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

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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

2010-07-01

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

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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.

Szafranek Angela

2007-11-01

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Restriction landmark genome scanning identifies culture-induced DNA methylation instability in the human embryonic stem cell epigenome.  

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Widespread provision of human embryonic stem cells (hESCs) for therapeutic use, drug screening and disease modelling will require cell lines sustainable over long periods in culture. Since the short-term, in vitro culture of mammalian embryos can result in DNA methylation changes, the epigenetic stability of hESCs warrants investigation. Existing hESC lines have been derived and cultured under diverse conditions, providing the potential for programming differential changes into the epigenome that may result in inter-line variability over and above that inherited from the embryo. By examining the DNA methylation profiles of > 2000 genomic loci by Restriction Landmark Genome Scanning, we identified substantial inter-line epigenetic distance between six independently derived hESC lines. Lines were found to inherit further epigenetic changes over time in culture, with most changes arising in the earliest stages post-derivation. The loci affected varied between lines. The majority of culture-induced changes (82.3-87.5%) were stably inherited both within the undifferentiated cells and post-differentiation. Adapting a line to a serum-free culture system resulted in additional epigenetic instability. Overall 80.5% of the unstable loci uncovered in hESCs have been associated previously with an adult tumour phenotype. Our study shows that current methods of hESC propagation can rapidly programme stable and unpredictable epigenetic changes in the stem cell genome. This highlights the need for (i) novel screening strategies to determine the experimental utility and biosafety of hESCs and (ii) optimization and standardization of procedures for the derivation and culture of hESC lines that minimize culture-induced instability. PMID:17409196

Allegrucci, Cinzia; Wu, Yue-Zhong; Thurston, Alexandra; Denning, Chris N; Priddle, Helen; Mummery, Christine L; Ward-van Oostwaard, Dorien; Andrews, Peter W; Stojkovic, Miodrag; Smith, Nigel; Parkin, Tony; Jones, Mark Edmondson; Warren, Graham; Yu, Li; Brena, Romulo Martin; Plass, Christoph; Young, Lorraine E

2007-05-15

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Arterial tree tracking from anatomical landmarks in magnetic resonance angiography scans  

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

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

2014-03-01

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

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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 2 min, 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

2013-12-01

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Clinical evaluation of semi-automatic landmark-based lesion tracking software for CT-scans  

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Background To evaluate a semi-automatic landmark-based lesion tracking software enabling navigation between RECIST lesions in baseline and follow-up CT-scans. Methods The software automatically detects 44 stable anatomical landmarks in each thoraco/abdominal/pelvic CT-scan, sets up a patient specific coordinate-system and cross-links the coordinate-systems of consecutive CT-scans. Accuracy of the software was evaluated on 96 RECIST lesions (target- and non-target lesions) in baseline and follow-up CT-scans of 32 oncologic patients (64 CT-scans). Patients had to present at least one thoracic, one abdominal and one pelvic RECIST lesion. Three radiologists determined the deviation between lesions’ centre and the software’s navigation result in consensus. Results The initial mean runtime of the system to synchronize baseline and follow-up examinations was 19.4?±?1.2 seconds, with subsequent navigation to corresponding RECIST lesions facilitating in real-time. Mean vector length of the deviations between lesions’ centre and the semi-automatic navigation result was 10.2?±?5.1 mm without a substantial systematic error in any direction. Mean deviation in the cranio-caudal dimension was 5.4?±?4.0 mm, in the lateral dimension 5.2?±?3.9 mm and in the ventro-dorsal dimension 5.3?±?4.0 mm. Conclusion The investigated software accurately and reliably navigates between lesions in consecutive CT-scans in real-time, potentially accelerating and facilitating cancer staging.

2014-01-01

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Identification of conserved lentiviral sequences as landmarks of genomic flexibility.  

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Considering that recombinations produce quasispecies in lentivirus spreading, we identified and localized highly conserved sequences that may play an important role in viral ontology. Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). They were located mainly in the structural genes forming hot spots particularly in the gag and pol genes and to a lesser extent in LTRs and regulatory genes. The CLS pattern was the same throughout the different HIV-1 subtypes, except for some HIV-1-O strains. Only CLS 3 and 4 were detected in both negative control HTLV-1 oncornaviruses and D-particle-forming simian viruses, which are not immunodeficiency inducers and display a genetic stability. CLSs divided the virus genomes into domains allowing us to distinguish sequence families leading to the notion of 'species self' besides that of 'lentiviral self'. Most of acutely localized CLSs in HIV-1s (82%) corresponded to wide recombination segments being currently reported. PMID:17027636

Moncany, Maurice L J; Dalet, Karine; Courtois, Pascal R R

2006-10-01

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

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

Ritter, M.

2007-04-27

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A note on generalized Genome Scan Meta-Analysis statistics  

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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 regio...

Feng Anne C; Koziol James A

2005-01-01

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

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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

2011-11-01

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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

2005-06-01

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A note on generalized Genome Scan Meta-Analysis statistics  

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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.

Feng Anne C

2005-02-01

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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.

Rogers Alan R

2010-01-01

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The Fibromyalgia Family Study: A Genome-Scan Linkage Study  

Science.gov (United States)

Objective Familial aggregation of fibromyalgia has been increasingly recognized. The goal of the current study was to conduct a genome wide linkage scan to identify susceptibility loci for fibromyalgia. Methods We genotyped members of 116 families from the Fibromyalgia Family Study and performed a model-free genome-wide linkage analysis of fibromyalgia with 341 microsatellite markers, using the Haseman-Elston regression approach. Results The estimated sibling recurrence risk ratio (?s) for fibromyalgia was 13.6 (95% CI: 10.0–18.5), based on a reported population prevalence of 2%. Genome-wide suggestive evidence of linkage was found at marker D17S2196 (Empirical P =0.00030) and D17S1294 (Empirical P =0.00035) on chromosome 17p11.2-q11.2. Conclusion The estimated sibling recurrence risk ratio suggests a strong genetic component of fibromyalgia. This is the first study to report genome-wide suggestive linkage of fibromyalgia to the chromosome 17p11.2-q11.2 region. Further investigation of these multi-case families from the Fibromyalgia Family Study is warranted to identify potential causal risk variants for fibromyalgia. PMID:23280346

Arnold, Lesley M.; Fan, Jinbo; Russell, I. Jon; Yunus, Muhammad B.; Khan, Muhammad Asim; Kushner, Irving; Olson, Jane M.; Iyengar, Sudha K.

2013-01-01

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Genome scan for meat quality traits in Nelore beef cattle.  

Science.gov (United States)

Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle. PMID:24022219

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

2013-11-01

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Genome-wide DNA polymorphism analyses using VariScan  

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BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the a...

Hutter, Stephan; Vilella Bertran, Albert; Rozas Liras, Julio A.

2006-01-01

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

Science.gov (United States)

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is an enduring public health problem globally, particularly in sub-Saharan Africa. Several studies have suggested a role for host genetic susceptibility in increased risk for TB but results across studies have been equivocal. As part of a household contact study of Mtb infection and disease in Kampala, Uganda, we have taken a unique approach to the study of genetic susceptibility to TB, by studying three phenotypes. First, we analyzed culture confirmed TB disease compared to latent Mtb infection (LTBI) or lack of Mtb infection. Second, we analyzed resistance to Mtb infection in the face of continuous exposure, defined by a persistently negative tuberculin skin test (PTST-); this outcome was contrasted to LTBI. Third, we analyzed an intermediate phenotype, tumor necrosis factor-alpha (TNFalpha) expression in response to soluble Mtb ligands enriched with molecules secreted from Mtb (culture filtrate). We conducted a full microsatellite genome scan, using genotypes generated by the Center for Medical Genetics at Marshfield. Multipoint model-free linkage analysis was conducted using an extension of the Haseman-Elston regression model that includes half sibling pairs, and HIV status was included as a covariate in the model. The analysis included 803 individuals from 193 pedigrees, comprising 258 full sibling pairs and 175 half sibling pairs. Suggestive linkage (p<10(-3)) was observed on chromosomes 2q21-2q24 and 5p13-5q22 for PTST-, and on chromosome 7p22-7p21 for TB; these findings for PTST- are novel and the chromosome 7 region contains the IL6 gene. In addition, we replicated recent linkage findings on chromosome 20q13 for TB (p = 0.002). We also observed linkage at the nominal alpha = 0.05 threshold to a number of promising candidate genes, SLC11A1 (PTST- p = 0.02), IL-1 complex (TB p = 0.01), IL12BR2 (TNFalpha p = 0.006), IL12A (TB p = 0.02) and IFNGR2 (TNFalpha p = 0.002). These results confirm not only that genetic factors influence the interaction between humans and Mtb but more importantly that they differ according to the outcome of that interaction: exposure but no infection, infection without progression to disease, or progression of infection to disease. Many of the genetic factors for each of these stages are part of the innate immune system. PMID:19116662

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

2008-01-01

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Genome scans and gene expression microarrays converge to identify gene regulatory loci relevant in schizophrenia  

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Multiple linkage regions have been reported in schizophrenia, and some appear to harbor susceptibility genes that are differentially expressed in postmortem brain tissue derived from unrelated individuals. We combined traditional genome-wide linkage analysis in a multiplex family with lymphocytic genome-wide expression analysis. A genome scan suggested linkage to a chromosome 4q marker (D4S1530, LOD 2.17, ?=0) using a dominant model. Haplotype analysis using flanking microsatellite markers d...

Vawter, Marquis P.; Atz, Mary E.; Rollins, Brandi L.; Cooper-casey, Kathleen M.; Shao, Ling; Byerley, William F.

2006-01-01

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Prioritizing genomic applications for action by level of evidence: a horizon-scanning method.  

Science.gov (United States)

As evidence accumulates on the use of genomic tests and other health-related applications of genomic technologies, decision makers may increasingly seek support in identifying which applications have sufficiently robust evidence to suggest they might be considered for action. As an interim working process to provide such support, we developed a horizon-scanning method that assigns genomic applications to tiers defined by availability of synthesized evidence. We illustrate an application of the method to pharmacogenomics tests. PMID:24398597

Dotson, W D; Douglas, M P; Kolor, K; Stewart, A C; Bowen, M S; Gwinn, M; Wulf, A; Anders, H M; Chang, C Q; Clyne, M; Lam, T K; Schully, S D; Marrone, M; Feero, W G; Khoury, M J

2014-04-01

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

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

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

2003-01-01

 
 
 
 
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Resampling methods to reduce the selection bias in genetic effect estimation in genome-wide scans  

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Abstract Using the simulated data of Problem 2 for Genetic Analysis Workshop 14 (GAW14), we investigated the ability of three bootstrap-based resampling estimators (a shrinkage, an out-of-sample, and a weighted estimator) to reduce the selection bias for genetic effect estimation in genome-wide linkage scans. For the given marker density in the preliminary genome scans (7 cM for microsatellite and 3 cM for SNP), we found that the two sets of markers produce comparable results in ter...

2005-01-01

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

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Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus?×?Brahman cattle crossbreds. We identified 24 POE–QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternall...

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

2011-01-01

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

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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.

Børglum Anders D

2011-07-01

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A Genome-wide Pleiotropy Scan for Prostate Cancer Risk  

DEFF Research Database (Denmark)

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

Panagiotou, Orestis A; Travis, Ruth C

2014-01-01

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

Science.gov (United States)

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

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

2010-09-01

26

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.

Wiuf Carsten

2009-07-01

27

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

28

Ordered Landmarks in Planning  

CERN Document Server

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

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

2011-01-01

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

International Nuclear Information System (INIS)

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

30

Genome scan for body mass index and height in the Framingham Heart Study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background Body mass index (BMI) and adult height are moderately and highly heritable traits, respectively. To investigate the genetic background of these quantitative phenotypes, we performed a linkage genome scan in the extended pedigrees of the Framingham Heart Study. Two variance-components approaches (SOLAR and MERLIN-VC) and one regression method (MERLIN-REGRESS) were applied to the data. Results Evidence for linkage to BMI was found on chromosome...

Görg Tilman; Dempfle Astrid; Geller Frank

2003-01-01

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Aberrant connectivity is implicated in many neurological and psychiatric disorders, including Alzheimer’s disease and schizophrenia. However, other than a few disease-associated candidate genes, we know little about the degree to which genetics play a role in the brain networks; we know even less about specific genes that influence brain connections. Twin and family-based studies can generate estimates of overall genetic influences on a trait, but genome-wide association scans (GWASs) can s...

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

2013-01-01

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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

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

Science.gov (United States)

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. PMID:22473089

Webb, Bradley T; Guo, An-Yuan; Maher, Brion S; Zhao, Zhongming; van den Oord, Edwin J; Kendler, Kenneth S; Riley, Brien P; Gillespie, Nathan A; Prescott, Carol A; Middeldorp, Christel M; Willemsen, Gonneke; de Geus, Eco Jc; Hottenga, Jouke-Jan; Boomsma, Dorret I; Slagboom, Eline P; Wray, Naomi R; Montgomery, Grant W; Martin, Nicholas G; Wright, Margie J; Heath, Andrew C; Madden, Pamela A; Gelernter, Joel; Knowles, James A; Hamilton, Steven P; Weissman, Myrna M; Fyer, Abby J; Huezo-Diaz, Patricia; McGuffin, Peter; Farmer, Anne; Craig, Ian W; Lewis, Cathryn; Sham, Pak; Crowe, Raymond R; Flint, Jonathan; Hettema, John M

2012-10-01

34

Whole genome scanning for mutations induced by chemical and physical mutagenes in barley  

International Nuclear Information System (INIS)

The presented research focuses on estimation of the types and frequencies of DNA changes induced by gamma rays and N-nitroso-N-methyl urea (MNU) in barley (Hordeum vulgare L.) genome. The analysis was performed in the M2 generation obtained after mutagenic treatment of doubled haploid (DH) line 'H930-36' with different doses of gamma rays (180, 210 Gy) and MNU (0.5, 1.0, 1.5 mM/3h). The main approach used in the study was the scanning of the whole genome for amplified fragment length polymorphism (AFLP). In the presented study, the combination of enzymes EcoRI/MseI and seven different primer combinations were used. The AFLP fragment sizes ranged from approximately 50 to 500 bp. The analysis was conducted on 1700 M2 plants derived from both populations. In all applied doses of mutagenes plants with changes in AFLP profile were observed. In total, 6,821 kb were scanned for AFLP polymorphism in the MNU treated population. Assuming that each polymorphic band (67 total) results from a single nucleotide change, this indicates 1 mutation per 102 kb. In gamma rays treated M2 population 5,600 kb barley genome sequence was scanned and only 18 polymorphic bands were detected, what corresponds to 1 mutation per 313 kb. The longest polymorphic AFLP bands were extracted from the polyacrylamide gels, cloned and sequenced. We found lack of homogeneity in all explored products. The NCBI database was used to find annotation for analyzed sequences. So far, the majority of investigated DNA fragment appear to be LTR retrotransposons. The repetitive sequences constitute the main part of barley genome. In order to determine the mutation type which caused an appearance of the additional band, the isolation of flanking regions was performed using thermal asymmetric interlaced (TAIL)-PCR method. (author)

35

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

DEFF Research Database (Denmark)

An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly, from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477-91). The latter was recently established when a causative coronavirus (SARS-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99% of all individuals of all major human populations (Sette & Sidney, Immunogenetics 1999: 50: 201-12). Foreach HLA supertype, we have selected the 15 top candidates for test in biochemical binding assays. At this time (approximately 2 6 months after the genome was established), we have tested the majority of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.

Nielsen, Morten; Lundegaard, Claus

2004-01-01

36

Genome scan meta-analysis of schizophrenia and bipolar disorder, part II: Schizophrenia.  

Science.gov (United States)

Schizophrenia is a common disorder with high heritability and a 10-fold increase in risk to siblings of probands. Replication has been inconsistent for reports of significant genetic linkage. To assess evidence for linkage across studies, rank-based genome scan meta-analysis (GSMA) was applied to data from 20 schizophrenia genome scans. Each marker for each scan was assigned to 1 of 120 30-cM bins, with the bins ranked by linkage scores (1 = most significant) and the ranks averaged across studies (R(avg)) and then weighted for sample size (N(sqrt)[affected casess]). A permutation test was used to compute the probability of observing, by chance, each bin's average rank (P(AvgRnk)) or of observing it for a bin with the same place (first, second, etc.) in the order of average ranks in each permutation (P(ord)). The GSMA produced significant genomewide evidence for linkage on chromosome 2q (PAvgRnk6q, 18q, 10p, 15q, 6q, and 17q. There is greater consistency of linkage results across studies than has been previously recognized. The results suggest that some or all of these regions contain loci that increase susceptibility to schizophrenia in diverse populations. PMID:12802786

Lewis, Cathryn M; Levinson, Douglas F; Wise, Lesley H; DeLisi, Lynn E; Straub, Richard E; Hovatta, Iiris; Williams, Nigel M; Schwab, Sibylle G; Pulver, Ann E; Faraone, Stephen V; Brzustowicz, Linda M; Kaufmann, Charles A; Garver, David L; Gurling, Hugh M D; Lindholm, Eva; Coon, Hilary; Moises, Hans W; Byerley, William; Shaw, Sarah H; Mesen, Andrea; Sherrington, Robin; O'Neill, F Anthony; Walsh, Dermot; Kendler, Kenneth S; Ekelund, Jesper; Paunio, Tiina; Lönnqvist, Jouko; Peltonen, Leena; O'Donovan, Michael C; Owen, Michael J; Wildenauer, Dieter B; Maier, Wolfgang; Nestadt, Gerald; Blouin, Jean-Louis; Antonarakis, Stylianos E; Mowry, Bryan J; Silverman, Jeremy M; Crowe, Raymond R; Cloninger, C Robert; Tsuang, Ming T; Malaspina, Dolores; Harkavy-Friedman, Jill M; Svrakic, Dragan M; Bassett, Anne S; Holcomb, Jennifer; Kalsi, Gursharan; McQuillin, Andrew; Brynjolfson, Jon; Sigmundsson, Thordur; Petursson, Hannes; Jazin, Elena; Zoëga, Tomas; Helgason, Tomas

2003-07-01

37

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

38

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

2011-12-01

39

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.

Regan Kelly R

2010-05-01

40

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.

Guimarães Simone EF

2010-04-01

 
 
 
 
41

Genome-Wide Association Scan for Variants Associated with Early-Onset Prostate Cancer  

Science.gov (United States)

Prostate cancer is the most common non-skin cancer and the second leading cause of cancer related mortality for men in the United States. There is strong empirical and epidemiological evidence supporting a stronger role of genetics in early-onset prostate cancer. We performed a genome-wide association scan for early-onset prostate cancer. Novel aspects of this study include the focus on early-onset disease (defined as men with prostate cancer diagnosed before age 56 years) and use of publically available control genotype data from previous genome-wide association studies. We found genome-wide significant (p<5×10?8) evidence for variants at 8q24 and 11p15 and strong supportive evidence for a number of previously reported loci. We found little evidence for individual or systematic inflated association findings resulting from using public controls, demonstrating the utility of using public control data in large-scale genetic association studies of common variants. Taken together, these results demonstrate the importance of established common genetic variants for early-onset prostate cancer and the power of including early-onset prostate cancer cases in genetic association studies. PMID:24740154

Lange, Ethan M.; Johnson, Anna M.; Wang, Yunfei; Zuhlke, Kimberly A.; Lu, Yurong; Ribado, Jessica V.; Keele, Gregory R.; Li, Jin; Duan, Qing; Li, Ge; Gao, Zhengrong; Li, Yun; Xu, Jianfeng; Isaacs, William B.; Zheng, Siqun; Cooney, Kathleen A.

2014-01-01

42

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.

Gut Ivo

2009-11-01

43

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.

Gasser Thomas

2007-07-01

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Genome-wide linkage scan of nonsyndromic orofacial clefting in 91 families of central European origin  

DEFF Research Database (Denmark)

Orofacial clefts are among the most common of all congenital disorders. Nonsyndromic cases of cleft lip with or without cleft palate (NSCL/P) and cleft palate only (NSCPO) are considered to have a multifactorial etiology which involves both genetic and environmental factors. We present the results of a genome-wide linkage scan in 91 families of central European descent with nonsyndromic orofacial clefts (NSC). The sample included 74 NSCL/P families, 15 NSCPO families, and 2 mixed families (a total of 217 affected and 230 unaffected individuals were genotyped). We genotyped 542 microsatellite markers (average intermarker distance = 6.9 cM). Multipoint nonparametric linkage analysis was performed using Allegro 2.0f. In addition to the factors investigated in previous genome-wide linkage analyses, we searched for sex-specific susceptibility loci, loci demonstrating parental imprinting and loci that are shared by NSCL/P and NSCPO. Several genomic regions likely to contain susceptibility loci for NSC were identified at the level of nominal significance. Some of these overlap with regions identified in previous studies. Suggestive evidence of linkage was obtained for the loci 4q21-q26 and 1p31-p21, with the chromosome 1 locus showing a male-specific genetic effect. Our study has identified promising chromosomal regions for the identification of NSC-associated genes, and demonstrates the importance of performing detailed statistical analyses which take into account complex genetic mechanisms such as sex-specific effects and genomic imprinting. Further research in large patient samples is necessary to identify factors common to NSCL/P and NSCPO.

Mangold, Elisabeth; Reutter, Heiko

2009-01-01

45

Ion Torrent sequencing for conducting genome-wide scans for mutation mapping analysis.  

Science.gov (United States)

Mutation mapping in mice can be readily accomplished by genome wide segregation analysis of polymorphic DNA markers. In this study, we showed the efficacy of Ion Torrent next generation sequencing for conducting genome-wide scans to map and identify a mutation causing congenital heart disease in a mouse mutant, Bishu, recovered from a mouse mutagenesis screen. The Bishu mutant line generated in a C57BL/6J (B6) background was intercrossed with another inbred strain, C57BL/10J (B10), and the resulting B6/B10 hybrid offspring were intercrossed to generate mutants used for the mapping analysis. For each mutant sample, a panel of 123 B6/B10 polymorphic SNPs distributed throughout the mouse genome was PCR amplified, bar coded, and then pooled to generate a single library used for Ion Torrent sequencing. Sequencing carried out using the 314 chip yielded >600,000 usable reads. These were aligned and mapped using a custom bioinformatics pipeline. Each SNP was sequenced to a depth >500×, allowing accurate automated calling of the B6/B10 genotypes. This analysis mapped the mutation in Bishu to an interval on the proximal region of mouse chromosome 4. This was confirmed by parallel capillary sequencing of the 123 polymorphic SNPs. Further analysis of genes in the map interval identified a splicing mutation in Dnaic1(c.204+1G>A), an intermediate chain dynein, as the disease causing mutation in Bishu. Overall, our experience shows Ion Torrent amplicon sequencing is high throughput and cost effective for conducting genome-wide mapping analysis and is easily scalable for other high volume genotyping analyses. PMID:24306492

Damerla, Rama Rao; Chatterjee, Bishwanath; Li, You; Francis, Richard J B; Fatakia, Sarosh N; Lo, Cecilia W

2014-04-01

46

Landmarks GIScience for intelligent services  

CERN Document Server

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

Richter, Kai-Florian

2014-01-01

47

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

2006-06-01

48

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 b...

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

2011-01-01

49

Genome-Wide Scan Identifies TNIP1, PSORS1C1, and RHOB as Novel Risk Loci for Systemic Sclerosis  

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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 ...

Cusi, Daniele Maria; Salvi, Erika

2011-01-01

50

Familial dyslexia in a large Swedish family: a whole genome linkage scan.  

Science.gov (United States)

There is a compelling body of evidence that developmental dyslexia runs in families and seems to be highly inheritable. Several investigations during the last two decades have shown possible locations of genes that might be involved in dyslexia, including regions of chromosomes 1, 2, 3, 6, 11, 13, 15 and 18. In addition, six candidate genes (KIAA0319, DYX1C1, DCDC2, ROBO1, MRPL19 and C2ORF3) seem to be related to dyslexia. The present study carried out a whole genome scan in a six-generation pedigree. In addition to literacy skills the assessment included cognitive skills and records concerning the history of reading and writing ability. Thirty-five percent were regarded as dyslexic in the family. A linkage analysis using both a quantitative and a qualitative approach has been performed. No evidence was obtained to support the hypothesis that the transmission of dyslexia in this pedigree is due to a highly penetrant major gene, and previous linkage findings were not replicated; however, power in this small study was not adequate to confirm linkage of genes with small to moderate effects. The results were discussed in relation to diagnostic procedures and sample characteristics. PMID:20862559

Svensson, Idor; Nilsson, Staffan; Wahlström, Jan; Jernås, Margareta; Carlsson, Lena M; Hjelmquist, Erland

2011-01-01

51

Acquistion of Structural versus Object Landmark Knowledge  

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Three experiments investigated the acquisition and retention of structural and object landmarks in virtual indoor environments. The experiments investigated the rate of acquisition and memory retention for hallway structure (structural landmarks) and pictures (object landmarks). The experiments investigated the rate of acquisition, the role of…

Stankiewicz, Brian J.; Kalia, Amy A.

2007-01-01

52

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

Science.gov (United States)

Genes for complex disorders have proven hard to find using linkage analysis. The results rarely reach the desired level of significance and researchers often have failed to replicate positive findings. There is, however, a wealth of information from other scientific approaches which enables the formation of hypotheses on groups of genes or genomic regions likely to be enriched in disease loci. Examples include genes belonging to specific pathways or producing proteins interacting with known risk factors, genes that show altered expression levels in patients or even the group of top scoring locations in a linkage study. We show here that this hypothesis of enrichment for disease loci can be tested using genome-wide linkage data, provided that these data are independent from the data used to generate the hypothesis. Our method is based on the fact that non-parametric linkage analyses are expected to show increased scores at each one of the disease loci, although this increase might not rise above the noise of stochastic variation. By using a summary statistic and calculating its empirical significance, we show that enrichment hypotheses can be tested with power higher than the power of the linkage scan data to identify individual loci. Via simulated linkage scans for a number of different models, we gain insight in the interpretation of genome scan results and test the power of our proposed method. We present an application of the method to real data from a late-onset Alzheimer's disease linkage scan as a proof of principle. PMID:16848972

Avramopoulos, Dimitrios; Zandi, Peter; Gherman, Adrian; Fallin, M Daniele; Bassett, Susan S

2006-06-01

53

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

Science.gov (United States)

Background Manual annotation of landmarks is a known source of variance, which exist in all fields of medical imaging, influencing the accuracy and interpretation of the results. However, the variability of human facial landmarks is only sparsely addressed in the current literature as opposed to e.g. the research fields of orthodontics and cephalometrics. We present a full facial 3D annotation procedure and a sparse set of manually annotated landmarks, in effort to reduce operator time and minimize the variance. Method Facial scans from 36 voluntary unrelated blood donors from the Danish Blood Donor Study was randomly chosen. Six operators twice manually annotated 73 anatomical and pseudo-landmarks, using a three-step scheme producing a dense point correspondence map. We analyzed both the intra- and inter-operator variability, using mixed-model ANOVA. We then compared four sparse sets of landmarks in order to construct a dense correspondence map of the 3D scans with a minimum point variance. Results The anatomical landmarks of the eye were associated with the lowest variance, particularly the center of the pupils. Whereas points of the jaw and eyebrows have the highest variation. We see marginal variability in regards to intra-operator and portraits. Using a sparse set of landmarks (n=14), that capture the whole face, the dense point mean variance was reduced from 1.92 to 0.54 mm. Conclusion The inter-operator variability was primarily associated with particular landmarks, where more leniently landmarks had the highest variability. The variables embedded in the portray and the reliability of a trained operator did only have marginal influence on the variability. Further, using 14 of the annotated landmarks we were able to reduced the variability and create a dense correspondences mesh to capture all facial features. PMID:25306436

2014-01-01

54

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

DEFF Research Database (Denmark)

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

Fagertun, Jens; Harder, Stine

2014-01-01

55

Genomic Scan Reveals Loci under Altitude Adaptation in Tibetan and Dahe Pigs  

Science.gov (United States)

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

Pu, Yabin; He, Xiaohong; Zhao, Qianjun; Luan, Yizhao; Guan, Weijun; Rao, Shaoqi; Ma, Yuehui

2014-01-01

56

Identification of Susceptibility Genes for Cancer in a Genome-wide Scan: Results from the Colon Neoplasia Sibling Study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in Americans and is the second leading cause of cancer mortality. Only a minority (?5%) of familial CRC can be explained by known genetic variants. To identify susceptibility genes for familial colorectal neoplasia, the colon neoplasia sibling study conducted a comprehensive, genome-wide linkage scan of 194 kindreds. Clinical information (histopathology, size and number of polyps, and other primary cancers) was used in conj...

Daley, Denise; Lewis, Susan; Platzer, Petra; Macmillen, Melissa; Willis, Joseph; Elston, Robert C.; Markowitz, Sanford D.; Wiesner, Georgia L.

