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1

Restriction landmark genome scanning for the detection of mutations.  

UK PubMed Central (United Kingdom)

There is a continuing need for more efficient methods to examine mutations in humans and other species resulting from exposures to environmental toxins and radiation. Environmental genomic studies, which often utilize nonmodel system species and as a result, there is a particular need for a method that does not rely on the availability of genome sequence information. Restriction landmark genome scanning (RLGS) is a two-dimensional electrophoresis (2-DE) of end-labeled DNA fragments. A vertical giant gel 2-DE system has been developed and applied to the RLGS. On a single RLGS pattern of mouse or human DNA, approx 2000 DNA fragments (spots) varying in size from 1.0 to 5.0 kb in the first dimension and 0.2 to 3.0 kb in the second dimension are visualized. In principle, this system will detect genomic alterations of two types: (1) that due to gain or loss of a cut site for the three restriction fragment enzymes employed in the study and (2) that due to insertion/deletion/rearrangement (I/D/R) events. After optimization of the sample preparation and electrophoresis conditions, the gel quality reached a level such that the electrophoresis patterns derived from a single DNA sample gave distribution patterns of spots able to be superimposed. This technology can visualize up to 3000 DNA fragments per gel without using any probes, and thus should be highly efficient in monitoring for mutations resulting in I/D/R events in DNA fragments distributed throughout the genome. This method relies on direct labeling of DNA fragments rather than hybridization and therefore precise information on genome sequences is not required. As a result this method is applicable to any species.

Asakawa J

2008-01-01

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Application of the Restriction Landmark Genome Scanning (RLGS) Method for Analysis of Genetic Diversity between Asian and African Sorghum  

Directory of Open Access Journals (Sweden)

Full Text Available Restriction Landmark Genome Scanning (RLGS) used to detect large numbers of restriction landmarks in a single experiment andapplied to analyze the genetic diversity of Asian and African sorghum accessions. This method is one of the genome analysistools based on the concept that restriction enzyme sites can serve as landmarks throughout a genome. RLGS uses direct endlabelingof the genomic DNA digested with a rare-cutting restriction enzyme and high-resolution two-dimensionalelectrophoresis. It has an advantage of providing precise information on a spot intensity that reflects the copy number ofrestriction landmarks and to visualize differences in methylation levels across the genome. RLGS becomes very useful for doingwhole genome scans that equals the work of thousands of polymerase chain reactions. A study was carried out using Sorghumaccessions collected from countries viz., Morocco, Nigeria, Sudan, South Africa, Japan, South Korea, and China. Onerepresentative sample was chosen from a country for analysis carried out at National Institute of Agrobiological Sciences(NIAS). Two dimensional spot images for seven accessions obtained and spot intensities were scanned. Totally, 119 spots weredetected of which 95 spots observed as polymorphic and 24 as non polymorphic. Unique presence and null spots werespecifically detected in all accessions taken for study. A total of 37 unique spots and 12 null spots, detected in this experiment.Principal Coordinate Analysis indicated, four African accessions scattered in the diagram were diverse and three Asianaccessions closely distributed with narrow diversity. The phylogenetic tree showed that Sudan and Nigerian accessions weredistant while Chinna, Japan and Korea accessions had close proximity

Hisato Okuizumi*, Tomotsugu Noguchi, Tatsuya Saguchi,Takuma Fujita, Eri Nonaka, Shinsuke Yamanaka, Koffi Kombate, Subbarayan Sivakumar , Kulandaivelu Ganesamurthy, Yasufumi Murakami

2010-01-01

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Identification of novel methylation markers in cervical cancer using restriction landmark genomic scanning.  

UK PubMed Central (United Kingdom)

Aberrant methylation of CpG islands in gene promoters often represents an early clonal event in carcinogenesis. Accordingly, defining methylation profiles may be useful for developing marker panels for early detection or predicting the risk of cancer precursors. To identify specific genes frequently methylated in cervical cancer, we conducted methylation profiling of 20 primary human cervical cancers using NotI-based restriction landmark genomic scanning (RLGS). Of 2,172 RLGS fragments analyzed (average, 1,753 CpG islands per patient), 186 RLGS fragments were lost in at least one tumor and 40 were lost in three or more. Methylation was identified in 19 (95%) of 20 tumor samples compared with normal DNA. Bisulfite sequencing was conducted to confirm RLGS results. Of the confirmed markers frequently methylated, we developed Methylight assays for two corresponding genes, nucleolar protein 4 (NOL4), and lipoma HMGIC fusion partner-like protein 4 (LHFPL4), which were methylated in 85% and 55% of cancers, respectively. Using these assays, we further confirmed frequent CpG island methylation in the original cancers and in another independent series of 15 cervical cancers. We also showed methylation at a reduced frequency in a set of carefully reviewed cytology specimens demonstrating cells exfoliated from cancer precursor lesions. In summary, we identified, for the first time, NOL4 and LHFPL4 as novel methylation targets specific for cervical cancer. Inclusion of NOL4 and LHFPL4 in evaluating methylation panels for early detection, risk prediction, and etiologic research on cervical cancer is warranted.

Wang SS; Smiraglia DJ; Wu YZ; Ghosh S; Rader JS; Cho KR; Bonfiglio TA; Nayar R; Plass C; Sherman ME

2008-04-01

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Restriction Landmark Genomic Scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Restriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning." Results We report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation. Conclusion The new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation.

Smiraglia Dominic J; Kazhiyur-Mannar Ramakrishnan; Oakes Christopher C; Wu Yue-Zhong; Liang Ping; Ansari Tahmina; Su Jian; Rush Laura J; Smith Laura T; Yu Li; Liu Chunhui; Dai Zunyan; Chen Shih-Shih; Wang Shu-Huei; Costello Joseph; Ioshikhes Ilya; Dawson David W; Hong Jason S; Teitell Michael A; Szafranek Angela; Camoriano Marta; Song Fei; Elliott Rosemary; Held William; Trasler Jacquetta M; Plass Christoph; Wenger Rephael

2007-01-01

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Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS)  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Understanding the role of ‘epigenetic’ changes such as DNA methylation and chromatin remodeling has now become critical in understanding many biological processes. In order to delineate the global methylation pattern in a given genomic DNA, computer software has been developed to create a virtual im...

Matsuyama, Tomoki; Kimura, Makoto T.; Koike, Kuniaki; Abe, Tomoko; Nakano, Takeshi; Asami, Tadao; Ebisuzaki, Toshikazu

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Methylation and downregulated expression of mac25/insulin-like growth factor binding protein-7 is associated with liver tumorigenesis in SV40T/t antigen transgenic mice, screened by restriction landmark genomic scanning for methylation (RLGS-M).  

UK PubMed Central (United Kingdom)

Restriction landmark genomic scanning for methylation (RLGS-M) was used to detect alterations in DNA methylation associated with murine SV40 T/t antigen-induced hepatocarcinogenesis. An altered locus/spot (S130) was cloned and found to correspond to sequences in the 5' flanking region and 5' portion of the cDNA for the murine mac25/insulin-like growth factor binding protein-7 (Igfbp-7) gene. IGFBPs are believed to be capable of binding insulin, Igf1, and Igf2 and modulating mitogenic effects. Previous studies have shown that Igf2 has an important role in promoting liver tumorigenesis. Quantitative PCR was used to access the methylation status of the NotI site just 5' to the coding region and the expression level of the mac25/igfbp-7 gene. The results indicated that the degree of methylation was inversely related to the expression level and is consistent with a role for DNA methylation in silencing mac25/Igfbp-7 gene expression and function for mac25/Igfbp-7 as a tumor suppressor gene.

Komatsu S; Okazaki Y; Tateno M; Kawai J; Konno H; Kusakabe M; Yoshiki A; Muramatsu M; Held WA; Hayashizaki Y

2000-01-01

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Automated landmarking and labeling of fully and partially scanned spinal columns in CT images.  

Science.gov (United States)

The spinal column is one of the most distinguishable structures in CT scans of the superior part of the human body. It is not necessary to segment the spinal column in order to use it as a frame of reference. It is sufficient to place landmarks and the appropriate anatomical labels at intervertebral disks and vertebrae. In this paper, we present an automated system for landmarking and labeling spinal columns in 3D CT datasets. We designed this framework with two goals in mind. First, we relaxed input data requirements found in the literature, and we label both full and partial spine scans. Secondly, we intended to fulfill the performance requirement for daily clinical use and developed a high throughput system capable of processing thousands of slices in just a few minutes. To accomplish the aforementioned goals, we encoded structural knowledge from training data in probabilistic boosting trees and used it to detect efficiently the spinal canal, intervertebral disks, and three reference regions responsible for initializing the landmarking and labeling. Final landmarks and labels are selected by Markov Random Field-based matches of newly introduced 3-disk models. The framework has been tested on 36 CT images having at least one of the regions around the thoracic first ribs, the thoracic twelfth ribs, or the sacrum. In an average time of 2min, we achieved a correct labeling in 35 cases with precision of 99.0% and recall of 97.2%. Additionally, we present results assuming none of the three reference regions could be detected. PMID:23978670

Major, David; Hlad?vka, Ji?í; Schulze, Florian; Bühler, Katja

2013-08-02

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Extracting actionable information from genome scans.  

UK PubMed Central (United Kingdom)

Genome-wide association studies discovered numerous genetic variants significantly associated with various phenotypes. However, significant signals explain only a small portion of the variation in many traits. One explanation is that missing variation is found in "suggestive signals," i.e., variants with reasonably small P-values. However, it is not clear how to capture this information and use it optimally to design and analyze future studies. We propose to extract the available information from a genome scan by accurately estimating the means of univariate statistics. The means are estimated by: (i) computing the sum of squares (SS) of a genome scan's univariate statistics, (ii) using SS to estimate the expected SS for the means (SSM) of univariate statistics, and (iii) constructing accurate soft threshold (ST) estimators for means of univariate statistics by requiring that the SS of these estimators equals the SSM. When compared to competitors, ST estimators explain a substantially higher fraction of the variability in true means. The accuracy of proposed estimators can be used to design two-tier follow-up studies in which regions close to variants having ST-estimated means above a certain threshold are sequenced at high coverage and the rest of the genome is sequenced at low coverage. This follow-up approach reduces the sequencing burden by at least an order of magnitude when compared to a high coverage sequencing of the whole genome. Finally, we suggest ways in which ST methodology can be used to improve signal detection in future sequencing studies and to perform general statistical model selection.

Bacanu SA; Kendler KS

2013-01-01

9

Electrochemical degradation of electrodeposited Pt particles on mask scratched substrate using a landmark for ex situ scanning electron microscopy  

Science.gov (United States)

Pt particles were deposited on a glassy carbon substrate using a landmark by a mask scratch-based Pt electrodeposition method to observe the same Pt particles by ex situ scanning electron microscopy before and after a potential cycling procedure. The potential cycling was conducted in a H2O2-containing 0.5 mol dm?3 H2SO4 solution. As a result, the Pt particle degradations are clearly observed in the solution containing 100 mmol dm?3 H2O2 in the potential range of 0.04-1.44 V vs. RHE; whereas, the degradations become more remarkable at 0.34-1.44 V vs. RHE. To clarify the reason for this potential cycling range-dependence of the Pt particle degradations, the weight change of a Pt electrode during potential cycling in the presence of H2O2 was measured using an electrochemical quartz crystal microbalance. The result suggests that the dissolved Pt is re-deposited on the Pt in ca. 0.01-0.40 V vs. RHE, which well explains the difference of the Pt particle degradations by the potential cyclings between 0.04-1.44 and 0.34-1.44 V vs. RHE.

Kishi, Akira; Inoue, Mitsuhiro; Shironita, Sayoko; Umeda, Minoru

2012-07-01

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PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes  

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Full Text Available Abstract Background EST-PCR markers normally represent specific products from target genes, and are therefore effective tools for genetic analysis. However, because wheat is an allohexaploid plant, PCR products derived from homoeologous genes are often simultaneously amplified. Such products may be easier to differentiate if they include intron sequences, which are more polymorphic than exon sequences. However, genomic sequence data for wheat are limited; therefore it is difficult to predict the location of introns. By using the similarities in gene structures between rice and wheat, we developed a system called PLUG (PCR-based Landmark Unique Gene) to design primers so that PCR products include intron sequences. We then investigated whether products amplified using such primers could serve as markers able to distinguish multiple products derived from homoeologous genes. Results The PLUG system consists of the following steps: (1) Single-copy rice genes (Landmark Unique Gene loci; LUGs) exhibiting high degrees of homology to wheat UniGene sequences are extracted; (2) Alignment analysis is carried out using the LUGs and wheat UniGene sequences to predict exon-exon junctions, and LUGs which can be used to design wheat primers flanking introns (TaEST-LUGs) are extracted; and (3) Primers are designed in an interactive manner. From a total of 4,312 TaEST-LUGs, 24 loci were randomly selected and used to design primers. With all of these primer sets, we obtained specific, intron-containing products from the target genes. These markers were assigned to chromosomes using wheat nullisomic-tetrasomic lines. By PCR-RFLP analysis using agarose gel electrophoresis, 19 of the 24 markers were located on at least one chromosome. Conclusion In the development of wheat EST-PCR markers capable of efficiently sorting products derived from homoeologous genes, it is important to design primers able to amplify products that include intron sequences with insertion/deletion polymorphisms. Using the PLUG system, wheat EST sequences that can be used for marker development are selected based on comparative genomics with rice, and then primer sets flanking intron sequences are prepared in an interactive, semi-automatic manner. Hence, the PLUG system is an effective tool for large-scale marker development.

Ishikawa Goro; Yonemaru Junichi; Saito Mika; Nakamura Toshiki

2007-01-01

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ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies.  

UK PubMed Central (United Kingdom)

UNLABELLED: ChromoScan is an implementation of a genome-based scan statistic that detects genomic regions, which are statistically significant for targeted measurements, such as genetic associations with disease, gene expression profiles, DNA copy number variations, as well as other genome-based measurements. A Java graphic user interface (GUI) is provided to allow users to select appropriate data transformations and thresholds for defining the significant events. AVAILABILITY: ChromoScan is freely available from http://www.epidkardia.sph.umich.edu/software/chromoscan/

Sun YV; Jacobsen DM; Kardia SL

2006-12-01

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Uninformative polymorphisms bias genome scans for signatures of selection  

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

Roesti Marius; Salzburger Walter; Berner Daniel

2012-01-01

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A genome scanning approach to assess the genetic effects of radiation in mice and humans.  

Science.gov (United States)

We used Restriction Landmark Genome Scanning (RLGS) to assess, on a genome-wide basis, the mutation induction rate in mouse germ cells after radiation exposure. Analyses of 1,115 autosomal NotI DNA fragments per mouse for reduced spot intensity, indicative of loss of one copy, in 506 progeny derived from X-irradiated spermatogonia (190, 237 and 79 mice in 0-, 3-, and 5-Gy groups, respectively), permitted us to identify 16 mutations affecting 23 fragments in 20 mice. The 16 mutations were composed of eight small changes (1-9 bp) at microsatellite sequences, five large deletions (more than 25 kb), and three insertions of SINE B2 or LINE1 transposable elements. The maximum induction rate of deletion mutations was estimated as (0.17 +/- 0.09) x 10(-5)/locus Gy(-1). The estimate is considerably lower than 1 x 10(-5)/locus Gy(-1), the mean induction rate of deletion mutations at Russell's 7 loci, which assumed that deletion mutations comprise 50% of all mutations. We interpret the results as indicating that the mean induction rate of mutations in the whole genome may be substantially lower than that at the 7 loci. We also demonstrate the applicability of RLGS for detection of human mutations, which allows direct comparisons between the two species. PMID:15038760

Asakawa, Jun-ichi; Kuick, Rork; Kodaira, Mieko; Nakamura, Nori; Katayama, Hiroaki; Pierce, Donald; Funamoto, Sachiyo; Preston, Dale; Satoh, Chiyoko; Neel, James V; Hanash, Samir

2004-04-01

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A genome scanning approach to assess the genetic effects of radiation in mice and humans.  

UK PubMed Central (United Kingdom)

We used Restriction Landmark Genome Scanning (RLGS) to assess, on a genome-wide basis, the mutation induction rate in mouse germ cells after radiation exposure. Analyses of 1,115 autosomal NotI DNA fragments per mouse for reduced spot intensity, indicative of loss of one copy, in 506 progeny derived from X-irradiated spermatogonia (190, 237 and 79 mice in 0-, 3-, and 5-Gy groups, respectively), permitted us to identify 16 mutations affecting 23 fragments in 20 mice. The 16 mutations were composed of eight small changes (1-9 bp) at microsatellite sequences, five large deletions (more than 25 kb), and three insertions of SINE B2 or LINE1 transposable elements. The maximum induction rate of deletion mutations was estimated as (0.17 +/- 0.09) x 10(-5)/locus Gy(-1). The estimate is considerably lower than 1 x 10(-5)/locus Gy(-1), the mean induction rate of deletion mutations at Russell's 7 loci, which assumed that deletion mutations comprise 50% of all mutations. We interpret the results as indicating that the mean induction rate of mutations in the whole genome may be substantially lower than that at the 7 loci. We also demonstrate the applicability of RLGS for detection of human mutations, which allows direct comparisons between the two species.

Asakawa J; Kuick R; Kodaira M; Nakamura N; Katayama H; Pierce D; Funamoto S; Preston D; Satoh C; Neel JV; Hanash S

2004-04-01

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Genomic scan for genes predisposing to schizophrenia  

Energy Technology Data Exchange (ETDEWEB)

We initiated a genome-wide search for genes predisposing to schizophrenia by ascertaining 9 families, each containing three to five cases of schizophrenia. The 9 pedigrees were initially genotyped with 329 polymorphic DNA loci distributed throughout the genome. Assuming either autosomal dominant or recessive inheritance, 254 DNA loci yielded lod scores less than -2.0 at {theta} = 0.0, 101 DNA markers gave lod scores less than -2.0 at {theta} = 0.05, while 5 DNA loci produced maximum lod scores greater than 1: D4S35, D14S17, D15S1, D22S84, and D22S55. Of the DNA markers yielding lod scores greater than 1, D4S35 and D22S55 also were suggestive of linkage when the Affected-Pedigree-Member method was used. The families were then genotyped with four highly polymorphic simple sequence repeat markers; possible linkage diminished with DNA markers mapping nearby D4S35, while suggestive evidence of linkage remained with loci in the region of D22S55. Although follow-up investigation of these chromosomal regions may be warranted, our linkage results should be viewed as preliminary observations, as 35 unaffected persons are not past the age of risk. 90 refs., 3 tabs.

Coon, H.; Jensen. S.; Holik, J. [Univ. of Utah Medical Center, Salt Lake City, UT (United States)] [and others

1994-03-15

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

Science.gov (United States)

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.

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

2013-02-01

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

Directory of Open Access Journals (Sweden)

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 intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.

Mei Lingling; Ding Xiaofan; Tsang Shui-Ying; Pun Frank W; Ng Siu-Kin; Yang Jianfeng; Zhao Cunyou; Li Dezhi; Wan Weiqing; Yu Chi-Hung; Tan Tze-Ching; Poon Wai-Sang; Leung Gilberto; Ng Ho-Keung; Zhang Liwei; Xue Hong

2011-01-01

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Genome scan for blood pressure loci in mice.  

UK PubMed Central (United Kingdom)

Hypertension is a complex trait of unknown cause in humans. Mice of the inbred strain BPH/2 serve as a rodent model of human hypertension and display elevated blood pressure compared with the hypotensive strain BPL/1. An F2 intercross of BPH/2 and BPL/1 and 2 backcrosses of BPL/1 with Mus spretus were used to perform interval linkage mapping for systolic blood pressure in a genome scan. Significant linkage was observed in the F2s on chromosome 10 (logarithm of the odds score [LOD]=4.9) and on chromosome 13 in the M spretus backcross (LOD=3.3), with additional suggestive LODs on chromosomes 2, 6, 8, and 18. In addition, several suggestive linkages were observed for phenotypes associated with human hypertension. Our study is the first reported genome-wide linkage scan for blood pressure genes in the mouse.

Wright FA; O'Connor DT; Roberts E; Kutey G; Berry CC; Yoneda LU; Timberlake D; Schlager G

1999-10-01

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Genome scan for blood pressure loci in mice.  

Science.gov (United States)

Hypertension is a complex trait of unknown cause in humans. Mice of the inbred strain BPH/2 serve as a rodent model of human hypertension and display elevated blood pressure compared with the hypotensive strain BPL/1. An F2 intercross of BPH/2 and BPL/1 and 2 backcrosses of BPL/1 with Mus spretus were used to perform interval linkage mapping for systolic blood pressure in a genome scan. Significant linkage was observed in the F2s on chromosome 10 (logarithm of the odds score [LOD]=4.9) and on chromosome 13 in the M spretus backcross (LOD=3.3), with additional suggestive LODs on chromosomes 2, 6, 8, and 18. In addition, several suggestive linkages were observed for phenotypes associated with human hypertension. Our study is the first reported genome-wide linkage scan for blood pressure genes in the mouse. PMID:10523337

Wright, F A; O'Connor, D T; Roberts, E; Kutey, G; Berry, C C; Yoneda, L U; Timberlake, D; Schlager, G

1999-10-01

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A note on generalized Genome Scan Meta-Analysis statistics  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Wise et al. introduced a rank-based statistical technique for meta-analysis of genome scans, the Genome Scan Meta-Analysis (GSMA) method. Levinson et al. recently described two generalizations of the GSMA statistic: (i) a weighted version of the GSMA statistic, so that different studies could be ascribed different weights for analysis; and (ii) an order statistic approach, reflecting the fact that a GSMA statistic can be computed for each chromosomal region or bin width across the various genome scan studies. Results We provide an Edgeworth approximation to the null distribution of the weighted GSMA statistic, and, we examine the limiting distribution of the GSMA statistics under the order statistic formulation, and quantify the relevance of the pairwise correlations of the GSMA statistics across different bins on this limiting distribution. We also remark on aggregate criteria and multiple testing for determining significance of GSMA results. Conclusion Theoretical considerations detailed herein can lead to clarification and simplification of testing criteria for generalizations of the GSMA statistic.

Koziol James A; Feng Anne C

2005-01-01

 
 
 
 
21

Genome-wide scans for loci under selection in humans  

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Full Text Available Abstract Natural selection, which can be defined as the differential contribution of genetic variants to future generations, is the driving force of Darwinian evolution. Identifying regions of the human genome that have been targets of natural selection is an important step in clarifying human evolutionary history and understanding how genetic variation results in phenotypic diversity, it may also facilitate the search for complex disease genes. Technological advances in high-throughput DNA sequencing and single nucleotide polymorphism genotyping have enabled several genome-wide scans of natural selection to be undertaken. Here, some of the observations that are beginning to emerge from these studies will be reviewed, including evidence for geographically restricted selective pressures (ie local adaptation) and a relationship between genes subject to natural selection and human disease. In addition, the paper will highlight several important problems that need to be addressed in future genome-wide studies of natural selection.

Ronald James; Akey Joshua M

2005-01-01

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Detecting positive selection from genome scans of linkage disequilibrium  

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Full Text Available Abstract Background Though a variety of linkage disequilibrium tests have recently been introduced to measure the signal of recent positive selection, the statistical properties of the various methods have not been directly compared. While most applications of these tests have suggested that positive selection has played an important role in recent human history, the results of these tests have varied dramatically. Results Here, we evaluate the performance of three statistics designed to detect incomplete selective sweeps, LRH and iHS, and ALnLH. To analyze the properties of these tests, we introduce a new computational method that can model complex population histories with migration and changing population sizes to simulate gene trees influenced by recent positive selection. We demonstrate that iHS performs substantially better than the other two statistics, with power of up to 0.74 at the 0.01 level for the variation best suited for full genome scans and a power of over 0.8 at the 0.01 level for the variation best suited for candidate gene tests. The performance of the iHS statistic was robust to complex demographic histories and variable recombination rates. Genome scans involving the other two statistics suffer from low power and high false positive rates, with false discovery rates of up to 0.96 for ALnLH. The difference in performance between iHS and ALnLH, did not result from the properties of the statistics, but instead from the different methods for mitigating the multiple comparison problem inherent in full genome scans. Conclusions We introduce a new method for simulating genealogies influenced by positive selection with complex demographic scenarios. In a power analysis based on this method, iHS outperformed LRH and ALnLH in detecting incomplete selective sweeps. We also show that the single-site iHS statistic is more powerful in a candidate gene test than the multi-site statistic, but that the multi-site statistic maintains a low false discovery rate with only a minor loss of power when applied to a scan of the entire genome. Our results highlight the need for careful consideration of multiple comparison problems when evaluating and interpreting the results of full genome scans for positive selection.

Huff Chad D; Harpending Henry C; Rogers Alan R

2010-01-01

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Genome scans for transmission ratio distortion regions in mice.  

Science.gov (United States)

Transmission ratio distortion (TRD) is the departure from the expected genotypic frequencies under Mendelian inheritance. This departure can be due to multiple physiological mechanisms during gametogenesis, fertilization, fetal and embryonic development, and early neonatal life. Although a few TRD loci have been reported in mouse, inheritance patterns have never been evaluated for TRD. In this article, we developed a Bayesian binomial model accounting for additive and dominant deviation TRD mechanisms. Moreover, this model was used to perform genome-wide scans for TRD quantitative trait loci (QTL) on six F2 mouse crosses involving between 296 and 541 mice and between 72 and 1854 genetic markers. Statistical significance of each model was checked at each genetic marker with Bayes factors. Genome scans revealed overdominance TRD QTL located in mouse chromosomes 1, 2, 12, 13, and 14 and additive TRD QTL in mouse chromosomes 2, 3, and 15, although these results did not replicate across mouse crosses. This research contributes new statistical tools for the analysis of specific genetic patterns involved in TRD in F2 populations, our results suggesting a relevant incidence of TRD phenomena in mouse with important implications for both statistical analyses and biological research. PMID:22367040

Casellas, Joaquim; Gularte, Rodrigo J; Farber, Charles R; Varona, Luis; Mehrabian, Margarete; Schadt, Eric E; Lusis, Aldon J; Attie, Alan D; Yandell, Brian S; Medrano, Juan F

2012-02-23

24

A genome-wide scan for modifier loci in schizophrenia.  

Science.gov (United States)

The purpose of this study was to detect genetic loci that influence clinical features of, but not necessarily susceptibility to, psychotic illness. In the Irish Study of High-Density Schizophrenia Families (n = 270 families, n = 1,408 individuals), subjects with non-affective psychosis were rated using the Operational Criteria Checklist for Psychotic Illness. Factor analysis identified hallucinations, delusions, and negative, manic, and depressive symptom factors. We performed autosomal genome-wide multipoint non-parametric quantitative trait locus linkage analysis, in affected individuals only, using these five factors, as well as age at onset, and course of illness. Determination of empirical significance and correction for multiple testing was implemented using 200 simulated genome scans. We also tested for pleiotropic loci by examining the sums of -log(10)'s of the empirical P values of multiple traits in selected regions. LODs of 2.42 and 2.35 were obtained near D9S934 (9q33.1) and D14S587 (14q24.2), respectively, for course of illness, and of 2.26 between D6S1040-D6S2420 (6q23.1-25.1) and age at onset. No other regions met criteria for suggestive linkage to any one trait. No loci were significant after correction for multiple testing. On 6q, however, the joint linkage of age of onset, course, delusions, and depressive symptoms resulted in a genome-wide P = 0.06. We conclude that genes located near 9q33.1 and 14q24.2 may modify the clinical course and severity of schizophrenia. A gene in 6q may affect several clinical features of illness. PMID:17262803

Fanous, Ayman H; Neale, Michael C; Webb, B Todd; Straub, Richard E; Amdur, Richard L; O'Neill, F Anthony; Walsh, Dermot; Riley, Brien P; Kendler, Kenneth S

2007-07-01

25

Landmarks in Hybrid Planning  

Directory of Open Access Journals (Sweden)

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.

Mohamed Elkawkagy; Heba Elbeh

2013-01-01

26

Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.  

UK PubMed Central (United Kingdom)

N-SCAN is a gene-prediction system that combines the methods of ab initio predictors like GENSCAN with information derived from genome comparison. It is the latest in the TWINSCAN series of programs. This unit describes the use of N-SCAN to identify gene structures in eukaryotic genomic sequences. Protocols for using N-SCAN through its Web interface and from the command line in a Linux environment are provided. Detailed discussion about the appropriate parameter settings, input-sequence processing, and choice of genome for comparison are included.

van Baren MJ; Koebbe BC; Brent MR

2007-12-01

27

Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.  

Science.gov (United States)

N-SCAN is a gene-prediction system that combines the methods of ab initio predictors like GENSCAN with information derived from genome comparison. It is the latest in the TWINSCAN series of programs. This unit describes the use of N-SCAN to identify gene structures in eukaryotic genomic sequences. Protocols for using N-SCAN through its Web interface and from the command line in a Linux environment are provided. Detailed discussion about the appropriate parameter settings, input-sequence processing, and choice of genome for comparison are included. PMID:18428682

van Baren, Marijke J; Koebbe, Brian C; Brent, Michael R

2007-12-01

28

Multiple loci influencing hippocampal degeneration identified by genome scan.  

UK PubMed Central (United Kingdom)

OBJECTIVE: Large genome-wide association studies (GWASs) have identified many novel genes influencing Alzheimer disease (AD) risk, but most of the genetic variance remains unexplained. We conducted a 2-stage GWAS for AD-related quantitative measures of hippocampal volume (HV), total cerebral volume (TCV), and white matter hyperintensities (WMH). METHODS: Brain magnetic resonance imaging measures of HV, TCV, and WMH were obtained from 981 Caucasian and 419 African American AD cases and their cognitively normal siblings in the MIRAGE (Multi Institutional Research in Alzheimer's Genetic Epidemiology) Study, and from 168 AD cases, 336 individuals with mild cognitive impairment, and 188 controls in the Alzheimer's Disease Neuroimaging Initiative Study. A GWAS for each trait was conducted in the 2 Caucasian data sets in stage 1. Results from the 2 data sets were combined by meta-analysis. In stage 2, 1 single nucleotide polymorphism (SNP) from each region that was nominally significant in each data set (p < 0.05) and strongly associated in both data sets (p < 1.0 × 10(-5)) was evaluated in the African American data set. RESULTS: Twenty-two markers (14 for HV, 3 for TCV, and 5 for WMH) from distinct regions met criteria for evaluation in stage 2. Novel genome-wide significant associations (p < 5.0 × 10(-8)) were attained for HV with SNPs in the APOE, F5/SELP, LHFP, and GCFC2 gene regions. All of these associations were supported by evidence in each data set. Associations with different SNPs in the same gene (p < 1 × 10(-5) in Caucasians and p < 2.2 × 10(-4) in African Americans) were also observed for PICALM with HV, SYNPR with TCV, and TTC27 with WMH. INTERPRETATION: Our study demonstrates the efficacy of endophenotypes for broadening our understanding of the genetic basis of AD.

Melville SA; Buros J; Parrado AR; Vardarajan B; Logue MW; Shen L; Risacher SL; Kim S; Jun G; DeCarli C; Lunetta KL; Baldwin CT; Saykin AJ; Farrer LA

2012-07-01

29

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

UK PubMed Central (United Kingdom)

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.

Aggarwal G; Ramaswamy R

2002-02-01

30

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

UK PubMed Central (United Kingdom)

In order to take into account the complex genomic distribution of SNP variations when identifying chromosomal regions with significant SNP effects, a single nucleotide polymorphism (SNP) association scan statistic was developed. To address the computational needs of genome wide association (GWA) studies, a fast Java application, which combines single-locus SNP tests and a scan statistic for identifying chromosomal regions with significant clusters of significant SNP effects, was developed and implemented. To illustrate this application, SNP associations were analyzed in a pharmacogenomic study of the blood pressure lowering effect of thiazide-diuretics (N=195) using the Affymetrix Human Mapping 100K Set. 55,335 tagSNPs (pair-wise linkage disequilibrium R(2)<0.5) were selected to reduce the frequency correlation between SNPs. A typical workstation can complete the whole genome scan including 10,000 permutation tests within 3 hours. The most significant regions locate on chromosome 3, 6, 13 and 16, two of which contain candidate genes that may be involved in the underlying drug response mechanism. The computational performance of ChromoScan-GWA and its scalability were tested with up to 1,000,000 SNPs and up to 4,000 subjects. Using 10,000 permutations, the computation time grew linearly in these datasets. This scan statistic application provides a robust statistical and computational foundation for identifying genomic regions associated with disease and provides a method to compare GWA results even across different platforms.

Sun YV; Jacobsen DM; Turner ST; Boerwinkle E; Kardia SL

2009-03-01

31

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

Science.gov (United States)

In order to take into account the complex genomic distribution of SNP variations when identifying chromosomal regions with significant SNP effects, a single nucleotide polymorphism (SNP) association scan statistic was developed. To address the computational needs of genome wide association (GWA) studies, a fast Java application, which combines single-locus SNP tests and a scan statistic for identifying chromosomal regions with significant clusters of significant SNP effects, was developed and implemented. To illustrate this application, SNP associations were analyzed in a pharmacogenomic study of the blood pressure lowering effect of thiazide-diuretics (N=195) using the Affymetrix Human Mapping 100K Set. 55,335 tagSNPs (pair-wise linkage disequilibrium R(2)<0.5) were selected to reduce the frequency correlation between SNPs. A typical workstation can complete the whole genome scan including 10,000 permutation tests within 3 hours. The most significant regions locate on chromosome 3, 6, 13 and 16, two of which contain candidate genes that may be involved in the underlying drug response mechanism. The computational performance of ChromoScan-GWA and its scalability were tested with up to 1,000,000 SNPs and up to 4,000 subjects. Using 10,000 permutations, the computation time grew linearly in these datasets. This scan statistic application provides a robust statistical and computational foundation for identifying genomic regions associated with disease and provides a method to compare GWA results even across different platforms. PMID:20161066

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

2009-03-15

32

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

Directory of Open Access Journals (Sweden)

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.

Hollegaard Mads V; Grove Jakob; Grauholm Jonas; Kreiner-Møller Eskil; Bønnelykke Klaus; Nørgaard Mette; Benfield Thomas L; Nørgaard-Pedersen Bent; Mortensen Preben B; Mors Ole; Sørensen Henrik T; Harboe Zitta B; Børglum Anders D; Demontis Ditte; Ørntoft Torben F; Bisgaard Hans; Hougaard David M

2011-01-01

33

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Schizophrenia is a common disorder with high heritability and a 10-fold increase in risk to siblings of probands. Replication has been inconsistent for reports of significant genetic linkage. To assess evidence for linkage across studies, rank-based genome scan meta-analysis (GSMA) was applied to da...

Lewis, Cathryn M.; Levinson, Douglas F.; Wise, Lesley H.; DeLisi, Lynn E.; Straub, Richard E.; Hovatta, Iiris; Williams, Nigel M.

34

A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2 tests  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We performed a genome-wide association scan on the North American Rheumatoid Arthritis Consortium (NARAC) data using Hotelling's T2 tests, i.e., TH based on allele coding and TG based on genotype coding. The objective was to identify associations between single-nucleotide polymorphisms (SNPs) or mar...

Chen, Lianfu; Zhong, Ming; Chen, Wei Vivien; Amos, Christopher I; Fan, Ruzong

35

Genome-wide scans using archived neonatal dried blood spot samples  

Directory of Open Access Journals (Sweden)

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.

Hollegaard Mads V; Grauholm Jonas; Børglum Anders; Nyegaard Mette; Nørgaard-Pedersen Bent; Ørntoft Torben; Mortensen Preben B; Wiuf Carsten; Mors Ole; Didriksen Michael; Thorsen Poul; Hougaard David M

2009-01-01

36

Genome-wide scans using archived neonatal dried blood spot samples  

DEFF Research Database (Denmark)

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.

Hollegaard, Mads; Grauholm, Jonas

2009-01-01

37

Landmark TAL CB CBS  

UK PubMed Central (United Kingdom)

d.3.0]Figure 5. Isolated cerebellum.Table 3. Landmark locations in all subjects.(mean [s.d.] reported in mm)Landmark TAL CB CBSAC-PC Distance 23.0 [fixed] 27.1 [1.1] 27.1 [1.0]Obex-PC distance 54.4 [3.7] 53.4 [3.0] 54.0 [fixed]AC localization fixed 2.2 [0.7] 2.1 [0.7]Obex localization 5.2 [2.6] 2.3 [1.9] fixedV4 apex localization 3.9 [2.1] 2.9 [1.5] 2.4 [1.5]Lingula localization 2.8 [1.2] 2.1 [0.9] 2.0 [0.9]Primary fissure 3.5 [1.5] 3.0 [1.6] 2.6 [1.6]Horizontal fissure 4.4 [2.1] 4.7 [1.8] 4.5 [1.9]Preculminate fissure 3.1 [1.9] 2.4 [1.3] 2.1 [1.3]Prepyramidal fissure 4.0 [1.8] 3.3 [2.0] 3.0 [1.9]Secondary fissure 4.1 [1.9] 3.1 [1.8] 2.5 [1.7]Yaw angle: 0.4 [s.d. 2.6] Roll angle: 2.4 [s.d. 2.8]Use of Cerebellar Landmarks To Define a Coordinate System and an Isolation StrategyKelly Rehm , David Rottenberg , Kirt Schaper , J

38

A genome-wide quantitative linkage scan of niacin skin flush response in families with schizophrenia.  

UK PubMed Central (United Kingdom)

Schizophrenia patients frequently display reduced niacin flush responses, and similar characteristics are also observed in their nonpsychotic relatives. This study aimed to identify loci influencing flush response to niacin in schizophrenia using genome-wide quantitative linkage scan. In a nationwide sample of families with at least 2 siblings affected with schizophrenia in each family, 115 families that had at least 2 affected siblings with information on the niacin skin test were subjected to quantitative trait loci linkage analysis, either involving affected individuals only or the whole family. Nonparametric linkage z (NPL-Z) scores were calculated for each of 386 microsatellite markers spaced at an average of 9-cM intervals. Niacin patches of 3 concentrations (0.001 M, 0.01, and 0.1 M) were applied to forearm skin, and the flush response was rated at 5, 10, and 15 minutes, respectively, with a 4-point scale. Determination of genome-wide empirical significance was implemented using 1000 simulated genome scans. One linkage peak attaining genome-wide significance was identified at chromosomal region 14q32.12 for 0.01 M concentration at 5 minutes (NPL-Z scores = 3.39, genome-wide empirical P = .03) in affected individuals, and the corresponding linkage signal remained strong (NPL-Z scores = 2.87) for the analyses of the whole family. This locus is distinct from the chromosomal region identified in the previous genome-wide scan for the diagnosis of schizophrenia, and the signal was higher than the peak linkage signal in that study. These findings indicate that there might be modifier or susceptibility-modifier genes at 14q32.12 for schizophrenia-related attenuation of flush response to niacin.

Lien YJ; Huang SS; Liu CM; Hwu HG; Faraone SV; Tsuang MT; Chen WJ

2013-01-01

39

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

International Nuclear Information System (INIS)

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

1998-01-01

40

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

UK PubMed Central (United Kingdom)

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

Paris M; Despres L

2012-04-01

 
 
 
 
41

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

DEFF Research Database (Denmark)

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 < 0.05) affected by the year of storage and storage conditions. Nine (0.2%) DBS samples failed whole-genome amplification. A total of 4,586 (98.8%) samples met our criterion of success of a genetic call-rate above 97%. The three studies used different arrays, with mean genotyping call-rates of 99.385% (Illumina Infinium Human610-Quad), 99.722% (Illumina Infinium HD HumanOmni1-Quad), and 99.206% (Affymetrix Axiom Genome-Wide CEU). We observed a concordance rate of 99.997% in the 38 methodological replications, and 99.999% in the 27 technical replications. Handling variables such as time of storage, storage conditions and type of filter paper were shown too significantly (P < 0.05) affect the genotype call-rates in some of the arrays, although the effect was minimal. 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.

Hollegaard, Mads V; Grove, Jakob

2011-01-01

42

Meta-analyses of genome-wide linkage scans of anxiety-related phenotypes.  

UK PubMed Central (United Kingdom)

Genetic factors underlying trait neuroticism, reflecting a tendency towards negative affective states, may overlap genetic susceptibility for anxiety disorders and help explain the extensive comorbidity amongst internalizing disorders. Genome-wide linkage (GWL) data from several studies of neuroticism and anxiety disorders have been published, providing an opportunity to test such hypotheses and identify genomic regions that harbor genes common to these phenotypes. In all, 11 independent GWL studies of either neuroticism (n=8) or anxiety disorders (n=3) were collected, which comprised of 5341 families with 15?529 individuals. The rank-based genome scan meta-analysis (GSMA) approach was used to analyze each trait separately and combined, and global correlations between results were examined. False discovery rate (FDR) analysis was performed to test for enrichment of significant effects. Using 10?cM intervals, bins nominally significant for both GSMA statistics, P(SR) and P(OR), were found on chromosomes 9, 11, 12, and 14 for neuroticism and on chromosomes 1, 5, 15, and 16 for anxiety disorders. Genome-wide, the results for the two phenotypes were significantly correlated, and a combined analysis identified additional nominally significant bins. Although none reached genome-wide significance, an excess of significant P(SR)P-values were observed, with 12 bins falling under a FDR threshold of 0.50. As demonstrated by our identification of multiple, consistent signals across the genome, meta-analytically combining existing GWL data is a valuable approach to narrowing down regions relevant for anxiety-related phenotypes. This may prove useful for prioritizing emerging genome-wide association data for anxiety disorders.

