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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
This theme issue on landmarks includes annotated listings of Web sites, CDROMs and computer software, videos, books, and additional resources that deal with landmarksnatural and manmade, ancient and modern, architectural and politicaland why they are important. Sidebars discuss fallen landmarks, landmark speeches, and linking landmarks. (AEF)
Online-Offline, 1999
Comparative genome mapping with mobile physical map landmarks.
We describe a method for comparative macrorestriction mapping of the chromosomes of Escherichia coli strains. In this method, a series of physically tagged E. coli K-12 alleles serve as mobile landmarks for mapping DNAs from other strains. This technique revealed evidence of strain-specific chromosomal additions or deletions in a pathogenic isolate and can be applied to most strains, yielding information on genealogy as well as virulence. In theory, the same strategy can be used to map and compare genomic DNAs from a wide variety of species. PMID:7961483
Bloch, C A; Rode, C K; Obreque, V; Russell, K Y
Arterial tree tracking from anatomical landmarks in magnetic resonance angiography scans
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
Comparative genome mapping with mobile physical map landmarks.
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We describe a method for comparative macrorestriction mapping of the chromosomes of Escherichia coli strains. In this method, a series of physically tagged E. coli K-12 alleles serve as mobile landmarks for mapping DNAs from other strains. This technique revealed evidence of strain-specific chromosomal additions or deletions in a pathogenic isolate and can be applied to most strains, yielding information on genealogy as well as virulence. In theory, the same strategy can be used to map and co...
Bloch, C. A.; Rode, C. K.; Obreque, V.; Russell, K. Y.
Detection of New Genomic Landmarks in the Maltese Goat Using Rapd PCR
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Full Text Available Since no information of the Maltese goat genome is available, RAPD technique has been used to identify a number of DNA landmarks. Genome Landmarks have been obtained from the DNA of 66 Maltese goats which were studied with Random Amplification of Polymorphic DNA (RAPD. Eleven (11 reproducible RAPD polymorphic zones were identified. For sequencing, the RAPD zones were cloned into the Puc 18 vector utilising E. coli and then sequenced using both the forward (universal and reverse primers specific for the Puc 18 vector. After sequencing a total of nine new markers (AF078170, AF078171, AF078172, AF078173, AF078174, AF078175, AF078176, AF078177, AF078178 amounting to approximately 5,500 bp of sequence from the goat genome were identified and their homologies with known nucleic acid and protein databases were described. The new sequences could provide useful anchors for more extensive mapping and sequencing and for genomics assisted breeding of the Maltese goat.
Blundell, R.
A landmark-based method for the geometrical 3D calibration of scanning microscopes
Energy Technology Data Exchange (ETDEWEB)
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.
Scanning the human genome at kilobase resolution
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Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ...
Chen, Jun; Kim, Yeong C.; Jung, Yong-chul; Xuan, Zhenyu; Dworkin, Geoff; Zhang, Yanming; Zhang, Michael Q.; Wang, San Ming
Clinical applications of Genome Polymorphism Scans
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Applications of Genome Polymorphism Scans range from the relatively simple such as gender determination and confirmation of biological relationships, to the relatively complex such as determination of autozygosity and propagation of genetic information throughout pedigrees. Unlike nearly all other clinical DNA tests, the Scan is a universal test � it covers all people and all genes. In balance, I argue that the Genome Polymorphism Scan is the most powerful, affordable clinical DNA test avai...
Weber, James L.
Clinical applications of Genome Polymorphism Scans
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Full Text Available Abstract Applications of Genome Polymorphism Scans range from the relatively simple such as gender determination and confirmation of biological relationships, to the relatively complex such as determination of autozygosity and propagation of genetic information throughout pedigrees. Unlike nearly all other clinical DNA tests, the Scan is a universal test � it covers all people and all genes. In balance, I argue that the Genome Polymorphism Scan is the most powerful, affordable clinical DNA test available today. Reviewers: This article was reviewed by Scott Weiss (nominated by Neil Smalheiser, Roberta Pagon (nominated by Jerzy Jurka and Val Sheffield (nominated by Neil Smalheiser.
Weber James L
Using Linkage Genome Scans to Improve Power of Association in Genome Scans
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Scanning the genome for association between markers and complex diseases typically requires testing hundreds of thousands of genetic polymorphisms. Testing such a large number of hypotheses exacerbates the trade-off between power to detect meaningful associations and the chance of making false discoveries. Even before the full genome is scanned, investigators often favor certain regions on the basis of the results of prior investigations, such as previous linkage scans. The remaining regions ...
Roeder, Kathryn; Bacanu, Silvi-alin; Wasserman, Larry; Devlin, B.
Electrochemical degradation of electrodeposited Pt particles on mask scratched substrate using a landmark for ex situ scanning electron microscopy
International Nuclear Information System (INIS)
Pt particles were deposited on a glassy carbon substrate using a landmark by a mask scratch-based Pt electrodeposition method to observe the same Pt particles by ex situ scanning electron microscopy before and after a potential cycling procedure. The potential cycling was conducted in a H2O2-containing 0.5 mol dm-3 H2SO4 solution. As a result, the Pt particle degradations are clearly observed in the solution containing 100 mmol dm-3 H2O2 in the potential range of 0.04-1.44 V vs. RHE; whereas, the degradations become more remarkable at 0.34-1.44 V vs. RHE. To clarify the reason for this potential cycling range-dependence of the Pt particle degradations, the weight change of a Pt electrode during potential cycling in the presence of H2O2 was measured using an electrochemical quartz crystal microbalance. The result suggests that the dissolved Pt is re-deposited on the Pt in ca. 0.01-0.40 V vs. RHE, which well explains the difference of the Pt particle degradations by the potential cyclings between 0.04-1.44 and 0.34-1.44 V vs. RHE.
Electrochemical degradation of electrodeposited Pt particles on mask scratched substrate using a landmark for ex situ scanning electron microscopy
Energy Technology Data Exchange (ETDEWEB)
Pt particles were deposited on a glassy carbon substrate using a landmark by a mask scratch-based Pt electrodeposition method to observe the same Pt particles by ex situ scanning electron microscopy before and after a potential cycling procedure. The potential cycling was conducted in a H{sub 2}O{sub 2}-containing 0.5 mol dm{sup -3} H{sub 2}SO{sub 4} solution. As a result, the Pt particle degradations are clearly observed in the solution containing 100 mmol dm{sup -3} H{sub 2}O{sub 2} in the potential range of 0.04-1.44 V vs. RHE; whereas, the degradations become more remarkable at 0.34-1.44 V vs. RHE. To clarify the reason for this potential cycling range-dependence of the Pt particle degradations, the weight change of a Pt electrode during potential cycling in the presence of H{sub 2}O{sub 2} was measured using an electrochemical quartz crystal microbalance. The result suggests that the dissolved Pt is re-deposited on the Pt in ca. 0.01-0.40 V vs. RHE, which well explains the difference of the Pt particle degradations by the potential cyclings between 0.04-1.44 and 0.34-1.44 V vs. RHE.
Kishi, Akira; Inoue, Mitsuhiro; Shironita, Sayoko [Department of Materials Science and Technology, Faculty of Engineering, Nagaoka University of Technology, Kamitomioka 1603-1, Nagaoka, Niigata 940-2188 (Japan); Umeda, Minoru, E-mail: email@example.com [Department of Materials Science and Technology, Faculty of Engineering, Nagaoka University of Technology, Kamitomioka 1603-1, Nagaoka, Niigata 940-2188 (Japan)
Sequential methods of analysis for genome scans.
As the preceding chapters illustrate, now that whole-genome scan analyses are becoming more common, there is considerable disagreement about the best way to balance between false positives and false negatives (traditionally called type I and type II errors in the statistical parlance). Type I and type II errors can be simultaneously controlled, if we are willing to let the sample size of analysis vary. This is the secret that Wald (1947) discovered in the 1940s that led to the theory of sequential sampling and was the inspiration for Newton Morton in developing the lod score method. We can exploit this idea further and capitalize on an old, but nearly forgotten theory: sequential multiple decision procedures (SMDP) (Bechhoffer, et al., 1968), which generalizes the standard "two-hypotheses" tests to consider multiple alternative hypotheses. Using this theory, we can develop a single, genome-wide test that simultaneously partitions all markers into "signal" and "noise" groups, with tight control over both type I and type II errors (Province, 2000). Conceiving this approach as an analysis tool for fixed sample designs (instead of a true sequential sampling scheme), we can let the data decide at which point we should move from the hypothesis generation phase of a genome scan (where multiple comparisons make the interpretation of p values and significance levels difficult and controversial), to a true hypothesis-testing phase (where the problem of multiple comparisons has been all but eliminated so that p values may be accepted at face value). PMID:11037338
Province, M A
PCR-based landmark unique gene (PLUG markers effectively assign homoeologous wheat genes to A, B and D genomes
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Full Text Available Abstract Background EST-PCR markers normally represent specific products from target genes, and are therefore effective tools for genetic analysis. However, because wheat is an allohexaploid plant, PCR products derived from homoeologous genes are often simultaneously amplified. Such products may be easier to differentiate if they include intron sequences, which are more polymorphic than exon sequences. However, genomic sequence data for wheat are limited; therefore it is difficult to predict the location of introns. By using the similarities in gene structures between rice and wheat, we developed a system called PLUG (PCR-based Landmark Unique Gene to design primers so that PCR products include intron sequences. We then investigated whether products amplified using such primers could serve as markers able to distinguish multiple products derived from homoeologous genes. Results The PLUG system consists of the following steps: (1 Single-copy rice genes (Landmark Unique Gene loci; LUGs exhibiting high degrees of homology to wheat UniGene sequences are extracted; (2 Alignment analysis is carried out using the LUGs and wheat UniGene sequences to predict exon-exon junctions, and LUGs which can be used to design wheat primers flanking introns (TaEST-LUGs are extracted; and (3 Primers are designed in an interactive manner. From a total of 4,312 TaEST-LUGs, 24 loci were randomly selected and used to design primers. With all of these primer sets, we obtained specific, intron-containing products from the target genes. These markers were assigned to chromosomes using wheat nullisomic-tetrasomic lines. By PCR-RFLP analysis using agarose gel electrophoresis, 19 of the 24 markers were located on at least one chromosome. Conclusion In the development of wheat EST-PCR markers capable of efficiently sorting products derived from homoeologous genes, it is important to design primers able to amplify products that include intron sequences with insertion/deletion polymorphisms. Using the PLUG system, wheat EST sequences that can be used for marker development are selected based on comparative genomics with rice, and then primer sets flanking intron sequences are prepared in an interactive, semi-automatic manner. Hence, the PLUG system is an effective tool for large-scale marker development.
Saito Mika
Microarray Analysis: Genome-scale hypothesis scanning
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Microarrays can survey genome-wide expression patterns. Not only can these gene expression profiles be used to identify a few genes of interest, they are now being creatively applied for hypothesis generation and testing
Gibson, Greg
Genome-wide DNA polymorphism analyses using VariScan
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Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.
Vilella Albert J
Ranks of Genuine Associations in Whole-Genome Scans
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With the recent advances in high-throughput genotyping techniques, it is now possible to perform whole-genome association studies to fine map causal polymorphisms underlying important traits that influence susceptibility to human diseases and efficacy of drugs. Once a genome scan is completed the results can be sorted by the association statistic value. What is the probability that true positives will be encountered among the first most associated markers? When a particular polymorphism is fo...
Zaykin, Dmitri V.; Zhivotovsky, Lev A.
Genome scans and microarrays: converging on genes for schizophrenia?
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Systematic genome-wide scans to date have shown that genes of major effect are not common causes of schizophrenia, but independent linkage studies looking for schizophrenia susceptibility genes are converging on a number of key chromosomal locations. Microarray expression analysis may identify new candidate genes and pathways, and a number of intriguing preliminary findings have already been reported.
A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
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Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation. Here, we present a genomic survey of recent local selective sweeps, especially aimed at those nearly or recently completed. A novel approach was developed for such signals, based on contrasting the extended haplotype homozygosity (EHH) profiles between populations. We applied this method to the genome single nucleotide polymorphism (SNP) data of both...
Genome-wide scanning with SSLPs in the rat.
Genome-wide linkage analysis is a powerful tool for the identification of genes underlying single gene and complex genetic disorders. The most commonly used technique for performing genome wide scans for genetic studies in the rat is by analysis of simple sequence length polymorphism (SSLPs) or microsatellite markers. A sensitive and flexible method for high-throughput genotyping is described. Addition of an M13 tail to the SSLP primer eliminates the need for direct conjugation of the fluorescent dye to the primers, allowing for any combination of primer and fluorophor, and therefore for easy multiplexing of primers in the same reaction. With the use of three different dyes, it is possible to run more than five hundred genotypes in each run of the automatic sequencer. Automation in the fluorescent detection system and data tracking software for processing genotypes, contributes to the ability to genotype large number of samples rapidly and accurately. PMID:16028680
Moreno, Carol; Kennedy, Kathleen; Andrae, Jaime Wendt; Jacob, Howard J
Genome-wide DNA methylation scan in major depressive disorder.
While genome-wide association studies are ongoing to identify sequence variation influencing susceptibility to major depressive disorder (MDD), epigenetic marks, such as DNA methylation, which can be influenced by environment, might also play a role. Here we present the first genome-wide DNA methylation (DNAm) scan in MDD. We compared 39 postmortem frontal cortex MDD samples to 26 controls. DNA was hybridized to our Comprehensive High-throughput Arrays for Relative Methylation (CHARM) platform, covering 3.5 million CpGs. CHARM identified 224 candidate regions with DNAm differences >10%. These regions are highly enriched for neuronal growth and development genes. Ten of 17 regions for which validation was attempted showed true DNAm differences; the greatest were in PRIMA1, with 12-15% increased DNAm in MDD (p = 0.0002-0.0003), and a concomitant decrease in gene expression. These results must be considered pilot data, however, as we could only test replication in a small number of additional brain samples (n = 16), which showed no significant difference in PRIMA1. Because PRIMA1 anchors acetylcholinesterase in neuronal membranes, decreased expression could result in decreased enzyme function and increased cholinergic transmission, consistent with a role in MDD. We observed decreased immunoreactivity for acetylcholinesterase in MDD brain with increased PRIMA1 DNAm, non-significant at p = 0.08.While we cannot draw firm conclusions about PRIMA1 DNAm in MDD, the involvement of neuronal development genes across the set showing differential methylation suggests a role for epigenetics in the illness. Further studies using limbic system brain regions might shed additional light on this role. PMID:22511943
Sabunciyan, Sarven; Aryee, Martin J; Irizarry, Rafael A; Rongione, Michael; Webster, Maree J; Kaufman, Walter E; Murakami, Peter; Lessard, Andree; Yolken, Robert H; Feinberg, Andrew P; Potash, James B
Genome-wide DNA polymorphism analyses using VariScan
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Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results ...
Hutter Stephan; Vilella Albert J; Rozas Julio
High-throughput genome scanning in constant tension fluidic funnels.
Genome Sequence Scanning (GSS) is a bacterial identification technology that detects sparse sequence-specific fluorescent tags on long DNA molecules linearized in a continuous-flow microfunnel. The efficiency and sensitivity of GSS depends on the detection throughput of well-stretched molecules. Previous studies have investigated the fundamental roles of elongational and shear flow on DNA stretching in continuous flow devices. Here, we present a novel compound funnel design that significantly improves effective molecule throughput over previously described devices. First, exploring the relationship between fluid strain rate and molecule tension allows for design of funnel geometries that accommodate high fluid velocities without compromising molecules due to overstretching under high tension. Second, a constant-strain detection channel is utilized to significantly reduce the number of molecules lost to further analysis due to shear-induced molecular tumbling and relaxation. Finally, application of the constant-strain detection channel allows for a priori prediction of spatial resolution bias due to accelerating flow. In all, the refined funnel geometries presented here yield over thirty-fold increase in effective molecule throughput due to increased fluid flow and improved retention of stretched molecules, compared to previously described devices. PMID:23202853
Griffis, Joshua W; Protozanova, Ekaterina; Cameron, Douglas B; Meltzer, Robert H
Genome-wide DNA polymorphism analyses using VariScan
Digital Repository Infrastructure Vision for European Research (DRIVER)
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...
Prioritizing genomic applications for action by level of evidence: a horizon-scanning method.
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
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Full Text Available Ever since the discovery of insulin and its role in the regulation of glucose uptake and utilization, there has been great interest in insulin, its structure and the way in which it interacts with its receptor and effects signal transduction. As the 90th anniversary of the discovery of insulin approaches, it is timely to provide an overview of the landmark discoveries relating to the structure and function of this remarkable molecule and its receptor.
Genome-wide linkage scan for loci associated with epilepsy in Belgian shepherd dogs
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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 info...
Oberbauer Anita M; Belanger Janelle M; Grossman Deborah I; Regan Kelly R; Famula Thomas R
Identification of the human chromosomal region containing the iridogoniodysgenesis anomaly locus by genomic-mismatch scanning.
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Genome-mismatch scanning (GMS) is a new method of linkage analysis that rapidly isolates regions of identity between two genomes. DNA molecules from regions of identity by descent from two relatives are isolated based on their ability to form extended mismatch-free heteroduplexes. We have applied this rapid technology to identify the chromosomal region shared by two fifth-degree cousins with autosomal dominant iridogoniodysgenesis anomaly (IGDA), a rare ocular neurocristopathy. Markers on the...
Mirzayans, F.; Mears, A. J.; Guo, S. W.; Pearce, W. G.; Walter, M. A.
A Genome Scan and Linkage Disequilibrium Analysis among Chromosomal Races of the Australian Grasshopper Vandiemenella viatica
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In the past decade the interest surrounding the role of recombination in speciation has been re-kindled by a new generation of chromosomal speciation models that invoke the recombination-suppression properties of some types of chromosomal rearrangement. A common prediction of recombination-suppression models is that gene exchange between diverging populations will be more restricted in regions of the genome that experience low recombination. We carried out a genome scan of three chromosomal r...
Resampling methods to reduce the selection bias in genetic effect estimation in genome-wide scans
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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 terms of power to dete...
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.
Extension of Type 2 Diabetes Genome-Wide Association Scan Results in the Diabetes Prevention Program
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OBJECTIVE� Genome-wide association scans (GWASs) have identified novel diabetes-associated genes. We evaluated how these variants impact diabetes incidence, quantitative glycemic traits, and response to preventive interventions in 3,548 subjects at high risk of type 2 diabetes enrolled in the Diabetes Prevention Program (DPP), which examined the effects of lifestyle intervention, metformin, and troglitazone versus placebo.
Moore, Allan F.; Jablonski, Kathleen A.; Mcateer, Jarred B.; Saxena, Richa; Pollin, Toni I.; Franks, Paul W.; Hanson, Robert L.; Shuldiner, Alan R.; Knowler, William C.; Altshuler, David; Florez, Jose C.
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
Parsing radiographs by integrating landmark set detection and multi-object active appearance models
This work addresses the challenging problem of parsing 2D radiographs into salient anatomical regions such as the left and right lungs and the heart. We propose the integration of an automatic detection of a constellation of landmarks via rejection cascade classifiers and a learned geometric constellation subset detector model with a multi-object active appearance model (MO-AAM) initialized by the detected landmark constellation subset. Our main contribution is twofold. First, we propose a recovery method for false positive and negative landmarks which allows to handle extreme ranges of anatomical and pathological variability. Specifically we (1) recover false negative (missing) landmarks through the consensus of inferences from subsets of the detected landmarks, and (2) choose one from multiple false positives for the same landmark by learning Gaussian distributions for the relative location of each landmark. Second, we train a MO-AAM using the true landmarks for the detectors and during test, initialize the model using the detected landmarks. Our model fitting allows simultaneous localization of multiple regions by encoding the shape and appearance information of multiple objects in a single model. The integration of landmark detection method and MO-AAM reduces mean distance error of the detected landmarks from 20.0mm to 12.6mm. We assess our method using a database of scout CT scans from 80 subjects with widely varying pathology.
Montillo, Albert; Song, Qi; Liu, Xiaoming; Miller, James V.
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)
Genome scan of Diabrotica virgifera virgifera for genetic variation associated with crop rotation tolerance
Digital Repository Infrastructure Vision for European Research (DRIVER)
Crop rotation has been a valuable technique for control of Diabrotica virgifera virgifera for almost a century. However, during the last two decades, crop rotation has ceased to be effective in an expanding area of the US corn belt. This failure appears to be due to a change in the insect's oviposition behaviour, which, in all probability, has an underlying genetic basis. A preliminary genome scan using 253 amplified fragment-length polymorphism (AFLP) markers sought to identify genetic varia...
Miller, N. J.; Ciosi, M.; Sappington, T. W.; Ratcliffe, S. T.; Spencer, J. L.; Guillemaud, T.
Linkage disequilibrium across two different single-nucleotide polymorphism genome scans
Digital Repository Infrastructure Vision for European Research (DRIVER)
Linkage disequilibrium (LD) content was calculated for the Genetic Analysis Workshop 14 Affymetrix and Illumina single-nucleotide polymorphism (SNP) genome scans of the Collaborative Study on the Genetics of Alcoholism samples. Pair-wise LD was measured as both D' and r2 on 505 pedigree founder individuals. The r2 estimates were then used to correct the multipoint identity by descent matrix (MIBD) calculation to account for LD and LOD scores on chromosomes 3 and 18 were calculated for COGA's ...
Peralta, Juan Manuel; Dyer, Thomas D.; Warren, Diane M.; Blangero, John; Almasy, Laura
Genetic Predisposition to Self-Curing Infection with the Protozoan Leishmania chagasi: A Genome Wide Scan
Digital Repository Infrastructure Vision for European Research (DRIVER)
The protozoan Leishmania chagasi can cause disseminated, fatal visceral leishmaniasis (VL) or asymptomatic human infection. We hypothesized that genetic factors contribute to this variable response to infection. A family study was performed in endemic neighborhoods near Natal, northeast Brazil. Subjects were assessed for VL or asymptomatic infection, defined as a positive delayed type hypersensitivity (DTH) skin test response to Leishmania antigen without disease symptoms. A genome scan of 40...
Jeronimo, Selma M. B.; Duggal, Priya; Ettinger, Nicholas A.; Nascimento, Eliana T.; Monteiro, Gloria R.; Cabral, Angela P.; Pontes, Nu?bia N.; Lacerda, He?nio G.; Queiroz, Paula V.; Maia, Carlos G.; Pearson, Richard D.; Blackwell, Jenefer M.; Beaty, Terri H.; Wilson, Mary E.