2008-01-01

57

An evaluation of cellular neural networks for the automatic identification of cephalometric landmarks on digital images.  

Science.gov (United States)

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. PMID:19753320

Leonardi, Rosalia; Giordano, Daniela; Maiorana, Francesco

2009-01-01

58

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

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s or mutation(s targeted by selection. This shortcoming is hopefully bound to disappear in the near future, thanks to the wealth of new genomic resources that are currently being developed for many species. In this article, we provide a foretaste of this exciting new era by conducting a genome scan in the mosquito Aedes aegypti with the aim to look for candidate genes involved in resistance to Bacillus thuringiensis subsp. israelensis (Bti insecticidal toxins. Results The genome of a Bti-resistant and a Bti-susceptible strains was surveyed using about 500 MITE-based molecular markers, and the loci showing the highest inter-strain genetic differentiation were sequenced and mapped on the Aedes aegypti genome sequence. Several good candidate genes for Bti-resistance were identified in the vicinity of these highly differentiated markers. Two of them, coding for a cadherin and a leucine aminopeptidase, were further examined at the sequence and gene expression levels. In the resistant strain, the cadherin gene displayed patterns of nucleotide polymorphisms consistent with the action of positive selection (e.g. an excess of high compared to intermediate frequency mutations, as well as a significant under-expression compared to the susceptible strain. Conclusion Both sequence and gene expression analyses agree to suggest a role for positive selection in the evolution of this cadherin gene in the resistant strain. However, it is unlikely that resistance to Bti is conferred by this gene alone, and further investigation will be needed to characterize other genes significantly associated with Bti resistance in Ae. aegypti. Beyond these results, this article illustrates how genome scans can build on the body of new genomic information (here, full genome sequence and MITE characterization to finally hold their promises and help pinpoint candidate genes for adaptation and speciation.

David Jean-Philippe

2009-11-01

59

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

Science.gov (United States)

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

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

2014-12-01

60

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.

Carlborg Örjan

2007-11-01

 
 
 
 
61

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

Science.gov (United States)

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

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

2010-01-01

62

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

Directory of Open Access Journals (Sweden)

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

Avramopoulos Dimitrios

2006-06-01

63

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

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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.

Bidanel Jean P

2009-12-01

64

Whole-Genome Scan, in a Complex Disease, Using 11,245 Single-Nucleotide Polymorphisms: Comparison with Microsatellites  

Science.gov (United States)

Despite the theoretical evidence of the utility of single-nucleotide polymorphisms (SNPs) for linkage analysis, no whole-genome scans of a complex disease have yet been published to directly compare SNPs with microsatellites. Here, we describe a whole-genome screen of 157 families with multiple cases of rheumatoid arthritis (RA), performed using 11,245 genomewide SNPs. The results were compared with those from a 10-cM microsatellite scan in the same cohort. The SNP analysis detected HLA*DRB1, the major RA susceptibility locus (P=.00004), with a linkage interval of 31 cM, compared with a 50-cM linkage interval detected by the microsatellite scan. In addition, four loci were detected at a nominal significance level (P<.05) in the SNP linkage analysis; these were not observed in the microsatellite scan. We demonstrate that variation in information content was the main factor contributing to observed differences in the two scans, with the SNPs providing significantly higher information content than the microsatellites. Reducing the number of SNPs in the marker set to 3,300 (1-cM spacing) caused several loci to drop below nominal significance levels, suggesting that decreases in information content can have significant effects on linkage results. In contrast, differences in maps employed in the analysis, the low detectable rate of genotyping error, and the presence of moderate linkage disequilibrium between markers did not significantly affect the results. We have demonstrated the utility of a dense SNP map for performing linkage analysis in a late-age-at-onset disease, where DNA from parents is not always available. The high SNP density allows loci to be defined more precisely and provides a partial scaffold for association studies, substantially reducing the resource requirement for gene-mapping studies. PMID:15154113

John, Sally; Shephard, Neil; Liu, Guoying; Zeggini, Eleftheria; Cao, Manqiu; Chen, Wenwei; Vasavda, Nisha; Mills, Tracy; Barton, Anne; Hinks, Anne; Eyre, Steve; Jones, Keith W.; Ollier, William; Silman, Alan; Gibson, Neil; Worthington, Jane; Kennedy, Giulia C.

2004-01-01

65

Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping.  

Science.gov (United States)

Identifying the molecular bases of adaptation is a key issue in evolutionary biology. Genome scan is an efficient approach for identifying important molecular variation involved in adaptation. Association mapping also offers an opportunity to gain insight into genotype-phenotype relationships. Using these two approaches coupled with environmental data should help to come up with a refined picture of the evolutionary process underlying adaptation. In this study, we first conducted a selection scan analysis on a transcription factor gene family. We focused on the MADS-box gene family, a gene family which plays a crucial role in vegetative and flower development. Twenty-one pearl millet populations were sampled along an environmental gradient in West Africa. We identified one gene, i.e. PgMADS11, using Bayesian analysis to detect selection signatures. Polymorphism at this gene was also associated with flowering time variation in an association mapping framework. Finally, we found that PgMADS11 allele frequencies were closely associated with annual rainfall. Overall, we determined an efficient way to detect functional polymorphisms associated with climate variation in non-model plants by combining genome scan and association mapping. These results should help monitor the impact of recent climatic changes on plant adaptation. PMID:21050293

Mariac, Cédric; Jehin, Léa; Saïdou, Abdoul-Aziz; Thuillet, Anne-Céline; Couderc, Marie; Sire, Pierre; Jugdé, Hélène; Adam, Hélène; Bezançon, Gilles; Pham, Jean-Louis; Vigouroux, Yves

2011-01-01

66

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

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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.

Law Andrew

2011-01-01

67

MRI-based anatomical landmarks for the identification of thoracic vertebral levels  

International Nuclear Information System (INIS)

Aim: To identify soft-tissue and bony anatomical landmarks on dedicated thoracic spine magnetic resonance imaging (MRI), and to assess their detectability, reproducibility, and accuracy in predicting specific thoracic vertebral levels. Materials and methods: One hundred dedicated thoracic MRI studies were retrospectively analysed by two radiologists independently. Ten bone and soft-tissue landmarks were localized to the adjacent vertebral level. The true numerical thoracic vertebral level was subsequently determined and recorded by cross referencing with a sagittal cervico-thoracic “counting scan”. Results: Six landmarks were defined in ?98% cases; however, there was a low interobserver percentage agreement for the defined vertebral levels (>70% for only one landmark). The most useful landmark for defining a specific vertebral level was the most superior rib (98% detection, 95% interobserver agreement, 98% at a single vertebral level, 0.07 SD). Eight landmarks localized to a specific thoracic segment in only 16–44% of cases, with a standard deviation of >0.5 vertebral levels and with a range which was greater than four vertebral levels. Conclusion: The C2 vertebra must be identified and cross referenced to the dedicated thoracic spine MRI, as other MRI-based anatomical landmarks are unreliable in determining the correct thoracic vertebral level

68

Genome-wide scan to detect quantitative trait loci for milk urea nitrogen in Dutch Holstein Friesian cows  

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Studies have reported genetic variation in milk urea nitrogen (MUN) between cows, suggesting genetic differences in nitrogen efficiency between cows. In this paper, the results of a genome-wide scan to identify quantitative trait loci (QTL) that contribute to genetic variation in MUN and MUN yield are presented. Two to 3 morning milk samples were taken from 1,926 cows, resulting in 5,502 test-day records. Test-day records were corrected for systematic environmental effects using a repeatabili...

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

2010-01-01

69

Retrosplenial Cortex Codes for Permanent Landmarks  

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Landmarks are critical components of our internal representation of the environment, yet their specific properties are rarely studied, and little is known about how they are processed in the brain. Here we characterised a large set of landmarks along a range of features that included size, visual salience, navigational utility, and permanence. When human participants viewed images of these single landmarks during functional magnetic resonance imaging (fMRI), parahippocampal cortex (PHC) and retrosplenial cortex (RSC) were both engaged by landmark features, but in different ways. PHC responded to a range of landmark attributes, while RSC was engaged by only the most permanent landmarks. Furthermore, when participants were divided into good and poor navigators, the latter were significantly less reliable at identifying the most permanent landmarks, and had reduced responses in RSC and anterodorsal thalamus when viewing such landmarks. The RSC has been widely implicated in navigation but its precise role remains uncertain. Our findings suggest that a primary function of the RSC may be to process the most stable features in an environment, and this could be a prerequisite for successful navigation. PMID:22912894

Auger, Stephen D.; Mullally, Sinead L.; Maguire, Eleanor A.

2012-01-01

70

A Practical Subspace Approach To Landmarking  

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Full Text Available 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 implementation issues, in order to minimize storage and processing requirements. In particular a fast approximate singular value decomposition method is proposed to speed up the training process and implementation of the landmarker in the Fourier domain is presented that will speed up the search process. A subspace method for outlier correction and an iterative implementation of the landmarker are both shown to improve its accuracy. The impact of carefully tuning the many parameters of the method is illustrated. The method is extensively tested and compared with alternatives.

Gert Beumer

2010-06-01

71

Autonomous Robot Navigation based on Visual Landmarks  

DEFF Research Database (Denmark)

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

Livatino, Salvatore

72

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

Directory of Open Access Journals (Sweden)

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

Prasad Aparna

2010-03-01

73

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

Science.gov (United States)

Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin (http://www.genomeutwin.org) consortium consists of eight twin cohorts (Australian, Danish, Dutch, Finnish, Italian, Norwegian, Swedish, and United Kingdom) with the total resource of hundreds of thousands of twin pairs. We performed quantitative trait locus (QTL) analysis of one of the most heritable human complex traits, adult stature (body height) using genome-wide scans performed for 3,817 families (8,450 individuals) derived from twin cohorts from Australia, Denmark, Finland, Netherlands, Sweden, and United Kingdom with an approximate ten-centimorgan microsatellite marker map. The marker maps for different studies differed and they were combined and related to the sequence positions using software developed by us, which is publicly available (https://apps.bioinfo.helsinki.fi/software/cartographer.aspx). Variance component linkage analysis was performed with age, sex, and country of origin as covariates. The covariate adjusted heritability was 81% for stature in the pooled dataset. We found evidence for a major QTL for human stature on 8q21.3 (multipoint logarithm of the odds 3.28), and suggestive evidence for loci on Chromosomes X, 7, and 20. Some evidence of sex heterogeneity was found, however, no obvious female-specific QTLs emerged. Several cohorts contributed to the identified loci, suggesting an evolutionarily old genetic variant having effects on stature in European-based populations. To facilitate the genetic studies of stature we have also set up a website that lists all stature genome scans published and their most significant loci (http://www.genomeutwin.org/stature_gene_map.htm). PMID:17559308

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

2007-01-01

74

Identification of novel susceptibility loci for Guam neurodegenerative disease: challenges of genome scans in genetic isolates  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Amyotrophic lateral sclerosis/parkinsonism–dementia complex (ALS/PDC) is a fatal neurodegenerative disease found in the Chamorro people of Guam and other Pacific Island populations. The etiology is unknown, although both genetic and environmental factors appear important. To identify loci for ALS/PDC, we conducted both genome-wide linkage and association analyses, using approximately 400 microsatellite markers, in the largest sample assembled to date, comprising a nearly complete sample of ...

Sieh, Weiva; Choi, Yoonha; Chapman, Nicola H.; Craig, Ulla-katrina; Steinbart, Ellen J.; Rothstein, Joseph H.; Oyanagi, Kiyomitsu; Garruto, Ralph M.; Bird, Thomas D.; Galasko, Douglas R.; Schellenberg, Gerard D.; Wijsman, Ellen M.

2009-01-01

75

Genome Scanning for Conditionally Essential Genes in Salmonella enterica Serotype Typhimurium  

Science.gov (United States)

As more whole-genome sequences become available, there is an increasing demand for high-throughput methods that link genes to phenotypes, facilitating discovery of new gene functions. In this study, we describe a new version of the Tn-seq method involving a modified EZ:Tn5 transposon for genome-wide and quantitative mapping of all insertions in a complex mutant library utilizing massively parallel Illumina sequencing. This Tn-seq method was applied to a genome-saturating Salmonella enterica serotype Typhimurium mutant library recovered from selection under 3 different in vitro growth conditions (diluted Luria-Bertani [LB] medium, LB medium plus bile acid, and LB medium at 42°C), mimicking some aspects of host stressors. We identified an overlapping set of 105 protein-coding genes in S. Typhimurium that are conditionally essential under at least one of the above selective conditions. Competition assays using 4 deletion mutants (pyrD, glnL, recD, and STM14_5307) confirmed the phenotypes predicted by Tn-seq data, validating the utility of this approach in discovering new gene functions. With continuously increasing sequencing capacity of next generation sequencing technologies, this robust Tn-seq method will aid in revealing unexplored genetic determinants and the underlying mechanisms of various biological processes in Salmonella and the other approximately 70 bacterial species for which EZ:Tn5 mutagenesis has been established. PMID:22367088

Khatiwara, Anita; Jiang, Tieshan; Sung, Sam-Sun; Dawoud, Turki; Kim, Jeong Nam; Bhattacharya, Dhruva; Kim, Hee-Bal; Ricke, Steven C.

2012-01-01

76

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

Science.gov (United States)

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777 000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty-one significant regions (P feed efficiency, meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high-density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome. PMID:25183526

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

2014-12-01

77

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Hunter, David J.; Peltonen, Leena; Guiducci, Candace; Crawford, Gabriel; Hirschhorn, Joel N.; Lyon, Helen N.; Speliotes, Elizabeth K.

2009-01-01

78

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 identi...

Lindgren, C. M.; Heid, I. M.; Randall, J. C.; Lamina, C.; Steinthorsdottir, V.; Qi, L.; Speliotes, E. K.; Thorleifsson, G.; Willer, C. J.; Herrera, B. M.; Jackson, A. U.; Lim, N.; Scheet, P.; Soranzo, N.; Amin, N.

2009-01-01

79

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

LENUS (Irish Health Repository)

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

Anney, Richard

2010-10-15

80

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

Science.gov (United States)

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10?8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10?8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C. PMID:20663923

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

2010-01-01

 
 
 
 
81

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

82

Landmarks selection in street map design  

Science.gov (United States)

In Taiwan many electrical maps present their landmarks according to the category of the feature, a designer short of knowledge about mental representation of space, can cause the map to lose its communication effects. To resolve this map design problem, in this research through long-term memory recall, navigation and observation, and short-term memory processing 111 participants were asked to select the proper landmark from study area. The results reveal that in Taiwan convenience stores are the most popular local landmark in rural and urban areas. Their commercial signs have a unique design and bright color. Contrasted to their background, this makes the convenience store a salient feature. This study also developed a rule to assess the priority of the landmarks to design them in different scale maps.

Kao, C. J.

2014-02-01

83

75 FR 69120 - National Natural Landmark Designations  

Science.gov (United States)

...Landmarks: Big Bone Lick, Boone County, Kentucky; Cave Without a Name, Kendall County, Texas; Chazy Fossil Reef...e., Federal, State, county or municipal governments...located within the State of Kentucky, southwest of...

2010-11-10

84

A Bayesian latent class analysis for whole-genome association analyses: an illustration using the GAW15 simulated rheumatoid arthritis dense scan data  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Although rheumatoid arthritis, a chronic and inflammatory disease affecting numerous adults, has a complex genetic component involving the human leukocyte antigen region, additional genomic regions most likely affects susceptibility. Whole-genome scans may assist in identifying these additional candidate regions, but a large number of false-positives are likely to occur using traditional statistical methods. Therefore, novel statistical approaches are needed. Here, we used ...

Schumacher Fredrick R; Kraft Peter

2007-01-01

85

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

86

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

DEFF Research Database (Denmark)

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

Sahana, Goutam; Kadlecová, Veronika

2013-01-01

87

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

Directory of Open Access Journals (Sweden)

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

Velculescu Victor E

2008-04-01

88

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

Science.gov (United States)

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

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

2014-10-01

89

Genome scan in familial late-onset Alzheimer's disease: a locus on chromosome 6 contributes to age-at-onset.  

Science.gov (United States)

Alzheimer's disease (AD) is a common, genetically complex, fatal neurodegenerative disorder of late life. Although several genes are known to play a role in early-onset AD, identification of the genetic basis of late onset AD (LOAD) has been challenging, with only the APOE gene known to have a high contribution to both AD risk and age-at-onset. Here, we present the first genome-scan analysis of the complete, well-characterized University of Washington LOAD sample of 119 pedigrees, using age-at-onset as the trait of interest. The analysis approach used allows for a multilocus trait model while at the same time accommodating age censoring, effects of APOE as a known genetic covariate, and full pedigree and marker information. The results provide strong evidence for linkage of loci contributing to age-at-onset to genomic regions on chromosome 6q16.3, and to 19q13.42 in the region of the APOE locus. There was evidence for interaction between APOE and the locus on chromosome 6q and suggestive evidence for linkage to chromosomes 11p13, 15q12-14, and 19p13.12. These results provide the first independent confirmation of an AD age-at-onset locus on chromosome 6 and suggest that further efforts towards identifying the underlying causal locus or loci are warranted. PMID:23355194

Zhao, Wei; Marchani, Elizabeth E; Cheung, Charles Y K; Steinbart, Ellen J; Schellenberg, Gerard D; Bird, Thomas D; Wijsman, Ellen M

2013-03-01

90

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

Directory of Open Access Journals (Sweden)

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

Cordell Heather J

2007-12-01

91

Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multilocus analysis surpasses genome scan.  

Science.gov (United States)

Wild populations of Atlantic salmon have declined worldwide. While the causes for this decline may be complex and numerous, increased mortality at sea is predicted to be one of the major contributing factors. Examining the potential changes occurring in the genome-wide composition of populations during this migration has the potential to tease apart some of the factors influencing marine mortality. Here, we genotyped 5568 SNPs in Atlantic salmon populations representing two distinct regional genetic groups and across two cohorts to test for differential allelic and genotypic frequencies between juveniles (smolts) migrating to sea and adults (grilses) returning to freshwater after 1 year at sea. Given the complexity of the traits potentially associated with sea mortality, we contrasted the outcomes of a single-locus FST based genome scan method with a new multilocus framework to test for genetically based differential mortality at sea. While numerous outliers were identified by the single-locus analysis, no evidence for parallel, temporally repeated selection was found. In contrast, the multilocus approach detected repeated patterns of selection for a multilocus group of 34 covarying SNPs in one of the two populations. No significant pattern of selective mortality was detected in the other population, suggesting different causes of mortality among populations. These results first support the hypothesis that selection mainly causes small changes in allele frequencies among many covarying loci rather than a small number of changes in loci with large effects. They also point out that moving away from the a strict 'selective sweep paradigm' towards a multilocus genetics framework may be a more useful approach for studying the genomic signatures of natural selection on complex traits in wild populations. PMID:24845361

Bourret, Vincent; Dionne, Mélanie; Bernatchez, Louis

2014-09-01

92

Evolutionary change driven by metal exposure as revealed by coding SNP genome scan in wild yellow perch (Perca flavescens).  

Science.gov (United States)

Pollution can drive rapid evolutionary change in wild populations. This study targets functional polymorphisms of chronically metal-contaminated wild yellow perch (Perca flavescens). A de novo transcriptome scan contrasted subsets of individuals from clean (n = 16) and contaminated (n = 16) lakes to identify 87 candidate annotated coding SNPs. Candidate genotypes and liver [metal] were obtained in 10 populations (n = 1,052) and a genome scan distinguished outliers: one nuclear (cyclin G1 gene) and two mitochondrial (cytochrome b and NADH dehydrogenase subunit 2 genes) also displaying allelic correlation to mean population [cadmium]. Whole mtDNA and 17 kb surrounding cyclin G1 were characterised through 454 sequencing thus revealing two non-synonymous substitutions involving dissimilar amino acids. Based on associated functions and inter-population differentiation, contaminated perch may have been selected for fast life cycle completion (p53 pathway) and memorization impairment mitigation (long-term potentiation pathway). In accordance with predicted evolutionary trajectory for stressed and energy deprived organisms, adapted perch would not compensate for repair mechanism inhibition, instead reallocating energy towards growth and favouring inexpensive impairment mitigation adaptations over costly detoxification. Overall, 85 years of selection could have driven rapid, potentially adaptive evolution by selecting alleles increasing perch fitness in polluted environments. PMID:23722603

Bélanger-Deschênes, Sébastien; Couture, Patrice; Campbell, Peter G C; Bernatchez, Louis

2013-07-01

93

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

Directory of Open Access Journals (Sweden)

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

Bumstead Nat

2005-09-01

94

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

DEFF Research Database (Denmark)

BACKGROUND: ?Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. METHODS: ?We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used population genetics approaches to investigate genetic diversity and population structure and identify loci under selection. RESULTS: ?High genetic diversity (? = 2.4 × 10(-4)), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known drug-resistance loci, including pfcrt, pfdhps, pfmdr1, and pfgch1. CONCLUSIONS: ?The sequence variations observed at drug-resistance loci reflect differences in each country's historical use of antimalarial drugs and may be useful in formulating local malaria treatment guidelines.

Ocholla, Harold; Preston, Mark D

2014-01-01

95

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

96

Landmark advances in the development of erythropoietin.  

Science.gov (United States)

This is a Minireview covering landmarks or milestones in the development of erythropoietin (EPO). Thirty-nine landmark advances have been identified, which cover the period 1863-2003. Several reports are included that directly support these original landmark advances. This Minireview also updates some of the advances in EPO research since my last Minireview update on EPO published in this journal in 2003. The areas of EPO research updated are: sites of production; purification, assay and standardization; regulation; action; use in anemias; extraerythropoietic actions; adverse effects; and blood doping. The new reports on the use of EPO in the therapy of myocardial infarction; stroke and other neurological diseases; diabetic retinopathy and other retinal diseases are also covered. PMID:21127338

Fisher, James W

2010-12-01

97

Landmark papers on photorefractive nonlinear optics  

CERN Document Server

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

98

36 CFR 62.6 - Natural landmark monitoring.  

Science.gov (United States)

... false Natural landmark monitoring. 62.6 Section 62...62.6 Natural landmark monitoring. (a) Owner contact...Offices of the NPS maintain periodic contacts with the owners...Offices are responsible for monitoring the condition of,...

2010-07-01

99

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

Science.gov (United States)

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

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

2004-01-01

100

Efficient fine mapping of the naked caryopsis gene ( nud) by HEGS (High Efficiency Genome Scanning)/AFLP in barley.  

Science.gov (United States)

The hulled or naked caryopsis character of barley ( Hordeum vulgare L.) is an important trait for edibility and to follow its domestication process. A single recessive gene, nud, controls the naked caryopsis character, and is located on the long arm of chromosome 7H. To develop a fine map around the nud locus efficiently, the HEGS (High Efficiency Genome Scanning) electrophoresis system was combined with amplified fragment length polymorphism (AFLP). From bulked segregant analysis of 1,894 primer combinations, 12 AFLP fragments were selected as linked markers. For mapping, an F(2 )population of 151 individuals derived from a cross between Kobinkatagi (naked type) and Triumph (hulled type) was used. Seven AFLP markers were localized near the nud region. A fine map was developed with one-order higher resolution than before, along with the seven anchor markers. Among the seven linked AFLP markers (KT1-7), KT1, KT2 and KT6 were co-dominant, and the former two were detected for their single-nucleotide polymorphisms (SNPs) in the same length of fragments after electrophoresis with the non-denaturing gels of HEGS. The nud locus has co-segregated with KT3 and KT7, and was flanked by KT2 and KT4, at the 0.3-cM proximal and the 1.2-cM distal side, respectively. Four of these AFLP markers were converted into sequence-characterized amplified region (SCAR) markers, one of which was a dominant marker co-segregating with the nud gene. PMID:12942174

Kikuchi, S; Taketa, S; Ichii, M; Kawasaki, S

2003-12-01

 
 
 
 
101

Genome-wide linkage scans for loci affecting total cholesterol, HDL-C, and triglycerides: the Family Blood Pressure Program.  

Science.gov (United States)

Atherosclerosis accounts for 75% of all deaths from cardiovascular disease and includes coronary heart disease (CHD), stroke, and other diseases of the arteries. More than half of all CHD is attributable to abnormalities in levels and metabolism of lipids. To locate genes that affect total cholesterol, high density lipoprotein cholesterol (HDL-C), and triglycerides, genome-wide linkage scans for quantitative trait loci were performed using variance components methods as implemented in SOLAR on a large diverse sample recruited as part of the Family Blood Pressure Program. Phenotype and genetic marker data were available for 9,299 subjects in 2,953 families for total cholesterol, 8,668 subjects in 2,736 families for HDL, and 7,760 subjects in 2,499 families for triglycerides. Mean lipid levels were adjusted for the effects of sex, age, age2, age-by-sex interaction, body mass index, smoking status, and field center. HDL-C and triglycerides were further adjusted for average total alcoholic drinks per week and estrogen use. Significant linkage was found for total cholesterol on chromosome 2 (LOD=3.1 at 43 cM) in Hispanics and for HDL-C on chromosome 3 (LOD=3.0 at 182 cM) and 12 (LOD=3.5 at 124 cM) in Asians. In addition, there were 13 regions that showed suggestive linkage (LOD >or= 2.0); 7 for total cholesterol, 4 for HDL, and 2 for triglycerides. The identification of these loci affecting lipid phenotypes and the apparent congruence with previous linkage results provides increased support that these regions contain genes influencing lipid levels. PMID:16868761

Bielinski, Suzette J; Tang, Weihong; Pankow, James S; Miller, Michael B; Mosley, Thomas H; Boerwinkle, Eric; Olshen, Richard A; Curb, J David; Jaquish, Cashell E; Rao, D C; Weder, Alan; Arnett, Donna K

2006-10-01

102

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

Science.gov (United States)

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

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

1998-01-01

103

78 FR 49975 - Energy Conservation Program for Consumer Products: Landmark Legal Foundation; Petition for...  

Science.gov (United States)

...the Landmark Legal Foundation. [[Page 49976...Reconsideration Landmark Legal Foundation (``Landmark...and existing power plants. See Justin Sink...Power Co. v. Nuclear Regulatory Com...everything from power plants to the Keystone...President Landmark Legal Foundation, 19415...

2013-08-16

104

Genome Scan for Loci Predisposing to Anxiety Disorders Using a Novel Multivariate Approach: Strong Evidence for a Chromosome 4 Risk Locus  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We conducted a 10-centimorgan linkage autosomal genome scan in a set of 19 extended American pedigrees (219 subjects) ascertained through probands with panic disorder. Several anxiety disorders—including social phobia, agoraphobia, and simple phobia—in addition to panic disorder segregate in these families. In previous studies of this sample, linkage analyses were based separately on each of the individual categorical affection diagnoses. Given the substantial comorbidity between anxiety ...

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

2006-01-01

105

A Genome Scan to Detect Quantitative Trait Loci for Economically Important Traits in Holstein Cattle Using Two Methods and a Dense Single Nucleotide Polymorphism Map  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Genome scans for detection of bovine quantitative trait loci (QTL) were performed via variance component linkage analysis and linkage disequilibrium single-locus regression (LDRM). Four hundred eighty-four Holstein sires, of which 427 were from 10 grandsire families, were genotyped for 9,919 single nucleotide polymorphisms (SNP) using the Affymetrix MegAllele GeneChip Bovine Mapping 10K SNP array. A hybrid of the granddaughter and selective genotyping designs was applied. Four thousand eight ...

Daetwyler, H. D.; Schenkel, F. S.; Sargolzaei, M.; Robinson, J. A. B.

2008-01-01

106

Robust Anatomical Landmark Detection for MR Brain Image Registration  

Science.gov (United States)

Correspondence matching between MR brain images is often challenging due to large inter-subject structural variability. In this paper, we propose a novel landmark detection method for robust establishment of correspondences between subjects. Specifically, we first annotate distinctive landmarks in the training images. Then, we use regression forest to simultaneously learn (1) the optimal set of features to best characterize each landmark and (2) the non-linear mappings from local patch appearances of image points to their displacements towards each landmark. The learned regression forests are used as landmark detectors to predict the locations of these landmarks in new images. Since landmark detection is performed in the entire image domain, our method can cope with large anatomical variations among subjects. We evaluated our method by applying it to MR brain image registration. Experimental results indicate that by combining our method with existing registration method, obvious improvement in registration accuracy can be achieved. PMID:25333117

Han, Dong; Gao, Yaozong; Wu, Guorong; Yap, Pew-Thian; Shen, Dinggang

2014-01-01

107

Navigation with two landmarks in rats (Rattus norvegicus): The role of landmark salience.  