Webb BT; Guo AY; Maher BS; Zhao Z; van den Oord EJ; Kendler KS; Riley BP; Gillespie NA; Prescott CA; Middeldorp CM; Willemsen G; de Geus EJ; Hottenga JJ; Boomsma DI; Slagboom EP; Wray NR; Montgomery GW; Martin NG; Wright MJ; Heath AC; Madden PA; Gelernter J; Knowles JA; Hamilton SP; Weissman MM; Fyer AJ; Huezo-Diaz P; McGuffin P; Farmer A; Craig IW; Lewis C; Sham P; Crowe RR; Flint J; Hettema JM

2012-10-01

43

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

UK PubMed Central (United Kingdom)

An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477-91). The latter was recently established when a causative coronavirus (SARS-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 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% of all individuals of all major human populations (Sette & Sidney, Immunogenetics 1999: 50: 201-12). For each HLA supertype, we have selected the 15 top candidates for test in biochemical binding assays. At this time (approximately 6 months after the genome was established), we have tested the majority of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.

Sylvester-Hvid C; Nielsen M; Lamberth K; Røder G; Justesen S; Lundegaard C; Worning P; Thomadsen H; Lund O; Brunak S; Buus S

2004-05-01

44

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

Science.gov (United States)

An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477-91). The latter was recently established when a causative coronavirus (SARS-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 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% of all individuals of all major human populations (Sette & Sidney, Immunogenetics 1999: 50: 201-12). For each HLA supertype, we have selected the 15 top candidates for test in biochemical binding assays. At this time (approximately 6 months after the genome was established), we have tested the majority of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design. PMID:15104671

Sylvester-Hvid, C; Nielsen, M; Lamberth, K; Røder, G; Justesen, S; Lundegaard, C; Worning, P; Thomadsen, H; Lund, O; Brunak, S; Buus, S

2004-05-01

45

Enhancing Planning Heuristic with Landmarks  

Directory of Open Access Journals (Sweden)

Full Text Available Recently, landmarks count heuristic can increase the number of problem instances solved and improve the quality of the solutions in satisfying non-optimal planning.  In order to make the heuristic optimal, we give the solution to solve the overestimate of landmarks count heuristic. We extend landmarks count heuristic without action cost assignments, and prove that the extension of heuristic is admissible. Our empirical evaluation shows that the extension of heuristic is admissible and can be competed with the state-of-the-art of heuristic.

Jingjing Zhao; Dayou Liu; Yongming Yang

2011-01-01

46

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

UK PubMed Central (United Kingdom)

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.

Jahanshad N; Rajagopalan P; Hua X; Hibar DP; Nir TM; Toga AW; Jack CR Jr; Saykin AJ; Green RC; Weiner MW; Medland SE; Montgomery GW; Hansell NK; McMahon KL; de Zubicaray GI; Martin NG; Wright MJ; Thompson PM

2013-03-01

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Two-dimensional DNA typing: A general method for scanning the total human genome  

Energy Technology Data Exchange (ETDEWEB)

Two-dimensional (2-D) DNA typing is a method that offers the possibility of analyzing hundreds of loci simultaneously in the human genome. This is done by electrophoretic separation of DNA restriction fragments in two dimensions: firstly according to size, and then in the second dimension by denaturing gradient gel electrophoresis (DGGE) according to base-pair sequence, followed by hybridization analysis using a micro- or minisatellite core probe. Depending on the core probe used in the hybridization analysis, between 150 and 700 restriction fragments are detected as spots in the 2-D DNA typing patterns. Many of the loci corresponding to these spots are polymorphic, and it is anticipated that 10 re-hybridizations with core probes, each detecting 150 informative spots, allow a scanning of the genome at 1500 loci. These properties of 2-D DNA typing make it possible to monitor genetic variability on a total genome scale. In families it is possible to follow the segregation of the 2-D spots, which are inherited in a Mendelian fashion as codominant markers. Due to the high degree of variability in the polymorphic loci, one spot (one allele) is often only represented once in the parents. A spot like that can function as an informative genetic marker without any further knowledge about the other alleles of the locus. We have followed the segregation of several such spots in 3 large CEPH pedigrees, and it has been possible by linkage analysis to map many of these spots. These results show that the spots are indeed inherited in a Mendelian manner, and that they can be scored reliably, and thus underlines the future perspective of 2-D DNA typing as a genetic marker system. An initial database has been set up on the basis of the computerized scanned image of 2-D DNA typings with informations which will mostly concern spot-data from studies on genomic alterations in different cancers, and studies on amplifications of trinucleotide repeats as disease-causing mutations.

Borglum, A.D.; Kvistgaard, A.B.; Kruse, T.A. [Aarhus Univ. (Denmark)] [and others

1994-09-01

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

DEFF Research Database (Denmark)

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

Zhang, Dongfeng; Pang, Zengchang

2012-01-01

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cisprimertool: software to implement a comparative genomics strategy for the development of conserved intron scanning (CIS) markers.  

Science.gov (United States)

The availability of complete, annotated genomic sequence information in model organisms is a rich resource that can be extended to understudied orphan crops through comparative genomic approaches. We report here a software tool (cisprimertool) for the identification of conserved intron scanning regions using expressed sequence tag alignments to a completely sequenced model crop genome. The method used is based on earlier studies reporting the assessment of conserved intron scanning primers (called CISP) within relatively conserved exons located near exon-intron boundaries from onion, banana, sorghum and pearl millet alignments with rice. The tool is freely available to academic users at http://www.icrisat.org/gt-bt/CISPTool.htm. PMID:21585836

Jayashree, B; Jagadeesh, V T; Hoisington, D

2008-05-01

50

Optimal Weighting of Landmarks for Face Recognition  

Directory of Open Access Journals (Sweden)

Full Text Available A new method named Landmark Model Matching was recently proposed for fully automatic face recognition. It was inspired by Elastic Bunch Graph Matching and Active Shape Model. Landmark Model Matching consists of four phases: creation of the landmark distribution model, face finding, landmark finding, and recognition. A drawback in Landmark Model Matching is that, in the recognition phase, the weights given to different landmarks or facial feature points were determined experimentally. In this work, we optimized the weights given to landmarks, and thereby improved the recognition rates for the two benchmarks used.

Rajinda S. Senaratne; Saman K. Halgamuge

2006-01-01

51

Genome scan of a nonword repetition phenotype in families with dyslexia: evidence for multiple loci.  

Science.gov (United States)

To understand the genetic architecture of dyslexia and identify the locations of genes involved, we performed linkage analyses in multigenerational families using a phonological memory phenotype--Nonword Repetition (NWR). A genome scan was first performed on 438 people from 51 families (DS-1) and linkage was assessed using variance components (VC), Bayesian oligogenic (BO), and parametric analyses. For replication, the genome scan and analyses were repeated on 693 people from 93 families (DS-2). For the combined set (DS-C), analyses were performed with all three methods in the regions that were identified in both samples. In DS-1, regions on chromosomes 4p, 6q, 12p, 17q, and 22q exceeded our initial threshold for linkage, with 17q providing a parametric LOD score of 3.2. Analysis with DS-2 confirmed the locations on chromosomes 4p and 12p. The strongest VC and BO signals in both samples were on chromosome 4p in DS-C, with a parametric multipoint LOD(max) of 2.36 for the 4p locus. Our linkage analyses of NWR in dyslexia provide suggestive and reproducible evidence for linkage to 4p12 and 12p in both samples, and significant evidence for linkage to 17q in one of the samples. These results warrant further studies of phonological memory and chromosomal regions identified here in other datasets. PMID:18607713

Brkanac, Zoran; Chapman, Nicola H; Igo, Robert P; Matsushita, Mark M; Nielsen, Kathleen; Berninger, Virginia W; Wijsman, Ellen M; Raskind, Wendy H

2008-07-08

52

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

Directory of Open Access Journals (Sweden)

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

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

2007-01-01

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

Directory of Open Access Journals (Sweden)

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.

Oberbauer Anita M; Belanger Janelle M; Grossman Deborah I; Regan Kelly R; Famula Thomas R

2010-01-01

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Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus)  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus) × Holstein (Bos taurus) cross. Results Through a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy) different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23. Conclusions The experimental F2 population derived from Gyr × Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle.

Machado Marco; S Azevedo Ana; Teodoro Roberto L; Pires Maria A; CD Peixoto Maria; de Freitas Célio; Prata Márcia; Furlong John; da Silva Marcos; Guimarães Simone EF; Regitano Luciana CA; Coutinho Luiz L; Gasparin Gustavo; Verneque Rui S

2010-01-01

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A genome scan for meat quality traits in Nelore beef cattle.  

UK PubMed Central (United Kingdom)

Meat quality traits are economically important because they impact 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 (GWAS) for Warner-Bratzler shear force (WBSF) measured at different times of meat aging, backfat thickness (BFT), ribeye muscle area (REA), scanning parameters (Lightness (L*), redness (a*) and yellowness (b*) to ascertain color characteristics of meat and fat, water-holding capacity (WHC), 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.

Tizioto PC; Decker JE; Taylor JF; Schnabel RD; Mudadu MA; Silva FL; Mourão GB; Coutinho LL; Tholon P; Sonstegard TS; Rosa AN; Alencar MM; Tullio RR; Medeiros SR; Nassu RT; Feijó GL; Silva LO; Torres RA; Siqueira F; Higa RH; Regitano LC

2013-09-01

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A whole genome Bayesian scan for adaptive genetic divergence in West African cattle  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposure to new pathogens. West African cattle populations thus represent an appealing model to unravel the genome response to adaptation to tropical conditions. The purpose of this study was to identify footprints of adaptive selection at the whole genome level in a newly collected data set comprising 36,320 SNPs genotyped in 9 West African cattle populations. Results After a detailed analysis of population structure, we performed a scan for SNP differentiation via a previously proposed Bayesian procedure including extensions to improve the detection of loci under selection. Based on these results we identified 53 genomic regions and 42 strong candidate genes. Their physiological functions were mainly related to immune response (MHC region which was found under strong balancing selection, CD79A, CXCR4, DLK1, RFX3, SEMA4A, TICAM1 and TRIM21), nervous system (NEUROD6, OLFM2, MAGI1, SEMA4A and HTR4) and skin and hair properties (EDNRB, TRSP1 and KRTAP8-1). Conclusion The main possible underlying selective pressures may be related to climatic conditions but also to the host response to pathogens such as Trypanosoma(sp). Overall, these results might open the way towards the identification of important variants involved in adaptation to tropical conditions and in particular to resistance to tropical infectious diseases.

Gautier Mathieu; Flori Laurence; Riebler Andrea; Jaffrézic Florence; Laloé Denis; Gut Ivo; Moazami-Goudarzi Katayoun; Foulley Jean-Louis

2009-01-01

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A high-density SNP genome-wide linkage scan in a large autism extended pedigree.  

Science.gov (United States)

We performed a high-density, single nucleotide polymorphism (SNP), genome-wide scan on a six-generation pedigree from Utah with seven affected males, diagnosed with autism spectrum disorder. Using a two-stage linkage design, we first performed a nonparametric analysis on the entire genome using a 10K SNP chip to identify potential regions of interest. To confirm potentially interesting regions, we eliminated SNPs in high linkage disequilibrium (LD) using a principal components analysis (PCA) method and repeated the linkage results. Three regions met genome-wide significance criteria after controlling for LD: 3q13.2-q13.31 (nonparametric linkage (NPL), 5.58), 3q26.31-q27.3 (NPL, 4.85) and 20q11.21-q13.12 (NPL, 5.56). Two regions met suggestive criteria for significance 7p14.1-p11.22 (NPL, 3.18) and 9p24.3 (NPL, 3.44). All five chromosomal regions are consistent with other published findings. Haplotype sharing results showed that five of the affected subjects shared more than a single chromosomal region of interest with other affected subjects. Although no common autism susceptibility genes were found for all seven autism cases, these results suggest that multiple genetic loci within these regions may contribute to the autism phenotype in this family, and further follow-up of these chromosomal regions is warranted. PMID:18283277

Allen-Brady, K; Miller, J; Matsunami, N; Stevens, J; Block, H; Farley, M; Krasny, L; Pingree, C; Lainhart, J; Leppert, M; McMahon, W M; Coon, H

2008-02-19

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Recurrent laryngeal nerve landmarks revisited.  

UK PubMed Central (United Kingdom)

BACKGROUND: The aim of this work was to evaluate, to prove their reliability, the different surgical landmarks previously proposed as a mean to locate the recurrent laryngeal nerve (RLN). METHODS: The necks of 143 (68 male and 76 female) human adult embalmed cadavers were examined. RLN origin and length and its relationship to different landmarks were recorded and results compared with those previously reported. Statistical comparisons were performed using the chi-square test (significance, p ? .05). RESULTS: Mostly, RLN is located anterior to the tracheoesophageal sulcus (41.6%), posterior to the inferior thyroid artery (35.8%), lateral to Berry's ligament (88.1%), below the inferior rim of the inferior constrictor muscle (90.4%), and entering the larynx before its terminal division (54.6%). CONCLUSIONS: The position of the RLN in relation to those structures classically considered as landmarks is highly variable. The most reliable relationships are those with Berry's ligament or the inferior constrictor muscle.

Asgharpour E; Maranillo E; Sañudo J; Pascual-Font A; Rodriguez-Niedenführ M; Valderrama FJ; Viejo F; Parkin IG; Vázquez T

2012-09-01

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A genome-wide scan for obesity in African-Americans.  

UK PubMed Central (United Kingdom)

A genome-wide scan using 387 short tandem repeat markers was conducted for obesity among 618 black individuals from 202 families residing in a suburb of Chicago. Evidence for linkage was evaluated with BMI and percent body fat (PBF) using a variance component analysis approach. Suggestive evidence for linkage was found for BMI on chromosome 5 (logarithm of odds [LOD] score = 1.9) and PBF on chromosome 6 (LOD score = 2.7). One additional region on chromosome 3 was linked to these phenotypes at a lower level of significance (LOD score = 1.8 and 0.95 for BMI and PBF, respectively); the linked marker on this chromosome lies in the same region implicated as harboring obesity genes in a previous study of a white population. The replication of linkage evidence using different ethnic groups reinforces the potential significance of this latter candidate region.

Zhu X; Cooper RS; Luke A; Chen G; Wu X; Kan D; Chakravarti A; Weder A

2002-02-01

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A genome-wide scan for obesity in African-Americans.  

Science.gov (United States)

A genome-wide scan using 387 short tandem repeat markers was conducted for obesity among 618 black individuals from 202 families residing in a suburb of Chicago. Evidence for linkage was evaluated with BMI and percent body fat (PBF) using a variance component analysis approach. Suggestive evidence for linkage was found for BMI on chromosome 5 (logarithm of odds [LOD] score = 1.9) and PBF on chromosome 6 (LOD score = 2.7). One additional region on chromosome 3 was linked to these phenotypes at a lower level of significance (LOD score = 1.8 and 0.95 for BMI and PBF, respectively); the linked marker on this chromosome lies in the same region implicated as harboring obesity genes in a previous study of a white population. The replication of linkage evidence using different ethnic groups reinforces the potential significance of this latter candidate region. PMID:11812767

Zhu, Xiaofeng; Cooper, Richard S; Luke, Amy; Chen, Guanjie; Wu, Xiaodong; Kan, Donghui; Chakravarti, Aravinda; Weder, Alan

2002-02-01

 
 
 
 
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Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis.  

Science.gov (United States)

Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium (LD) and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, whereas no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error using multiple outlier detection approaches, multitest corrections and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan. PMID:21605221

Tice, K A; Carlon, D B

2011-05-23

62

Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis.  

UK PubMed Central (United Kingdom)

Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium (LD) and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, whereas no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error using multiple outlier detection approaches, multitest corrections and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan.

Tice KA; Carlon DB

2011-08-01

63

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

UK PubMed Central (United Kingdom)

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

Mattersdorfer K; Koblmüller S; Sefc KM

2012-07-01

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

UK PubMed Central (United Kingdom)

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

Apple JL; Grace T; Joern A; St Amand P; Wisely SM

2010-09-01

65

Genome-wide linkage scan for psoriasis susceptibility loci in multiplex Tunisian families.  

UK PubMed Central (United Kingdom)

BACKGROUND: Psoriasis is a relapsing chronic inflammatory skin disease affecting all population groups, with a peak prevalence of 3% in northern European and Scandinavian caucasians. Epidemiological studies have implicated a genetic component to psoriasis. In the past 12 years multiple genome-wide linkage analyses have identified putative susceptibility loci on several chromosomes, with a major locus in the major histocompatibility complex region. OBJECTIVES: To investigate the genetic basis of familial psoriasis in the Tunisian population using a genome-wide linkage scan in seven ultiplex psoriatic families from Tunisia. METHODS: Following single nucleotide polymorphism (SNP) genotyping on the Affymetrix 10K SNP array, we performed nonparametric linkage (NPL) multipoint analyses to identify genotypes and obtain evidence for linkage with psoriasis across the genome. RESULTS: No chromosomal region gave consistent evidence for linkage, providing evidence for genetic heterogeneity in Tunisian psoriasis families. Significant evidence for linkage of psoriasis to chromosome 2p12 was seen in one family. We also identified several regions of tentative psoriasis linkage on chromosomes 2q, 4q, 6p, 11q, 12q, 9q and 13q. One family exhibiting suggestive evidence for linkage to 17q25 (PSORS2) was identified and all affected members harboured a p.Gly117Ser mutation in CARD14 (caspase recruitment domain family, member 14), recently reported to lead to psoriasis in a large family from the U.S.A. CONCLUSIONS: Our results support the genetic heterogeneity of psoriasis in the Tunisian population, provide confirmatory evidence for a novel psoriasis locus at chromosome 2p12 and reveal a psoriasis family with a mutation at PSORS2.

Ammar M; Bouchlaka-Souissi C; Helms CA; Zaraa I; Jordan CT; Anbunathan H; Bouhaha R; Kouidhi S; Doss N; Dhaoui R; Ben Osman A; Ben Ammar El Gaied A; Marrakchi R; Mokni M; Bowcock AM

2013-03-01

66

Landmark Discrimination Learning in the Dog  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Allocentric spatial memory was studied in dogs of varying ages and sources using a landmark discrimination task. The primary goal of this study was to develop a protocol to test landmark discrimination learning in the dog. Using a modified version of a landmark test developed for use in monkeys, we ...

Milgram, Norton W.; Adams, Beth; Callahan, Heather; Head, Elizabeth; Mackay, Bill; Thirlwell, Celeste; Cotman, Carl W.

67

A Practical Subspace Approach To Landmarking  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A probabilistic, maximum aposteriori approach to finding landmarks in a face image is proposed, which provides a theoretical framework for template based landmarkers. One such landmarker, based on a likelihood ratio detector, is discussed in detail. Special attention is paid to training and implemen...

Gert Beumer; Raymond Veldhuis

68

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

DEFF Research Database (Denmark)

Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma. In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764, and D8S2324, respectively. The results from chromosomes 1 and 3 replicate previous reports of linkage. We also replicate linkage to 5q with peak LODs of 1.96 (SPT(per)) and 1.77 (IgE) at or near marker D5S1480. Our results provide further evidence implicating chromosomes 1, 3, and 5q. The current report represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders.

Webb, BT; van den Oord, E

2007-01-01

69

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

UK PubMed Central (United Kingdom)

Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma. In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD > or = 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764, and D8S2324, respectively. The results from chromosomes 1 and 3 replicate previous reports of linkage. We also replicate linkage to 5q with peak LODs of 1.96 (SPT(per)) and 1.77 (IgE) at or near marker D5S1480. Our results provide further evidence implicating chromosomes 1, 3, and 5q. The current report represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders.

Webb BT; van den Oord E; Akkari A; Wilton S; Ly T; Duff R; Barnes KC; Carlsen K; Gerritsen J; Lenney W; Silverman M; Sly P; Sundy J; Tsanakas J; von Berg A; Whyte M; Blumenthal M; Vestbo J; Middleton L; Helms PJ; Anderson WH; Pillai SG

2007-03-01

70

A genome-wide linkage scan for body mass index on Framingham Heart Study families  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Genome-wide scan data from a community-based sample was used to identify the genetic factors that affect body mass index (BMI). BMI was defined as weight (kg) over the square of height (m), where weight and height were obtained from the first measurement available between the ages of 40 and 50 years. Results Significant familial correlations were observed in mother:father (spouse) relative pairs and in all relative pairs examined except parent:daughter pairs. Single-point sib-pair regression analysis provided nominal evidence for linkage (p p-values showed results consistent with the multi-point results; all but three of the loci identified by multi-point analysis were also significant. Conclusion The largest regions of nominally significant linkage were found on chromosomes 2, 3, and 11. The most significant evidence for linkage was obtained with markers D2S1788, D2S1356, D2S1352, D3S1744, and D11S912 from multi-point sib-pair single-trait regression analysis. Our results are in agreement with some of the recently published reports on BMI using various data sets including the Framingham Heart Study data.

Moslehi Roxana; Goldstein Alisa M; Beerman Michael; Goldin Lynn; Bergen Andrew W

2003-01-01

71

A QTL genome scan of the metabolic syndrome and its component traits  

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Full Text Available Abstract Background Because high blood pressure, altered lipid levels, obesity, and diabetes so frequently occur together, they are sometimes collectively referred to as the metabolic syndrome. While there have been many studies of each metabolic syndrome trait separately, few studies have attempted to analyze them combined, i.e., as one composite variable, in quantitative trait linkage or association analysis. We used genotype and phenotype data from the Framingham Heart Study to perform a full-genome scan for quantitative trait loci underlying the metabolic syndrome. Results Heritability estimates for all of the covariate-adjusted and age- and gender-standardized individual traits, and the composite metabolic syndrome trait, were all fairly high (0.39–0.62), and the composite trait was among the highest at 0.61. The composite trait yielded no regions with suggestive linkage by Lander and Kruglyak's criteria, although there were several noteworthy regions for individual traits, some of which were also observed for the composite variable. Conclusion Despite its high heritability, the composite metabolic syndrome trait variable did not increase the power to detect or localize linkage peaks in this sample. However, this strategy and related methods of combining correlated individual traits deserve further investigation, particularly in settings with complex causal pathways.

McQueen Matthew B; Bertram Lars; Rimm Eric B; Blacker Deborah; Santangelo Susan L

2003-01-01

72

Primary genome scan for complex body shape-related traits in the common carp Cyprinus carpio.  

Science.gov (United States)

To identify quantitative trait loci (QTL) that affect body shape in common carp Cyprinus carpio, a linkage map, 2159·23 cM long, was constructed with a total of 307 markers covering 51 linkage groups (LG). The map included 167 new single nucleotide polymorphism (SNP) markers derived from expressed sequence tags (EST) together with 140 microsatellite markers reported earlier. A primary genome scan was conducted for QTL for standard length (L(S)), head length (L(H)), body height (H(B)), body width (W(B)) and tail length (L(TAIL)) in an F1 line containing 92 offspring. A total of 15 suggestive QTL on six LGs were found to associate with L(S), L(H), H(B), W(B) and L(TAIL) which explained 10·7-17·4% of the variance. Five significant QTL were detected for body-shape related traits and located for LGs (lg1, 12 and 20). These QTL included: one associated with L(S) (21·1% variance explained), three for H(B) (almost 20% variance explained) and one for W(B) (20·7% variance explained). PMID:23331142

Zhang, Y; Wang, S; Li, J; Zhang, X; Jiang, L; Xu, P; Lu, C; Wan, Y; Sun, X

2012-11-07

73

Primary genome scan for complex body shape-related traits in the common carp Cyprinus carpio.  

UK PubMed Central (United Kingdom)

To identify quantitative trait loci (QTL) that affect body shape in common carp Cyprinus carpio, a linkage map, 2159·23 cM long, was constructed with a total of 307 markers covering 51 linkage groups (LG). The map included 167 new single nucleotide polymorphism (SNP) markers derived from expressed sequence tags (EST) together with 140 microsatellite markers reported earlier. A primary genome scan was conducted for QTL for standard length (L(S)), head length (L(H)), body height (H(B)), body width (W(B)) and tail length (L(TAIL)) in an F1 line containing 92 offspring. A total of 15 suggestive QTL on six LGs were found to associate with L(S), L(H), H(B), W(B) and L(TAIL) which explained 10·7-17·4% of the variance. Five significant QTL were detected for body-shape related traits and located for LGs (lg1, 12 and 20). These QTL included: one associated with L(S) (21·1% variance explained), three for H(B) (almost 20% variance explained) and one for W(B) (20·7% variance explained).

Zhang Y; Wang S; Li J; Zhang X; Jiang L; Xu P; Lu C; Wan Y; Sun X

2013-01-01

74

A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2 tests  

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Full Text Available Abstract We performed a genome-wide association scan on the North American Rheumatoid Arthritis Consortium (NARAC) data using Hotelling's T2 tests, i.e., TH based on allele coding and TG based on genotype coding. The objective was to identify associations between single-nucleotide polymorphisms (SNPs) or markers and rheumatoid arthritis. In specific candidate gene regions, we evaluated the performance of Hotelling's T2 tests. Then Hotelling's T2 tests were used as a tool to identify new regions that contain SNPs showing strong associations with disease. As expected, the strongest association evidence was found in the region of the HLA-DRB1 locus on chromosome 6. In the region of the TRAF1-C5 genes, we identified two SNPs, rs2900180 and rs3761847, with the largest and the second largest TH and TG scores among all SNPs on chromosome 9. We also identified one SNP, rs2476601, in the region of the PTPN22 gene that had the largest TH score and the second largest TG score among all SNPs on chromosome 1. In addition, SNPs with the largest TH score on each chromosome were identified. These SNPs may be located in the regions of genes that have modest effects on rheumatoid arthritis. These regions deserve further investigation.

Chen Lianfu; Zhong Ming; Chen Wei; Amos Christopher I; Fan Ruzong

2009-01-01

75

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

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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.

Rosalia Leonardi; Daniela Giordano; Francesco Maiorana

2009-01-01

76

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

UK PubMed Central (United Kingdom)

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

Perakis P; Passalis G; Theoharis T; Kakadiaris IA

2013-07-01

77

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

UK PubMed Central (United Kingdom)

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.

Tollenaere C; Jacquet S; Ivanova S; Loiseau A; Duplantier JM; Streiff R; Brouat C

2013-01-01

78

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

UK PubMed Central (United Kingdom)

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.

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

2012-12-01

79

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

Science.gov (United States)

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. PMID:22767094

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

2012-07-05

80

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

UK PubMed Central (United Kingdom)

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

Moore AF; Jablonski KA; McAteer JB; Saxena R; Pollin TI; Franks PW; Hanson RL; Shuldiner AR; Knowler WC; Altshuler D; Florez JC

2008-09-01

 
 
 
 
81

A genome wide linkage scan for dizygotic twinning in 525 families of mothers of dizygotic twins.  

UK PubMed Central (United Kingdom)

BACKGROUND: The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning, we conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism marker panels. METHODS AND RESULTS: Non-parametric linkage analyses, including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL), produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential logarithm of odds [(exp)LOD] score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (P = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5' untranslated region of FSHR that segregated with the DZ twinning phenotype in the Utah family. CONCLUSION: Our data provide further evidence for complex inheritance of familial DZ twinning.

Painter JN; Willemsen G; Nyholt D; Hoekstra C; Duffy DL; Henders AK; Wallace L; Healey S; Cannon-Albright LA; Skolnick M; Martin NG; Boomsma DI; Montgomery GW

2010-06-01

82

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

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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.

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

2011-01-01

83

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

UK PubMed Central (United Kingdom)

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.

Nishiyama T; Takahashi K; Tango T; Pinto D; Scherer SW; Takami S; Kishino H

2011-01-01

84

Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species.  

UK PubMed Central (United Kingdom)

Recent advances in population genomics have triggered great interest in the genomic landscape of divergence in taxa with 'porous' species boundaries. One important obstable of previous studies of this topic was the low genomic coverage achieved. This issue can now be overcome by the use of 'next generation' or short-read DNA-sequencing approaches capable of assaying many thousands of single nucleotide polymorphisms (SNPs) in divergent species. We have scanned the 'porous' genomes of Populus alba and Populus tremula, two ecologically divergent hybridizing forest trees, using >38,000 SNPs assayed by restriction site associated DNA (RAD) sequencing. Windowed analyses indicate great variation in genetic divergence (e.g. the proportion of fixed SNPs) between species, and these results are unlikely to be strongly biased by genomic features of the Populus trichocarpa reference genome used for SNP calling. Divergence estimates were significantly autocorrelated (P < 0.01; Moran's I up to 0.6) along 11 of 19 chromosomes. Many of these autocorrelations involved low divergence blocks, thus suggesting that allele sharing was caused by recurrent gene flow rather than shared ancestral polymorphism. A conspicuous low divergence block of three megabases was detected on chromosome XIX, recently put forward as an incipient sex chromosome in Populus, and was largely congruent with introgression of mapped microsatellites in two natural hybrid zones (N > 400). Our results help explain the origin of the 'genomic mosaic' seen in these taxa with 'porous' genomes and suggest rampant introgression or extensive among-species conservation of an incipient plant sex chromosome. RAD sequencing holds great promise for detecting patterns of divergence and gene flow in highly divergent hybridizing species.

Stölting KN; Nipper R; Lindtke D; Caseys C; Waeber S; Castiglione S; Lexer C

2013-02-01

85

A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL  

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Full Text Available Abstract Background Identity by descent (IBD) matrix estimation is a central component in mapping of Quantitative Trait Loci (QTL) using variance component models. A large number of algorithms have been developed for estimation of IBD between individuals in populations at discrete locations in the genome for use in genome scans to detect QTL affecting various traits of interest in experimental animal, human and agricultural pedigrees. Here, we propose a new approach to estimate IBD as continuous functions rather than as discrete values. Results Estimation of IBD functions improved the computational efficiency and memory usage in genome scanning for QTL. We have explored two approaches to obtain continuous marker-bracket IBD-functions. By re-implementing an existing and fast deterministic IBD-estimation method, we show that this approach results in IBD functions that produces the exact same IBD as the original algorithm, but with a greater than 2-fold improvement of the computational efficiency and a considerably lower memory requirement for storing the resulting genome-wide IBD. By developing a general IBD function approximation algorithm, we show that it is possible to estimate marker-bracket IBD functions from IBD matrices estimated at marker locations by any existing IBD estimation algorithm. The general algorithm provides approximations that lead to QTL variance component estimates that even in worst-case scenarios are very similar to the true values. The approach of storing IBD as polynomial IBD-function was also shown to reduce the amount of memory required in genome scans for QTL. Conclusion In addition to direct improvements in computational and memory efficiency, estimation of IBD-functions is a fundamental step needed to develop and implement new efficient optimization algorithms for high precision localization of QTL. Here, we discuss and test two approaches for estimating IBD functions based on existing IBD estimation algorithms. Our approaches provide immediately useful techniques for use in single QTL analyses in the variance component QTL mapping framework. They will, however, be particularly useful in genome scans for multiple interacting QTL, where the improvements in both computational and memory efficiency are the key for successful development of efficient optimization algorithms to allow widespread use of this methodology.

Besnier Francois; Carlborg Örjan

2007-01-01

86

Looking for landmarks in medial orbital trauma surgery.  

Science.gov (United States)

Knowledge of the precise location of anatomical landmarks such as the anterior (AEC) and posterior ethmoid (PEC) canals facilitates medial orbital wall surgery and is of major importance for the protection of the orbital nerve. The aim of this study was to identify these anatomical structures in 100 consecutive CT scans and measure the distance between them. The authors investigated whether a predictable symmetry existed between the left and right side. The AEC was not identified unilaterally in one patient, the PEC was not identified unilaterally in six patients and not bilaterally in one patient. An additional PEC was found unilaterally in 12 and bilaterally in five patients. If an anatomical structure was found bilaterally, the authors obtained a strong Pearson's correlation between the sides (r=0.798-0.903, pAEC as reliable surgical landmarks in medial orbital surgery. PMID:23287107

Lethaus, B; Weigl, S; Kloss-Brandstätter, A; Kloss, F R; Kessler, P; Hölzle, F; Bangard, C

2013-01-01

87

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

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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.).

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

1994-05-01

88

Anatomic Landmarks for the First Dorsal Compartment  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Objective: Knowledge of anatomic landmarks for the first dorsal compartment can assist clinicians with management of de Quervain's disease. The radial styloid, the scaphoid tubercle, and Lister's tubercle can be used as superficial landmarks for the first dorsal compartment. Methods: Thirty-two cada...

Hazani, Ron; Engineer, Nitin J.; Cooney, Damon; Wilhelmi, Bradon J.

89

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

Directory of Open Access Journals (Sweden)

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.

Noguera José L; Rodríguez Carmen; Varona Luis; Tomàs Anna; Muñoz Gloria; Ramírez Oscar; Barragán Carmen; Arqué Meritxell; Bidanel Jean P; Amills Marcel; Ovilo Cristina; Sánchez Armand

2009-01-01

90

A genome-wide scan for human obesity genes reveals a major susceptibility locus on chromosome 10.  

Science.gov (United States)

Obesity, a common multifactorial disorder, is a major risk factor for type 2 diabetes, hypertension and coronary heart disease (CHD). According to the definition of the World Health Organization (WHO), approximately 6-10% of the population in Westernized countries are considered obese. Epidemiological studies have shown that 30-70% of the variation in body weight may be attributable to genetic factors. To date, two genome-wide scans using different obesity-related quantitative traits have provided candidate regions for obesity. We have undertaken a genome-wide scan in affected sibpairs to identify chromosomal regions linked to obesity in a collection of French families. Model-free multipoint linkage analyses revealed evidence for linkage to a region on chromosome 10p (MLS=4.85). Two further loci on chromosomes 5cen-q and 2p showed suggestive evidence for linkage of serum leptin levels in a genome-wide context. The peak on chromosome 2 coincided with the region containing the gene (POMC) encoding pro-opiomelanocortin, a locus previously linked to leptin levels and fat mass in a Mexican-American population and shown to be mutated in obese humans. Our results suggest that there is a major gene on chromosome 10p implicated in the development of human obesity, and the existence of two further loci influencing leptin levels. PMID:9806554

Hager, J; Dina, C; Francke, S; Dubois, S; Houari, M; Vatin, V; Vaillant, E; Lorentz, N; Basdevant, A; Clement, K; Guy-Grand, B; Froguel, P

1998-11-01

91

A model-based, semi-global segmentation approach for automatic 3-D point landmark localization in neuroimages.  

UK PubMed Central (United Kingdom)

The existing differential approaches for localization of 3-D anatomic point landmarks in 3-D images are sensitive to noise and usually extract numerous spurious landmarks. The parametric model-based approaches are not practically usable for localization of landmarks that can not be modeled by simple parametric forms. Some dedicated methods using anatomic knowledge to identify particular landmarks are not general enough to cope with other landmarks. In this paper, we propose a model-based, semi-global segmentation approach to automatically localize 3-D point landmarks in neuroimages. To localize a landmark, the semi-global segmentation (meaning the segmentation of a part of the studied structure in a certain neighborhood of the landmark) is first achieved by an active surface model, and then the landmark is localized by analyzing the segmented part only. The joint use of global model-to-image registration, semi-global structure registration, active surface-based segmentation, and point-anchored surface registration makes our method robust to noise and shape variation. To evaluate the method, we apply it to the localization of ventricular landmarks including curvature extrema, centerline intersections, and terminal points. Experiments with 48 clinical and 18 simulated magnetic resonance (MR) volumetric images show that the proposed approach is able to localize these landmarks with an average accuracy of 1 mm (i.e., at the level of image resolution). We also illustrate the use of the proposed approach to cortical landmark identification and discuss its potential applications ranging from computer-aided radiology and surgery to atlas registration with scans.

Liu J; Gao W; Huang S; Nowinski WL

2008-08-01

92

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

Directory of Open Access Journals (Sweden)

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

Wiener Pamela; Edriss Mohammad A; Williams John L; Waddington David; Law Andrew; Woolliams John A; Gutiérrez-Gil Beatriz

2011-01-01

93

Genome scans and candidate gene approaches in the study of common diseases and variable drug responses  

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There is both tremendous enthusiasm and controversy surrounding genetic association studies. In this article we use new methods for representing variation in the human genome that suggest as a few as 170 000 carefully selected single nucleotide polymorphisms (SNPs) are sufficient to represent all th...

Goldstein, D.B.; Ahmadi, K.R.; Weale, M.E.; Wood, N.W.

94

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Anney, Richard; Klei, Lambertus; Pinto, Dalila; Regan, Regina; Conroy, Judith; Magalhaes, Tiago; Correia, Catarina

95

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

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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...

Anney, Richard; Klei, Lambertus; Pinto, Dalila; Regan, Regina; Conroy, Judith; Magalhaes, Tiago R.; Correia, Catarina

96

Dewatering induced settlement of a historic landmark  

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Construction related dewatering in urban areas often induces damage of existing structures. The following forensic investigation highlights the complexities of such a phenomenon. Somerset plantation, a national historic landmark located in northeastern North Carolina is currently exhibiting distress...

Laefer, Debra F.; Frazier, Jon; Evans, Ashely

97

Anatomical landmarks of radical prostatecomy.  

UK PubMed Central (United Kingdom)

INTRODUCTION: In the present study, we review current literature and based on our experience, we present the anatomical landmarks of open and laparoscopic/endoscopic radical prostatectomy. METHODS: A thorough literature search was performed with the Medline database on the anatomy and the nomenclature of the structures surrounding the prostate gland. The correct handling of puboprostatic ligaments, external urethral sphincter, prostatic fascias and neurovascular bundle is necessary for avoiding malfunction of the urogenital system after radical prostatectomy. RESULTS: When evaluating new prostatectomy techniques, we should always take into account both clinical and final oncological outcomes. The present review adds further knowledge to the existing "postprostatectomy anatomical hazard" debate. It emphasizes upon the role of the puboprostatic ligaments and the course of the external urethral sphincter for urinary continence. When performing an intrafascial nerve sparing prostatectomy most urologists tend to approach as close to the prostatic capsula as possible, even though there is no concurrence regarding the nomenclature of the surrounding fascias and the course of the actual neurovascular bundles. After completion of an intrafascial technique the specimen does not contain any periprostatic tissue and thus the detection of pT3a disease is not feasible. This especially becomes problematic if the tumour reaches the resection margin. DISCUSSION: Nerve sparing open and laparoscopic radical prostatectomy should aim in maintaining sexual function, recuperating early continence after surgery, without hindering the final oncological outcome to the procedure. Despite the different approaches for radical prostatectomy the key for better results is the understanding of the anatomy of the bladder neck and the urethra.

Stolzenburg JU; Schwalenberg T; Horn LC; Neuhaus J; Constantinides C; Liatsikos EN

2007-03-01

98

Siblings with ischemic stroke study: results of a genome-wide scan for stroke loci.  

UK PubMed Central (United Kingdom)

BACKGROUND AND PURPOSE: Ischemic stroke has a strong familial component to risk. The Siblings With Ischemic Stroke Study (SWISS) is a genome-wide, family-based analysis that included use of imputed genotypes. The Siblings With Ischemic Stroke Study was conducted to examine the associations between single-nucleotide polymorphisms (SNPs) and risk of stroke and stroke subtypes within pairs. METHODS: The Siblings With Ischemic Stroke Study enrolled 312 probands with ischemic stroke from 70 US and Canadian centers. Affected siblings were ascertained by centers and confirmed by central record review; unaffected siblings were ascertained by telephone contact. Ischemic stroke was subtyped according to Trial of Org 10172 in Acute Stroke Treatment criteria. Genotyping was performed with an Illumina 610 quad array (probands) and an Illumina linkage V array (affected siblings). SNPs were imputed by using 1000 Genomes Project data and MACH software. Family-based association analyses were conducted by using the sibling transmission-disequilibrium test. RESULTS: For all pairs, the correlation of age at stroke within pairs of affected siblings was r=0.83 (95% CI, 0.78-0.86; P<2.2×10(-16)). The correlation did not differ substantially by subtype. The concordance of stroke subtypes among affected pairs was 33.8% (kappa=0.13; P=5.06×10(-4)) and did not differ by age at stroke in the proband. Although no SNP achieved genome-wide significance for risk of ischemic stroke, there was clustering of the most associated SNPs on chromosomes 3p (neuronal nitric oxide synthase) and 6p. CONCLUSIONS: Stroke subtype and age at stroke in affected sibling pairs exhibit significant clustering. No individual SNP reached genome-wide significance. However, 2 promising candidate loci were identified, including 1 that contains neuronal nitric oxide synthase, although these risk loci warrant further examination in larger sample collections.