Genomic Scan as a Tool for Assessing the Genetic Component of Phenotypic Variance in Wild Populations
Digital Repository Infrastructure Vision for European Research (DRIVER)
Methods for estimating quantitative trait heritability in wild populations have been developed in recent years which take advantage of the increased availability of genetic markers to reconstruct pedigrees or estimate relatedness between individuals, but their application to real-world data is not exempt from difficulties. This chapter describes a recent marker-based technique which, by adopting a genomic scan approach and focusing on the relationship betwe...
Herrera, Carlos M.
A genome-wide linkage scan for body mass index on Framingham Heart Study families
Digital Repository Infrastructure Vision for European Research (DRIVER)
Abstract Background Genome-wide scan data from a community-based sample was used to identify the genetic factors that affect body mass index (BMI). BMI was defined as weight (kg) over the square of height (m), where weight and height were obtained from the first measurement available between the ages of 40 and 50 years. Results Significant familial correlations were observed in mother:father (spouse) relative pairs and in all relative pairs examined except paren...
Moslehi Roxana; Goldstein Alisa M; Beerman Michael; Goldin Lynn; Bergen Andrew W
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
Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing.
AFLP-based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection owing to the difficulties of obtaining DNA sequences from AFLP fragments. Here, we combine classical AFLP outlier detection with 454 sequencing of AFLP fragments to obtain sequences from outlier loci. We applied this approach to the study of resistance to Bacillus thuringiensis israelensis (Bti) toxins in the dengue vector Aedes aegypti. A genome scan of Bti-resistant and Bti-susceptible A.�aegypti laboratory strains was performed based on 432 AFLP markers. Fourteen outliers were detected using two different population genetic algorithms. Out of these, 11 were successfully sequenced. Three contained transposable elements (TEs) sequences, and the 10 outliers that could be mapped at a unique location in the reference genome were located on different supercontigs. One outlier was in the vicinity of a gene coding for an aminopeptidase potentially involved in Bti toxin-binding. Patterns of sequence variability of this gene showed significant deviation from neutrality in the resistant strain but not in the susceptible strain, even after taking into account the known demographic history of the selected strain. This gene is a promising candidate for future functional analysis. PMID:22348648
Paris, Margot; Despres, Laurence
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
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)
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.
Sylvester-Hvid, C.; Nielsen, Morten
Homozygous deletion scanning of the lung cancer genome at a 100-kb resolution.
Whole genome scanning of 43 lung cancer cell lines at a 100-kb resolution led to identification of 51 genomic regions with homozygous deletions (HDs). The regions contained 113 genes, including two known tumor suppressor genes, RBl (RB) and CDKN2A (p16), and eight genes previously reported as being candidate tumor suppressor genes, such as PTPRD and LRP1B. Three miRNA genes, MIRNLET7C (let-7c), MIRN99A (hsa-mir-99a), and MIRN125B2 (hsa-mir-125b-2), were also mapped in a region with HD at 21q11-q21. The present study provides a list of protein- and miRNA-encoding genes whose inactivation is possibly involved in lung carcinogenesis. PMID:17674361
Nagayama, Kazuhiro; Kohno, Takashi; Sato, Masanori; Arai, Yasuhito; Minna, John D; Yokota, Jun
Genome scan meta-analysis of schizophrenia and bipolar disorder, part III: Bipolar disorder.
Genome scans of bipolar disorder (BPD) have not produced consistent evidence for linkage. The rank-based genome scan meta-analysis (GSMA) method was applied to 18 BPD genome scan data sets in an effort to identify regions with significant support for linkage in the combined data. The two primary analyses considered available linkage data for "very narrow" (i.e., BP-I and schizoaffective disorder-BP) and "narrow" (i.e., adding BP-II disorder) disease models, with the ranks weighted for sample size. A "broad" model (i.e., adding recurrent major depression) and unweighted analyses were also performed. No region achieved genomewide statistical significance by several simulation-based criteria. The most significant P values (chromosomes 9p22.3-21.1 (very narrow), 10q11.21-22.1 (very narrow), and 14q24.1-32.12 (narrow). Nominally significant P values were observed in adjacent bins on chromosomes 9p and 18p-q, across all three disease models on chromosomes 14q and 18p-q, and across two models on chromosome 8q. Relatively few BPD pedigrees have been studied under narrow disease models relative to the schizophrenia GSMA data set, which produced more significant results. There was no overlap of the highest-ranked regions for the two disorders. The present results for the very narrow model are promising but suggest that more and larger data sets are needed. Alternatively, linkage might be detected in certain populations or subsets of pedigrees. The narrow and broad data sets had considerable power, according to simulation studies, but did not produce more highly significant evidence for linkage. We note that meta-analysis can sometimes provide support for linkage but cannot disprove linkage in any candidate region. PMID:12802785
Segurado, Ricardo; Detera-Wadleigh, Sevilla D; Levinson, Douglas F; Lewis, Cathryn M; Gill, Michael; Nurnberger, John I; Craddock, Nick; DePaulo, J Raymond; Baron, Miron; Gershon, Elliot S; Ekholm, Jenny; Cichon, Sven; Turecki, Gustavo; Claes, Stephan; Kelsoe, John R; Schofield, Peter R; Badenhop, Renee F; Morissette, J; Coon, Hilary; Blackwood, Douglas; McInnes, L Alison; Foroud, Tatiana; Edenberg, Howard J; Reich, Theodore; Rice, John P; Goate, Alison; McInnis, Melvin G; McMahon, Francis J; Badner, Judith A; Goldin, Lynn R; Bennett, Phil; Willour, Virginia L; Zandi, Peter P; Liu, Jianjun; Gilliam, Conrad; Juo, Suh-Hang; Berrettini, Wade H; Yoshikawa, Takeo; Peltonen, Leena; L�nnqvist, Jouko; N�then, Markus M; Schumacher, Johannes; Windemuth, Christine; Rietschel, Marcella; Propping, Peter; Maier, Wolfgang; Alda, Martin; Grof, Paul; Rouleau, Guy A; Del-Favero, Jurgen; Van Broeckhoven, Christine; Mendlewicz, Julien; Adolfsson, Rolf; Spence, M Anne; Luebbert, Hermann; Adams, Linda J; Donald, Jennifer A; Mitchell, Philip B; Barden, Nicholas; Shink, Eric; Byerley, William; Muir, Walter; Visscher, Peter M; Macgregor, Stuart; Gurling, Hugh; Kalsi, Gursharan; McQuillin, Andrew; Escamilla, Michael A; Reus, Victor I; Leon, Pedro; Freimer, Nelson B; Ewald, Henrik; Kruse, Torben A; Mors, Ole; Radhakrishna, Uppala; Blouin, Jean-Louis; Antonarakis, Stylianos E; Akarsu, Nurten
Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity
Aberrant connectivity is implicated in many neurological and psychiatric disorders, including Alzheimer�s disease and schizophrenia. However, other than a few disease-associated candidate genes, we know little about the degree to which genetics play a role in the brain networks; we know even less about specific genes that influence brain connections. Twin and family-based studies can generate estimates of overall genetic influences on a trait, but genome-wide association scans (GWASs) can screen the genome for specific variants influencing the brain or risk for disease. To identify the heritability of various brain connections, we scanned healthy young adult twins with high-field, high-angular resolution diffusion MRI. We adapted GWASs to screen the brain�s connectivity pattern, allowing us to discover genetic variants that affect the human brain�s wiring. The association of connectivity with the SPON1 variant at rs2618516 on chromosome 11 (11p15.2) reached connectome-wide, genome-wide significance after stringent statistical corrections were enforced, and it was replicated in an independent subsample. rs2618516 was shown to affect brain structure in an elderly population with varying degrees of dementia. Older people who carried the connectivity variant had significantly milder clinical dementia scores and lower risk of Alzheimer�s disease. As a posthoc analysis, we conducted GWASs on several organizational and topological network measures derived from the matrices to discover variants in and around genes associated with autism (MACROD2), development (NEDD4), and mental retardation (UBE2A) significantly associated with connectivity. Connectome-wide, genome-wide screening offers substantial promise to discover genes affecting brain connectivity and risk for brain diseases.
Jahanshad, Neda; Rajagopalan, Priya; Hua, Xue; Hibar, Derrek P.; Nir, Talia M.; Toga, Arthur W.; Jack, Clifford R.; Saykin, Andrew J.; Green, Robert C.; Weiner, Michael W.; Medland, Sarah E.; Montgomery, Grant W.; Hansell, Narelle K.; McMahon, Katie L.; de Zubicaray, Greig I.; Martin, Nicholas G.; Wright, Margaret J.; Thompson, Paul M.; Weiner, Michael; Aisen, Paul; Weiner, Michael; Aisen, Paul; Petersen, Ronald; Jack, Clifford R.; Jagust, William; Trojanowski, John Q.; Toga, Arthur W.; Beckett, Laurel; Green, Robert C.; Saykin, Andrew J.; Morris, John; Liu, Enchi; Green, Robert C.; Montine, Tom; Petersen, Ronald; Aisen, Paul; Gamst, Anthony; Thomas, Ronald G.; Donohue, Michael; Walter, Sarah; Gessert, Devon; Sather, Tamie; Beckett, Laurel; Harvey, Danielle; Gamst, Anthony; Donohue, Michael; Kornak, John; Jack, Clifford R.; Dale, Anders; Bernstein, Matthew; Felmlee, Joel; Fox, Nick; Thompson, Paul; Schuff, Norbert; Alexander, Gene; DeCarli, Charles; Jagust, William; Bandy, Dan; Koeppe, Robert A.; Foster, Norm; Reiman, Eric M.; Chen, Kewei; Mathis, Chet; Morris, John; Cairns, Nigel J.; Taylor-Reinwald, Lisa; Trojanowki, J.Q.; Shaw, Les; Lee, Virginia M.Y.; Korecka, Magdalena; Toga, Arthur W.; Crawford, Karen; Neu, Scott; Saykin, Andrew J.; Foroud, Tatiana M.; Potkin, Steven; Shen, Li; Khachaturian, Zaven; Frank, Richard; Snyder, Peter J.; Molchan, Susan; Kaye, Jeffrey; Quinn, Joseph; Lind, Betty; Dolen, Sara; Schneider, Lon S.; Pawluczyk, Sonia; Spann, Bryan M.; Brewer, James; Vanderswag, Helen; Heidebrink, Judith L.; Lord, Joanne L.; Petersen, Ronald; Johnson, Kris; Doody, Rachelle S.; Villanueva-Meyer, Javier; Chowdhury, Munir; Stern, Yaakov; Honig, Lawrence S.; Bell, Karen L.; Morris, John C.; Ances, Beau; Carroll, Maria; Leon, Sue; Mintun, Mark A.; Schneider, Stacy; Marson, Daniel; Griffith, Randall; Clark, David; Grossman, Hillel; Mitsis, Effie; Romirowsky, Aliza; deToledo-Morrell, Leyla; Shah, Raj C.; Duara, Ranjan; Varon, Daniel; Roberts, Peggy; Albert, Marilyn; Onyike, Chiadi; Kielb, Stephanie; Rusinek, Henry; de Leon, Mony J.; Glodzik, Lidia; De Santi, Susan; Doraiswamy, P. Murali; Petrella, Jeffrey R.; Coleman, R. Edward; Arnold, Steven E.; Karlawish, Jason H.; Wolk, David; Smith, Charles D.; Jicha, Greg; Hardy, Peter; Lopez, Oscar L.; Oakley, MaryAnn; Simpson, Donna M.; Porsteinsson, Anton P.; Goldstein, Bonnie S.; Martin, Kim; Makino, Kelly M.; Ismail, M. Saleem; Brand, Connie; Mulnard, Ruth A.; Thai, Gaby; Mc-Adams-Ortiz, Catherine; Womack, Kyle; Mathews, Dana; Quiceno, Mary; Diaz-Arrastia, Ramon; King, Richard; Weiner, Myron; Martin-Cook, Kristen; DeVous, Michael; Levey, Allan I.; Lah, James J.; Cellar, Janet S.; Burns, Jeffrey M.; Anderson, Heather S.; Swerdlow, Russell H.; Apostolova, Liana; Lu, Po H.; Bartzokis, George; Silverman, Daniel H.S.; Graff-Radford, Neill R.; Parfitt, Francine; Johnson, Heather; Farlow, Martin R.; Hake, Ann Marie; Matthews, Brandy R.; Herring, Scott; van Dyck, Christopher H.; Carson, Richard E.; MacAvoy, Martha G.; Chertkow, Howard; Bergman, Howard; Hosein, Chris; Black, Sandra; Stefanovic, Bojana; Caldwell, Curtis; Hsiung, Ging-Yuek Robin; Feldman, Howard; Mudge, Benita; Assaly, Michele; Kertesz, Andrew; Rogers, John; Trost, Dick; Bernick, Charles; Munic, Donna; Kerwin, Diana; Mesulam, Marek-Marsel; Lipowski, Kristina; Wu, Chuang-Kuo; Johnson, Nancy; Sadowsky, Carl; Martinez, Walter; Villena, Teresa; Turner, Raymond Scott; Johnson, Kathleen; Reynolds, Brigid; Sperling, Reisa A.; Johnson, Keith A.; Marshall, Gad; Frey, Meghan; Yesavage, Jerome; Taylor, Joy L.; Lane, Barton; Rosen, Allyson; Tinklenberg, Jared; Sabbagh, Marwan; Belden, Christine; Jacobson, Sandra; Kowall, Neil; Killiany, Ronald; Budson, Andrew E.; Norbash, Alexander; Johnson, Patricia Lynn; Obisesan, Thomas O.; Wolday, Saba; Bwayo, Salome K.; Lerner, Alan; Hudson, Leon; Ogrocki, Paula; Fletcher, Evan; Carmichael, Owen; Olichney, John; DeCarli, Charles; Kittur, Smita; Borrie, Michael; Lee, T.-Y.; Bartha, Rob; Johnson, Sterling; Asthana, Sanjay; Carlsson, Cynthia M.; Potkin, Steven G.; Preda, Adrian; Nguyen, Dana; Tariot, Pierre; Fleisher, Adam; Reeder, Stephanie; Bates, Vernice; Capote, Horacio; Rainka, Michelle; Scharre, Douglas W.; Kataki, Maria; Zimmerman, Earl A.; Celmins, Dzintra; Brown, Alice D.; Pearlson, Godfrey D.; Blank, Karen; Anderson, Karen; Saykin, Andrew J.; Santulli, Robert B.; Schwartz, Eben S.; Sink, Kaycee M.; Williamson, Jeff D.; Garg, Pradeep; Watkins, Franklin; Ott, Brian R.; Querfurth, Henry; Tremont, Geoffrey; Salloway, Stephen; Malloy, Paul; Correia, Stephen; Rosen, Howard J.; Miller, Bruce L.; Mintzer, Jacobo
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
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.
Guimar�es Simone EF
Landmark Discrimination Learning in the Dog
Digital Repository Infrastructure Vision for European Research (DRIVER)
Allocentric spatial memory was studied in dogs of varying ages and sources using a landmark discrimination task. The primary goal of this study was to develop a protocol to test landmark discrimination learning in the dog. Using a modified version of a landmark test developed for use in monkeys, we successfully trained dogs to make a spatial discrimination on the basis of the position of a visual landmark relative to two identical discriminanda. Task performance decreased, however, as the dis...
Milgram, Norton W.; Adams, Beth; Callahan, Heather; Head, Elizabeth; Mackay, Bill; Thirlwell, Celeste; Cotman, Carl W.
InterProScan 5: genome-scale protein function classification
Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code. Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/. Contact: http://www.ebi.ac.uk/support or email@example.com or email@example.com
Jones, Philip; Binns, David; Chang, Hsin-Yu; Fraser, Matthew; Li, Weizhong; McAnulla, Craig; McWilliam, Hamish; Maslen, John; Mitchell, Alex; Nuka, Gift; Pesseat, Sebastien; Quinn, Antony F.; Sangrador-Vegas, Amaia; Scheremetjew, Maxim; Yong, Siew-Yit; Lopez, Rodrigo; Hunter, Sarah
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
HybGFS: a hybrid method for genome-fingerprint scanning
Directory of Open Access Journals (Sweden)
Full Text Available Abstract Background Protein identification based on mass spectrometry (MS has previously been performed using peptide mass fingerprinting (PMF or tandem MS (MS/MS database searching. However, these methods cannot identify proteins that are not already listed in existing databases. Moreover, the alternative approach of de novo sequencing requires costly equipment and the interpretation of complex MS/MS spectra. Thus, there is a need for novel high-throughput protein-identification methods that are independent of existing predefined protein databases. Results Here, we present a hybrid method for genome-fingerprint scanning, known as HybGFS. This technique combines genome sequence-based peptide MS/MS ion searching with liquid-chromatography elution-time (LC-ET prediction, to improve the reliability of identification. The hybrid method allows the simultaneous identification and mapping of proteins without a priori information about their coding sequences. The current study used standard LC-MS/MS data to query an in silico-generated six-reading-frame translation and the enzymatic digest of an entire genome. Used in conjunction with precursor/product ion-mass searching, the LC-ETs increased confidence in the peptide-identification process and reduced the number of false-positive matches. The power of this method was demonstrated using recombinant proteins from the Escherichia coli K12 strain. Conclusion The novel hybrid method described in this study will be useful for the large-scale experimental confirmation of genome coding sequences, without the need for transcriptome-level expression analysis or costly MS database searching.
Sugiyama Naoyuki
Ion Torrent sequencing for conducting genome-wide scans for mutation mapping analysis.
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
A Genome Scan Conducted in a Multigenerational Pedigree with Convergent Strabismus Supports a Complex Genetic Determinism
A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromosome regions with near-suggestive evidence for linkage, respectively on chromosomes 8 and 18. The chromosome 8 linkage implied a penetrance of 0.80 and a rate of phenocopy of 0.11, while the chromosome 18 linkage implied a penetrance of 0.64 and a rate of phenocopy of 0. Our analysis excludes a simple genetic determinism of strabismus in this pedigree.
Georges, Anouk; Cambisano, Nadine; Ahariz, Naima; Karim, Latifa; Georges, Michel
Information content in genome-wide scans: concordance between patterns of genetic differentiation and linkage mapping associations
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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...
Wiener Pamela; Edriss Mohammad A; Williams John L; Waddington David; Law Andrew; Woolliams John A; Guti�rrez-Gil Beatriz
Position-Based Scanning for Comparative Genomics and Identification of Genetic Islands in Haemophilus influenzae Type b
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Bacteria exhibit extensive genetic heterogeneity within species. In many cases, these differences account for virulence properties unique to specific strains. Several such loci have been discovered in the genome of the type b serotype of Haemophilus influenzae, a human pathogen able to cause meningitis, pneumonia, and septicemia. Here we report application of a PCR-based scanning procedure to compare the genome of a virulent type b (Hib) strain with that of the laboratory-passaged Rd KW20 str...
Bergman, Nicholas H.; Akerley, Brian J.
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 ...
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 ...
By the end of 2002, we witnessed the landmark submission of the 100th complete genome sequence in the databases. An overview of these genomes reveals certain interesting trends and provides valuable insights into possible future developments. PMID:12734008
Janssen, Paul; Audit, Benjamin; Cases, Ildefonso; Darzentas, Nikos; Goldovsky, Leon; Kunin, Victor; Lopez-Bigas, Nuria; Peregrin-Alvarez, Jos� Manuel; Pereira-Leal, Jos� B; Tsoka, Sophia; Ouzounis, Christos A
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By the end of 2002, we witnessed the landmark submission of the 100th complete genome sequence in the databases. An overview of these genomes reveals certain interesting trends and provides valuable insights into possible future developments.
Janssen, Paul; Audit, Benjamin; Cases, Ildefonso; Darzentas, Nikos; Goldovsky, Leon; Kunin, Victor; Lopez-bigas, Nuria; Peregrin-alvarez, Jose? Manuel; Pereira-leal, Jose? B.; Tsoka, Sophia; Ouzounis, Christos A.
Quantitative linkage genome scan for atopy in a large collection of Caucasian families.
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Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma. In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764, and D8S2324, respectively. The results from chromosomes 1 and 3 replicate previous reports of linkage. We also replicate linkage to 5q with peak LODs of 1.96 (SPT(per)) and 1.77 (IgE) at or near marker D5S1480. Our results provide further evidence implicating chromosomes 1, 3, and 5q. The current report represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders.
Webb, BT; van den Oord, E
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 r...
Auger, Stephen D.; Mullally, Sine?ad L.; Maguire, Eleanor A.
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 r...
Desert Ants Learn Vibration and Magnetic Landmarks
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The desert ants Cataglyphis navigate not only by path integration but also by using visual and olfactory landmarks to pinpoint the nest entrance. Here we show that Cataglyphis noda can additionally use magnetic and vibrational landmarks as nest-defining cues. The magnetic field may typically provide directional rather than positional information, and vibrational signals so far have been shown to be involved in social behavior. Thus it remains questionable if magnetic and vibration landmarks a...
Buehlmann, Cornelia; Hansson, Bill S.; Knaden, Markus
Adaptive bioinspired landmark identification for navigation control
In this paper a new methodology for landmark navigation will be introduced. Either for animals or for artificial agents, the whole problem of landmark navigation can be divided into two parts: first, the agent has to recognize, from the dynamic environment, space invariant objects which can be considered as suitable landmarks for driving the motion towards a goal position; second, it has to use the information on the landmarks to effectively navigate within the environment. Here, the problem of determining landmarks has been addressed by processing the external information through a spiking network with dynamic synapses plastically tuned by an STDP algorithm. The learning processes establish correlations between the incoming stimuli, allowing the system to extract from the scenario important features which can play the role of landmarks. Once established the landmarks, the agent acquires geometric relationships between them and the goal position. This process defines the parameters of a recurrent neural network (RNN). This in turn drives the agent navigation, filtering the information about landmarks given within an absolute reference system (e.g the North). When the absolute reference is not available, a safety mechanism acts to control the motion maintaining a correct heading. Simulation results showed the potentiality of the proposed architecture: this is able to drive an agent towards the desired position in presence of stimuli subject to noise and also in the case of partially obscured landmarks.
Arena, Paolo; Cruse, Holk; Fortuna, Luigi; Lombardo, Davide; Patan�, Luca; Rapisarda, Rosa
Estimation of genetic parameters and genome scan for 15 semen characteristics traits of Holstein bulls.