Science.gov (United States)

In two experiments, male and female rats were trained in a Morris pool in the presence of 1 (Experiment 1) or 2 (Experiment 2) landmarks, which were placed relatively close in relation to a hidden platform. Experiment 1 established the relative salience of 3 landmarks. Two of them revealed a similar salience, and smaller than a third one, the most salient landmark, both in training and on a test trial without the platform. Then in Experiment 2 rats were extensively trained to find a hidden platform in the presence of a configuration formed by 2 landmarks and the effects of varying the salience of one of the landmarks were studied. Subsequent test trials without the platform revealed that finding the platform was controlled by different strategies and that the rats were taking advantage of this redundancy depending on the nature of the test trials. Surprisingly, in Experiment 2 a clear sex difference was found on escape trials only, with males reaching the platform faster than females. (PsycINFO Database Record (c) 2014 APA, all rights reserved). PMID:24749502

Rodrigo, Teresa; Gimeno, Elisabet; Ayguasanosa, Meritxell; Chamizo, Victoria D

2014-11-01

108

Identification of susceptibility genes for cancer in a genome-wide scan: results from the colon neoplasia sibling study.  

Science.gov (United States)

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in Americans and is the second leading cause of cancer mortality. Only a minority ( approximately 5%) of familial CRC can be explained by known genetic variants. To identify susceptibility genes for familial colorectal neoplasia, the colon neoplasia sibling study conducted a comprehensive, genome-wide linkage scan of 194 kindreds. Clinical information (histopathology, size and number of polyps, and other primary cancers) was used in conjunction with age at onset and family history for classification of the families into five phenotypic subgroups (severe histopathology, oligopolyposis, young, colon/breast, and multiple cancer) prior to analysis. By expanding the traditional affected-sib-pair design to include unaffected and discordant sib pairs, analytical power and robustness to type I error were increased. Sib-pair linkage statistics and Haseman-Elston regression identified 19 linkage peaks, with interesting results for chromosomes 1p31.1, 15q14-q22, 17p13.3, and 21. At marker D1S1665 (1p31.1), there was strong evidence for linkage in the multiple-cancer subgroup (p = 0.00007). For chromosome 15q14-q22, a linkage peak was identified in the full-sample (p = 0.018), oligopolyposis (p = 0.003), and young (p = 0.0009) phenotypes. This region includes the HMPS/CRAC1 locus associated with hereditary mixed polyposis syndrome (HMPS) in families of Ashkenazi descent. We provide compelling evidence linking this region in families of European descent with oligopolyposis and/or young age at onset (

Daley, Denise; Lewis, Susan; Platzer, Petra; MacMillen, Melissa; Willis, Joseph; Elston, Robert C; Markowitz, Sanford D; Wiesner, Georgia L

2008-03-01

109

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

Science.gov (United States)

As part of an extensive study in the Portuguese Island population of families with multiple patients suffering from bipolar disorder and schizophrenia, we performed an initial genome-wide scan of 16 extended families with bipolar disorder that identified three regions on chromosomes 2, 11, and 19 with genome-wide suggestive linkage and several other regions, including chromosome 6q, also approached suggestive levels of significance. Dick et al. [2003: Am J Hum Genet 73:107-114] recently reported in a study of 250 families with bipolar disorder a maxLOD score of 3.61 near marker D6S1021 on chromosome 6q. This study replicates this finding having detected a peak NPL = 2.02 (P = 0.025) with the same marker D6S1021(104.7 Mb). Higher-density mapping provided additional support for loci on chromosome 6 including marker D6S1021 with an NPL = 2.59 (P = 0.0068) and peaking at marker D6S1639 (125 Mb) with an NPL = 3.06 (P = 0.0019). A similar pattern was detected with higher-density mapping of chromosome 11 with an NPL = 3.15 (P = 0.0014) at marker D11S1883 (63.1 Mb). Simulations at the density of our fine mapping data indicate that less than 1 scan out of 10 would find two such scores genome-wide in the same scan by chance. Our findings provide additional support for a susceptibility locus for bipolar disorder on 6q, as well as, suggesting the importance of denser scans. Published 2004 Wiley-Liss, Inc. PMID:15108176

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

2004-05-15

110

The behavioural relevance of landmark texture for honeybee homing  

Directory of Open Access Journals (Sweden)

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

LauraDittmar

2011-04-01

111

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

2012-12-01

112

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 a...

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.

2013-01-01

113

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

114

Concurrent map building and localization with landmark validation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Andrade Cetto, Juan; Sanfeliu Corte?s, Alberto

2002-01-01

115

Detection of natural landmarks through multiscale opponent features  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Todt, Eduardo; Torras Geni?s, Carme

2000-01-01

116

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

A genome-wide scan was performed to identify quantitative trait loci (QTL) for short- and medium-chain fatty acids (expressed in wt/wt %). Milk samples were available from 1,905 cows from 398 commercial herds in the Netherlands, and milk-fat composition was measured by gas chromatography. DNA was available from 7 of the paternal half-sib families: 849 cows and their 7 sires. A genetic map was constructed comprising 1,341 SNP and 2,829 cM, with an average information content of 0.83. Multimark...

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

2009-01-01

117

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present the results of a genome-wide scan to identify quantitative trait loci (QTL) that contribute to genetic variation in long-chain milk fatty acids. Milk-fat composition phenotypes were available on 1,905 Dutch Holstein-Friesian cows. A total of 849 cows and their 7 sires were genotyped for 1,341 single nucleotide polymorphisms across all Bos taurus autosomes (BTA). We detected significant QTL on BTA14, BTA15, and BTA16: for C18:1 cis-9, C18:1 cis-12, C18:2 cis-9,12, CLA cis-9,trans-11...

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

2009-01-01

118

Landmark vs. Geometry Learning: Explaining Female Rats' Selective Preference for a Landmark  

Science.gov (United States)

Rats were trained in a triangular-shaped pool to find a hidden platform, whose location was defined in terms of two sources of information, a landmark outside the pool and a particular corner of the pool. Subsequent test trials without the platform pitted these two sources of information against one another. In Experiment 1 this test revealed a…

Torres, Marta N.; Rodríguez, Clara A.; Chamizo, V. D.; Mackintosh, N. J.

2014-01-01

119

Active shape models incorporating isolated landmarks for medical image annotation  

Science.gov (United States)

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

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

2014-03-01

120

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

Directory of Open Access Journals (Sweden)

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

Moradi Mohammad Hossein

2012-02-01

 
 
 
 
121

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

2007-01-01

122

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

123

Genetics of Type 2 Diabetes and Metabolic Syndrome: From Genome Wide Linkage Scan and Candidate Genes to Genome Wide Association Studies  

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Type 2 diabetes (T2D) and metabolic syndrome (MetS) are major health problems associated with cardiovascular disease. Both diseases are influenced by a combination of genetic and environmental factors. The aim of this thesis was to identify genetic risk factors for T2D, particularly T2D associated with obesity, and for MetS. To achieve this goal, we 1) followed-up a region linked to obese T2D in an earlier genome wide linkage study; 2) studied IRS1 as a candidate gene for T2D and MetS and 3) ...

Sjo?gren, Marketa

2008-01-01

124

A genome scan for familial combined hyperlipidemia reveals evidence of linkage with a locus on chromosome 11.  

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Familial combined hyperlipidemia (FCHL) is a common familial lipid disorder characterized by a variable pattern of elevated levels of plasma cholesterol and/or triglycerides. It is present in 10%-20% of patients with premature coronary heart disease. The genetic etiology of the disease, including the number of genes involved and the magnitude of their effects, is unknown. Using a subset of 35 Dutch families ascertained for FCHL, we screened the genome, with a panel of 399 genetic markers, for...

Aouizerat, B. E.; Allayee, H.; Cantor, R. M.; Davis, R. C.; Lanning, C. D.; Wen, P. Z.; Dallinga-thie, G. M.; Bruin, T. W.; Rotter, J. I.; Lusis, A. J.

1999-01-01

125

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

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Abstract Genes for complex disorders have proven hard to find using linkage analysis. The results rarely reach the desired level of significance and researchers often have failed to replicate positive findings. There is, however, a wealth of information from other scientific approaches which enables the formation of hypotheses on groups of genes or genomic regions likely to be enriched in disease loci. Examples include genes belonging to specific pathways or producing proteins inter...

Avramopoulos Dimitrios; Zandi Peter; Gherman Adrian; Fallin M; Bassett Susan S

2006-01-01

126

MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans  

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Full Text Available Abstract Background MicroRNAs (miRNAs are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hundreds of miRNAs have been identified by direct cloning and computational approaches in several species. However, there are still many miRNAs that remain to be identified due to lack of either sequence features or robust algorithms to efficiently identify them. Results We have evaluated features valuable for pre-miRNA prediction, such as the local secondary structure differences of the stem region of miRNA and non-miRNA hairpins. We have also established correlations between different types of mutations and the secondary structures of pre-miRNAs. Utilizing these features and combining some improvements of the current pre-miRNA prediction methods, we implemented a computational learning method SVM (support vector machine to build a high throughput and good performance computational pre-miRNA prediction tool called MiRFinder. The tool was designed for genome-wise, pair-wise sequences from two related species. The method built into the tool consisted of two major steps: 1 genome wide search for hairpin candidates and 2 exclusion of the non-robust structures based on analysis of 18 parameters by the SVM method. Results from applying the tool for chicken/human and D. melanogaster/D. pseudoobscura pair-wise genome alignments showed that the tool can be used for genome wide pre-miRNA predictions. Conclusion The MiRFinder can be a good alternative to current miRNA discovery software. This tool is available at http://www.bioinformatics.org/mirfinder/.

Li Kui

2007-09-01

127

A genome-wide SNP scan reveals novel loci for egg production and quality traits in white leghorn and brown-egg dwarf layers.  

Science.gov (United States)

Availability of the complete genome sequence as well as high-density SNP genotyping platforms allows genome-wide association studies (GWAS) in chickens. A high-density SNP array containing 57,636 markers was employed herein to identify associated variants underlying egg production and quality traits within two lines of chickens, i.e., White Leghorn and brown-egg dwarf layers. For each individual, age at first egg (AFE), first egg weight (FEW), and number of eggs (EN) from 21 to 56 weeks of age were recorded, and egg quality traits including egg weight (EW), eggshell weight (ESW), yolk weight (YW), eggshell thickness (EST), eggshell strength (ESS), albumen height(AH) and Haugh unit(HU) were measured at 40 and 60 weeks of age. A total of 385 White Leghorn females and 361 brown-egg dwarf dams were selected to be genotyped. The genome-wide scan revealed 8 SNPs showing genome-wise significant (P<1.51E-06, Bonferroni correction) association with egg production and quality traits under the Fisher's combined probability method. Some significant SNPs are located in known genes including GRB14 and GALNT1 that can impact development and function of ovary, but more are located in genes with unclear functions in layers, and need to be studied further. Many chromosome-wise significant SNPs were also detected in this study and some of them are located in previously reported QTL regions. Most of loci detected in this study are novel and the follow-up replication studies may be needed to further confirm the functional significance for these newly identified SNPs. PMID:22174844

Liu, Wenbo; Li, Dongfeng; Liu, Jianfeng; Chen, Sirui; Qu, Lujiang; Zheng, Jiangxia; Xu, Guiyun; Yang, Ning

2011-01-01

128

Evolution of the pygmy phenotype: evidence of positive selection fro genome-wide scans in African, Asian, and Melanesian pygmies.  

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Human pygmy populations inhabit different regions of the world, from Africa to Melanesia. In Asia, short-statured populations are often referred to as "negritos." Their short stature has been interpreted as a consequence of thermoregulatory, nutritional, and/or locomotory adaptations to life in tropical forests. A more recent hypothesis proposes that their stature is the outcome of a life history trade-off in high-mortality environments, where early reproduction is favored and, consequently, early sexual maturation and early growth cessation have coevolved. Some serological evidence of deficiencies in the growth hormone/insulin-like growth factor axis have been previously associated with pygmies' short stature. Using genome-wide single-nucleotide polymorphism genotype data, we first tested whether different negrito groups living in the Philippines and Papua New Guinea are closely related and then investigated genomic signals of recent positive selection in African, Asian, and Papuan pygmy populations. We found that negritos in the Philippines and Papua New Guinea are genetically more similar to their nonpygmy neighbors than to one another and have experienced positive selection at different genes. These results indicate that geographically distant pygmy groups are likely to have evolved their short stature independently. We also found that selection on common height variants is unlikely to explain their short stature and that different genes associated with growth, thyroid function, and sexual development are under selection in different pygmy groups. PMID:24297229

Migliano, Andrea Bamberg; Romero, Irene Gallego; Metspalu, Mait; Leavesley, Matthew; Pagani, Luca; Antao, Tiago; Huang, Da-Wei; Sherman, Brad T; Siddle, Katharine; Scholes, Clarissa; Hudjashov, Georgi; Kaitokai, Elton; Babalu, Avis; Belatti, Maggie; Cagan, Alex; Hopkinshaw, Byrony; Shaw, Colin; Nelis, Mari; Metspalu, Ene; Mägi, Reedik; Lempicki, Richard A; Villems, Richard; Lahr, Marta Mirazon; Kivisild, Toomas

2013-01-01

129

DETEKSI LANDMARK CITRA WAJAH DENGAN EXTRAKSI FITUR GABOR ANALISA FUZZY  

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Full Text Available This paper proposes a method that automatically finds human faces as well as its landmark points in color images based on a fuzzy analysis. The proposed approach first uses color information to detect face candidate regions and then uses a fuzzy analysis of the color, shape, symmetry and interior facial features. A deformable Gabor wavelet graph matching is used to locate the facial landmark points describing the face. The latter allows for size and orientation variation since the search for landmark points allows for affine transformations as well as local deformations of the Gabor wavelet graph. The search is performed using a genetic algorithm that is essential because it effectively searches the solution space. Results based on the proposed method are included to verify the effectiveness of the proposed approach. Abstract in Bahasa Indonesia : Paper ini mengusulkan sebuah metode deteksi wajah beserta dengan titik landmarknya pada citra berwarna menggunakan analisa fuzzy. Proses awal menggunakan informasi warna kulit untuk menseleksi calon-calon obyek lantas dilanjukan dengan analisa fuzzy terhadap warna, bentuk, simetri dan fitur/landmark wajah. Proses lokalisasi landmark wajah menggunakan Gabor wavelet graph matching dengan memaksimalkan kemiripan antara landmark wajah model dengan obyek inputan. Proses maksimalisasi kemiripan ini menggunakan algoritma genetika. Hasil-hasil percobaan ditampilkan untuk memberikan gambaran keberhasilan dari metode yang diusulkan. Kata kunci: lokalisasi landmark wajah, analisa fuzzy, graph matching, algoritma genetika, Gabor wavelet.

Resmana Lim

2003-01-01

130

Landmarks and ant search strategies after interrupted tandem runs.  

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During a tandem run, a single leading ant recruits a single follower to an important resource such as a new nest. To examine this process, we used a motorized gantry, which has not previously been used in ant studies, to track tandem running ants accurately in a large arena and we compared their performance in the presence of different types of landmark. We interrupted tandem runs by taking away the leader and moved a large distant landmark behind the new nest just at the time of this separation. Our aim was to determine what information followers might have obtained from the incomplete tandem run they had followed, and how they behaved after the tandem run had been interrupted. Our results show that former followers search by using composite random strategies with elements of sub-diffusive and diffusive movements. Furthermore, when we provided more landmarks former followers searched for longer. However, when all landmarks were removed completely from the arena, the ants' search duration lasted up to four times longer. Hence, their search strategy changes in the presence or absence of landmarks. Even after extensive search of this kind, former followers headed back to their old nest but did not return along the path of the tandem run they had followed. The combination of the position to which the large distant landmark behind the new nest was moved and the presence or absence of additional landmarks influenced the orientation of the former followers' paths back to the old nest. We also found that these ants exhibit behavioural lateralization in which they possibly use their right eye more than their left eye to recognize landmarks for navigation. Our results suggest that former follower ants learn landmarks during tandem running and use this information to make strategic decisions. PMID:24198259

Basari, Norasmah; Bruendl, Aisha C; Hemingway, Charlotte E; Roberts, Nicholas W; Sendova-Franks, Ana B; Franks, Nigel R

2014-03-15

131

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

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

N. Ivalú Cacho

2013-07-01

132

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

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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, Henriette Svarre

2011-01-01

133

Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus.  

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The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here, we combine genome scans, population genetics and sequence-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear colour)- and Andean (white colour)-derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world's most diverse and iconic ecosystems. PMID:22512735

Cooke, Georgina M; Chao, Ning L; Beheregaray, Luciano B

2012-05-01

134

A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number.  

Science.gov (United States)

A genome-wide scan to detect evidence of selection was conducted in the Golden Glow maize long-term selection population. The population had been subjected to selection for increased number of ears per plant for 30 generations, with an empirically estimated effective population size ranging from 384 to 667 individuals and an increase of more than threefold in the number of ears per plant. Allele frequencies at >1.2 million single-nucleotide polymorphism loci were estimated from pooled whole-genome resequencing data, and FST values across sliding windows were employed to assess divergence between the population preselection and the population postselection. Twenty-eight highly divergent regions were identified, with half of these regions providing gene-level resolution on potentially selected variants. Approximately 93% of the divergent regions do not demonstrate a significant decrease in heterozygosity, which suggests that they are not approaching fixation. Also, most regions display a pattern consistent with a soft-sweep model as opposed to a hard-sweep model, suggesting that selection mostly operated on standing genetic variation. For at least 25% of the regions, results suggest that selection operated on variants located outside of currently annotated coding regions. These results provide insights into the underlying genetic effects of long-term artificial selection and identification of putative genetic elements underlying number of ears per plant in maize. PMID:24381334

Beissinger, Timothy M; Hirsch, Candice N; Vaillancourt, Brieanne; Deshpande, Shweta; Barry, Kerrie; Buell, C Robin; Kaeppler, Shawn M; Gianola, Daniel; de Leon, Natalia

2014-03-01

135

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

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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.

Conord Cyrille

2009-12-01

136

Genome-Wide Scan of the Gene Expression Kinetics of Salmonella enterica Serovar Typhi during Hyperosmotic Stress  

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Full Text Available Salmonella enterica serovar Typhi is a human enteroinvasive pathogen that canovercome the stress caused by the high osmolarity of the human small intestine and causesystemic infection. To investigate the global transcriptional regulations of S. entericaserovar Typhi exposed to a hyperosmotic environment, a genomic oligo-DNA microarraycontaining 4474 Salmonella genes was prepared. A wild strain of S. enterica serovar TyphiGIFU10007 was grown in LB medium containing 50 mM NaCl to simulate a low osmoticenvironment. The hyperosmotic stress was simulated by an osmotic up-shift, whichincreased the concentration of NaCl in the LB from 50 mM to 300 mM. Genome-wide geneexpressions of S. enterica serovar Typhi at 15 min, 30 min, 60 min, and 120 min after theosmotic up-shift were investigated by the microarray analysis. Gene expression profiles insomewhat later stage (60 ~120 min of the stress were quite different from those in the earlystage (0 ~ 30 min of the stress. At 120 min after the osmotic stress, the expression levels of889 genes were obviously changed. However, expression levels of only 382 genes weresignificantly changed at 15 min after the osmotic stress. The expression levels of most SPI-1genes associated with invasion of the pathogen were increased at 120 min after the osmoticup-shift, but were not obviously changed at 15 min or 30 min after the osmotic stress.Expressions of a central regulatory gene, phoP, and sigma factor genes rpoE, rpoD, andrpoS were also changed with different profiles during the osmotic stress. These resultsindicated that the invasive ability of the pathogen is significantly increased after 2 h of hyperosmotic stress, and regulator PhoP and sigma factors RpoE, RpoD appear to participate in the network regulatory mechanisms that benefit the pathogen to adapt hyperosmotic environmental conditions. The later increased invasive ability of S. enterica serovar Typhi after hyperosmotic stress may be one reason why the pathogen performs invading in the distal ileum of human and not in areas of the upper small intestine.

Takayuki Ezaki

2007-02-01

137

Automatic Evaluation of Landmarks for Image-Based Navigation Update  

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

Stefan Lang

2009-01-01

138

Route and landmark selection tool (RULST) : user's manual.; TOPICAL  

International Nuclear Information System (INIS)

The Route and Landmark Selection Tool (RULST) is a software program designed to assist military planners in defining geographical objects, such as routes, landmarks, spurs, and yards, at a given facility. Argonne National Laboratory is currently developing a prototype of this tool for use by the Military Traffic Management Command Transportation Engineering Agency (MTMCTEA). The primary objective of RULST is to populate database tables of facility objects for use in MTMCTEA models. RULST defines facility data for use in models such as Port Simulation (PORTSIM) and Transportation System Capability (TRANSCAP), which simulate the transportation of equipment through ports and military installations. The main purpose of RULST is to allow you to specify the relationships between landmarks and routes. The nodes, links, and landmarks that describe a facility are often predefined on the basis of the layout of the physical site

139

36 CFR 65.5 - Designation of National Historic Landmarks.  

Science.gov (United States)

...property with multiple ownership it...appropriate. In making its recommendation...finds that the criteria of the landmarks...based on the criteria set forth herein, makes a decision on National Historic...properties with multiple...

2010-07-01

140

A genome scan for familial combined hyperlipidemia reveals evidence of linkage with a locus on chromosome 11.  

Science.gov (United States)

Familial combined hyperlipidemia (FCHL) is a common familial lipid disorder characterized by a variable pattern of elevated levels of plasma cholesterol and/or triglycerides. It is present in 10%-20% of patients with premature coronary heart disease. The genetic etiology of the disease, including the number of genes involved and the magnitude of their effects, is unknown. Using a subset of 35 Dutch families ascertained for FCHL, we screened the genome, with a panel of 399 genetic markers, for chromosomal regions linked to genes contributing to FCHL. The results were analyzed by use of parametric-linkage methods in a two-stage study design. Four loci, on chromosomes 2p, 11p, 16q, and 19q, exhibited suggestive evidence for linkage with FCHL (LOD scores of 1.3-2.6). Markers within each of these regions were then examined in the original sample and in additional Dutch families with FCHL. The locus on chromosome 2 failed to show evidence for linkage, and the loci on chromosome 16q and 19q yielded only equivocal or suggestive evidence for linkage. However, one locus, near marker D11S1324 on the short arm of human chromosome 11, continued to show evidence for linkage with FCHL, in the second stage of this design. This region does not contain any strong candidate genes. These results provide evidence for a candidate chromosomal region for FCHL and support the concept that FCHL is complex and heterogeneous. PMID:10417282

Aouizerat, B E; Allayee, H; Cantor, R M; Davis, R C; Lanning, C D; Wen, P Z; Dallinga-Thie, G M; de Bruin, T W; Rotter, J I; Lusis, A J

1999-01-01

 
 
 
 
141

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

Science.gov (United States)

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

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

2014-01-01

142

3D face analysis : landmarking, expression recognition and beyond  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This Ph.D thesis work is dedicated to automatic facial analysis in 3D, including facial landmarking and facial expression recognition. Indeed, facial expression plays an important role both in verbal and non verbal communication, and in expressing emotions. Thus, automatic facial expression recognition has various purposes and applications and particularly is at the heart of "intelligent" human-centered human/computer(robot) interfaces. Meanwhile, automatic landmarking provides aprior knowled...

Zhao, Xi

2010-01-01

143

Detecting corpus callosum abnormalities in autism based on anatomical landmarks  

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Autism is a severe developmental disorder whose neurological basis is largely unknown. Autism is a subtype of autism that displays more homogeneous features within group. The aim of this study was to identify the shape differences of the corpus callosum between patients with autism and the controls. Anatomical landmarks were collected from mid-sagittal MRI of 25 patients and 18 controls. Euclidean distance matrix analysis and thin-plate spline were used to analyze the landmark forms. Point-by...

Duan, Ye; Karsch, Kevin; Miles, Judith

2010-01-01

144

Indoor Localization System based on Artificial Landmarks and Monocular Vision  

Directory of Open Access Journals (Sweden)

Full Text Available This paper presents a visual localization approach well suited for the domestic and industrial environments due to its ability to provide an accurate, reliable and robust pose estimation.The mobile robot is equipped with a single camera to update their pose whenever a landmark is available on the field of view.The innovation presented by this research focus, especially, on the artificial landmark that has the ability to detect the presence of the robot, sinceboth entities communicates with each other using an infrared signal protocol modulated in frequency. Besides this communication ability, each landmark has several high intensity light-emitting diodes (leds that shine only for some instances according with the communication, which enables a synchronization between the camera shutter and the blinking of leds. This synchronization increases the system tolerance concerning to the changes in brightness of the ambient lights over time, independently of the landmarks location. The environment’s ceiling is populated with theselandmarks and an Extended Kalman Filter is usedto combine the dead-reckoning and landmark information. This increases the flexibility of the system by reducing the number of landmarks needed. The experimental evaluation of the proposed system was conducted in a real indoor environment with an autonomous wheelchair prototype.

Paulo G. Costa

2012-12-01

145

Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia.  

Science.gov (United States)

Despite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high- versus low-altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed using both D' and r(2) between adjacent SNPs. We calculated FST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between high- and low-altitude populations following the hierarchical island model approach. We identified 816 loci (p genes that might have roles in local adaptation. Some of them are associated with candidate genes that are involved in metabolism (ATP2A3, CA2, MYO18B, SIK3, INPP4A, and IREB2), hypoxia response (BDNF, TFRC, and PML) and heat stress (PRKDC, CDK1, and TFDC). Average r(2) and D' values were 0.14 ± 0.21 and 0.57 ± 0.34, respectively, for a minor allele frequency (MAF) ? 0.05 and were found to increase with increasing MAF value. The outlier loci identified in the studied Ethiopian cattle populations indicate the presence of genetic variation produced/shaped by adaptation to different environmental conditions and provide a basis for further validation and functional analysis using a reasonable sample size and high-density markers. PMID:24602159

Edea, Z; Dadi, H; Kim, S-W; Park, J-H; Shin, G-H; Dessie, T; Kim, K-S

2014-10-01

146

Genome-wide scan for loci influencing quantitative immune response traits in the Belém family study: comparison of methods and summary of results.  

Science.gov (United States)

Here we report the results from a genome-wide linkage scan to identify genes and chromosomal regions that influence quantitative immune response traits, using multi-case leprosy and tuberculosis families from north-eastern Brazil. Total plasma IgE, antigen-specific IgG to Mycobacterium leprae soluble antigen (MLSA), M. tuberculosis soluble antigen (MTSA) and M. tuberculosis purified protein derivative (PPD), and antigen-specific lymphocyte proliferation (stimulation index or SI) and interferon-gamma (IFN-gamma) release to MLSA and PPD, were measured in 16 tuberculosis (184 individuals) and 21 leprosy (177 individuals) families. The individuals were genotyped at 382 autosomal microsatellite markers across the genome. The adjusted immune-response phenotypes were analysed using a variety of variance components and regression-based methods. These analyses highlighted a number of practical issues and problems with regard to implementation of the methods and, interestingly, differences were observed between several standard statistical and genetic analysis packages used. From this we determined that, for this set of traits in these pedigrees, significant p values for linkage using variance components analysis, supported by significance using the Visscher-Hopper modification of the Haseman-Elston method, provided the most compelling evidence for linkage. Using these criteria, linkage (5.8 x 10(-5) < p < 0.008) was seen for: total plasma IgE on chromosome 2; IgG to MLSA on chromosomes 8, 17 and 21; IgG to PPD on chromosome 12; SI to PPD on chromosome 1; IFN-gamma to MLSA on chromosomes 6, 7, 10, 12 and 14; and IFN-gamma to PPD on chromosomes 1, 16 and 19. PMID:16441259

Wheeler, E; Miller, E N; Peacock, C S; Donaldson, I J; Shaw, M-A; Jamieson, S E; Blackwell, J M; Cordell, H J

2006-01-01

147

A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle.  

Science.gov (United States)

To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ? 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle. PMID:20477797

McClure, M C; Morsci, N S; Schnabel, R D; Kim, J W; Yao, P; Rolf, M M; McKay, S D; Gregg, S J; Chapple, R H; Northcutt, S L; Taylor, J F

2010-12-01

148

Honey bees store landmarks in an egocentric frame of reference.  

Science.gov (United States)

Honey bees are well known to rely on stored landmark information to locate a previously visited site. While various mechanisms underlying insect navigation have been thoroughly explored, little is yet known about the degree of integration of spatial parameters to form higher-level spatial representations. In this paper we explore the basic interactions between landmark cues and directional cues, which stand at the basis of our understanding of piloting mechanisms. A novel experimental paradigm allowed us independent manipulation of each parameter in a highly controlled environment. The approach taken was twofold: cue-conflict experiments were first conducted to examine the interactions between positional cues and directional cues. The bees were then successively deprived of sensory cues to question the dependence of landmark navigation on context cues. Our results confirm previous findings that landmark cues are used in concert with external directional cues if present. Conversely, the bees' ability to locate a food site was not disrupted in the absence of an external directional reference. Thus, bees store landmark memories in an egocentric frame of reference and only loose and facultative associations between visual memories and compass cues are formed. PMID:11913810

Fry, Steven N; Wehner, Rüdiger

2002-01-01

149

Interactions of visual odometry and landmark guidance during food search in honeybees.  