Meschia JF; Nalls M; Matarin M; Brott TG; Brown RD Jr; Hardy J; Kissela B; Rich SS; Singleton A; Hernandez D; Ferrucci L; Pearce K; Keller M; Worrall BB

2011-10-01

99

[Genome-wide scanning in the study of risk for cerebral stroke].  

UK PubMed Central (United Kingdom)

The role of genetic predisposition to the formation of most multifactorial diseases, including stroke, was demonstrated in a number of investigations. To determine the individual genetic risk of a polygenic disease, the candidate gene approach is used most often. It is based on the analysis of polymorphic variants of certain genes taking into consideration the function of their protein product. But this approach is limited by the analysis of defined genes and does not detect new groups of genes, which involved in the pathogenesis of cerebral stroke. Genome-wide association study is a wide-range analysis of whole-genome polymorphisms, which allows to compare the distribution of allele frequencies in stroke patients and healthy individuals. The use of this method for the determination of individual genetic risk of acute stroke allows to perform molecular-genetic screening of most significant markers of stroke predisposition; to determine patients with the highest risk of stroke and to perform the mass health examination with preventive therapy prescription. The genome-wide association study to determine the individual genetic risk of stroke, taking into account ethnic origin, is performed in the Russian Federation since 2008 on the basis of the Neurological clinic of the Russian State Medical University in collaboration with the Institute of Molecular Genetics, Russian Academy of Sciences.

Skvortsova VI; Limborskaia SA; Shetova IM; Slominski? PA; Botsina AIu; Shamalov NA; Tupitsyna TV

2009-01-01

100

A genome wide association scan of bovine tuberculosis susceptibility in Holstein-Friesian dairy cattle.  

UK PubMed Central (United Kingdom)

BACKGROUND: Bovine tuberculosis is a significant veterinary and financial problem in many parts of the world. Although many factors influence infection and progression of the disease, there is a host genetic component and dissection of this may enlighten on the wider biology of host response to tuberculosis. However, a binary phenotype of presence/absence of infection presents a noisy signal for genomewide association study. METHODOLOGY/PRINCIPAL FINDINGS: We calculated a composite phenotype of genetic merit for TB susceptibility based on disease incidence in daughters of elite sires used for artificial insemination in the Irish dairy herd. This robust measure was compared with 44,426 SNP genotypes in the most informative 307 subjects in a genome wide association analysis. Three SNPs in a 65 kb genomic region on BTA 22 were associated (i.e. p<10(-5), peaking at position 59588069, p?=?4.02×10(-6)) with tuberculosis susceptibility. CONCLUSIONS/SIGNIFICANCE: A genomic region on BTA 22 was suggestively associated with tuberculosis susceptibility; it contains the taurine transporter gene SLC6A6, or TauT, which is known to function in the immune system but has not previously been investigated for its role in tuberculosis infection.

Finlay EK; Berry DP; Wickham B; Gormley EP; Bradley DG

2012-01-01

 
 
 
 
101

Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins.  

UK PubMed Central (United Kingdom)

Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We resequenced some of the positively selected sites (PSSs), within the positively selected genes, and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment.

Sun YB; Zhou WP; Liu HQ; Irwin DM; Shen YY; Zhang YP

2013-01-01

102

Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient.  

UK PubMed Central (United Kingdom)

Identification of loci with adaptive importance is a key step to understand the speciation process in natural populations, because those loci are responsible for phenotypic variation that affects fitness in different environments. We conducted an AFLP genome scan in populations of ocellated lizards (Lacerta lepida) to search for candidate loci influenced by selection along an environmental gradient in the Iberian Peninsula. This gradient is strongly influenced by climatic variables, and two subspecies can be recognized at the opposite extremes: L. lepida iberica in the northwest and L. lepida nevadensis in the southeast. Both subspecies show substantial morphological differences that may be involved in their local adaptation to the climatic extremes. To investigate how the use of a particular outlier detection method can influence the results, a frequentist method, DFDIST, and a Bayesian method, BayeScan, were used to search for outliers influenced by selection. Additionally, the spatial analysis method was used to test for associations of AFLP marker band frequencies with 54 climatic variables by logistic regression. Results obtained with each method highlight differences in their sensitivity. DFDIST and BayeScan detected a similar proportion of outliers (3-4%), but only a few loci were simultaneously detected by both methods. Several loci detected as outliers were also associated with temperature, insolation or precipitation according to spatial analysis method. These results are in accordance with reported data in the literature about morphological and life-history variation of L. lepida subspecies along the environmental gradient.

Nunes VL; Beaumont MA; Butlin RK; Paulo OS

2011-01-01

103

A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.  

UK PubMed Central (United Kingdom)

Crohn's disease (CD) is a complex disorder resulting from the interaction of intestinal microbiota with the host immune system in genetically susceptible individuals. The largest meta-analysis of genome-wide association to date identified 71 CD-susceptibility loci in individuals of European ancestry. An important epidemiological feature of CD is that it is 2-4 times more prevalent among individuals of Ashkenazi Jewish (AJ) descent compared to non-Jewish Europeans (NJ). To explore genetic variation associated with CD in AJs, we conducted a genome-wide association study (GWAS) by combining raw genotype data across 10 AJ cohorts consisting of 907 cases and 2,345 controls in the discovery stage, followed up by a replication study in 971 cases and 2,124 controls. We confirmed genome-wide significant associations of 9 known CD loci in AJs and replicated 3 additional loci with strong signal (p<5×10??). Novel signals detected among AJs were mapped to chromosomes 5q21.1 (rs7705924, combined p?=?2×10??; combined odds ratio OR?=?1.48), 2p15 (rs6545946, p?=?7×10??; OR?=?1.16), 8q21.11 (rs12677663, p?=?2×10??; OR?=?1.15), 10q26.3 (rs10734105, p?=?3×10??; OR?=?1.27), and 11q12.1 (rs11229030, p?=?8×10??; OR?=?1.15), implicating biologically plausible candidate genes, including RPL7, CPAMD8, PRG2, and PRG3. In all, the 16 replicated and newly discovered loci, in addition to the three coding NOD2 variants, accounted for 11.2% of the total genetic variance for CD risk in the AJ population. This study demonstrates the complementary value of genetic studies in the Ashkenazim.

Kenny EE; Pe'er I; Karban A; Ozelius L; Mitchell AA; Ng SM; Erazo M; Ostrer H; Abraham C; Abreu MT; Atzmon G; Barzilai N; Brant SR; Bressman S; Burns ER; Chowers Y; Clark LN; Darvasi A; Doheny D; Duerr RH; Eliakim R; Giladi N; Gregersen PK; Hakonarson H; Jones MR; Marder K; McGovern DP; Mulle J; Orr-Urtreger A; Proctor DD; Pulver A; Rotter JI; Silverberg MS; Ullman T; Warren ST; Waterman M; Zhang W; Bergman A; Mayer L; Katz S; Desnick RJ; Cho JH; Peter I

2012-01-01

104

Automated landmark extraction for orthodontic measurement of faces using the 3-camera photogrammetry methodology.  

UK PubMed Central (United Kingdom)

OBJECTIVES: To set up a three-dimensional photogrammetric scanning system for precise landmark measurements, without any physical contact, using a low-cost and noninvasive digital photogrammetric solution, for supporting several necessity in clinical orthodontics and/or surgery diagnosis. MATERIALS AND METHODS: Thirty coded targets were directly applied onto the subject's face on the soft tissue landmarks, and then, 3 simultaneous photos were acquired using photogrammetry, at room light conditions. For comparison, a dummy head was digitized both with a photogrammetric technique and with the laser scanner Minolta Vivid 910i (Konica Minolta, Tokyo, Japan). RESULTS: The precise measurement of the landmarks is ranged between 0.017 and 0.029 mm. The system automatically measures spatial position of face landmarks, from which distances and angles can be obtained. The facial measurements were compared with those done using laser scanning and manual caliper. The adopted method gives higher precision than the others (0.022-mm mean value on points and 0.038-mm mean value on linear distances on a dummy head), is simple, and can be used easily as a standard routine. CONCLUSIONS: The study demonstrated the validity of photogrammetry for accurate digitization of human face landmarks. This research points out the potential of this low-cost photogrammetry approach for medical digitization.

Deli R; Di Gioia E; Galantucci LM; Percoco G

2010-01-01

105

[Genome-wide linkage scan for an ethnic Han Chinese pedigree affected with schizophrenia].  

UK PubMed Central (United Kingdom)

OBJECTIVE: To perform genome-wide linkage analysis for an ethnic Han Chinese pedigree with schizophrenia in order to locate the susceptibility genes. METHODS: Genomic DNA was extracted from 4 mL of peripheral blood using conventional phenol-chloroform method. Illumina Infinium Linkage 24 BeadChips chip was used for determining the genotypes through detection of single nucleotide polymorphisms (SNPs). After processing the raw data using Illumina BeadStudio software, two-point nonparametric linkage analysis and two-point parametric linkage analysis were performed with Merlin software. RESULTS: By two-point nonparametric linkage analysis, 27 sites with high LOD scores (LOD=0.63-0.75, P U+003C 0.05) were identified. Among these, 3 SNPs(rs993694, rs992690 rs1861577) were located in 12p12.3 region, whilst the remainders were located in 4p12-q22 region. Two-point parametric linkage analysis under a dominant model has yielded almost identical results. CONCLUSION: Chromosomal regions 4p12-q22 and 12p12.3 probably contain susceptibility genes for schizophrenia.

Zhao LS; Wang YC; Wei JX; Liu X; Yang ZX; Li T; Chen XG; Ma XH

2013-02-01

106

Genome-wide scan for copy number variation association with age at onset of Alzheimer's disease.  

UK PubMed Central (United Kingdom)

Alzheimer's disease (AD) is a progressive neurodegenerative disease with high prevalence, which imposes a substantial public health problem. The heritability of AD is estimated at 60-80% forecasting the potential use of genetic biomarkers for risk stratification in the future. Several large scale genome-wide association studies using high frequency variants identified 10 loci accountable for only a fraction of the estimated heritability. To find the missing heritability, systematic assessment of various mutational mechanisms needs to be performed. This copy number variation (CNV) genome-wide association study with age at onset (AAO) of AD identified 5 CNV regions that may contribute to the heritability of AAO of AD. Two CNV events are intragenic causing a deletion in CPNE4. In addition, to further study the mutational load at the 10 known susceptibility loci, CNVs overlapping with these loci were also catalogued. We identified rare small events overlapping CR1 and BIN1 in AD and normal controls with opposite CNV dosage. The CR1 events are consistent with previous reports. Larger scale studies with deeper genotyping specifically addressing CNV are needed to evaluate the significance of these findings.

Szigeti K; Lal D; Li Y; Doody RS; Wilhelmsen K; Yan L; Liu S; Ma C

2013-01-01

107

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

DEFF Research Database (Denmark)

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.

Nielsen, Rasmus; Bustamente, Carlos

2005-01-01

108

Results of a whole genome scan targeting QTL for growth and carcass traits in a Piétrain × Large White intercross  

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Full Text Available Abstract We herein report the results of a whole genome scan performed in a Piétrain × Large White intercross counting 525 offspring to map QTL influencing economically important growth and carcass traits. We report experiment-wide significant lod scores (> 4.6 for meatiness and fat deposition on chromosome SSC2, and for average daily gain and carcass length on chromosome SSC7. Additional suggestive lod scores (> 3.3) for fat deposition are reported on chromosomes SSC1, SSC7 and SSC13. A significant dominance deviation was found for the QTL on SSC1, while the hypothesis of an additive QTL could not be rejected for the QTL on SSC7 and SSC13. No evidence for imprinted QTL could be found for QTL other than the one previously reported on SSC2.

Nezer Carine; Moreau Laurence; Wagenaar Danny; Georges Michel

2002-01-01

109

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

UK PubMed Central (United Kingdom)

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

Zeng YN; Shen YY; Zhang YP

2013-06-01

110

Genome-wide scan for loci of adolescent obesity and their relationship with blood pressure.  

UK PubMed Central (United Kingdom)

CONTEXT: Hypertension, typically considered a disorder of adulthood, is now emerging in adolescence. This is mainly due to the growing prevalence of obesity and the fact that excess body fat increases blood pressure (BP). OBJECTIVE: The objective of the study was to investigate whether genome-wide identified gene loci of obesity are associated with elevated BP in adolescence. DESIGN: This was a genotype-phenotype association study. SETTING: The study was conducted in a French-Canadian founder population. PARTICIPANTS: Participants included 598 adolescents, aged 12-18 yr. INTERVENTION: Testing associations between 530,011 single-nucleotide polymorphisms (SNP; Human610W-Quad BeadChip) and obesity measures and between identified SNP and BP. PRIMARY OUTCOME MEASURES: Total fat mass (TFM) was assessed with bioelectrical impedance, and body mass index (BMI) was determined with anthropometry. BP was measured beat by beat during an hour-long protocol. RESULTS: The genome-wide association studies of TFM and BMI revealed two novel and several previously identified loci of obesity. The former were PAX5 (rs16933812, TFM: P = 9.3 × 10(-9)) and MRPS22 (rs7638110, BMI: P = 4.6 × 10(-8)), and the top ones among the latter (P < 5 × 10(-4)) were MC4R (rs17773430, BMI: P = 5.8 × 10(-6)), FTO (rs9930333, BMI: P = 1.9 × 10(-4)), and MTCH2 (rs7120548, BMI: P = 1.9 × 10(-4)). From these five, only the PAX5, MRPS22, and FTO were also associated with BP; their minor allele homozygotes vs. major allele homozygotes showed greater TFM by 2.9-8.0 kg and higher BP by 3.3-6.7 mm Hg. CONCLUSIONS: Genome-wide association studies conducted in an adolescent founder population revealed two new and a number of previously identified loci of obesity and demonstrated that several but not all of these loci are also associated with elevated BP. These results begin to reveal the genetic architecture of obesity-induced hypertension.

Melka MG; Bernard M; Mahboubi A; Abrahamowicz M; Paterson AD; Syme C; Lourdusamy A; Schumann G; Leonard GT; Perron M; Richer L; Veillette S; Gaudet D; Paus T; Pausova Z

2012-01-01

111

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

Directory of Open Access Journals (Sweden)

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

Wang Xiaojing; Shaffer John R; Zeng Zhen; Begum Ferdouse; Vieira Alexandre R; Noel Jacqueline; Anjomshoaa Ida; Cuenco Karen T; Lee Myoung-Keun; Beck James; Boerwinkle Eric; Cornelis Marilyn C; Hu Frank B; Crosslin David R; Laurie Cathy C; Nelson Sarah C; Doheny Kimberly F; Pugh Elizabeth W; Polk Deborah E; Weyant Robert J; Crout Richard; McNeil Daniel W; Weeks Daniel E; Feingold Eleanor; Marazita Mary L

2012-01-01

112

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

DEFF Research Database (Denmark)

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

Kolte, Astrid Marie; Nielsen, H S

2011-01-01

113

Whole mitochondrial genome scan for population structure and selection in the Atlantic herring  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Marine fish, such as the Atlantic herring (Clupea harengus), often show a low degree of differentiation over large geographical regions. Despite strong environmental gradients (salinity and temperature) in the Baltic Sea, population genetic studies have shown little genetic differentiation among herring in this area, but some evidence for environmentally-induced selection has been uncovered. The mitochondrial genome is a likely target for selection in this system due to its functional role in metabolism. Results We sequenced whole mitochondrial genomes for herring from throughout the Baltic region (n=98) in order to investigate evidence for geographical structuring, selection, and associations between genetic and environmental variation. Three well-supported clades that predate the formation of the Baltic Sea were identified, but geographic structuring of this variation was weak (?ST = 0.036). There was evidence for significant positive selection, particularly in the ND2, ND4 and ND5 genes, and amino acids under significant selection in these genes explained some of the clade formation. Despite uncovering evidence for selection, correlations between genetic diversity or differentiation with environmental factors (temperature, salinity, latitude) were weak. Conclusions The results indicate that most of the current mtDNA diversity in herring predates the formation of the Baltic Sea, and that little structuring has evolved since. Thus, fisheries management units in this region cannot be determined on the basis of mtDNA variability. Preliminary evidence for selection underlying clade formation indicates that the NADH complex may be useful for examining adaptation and population structuring at a broader geographical scale.

Teacher Amber GF; André Carl; Merilä Juha; Wheat Christopher W

2012-01-01

114

A genome-wide linkage scan for steroids and SHBG levels in black and white families: the HERITAGE Family Study.  

UK PubMed Central (United Kingdom)

To identify loci-harboring genes affecting steroid hormone and SHBG plasma levels, a genomic-wide scan was performed in the HERITAGE Family Study at baseline. The following steroid hormones were assayed: androstane-3 alpha, 17 beta-diol glucuronide, androsterone glucuronide, cortisol, dihydrotestosterone, estradiol, 17-hydroxyprogesterone (OH-PROG), progesterone (PROG), pregnenolone ester, and testosterone. A total of 509 markers on the 22 autosomes were genotyped, and a maximum of 357 pairs of siblings from white families and 103 from black families were available for the study. Significant linkages with LOD scores over 3.6 (P < 2.2 x 10(-5)) for SHBG were observed in blacks on 1q44 (D1S321), 5p13.3 (D5S1986), 10q24.1 (D10S1239), and 12q12 (D12S1653) in both singlepoint and multipoint analyses. Promising evidence of linkage (1.75 < LOD < 3.6; 2.2 x 10(-5) < P < 0.0023) for SHBG was observed on 1q44 in singlepoint analysis in whites. In addition, several other loci in blacks exhibited promising evidence of linkage, suggesting that many genes can potentially regulate SHBG levels. In the case of C21 steroids, promising linkages were found on 1q43 (D1S517) for PROG, 2p25.1 (D2S1400) for pregnenolone ester, and 18q21.32 (D18S38) for OH-PROG in whites and on 3q25.33 (D3S1763) for OH-PROG in blacks, both singlepoint and multipoint analyses (P < 0.0023). The strongest signals for C19 steroids were found on 22q12.3 for testosterone in whites (P = 0.0024 in multipoint) and on 8q22.1 for dihydrotestosterone in blacks. In blacks, the strongest evidence of linkage for estradiol (C18 steroid) was provided by marker D1S1588 on 1p21.3 and in whites by markers D2S2374 and D2S2347 on 2p21, and D6S465 on 6p12.3. Several genes encoding enzymes of the steroid biosynthesis pathways but also other potential candidate genes were located in the vicinity of the genomic regions showing evidence of linkage in this genomic scan.

Ukkola O; Rankinen T; Gagnon J; Leon AS; Skinner JS; Wilmore JH; Rao DC; Bouchard C

2002-08-01

115

A genome-wide linkage scan for steroids and SHBG levels in black and white families: the HERITAGE Family Study.  

Science.gov (United States)

To identify loci-harboring genes affecting steroid hormone and SHBG plasma levels, a genomic-wide scan was performed in the HERITAGE Family Study at baseline. The following steroid hormones were assayed: androstane-3 alpha, 17 beta-diol glucuronide, androsterone glucuronide, cortisol, dihydrotestosterone, estradiol, 17-hydroxyprogesterone (OH-PROG), progesterone (PROG), pregnenolone ester, and testosterone. A total of 509 markers on the 22 autosomes were genotyped, and a maximum of 357 pairs of siblings from white families and 103 from black families were available for the study. Significant linkages with LOD scores over 3.6 (P 10q24.1 (D10S1239), and 12q12 (D12S1653) in both singlepoint and multipoint analyses. Promising evidence of linkage (1.75 < LOD < 3.6; 2.2 x 10(-5) < P < 0.0023) for SHBG was observed on 1q44 in singlepoint analysis in whites. In addition, several other loci in blacks exhibited promising evidence of linkage, suggesting that many genes can potentially regulate SHBG levels. In the case of C21 steroids, promising linkages were found on 1q43 (D1S517) for PROG, 2p25.1 (D2S1400) for pregnenolone ester, and 18q21.32 (D18S38) for OH-PROG in whites and on 3q25.33 (D3S1763) for OH-PROG in blacks, both singlepoint and multipoint analyses (P < 0.0023). The strongest signals for C19 steroids were found on 22q12.3 for testosterone in whites (P = 0.0024 in multipoint) and on 8q22.1 for dihydrotestosterone in blacks. In blacks, the strongest evidence of linkage for estradiol (C18 steroid) was provided by marker D1S1588 on 1p21.3 and in whites by markers D2S2374 and D2S2347 on 2p21, and D6S465 on 6p12.3. Several genes encoding enzymes of the steroid biosynthesis pathways but also other potential candidate genes were located in the vicinity of the genomic regions showing evidence of linkage in this genomic scan. PMID:12161500

Ukkola, Olavi; Rankinen, Tuomo; Gagnon, Jacques; Leon, Arthur S; Skinner, James S; Wilmore, Jack H; Rao, D C; Bouchard, Claude

2002-08-01

116

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

Science.gov (United States)

To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N?=?38,580) informative for adult waist circumference (WC) and waist–hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P?=?1.9×10?11) and MSRA (WC, P?=?8.9×10?9). A third locus, near LYPLAL1, was associated with WHR in women only (P?=?2.6×10?8). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.

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

2009-01-01

117

TINA manual landmarking tool: software for the precise digitization of 3D landmarks.  

UK PubMed Central (United Kingdom)

BACKGROUND: Interest in the placing of landmarks and subsequent morphometric analyses of shape for 3D data has increased with the increasing accessibility of computed tomography (CT) scanners. However, current computer programs for this task suffer from various practical drawbacks. We present here a free software tool that overcomes many of these problems. RESULTS: The TINA Manual Landmarking Tool was developed for the digitization of 3D data sets. It enables the generation of a modifiable 3D volume rendering display plus matching orthogonal 2D cross-sections from DICOM files. The object can be rotated and axes defined and fixed. Predefined lists of landmarks can be loaded and the landmarks identified within any of the representations. Output files are stored in various established formats, depending on the preferred evaluation software. CONCLUSIONS: The software tool presented here provides several options facilitating the placing of landmarks on 3D objects, including volume rendering from DICOM files, definition and fixation of meaningful axes, easy import, placement, control, and export of landmarks, and handling of large datasets. The TINA Manual Landmark Tool runs under Linux and can be obtained for free from http://www.tina-vision.net/tarballs/.

Schunke AC; Bromiley PA; Tautz D; Thacker NA

2012-01-01

118

TINA manual landmarking tool: software for the precise digitization of 3D landmarks  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Interest in the placing of landmarks and subsequent morphometric analyses of shape for 3D data has increased with the increasing accessibility of computed tomography (CT) scanners. However, current computer programs for this task suffer from various practical drawbacks. We present here a free software tool that overcomes many of these problems. Results The TINA Manual Landmarking Tool was developed for the digitization of 3D data sets. It enables the generation of a modifiable 3D volume rendering display plus matching orthogonal 2D cross-sections from DICOM files. The object can be rotated and axes defined and fixed. Predefined lists of landmarks can be loaded and the landmarks identified within any of the representations. Output files are stored in various established formats, depending on the preferred evaluation software. Conclusions The software tool presented here provides several options facilitating the placing of landmarks on 3D objects, including volume rendering from DICOM files, definition and fixation of meaningful axes, easy import, placement, control, and export of landmarks, and handling of large datasets. The TINA Manual Landmark Tool runs under Linux and can be obtained for free from http://www.tina-vision.net/tarballs/.

Schunke Anja C; Bromiley Paul A; Tautz Diethard; Thacker Neil A

2012-01-01

119

Genome-wide scan identifies loci associated with classical BSE occurrence.  

UK PubMed Central (United Kingdom)

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. Sequence variations in the coding region of the prion gene (PRNP) have been associated with acquired transmissible spongiform encephalopathy (TSE) susceptibility in mammals; however, this is not the case in cattle. It has been hypothesized that genes, in addition to the prion gene, contribute to genetic susceptibility of acquired TSEs. Accordingly, genetic studies of classical BSE in cattle identified loci other than PRNP that are associated with disease incidence. The objective of this study was to utilize a genome-wide association study to test for genetic loci associated with classical BSE. The samples include 143 BSE affected (case) and 173 unaffected half sib (control) animals collected in the mid 1990s in Southern England. The data analysis identifies loci on two different chromosomes associated with BSE disease occurrence. Most notable is a single nucleotide polymorphism on chromosome 1 at 29.15 Mb that is associated with BSE disease (p = 3.09E-05). Additionally, a locus on chromosome 14, within a cluster of SNPs showed a trend toward significance (p = 5.24E-05). It is worth noting that in a human vCJD study markers on human chromosome 8, a region with shared synteny to the region identified on cattle chromosome 14, were associated with disease. Further, our candidate genes appear to have plausible biological relevance with the known etiology of TSE disease. One of the candidate genes is hypothetical gene LOC521010, similar to FK506 binding protein 2 located on chromosome 1 at 29.32 Mb. This gene encodes a protein that is a member of the immunophilin protein family and is involved in basic cellular processes including protein folding. The chromosomal regions identified in this study and candidate genes within these regions merit further investigation.

Murdoch BM; Murdoch GK; Settles M; McKay S; Williams JL; Moore SS

2011-01-01

120

Genome-wide scan identifies loci associated with classical BSE occurrence.  

Science.gov (United States)

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. Sequence variations in the coding region of the prion gene (PRNP) have been associated with acquired transmissible spongiform encephalopathy (TSE) susceptibility in mammals; however, this is not the case in cattle. It has been hypothesized that genes, in addition to the prion gene, contribute to genetic susceptibility of acquired TSEs. Accordingly, genetic studies of classical BSE in cattle identified loci other than PRNP that are associated with disease incidence. The objective of this study was to utilize a genome-wide association study to test for genetic loci associated with classical BSE. The samples include 143 BSE affected (case) and 173 unaffected half sib (control) animals collected in the mid 1990s in Southern England. The data analysis identifies loci on two different chromosomes associated with BSE disease occurrence. Most notable is a single nucleotide polymorphism on chromosome 1 at 29.15 Mb that is associated with BSE disease (p = 3.09E-05). Additionally, a locus on chromosome 14, within a cluster of SNPs showed a trend toward significance (p = 5.24E-05). It is worth noting that in a human vCJD study markers on human chromosome 8, a region with shared synteny to the region identified on cattle chromosome 14, were associated with disease. Further, our candidate genes appear to have plausible biological relevance with the known etiology of TSE disease. One of the candidate genes is hypothetical gene LOC521010, similar to FK506 binding protein 2 located on chromosome 1 at 29.32 Mb. This gene encodes a protein that is a member of the immunophilin protein family and is involved in basic cellular processes including protein folding. The chromosomal regions identified in this study and candidate genes within these regions merit further investigation. PMID:22073200

Murdoch, Brenda M; Murdoch, Gordon K; Settles, Matthew; McKay, Stephanie; Williams, John L; Moore, Stephen S

2011-11-04

 
 
 
 
121

A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Identifying the genes that influence levels of pro-inflammatory molecules can help to elucidate the mechanisms underlying this process. We first conducted a two-stage genome-wide association scan (GWAS) for the key inflammatory biomarkers Interleukin-6 (IL-6), the general measure of inflammation ery...

Naitza, Silvia; Porcu, Eleonora; Steri, Maristella; Taub, Dennis D.; Mulas, Antonella; Xiao, Xiang; Strait, James

122

Landmark papers on photorefractive nonlinear optics  

CERN Multimedia

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

Yeh, Pochi

1995-01-01

123

A Genome-wide Admixture Scan for Ancestry-linked Genes Predisposing to Sarcoidosis in African Americans  

Science.gov (United States)

Genome-wide linkage and association studies have uncovered variants associated with sarcoidosis, a multi-organ granulomatous inflammatory disease. African ancestry may influence disease pathogenesis since African Americans are more commonly affected by sarcoidosis. Therefore, we conducted the first sarcoidosis genome-wide ancestry scan using a map of 1,384 highly ancestry informative single nucleotide polymorphisms genotyped on 1,357 sarcoidosis cases and 703 unaffected controls self-identified as African American. The most significant ancestry association was at marker rs11966463 on chromosome 6p22.3 (ancestry association risk ratio (aRR)= 1.90; p=0.0002). When we restricted the analysis to biopsy-confirmed cases, the aRR for this marker increased to 2.01; p=0.00007. Among the eight other markers that demonstrated suggestive ancestry associations with sarcoidosis were rs1462906 on chromosome 8p12 which had the most significant association with European ancestry (aRR=0.65; p=0.002), and markers on chromosomes 5p13 (aRR=1.46; p=0.005) and 5q31 (aRR=0.67; p=0.005), which correspond to regions we previously identified through sib pair linkage analyses. Overall, the most significant ancestry association for Scadding stage IV cases was to marker rs7919137 on chromosome 10p11.22 (aRR=0.27; p=2×10?5), a region not associated with disease susceptibility. In summary, through admixture mapping of sarcoidosis we have confirmed previous genetic linkages and identified several novel putative candidate loci for sarcoidosis.

Rybicki, Benjamin A.; Levin, Albert M.; McKeigue, Paul; Datta, Indrani; Gray-McGuire, Courtney; Colombo, Marco; Reich, David; Burke, Robert R.; Iannuzzi, Michael C.

2010-01-01

124

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

2000-03-01

125

Looking for landmarks in medial orbital trauma surgery.  

UK PubMed Central (United Kingdom)

Knowledge of the precise location of anatomical landmarks such as the anterior (AEC) and posterior ethmoid (PEC) canals facilitates medial orbital wall surgery and is of major importance for the protection of the orbital nerve. The aim of this study was to identify these anatomical structures in 100 consecutive CT scans and measure the distance between them. The authors investigated whether a predictable symmetry existed between the left and right side. The AEC was not identified unilaterally in one patient, the PEC was not identified unilaterally in six patients and not bilaterally in one patient. An additional PEC was found unilaterally in 12 and bilaterally in five patients. If an anatomical structure was found bilaterally, the authors obtained a strong Pearson's correlation between the sides (r=0.798-0.903, p<0.001). An anatomical variation was found in nearly every fourth patient. The authors think that these data call into question the use of the PEC and AEC as reliable surgical landmarks in medial orbital surgery.

Lethaus B; Weigl S; Kloss-Brandstätter A; Kloss FR; Kessler P; Hölzle F; Bangard C

2013-02-01

126

Bivariate genome scans incorporating factor and principal component analyses to identify common genetic components of alcoholism, event-related potential, and electroencephalogram phenotypes  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Genetic components significantly contribute to the susceptibilities of alcoholism and its endophenotypes, such as event-related potential measures and electroencephalogram. An endophenotype is a correlated trait which identifies individuals at risk. Correlated traits could be influenced by shared genes. This study is intended to identify chromosome regions that may harbor common genetic loci contributing to alcoholism, event related potential measures and electroencephalogram. All 143 Collaborative Study on the Genetics of Alcoholism families with 1,614 individuals provided by the Genetic Analysis Workshop 14 were used for the analysis with aldx1 as an alcoholism diagnosis. We carried out factor and principal component analyses on the 12 event-related potentials, then bivariate genome scans on aldx1 and electroencephalogram (ecb21), as well as alcoholism and the principal component scores of the event-related potential measures. A univariate genome scan was also carried out on each trait. Factor and principal component analysis on the event-related potential measures showed that the 4 ttths and 4 ntths belong to one cluster (cluster 1), while the 4 ttdts belonged to another (cluster 2). From each cluster, one principal component was extracted and saved as pc1 (for cluster 1) and pc2 (for cluster 2). The results of genome scans revealed only one chromosome region, chromosome 4 q at about 100 cM, identified by several univariate genome scans including aldx1, ecb21, and pc2, and the evidence of linkage increased significantly in the bivariate genome scans of aldx1 and ecb21 and aldx1 and pc2. Our study suggests that the same quantitative trait locus on the chromosome 4 q region, where ADH3 is located, may influence the risk of alcoholism, variations of electroencephalogram, and the 4 ttdts of the event-related potential measures.

Lin Jing-Ping; Wu Colin

2005-01-01

127

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

UK PubMed Central (United Kingdom)

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 association with TNIP1 variants, together with tissular and cellular investigations, suggests that this pathway has a critical role in regulating autoimmunity and SSc pathogenesis.

Allanore Y; Saad M; Dieudé P; Avouac J; Distler JH; Amouyel P; Matucci-Cerinic M; Riemekasten G; Airo P; Melchers I; Hachulla E; Cusi D; Wichmann HE; Wipff J; Lambert JC; Hunzelmann N; Tiev K; Caramaschi P; Diot E; Kowal-Bielecka O; Valentini G; Mouthon L; Czirják L; Damjanov N; Salvi E; Conti C; Müller M; Müller-Ladner U; Riccieri V; Ruiz B; Cracowski JL; Letenneur L; Dupuy AM; Meyer O; Kahan A; Munnich A; Boileau C; Martinez M

2011-07-01

128

Remembered landmarks enhance the precision of path integration  

Directory of Open Access Journals (Sweden)

Full Text Available When navigating by path integration, knowledge of one?s position becomes increasingly uncertain as one walks from a known location. This uncertainty decreases if one perceives a known landmark location nearby. We hypothesized that remembering landmarks might serve a similar purpose for path integration as directly perceiving them. If this is true, walking near a remembered landmark location should enhance response consistency in path integration tasks. To test this, we asked participants to view a target and then attempt to walk to it without vision. Some participants saw the target plus a landmark during the preview. Compared with no-landmark trials, response consistency nearly doubled when participants passed near the remembered landmark location. Similar results were obtained when participants could audibly perceive the landmark while walking. A control experiment ruled out perceptual context effects during the preview. We conclude that remembered landmarks can enhance path integration even though they are not directly perceived.

John W. Philbeck; Shannon O´Leary

2005-01-01

129

The genetics of obesity in Mexican Americans: the evidence from genome scanning efforts in the San Antonio family heart study.  

UK PubMed Central (United Kingdom)

Recent estimates indicate that approximately 18% of the population in the United States can be considered obese (defined as a body mass index [BMI] > or = 30), and this rate is even higher among ethnic populations such as Mexican Americans. This figure becomes very significant given the strong evidence for obesity as a major risk factor for a variety of chronic diseases including type 2 diabetes mellitus and coronary heart disease. The search for genes involved in the expression of obesity has been one of the focal points of the San Antonio Family Heart Study (SAFHS), a large, family-based study to examine the genetics of risk for atherosclerosis in Mexican Americans. To date, our genome scanning effort has reported two quantitative trait loci (QTLs) with pronounced effects on the expression of a variety of obesity--related phenotypes (e.g., leptin levels, fat mass, and BMI) located on chromosomes 2 and 8. We are currently working to further refine these signals and to identify the genes and allelic variants involved. Here, we summarize the latest results from our ongoing efforts to identify obesity genes in the San Antonio Family Heart Study.

Comuzzie AG; Mitchell BD; Cole S; Martin LJ; Hsueh WC; Rainwater DL; Almasy L; Stern MP; Hixson J; MacCluer JW; Blangero J

2003-10-01

130

The genetics of obesity in Mexican Americans: the evidence from genome scanning efforts in the San Antonio family heart study.  

Science.gov (United States)

Recent estimates indicate that approximately 18% of the population in the United States can be considered obese (defined as a body mass index [BMI] > or = 30), and this rate is even higher among ethnic populations such as Mexican Americans. This figure becomes very significant given the strong evidence for obesity as a major risk factor for a variety of chronic diseases including type 2 diabetes mellitus and coronary heart disease. The search for genes involved in the expression of obesity has been one of the focal points of the San Antonio Family Heart Study (SAFHS), a large, family-based study to examine the genetics of risk for atherosclerosis in Mexican Americans. To date, our genome scanning effort has reported two quantitative trait loci (QTLs) with pronounced effects on the expression of a variety of obesity--related phenotypes (e.g., leptin levels, fat mass, and BMI) located on chromosomes 2 and 8. We are currently working to further refine these signals and to identify the genes and allelic variants involved. Here, we summarize the latest results from our ongoing efforts to identify obesity genes in the San Antonio Family Heart Study. PMID:14763601

Comuzzie, Anthony G; Mitchell, Braxton D; Cole, Shelley; Martin, Lisa J; Hsueh, Wen-Chi; Rainwater, David L; Almasy, Laura; Stern, Michael P; Hixson, James; MacCluer, Jean W; Blangero, John

2003-10-01

131

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

DEFF Research Database (Denmark)

Maturity-onset diabetes of the young (MODY) is a heterogeneous single gene disorder characterized by non-insulin-dependent diabetes, an early onset and autosomal dominant inheritance. Mutations in six genes have been shown to cause MODY. Approximately 15-20% of families fitting MODY criteria do not have mutations in any of the known genes. These families provide a rich resource for the identification of new MODY genes. This will potentially enable further dissection of clinical heterogeneity and bring new insights into mechanisms of beta-cell dysfunction. To facilitate the identification of novel MODY loci, we combined the results from three genome-wide scans on a total of 23 families fitting MODY criteria. We used both a strict parametric model of inheritance with heterogeneity and a model-free analysis. We did not identify any single novel locus but provided putative evidence for linkage to chromosomes 6 (nonparametric linkage [NPL]score 2.12 at 71 cM) and 10 (NPL score 1.88 at 169-175 cM), and to chromosomes 3 (heterogeneity LOD [HLOD] score 1.27 at 124 cM) and 5 (HLOD score 1.22 at 175 cM) in 14 more strictly defined families. Our results provide evidence for further heterogeneity in MODY.

Frayling, Timothy M; Lindgren, Cecilia M

2003-01-01

132

Genome scan of the mitten crab Eriocheir sensu stricto in East Asia: population differentiation, hybridization and adaptive speciation.  

Science.gov (United States)

We examine the genetic structure and evolutionary history of the mitten crab Eriocheir sensu stricto in East Asia by employing a genome scan - amplified fragment length polymorphism. Population analysis reveals three divergent clades in Eriocheir s. s., which dominate the East China Sea-Yellow Sea, the Sea of Japan (plus Okinawa) and the South China Sea, respectively, mostly in agreement with our previous mtDNA analysis. With the tropical South China Sea inferred as the origin, the East China Sea-Yellow Sea and the Sea of Japan clades in the north diverged successively from the ancestral clade during the mid-Pleistocene. The divergence of the three clades likely resulted from isolation of the three marginal seas caused by sea level change in the Pleistocene. Two sympatric zones, one of the East China Sea-Yellow Sea and the South China Sea clades in southeast China and the other of the East China Sea-Yellow Sea and the Sea of Japan clades in Vladivostok, are demonstrated to be hybrid zones, with hybridization occurring currently in the former but historically in the latter. Adaptive speciation is observed in the divergence process of the three clades, possibly because of selection from accumulated temperature. Our study indicates that the genetic structure and evolutionary history of Eriocheir s. s. have been primarily affected by Pleistocene glacial cycles, secondarily by divergent selection and drainage isolation, but only minimally by human activities. PMID:22465485

Xu, Jiawu; Chu, Ka Hou

2012-03-24

133

Genome scan of the mitten crab Eriocheir sensu stricto in East Asia: population differentiation, hybridization and adaptive speciation.  

UK PubMed Central (United Kingdom)

We examine the genetic structure and evolutionary history of the mitten crab Eriocheir sensu stricto in East Asia by employing a genome scan - amplified fragment length polymorphism. Population analysis reveals three divergent clades in Eriocheir s. s., which dominate the East China Sea-Yellow Sea, the Sea of Japan (plus Okinawa) and the South China Sea, respectively, mostly in agreement with our previous mtDNA analysis. With the tropical South China Sea inferred as the origin, the East China Sea-Yellow Sea and the Sea of Japan clades in the north diverged successively from the ancestral clade during the mid-Pleistocene. The divergence of the three clades likely resulted from isolation of the three marginal seas caused by sea level change in the Pleistocene. Two sympatric zones, one of the East China Sea-Yellow Sea and the South China Sea clades in southeast China and the other of the East China Sea-Yellow Sea and the Sea of Japan clades in Vladivostok, are demonstrated to be hybrid zones, with hybridization occurring currently in the former but historically in the latter. Adaptive speciation is observed in the divergence process of the three clades, possibly because of selection from accumulated temperature. Our study indicates that the genetic structure and evolutionary history of Eriocheir s. s. have been primarily affected by Pleistocene glacial cycles, secondarily by divergent selection and drainage isolation, but only minimally by human activities.