A QTL detection experiment was performed in French dairy cattle to search for QTL related to male fertility. Ten families, involving a total of 515 bulls, were phenotyped for ejaculated volume and sperm concentration, number of spermatozoa, motility, velocity, percentage of motile spermatozoa after thawing and abnormal spermatozoa. A set of 148 microsatellite markers were used to realize a genome scan. First, genetic parameters were estimated for all traits. Semen production traits were found to have moderate heritabilities (from 0.15 to 0.30) while some of the semen quality traits such as motility had high heritabilities (close to 0.60). Genetic correlations among traits showed negative relationships between volume and concentration and between volume and most quality traits such as motility or abnormal sperm while correlations between concentration and these traits were rather favourable. Percentages of abnormal sperm were negatively related to quality traits, especially with motility and velocity of spermatozoa. Three QTL related to abnormal sperm frequencies were significant at p < 0.01. In total, 11 QTL (p < 0.05) were detected. However, the number of QTL detected was within the range of expected false positives. Because of the lack of power to find QTL in this design further analyses are required to confirm these QTL. PMID:19630877
Druet, T; Fritz, S; Sellem, E; Basso, B; G�rard, O; Salas-Cortes, L; Humblot, P; Druart, X; Eggen, A
QTLs for height: results of a full genome scan in Dutch sibling pairs.
Height is a highly heritable, complex trait. At present, the genes responsible for the variation in height have not yet been identified. This paper summarizes the results of previous linkage studies and presents results of an additional linkage analysis. Using data from the Netherlands Twin Register, a sib-pair-based linkage analysis for adult height was conducted. For 513 sib-pairs from 174 families complete genome scans and adult height were available. The strongest evidence for linkage was found for a region on chromosome 6, near markers D6S1053 and D6S1031 (LOD = 2.32). This replicated previous findings in other data sets. LOD scores ranging from 1.53 to 2.04 were found for regions on chromosomes 1, 5, 8, 10, and 18. The region on chromosome 18 (LOD = 1.83) also corresponded with the results of previous studies. Several chromosomal regions are now implied in the variance in height, but further study is needed to draw definite conclusions with regard to the significance of these regions for adult height. PMID:15305175
Willemsen, Gonneke; Boomsma, Dorret I; Beem, A Leo; Vink, Jacqueline M; Slagboom, P Eline; Posthuma, Danielle
A genome-wide scan suggests a susceptibility locus on 5p 13 for nasopharyngeal carcinoma.
Nasopharyngeal carcinoma (NPC) occurs with high frequency in Southeast Asian populations. The high prevalence and familial clustering of NPC in these populations suggest that genetic factors may contribute to the increased cancer risk by affecting susceptibility. The aim of the present study was to map chromosomal loci linked to susceptibility genes predisposing for NPC. We carried out a genome-wide scan by multipoint affected-only allele-sharing methods in 15 Chinese NPC families with two to six affected members per family. The families were from the Guangdong province in the south of China, where the highest risk of NPC is documented. These samples were genotyped using 800 microsatellite markers covering all autosomal chromosomes with an average marker distance of 5 cM. Using multipoint linkage analysis, four loci (2q, 5p, 12p, and 18p) showed LOD scores above 1.5. After genotyping additional markers in these four regions, only one locus on 5p13 showed an increased LOD of 2.1. In further haplotype analysis, affected individuals in six families shared three marker haplotypes between D5S674 and D5S418. In conclusion, a region on 5p13 may harbor a susceptibility gene for NPC. PMID:18197201
Hu, Li-Fu; Qiu, Qian-Hui; Fu, Sheng-Miao; Sun, Di; Magnusson, Kristinn; He, Bing; Lindblom, Annika; Ernberg, Ingemar
Genome-Wide Association Scan Shows Genetic Variants in the FTO Gene Are Associated with Obesity-Related Traits
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The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated po...
Scuteri, Angelo; Sanna, Serena; Chen, Wei-min; Uda, Manuela; Albai, Giuseppe; Strait, James; Najjar, Samer; Nagaraja, Ramaiah; Orru?, Marco; Usala, Gianluca; Dei, Mariano; Lai, Sandra; Maschio, Andrea; Busonero, Fabio; Mulas, Antonella
A genome-wide linkage scan reveals CD53 as an important regulator of innate TNF-? levels
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Cytokines are major immune system regulators. Previously, innate cytokine profiles determined by lipopolysaccharide stimulation were shown to be highly heritable. To identify regulating genes in innate immunity, we analyzed data from a genome-wide linkage scan using microsatellites in osteoarthritis (OA) patients (The GARP study) and their innate cytokine data on interleukin (IL)-1?, IL-1Ra, IL-10 and tumor necrosis factor (TNF)?. A confirmation cohort consisted of the Leiden 85-Plus study....
Bos, Steffan D.; Lakenberg, Nico; Breggen, Ruud; Houwing-duistermaat, Jeanine J.; Kloppenburg, Margreet; Craen, Anton Jm; Beekman, Marian; Meulenbelt, Ingrid; Slagboom, P. Eline
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
GDT Large Area Landmarks represents common landmark areas within United States including military areas, prisons, educational institutions, amusement centers, government centers, sport centers, golf courses, and cemeteries....
Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan
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Multiple displacement amplification (MDA) has emerged as a promising new method of whole genome amplification (WGA) with the potential to generate virtually unlimited genome-equivalent DNA from only a small amount of seed DNA. To date, genome-wide high marker density assessments of MDA�DNA have focussed mainly upon suitability for single nucleotide polymorphism (SNP) genotyping applications. Suitability for short tandem repeat (STR) genotyping has not been investigated in great detail, desp...
Dickson, Peter A.; Montgomery, Grant W.; Henders, Anjali; Campbell, Megan J.; Martin, Nicholas G.; James, Michael R.
A genome-wide scan for attention-deficit/hyperactivity disorder in 155 German sib-pairs.
Three groups have previously performed genome scans in attention-deficit/hyperactivity disorder (ADHD); linkage to chromosome 5p13 was detected in all of the respective studies. In the current study, we performed a whole-genome scan with 102 German families with two or more offspring who currently fulfilled the diagnostic criteria for ADHD. Including subsequent fine mapping on chromosome 5p, a total of 523 markers were genotyped. The highest nonparametric multipoint LOD score of 2.59 (empirical genome-wide significance 0.1) was obtained for chromosome 5p at 17 cM (according to the Marshfield map). Subsequent analyses revealed (a) a higher LOD score of 3.37 at 39 cM for a quantitative severity score based on symptoms of inattention than for hyperactivity/impulsivity (LOD score of 1.11 at 59 cM), and (b) an HLOD of 4.75 (empirical genome-wide significance 0.001) based on a parametric model assuming dominant inheritance. The locus of the solute carrier 6A3 (SLC6A3; dopamine transporter 1; DAT1) localizes to 5p15.33; the gene has repeatedly been implicated in the etiology of ADHD. However, in our sample the DAT1 VNTR did not show association with ADHD. We additionally identified nominal evidence for linkage to chromosomes 6q, 7p, 9q, 11 q, 12q and 17p, which had also been identified in previous scans. Despite differences in ethnicity, ascertainment and phenotyping schemes, linkage results in ADHD appear remarkably consistent. PMID:16222334
Hebebrand, J; Dempfle, A; Saar, K; Thiele, H; Herpertz-Dahlmann, B; Linder, M; Kiefl, H; Remschmidt, H; Hemminger, U; Warnke, A; Kn�lker, U; Heiser, P; Friedel, S; Hinney, A; Sch�fer, H; N�rnberg, P; Konrad, K
Landmarks selection in street map design
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.
LocusZoom: regional visualization of genome-wide association scan results
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Summary: Genome-wide association studies (GWAS) have revealed hundreds of loci associated with common human genetic diseases and traits. We have developed a web-based plotting tool that provides fast visual display of GWAS results in a publication-ready format. LocusZoom visually displays regional information such as the strength and extent of the association signal relative to genomic position, local linkage disequilibrium (LD) and recombination patterns and the positions of genes in the reg...
Pruim, Randall J.; Welch, Ryan P.; Sanna, Serena; Teslovich, Tanya M.; Chines, Peter S.; Gliedt, Terry P.; Boehnke, Michael; Abecasis, Gonc?alo R.; Willer, Cristen J.
A genome-wide linkage and association scan reveals novel loci for autism
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Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success. Genome-wide association studies using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits. Consequently, we initiated a linkage and association mapping study using half a million genome-wide single nucleo...
Weiss, La; Arking, DE; Daly, Mj; Chakravarti, A.; Brune, Cw; West, K.; O Connor, A.; Hilton, G.; Tomlinson, Rl; West, Ab; Cook Jr, Eh; Green, T.; Chang, S-c; Gabriel, S.; Gates, C.
A Genome Wide Linkage Scan for Cleft Lip and Palate and Dental Anomalies
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We revisited 46 families with two or more siblings affected with an orofacial cleft that participated in previous genome wide studies and collected complete dental information. Genotypes from 392 microsatellite markers at 10 cM intervals were reanalyzed. We carried out four sets of genome wide analyses. First, we ran the analysis solely on the cleft status. Second, we assigned to any dental anomaly (tooth agenesis, supernumerary teeth, and microdontia) an affection status, and repeated the an...
Vieira, Alexandre R.; Mchenry, Toby G.; Daack-hirsch, Sandra; Murray, Jeffrey C.; Marazita, Mary L.
Optimization of Landmark Selection for Cortical Surface Registration
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Manually labeled landmark sets are often required as inputs for landmark-based image registration. Identifying an optimal subset of landmarks from a training dataset may be useful in reducing the labor intensive task of manual labeling. In this paper, we present a new problem and a method to solve it: given a set of N landmarks, find the k(< N) best landmarks such that aligning these k landmarks that produce the best overall alignment of all N landmarks. The resulting procedure allows us to s...
Joshi, Anand; Pantazis, Dimitrios; Damasio, Hanna; Shattuck, David; Li, Quanzheng; Leahy, Richard
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.
A genome-wide scan for signatures of recent selection in Holstein cattle.
The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding. PMID:20096028
Qanbari, S; Pimentel, E C G; Tetens, J; Thaller, G; Lichtner, P; Sharifi, A R; Simianer, H
Meta-Analysis of Genome-Wide Scans for Human Adult Stature Identifies Novel Loci and Associations with Measures of Skeletal Frame Size
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Recent genome-wide (GW) scans have identified several independent loci affecting human stature, but their contribution through the different skeletal components of height is still poorly understood. We carried out a genome-wide scan in 12,611 participants, followed by replication in an additional 7,187 individuals, and identified 17 genomic regions with GW-significant association with height. Of these, two are entirely novel (rs11809207 in CATSPER4, combined P-value=6.1x10(-8) and rs910316 in...
Soranzo, N.; Rivadeneira Ramirez, F.; Chinappen-horsley, U.; Malkina, I.; Richards, J. B.; Hammond, N.; Stolk, L.; Nica, A.; Inouye, M.; Hofman, A.; Stephens, J.; Wheeler, E.; Arp, P. P.; Gwilliam, R.; Jhamai, P. M.
Combined Genome Scans for Body Stature in 6,602 European Twins: Evidence for Common Caucasian Loci
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).
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
Genome-wide linkage scans for major depression in individuals with alcohol dependence
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Major depression is more prevalent among individuals with alcoholism than in the general population. Twin studies have found a moderate degree of genetic correlation for alcohol dependence (AD) and major depression (MD), suggesting the existence of loci that confer susceptibility to both disorders. The aim of the present study was to conduct genome-wide linkage analyses to identify loci and to replicate prior evidence for linkage to MD, and to search for linkage regions that may confer risk t...
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
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Motivation: Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins, UGA is recoded to Sec in presence of specific features on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks, and even known selenoproteins are often misannotated in genome databases.
Mariotti, M.; Guigo?, R.
Genome-wide Association Scan Yields New Insights into the Immunopathogenesis of Psoriasis
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Psoriasis is a common, immunologically-mediated, inflammatory and hyperproliferative disease of the skin and joints, with a multifactorial genetic basis. We previously mapped PSORS1, the major psoriasis susceptibility gene in the major histocompatibility complex, to within or very near HLA-Cw6. In an effort to identify non-MHC psoriasis genes, we carried out a collaborative genome-wide association study. After initial follow-up genotyping of 21 SNPs from 18 loci showing strong evidence of ass...
Elder, James T.
A genome-wide scan for common alleles affecting risk for autism
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Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD 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...
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
A genome-wide scan for common alleles affecting risk for autism.
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Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD 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...
Anney, Richard; Klei, Lambertus; Pinto, Dalila; Regan, Regina; Conroy, Judith; Magalhaes, Tiago; Correia, Catarina; Abrahams, Brett; Sykes, Nuala; Pagnamenta, Alistair; Almeida, Joana; Bacchelli, Elena; Bailey, Anthony; Baird, Gillian; Battaglia, Agatino
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
Crohn's disease (CD) is a complex disorder resulting from the interaction of intestinal microbiota with the host immune system in genetically susceptible individuals. The largest meta-analysis of genome-wide association to date identified 71 CD-susceptibility loci in individuals of European ancestry. An important epidemiological feature of CD is that it is 2-4 times more prevalent among individuals of Ashkenazi Jewish (AJ) descent compared to non-Jewish Europeans (NJ). To explore genetic variation associated with CD in AJs, we conducted a genome-wide association study (GWAS) by combining raw genotype data across 10 AJ cohorts consisting of 907 cases and 2,345 controls in the discovery stage, followed up by a replication study in 971 cases and 2,124 controls. We confirmed genome-wide significant associations of 9 known CD loci in AJs and replicated 3 additional loci with strong signal (pCPAMD8, PRG2, and PRG3. In all, the 16 replicated and newly discovered loci, in addition to the three coding NOD2 variants, accounted for 11.2% of the total genetic variance for CD risk in the AJ population. This study demonstrates the complementary value of genetic studies in the Ashkenazim. PMID:22412388
Kenny, Eimear E; Pe'er, Itsik; Karban, Amir; Ozelius, Laurie; Mitchell, Adele A; Ng, Sok Meng; Erazo, Monica; Ostrer, Harry; Abraham, Clara; Abreu, Maria T; Atzmon, Gil; Barzilai, Nir; Brant, Steven R; Bressman, Susan; Burns, Edward R; Chowers, Yehuda; Clark, Lorraine N; Darvasi, Ariel; Doheny, Dana; Duerr, Richard H; Eliakim, Rami; Giladi, Nir; Gregersen, Peter K; Hakonarson, Hakon; Jones, Michelle R; Marder, Karen; McGovern, Dermot P B; Mulle, Jennifer; Orr-Urtreger, Avi; Proctor, Deborah D; Pulver, Ann; Rotter, Jerome I; Silverberg, Mark S; Ullman, Thomas; Warren, Stephen T; Waterman, Matti; Zhang, Wei; Bergman, Aviv; Mayer, Lloyd; Katz, Seymour; Desnick, Robert J; Cho, Judy H; Peter, Inga
Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever
Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 (IL21), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21. Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit.
Andersen, Kristian G.; Shylakhter, Ilya; Tabrizi, Shervin; Grossman, Sharon R.; Happi, Christian T.; Sabeti, Pardis C.
TINA manual landmarking tool: software for the precise digitization of 3D landmarks
Directory of Open Access Journals (Sweden)
Full Text Available Abstract Background Interest in the placing of landmarks and subsequent morphometric analyses of shape for 3D data has increased with the increasing accessibility of computed tomography (CT scanners. However, current computer programs for this task suffer from various practical drawbacks. We present here a free software tool that overcomes many of these problems. Results The TINA Manual Landmarking Tool was developed for the digitization of 3D data sets. It enables the generation of a modifiable 3D volume rendering display plus matching orthogonal 2D cross-sections from DICOM files. The object can be rotated and axes defined and fixed. Predefined lists of landmarks can be loaded and the landmarks identified within any of the representations. Output files are stored in various established formats, depending on the preferred evaluation software. Conclusions The software tool presented here provides several options facilitating the placing of landmarks on 3D objects, including volume rendering from DICOM files, definition and fixation of meaningful axes, easy import, placement, control, and export of landmarks, and handling of large datasets. The TINA Manual Landmark Tool runs under Linux and can be obtained for free from http://www.tina-vision.net/tarballs/.
Schunke Anja C
A genome scan for quantitative trait loci affecting three ear traits in a White Duroc x Chinese Erhualian resource population.
Chinese Erhualian pigs have larger and floppier ears compared with White Duroc pigs (small, half- or fully-pricked ears). To identify quantitative trait loci (QTL) for ear weight and area as well as erectness, a genome-wide scan with 194 microsatellites was performed in a White Duroc x Chinese Erhualian resource population (>1000 F(2) animals). Twenty-three genome-wide significant QTL and 12 suggestive QTL were identified. All QTL for ear erectness and size detected in two previous studies, bar two on SSC6 and 9, were confirmed here. The 1% genome-wide significant QTL at 70 cM on SSC5 and at 58 cM on SSC7 have profound and pleiotropic effects on the three ear traits, with Erhualian alleles increasing weight and area but decreasing erectness. Notably, the 95% confidence interval of the QTL for weight and area on SSC7 spanned only 3 cM. New QTL reaching 1% genome-wide significance were found on SSC8 (at 37 cM) for all three ear traits, on SSC4 and 16 for weight and area, and on SSCX for area. Unexpectedly, Erhualian alleles at these loci were associated with lighter and smaller or erect ear. Some new suggestive QTL were also found on other chromosome regions. Almost all the QTL for weight and area had essentially additive effects, while the QTL for erectness on SSC2, 5 and 7 showed not only additive effects but also partial dominance effects of Erhualian alleles. The two most significant QTL on SSC7 and SSC5 could be promising targets for fine mapping and identification of the causative mutations. PMID:19392826
Ma, J; Qi, W; Ren, D; Duan, Y; Qiao, R; Guo, Y; Yang, Z; Li, L; Milan, D; Ren, J; Huang, L
Impact of different anatomical landmarks on registration in imaging-guided radiation for lung cancer
International Nuclear Information System (INIS)
Objective: To evaluate the impact of different anatomical landmarks on registration in imaging-guided radiation (IGRT) for lung cancer. Methods: For 20 patients with non-small cell lung cancer receiving stereotactic body radiotherapy (SBRT) in Fudan University Cancer Hospital, 100 frames of kilo-voltage cone-beam computed tomography scanning were evaluated in this study. The spine, carina and tumor were selected as landmarks for registration, respectively. Results of registration using different landmarks were documented and compared. Results: The average set-up errors in the left-right, superior inferior and anterior-posterior directions were -0.08 cm �0.32 cm, -0.16 cm �0.45 cm and 0.06 cm �0.23 cm with the spine for registration; 0.06 cm �0.34 cm, -0.13 cm �0.45 cm and -0.02 cm�0.23 cm with the carina; and -0.17 cm �0.25 cm, 0.03 cm �0.47 cm and 0.15 cm �0.38 cm with tumor. The registration results between using the carina and tumor as landmarks were statistically significant different (q=4.61, P=0.002; q = 2.23 , P=0.118; q=3.44, P=0.017). The registration results were equal when using the spine and tumor as landmarks (q =1.85, P = 0.195; q = 2.54, P = 0.075; q = 1.89, P=0.185), as well as using the carina and tumor as landmarks (q=2.76, P=0.054; q=0.31, P=0.826; q=1.55, P=0.276). Conclusions: For early stage lung cancer, the spine and tumor can be used equally as registration landmarks in imaging-guided SBRT. The carina is not suggested for its poor reproducible position. (authors)
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...
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 t...
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 t...
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 t...
VISITO Tuscany: landmark recognition for cultural heritage
Digital Repository Infrastructure Vision for European Research (DRIVER)
VISITO Tuscany (VIsual Support to Interactive TOurism in Tuscany) is a research project which investigates techniques for producing an interactive guide, accessible via smartphone, for tourists visiting cities of art. The system applies image analysis and content recognition techniques to recognize photographed monuments. The user just has to take a picture of a tourist landmark to obtain pertinent information on his or her smartphone.
Amato, Giuseppe; Falchi, Fabrizio; Bolettieri, Paolo
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
A sensitive scanning technology for low frequency nuclear point mutations in human genomic DNA
Digital Repository Infrastructure Vision for European Research (DRIVER)
Knowledge of the kinds and numbers of nuclear point mutations in human tissues is essential to the understanding of the mutation mechanisms underlying genetic diseases. However, nuclear point mutant fractions in normal humans are so low that few methods exist to measure them. We have now developed a means to scan for point mutations in 100 bp nuclear single copy sequences at mutant fractions as low as 10�6. Beginning with about 108 human cells we first enrich for the desired nuclear sequenc...
Li-sucholeiki, Xiao-cheng; Thilly, William G.
Genome-wide association Scan of dental caries in the permanent dentition
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Full Text Available Abstract Background Over 90% of adults aged 20 years or older with permanent teeth have suffered from dental caries leading to pain, infection, or even tooth loss. Although caries prevalence has decreased over the past decade, there are still about 23% of dentate adults who have untreated carious lesions in the US. Dental caries is a complex disorder affected by both individual susceptibility and environmental factors. Approximately 35-55% of caries phenotypic variation in the permanent dentition is attributable to genes, though few specific caries genes have been identified. Therefore, we conducted the first genome-wide association study (GWAS to identify genes affecting susceptibility to caries in adults. Methods Five independent cohorts were included in this study, totaling more than 7000 participants. For each participant, dental caries was assessed and genetic markers (single nucleotide polymorphisms, SNPs were genotyped or imputed across the entire genome. Due to the heterogeneity among the five cohorts regarding age, genotyping platform, quality of dental caries assessment, and study design, we first conducted genome-wide association (GWA analyses on each of the five independent cohorts separately. We then performed three meta-analyses to combine results for: (i the comparatively younger, Appalachian cohorts (N?=?1483 with well-assessed caries phenotype, (ii the comparatively older, non-Appalachian cohorts (N?=?5960 with inferior caries phenotypes, and (iii all five cohorts (N?=?7443. Top ranking genetic loci within and across meta-analyses were scrutinized for biologically plausible roles on caries. Results Different sets of genes were nominated across the three meta-analyses, especially between the younger and older age cohorts. In general, we identified several suggestive loci (P-value???10E-05 within or near genes with plausible biological roles for dental caries, including RPS6KA2 and PTK2B, involved in p38-depenedent MAPK signaling, and RHOU and FZD1, involved in the Wnt signaling cascade. Both of these pathways have been implicated in dental caries. ADMTS3 and ISL1 are involved in tooth development, and TLR2 is involved in immune response to oral pathogens. Conclusions As the first GWAS for dental caries in adults, this study nominated several novel caries genes for future study, which may lead to better understanding of cariogenesis, and ultimately, to improved disease predictions, prevention, and/or treatment.