Science.gov (United States)

How do honeybees use visual odometry and goal-defining landmarks to guide food search? In one experiment, bees were trained to forage in an optic-flow-rich tunnel with a landmark positioned directly above the feeder. Subsequent food-search tests indicated that bees searched much more accurately when both odometric and landmark cues were available than when only odometry was available. When the two cue sources were set in conflict, by shifting the position of the landmark in the tunnel during test, bees overwhelmingly used landmark cues rather than odometry. In another experiment, odometric cues were removed by training and testing in axially striped tunnels. The data show that bees did not weight landmarks as highly as when odometric cues were available, tending to search in the vicinity of the landmark for shorter periods. A third experiment, in which bees were trained with odometry but without a landmark, showed that a novel landmark placed anywhere in the tunnel during testing prevented bees from searching beyond the landmark location. Two further experiments, involving training bees to relatively longer distances with a goal-defining landmark, produced similar results to the initial experiment. One caveat was that, with the removal of the familiar landmark, bees tended to overshoot the training location, relative to the case where bees were trained without a landmark. Taken together, the results suggest that bees assign appropriate significance to odometric and landmark cues in a more flexible and dynamic way than previously envisaged. PMID:16244171

Vladusich, Tony; Hemmi, Jan M; Srinivasan, Mandyam V; Zeil, Jochen

2005-11-01

150

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

151

Adaptive Landmark-Based Navigation System Using Learning Techniques  

DEFF Research Database (Denmark)

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

Zeidan, Bassel; Dasgupta, Sakyasingha

2014-01-01

152

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

Science.gov (United States)

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. PMID:19728873

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

2009-01-01

153

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.

Tekely Kathleen

2009-09-01

154

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

Science.gov (United States)

Few studies have examined how landmarks affect territories' fundamental characteristics. In this field study, we investigated effects of landmarks on territory size, shape and location in a cichlid fish (Amatitlania siquia). We provided cans as breeding sites and used plastic plants as landmarks. During 10 min trials, we recorded locations where residents chased intruders and used those locations to outline and measure the territory. In two experiments, we observed pairs without landmarks and with either a point landmark (one plant) or linear landmark (four plants) placed near the nest can. We alternated which trial occurred first and performed the second trial 24 h after the first. Territories were approximately round without landmarks or with a point landmark but were significantly more elongated when we added a linear landmark. Without landmarks, nests were centrally located; however, with any landmark, pairs set territory boundaries closer to the landmark and thus the nest. Territory size was significantly reduced in the presence of any landmark. This reduction suggests that a smaller territory with well-defined boundaries has greater benefits than a larger territory with less well-defined borders. PMID:24759367

Suriyampola, Piyumika S; Eason, Perri K

2014-01-01

155

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

Science.gov (United States)

We conducted a 10-centimorgan linkage autosomal genome scan in a set of 19 extended American pedigrees (219 subjects) ascertained through probands with panic disorder. Several anxiety disorders--including social phobia, agoraphobia, and simple phobia--in addition to panic disorder segregate in these families. In previous studies of this sample, linkage analyses were based separately on each of the individual categorical affection diagnoses. Given the substantial comorbidity between anxiety disorders and their probable shared genetic liability, it is clear that this method discards a considerable amount of information. In this article, we propose a new approach that considers panic disorder, simple phobia, social phobia, and agoraphobia as expressions of the same multivariate, putatively genetically influenced trait. We applied the most powerful multipoint Haseman-Elston method, using the grade of membership score generated from a fuzzy clustering of these phenotypes as the dependent variable in Haseman-Elston regression. One region on chromosome 4q31-q34, at marker D4S413 (with multipoint and single-point nominal P values < .00001), showed strong evidence of linkage (genomewide significance at P<.05). The same region is known to be the site of a neuropeptide Y receptor gene, NPY1R (4q31-q32), that was recently connected to anxiolytic-like effects in rats. Several other regions on four chromosomes (4q21.21-22.3, 5q14.2-14.3, 8p23.1, and 14q22.3-23.3) met criteria for suggestive linkage (multipoint nominal P values < .01). Family-by-family analysis did not show any strong evidence of heterogeneity. Our findings support the notion that the major anxiety disorders, including phobias and panic disorder, are complex traits that share at least one susceptibility locus. This method could be applied to other complex traits for which shared genetic-liability factors are thought to be important, such as substance dependencies. PMID:16532386

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

2006-04-01

156

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

157

On-line SLAM using clustered landmarks with omnidirectional vision  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English 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 inhe [...] rent to the sensors. One common solution consists of establishing landmarks in the environment which are used as reference points for absolute localization estimates and form a sparse map that is iteratively refined as more information is obtained. This paper introduces a method of landmark selection and clustering in omnidirectional images for on-line SLAM, using the SIFT algorithm for initial feature extraction and assuming no prior knowledge of the environment. Visual sensors are an attractive way of collecting information from the environment, but tend to create an excessive amount of landmarks that are individually prone to false matches due to image noise and object similarities. By clustering several features in single objects, our approach eliminates landmarks that do not consistently represent the environment, decreasing computational cost and increasing the reliability of information incorporated. Tests conducted in real navigational situations show a significant improvement in performance without loss of quality.

Jun, Okamoto Jr.; Vitor Campanholo, Guizilini.

2010-12-01

158

Cuttlefish rely on both polarized light and landmarks for orientation.  

Science.gov (United States)

Cuttlefish are sensitive to linear polarization of light, a sensitivity that they use in predation and possibly in intraspecific communication. It has also been shown that cuttlefish are able to solve a maze using visual landmarks. In this study, cuttlefish were trained to solve a Y-maze with the e-vector of a polarized light and landmarks as redundant spatial information. The results showed that cuttlefish can use the e-vector orientation and landmarks in parallel to orient and that they are able to use either type of cue when the other one is missing. When they faced conflicting spatial information in the experimental apparatus, the majority of cuttlefish followed the e-vector rather than landmarks. Differences in response latencies in the different conditions of testing (training with both types of cue, tests with single cue or with conflicting information) were observed and discussed in terms of decision making. The ability to use near field and far field information may enable animals to interpret the partially occluded underwater light field. PMID:22460628

Cartron, Lelia; Darmaillacq, Anne-Sophie; Jozet-Alves, Christelle; Shashar, Nadav; Dickel, Ludovic

2012-07-01

159

Identifying landmark articles for advancing the practice of geriatrics.  

Science.gov (United States)

Landmark articles from the peer-reviewed literature can be used to teach the fundamental principles of geriatric medicine. Three approaches were used in sequential combination to identify landmark articles as a resource for geriatricians and other healthcare practitioners. Candidate articles were identified first through a literature review and expert opinion survey of geriatric medicine faculty. Candidate articles in a winnowed list (n = 30) were then included in a bibliometric analysis that incorporated the journal impact factor and average monthly citation index. Finally, a consensus panel reviewed articles to assess each manuscript's clinical relevance. For each article, a final score was determined by averaging, with equal weight, the opinion survey, bibliometric analysis, and consensus panel review. This process ultimately resulted in the identification of 27 landmark articles. Overall, there was weak correlation between articles that the expert opinion survey and bibliometric analysis both rated highly. This process demonstrates a feasible method combining subjective and objective measures that can be used to identify landmark papers in geriatric medicine for the enhancement of geriatrics education and practice. PMID:25366821

Vaughan, Camille P; Fowler, Rachel; Goodman, Richard A; Graves, Taylor R; Flacker, Jonathan M; Johnson, Theodore M

2014-11-01

160

Multiplanar transcranial ultrasound imaging: standards, landmarks and correlation with magnetic resonance imaging.  

Science.gov (United States)

The purpose of this study was to define a standardized multiplanar approach for transcranial ultrasound (US) imaging of brain parenchyma based on matched data from 3-D US and 3-D magnetic resonance imaging (MRI). The potential and limitations of multiple insonation planes in transverse and coronal orientation were evaluated for the visualization of intracranial landmarks in 60 healthy individuals (18 to 83 years old, mean 41.4 years) with sufficient temporal bone windows. Landmarks regularly visualized even in moderate sonographic conditions with identification rates of >75% were mesencephalon, pons, third ventricle, lateral ventricles, falx, thalamus, basal ganglia, pineal gland and temporal lobe. Identification of medulla oblongata, fourth ventricle, cerebellar structures, hippocampus, insula, frontal, parietal and occipital lobes was more difficult (<75%). We hypothesize that multiplanar transcranial US images, with standardized specification of tilt angles and orientation, not only allow comparison with other neuroimaging modalities, but may also provide a more objective framework for US monitoring of cerebral disease than freehand scanning. PMID:15749552

Kern, Rolf; Perren, Fabienne; Kreisel, Stefan; Szabo, Kristina; Hennerici, Michael; Meairs, Stephen

2005-03-01

 
 
 
 
161

36 CFR 65.9 - Withdrawal of National Historic Landmark designation.  

Science.gov (United States)

(a) National Historic Landmarks will be considered for withdrawal of designation only at the request of the owner or upon the initiative of the Secretary. (b) Four justifications exist for the withdrawal of National Historic Landmark...

2010-07-01

162

Automatic landmarking of cephalograms using active appearance models.  

Science.gov (United States)

There have been many attempts to further improve and automate cephalometric analysis in order to increase accuracy, reduce errors due to subjectivity, and to provide more efficient use of clinicians' time. The aim of this research was to evaluate an automated system for landmarking of cephalograms based on the use of an active appearance model (AAM) that contains a statistical model of shape and grey-level appearance of an object of interest and represents both shape and texture variations of the region covered by the model. Multi-resolution implementation was used, in which the AAM iterate to convergence at each level before projecting the current solution to the next level of the model. The AAM system was trained using 60 randomly selected, hand-annotated digital cephalograms of subjects between 7.2 and 25.6 years of age, and tested with a leave-five-out method that enabled testing not only of the accuracy of the AAM system but also the accuracy of each AAM. Differences between methods were examined using the non-parametric Wilcoxon signed rank test. An average accuracy of 1.68 mm was obtained, with 61 per cent of landmarks detected within 2 mm and 95 per cent of landmarks detected within 5 mm precision. A noticeable increase in overall precision and detection of low-contrast cephalometric landmarks was achieved compared with other automated systems. These results suggest that the AAM approach can adequately represent the average shape and texture variations of craniofacial structures on digital radiographs. As such it can successfully be implemented for automatic localization of cephalometric landmarks. PMID:20203126

Vucini?, Predrag; Trpovski, Zeljen; S?epan, Ivana

2010-06-01

163

Group-wise FMRI activation detection on corresponding cortical landmarks.  

Science.gov (United States)

Group-wise activation detection in task-based fMRI has been widely used because of its robustness to noises and statistical power to deal with variability of individual brains. However, current group-wise fMRI activation detection methods typically rely on the spatial alignment established by coregistration of individual brains' fMRI images into the same template space, which has difficulty in dealing with the remarkable anatomic variation of different brains. As a consequence, the resulted misalignment among multiple brains could substantially degrade the accuracy and specificity of group-wise fMRI activation detection. To address these challenges, this paper presents a novel methodology to detect group-wise fMRI activation based on a publicly released dense map of DTI-derived structural cortical landmarks, which possess intrinsic correspondences across individuals and populations. The basic idea here is that a first-level general linear model (GLM) analysis is performed on fMRI signals of each corresponding cortical landmark in each individual brain's own space, and then the single-subject effect size of the same landmark from a group of subjects are statistically integrated and assessed at the group level using the mixed-effects model. As a result, the consistently activated cortical landmarks are determined and declared group-wisely in response to external block-based stimuli. Our experimental results demonstrated that the proposed approach can map meaningful group-wise activation patterns on the atlas of cortical landmarks without image registration between subjects and spatial smoothing. PMID:24579198

Lv, Jinglei; Zhu, Dajiang; Hu, Xintao; Zhang, Xin; Zhang, Tuo; Han, Junwei; Guo, Lei; Liu, Tianming

2013-01-01

164

Solving small spaces: investigating the use of landmark cues in brown capuchins (Cebus apella).  

Science.gov (United States)

Some researchers have recently argued that humans may be unusual among primates in preferring to use landmark information when reasoning about some kinds of spatial problems. Some have explained this phenomenon by positing that our species' tendency to prefer landmarks stems from a human-unique trait: language. Here, we test this hypothesis-that preferring to use landmarks to solve such tasks is related to language ability-by exploring landmark use in a spatial task in one non-human primate, the brown capuchin monkey (Cebus apella). We presented our subjects with the rotational displacement task, in which subjects attempt to relocate a reward hidden within an array of hiding locations which are subsequently rotated to a new position. Over several experiments, we varied the availability and the salience of a landmark cue within the array. Specifically, we varied (1) visual access to the array during rotation, (2) the type of landmark, (3) the consistency of the landmark qualities, and (4) the amount of exposure to the landmark. Across Experiments 1 through 4, capuchins did not successfully use landmarks cues, suggesting that non-linguistic primates may not spontaneously use landmarks to solve some spatial problems, as in this case of a small-scale dynamic spatial task. Importantly, we also observed that capuchins demonstrated some capacity to learn to use landmarks in Experiment 4, suggesting that non-linguistic creatures may be able to use some landmarks cues in similar spatial tasks with extensive training. PMID:23430144

Hughes, Kelly D; Mullo, Enma; Santos, Laurie R

2013-09-01

165

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.

Yanagihara Kazuyoshi

2009-06-01

166

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

Science.gov (United States)

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

Ghimire, Deepak; Lee, Joonwhoan

2014-01-01

167

Safe Treatment of Trigger Thumb With Longitudinal Anatomic Landmarks  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Objective: Stenosing tenosynovitis of the thumb flexor tendon sheath is also known as trigger thumb. It is an inflammatory process that involves the flexor tendon sheath at the A1 pulley. Successful percutaneous or open treatment of trigger thumb depends on the ability of the clinician to properly predict the location of the A1 pulley. Longitudinal anatomic landmarks can facilitate safe treatment for the trigger thumb while circumventing injury to the neurovascular bundles. Methods: Fourteen ...

Hazani, Ron; Elston, Josh; Whitney, Ryan D.; Redstone, Jeremiah; Chowdhry, Saeed; Wilhelmi, Bradon J.

2010-01-01

168

Color-contrast landmark detection and encoding in outdoor images  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper describes a system to extract salient regions from an outdoor image and match them against a database of previously acquired landmarks. Region saliency is based mainly on color contrast, although intensity and texture orientation are also taken into account. Remarkably, color constancy is embedded in the saliency detection process through a novel color ratio algorithm that makes the system robust to illumination changes, so common in outdoor environments. A region is characterized ...

Todt, Eduardo; Torras Geni?s, Carme

2005-01-01

169

Ageing effects on path integration and landmark navigation.  

Science.gov (United States)

Navigation abilities show marked decline in both normal ageing and dementia. Path integration may be particularly affected, as it is supported by the hippocampus and entorhinal cortex, both of which show severe degeneration with ageing. Age differences in path integration based on kinaesthetic and vestibular cues have been clearly demonstrated, but very little research has focused on visual path integration, based only on optic flow. Path integration is complemented by landmark navigation, which may also show age differences, but has not been well studied either. Here we present a study using several simple virtual navigation tasks to explore age differences in path integration both with and without landmark information. We report that, within a virtual environment that provided only optic flow information, older participants exhibited deficits in path integration in terms of distance reproduction, rotation reproduction, and triangle completion. We also report age differences in triangle completion within an environment that provided landmark information. In all tasks, we observed a more restricted range of responses in the older participants, which we discuss in terms of a leaky integrator model, as older participants showed greater leak than younger participants. Our findings begin to explain the mechanisms underlying age differences in path integration, and thus contribute to an understanding of the substantial decline in navigation abilities observed in ageing. PMID:22431367

Harris, Mathew A; Wolbers, Thomas

2012-08-01

170

Quality-Aware Estimation of Facial Landmarks in Video Sequences  

DEFF Research Database (Denmark)

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

Haque, Mohammad Ahsanul; Nasrollahi, Kamal

2015-01-01

171

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

2013-01-01

172

Microarray data mining using landmark gene-guided clustering  

Directory of Open Access Journals (Sweden)

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

Cho HyungJun

2008-02-01

173

Genome scan of schizophrenia families in a large Veterans Affairs Cooperative Study sample: evidence for linkage to 18p11.32 and for racial heterogeneity on chromosomes 6 and 14.  

Science.gov (United States)

Genome-wide linkage analyses of schizophrenia have identified several regions that may harbor schizophrenia susceptibility genes but, given the complex etiology of the disorder, it is unlikely that all susceptibility regions have been detected. We report results from a genome scan of 166 schizophrenia families collected through the Department of Veterans Affairs Cooperative Studies Program. Our definition of affection status included schizophrenia and schizoaffective disorder, depressed type and we defined families as European American (EA) and African American (AA) based on the probands' and parents' races based on data collected by interviewing the probands. We also assessed evidence for racial heterogeneity in the regions most suggestive of linkage. The maximum LOD score across the genome was 2.96 for chromosome 18, at 0.5 cM in the combined race sample. Both racial groups showed LOD scores greater than 1.0 for chromosome 18. The empirical P-value associated with that LOD score is 0.04 assuming a single genome scan for the combined sample with race narrowly defined, and 0.06 for the combined sample allowing for broad and narrow definitions of race. The empirical P-value of observing a LOD score as large as 2.96 in the combined sample, and of at least 1.0 in each racial group, allowing for narrow and broad racial definitions, is 0.04. Evidence for the second and third largest linkage signals come solely from the AA sample on chromosomes 6 (LOD = 2.11 at 33.2 cM) and 14 (LOD = 2.13 at 51.0). The linkage evidence differed between the AA and EA samples (chromosome 6 P-value = 0.007 and chromosome 14 P-value = 0.004). PMID:16152571

Faraone, S V; Skol, A D; Tsuang, D W; Young, K A; Haverstock, S L; Prabhudesai, S; Mena, F; Menon, A S; Leong, L; Sautter, F; Baldwin, C; Bingham, S; Weiss, D; Collins, J; Keith, T; Vanden Eng, J L; Boehnke, M; Tsuang, M T; Schellenberg, G D

2005-11-01

174

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

International Nuclear Information System (INIS)

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

175

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

International Nuclear Information System (INIS)

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

176

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

2012-01-01

177

Defining esophageal landmarks, gastroesophageal reflux disease, and Barrett's esophagus.  

Science.gov (United States)

The following paper on gastroesophageal reflux disease (GERD) and Barrett's esophagus (BE) includes commentaries on defining esophageal landmarks; new techniques for evaluating upper esophageal sphincter (UES) tone; differential diagnosis of GERD, BE, and hiatal hernia (HH); the use of high-resolution manometry for evaluation of reflux; the role of fundic relaxation in reflux; the use of 24-h esophageal pH-impedance testing in differentiating acid from nonacid reflux and its potential inclusion in future Rome criteria; classification of endoscopic findings in GERD; the search for the cell origin that generates BE; and the relationship between BE, Barrett's carcinoma, and obesity. PMID:24117649

DeVault, Kenneth; McMahon, Barry P; Celebi, Altay; Costamagna, Guido; Marchese, Michele; Clarke, John O; Hejazi, Reza A; McCallum, Richard W; Savarino, Vincenzo; Zentilin, Patrizia; Savarino, Edoardo; Thomson, Mike; Souza, Rhonda F; Donohoe, Claire L; O'Farrell, Naoimh J; Reynolds, John V

2013-10-01

178

CAT Scan  

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Full Text Available ... reviews the benefits and risks of this scan. Test A CT scan uses x-ray technology and ... the scanning. This allows for sharper pictures. The test takes from a few minutes to approximately half ...

179

Characteristics of anatomical landmarks in the mandibular interforaminal region: A cone-beam computed tomography study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Objectives: This study was conducted to assess appearance, visibility, location and course of anatomical landmarks in mandibular interforaminal region using cone-beam computed tomography (CBCT). Study design: A total of 96 CBCT examinations was re-evaluated to exploit anatomical landmarks. The examinations used the Promax 3D CBCT unit. A sole examiner carried out all the measurements. Visibilities of the anatomical landmarks were scored using a four-point rating scale. Results: The mand...

Parnia, Fereidoun; Moslehifard, Elnaz; Hafezeqoran, Ali; Mahboub, Farhang; Mojaver-kahnamoui, Haniye

2012-01-01

180

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

 
 
 
 
181

A genome-wide linkage scan of bipolar disorder in Latino families identifies susceptibility loci at 8q24 and 14q32.  

Science.gov (United States)

A genome-wide nonparametric linkage screen was performed to localize Bipolar Disorder (BP) susceptibility loci in a sample of 3757 individuals of Latino ancestry. The sample included 963 individuals with BP phenotype (704 relative pairs) from 686 families recruited from the US, Mexico, Costa Rica, and Guatemala. Non-parametric analyses were performed over a 5 cM grid with an average genetic coverage of 0.67 cM. Multipoint analyses were conducted across the genome using non-parametric Kong & Cox LOD scores along with Sall statistics for all relative pairs. Suggestive and significant genome-wide thresholds were calculated based on 1000 simulations. Single-marker association tests in the presence of linkage were performed assuming a multiplicative model with a population prevalence of 2%. We identified two genome-wide significant susceptibly loci for BP at 8q24 and 14q32, and a third suggestive locus at 2q13-q14. Within these three linkage regions, the top associated single marker (rs1847694, P = 2.40 × 10(-5)) is located 195 Kb upstream of DPP10 in Chromosome 2. DPP10 is prominently expressed in brain neuronal populations, where it has been shown to bind and regulate Kv4-mediated A-type potassium channels. Taken together, these results provide additional evidence that 8q24, 14q32, and 2q13-q14 are susceptibly loci for BP and these regions may be involved in the pathogenesis of BP in the Latino population. PMID:25044503

Gonzalez, Suzanne; Camarillo, Cynthia; Rodriguez, Marco; Ramirez, Mercedes; Zavala, Juan; Armas, Regina; Contreras, Salvador A; Contreras, Javier; Dassori, Albana; Almasy, Laura; Flores, Deborah; Jerez, Alvaro; Raventós, Henriette; Ontiveros, Alfonso; Nicolini, Humberto; Escamilla, Michael

2014-09-01

182

Genome-wide linkage scan for prostate cancer susceptibility in Finland: evidence for a novel locus on 2q37.3 and confirmation of signal on 17q21-q22.  

Science.gov (United States)

Genome-wide linkage studies have been used to localize rare and highly penetrant prostate cancer (PRCA) susceptibility genes. Linkage studies performed in different ethnic backgrounds and populations have been somewhat disparate, resulting in multiple, often irreproducible signals because of genetic heterogeneity and high sporadic background of the disease. Our first genome-wide linkage study and subsequent fine-mapping study of Finnish hereditary prostate cancer (HPC) families gave evidence of linkage to one region. Here, we conducted subsequent scans with microsatellites and SNPs in a total of 69 Finnish HPC families. GENEHUNTER-PLUS was used for parametric and nonparametric analyses. Our microsatellite genome-wide linkage study provided evidence of linkage to 17q12-q23, with a heterogeneity LOD (HLOD) score of 3.14 in a total of 54 of the 69 families. Genome-wide SNP analysis of 59 of the 69 families gave a highest HLOD score of 3.40 at 2q37.3 under a dominant high penetrance model. Analyzing all 69 families by combining microsatellite and SNP maps also yielded HLOD scores of > 3.3 in two regions (2q37.3 and 17q12-q21.3). These significant linkage peaks on chromosome 2 and 17 confirm previous linkage evidence of a locus on 17q from other populations and provide a basis for continued research into genetic factors involved in PRCA. Fine-mapping analysis of these regions is ongoing and candidate genes at linked loci are currently under analysis. PMID:21207418

Cropp, Cheryl D; Simpson, Claire L; Wahlfors, Tiina; Ha, Nati; George, Asha; Jones, MaryPat S; Harper, Ursula; Ponciano-Jackson, Damaris; Green, Tiffany A; Tammela, Teuvo L J; Bailey-Wilson, Joan; Schleutker, Johanna

2011-11-15

183

Automatic corpus callosum segmentation for standardized MR brain scanning  

Science.gov (United States)

Magnetic Resonance (MR) brain scanning is often planned manually with the goal of aligning the imaging plane with key anatomic landmarks. The planning is time-consuming and subject to inter- and intra- operator variability. An automatic and standardized planning of brain scans is highly useful for clinical applications, and for maximum utility should work on patients of all ages. In this study, we propose a method for fully automatic planning that utilizes the landmarks from two orthogonal images to define the geometry of the third scanning plane. The corpus callosum (CC) is segmented in sagittal images by an active shape model (ASM), and the result is further improved by weighting the boundary movement with confidence scores and incorporating region based refinement. Based on the extracted contour of the CC, several important landmarks are located and then combined with landmarks from the coronal or transverse plane to define the geometry of the third plane. Our automatic method is tested on 54 MR images from 24 patients and 3 healthy volunteers, with ages ranging from 4 months to 70 years old. The average accuracy with respect to two manually labeled points on the CC is 3.54 mm and 4.19 mm, and differed by an average of 2.48 degrees from the orientation of the line connecting them, demonstrating that our method is sufficiently accurate for clinical use.

Xu, Qing; Chen, Hong; Zhang, Li; Novak, Carol L.

2007-03-01

184

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

2012-06-01

185

Multifunction Digital Research Scanning System  

International Nuclear Information System (INIS)

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

186

Brain activity during landmark and line bisection tasks  

Directory of Open Access Journals (Sweden)

Full Text Available Neglect patients bisect lines far rightward of center whereas normal subjects typically bisect lines with a slight leftward bias supporting a right hemisphere bias for attention allocation. We used fMRI to assess the brain regions related to this function in normals, using two complementary tasks. In the Landmark task subjects were required to judge whether or not a presented line was bisected correctly. During the line bisection task, subjects moved a cursor and indicated when it reached the center of the line. The conjunction of BOLD activity for both tasks showed right lateralized intraparietal sulcus and lateral peristriate cortex activity. The results provide evidence that predominantly right hemisphere lateralized processes are engaged in normal subjects during tasks that are failed in patients with unilateral neglect and highlight the importance of a right fronto-parietal network in attention allocation.

MetehanCicek

2009-05-01

187

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

2013-01-01

188

Robust Mobile Robot Localization by Tracking Natural Landmarks  

Science.gov (United States)

This article presents a feature-based localization framework to use with conventional 2D laser rangefinder. The system is based on the Unscented Kalman Filter (UKF) approach, which can reduce the errors in the calculation of the robot's position and orientation. The framework consists of two main parts: feature extraction and multi-sensor fusing localization. The novelty of this system is that a new segmentation algorithm based-on the micro-tangent line (MTL) is introduced. Features, such as lines, corners and curves, can be characterized from the segments. For each landmark, the geometrical parameters are provided with statistical information, which are used in the subsequent matching phase, together with a priori map, so as to get an optimal estimate of the robot pose. Experimental results show that the proposed localization method is efficient in office-like environment.

Feng, Xiaowei; Guo, Shuai; Li, Xianhua; He, Yongyi

189

Morphometric analysis of facial landmark data to characterize the facial phenotype associated with fetal alcohol syndrome  

Science.gov (United States)

Procrustes analysis and principal component analysis were applied to stereo-photogrammetrically obtained landmarks to compare the facial features associated with fetal alcohol syndrome (FAS) in subjects with FAS and normal controls. Two studies were performed; both compared facial landmark data of FAS and normal subjects, but they differed in the number of landmarks chosen. The first study compared landmarks representing palpebral fissure length, upper lip thinness and philtrum smoothness and revealed no significant difference in shape. The second study added to the landmarks used in the first those affected by mid-face hypoplasia, and revealed significant differences in shape between the two groups, broadly confirming the FAS gestalt reported in the literature. Some disagreement in the characteristic FAS facial shape between our results and those reported in the literature may be due to ethnic variation. PMID:17310546

Mutsvangwa, Tinashe; Douglas, Tania S

2007-01-01

190

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

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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

2010-06-01

191

Genome-wide linkage scan in a large bipolar disorder sample from the National Institute of Mental Health genetics initiative suggests putative loci for bipolar disorder, psychosis, suicide, and panic disorder.  