Xu J; Chu KH

2012-07-01

134

Linkage analysis of alcoholism-related electrophysiological phenotypes: genome scans with microsatellites compared to single-nucleotide polymorphisms  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract P300 amplitude is an electrophysiological quantitative trait that is correlated with both alcoholism and smoking status. Using the Collaborative Study on the Genetics of Alcoholism data, we performed model-free linkage analysis to investigate the relationship between alcoholism, P300 amplitude, and habitual smoking. We also analyzed the effect of parent-of-origin on alcoholism, and utilized both microsatellites (MS) markers and single-nucleotide polymorphisms (SNPs). We found significant evidence of linkage for alcoholism to chromosome 10; inclusion of P300 amplitude as a covariate provided additional evidence of linkage to chromosome 12. This same region on chromosome 12 showed some evidence for a parent-of-origin effect. We found evidence of linkage for the P300 phenotype to chromosome 7 in non-smokers, and to chromosome 17 in alcoholics. The effects of alcoholism and habitual smoking on P300 amplitude appear to have separate genetic determinants. Overall, there were few differences between MS and SNP genome scans. The use of covariates and parent-of-origin effects allowed detection of linkage not seen otherwise.

Bautista Jocelyn F; Quade Shannon RE; Parrado Antonio R; Goddard Katrina AB

2005-01-01

135

A study on the reproducibility of cephalometric landmarks when undertaking a three-dimensional (3D) cephalometric analysis.  

UK PubMed Central (United Kingdom)

OBJECTIVES: Cone Beam Computerized Tomography (CBCT) allows the possibility of modifying some of the diagnostic tools used in orthodontics, such as cephalometry. The first step must be to study the characteristics of these devices in terms of accuracy and reliability of the most commonly used landmarks. The aims were 1- To assess intra and inter-observer reliability in the location of anatomical landmarks belonging to hard tissues of the skull in images taken with a CBCT device, 2- To determine which of those landmarks are more vs. less reliable and 3- To introduce planes of reference so as to create cephalometric analyses appropriated to the 3D reality. STUDY DESIGN: Fifteen patients who had a CBCT (i-CAT) as a diagnostic register were selected. To assess the reproducibility on landmark location and the differences in the measurements of two observers at different times, 41 landmarks were defined on the three spatial axes (X,Y,Z) and located. 3.690 measurements were taken and, as each determination has 3 coordinates, 11.070 data were processed with SPSS statistical package. To discover the reproducibility of the method on landmark location, an ANOVA was undertaken using two variation factors: time (t1, t2 and t3) and observer (Ob1 and Ob2) for each axis (X, Y and Z) and landmark. The order of the CBCT scans submitted to the observers (Ob1, Ob2) at t1, t2, and t3, were different and randomly allocated. Multiple comparisons were undertaken using the Bonferroni test. The intra- and inter-examiner ICC's were calculated. RESULTS: Intra- and interexaminer reliability was high, both being ICC ? 0.99, with the best frequency on axis Z. CONCLUSIONS: The most reliable landmarks were: Nasion, Sella, Basion, left Porion, point A, anterior nasal spine, Pogonion, Gnathion, Menton, frontozygomatic sutures, first lower molars and upper and lower incisors. Those with less reliability were the supraorbitals, right zygion and posterior nasal spine.

Zamora N; Llamas JM; Cibrián R; Gandia JL; Paredes V

2012-07-01

136

Precision of identifying cephalometric landmarks with cone beam computed tomography in vivo.  

UK PubMed Central (United Kingdom)

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 two types of images: 1. axial, coronal, and sagittal MPR images and 2. 3D surface models. Eleven observers identified 22 cephalometric landmarks on 3D surface models first and then using 3D in combination with MPR images twice independently. Tracing time was recorded in both methods. Precision was defined as the absolute difference between an observer's repeated measurements and the mean of all measurements per landmark. Inter- and intra-observer agreements were defined as the absolute difference of the observers' measurements from each other and from their repeated measurements averaged over all landmarks, respectively. The precision of measurements ranged between 0.29 ± 0.17 and 2.82 ± 7.53. Adding MPR alongside, 3D surfaces improved the precision of tracing for 15 of 22 of the landmark but it took on average twice as much time. Mean time required to trace one patient was 6:03 ± 2:48 and 10:41 ± 4:01 minutes for 3D and 3D + MPR, respectively (P = 0.0001).

Hassan B; Nijkamp P; Verheij H; Tairie J; Vink C; van der Stelt P; van Beek H

2013-02-01

137

Anatomic landmarks in the sleeve gastrectomy.  

UK PubMed Central (United Kingdom)

BACKGROUND AND OBJECTIVES: The vertical sleeve gastrectomy is a common bariatric procedure. The operation is relatively standard, but there are still variations among surgeons. The two main variations are bougie size and extent of distal resection. Some surgeons will start the gastric resection at 2 cm proximal to the pylorus, whereas others start at 6 cm. Our hypothesis is that there are anatomic landmarks that are constant and can be used to help standardize the procedure. METHODS: Twenty-eight morbidly obese patients undergoing laparoscopic bariatric surgery (gastric bypass or sleeve gastrectomy) had the distance from the pylorus to the second branch of the right gastroepiploic artery on the inferior border of the greater curvature of the stomach measured. Body mass index, height, weight, age, and sex were also analyzed. RESULTS: The study comprised 22 women and 6 men with a mean age of 46.2 years (range, 22-68 years). The mean body mass index was 43.2 kg/m(2) (range, 37.2-62.4 kg/m(2)). The mean distance from the pylorus to the second branch of the right gastroepiploic vessel was 4.52 cm (range, 3.5-5.5 cm). CONCLUSION: The second branch of the right gastroepiploic artery can be used as a constant anatomic landmark. It is found about 4.5 cm from the pylorus. This can be safely used as a landmark for marking the distal extent of resection during a vertical sleeve gastrectomy and obviates the need to formally measure the distance from the pylorus.

Clapp B

2013-01-01

138

Acetabular orientation with different pelvic registration landmarks.  

Science.gov (United States)

This study determined the relationship of various pelvic landmarks to the pelvic plane in the lateral position. Five whole-body cadavers were used in this study. All navigation data were collected using the OrthoPilot navigation system (B. Braun Aesculap, Tuttlingen, Germany) to register all landmarks. The pelvic plane was registered with the body in the supine position for comparison. The ipsilateral posterosuperior iliac spine (PSIS) and contralateral PSIS were registered for comparison of the line made by the 2 anterosuperior iliac spines (ASIS) in the supine position. Registration points along the acetabular rim at the 12-, 3-, and 9-o'clock positions were recorded, and the transverse acetabular ligament (TAL) was registered using the ends and middle of the ligament for the 3 registration points. Inclination as determined by the TAL was 49.7 degrees +/-25.8 degrees , whereas the acetabular rim resulted in an inclination of 36.3 degrees +/-7.2 degrees . When the interspinal posterior line was calculated, the difference in inclination compared with the pelvic plane was 1.8 degrees +/-1.7 degrees . Anteversion using the acetabular rim resulted in a difference of 8.1 degrees +/-4.9 degrees and using the TAL resulted in a difference of 13.4 degrees +/-7.9 degrees . The difference in anteversion using the pelvic plane and the posterior interspinal line was 1.2 degrees +/-1.3 degrees . This study determined that the alternative landmarks of the acetabular rim and the TAL were not as accurate as using the posterior interspinal line as determined by registering the PSIS. PMID:19835300

Mihalko, William M; Kammerzell, Sergej; Saleh, Khaled J

2009-10-01

139

Acetabular orientation with different pelvic registration landmarks.  

UK PubMed Central (United Kingdom)

This study determined the relationship of various pelvic landmarks to the pelvic plane in the lateral position. Five whole-body cadavers were used in this study. All navigation data were collected using the OrthoPilot navigation system (B. Braun Aesculap, Tuttlingen, Germany) to register all landmarks. The pelvic plane was registered with the body in the supine position for comparison. The ipsilateral posterosuperior iliac spine (PSIS) and contralateral PSIS were registered for comparison of the line made by the 2 anterosuperior iliac spines (ASIS) in the supine position. Registration points along the acetabular rim at the 12-, 3-, and 9-o'clock positions were recorded, and the transverse acetabular ligament (TAL) was registered using the ends and middle of the ligament for the 3 registration points. Inclination as determined by the TAL was 49.7 degrees +/-25.8 degrees , whereas the acetabular rim resulted in an inclination of 36.3 degrees +/-7.2 degrees . When the interspinal posterior line was calculated, the difference in inclination compared with the pelvic plane was 1.8 degrees +/-1.7 degrees . Anteversion using the acetabular rim resulted in a difference of 8.1 degrees +/-4.9 degrees and using the TAL resulted in a difference of 13.4 degrees +/-7.9 degrees . The difference in anteversion using the pelvic plane and the posterior interspinal line was 1.2 degrees +/-1.3 degrees . This study determined that the alternative landmarks of the acetabular rim and the TAL were not as accurate as using the posterior interspinal line as determined by registering the PSIS.

Mihalko WM; Kammerzell S; Saleh KJ

2009-10-01

140

Anatomic landmarks for Basal joint injections.  

UK PubMed Central (United Kingdom)

Objective: Basal joint arthritis is a common cause of pain and disability, particularly in elderly women. Corticosteroid injection with splinting provides a reliable long-term relief for patients with mild arthritis. Proper location of the basal joint with anatomic landmarks can facilitate diagnosis and treatment of basal joint arthritis while avoiding inadvertent injury to local structures. The purpose of this study is to identify bony anatomic landmarks for basal joint injections and aid clinicians in avoiding inadvertent injury to surrounding structures on the radial side of the wrist. Methods: Twenty fresh cadaveric wrists were dissected with the aid of loupe magnification. The distal edge of the radial styloid and the palpable dorsal aspect of the thumb metacarpophalangeal joint were used as bony anatomic landmarks for the identification of the basal joint along a longitudinal vector. Measurements of the distance from our anatomic landmarks to the basal joint space were recorded. The locations of the radial artery and the superficial branch of the radial nerve were noted in relation to the borders of the anatomic snuffbox at the basal joint level. Results: The basal joint of the thumb is located 2.44 ± 0.34 cm distal to the distal edge of the radial styloid, and 4.47 ± 0.29 cm proximal to the metacarpophalangeal joint. At the level of the basal joint, the radial artery is found 0.76 ± 0.12 cm dorsal to the extensor pollicis brevis tendon. The first branch of the superficial branch of the radial nerve is volar to the abductor pollicis longus tendon in 84% of the specimens and courses over the abductor pollicis longus tendon in 16%. Conclusion: The basal joint of the thumb is approximately 2.4 cm distal to the radial styloid and 4.5 cm proximal to the metacarpophalangeal joint. Placement of a needle in the basal joint space immediately dorsal to extensor pollicis brevis tendon while applying longitudinal traction on the thumb is more likely to avoid damage to the radial artery and the superficial branch of the radial nerve.

Hazani R; Engineer NJ; Elston J; Wilhelmi BJ

2012-01-01

 
 
 
 
141

Combining Path Integration and Remembered Landmarks When Navigating without Vision  

Science.gov (United States)

This study investigated the interaction between remembered landmark and path integration strategies for estimating current location when walking in an environment without vision. We asked whether observers navigating without vision only rely on path integration information to judge their location, or whether remembered landmarks also influence judgments. Participants estimated their location in a hallway after viewing a target (remembered landmark cue) and then walking blindfolded to the same or a conflicting location (path integration cue). We found that participants averaged remembered landmark and path integration information when they judged that both sources provided congruent information about location, which resulted in more precise estimates compared to estimates made with only path integration. In conclusion, humans integrate remembered landmarks and path integration in a gated fashion, dependent on the congruency of the information. Humans can flexibly combine information about remembered landmarks with path integration cues while navigating without visual information.

Kalia, Amy A.; Schrater, Paul R.; Legge, Gordon E.

2013-01-01

142

Estimation of mutation induction rates in AT-rich sequences using a genome scanning approach after X irradiation of mouse spermatogonia.  

UK PubMed Central (United Kingdom)

We have previously used NotI as the marker enzyme (recognizing GCGGCCGC) in a genome scanning approach for detection of mutations induced in mouse spermatogonia and estimated the mutation induction rate as about 0.7 x 10(-5) per locus per Gy. To see whether different parts of the genome have different sensitivities for mutation induction, we used AflII (recognizing CTTAAG) as the marker enzyme in the present study. After the screening of 1,120 spots in each mouse offspring, we found five mutations among 92,655 spots from the unirradiated paternal genome, five mutations among 218,411 spots from the unirradiated maternal genome, and 13 mutations among 92,789 spots from 5 Gy-exposed paternal genome. Among the 23 mutations, 11 involved mouse satellite DNA sequences (AT-rich), and the remaining 12 mutations also involved AT-rich but non-satellite sequences. Both types of sequences were found as multiple, similar-sequence blocks in the genome. Counting each member of cluster mutations separately and excluding results on one hypermutable spot, the spontaneous mutation rates were estimated as 3.2 (+/- 1.9) x 10(-5) and 2.3 (+/- 1.0) x 10(-5) per locus per generation in the male and female genomes, respectively, and the mutation induction rate as 1.1 (+/- 1.2) x 10(-5) per locus per Gy. The induction rate would be reduced to 0.9 x 10(-5) per locus per Gy if satellite sequence mutations were excluded from this analysis. The results indicate that mutation induction rates do not largely differ between GC-rich and AT-rich regions: 1 x 10(-5) per locus per Gy or less, which is close to 1.08 x 10(-5) per locus per Gy, the current estimate for the mean mutation induction rate in mice.

Asakawa J; Nakamura N; Katayama H; Cullings HM

2007-08-01

143

Reorienting with terrain slope and landmarks.  

UK PubMed Central (United Kingdom)

Orientation (or reorientation) is the first step in navigation, because establishing a spatial frame of reference is essential for a sense of location and heading direction. Recent research on nonhuman animals has revealed that the vertical component of an environment provides an important source of spatial information, in both terrestrial and aquatic settings. Nonetheless, humans show large individual and sex differences in the ability to use terrain slope for reorientation. To understand why some participants--mainly women--exhibit a difficulty with slope, we tested reorientation in a richer environment than had been used previously, including both a tilted floor and a set of distinct objects that could be used as landmarks. This environment allowed for the use of two different strategies for solving the task, one based on directional cues (slope gradient) and one based on positional cues (landmarks). Overall, rather than using both cues, participants tended to focus on just one. Although men and women did not differ significantly in their encoding of or reliance on the two strategies, men showed greater confidence in solving the reorientation task. These facts suggest that one possible cause of the female difficulty with slope might be a generally lower spatial confidence during reorientation.

Nardi D; Newcombe NS; Shipley TF

2013-02-01

144

A Simple and Fast Method of 3D Registration and Statistical Landmark Localization for Sparse Multi-Modal/Time-Series Neuroimages Based on Cortex Ellipse Fitting.  

Science.gov (United States)

Existing methods of neuroimage registration typically require high quality scans and are time-consuming. We propose a simple and fast method which allows intra-patient multi-modal and time-series neuroimage registration as well as landmark identification (including commissures and superior/inferior brain landmarks) for sparse data. The method is based on elliptical approximation of the brain cortical surface in the vicinity of the midsagittal plane (MSP). Scan registration is performed by a 3D affine transformation based on parameters of the cortex elliptical fit and by aligning the MSPs. The landmarks are computed using a statistical localization method based on analysis of 53 structural scans without detectable pathology. The method is illustrated for multi-modal registration, analysis of hemorrhagic stroke time series, and ischemic stroke follow ups, as well as for localization of hardly visible or not discernible landmarks in sparse neuroimages. The method also enables a statistical localization of landmarks in sparse morphological/non-morphological images, where landmark points may be invisible. PMID:24028883

Volkau, I; Puspitasari, F; Ng, T T; Bhanu Prakash, K N; Gupta, V; Nowinski, W L

2012-03-01

145

A Simple and Fast Method of 3D Registration and Statistical Landmark Localization for Sparse Multi-Modal/Time-Series Neuroimages Based on Cortex Ellipse Fitting.  

UK PubMed Central (United Kingdom)

Existing methods of neuroimage registration typically require high quality scans and are time-consuming. We propose a simple and fast method which allows intra-patient multi-modal and time-series neuroimage registration as well as landmark identification (including commissures and superior/inferior brain landmarks) for sparse data. The method is based on elliptical approximation of the brain cortical surface in the vicinity of the midsagittal plane (MSP). Scan registration is performed by a 3D affine transformation based on parameters of the cortex elliptical fit and by aligning the MSPs. The landmarks are computed using a statistical localization method based on analysis of 53 structural scans without detectable pathology. The method is illustrated for multi-modal registration, analysis of hemorrhagic stroke time series, and ischemic stroke follow ups, as well as for localization of hardly visible or not discernible landmarks in sparse neuroimages. The method also enables a statistical localization of landmarks in sparse morphological/non-morphological images, where landmark points may be invisible.

Volkau I; Puspitasari F; Ng TT; Bhanu Prakash KN; Gupta V; Nowinski WL

2012-03-01

146

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

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF. Results A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (PRB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens. Conclusions We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.

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

2012-01-01

147

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

Energy Technology Data Exchange (ETDEWEB)

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

Peters, Anton R.; Herk, Marcel van [Department of Radiotherapy, The Netherlands Cancer Institute/Antoni van Leeuwenhoek Huis (NKI/AVL), Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Muller, Sara H. [Department of Radiotherapy, The Netherlands Cancer Institute/Antoni van Leeuwenhoek Huis (NKI/AVL), Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Department of Radiology, NKI/AVL, Amsterdam (Netherlands); Munck, Jan C. de [MEG Centrum KNAW, Free University Hospital, De Boelelaan 1117, 1081 HV Amsterdam (Netherlands)

2000-08-01

148

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

Directory of Open Access Journals (Sweden)

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.

Xiaohong W. Gao; Sergey Anishenko; Dmitry Shaposhnikov; Lubov Podlachikova; Stephen Batty; John Clark

2007-01-01

149

Electronic and film portal images: a comparison of landmark visibility and review accuracy  

International Nuclear Information System (INIS)

Purpose: To quantitatively compare a scanning liquid ion chamber electronic portal imaging device (SLIC-EPID) and an amorphous silicon flat panel (aSi) EPID with portal film in clinical applications using measures of landmark visibility and treatment review accuracy. Methods and Materials: Six radiation oncologists viewed 39 electronic portal images (EPIs) from the SLIC-EPID, 36 EPIs from the aSi-EPID, and portal films of each of these treatment fields. The physicians rated the clarity of anatomic landmarks in the portal images, and the scores were compared between EPID and film. Nine hundred portal image reviews were performed. EPID and film portal images were acquired with known setup errors in either phantom or cadaver treatments. Physicians identified the errors visually in portal films and with computerized analysis for EPID. Results: There were no statistically significant (p

2002-10-01

150

Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii?RW1.  

UK PubMed Central (United Kingdom)

Sphingomonas wittichii?RW1 is a dibenzofuran and dibenzodioxin-degrading bacterium with potentially interesting properties for bioaugmentation of contaminated sites. In order to understand the capacity of the microorganism to survive in the environment we used a genome-wide transposon scanning approach. RW1 transposon libraries were generated with around 22?000 independent insertions. Libraries were grown for an average of 50 generations (five successive passages in batch liquid medium) with salicylate as sole carbon and energy source in presence or absence of salt stress at -1.5?MPa. Alternatively, libraries were grown in sand with salicylate, at 50% water holding capacity, for 4 and 10 days (equivalent to 7 generations). Library DNA was recovered from the different growth conditions and scanned by ultrahigh throughput sequencing for the positions and numbers of inserted transposed kanamycin resistance gene. No transposon reads were recovered in 579 genes (10% of all annotated genes in the RW1 genome) in any of the libraries, suggesting those to be essential for survival under the used conditions. Libraries recovered from sand differed strongly from those incubated in liquid batch medium. In particular, important functions for survival of cells in sand at the short term concerned nutrient scavenging, energy metabolism and motility. In contrast to this, fatty acid metabolism and oxidative stress response were essential for longer term survival of cells in sand. Comparison to transcriptome data suggested important functions in sand for flagellar movement, pili synthesis, trehalose and polysaccharide synthesis and putative cell surface antigen proteins. Interestingly, a variety of genes were also identified, interruption of which cause significant increase in fitness during growth on salicylate. One of these was an Lrp family transcription regulator and mutants in this gene covered more than 90% of the total library after 50 generations of growth on salicylate. Our results demonstrate the power of genome-wide transposon scanning approaches for analysis of complex traits.

Roggo C; Coronado E; Moreno-Forero SK; Harshman K; Weber J; van der Meer JR

2013-03-01

151

Vision-Based Navigation Using Natural Landmarks  

UK PubMed Central (United Kingdom)

MYNORCA is a vision-based navigation systemfor mobile robots, designed principally foroperation in indoor environments. The systemuses vision for detecting obstacles and locatingnatural landmarks. In addition, it is able tosolve navigation problems in which the robot'sinitial location is completely unknown. In thispaper, we present an overview of MYNORCA,describe its implementation and present someexperimental results.1 IntroductionMYNORCA is a vision-based navigation system for mobilerobots, designed principally for operation in indoorenvironments, such as office buildings. MYNORCA dividesthe overall navigation problem into two parts: localand global navigation. Local navigation is defined asthe immediate problem of detecting and avoiding obstacles,whilst global navigation is defined as the problem ofreaching distant goals. This division of responsibilitieshas a double benefit: global navigation can be treated asa fairly abstract planning problem, since ...

Andrew Howard; Les Kitchen

152

Robot Navigation Using Panoramic Landmark Tracking  

UK PubMed Central (United Kingdom)

A vision based navigation system is presented for determininga mobile robot's position and orientation usingpanoramic imagery. Omni-directional sensors are usefulin obtaining afield of view, permitting objects in thevicinity of a robot to be imaged simultaneously. Recognizinglandmarks in a panoramic image from an a priori modelof distinct features in an environment allows a robot's locationinformation to be updated. A system is shown fortracking vertex and line features for omni-directional camerasconstructed with catadioptric (containing both mirrorsand lenses) optics. With the aid of the Panoramic HoughTransform, line features can be tracked without restrictingthe mirror geometry to that which satisfies the single viewpointcriteria. Two paradigms for landmark tracking are explored,with experiments shown with synthetic and real imagesreported. A working implementation on a mobile robotis shown.

Mark Fiala; Anup Basu

153

Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation.  

Science.gov (United States)

Although the sexual transfer of genetic material between species (i.e. introgression) has been documented in many groups of plants and animals, genome-wide patterns of introgression are poorly understood. Is most of the genome permeable to interspecific gene flow, or is introgression typically restricted to a handful of genomic regions? Here, we assess the genomic extent and direction of introgression between three sunflowers from the south-central USA: the common sunflower, Helianthus annuus ssp. annuus; a near-endemic to Texas, Helianthus debilis ssp. cucumerifolius; and their putative hybrid derivative, thought to have recently colonized Texas, H. annuus ssp. texanus. Analyses of variation at 88 genetically mapped microsatellite loci revealed that long-term migration rates were high, genome-wide and asymmetric, with higher migration rates from H. annuus texanus into the two parental taxa than vice versa. These results imply a longer history of intermittent contact between H. debilis and H. annuus than previously believed, and that H. annuus texanus may serve as a bridge for the transfer of alleles between its parental taxa. They also contradict recent theory suggesting that introgression should predominantly be in the direction of the colonizing species. As in previous studies of hybridizing sunflower species, regions of genetic differentiation appear small, whether estimated in terms of FST or unidirectional migration rates. Estimates of recent immigration and admixture were inconsistent, depending on the type of analysis. At the individual locus level, one marker showed striking asymmetry in migration rates, a pattern consistent with tight linkage to a Bateson-Dobzhansky-Muller incompatibility. PMID:20355258

Scascitelli, M; Whitney, K D; Randell, R A; King, Matthew; Buerkle, C A; Rieseberg, L H

2010-02-01

154

Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation.  

UK PubMed Central (United Kingdom)

Although the sexual transfer of genetic material between species (i.e. introgression) has been documented in many groups of plants and animals, genome-wide patterns of introgression are poorly understood. Is most of the genome permeable to interspecific gene flow, or is introgression typically restricted to a handful of genomic regions? Here, we assess the genomic extent and direction of introgression between three sunflowers from the south-central USA: the common sunflower, Helianthus annuus ssp. annuus; a near-endemic to Texas, Helianthus debilis ssp. cucumerifolius; and their putative hybrid derivative, thought to have recently colonized Texas, H. annuus ssp. texanus. Analyses of variation at 88 genetically mapped microsatellite loci revealed that long-term migration rates were high, genome-wide and asymmetric, with higher migration rates from H. annuus texanus into the two parental taxa than vice versa. These results imply a longer history of intermittent contact between H. debilis and H. annuus than previously believed, and that H. annuus texanus may serve as a bridge for the transfer of alleles between its parental taxa. They also contradict recent theory suggesting that introgression should predominantly be in the direction of the colonizing species. As in previous studies of hybridizing sunflower species, regions of genetic differentiation appear small, whether estimated in terms of FST or unidirectional migration rates. Estimates of recent immigration and admixture were inconsistent, depending on the type of analysis. At the individual locus level, one marker showed striking asymmetry in migration rates, a pattern consistent with tight linkage to a Bateson-Dobzhansky-Muller incompatibility.

Scascitelli M; Whitney KD; Randell RA; King M; Buerkle CA; Rieseberg LH

2010-02-01

155

Bony landmarks as an aid for intraoperative facial nerve identification  

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Identification of the facial nerve trunk is essential during surgery of the parotid gland. Numerous landmarks have been researched and used. The relation between the facial nerve to two constant bony landmarks, the tip of the mastoid process and the central point of the transverse process of the atl...

Greyling, Linda M.; Glanvill, R.; Boon, J.M.; Schabort, D.; Meiring, J.H.; Pretorius, Jan P.; Van Schoor, Albert-Neels

156

Craniofacial osseous landmark determination from stereo computer tomography reconstructions.  

UK PubMed Central (United Kingdom)

The accurate and reproducible determination of the three dimensional (3D) co-ordinate positions of anatomical landmarks from computer tomography (CT) images has been limited even though potentially the data have been available for several years. This paper describes a method of acquisition of osseous landmark positions using an off-line computing technique based on multiple stereo images of 3D CT reconstructions. The use of stereo pairs greatly enhances the consistent identification of osseous landmarks. Further, the technique is of particular value where access to the CT scanner is restricted due to heavy clinical demand and separate high quality graphics facilities are unavailable. Osseous landmark position data were determined for dried skulls and patients with craniofacial conditions. Accuracies of the order 1.7mm (median) were obtained. These results encourage the use of the technique for acquisition of landmark positions for the study of the craniofacial complex in three dimensions.

Abbott AH; Netherway DJ; David DJ; Brown T

1990-09-01

157

Craniofacial osseous landmark determination from stereo computer tomography reconstructions.  

Science.gov (United States)

The accurate and reproducible determination of the three dimensional (3D) co-ordinate positions of anatomical landmarks from computer tomography (CT) images has been limited even though potentially the data have been available for several years. This paper describes a method of acquisition of osseous landmark positions using an off-line computing technique based on multiple stereo images of 3D CT reconstructions. The use of stereo pairs greatly enhances the consistent identification of osseous landmarks. Further, the technique is of particular value where access to the CT scanner is restricted due to heavy clinical demand and separate high quality graphics facilities are unavailable. Osseous landmark position data were determined for dried skulls and patients with craniofacial conditions. Accuracies of the order 1.7mm (median) were obtained. These results encourage the use of the technique for acquisition of landmark positions for the study of the craniofacial complex in three dimensions. PMID:2260813

Abbott, A H; Netherway, D J; David, D J; Brown, T

1990-09-01

158

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

UK PubMed Central (United Kingdom)

BACKGROUND: Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF. RESULTS: A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (P<0.01), respectively. A number of genes in the significant core regions, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens. CONCLUSIONS: We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.

Zhang H; Wang SZ; Wang ZP; Da Y; Wang N; Hu XX; Zhang YD; Wang YX; Leng L; Tang ZQ; Li H

2012-01-01

159

Genome-Wide Scan for Bats and Dolphin to Detect Their Genetic Basis for New Locomotive Styles  

Digital Repository Infrastructure Vision for European Research (DRIVER)

For most mammals, running is their major locomotive style, however, cetaceans and bats are two mammalian groups that have independently developed new locomotive styles (swimming and flying) from their terrestrial ancestors. In this study, we used a genome-wide comparative analysis in an attempt to i...

Shen, Yong-Yi; Zhou, Wei-Ping; Zhou, Tai-Cheng; Zeng, Yan-Ni; Li, Gui-Mei; Irwin, David M.; Zhang, Ya-Ping

160

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

Directory of Open Access Journals (Sweden)

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.

Wang Chun; Lo Loong; Zhu Ze; Yue Gen

2006-01-01

 
 
 
 
161

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

UK PubMed Central (United Kingdom)

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 (approximately 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.

Wang CM; Lo LC; Zhu ZY; Yue GH

2006-01-01

162

Landmark detection and coupled patch registration for cardiac motion tracking  

Science.gov (United States)

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.

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

2013-03-01

163

A genome-wide SNP scan reveals two loci associated with the chicken resistance to Marek's disease.  

UK PubMed Central (United Kingdom)

Marek's disease (MD) is a neoplastic disease in chickens, caused by the Marek's disease virus (MDV). To investigate host genetic resistance to MD, we conducted a genome-wide association study (GWAS) on 67 MDV-infected chickens based on a case and control design, including 57 susceptible chickens in the case group and 10 resistant chickens as controls. After searching 38 655 valid genomic markers, two SNPs were found to be associated with host resistance to MD. One SNP, rs14527240, reaching chromosome-wide significance level (P < 0.01) was located in the SPARC-related modular calcium-binding 1 (SMOC1) gene on GGA5. The other one, GGaluGA156129, reaching genome-wide significance (P < 0.05), was located in the protein tyrosine phosphatase, non-receptor type 3 (PTPN3) gene on GGA2. In addition, expression patterns of these two genes in spleens were detected by qPCR. The expression of SMOC1 was significantly up-regulated (P < 0.05), whereas the expression of PTNP3 did not show significance when the case group was compared with the control group. Up-regulation of SMOC1 in susceptible spleens suggests its important roles in MD tumorigenesis. This is the first study to investigate MD-resistant loci, and it demonstrates the power of GWASs for mapping genes associated with MD resistance.

Li DF; Lian L; Qu LJ; Chen YM; Liu WB; Chen SR; Zheng JX; Xu GY; Yang N

2013-04-01

164

PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Periodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions and in the organization of chromosomes in both eukaryotes and prokaryotes. Local differences in DNA sequence periodicity have been linked to differences in gene expression in some organisms. Despite the significance of these periodic patterns, there are virtually no publicly accessible tools for their analysis. Results We present novel tools suitable for assessments of DNA curvature-related sequence periodicity in nucleotide sequences at the genome scale. Utility of the present software is demonstrated on a comparison of sequence periodicities in the genomes of Haemophilus influenzae, Methanocaldococcus jannaschii, Saccharomyces cerevisiae, and Arabidopsis thaliana. The software can be accessed through a web interface and the programs are also available for download. Conclusions The present software is suitable for comparing DNA curvature-related sequence periodicity among different genomes as well as for analysis of intrachromosomal heterogeneity of the sequence periodicity. It provides a quick and convenient way to detect anomalous regions of chromosomes that could have unusual structural and functional properties and/or distinct evolutionary history.

Mrázek Jan; Chaudhari Tejas; Basu Aryabrata

2011-01-01

165

An image processing system for locating craniofacial landmarks  

Energy Technology Data Exchange (ETDEWEB)

A new automatic target recognition algorithm has been developed to extract craniofacial landmarks from lateral skull x-rays (cephalograms). The locations of these landmarks are used by orthodontists in what is referred to as a cephalometric evaluation. The evaluation assists in the diagnosis of anomalies and in the monitoring of treatments. The algorithm is based on gray-scale mathematical morphology. A statistical approach to training was used to overcome subtle differences in skeletal topographies. Decomposition was used to desensitize the algorithm to size differences. A system was trained to locate 20 landmarks. Tests on 40 x-rays showed an 85% recognition rate on average.

Cardillo, J.; Sid-Ahmed, M.A. (Univ. of Windsor, Ontario (Canada). Dept. of Electrical Engineering)

1994-06-01

166

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

UK PubMed Central (United Kingdom)

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

Simino J; Shi G; Kume R; Schwander K; Province MA; Gu CC; Kardia S; Chakravarti A; Ehret G; Olshen RA; Turner ST; Ho LT; Zhu X; Jaquish C; Paltoo D; Cooper RS; Weder A; Curb JD; Boerwinkle E; Hunt SC; Rao DC

2011-03-01

167

Taiwan schizophrenia linkage study: Lessons learned from endophenotype-based genome-wide linkage scans and perspective.  

Science.gov (United States)

Taiwan Schizophrenia Linkage Study (TSLS) was initiated with a linkage strategy for locating multiple genes, each of small to moderate effect, and aimed to recruit a large enough sample of pairs of affected siblings and their families ascertained from a multisite study. With a sample of 607 families successfully recruited, a total of 2,242 individuals (1,207 affected and 1,035 unaffected) from 557 families were genotyped using 386 microsatellite markers spaced at an average of 9-cM intervals. Here the author reviews the establishment of TSLS and initial signal derived from linkage scan using the diagnosis of schizophrenia. Based on the limited success of the initial linkage analysis, a sufficient-component causal model is proposed to incorporate endophenotypes and genes for schizophrenia. Four types of candidate endophenotype measured in TSLS, including schizotypal personality, Continuous Performance Test, Wisconsin Card Sorting Test, and niacin skin flush test, are briefly described. The author discusses different strategies of linkage analysis incorporating these endophenotypes, including quantitative trait loci (QTL) linkage analysis, clustering-derived subgroups, ordered subset analysis (OSA), and latent classes for linkage scan. Then the author summarizes the linkage signals generated from seven studies of endophenotype-based linkage analysis using TSLS, including QTL scan of neurocognitive performance, QTL scan of niacin skin flush, the family cluster of attention deficit and execution deficit, OSA by schizophrenia-schizotypy factors, nested OSA by age at onset and neurocognitive performance, and the latent class of deficit schizophrenia for linkage analysis. The perspective of combining next-generation sequencing with linkage analysis of families is also discussed. © 2013 Wiley Periodicals, Inc. PMID:24132895

Chen, Wei J

2013-10-01

168

Technical note: A new method for measuring long bone curvature using 3D landmarks and semi-landmarks.  

UK PubMed Central (United Kingdom)

Here we describe and evaluate a new method for quantifying long bone curvature using geometric morphometric and semi-landmark analysis of the human femur. The technique is compared with traditional ways of measuring subtense and point of maximum curvature using either coordinate calipers or projection onto graph paper. Of the traditional methods the graph paper method is more reliable than using coordinate calipers. Measurement error is consistently lower for measuring point of maximum curvature than for measuring subtense. The results warrant caution when comparing data collected by the different traditional methods. Landmark data collection proves reliable and has a low measurement error. However, measurement error increases with the number of semi-landmarks included in the analysis of curvature. Measurements of subtense can be estimated more reliably using 3D landmarks along the curve than using traditional techniques. We use equidistant semi-landmarks to quantify the curve because sliding the semi-landmarks masks the curvature signal. Principal components analysis of these equidistant semi-landmarks provides the added benefit of describing the shape of the curve. These results are promising for functional and forensic analysis of long bone curvature in modern human populations and in the fossil record.

De Groote I; Lockwood CA; Aiello LC

2010-04-01

169

A new guide to the human genome  

Energy Technology Data Exchange (ETDEWEB)

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.

Marx, J.

1995-12-22

170

Genome scan study of prostate cancer in Arabs: identification of three genomic regions with multiple prostate cancer susceptibility loci in Tunisians.  

UK PubMed Central (United Kingdom)

BACKGROUND: Large databases focused on genetic susceptibility to prostate cancer have been accumulated from population studies of different ancestries, including Europeans and African-Americans. Arab populations, however, have been only rarely studied. METHODS: Using Affymetrix Genome-Wide Human SNP Array 6, we conducted a genome-wide association study (GWAS) in which 534,781 single nucleotide polymorphisms (SNPs) were genotyped in 221 Tunisians (90 prostate cancer patients and 131 age-matched healthy controls). TaqMan SNP Genotyping Assays on 11 prostate cancer associated SNPs were performed in a distinct cohort of 337 individuals from Arab ancestry living in Qatar and Saudi Arabia (155 prostate cancer patients and 182 age-matched controls). In-silico expression quantitative trait locus (eQTL) analysis along with mRNA quantification of nearby genes was performed to identify loci potentially cis-regulated by the identified SNPs. RESULTS: Three chromosomal regions, encompassing 14 SNPs, are significantly associated with prostate cancer risk in the Tunisian population (P = 1 × 10-4 to P = 1 × 10-5). In addition to SNPs located on chromosome 17q21, previously found associated with prostate cancer in Western populations, two novel chromosomal regions are revealed on chromosome 9p24 and 22q13. eQTL analysis and mRNA quantification indicate that the prostate cancer associated SNPs of chromosome 17 could enhance the expression of STAT5B gene. CONCLUSION: Our findings, identifying novel GWAS prostate cancer susceptibility loci, indicate that prostate cancer genetic risk factors could be ethnic specific.

Shan J; Al-Rumaihi K; Rabah D; Al-Bozom I; Kizhakayil D; Farhat K; Al-Said S; Kfoury H; Dsouza SP; Rowe J; Khalak HG; Jafri S; Aigha II; Chouchane L

2013-01-01

171

Development of a novel constellation based landmark detection algorithm  

Science.gov (United States)

Anatomical landmarks such as the anterior commissure (AC) and posterior commissure (PC) are commonly used by researchers for co-registration of images. In this paper, we present a novel, automated approach for landmark detection that combines morphometric constraining and statistical shape models to provide accurate estimation of landmark points. This method is made robust to large rotations in initial head orientation by extracting extra information of the eye centers using a radial Hough transform and exploiting the centroid of head mass (CM) using a novel estimation approach. To evaluate the effectiveness of this method, the algorithm is trained on a set of 20 images with manually selected landmarks, and a test dataset is used to compare the automatically detected against the manually detected landmark locations of the AC, PC, midbrain-pons junction (MPJ), and fourth ventricle notch (VN4). The results show that the proposed method is accurate as the average error between the automatically and manually labeled landmark points is less than 1 mm. Also, the algorithm is highly robust as it was successfully run on a large dataset that included different kinds of images with various orientation, spacing, and origin.

Ghayoor, Ali; Vaidya, Jatin G.; Johnson, Hans J.

2013-03-01

172

Evaluation of the genetic overlap between osteoarthritis with body mass index and height using genome-wide association scan data.  

UK PubMed Central (United Kingdom)

OBJECTIVES: Obesity as measured by body mass index (BMI) is one of the major risk factors for osteoarthritis. In addition, genetic overlap has been reported between osteoarthritis and normal adult height variation. We investigated whether this relationship is due to a shared genetic aetiology on a genome-wide scale. METHODS: We compared genetic association summary statistics (effect size, p value) for BMI and height from the GIANT consortium genome-wide association study (GWAS) with genetic association summary statistics from the arcOGEN consortium osteoarthritis GWAS. Significance was evaluated by permutation. Replication of osteoarthritis association of the highlighted signals was investigated in an independent dataset. Phenotypic information of height and BMI was accounted for in a separate analysis using osteoarthritis-free controls. RESULTS: We found significant overlap between osteoarthritis and height (p=3.3×10(-5) for signals with p?0.05) when the GIANT and arcOGEN GWAS were compared. For signals with p?0.001 we found 17 shared signals between osteoarthritis and height and four between osteoarthritis and BMI. However, only one of the height or BMI signals that had shown evidence of association with osteoarthritis in the arcOGEN GWAS was also associated with osteoarthritis in the independent dataset: rs12149832, within the FTO gene (combined p=2.3×10(-5)). As expected, this signal was attenuated when we adjusted for BMI. CONCLUSIONS: We found a significant excess of shared signals between both osteoarthritis and height and osteoarthritis and BMI, suggestive of a common genetic aetiology. However, only one signal showed association with osteoarthritis when followed up in a new dataset.

Elliott KS; Chapman K; Day-Williams A; Panoutsopoulou K; Southam L; Lindgren CM; Arden N; Aslam N; Birrell F; Carluke I; Carr A; Deloukas P; Doherty M; Loughlin J; McCaskie A; Ollier WE; Rai A; Ralston S; Reed MR; Spector TD; Valdes AM; Wallis GA; Wilkinson M; Zeggini E

2013-06-01

173

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

UK PubMed Central (United Kingdom)

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.

Utsunomiya YT; Pérez O'Brien AM; Sonstegard TS; Van Tassell CP; do Carmo AS; Mészáros G; Sölkner J; Garcia JF

2013-01-01

174

Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods  

Science.gov (United States)

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.