Wang Xiaojing
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
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
A genome-wide scan in affected sibling pairs with idiopathic recurrent miscarriage suggests genetic linkage.
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. PMID:21257601
Kolte, A M; Nielsen, H S; Moltke, I; Degn, B; Pedersen, B; Sunde, L; Nielsen, F C; Christiansen, O B
Ultrasound of the elbow: A systematic approach using bony landmarks
International Nuclear Information System (INIS)
The use of bony landmarks can be helpful in performing an ultrasound study of the elbow. We discuss bony landmarks that can be used for evaluation of the common extensor tendon, ulnar collateral ligament and common flexor tendon, coronoid and olecranon fossa, ulnar nerve, and biceps tendon. We discuss bony landmarks for each of these structures.
Strategies in Landmark Use by Children, Adults, and Marmoset Monkeys
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
A genome scan for quantitative trait loci affecting the Salmonella carrier-state in the chicken.
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 6(1) 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 x 6(1)) x 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. PMID:16093014
Tilquin, Pierre; Barrow, Paul A; Marly, Jos�; Pitel, Fr�d�rique; Plisson-Petit, Florence; Velge, Philippe; Vignal, Alain; Baret, Philippe V; Bumstead, Nat; Beaumont, Catherine
Genome-Wide Association Scan Meta-Analysis Identifies Three Loci Influencing Adiposity and Fat Distribution
To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N?=?38,580) informative for adult waist circumference (WC) and waist�hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P?=?1.9�10?11) and MSRA (WC, P?=?8.9�10?9). A third locus, near LYPLAL1, was associated with WHR in women only (P?=?2.6�10?8). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.
Qi, Lu; Speliotes, Elizabeth K.; Thorleifsson, Gudmar; Willer, Cristen J.; Herrera, Blanca M.; Jackson, Anne U.; Lim, Noha; Scheet, Paul; Soranzo, Nicole; Amin, Najaf; Aulchenko, Yurii S.; Chambers, John C.; Drong, Alexander; Luan, Jian'an; Lyon, Helen N.; Rivadeneira, Fernando; Sanna, Serena; Timpson, Nicholas J.; Zillikens, M. Carola; Zhao, Jing Hua; Almgren, Peter; Bandinelli, Stefania; Bennett, Amanda J.; Bergman, Richard N.; Bonnycastle, Lori L.; Bumpstead, Suzannah J.; Chanock, Stephen J.; Cherkas, Lynn; Chines, Peter; Coin, Lachlan; Cooper, Cyrus; Crawford, Gabriel; Doering, Angela; Dominiczak, Anna; Doney, Alex S. F.; Ebrahim, Shah; Elliott, Paul; Erdos, Michael R.; Estrada, Karol; Ferrucci, Luigi; Fischer, Guido; Forouhi, Nita G.; Gieger, Christian; Grallert, Harald; Groves, Christopher J.; Grundy, Scott; Guiducci, Candace; Hadley, David; Hamsten, Anders; Havulinna, Aki S.; Hofman, Albert; Holle, Rolf; Holloway, John W.; Illig, Thomas; Isomaa, Bo; Jacobs, Leonie C.; Jameson, Karen; Jousilahti, Pekka; Karpe, Fredrik; Kuusisto, Johanna; Laitinen, Jaana; Lathrop, G. Mark; Lawlor, Debbie A.; Mangino, Massimo; McArdle, Wendy L.; Meitinger, Thomas; Morken, Mario A.; Morris, Andrew P.; Munroe, Patricia; Narisu, Narisu; Nordstrom, Anna; Nordstrom, Peter; Oostra, Ben A.; Palmer, Colin N. A.; Payne, Felicity; Peden, John F.; Prokopenko, Inga; Renstrom, Frida; Ruokonen, Aimo; Salomaa, Veikko; Sandhu, Manjinder S.; Scott, Laura J.; Scuteri, Angelo; Silander, Kaisa; Song, Kijoung; Yuan, Xin; Stringham, Heather M.; Swift, Amy J.; Tuomi, Tiinamaija; Uda, Manuela; Vollenweider, Peter; Waeber, Gerard; Wallace, Chris; Walters, G. Bragi; Weedon, Michael N.; Witteman, Jacqueline C. M.; Zhang, Cuilin; Zhang, Weihua; Caulfield, Mark J.; Collins, Francis S.; Davey Smith, George; Day, Ian N. M.; Franks, Paul W.; Hattersley, Andrew T.; Hu, Frank B.; Jarvelin, Marjo-Riitta; Kong, Augustine; Kooner, Jaspal S.; Laakso, Markku; Lakatta, Edward; Mooser, Vincent; Morris, Andrew D.; Peltonen, Leena; Samani, Nilesh J.; Spector, Timothy D.; Strachan, David P.; Tanaka, Toshiko; Tuomilehto, Jaakko; Uitterlinden, Andre G.; van Duijn, Cornelia M.; Wareham, Nicholas J.; Watkins for the PROCARDIS consortia, Hugh; Waterworth, Dawn M.; Boehnke, Michael; Deloukas, Panos; Groop, Leif; Hunter, David J.; Thorsteinsdottir, Unnur; Schlessinger, David; Wichmann, H.-Erich; Frayling, Timothy M.; Abecasis, Goncalo R.; Hirschhorn, Joel N.; Loos, Ruth J. F.; Stefansson, Kari; Mohlke, Karen L.; Barroso, Ines; McCarthy for the GIANT consortium, Mark I.
Genome-wide linkage scan for factors of metabolic syndrome in a Chinese population
Directory of Open Access Journals (Sweden)
Full Text Available Abstract Background Shared genetic factors may contribute to the phenotypic clustering of different components of the metabolic syndrome (MES. This study aims to identify genetic loci that contribute to individual or multiple factors related to MES. Results We studied 478 normoglycemic subjects ascertained through 163 families participating in the Hong Kong Family Diabetes Study. Factor analysis on 15 MES-related traits yielded 6 factors including adiposity factor (body mass index, waist and hip circumferences, insulin factor (fasting insulin and insulin AUC during OGTT, glucose factor (fasting glucose and glucose AUC during OGTT, TC-LDLC factor (total cholesterol and LDL-cholesterol, blood pressure factor (systolic and diastolic blood pressure and TG-HDLC factor (triglycerides and HDL-cholesterol. Genome-wide linkage analyses were performed on these factors using variance component approach. Suggestive evidence for linkage (LOD = 1.24 - 2.46 were observed for adiposity factor (chromosome 1 at 187 cM, chromosome 9 at 34 cM and chromosome 17 at 10 cM, insulin factor (chromosome 2 at 128 cM, chromosome 5 at 21 cM and chromosome 12 at 7 cM, glucose factor (chromosome 7 at 155 cM, TC-LDLC factor (chromosome 7 at 151 cM and chromosome 13 at 15 cM and TG-HDLC factor (chromosome 7 at 155 cM. Conclusions In summary, our findings suggest the presence of susceptibility loci that influence either single (chromosomes 1, 2, 5, 9, 12, 13 and 17 or multiple factors (chromosome 7 for MES in Hong Kong Chinese without diabetes.
Chan Juliana CN
Mapped Landmark Algorithm for Precision Landing
A report discusses a computer vision algorithm for position estimation to enable precision landing during planetary descent. The Descent Image Motion Estimation System for the Mars Exploration Rovers has been used as a starting point for creating code for precision, terrain-relative navigation during planetary landing. The algorithm is designed to be general because it handles images taken at different scales and resolutions relative to the map, and can produce mapped landmark matches for any planetary terrain of sufficient texture. These matches provide a measurement of horizontal position relative to a known landing site specified on the surface map. Multiple mapped landmarks generated per image allow for automatic detection and elimination of bad matches. Attitude and position can be generated from each image; this image-based attitude measurement can be used by the onboard navigation filter to improve the attitude estimate, which will improve the position estimates. The algorithm uses normalized correlation of grayscale images, producing precise, sub-pixel images. The algorithm has been broken into two sub-algorithms: (1) FFT Map Matching (see figure), which matches a single large template by correlation in the frequency domain, and (2) Mapped Landmark Refinement, which matches many small templates by correlation in the spatial domain. Each relies on feature selection, the homography transform, and 3D image correlation. The algorithm is implemented in C++ and is rated at Technology Readiness Level (TRL) 4.
Johnson, Andrew; Ansar, Adnan; Matthies, Larry
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.
A genomic scan of porcine reproductive traits reveals possible quantitative trait loci (QTLs) for number of corpora lutea.
Reproductive traits have low heritabilities, are expressed in only one sex, and are not measurable until sexual maturity (Avalos and Smith, Anim Prod 44:153, 1987). Using traditional methods, selection for reproductive traits is relatively less effective than selecting for growth or carcass traits. Traits most affected by a small number of genes with major effects rather than many genes with small effects are most amenable to MAS. As part of our porcine genome scan to identify quantitative trait loci (QTLs) of economic importance in marker-assisted selective (MAS) breeding programs, we examined 8 reproductive and farrowing traits in the University of Illinois (UI) Meishan x Yorkshire Resource Family. Gilts were genotyped with 119 microsatellite markers (MS) with intervals averaging 24 cM over all 18 porcine autosomes. F-ratios supporting QTL location were calculated by the least squares regression method. Results suggestive of linkage at the 5% genome-wide level were observed for the number of stillborn piglets on Chromosome (Chr) 4 (SSC4) (p-value = 0.0001), corpora lutea on SSC8 (p-value = 0.00027), and gestation length on SSC9 (p-value = 0.00019). Results for additional loci relevant to litter size, number of corpora lutea on SSC15 and 7 (p-value = 0.0029 and 0.0028 at 107 and 150 cM, respectively), gestation length on SSC15 and 1 (p-value = 0.0017 and 0.0069 at 96 and 166 cM, respectively), uterine length on SSC7 and 5 (p-value = 0.0044 and 0.0075 at 148 and 1 cM, respectively) and piglets born per litter on SSC6 (p-value = 0.0075 at 102 cM), were not statistically significant at the 5% genome-wide level. Thus, the use of a linked marker to facilitate selection for reproductive traits has considerable potential. By using linked markers, selection can be applied to both sexes before sexual maturity, making genetic selection considerably more efficient and less costly. PMID:10341088
Wilkie, P J; Paszek, A A; Beattie, C W; Alexander, L J; Wheeler, M B; Schook, L B
A genome-wide scan in families with maturity-onset diabetes of the young : evidence for further genetic heterogeneity
DEFF Research Database (Denmark)
Maturity-onset diabetes of the young (MODY) is a heterogeneous single gene disorder characterized by non-insulin-dependent diabetes, an early onset and autosomal dominant inheritance. Mutations in six genes have been shown to cause MODY. Approximately 15-20% of families fitting MODY criteria do not have mutations in any of the known genes. These families provide a rich resource for the identification of new MODY genes. This will potentially enable further dissection of clinical heterogeneity and bring new insights into mechanisms of beta-cell dysfunction. To facilitate the identification of novel MODY loci, we combined the results from three genome-wide scans on a total of 23 families fitting MODY criteria. We used both a strict parametric model of inheritance with heterogeneity and a model-free analysis. We did not identify any single novel locus but provided putative evidence for linkage to chromosomes 6 (nonparametric linkage [NPL]score 2.12 at 71 cM) and 10 (NPL score 1.88 at 169-175 cM), and to chromosomes 3 (heterogeneity LOD [HLOD] score 1.27 at 124 cM) and 5 (HLOD score 1.22 at 175 cM) in 14 more strictly defined families. Our results provide evidence for further heterogeneity in MODY.
Frayling, Timothy M; Lindgren, Cecilia M
The behavioural relevance of landmark texture for honeybee homing
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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.
Landmark vs. Geometry Learning: Explaining Female Rats' Selective Preference for a Landmark
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.; Rodr�guez, Clara A.; Chamizo, V. D.; Mackintosh, N. J.
The behavioural relevance of landmark texture for honeybee homing
Digital Repository Infrastructure Vision for European Research (DRIVER)
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, suggest...
The Behavioral Relevance of Landmark Texture for Honeybee Homing
Digital Repository Infrastructure Vision for European Research (DRIVER)
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 color. Recently, we showed that honeybees can use landmarks that are statically camouflaged, suggesti...
Active shape models incorporating isolated landmarks for medical image annotation
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.
A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation
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Identifying the genes that influence levels of pro-inflammatory molecules can help to elucidate the mechanisms underlying this process. We first conducted a two-stage genome-wide association scan (GWAS) for the key inflammatory biomarkers Interleukin-6 (IL-6), the general measure of inflammation erythrocyte sedimentation rate (ESR), monocyte chemotactic protein-1 (MCP-1), and high-sensitivity C-reactive protein (hsCRP) in a large cohort of individuals from the founder population of Sardinia. ...
Naitza, Silvia; Porcu, Eleonora; Steri, Maristella; Taub, Dennis D.; Mulas, Antonella; Xiao, Xiang; Strait, James; Dei, Mariano; Lai, Sandra; Busonero, Fabio; Maschio, Andrea; Usala, Gianluca; Zoledziewska, Magdalena; Sidore, Carlo; Zara, Ilenia
A Genome-wide association scan on the levels of markers of inflammation in Sardinians reveals associations that underpin its complex regulation
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Identifying the genes that influence levels of pro-inflammatory molecules can help to elucidate the mechanisms underlying this process. We first conducted a two-stage genome-wide association scan (GWAS) for the key inflammatory biomarkers Interleukin-6 (IL-6), the general measure of inflammation erythrocyte sedimentation rate (ESR), monocyte chemotactic protein-1 (MCP-1), and high-sensitivity C-reactive protein (hsCRP) in a large cohort of individuals from the founder population of Sardinia. ...
Naitza, Silvia; Porcu, Elenora; Steri, Maristella; Taub, Dennis Daniel; Mulas, Antonella; Xiao, Xiang; Strait, James; Dei, Mariano; Lai, Sandra; Busonero, Fabio; Maschio, Andrea; Usala, Gianluca; Zoledziewska, Magdalena; Sidore, Carlo; Zara, Ilenia
Results of a whole-genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four-way cross.
A whole-genome quantitative trait locus (QTL) scan for 31 phenotypes related to growth, carcass composition and meat quality was conducted using 1187 progeny of a commercial four-way cross. Animals were genotyped for 198 microsatellite markers that spanned the entire porcine genome. QTL analysis was conducted to extract information from paternal and maternal meioses separately using a rank-based nonparametric approach for half-sib designs. Nine QTL exceeded genome-wide significance: one QTL affecting growth (average daily gain on SSC1), two QTL influencing carcass composition (fatness on SSC3 and muscle mass on SSC15) and six QTL influencing meat quality (tenderness on SSC4 and SSC14; colour on SSC5, SSC6 and SSCX; and conductivity on SSC16). All but one of these coincided with previously reported QTL. In addition, we present evidence for 78 suggestive QTL with a combined false discovery rate of 40%. PMID:17121599
Harmegnies, N; Davin, F; De Smet, S; Buys, N; Georges, M; Coppieters, W
Genome scanning using endogenous LTR-like elements for rapid DNA-fingerprinting of breast-cancer and transformed human breast epithelial-cells.
In the present work genomic DNAs from nine primary breast cancers and transformed human breast epithelial cell lines obtained by treatment of MCF 10F, a spontaneously immortalized human breast epithelial cell line, with benzo(a)pyrene (BP) or 7,12 dimethyl benz(a)anthracene (DMBA), were used for genomic scanning. The treatment of MCF 10F with BP gave rise to different clones designated BP1 and BP1E, the latter being a tumorigenic cell line. Treatment with DMBA gave rise to D3 and D3-1 clones. The clones D3-1 and BP1 have been transfected with the plasmid pH06T1 containing the mutated c-Ha-ras oncogene resulting in the D3-1Tras and BP1T-ras cell lines, that are highly tumorigenic in SCID mice. Genomic DNA are separately hybridized to two different probes representing different families of human endogenous retrovirus like sequences (RTLV-H and HERV-K LTR). The technique of genomic scanning allows the mapping of each tumor or cell line and comparison with its counterpart obtained from the adjacent normal tissue of the same patient or with the untreated MCF 10F cells. DNA changes such as deletions, amplifications and/or rearrangements were detected in 5 of the tumor pairs studied. We have identified genomic alterations that involved amplification of a 10 kb band in the transformed cell lines. The cell lines D3-1Tras and BP1T-ras show, in addition, the presence of a second band of 4.5 kb in size. A third band of 500 bp size was found in clones D3-1 and BP1E that have a more aggressive behavior in vitro than their precursors D3 and BP1 cells respectively. In conclusion the present report indicates that genomic scanning detects DNA aberrations in primary primary tumors and in human breast epithelial cells transformed with chemical carcinogens and/or oncogene transfection that are not present in their normal counterpart. These results further indicate that detection of endogenous retrovirus elements may help in genome mapping and can be a useful tool for detecting genomic changes in the preliminary screening of DNA extracted from primary breast cancer and transformed cells. PMID:21552801
Wahab, I; Barnabas, N; Calaf, G; Russo, J
77 FR 44670 - Information Collection Activities: National Historic Landmarks (NHL) Condition Survey
...Activities: National Historic Landmarks (NHL) Condition Survey AGENCY: National Park...1024-NEW, National Historic Landmarks (NHL) Condition Survey in the subject line...Abstract National Historic Landmarks (NHL) are nationally significant historic...
A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content
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 (PLRP1B, 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.
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
Directory of Open Access Journals (Sweden)
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
BR-squared: a practical solution to the winner�s curse in genome-wide scans
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The detrimental effects of the winner�s curse, including overestimation of the genetic effects of associated variants and underestimation of sufficient sample sizes for replication studies are well-recognized in genome-wide association studies (GWAS). These effects can be expected to worsen as the field moves from GWAS into whole genome sequencing. To date, few studies have reported statistical adjustments to the naive estimates, due to the lack of suitable statistical methods and computati...
Sun, Lei; Dimitromanolakis, Apostolos; Faye, Laura L.; Paterson, Andrew D.; Waggott, Daryl; Bull, Shelley B.
A genome-wide scan for quantitative trait loci affecting serum glucose and lipids in a White Duroc x Erhualian intercross F(2) population.
Serum glucose and lipid levels are associated with diabetes mellitus and cardiovascular disease. The purpose of this study was to identify quantitative trait loci (QTL) for serum glucose and lipids in a White Duroc x Erhualian resource population. Serum glucose, glycosylated serum proteins (GSP), and serum lipid levels were measured in a total of 760 F(2) animals at 240 days. Strong positive correlations were observed between total cholesterol (TC) and low-density-lipoprotein cholesterol (LDL-C)/high-density-lipoprotein cholesterol (HDL-C). A whole-genome scan was performed with 194 microsatellites covering the pig genome across the entire resource population, revealing 2 QTL for serum glucose and 15 QTL for serum lipids. Of them, three 1% genome-wide significant QTL were identified for LDL-C, TC, and triglycerides (TG) in an adjacent region (67-73 cM) on chromosome 2 (SSC2), and the QTL for LDL-C showed the largest effect with a 95% confidence interval of 5 cM. Another 1% genome-wide significant QTL was found for LDL-C at 87 cM on SSC8. Other QTL showed 5% genome-wide significant or suggestive effects on SSC4, 5, 7, 9, 11, 14, and 15. In total, five significant QTL for serum lipids and a suggestive QTL for GSP on SSC4 were identified for the first time in pigs. Most of the identified QTL are homologous to the previously reported QTL for serum lipids in humans and mice. As correlated traits, QTL for TC and LDL-C were always located in the same genomic regions. The results shed new light on studies of human atherosclerosis and cardiovascular-related diseases. PMID:19495872
Chen, Rongrong; Ren, Jun; Li, Wanbo; Huang, Xiang; Yan, Xueming; Yang, Bin; Zhao, Yinggong; Guo, Yuanmei; Mao, Huirong; Huang, Lusheng
Landmarks and ant search strategies after interrupted tandem runs.
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
A genome scan for quantitative trait loci affecting the length of small intestine in a White Duroc x Chinese Erhualian intercross resource population.
The small intestine is a vital organ in animal gastrointestinal system, in which a large variety of nutrients are absorbed. To identify quantitative trait loci (QTL) for the length of porcine small intestine, phenotypic values were measured in 1034 individuals at 240 d from a White Duroc x Chinese Erhualian intercross F(2) population. The length of small intestine showed strong correlation with growth traits and carcass length in the F2 population. A whole-genome scan was performed based on 183 microsatellites covering the pig genome in the F(2) population. A total of 10 QTL for this trait were identified on 8 pig chromosomes (SSC), including four 1% genome-wide significant QTL on SSC2, 4, 7 and 8, one 5% genome-wide significant QTL on SSC12, and five 5% chromosome-wide significant QTL on SSC5, 7, 13 and 14. The Erhualian alleles were generally associated with shorter length of the small intestine except the alleles on SSC7 and 13. The QTL on SSC4 overlapped with the previously reported QTL for the length of small intestine. Several significant QTL on SSC2, 8, and 12 were consistent with previous reports. The significant QTL detected on SSC7 was reported for the first time. All QTL identified in this study corresponded to the known region significantly associated with growth traits, supporting the important role of the length of small intestine in pig growth. PMID:20433520
Gao, J; Ren, J; Zhou, L H; Ren, D R; Li, L; Xiao, S J; Yang, B; Huang, L S
A genome-wide admixture scan identifies MYH9 as a candidate locus associated with non-diabetic end stage renal disease in African Americans
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End stage renal disease (ESRD) has a four times higher incidence in African Americans compared to European Americans. This led to the hypothesis that susceptibility alleles for ESRD have a higher frequency in West African than European gene pool. We performed a genome-wide admixture scan in 1,372 ESRD cases and 806 controls and demonstrated a highly significant association between excess African ancestry and non-diabetic ESRD (LOD 5.70) but not diabetic ESRD (LOD 0.47) on chromosome 22q12. Ea...
Linda Kao, Wh; Klag, Michael J.; Meoni, Lucy A.; Reich, David; Berthier-schaad, Yvette; Li, Man; Coresh, Josef; Patterson, Nick; Tandon, Arti; Powe, Neil R.; Fink, Nancy E.; Sadler, John H.; Weir, Matthew R.; Abboud, Hanna E.; Adler, Sharon
Meta-Analysis of 13 Genome Scans Reveals Multiple Cleft Lip/Palate Genes with Novel Loci on 9q21 and 2q32-35
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Isolated or nonsyndromic cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex etiology. A 10-cM genome scan of 388 extended multiplex families with CL/P from seven diverse populations (2,551 genotyped individuals) revealed CL/P genes in six chromosomal regions, including a novel region at 9q21 (heterogeneity LOD score [HLOD]=6.6). In addition, meta-analyses with the addition of results from 186 more families (six populations; 1,033 genotyped individuals) showe...