Science.gov (United States)

We conducted a 9-cM genome scan in a large bipolar pedigree sample from the National Institute of Mental Health genetics initiative (1060 individuals from 154 multiplex families). We performed parametric and nonparametric analyses using both standard diagnostic models and comorbid conditions thought to identify phenotypic subtypes: psychosis, suicidal behavior, and panic disorder. Our strongest linkage signals (genome-wide significance) were observed on chromosomes 10q25, 10p12, 16q24, 16p13, and 16p12 using standard diagnostic models, and on 6q25 (suicidal behavior), 7q21 (panic disorder) and 16p12 (psychosis) using phenotypic subtypes. Several other regions were suggestive of linkage, including 1p13 (psychosis), 1p21 (psychosis), 1q44, 2q24 (suicidal behavior), 2p25 (psychosis), 4p16 (psychosis, suicidal behavior), 5p15, 6p25 (psychosis), 8p22 (psychosis), 8q24, 10q21, 10q25 (suicidal behavior), 10p11 (psychosis), 13q32 and 19p13 (psychosis). Over half the implicated regions were identified using phenotypic subtypes. Several regions - 1p, 1q, 6q, 8p, 13q and 16p - have been previously reported to be linked to bipolar disorder. Our results suggest that dissection of the disease phenotype can enrich the harvest of linkage signals and expedite the search for susceptibility genes. This is the first large-scale linkage scan of bipolar disorder to analyze simultaneously bipolar disorder, psychosis, suicidal behavior, and panic disorder. PMID:16402137

Cheng, R; Juo, S H; Loth, J E; Nee, J; Iossifov, I; Blumenthal, R; Sharpe, L; Kanyas, K; Lerer, B; Lilliston, B; Smith, M; Trautman, K; Gilliam, T C; Endicott, J; Baron, M

2006-03-01

192

CAT Scan  

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Full Text Available ... scan. Test A CT scan uses x-ray technology and sophisticated computers to come up with the ... However, this amount could be dangerous for unborn children. It is therefore very important to make sure ...

193

CAT Scan  

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Full Text Available ... CT scan uses x-ray technology and sophisticated computers to come up with the final pictures. The ... be done if you are not sure. Recently studies have suggested that repeated CT scans can potentially ...

194

CAT Scan  

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Full Text Available ... machine looks like a giant donut and the “gantry” is its hole. CT Scan You will be ... to be scanned will be placed inside the gantry of the machine. It is important that you ...

195

Renal scan  

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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 . ...

196

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

Directory of Open Access Journals (Sweden)

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

Marcelo Jangarelli

2010-12-01

197

From objects to landmarks: the function of visual location information in spatial navigation  

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Full Text Available Landmarks play an important role in guiding navigational behavior. A host of studies in the last 15 years has demonstrated that environmental objects can act as landmarks for navigation in different ways. In this review, we propose a parsimonious four-part taxonomy for conceptualizing object location information during navigation. We begin by outlining object properties that appear to be important for a landmark to attain salience. We then systematically examine the different functions of objects as navigational landmarks based on previous behavioral and neuroanatomical findings in rodents and humans. Evidence is presented showing that single environmental objects can function as navigational beacons, or act as associative or orientation cues. In addition, we argue that extended surfaces or boundaries can act as landmarks by providing a frame of reference for encoding spatial information. The present review provides a concise taxonomy of the use of visual objects as landmarks in navigation and should serve as a useful reference for future research into landmark-based spatial navigation.

OliverBaumann

2012-08-01

198

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

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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

2009-01-01

199

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

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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

200

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.

 
 
 
 
201

Is there consistency in cephalometric landmark identification amongst oral and maxillofacial surgeons?  

Science.gov (United States)

There may be significant variation amongst oral and maxillofacial surgeons (OMFS) in the identification and placement of cephalometric landmarks for orthognathic surgery, and this could impact upon the surgical plan and final treatment outcome. In an effort to assess this variability, 10 lateral cephalometric radiographs were selected for evaluation by 16 OMFS with different levels of surgical knowledge and experience, and the position of 21 commonly used cephalometric landmarks were identified on radiographs displayed on a computer screen using a computer mouse on a pen tablet. The database consisted of real position measurements (x, y) to determine the consistency of landmark identification between surgeons and within individual surgeons. Inter-examiner analysis demonstrated that most landmark points had excellent reliability (intra-class correlation coefficient >0.90). Regardless of the level of surgeon experience, certain landmarks presented consistently poor reliability, and intra-examiner reliability analysis demonstrated that some locations had a higher average difference for both x and y axes. In particular, porion, condylion, and gonion showed poor agreement and reliability between examiners. The identification of most landmarks showed some inconsistencies within different parameters of evaluation. Such variability among surgeons may be addressed by the consistent use of high-quality images, and also by periodic surgeon education of the definition of the specific landmarks. PMID:24055177

Miloro, M; Borba, A M; Ribeiro-Junior, O; Naclério-Homem, M G; Jungner, M

2014-04-01

202

Landmarks of History of Soil Science in Sri Lanka  

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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

203

A genome-wide scan for quantitative trait loci affecting limb bone lengths and areal bone mineral density of the distal femur in a White Duroc × Erhualian F2 population  

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Full Text Available Abstract Background Limb bone lengths and bone mineral density (BMD have been used to assess the bone growth and the risk of bone fractures in pigs, respectively. It has been suggested that limb bone lengths and BMD are under genetic control. However, the knowledge about the genetic basis of the limb bone lengths and mineralisatinon is limited in pigs. The aim of this study was to identify quantitative trait loci (QTL affecting limb bone lengths and BMD of the distal femur in a White Duroc × Erhualian resource population. Results Limb bone lengths and femoral bone mineral density (fBMD were measured in a total of 1021 and 116 F2 animals, respectively. There were strong positive correlations among the lengths of limb bones and medium positive correlations between the lengths of limb bones and fBMD. A whole-genome scan involving 183 microsatellite markers across the pig genome revealed 35 QTL for the limb bone lengths and 2 for femoral BMD. The most significant QTL for the lengths of five limb bones were mapped on two chromosomes affecting all 5 limb bones traits. One was detected around 57 cM on pig chromosome (SSC 7 with the largest F-value of more than 26 and 95% confidence intervals of less than 5 cM, providing a crucial start point to identify the causal genes for these traits. The Erhualian alleles were associated with longer limb bones. The other was located on SSCX with a peak at 50–53 cM, whereas alleles from the White Duroc breed increased the bone length. Many QTL identified are homologous to the human genomic regions containing QTL for bone-related traits and a list of interesting candidate genes. Conclusion This study detected the QTL for the lengths of scapula, ulna, humerus and tibia and fBMD in the pig for the first time. Moreover, several new QTL for the pig femoral length were found. As correlated traits, QTL for the lengths of five limb bones were mainly located in the same genomic regions. The most promising QTL for the lengths of five limb bones on SSC7 merits further investigation.

Ma Junwu

2008-10-01

204

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

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

2010-12-01

205

77 FR 14420 - Landmarks Committee of the National Park System Advisory Board Meeting  

Science.gov (United States)

...May 16 at 9 a.m. Location: The Charles Sumner School Museum and Archives, 3rd...FURTHER INFORMATION CONTACT: Patricia Henry, National Historic Landmarks Program...Telephone (202) 354-2216; Email: Patty_Henry@nps.gov. SUPPLEMENTARY...

2012-03-09

206

36 CFR 62.4 - Natural landmark designation and recognition process.  

Science.gov (United States)

...that may affect the area's natural values, integrity, or other matters of...owner's interest in protecting and managing the area in a manner that prevents the loss or deterioration of the natural values on which landmark designation is...

2010-07-01

207

Numerical landmarks are useful--except when they're not.  

Science.gov (United States)

Placing landmarks on number lines, such as marking each tenth on a 0-1 line with a hatch mark and the corresponding decimal, has been recommended as a useful tool for improving children's number sense. Four experiments indicated that some landmarks do have beneficial effects, others have harmful effects, and yet others have no effects on representations of common fractions (N/M). The effects of the landmarks were seen not only on the number line task where they appeared but also on a subsequent magnitude comparison task and on correlations with mathematics achievement tests. Landmarks appeared to exert their effects through the encodings and strategies that they promoted. Theoretical and educational implications are discussed. PMID:24382407

Siegler, Robert S; Thompson, Clarissa A

2014-04-01

208

CAT Scan  

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Full Text Available ... will be placed inside the gantry of the machine. It is important that you remain still during the scanning. This allows for sharper pictures. The test takes from a few minutes to approximately half an hour. CT scan technologists sit in the next room and are able to see you through a ...

209

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  

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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.

Ellison R Curtis

2006-03-01

210

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

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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, di...

Rosalia Leonardi; Daniela Giordano; Francesco Maiorana

2009-01-01

211

Assessment of the reliability and repeatability of landmarks using 3-D cephalometry software.  

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The aim of this study was to analyze the reliability and repeatability of identification landmarks using 3-D cephalometric software. Ten orthognathic patients were selected for this study and underwent the following protocol: 1. radiographic evaluation (CBCT technique); 2. stone casts; 3. photos; and 4. 3-D cephalometric evaluation. Twenty-one hard tissue landmarks and 14 cephalometric measurements were taken three times (T1, T2, and T3) on each patient, with an interval of one week by two ex...

Frongia, Gianluigi; Piancino, Maria Grazia; Bracco, Pietro

2012-01-01

212

A comparison of two methods for natural landmark classification with Biosonar  

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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 trees that they use during their nocturnal flights. In this paper we compare two methods for natural landmark classification by a biomimetic sonar consisting of one sender (mouth) and two receivers ...

Wang, Maosen; Zell, Andreas; Mu?ller, Rolf; Wilhelm-schickard-institut Fu?r Informatik, Tu?bingen

2004-01-01

213

Detection and location of 127 anatomical landmarks in diverse CT datasets  

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

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

2014-03-01

214

Influence of Landmarks on Spatial Memory in Short-nosed Fruit Bat, Cynopterus sphinx.  

Science.gov (United States)

In order to study the relationship between landmarks and spatial memory in short-nosed fruit bat, Cynopterus sphinx (Megachiroptera, Pteropodidae), we simulated a foraging environment in the laboratory. Different landmarks were placed to gauge the spatial memory of C. sphinx. We changed the number of landmarks every day with 0 landmarks again on the fifth day (from 0, 2, 4, 8 to 0). Individuals from the control group were exposed to the identical artificial foraging environment, but without landmarks. The results indicated that there was significant correlation between the time of the first foraging and the experimental days in both groups (Pearson Correlation: experimental group: r=-0.593, P0.05), but there was significant correlation between the success rates of foraging and the experimental days in the control groups (Pearson Correlation: r=0.445, P0.05); also, there was no significant difference in success rates of foraging between these two groups (GLM: F(0.05,1 )=0.849, P>0.05). The results of our experiment suggest that spatial memory in C. sphinx was formed gradually and that the placed landmarks appeared to have no discernable effects on the memory of the foraging space. PMID:20545006

Zeng, Yu; Zhang, Xin-Wen; Zhu, Guang-Jian; Gong, Yan-Yan; Yang, Jian; Zhang, Li-Biao

2010-04-01

215

IAEA Director General welcomes landmark convention to combat nuclear terrorism  

International Nuclear Information System (INIS)

Full text: IAEA Director General Mohamed ElBaradei welcomed the adoption of an International convention against nuclear terrorism. 'This is a landmark achievement which will bolster global efforts to combat nuclear terrorism,' Dr. ElBaradei said. 'It will be a key part of international efforts to prevent terrorists from gaining access to nuclear weapons'. The United Nations General Assembly adopted the convention, The International Convention for the Suppression of Acts of Nuclear Terrorism, on 13 April 2005. The Convention strengthens the global legal framework to counter terrorist threats. Based on a proposal by the Russian Federation in 1998, the Convention focuses on criminal offences related to nuclear terrorism and covers a broad range of possible targets, including nuclear reactors as well as nuclear material and radioactive substances. Under its provisions, alleged offenders - for example any individual or group that unlawfully and intentionally possesses or uses radioactive material with the intent to cause harm - must be either extradited or prosecuted. States are also encouraged to cooperate with each other in connection with criminal investigations and extradition proceedings. The Convention further requires that any seized nuclear or radiological material be held in accordance with IAEA safeguards, and handled in keeping with the IAEA's health, safety and physical protection standards. Dr. ElBaradei also recalled that the Agency is in the process of amending the Convention on the Physical Protection of Nuclear Material, in order to broaden its scope, and in so doing, strengthen the current legal framework for securing nuclear material against illicit uses. A conference will be held from 4 to 8 July in Vienna to consider and adopt the amendments. The Convention opens for signature in September this year. Dr ElBaradei urged all States to 'sign and ratify the Convention without delay so nuclear terrorism will have no chance'. (IAEA)

216

Insite: Canada's landmark safe injecting program at risk  

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Full Text Available Abstract InSite is North Americas first supervised injection site and a landmark public heath initiative operating in Vancouver since 2003. The program is a vital component of that cities internationally recognized harm reduction approach to its serious problems with drugs, crime, homelessness and AIDS. InSite currently operates under a waiver of Federal rules that allow it to provide services as a research project. An extensive evaluation has produced very positive results for thousands of users. Normally such strong evidence documenting the successes of such a program, and the medical and public health significance of these positive outcomes, would be the basis for celebration and moves to expand the model and provide similar services elsewhere in Canada. Instead, there is a distinct possibility that InSite will be closed by the newly elected Canadian Prime Minister Paul Harper – a conservative who has traveled to the US to visit George WQ Bush and come back antagonistic to harm reduction in all its forms. Because InSites federal waiver is expiring and up for renewal in September, the fear is that Mr. Harpers will not renew the approval and that the program will be forced to close down. The risks associated with the potential closure of InSite need to be fully understood. This editorial lays out these public health risks and the associated economic impact if InSite were to be closed. In addition to preventable deaths and disease, InSites closure will cost Vancouver and British Columbia between $3.8 and $ 8.8 million in preventable health care expenses over the next two years.

Drucker Ernest

2006-08-01

217

CAT Scan  

Medline Plus

Full Text Available ... a test that provides very clear pictures of structures inside the body. Doctors may recommend a CT ... CT scan uses x-ray technology and sophisticated computers to come up with ...

218

CAT Scan  

Medline Plus

Full Text Available ... up with the final pictures. The CT scan machine looks like a giant donut and the “gantry” ... will be placed inside the gantry of the machine. It is important that you remain still during ...

219

CAT Scan  

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Full Text Available ... failure, especially if the patient is taking Glucophage® (metformin), a diabetic medication. X-rays are used during ... potentially increase a patient’s risk of developing future cancers or tumors in the areas scanned. This risk ...

220

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)

 
 
 
 
221

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

Science.gov (United States)

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

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

2012-06-01

222

Spatial cognition based on geometry and landmarks in the domestic chick (Gallus gallus).  

Science.gov (United States)

Recent evidence suggest that encoding of spatial information based on extended surfaces may differ from encoding based on discrete arrays of local elements. Here we investigated the use of these different frames of reference in domestic chicks. Chicks were trained to search for food hidden under sawdust in the center of the floor of a square-shaped landmark array, with its center in coincidence with the center of a square-shaped enclosure. Displacement of the array to a corner caused a shift of searching behavior toward the array, the search activity spanning between the center of the arena and the center of the array. After changing distances between landmarks, chicks still searched in the central area. Asymmetries were apparent in chicks tested in monocular conditions, with left-eyed chicks being more affected by the overall enclosure and right-eyed chicks by local landmarks. These results suggest that chicks can use both distances from extended surfaces and local information provided by the landmarks of the array to orient in space. However, chicks do not seem to perceive the array as a whole configuration, rather they tend to rely only on single landmarks to locate the goal. PMID:16979247

Chiesa, A Della; Speranza, M; Tommasi, L; Vallortigara, G

2006-11-25

223

Scan Statistics  

CERN Document Server

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

224

CAT Scan  

Medline Plus

Full Text Available ... CT scan uses x-ray technology and sophisticated computers to come up with the final pictures. The ... for your specific condition. ©1995-2013, The Patient Education Institute, Inc. www.X-Plain.com rd050105 Last ...

225

Genome-Wide Linkage Scan of Bipolar Disorder in a Colombian Population Isolate Replicates Loci on Chromosomes 7p21–22, 1p31, 16p12 and 21q21–22 and Identifies a Novel Locus on Chromosome 12q  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Background/Aims: Bipolar disorder (BP) is a severe psychiatric illness, characterised by alternating episodes of depression and mania, which ranks among the top ten causes of morbidity and life-long disability world-wide. We have previously performed a whole-genome linkage scan on 6 pedigrees segregating severe BP from the well-characterised population isolate of Antioquia, Colombia. We recently collected genotypes for the same set of 382 autosomal microsatellite markers in 9 additional Antio...

Kremeyer, B.; Garci?a, J.; Mu?ller, H.; Burley, M. W.; Herzberg, I.; Parra, M. V.; Duque, C.; Vega, J.; Montoya, P.; Lo?pez, M. C.; Bedoya, G.; Reus, V.; Palacio, C.; Lo?pez, C.; Ospina-duque, J.

2010-01-01

226

Landmark matching based retinal image alignment by enforcing sparsity in correspondence matrix.  

Science.gov (United States)

Retinal image alignment is fundamental to many applications in diagnosis of eye diseases. In this paper, we address the problem of landmark matching based retinal image alignment. We propose a novel landmark matching formulation by enforcing sparsity in the correspondence matrix and offer its solutions based on linear programming. The proposed formulation not only enables a joint estimation of the landmark correspondences and a predefined transformation model but also combines the benefits of the softassign strategy (Chui and Rangarajan, 2003) and the combinatorial optimization of linear programming. We also introduced a set of reinforced self-similarities descriptors which can better characterize local photometric and geometric properties of the retinal image. Theoretical analysis and experimental results with both fundus color images and angiogram images show the superior performances of our algorithms to several state-of-the-art techniques. PMID:24238743

Zheng, Yuanjie; Daniel, Ebenezer; Hunter, Allan A; Xiao, Rui; Gao, Jianbin; Li, Hongsheng; Maguire, Maureen G; Brainard, David H; Gee, James C

2014-08-01

227

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

Directory of Open Access Journals (Sweden)

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

Nihat Y?lmaz

2006-06-01

228

Use of Landmark Features and Geometry by Children and Adults during a Two-Dimensional Search Task  

Science.gov (United States)

Three- to six-year-old children (n=28) and adults (n=46) participated in a two-dimensional search task that included geometry and feature conditions. During each of 24 trials, participants watched as a cartoon character hid behind one of three landmarks arranged in a triangle on a computer screen. The landmarks and character then disappeared and…

Gibson, Brett M.; Leichtman, Michelle D.; Kung, Deborah A.; Simpson, Michael J.

2007-01-01

229

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

Scientific Electronic Library Online (English)

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

Germán, Robledo; Guillermo, Seijo.

230

Origin of the anterior cruciate ligament and the surrounding osseous landmarks of the femur.  

Science.gov (United States)

The aims of this study were to evaluate the discernibility of the LIR (lateral intercondylar ridge) and the LBR (lateral bifurcate ridge) and show their reliability in femoral tunnel placement in ACL (anterior cruciate ligament) reconstruction. Additionally, their position to the femoral axis, their course, and the ACL footprint were analyzed. For this study, 235 human femora were evaluated. Of these, 166 specimens originated from the Museum of Natural History (group A), and 69 were obtained from fixed cadavers at the Anatomic Institute (group B). The femoral footprint and the osseous landmarks were identified macroscopically and labeled in the photographs. A coordinate system was outlined, and the dimensions, position, and orientation of the femoral footprint of the ACL were measured. The LBR was found in 24.7% of the specimens in group A and in only 13.2% of the specimens in group B. The LIR was found in 97.9% and 85.3% of the specimens in groups A and B, respectively. The area of the ACL footprint was 127.21?±?32.54 mm(2) in group A and 119.58?±?34.84 mm(2) in group B. The shapes and angles of the osseous landmarks near the line of Blumensaat were highly variable. The LBR is an unreliable intraoperative landmark for arthroscopic ACL reconstruction due to its low incidence. Other anatomical structures, such as the LIR or the osteochondral border, may be more helpful and reliable landmarks to guide proper tunnel placement. PMID:25065356

Zauleck, Max Konstantin; Gabriel, Sebastian; Fischmeister, Martin Franz; Hirtler, Lena

2014-10-01

231

Evaluating the City Image: A Focus on Landmarks of Kuala Lumpur, Malaysia  

Directory of Open Access Journals (Sweden)

Full Text Available One of the main issues that have been considered about Kuala Lumpur city is its indistinguishable identity and image, partly due to the rapid development and expansion of the city structure over many decades. Inevitably, forming a distinctive city image is not an easy task as it depends primarily on the manner of reciprocal interactions between people and their surrounding built environment. This paper examines the relationship and interaction between people and the city structure, specifically through public evaluation of landmarks as one of the five elements of the city image. The people’s background and their evaluation of the landmarks’ features are examined in this study. To achieve this objective, both quantitative and qualitative data were collected using mixed-techniques involving a questionnaire survey of 120 respondents followed by an unstructured interview. The results show significant differences in the public evaluation of landmarks based on the respondents’ nationality and ethnicity. Differences in the evaluation are related to the landmark factors namely unique; memorable; legible; historic; design; scale; meaningful and color. Much effort by the local authorities is necessary to create a distinguishable image of Kuala Lumpur that reflects the city’s fusion of modern and traditional lifestyles, and diversified cultures and values.

Ahmed Raad Al Shams

2014-01-01

232

36 CFR 62.4 - Natural landmark designation and recognition process.  

Science.gov (United States)

...area's natural values, integrity, or...official land or tax records, whichever...State the land or tax records are not helpful...purposes of NEPA which impacts the NNL or these...natural landmarks are added to the National Registry...deterioration of the natural values on which...

2010-07-01

233

Robust 3D Face Landmark Localization Based on Local Coordinate Coding.  

Science.gov (United States)

In the 3D facial animation and synthesis community, input faces are usually required to be labeled by a set of landmarks for parameterization. Because of the variations in pose, expression and resolution, automatic 3D face landmark localization remains a challenge. In this paper, a novel landmark localization approach is presented. The approach is based on local coordinate coding (LCC) and consists of two stages. In the first stage, we perform nose detection, relying on the fact that the nose shape is usually invariant under the variations in the pose, expression, and resolution. Then, we use the iterative closest points algorithm to find a 3D affine transformation that aligns the input face to a reference face. In the second stage, we perform resampling to build correspondences between the input 3D face and the training faces. Then, an LCC-based localization algorithm is proposed to obtain the positions of the landmarks in the input face. Experimental results show that the proposed method is comparable to state of the art methods in terms of its robustness, flexibility, and accuracy. PMID:25296404

Song, Mingli; Tao, Dacheng; Sun, Shengpeng; Chen, Chun; Maybank, Stephen J

2014-12-01

234

Landmarks in the Professional and Academic Development of Mid-Career Teacher Educators  

Science.gov (United States)

This paper focuses on the professional and academic development of mid-career teacher educators from two universities in England. The objectives of the study were to analyse and compare the career experiences of teacher educators; in particular, to identify stages of development, landmark events and contextual factors affecting professional…

Griffiths, Vivienne; Thompson, Simon; Hryniewicz, Liz

2014-01-01

235

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

2000-06-01

236

Characteristics of anatomical landmarks in the mandibular interforaminal region: A cone-beam computed tomography study  

Science.gov (United States)

Objectives: This study was conducted to assess appearance, visibility, location and course of anatomical landmarks in mandibular interforaminal region using cone-beam computed tomography (CBCT). Study design: A total of 96 CBCT examinations was re-evaluated to exploit anatomical landmarks. The examinations used the Promax 3D CBCT unit. A sole examiner carried out all the measurements. Visibilities of the anatomical landmarks were scored using a four-point rating scale. Results: The mandibular foramen, anterior loop, incisive canal and lingual foramen were observed in 100,84,83,49 % of the images, respectively. The mean size, diameter and width of anterior loop, incisive canal and lingual foramen were obtained 3.54± 1.41, 1.47±0.50 and 0.8 ± 0.09mm, respectively. Conclusion: It is not safe to recommend any definite distance mesially from the mental foramen. The diameter of the canals and foramens should be determined on a case-by-case basis to exploit the appropriate location for each individual. Key words:Anatomical landmarks, cone-beam computed tomography, implant surgery, radiographic evaluation, surgical complications. PMID:22143718

Parnia, Fereidoun; Hafezeqoran, Ali; Mahboub, Farhang; Mojaver-Kahnamoui, Haniye

2012-01-01

237

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

International Nuclear Information System (INIS)

rebrain development with fetal MRI before gw 27. Several anatomical structures are readily detectable with routine fetal MRI sequences; thus, if these landmarks are not delineable, it should raise the suspicion of a pathology. Recommendations regarding favorable sequences/planes are provided. (orig.)

238

Toward a model for lexical access based on acoustic landmarks and distinctive features  

Science.gov (United States)

This article describes a model in which the acoustic speech signal is processed to yield a discrete representation of the speech stream in terms of a sequence of segments, each of which is described by a set (or bundle) of binary distinctive features. These distinctive features specify the phonemic contrasts that are used in the language, such that a change in the value of a feature can potentially generate a new word. This model is a part of a more general model that derives a word sequence from this feature representation, the words being represented in a lexicon by sequences of feature bundles. The processing of the signal proceeds in three steps: (1) Detection of peaks, valleys, and discontinuities in particular frequency ranges of the signal leads to identification of acoustic landmarks. The type of landmark provides evidence for a subset of distinctive features called articulator-free features (e.g., [vowel], [consonant], [continuant]). (2) Acoustic parameters are derived from the signal near the landmarks to provide evidence for the actions of particular articulators, and acoustic cues are extracted by sampling selected attributes of these parameters in these regions. The selection of cues that are extracted depends on the type of landmark and on the environment in which it occurs. (3) The cues obtained in step (2) are combined, taking context into account, to provide estimates of ``articulator-bound'' features associated with each landmark (e.g., [lips], [high], [nasal]). These articulator-bound features, combined with the articulator-free features in (1), constitute the sequence of feature bundles that forms the output of the model. Examples of cues that are used, and justification for this selection, are given, as well as examples of the process of inferring the underlying features for a segment when there is variability in the signal due to enhancement gestures (recruited by a speaker to make a contrast more salient) or due to overlap of gestures from neighboring segments.

Stevens, Kenneth N.

2002-04-01

239

RNIE: genome-wide prediction of bacterial intrinsic terminators  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most accurate computational tools for predicting homology in structural non-coding RNAs. We show that RNIE has superior performance in model species from a spectrum of bacterial phyla....

Gardner, Paul P.; Barquist, Lars; Bateman, Alex; Nawrocki, Eric P.; Weinberg, Zasha

2011-01-01

240

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

Science.gov (United States)

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

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

2014-01-01

 
 
 
 
241

Evaluation of soft tissue thicknesses of facial midline landmarks before and after puberty  

Directory of Open Access Journals (Sweden)

Full Text Available Introduction: In recent years, proportions and harmony of orofacial soft tissues have gained great importance in orthodontics. The aim of this research was to evaluate soft tissue thickness changes of facial midline landmarks during growth in both genders.Materials and methods: In this analytical-descriptive study, lateral cephalometric views of ninety-eight 6-18 year-old patients referring to the Orthodontics Department of Khorasegan Azad University were evaluated. The positions of 7 facial midline landmarks, including glabella, soft tissue nasion, soft tissue points A and B, soft tissue pogonion, and superior and inferior labrale, were determined and then the thicknesses of the landmarks were measured. Data was compared between two groups of under and above 12 years of age between males and females using independent t-test (?=0.05.Results: There were no statistically significant differences between the soft tissue thicknesses of both sexes in any of the landmarks except nasion (p value=0.026 and point B (p value=0.043 in the group under 12 years of age. Differences between the soft tissue thicknesses in both sexes over 12 years of age were statistically significant in nasion (p value = 0.043, point A (p value=0.001, and superior labrale (p value<0.001. Differences between soft tissue thicknesses of all the landmarks were statistically significant between the two age groups in males except point B (p value=0.119; however, in females only the thickness of soft tissue nasion (p value=0.105 and superior labrale (p value=0.968 were not statistically significant between the two age groups.Conclusion: Soft tissue thicknesses were almost the same in boys and girls except nasion and point B before puberty. After puberty upper face soft tissue thicknesses, including glabella and point A, were greater in boys compared to girls. However, in both sexes, soft tissue thicknesses of facial midline landmarks increased after 12 years of age. Key words: Soft tissue, Orthodontics, Radiography.

Soosan Sadeghian

2011-01-01

242

Modeling and matching of landmarks for automation of Mars Rover localization  

Science.gov (United States)

The Mars Exploration Rover (MER) mission, begun in January 2004, has been extremely successful. However, decision-making for many operation tasks of the current MER mission and the 1997 Mars Pathfinder mission is performed on Earth through a predominantly manual, time-consuming process. Unmanned planetary rover navigation is ideally expected to reduce rover idle time, diminish the need for entering safe-mode, and dynamically handle opportunistic science events without required communication to Earth. Successful automation of rover navigation and localization during the extraterrestrial exploration requires that accurate position and attitude information can be received by a rover and that the rover has the support of simultaneous localization and mapping. An integrated approach with Bundle Adjustment (BA) and Visual Odometry (VO) can efficiently refine the rover position. However, during the MER mission, BA is done manually because of the difficulty in the automation of the cross-sitetie points selection. This dissertation proposes an automatic approach to select cross-site tie points from multiple rover sites based on the methods of landmark extraction, landmark modeling, and landmark matching. The first step in this approach is that important landmarks such as craters and rocks are defined. Methods of automatic feature extraction and landmark modeling are then introduced. Complex models with orientation angles and simple models without those angles are compared. The results have shown that simple models can provide reasonably good results. Next, the sensitivity of different modeling parameters is analyzed. Based on this analysis, cross-site rocks are matched through two complementary stages: rock distribution pattern matching and rock model matching. In addition, a preliminary experiment on orbital and ground landmark matching is also briefly introduced. Finally, the reliability of the cross-site tie points selection is validated by fault detection, which considers the mapping capability of MER cameras and the reason for mismatches. Fault detection strategies are applied in each step of the cross-site tie points selection to automatically verify the accuracy. The mismatches are excluded and localization errors are minimized. The method proposed in this dissertation is demonstrated with the datasets from the 2004 MER mission (traverse of 318 m) as well as the simulated test data at Silver Lake (traverse of 5.5 km), California. The accuracy analysis demonstrates that the algorithm is efficient at automatically selecting a sufficient number of well-distributed high-quality tie points to link the ground images into an image network for BA. The method worked successfully along with a continuous 1.1 km stretch. With the BA performed, highly accurate maps can be created to help the rover to navigate precisely and automatically. The method also enables autonomous long-range Mars rover localization.