Utsunomiya, Yuri Tani; Perez O'Brien, Ana Maria; Sonstegard, Tad Stewart; Van Tassell, Curtis Paul; do Carmo, Adriana Santana; Meszaros, Gabor; Solkner, Johann; Garcia, Jose Fernando

2013-01-01

175

Genome scan to assess the respective role of host-plant and environmental constraints on the adaptation of a widespread insect  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The evolutionary success of phytophagous insects could result from their adaptation to different host-plants. Alternatively, the diversification of widespread species might be driven by adaptation along environmental gradients. To disentangle the respective roles of host-plant versus abiotic environmental variables acting on the genome of an oligophagous insect, we performed a genome scan using 83 unlinked AFLP markers on larvae of the large pine weevil collected on two host-plants (pine and spruce) in four forestry regions across Europe. Results At this large geographic scale, the global genetic differentiation was low and there was no isolation by distance pattern, suggesting that migration is overwhelming genetic drift in this species. In this context, the widely used frequentist methods to detect outliers (e.g. Dfdist), which assume migration - drift equilibrium are not the most appropriate approach. The implementation of a recently developed Bayesian approach, conceived to detect outliers even in non-equilibrium situations, consistently detected 9 out of 83 loci as outliers. Eight of these were validated as outliers by multiple logistic regressions: six correlated with environmental variables, one with host-plant and one with the interaction between environmental variables and host-plant. Conclusion These results suggest a relatively greater importance of abiotic environmental variables, as opposed to factors linked with the host-plant, in shaping genetic differentiation across the genome in this species. Logistic regression allows the nature of factors involved in locus-specific selection to be precisely identified and represents another step forward in the process of identifying adaptive loci.

Manel Stéphanie; Conord Cyrille; Després Laurence

2009-01-01

176

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

UK PubMed Central (United Kingdom)

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

Chávez-Galarza J; Henriques D; Johnston JS; Azevedo JC; Patton JC; Muñoz I; de La Rúa P; Pinto MA

2013-09-01

177

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

DEFF Research Database (Denmark)

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

Gregersen, Vivi R; Conley, Lene N

2012-01-01

178

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

UK PubMed Central (United Kingdom)

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

Gregersen VR; Conley LN; Sørensen KK; Guldbrandtsen B; Velander IH; Bendixen C

2012-01-01

179

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

Directory of Open Access Journals (Sweden)

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.

Schosser Alexandra; Pirlo Katrina; Gaysina Darya; Cohen-Woods Sarah; Schalkwyk Leonard C; Elkin Amanda; Korszun Ania; Gunasinghe Cerisse; Gray Joanna; Jones Lisa; Meaburn Emma; Farmer Anne E; Craig Ian W; McGuffin Peter

2010-01-01

180

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

UK PubMed Central (United Kingdom)

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

Shen YY; Zhou WP; Zhou TC; Zeng YN; Li GM; Irwin DM; Zhang YP

2012-01-01

 
 
 
 
181

Asymmetric introgression in the horticultural living fossil cycas sect. Asiorientales using a genome-wide scanning approach.  

UK PubMed Central (United Kingdom)

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.

Chiang YC; Huang BH; Chang CW; Wan YT; Lai SJ; Huang S; Liao PC

2013-01-01

182

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

Directory of Open Access Journals (Sweden)

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.

Yu-Chung Chiang; Bing-Hong Huang; Chun-Wen Chang; Yu-Ting Wan; Shih-Jie Lai; Shong Huang; Pei-Chun Liao

2013-01-01

183

Schizophrenia: A genome scan targets chromosomes 3p and 8p as potential sites of susceptibility genes  

Energy Technology Data Exchange (ETDEWEB)

Using a systematically ascertained sample of 57 families, each having 2 or more members with a consensus diagnosis of schizophrenia (DSM-III-R criteria), we have carried out linkage studies of 520 loci, covering approximately 70% of the genome for susceptibility loci for schizophrenia. A two-stage strategy based on lod score thresholds from simulation studies of our sample identified regions for further exploration. In each region, a dense map of highly informative dinucleotide repeat polymorphisms (heterozygosity greater than .70) was analyzed using dominant, recessive, and {open_quotes}affected only{close_quotes} models and nonparametric sib pair identity-by-descent methods. For one region, 8p22-p21, affected sib-pair analyses gave a P value = .0001, corresponding to a lod score approximately equal to 3.00. For 8p22-p21, the maximum two-point lod score occurred using the {open_quotes}affected only{close_quotes} recessive model (Z{sub max} = 2.35; {theta}{sub M} = {theta}{sub F}); allowing for a constant sex difference in recombination fractions found in reference pedigrees, Z{sub max} = 2.78 ({theta}{sub M}/{theta}{sub F} = 3). For a second region, 3p26-p24, the maximum two-point lod score was 2.34 ({open_quotes}affected only{close_quotes} dominant model), and the affected sib-pair P value was .01. These two regions are worthy of further exploration as potential sites of susceptibility genes for schizophrenia. 59 refs., 2 figs., 4 tabs.

Pulver, A.E.; Lasseter, V.K.; Kasch, L. [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)] [and others

1995-06-19

184

A genome-wide scan for common variants affecting the rate of age-related cognitive decline  

Science.gov (United States)

Age-related cognitive decline is likely promoted by accumulated brain injury due to chronic conditions of aging, including neurodegenerative and vascular disease. Since common neuronal mechanisms may mediate the adaptation to diverse cerebral insults, we hypothesized that susceptibility for age-related cognitive decline may be due in part to a shared genetic network. We have therefore performed a genome-wide association study using a quantitative measure of global cognitive decline slope, based on repeated measures of 17 cognitive tests in 749 subjects from the Religious Orders Study. Top results were evaluated in three independent replication cohorts, consisting of 2,279 additional subjects with repeated cognitive testing. As expected, we find that the Alzheimer’s disease (AD) susceptibility locus, APOE, is strongly associated with rate of cognitive decline (PDISC=5.6×10?9; PJOINT=3.7×10?27). We additionally discover a variant, rs10808746, which shows consistent effects in the replication cohorts and modestly improved evidence of association in the joint analysis (PDISC=6.7×10?5; PREP=9.4×10?3; PJOINT=2.3×10?5). This variant influences the expression of two adjacent genes, PDE7A and MTFR1, which are potential regulators of inflammation and oxidative injury, respectively. Using aggregate measures of genetic risk, we find that known susceptibility loci for cardiovascular disease, type II diabetes, and inflammatory diseases are not significantly associated with cognitive decline in our cohort. Our results suggest that intermediate phenotypes, when coupled with larger sample sizes, may be a useful tool to dissect susceptibility loci for age-related cognitive decline and uncover shared molecular pathways with a role in neuronal injury.

De Jager, Philip L.; Shulman, Joshua M.; Chibnik, Lori B.; Keenan, Brendan T.; Raj, Towfique; Wilson, Robert S.; Yu, Lei; Leurgans, Sue E.; Tran, Dong; Aubin, Cristin; Anderson, Christopher D.; Biffi, Alessandro; Corneveaux, Jason J.; Huentelman, Matthew J.; Rosand, Jonathan; Daly, Mark J.; Myers, Amanda J.; Reiman, Eric M.; Bennett, David A.; Evans, Denis A.

2011-01-01

185

A Replication Study and Genome-wide Scan of Single Nucleotide Polymorphisms Associated with Pancreatic Cancer Risk and Overall Survival  

Science.gov (United States)

Purpose To explore the effects of single nucleotide polymorphisms (SNPs) on pancreatic cancer risk and overall survival. Experimental Design The germline DNA of 531 pancreatic cancer cases and 305 healthy controls from a hospital-based study was genotyped at SNPs previously reported to be associated with pancreatic cancer risk or clinical outcome. We analyzed putative risk SNPs for replication of their reported effects on risk and tested for novel effects on overall survival (OS). Similarly, we analyzed putative survival-associated SNPs for replication of their reported effects on OS and tested for novel effects on risk. Lastly, we performed a genome-wide association study of OS using a subset of 252 cases, with two subsequent validation sets of 261 and 572 patients, respectively. Results Among seven risk SNPs analyzed, two (rs505922, rs9543325) were associated with risk (p<0.05). Among 24 survival-associated SNPs analyzed, one (rs9350) was associated with OS (p<0.05). No putative risk SNPs or putative survival-associated SNPs were found to be associated with OS or risk, respectively. Further, our GWAS identified a novel SNP (rs1482426, combined stage 1 and 2 p = 1.7 ×10?6, per-allele HR = 1.74, 95% CI 1.38–2.18) to be putatively associated with OS. Conclusions The effects of SNPs on pancreatic cancer risk and overall survival were replicated in our study, though further work is necessary to understand the functional mechanisms underlying these effects. More importantly, the putative association with OS identified by GWAS suggests that GWAS may be useful in identifying SNPs associated with clinical outcome in pancreatic cancer.

Willis, Jason A.; Olson, Sara H.; Orlow, Irene; Mukherjee, Semanti; McWilliams, Robert R.; Kurtz, Robert C.; Klein, Robert J.

2013-01-01

186

Landmark learning by the Ozark zigzag salamander Plethodon angusticlavius  

Directory of Open Access Journals (Sweden)

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].

Adam L. CRANE, Alicia MATHIS

2011-01-01

187

Discriminative BoW Framework for Mobile Landmark Recognition.  

UK PubMed Central (United Kingdom)

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

Chen T; Yap KH

2013-07-01

188

Progressive data transmission for anatomical landmark detection in a cloud.  

UK PubMed Central (United Kingdom)

BACKGROUND: In the concept of cloud-computing-based systems, various authorized users have secure access to patient records from a number of care delivery organizations from any location. This creates a growing need for remote visualization, advanced image processing, state-of-the-art image analysis, and computer aided diagnosis. OBJECTIVES: This paper proposes a system of algorithms for automatic detection of anatomical landmarks in 3D volumes in the cloud computing environment. The system addresses the inherent problem of limited bandwidth between a (thin) client, data center, and data analysis server. METHODS: The problem of limited bandwidth is solved by a hierarchical sequential detection algorithm that obtains data by progressively transmitting only image regions required for processing. The client sends a request to detect a set of landmarks for region visualization or further analysis. The algorithm running on the data analysis server obtains a coarse level image from the data center and generates landmark location candidates. The candidates are then used to obtain image neighborhood regions at a finer resolution level for further detection. This way, the landmark locations are hierarchically and sequentially detected and refined. RESULTS: Only image regions surrounding landmark location candidates need to be trans- mitted during detection. Furthermore, the image regions are lossy compressed with JPEG 2000. Together, these properties amount to at least 30 times bandwidth reduction while achieving similar accuracy when compared to an algorithm using the original data. CONCLUSIONS: The hierarchical sequential algorithm with progressive data transmission considerably reduces bandwidth requirements in cloud-based detection systems.

Sofka M; Ralovich K; Zhang J; Zhou SK; Comaniciu D

2012-01-01

189

Automated landmark identification for human cortical surface-based registration.  

UK PubMed Central (United Kingdom)

Volume-based registration (VBR) is the predominant method used in human neuroimaging to compensate for individual variability. However, surface-based registration (SBR) techniques have an inherent advantage over VBR because they respect the topology of the convoluted cortical sheet. There is evidence that existing SBR methods indeed confer a registration advantage over affine VBR. Landmark-SBR constrains registration using explicit landmarks to represent corresponding geographical locations on individual and atlas surfaces. The need for manual landmark identification has been an impediment to the widespread adoption of Landmark-SBR. To circumvent this obstacle, we have implemented and evaluated an automated landmark identification (ALI) algorithm for registration to the human PALS-B12 atlas. We compared ALI performance with that from two trained human raters and one expert anatomical rater (ENR). We employed both quantitative and qualitative quality assurance metrics, including a biologically meaningful analysis of hemispheric asymmetry. ALI performed well across all quality assurance tests, indicating that it yields robust and largely accurate results that require only modest manual correction (<10 min per subject). ALI largely circumvents human error and bias and enables high throughput analysis of large neuroimaging datasets for inter-subject registration to an atlas.

Anticevic A; Repovs G; Dierker DL; Harwell JW; Coalson TS; Barch DM; Van Essen DC

2012-02-01

190

Evidence for discrete landmark use by pigeons during homing.  

UK PubMed Central (United Kingdom)

Considerable efforts have been made to investigate how homing pigeons (Columba livia f. domestica) are able to return to their loft from distant, unfamiliar sites while the mechanisms underlying navigation in familiar territory have received less attention. With the recent advent of global positioning system (GPS) data loggers small enough to be carried by pigeons, the role of visual environmental features in guiding navigation over familiar areas is beginning to be understood, yet, surprisingly, we still know very little about whether homing pigeons can rely on discrete, visual landmarks to guide navigation. To assess a possible role of discrete, visual landmarks in navigation, homing pigeons were first trained to home from a site with four wind turbines as salient landmarks as well as from a control site without any distinctive, discrete landmark features. The GPS-recorded flight paths of the pigeons on the last training release were straighter and more similar among birds from the turbine site compared with those from the control site. The pigeons were then released from both sites following a clock-shift manipulation. Vanishing bearings from the turbine site continued to be homeward oriented as 13 of 14 pigeons returned home. By contrast, at the control site the vanishing bearings were deflected in the expected clock-shift direction and only 5 of 13 pigeons returned home. Taken together, our results offer the first strong evidence that discrete, visual landmarks are one source of spatial information homing pigeons can utilize to navigate when flying over a familiar area.

Mora CV; Ross JD; Gorsevski PV; Chowdhury B; Bingman VP

2012-10-01

191

Genome-wide scan of 500,000 single-nucleotide polymorphisms among responders and nonresponders to interferon beta therapy in multiple sclerosis.  

UK PubMed Central (United Kingdom)

BACKGROUND: Interferon beta is 1 of 2 first-line treatments for relapsing-remitting multiple sclerosis (MS). However, not all patients respond to interferon beta therapy, and to date there is a lack of surrogate markers that reliably correlate with responsiveness to interferon beta therapy in MS. OBJECTIVE: To identify allelic variants that influence response to interferon beta therapy in patients with MS. DESIGN: Genome-wide scan. SETTING: Academic research. Patients Two hundred patients having relapsing-remitting MS treated with interferon beta and having a follow-up period of at least 2 years were classified as responders or nonresponders to treatment based on stringent clinical criteria. MAIN OUTCOME MEASURES: In the first phase of the study, a pooling-based genome-wide association study of 428 867 single-nucleotide polymorphisms (SNPs) was performed in 53 responders and 53 nonresponders to interferon beta therapy. After applying several selection criteria, 383 SNPs were individually genotyped in an independent validation cohort of 49 responders and 45 nonresponders to interferon beta therapy using a different genotyping platform. RESULTS: Eighteen SNPs had uncorrected P < .05 associated with interferon beta responder status in the validation cohort. Of these, 7 SNPs were located in genes that code for alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid-type glutamate receptor GRIA3, type 1 interferon-related proteins ADAR and IFNAR2, cell cycle-dependent protein CIT, zinc finger proteins ZFAT and ZFHX4, and guanosine triphosphatase-activating protein STARD13. CONCLUSIONS: This study supports an underlying polygenic response to interferon beta treatment in MS and highlights the importance of the glutamatergic system in patient response to interferon beta therapy.

Comabella M; Craig DW; Morcillo-Suárez C; Río J; Navarro A; Fernández M; Martin R; Montalban X

2009-08-01

192

Cardiac Conduction System: Delineation of Anatomic Landmarks With Multidetector CT  

Directory of Open Access Journals (Sweden)

Full Text Available Major components of the cardiac conduction system including the sinoatrial node (SAN), atrioventricular node (AVN), the His Bundle, and the right and left bundle branches are too small to be directly visualized by multidetector CT (MDCT) given the limited spatial resolution of current scanners. However, the related anatomic landmarks and variants of this system a well as the areas with special interest to electrophysiologists can be reliably demonstrated by MDCT. Some of these structures and landmarks include the right SAN artery, right atrial cavotricuspid isthmus, Koch triangle, AVN artery, interatrial muscle bundles, and pulmonary veins. In addition, MDCT has an imperative role in demarcating potential arrhythmogenic structures. The aim of this review will be to assess the extent at which MDCT can outline the described anatomic landmarks and therefore provide crucial information used in clinical practice.

Farhood Saremi; Maria Torrone; Nooshin Yashar

2009-01-01

193

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

UK PubMed Central (United Kingdom)

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

Prunier J; Laroche J; Beaulieu J; Bousquet J

2011-04-01

194

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

UK PubMed Central (United Kingdom)

Allergic rhinitis is a common disease of complex inheritance and is characterised by mucosal inflammation caused by allergen exposure. The genetics of closely related phenotypes such as asthma, atopy and to some extend atopic dermatitis has attracted attention in recent years. Genetic reports of allergic rhinitis on the contrary have as yet been most sparse. To identify candidate regions holding genes for allergic rhinitis we performed a total genome-scan on affected sib-pair families. From 100 Danish sib-pair families selected for allergy, families containing sib-pairs matching a phenotype definition of both clinical allergic rhinitis and confirmed specific allergy were chosen. Thirty-three affected sib-pair families qualified for the scan that was undertaken using 446 microsatellite markers. Non-parametric linkage results were obtained from MAPMAKER/SIBS computer program. The study revealed one major candidate region on chromosome 4q24-q27 (LOD=2.83) and eight minor candidate regions 2q12-q33, 3q13, 4p15-q12, 5q13-q15, 6p24-p23, 12p13, 22q13, and Xp21 (LOD=1.04-1.63) likely to contain susceptibility genes for allergic rhinitis. Our findings did not support a previous report of linkage of allergic rhinitis to chromosome 12q14-q24 but they added positive evidence to the asthma and atopy candidate regions 2q33 and 6p23. Further identification of the specific genes involved in allergic rhinitis will give opportunities for improved diagnosis and treatment.

Haagerup A; Bjerke T; Schøitz PO; Binderup HG; Dahl R; Kruse TA

2001-12-01

195

Pontos referenciais nos acessos cranianos Landmarks to the cranial approaches  

Directory of Open Access Journals (Sweden)

Full Text Available O conhecimento da topografia cranioencefálica permite delimitar os acessos cranianos. Sistematiza-se os pontos referenciais, definidos em relação aos pontos craniométricos, usados nos diferentes acessos cranianos. Dos 22 pontos referenciais descritos, os doze primeiros estão em relação com a base do crânio e os demais com a convexidade.The knowledge of the craniotopography allows the delimitation of the cranial approaches. In this study the landmarks, defined in relation to the craniometric points and used in the different cranial approaches, were systematized. Twenty two landmarks are described: the first twelve are in relation to the skull base and the remainder are in relation to the skull vertex.

Sebastião Gusmão; Roberto Leal Silveira; Aluízio Arantes

2003-01-01

196

Endoscopic endonasal transpterygoid approaches: anatomical landmarks for planning the surgical corridor.  

UK PubMed Central (United Kingdom)

OBJECTIVES/HYPOTHESIS: Endoscopic endonasal transpterygoid approaches (EETA) use the pneumatization of the sinonasal corridor to control lesions of the middle and posterior skull base. These surgical areas are complex and the required surgical corridors are difficult to predict. AIM: Define anatomical landmarks for the preoperative planning of EETAs. STUDY DESIGN: Anatomical study. METHODS: We reviewed images from high-resolution maxillofacial CT scans with (0.6-mm axial slice acquisition). Cephalometric measurements were obtained using Kodak Carestream Image Software (Rochester, NY). RESULTS: Average distance from midline to the vidian canal was 12.78 mm (range 9.4-15.8 mm). Average horizontal distance from the vidian canal to the foramen rotundum was 5.6 mm (range 2.8-11.5 mm). Average vertical distance from the vidian canal to the foramen rotundum was 6.22 mm (range 4.3-9.3 mm). These landmarks are consequential during the preoperative planning of the surgical corridor. To facilitate communication, we classified EETAs as: A) Partial removal of the pterygoid plates (transposition of temporo-parietal fascia); B) removal of anteromedial aspect of the pterygoid process (lesions involving the lateral recess of the sphenoid sinus); C) involves dissecting the vidian nerve to control the petrous ICA and removing the pterygoid plates base to reach the petrous apex, Meckel's cave, or cavernous sinus; D) variable removal of the pterygoid plates to access the infratemporal fossa; and E) removal of pterygoid process and medial third of the Eustachian tube to expose the nasopharynx. CONCLUSIONS: Our novel classification and landmarks system helps to understand the anatomy of this complex area and to accurately plan the EETA.

Kasemsiri P; Solares CA; Carrau RL; Prosser JD; Prevedello DM; Otto BA; Old M; Kassam AB

2013-04-01

197

Genetic analysis of albuminuria in the aging mouse and concordance with loci for diabetic nephropathy found in a genome-wide association scan  

Science.gov (United States)

Aging is a physiological process involving both genetic factors and environmental agents that can lead to function loss in organs. In the kidney, aging can cause leakage of proteins in urine, starting with albumin. Discovering molecular mechanisms responsible for albuminuria during aging could offer new perspectives on the etiology of this abnormality. Haplotype association mapping in the mouse is a novel approach which uses the haplotypes of the relatively closely related mouse inbred strains and the variation of the phenotypes among these strains to find associations between haplotypes and phenotype. Albumin-to-creatinine ratios, measures of urinary albumin excretion, were determined in 30 inbred mouse strains at 12, 18, and 24 months of age. To determine genetic loci that are involved in albuminuria, haplotype association mapping was performed for males and females separately at all 3 time points using a set of 63,222 SNPs. One significant and 8 suggestive loci were identified, some of which map to previously identified loci for traits associated with kidney damage in the mouse, but with a much higher resolution, which narrowed the mapped loci. These 9 loci were then investigated in the data of the genome-wide association scan for diabetic nephropathy in human type 1 diabetes. Two of the 9 mouse loci were found to be significantly associated with diabetic nephropathy, suggesting common underlying genes predisposing to kidney disease in mice and humans.

Tsaih, Shirng-Wern; Pezzolesi, Marcus G.; Yuan, Rong; Warram, James H.; Krolewski, Andrzej S.; Korstanje, Ron

2009-01-01

198

Genetic analysis of albuminuria in aging mice and concordance with loci for human diabetic nephropathy found in a genome-wide association scan.  

Science.gov (United States)

Aging in the kidney can cause albuminuria, and discovering molecular mechanisms responsible for this might offer a new perspective on the etiology of this abnormality. Haplotype association mapping in the mouse is a novel approach which uses the haplotypes of the relatively closely related mouse inbred strains and the phenotypic variation among these strains to find associations between haplotypes and phenotype. The albumin-to-creatinine ratios, a measure of urinary albumin excretion, were determined in 30 inbred mouse strains at 12, 18, and 24 months of age. Mapping was performed for males and females separately at all three time points using a high density set of 63,222 single-nucleotide polymorphisms to determine genetic loci involved in albuminuria. One significant and eight suggestive loci were found, some of which map to previously identified loci for traits associated with kidney damage in the mouse, but with a much higher resolution thus narrowing their chromosomal location. These nine loci were then compared with genome-wide association scans for diabetic nephropathy (DN) in human type I diabetes. Our study found that two of the nine mouse loci for age-related albuminuria were significantly associated with DN and consistent across male and female strata. This suggests common underlying genes predispose to kidney disease in mice and humans. PMID:19924099

Tsaih, Shirng-Wern; Pezzolesi, Marcus G; Yuan, Rong; Warram, James H; Krolewski, Andrzej S; Korstanje, Ron

2009-11-18

199

Genetic analysis of albuminuria in aging mice and concordance with loci for human diabetic nephropathy found in a genome-wide association scan.  

UK PubMed Central (United Kingdom)

Aging in the kidney can cause albuminuria, and discovering molecular mechanisms responsible for this might offer a new perspective on the etiology of this abnormality. Haplotype association mapping in the mouse is a novel approach which uses the haplotypes of the relatively closely related mouse inbred strains and the phenotypic variation among these strains to find associations between haplotypes and phenotype. The albumin-to-creatinine ratios, a measure of urinary albumin excretion, were determined in 30 inbred mouse strains at 12, 18, and 24 months of age. Mapping was performed for males and females separately at all three time points using a high density set of 63,222 single-nucleotide polymorphisms to determine genetic loci involved in albuminuria. One significant and eight suggestive loci were found, some of which map to previously identified loci for traits associated with kidney damage in the mouse, but with a much higher resolution thus narrowing their chromosomal location. These nine loci were then compared with genome-wide association scans for diabetic nephropathy (DN) in human type I diabetes. Our study found that two of the nine mouse loci for age-related albuminuria were significantly associated with DN and consistent across male and female strata. This suggests common underlying genes predispose to kidney disease in mice and humans.

Tsaih SW; Pezzolesi MG; Yuan R; Warram JH; Krolewski AS; Korstanje R

2010-02-01

200

Accuracy of computerized automatic identification of cephalometric landmarks by a designed software.  

UK PubMed Central (United Kingdom)

OBJECTIVES: The purpose of this study was to design software for localization of cephalometric landmarks and to evaluate its accuracy in finding landmarks. METHODS: 40 digital cephalometric radiographs were randomly selected. 16 landmarks which were important in most cephalometric analyses were chosen to be identified. Three expert orthodontists manually identified landmarks twice. The mean of two measurements of each landmark was defined as the baseline landmark. The computer was then able to compare the automatic system's estimate of a landmark with the baseline landmark. The software was designed using Delphi and Matlab programming languages. The techniques were template matching, edge enhancement and some accessory techniques. RESULTS: The total mean error between manually identified and automatically identified landmarks was 2.59 mm. 12.5% of landmarks had mean errors less than 1 mm. 43.75% of landmarks had mean errors less than 2 mm. The mean errors of all landmarks except the anterior nasal spine were less than 4 mm. CONCLUSIONS: This software had significant accuracy for localization of cephalometric landmarks and could be used in future applications. It seems that the accuracy obtained with the software which was developed in this study is better than previous automated systems that have used model-based and knowledge-based approaches.

Shahidi Sh; Shahidi S; Oshagh M; Gozin F; Salehi P; Danaei SM

2013-01-01

 
 
 
 
201

Object-oriented landmark recognition for UAV-navigation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Computer vision is an ever more important means for the navigation of UAVs. Here we propose a landmark recognition system looking for salient man-made infrastructure. An object-oriented structural system is preferred since it can utilize known properties of these objects such as part-of hierarchies,...

Michaelsen, E.; Roschkowski, D.; Doktorski, L.; Jaeger, K.; Arens, M.

202

On-line SLAM using clustered landmarks with omnidirectional vision  

Scientific Electronic Library Online (English)

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

Okamoto Jr., Jun; Guizilini, Vitor Campanholo

2010-12-01

203

Pigeons combine compass and landmark guidance in familiar route navigation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

How do birds orient over familiar terrain? In the best studied avian species, the homing pigeon (Columba livia), two apparently independent primary mechanisms are currently debated: either memorized visual landmarks provide homeward guidance directly, or birds rely on a compass to home from familiar...

Biro, Dora; Freeman, Robin; Meade, Jessica; Roberts, Stephen; Guilford, Tim

204

On-line SLAM using clustered landmarks with omnidirectional vision  

Directory of Open Access Journals (Sweden)

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

Jun Okamoto Jr.; Vitor Campanholo Guizilini

2010-01-01

205

The Landmark Decision that Faded into Historical Obscurity  

Science.gov (United States)

This article takes a look at the Mendez v. Westminster School District, a landmark case that faded into historical obscurity. In the 1940s, Gonzalo and Felicita Mendez wanted their three children to attend the school nearest their farm, which was the 17th Street Elementary School in Westminster. But in the Westminster, Orange County, El Medina,…

Nance, Molly

2007-01-01

206

An Adaptive Algorithm for Finding Frequent Sets in Landmark Windows  

DEFF Research Database (Denmark)

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

Dang, Xuan-Hong; Ong, Kok-Leong

2012-01-01

207

The Giessen virtual environment laboratory: human wayfinding and landmark salience.  

UK PubMed Central (United Kingdom)

In our virtual environment laboratory, we focus on different topics in human spatial cognition with projects on landmark salience, route knowledge, and survey knowledge. Within this laboratory note, we provide an overview of previous, current, and future work with our virtual environment SQUARELAND.

Röser F; Hamburger K; Knauff M

2011-05-01

208

Reliability of bony landmarks for restoration of the joint line in revision knee arthroplasty.  

Science.gov (United States)

The aim of this study was to determine the reliability of bone landmarks for restoring the joint line in revision knee arthroplasty. The relationship of the femoral epicondyles, the tibial tubercle (TT) and the fibular head (FH) to the joint line was measured on 200 magnetic resonance imaging (MRI, 100 females, 100 males), including assessment on intraobserver and interobserver reliability. MRI scans demonstrating chondral lesions and osteoarthritis were excluded, as were patients with immature skeletons or a history of previous knee surgery. Sequences in sagittal, coronal and axial planes were used as well as cross-referencing with the same computer software. In order to account for size differences between patients, each bony landmark measurement was converted to a ratio relative to the femoral or/and tibial width. We found a transepicondylar axis equal to 3.11 degrees (+/-1.9). The average distance from the epicondyles to the joint line was respectively 23 mm on the lateral side and 28 mm on the medial side. However there was a variation of distance from the epicondyles of the joint line up to 11 mm and a significative difference was found between male and female. We determined the distances from the tip of the FH and from the TT to the joint line. The joint line-FH distance averaged 14 mm (range 4.1-22.13) with no gender difference. The joint line-TT distance was averaged 22 mm (range 10.61-32.09). We determined an epicondylar ratio (distance from the lateral epicondyle to the joint line related to the femoral width). We found this ratio averaged 28% with no gender difference (P = 0.09). There is a large variation of bony landmarks depending on the size of the individual. Considering this findings, the FH is not a reliable guide for the joint line in revision surgery. Previous studies have measured the absolute values from various landmarks to the joint line. This study provides a significant advantage, in that the level of the joint line can be determined for each individual by using a ratio to account for gender and size differences. PMID:18046537

Servien, Elvire; Viskontas, Darius; Giuffrè, Bruno M; Coolican, Myles R J; Parker, David A

2007-11-29

209

Improving Detection Rate in Intrusion Detection Systems Using FCM Clustering to Select Meaningful Landmarks in Incremental Landmark Isomap Algorithm  

Directory of Open Access Journals (Sweden)

Full Text Available Dimension reduction is crucial when it is applied on intrusion detection systems. Many data mining algorithms have been used for this purpose. For example, manifold learning algorithms, especially Isometric feature mapping (Isomap) have been investigated. Researchers successfully applied Isomap on intrusion detection system as a nonlinear dimension reduction method. But it had some problems such as operation on batch mode and being disabled to handle new data points, additionally, it had computational cost and could not be properly applied on huge datasets. Losing time and reducing speed of detection is another problem of Isomap in intrusion detection systems. Incremental Landmark Isomap which selects landmarks among whole data points has been invented for solving these problems. In this paper, we use FCM as a data reduction method to select meaningful landmarks for Incremental L-Isomap instead of choosing them randomly. This method is implemented and applied on some UCI datasets and also NSLKDD dataset. The results demonstrate higher detection rate for the proposed method, comparing to classical Incremental L-Isomap which chooses landmarks randomly.

Seyed Mehdi Iranmanesh; Mehdi Mohammadi; Ahmad Akbari; Babak Nassersharif

2012-01-01

210

Otitis media: a genome-wide linkage scan with evidence of susceptibility loci within the 17q12 and 10q22.3 regions  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Otitis media (OM) is a common worldwide pediatric health care problem that is known to be influenced by genetics. The objective of our study was to use linkage analysis to map possible OM susceptibility genes. Methods Using a stringent diagnostic model in which only those who underwent tympanostomy tube insertion at least once for recurrent/persistent OM are considered affected, we have carried out a genome-wide linkage scan using the 10K Affymetrix SNP panel. We genotyped 403 Caucasian families containing 1,431 genotyped individuals and 377 genotyped affected sib pairs, and 26 African American families containing 75 genotyped individuals and 27 genotyped affected sib pairs. After careful quality control, non-parametric linkage analysis was carried out using 8,802 SNPs. Results In the Caucasian-only data set, our most significant linkage peak is on chromosome 17q12 at rs226088 with a p-value of 0.00007. Other peaks of potential interest are on 10q22.3 (0.00181 at rs1878001), 7q33 (0.00105 at rs958408), 6p25.1 (0.00261 at rs554653), and 4p15.2 (0.00301 at rs2133507). In the combined Caucasian and African American dataset, the 10q22.3 peak becomes more significant, with a minimal p-value of 0.00026 at rs719871. Family-based association testing reveals signals near previously implicated genes: 513 kb from SFTPA2 (10q22.3), 48 kb from IFNG (12q14), and 870 kb from TNF (6p21.3). Conclusion Our scan does not provide evidence for linkage in the previously reported regions of 10q26.3 and 19q13.43. Our best-supported linkage regions may contain susceptibility genes that influence the risk for recurrent/persistent OM. Plausible candidates in 17q12 include AP2B1, CCL5, and a cluster of other CCL genes, and in 10q22.3, SFTPA2.

Casselbrant Margaretha L; Mandel Ellen M; Jung Jeesun; Ferrell Robert E; Tekely Kathleen; Szatkiewicz Jin P; Ray Amrita; Weeks Daniel E

2009-01-01

211

A whole genome scan for QTL affecting milk protein percentage in Italian Holstein cattle, applying selective milk DNA pooling and multiple marker mapping in a daughter design.  

UK PubMed Central (United Kingdom)

We report on a complete genome scan for quantitative trait loci (QTL) affecting milk protein percentage (PP) in the Italian Holstein-Friesian cattle population, applying a selective DNA pooling strategy in a daughter design. Ten Holstein-Friesian sires were chosen, and for each sire, about 200 daughters, each from the high and low tails of estimated breeding value for PP, were used to construct milk DNA pools. Sires and pools were genotyped for 181 dinucleotide microsatellites covering all cattle autosomes. Sire marker allele frequencies in the pools were obtained by shadow correction of peak height in the electropherograms. After quality control, pool data from eight sires were used for all subsequent analyses. The QTL heterozygosity estimate was lower than that of similar studies in other cattle populations. Multiple marker mapping identified 19 QTL located on 14 chromosomes (BTA1, 2, 3, 4, 5, 6, 8, 9, 12, 14, 17, 20, 23 and 27). The sires were also genotyped for seven polymorphic sites in six candidate genes (ABCG2, SPP1, casein kappa, DGAT1, GHR and PRLR) located within QTL regions of BTA6, 14 and 20 found in this study. The results confirmed or excluded the involvement of some of the analysed markers as the causative polymorphic sites of the identified QTL. The QTL identified, combined with genotype data of these candidate genes, will help to identify other quantitative trait genes and clarify the complex QTL patterns observed for a few chromosomes. Overall, the results are consistent with the Italian Holstein population having been under long-term selection for high PP.

Russo V; Fontanesi L; Dolezal M; Lipkin E; Scotti E; Zambonelli P; Dall'Olio S; Bigi D; Davoli R; Canavesi F; Medugorac I; Föster M; Sölkner J; Schiavini F; Bagnato A; Soller M

2012-07-01

212

The landmark citation method: analysis of a citation pattern as a collection assessment method.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The landmark citation method is a new collection assessment method based on the citation record of a single landmark article. This citation record is developed by identifying sources which cite the landmark article. A bibliography, extracted from the citation record, is then used to complete an asse...

Soehner, C B; Wray, S T; Richards, D T

213

CT Scan (CAT Scan)  

Science.gov (United States)

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

2008-08-20

214

Accuracy of surface landmark identification for cannula cricothyroidotomy.  

UK PubMed Central (United Kingdom)

Cannula cricothyroidotomy is recommended for emergency transtracheal ventilation by all current airway guidelines. Success with this technique depends on the accurate and rapid identification of percutaneous anatomical landmarks. Six healthy subjects underwent neck ultrasound to delineate the borders of the cricothyroid membrane. The midline and bisecting transverse planes through the membrane were marked with an invisible ink pen which could be revealed with an ultraviolet light. Eighteen anaesthetists were then invited to mark an entry point for cricothyroid membrane puncture. Only 32 (30%) attempts by anaesthetists accurately marked the skin area over the cricothyroid membrane. Of these only 11 (10%) marked over the centre point of the membrane. Entry point accuracy was not significantly affected by subjects' weight, height, body mass index, neck circumference or cricothyroid dimensions. Consultant and registrar anaesthetists were significantly more accurate than senior house officers at correctly identifying the cricothyroid membrane. Accuracy of percutaneously identifying the cricothyroid membrane was poor. Ultrasound may assist in identifying anatomical landmarks for cricothyroidotomy.

Elliott DS; Baker PA; Scott MR; Birch CW; Thompson JM

2010-09-01

215

Automatic identification of the reference system based on the fourth ventricular landmarks in T1-weighted MR images.  

UK PubMed Central (United Kingdom)

RATIONALE AND OBJECTIVES: The reference system based on the fourth ventricular landmarks (including the fastigial point and ventricular floor plane) is used in medical image analysis of the brain stem. The objective of this study was to develop a rapid, robust, and accurate method for the automatic identification of this reference system on T1-weighted magnetic resonance images. MATERIALS AND METHODS: The fully automated method developed in this study consisted of four stages: preprocessing of the data set, expectation-maximization algorithm-based extraction of the fourth ventricle in the region of interest, a coarse-to-fine strategy for identifying the fastigial point, and localization of the base point. The method was evaluated on 27 Brain Web data sets qualitatively and 18 Internet Brain Segmentation Repository data sets and 30 clinical scans quantitatively. RESULTS: The results of qualitative evaluation indicated that the method was robust to rotation, landmark variation, noise, and inhomogeneity. The results of quantitative evaluation indicated that the method was able to identify the reference system with an accuracy of 0.7 +/- 0.2 mm for the fastigial point and 1.1 +/- 0.3 mm for the base point. It took <6 seconds for the method to identify the related landmarks on a personal computer with an Intel Core 2 6300 processor and 2 GB of random-access memory. CONCLUSION: The proposed method for the automatic identification of the reference system based on the fourth ventricular landmarks was shown to be rapid, robust, and accurate. The method has potentially utility in image registration and computer-aided surgery.

Fu Y; Gao W; Chen X; Zhu M; Shen W; Wang S

2010-01-01

216

Design Guidelines for Landmarks to Support Navigation in Virtual Environments  

CERN Multimedia

Unfamiliar, large-scale virtual environments are difficult to navigate. This paper presents design guidelines to ease navigation in such virtual environments. The guidelines presented here focus on the design and placement of landmarks in virtual environments. Moreover, the guidelines are based primarily on the extensive empirical literature on navigation in the real world. A rationale for this approach is provided by the similarities between navigational behavior in real and virtual environments.

Vinson, N G

2003-01-01

217

Dung beetles ignore landmarks for straight-line orientation.  

Science.gov (United States)

Upon locating a suitable dung pile, ball-rolling dung beetles shape a piece of dung into a ball and roll it away in a straight line. This guarantees that they will not return to the dung pile, where they risk having their ball stolen by other beetles. Dung beetles are known to use celestial compass cues such as the sun, the moon and the pattern of polarised light formed around these light sources to roll their balls of dung along straight paths. Here, we investigate whether terrestrial landmarks have any influence on straight-line orientation in dung beetles. We find that the removal or re-arrangement of landmarks has no effect on the beetle's orientation precision. Celestial compass cues dominate straight-line orientation in dung beetles so strongly that, under heavily overcast conditions or when prevented from seeing the sky, the beetles can no longer orient along straight paths. To our knowledge, this is the only animal with a visual compass system that ignores the extra orientation precision that landmarks can offer. PMID:23076443

Dacke, Marie; Byrne, Marcus; Smolka, Jochen; Warrant, Eric; Baird, Emily

2012-10-18

218

Dung beetles ignore landmarks for straight-line orientation.  

UK PubMed Central (United Kingdom)

Upon locating a suitable dung pile, ball-rolling dung beetles shape a piece of dung into a ball and roll it away in a straight line. This guarantees that they will not return to the dung pile, where they risk having their ball stolen by other beetles. Dung beetles are known to use celestial compass cues such as the sun, the moon and the pattern of polarised light formed around these light sources to roll their balls of dung along straight paths. Here, we investigate whether terrestrial landmarks have any influence on straight-line orientation in dung beetles. We find that the removal or re-arrangement of landmarks has no effect on the beetle's orientation precision. Celestial compass cues dominate straight-line orientation in dung beetles so strongly that, under heavily overcast conditions or when prevented from seeing the sky, the beetles can no longer orient along straight paths. To our knowledge, this is the only animal with a visual compass system that ignores the extra orientation precision that landmarks can offer.

Dacke M; Byrne M; Smolka J; Warrant E; Baird E

2013-01-01

219

Perceptual organization and artificial attention for visual landmarks detection.  

UK PubMed Central (United Kingdom)

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

Antúnez E; Palomino AJ; Marfil R; Bandera JP

2013-03-01

220

A physical map of the human genome.  

UK PubMed Central (United Kingdom)

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.