Marazita, Mary L.; Murray, Jeffrey C.; Lidral, Andrew C.; Arcos-burgos, Mauricio; Cooper, Margaret E.; Goldstein, Toby; Maher, Brion S.; Daack-hirsch, Sandra; Schultz, Rebecca; Mansilla, M. Adela; Field, L. Leigh; Liu, You-e; Prescott, Natalie; Malcolm, Sue; Winter, Robin
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci
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Systemic lupus erythematosus (SLE) is a common systemic autoimmune disease with complex etiology but strong clustering in families (?S = ~30). We performed a genome-wide association scan using 317,501 SNPs in 720 women of European ancestry with SLE and in 2,337 controls, and we genotyped consistently associated SNPs in two additional independent sample sets totaling 1,846 affected women and 1,825 controls. Aside from the expected strong association between SLE and the HLA region on chromosom...
Harley, John B.; Alarco?n-riquelme, Marta E.; Criswell, Lindsey A.; Jacob, Chaim O.; Kimberly, Robert P.; Moser, Kathy L.; Tsao, Betty P.; Vyse, Timothy J.; Langefeld, Carl D.; Nath, Swapan K.; Guthridge, Joel M.; Cobb, Beth L.; Mirel, Daniel B.; Marion, Miranda C.; Williams, Adrienne H.
A new guide to the human genome
Energy Technology Data Exchange (ETDEWEB)
The construction of a detailed physical map of the human genome, with 15,000 sequence-based landmarks, opens the door to genome-wide sequencing. This article summarizes the researchers, the research, the approach, and the usefulness of a new physical map of the human genome.
Marx, J.
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
Digital Repository Infrastructure Vision for European Research (DRIVER)
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 ...
Resmana Lim
Pigeons combine compass and landmark guidance in familiar route navigation
Digital Repository Infrastructure Vision for European Research (DRIVER)
How do birds orient over familiar terrain? In the best studied avian species, the homing pigeon (Columba livia), two apparently independent primary mechanisms are currently debated: either memorized visual landmarks provide homeward guidance directly, or birds rely on a compass to home from familiar locations. Using miniature Global Positioning System tracking technology and clock-shift procedures, we set sun-compass and landmark information in conflict, showing that experienced birds can acc...
Biro, Dora; Freeman, Robin; Meade, Jessica; Roberts, Stephen; Guilford, Tim
3D face analysis : landmarking, expression recognition and beyond
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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
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...
He, Qing; Duan, Ye; Karsch, Kevin; Miles, Judith
Automatic Evaluation of Landmarks for Image-Based Navigation Update
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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...
Visual Homing in the Absence of Feature-Based Landmark Information
Despite that fact that landmarks play a prominent role in human navigation, experimental evidence on how landmarks are selected and defined by human navigators remains elusive. Indeed, the concept of a "landmark" is itself not entirely clear. In everyday language, the term landmark refers to salient, distinguishable, and usually nameable objects,�
Gillner, Sabine; Weiss, Anja M.; Mallot, Hanspeter A.
Genome-wide SNP-based linkage scan identifies a locus on 8q24 for an age-related hearing impairment trait
DEFF Research Database (Denmark)
Age-related hearing impairment (ARHI), or presbycusis, is a very common multifactorial disorder. Despite the knowledge that genetics play an important role in the etiology of human ARHI as revealed by heritability studies, to date, its precise genetic determinants remain elusive. Here we report the results of a cross-sectional family-based genetic study employing audiometric data. By using principal component analysis, we were able to reduce the dimensionality of this multivariate phenotype while capturing most of the variation and retaining biologically important features of the audiograms. We conducted a genome-wide association as well as a linkage scan with high-density SNP microarrays. Because of the presence of genetic population substructure, association testing was stratified after which evidence was combined by meta-analysis. No association signals reaching genome-wide significance were detected. Linkage analysis identified a linkage peak on 8q24.13-q24.22 for a trait correlated to audiogram shape. The signal reached genome-wide significance, as assessed by simulations. This finding represents the first locus for an ARHI trait Udgivelsesdato: 2008/9/12
Huyghe, J.R.; Laer, L. Van
A whole genome scan for quantitative trait loci for leg weakness and its related traits in a large F2 intercross population between White Duroc and Erhualian.
To detect QTL for leg weakness and its related traits in pigs, a total of 1,484 F(2) pigs were recorded for leg (at 76 and 213 d) and gait scores (at 153 and 223 d) in a White Duroc x Erhualian intercross. The length and weight of the biceps brachii muscle were measured after slaughter at 240 d. A genome scan was performed with 183 microsatellite markers in the population. A total of 42 QTL were detected, including 16 at the 1% genome-wide significant level and 6 at the 5% genome-wide significant level. Thirty-eight of the 42 QTL showed significant additive effects, and 14 had significant dominance effects. At least 2 QTL were detected for each trait except for leg score at 76 d, for which no QTL was identified. Some of the QTL for leg and gait scores confirmed previous findings. Eighteen QTL were detected for weight and length of the biceps brachii muscle. To our knowledge, this was the first report about QTL for weight and length of the biceps brachii muscle in pigs. Two chromosome regions each on SSC4 and SSC7 showed significant and multiple associations with both leg weakness and growth of the biceps brachii muscle, which are worthwhile for further investigation. PMID:19151150
Guo, Y M; Ai, H S; Ren, J; Wang, G J; Wen, Y; Mao, H R; Lan, L T; Ma, J W; Brenig, B; Rothschild, M F; Haley, C S; Huang, L S
A Genome-Wide �Pleiotropy Scan� Does Not Identify New Susceptibility Loci for Estrogen Receptor Negative Breast Cancer
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Approximately 15�30% of all breast cancer tumors are estrogen receptor negative (ER?). Compared with ER-positive (ER+) disease they have an earlier age at onset and worse prognosis. Despite the vast number of risk variants identified for numerous cancer types, only seven loci have been unambiguously identified for ER-negative breast cancer. With the aim of identifying new susceptibility SNPs for this disease we performed a pleiotropic genome-wide association study (GWAS). We selected 3079...
Campa, Daniele; Barrdahl, Myrto; Tsilidis, Konstantinos K.; Severi, Gianluca; Diver, W. Ryan; Siddiq, Afshan; Chanock, Stephen; Hoover, Robert N.; Ziegler, Regina G.; Berg, Christine D.; Buys, Saundra S.; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick R.; Le Marchand, Loi?c
A genome-wide scan for common variants affecting the rate of age-related cognitive decline
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Age-related cognitive decline is likely promoted by accumulated brain injury due to chronic conditions of aging, including neurodegenerative and vascular disease. Since common neuronal mechanisms may mediate the adaptation to diverse cerebral insults, we hypothesized that susceptibility for age-related cognitive decline may be due in part to a shared genetic network. We have therefore performed a genome-wide association study using a quantitative measure of global cognitive decline slope, bas...
Jager, Philip L.; Shulman, Joshua M.; Chibnik, Lori B.; Keenan, Brendan T.; Raj, Towfique; Wilson, Robert S.; Yu, Lei; Leurgans, Sue E.; Tran, Dong; Aubin, Cristin; Anderson, Christopher D.; Biffi, Alessandro; Corneveaux, Jason J.; Huentelman, Matthew J.; Rosand, Jonathan
Genome-Wide Scan for Bats and Dolphin to Detect Their Genetic Basis for New Locomotive Styles
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For most mammals, running is their major locomotive style, however, cetaceans and bats are two mammalian groups that have independently developed new locomotive styles (swimming and flying) from their terrestrial ancestors. In this study, we used a genome-wide comparative analysis in an attempt to identify the selective imprint of the development of new locomotive styles by cetaceans and bats to adapt to their new ecological niches. We found that an elevated proportion of mitochondrion-associ...
Shen, Yong-yi; Zhou, Wei-ping; Zhou, Tai-cheng; Zeng, Yan-ni; Li, Gui-mei; Irwin, David M.; Zhang, Ya-ping
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
PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
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Full Text Available Abstract Background Periodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions and in the organization of chromosomes in both eukaryotes and prokaryotes. Local differences in DNA sequence periodicity have been linked to differences in gene expression in some organisms. Despite the significance of these periodic patterns, there are virtually no publicly accessible tools for their analysis. Results We present novel tools suitable for assessments of DNA curvature-related sequence periodicity in nucleotide sequences at the genome scale. Utility of the present software is demonstrated on a comparison of sequence periodicities in the genomes of Haemophilus influenzae, Methanocaldococcus jannaschii, Saccharomyces cerevisiae, and Arabidopsis thaliana. The software can be accessed through a web interface and the programs are also available for download. Conclusions The present software is suitable for comparing DNA curvature-related sequence periodicity among different genomes as well as for analysis of intrachromosomal heterogeneity of the sequence periodicity. It provides a quick and convenient way to detect anomalous regions of chromosomes that could have unusual structural and functional properties and/or distinct evolutionary history.
Mr�zek Jan
A whole-genome scan in a large family with leukodystrophy and oligodontia reveals linkage to 10q22.
Dentoleukoencephalopathies with autosomal recessive inheritance are very rare. Recently, a large inbred Syrian pedigree was reported with oligodontia in association with a degenerative neurologic condition characterized by progressive ataxia and pyramidal syndrome and abnormalities in the white matter and cortical atrophy. A whole-genome screening of this family using 382 microsatellite markers was completed, but no evidence was found of linkage to any chromosomal region. A genome-wide linkage analysis using the 260K single nucleotide polymorphism Affymetrix array was then undertaken and a maximum multipoint logarithm of the odds score of 5.66 (NPL score = 7.65) was detected on chromosome 10q22 region. This genomic interval contains 95 known genes including the Prosaposin gene (PSAP) responsible for metachromatic leukodystrophy, which was excluded. Seventeen additional candidate genes were tested and excluded. Sequencing of the whole candidate locus is in progress and should allow the identification of the causative gene in this rare disease, thereby improving the understanding of the physiopathology of this disease. PMID:20721593
Chouery, Eliane; Delague, Val�rie; Jalkh, Nadine; Salem, Nabiha; Kfoury, Jessy; Rodriguez, Diana; Chabrol, Brigitte; Boespflug-Tanguy, Odile; L�vy, Nicolas; Serre, Jean Louis; M�garban�, Andr�
Automated landmarking and geometric characterization of the carotid siphon.
The geometry of the carotid siphon has a large variability between subjects, which has prompted its study as a potential geometric risk factor for the onset of vascular pathologies on and off the internal carotid artery (ICA). In this work, we present a methodology for an objective and extensive geometric characterization of carotid siphon parameterized by a set of anatomical landmarks. We introduce a complete and automated characterization pipeline. Starting from the segmentation of vasculature from angiographic image and its centerline extraction, we first identify ICA by characterizing vessel tree bifurcations and training a support vector machine classifier to detect ICA terminal bifurcation. On ICA centerline curve, we detect anatomical landmarks of carotid siphon by modeling it as a sequence of four bends and selecting their centers and interfaces between them. Bends are detected from the trajectory of the curvature vector expressed in the parallel transport frame of the curve. Finally, using the detected landmarks, we characterize the geometry in two complementary ways. First, with a set of local and global geometric features, known to affect hemodynamics. Second, using large deformation diffeomorphic metric curve mapping (LDDMCM) to quantify pairwise shape similarity. We processed 96 images acquired with 3D rotational angiography. ICA identification had a cross-validation success rate of 99%. Automated landmarking was validated by computing limits of agreement with the reference taken to be the locations of the manually placed landmarks averaged across multiple observers. For all but one landmark, either the bias was not statistically significant or the variability was within 50% of the inter-observer one. The subsequently computed values of geometric features and LDDMCM were commensurate to the ones obtained with manual landmarking. The characterization based on pair-wise LDDMCM proved better in classifying the carotid siphon shape classes than the one based on geometric features. The proposed characterization provides a rich description of geometry and is ready to be applied in the search for geometric risk factors of the carotid siphon. PMID:22377655
Bogunovi?, Hrvoje; Pozo, Jos� Mar�a; C�rdenes, Rub�n; Villa-Uriol, Mar�a Cruz; Blanc, Rapha�l; Piotin, Michel; Frangi, Alejandro F
A Landmark Based Position Estimation for Pinpoint Landing on Mars
Real-time position estimation for a descent lander is a critical technological need for many of NASA's planned in situ missions including landing on a number of bodies at locations of greatest scientific interest and sample return. In particular, it enables the capability to land precisely and safely in a scientifically promising but hazardous site and is a key technology to be demonstrated by NASA in the next decade. The key challenge of pinpoint landing (PPL) is how to localize the lander by recognizing the landmarks (craters) in the landing area and match them positively to a preexisting landmark database while the spacecraft is descending. In this paper, a real-time landmark based position estimation technique for pinpoint landing is suggested. This system includes three crucial components: (1) real time landmark detection, (2) real-time landmark matching and (3) state (both position and velocity) estimation. We discuss the performance analysis of this system. Finally, we show that the suggested technology is able to deliver a spacecraft to less than 100 m from a pre-selected landing site on Mars.
Cheng, Yang; Ansar, Adnan
Landmark learning by the Ozark zigzag salamander Plethodon angusticlavius
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Full Text Available Although salamanders have been shown to respond to classical conditioning, spatial learning has been largely unstudied. We tested whether salamanders could learn to locate foraging areas by using landmarks. We trained 10 salamanders Plethodon angusticlavius to use landmarks (small rocks to locate patches within the arena containing food (blackworms Lumbriculus variegatus. At the corners of each square testing arena were four plastic dishes, one containing blackworms and the other three empty. A rock was placed in front of the dish containing blackworms, and the location of the food-dish was randomly chosen for each training trial. A control group was also trained to feed on blackworms in the presence of a rock, but the rock was positioned randomly among the four dish locations so that the rock was not a reliable landmark for the worms. Although the length of the training period for individual salamanders varied (22�38 trainings per individual, the mean number of trainings for salamanders in the control and experimental groups was equal (30 training trials. During testing, no blackworms were present to eliminate any visual or chemical cues emanating directly from the prey. Individuals trained with the rock landmarks spent significantly more time in the area of the landmark than did control salamanders [Current Zoology 57 (4: 485�490, 2011].
Adam L. CRANE, Alicia MATHIS
Detecting corpus callosum abnormalities in autism based on anatomical landmarks
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-point shape comparison was performed both globally and locally. A new local shape comparison scheme was proposed which compared each part of the shape in its local coordinate system. Point correspondence was established among individual shapes based on the inherent landmark correspondence. No significant difference was found in the landmark form between patients and controls, but the distance between interior genu and posterior most was found significantly shorter in patients. Thin-plate spline analysis showed significant group difference between the landmark configurations in terms of the deformation from the overall mean configuration. Significant global shape differences were found in the anterior lower body and posterior bottom, and local shape difference existed in the anterior bottom. This study can serve as both clinical reference and a detailed procedure guideline for similar studies in the future.
He, Qing; Duan, Ye; Karsch, Kevin; Miles, Judith
A statistical method for 2-D facial landmarking.
Many facial-analysis approaches rely on robust and accurate automatic facial landmarking to correctly function. In this paper, we describe a statistical method for automatic facial-landmark localization. Our landmarking relies on a parsimonious mixture model of Gabor wavelet features, computed in coarse-to-fine fashion and complemented with a shape prior. We assess the accuracy and the robustness of the proposed approach in extensive cross-database conditions conducted on four face data sets (Face Recognition Grand Challenge, Cohn-Kanade, Bosphorus, and BioID). Our method has 99.33% accuracy on the Bosphorus database and 97.62% accuracy on the BioID database on the average, which improves the state of the art. We show that the method is not significantly affected by low-resolution images, small rotations, facial expressions, and natural occlusions such as beard and mustache. We further test the goodness of the landmarks in a facial expression recognition application and report landmarking-induced improvement over baseline on two separate databases for video-based expression recognition (Cohn-Kanade and BU-4DFE). PMID:21803691
Dibeklio?lu, Hamdi; Salah, Albert Ali; Gevers, Theo
Discriminative BoW framework for mobile landmark recognition.
This paper proposes a new soft bag-of-words (BoW) method for mobile landmark recognition based on discriminative learning of image patches. Conventional BoW methods often consider the patches/regions in the images as equally important for learning. Amongst the few existing works that consider the discriminative information of the patches, they mainly focus on selecting the representative patches for training, and discard the others. This binary hard selection approach results in underutilization of the information available, as some discarded patches may still contain useful discriminative information. Further, not all the selected patches will contribute equally to the learning process. In view of this, this paper presents a new discriminative soft BoW approach for mobile landmark recognition. The main contribution of the method is that the representative and discriminative information of the landmark is learned at three levels: patches, images, and codewords. The patch discriminative information for each landmark is first learned and incorporated through vector quantization to generate soft BoW histograms. Coupled with the learned representative information of the images and codewords, these histograms are used to train an ensemble of classifiers using fuzzy support vector machine. Experimental results on two different datasets show that the proposed method is effective in mobile landmark recognition. PMID:23846513
Chen, Tao; Yap, Kim-Hui
Cardiac Conduction System: Delineation of Anatomic Landmarks With Multidetector CT
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Full Text Available Major components of the cardiac conduction system including the sinoatrial node (SAN, atrioventricular node (AVN, the His Bundle, and the right and left bundle branches are too small to be directly visualized by multidetector CT (MDCT given the limited spatial resolution of current scanners. However, the related anatomic landmarks and variants of this system a well as the areas with special interest to electrophysiologists can be reliably demonstrated by MDCT. Some of these structures and landmarks include the right SAN artery, right atrial cavotricuspid isthmus, Koch triangle, AVN artery, interatrial muscle bundles, and pulmonary veins. In addition, MDCT has an imperative role in demarcating potential arrhythmogenic structures. The aim of this review will be to assess the extent at which MDCT can outline the described anatomic landmarks and therefore provide crucial information used in clinical practice.
Farhood Saremi
The importance of context to the genetic architecture of diabetes-related traits is revealed in a genome-wide scan of a LG/J x SM/J murine model
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Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci affecting serum glucose and insulin levels and response to glucose stress in an F16 Advan...
Lawson, Heather A.; Lee, Arthur; Fawcett, Gloria L.; Wang, Bing; Pletscher, L. Susan; Maxwell, Taylor J.; Ehrich, Thomas H.; Kenney-hunt, Jane P.; Wolf, Jason B.; Semenkovich, Clay F.; Cheverud, James M.
Genetic diversity and features analysis of type VI secretion systems loci in avian pathogenic Escherichia coli by wide genomic scanning.
Avian pathogenic Escherichia coli (APEC) strains frequently cause extra-intestinal infections and significant economic losses. Recent studies revealed that the type VI secretion system (T6SS) is involved in APEC pathogenesis. Here we provide the first evidence of three distinguishable and conserved T6SS loci in APEC genomes. In addition, we present the prevalence and comparative genomic analysis of these three T6SS loci in 472 APEC isolates. The prevalence of T6SS1, T6SS2 and T6SS3 loci were 14.62% (69/472), 2.33% (11/472) and 0.85% (4/472) positive in the APEC collections, respectively, and revealed that >85% of the strains contained T6SS loci which consisted of the virulent phylogenetic groups D and B2. Comprehensive analysis showed prominent characteristics of T6SS1 locus, including wildly prevalence, rich sequence diversity, versatile VgrG islands and excellent expression competence in various E. coli pathotypes. Whereas the T6SS2 locus infatuated with ECOR groups B2 and sequence conservation, of which are only expressed in meningitis E. coli. Regrettably, the T6SS3 locus was encoded in negligible APEC isolates and lacked several key genes. An in-depth analysis about VgrG proteins indicated that their COG4253 and gp27 domain were involved in the transport of putative effector islands and recognition of host cells respectively, which revealed that VgrG proteins played an important role in functions formation of T6SS. PMID:24120694
Ma, Jiale; Sun, Min; Bao, Yinli; Pan, Zihao; Zhang, Wei; Lu, Chengping; Yao, Huochun
Detection of novel quantitative trait loci for cutaneous melanoma by genome-wide scan in the MeLiM swine model.
Human cutaneous melanoma is a complex trait inherited in about 10% of cases. Although 2 high-risk genes, CDKN2A and CDK4, and 1 low risk gene, MC1R, have been identified, susceptibility genes remain to be discovered. Here, we attempted to determine new genomic regions linked to melanoma using the pig MeLiM strain, which develops hereditary cutaneous melanomas. We applied quantitative trait loci (QTL) mapping method to a significant genome-wide scan performed on 331 backcross pigs derived from this strain. QTLs were detected at chromosome-wide level for a melanoma synthetic trait corresponding to the development of melanoma. The peak positions on Sus scrofa chromosomes (SSC) were at 49.4 and 88.0 cM (SSC1), 56.0 cM (SSC13), 86.5 cM (SSC15) and 39.8 cM (SSC17), and, on SSC2, at 16.9 cM, in families derived from F1 males only (p black coat colour in pigs, predisposes significantly to melanoma. Interactions were observed between MC1R and markers located on SSC1 (p < 0.05). Taken together, these results indicate that MeLiM swine is a model for human multigenic diseases. Comparative mapping revealed human regions of interest to search for new melanoma susceptibility candidates. PMID:17066441
Du, Zhi-Qiang; Vincent-Naulleau, Silvia; Gilbert, H�l�ne; Vignoles, Florence; Cr�chet, Fran�oise; Shimogiri, Takeshi; Yasue, Hiroshi; Leplat, Jean-Jacques; Bouet, Stephan; Gruand, Joseph; Horak, Vratislav; Milan, Denis; Le Roy, Pascale; Geffrotin, Claudine
Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms.