Wang, Jue

243

Proper name retrieval in temporal lobe epilepsy: naming of famous faces and landmarks.  

Science.gov (United States)

The objective of this study was to further explore proper name (PN) retrieval and conceptual knowledge in patients with left and right temporal lobe epilepsy (69 patients with LTLE and 62 patients with RTLE) using a refined assessment procedure. Based on the performance of a large group of age- and education-matched normals, a new test of famous faces and famous landmarks was designed. Recognition, naming, and semantic knowledge were assessed consecutively, allowing for a better characterization of deficient levels in the naming system. Impairment in PN retrieval was common in the cohort with TLE. Furthermore, side of seizure onset impaired stages of name retrieval differently: LTLE impaired the lexico-phonological processing, whereas RTLE mainly impaired the perceptual-semantic stage of object recognition. In addition to deficient PN retrieval, patients with TLE had reduced conceptual knowledge regarding famous persons and landmarks. PMID:23542541

Benke, Thomas; Kuen, Eva; Schwarz, Michael; Walser, Gerald

2013-05-01

244

[Anatomical key points and operative principle of "two planes and four landmarks" in extralevator abdominoperineal excision].  

Science.gov (United States)

Abominoperineal resection (APR) is the main approach of lower rectal cancer treatment. Recently, it was found that conventional APR had higher incidence rate of positive circumferential resection margin(CRM) and intraoperative perforation (IOP), which was the crucial reason of local recurrence and worse prognosis. Extralevator abdominoperineal excision(ELAPE) procedure was proposed by European panels including surgeons, radiologist and pathologists, and considered to lower the positive rates of CRM and IOP. Definitive surgical planes and anatomic landmarks are the cores of this procedure, which are the prerequisite for the guarantee of safety and smoothness of surgery. To realize the anatomy of muscles, fascias, blood vessels and nervous of perineal region is the base of carrying out ELAPE procedure. In this paper, we introduce the key anatomy related to ELAPE procedure and summarize the principle of ELAPE procedure as "two planes and four landmarks", which will be beneficial to the popularization and application. PMID:25421764

Ye, Yingjiang; Shen, Zhanlong; Wang, Shan

2014-11-01

245

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

International Nuclear Information System (INIS)

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

246

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

1995-01-01

247

Towards a new speech event detection approach for landmark-based speech recognition  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this work, we present a new approach for the classification and detection of speech units for the use in landmark or eventbased speech recognition systems. We use segmentation to model any time-variable speech unit by a fixed-dimensional observation vector, in order to train a committee of boosted decision stumps on labeled training data. Given an unknown speech signal, the presence of a desired speech unit is estimated by searching for each time frame the corresponding segment, that provi...

Ziegler, Stefan; Ludusan, Bogdan; Gravier, Guillaume

2012-01-01

248

Muscle fibre direction of longissimus, iliocostalis and multifidus: landmark-derived reference lines.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Considerable inter-individual variations in the fibre direction angles of the iliocostalis lumborum, longissimus and multifidus were observed, thus bringing the applicability of a two dimensional fixed angle grid system for fibre direction determination into question. However, the angulation of the fibres of the multifidus and iliocostalis lumborum were found to be easily identifiable by the use of three surface anatomical landmarks: the caudal tip of the superior iliac spine, the lateral bor...

Foa, J. L.; Forrest, W.; Biedermann, H. J.

1989-01-01

249

Opacification of tympanic membrane: As an anatomic landmark of oto-radiology  

International Nuclear Information System (INIS)

Opacification of tympanic membrane was done by attachment of a cotton patch soaked with contrast media through external meatus. Detailed evaluation of fine structures in middle ear of normal adult is easily done after opacification of tympanic membrane. It was believed that opacified tympanic membrane would be an useful landmark for early detection of cholesteatoma and a good marker also in tomography of temporal bone.

250

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

Science.gov (United States)

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

Wang, Hongsheng; Zheng, Naiqaun Nigel

2010-12-01

251

Leg CT scan  

Science.gov (United States)

CAT scan - leg; Computed axial tomography scan - leg; Computed tomography scan - leg; CT scan - leg ... printed on film. Three-dimensional models of the leg can be created by adding the slices together. ...

252

Blocking between landmarks during 2-D (touchscreen) and 3-D (ARENA) search tasks with pigeons.  

Science.gov (United States)

Many studies investigating cue competition have focused on the blocking effect. We investigated the blocking effect with pigeons using a landmark-based spatial search task in both a touchscreen preparation (Exp. 1a) and an automated remote environmental navigation apparatus (Exp. 1b). In Phase 1, two landmarks (LMs: A and Z) appeared on separate trials as colored circles among a row of eight (touchscreen) or six (ARENA) identical response units. Subjects were rewarded for pecking at a target response unit to the right of LM A and to the left of an extraneous LM, Z. During the blocking trials in Phase 2, LM X was presented in compound with a second LM (A) that had been previously trained. On control trials, LM Y was presented in compound with LM B and a target in the same manner as in the trials of AX, except that neither landmark had previously been trained with the target. All subjects were then tested with separate trials of A, X, B, and Y. Testing revealed poor spatial control by X relative to A and Y. We report the first evidence for a spatial-blocking effect in pigeons and additional support for associative effects (e.g., blocking) occurring under similar conditions (e.g., training sessions, spatial relationships, etc.) in 3-D and 2-D search tasks. PMID:25209533

Leising, Kenneth J; Wong, Jared; Ruprecht, Chad M; Blaisdell, Aaron P

2014-12-01

253

A new automatic landmark extraction framework on ultrasound images of femoral condyles  

Science.gov (United States)

In Computer Assisted Orthopaedic Surgery (CAOS), surgeons have to acquire some anatomical landmarks as inputs to the system. To do so, they use manual pointers that are localized in the Operating Room (OR) space using an infrared camera. When the needed landmark is not reachable through an opening, it is palpated directly on skin and there is a loss of precision that can vary from several millimeters to centimeters depending on the thickness of soft tissues. In this paper, we propose a new framework based on three main steps to register the bone surface and extract automatically anatomical landmarks with an ultrasound probe. This framework is based on an oriented gradient calculation, a simulated-compound and a contour closure using a graph representation. The oriented gradient allows extracting a set of pixels that probably belong to the bone surface. The simulatedcompound step allows using ultrasound images properties to define a set of small segments which may belong to the bone surface, and the graph representation allows eliminating false positive detection among remaining segments. The proposed method has been validated on a database of 230 ultrasound images of anterior femoral condyles (on the knee). The average computation time is 0.11 sec per image, and average errors are: 0.54 mm for the bone surface extraction, 0.31 mm for the condylar line, and 1.4 mm for the trochlea middle.

Masson-Sibut, Agnès; Nakib, Amir; Petit, Eric; Leitner, François

2012-03-01

254

Describing Wing Geometry of Aedes Aegypti Using Landmark-Based Geometric Morphometrics  

Directory of Open Access Journals (Sweden)

Full Text Available Insect wing morphology has been used in many studies to describe variations among species and populations using traditional morphometrics and more recently, geometric morphometrics. This study was conducted to determine intraspecific divergence in wing shape and venation in Aedes aegypti using landmark-based geometric morphometrics. In the Philippines, Ae. aegypti has been identified as a common dengue vector species. With the increasing cases of dengue, mosquito control programs are faced with problems on vector species diversification and proper identification. Variation in wing geometry may provide relevant information on proper identification of species and in describing population diversity. In this study, the geometry of 30 wings of female Ae. Aegypti was described using 18 anatomical landmarks and subjected to Procrustes superimposition and relative warp analysis. Results of the relative warp analysis showed some intraspecific variation in the wing outline of Ae. aegypti. The observed morphological disparity in wing shape suggest a possible morphological divergence among populations of Ae. aegypti. Based from the results of the study, landmark-based geometric morphometrics is a good tool in describing quantitatively variations in wing shape of the mosquitoes.

udy P. Sendaydiego

2013-07-01

255

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

2007-04-01

256

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

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

Mertes, Marcel; Dittmar, Laura; Egelhaaf, Martin; Boeddeker, Norbert

2014-01-01

257

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Martino?n-torres, Marcos

2001-01-01

258

Automated planning of MRI scans of knee joints  

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

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

2007-03-01

259

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Stereotactic targeting is a commonly used technique for performing injections in the brains of mice and other animals. The most common method for targeting stereoscopic injections uses the skull indentations bregma and lambda as reference points and is limited in its precision by factors such as skull curvature and individual variation, as well as an incomplete correspondence between skull landmarks and brain locations. In this software tool, a 3D laser scan of the mouse sku...

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

2014-01-01

260

Heart PET scan  

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

 
 
 
 
261

Coronary Calcium Scan  

Science.gov (United States)

... the NHLBI on Twitter. What Is a Coronary Calcium Scan? A coronary calcium scan is a test ... you have calcifications in your coronary arteries. Coronary Calcium Scan Figure A shows the position of the ...

262

The Genome Sequence of Drosophila melanogaster  

Science.gov (United States)

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

Ramanujan, Krishna.

263

CT scan method accurately assesses humeral head retroversion.  

Science.gov (United States)

Humeral head retroversion is not well described with the literature controversial regarding accuracy of measurement methods and ranges of normal values. We therefore determined normal humeral head retroversion and assessed the measurement methods. We measured retroversion in 65 cadaveric humeri, including 52 paired specimens, using four methods: radiographic, computed tomography (CT) scan, computer-assisted, and direct methods. We also assessed the distance between the humeral head central axis and the bicipital groove. CT scan methods accurately measure humeral head retroversion, while radiographic methods do not. The retroversion with respect to the transepicondylar axis was 17.9 degrees and 21.5 degrees with respect to the trochlear tangent axis. The difference between the right and left humeri was 8.9 degrees. The distance between the central axis of the humeral head and the bicipital groove was 7.0 mm and was consistent between right and left humeri. Humeral head retroversion may be most accurately obtained using the patient's own anatomic landmarks or, if not, identifiable retroversion as measured by those landmarks on contralateral side or the bicipital groove. PMID:18264854

Boileau, P; Bicknell, R T; Mazzoleni, N; Walch, G; Urien, J P

2008-03-01

264

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

Science.gov (United States)

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

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

2011-01-01

265

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.

266

Geometry and landmark representation by pigeons: evidence for species-differences in the hemispheric organization of spatial information processing?  

Science.gov (United States)

In this study, we investigated how pigeons (Columba livia) represent environmental geometry and landmark information. Birds learned to locate the centre of a square arena by means of geometric cues alone, or by means of both geometric and landmark cues. By manipulating the type of information available at training and testing, we assessed which cues the birds had encoded, and through the use of monocular occlusion we examined how the information was represented by the two brain hemispheres. Our results show that both brain hemispheres encoded geometric and landmark information. During all viewing conditions, the geometric representation was based mainly on an absolute metric for distance. The relative use of geometry and landmarks was experience dependent. With both brain hemispheres available birds relied, to a greater degree, on geometric information and used it in a more integrated way than with either hemisphere alone. Overall, our findings show a different pattern for the hemispheric encoding of geometric and landmark information by the pigeon than that previously reported for the domestic chick. Our results suggest that the organization of spatial information processing in the left and right brain hemispheres of birds may be more diverse than what is currently known. PMID:19200073

Wilzeck, Christiane; Prior, Helmut; Kelly, Debbie M

2009-02-01

267

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

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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

2010-01-01

268

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

2010-07-01

269

The resident's ridge as an arthroscopic landmark for anatomical femoral tunnel drilling in ACL reconstruction.  

Science.gov (United States)

The purposes of this study were to establish the technique to arthroscopically identify the resident's ridge without bony notchplasty even in patients with chronic ACL insufficiency and to elucidate if the ridge could be used as a landmark for anatomical femoral tunnel for ACL graft. There were 50 consecutive patients undergoing arthroscopic ACL reconstruction. With the thigh kept horizontal using a leg holder, a meticulous effort was made to find out a linear ridge running proximo-distal in a posterior one-third of the lateral notch wall, after removal of superficial soft tissue with radiofrequency energy. If the ridge was found, a socket with a rectangular aperture of 5 x 10 mm was created just behind the ridge. At 3-4-weeks post surgery, three-dimensional computed tomography (3-D CT) was performed to geographically identify the location of the ridge using the socket as a reference. Arthroscopically, a linear ridge running from superior-anterior to inferior-posterior on the lateral notch wall was consistently observed 7-10 mm anterior to the posterior articular cartilage margin of the lateral femoral condyle in all of the patients. The 3-D CT pictures proved the arthroscopically identified ridge to be the resident's ridge. The resident's ridge is arthroscopically identifiable after non-mechanical removal of the soft tissues without bony notchplasty. The ridge is a useful landmark for anatomical femoral tunnel drilling in arthroscopic ACL reconstruction. PMID:19915823

Shino, Konsei; Suzuki, Tomoyuki; Iwahashi, Takehiko; Mae, Tatsuo; Nakamura, Norimasa; Nakata, Ken; Nakagawa, Shigeto

2010-09-01

270

Computed tomographic scanning and radioisotope bone scanning  

International Nuclear Information System (INIS)

We report here a comparative study of bone scans, radiographs, and computed tomographic (CT) scanning in 30 patients with cancer of the breast. All the bone scans had focally increased uptake in the axial skeleton and were assessed with the corresponding radiographs. CT scans were made of the regions of focally increased uptake. In three patients with solitary bone scan abnormalities, two were shown on CT scans to have lytic and sclerotic lesions when the conventional radiographs showed only osteophytes and degenerative joint disease, and in one patient CT scans demonstrated degenerative disease of a costovertebral joint not shown on the radiographs. In two patients with multifocal abnormalities in the lumbar spine that could be accounted for by benign disease shown on the CT scans, radiography could explain only one lesion. In the remaining patients, there was agreement between the three methods. The results confirm the importance of excluding benign causes for bone scan abnormalities. (orig./MG) 891 MG/orig.- 892 MB

271

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

Science.gov (United States)

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

Little, J P; Adam, C J

2015-05-01

272

Cryptosporidium Parvum Genome Project  

Directory of Open Access Journals (Sweden)

Full Text Available A lack of basic understanding of parasite biology has been a limiting factor in designing effective means of treating and preventing disease caused by Cryptosporidium parvum. Since the genomic DNA sequence encodes all of the heritable information responsible for development, disease pathogenesis, virulence, species permissiveness and immune resistance, a comprehensive knowledge of the C. parvum genome will provide the necessary information required for cost-effective and targeted research into disease prevention and treatment. With the recent advances in high-throughput automated DNA sequencing capabilities, large-scale genomic sequencing has become a cost-effective and time-efficient approach to understanding the biology of an organism. In addition, the continued development and implementation of new software tools that can scan raw sequences for signs of genes and then identify clues as to potential functions, has provided the final realization of the potential rewards of genome sequencing. To further our understanding of C. parvum biology, we have initiated a random shotgun sequencing approach to obtain the complete sequence of the IOWA isolate of C. parvum. Our progress to date has demonstrated that sequencing of the C. parvum genome will be an efficient and costeffective method for gene discovery of this important eukaryotic pathogen. This will allow for the identification of key metabolic and immunological features of the organism that will provide the basis for future development of safe and effective strategies for prevention and treatment of disease in AIDS patients, as well as immunocompetent hosts. Moreover, by obtaining the complete sequence of the C. parvum genome, effective methods for subspecific differentiation (strain typing and epidemiologic surveillance (strain tracking of this pathogen can be developed.

Mitchell S. Abrahamsen

2006-04-01

273

Assessing the role of the biomaterial Aquavene in patient reactions to Landmark midline catheters.  

Science.gov (United States)

Landmark midline catheters (Menlo Care, Inc., Palo Alto, CA) provide peripheral venous access for the infusion of medications or fluids. They are constructed of an inner layer of polyurethane and an outer layer of the biomaterial Aquavene, a blend of polyurethane and polyethylene oxide to which butylated hyroxyanisole (BHA), butylated hydroxytoluene (BHT), and triallyl-s-triazine trione (TTT) are added. Once inside the vein, the Aquavene material becomes hydrated and the catheter swells resulting in minimal trauma to the vein. It is well recognized that some patients experience reactions to catheterization. Recent reports of hypersensitivity-like reactions in some patients catheterized with Landmark catheters have prompted the manufacturer to reexamine biocompatibility data and clinical data to assess whether Aquavene was the source of the patient responses. None of the biocompatibility studies provided by Menlo Care in support of U.S. registration and marketing of Aquavene-based catheters demonstrated any tendency for Aquavene or material extracted from Aquavene to invoke an immunological or toxicological response. Examination of potential catheter residuals revealed that significant amounts of BHA and BHT were unlikely to be released from the catheters during expected use. The amounts of polyethylene oxide and TTT expected to be released during the first few minutes after catheter insertion (when most of the patient reactions were reported) are almost 92,500 and 270,000 times lower, respectively, than nontoxic animal exposures. These analyses do not support chemically mediated toxicity as an explanation for the adverse events experienced by some patients. A review of the postmarket surveillance data on Aquavene-based catheters revealed that the reported events were not consistent with a hypersensitivity (immunogenic) response to the biomaterial. The rare reported adverse events tend to occur quickly, most often after flushing of the catheter, and resolve quickly, even when the catheter remains in place. Determining the frequency and severity of adverse events reported in association with the use of Landmark catheters will ultimately require a controlled prospective study, preferably one with a concurrent control group using alternative products. PMID:9056501

Silverstein, B; Witkin, K M; Frankos, V H; Terr, A I

1997-02-01

274

Primate genomes.  

Science.gov (United States)

A particular interest in primate genetics was fueled by the release of the complete human genome sequence drafts reported in 2001 by the IHGSC and Celera Genomics. Postgenomic comparative analyses based on the complete genome sequence of the mouse started focusing on functional, evolutionary and diversity aspects of human DNA. By analyzing molecular character states in the representatives of the major primate groups one is able to reconstruct the processes that shape genomes on the lineage to humans after the mouse-human divergence. Consequently, several primate genome sequences are about to be generated during Whole Genome Shotgun (WGS) sequencing projects and are already available for two representatives of the Old World monkeys and hominoids (rhesus monkey, chimpanzee). Comparative data restricted to functional genome parts of a meaningful primate sample (ENCODE project) are underway. These data will yield a definite phylogenetic framework linking the mouse, primate related eutherians and the major primate groups, which is indispensable for any analysis of character evolution. Concerning the functional site comparative genetic research in primates on molecular phenomena that control the spatiotemporal profile of the cellular RNA and protein composition will contribute to our understanding of genotype-phenotype correlations and the emergence of human specific traits. PMID:18753766

Herlyn, H; Zischler, H

2006-01-01

275

Maximized Posteriori Attributes Selection from Facial Salient Landmarks for Face Recognition  

Science.gov (United States)

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

Gupta, Phalguni; Kisku, Dakshina Ranjan; Sing, Jamuna Kanta; Tistarelli, Massimo

276

Maximized Posteriori Attributes Selection from Facial Salient Landmarks for Face Recognition  

CERN Document Server

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

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

2010-01-01

277

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

278

Physics-based elastic image registration using splines and including landmark localization uncertainties.  

Science.gov (United States)

We introduce an elastic registration approach which is based on a physical deformation model and uses Gaussian elastic body splines (GEBS). We formulate an extended energy functional related to the Navier equation under Gaussian forces which also includes landmark localization uncertainties. These uncertainties are characterized by weight matrices representing anisotropic errors. Since the approach is based on a physical deformation model, cross-effects in elastic deformations can be taken into account. Moreover, we have a free parameter to control the locality of the transformation for improved registration of local geometric image differences. We demonstrate the applicability of our scheme based on 3D CT images from the Truth Cube experiment, 2D MR images of the brain, as well as 2D gel electrophoresis images. It turns out that the new scheme achieves more accurate results compared to previous approaches. PMID:17354831

Wörz, Stefan; Rohr, Karl

2006-01-01

279

Landmark-based shape analysis of the archaic Homo calvarium from Ceprano (Italy).  

Science.gov (United States)

The Ceprano calvarium represents one of the most important sources of information about both the dynamics of the earliest hominid dispersal toward Europe and the evolution of the genus Homo in the early-to-middle Pleistocene. In this paper, the midsagittal vault profile and the 3D frontal bone morphology of Ceprano are investigated comparatively, using landmark coordinates and Procrustes superimposition. In fact, despite the fact that the skull appears partially distorted by diagenetic pressures (thus precluding a comprehensive landmark-based analysis), some aspects of the overall morphology are suitable for consideration in terms of geometric morphometrics. The midsagittal profile shows an archaic shape, comparable with the H. ergaster/erectus range of variation because of the fronto-parietal flattening, the development of the supraorbital and nuchal structures, and the occurrence of a slightly larger occipital bone. By contrast, the frontal bone displays a derived 3D shape that, mostly because of the widening of the frontal squama, appears comparable with the Afro-European variation of the Middle Pleistocene (i.e., H. heidelbergensis/rhodesiensis). Taking into account the unique morphological pattern displayed by Ceprano, its role as a link between early Homo and the Middle Pleistocene populations of Europe and Africa is not falsified. Thus, when aspects of the Ceprano's morphology are described within the analytical framework provided by geometric morphometrics, the relationships between Ceprano and the subsequent Afro-European fossil record are emphasized, suggesting the occurrence of an ancestral stock of H. heidelbergensis/rhodesiensis that is properly represented by the Italian specimen. PMID:17177181

Bruner, Emiliano; Manzi, Giorgio

2007-03-01

280

Asynchrony of the early maturation of white matter bundles in healthy infants: Quantitative landmarks revealed noninvasively by diffusion tensor imaging  

International Nuclear Information System (INIS)

ate and inferior longitudinal fascicles, then the spino-thalamic tract and fornix, and finally the cortico-spinal tract as the most mature bundle. Thus, this approach provides new quantitative landmarks for further noninvasive research on brain-behavior relationships during normal and abnormal development. (authors)

 
 
 
 
281

Nucleomorph genomes.  

Science.gov (United States)

Nucleomorphs are the remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes, two evolutionarily distinct unicellular eukaryotic lineages that acquired photosynthesis secondarily by the engulfment of red and green algae, respectively. At less than one million base pairs in size, nucleomorph genomes are the most highly reduced nuclear genomes known, with three small linear chromosomes and a gene density similar to that seen in prokaryotes. The independent origin of nucleomorphs in cryptophytes and chlorarachniophytes presents an interesting opportunity to study the reductive evolutionary forces that have led to their remarkable convergence upon similar genome architectures and coding capacities. In this article, we review the current state of knowledge with respect to the structure, function, origin, and evolution of nucleomorph genomes across the known diversity of cryptophyte and chlorarachniophyte algae. PMID:19686079

Moore, Christa E; Archibald, John M

2009-01-01

282

Lung PET scan  

Science.gov (United States)

Chest PET scan; Lung positron emission tomography; PET - chest; PET - lung; PET - tumor imaging ... A PET scan requires a small amount of radioactive material (tracer). This tracer is given through a vein (IV), ...

283

Getting a CAT Scan  

Medline Plus

Full Text Available ... Games Kids' Medical Dictionary En Español What Other Kids Are Reading Moving to Middle School Going Back ... Locker Society Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) ...

284

Getting a CAT Scan  

Medline Plus

Full Text Available ... Works Main Page 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 ...

285

Radiopharmaceutical scanning agents  

International Nuclear Information System (INIS)

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

286

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

287

A genome scan for quantitative trait loci affecting milk somatic cell score in Israeli and Italian Holstein cows by means of selective DNA pooling with single- and multiple-marker mapping.  

Science.gov (United States)

Mastitis is an important and common dairy cattle disease affecting milk yield, quality, and consumer safety as well as cheese yields and quality. Animal welfare and residues of the antibiotics used to treat mastitis cause public concern. Considerable genetic variation may allow selection for increased resistance to mastitis. Because of high genetic correlation to milk somatic cell score (SCS), SCS can serve as a surrogate trait for mastitis resistance. The present study intended to identify quantitative trait loci (QTL) affecting SCS in Israeli and Italian Holstein dairy cattle (IsH and ItH, respectively), using selective DNA pooling with single and multiple marker mapping. Milk samples of 4,788 daughters of 6 IsH and 7 ItH sires were used to construct sire-family high- and low-tail pools, which were genotyped at 123 (IsH) and 133 (ItH) microsatellite markers. Shadow correction was used to obtain pool allele frequency estimates. Frequency difference between the tails and empirical standard error of D, SE(D), were used to obtain P-values. All markers significant by single marker mapping were also significant by multiple marker mapping, but not vice versa. Combining both populations, 22 QTL on 21 chromosomes were identified; all corresponded to previous reports in the literature. Confidence intervals were set by chi-squared drop method. Heterozygosity of QTL was estimated at 44.2%. Allele substitution effects ranged from 1,782 to 4,930 cells/mL in estimated breeding value somatic cell count units. Most (80%) of the observed variation in estimated breeding value somatic cell score could be explained by the QTL identified under the stringent criteria. The results found here can be used as a basis for further genome-wide association studies for the same trait. PMID:20855026

Tal-Stein, R; Fontanesi, L; Dolezal, M; Scotti, E; Bagnato, A; Russo, V; Canavesi, F; Friedmann, A; Soller, M; Lipkin, E

2010-10-01

288

Radiographic scanning agent  

International Nuclear Information System (INIS)

A composition and method for the preparation of a technetium-99m -based scanning agent are disclosed. The scanning agent is prepared from /sup 99m/Tc, in a +3, +4 and/or +5 oxidation state, and a methanehydroxydiphosphonate bone-seeking agent which carries the radionuclide to bone mineral. The methanehydroxydiphosphonate agent provides scan sharpness equivalent or superior to commercial scanning agents, and is superior for detecting myocardial infarcts, as compared with commercial scanning agents such as ethane-1-hydroxy-1,1-diphosphonate and methanediphosphonate

289

Algorithms For Automatic And Robust Registration Of 3D Head Scans  

Directory of Open Access Journals (Sweden)

Full Text Available Two methods for registering laser-scans of human heads and transforming them to a new semantically consistent topology defined by a user-provided template mesh are described. Both algorithms are stated within the Iterative Closest Point framework. The first method is based on finding landmark correspondences by iteratively registering the vicinity of a landmark with a re-weighted error function. Thin-plate spline interpolation is then used to deform the template mesh and finally the scan is resampled in the topology of the deformed template. The second algorithm employs a morphable shape model, which can be computed from a database of laser-scans using the first algorithm. It directly optimizes pose and shape of the morphable model. The use of the algorithm with PCA mixture models, where the shape is split up into regions each described by an individual subspace, is addressed. Mixture models require either blending or regularization strategies, both of which are described in detail. For both algorithms, strategies for filling in missing geometry for incomplete laser-scans are described. While an interpolation-based approach can be used to fill in small or smooth regions, the model-driven algorithm is capable of fitting a plausible complete head mesh to arbitrarily small geometry, which is known as "shape completion". The importance of regularization in the case of extreme shape completion is shown.

Peter Eisert

2010-12-01

290

The RHIC Beam Energy Scan - STAR'S Perspective  

CERN Document Server

The first decade of RHIC running has established the existence of a strongly coupled Quark Gluon Plasma (sQGP), a new state of nuclear matter with partonic degrees of freedom. Theory predicts how transitions to this sQGP depend on the baryon chemical potential, mu_B, and temperature, T. At low mu_B and high T a cross-over transition occurs. At high mu_B and low T the transition is of first order. Hence, at intermediate values, a critical point should occur. Experimentally we can vary these initial conditions by altering the beam energy. Thus a beam energy scan (BES) will allow us to explore the QCD phase diagram close to the QGP-hadron gas boundary and locate such key "landmarks" as the critical point. Establishing the existence of this critical point would be a seminal step forwards for QCD physics. I discuss below the physics case for a BES, and explain why RHIC and the STAR experiment are ideally designed for such a program.