McPherson JD; Marra M; Hillier L; Waterston RH; Chinwalla A; Wallis J; Sekhon M; Wylie K; Mardis ER; Wilson RK; Fulton R; Kucaba TA; Wagner-McPherson C; Barbazuk WB; Gregory SG; Humphray SJ; French L; Evans RS; Bethel G; Whittaker A; Holden JL; McCann OT; Dunham A; Soderlund C; Scott CE; Bentley DR; Schuler G; Chen HC; Jang W; Green ED; Idol JR; Maduro VV; Montgomery KT; Lee E; Miller A; Emerling S; Kucherlapati; Gibbs R; Scherer S; Gorrell JH; Sodergren E; Clerc-Blankenburg K; Tabor P; Naylor S; Garcia D; de Jong PJ; Catanese JJ; Nowak N; Osoegawa K; Qin S; Rowen L; Madan A; Dors M; Hood L; Trask B; Friedman C; Massa H; Cheung VG; Kirsch IR; Reid T; Yonescu R; Weissenbach J; Bruls T; Heilig R; Branscomb E; Olsen A; Doggett N; Cheng JF; Hawkins T; Myers RM; Shang J; Ramirez L; Schmutz J; Velasquez O; Dixon K; Stone NE; Cox DR; Haussler D; Kent WJ; 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 XN; Fujiyama A; Hattori M; Toyoda A; Yada T; Park HS; 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

2001-02-01

 
 
 
 
221

A physical map of the human genome  

Energy Technology Data Exchange (ETDEWEB)

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.

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

222

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.  

UK PubMed Central (United Kingdom)

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

Mita H; Toyota M; Aoki F; Akashi H; Maruyama R; Sasaki Y; Suzuki H; Idogawa M; Kashima L; Yanagihara K; Fujita M; Hosokawa M; Kusano M; Sabau SV; Tatsumi H; Imai K; Shinomura Y; Tokino T

2009-01-01

223

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

Directory of Open Access Journals (Sweden)

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

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

2009-01-01

224

Errors in landmarking and the evaluation of the accuracy of traditional and 3D anthropometry.  

UK PubMed Central (United Kingdom)

Body dimensions are based on landmarks of the body, but the magnitude of error in landmark determination is not well known. Therefore, a study was performed in which 40 subjects were marked five times in total by one highly skilled marker and a novice marker. Immediately after marking, a skilled measurer determined 34 body dimensions that were based on the mark locations. Intra- and inter-observer errors in landmarking of 35 landmarks, as well as those in 34 body dimensions were quantified. The error in landmarking was defined as the distance between two marks made on the same landmark by the same marker (intra-observer error) or by two different markers (inter-observer error). To make the first mark invisible when the second mark was made, the first mark was made using an invisible ink pen under black light. Landmarks with large intra-observer errors also had large inter-observer errors. Errors in body dimensions were smaller than landmarking errors in 23 measurements, which suggested that the magnitude of landmarking error would be underestimated from errors in body dimensions. In 15 body dimensions, measurements based on marks made by two different markers were not comparable according to the ISO 20685 criterion. Examination of body dimensions and landmarks with large inter-observer errors suggested that reducing inter-observer landmarking errors was necessary to reduce inter-observer measurement errors, and that a possible solution was to explicitly define landmarks with large errors in more detail so that anthropometrists can pinpoint them on the skin. Quantitative data on the intra- and inter-observer landmarking errors in the present study may be useful as a reference when evaluating and comparing the performance of software for calculating landmark locations for 3D anthropometry.

Kouchi M; Mochimaru M

2011-03-01

225

CAT Scan  

Medline Plus

Full Text Available X-Plain Computed Axial Tomography (CT) Scan Reference Summary Introduction A Computed Axial Tomography Scan or CT scan is a test that provides very clear pictures of structures inside the body. ...

226

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

UK PubMed Central (United Kingdom)

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

Peetz J; Wilson AE

2013-02-01

227

Intensity-based elastic registration incorporating anisotropic landmark errors and rotational information.  

UK PubMed Central (United Kingdom)

PURPOSE: Thin-plate splines (TPS) represent an effective tool for estimating the deformation that warps one set of landmarks to another based on the physical equivalent of thin metal sheets. In the original formulation, data used to estimate the deformation field are restricted to landmark locations only and thus does not allow to incorporate information about the rotation of the image around the landmark. It furthermore assumes that landmark positions are known exactly which is not the case in real world applications. These localization inaccuracies are propagated to the entire deformation field as each landmark has a global influence. We propose to use a TPS approximation method that incorporates anisotropic landmark errors and rotational information and integrate it into a hierarchical elastic registration framework (HERA). The improvement of the registration performance has been evaluated. METHODS: The proposed TPS approximation scheme integrates anisotropic landmark errors with rotational information of the landmarks. The anisotropic landmark errors are represented by their covariance matrices estimated directly from the image data as a minimal stochastic localization error, i.e. the Cramér-Rao bound. The rotational attribute of each landmark is characterized by an additional angular landmark, thus doubling the number of landmarks in the TPS model. This allows the TPS approximation to better cope up with local deformations. RESULTS: We integrated the proposed TPS approach into the HERA registration framework and applied it to register 161 image pairs from a digital mammogram database. Experiments showed that the mean squared error using the proposed TPS approximation was superior to pure TPS interpolation. On artificially deformed breast images HERA, with the proposed TPS approximation, performed significantly better than the state-of-the-art registration method presented by Rueckert. CONCLUSION: The TPS approximation approach proposed in this publication allows to incorporate anisotropic landmark errors as well as rotational information. The integration of the method into an intensity-based hierarchical non-rigid registration framework is straightforward and improved the registration quality significantly.

Serifovi?-Trbali? A; Demirovi? D; Prljaca N; Szekely G; Cattin PC

2009-09-01

228

Volumetric image guidance using carina vs spine as registration landmarks for conventionally fractionated lung radiotherapy.  

UK PubMed Central (United Kingdom)

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.

Lavoie C; Higgins J; Bissonnette JP; Le LW; Sun A; Brade A; Hope A; Cho J; Bezjak A

2012-12-01

229

Anatomical landmarks for transnasal endoscopic skull base surgery.  

UK PubMed Central (United Kingdom)

Resection of midline skull base lesions involve approaches needing extensive neurovascular manipulation. Transnasal endoscopic approach (TEA) is minimally invasive and ideal for certain selected lesions of the anterior skull base. A thorough knowledge of endonasal endoscopic anatomy is essential to be well versed with its surgical applications and this is possible only by dedicated cadaveric dissections. The goal in this study was to understand endoscopic anatomy of the orbital apex, petrous apex and the pterygopalatine fossa. Six cadaveric heads (3 injected and 3 non injected) and 12 sides, were dissected using a TEA outlining systematically, the steps of surgical dissection and the landmarks encountered. Dissection done by the "2 nostril, 4 hands" technique, allows better transnasal instrumentation with two surgeons working in unison with each other. The main surgical landmarks for the orbital apex are the carotid artery protuberance in the lateral sphenoid wall, optic nerve canal, lateral optico-carotid recess, optic strut and the V2 nerve. Orbital apex includes structures passing through the superior and inferior orbital fissure and the optic nerve canal. Vidian nerve canal and the V2 are important landmarks for the petrous apex. Identification of the sphenopalatine artery, V2 and foramen rotundum are important during dissection of the pterygopalatine fossa. In conclusion, the major potential advantage of TEA to the skull base is that it provides a direct anatomical route to the lesion without traversing any major neurovascular structures, as against the open transcranial approaches which involve more neurovascular manipulation and brain retraction. Obviously, these approaches require close cooperation and collaboration between otorhinolaryngologists and neurosurgeons.

Sandu K; Monnier P; Pasche P

2012-01-01

230

Anatomical landmarks for transnasal endoscopic skull base surgery.  

Science.gov (United States)

Resection of midline skull base lesions involve approaches needing extensive neurovascular manipulation. Transnasal endoscopic approach (TEA) is minimally invasive and ideal for certain selected lesions of the anterior skull base. A thorough knowledge of endonasal endoscopic anatomy is essential to be well versed with its surgical applications and this is possible only by dedicated cadaveric dissections. The goal in this study was to understand endoscopic anatomy of the orbital apex, petrous apex and the pterygopalatine fossa. Six cadaveric heads (3 injected and 3 non injected) and 12 sides, were dissected using a TEA outlining systematically, the steps of surgical dissection and the landmarks encountered. Dissection done by the "2 nostril, 4 hands" technique, allows better transnasal instrumentation with two surgeons working in unison with each other. The main surgical landmarks for the orbital apex are the carotid artery protuberance in the lateral sphenoid wall, optic nerve canal, lateral optico-carotid recess, optic strut and the V2 nerve. Orbital apex includes structures passing through the superior and inferior orbital fissure and the optic nerve canal. Vidian nerve canal and the V2 are important landmarks for the petrous apex. Identification of the sphenopalatine artery, V2 and foramen rotundum are important during dissection of the pterygopalatine fossa. In conclusion, the major potential advantage of TEA to the skull base is that it provides a direct anatomical route to the lesion without traversing any major neurovascular structures, as against the open transcranial approaches which involve more neurovascular manipulation and brain retraction. Obviously, these approaches require close cooperation and collaboration between otorhinolaryngologists and neurosurgeons. PMID:21744072

Sandu, Kishore; Monnier, Philippe; Pasche, Philippe

2011-07-09

231

Landmark risk prediction of residual life for breast cancer survival.  

Science.gov (United States)

The importance of developing personalized risk prediction estimates has become increasingly evident in recent years. In general, patient populations may be heterogenous and represent a mixture of different unknown subtypes of disease. When the source of this heterogeneity and resulting subtypes of disease are unknown, accurate prediction of survival may be difficult. However, in certain disease settings, the onset time of an observable short-term event may be highly associated with these unknown subtypes of disease and thus may be useful in predicting long-term survival. One approach to incorporate short-term event information along with baseline markers for the prediction of long-term survival is through a landmark Cox model, which assumes a proportional hazards model for the residual life at a given landmark point. In this paper, we use this modeling framework to develop procedures to assess how a patient's long-term survival trajectory may change over time given good short-term outcome indications along with prognosis on the basis of baseline markers. We first propose time-varying accuracy measures to quantify the predictive performance of landmark prediction rules for residual life and provide resampling-based procedures to make inference about such accuracy measures. Simulation studies show that the proposed procedures perform well in finite samples. Throughout, we illustrate our proposed procedures by using a breast cancer dataset with information on time to metastasis and time to death. In addition to baseline clinical markers available for each patient, a chromosome instability genetic score, denoted by CIN25, is also available for each patient and has been shown to be predictive of survival for various types of cancer. We provide procedures to evaluate the incremental value of CIN25 for the prediction of residual life and examine how the residual life profile changes over time. This allows us to identify an informative landmark point, t0 , such that accurate risk predictions of the residual life could be made for patients who survive past t0 without metastasis. Copyright © 2013 John Wiley & Sons, Ltd. PMID:23494768

Parast, Layla; Cai, Tianxi

2013-03-14

232

Landmark trials affecting the surgical management of invasive breast cancer.  

UK PubMed Central (United Kingdom)

Significant progress has been made in the surgical management of breast cancer. Most women diagnosed with early stage invasive breast cancer can now be managed with breast-conserving therapy to include a segmental mastectomy followed by radiation. Axillary lymph nodes are routinely assessed by sentinel lymph node biopsy. Axillary lymph node dissection is reserved for patients with documented nodal metastasis; however, here too progress has been made because a population of low-risk patients has been identified in whom a complete dissection is not required even in the setting of a positive sentinel lymph node. This article details the landmark clinical trials that have guided the surgical management of breast cancer.

Black DM; Mittendorf EA

2013-04-01

233

Preliminary study of automatic detection method for anatomical landmarks in body trunk CT images  

International Nuclear Information System (INIS)

In the research field of medical image processing and analysis, it is important to develop medical image understanding methods which are robust for individual and case differences, since they often interfere with accurate medical image processing and analysis. Location of anatomical landmarks, which are localized regions with anatomical reference to the human body, allows for robust medical understanding since the relative position of anatomical landmarks is basically the same among cases. This is a preliminary study for detecting anatomical point landmarks by using a technique of local area model matching. The model for matching process, which is called appearance model, shows the spatial appearance of voxel values at the detection target landmark and its surrounding region, while the Principal Component Analysis (PCA) is used to train appearance models. In this study, we experimentally investigate the optimal appearance model for landmark detection and analyze detection accuracy of anatomical point landmarks. (author)

2010-01-01

234

Toward 959 nematode genomes.  

UK PubMed Central (United Kingdom)

The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism. The success of the C. elegans genome sequencing project also inspired communities working on other organisms to approach genome sequencing of their species. The phylum Nematoda is rich and diverse and of interest to a wide range of research fields from basic biology through ecology and parasitic disease. For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases. The advent of second-generation sequencing technologies, improvements in computing algorithms and infrastructure and growth in bioinformatics and genomics literacy is making the addition of genome sequencing to the research goals of any nematode research program a less daunting prospect. To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/). Just as the deciphering of the developmental lineage of the 959 cells of the adult hermaphrodite C. elegans was the gateway to broad advances in biomedical science, we hope that a nematode phylogeny with (at least) 959 sequenced species will underpin further advances in understanding the origins of parasitism, the dynamics of genomic change and the adaptations that have made Nematoda one of the most successful animal phyla.

Kumar S; Koutsovoulos G; Kaur G; Blaxter M

2012-01-01

235

The use of radial symmetry to localize retinal landmarks.  

UK PubMed Central (United Kingdom)

Locating the optic disc center and the fovea in digital fundus images is surprisingly difficult due to the variation range in color and contrast and the possible presence of pathologies creating bright spots or changing the appearance of retinal landmarks. These reasons make it difficult to find good templates of optic disc and fovea shape and color for pattern matching. In this paper we propose radial symmetry as the principal cue to locate both optic disc and macula centers. Centers of bright and dark circularly symmetrical regions with arbitrary radii, can be found robustly against changes in brightness and contrast by using the Fast Radial Symmetry transform. Detectors based on this transform coupled with a weak hypothesis on vessel density (optic disc intersects large vessels while the fovea lies in an avascular region), can provide a fast location of both OD and macula with accuracy similar or better than state-of-the-art methods. The approach has been chosen as the default technique for fast localization of the two landmarks in the VAMPIRE software suite.

Giachetti A; Ballerini L; Trucco E; Wilson PJ

2013-07-01

236

Dominance of the odometer over serial landmark learning in honeybee navigation  

Science.gov (United States)

Honeybees use their visual flow field to measure flight distance. It has been suggested that the experience of serial landmarks encountered on the flight toward a feeding place contributes to distance estimation. Here, we address this question by tracing the flight paths of individual bees with a harmonic radar system. Bees were trained along an array of three landmarks (tents), and the distance between these landmarks was either increased or decreased under two test conditions. We find that absolute distance estimation dominates the search for the feeding place, but serial position effects are also found. In the latter case, bees search only or additionally at locations determined by serial experience of the landmarks.

Menzel, Randolf; Fuchs, Jacqueline; Nadler, Leonard; Weiss, Benjamin; Kumbischinski, Nicole; Adebiyi, Daniel; Hartfil, Sergej; Greggers, Uwe

2010-08-01

237

A game-theoretic framework for landmark-based image segmentation.  

UK PubMed Central (United Kingdom)

A novel game-theoretic framework for landmark-based image segmentation is presented. Landmark detection is formulated as a game, in which landmarks are players, landmark candidate points are strategies, and likelihoods that candidate points represent landmarks are payoffs, determined according to the similarity of image intensities and spatial relationships between the candidate points in the target image and their corresponding landmarks in images from the training set. The solution of the formulated game-theoretic problem is the equilibrium of candidate points that represent landmarks in the target image and is obtained by a novel iterative scheme that solves the segmentation problem in polynomial time. The object boundaries are finally extracted by applying dynamic programming to the optimal path searching problem between the obtained adjacent landmarks. The performance of the proposed framework was evaluated for segmentation of lung fields from chest radiographs and heart ventricles from cardiac magnetic resonance cross sections. The comparison to other landmark-based segmentation techniques shows that the results obtained by the proposed game-theoretic framework are highly accurate and precise in terms of mean boundary distance and area overlap. Moreover, the framework overcomes several shortcomings of the existing techniques, such as sensitivity to initialization and convergence to local optima.

Ibragimov B; Likar B; Pernus F; Vrtovec T

2012-09-01

238

Do individuals with intellectual disability select appropriate objects as landmarks when learning a new route?  

UK PubMed Central (United Kingdom)

BACKGROUND: The present study was aimed at investigating the selection of landmarks by individuals with intellectual disability (ID). The hypothesis was that they would be less efficient than individuals without IDs in the selection of landmarks when learning a new route. METHODS: The experiment took place in a natural setting with a group of participants with ID and a group of control participants matched by chronological age. The participants were first guided along a route situated in an unfamiliar district. Then, they had to guide the experimenter along the route while pointing to all the objects and features they found useful for wayfinding. RESULTS: The designated objects were categorised as a function of their landmarks properties. There were significant differences between the two groups for non-permanent landmarks, distant landmarks and non-unique landmarks. The two groups selected landmarks near intersections in the same proportions. However, the individuals with ID selected more non-unique landmarks and less textual signage than the control group at these decision points. CONCLUSION: Individuals with ID seem to be less efficient than individuals without disability in landmark selection. This may limit their wayfinding abilities in their day-to-day travelling. This may also account for their difficulties in obtaining the kind of spatial knowledge which relates to the configural structure of their environment.

Courbois Y; Blades M; Farran EK; Sockeel P

2013-01-01

239

Genome-Wide Scan Identifies Variant in TNFSF13 Associated with Serum IgM in a Healthy Chinese Male Population  

Digital Repository Infrastructure Vision for European Research (DRIVER)

IgM provides a first line of defense during microbial infections. Serum IgM levels are detected routinely in clinical practice. And IgM is a genetically complex trait. We conducted a two-stage genome-wide association study (GWAS) to identify genetic variants affecting serum IgM levels in a Chinese p...

Yang, Ming; Wu, Yongming; Lu, Yanmei; Liu, Changyuan; Sun, Jielin; Liao, Ming; Qin, Min; Mo, Linjian; Gao, Yong; Lu, Zheng

240

The genetic risk in mice from radiation: an estimate of the mutation induction rate per genome.  

UK PubMed Central (United Kingdom)

Restriction Landmark Genome Scanning (RLGS) is a method that uses end-labeled (32)P NotI sites that are mostly associated with coding genes to visualizes thousands of DNA fragments as spots in two-dimensional autoradiograms. This approach allows direct detection of autosomal deletions as spots with half normal intensity. The method was applied to mouse offspring derived from spermatogonia exposed to 4 Gy of X rays. A genome-wide assessment of the mutation induction rate was estimated from the detected deletions. Examinations were made of 1,007 progeny (502 derived from control males and 505 from irradiated males) and 1,190 paternal and 1,240 maternal spots for each mouse. The results showed one deletion mutation in the unirradiated paternal genomes of 502 offspring (0.2%) and 5 deletions in the irradiated paternal genomes of 505 offspring (1%). The difference was marginally significant, with the deletion sizes ranged from 2-13 Mb. If the frequencies are taken at face value, the net increase was 0.8% after an exposure of 4 Gy, or 0.2% per Gy per individual if a linear dose response is assumed. Since the present RLGS analysis examined 1,190 NotI sites, while the mouse genome contains ?25,000 genes, the genomic probability of any gene undergoing a deletion mutation would be 25× 0.2%, or 5% per Gy. Furthermore, since the present RLGS screened about 0.2% of the total genome, the probability of detecting a deletion anywhere in the total genome would be estimated to be 500 times 0.2% or 100% (i.e., 1 deletion per Gy). These results are discussed with reference to copy number variation in the human genome.

Asakawa J; Kodaira M; Cullings HM; Katayama H; Nakamura N

2013-03-01

 
 
 
 
241

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

UK PubMed Central (United Kingdom)

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.

Kettunen P; Irvankoski K; Krause CM; Sarjakoski LT

2013-08-01

242

The use of anatomical landmarks for percutaneous nephrolithotomy  

Directory of Open Access Journals (Sweden)

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

Esat Kaan Akbay; Burak Turna; Servet Çelik; Emil Mukhtarov; Ahmet Bar?? Altay; Oktay Nazl?

2012-01-01

243

Bone scan  

Science.gov (United States)

A bone scan involves injecting a radioactive material (radiotracer) into a vein. The substance travels through your ... body. The camera takes pictures of how much radiotracer collects in the bones. If a bone scan ...

244

Renal scan  

Science.gov (United States)

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

245

CAT Scans  

Science.gov (United States)

This Physics 2000 page uses characters and dialogue to help explain what CAT scans are and how they work. Java applets show the relationship between traditional x-rays and the CAT scan. Links for more information are provided.

2007-07-16

246

CT Scan  

Science.gov (United States)

CT scan Basics In-Depth Multimedia Expert Answers Resources Reprints A single copy of this article may be reprinted for personal, noncommercial use only. CT scan By Mayo Clinic staff Original Article: http:// ...

247

Brain scanning  

International Nuclear Information System (INIS)

In this paper we will consider the brain scan and the knowledge the nurse will need to understand in order to give intelligent care to the patient having this neurodiagnostic study. We will include indications for the study, radiopharmaceuticals, physiology, scanning instruments, prior preparation, procedure, brain scan interpretation, and the implications for nursing management

1974-01-01

248

Elections and landmark policies in Tanzania and Uganda  

DEFF Research Database (Denmark)

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

Kjær, Anne Mette; Therkildsen, Ole

2012-01-01

249

Intra-articular hip injection using anatomic surface landmarks.  

UK PubMed Central (United Kingdom)

Intra-articular hip injection is a frequently used technique for diagnostic and therapeutic purposes and is gaining more importance for the early diagnosis of hip disease. It is commonly performed with imaging guidance such as ultrasonographic or fluoroscopic control. We describe our technique of injection of the hip using relative distances from anatomic surface landmarks, with the needle insertion point at the site of the proximal anterolateral portal for hip arthroscopy, with a posterior direction of 30° and targeted toward a junctional point between 2 perpendicular lines, 1 distal from the anterior superior iliac spine and the second anterior from the tip of the greater trochanter. This technique can be used without imaging guidance in the outpatient clinic. Moreover, it minimizes the need for radiographic exposure for more critical injections, such as the injection of contrast material before conducting magnetic resonance arthrogaphy of the hip.

Masoud MA; Said HG

2013-05-01

250

A neural wayfinding mechanism adjusts for ambiguous landmark information.  

UK PubMed Central (United Kingdom)

Objects along a route can serve as crucial landmarks that facilitate successful navigation. Previous functional magnetic resonance imaging (fMRI) evidence indicated that the human parahippocampal gyrus automatically distinguishes between objects placed at navigationally relevant (decision points) and irrelevant locations (non-decision points). This storage of relevant objects can provide a neural mechanism underlying successful navigation. However, only objects that actually support wayfinding need to be stored. Objects can also provide misleading information if similar objects appear at different locations along a route. An efficient mechanism needs to specifically adjust for ambiguous landmark information. We investigated this by placing identical objects twice in a virtual labyrinth at places with the same as well as with a different navigational relevance. Twenty right-handed volunteers moved through a virtual maze. They viewed the same object either at two different decision points, at two different non-decision points, or at a decision as well as at a non-decision point. Afterwards, event-related fMRI data were acquired during object recognition. Participants decided whether they had seen the objects in the maze or not. The results showed that activity in the parahippocampal gyrus was increased for objects placed at a decision and at a non-decision point as compared to objects placed at two non-decision points. However, ambiguous information resulting from the same object placed at two different decision points revealed increased activity in the right middle frontal gyrus. These findings suggest a neural wayfinding mechanism that differentiates between helpful and misleading information.

Janzen G; Jansen C

2010-08-01

251

Impact of landmark parametrization on monocular EKF-SLAM with points and lines  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper explores the impact that landmark parametrization has in the performance of monocular, EKF-based, 6-DOF simultaneous localization and mapping (SLAM) in the context of undelayed landmark initialization. Undelayed initialization in monocular SLAM challenges EKF because of the combination of...

Solà, Joan; Vidal-Calleja, Teresa; Civera, Javier; Martinez-Monti, Jose Maria

252

First Steps toward Location of Landmarks on X-Ray Images  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We address the problem of locating some anatomical bone structures on lateral cranial X-ray images. These structures are landmarks used in orthodontic therapy. The main problem in this pattern recognition application is that the landmarks are difficult to distinguish on images even for the human exp...

Desvignes, Michel; Romaniuk, Barbara; Clouard, Régis; Demoment, Ronan; Revenu, Marinette; Deshayes, Marie-Josèphe

253

Validation of anatomical landmarks-based registration for image-guided surgery: An in-vitro study.  

UK PubMed Central (United Kingdom)

INTRODUCTION: Perioperative navigation is a recent addition to orthognathic surgery. This study aimed to evaluate the accuracy of anatomical landmarks-based registration. MATERIALS AND METHODS: Eighty-five holes (1.2 mm diameter) were drilled in the surface of a plastic skull model, which was then scanned using a SkyView cone beam computed tomography scanner. DICOM files were imported into BrainLab ENT 3.0.0 to make a surgical plan. Six anatomical points were selected for registration: the infraorbital foramena, the anterior nasal spine, the crown tips of the upper canines, and the mesial contact point of the upper incisors. Each registration was performed five times by two separate observers (10 times total). RESULTS: The mean target registration error (TRE) in the anterior maxillary/zygomatic region was 0.93 ± 0.31 mm (p < 0.001 compared with other anatomical regions). The only statistically significant inter-observer difference of mean TRE was at the zygomatic arch, but was not clinically relevant. CONCLUSION: With six anatomical landmarks used, the mean TRE was clinically acceptable in the maxillary/zygomatic region. This registration technique may be used to access occlusal changes during bimaxillary surgery, but should be used with caution in other anatomical regions of the skull because of the large TRE observed.

Sun Y; Luebbers HT; Agbaje JO; Schepers S; Vrielinck L; Lambrichts I; Politis C

2013-09-01

254

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

Directory of Open Access Journals (Sweden)

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

Hampe O Baszio S

2010-01-01

255

Assessment of landmark measurements of craniofacial images from 2D and 3D reconstructions of spiral CT  

Science.gov (United States)

Purpose: The purpose of this study is to compare the accuracy of facial linear measurements obtained from volumetric spiral CT using 2D versus 3D reconstruction, and test the repeatability of these measurements. Material and Methods: The population consisted of 5 cadaver heads that were scanned to a Spiral CT scanner (120 Kvp and 200 mA, Toshiba Xpress S/X Toshiba-America, Medical System Inc., Tustin, CA) with high- resolution contiguous slices. Heads were scanned with 3 mm thick axial slices and a 2 mm/sec table feed. The CT data were archived on optical disks, and then transferred to a networked computer workstation (Sun Microsystems with Cemax version 1.4 software, Fremont, CA), to generate 2D and 3D images for manipulation and analyses. Repeated measurements were done on 2D and 3D images reconstructed from spiral CT scans on the workstation. Linear measurements were done by 2 observers with 2 sessions each, using several unique and conventional craniometric anatomic landmarks. The soft tissues were then partially removed and physical measurements of the same landmarks were repeated by an electromagnetic (3 space) digitizer (Polhemus Navigation Sciences Division, Mc Donnell Douglas Electronic Company, Colchester, VE). Analyses of variance were done to compare 2D versus 3D methods, and the accuracy of measurements between both imaging techniques. Results: The results showed statistically significant differences between 2D and 3D images for the majority of measurements. The 3D image measurements were not statistically different from the physical measurements. However, some of the 2D image landmarks differed from physical measurements. The repeatability of measurements was high by spiral CT-based craniofacial imaging. Conclusion: New computer graphics technology combined with 3D volumetric imaging by spiral CT can distinguish the craniofacial anatomy with greater accuracy than previously reported measurements and with greater accuracy than measurements from 2DCT images. These 3D measurements are essential to diagnostic and treatment planning of craniofacial injuries, anomalies and for craniofacial identification.

Cavalcanti, Marcelo G.; Haller, John W.; Vannier, Michael W.

1998-06-01

256

Genome-wide scan with nearly 700,000 SNPs in two Sardinian sub-populations suggests some regions as candidate targets for positive selection.  

Science.gov (United States)

This paper explores the genetic structure and signatures of natural selection in different sub-populations from the Island of Sardinia, exploiting information from nearly 700,000 autosomal SNPs genotyped with the Affymetrix Genome-Wide Human SNP 6.0 Array. The genetic structure of the Sardinian population and its position within the context of other Mediterranean and European human groups were investigated in depth by comparing our data with publicly available data sets. Principal components and admixture analyses suggest a clustering of the examined samples in two significantly differentiated sub-populations (Ogliastra and Southern Sardinia), as confirmed by AMOVA (F(ST)=0.011; P<0.001). Differentiation of these sub-populations was still evident when they were pooled together with supplementary Sardinian samples from HGDP and compared with several other European, North-African and Near Eastern populations, confirming the uniqueness of the Sardinian genetic background. Moreover, by applying several statistical approaches aimed at assessing differences at the SNP level, the highest differentiated genomic regions between Ogliastra and Southern Sardinia were thus investigated via an extended haplotype homozygosity (EHH)-based test to point out potential selective sweeps. Using this approach, 40 genomic regions were detected, with significant differences between Ogliastra and Southern Sardinia. These regions were subsequently investigated using a long-range haplotype test, which found significant REHH values for SNPs rs11070188 and rs11070192 in the Ogliastra sub-population. In the light of these results and the overlap of the different computed statistics, the region encompassing these loci can be considered a strong candidate to have undergone selective pressure in Ogliastra. PMID:22535185

Piras, Ignazio Stefano; De Montis, Antonella; Calò, Carla Maria; Marini, Monica; Atzori, Manuela; Corrias, Laura; Sazzini, Marco; Boattini, Alessio; Vona, Giuseppe; Contu, Licinio

2012-04-25

257

Automated positioning of scan plane and navigator tracker in MRI liver scan  

International Nuclear Information System (INIS)

[en] This paper presents a new method of the automatic scan prescription planning both the scan planes and Navigator Tracker locations in MRI liver scan. 3D dataset acquired by fast T1 sequence is preprocessed and converted into a 2D projection images to avoid the complicated and time-consuming 3D segmentation. 2D Active Shape Model is applied to the 2D Coronal projection data and extracts the outer shape of the liver dataset initially using the rough estimation of the inferior edge of the liver from the 2D projection dataset. The scan plane locations are identified from the inferior and superior edges of the shape model and Navigator tracker, which is used for motion compensated MR abdominal MR scanning, establishes the location selecting one of landmarks in the ASM. 38 volunteers datasets were tested and showed the good results to evolve into clinical test. (author)

2010-01-01

258

Landmarks of History of Soil Science in Sri Lanka  

Science.gov (United States)

Sri Lanka is a tropical Island in the Southern tip of Indian subcontinent positioned at 50 55' to 90 50' N latitude and 790 42' to 810 53' E longitude surrounded by the Indian Ocean. It is an island 435 km in length and 224 km width consisting of a land are of 6.56 million ha with a population of 20 million. In area wise it is ranked as 118th in the world, where at present ranked as 47 in population wise and ranked 19th in population density. The country was under colonial rule under Portuguese, Dutch and British from 1505 to 1948. The majority of the people in the past and present earn their living from activities based on land, which indicates the important of the soil resource. The objective of this paper is to describe the landmarks of the history of Soil Science to highlight the achievements and failures, which is useful to enrich our present understanding of Sri Lankan soils. The landmarks of the history of Soil Science in Sri Lanka can be divided to three phases namely, the early period (prior to 1956), the middle period (1956 to 1972) and the present period (from 1972 onwards). During the early period, detailed analytical studies of coffee and tea soils were compiled, and these gave mainly information on up-country soils which led to fertilizer recommendations based on field trials. In addition, rice and forest soils were also studied in less detail. The first classification of Sri Lankan soils and a provisional soil map based on parent material was published by Joachim in 1945 which is a major landmark of history of Soil Science in Sri Lanka. In 1959 Ponnamperuma proposed a soil classification system for wetland rice soils. From 1963 to 1968 valuable information on the land resource was collected and documented by aerial resource surveys funded by Canada-Ceylon Colombo plan aid project. This covered 18 major river basins and about 1/4th of Sri Lanka, which resulted in producing excellent soil maps and information of the areas called the Kelani Aruvi Ara and Walawe basins. The provisional soil map was updated by many other workers as Moorman and Panabokke in 1961 and 1972 using this information. The soil map produced by De Alwis and Panabokke in 1972 at a scale of 1:500,000 was the soil maps mostly used during the past years During the present era, the need for classification of Soils of Sri Lanka according to international methods was felt. A major leap forward in Soil Survey, Classification leading to development of a soil data base was initiated in 1995 with the commencement of the "SRICANSOL" project which was a twining project between the Soil Science Societies of Sri Lanka and Canada. This project is now completed with detail soil maps at a scale of 1:250,000 and soil classified according to international methods for the Wet, Intermediate and Dry zones of Sri Lanka. A digital database consisting of soil profile description and physical and chemical data is under preparation for 28, 40 and 51 benchmark sites of the Wet, Intermediate and Dry zones respectively. The emphases on studies on Soil Science in the country at present is more towards environmental conservation related to soil erosion control, reducing of pollution of soil and water bodies from nitrates, pesticide residues and heavy metal accumulation. Key words: Sri Lanka, Provisional soil map

Mapa, R.

2012-04-01

259

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

Science.gov (United States)

Job-related exhaustion is the core dimension of burnout, a work-related stress syndrome that has several negative health consequences. In this study, we explored the molecular genetic background of job-related exhaustion. A genome-wide analysis of job-related exhaustion was performed in the GENMETS subcohort (n = 1256) of the Finnish population-based Health 2000 study. Replication analyses included an analysis of the strongest associations in the rest of the Health 2000 sample (n = 1660 workers) and in three independent populations (the FINRISK population cohort, n = 10 753; two occupational cohorts, total n = 1451). Job-related exhaustion was ascertained using a standard self-administered questionnaire (the Maslach Burnout Inventory (MBI)-GS exhaustion scale in the Health 2000 sample and the occupational cohorts) or a single question (FINRISK). A variant located in an intron of UST, uronyl-2-sulfotransferase (rs13219957), gave the strongest statistical evidence in the initial genome-wide study (P = 1.55 × 10(-7)), and was associated with job-related exhaustion in all the replication sets (P UST in four separate samples suggest that this variant might be a weak risk factor for job-related exhaustion. Together with the previously reported associations of other dermatan/chondroitin sulfate genes with mood disorders, these results indicate a potential molecular pathway for stress-related traits and mark a candidate region for further studies of job-related and general exhaustion. PMID:23620144

Sulkava, Sonja; Ollila, Hanna M; Ahola, Kirsi; Partonen, Timo; Viitasalo, Katriina; Kettunen, Johannes; Lappalainen, Maarit; Kivimäki, Mika; Vahtera, Jussi; Lindström, Jaana; Härmä, Mikko; Puttonen, Sampsa; Salomaa, Veikko; Paunio, Tiina

2013-04-24

260

Radiographic landmarks for tunnel positioning in posterior cruciate ligament reconstructions.  

UK PubMed Central (United Kingdom)

BACKGROUND: Consistent radiographic guidelines for tunnel placement in single- or double-bundle posterior cruciate ligament (PCL) reconstructions are not well defined. Quantitative guidelines reporting the location of the individual PCL bundle attachments would aid in intraoperative tunnel placement and postoperative assessment of a PCL reconstruction. HYPOTHESIS: Consistent and reproducible measurements in relation to radiographic landmarks for the entire PCL and its individual bundle attachments are achievable. STUDY DESIGN: Controlled laboratory study. METHODS: The femoral and tibial PCL bundle attachment centers of 20 nonpaired fresh-frozen cadaveric knees were labeled using radio-opaque spheres and the attachment areas were labeled using barium sulfate. Anteroposterior (AP) and lateral radiographs of the femur and tibia were obtained, and measurements of the distances between the PCL bundle centers and landmarks were acquired. RESULTS: On the AP femur view, the anterolateral bundle (ALB) and posteromedial bundle (PMB) centers were 34.1 ± 3.0 mm and 29.2 ± 3.0 mm lateral to the most medial border of the medial femoral condyle, respectively. The lateral femur images revealed that the ALB center was 17.4 ± 1.7 mm and the PMB center was 23.9 ± 2.7 mm posteroproximal to a line perpendicular to the Blumensaat line that intersected the anterior margin of the medial femoral condyle cortex. Anteroposterior tibia images revealed that the ALB and PMB centers were located 0.2 ± 2.1 mm proximal and 4.9 ± 2.9 mm distal to the proximal joint line, respectively. The PCL attachment center was 1.6 ± 2.5 mm distal to the proximal joint line. On the lateral tibia view, the ALB center was 8.4 ± 1.8 mm, the PCL attachment center was 5.5 ± 1.7 mm, and the PMB center was 2.5 ± 1.5 mm superior to the champagne glass drop-off of the posterior tibia. CONCLUSION: Radiographic measurements from several clinically relevant views of the femur and tibia were reproducible with regard to the anatomic locations of the ALB and PMB centers. The measurements from the lateral femur and tibia views provided the most clinically pertinent radiographic measurements intraoperatively. CLINICAL RELEVANCE: This study established a set of clinically relevant radiographic guidelines for anatomic reconstruction of the PCL. The parameters set forth in this study can be used in both the intraoperative and postoperative settings for both single- and double-bundle PCL reconstructions.

Johannsen AM; Anderson CJ; Wijdicks CA; Engebretsen L; LaPrade RF

2013-01-01

 
 
 
 
261

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

Directory of Open Access Journals (Sweden)

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.

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

2009-01-01

262

A framework for evaluation of deformable image registration spatial accuracy using large landmark point sets  

International Nuclear Information System (INIS)

Expert landmark correspondences are widely reported for evaluating deformable image registration (DIR) spatial accuracy. In this report, we present a framework for objective evaluation of DIR spatial accuracy using large sets of expert-determined landmark point pairs. Large samples (>1100) of pulmonary landmark point pairs were manually generated for five cases. Estimates of inter- and intra-observer variation were determined from repeated registration. Comparative evaluation of DIR spatial accuracy was performed for two algorithms, a gradient-based optical flow algorithm and a landmark-based moving least-squares algorithm. The uncertainty of spatial error estimates was found to be inversely proportional to the square root of the number of landmark point pairs and directly proportional to the standard deviation of the spatial errors. Using the statistical properties of this data, we performed sample size calculations to estimate the average spatial accuracy of each algorithm with 95% confidence intervals within a 0.5 mm range. For the optical flow and moving least-squares algorithms, the required sample sizes were 1050 and 36, respectively. Comparative evaluation based on fewer than the required validation landmarks results in misrepresentation of the relative spatial accuracy. This study demonstrates that landmark pairs can be used to assess DIR spatial accuracy within a narrow uncertainty range.

263

A framework for evaluation of deformable image registration spatial accuracy using large landmark point sets  

Energy Technology Data Exchange (ETDEWEB)

Expert landmark correspondences are widely reported for evaluating deformable image registration (DIR) spatial accuracy. In this report, we present a framework for objective evaluation of DIR spatial accuracy using large sets of expert-determined landmark point pairs. Large samples (>1100) of pulmonary landmark point pairs were manually generated for five cases. Estimates of inter- and intra-observer variation were determined from repeated registration. Comparative evaluation of DIR spatial accuracy was performed for two algorithms, a gradient-based optical flow algorithm and a landmark-based moving least-squares algorithm. The uncertainty of spatial error estimates was found to be inversely proportional to the square root of the number of landmark point pairs and directly proportional to the standard deviation of the spatial errors. Using the statistical properties of this data, we performed sample size calculations to estimate the average spatial accuracy of each algorithm with 95% confidence intervals within a 0.5 mm range. For the optical flow and moving least-squares algorithms, the required sample sizes were 1050 and 36, respectively. Comparative evaluation based on fewer than the required validation landmarks results in misrepresentation of the relative spatial accuracy. This study demonstrates that landmark pairs can be used to assess DIR spatial accuracy within a narrow uncertainty range.

Castillo, Richard [Department of Imaging Physics, University of Texas M. D. Anderson Cancer Center, Houston, TX (United States); Castillo, Edward [Department of Mathematics, University of California, Irvine, CA (United States); Guerra, Rudy [Department of Statistics, Rice University, Houston, TX (United States); Johnson, Valen E [Department of Biostatistics and Applied Mathematics, University of Texas M. D. Anderson Cancer Center, Houston, TX (United States); McPhail, Travis [Department of Computer Science, Rice University, Houston, TX (United States); Garg, Amit K; Guerrero, Thomas [Department of Radiation Oncology, University of Texas M. D. Anderson Cancer Center, Houston, TX (United States)], E-mail: tguerrero@mdanderson.org

2009-04-07

264

Landmark-based elastic registration using approximating thin-plate splines.  