Understanding the genetic mechanisms of adaptive population divergence is one of the most fundamental endeavours in evolutionary biology and is becoming increasingly important as it will allow predictions about how organisms will respond to global environmental crisis. This is particularly important for the honey bee, a species of unquestionable ecological and economical importance that has been exposed to increasing human-mediated selection pressures. Here, we conducted a single nucleotide polymorphism (SNP)-based genome scan in honey bees collected across an environmental gradient in Iberia and used four FST -based outlier tests to identify genomic regions exhibiting signatures of selection. Additionally, we analysed associations between genetic and environmental data for the identification of factors that might be correlated or act as selective pressures. With these approaches, 4.4% (17 of 383) of outlier loci were cross-validated by four FST -based methods, and 8.9% (34 of 383) were cross-validated by at least three methods. Of the 34 outliers, 15 were found to be strongly associated with one or more environmental variables. Further support for selection, provided by functional genomic information, was particularly compelling for SNP outliers mapped to different genes putatively involved in the same function such as vision, xenobiotic detoxification and innate immune response. This study enabled a more rigorous consideration of selection as the underlying cause of diversity patterns in Iberian honey bees, representing an important first step towards the identification of polymorphisms implicated in local adaptation and possibly in response to recent human-mediated environmental changes. PMID:24118235
Ch�vez-Galarza, Julio; Henriques, Dora; Johnston, J Spencer; Azevedo, Jo�o C; Patton, John C; Mu�oz, Irene; De la R�a, Pilar; Pinto, M Alice
The Landmark on Film: Representations of Place and Identity
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Full Text Available This paper examines two documentary essays focusing on landmark architecture in the transnational �resund region comprising Copenhagen and Malm�. I argue that the motif of construction and deconstruction is congruous to our understanding of the ways identities are negotiated vis-�-vis spatial experience. In the films, the multiple trajectories of characters of diverse nationalities and cultures are woven into the (deconstruction of the landmark structures, producing a visual space that interrogates what �identity� means in an increasingly networked and global world.
Pei-Sze Chow
Pontos referenciais nos acessos cranianos Landmarks to the cranial approaches
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Full Text Available O conhecimento da topografia cranioencef�lica permite delimitar os acessos cranianos. Sistematiza-se os pontos referenciais, definidos em rela��o aos pontos craniom�tricos, usados nos diferentes acessos cranianos. Dos 22 pontos referenciais descritos, os doze primeiros est�o em rela��o com a base do cr�nio e os demais com a convexidade.The knowledge of the craniotopography allows the delimitation of the cranial approaches. In this study the landmarks, defined in relation to the craniometric points and used in the different cranial approaches, were systematized. Twenty two landmarks are described: the first twelve are in relation to the skull base and the remainder are in relation to the skull vertex.
Sebasti�o Gusm�o
Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds
DEFF Research Database (Denmark)
BACKGROUND: Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole). The steroid androstenone is a sex pheromone produced in the testis of the boars. Skatole is produced from tryptophan by bacteria in the intestine of the pigs. In many countries pigs are castrated as piglets to avoid boar taint, however, this is undesirable for animal welfare reasons. Genetic variations affecting the level of boar taint have previously been demonstrated in many breeds. In the study presented in this paper, markers and haplotypes, which can be applied to DNA-based selection schemes in order to reduce or eliminate the boar taint problem, are identified. RESULTS: Approximately 30,000 SNPs segregating in 923 boars from three Danish breeds; Duroc, Landrace, and Yorkshire, were used to conduct genome wide association studies of boar taint compounds. At 46 suggestive quantitative trait loci (QTL), 25 haplotypes and three single markers with effects were identified. Furthermore, 40% of the haplotypes mapped to previously identified regions. Haplotypes were also analysed for effects of slaughter weight and meat content. The most promising haplotype was identified on Sus scrofa chromosome 1. The gain in fixed effect of having this haplotype on level of androstenone in Landrace was identified to be high (1.279 micro gram/g). In addition, this haplotype explained 16.8% of the phenotypic variation within the trait. The haplotype was identified around the gene CYB5A which is known to have an indirect impact on the amount of androstenone. In addition to CYB5A, the genes SRD5A2, LOC100518755, and CYP21A2 are candidate genes for other haplotypes affecting androstenone, whereas, candidate genes for the indolic compounds were identified to be SULT1A1 and CYP2E1. CONCLUSIONS: Despite the small sample size, a total of 25 haplotypes and three single markers were identified including genomic regions not previously reported. The haplotypes that were analysed showed large effects on trait level. However, little overlap of QTL between breeds was observed.
Gregersen, Vivi R; Conley, Lene N
Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds
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Full Text Available Abstract Background Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole. The steroid androstenone is a sex pheromone produced in the testis of the boars. Skatole is produced from tryptophan by bacteria in the intestine of the pigs. In many countries pigs are castrated as piglets to avoid boar taint, however, this is undesirable for animal welfare reasons. Genetic variations affecting the level of boar taint have previously been demonstrated in many breeds. In the study presented in this paper, markers and haplotypes, which can be applied to DNA-based selection schemes in order to reduce or eliminate the boar taint problem, are identified. Results Approximately 30,000 SNPs segregating in 923 boars from three Danish breeds; Duroc, Landrace, and Yorkshire, were used to conduct genome wide association studies of boar taint compounds. At 46 suggestive quantitative trait loci (QTL, 25 haplotypes and three single markers with effects were identified. Furthermore, 40% of the haplotypes mapped to previously identified regions. Haplotypes were also analysed for effects of slaughter weight and meat content. The most promising haplotype was identified on Sus scrofa chromosome 1. The gain in fixed effect of having this haplotype on level of androstenone in Landrace was identified to be high (1.279 ?g/g. In addition, this haplotype explained 16.8% of the phenotypic variation within the trait. The haplotype was identified around the gene CYB5A which is known to have an indirect impact on the amount of androstenone. In addition to CYB5A, the genes SRD5A2, LOC100518755, and CYP21A2 are candidate genes for other haplotypes affecting androstenone, whereas, candidate genes for the indolic compounds were identified to be SULT1A1 and CYP2E1. Conclusions Despite the small sample size, a total of 25 haplotypes and three single markers were identified including genomic regions not previously reported. The haplotypes that were analysed showed large effects on trait level. However, little overlap of QTL between breeds was observed.
Gregersen Vivi R
(ps3) EN Route to the ERA of Genomic Medicine
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The Human Genome Project s completion of the human genome sequence in 2003 was a landmark scientific achievement of historic significance. It also signified a critical transition for the field of genomics, as the new foundation of genomic knowledge started to be used in powerful ways by researchers and clinicians to tackle increasingly complex problems in biomedicine. To exploit the opportunities provided by the human genome sequence and to ensure the productive growth of genomics as one of t...
Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis.
The prediction of response (or non-response) to anti-TNF treatment for rheumatoid arthritis (RA) is a pressing clinical problem. We conducted a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning anti-TNF therapy as part of Autoimmune Biomarkers Collaborative Network (ABCoN [Autoimmune Bio-markers Collaborative Network]) patient cohort. Response to therapy was determined by the change in Disease Activity Score (DAS28) observed after 14 wks. We used a two-part analysis that treated the change in DAS28 as a continuous trait and then incorporated it into a dichotomous trait of "good responder" and "nonresponder" by European League Against Rheumatism (EULAR) criteria. We corrected for multiple tests by permutation, and adjusted for potential population stratification using EIGENSTRAT. Multiple single nucleotide polymorphism (SNP) markers showed significant associations near or within loci including: the v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB) gene on chromosome 20; the type I interferon gene IFNk on chromosome 9; and in a locus on chromosome 7 that includes the paraoxonase I (PON1) gene. An SNP in the IL10 promoter (rs1800896) that was previously reported as associated with anti-TNF response was weakly associated with response in this cohort. Replications of these results in independent and larger data sets clearly are required. We provide a reference list of candidate SNPs (P < 0.01) that can be investigated in future pharmacogenomic studies. PMID:18615156
Liu, Chunyu; Batliwalla, Franak; Li, Wentian; Lee, Annette; Roubenoff, Ronenn; Beckman, Evan; Khalili, Houman; Damle, Aarti; Kern, Marlena; Furie, Richard; Dupuis, Jos�e; Plenge, Robert M; Coenen, Marieke J H; Behrens, Timothy W; Carulli, John P; Gregersen, Peter K
A field study investigating effects of landmarks on territory size and shape.
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
Asymmetric introgression in the horticultural living fossil cycas sect. Asiorientales using a genome-wide scanning approach.
The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. Consistent results tested by all neutral loci, and the species-associated loci, specify the recent introgression from the paradox of sharing of ancestral polymorphisms. Phenomenon of introgression of cultivated cycads implies niche conservation among two geographic-isolated cycads, even though the habitats of the extant wild populations of two species are distinct. PMID:23591840
Chiang, Yu-Chung; Huang, Bing-Hong; Chang, Chun-Wen; Wan, Yu-Ting; Lai, Shih-Jie; Huang, Shong; Liao, Pei-Chun
On-line SLAM using clustered landmarks with omnidirectional vision
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Full Text Available The problem of SLAM (simultaneous localization and mapping is a fundamental problem in autonomous robotics. It arises when a robot must create a map of the regions it has navigated while localizing itself on it, using results from one step to increase precision in another by eliminating errors inherent to the sensors. One common solution consists of establishing landmarks in the environment which are used as reference points for absolute localization estimates and form a sparse map that is iteratively refined as more information is obtained. This paper introduces a method of landmark selection and clustering in omnidirectional images for on-line SLAM, using the SIFT algorithm for initial feature extraction and assuming no prior knowledge of the environment. Visual sensors are an attractive way of collecting information from the environment, but tend to create an excessive amount of landmarks that are individually prone to false matches due to image noise and object similarities. By clustering several features in single objects, our approach eliminates landmarks that do not consistently represent the environment, decreasing computational cost and increasing the reliability of information incorporated. Tests conducted in real navigational situations show a significant improvement in performance without loss of quality.
Jun Okamoto Jr.
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.
Okamoto Jr., Jun; Guizilini, Vitor Campanholo.
Evolving a Multiagent System for Landmark-based Robot Navigation
Digital Repository Infrastructure Vision for European Research (DRIVER)
In this article, we build upon a multiagent architecture for landmark-based navigation in unknown environments. In this architecture, each of the agents in the navigation system has a bidding function that is controlled by a set of parameters. We show here the good results obtained by an evolutionary approach that tunes the parameter set values for two navigation tasks.
Ambastha, Madhur; Busquets, Didac; Lopez Mantaras, Ramon; Sierra, Carles
Improving Detection Rate in Intrusion Detection Systems Using FCM Clustering to Select Meaningful Landmarks in Incremental Landmark Isomap Algorithm
Directory of Open Access Journals (Sweden)
Full Text Available Dimension reduction is crucial when it is applied on intrusion detection systems. Many data mining algorithms have been used for this purpose. For example, manifold learning algorithms, especially Isometric feature mapping (Isomap have been investigated. Researchers successfully applied Isomap on intrusion detection system as a nonlinear dimension reduction method. But it had some problems such as operation on batch mode and being disabled to handle new data points, additionally, it had computational cost and could not be properly applied on huge datasets. Losing time and reducing speed of detection is another problem of Isomap in intrusion detection systems. Incremental Landmark Isomap which selects landmarks among whole data points has been invented for solving these problems. In this paper, we use FCM as a data reduction method to select meaningful landmarks for Incremental L-Isomap instead of choosing them randomly. This method is implemented and applied on some UCI datasets and also NSLKDD dataset. The results demonstrate higher detection rate for the proposed method, comparing to classical Incremental L-Isomap which chooses landmarks randomly.
Babak Nassersharif
Algorithms For Automatic And Robust Registration Of 3D Head Scans
Digital Repository Infrastructure Vision for European Research (DRIVER)
wo 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 re...
Personal genomics services: whose genomes?
Digital Repository Infrastructure Vision for European Research (DRIVER)
New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States,...
Gurwitz, David; Bregman-eschet, Yael
Pontos referenciais nos acessos cranianos / Landmarks to the cranial approaches
Scientific Electronic Library Online (English)
Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese O conhecimento da topografia cranioencef�lica permite delimitar os acessos cranianos. Sistematiza-se os pontos referenciais, definidos em rela��o aos pontos craniom�tricos, usados nos diferentes acessos cranianos. Dos 22 pontos referenciais descritos, os doze primeiros est�o em rela��o com a base do [...] cr�nio e os demais com a convexidade. Abstract in english The knowledge of the craniotopography allows the delimitation of the cranial approaches. In this study the landmarks, defined in relation to the craniometric points and used in the different cranial approaches, were systematized. Twenty two landmarks are described: the first twelve are in relation t [...] o the skull base and the remainder are in relation to the skull vertex.
Gusm�o, Sebasti�o; Silveira, Roberto Leal; Arantes, Alu�zio.
Automatic facial expression recognition based on features extracted from tracking of facial landmarks
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
Genome Paths: A Way to Personalized and Predictive Medicine
Digital Repository Infrastructure Vision for European Research (DRIVER)
The review is devoted to the impact of human genome research on progress in modern medicine. Basic achievements in genome research have resulted in the deciphering of the human genome and creation of a molecular landmarks map of the human haploid genome (HapMap Project), which has made a tremendous contribution to our understanding of common genetic and multifactorial (complex) disorders. Current genome studies mainly focus on genetic testing and gene association studies of multifactorial (co...
Discovering landmark preferences and movement patterns from photo postings
Digital Repository Infrastructure Vision for European Research (DRIVER)
This article presents a geovisual analytics approach to discovering people's preferences for landmarks and movement patterns from photos posted on the Flickr website. The approach combines an exploratory spatio-temporal analysis of geographic coordinates and dates representing locations and time of taking photos with basic thematic information available through the Google Maps Web mapping service, and interpretation of the analyzed area. The article describes data aggregation and filtering te...
Cardiac Conduction System: Delineation of Anatomic Landmarks With Multidetector CT
Digital Repository Infrastructure Vision for European Research (DRIVER)
Major components of the cardiac conduction system including the sinoatrial node (SAN), atrioventricular node (AVN), the His Bundle, and the right and left bundle branches are too small to be directly visualized by multidetector CT (MDCT) given the limited spatial resolution of current scanners. However, the related anatomic landmarks and variants of this system a well as the areas with special interest to electrophysiologists can be reliably demonstrated by MDCT. Some of these structures and ...
Visual landmarks facilitate rodent spatial navigation in virtual reality environments
Digital Repository Infrastructure Vision for European Research (DRIVER)
Because many different sensory modalities contribute to spatial learning in rodents, it has been difficult to determine whether spatial navigation can be guided solely by visual cues. Rodents moving within physical environments with visual cues engage a variety of nonvisual sensory systems that cannot be easily inhibited without lesioning brain areas. Virtual reality offers a unique approach to ask whether visual landmark cues alone are sufficient to improve performance in a spatial task. We ...
Youngstrom, Isaac A.; Strowbridge, Ben W.
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.
[Lymphoscintigrams with anatomical landmarks obtained with vector graphics].
Nuclear medicine images are difficult to interpret because they do not include anatomical details. The aim of this study was to obtain lymphoscintigrams with anatomical landmarks that could be easily interpreted by General Physicians. Traditional lymphoscintigrams were processed with Adobe� Photoshop� CS6 and converted into vector images created by Illustrator�. The combination with a silhouette vector improved image interpretation, without resulting in longer radiation exposure or acquisition times. PMID:23096740
Rubini, Giuseppe; Antonica, Filippo; Renna, Maria Antonia; Ferrari, Cristina; Iuele, Francesca; Stabile Ianora, Antonio Amato; Losco, Matteo; Niccoli Asabella, Artor
Probing navigation strategies of honeybees � landmark experiments and simulations
Digital Repository Infrastructure Vision for European Research (DRIVER)
In this study we probed the content of the spatial memory of honeybees in two landmark manipulation experiments accompanied by computer modelling. While the results of the first experiments are in line with an image-like representation of places, the findings of the second experiment suggest that bees also memorize the depth structure of a scene, most probably inferred from optic flow. This is supported by the fact that bees actively control their visual input.
Associative Basis of Landmark Learning and Integration in Vertebrates
Digital Repository Infrastructure Vision for European Research (DRIVER)
Early work on spatial navigation evaluated what stimuli (kinesthetic or extra-maze) support small-scale navigation and the nature of the underlying learning (place versus response) process. Contemporary research has focused primarily on how cues interact to determine spatial search. This review covers three general findings from research on landmark-based spatial search in vertebrates. First, pigeons and rats encode simple spatial maps in both open-field and touchscreen environments. Second, ...
Leising, Kenneth J.; Blaisdell, Aaron P.
Neural Network Based Sensory Fusion for Landmark Detection
NASA is planning to send numerous unmanned planetary missions to explore the space. This requires autonomous robotic vehicles which can navigate in an unstructured, unknown, and uncertain environment. Landmark based navigation is a new area of research which differs from the traditional goal-oriented navigation, where a mobile robot starts from an initial point and reaches a destination in accordance with a pre-planned path. The landmark based navigation has the advantage of allowing the robot to find its way without communication with the mission control station and without exact knowledge of its coordinates. Current algorithms based on landmark navigation however pose several constraints. First, they require large memories to store the images. Second, the task of comparing the images using traditional methods is computationally intensive and consequently real-time implementation is difficult. The method proposed here consists of three stages, First stage utilizes a heuristic-based algorithm to identify significant objects. The second stage utilizes a neural network (NN) to efficiently classify images of the identified objects. The third stage combines distance information with the classification results of neural networks for efficient and intelligent navigation.
Kumbla, Kishan -K.; Akbarzadeh, Mohammad R.
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.
A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation
Identifying the genes that influence levels of pro-inflammatory molecules can help to elucidate the mechanisms underlying this process. We first conducted a two-stage genome-wide association scan (GWAS) for the key inflammatory biomarkers Interleukin-6 (IL-6), the general measure of inflammation erythrocyte sedimentation rate (ESR), monocyte chemotactic protein-1 (MCP-1), and high-sensitivity C-reactive protein (hsCRP) in a large cohort of individuals from the founder population of Sardinia. By analysing 731,213 autosomal or X chromosome SNPs and an additional ?1.9 million imputed variants in 4,694 individuals, we identified several SNPs associated with the selected quantitative trait loci (QTLs) and replicated all the top signals in an independent sample of 1,392 individuals from the same population. Next, to increase power to detect and resolve associations, we further genotyped the whole cohort (6,145 individuals) for 293,875 variants included on the ImmunoChip and MetaboChip custom arrays. Overall, our combined approach led to the identification of 9 genome-wide significant novel independent signals�5 of which were identified only with the custom arrays�and provided confirmatory evidence for an additional 7. Novel signals include: for IL-6, in the ABO gene (rs657152, p?=?2.13�10?29); for ESR, at the HBB (rs4910472, p?=?2.31�10?11) and UCN119B/SPPL3 (rs11829037, p?=?8.91�10?10) loci; for MCP-1, near its receptor CCR2 (rs17141006, p?=?7.53�10?13) and in CADM3 (rs3026968, p?=?7.63�10?13); for hsCRP, within the CRP gene (rs3093077, p?=?5.73�10?21), near DARC (rs3845624, p?=?1.43�10?10), UNC119B/SPPL3 (rs11829037, p?=?1.50�10?14), and ICOSLG/AIRE (rs113459440, p?=?1.54�10?08) loci. Confirmatory evidence was found for IL-6 in the IL-6R gene (rs4129267); for ESR at CR1 (rs12567990) and TMEM57 (rs10903129); for MCP-1 at DARC (rs12075); and for hsCRP at CRP (rs1205), HNF1A (rs225918), and APOC-I (rs4420638). Our results improve the current knowledge of genetic variants underlying inflammation and provide novel clues for the understanding of the molecular mechanisms regulating this complex process.
Naitza, Silvia; Porcu, Eleonora; Steri, Maristella; Taub, Dennis D.; Mulas, Antonella; Xiao, Xiang; Strait, James; Dei, Mariano; Lai, Sandra; Busonero, Fabio; Maschio, Andrea; Usala, Gianluca; Zoledziewska, Magdalena; Sidore, Carlo; Zara, Ilenia; Pitzalis, Maristella; Loi, Alessia; Virdis, Francesca; Piras, Roberta; Deidda, Francesca; Whalen, Michael B.; Crisponi, Laura; Concas, Antonio; Podda, Carlo; Uzzau, Sergio; Scheet, Paul; Longo, Dan L.; Lakatta, Edward; Abecasis, Goncalo R.; Cao, Antonio; Schlessinger, David; Uda, Manuela
A novel method, digital genome scanning detects
Digital Repository Infrastructure Vision for European Research (DRIVER)
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 inv...
Mita Hiroaki; Toyota Minoru; Aoki Fumio; Akashi Hirofumi; Maruyama Reo; Sasaki Yasushi; Suzuki Hiromu; Idogawa Masashi; Kashima Lisa; Yanagihara Kazuyoshi; Fujita Masahiro; Hosokawa Masao; Kusano Masanobu; Sabau Sorin; Tatsumi Haruyuki
New Statistical Method to Analyze Three-Dimensional Landmark Configurations Obtained with Cone-Beam CT: Basic Features and Clinical Application for Rapid Maxillary Expansion
Energy Technology Data Exchange (ETDEWEB)
To describe a statistical method of three-dimensional landmark configuration data and apply it to an orthodontic data set comparing two types of rapid maxillary expansion (RME) treatments. Landmark configurations obtained from cone beam CT scans were used to represent patients in two types (please describe what were two types) of RME groups and a control group over four time points. A method using tools from persistent homology and dimensionality reduction is presented and used to identify variability between the subjects. The analysis was in agreement with previous results using conventional methods, which found significant differences between treatment groups and the control, but no distinction between the types of treatment. Additionally, it was found that second molar eruption varied considerably between the subjects, and this has not been evaluated in previous analyses. This method of analysis allows entire configurations to be considered as a whole, and does not require specific inter-landmark distances or angles to be selected. Sources of variability present themselves, without having to be individually sought after. This method is suggested as an additional tool for the analysis of landmark configuration data.
Gamble, Jennifer; Lagravere, Manuel O.; Major, Paul W.; Heo, Giseon [University of Alberta, Edmonton (Canada)
New Statistical Method to Analyze Three-Dimensional Landmark Configurations Obtained with Cone-Beam CT: Basic Features and Clinical Application for Rapid Maxillary Expansion
International Nuclear Information System (INIS)
To describe a statistical method of three-dimensional landmark configuration data and apply it to an orthodontic data set comparing two types of rapid maxillary expansion (RME) treatments. Landmark configurations obtained from cone beam CT scans were used to represent patients in two types (please describe what were two types) of RME groups and a control group over four time points. A method using tools from persistent homology and dimensionality reduction is presented and used to identify variability between the subjects. The analysis was in agreement with previous results using conventional methods, which found significant differences between treatment groups and the control, but no distinction between the types of treatment. Additionally, it was found that second molar eruption varied considerably between the subjects, and this has not been evaluated in previous analyses. This method of analysis allows entire configurations to be considered as a whole, and does not require specific inter-landmark distances or angles to be selected. Sources of variability present themselves, without having to be individually sought after. This method is suggested as an additional tool for the analysis of landmark configuration data.