Caines, Helen

2009-01-01

291

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2010-09-15

292

Listeria Genomics  

Science.gov (United States)

The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

293

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

Directory of Open Access Journals (Sweden)

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

F. Esfandiarpour

2009-12-01

294

Laser Scanning in Forests  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Håkan Olsson; Juha Hyyppä; Markus Holopainen

2012-01-01

295

The scanning proton microprobe  

International Nuclear Information System (INIS)

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

296

Bone scanning in lymphoma  

International Nuclear Information System (INIS)

The results of bone scanning with the newer technetium-99m complexes were correlated with clinical, laboratory, and radiographic findings in 26 patients with malignant lymphoma (10 with Hodgkin's disease and 16 with non-Hodgkin's lymphomas). Abnormalities on bone scan compatible with lymphomatous involvement of the skeleton appeared to occur more commonly in patients with diffuse lymphomas than in patients with nodular lymphomas and were generally observed in the setting of advanced disease (15 of 23 patients). Twenty-seven (73 percent) of the 37 scans obtained were abnormal. Although abnormal scans were observed with the greatest frequency in patients with bone pain (11 of 11), bone marrow involvement (11 of 12), abnormal skeletal radiographs (11 of 11), and elevated serum alkaline phosphatase levels (5 of 6), bone scanning also detected lymphomatous involvement in patients free of pain or with normal laboratory tests. Moreover, conventional radiography was entirely normal in six (35 percent) of 17 patients with abnormal scans and revealed only nonspecific osteopenia in another two patients (12 percent). Serial bone scans in nine patients reflected their response to chemotherapy. Of the 37 scans, only one was judged falsely positive and one falsely negative. Bone scanning with /sup 99m/Tc complexes is a safe, simple, and sensitive screening procedure for detecting both extensive and focal lymphomatous involvement of the skeletal system and is a useful means of following such involvement in response to treatment

297

Advanced scanning probe lithography  

Science.gov (United States)

The nanoscale control afforded by scanning probe microscopes has prompted the development of a wide variety of scanning-probe-based patterning methods. Some of these methods have demonstrated a high degree of robustness and patterning capabilities that are unmatched by other lithographic techniques. However, the limited throughput of scanning probe lithography has prevented its exploitation in technological applications. Here, we review the fundamentals of scanning probe lithography and its use in materials science and nanotechnology. We focus on robust methods, such as those based on thermal effects, chemical reactions and voltage-induced processes, that demonstrate a potential for applications.

Garcia, Ricardo; Knoll, Armin W.; Riedo, Elisa

2014-08-01

298

Scanning of bone metastases  

International Nuclear Information System (INIS)

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

299

Anatomic landmarks of fluoroscopy guided puncture of the pulseless femoral artery  

International Nuclear Information System (INIS)

We wanted to improve puncturing the pulseless femoral artery by evaluating the anatomic landmarks that suggest the course of the femoral artery on fluoroscopy. We analyzed 37 hemipelvis spot images that were centered on the arterial sheath after puncture of the femoral artery. The inguinal angles were measured between the inguinal line connecting the anterior superior iliac spine and the symphysis pubis, and the line of the arterial sheath. Inguinal ligament ratios were measured as the distance from the symphysis pubis to the arterial sheath to the length of the inguinal ligament on the inguinal line. The femoral head ratios were measured as the distance from the medial margin of the femur head to the arterial sheath to the transverse length of the femur head. The mean inguinal angle was 66.5 and the mean inguinal ligament ratio was 0.42 (± 0.03). The mean femoral head ratio was 0.08 (± 0.18). In comparing the men and women, there was no significant difference in the inguinal angle and the femoral head ratio, but the inguinal distance ratio was larger in women (men: 0.41 ± 0.033, women: 0.44 ± 0.031, ? < 0.05). The femoral artery generally courses just lateral to the medial margin of the femur head (femoral head ratio: 0.08) and the medial 40% of the inguinal ligament (inguinal ligament ratio: 0.42). So, consideration of these relations may be helpful for puncturing the pulseless femoral artery

300

Truncation of the flash-lag effect by a fixed spatial landmark.  

Science.gov (United States)

The flash-lag effect is a visual illusion where a moving image is perceived to be advanced in its spatial location relative to a flashed image. Multiple studies have shown that the flash-lag effect can be enhanced by increasing the uncertainty of the moving and/or flashed images. However, little is known about the effect of task-irrelevant visual objects on the flash-lag effect. We were interested to see whether a task-irrelevant spatial landmark might reduce uncertainty and hence reduce the flash-lag effect. We placed a fixed bar between moving and flashed bars while measuring the flash-lag effect in six participants. For most participants, the fixed bar substantially truncated the flash-lag effect. The effect was maximal when the fixed bar was aligned with the flashed bar and decreased when the fixed bar was positioned more peripherally. A second experiment with two participants used a smaller fixed bar; the smaller bar had less truncation effect in one participant, while the other participant showed similar truncation regardless of the fixed bar size. Our results support models that place the locus of the flash-lag effect in higher-order brain areas, e.g., the parietal lobe. PMID:25401439

Paschall, Jacob D; Mazurek, Mark E

2014-09-01

 
 
 
 
301

Enhancer Identification through Comparative Genomics  

Energy Technology Data Exchange (ETDEWEB)

With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

Visel, Axel; Bristow, James; Pennacchio, Len A.

2006-10-01

302

Comparing the Effectiveness of GPS-Enhanced Voice Guidance for Pedestrians with Metric- and Landmark-Based Instruction Sets  

Science.gov (United States)

This paper reports on a field experiment comparing two different kinds of verbal turn instructions in the context of GPS-based pedestrian navigation. The experiment was conducted in the city of Salzburg with 20 participants. Both instruction sets were based on qualitative turn direction concepts. The first one was enhanced with metric distance information and the second one was enhanced with landmark-anchored directions gathered from participants of a previous field experiment. The results show that in context of GPS-enhanced pedestrian navigation both kinds of instruction sets lead to similar navigation performance. Results also demonstrate that effective voice-only guidance of pedestrians in unfamiliar environments at a minimal error rate and without stopping the walk is feasible. Although both kinds of instructions lead to similar navigation performance, participants clearly preferred landmark-enhanced instructions.

Rehrl, Karl; Häusler, Elisabeth; Leitinger, Sven

303

Environmental Scanning Report.  

Science.gov (United States)

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

Truckee Meadows Community Coll., Sparks, NV.

304

Getting a CAT Scan  

Medline Plus

Full Text Available ... Main Page 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 ...

305

Using the C7-T3 spinous processes as landmarks for the localization of thoracic spinal lesions: technique notes.  

Science.gov (United States)

The authors describe a method of using the C7-T3 spinous processes visualized on MRI as landmarks for localizing thoracic spinal lesions in 19 cases. This method included six steps. First, the "spinous process nearest to the lesion that was visible on the MRI image" was identified. Second, a dashed line was drawn on the image through the tip of the identified spinous process perpendicular to the skin surface. Third, two additional dashed lines parallel to the first dashed line were drawn from the upper and lower margins of the lesion. Fourth, the distances between the identified process and the two additional dashed lines were measured. Fifth, the same "spinous process nearest to the lesion" was identified by palpation and marked on the patient's skin. Sixth, the upper and lower margins of the lesion were marked on the skin according to the two distances measured in step 4. After the lesion was exposed, the deviations of the lesion margins were measured. All 19 cases of the thoracic spinal lesions were localized correctly using the C7-T3 spinous processes visualized on the MRI images as landmarks without any other evaluation methods. The deviation value for the localization of the tumor margin was 4.1?±?1.47 mm. Using the C7-T3 spinous processes as landmarks is an accurate, simple, and economic method for lesion localization during thoracic spinal surgery. PMID:24030754

Xiao, Xinru; Wu, Zhen; Zhang, Liwei; Jia, Guijun; Zhang, Junting; Tang, Jie; Meng, Guolu

2014-01-01

306

Endoscopic orientation of the parasellar region in sphenoid sinus with ill-defined bony landmarks: an anatomic study.  

Science.gov (United States)

The sphenoid bony landmarks are important for endoscopic orientation in skull base surgery but show a wide range of variations. We aimed to describe an instructional model for the endoscopic parasellar anatomy in sphenoid sinuses with ill-defined bony landmarks. Five preserved injected cadaveric heads and four sides of dry skulls were studied endoscopically via transethmoid, transsphenoidal approach. The parasellar region was exposed by drilling along the maxillary nerve (V2) canal [the length of the foramen rotundum (FR) between the middle cranial fossa and the pterygopalatine fossa]. This was achieved by drilling in the inferior part of the lateral wall of posterior ethmoids immediately above the sphenopalatine foramen. Cavernous V2 was traced to the paraclival internal carotid artery (ICA). Cavernous sinus (CS) apex was exposed by drilling a triangle bounded by V2 and its canal inferiorly, bone between FR and superior orbital fissure (SOF) anteriorly, and ophthalmic nerve (V1) superiorly. Drilling was continued toward the annulus of Zinn (AZ) and optic nerve superiorly and over the intracavernous ICA posteriorly. Endoscopic measurements between V2, SOF, AZ, and opticocarotid recess were obtained. Endoscopic systematic orientation of parasellar anatomy is presented that can be helpful for approaching sphenoid sinus with ill-defined bony landmarks. PMID:21772799

Amin, Sameh M; Nasr, Ashraf Y; Saleh, Hamid A; Foad, Mohamed M; Herzallah, Islam R

2010-11-01

307

Beam scanning system  

International Nuclear Information System (INIS)

A system for deflecting a beam of particles having different momenta, preferably through a 900 angle, so as to cause the beam to impinge upon a moving target and to scan across the target is described. The system includes a means responsive to a beam from a suitable source for causing the beam to periodically scan in a scanning plane and further means for deflecting the periodically scanned beam through the desired angle in a deflection plane so that the deflected beam impinges on the target. Means are included in the system for reducing the momentum dispersion at the target in both the deflection and the scanning planes and for spatially focussing the beam so as to produce a desired beam diameter at the target

308

Transverse section scanning mechanism  

International Nuclear Information System (INIS)

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

309

Radionuclide bone scan  

International Nuclear Information System (INIS)

Recently, the clinical use of radionuclide bone scan has been populized for the detection of bone lesions. For the sensitivity rate of this modality is superior to that of the radiography in the reflexion of local bone pathology. Especially, bone scanning offers reliable means for establishing the early detection, determining the extent of the disease and assessing the therapeutic response in bone tumor, infection and trauma. A comparative study of bone scans to radiographies with 45 proven cases of bone tumors, inflammations and fractures was tried at Department of Radiology, Chung Ang university hospital, during January 1980 to October 1980. Results were as follows: 1. Increased radioactivities were seen in all primary malignant bone tumors, but exostosis and bone cyst were showed negative finding in bone scans. 2. No evidence of increases uptake was noted in one case of destructive metastatic lesion without osteoblastic reaction. 3. Inflammations of skeletal system were detected by bone scan at early time than by orthodox radiography. It was difficult to differentiate osteomyelitis from other inflammatory disease, such as cellulitis or septic arthritis, by bone scan only. 4. Fresh fractures were identified as increased radioactivity, but healed fractures were negative in bone scans. Prolongation of increased uptake

310

Radionuclide bone scan  

Energy Technology Data Exchange (ETDEWEB)

Recently, the clinical use of radionuclide bone scan has been popularized for the detection of bone lesions. For the sensitivity rate of this modality is superior to that of the radiography in the reflexion of local bone pathology. Especially, bone scanning offers reliable means for establishing the early detection, determining the extent of the disease and assessing the therapeutic response in bone tumor, infection and trauma. A comparative study of bone scans to radiographies with 45 proven cases of bone tumors, inflammations and fractures was tried at Department of Radiology, Chung Ang university hospital, during January 1980 to October 1980. Results were as follows: 1. Increased radioactivities were seen in all primary malignant bone tumors, but exostosis and bone cyst were showed negative finding in bone scans. 2. No evidence of increased uptake was noted in one case of destructive metastatic lesion without osteoblastic reaction. 3. Inflammations of skeletal system were detected by bone scan at an earlier time than by orthodox radiography. It was difficult to differentiate osteomyelitis from other inflammatory disease, such as cellulitis or septic arthritis, by bone scan only. 4. Fresh fractures were identified as increased radioactivity, but healed fractures were negative in bone scans. Prolongation increased uptake.

Park, J.H.; Lee, Y.C.; Lee, K.S.; Kim, K.S.; Park, S.S. (Chungang Univ., Seoul (Republic of Korea))

1982-03-01

311

Laser Scanning in Forests  

Directory of Open Access Journals (Sweden)

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

Håkan Olsson

2012-09-01

312

Scanning with Iodine-125  

International Nuclear Information System (INIS)

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

313

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

International Nuclear Information System (INIS)

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

314

CLIC Energy Scans  

CERN Document Server

The physics experiments at CLIC will require that the machine scans lower than nominal centre-of-mass energy. We present different options to achieve this and discuss the implications for luminosity and the machine design.

Schulte, D; Corsini, R; Dalena, B; Delahaye, JP; Doebert, S; Geschonke, G; Grudiev, A; Jeanneret, B; Jensen, E; Lebrun, Ph; Papaphilippou, Y; Rinolfi, L; Rumolo, G; Schmickler, H; Stulle, F; Syratchev, I; Tomas, R; Wuensch, W

2010-01-01

315

The conical scan radiometer  

Science.gov (United States)

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

Prosch, T.; Hennings, D.

1982-07-01

316

Skeletal Scintigraphy (Bone Scan)  

Science.gov (United States)

... abnormalities that may be missed in a Bone Radiography or X-ray (http://www.radiologyinfo.org/en/ ... radiopharmaceuticals can be transmitted to the baby through breast milk. top of page • Limitations Bone scans cannot ...

317

Terahertz Scanning Array Radiometers  

International Science & Technology Center (ISTC)

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

318

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

Energy Technology Data Exchange (ETDEWEB)

Purpose: To analyze primary tumor (PT) and lymph node (LN) position changes relative to each other and relative to anatomic landmarks during conventionally fractionated radiation therapy for patients with locally advanced lung cancer. Methods and Materials: In 12 patients with locally advanced non-small cell lung cancer PT, LN, carina, and 1 thoracic vertebra were manually contoured on weekly 4-dimensional fan-beam CT scans. Systematic and random interfraction displacements of all contoured structures were identified in the 3 cardinal directions, and resulting setup margins were calculated. Time trends and the effect of volume changes on displacements were analyzed. Results: Three-dimensional displacement vectors and systematic/random interfraction displacements were smaller for carina than for vertebra both for PT and LN. For PT, mean (SD) 3-dimensional displacement vectors with carina-based alignment were 7 (4) mm versus 9 (5) mm with bony anatomy (P<.0001). For LN, smaller displacements were found with carina- (5 [3] mm, P<.0001) and vertebra-based (6 [3] mm, P=.002) alignment compared with using PT for setup (8 [5] mm). Primary tumor and LN displacements relative to bone and carina were independent (P>.05). Displacements between PT and bone (P=.04) and between PT and LN (P=.01) were significantly correlated with PT volume regression. Displacements between LN and carina were correlated with LN volume change (P=.03). Conclusions: Carina-based setup results in a more reproducible PT and LN alignment than bony anatomy setup. Considering the independence of PT and LN displacement and the impact of volume regression on displacements over time, repeated CT imaging even with PT-based alignment is recommended in locally advanced disease.

Jan, Nuzhat; Balik, Salim; Hugo, Geoffrey D. [Department of Radiation Oncology, Virginia Commonwealth University, Richmond, Virginia (United States); Mukhopadhyay, Nitai [Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia (United States); Weiss, Elisabeth, E-mail: eweiss@mcvh-vcu.edu [Department of Radiation Oncology, Virginia Commonwealth University, Richmond, Virginia (United States)

2014-01-01

319

Scanning Tunneling Microscopy  

Science.gov (United States)

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

Consortium, The C.

2011-12-11

320

Josephson scanning tunneling microscopy  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2000-01-01

 
 
 
 
321

The personal genome browser: visualizing functions of genetic variants.  

Science.gov (United States)

Advances in high-throughput sequencing technologies have brought us into the individual genome era. Projects such as the 1000 Genomes Project have led the individual genome sequencing to become more and more popular. How to visualize, analyse and annotate individual genomes with knowledge bases to support genome studies and personalized healthcare is still a big challenge. The Personal Genome Browser (PGB) is developed to provide comprehensive functional annotation and visualization for individual genomes based on the genetic-molecular-phenotypic model. Investigators can easily view individual genetic variants, such as single nucleotide variants (SNVs), INDELs and structural variations (SVs), as well as genomic features and phenotypes associated to the individual genetic variants. The PGB especially highlights potential functional variants using the PGB built-in method or SIFT/PolyPhen2 scores. Moreover, the functional risks of genes could be evaluated by scanning individual genetic variants on the whole genome, a chromosome, or a cytoband based on functional implications of the variants. Investigators can then navigate to high risk genes on the scanned individual genome. The PGB accepts Variant Call Format (VCF) and Genetic Variation Format (GVF) files as the input. The functional annotation of input individual genome variants can be visualized in real time by well-defined symbols and shapes. The PGB is available at http://www.pgbrowser.org/. PMID:24799434

Juan, Liran; Teng, Mingxiang; Zang, Tianyi; Hao, Yafeng; Wang, Zhenxing; Yan, Chengwu; Liu, Yongzhuang; Li, Jie; Zhang, Tianjiao; Wang, Yadong

2014-07-01

322

GenomeViz: visualizing microbial genomes  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis of diversity and mechanisms that lead to the acquisition of new genetic traits. These exercises have necessitated the requirement for visualizing microbial genomes and performing genome comparisons on a finer scale. We have developed GenomeViz to enable rapid visualization and subsequent comparisons of several microbial genomes in an interactive environment. Results Here we describe a program that allows visualization of both qualitative and quantitative information from complete and partially sequenced microbial genomes. Using GenomeViz, data deriving from studies on genomic islands, gene/protein classifications, GC content, GC skew, whole genome alignments, microarrays and proteomics may be plotted. Several genomes can be visualized interactively at the same time from a comparative genomic perspective and publication quality circular genome plots can be created. Conclusions GenomeViz should allow researchers to perform visualization and comparative analysis of up to eight different microbial genomes simultaneously.

Chakraborty Trinad

2004-12-01

323

Factors Influencing Superimposition Error of 3D Cephalometric Landmarks by Plane Orientation Method Using 4 Reference Points: 4 Point Superimposition Error Regression Model  

Science.gov (United States)

Superimposition has been used as a method to evaluate the changes of orthodontic or orthopedic treatment in the dental field. With the introduction of cone beam CT (CBCT), evaluating 3 dimensional changes after treatment became possible by superimposition. 4 point plane orientation is one of the simplest ways to achieve superimposition of 3 dimensional images. To find factors influencing superimposition error of cephalometric landmarks by 4 point plane orientation method and to evaluate the reproducibility of cephalometric landmarks for analyzing superimposition error, 20 patients were analyzed who had normal skeletal and occlusal relationship and took CBCT for diagnosis of temporomandibular disorder. The nasion, sella turcica, basion and midpoint between the left and the right most posterior point of the lesser wing of sphenoidal bone were used to define a three-dimensional (3D) anatomical reference co-ordinate system. Another 15 reference cephalometric points were also determined three times in the same image. Reorientation error of each landmark could be explained substantially (23%) by linear regression model, which consists of 3 factors describing position of each landmark towards reference axes and locating error. 4 point plane orientation system may produce an amount of reorientation error that may vary according to the perpendicular distance between the landmark and the x-axis; the reorientation error also increases as the locating error and shift of reference axes viewed from each landmark increases. Therefore, in order to reduce the reorientation error, accuracy of all landmarks including the reference points is important. Construction of the regression model using reference points of greater precision is required for the clinical application of this model. PMID:25372707

Hwang, Jae Joon; Kim, Kee-Deog; Park, Hyok; Park, Chang Seo; Jeong, Ho-Gul

2014-01-01

324

Confocal Line Scanning Sensor  

Energy Technology Data Exchange (ETDEWEB)

We have developed a novel confocal-based imaging sensor for surface characterization. In this case, a tilted-plane technique is incorporated in a confocal imaging system to create a new parallel scanning scheme, enabling the sensor to be designed and developed as a robust and simple configuration. With a tilted disk consisting of in-line pinholes, a motionless parallel z scanning scheme is manifested when the specimen is transversely scanned through the stationary diffraction-foci projecting at different depths. This sensor uses a line scanning approach, so that it is entitled as a Confocal Line Scanning Sensor (CLSS). In this paper, the CLSS principle, the concept of data processing, and major calibration are described. The sensor was first developed as a two-dimensional profiler to cover the measurement ranges of up to 50 {mu}m in depth and up to 15 mm in lateral length. Experimental results were carried out using calibrated specimens for roughness measurement. In this system, the optical lateral resolution is 0.5 {mu}m, and the depth resolution, defined by noise-limited approach, is 15 nm.

Chanbai, S; Wiora, G; Wewer, L [NanoFocus AG, Lindnerstr. 98, 46149 Oberhausen (Germany); Zafarullah, I [Applied Scientific Imaging Inc., Toronto (Canada); Roth, H, E-mail: chanbai@nanofocus.de, E-mail: wiora@nanofocus.de [Institute of Automatic Control Engineering, University of Siegen, Hoelderlinstr. 3, 57068 Siegen (Germany)

2011-08-19

325

Confocal Line Scanning Sensor  

Science.gov (United States)

We have developed a novel confocal-based imaging sensor for surface characterization. In this case, a tilted-plane technique is incorporated in a confocal imaging system to create a new parallel scanning scheme, enabling the sensor to be designed and developed as a robust and simple configuration. With a tilted disk consisting of in-line pinholes, a motionless parallel z scanning scheme is manifested when the specimen is transversely scanned through the stationary diffraction-foci projecting at different depths. This sensor uses a line scanning approach, so that it is entitled as a Confocal Line Scanning Sensor (CLSS). In this paper, the CLSS principle, the concept of data processing, and major calibration are described. The sensor was first developed as a two-dimensional profiler to cover the measurement ranges of up to 50 ?m in depth and up to 15 mm in lateral length. Experimental results were carried out using calibrated specimens for roughness measurement. In this system, the optical lateral resolution is 0.5 ?m, and the depth resolution, defined by noise-limited approach, is 15 nm.

Chanbai, S.; Zafarullah, I.

2011-08-01

326

Confocal Line Scanning Sensor  

International Nuclear Information System (INIS)

We have developed a novel confocal-based imaging sensor for surface characterization. In this case, a tilted-plane technique is incorporated in a confocal imaging system to create a new parallel scanning scheme, enabling the sensor to be designed and developed as a robust and simple configuration. With a tilted disk consisting of in-line pinholes, a motionless parallel z scanning scheme is manifested when the specimen is transversely scanned through the stationary diffraction-foci projecting at different depths. This sensor uses a line scanning approach, so that it is entitled as a Confocal Line Scanning Sensor (CLSS). In this paper, the CLSS principle, the concept of data processing, and major calibration are described. The sensor was first developed as a two-dimensional profiler to cover the measurement ranges of up to 50 ?m in depth and up to 15 mm in lateral length. Experimental results were carried out using calibrated specimens for roughness measurement. In this system, the optical lateral resolution is 0.5 ?m, and the depth resolution, defined by noise-limited approach, is 15 nm.

327

Surgical anatomy of the superior gluteal nerve and landmarks for its localization during minimally invasive approaches to the hip.  

Science.gov (United States)

The superior gluteal nerve (SGN) is vulnerable to damage during total hip arthroplasty and various pelvic surgeries. Recently introduced minimally invasive approaches to the hip show promise for less muscle trauma compared to conventional approaches. However, the risk of damaging the SGN has not been well documented for such alternative approaches. Therefore, we aimed to investigate the anatomic course of the SGN and to define anatomical landmarks that may be used by surgeons during minimally invasive approaches to the hip. Twenty-eight gluteal regions from 14 formalin-fixed cadavers were dissected and the course and the distances of the SGN and its branches to the tip of the greater trochanter (GT) were measured. The landmarks for standardizing the course of the SGN included the posterior inferior iliac spine (PIIS), GT, and a line (PIIS-GT) connecting these two points. The exit of the SGN was found to be at the medial one third of the PIIS-GT line and 5.4 cm from the GT. Two branching patterns were noted. The branches of the SGN were distributed lateral to the PIIS-GT line. On the basis of our study, the safe zone for the SGN was smaller than previously reported. Posterior, lateral, or anterolateral minimally invasive approaches to the hip should take into account the point of exit of the SGN and the area of distribution of its branches. A minimally invasive anterolateral approach may particularly compromise branches to the tensor fasciae latae muscle. Localization of the SGN and its branches using the anatomic landmarks defined in this study may decrease surgical morbidity. PMID:22374811

Apaydin, Nihal; Kendir, Simel; Loukas, Marios; Tubbs, R Shane; Bozkurt, Murat

2013-07-01

328

Objects and landmarks: Hippocampal place cells respond differently to manipulations of visual cues depending on size, perspective, and experience.  

Science.gov (United States)

Human navigation studies show that landmarks are used for orientation, whereas objects contribute to the contextual representation of an environment. What constitutes a landmark? Classic rodent studies show that hippocampal place fields are controlled by distal, polarizing cues. Place fields, however, are also influenced by local cues. One difficulty in examining mechanisms by which distal and local cues influence the activity of hippocampal cells is that distant cues are necessarily processed visually, whereas local cues are generally multimodal. Here, we compared the effects of 90° rotations under different cue conditions in which cues were restricted to the visual modality. Three two-dimensional visual cue conditions were presented in a square open field: a large vertical cue on one wall, a large floor cue in a corner abutting two walls, and a smaller complex floor cue in a corner adjacent to two walls. We show that rotations of large distal cues, whether on the wall or floor, were equally effective in controlling place fields. Rotations of the smaller floor cues were significantly more likely to result in remapping, whether or not animals were also exposed to the distal polarizing cues. Responses of distal and local cues were affected differently by extended experience. Our data provide evidence that hippocampal place cell responses to visual cues are influenced by perspective, salience of the cue, and prior experience. The hippocampus processes visual cues either as stable landmarks useful for orientation and navigation or as nonstationary objects or features of the local environment available for associative learning or binding items in context. © 2014 Wiley Periodicals, Inc. PMID:25045010

Scaplen, Kristin M; Gulati, Arune A; Heimer-McGinn, Victoria L; Burwell, Rebecca D

2014-11-01

329

Shipborne hydrographic laser scanning  

Science.gov (United States)

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

Pfennigbauer, Martin; Rieger, Peter; Schaich, Martin

2011-11-01

330

Scanning microarray slides.  

Science.gov (United States)

Here we describe some practical concerns surrounding the scanning of microarray slides that have been hybridized with fluorescent dyes. We use a laser scanner that has two lasers, each set to excite a different fluor, and separate detectors to capture emission from each fluor. The laser passes over an address (position on the scanned surface) and the detectors capture photons emitted from each address. Two superimposed image files are written that carry intensities for each channel for each pixel of the image scan. These are the raw data. Image analysis software is used to identify and summarize the intensities of the pixels that make up each spot. After comparison to background pixels, the processed intensity levels representing the gene expression measurements are associated with the identity of each spot. PMID:24492780

Ares, Manuel

2014-02-01

331

Scanning Nearfield Infrared Microscopy  

International Nuclear Information System (INIS)

Commonly, location specific chemical identification by means of vibrational spectroscopy in the infrared region is largely restricted to samples of macroscopic dimensions, on the order of one to several microns; the scale of the examined area is completely determined by the diffraction limit of the incident radiation. However, chemical identification at length scales less than the diffraction limit is possible using a scanned probe technique, the Scanning Near-Field Infrared Microscope (SNFIM). Using a scanned probe technique in the near-field, resolution of chemical features on the order of h/20 or ? 100 nm can be achieved. An overview of previous experimental results using a free electron laser (FEL) and more conventional infrared sources will be discussed. Recent results from the SNFIM experiment at Jefferson Lab will also be presented

332

Radiation scanning system  

International Nuclear Information System (INIS)

In the radiation scanning system the radiation emitted from an image field is scanned by a field of radiosensitive detector elements, and the signals transmitted are used to control the video input of a scanning-pattern image display unit. By the variations of the transmitting properties of the detector elements and the electronic equipment spurious patterns are produced on the projected picture. In order to prevent this there is provided for a compensating circuit and a comparator by means of which the variations of the transmitting properties are compensated. It works synchronous by together with a multipler device and carries out a measurement of the statistic moment of the voltage of each channel. The compensating device may be designed as an open or closed control loop. (orig.)