UK PubMed Central (United Kingdom)

We consider elastic image registration based on a set of corresponding anatomical point landmarks and approximating thin-plate splines. This approach is an extension of the original interpolating thin-plate spline approach and allows to take into account landmark localization errors. The extension is important for clinical applications since landmark extraction is always prone to error. Our approach is based on a minimizing functional and can cope with isotropic as well as anisotropic landmark errors. In particular, in the latter case it is possible to include different types of landmarks, e.g., unique point landmarks as well as arbitrary edge points. Also, the scheme is general with respect to the image dimension and the order of smoothness of the underlying functional. Optimal affine transformations as well as interpolating thin-plate splines are special cases of this scheme. To localize landmarks we use a semi-automatic approach which is based on three-dimensional (3-D) differential operators. Experimental results are presented for two-dimensional as well as 3-D tomographic images of the human brain.

Rohr K; Stiehl HS; Sprengel R; Buzug TM; Weese J; Kuhn MH

2001-06-01

265

CAT Scan  

Medline Plus

Full Text Available ... of this scan. Test A CT scan uses x-ray technology and sophisticated computers to come up with ... com rd050104 Last reviewed: 07/14/2010 1 X-rays are used during this procedure. The amount of ...

266

The Finland-United States Investigation of Non-Insulin-Dependent Diabetes Mellitus Genetics (FUSION) Study. II. An Autosomal Genome Scan for Diabetes-Related Quantitative-Trait Loci  

Science.gov (United States)

Type 2 diabetes mellitus is a complex disorder encompassing multiple metabolic defects. We report results from an autosomal genome scan for type 2 diabetes–related quantitative traits in 580 Finnish families ascertained for an affected sibling pair and analyzed by the variance components-based quantitative-trait locus (QTL) linkage approach. We analyzed diabetic and nondiabetic subjects separately, because of the possible impact of disease on the traits of interest. In diabetic individuals, our strongest results were observed on chromosomes 3 (fasting C-peptide/glucose: maximum LOD score [MLS] = 3.13 at 53.0 cM) and 13 (body-mass index: MLS = 3.28 at 5.0 cM). In nondiabetic individuals, the strongest results were observed on chromosomes 10 (acute insulin response: MLS = 3.11 at 21.0 cM), 13 (2-h insulin: MLS = 2.86 at 65.5 cM), and 17 (fasting insulin/glucose ratio: MLS = 3.20 at 9.0 cM). In several cases, there was evidence for overlapping signals between diabetic and nondiabetic individuals; therefore we performed joint analyses. In these joint analyses, we observed strong signals for chromosomes 3 (body-mass index: MLS = 3.43 at 59.5 cM), 17 (empirical insulin-resistance index: MLS = 3.61 at 0.0 cM), and 19 (empirical insulin-resistance index: MLS = 2.80 at 74.5 cM). Integrating genome-scan results from the companion article by Ghosh et al., we identify several regions that may harbor susceptibility genes for type 2 diabetes in the Finnish population.

Watanabe, Richard M.; Ghosh, Soumitra; Langefeld, Carl D.; Valle, Timo T.; Hauser, Elizabeth R.; Magnuson, Victoria L.; Mohlke, Karen L.; Silander, Kaisa; Ally, Delphine S.; Chines, Peter; Blaschak-Harvan, Jillian; Douglas, Julie A.; Duren, William L.; Epstein, Michael P.; Fingerlin, Tasha E.; Kaleta, Hong Shi; Lange, Ethan M.; Li, Chun; McEachin, Richard C.; Stringham, Heather M.; Trager, Edward; White, Peggy P.; Balow, Jr., James; Birznieks, Gunther; Chang, Jennie; Eldridge, William; Erdos, Michael R.; Karanjawala, Zarir E.; Knapp, Julie I.; Kudelko, Kristina; Martin, Colin; Morales-Mena, Anabelle; Musick, Anjene; Musick, Tiffany; Pfahl, Carrie; Porter, Rachel; Rayman, Joseph B.; Rha, David; Segal, Leonid; Shapiro, Shane; Sharaf, Ravi; Shurtleff, Ben; So, Alistair; Tannenbaum, Joyce; Te, Catherine; Tovar, Jason; Unni, Arun; Welch, Christian; Whiten, Ray; Witt, Alyson; Kohtamaki, Kimmo; Ehnholm, Christian; Eriksson, Johan; Toivanen, Liisa; Vidgren, Gabriele; Nylund, Stella J.; Tuomilehto-Wolf, Eva; Ross, Edna H.; Demirchyan, Elza; Hagopian, William A.; Buchanan, Thomas A.; Tuomilehto, Jaakko; Bergman, Richard N.; Collins, Francis S.; Boehnke, Michael

2000-01-01

267

Reproducibility of facial soft tissue landmarks on facial images captured on a 3D camera.  

UK PubMed Central (United Kingdom)

OBJECTIVE: Fast and non-invasive systems of the three-dimensional (3D) technology are a recent trend in orthodontics. The reproducibility of facial landmarks is important so that 3D facial measurements are accurate and may-be applied clinically. The aim of this study is to evaluate the reproducibility of facial soft tissue landmarks using a non-invasive stereo-photogrammetry 3D camera. MATERIAL AND METHODS: Twenty-four soft tissue landmarks on 3D facial images captured using a VECTRA-3D dual module camera system for full face imaging (Canfield Scientific inc, Fairfield, NJ, USA) were viewed and analysed using Mirror software on 30 adult subjects (15 males and 15 females, in the age range of 20-25 years). The landmarks were identified, recorded and measured twice on each 3D facial image by one examiner after a 2-week interval. Intra-class correlations and paired t-test or Wilcoxon Rank test were performed for each landmark to assess intra-examiner reproducibility. RESULTS: Intra-class correlation coefficients for all 24 landmarks ranged from 0.68 to 0.97, indicating moderate to high reliability and reproducibility of all facial soft tissue landmarks. Paired t-tests and Wilcoxon Rank test also revealed that there were no significant differences in all 24 facial soft tissue landmarks measurements (p = 0. 17 - 0.99). CONCLUSION: The results indicated that the reproducibility of identification of landmarks by one operator on facial images captured using a VECTRA-3D camera was acceptable. This device may be useful in treatment planning and may provide accurate information in making clinical decisions. However, it is suggested that further studies on inter-examiner reproducibility should be undertaken.

Othman SA; Ahmad R; Mericant AF; Jamaludin M

2013-05-01

268

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

UK PubMed Central (United Kingdom)

Job-related exhaustion is the core dimension of burnout, a work-related stress syndrome that has several negative health consequences. In this study, we explored the molecular genetic background of job-related exhaustion. A genome-wide analysis of job-related exhaustion was performed in the GENMETS subcohort (n = 1256) of the Finnish population-based Health 2000 study. Replication analyses included an analysis of the strongest associations in the rest of the Health 2000 sample (n = 1660 workers) and in three independent populations (the FINRISK population cohort, n = 10 753; two occupational cohorts, total n = 1451). Job-related exhaustion was ascertained using a standard self-administered questionnaire (the Maslach Burnout Inventory (MBI)-GS exhaustion scale in the Health 2000 sample and the occupational cohorts) or a single question (FINRISK). A variant located in an intron of UST, uronyl-2-sulfotransferase (rs13219957), gave the strongest statistical evidence in the initial genome-wide study (P = 1.55 × 10(-7)), and was associated with job-related exhaustion in all the replication sets (P < 0.05; P = 6.75 × 10(-7) from the meta-analysis). Consistent with studies of mood disorders, individual common genetic variants did not have any strong effect on job-related exhaustion. However, the nominally significant signals from the allelic variant of UST in four separate samples suggest that this variant might be a weak risk factor for job-related exhaustion. Together with the previously reported associations of other dermatan/chondroitin sulfate genes with mood disorders, these results indicate a potential molecular pathway for stress-related traits and mark a candidate region for further studies of job-related and general exhaustion.

Sulkava S; Ollila HM; Ahola K; Partonen T; Viitasalo K; Kettunen J; Lappalainen M; Kivimäki M; Vahtera J; Lindström J; Härmä M; Puttonen S; Salomaa V; Paunio T

2013-08-01

269

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

Science.gov (United States)

Abnormal lipid levels are important risk factors for cardiovascular diseases. We conducted genome-wide variance component linkage analyses to search for loci influencing total cholesterol (TC), LDL, HDL and triglyceride in families residing in American Samoa and Samoa as well as in a combined sample from the two polities. We adjusted the traits for a number of environmental covariates, such as smoking, alcohol consumption, physical activity, and material lifestyle. We found suggestive univariate linkage with log of the odds (LOD) scores > 3 for LDL on 6p21-p12 (LOD 3.13) in Samoa and on 12q21-q23 (LOD 3.07) in American Samoa. Furthermore, in American Samoa on 12q21, we detected genome-wide linkage (LOD(eq) 3.38) to the bivariate trait TC-LDL. Telomeric of this region, on 12q24, we found suggestive bivariate linkage to TC-HDL (LOD(eq) 3.22) in the combined study sample. In addition, we detected suggestive univariate linkage (LOD 1.9-2.93) on chromosomes 4p-q, 6p, 7q, 9q, 11q, 12q 13q, 15q, 16p, 18q, 19p, 19q and Xq23 and suggestive bivariate linkage (LOD(eq) 2.05-2.62) on chromosomes 6p, 7q, 12p, 12q, and 19p-q. In conclusion, chromosome 6p and 12q may host promising susceptibility loci influencing lipid levels; however, the low degree of overlap between the three study samples strongly encourages further studies of the lipid-related traits. PMID:18594117

Aberg, Karolina; Dai, Feng; Sun, Guangyun; Keighley, Ember; Indugula, Subba Rao; Bausserman, Linda; Viali, Satupaitea; Tuitele, John; Deka, Ranjan; Weeks, Daniel E; McGarvey, Stephen T

2008-07-01

270

The landmark citation method: analysis of a citation pattern as a collection assessment method.  

Science.gov (United States)

The landmark citation method is a new collection assessment method based on the citation record of a single landmark article. This citation record is developed by identifying sources which cite the landmark article. A bibliography, extracted from the citation record, is then used to complete an assessment of the collection. This method was developed and used to assess the biotechnology collection of the National Library of Medicine. The information gained from this study, in addition to demonstrating the technique, also provided insight into the evolution of the biotechnology literature. PMID:1422507

Soehner, C B; Wray, S T; Richards, D T

1992-10-01

271

The landmark citation method: analysis of a citation pattern as a collection assessment method.  

UK PubMed Central (United Kingdom)

The landmark citation method is a new collection assessment method based on the citation record of a single landmark article. This citation record is developed by identifying sources which cite the landmark article. A bibliography, extracted from the citation record, is then used to complete an assessment of the collection. This method was developed and used to assess the biotechnology collection of the National Library of Medicine. The information gained from this study, in addition to demonstrating the technique, also provided insight into the evolution of the biotechnology literature.

Soehner CB; Wray ST; Richards DT

1992-10-01

272

Landmark image super-resolution by retrieving web images.  

UK PubMed Central (United Kingdom)

This paper proposes a new super-resolution (SR) scheme for landmark images by retrieving correlated web images. Using correlated web images significantly improves the exemplar-based SR. Given a low-resolution (LR) image, we extract local descriptors from its up-sampled version and bundle the descriptors according to their spatial relationship to retrieve correlated high-resolution (HR) images from the web. Though similar in content, the retrieved images are usually taken with different illumination, focal lengths, and shot perspectives, resulting in uncertainty for the HR detail approximation. To solve this problem, we first propose aligning these images to the up-sampled LR image through a global registration, which identifies the corresponding regions in these images and reduces the mismatching. Second, we propose a structure-aware matching criterion and adaptive block sizes to improve the mapping accuracy between LR and HR patches. Finally, these matched HR patches are blended together by solving an energy minimization problem to recover the desired HR image. Experimental results demonstrate that our SR scheme achieves significant improvement compared with four state-of-the-art schemes in terms of both subjective and objective qualities.

Yue H; Sun X; Yang J; Wu F

2013-12-01

273

Landmark Image Super-resolution by Retrieving Web Images.  

UK PubMed Central (United Kingdom)

This paper proposes a new super-resolution (SR) scheme for landmark images by retrieving correlated web images. Using correlated web images significantly improves the exemplarbased SR. Given a low-resolution (LR) image, we extract local descriptors from its up-sampled version and bundle the descriptors according to their spatial relationship to retrieve correlated highresolution (HR) images from the web. Though similar in content, the retrieved images are usually taken with different illumination, focal lengths, and shot perspectives, resulting in uncertainty for the HR detail approximation. To solve this problem, we first propose aligning these images to the up-sampled LR image through a global registration, which identifies the corresponding regions in these images and reduces the mismatching. Second, we propose a structure-aware matching criterion and adaptive block sizes to improve the mapping accuracy between LR and HR patches. Finally, these matched HR patches are blended together by solving an energy minimization problem to recover the desired HR image. Experimental results demonstrate that our SR scheme achieves significant improvement compared with four state-of-the-art schemes in terms of both subjective and objective qualities.

Yue H; Sun X; Yang J; Wu F

2013-08-01

274

Landmark image super-resolution by retrieving web images.  

Science.gov (United States)

This paper proposes a new super-resolution (SR) scheme for landmark images by retrieving correlated web images. Using correlated web images significantly improves the exemplar-based SR. Given a low-resolution (LR) image, we extract local descriptors from its up-sampled version and bundle the descriptors according to their spatial relationship to retrieve correlated high-resolution (HR) images from the web. Though similar in content, the retrieved images are usually taken with different illumination, focal lengths, and shot perspectives, resulting in uncertainty for the HR detail approximation. To solve this problem, we first propose aligning these images to the up-sampled LR image through a global registration, which identifies the corresponding regions in these images and reduces the mismatching. Second, we propose a structure-aware matching criterion and adaptive block sizes to improve the mapping accuracy between LR and HR patches. Finally, these matched HR patches are blended together by solving an energy minimization problem to recover the desired HR image. Experimental results demonstrate that our SR scheme achieves significant improvement compared with four state-of-the-art schemes in terms of both subjective and objective qualities. PMID:23974626

Yue, Huanjing; Sun, Xiaoyan; Yang, Jingyu; Wu, Feng

2013-08-21

275

Desert ants benefit from combining visual and olfactory landmarks.  

UK PubMed Central (United Kingdom)

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

Steck K; Hansson BS; Knaden M

2011-04-01

276

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

Scientific Electronic Library Online (English)

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

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

2010-12-01

277

Accuracy of laser-scanned models compared to plaster models and cone-beam computed tomography.  

UK PubMed Central (United Kingdom)

Objective: To compare the accuracy of measurements obtained from the three-dimensional (3D) laser scans to those taken from the cone-beam computed tomography (CBCT) scans and those obtained from plaster models. Materials and Methods: Eighteen different measurements, encompassing mesiodistal width of teeth and both maxillary and mandibular arch length and width, were selected using various landmarks. CBCT scans and plaster models were prepared from 60 patients. Plaster models were scanned using the Ortho Insight 3D laser scanner, and the selected landmarks were measured using its software. CBCT scans were imported and analyzed using the Avizo software, and the 26 landmarks corresponding to the selected measurements were located and recorded. The plaster models were also measured using a digital caliper. Descriptive statistics and intraclass correlation coefficient (ICC) were used to analyze the data. Results: The ICC result showed that the values obtained by the three different methods were highly correlated in all measurements, all having correlations >0.808. When checking the differences between values and methods, the largest mean difference found was 0.59 mm ± 0.38 mm. Conclusions: In conclusion, plaster models, CBCT models, and laser-scanned models are three different diagnostic records, each with its own advantages and disadvantages. The present results showed that the laser-scanned models are highly accurate to plaster models and CBCT scans. This gives general clinicians an alternative to take into consideration the advantages of laser-scanned models over plaster models and CBCT reconstructions.

Kim J; Heo G; Lagravère MO

2013-08-01

278

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

UK PubMed Central (United Kingdom)

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.

García-Gámez E; Reverter A; Whan V; McWilliam SM; Arranz JJ; Kijas J

2011-01-01

279

Genome-Wide Scan Identifies Variant in TNFSF13 Associated with Serum IgM in a Healthy Chinese Male Population  

Science.gov (United States)

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

Sun, Jielin; Liao, Ming; Qin, Min; Mo, Linjian; Gao, Yong; Lu, Zheng; Wu, Chunlei; Zhang, Youjie; Zhang, Haiying; Qin, Xue; Hu, Yanling; Zhang, Shijun; Li, Jianling; Dong, Min; Zheng, S. Lilly; Xu, Jianfeng; Yang, Xiaobo; Tan, Aihua; Mo, Zengnan

2012-01-01

280

77 FR 53230 - Landmarks Committee of the National Park System Advisory Board Meeting  

Science.gov (United States)

...Landmarks Committee may consider the following nominations: Alabama EDMUND PETTUS BRIDGE, Dallas County Connecticut HARRIET BEECHER STOWE HOUSE, Hartford Illinois SECOND PRESBYTERIAN CHURCH, Chicago Kentucky CAMP NELSON HISTORIC AND...

2012-08-31

 
 
 
 
281

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

UK PubMed Central (United Kingdom)

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.

Cheng E; Chen J; Yang J; Deng H; Wu Y; Megalooikonomou V; Gable B; Ling H

2011-01-01

282

Accuracy and landmark error calculation using cone-beam computed tomography-generated cephalograms.  

UK PubMed Central (United Kingdom)

OBJECTIVE: To evaluate systematic differences in landmark position between cone-beam computed tomography (CBCT)-generated cephalograms and conventional digital cephalograms and to estimate how much variability should be taken into account when both modalities are used within the same longitudinal study. MATERIALS AND METHODS: Landmarks on homologous cone-beam computed tomographic-generated cephalograms and conventional digital cephalograms of 46 patients were digitized, registered, and compared via the Hotelling T(2) test. RESULTS: There were no systematic differences between modalities in the position of most landmarks. Three landmarks showed statistically significant differences but did not reach clinical significance. A method for error calculation while combining both modalities in the same individual is presented. CONCLUSION: In a longitudinal follow-up for assessment of treatment outcomes and growth of one individual, the error due to the combination of the two modalities might be larger than previously estimated.

Grauer D; Cevidanes LS; Styner MA; Heulfe I; Harmon ET; Zhu H; Proffit WR

2010-03-01

283

Milestones in movement disorders clinical trials: advances and landmark studies.  

UK PubMed Central (United Kingdom)

Over the past 25 years clinical trials testing in movement disorders has evolved in order to more effectively and efficiently analyze the safety and efficacy of new interventions. Studies today regularly incorporate methods to decrease placebo and bias effects and to ensure more rigorous statistical analyses. Newer, standardized, and validated rating scales such as the Unified Parkinson's Disease Rating Scale and the Unified Huntington's Disease Rating Scale are routinely employed in an effort to produce results that are comparable across different sites and studies. Several landmark studies in movement disorder research highlight these and other prominent procedural advances. The Deprenyl and Tocopherol Antioxidative Therapy of Parkinsonism trial pioneered the use of functional clinical end points, utilized a 2 × 2 factorial design to more efficiently analyze multiple interventions, and employed a washout design to assist in sorting putative neuroprotective from symptomatic effects. PRECEPT included neuroimaging as an outcome measure and highlighted the importance of futility studies in more efficiently directing resources. TEMPO and ADAGIO introduced the use of delayed-start (or 2-period) trials to try to identify disease-modifying interventions. NET-PD used futility studies to streamline the evaluation of potentially valuable treatments, followed by a large, long-term simple study design to assess the clinical significance of a new intervention. There have also been advances in clinical trials testing new surgical interventions, with the introduction of blinded outcome assessments and sham-surgery control groups. Collectively, methodological advances in clinical trials have permitted the safety and efficacy of new interventions to be tested more efficiently and economically and with a higher level of certainty that the potential benefits and adverse effects of interventions recommended for general use are well understood.

Olanow CW; Wunderle KB; Kieburtz K

2011-05-01

284

Genetic variants in vitamin D metabolism-related genes and body mass index: analysis of genome-wide scan data of approximately 7000 Chinese women.  

Science.gov (United States)

Vitamin D deficiency has been consistently associated with obesity. However, it is unclear whether vitamin D deficiency is the cause or consequence of obesity. We investigated this question by evaluating the association between genetic variants in vitamin D metabolism pathway genes and obesity-related traits. Using directly genotyped and imputed data from a genome-wide association study of 6922 women aged 25-70 years, we examined the association of 198 single-nucleotide polymorphisms (SNPs) in vitamin D pathway genes (CYP27A1, CYP27B1, CYP24A1, CYP2R1, group-specific component (GC) and vitamin D nuclear receptor (VDR)) with body mass index (BMI) and body weight. Per allele beta (?) estimates were calculated for this association using linear regression models, controlling for age, square of age, menopausal status and sample sets. Overall, only two SNPs (rs2248359 in CYP24A1 and rs10832313 in CYP2R1) had a nominally significant association with BMI and weight (P<0.05 for all), with no variation observed by menopausal status, physical activity or dietary energy intake. None of the SNPs examined in the VDR gene were associated with BMI or weight. Our findings suggest that common genetic variants in vitamin D pathway genes do not have a major role in obesity among Chinese women. This comprehensive evaluation of genetic polymorphisms in vitamin D metabolism-related genes and obesity-related traits did not provide strong evidence to support low vitamin D levels as a cause of obesity. PMID:22158264

Dorjgochoo, T; Shi, J; Gao, Y T; Long, J; Delahanty, R; Xiang, Y B; Cai, Q; Shu, X O

2011-12-13

285

Toward 959 nematode genomes.  

Science.gov (United States)

The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism. The success of the C. elegans genome sequencing project also inspired communities working on other organisms to approach genome sequencing of their species. The phylum Nematoda is rich and diverse and of interest to a wide range of research fields from basic biology through ecology and parasitic disease. For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases. The advent of second-generation sequencing technologies, improvements in computing algorithms and infrastructure and growth in bioinformatics and genomics literacy is making the addition of genome sequencing to the research goals of any nematode research program a less daunting prospect. To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/). Just as the deciphering of the developmental lineage of the 959 cells of the adult hermaphrodite C. elegans was the gateway to broad advances in biomedical science, we hope that a nematode phylogeny with (at least) 959 sequenced species will underpin further advances in understanding the origins of parasitism, the dynamics of genomic change and the adaptations that have made Nematoda one of the most successful animal phyla. PMID:24058822

Kumar, Sujai; Koutsovoulos, Georgios; Kaur, Gaganjot; Blaxter, Mark

2012-01-01

286

Compensation for fluctuations in crosswind drift without stationary landmarks in butterflies migrating over seas.  

UK PubMed Central (United Kingdom)

Migrating insects may fly over large bodies of water that lack landmarks, but little is known about their ability to navigate in such a fluid environment. Using boat navigation instruments to measure compensation for fluctuations in crosswind drift, I investigated the ability of butterflies (Lepidoptera: Hesperiidae, Nymphalidae and Pieridae) to orient with and without landmarks as they migrated naturally over the Caribbean Sea. I used the presence or absence of landmarks or clouds to evaluate their use by the butterflies as guides for compensation. Forty-one per cent of the butterflies compensated for crosswind drift, whereas only 16% did not compensate. No conclusion could be drawn for the remainder. Without landmarks or clouds, butterflies were significantly less likely to compensate for drift than when these local cues were present. Butterflies were more likely to compensate fully in the presence of a landmark than when only clouds were present. Phoebis sennae butterflies drifted in the morning and overcompensated for drift in the afternoon, a pattern found both within and between individuals independent of landmarks. Although I cannot exclude the use of clouds, this would probably result in undercompensation. Hence, a ground reference in conjunction with a sun or magnetic compass is the most likely orientation cue. In the absence of clouds, one butterfly compensated, at least in part, indicating that it was using ripples on the sea surface as a ground reference in conjunction with a sun or magnetic compass. Copyright 2001 The Association for the Study of Animal Behaviour.

Srygley RB

2001-01-01

287

Multiobjective optimization framework for landmark measurement error correction in three-dimensional cephalometric tomography.  

UK PubMed Central (United Kingdom)

The purpose of this study is to minimize errors that occur when using a four vs six landmark superimpositioning method in the cranial base to define the co-ordinate system. Cone beam CT volumetric data from ten patients were used for this study. Co-ordinate system transformations were performed. A co-ordinate system was constructed using two planes defined by four anatomical landmarks located by an orthodontist. A second co-ordinate system was constructed using four anatomical landmarks that are corrected using a numerical optimization algorithm for any landmark location operator error using information from six landmarks. The optimization algorithm minimizes the relative distance and angle between the known fixed points in the two images to find the correction. Measurement errors and co-ordinates in all axes were obtained for each co-ordinate system. Significant improvement is observed after using the landmark correction algorithm to position the final co-ordinate system. The errors found in a previous study are significantly reduced. Errors found were between 1 mm and 2 mm. When analysing real patient data, it was found that the 6-point correction algorithm reduced errors between images and increased intrapoint reliability. A novel method of optimizing the overlay of three-dimensional images using a 6-point correction algorithm was introduced and examined. This method demonstrated greater reliability and reproducibility than the previous 4-point correction algorithm.

DeCesare A; Secanell M; Lagravère MO; Carey J

2013-01-01

288

Anatomical confirmation of the use of radiographic landmarks in medial patellofemoral ligament reconstruction.  

UK PubMed Central (United Kingdom)

BACKGROUND: A recent study has described radiographic landmarks for femoral insertion of the medial patellofemoral ligament. Clinical relevance and application of these landmarks for surgical reconstruction have yet to be determined. HYPOTHESIS: Radiographic landmarks can be used to accurately determine the femoral insertion of the medial patellofemoral ligament in a percutaneous fluoroscopically guided surgical technique. STUDY DESIGN: Descriptive laboratory study. METHODS: The femoral insertion of the medial patellofemoral ligament was estimated using fluoroscopy in 8 fresh-frozen human cadaveric knees. The knees were dissected and the true anatomical medial patellofemoral ligament femoral insertion was identified. Radiographic markers were placed on both the estimated and anatomical medial patellofemoral ligament and a repeat lateral radiograph was performed. Using imaging software, the distance between the true anatomical insertion and the fluoroscopically determined insertion was calculated. Results All 8 points determined by fluoroscopically guided pin placement averaged less than 4 mm from the anatomical insertion. The radiographic landmark method consistently placed the origin on average 2.5 mm anterior and 0.6 mm distal to the anatomical insertion. CONCLUSION: Radiographic landmarks determined by fluoroscopy can be used to accurately reproduce the femoral insertion of the medial patellofemoral ligament in ligament reconstruction. CLINICAL RELEVANCE: Confirming the use of radiographic landmarks to determine the medial patellofemoral ligament femoral insertion may help to increase accuracy and precision in ligament reconstruction and minimize surgical dissection.

Redfern J; Kamath G; Burks R

2010-02-01

289

Pitfalls at the root of facial assessment on photographs: a quantitative study of accuracy in positioning facial landmarks.  

UK PubMed Central (United Kingdom)

In the last years, facial analysis has gained great interest also for forensic anthropology. The application of facial landmarks may bring about relevant advantages for the analysis of 2D images by measuring distances and extracting quantitative indices. However, this is a complex task which depends upon the variability in positioning facial landmarks. In addition, literature provides only general indications concerning the reliability in positioning facial landmarks on photographic material, and no study is available concerning the specific errors which may be encountered in such an operation. The aim of this study is to analyze the inter- and intra-observer error in defining facial landmarks on photographs by using a software specifically developed for this purpose. Twenty-four operators were requested to define 22 facial landmarks on frontal view photographs and 11 on lateral view images; in addition, three operators repeated the procedure on the same photographs 20 times (at distance of 24 h). In the frontal view, the landmarks with less dispersion were the pupil, cheilion, endocanthion, and stomion (sto), and the landmarks with the highest dispersion were gonion, zygion, frontotemporale, tragion, and selion (se). In the lateral view, the landmarks with the least dispersion were se, pronasale, subnasale, and sto, whereas landmarks with the highest dispersion were gnathion, pogonion, and tragion. Results confirm that few anatomical points can be defined with the highest accuracy and show the importance of the preliminary investigation of reliability in positioning facial landmarks.

Cummaudo M; Guerzoni M; Marasciuolo L; Gibelli D; Cigada A; Obertovà Z; Ratnayake M; Poppa P; Gabriel P; Ritz-Timme S; Cattaneo C

2013-05-01

290

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

Directory of Open Access Journals (Sweden)

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

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

2006-01-01

291

Scan Statistics  

CERN Multimedia

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.

Glaz, Joseph

2009-01-01

292

Usefulness of the anterior surface and supracondylar region of the femur as a landmark for femoral rotational alignment in knee surgery  

International Nuclear Information System (INIS)

We investigated the possibility that a line tangential to the anterior surface of the femur could serve as a landmark for rotational alignment of the femoral component in total knee arthroplasty (TKA). The subjects were 37 women treated with TKA for medial knee osteoarthritis. Before surgery X-ray films and computed tomography scans were obtained. The three axes -the posterior condylar axis, the transepicondylar axis, and the anterior surface at the supracondyle- were constructed on each CT scan, and the angles between two axes were measured with the X-Caliper system. The results obtained from 35 subjects showed that the angle between the transepicondylar axis and the posterior condylar axis ranged from 3.1 to 10.7 degrees and bad a mean value of 6.35±1.93 degrees. The angle between the transepicondylar axis and the anterior femoral surface at the supracondyle ranged from 6.1 to 15.4 degrees and had a mean value of 11.21±2.48 degrees. The anterior surface was internally rotated relative to the posterior condylar axis in all cases, and its value indicated the degree of anterolateral notching. The anterior femoral surface at the supracondylar level is easy to identify during surgery. Thus, it may be a useful landmark for determining the correct rotational alignment of the femoral component in TKA. (author)

2007-01-01

293

The Finland-United States Investigation of Non-Insulin-Dependent Diabetes Mellitus Genetics (FUSION) Study. I. An Autosomal Genome Scan for Genes That Predispose to Type 2 Diabetes  

Science.gov (United States)

We performed a genome scan at an average resolution of 8 cM in 719 Finnish sib pairs with type 2 diabetes. Our strongest results are for chromosome 20, where we observe a weighted maximum LOD score (MLS) of 2.15 at map position 69.5 cM from pter and secondary weighted LOD-score peaks of 2.04 at 56.5 cM and 1.99 at 17.5 cM. Our next largest MLS is for chromosome 11 (MLS = 1.75 at 84.0 cM), followed by chromosomes 2 (MLS = 0.87 at 5.5 cM), 10 (MLS = 0.77 at 75.0 cM), and 6 (MLS = 0.61 at 112.5 cM), all under an additive model. When we condition on chromosome 2 at 8.5 cM, the MLS for chromosome 20 increases to 5.50 at 69.0 cM (P=.0014). An ordered-subsets analysis based on families with high or low diabetes-related quantitative traits yielded results that support the possible existence of disease-predisposing genes on chromosomes 6 and 10. Genomewide linkage-disequilibrium analysis using microsatellite marker data revealed strong evidence of association for D22S423 (P=.00007). Further analyses are being carried out to confirm and to refine the location of these putative diabetes-predisposing genes.

Ghosh, Soumitra; Watanabe, Richard M.; Valle, Timo T.; Hauser, Elizabeth R.; Magnuson, Victoria L.; Langefeld, Carl D.; Ally, Delphine S.; Mohlke, Karen L.; Silander, Kaisa; Kohtamaki, Kimmo; Chines, Peter; Balow, Jr., James; Birznieks, Gunther; Chang, Jennie; Eldridge, William; Erdos, Michael R.; Karanjawala, Zarir E.; Knapp, Julie I.; Kudelko, Kristina; Martin, Colin; Morales-Mena, Anabelle; Musick, Anjene; Musick, Tiffany; Pfahl, Carrie; Porter, Rachel; Rayman, Joseph B.; Rha, David; Segal, Leonid; Shapiro, Shane; Sharaf, Ravi; Shurtleff, Ben; So, Alistair; Tannenbaum, Joyce; Te, Catherine; Tovar, Jason; Unni, Arun; Welch, Christian; Whiten, Ray; Witt, Alyson; Blaschak-Harvan, Jillian; Douglas, Julie A.; Duren, William L.; Epstein, Michael P.; Fingerlin, Tasha E.; Kaleta, Hong Shi; Lange, Ethan M.; Li, Chun; McEachin, Richard C.; Stringham, Heather M.; Trager, Edward; White, Peggy P.; Eriksson, Johan; Toivanen, Liisa; Vidgren, Gabriele; Nylund, Stella J.; Tuomilehto-Wolf, Eva; Ross, Edna H.; Demirchyan, Elza; Hagopian, William A.; Buchanan, Thomas A.; Tuomilehto, Jaakko; Bergman, Richard N.; Collins, Francis S.; Boehnke, Michael

2000-01-01

294

Gaze-centered spatial updating in delayed reaching even in the presence of landmarks.  

Science.gov (United States)

Previous results suggest that the brain predominantly relies on a constantly updated gaze-centered target representation to guide reach movements when no other visual information is available. In the present study, we investigated whether the addition of reliable visual landmarks influences the use of spatial reference frames for immediate and delayed reaching. Subjects reached immediately or after a delay of 8 or 12s to remembered target locations, either with or without landmarks. After target presentation and before reaching they shifted gaze to one of five different fixation points and held their gaze at this location until the end of the reach. With landmarks present, gaze-dependent reaching errors were smaller and more precise than when reaching without landmarks. Delay influenced neither reaching errors nor variability. These findings suggest that when landmarks are available, the brain seems to still use gaze-dependent representations but combine them with gaze-independent allocentric information to guide immediate or delayed reach movements to visual targets. PMID:23770521

Schütz, I; Henriques, D Y P; Fiehler, K

2013-06-12

295

Bilateral participation of the hippocampus in familiar landmark navigation by homing pigeons.  

Science.gov (United States)

Recent findings indicate a different role of the left and right hippocampal formation (RHF) in homing pigeon navigational map learning. However, it remains uncertain whether the left or the RHF may play a more important role in navigation based on familiar landmarks. In the present study, we attempted to answer this question by experimentally releasing control and left and right hippocampal ablated pigeons from familiar training sites under anosmia, to render their navigational map dysfunctional, and after a phase-shift of the light-dark cycle, to place into conflict a pilotage-like landmark navigational strategy and a site-specific compass orientation landmark navigational strategy. Both left and right hippocampal ablated birds succeeded in learning to navigate by familiar landmarks, and both preferentially relied on sun-compass based, site-specific compass orientation to home. Like bilateral hippocampal lesioned birds, and in contrast to intact controls, neither ablation group adopted a pilotage-like strategy. We conclude that both the left and RHF are necessary if pilotage-like, familiar landmark navigation is to be learned or preferentially used for navigation. PMID:12385806

Gagliardo, Anna; Odetti, Francesca; Ioalè, Paolo; Bingman, Verner P; Tuttle, Sarah; Vallortigara, Giorgio

2002-10-17

296

Bilateral participation of the hippocampus in familiar landmark navigation by homing pigeons.  

UK PubMed Central (United Kingdom)

Recent findings indicate a different role of the left and right hippocampal formation (RHF) in homing pigeon navigational map learning. However, it remains uncertain whether the left or the RHF may play a more important role in navigation based on familiar landmarks. In the present study, we attempted to answer this question by experimentally releasing control and left and right hippocampal ablated pigeons from familiar training sites under anosmia, to render their navigational map dysfunctional, and after a phase-shift of the light-dark cycle, to place into conflict a pilotage-like landmark navigational strategy and a site-specific compass orientation landmark navigational strategy. Both left and right hippocampal ablated birds succeeded in learning to navigate by familiar landmarks, and both preferentially relied on sun-compass based, site-specific compass orientation to home. Like bilateral hippocampal lesioned birds, and in contrast to intact controls, neither ablation group adopted a pilotage-like strategy. We conclude that both the left and RHF are necessary if pilotage-like, familiar landmark navigation is to be learned or preferentially used for navigation.

Gagliardo A; Odetti F; Ioalè P; Bingman VP; Tuttle S; Vallortigara G

2002-10-01

297

Gaze-centered spatial updating in delayed reaching even in the presence of landmarks.  

UK PubMed Central (United Kingdom)

Previous results suggest that the brain predominantly relies on a constantly updated gaze-centered target representation to guide reach movements when no other visual information is available. In the present study, we investigated whether the addition of reliable visual landmarks influences the use of spatial reference frames for immediate and delayed reaching. Subjects reached immediately or after a delay of 8 or 12s to remembered target locations, either with or without landmarks. After target presentation and before reaching they shifted gaze to one of five different fixation points and held their gaze at this location until the end of the reach. With landmarks present, gaze-dependent reaching errors were smaller and more precise than when reaching without landmarks. Delay influenced neither reaching errors nor variability. These findings suggest that when landmarks are available, the brain seems to still use gaze-dependent representations but combine them with gaze-independent allocentric information to guide immediate or delayed reach movements to visual targets.

Schütz I; Henriques DY; Fiehler K

2013-07-01

298

Using the landmark-route-survey framework to evaluate spatial knowledge obtained from synthetic vision systems.  

UK PubMed Central (United Kingdom)

OBJECTIVE: Using the landmark-route-survey framework, this research investigated the effect of synthetic vision systems (SVS) in either low or high visibility conditions on performance in wayfinding and spatial-knowledge-based tasks that probed spatial awareness. BACKGROUND: SVS are cockpit displays that depict computer-generated views of the terrain surrounding an aircraft and have been developed to support flight efficiency through improved spatial awareness. No studies have directly measured SVS impact on the three levels of spatial knowledge (landmark, route, and survey). METHOD: A total of 55 nonpilots learned a route in four different experimental conditions (high or low visibility, either with or without SVS). Subsequently, they underwent four recall tasks: way finding, scene recognition, scene classification, and sketch map. Six dependent measures were used to probe the three levels of spatial knowledge (selection errors, sorting errors, number of landmarks depicted, bidimensional regression) and their use in the wayfinding task (direction errors, designated landmark errors, and wayfinding verbalized hesitations). RESULTS: SVS produced higher performance in all four tasks. The low visibility condition lowered the wayfinding and scene-recognition performance. CONCLUSION: The overall results indicated that visibility mostly affected the first level of spatial knowledge (landmark) inducing a decreased wayfinding performance, whereas the use of SVS influenced the three levels of spatial knowledge (route and survey) inducing an increased wayfinding performance. APPLICATION: Potential applications of this work include spatial knowledge-based measures to evaluate SVS prototypes as well as to assess the relationship between spatial knowledge and spatial awareness.

Lapeyre B; Hourlier S; Servantie X; N'Kaoua B; Sauzéon H

2011-12-01

299

Wayfinding behavior and spatial knowledge of adults and children in a virtual environment: The role of landmarks.  

UK PubMed Central (United Kingdom)

This study investigated the effect of different organizations of landmark-location pairings as fine-space information on wayfinding behavior and spatial knowledge on a total of 90 participants: 30 second graders, 30 sixth graders, and 30 adults. All participants had to find their way to a goal in a virtual environment with either randomized or categorical landmarks, or without any landmarks. Thereafter, they had to find the shortest way from the start position to the goal in two consecutive trials (wayfinding performance), and they had to solve a number of spatial knowledge tasks. The results showed that independent of their categorical function, the existence of landmarks influenced the way-finding performance of adults and children in the same way. Whereas the presence of landmarks had no effect on spatial survey knowledge, landmark knowledge itself was influenced by the categorical function of the landmarks presented. Moreover, second graders showed limited achievement compared to adults independent of the existence of landmarks. The main results implicate firstly that children at school age indeed are able to use landmark-location pairings as fine-space information like adults during learning an unknown environmental space, and secondly that a dissociation between wayfinding behavior and spatial knowledge might exist.

Jansen-Osmann P; Fuchs P

2006-01-01

300

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

Scientific Electronic Library Online (English)

Full Text Available Abstract in english 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 plac (more) ement, 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

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

2009-01-01

 
 
 
 
301

The influence of excitatory and inhibitory landmarks on choice in environments with a distinctive shape.  

UK PubMed Central (United Kingdom)

In two experiments rats were trained to find one of two submerged platforms that were located in diagonally opposite corners-the correct corners-of a rectangular pool. Additional training was given to endow two different landmarks with excitatory and inhibitory properties, by using them to indicate where a platform was or was not located in either a rectangular (Experiment 1) or a square pool (Experiment 2). Subsequent test trials, with the platforms removed from the pool, revealed that placing the excitatory landmark in each of the four corners of the rectangle resulted in more time being spent in the correct corners than when the four corners contained inhibitory landmarks. This result is contrary to predictions derived from a choice rule for spatial behavior proposed by Miller and Shettleworth (2007).

Horne MR; León SP; Pearce JM

2013-01-01

302

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

UK PubMed Central (United Kingdom)

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.

Frankenstein J; Brüssow S; Ruzzoli F; Hölscher C

2012-08-01

303

Influence of local objects on hippocampal representations: Landmark vectors and memory.  