New Statistical Method to Analyze Three-Dimensional Landmark Configurations Obtained with Cone-Beam CT: Basic Features and Clinical Application for Rapid Maxillary Expansion
Objective To describe a statistical method of three-dimensional landmark configuration data and apply it to an orthodontic data set comparing two types of rapid maxillary expansion (RME) treatments. Materials and Methods Landmark configurations obtained from cone beam CT scans were used to represent patients in two types (please describe what were two types) of RME groups and a control group over four time points. A method using tools from persistent homology and dimensionality reduction is presented and used to identify variability between the subjects. Results The analysis was in agreement with previous results using conventional methods, which found significant differences between treatment groups and the control, but no distinction between the types of treatment. Additionally, it was found that second molar eruption varied considerably between the subjects, and this has not been evaluated in previous analyses. Conclusion This method of analysis allows entire configurations to be considered as a whole, and does not require specific inter-landmark distances or angles to be selected. Sources of variability present themselves, without having to be individually sought after. This method is suggested as an additional tool for the analysis of landmark configuration data.
Gamble, Jennifer; Lagravere, Manuel O.; Major, Paul W.
Volumetric Image Guidance Using Carina vs Spine as Registration Landmarks for Conventionally Fractionated Lung Radiotherapy
Energy Technology Data Exchange (ETDEWEB)
Purpose: To compare the relative accuracy of 2 image guided radiation therapy methods using carina vs spine as landmarks and then to identify which landmark is superior relative to tumor coverage. Methods and Materials: For 98 lung patients, 2596 daily image-guidance cone-beam computed tomography scans were analyzed. Tattoos were used for initial patient alignment; then, spine and carina registrations were performed independently. A separate analysis assessed the adequacy of gross tumor volume, internal target volume, and planning target volume coverage on cone-beam computed tomography using the initial, middle, and final fractions of radiation therapy. Coverage was recorded for primary tumor (T), nodes (N), and combined target (T+N). Three scenarios were compared: tattoos alignment, spine registration, and carina registration. Results: Spine and carina registrations identified setup errors {>=}5 mm in 35% and 46% of fractions, respectively. The mean vector difference between spine and carina matching had a magnitude of 3.3 mm. Spine and carina improved combined target coverage, compared with tattoos, in 50% and 34% (spine) to 54% and 46% (carina) of the first and final fractions, respectively. Carina matching showed greater combined target coverage in 17% and 23% of fractions for the first and final fractions, respectively; with spine matching, this was only observed in 4% (first) and 6% (final) of fractions. Carina matching provided superior nodes coverage at the end of radiation compared with spine matching (P=.0006), without compromising primary tumor coverage. Conclusion: Frequent patient setup errors occur in locally advanced lung cancer patients. Spine and carina registrations improved combined target coverage throughout the treatment course, but carina matching provided superior combined target coverage.
Lavoie, Caroline; Higgins, Jane; Bissonnette, Jean-Pierre [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada); Le, Lisa W. [Department of Biostatistics, Princess Margaret Hospital, Toronto, Ontario, M5G 2M9 (Canada); Sun, Alexander; Brade, Anthony; Hope, Andrew; Cho, John [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada); Bezjak, Andrea, E-mail: firstname.lastname@example.com [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada)
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 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.
Human Genome Anatomy: BACs Integrating the Genetic and Cytogenetic Maps for Bridging Genome and Biomedicine
Digital Repository Infrastructure Vision for European Research (DRIVER)
Human genome sequencing is accelerating rapidly. Multiple genome maps link this sequence to problems in biology and clinical medicine. Because each map represents a different aspect of the structure, content, and behavior of human chromosomes, these fundamental properties must be integrated with the genome to understand disease genes, cancer instability, and human evolution. Cytogenetic maps use 400�850 visible band landmarks and are the primary means for defining prenatal defects and novel...
Korenberg, Julie R.; Chen, Xiao-ning; Sun, Zhiguang; Shi, Zheng-yang; Ma, Shaowu; Vataru, Eddy; Yimlamai, Dean; Weissenbach, Jean S.; Shizuya, Hiroaki; Simon, Melvin I.; Gerety, Sebastian S.; Nguyen, Huy; Zemsteva, Irina S.; Hui, Lester; Silva, James
Statistical analysis of shape through triangulation of landmarks: A study of sexual dimorphism in hominids
Digital Repository Infrastructure Vision for European Research (DRIVER)
Two objects with homologous landmarks are said to be of the same shape if the configuration of landmarks of one object can be exactly matched with that of the other by translation, rotation/reflection, and scaling. In an earlier paper, the authors proposed statistical analysis of shape by considering logarithmic differences of all possible Euclidean distances between landmarks. Tests of significance for differences in the shape of objects and methods of discrimination between populations were...
[Surgical landmarks of course of atrioventricular conduction system].
There is a certain tendency in the relationship between the distribution of the conduction system and the type of VSD as classified by Soto and coworkers. The course of the conduction system and its surgical landmarks were investigated histologically in various cardiac anomalies. In perimembranous inlet VSD, the His bundle ran superficially on the crest of the ventricular septum. It ran on the left ventricular aspect and somewhat deeply in trabecular VSD and far deeply in infundibular VSD. In perimembranous inlet or trabecular VSD, the RBB laid beneath or just anterior to a series of upper-uppermost accessory papillary muscle when these were present and descended posteroinferior to the MPM, basically as in the normal heart. The upper-uppermost AcPM are reliable landmarks for the RBB. The RBB descended just anterior to the so called MPM (embryologically the uppermost AcPM--Van Mierop) in infundibular VSD and TOF. These findings have provided us useful bases for suture placement to avoid conduction disturbance. PMID:9301911
Yamashiro, T; Matsumoto, T; Kiyoku, H; Tamiya, T
MR arthrography of the shoulder and hip after fluoroscopic landmarking
International Nuclear Information System (INIS)
Purpose. To describe a technique for intra-articular injection in the MR suite after conventional fluoroscopic landmarking in order to streamline MR arthrography.Design and patients. This technique was performed on 33 consecutive patients referred for MR arthrography of the shoulder to evaluate the glenoid labrum and on 15 consecutive patients referred for MR arthrography of the hip to evaluate the acetabular labrum. The patients were landmarked in the fluoroscopy suite, followed by a conventional MR examination. The intra-articular injection was then performed on the MR table and the MR arthrographic sequences obtained.Results. One of the 48 injections was extra-articular, requiring a second injection. The other injections were performed without incident, and the average total procedure time for all injections was 10 min.Conclusions. This technique is a reliable method of streamlining intra-articular injections when performing conventional MR imaging prior to the MR arthrographic portion of the examination. It shortens the total MR examination time by eliminating a visit to the fluoroscopy suite in the middle of the MR study, and its use of a straight anterior approach for both the shoulder and hip joints should be familiar to most people who perform conventional arthrography. (orig.)
Dominance of the odometer over serial landmark learning in honeybee navigation
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
Landmarks in nature to support wayfinding: the effects of seasons and experimental methods.
Landmarks constitute an essential basis for a structural understanding of the spatial environment. Therefore, they are crucial factors in external spatial representations such as maps and verbal route descriptions, which are used to support wayfinding. However, selecting landmarks for these representations is a difficult task, for which an understanding of how people perceive and remember landmarks in the environment is needed. We investigated the ways in which people perceive and remember landmarks in nature using the thinking aloud and sketch map methods during both the summer and the winter seasons. We examined the differences between methods to identify those landmarks that should be selected for external spatial representations, such as maps or route descriptions, in varying conditions. We found differences in the use of landmarks both in terms of the methods and also between the different seasons. In particular, the participants used passage and tree-related landmarks at significantly different frequencies with the thinking aloud and sketch map methods. The results are likely to reflect the different roles of the landmark groups when using the two methods, but also the differences in counting landmarks when using both methods. Seasonal differences in the use of landmarks occurred only with the thinking aloud method. Sketch maps were drawn similarly in summertime and wintertime; the participants remembered and selected landmarks similarly independent of the differences in their perceptions of the environment due to the season. The achieved results may guide the planning of external spatial representations within the context of wayfinding as well as when planning further experimental studies. PMID:23392783
Kettunen, Pyry; Irvankoski, Katja; Krause, Christina M; Sarjakoski, L Tiina
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�13� (range 30-70�, (b was 41�13� (range 20-70� and (g was 61�13� (range 28-80�. 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
Die Reproduzierbarkeit von radiologisch-anatomischen Landmarks zur Determination der Gelenkspaltgrenzen des Articulatio temporomandibularis
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Zur dreidimensionalen Evaluation des Kiefergelenkspaltes ist eine exakte Ausrichtung des Gelenkes an eine Referenzebene notwendig. Um diese Ebene zu determinieren wurden an Computer-Tomogrammen des menschlichen Sch�dels radiologisch-anatomische landmarks definiert und auf ihre interindividuelle Reproduzierbarkeit hin �berpr�ft. F�nf Untersucher haben an achtzehn CT-Datens�tzen jeweils neunzehn landmarks identifiziert. Aus der Euklidischen Distanz zwischen gleichen Punkten verschiedener U...
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 ...
Nuclear scans use radioactive substances to see structures and functions inside your body. They use a special ... images. Most scans take 20 to 45 minutes. Nuclear scans can help doctors diagnose many conditions, including ...
Full Text Available X-Plain Computed Axial Tomography (CT) Scan Reference Summary Introduction A Computed Axial Tomography Scan or CT scan is a test that provides very clear pictures of structures inside the body. ...
Meta-Analysis of Genome-Wide Scans for Total Body BMD in Children and Adults Reveals Allelic Heterogeneity and Age-Specific Effects at the WNT16 Locus
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To identify genetic loci influencing bone accrual, we performed a genome-wide association scan for total-body bone mineral density (TB-BMD) variation in 2,660 children of different ethnicities. We discovered variants in 7q31.31 associated with BMD measurements, with the lowest P?=?4.1�10?11 observed for rs917727 with minor allele frequency of 0.37. We sought replication for all SNPs located �500 kb from rs917727 in 11,052 additional individuals from five independent studies including ...
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
A Genome-Wide SNP Scan Reveals Novel Loci for Egg Production and Quality Traits in White Leghorn and Brown-Egg Dwarf Layers
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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 ag...
Liu, Wenbo; Li, Dongfeng; Liu, Jianfeng; Chen, Sirui; Qu, Lujiang; Zheng, Jiangxia; Xu, Guiyun; Yang, Ning
Landmarks of History of Soil Science in Sri Lanka
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.
Is there consistency in cephalometric landmark identification amongst oral and maxillofacial surgeons?
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; Nacl�rio-Homem, M G; Jungner, M
Distal landmarks and hippocampal place cells: effects of relative translation versus rotation.
Hippocampal neurons are selectively active when a rat occupies restricted locations in an environment. These place cells derive their specificity from a multitude of sources, including idiothetic cues and sensory input derived from both distal and local landmarks. Most experiments have attempted to dissociate the relative strengths and roles played by these sources by rotating one set against the other. Few studies have addressed the effects of relative translation of the local cue set versus salient distal landmarks. To address this question, ensembles of place cells were recorded as a rectangular or circular track was moved to different locations in a room with controlled visual landmarks. Place cells primarily maintained their firing fields relative to the track (i.e., occupying new locations relative to the distal landmarks), even though the track could occupy completely nonoverlapping regions of the room. When the distal landmarks were rotated around the circular track, however, the place fields rotated with the landmarks, demonstrating that the cues were perceptible to the rat. These results suggest that, under these conditions, the spatial tuning of place cells may derive from an interaction between local and idiothetic cues, which define the precise firing locations of the cells and the relationships between them, and distal landmarks, which set the orientation of the ensemble representation relative to the external environment. PMID:12921350
Knierim, James J; Rao, Geeta
Learning of landmark stability and instability by hippocampal place cells.
Place cells in the rat hippocampus fire whenever the animal is in a particular location. In a symmetrical environment, their receptive fields (place fields) are oriented by visual cues, and if these are unavailable they are oriented by movement-generated (idiothetic) cues. The present study tested the hypothesis that the cells would learn not to 'trust' a visual cue if the rat experienced it to be unstable (Knierim et al., 1995. Place cells, head direction cells and the learning of landmark stability. J. Neurosci. 15, 1648-1659). In an otherwise symmetrical environment, a visual cue was moved with respect to the idiothetic cues, either in sight or out-of-sight of the rat. When the visual cue was moved out-of-sight of the rat, place fields were initially oriented by this cue in preference to the idiothetic cues. However, if the cue was seen by the rat to be mobile, place fields ceased following the visual cue and became oriented by the idiothetic cues instead. If the cue was not seen to be mobile until the rat had had several days of experience in the environment, then the fields continued to be oriented by the (now visibly mobile) visual cue. It thus appears that the orienting influence of a visual cue on place fields can be either strengthened or weakened relative to the idiothetic cues, depending on the experience of the rat. PMID:9705005
Jeffery, K J
Using Regulatory and Epistatic Networks to Extend the Findings of a Genome Scan: Identifying the Gene Drivers of Pigmentation in Merino Sheep
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Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific micr...
Garci?a-ga?mez, Elsa; Reverter, Antonio; Whan, Vicki; Mcwilliam, Sean M.; Arranz, Juan Jose?; Kijas, James
Global Nature of Dynamic Protein-Chromatin Interactions In Vivo: Three-Dimensional Genome Scanning and Dynamic Interaction Networks of Chromatin Proteins
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Genome structure and gene expression depend on a multitude of chromatin-binding proteins. The binding properties of these proteins to native chromatin in intact cells are largely unknown. Here, we describe an approach based on combined in vivo photobleaching microscopy and kinetic modeling to analyze globally the dynamics of binding of chromatin-associated proteins in living cells. We have quantitatively determined basic biophysical properties, such as off rate constants, residence time, and ...
Phair, Robert D.; Scaffidi, Paola; Elbi, Cem; Vecerova?, Jaromi?ra; Dey, Anup; Ozato, Keiko; Brown, David T.; Hager, Gordon; Bustin, Michael; Misteli, Tom
Evidence for a colorectal cancer susceptibility locus on chromosome 3q21-q24 from a high-density SNP genome-wide linkage scan.
To identify a novel susceptibility gene for colorectal cancer (CRC), we conducted a genome-wide linkage analysis of 69 pedigrees segregating colorectal neoplasia in which involvement of known loci had been excluded, using a high-density single nucleotide polymorphism (SNP) array containing 10,204 markers. Multipoint linkage analyses were undertaken using both non-parametric (model-free) and parametric (model-based) methods. After the removal of SNPs in strong linkage disequilibrium, we obtained a maximum non-parametric linkage statistic of 3.40 (P=0.0003) at chromosomal region 3q21-q24. The same genomic position also yielded the highest multipoint heterogeneity LOD (HLOD) score under a dominant model (HLOD=3.10, genome-wide P=0.038) with 62% of families linked to the locus. We provide evidence for a novel CRC susceptibility gene. Further studies are needed to confirm this localization and to evaluate the contribution of this locus to disease incidence. PMID:16923799
Kemp, Zoe; Carvajal-Carmona, Luis; Spain, Sarah; Barclay, Ella; Gorman, Margaret; Martin, Lynn; Jaeger, Emma; Brooks, Neil; Bishop, D Timothy; Thomas, Huw; Tomlinson, Ian; Papaemmanuil, Elli; Webb, Emily; Sellick, Gabrielle S; Wood, Wendy; Evans, Gareth; Lucassen, Anneke; Maher, Eamonn R; Houlston, Richard S
Follow-up study of the first genome-wide association scan in alopecia areata: IL13 and KIAA0350 as susceptibility loci supported with genome-wide significance.
Recently, the first genome-wide association study (GWAS) of alopecia areata (AA) was conducted in a North-American sample, and this identified eight susceptibility loci surpassing genome-wide significance. The aim of the present follow-up association analysis was to confirm five of these eight loci (single-nucleotide polymorphisms (SNPs) from the CTLA4, IL-2RA, and HLA regions were not included due to previous own findings) and test 12 other loci from the GWAS, which did not surpass the threshold for genome-wide significance. Twenty-three SNPs from the 17 loci were investigated using a sample of 1,702 Central European AA patients and 1,723 controls. Of the five loci with previously reported genome-wide significance, association was confirmed for all of these: ULBP3/ULBP6, PRDX5, IL-2/IL-21, STX17, and IKZF4/ERBB3 (P-value <0.05). To detect robust evidence for association among the 12 other loci, a meta-analysis of the present association data and the data of the recent GWAS was performed. Genome-wide significant association was found for rs20541 (P(comb)=7.52 � 10(-10); odds ratio (OR)=1.30 (1.23-1.38)) and rs998592 (P(comb)=1.11 � 10(-11); OR=1.28 (1.21-1.36)), thus establishing IL-13 and KIAA0350/CLEC16A as susceptibility loci for AA. Interestingly, IL-13 and KIAA0350/CLEC16A are susceptibility loci for other autoimmune diseases, supporting the hypothesis of shared pathways of autoimmune susceptibility. PMID:22534877
Jagielska, Dagny; Redler, Silke; Brockschmidt, Felix F; Herold, Christine; Pasternack, Sandra M; Garcia Bartels, Natalie; Hanneken, Sandra; Eigelshoven, Sibylle; Refke, Melanie; Barth, Sandra; Giehl, Kathrin A; Kruse, Roland; Lutz, Gerhard; Wolff, Hans; Blaumeiser, Bettina; B�hm, Markus; Blume-Peytavi, Ulrike; Becker, Tim; N�then, Markus M; Betz, Regina C
Full Text Available ... scan is a test that provides very clear pictures of structures inside the body. Doctors may recommend ... sophisticated computers to come up with the final pictures. The CT scan machine looks like a giant ...
Liver gallium scan; Bony gallium scan ... You will get a radioactive material called gallium injected into your vein. The gallium travels through the bloodstream and collects in the bones and certain organs. Your health care provider will ...
78 FR 69437 - Landmarks Committee of the National Park System Advisory Board Meeting
...the National Park System Advisory Board of the qualifications of each property being proposed for National Historic Landmark (NHL) designation, and to make recommendations regarding the possible designation of those properties as National Historic...
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The author comments on the current situation in the area of lung scanning by appraising the standard of lung scanning in Australia, by outlining areas of development and by assessing how lung scanning can serve the medical community as a means of assessing lung function
Color Atlas of Skeletal landmark definitions. Guidelines for reproducible manual and virtual palpations.
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This book defines the location of anatomic landmarks by means of two palpation protocols: manual palpation, which allows spatial location of landmarks using hands combined or not with threedimensional (3D) digitizing, and virtual palpation on 3D computer models obtained, for example, from medical imaging. These protocols can be used independently or in combination. Manual palpation is used clinically for variouspurposes:� Identification of painful areas� Positioning of particular pieces o...
Sint Jan, Serge
Learning Compact Visual Descriptors for Low Bit Rate Mobile Landmark Search
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Coming with the ever growing computational power of mobile devices, mobile visual search have undergone an evolution in techniques and applications. A significant trend is low bit rate visual search, where compact visual descriptors are extracted directly over a mobile and delivered as queries rather than raw images to reduce the query transmission latency. In this article, we introduce our work on low bit rate mobile landmark search, in which a compact yet discriminative landmark image descr...
Duan, Ling-yu Peking University; Chen, Jie Peking University; Ji, Rongrong Peking University; Huang, Tiejun Peking University; Gao, Wen Peking University
Coupling between place cells and head direction cells during relative translations and rotations of distal landmarks.
Hippocampal place cells are selectively active when a rat occupies restricted locations in an environment, and head direction cells fire selectively when the rat's head is pointed in a particular direction in allocentric space. Both place cells and head direction cells are usually coupled, and they are controlled by a complex interaction between external landmarks and idiothetic cues. Most studies have investigated this interaction by rotating the landmarks in the environment. In contrast, a recent study translated the apparatus relative to the landmarks in an environment and found that most place cells maintained the same preferred location on the apparatus regardless of the location of the apparatus in the room. Because head direction cells are insensitive to the rat's location in an environment, the distal landmarks may influence the place field firing locations primarily by controlling the bearing of the head direction cell system. To address this question, ensembles of CA1 place cells and head direction cells of the anterior thalamus were recorded simultaneously, as a rectangular or circular track was moved to different locations in a room with distinct visual landmarks. Most place cells maintained their firing fields relative to the track when the track was translated, and head direction cells maintained the same preferred firing direction. When the distal landmarks were rotated around the track, the firing fields of place cells and the preferred directions of head direction cells rotated with the cues. These results suggest that the precise firing locations of place cells are controlled by an interaction between local and idiothetic cues, and the orientation of the CA1 ensemble representation relative to the distal landmarks may be controlled indirectly by the distal landmarks' influence over the bearing of the head direction cell system. PMID:15340767
Yoganarasimha, D; Knierim, James J
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
IAEA Director General welcomes landmark convention to combat nuclear terrorism
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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)
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
Compensation for fluctuations in crosswind drift without stationary landmarks in butterflies migrating over seas.
Migrating insects may fly over large bodies of water that lack landmarks, but little is known about their ability to navigate in such a fluid environment. Using boat navigation instruments to measure compensation for fluctuations in crosswind drift, I investigated the ability of butterflies (Lepidoptera: Hesperiidae, Nymphalidae and Pieridae) to orient with and without landmarks as they migrated naturally over the Caribbean Sea. I used the presence or absence of landmarks or clouds to evaluate their use by the butterflies as guides for compensation. Forty-one per cent of the butterflies compensated for crosswind drift, whereas only 16% did not compensate. No conclusion could be drawn for the remainder. Without landmarks or clouds, butterflies were significantly less likely to compensate for drift than when these local cues were present. Butterflies were more likely to compensate fully in the presence of a landmark than when only clouds were present. Phoebis sennae butterflies drifted in the morning and overcompensated for drift in the afternoon, a pattern found both within and between individuals independent of landmarks. Although I cannot exclude the use of clouds, this would probably result in undercompensation. Hence, a ground reference in conjunction with a sun or magnetic compass is the most likely orientation cue. In the absence of clouds, one butterfly compensated, at least in part, indicating that it was using ripples on the sea surface as a ground reference in conjunction with a sun or magnetic compass. Copyright 2001 The Association for the Study of Animal Behaviour. PMID:11170709
Srygley, Robert B.
Multiobjective optimization framework for landmark measurement error correction in three-dimensional cephalometric tomography.