333

Lung scans and malignancy  

International Nuclear Information System (INIS)

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

334

Liver Scanning with Radiomolybdate  

International Nuclear Information System (INIS)

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

335

Improved vertical scanning interferometry  

Science.gov (United States)

Vertical scanning interferometers are routinely used for the measurement of optical fiber connectors. There are increasing needs for measurements of such items as machined surfaces, contact lenses, paint texture, cell structure, and integrated circuit devices, to name a few. These structures have too much depth, or are too rough, to measure with standard interferometry methods. Phase- measurement interferometry methods are limited to surfaces that do not have any discontinuities larger than one quarter of the operating wavelength. On the other hand, vertical scanning interferometers can be very effective, even though they have low height resolution compared to that of phase-measurement interferometers. Improving the height resolution of vertical scanning interferometers from the point of hardware improvement and signal processing has been one of the major research interests in the surface metrology area. This work provides a new algorithm, which called here ``PSI on the Fly'' technique, as a solution for improving height resolution of vertical scanning interferometers. This dissertation begins with a review of white-light interference microscopes. The height and lateral resolutions are derived based on scalar diffraction theory. Next, various well-established. algorithms for finding a topographic map of the small object surface are discussed. The work proceeds with a discussion of the phase change upon reflection and its influence on the coherence envelope. Then phase measurement interferometry methods are reviewed. The emphasis is in errors in phase measurement resulting from using a white light source instead of a monochromatic light source as in the usual case. The following chapter describes and examines an often- observed artifact of vertical-scanning interferometry when applied to step heights. The artifact is called ``bat wings'' because of its appearance. The physical cause of the ``bat wings'' artifact is discussed through a diffraction model. The next chapter proposes an improved vertical-scanning interferometry algorithm. The method, called here ``PSI on the Fly'' technique, has been developed by combining regular vertical-scanning interferometry and a monochromatic phase-shifting interferometry technique. The PSI on the Fly technique improves the surface height resolution of vertical scanning interferometry to that of a phase-shifting interferometry measurement. In addition to the resolution improvement, the algorithm also successfully removes the ``bat wings'' artifact.

Harasaki, Akiko

2000-11-01

336

Translational genomics  

Directory of Open Access Journals (Sweden)

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

Martin Kussmann

2014-09-01

337

Ultrafast scanning probe microscopy  

Science.gov (United States)

An ultrafast scanning probe microscopy method is described for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample. 6 Figs.

Weiss, S.; Chemla, D.S.; Ogletree, D.F.; Botkin, D.

1995-05-16

338

Virtual Scanning Electron Microscopy  

Science.gov (United States)

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

Davidson, Michael W.; Kunkel, Dennis; Parry-Hill, Matthew J.; University, Florida S.

339

Getting a CAT Scan  

Medline Plus

Full Text Available ... The scan itself is painless. All you'll need to do is hold still for a few minutes at a time so the pictures come out ... All information on KidsHealth® is for educational purposes only. For specific medical advice, diagnoses, and ...

340

Stabilized radiographic scanning agents  

International Nuclear Information System (INIS)

A stable composition, useful in the preparation of technetium-99m-based radiographic scanning agents, comprises a pertechnetate reducing agent and a stabilizing amount of a gentisate stabilizer selected from gentisic acid and its soluble, pharmaceutically-acceptable salts and esters. The composition may additionally comprise an organ-specific carrier

 
 
 
 
341

Scanning bubble chamber pictures  

CERN Multimedia

These were taken at the 2 m hydrogen bubble chamber. The photo shows an early Shiva system where the pre-measurements needed to qualify the event were done manually (cf photo 7408136X). The scanning tables were located in bld. 12. Gilberte Saulmier sits on foreground, Inge Arents at centre.

1974-01-01

342

Scan This Book!  

Science.gov (United States)

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

Albanese, Andrew Richard

2007-01-01

343

Scanning tunneling microscopy  

International Nuclear Information System (INIS)

Based on vacuum tunneling, a novel type of microscope, the scanning tunneling microscope (STM) was developed. It has an unprecedented resolution in real space on an atomic scale. The authors review the important technical features, illustrate the power of the STM for surface topographies and discuss its potential in other areas of science and technology. (Auth.)

344

Getting a CAT Scan  

Medline Plus

Full Text Available ... the Body Works Main Page The Pink Locker Society Getting a CAT Scan (Video) KidsHealth > Kids > Movies & ... Use Visit the Nemours Web site. Note: All information on KidsHealth® is for educational purposes only. For ...

345

Ultrafast scanning probe microscopy  

Science.gov (United States)

An ultrafast scanning probe microscopy method for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample.

Weiss, Shimon (El Cerrito, CA); Chemla, Daniel S. (Kensington, CA); Ogletree, D. Frank (El Cerrito, CA); Botkin, David (San Francisco, CA)

1995-01-01

346

Bone scan in rheumatology  

International Nuclear Information System (INIS)

In this chapter a revision is made concerning different uses of bone scan in rheumatic diseases. These include reflex sympathetic dystrophy, osteomyelitis, spondyloarthropaties, metabolic bone diseases, avascular bone necrosis and bone injuries due to sports. There is as well some comments concerning pediatric pathology and orthopedics. (authors). 19 refs., 9 figs

347

Mobile element scanning (ME-Scan by targeted high-throughput sequencing  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Mobile elements (MEs are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and substrates for further genomic rearrangements. Research on the impacts, population dynamics, and evolution of MEs is constrained by the difficulty of ascertaining rare polymorphic ME insertions that occur against a large background of pre-existing fixed elements and then genotyping them in many individuals. Results Here we present a novel method for identifying nearly all insertions of a ME subfamily in the whole genomes of multiple individuals and simultaneously genotyping (for presence or absence those insertions that are variable in the population. We use ME-specific primers to construct DNA libraries that contain the junctions of all ME insertions of the subfamily, with their flanking genomic sequences, from many individuals. Individual-specific "index" sequences are designed into the oligonucleotide adapters used to construct the individual libraries. These libraries are then pooled and sequenced using a ME-specific sequencing primer. Mobile element insertion loci of the target subfamily are uniquely identified by their junction sequence, and all insertion junctions are linked to their individual libraries by the corresponding index sequence. To test this method's feasibility, we apply it to the human AluYb8 and AluYb9 subfamilies. In four individuals, we identified a total of 2,758 AluYb8 and AluYb9 insertions, including nearly all those that are present in the reference genome, as well as 487 that are not. Index counts show the sequenced products from each sample reflect the intended proportions to within 1%. At a sequencing depth of 355,000 paired reads per sample, the sensitivity and specificity of ME-Scan are both approximately 95%. Conclusions Mobile Element Scanning (ME-Scan is an efficient method for quickly genotyping mobile element insertions with very high sensitivity and specificity. In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species.

Watkins W Scott

2010-06-01

348

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

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

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

Martinón-Torres, Marcos

2001-06-01

349

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

Science.gov (United States)

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

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

2007-06-01

350

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

CERN Document Server

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

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

2014-01-01

351

Lung Ventilation/Perfusion Scan  

Science.gov (United States)

... from the NHLBI on Twitter. What Is a Lung Ventilation/Perfusion Scan? A lung ventilation/perfusion scan, or VQ scan, is a ... that measures air and blood flow in your lungs. A VQ scan most often is used to ...

352

Whole Genome Sequencing  

Science.gov (United States)

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

353

Scanning temperature gradient focusing.  

Science.gov (United States)

Temperature gradient focusing (TGF) is a recently developed technique for the simultaneous concentration and electrophoretic separation of ionic analytes in microfluidic channels. One drawback to TGF as it has previously been described is the limited peak capacity; only a small number of analyte peaks (approximately 2-3) can be simultaneously focused and separated. In this paper, we report on a variation of the TGF method whereby the bulk flow rate is varied over time so that a large number of analytes can be sequentially focused, moved past a fixed detection point, and flushed to waste. In addition to improved peak capacity, the detection limits of the scanning TGF method can be adjusted on-the-fly, as needed for different samples. Finally, scanning TGF provides a technique by which high-resolution, high-peak-capacity electrophoretic separations can be performed in simple, straight, and short microfluidic channels. PMID:17037919

Hoebel, Stacey J; Balss, Karin M; Jones, Barbara J; Malliaris, Constantin D; Munson, Matthew S; Vreeland, Wyatt N; Ross, David

2006-10-15

354

Scanning in Thyroid Cancer  

International Nuclear Information System (INIS)

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

355

Scanning probe microscopy  

International Nuclear Information System (INIS)

In late 1959, Richard Feynman observed that manoeuvring atoms was something that could be done in principle but has not been done, 'because we are too big'. In 1982, the scanning tunnelling microscope (STM) was invented and is now a central tool for the construction of nanoscale devices in what was known as molecular engineering, and now, nanotechnology. The principles of the microscope are outlined and references are made to other scanning devices which have evolved from the original invention. The method of employment of the STM as a machine tool is described and references are made to current speculations on applications of the instrument in nanotechnology. A short bibliography on this topic is included. 27 refs., 7 figs

356

FibroScan?????????????????????????????  

Directory of Open Access Journals (Sweden)

Full Text Available ObjectiveTo evaluate the value of FibroScan in assessing liver fibrosis in chronic hepatitis B (CHB patients with hepatocyte steatosis. MethodsFour hundred and eighteen CHB patients who had undergone liver biopsy in Shanghai Ruijin Hospital from January 2009 to December 2011 were enrolled in this study. These patients were divided into hepatocyte steatosis group (n=211 and non-hepatocyte steatosis group (n=207. FibroScan was performed in both groups on the same day. Comparisons of liver stiffness measurement (LSM and liver fibrosis stage determined by FibroScan and Ishak scoring system were made. Comparisons between groups were made by independent-samples t test, Kruskal-Wallis H test, and Nemenyi test. Comparison of categorical data was made by chi-square analysis. Bivariate correlation analysis was performed using the Spearman Rank Correlation coefficient. The influential factors for LSM were determined by stepwise regression analysis. ResultsThere was no significant difference in LSM between the patients of the same liver fibrosis stage in the two groups (P?0.05, and LSM had a significant positive correlation with liver fibrosis stage in the non-hepatocyte steatosis group (rs=0.650 35, P?0.000?1 and hepatocyte steatosis group (rs=0?637 93, P?0.000?1. The stepwise regression analysis showed that aspartate aminotransferase (AST, alanine aminotransferase, albumin (Alb, total bilirubin, and platelet (PLT were significant influential factors for LSM in the non-hepatocyte steatosis group and that PLT, AST, age, Alb, and body mass index were significant influential factors for LSM in the hepatocyte steatosis group. ConclusionFibroScan can be used as a useful tool for assessing liver fibrosis in CHB patients with hepatocyte steatosis.

LIU Kehui

2014-02-01

357

IMEF gamma scanning system  

International Nuclear Information System (INIS)

The gamma scanning system which is installed in IMEF is the equipment obtaining the gamma ray spectrum from irradiated fuels. This equipment could afford the useful data relating spent fuels like as burn-up measurements. We describe the specifications of the equipment and its accessories, and also described its operation procedure so that an operator can use this report as the operation procedure. (author). 1 tab., 11 figs., 11 refs

358

A Scanning Cavity Nanoscope  

Science.gov (United States)

Techniques for imaging and manipulating individual quantum emitters with high spatial resolution are essential in areas ranging from single molecule spectroscopy to interfacing emitters in quantum networks. Optical cavities enable strong light-matter interaction and, when coupled to suitable imaging platforms, enable new approaches for single-atom microscopy. Here we demonstrate a scanning cavity nanoscope (SCN), based on a photonic crystal cavity, that enables simultaneous nanoscale localization of solid-state quantum emitters and modification of emitter properties via the Purcell Effect. We illustrate the power of the SCN by coupling individual nitrogen vacancy (NV) centres in diamond to the nanocavity. Scanning over an NV results in strong position-dependent modification of the spontaneous emission (SE) spectrum, including a six-fold enhancement of the SE intensity at the cavity frequency. The scanning nanocavity overcomes the traditional trade-off between spatial resolution and collection efficiency of near-field optical probes and enables a deterministic photonic interface for a wide range of quantum emitters.

Shields, Brendan; Englund, Dirk; Rivoire, Kelley; Hatami, Fariba; Vuckovic, Jelena; Park, Hongkun; Lukin, Mikhail

2010-03-01

359

Adaptive Processing of Range Scanned Head: Synthesis of Personalized Animated Human Face Representation with Multiple-Level Radial Basis Function  

Directory of Open Access Journals (Sweden)

Full Text Available We propose an animation system for personalized human head. Landmarks compliant to MPEG-4 facial definition parameters (FDP are initially labeled on both template model and any target human head model as priori knowledge. The deformation from the template model to the target head is through a multilevel training process. Both general radial basis function (RBF and compactly supported radial basis function (CSRBF are applied to ensure the fidelity of the global shape and face features. Animation factor is also adapted so that the deformed model still can be considered as an animated head. Situations with defective scanned data are also discussed in this paper.

Prakash Edmond C

2007-01-01

360

Identifying Synonymous Regulatory Elements in Vertebrate Genomes  

Energy Technology Data Exchange (ETDEWEB)

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

Ovcharenko, I; Nobrega, M A

2005-02-07

 
 
 
 
361

ABrowse - a customizable next-generation genome browser framework  

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

Kong Lei

2012-01-01

362

GENOMIC MEDICINE  

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Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease; thus, conducts may be undertaken like selection of embryos or opting for adoption.Although genetic studies of molecular profiles are promissory, there are questions on how these are requested and how the results are communicated to the patients, their clinical use, application of the pre-symptomatic diagnosis – especially in children, the bad intended use of this information by medical insurance companies considering pre-existing conditions, and finally, the great amount of information and its application in populations where prior studies of association have not been conducted may be cause for concern.In developed nations, these types of exams are requested without medical prescription in pharmacies that mail the results directly to the interested party. It is worrisome what can happen to patients upon receiving this information; for example, if the report indicates susceptibility to Alzheimer’s or cancer, without medical support to identify the presentation risks and the possibility of transmitting the disease to their offspring. This suggests the validity, more than ever, of genetic counseling when delivering analysis results.On the other hand, insurance companies must consider molecular genetic profiles as a preventive tool that permits improving service quality while lowering costs; for instance, in cancer cases where prophylaxis measures are notably less costly than treatment.Another aspect to bear in mind is that association studies of genetic polymorphism and disease need thousands of cases and controls, making them very costly for implementation in Colombia. For this reason, the exams include the ancestral report for the purpose of interpreting the results according to ethnic origin. For now, this is the most adequate conduct considering that it will take a long time before validation studies can be conducted.As with all great progress in medicine, genomics opens a path that will bring enormous benefit inasmuch as the criteria for good medical practices are considered.

Ignacio Briceño Balcázar

2011-03-01

363

Acetabular orientation variability and symmetry based on CT scans of adults  

International Nuclear Information System (INIS)

Understanding acetabular orientation is important in many orthopaedic procedures. Acetabular orientation, usually described by anteversion and abduction angles, has uncertain measurement variability in adult patients. The goals of this study are threefold: (1) to describe a new method for computing patient-specific abduction/anteversion angles from a single CT study based on the identification of anatomical landmarks and acetabular rim points; (2) to quantify the inaccuracies associated with landmark selection in computing the acetabular angles; and (3) to quantify the variability and symmetry of acetabular orientation. A total of 25 CT studies from adult patients scanned for non-orthopaedic indications were retrospectively reviewed. The patients were randomly selected from the hospital's database. Inclusion criteria were adults 20-65 years of age. Acetabular landmark coordinates were identified by expert observers and tabulated in a spreadsheet. Two sets of calculations were done using the data: (1) computation of the abduction and anteversion for each patient, and (2) evaluation of the variability of measurements in the same individual by the same surgeon. The results were tabulated and summary statistics computed. This retrospective study showed that acetabular abduction and anteversion angles averaged 54 and 17 , respectively, in adults. A clinically significant intra-patient variability of >20 was found. We also found that the right and left side rim plane orientt the right and left side rim plane orientation were significantly correlated, but were not always symmetric. A new method of computing patient-specific abduction and anteversion angles from a CT study of the anterior pelvic plane and the left and right acetabular rim planes was reliable and accurate. We found that the acetabular rim plane can be reliably and accurately computed from identified points on the rim. The novelty of this work is that angular measurements are performed between planes on a 3-D model rather than lines on 2-D projections, as was done in the past. (orig.)

364

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

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

Soraia Ale Souza

2009-02-01

365

Unexpected cross-species contamination in genome sequencing projects  

Science.gov (United States)

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

Merchant, Samier; Wood, Derrick E.

2014-01-01

366

Design of an Enterobacteriaceae Pan-genome Microarray Chip  

DEFF Research Database (Denmark)

Abstract. Microarrays are a common method for evaluating genomic content of bacterial species and comparing unsequenced bacterial genomes. This technology allows for quick scans of characteristic genes and chromosomal regions, and to search for indications of horizontal transfer. A high-density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination of the genetic makeup of unknown strains within this bacterial family and can introduce insights into phylogenetic relationships.

Lukjancenko, Oksana; Ussery, David

2010-01-01

367

Verification of selected anatomic landmarks used as reference points for universal goniometer positioning during knee joint mobility range measurements.  

Science.gov (United States)

The study was concerned with verification of the selection of reference points used for knee joint mobility range goniometry. The verification was based on photometric and electrogoniometric methods of femorotibial angle measurements. The material for measurements were three knee joint preparations. The obtained data were subjected to descriptive analysis; photographic documentation of geometric relations between the reference points was also prepared. Considerable divergence of measurement results was observed with respect to the actual knee joint flexion angle, amounting even to 16 degrees. The differences are due to the selection of anatomic landmarks, and depend in particular on the distance of the point to which the goniometer axis is applied from the approximate location of the mechanical joint axis. The corrections of knee joint flexion angle measurements were also estimated on the basis of data obtained from the photographs and the derived mathematical formula. PMID:11257742

Szulc, P; Lewandowski, J; Marecki, B

2001-01-01

368

Radiographic scanning agent  

International Nuclear Information System (INIS)

This invention relates to radiodiagnostic agents and more particularly to a composition and method for preparing a highly effective technetium-99m-based bone scanning agent. One deficiency of x-ray examination is the inability of that technique to detect skeletal metastases in their incipient stages. It has been discovered that the methanehydroxydiphosphonate bone mineral-seeking agent is unique in that it provides the dual benefits of sharp radiographic imaging and excellent lesion detection when used with technetium-99m. This agent can also be used with technetium-99m for detecting soft tissue calcification in the manner of the inorganic phosphate radiodiagnostic agents

369

The proton scanning microprobe  

International Nuclear Information System (INIS)

The beam properties of a simple doublet configuration have been investigated systematically. The beam optical parameters have been calculated up to the chromatic and the third order aberration coefficients. By scanning a 250 lines/inch copper electron microscope mesh, the beam spot size was determined to be 16 x 18 ?m2 with the object aperture of 50 ?m in diameter. The beam spot size was not decreased proportionally by replacing the object aperture size from 100 ?m to 50 ?m. In the present experimental arrangement, it is concluded that the beam size was restricted by chromatic aberration. (author)

370

Scanning apparatus and method  

International Nuclear Information System (INIS)

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

371

A Descriptive Comparison of Ultrasound Guided Central Venous Cannulation of the Internal Jugular to Landmark Based Subclavian Vein Cannulation  

Science.gov (United States)

The safest site for central venous cannulation (CVC) remains debated. Many emergency medicine physicians advocate the ultrasound guided internal jugular approach (USIJ) because of data supporting its efficiency. However, a number of physicians prefer, and are most comfortable with, the subclavian vein approach. The purpose of this study was to describe adverse event rates among operators using the USIJ approach and the landmark subclavian vein approach without ultrasound (SC). Methods This was a prospective observational trial of patients undergoing CVC of the subclavian or internal jugular veins in the Emergency Department (ED). Physicians performing the procedures did not undergo standardized training in either technique. The primary outcome was a composite of adverse events defined as hematoma, arterial cannulation, pneumothorax, and failure to cannulate. Physicians recorded the anatomical site of cannulation, ultrasound assistance, indications and acute complications. Variables of interest were collected from the pharmacy and ED record. Physician experience was based on a self-reported survey. We followed outcomes of central line insertion until device removal or patient discharge. Results Physicians attempted 236 USIJ and 132 SC cannulations on 333 patients. The overall adverse event rate was 22% with failure to cannulate being the most common. Adverse events occurred in 19% of USIJ attempts compared to 29% of non-ultrasound guided subclavian attempts. Among highly experienced operators CVCs placed at the subclavian site resulted in more adverse events than those performed using USIJ (RR=1.89, 95%CI 1.05 to 3.39). Conclusions While limited by observational design, our results suggest that the USIJ technique may result in fewer adverse events compared to the landmark SC approach. PMID:20370781

Theodoro, Daniel; Bausano, Brian; Lewis, Lawrence; Evanoff, Bradley; Kollef, Marin

2013-01-01

372

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

Directory of Open Access Journals (Sweden)

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

Leeder J Steven

2003-09-01

373

Free Motion Scanning System  

Energy Technology Data Exchange (ETDEWEB)

The present invention relates to an ultrasonic scanner and method for the imaging of a part surface, the scanner comprising: a probe assembly spaced apart from the surface including at least two tracking signals for emitting electromagnetic radiation and a transmitter for emitting ultrasonic waves onto a surface in order to induce at least a portion of said waves to be reflected from the surface, at least one detector for receiving the electromagnetic radiation wherein the detector is positioned to receive said radiation from the tracking signals, an analyzing means for recognizing a three-dimensional location of the tracking signals based on said emitted electromagnetic radiation, a differential conversion means for generating an output signal representative of the waveform of the reflected waves, and a means for relating said tracking signal location with the output signal and projecting an image of the resulting data. The scanner and method are particularly useful to acquire ultrasonic inspection data by scanning the probe-over a complex part surface in an arbitrary scanning pattern.

Sword, Charles K.

1998-06-18

374

Major cytogenetic landmarks and karyotype analysis inDaucus carota and other Apiaceae.  

Science.gov (United States)

Karyotype analysis provides insights into genome organization at the chromosome level and into chromosome evolution. Chromosomes were marked for comparative karyotype analysis using FISH localization of rDNA genes for the first time in Apioideae species including taxa of economic importance and several wild Daucus relatives. Interestingly, Daucus species did not vary in number of rDNA loci despite variation in chromosome number (2n = 18, 20, 22, and 44) and previous publications suggesting multiple loci. All had single loci for both 5S and 18S-25S (nucleolar organizing region) rDNA, located on two different chromosome pairs. The 5S rDNA was on the short arm of a metacentric chromosome pair in D. crinitus (2n = 22) and D. glochidiatus (2n = 44) and on the long arm of a metacentric pair in other Daucus species, suggesting possible rearrangement of this chromosome. For other Apiaceae, from two (Apium graveolens), to three (Orlaya grandiflora), to four (Cuminum cyminum) chromosomes had 18S-25S rDNA sites. Variability for number and position of the 5S rDNA was also observed. FISH signals enabled us to identify 20-40% of the chromosome complement among species examined. Comparative karyotype analysis provides insights into the fundamental aspects of chromosome evolution in Daucus. PMID:21632405

Iovene, Marina; Grzebelus, Ewa; Carputo, Domenico; Jiang, Jiming; Simon, Philipp W

2008-07-01

375

Overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applications.  

Science.gov (United States)

During the early days of molecular biology, cell-free protein synthesis played an essential role in deciphering the genetic code and contributed to our understanding of translation of protein from messenger RNA. Owing to several decades of major and incremental improvements, modern cell-free systems have achieved higher protein synthesis yields at lower production costs. Commercial cell-free systems are now available from a variety of material sources, ranging from "traditional" E. coli, rabbit reticulocyte lysate, and wheat germ extracts, to recent insect and human cell extracts, to defined systems reconstituted from purified recombinant components. Although each cell-free system has certain advantages and disadvantages, the diversity of the cell-free systems allows in vitro synthesis of a wide range of proteins for a variety of downstream applications. In the post-genomic era, cell-free protein synthesis has rapidly become the preferred approach for high-throughput functional and structural studies of proteins and a versatile tool for in vitro protein evolution and synthetic biology. This unit provides a brief history of cell-free protein synthesis and describes key advances in modern cell-free systems, practical differences between widely used commercial cell-free systems, and applications of this important technology. Curr. Protoc. Mol. Biol. 108:16.30.1-16.30.11. © 2014 by John Wiley & Sons, Inc. PMID:25271714

Chong, Shaorong

2014-01-01

376

Factors influencing bone scan quality  

International Nuclear Information System (INIS)

A reliable subjective method of assessing bone scan quality is described. A large number of variables which theoretically could influence scan quality were submitted to regression and factor analysis. Obesity, age, sex and abnormality of scan were found to be significant but weak variables. (orig.)

377

Establishing Cephalometric Landmarks for the Translational Study of Le Fort-based Facial Transplantation in Swine: Enhanced applications using computer-assisted surgery and custom cutting guides  

Science.gov (United States)

Background Le Fort-based, maxillofacial allotransplantation is a reconstructive alternative gaining clinical acceptance. However, the vast majority of single-jaw transplant recipients demonstrate less-than-ideal skeletal and dental relationships with suboptimal aesthetic harmony. The purpose of this study was to investigate reproducible cephalometric landmarks in a large animal model, where refinement of computer-assisted planning, intra-operative navigational guidance, translational bone osteotomies, and comparative surgical techniques could be performed. Methods Cephalometric landmarks that could be translated into the human craniomaxillofacial skeleton, and would remain reliable following maxillofacial osteotomies with mid-facial alloflap inset, were sought on six miniature swine. Le Fort I-and Le Fort III-based alloflaps were harvested in swine with osteotomies, and all alloflaps were either auto-replanted or transplanted. Cephalometric analyses were performed on lateral cephalograms pre- and post-operatively. Critical cephalometric data sets were identified with the assistance of surgical planning and virtual prediction software, and evaluated for reliability and translational predictability. Results Several pertinent landmarks and human analogues were identified including pronasale (PRN), zygion (Zy), parietale (PA), gonion (GO), gnathion (GN), lower incisior base (LIB), and alveolare (ALV). PA-PRN-ALV and PA-PRN-LIB were found to be reliable correlates of SNA and SNB measurements in humans, respectively. Conclusions There is a set of reliable cephalometric landmarks and measurement angles pertinent for utilization within a translational large animal model. These craniomaxillofacial landmarks will allow us to develop novel navigational software technology, improve our cutting guide designs, and explore new avenues for investigation and collaboration. Level of Evidence N/A (Large Animal Study) PMID:24445879

Santiago, Gabriel F.; Susarla, Srinivas M.; Al Rakan, Mohammed; Coon, Devin; Rada, Erin M.; Sarhane, Karim; Shores, Jamie T.; Bonawitz, Steven C.; Cooney, Damon; Sacks, Justin; Murphy, Ryan J.; Fishman, Elliot K.; Brandacher, Gerald; Lee, WP Andrew; Liacouras, Peter; Grant, Gerald; Armand, Mehran; Gordon, Chad R.

2014-01-01

378

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

Directory of Open Access Journals (Sweden)

Full Text Available In 2003, the National Institute for Occupational Safety and Health (NIOSH conducted a head-and-face anthropometric survey of diverse, civilian respirator users. Of the 3,997 subjects measured using traditional anthropometric techniques, surface scans and 26 three-dimensional (3D landmark locations were collected for 947 subjects. The objective of this study was to report the size and shape variation of the survey participants using the 3D data. Generalized Procrustes Analysis (GPA was conducted to standardize configurations of landmarks associated with individuals into a common coordinate system. The superimposed coordinates for each individual were used as commensurate variables that describe individual shape and were analyzed using Principal Component Analysis (PCA to identify population variation. The first four principal components (PC account for 49% of the total sample variation. The first PC indicates that overall size is an important component of facial variability. The second PC accounts for long and narrow or short and wide faces. Longer narrow orbits versus shorter wider orbits can be described by PC3, and PC4 represents variation in the degree of ortho/prognathism. Geometric Morphometrics provides a detailed and interpretable assessment of morphological variation that may be useful in assessing respirators and devising new test and certification standards.

Stephanie Lynch

2010-01-01

379

The study of craniofacial growth patterns using 3D laser scanning and geometric morphometrics  

Science.gov (United States)

Throughout childhood, braincase and face grow at different rates and therefore exhibit variable proportions and positions relative to each other. Our understanding of the direction and magnitude of these growth patterns is crucial for many ergonomic applications and can be improved by advanced 3D morphometrics. The purpose of this study is to investigate this known growth allometry using 3D imaging techniques. The geometry of the head and face of 840 children, aged 2 to 19, was captured with a laser surface scanner and analyzed statistically. From each scan, 18 landmarks were extracted and registered using General Procrustes Analysis (GPA). GPA eliminates unwanted variation due to position, orientation and scale by applying a least-squares superimposition algorithm to individual landmark configurations. This approach provides the necessary normalization for the study of differences in size, shape, and their interaction (allometry). The results show that throughout adolescence, boys and girls follow a different growth trajectory, leading to marked differences not only in size but also in shape, most notably in relative proportions of the braincase. These differences can be observed during early childhood, but become most noticeable after the age of 13 years, when craniofacial growth in girls slows down significantly, whereas growth in boys continues for at least 3 more years.

Friess, Martin

2006-02-01

380

Not just another genome  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. It establishes Daphnia as an eco-genetical model organism par excellence.

2011-01-01