Science.gov (United States)

The hippocampus is thought to represent nonspatial information in the context of spatial information. An animal can derive both spatial information as well as nonspatial information from the objects (landmarks) it encounters as it moves around in an environment. In this article, correlates of both object-derived spatial as well as nonspatial information in the hippocampus of rats foraging in the presence of objects are demonstrated. A new form of CA1 place cells, called landmark-vector cells, that encode spatial locations as a vector relationship to local landmarks is described. Such landmark vector relationships can be dynamically encoded. Of the 26 CA1 neurons that developed new fields in the course of a day's recording sessions, in eight cases, the new fields were located at a similar distance and direction from a landmark as the initial field was located relative to a different landmark. In addition, object-location memory in the hippocampus is also described. When objects were removed from an environment or moved to new locations, a small number of neurons in CA1 and CA3 increased firing at the locations where the objects used to be. In some neurons, this increase occurred only in one location, indicating object + place conjunctive memory; in other neurons, the increase in firing was seen at multiple locations where an object used to be. Taken together, these results demonstrate that the spatially restricted firing of hippocampal neurons encode multiple types of information regarding the relationship between an animal's location and the location of objects in its environment. PMID:23447419

Deshmukh, Sachin S; Knierim, James J

2013-02-27

304

Influence of local objects on hippocampal representations: Landmark vectors and memory.  

UK PubMed Central (United Kingdom)

The hippocampus is thought to represent nonspatial information in the context of spatial information. An animal can derive both spatial information as well as nonspatial information from the objects (landmarks) it encounters as it moves around in an environment. In this article, correlates of both object-derived spatial as well as nonspatial information in the hippocampus of rats foraging in the presence of objects are demonstrated. A new form of CA1 place cells, called landmark-vector cells, that encode spatial locations as a vector relationship to local landmarks is described. Such landmark vector relationships can be dynamically encoded. Of the 26 CA1 neurons that developed new fields in the course of a day's recording sessions, in eight cases, the new fields were located at a similar distance and direction from a landmark as the initial field was located relative to a different landmark. In addition, object-location memory in the hippocampus is also described. When objects were removed from an environment or moved to new locations, a small number of neurons in CA1 and CA3 increased firing at the locations where the objects used to be. In some neurons, this increase occurred only in one location, indicating object + place conjunctive memory; in other neurons, the increase in firing was seen at multiple locations where an object used to be. Taken together, these results demonstrate that the spatially restricted firing of hippocampal neurons encode multiple types of information regarding the relationship between an animal's location and the location of objects in its environment.

Deshmukh SS; Knierim JJ

2013-04-01

305

Observer Reliability in identification of Three-Dimensional Cephalometric Landmarks on CBCT Images  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract:Background and Aim: An important step before establishing CBCT as a common orthodontic diagnostic approach is to assess landmark reliability. The purpose of the present study was to evaluate intra- and inter observer reliability in 3D landmark identification using CBCT images.Materials and Methods: A total of 30 CBCT images were selected for this experimental study. Working independently, two observers identified 14 landmarks, twice in the CBCT images. Selecting the most appropriate slice in the axial, coronal, and sagittal views, the position of the landmark was recorded in millimeters for the X, Y, and Z coordinates respectively. Intra- and inter observer reliability values were determined using Pearson’s correlation test.Results: The Intra class correlation (ICC) was >0.7 for 97.6% of intra observer assessments and 92.8% of inter observer assessments. None of the ICCs were <0.6. The ICC was ?0.9 for 25 (59.5%) of the intra observer assessments. The ICC was ?0.9 for 28 (66.67%) of the inter observer assessments. The mean differences between the two observers in 95.2% of the cases were less than 2 millimeters.Conclusions: Considering the limitations and the results of the present study, the intra- and inter observer reliability was high. With proper training of the operator, the three-dimensional landmark identification using CBCT can offer consistent and reproducible data.Key words: Anatomic Landmarks; Cephalometry; Cone Beam CTJournal Res Dent Sci 2013;10(3): 192-199

Ghaffari R; Saghaie; Sheikhi M

2013-01-01

306

Ultrasonographic identification of the anatomical landmarks that define cervical lymph nodes spaces.  

UK PubMed Central (United Kingdom)

The localization of cervical lymph nodes is extremely important in practice for the positive and differential diagnosis as well as the staging of cervical lymphadenopathies. Ultrasonography represents the first line imaging method in the diagnosis of cervical lymphadenopathies due to its excellent resolution and high diagnosis accuracy. The present paper aims to illustrate the ultrasonographic identification of the anatomical landmarks used for the definition of cervical lymphatic spaces. The application of standardized views allows a delineation of clear anatomical landmarks and an accurate localization of the cervical lymph nodes.

Lenghel LM; Baciu? G; Botar-Jid C; Vasilescu D; Bojan A; Dudea SM

2013-03-01

307

Homing in pigeons: the role of the hippocampal formation in the representation of landmarks used for navigation.  

UK PubMed Central (United Kingdom)

When given repeated training from a location, homing pigeons acquire the ability to use familiar landmarks to navigate home. Both control and hippocampal-lesioned pigeons succeed in learning to use familiar landmarks for homing. However, the landmark representations that guide navigation are strikingly different. Control and hippocampal-lesioned pigeons were initially given repeated training flights from two locations. On subsequent test days from the two training locations, all pigeons were rendered anosmic to eliminate use of their navigational map and were phase- or clock-shifted to examine the extent to which their learned landmark representations were dependent on the use of the sun as a compass. We show that control pigeons acquire a landmark representation that allows them to directly use landmarks without reference to the sun to guide their flight home, called "pilotage". Hippocampal-lesioned birds only learn to use familiar landmarks at the training location to recall the compass direction home, based on the sun, flown during training, called "site-specific compass orientation." The results demonstrate that for navigation of 20 km or more in a natural field setting, the hippocampal formation is necessary if homing pigeons are to learn a spatial representation based on numerous independent landmark elements that can be used to directly guide their return home.

Gagliardo A; Ioalé P; Bingman VP

1999-01-01

308

Homing in pigeons: the role of the hippocampal formation in the representation of landmarks used for navigation.  

Science.gov (United States)

When given repeated training from a location, homing pigeons acquire the ability to use familiar landmarks to navigate home. Both control and hippocampal-lesioned pigeons succeed in learning to use familiar landmarks for homing. However, the landmark representations that guide navigation are strikingly different. Control and hippocampal-lesioned pigeons were initially given repeated training flights from two locations. On subsequent test days from the two training locations, all pigeons were rendered anosmic to eliminate use of their navigational map and were phase- or clock-shifted to examine the extent to which their learned landmark representations were dependent on the use of the sun as a compass. We show that control pigeons acquire a landmark representation that allows them to directly use landmarks without reference to the sun to guide their flight home, called "pilotage". Hippocampal-lesioned birds only learn to use familiar landmarks at the training location to recall the compass direction home, based on the sun, flown during training, called "site-specific compass orientation." The results demonstrate that for navigation of 20 km or more in a natural field setting, the hippocampal formation is necessary if homing pigeons are to learn a spatial representation based on numerous independent landmark elements that can be used to directly guide their return home. PMID:9870960

Gagliardo, A; Ioalé, P; Bingman, V P

1999-01-01

309

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

Directory of Open Access Journals (Sweden)

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

Leslie Marcus; Erika Hingst-Zaher; Hussam Zaher

2000-01-01

310

Consistency of the monocular EKF-SLAM algorithm for 3 different landmark parametrizations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We benchmark in this article three different parametrizations for punctual landmarks in monocular 6DOF EKF-SLAM. These parametrizations are homogeneous points (HM), inverse-distance points (IDP, better known as \\emph{inverse-depth}), and the new anchored homogeneous points (AHP). The discourse used ...

Solà, Joan

311

A comparison of two methods for natural landmark classification with Biosonar  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Most current sonar systems for mobile robots only yield time of flight distance information produced by measuring the time of a single sonar pulse. However, sonar systems of animals like sonar bats are much more sophisticated, allowing to recognize not only the shape, but also the type of landmark t...

Wang, Maosen; Zell, Andreas; Müller, Rolf; Wilhelm-Schickard-Institut für Informatik, Tübingen

312

Direct and continuous localization of anatomical landmarks for image-guided orthognathic surgery.  

UK PubMed Central (United Kingdom)

OBJECTIVE: The accuracy and consistency of a new image-guided method for orthognathic surgery using direct and continuous landmark localization was compared with that of a conventional method. STUDY DESIGN: Maxillary and mandibular dental casts mounted on an articulator were used as a surgery phantom. We planned six types of surgeries including translations and rotations. The sequential positions of the landmarks determined before surgery could be traced and the difference between planned and actual positions of the landmarks could be visualized during surgery. The final deviation errors were determined with and without applying the pointing instrument to the landmarks. RESULTS: The mean RMS accuracy of 0.47 ± 0.22 mm by direct localization was significantly higher than that of 1.06 ± 0.49 mm by the manual localization. There were no significant differences in accuracies for surgeries using the direct localization method. CONCLUSION: The direct and continuous localization method showed higher accuracy and consistency than conventional manual localization in all phantom surgeries.

Kim SH; Kim DS; Huh KH; Lee SS; Heo MS; Choi SC; Hwang SJ; Yi WJ

2013-10-01

313

A New 2D Corner Detector for Extracting Landmarks from Brain MR Images  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Point-based registration of images strongly depends on the extraction of suitable landmarks. Recently, various 2D operators have been proposed for the detection of corner points but most of them are not effective for medical images that need a high accuracy. In this paper we have proposed a new auto...

Mohammadi, Gelareh; Fatemizadeh, Emad

314

Look and turn: landmark-based goal navigation in honey bees.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This report describes the piloting mechanisms employed by honey bees during their final approach to a goal. Conceptually applying a bottom-up approach, we systematically varied the position, number and appearance landmarks associated with a rewarded target location within a large, homogenous flight ...

Fry, S N; Wehner, R

315

Smells like home: Desert ants, Cataglyphis fortis, use olfactory landmarks to pinpoint the nest  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Cataglyphis fortis ants forage individually for dead arthropods in the inhospitable salt-pans of Tunisia. Locating the inconspicuous nest after a foraging run of more than 100 meters demands a remarkable orientation capability. As a result of high temperatures and the unpredictable distribution of food, Cataglyphis ants do not lay pheromone trails. Instead, path integration is the fundamental system of long-distance navigation. This system constantly informs a foraging ant about its position relative to the nest. In addition, the ants rely on visual landmarks as geocentric navigational cues to finally pinpoint the nest entrance. Results Apart from the visual cues within the ants' habitat, we found potential olfactory landmark information with different odour blends coupled to various ground structures. Here we show that Cataglyphis ants can use olfactory information in order to locate their nest entrance. Ants were trained to associate their nest entrance with a single odour. In a test situation, they focused their nest search on the position of the training odour but not on the positions of non-training odours. When trained to a single odour, the ants were able to recognise this odour within a mixture of four odours. Conclusion The uniform salt-pans become less homogenous if one takes olfactory landmarks into account. As Cataglyphis ants associate environmental odours with the nest entrance they can be said to use olfactory landmarks in the vicinity of the nest for homing.

Steck Kathrin; Hansson Bill S; Knaden Markus

2009-01-01

316

Image-guided surgical planning using anatomical landmarks in the retrosigmoid approach.  

UK PubMed Central (United Kingdom)

OBJECTIVE: The suboccipital lateral or retrosigmoid approach is the main neurosurgical approach to the cerebellopontine angle (CPA). It is mainly used in the treatment of CPA tumors and vascular decompression of cranial nerves. A prospective study using navigation registered with anatomical landmarks in order to identify the transverse and sigmoid sinuses junction (TSSJ) was carried out in a series of 30 retrosigmoid craniotomies. The goal of this study was to determine the accuracy of this navigation technique and to establish the relationship between the location of the asterion and the TSSJ. METHODS: From March through November 2008, 30 patients underwent a retrosigmoid craniotomy for removal of CPA tumors or for surgical treatment of neurovascular syndromes. Magnetic resonance imaging (MRI) T1 sequences with gadolinium (FSPGR with FatSst, 1.5 T GE Signa) and frameless navigation (Vector vision, Brainlab) were used for surgical planning. Registration was performed using six anatomical landmarks. The position of the TSSJ indicated by navigation was the landmark to guide the craniotomy. The location of the asterion was compared with the position of the TSSJ. After craniotomy, the real TSSJ position was compared with the virtual position, as demonstrated by navigation. RESULTS: There were 19 cases of vestibular schwannomas, 5 petroclival meningiomas, 3 trigeminal neuralgias, 1 angioblastoma, 1 epidermoid cyst and 1 hemifacial spasm. In all cases, navigation enabled the location of the TSSJ and the emissary vein, with an accuracy flaw below 2 mm. The asterion was located directly over the TSSJ in only seven cases. One patient had a laceration of the sigmoid sinus during the craniotomy. CONCLUSIONS: Navigation using anatomical landmarks for registration is a reliable method in the localization of the TSSJ for retrosigmoid craniotomies and thereby avoiding unnecessary sinus exposure. In addition, the method proved to be fast and accurate. The asterion was found to be a less accurate landmark for the localization of the TSSJ using navigation.

da Silva EB Jr; Leal AG; Milano JB; da Silva LF Jr; Clemente RS; Ramina R

2010-05-01

317

Arm CT scan  

Science.gov (United States)

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

318

Cranial CT scan  

Science.gov (United States)

Brain CT; Head CT; CT scan - skull; CT scan - head; CT scan - orbits; CT scan - sinuses; Computed tomography - cranial ... table that slides into the center of the CT scanner. While inside the scanner, the machine's x- ...

319

A new method for automatic tracking of facial landmarks in 3D motion captured images (4D).  

UK PubMed Central (United Kingdom)

The aim of this study was to validate the automatic tracking of facial landmarks in 3D image sequences. 32 subjects (16 males and 16 females) aged 18-35 years were recruited. 23 anthropometric landmarks were marked on the face of each subject with non-permanent ink using a 0.5mm pen. The subjects were asked to perform three facial animations (maximal smile, lip purse and cheek puff) from rest position. Each animation was captured by the 3D imaging system. A single operator manually digitised the landmarks on the 3D facial models and their locations were compared with those of the automatically tracked ones. To investigate the accuracy of manual digitisation, the operator re-digitised the same set of 3D images of 10 subjects (5 male and 5 female) at 1 month interval. The discrepancies in x, y and z coordinates between the 3D position of the manual digitised landmarks and that of the automatic tracked facial landmarks were within 0.17mm. The mean distance between the manually digitised and the automatically tracked landmarks using the tracking software was within 0.55 mm. The automatic tracking of facial landmarks demonstrated satisfactory accuracy which would facilitate the analysis of the dynamic motion during facial animations.

Al-Anezi T; Khambay B; Peng MJ; O'Leary E; Ju X; Ayoub A

2013-01-01

320

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

UK PubMed Central (United Kingdom)

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.

Austen JM; Kosaki Y; McGregor A

2013-07-01

 
 
 
 
321

Automated positioning of scan planes and navigator tracker locations in MRI liver scanning  

International Nuclear Information System (INIS)

This report presents a new method for automatic scan prescription planning of both the scan planes and Navigator Tracker locations in MRI liver scanning. A 3D dataset acquired using a fast T1 sequence is preprocessed and converted to 2D projection images to avoid the need for complicated and time-consuming 3D segmentation. A 2D active shape model (ASM) is applied to the 2D coronal projection data, and the external shape of the liver dataset is initially extracted based on a rough estimate of the inferior edge of the liver from the 2D projection dataset. The scan plane locations are determined from the inferior and superior edges of the shape model. Navigator Tracker, which is used for motion-compensated MR abdominal MR scanning, establishes the location by selecting one of the landmarks in the ASM. Datasets obtained from 38 volunteers were tested. Good results were obtained, suggesting that this method may prove to be useful for clinical diagnosis. (author)

2010-01-01

322

On landmark selection and sampling in high-dimensional data analysis  

CERN Multimedia

In recent years, the spectral analysis of appropriately defined kernel matrices has emerged as a principled way to extract the low-dimensional structure often prevalent in high-dimensional data. Here we provide an introduction to spectral methods for linear and nonlinear dimension reduction, emphasizing ways to overcome the computational limitations currently faced by practitioners with massive datasets. In particular, a data subsampling or landmark selection process is often employed to construct a kernel based on partial information, followed by an approximate spectral analysis termed the Nystrom extension. We provide a quantitative framework to analyse this procedure, and use it to demonstrate algorithmic performance bounds on a range of practical approaches designed to optimize the landmark selection process. We compare the practical implications of these bounds by way of real-world examples drawn from the field of computer vision, whereby low-dimensional manifold structure is shown to emerge from high-di...

Belabbas, Mohamed-Ali

2009-01-01

323

Sex differences in a landmark environmental re-orientation task only during the learning phase.  

UK PubMed Central (United Kingdom)

Sex differences are consistently reported in human navigation. Indeed, to orient themselves during navigation women are more likely to use landmark-based strategies and men Euclidean-based strategies. The difference could be due to selective social pressure, which fosters greater spatial ability in men, or biological factors. And the great variability of the results reported in the literature could be due to the experimental setting more than real differences in ability. In this study, navigational behaviour was assessed by means of a place-learning task in which a modified version of the Morris water maze for humans was used to evaluate sex differences. In using landmarks, sex differences emerged only during the learning phase. Although the men were faster than the women in locating the target position, the differences between the sexes disappeared in delayed recall.

Piccardi L; Bianchini F; Iasevoli L; Giannone G; Guariglia C

2011-10-01

324

Accuracy of a transformation method to estimate muscle attachments based on three bony landmarks.  

UK PubMed Central (United Kingdom)

In this work, the accuracy of a transformation method to estimate muscle attachments based on three bony landmarks was assessed. A concept of mathematical error was introduced and applied to a data-set of 17 muscles' attachment lines from the shoulders of seven cadavers. Within the muscles' attachment lines from the studied data-set, mathematical error and anatomical variability average percentage values were 37.3 and 62.7%, respectively, for the scapula, and 54.4 and 45.6%, respectively, for the humerus. To reduce mathematical error in the transformation method presented, the plane formed by the three landmarks of the segment corresponding to the scaled muscles should neither be too close to the origin of the global coordinate system, nor too far away from muscle attachment locations to be transformed. The procedure outlined in this work allows the researcher to analyse the anatomical variability within a data-set.

Matias R; Andrade C; Veloso AP

2011-01-01

325

Radiographic landmarks for measurement of cranial tibial subluxation in the canine cruciate ligament deficient stifle.  

UK PubMed Central (United Kingdom)

OBJECTIVES: The primary objective was to develop a repeatable radiographic technique for assessment of cranial tibial subluxation (CTS) and test the intra-observer and inter-observer repeatability of the chosen landmarks. A secondary objective was to determine the effects of digital radiographic magnification on CTS measurement repeatability. METHODS: Twenty-three normal canine pelvic limbs were used to determine the magnitude of CTS before and after transection of the cranial cruciate ligament. Mediolateral radiographs were taken with and without fiduciary markers in place. Three investigators measured the CTS using radiographically visible anatomic landmarks at two different magnifications. The total observed variabilities were assessed by inter-observer and intra-observer differences. Paired t-tests were used to determine the effect of magnification and marker presence on CTS measures. RESULTS: Measurement of the CTS from the caudal margin of the intercondylar fossa on the femur to the intercondylar eminence was the most repeatable. Poor correlation between the anatomic landmarks and the fiduciary bone markers was observed. We found no effect of magnification or presence or absence of bone markers on measurement of CTS. CLINICAL SIGNIFICANCE: Cranial tibial subluxation can be detected with the most repeatability by measuring between the caudal margin of the intercondylar fossa and the intercondylar eminence. Magnification of the digitized radiographic image had minimal effect on repeatability. This technique can be used for in vivo analysis of the canine cruciate ligament deficient stifle joint.

Plesman R; Sharma A; Gilbert P; Campbell J; Johnston JD; Shmon C; Linn K

2012-11-01

326

Precise visual navigation using multi-stereo vision and landmark matching  

Science.gov (United States)

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

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

2007-05-01

327

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

UK PubMed Central (United Kingdom)

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

Wang L; Beyer ST; Cronk QC; Walus K

2011-01-01

328

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

Directory of Open Access Journals (Sweden)

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

Wang Lisheng; Beyer Simon T; Cronk Quentin CB; Walus Konrad

2011-01-01

329

[Dyspraxia: landmarks].  

UK PubMed Central (United Kingdom)

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.

Mazeau M

2010-03-01

330

[Dyspraxia: landmarks].  

Science.gov (United States)

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. PMID:19942418

Mazeau, M

2009-11-25

331

Heart PET scan  

Science.gov (United States)

Heart nuclear medicine scan; Heart positron emission tomography; Myocardial PET scan ... and collects in organs and tissues, including your heart. The tracer helps the radiologist see certain areas ...

332

The dorsal pedis artery as a new distal landmark for extramedullary tibial alignment in total knee arthroplasty.  

UK PubMed Central (United Kingdom)

PURPOSE: It is better to use multiple anatomical landmarks to reduce errors in component alignment in total knee arthroplasty. Therefore, it is worthwhile to find a new landmark that can be used as an addition to conventional ones. Herein, we assessed the dorsal pedis artery as a new distal landmark for extramedullary tibial alignment. METHODS: Fifty-two ankles in patients undergoing total knee arthroplasty and 10 ankles in normal controls were included. Color Doppler ultrasonography was used to locate the dorsal pedis artery at the level of the ankle joint. Conventional landmarks, including the tibialis anterior tendon, the extensor hallucis longus tendon, the extensor digitorum longus tendon, and the malleolar centre, were also located on ultrasound images. The distances between the ankle centre and each landmark were measured and compared. RESULTS: The dorsal pedis artery was absent in 2 patients and impalpable but visible with ultrasonography in other 2 patients. The dorsal pedis artery was located anatomically closest to the ankle centre in patients (0.4 ± 3.4 mm lateral). Statistical analysis showed that the dorsal pedis artery, the extensor hallucis longus tendon, and the malleolar centre were located significantly closer to the ankle centre comparing with the extensor digitorum longus tendon and the tibialis anterior tendon in both patients and controls (p < 0.001). CONCLUSIONS: As long as the dorsal pedis artery exists, it can be used as an addition to the conventional landmarks in total knee arthroplasty. Using this new landmark will help reduce errors in coronal plane alignment of tibial component. LEVEL OF EVIDENCE: II.

Sugimura N; Ikeuchi M; Izumi M; Aso K; Ushida T; Tani T

2013-02-01

333

The lumbar sympathetic trunk: its visibility and distance to two anatomical landmarks.  

UK PubMed Central (United Kingdom)

OBJECTIVE: The lumbar sympathetic trunk's (LST) distance to two anatomical landmarks, the costal process and medial margin of the psoas muscle, was assessed due to its use as landmarks for lumbar sympathetic blocks: the costal process for fluoroscopic guided techniques and the psoas major for CT- and MRI-guided techniques. Based on the measurements, we evaluate the trunk's visibility in MR and CT images for accurate positioning of the needle. METHODS: A total of 54 cadavers embalmed with Thiel's method were investigated. The LST's distances to the psoas major's medial margin and to the base of the lumbar vertebrae's costal process were measured on the levels L2/3, L3/4 and L4/5. The measurements were compared to MR and CT images of 20 anonymous patients to identify the LST. RESULTS: LST's mean distance to the psoas major was 0.3 mm at L2/3, 3.1 mm at L3/4 and 4.6 mm at L4/5. The mean distance to the costal process was 31 mm at L2/3, 34 mm at L3/4 and 32.6 mm at L4/5. In both MR and CT imaging, a structure could be determined as the LST correlating to the measurements with decreasing possible identification from cephalad to caudad levels. CONCLUSIONS: The costal process is a usable landmark for fluoroscopic guidance and the psoas major for CT- and MRI-guided techniques. The LST is clearly visible in MR and CT images, which gives both techniques a decisive advantage over fluoroscopy concerning the block of the LST due to a visible target.

Feigl GC; Kastner M; Ulz H; Breschan C; Pixner T; Dreu M; Umschaden HW; Likar R

2013-03-01

334

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

Scientific Electronic Library Online (English)

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

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

2013-01-01

335

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

DEFF Research Database (Denmark)

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 configuration graphs of Turing machines. I will discuss some of the natural habitats of undecidable temporal logics, such as first-order, interval-based and real time temporal logics, as well as some extensions that often lead to undecidability, such as two-dimensional temporal logics and temporal-epistemic logics.

Goranko, Valentin

2012-01-01

336

Orbit and attitude refinement of a spinning satellite using landmark data  

Science.gov (United States)

A methodology is presented for the orbit and attitude refinement of a spinning satellite using landmarks extracted from the imagery obtained from its sensors. The search strategy comprises both random and deterministic searches whose order of deployment is chosen in such a way as to exploit the relative inherent advantages of both types of methods. Findings of extensive simulation exercises are presented that include several trend analyses like radius of convergence, effect of observation errors and data span. The feasibility of the proposed methodology is demonstrated by application to actual data of the Indian satellite RSD2 which carried a 'Smart' sensor onboard.

Sheela, B. V.; Nagarajan, N.; Padmanabhan, P.; Bhat, R. S.; Prakasarao, A. S.

337

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

International Nuclear Information System (INIS)

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

2011-01-01

338

A New Anatomical and Surgical Landmark in Internal Abdominal Oblique Muscle Fat Triangle  

Directory of Open Access Journals (Sweden)

Full Text Available Purpose: To determine the anatomical landmark within the internal oblique muscle. Materials and Methods: In a prospective study, the abdominal wall was examined for internal oblique muscle land marks in 900 patients undergoing laparatomy. Results: There was a fat line at anterior superior iliac spine level to access the underlying layers and then to the abdominal cavity. Conclusion: A fat triangle within the internal oblique muscle provides a suitable region of surgical incision at the lower part of the abdominal wall.

Kazem Madaen; Behrooz Niknafs

2012-01-01

339

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

International Nuclear Information System (INIS)

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

2010-11-21

340

The use of pseudo-landmarks for craniofacial analysis: A comparative study with L1-regularized logistic regression.  

UK PubMed Central (United Kingdom)

Morphometrics, the quantitative analysis of shape, is used by craniofacial researchers to study abnormalities in human face shapes. Most of the work in craniofacial morphometrics uses landmark points that are manually marked on 3D face data and processed via a generalized Procrustes analysis. For large data sets this manual process is very time-consuming. Dense sets of pseudo-landmarks have also been proposed and successfully used for classification and clustering, but the two main methods in the literature are very computationally intensive. We have developed a computationally simple method that can compute pseudo-landmark points at different resolutions from 3D meshes of human faces. In this paper, we perform a comparative study employing L1-regularized logistic regression to train a classifier that predicts the sex of 500 normal adult face meshes in order to compare our method to two alternative pseudo-landmark methods and a distance matrix approach.Our results show that our method, which is fully automatic, achieved similar results to the best-scoring methods with no manual landmarking and with much lower computation time. Use of the distance matrix did not improve classification results.

Mercan E; Shapiro LG; Weinberg SM; Lee SI

2013-07-01

 
 
 
 
341

The use of pseudo-landmarks for craniofacial analysis: A comparative study with L1-regularized logistic regression.  

Science.gov (United States)

Morphometrics, the quantitative analysis of shape, is used by craniofacial researchers to study abnormalities in human face shapes. Most of the work in craniofacial morphometrics uses landmark points that are manually marked on 3D face data and processed via a generalized Procrustes analysis. For large data sets this manual process is very time-consuming. Dense sets of pseudo-landmarks have also been proposed and successfully used for classification and clustering, but the two main methods in the literature are very computationally intensive. We have developed a computationally simple method that can compute pseudo-landmark points at different resolutions from 3D meshes of human faces. In this paper, we perform a comparative study employing L1-regularized logistic regression to train a classifier that predicts the sex of 500 normal adult face meshes in order to compare our method to two alternative pseudo-landmark methods and a distance matrix approach.Our results show that our method, which is fully automatic, achieved similar results to the best-scoring methods with no manual landmarking and with much lower computation time. Use of the distance matrix did not improve classification results. PMID:24111127

Mercan, Ezgi; Shapiro, Linda G; Weinberg, Seth M; Lee, Su-In

2013-07-01

342

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

Science.gov (United States)

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

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

2010-11-01

343

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

UK PubMed Central (United Kingdom)

BACKGROUND: The acquisition of new knowledge is a primary goal of residency training. Retrieving and retaining influential primary and secondary medical literature can be challenging for house officers. We set out to investigate the effect of a Universal Serial Bus (USB) drive loaded with landmark scientific articles on housestaff education in a pilot study. METHODS: We created a USB syllabus that contains 187 primary scientific research articles. The electronic syllabus had links to the full-text articles and was organized using an html webpage with a table of contents according to medical subspecialties. We performed a prospective cohort study of 53 house officers in the internal medicine residency program who received the USB syllabus. We evaluated the impact of the USB syllabus on resident education with surveys at the beginning and conclusion of the nine-month study period. RESULTS: All 50 respondents (100%) reported to have used the USB syllabus. The self-reported number of original articles read each month was higher at the end of the nine-month study period compared to baseline. Housestaff rated original articles as being a more valuable educational resource after the intervention. CONCLUSIONS: An electronic syllabus with landmark scientific articles placed on a USB drive was widely utilized by housestaff, increased the self-reported reading of original scientific articles and seemed to have positively influenced residents' attitude toward original medical literature.

Chahla M; Eberlein M; Wright S

2010-01-01

344

Evaluation of facial nerve and its landmarks in adult temporal bones  

Directory of Open Access Journals (Sweden)

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.

Saeid Soheilipour; Ali Asghar Narimani; Abdollah Noorbakhsh

2010-01-01

345

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

Directory of Open Access Journals (Sweden)

Full Text Available Background: The acquisition of new knowledge is a primary goal of residency training. Retrieving and retaining influential primary and secondary medical literature can be challenging for house officers. We set out to investigate the effect of a Universal Serial Bus (USB) drive loaded with landmark scientific articles on housestaff education in a pilot study. Methods: We created a USB syllabus that contains 187 primary scientific research articles. The electronic syllabus had links to the full-text articles and was organized using an html webpage with a table of contents according to medical subspecialties. We performed a prospective cohort study of 53 house officers in the internal medicine residency program who received the USB syllabus. We evaluated the impact of the USB syllabus on resident education with surveys at the beginning and conclusion of the nine-month study period. Results: All 50 respondents (100%) reported to have used the USB syllabus. The self-reported number of original articles read each month was higher at the end of the nine-month study period compared to baseline. Housestaff rated original articles as being a more valuable educational resource after the intervention. Conclusions: An electronic syllabus with landmark scientific articles placed on a USB drive was widely utilized by housestaff, increased the self-reported reading of original scientific articles and seemed to have positively influenced residents’ attitude toward original medical literature.

Mayy Chahla; Michael Eberlein; Scott Wright

2010-01-01

346

Sex differences in memory for landmark arrays in C57BL/J6 mice.  

Science.gov (United States)

The most robust sex differences in cognition across polygynous mammalian species are the sex-specific patterns of the use of spatial cues during encoding and orientation. In laboratory rats, wild rodents, and humans, females orient preferentially to the features and arrangement of local landmarks, while males preferentially attend to distant landmarks. Yet this sex-specific pattern is often absent or reversed in the laboratory mouse, a species representing a major laboratory model of neural mechanisms. We explored sex differences in the C57BL/J6 strain of laboratory mouse by employing tasks that were motivated by the natural patterns of exploration. We predicted that such tasks would unmask the predicted default polygynous patterns of cue use by females and males. We used two standard tasks, a novel object recognition task and a five-stage serial object dishabituation task. On the first task, the results showed a female advantage in detecting the novel object, as predicted by prior results from other polygynous species. In the second task, we found, also as predicted, a male advantage in performance when the polarization of the array was distorted and a female advantage in performance when the local array was re-arranged. The pattern of sex-specific advantages in performance in C57BL/J6 mouse is thus concordant with that found in other polygynous mammals. PMID:23526160

Bettis, Tania J; Jacobs, Lucia F

2013-03-23

347

Sex differences in memory for landmark arrays in C57BL/J6 mice.  

UK PubMed Central (United Kingdom)

The most robust sex differences in cognition across polygynous mammalian species are the sex-specific patterns of the use of spatial cues during encoding and orientation. In laboratory rats, wild rodents, and humans, females orient preferentially to the features and arrangement of local landmarks, while males preferentially attend to distant landmarks. Yet this sex-specific pattern is often absent or reversed in the laboratory mouse, a species representing a major laboratory model of neural mechanisms. We explored sex differences in the C57BL/J6 strain of laboratory mouse by employing tasks that were motivated by the natural patterns of exploration. We predicted that such tasks would unmask the predicted default polygynous patterns of cue use by females and males. We used two standard tasks, a novel object recognition task and a five-stage serial object dishabituation task. On the first task, the results showed a female advantage in detecting the novel object, as predicted by prior results from other polygynous species. In the second task, we found, also as predicted, a male advantage in performance when the polarization of the array was distorted and a female advantage in performance when the local array was re-arranged. The pattern of sex-specific advantages in performance in C57BL/J6 mouse is thus concordant with that found in other polygynous mammals.

Bettis TJ; Jacobs LF

2013-03-01

348

Intercostobrachial nerves as a novel anatomic landmark for dividing the axillary space in lymph node dissection.  

UK PubMed Central (United Kingdom)

Purpose. Our aim was to assess the feasibility of using the intercostobrachial nerves (ICBNs) as a possible new anatomic landmark for axillaries lymph node dissection in breast cancer patients. Background Data Summary. The preservation of ICBN is now an accepted procedure in this type of dissection; however, it could be improved further to reduce the number of postoperative complications. The axillary space is divided into lower and upper parts by the ICBN-a thorough investigation of the metastasis patterns in lymph nodes found in this area could supply new information leading to such improvements. Methods. Seventy-two breast cancer patients, all about to undergo lymph node dissection and with sentinel lymph nodes identified, were included in this trial. The lymph nodes were collected in two groups, from lower and upper axillary spaces, relative to the intercostobrachial nerves. The first group was further subdivided into sentinel (SLN) and nonsentinel (non-SLN) nodes. All lymph nodes were tested to detect macro- and micrometastasis. Results. All the sentinel lymph nodes were found under the intercostobrachial nerves; more than 10 lymph nodes were located in that space. Moreover, when lymph nodes macrometastasize or micrometastasize above the intercostobrachial nerves, we also observe metastasis-positive nodes under the nerves; when the lower group nodes show no metastasis, the upper group is also metastasis free. Conclusions. Our results show that the intercostobrachial nerves are good candidates for a new anatomic landmark to be used in lymph node dissection procedure.

Li J; Zhang Y; Zhang W; Jia S; Gu X; Ma Y; Li D

2013-01-01

349

Landmarks of the sacral hiatus for caudal epidural block: an anatomical study.  

UK PubMed Central (United Kingdom)

BACKGROUND: This study determined the landmarks for caudal epidural block (CEB) after morphometric measurements of the sacral hiatus on dry sacral bones. Anatomical features of the sacral hiatus of clinical importance during CEB, along with distances and angles of use in detecting the apex, were measured. This provides detailed knowledge of the anatomy of the sacral hiatus and practical landmarks. METHODS: Ninety-six dry sacral bones were used. Anatomical measurements were made with a Vernier caliper accurate to 0.1 mm. RESULTS: Two sacral bones were excluded since they had total posterior closure defect. Agenesis of the sacral hiatus was detected in six sacral bones. As the posterior superior iliac spines impose on the superolateral sacral crests of the sacrum, the latter were accepted as forming the base of a triangle. The distance between the two superolateral sacral crests and the distances between the sacral apex and the right and left superolateral sacral crest were 66.5 (SD 53.5), 67.1 (10.0) and 67.5 (9.5) mm respectively, on average. CONCLUSION: The triangle formed between the apex of the sacral hiatus and the superolateral sacral crests was found to have the features of an equilateral triangle. The sacrum and sacral hiatus are variable anatomical structures. However, the equilateral triangle located between the apex of the sacral hiatus and superolateral sacral crests will certainly be of use in determining the location of the sacral hiatus during CEB.

Senoglu N; Senoglu M; Oksuz H; Gumusalan Y; Yuksel KZ; Zencirci B; Ezberci M; Kizilkanat E

2005-11-01

350

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

Directory of Open Access Journals (Sweden)

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

Alejandro González; Flavio Prieto

2010-01-01

351

HIDA Scan (Cholescintigraphy)  

Science.gov (United States)

HIDA scan Basics In-Depth Multimedia Resources Reprints A single copy of this article may be reprinted for personal, noncommercial use only. HIDA scan By Mayo Clinic staff Original Article: http:// ...

352

Scanning Cursor Adaptability.  

Science.gov (United States)

This report details the research and findings related to the Scanning Cursor Adaptability Study. The data herein pertains to the review of automated cartographic and scanning cursor programs, digitizing device vendors, the analysis of interface requiremen...

A. J. Kreutzer G. W. Hunka T. B. Kolassa P. N. Mandryck

1981-01-01

353

Getting a CAT Scan  

Medline Plus

Full Text Available ... Story: Power Player The Pink Locker Society Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) Print A A A Text Size CAT stands for "computerized ...

354

Getting a CAT Scan  

Science.gov (United States)

... Power Player The Pink Locker Society Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) Print A A A Text Size CAT stands for "computerized axial tomography." Translated, that means ...

355

Heart CT scan  

Science.gov (United States)

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

356

Scanning gamma camera  

International Nuclear Information System (INIS)

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

1977-01-01

357

Proposal of landmarks for clamping neurovascular elements during endoscopic surgery of the supraglottic region.  

UK PubMed Central (United Kingdom)

BACKGROUND: Bleeding within the supraglottic region can be a lethal complication after CO(2) laser microsurgery. Our aim was to propose endoluminal anatomical landmarks to locate the superior laryngeal vessels resulting in a safer microsurgery. METHODS: Endoluminal dissections were made in 22 larynges without laryngeal disease. RESULTS: The neurovascular structures were in the superior third of a triangle defined by the vocal process, the anterior commissure, and the epiglottic attachment of the aryepiglottic fold. They overlapped in 4 different ways: pattern I (70.4%): superior laryngeal vein (SLV), superior laryngeal artery (SLA), and internal laryngeal nerve (ILN); pattern II (13.6%): SLA, SLV, ILN; pattern III (4.6%): SLV, ILN, and SLA; pattern IV (4.6%): SLA, ILN, and SLV. CONCLUSION: Microsurgery in the supraglottic region may be safer if surgeons are aware of the superior third of the above-defined triangle, "danger area", where the vascular elements of this region are located.

Souvirón R; Maranillo E; Vázquez T; Patel N; McHanwell S; Cobeta I; Scola B; Sañudo J

2013-01-01

358

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

International Nuclear Information System (INIS)

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

1987-01-01

359

Environmental Genomics ??????  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The Environmental Genomics thematic programme aims to facilitate the exploitation and, where appropriate, acquisition of whole or partial genome sequence data in environmental biology. Central to this aim is the establishment of a community of researchers, comprising empiricists and theoretic...

Wang, Nan????

360

Anatomy and surgical landmarks for the ansa pectoralis: application to pectoralis major nerve selective neurotomy.  

UK PubMed Central (United Kingdom)

BACKGROUND: Ansa pectoralis neurotomy is a surgical approach in the treatment of the pectoralis major muscle spasticity causing an attitude in adduction and internal rotation of the shoulder. OBJECTIVE: To establish the anatomical landmarks allowing an easier localisation of the ansa pectoralis during neurotomy. MATERIAL AND METHODS: Fifteen adult human cadavers (10 embalmed and 5 fresh) were dissected in order to determine anatomical landmarks allowing an easier localization of the ansa pectoralis during neurotomy. RESULTS: In all the cadavers, the lateral pectoral nerve arose from the lateral cord of the brachial plexus, 0.2 cm above to 1.5 cm below the inferior border of the clavicle with a mean distance of 0.76 cm for left and right side, whereas the medial pectoral nerve arose from the medial cord of the brachial plexus, 0.7-2.3 cm below the inferior border of the clavicle with a mean distance of 0.61 cm for the left side and 0.68 cm for the right side. We systematically found both the origin of pectoral nerves and the ansa pectoralis at the level of the middle third of the distance between the sternoclavicular and the acromioclavicular joints. Moreover, ansa pectoralis was constantly localized lateral to the thoracoacromial artery. In four cases, the division of the lateral pectoral nerve was not found. In one case, medial pectoral nerve did not exist. CONCLUSION: Ansa pectoralis can be found by a curved incision made at the mid-third of the distance between the sternoclavicular and the acromioclavicular joints, the medial point being located just below the lower edge of the clavicle and the lateral point 2 cm below the inferior edge of the clavicle.

Creze M; Peltier J; Havet E; Potier A; Lefranc M; Foulon P; Le Gars D

2012-12-01