The purpose of this study is to minimize errors that occur when using a four vs six landmark superimpositioning method in the cranial base to define the co-ordinate system. Cone beam CT volumetric data from ten patients were used for this study. Co-ordinate system transformations were performed. A co-ordinate system was constructed using two planes defined by four anatomical landmarks located by an orthodontist. A second co-ordinate system was constructed using four anatomical landmarks that are corrected using a numerical optimization algorithm for any landmark location operator error using information from six landmarks. The optimization algorithm minimizes the relative distance and angle between the known fixed points in the two images to find the correction. Measurement errors and co-ordinates in all axes were obtained for each co-ordinate system. Significant improvement is observed after using the landmark correction algorithm to position the final co-ordinate system. The errors found in a previous study are significantly reduced. Errors found were between 1 mm and 2 mm. When analysing real patient data, it was found that the 6-point correction algorithm reduced errors between images and increased intrapoint reliability. A novel method of optimizing the overlay of three-dimensional images using a 6-point correction algorithm was introduced and examined. This method demonstrated greater reliability and reproducibility than the previous 4-point correction algorithm. PMID:23640988
DeCesare, A; Secanell, M; Lagrav�re, M O; Carey, J
Detection and location of 127 anatomical landmarks in diverse CT datasets
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
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements
Motivation The transcription start site (TSS) has been located for an increasing number of genes across several organisms. Statistical tests have shown that some cis-acting regulatory elements have positional preferences with respect to the TSS, but few strategies have emerged for locating elements by their positional preferences. This paper elaborates such a strategy. First, we align promoter regions without gaps, anchoring the alignment on each promoter�s TSS. Second, we apply a novel word-specific mask. Third, we apply a clustering test related to gapless BLAST statistics. The test examines whether any specific word is placed unusually consistently with respect to the TSS. Finally, our program A-GLAM, an extension of the GLAM program, uses significant word positions as new �anchors� to realign the sequences. A Gibbs sampling algorithm then locates putative cis-acting regulatory elements. Usually, Gibbs sampling requires a preliminary masking step, to avoid convergence onto a dominant but uninteresting signal from a DNA repeat. However, since the positional anchors focus A-GLAM on the motif of interest, masking DNA repeats during Gibbs sampling becomes unnecessary. Results In a set of human DNA sequences with experimentally characterized TSSs, the placement of 791 octonucleotide words was unusually consistent (multiple test corrected P < 0.05). Alignments anchored on these words sometimes located statistically significant motifs inaccessible to GLAM or AlignACE. Availability The A-GLAM program and a list of statistically significant words are available at ftp://ftp.ncbi.nih.gov/pub/spouge/papers/archive/AGLAM/. Contact email@example.com
Tharakaraman, Kannan; Marino-Ramirez, Leonardo; Sheetlin, Sergey; Landsman, David; Spouge, John L.
Sequence variations in the public human genome data reflect a bottlenecked population history
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Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving population structure. Redundant coverage in overlaps of large-insert genomic clones, sequenced as part of the Human Genome Project, comprises a quarter of the genome, and it is representative in terms of base compositional and functional sequence features. We mined these regions to produce 500,000 ...
Involvement of the hippocampus and associative parietal cortex in the use of proximal and distal landmarks for navigation.
Rats with dorsal hippocampus or associative parietal cortex (APC) lesions and sham-operated controls were trained on variants of the Morris water maze navigation task. In the 'proximal landmark condition', the rats had to localize the hidden platform solely on the basis of three salient object landmarks placed directly in the swimming pool. In the 'distal landmark condition', rats could rely only on distal landmarks (room cues) to locate the platform. In the 'beacon condition', the platform location was signaled by a salient cue directly attached to it. Rats with hippocampal lesions were impaired in the distal and to a less extent in the proximal landmark condition whereas rats with parietal lesions were impaired only in the proximal landmark condition. None of the lesioned groups was impaired in the beacon condition. These results suggest that the processing of information related to proximal, distal landmarks or associated beacon are mediated by different neural systems. The hippocampus would contribute to both proximal and distal landmark processing whereas the APC would be involved in the processing of proximal landmarks only. Navigation relying on a cued-platform would not require participation of the hippocampus nor the APC. Assuming that the processing of proximal landmarks heavily depends on the integration of visuospatial and idiothetic information, these results are consistent with the hypothesis that the APC plays a role in the combination of multiple sensory information and contributes to the formation of an allocentric spatial representation. PMID:10762689
Save, E; Poucet, B
Genome-wide linkage scan to identify loci associated with type 2 diabetes and blood lipid phenotypes in the Sikh Diabetes Study.
In this investigation, we have carried out an autosomal genome-wide linkage analysis to map genes associated with type 2 diabetes (T2D) and five quantitative traits of blood lipids including total cholesterol, high-density lipoprotein (HDL) cholesterol, low-density lipoprotein (LDL) cholesterol, very low-density lipoprotein (VLDL) cholesterol, and triglycerides in a unique family-based cohort from the Sikh Diabetes Study (SDS). A total of 870 individuals (526 male/344 female) from 321 families were successfully genotyped using 398 polymorphic microsatellite markers with an average spacing of 9.26 cM on the autosomes. Results of non-parametric multipoint linkage analysis using S(all) statistics (implemented in Merlin) did not reveal any chromosomal region to be significantly associated with T2D in this Sikh cohort. However, linkage analysis for lipid traits using QTL-ALL analysis revealed promising linkage signals with p?0.005 for total cholesterol, LDL cholesterol, and HDL cholesterol at chromosomes 5p15, 9q21, 10p11, 10q21, and 22q13. The most significant signal (p?=?0.0011) occurred at 10q21.2 for HDL cholesterol. We also observed linkage signals for total cholesterol at 22q13.32 (p?=?0.0016) and 5p15.33 (p?=?0.0031) and for LDL cholesterol at 10p11.23 (p?=?0.0045). Interestingly, some of linkage regions identified in this Sikh population coincide with plausible candidate genes reported in recent genome-wide association and meta-analysis studies for lipid traits. Our study provides the first evidence of linkage for loci associated with quantitative lipid traits at four chromosomal regions in this Asian Indian population from Punjab. More detailed examination of these regions with more informative genotyping, sequencing, and functional studies should lead to rapid detection of novel targets of therapeutic importance. PMID:21698157
Sanghera, Dharambir K; Been, Latonya F; Ralhan, Sarju; Wander, Gurpreet S; Mehra, Narinder K; Singh, Jai Rup; Ferrell, Robert E; Kamboh, Mohammed I; Aston, Christopher E
Femoral arterial puncture: comparison of using the inguinal crease and bony landmarks
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We tried to compare the accuracy of using bony landmarks and inguinal crease landmarks for performing femoral artery puncture and to determine an ideal puncture site. We studied ninety consecutive patients who underwent femoral arterial puncture for performing angiogram. For the evaluation of bony landmarks, the pelvis and inguinal areas were divided into 8 zones according to 7 lines that were drawn parallel to the line drawn between the anterior superior iliac spine and the pubic tubercle. For evaluation of the inguinal crease as a landmark, the 8 zones above and 4 zones below the inguinal crease were determined. The zones were divided by 11 lines drawn parallel to the inguinal crease, and the interval between each line was 1 cm. Locations of the inguinal ligament and femoral bifurcation were recorded for every patient according to the above zones, and an ideal zone for the femoral arterial puncture was decided upon. The ideal zone was considered if the locations of all of inguinal ligaments were above the zone and the least possibility to puncture was below the femoral bifurcation. On the bony landmark, the femoral bifurcations were located at zone 3 in 1 patient (1.1%), at zone 4 in 2 patients (2.2%), at zone 5 in 3 patients (3.3%), at zone 6 in 24 patients (26.7%), and at zone 7 in 44 patients (48.9%). Inguinal ligaments were at zone 1 in 2 patient (3.0%), at zone 2 in 34 patients (50.7%), at zone 3 in 25 patients (37.3%), and at zone 4 in 6 patients (8.9%). When the inguinal creases were used as a landmark, the femoral bifurcations were located at zone 4 in 4 patients (4.4%), at zone 3 in 19 patients (21.1%). at zone 2 in 30 patients (33.3%), at zone 1 in 19 patients (21.1%), at zone -1 in 13 patients (14.4%), at zone -2 in 3 patients (3.3%) and at zone -4 in 2 patients (2.2%). Inguinal ligaments were at zone 8 in 7 patients (10.4%), at zone 7 in 11 patients (16.4%), at zone 6 in 19 patients (28.4%), at zone 5 in 20 patients (29.9%), at zone 4 in 7 patients (10.4%), and at zone 3 in 3 patients (4.5%). Therefore, the best zone for femoral arterial puncture was zone 5 with using bony landmarks and zone 2 with using inguinal crease landmarks. In terms of zone 5 on the bony landmark, every locations of inguinal ligaments was above it and 84 patients (93.4%) had their femoral bifurcation below it, excluding the 6 patients who had their femoral bifurcations at zones 3, 4, and 5. Therefore, zone 5 with using the bony landmarks was a good indicator for femoral arterial puncture. In case of zone 2 on the inguinal crease landmark, although every location of the inguinal ligament was above it, 53 patients (58.8%) had their femoral bifurcation above it at zone 4, 3, and 2. So, it was not a good indicator for femoral arterial puncture. Bony landmarks are more accurate indicators for performing femoral arterial puncture than the inguinal crease landmark. Zone 5 on the bony landmark is an ideal location for femoral arterial puncture.
Chung, Hwan Hoon; Ha, Jong Soo; Cha, Sang Hoon; Kim, Baek Hyun; Lee, Kee Yeol; Kim, Taik Kun; Lee, Seung Hwa; Kim, Jung Hyuck; Seol, Hae Seol [Korea University College of Medicine, Seoul (Korea, Republic of)
A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21.
Much of the variation in inherited risk of colorectal cancer (CRC) is probably due to combinations of common low risk variants. We conducted a genome-wide association study of 550,000 tag SNPs in 930 familial colorectal tumor cases and 960 controls. The most strongly associated SNP (P = 1.72 x 10(-7), allelic test) was rs6983267 at 8q24.21. To validate this finding, we genotyped rs6983267 in three additional CRC case-control series (4,361 affected individuals and 3,752 controls; 1,901 affected individuals and 1,079 controls; 1,072 affected individuals and 415 controls) and replicated the association, providing P = 1.27 x 10(-14) (allelic test) overall, with odds ratios (ORs) of 1.27 (95% confidence interval (c.i.): 1.16-1.39) and 1.47 (95% c.i.: 1.34-1.62) for heterozygotes and rare homozygotes, respectively. Analyses based on 1,477 individuals with colorectal adenoma and 2,136 controls suggest that susceptibility to CRC is mediated through development of adenomas (OR = 1.21, 95% c.i.: 1.10-1.34; P = 6.89 x 10(-5)). These data show that common, low-penetrance susceptibility alleles predispose to colorectal neoplasia. PMID:17618284
Tomlinson, Ian; Webb, Emily; Carvajal-Carmona, Luis; Broderick, Peter; Kemp, Zoe; Spain, Sarah; Penegar, Steven; Chandler, Ian; Gorman, Maggie; Wood, Wendy; Barclay, Ella; Lubbe, Steven; Martin, Lynn; Sellick, Gabrielle; Jaeger, Emma; Hubner, Richard; Wild, Ruth; Rowan, Andrew; Fielding, Sarah; Howarth, Kimberley; Silver, Andrew; Atkin, Wendy; Muir, Kenneth; Logan, Richard; Kerr, David; Johnstone, Elaine; Sieber, Oliver; Gray, Richard; Thomas, Huw; Peto, Julian; Cazier, Jean-Baptiste; Houlston, Richard
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
Anatomy-guided discovery of large-scale consistent connectivity-based cortical landmarks.
Establishment of structural and functional correspondences across different brains is one of the most fundamental issues in the human brain mapping field. Recently, several multimodal DTI/fMRI studies have demonstrated that consistent white matter fiber connection patterns can predict brain function and represent common brain architectures across individuals and populations, and along this direction, several approaches have been proposed to discover large-scale cortical landmarks with common structural connection profiles. However, an important limitation of previous approaches is that the rich anatomical information such as gyral/sulcal folding patterns has not been incorporated into the landmark discovery procedure yet. In this paper, we present a novel anatomy-guided discovery framework that defines and optimizes a dense map of cortical landmarks that possess group-wise consistent anatomical and fiber connectional profiles. This framework effectively integrates reliable and rich anatomical, morphological, and fiber connectional information for landmark initialization, optimization and prediction, which are formulated and solved as an energy minimization problem. Validation results based on fMRI data demonstrate that the identified 555 cortical landmarks are producible, predictable and exhibit accurate structural and functional correspondences across individuals and populations, offering a universal and individualized brain reference system for neuroimaging research. PMID:24505813
Jiang, Xi; Zhang, Tuo; Zhu, Dajiang; Li, Kaiming; Lv, Jinglei; Guo, Lei; Liu, Tianming
Simplifying subclavian vein cannulation using innovative landmarks: a radiologic, anatomic, and clinical study.
The objective of this study was to investigate novel and optimal landmarks for subclavian vein (SV) cannulation. We conducted the study in three phases: (a) Various possible markers for SV cannulation were evaluated by anatomic measurements in patients from intensive care unit and the course of SV was evaluated by radiologic means; (b) Results acquired by the two means were compared and adjusted, then innovative landmarks and a new approach for SV cannulation was proposed; (c) The efficacy of new approach for SV cannulation was compared with that of a traditional one by a prospective, randomized, controlled study. Point A (the junction of the lateral border of sternocleidomastoideus clavicular head and inferior border of clavicle), point B (a point on the lower border of clavicle just above the middle of the line joining the coracoid process and midline of the body), and point D (where SV crosses the inferior border of clavicle) were close in proximity. Points A and B could be considered as innovative landmarks for SV cannulation. Beginners using the new method had significantly higher success rate (86.9% vs. 70.2%, p = 0.008); the time consumed by new method was significant shorter than that by traditional one (5.9 vs. 10.4 min, p = 0.001). Points A and B could be considered as landmarks for identifying puncture site for SV cannulation. Beginners using innovative landmarks for SV cannulation could significantly reduce operation time and increase success rate. PMID:22561227
Hu, Bin; Hu, Mei; Wang, Yan; Wang, Dao Wen
An�lise de agrupamento de diferentes densidades de marcadores no mapeamento gen�tico por varredura gen�mica / 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 simula��o tem contribu�do para o avan�o da gen�mica nas diversas �reas do melhoramento gen�tico. Foram simulados mapeamentos gen�ticos utilizando diferentes densidades de marcadores para estimar os valores fenot�picos na sele��o assistida por marcadores (SAM), em caracter�sticas quantitativas com [...] valores de herdabilidade de 0,10; 0,40; e 0,70. Procedeu-se a an�lise de agrupamento com os desempenhos fenot�picos, cuja finalidade foi obter estruturas de classifica��o entre as densidades visando � otimiza��o na detec��o de QTL. O sistema de simula��o gen�tica (Genesys) foi utilizado para tr�s genomas (cada qual constitu�do de uma �nica caracter�stica cuja distin��o estava no valor da herdabilidade) e para as popula��es base e inicial. Cada popula��o inicial foi submetida � sele��o assistida por marcadores por 20 gera��es consecutivas, em que os genitores selecionados acasalavam-se seletivamente entre os melhores e os piores. O mapeamento empregando de m�dia a alta densidade de marcadores assinalou efici�ncia nos progressos fenot�picos obtidos com a SAM. Menores quantidades de marcadores s�o requeridas para manter determinado poder de detec��o de QTL � medida que se eleva a magnitude da herdabilidade. A an�lise de agrupamento indicou otimiza��o e correspond�ncia nos incrementos fenot�picos 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 Dami�o, Cruz; Paulo Roberto, Cecon; Antonio Policarpo Souza, Carneiro.
Landmark matching based retinal image alignment by enforcing sparsity in correspondence matrix.
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
Internal jugular vein cannulation: an ultrasound-guided technique versus a landmark-guided technique
Scientific Electronic Library Online (English)
Full Text Available SciELO Brazil | Language: English Abstract in english OBJECTIVES: To compare the landmark-guided technique versus the ultrasound-guided technique for internal jugular vein cannulation in spontaneously breathing patients. METHODS: A total of 380 patients who required internal jugular vein cannulation were randomly assigned to receive internal jugular ve [...] in cannulation using either the landmark- or ultrasound-guided technique in Bursa, Uludag University Faculty of Medicine, between April and November, 2008. Failed catheter placement, risk of complications from placement, risk of failure on first attempt at placement, number of attempts until successful catheterization, time to successful catheterization and the demographics of each patient were recorded. RESULTS: The overall complication rate was higher in the landmark group than in the ultrasound-guided group (p
Gurkan, Turker; Fatma Nur, Kaya; Alp, Gurbet; Hale, Aksu; Cuneyt, Erdogan; Ahmet, Atlas.
Landmark Detection via Ann for a Web Based Autonomous Mobile Robot: Sunar
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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
Full Text Available ... CT scans can be helpful in detecting some problems in the body. Though it may take up ... your specific condition. �1995-2013, The Patient Education Institute, Inc. www.X-Plain.com rd050105 Last reviewed: ...
... radioactive material (radioisotope) is used to measure the function of the kidneys. ... blood pressure medications. These drugs might affect the test. You may be asked to drink additional fluids before the scan.
Magnetic resonance imaging (MRI) uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from ...
International Nuclear Information System (INIS)
A survey of nine Atlanta area hospitals, each with over 200 beds revealed that in the years 1970 through 1972 most hospitals were performing 10 to 30 bone scans annually. There was a dramatic increase to 100 to 200 bone scans in 1973 and a continued increase to 200 to 500 in 1974. Although the 1975 figures are not yet complete it appears four hospitals will be over 500 and Emory University Hospital will be over 1000 bone scans. The sudden increase in utilization of bone scans in 1973 can be attributed to the introduction of /sup 99m/Tc-polyphosphate in July 1972. Two previous radiopharmaceuticals had been used, Strontium-85 and Fluorine-18. The beta particle radiation dosage from 85Sr was so high that the Atomic Energy Commission would allow its use only in cancer patients or in patients with a strong likelihood of cancer. Another detriment to 85Sr was its slow, colonic excretion necessitating cleansing enemas and a four to five day delay in scanning. Although 18F was excreted quickly via the urinary tract which obviated the enemas and the delay in scanning, it had a high cost and a mere two hour half-life. Since the only source of intravenous 18F was in California, only cities with direct air routes to San Francisco could hope to obtain it. Several times we had to cancel our patients anyway due to ''shipping difficulties.'' We then attempted to obtain non-pyrogen free material from the Georgia Tech Reactor and give the radionuclide orally but this often resulted in a large accumulation of the tracer in the stomach which obscured uptake in the lower thoracic-upper lumbar spine
Pooled association genome scanning for alcohol dependence using 104,268 SNPs: validation and use to identify alcoholism vulnerability loci in unrelated individuals from the collaborative study on the genetics of alcoholism.
Association genome scanning can identify markers for the allelic variants that contribute to vulnerability to complex disorders, including alcohol dependence. To improve the power and feasibility of this approach, we report validation of "100k" microarray-based allelic frequency assessments in pooled DNA samples. We then use this approach with unrelated alcohol-dependent versus control individuals sampled from pedigrees collected by the Collaborative Study on the Genetics of Alcoholism (COGA). Allele frequency differences between alcohol-dependent and control individuals are assessed in quadruplicate at 104,268 autosomal SNPs in pooled samples. One hundred eighty-eight SNPs provide (1) the largest allele frequency differences between dependent versus control individuals; (2) t values >or= 3 for these differences; and (3) clustering, so that 51 relatively small chromosomal regions contain at least three SNPs that satisfy criteria 1 and 2 above (Monte Carlo P = 0.00034). These positive SNP clusters nominate interesting genes whose products are implicated in cellular signaling, gene regulation, development, "cell adhesion," and Mendelian disorders. The results converge with linkage and association results for alcohol and other addictive phenotypes. The data support polygenic contributions to vulnerability to alcohol dependence. These SNPs provide new tools to aid the understanding, prevention, and treatment of alcohol abuse and dependence. PMID:16894614
Johnson, Catherine; Drgon, Tomas; Liu, Qing-Rong; Walther, Donna; Edenberg, Howard; Rice, John; Foroud, Tatiana; Uhl, George R
Automatic recognition of surface landmarks of anatomical structures of back and posture
Faulty postures, scoliosis and sagittal plane deformities should be detected as early as possible to apply preventive and treatment measures against major clinical consequences. To support documentation of the severity of deformity and diminish x-ray exposures, several solutions utilizing analysis of back surface topography data were introduced. A novel approach to automatic recognition and localization of anatomical landmarks of the human back is presented that may provide more repeatable results and speed up the whole procedure. The algorithm was designed as a two-step process involving a statistical model built upon expert knowledge and analysis of three-dimensional back surface shape data. Voronoi diagram is used to connect mean geometric relations, which provide a first approximation of the positions, with surface curvature distribution, which further guides the recognition process and gives final locations of landmarks. Positions obtained using the developed algorithms are validated with respect to accuracy of manual landmark indication by experts. Preliminary validation proved that the landmarks were localized correctly, with accuracy depending mostly on the characteristics of a given structure. It was concluded that recognition should mainly take into account the shape of the back surface, putting as little emphasis on the statistical approximation as possible.
Micho?ski, Jakub; Glinkowski, Wojciech; Witkowski, Marcin; Sitnik, Robert
Shape shifting: Local landmarks interfere with navigation by, and recognition of, global shape.
An influential theory of spatial navigation states that the boundary shape of an environment is preferentially encoded over and above other spatial cues, such that it is impervious to interference from alternative sources of information. We explored this claim with 3 intradimensional-extradimensional shift experiments, designed to examine the interaction of landmark and geometric features of the environment in a virtual navigation task. In Experiments 1 and 2, participants were first required to find a hidden goal using information provided by the shape of the arena or landmarks integrated into the arena boundary (Experiment 1) or within the arena itself (Experiment 2). Participants were then transferred to a different-shaped arena that contained novel landmarks and were again required to find a hidden goal. In both experiments, participants who were navigating on the basis of cues that were from the same dimension that was previously relevant (intradimensional shift) learned to find the goal significantly faster than participants who were navigating on the basis of cues that were from a dimension that was previously irrelevant (extradimensional shift). This suggests that shape information does not hold special status when learning about an environment. Experiment 3 replicated Experiment 2 and also assessed participants' recognition of the global shape of the navigated arenas. Recognition was attenuated when landmarks were relevant to navigation throughout the experiment. The results of these experiments are discussed in terms of associative and non-associative theories of spatial learning. PMID:24245537
Buckley, Matthew G; Smith, Alastair D; Haselgrove, Mark
Application of landmark morphometrics to skulls representing the orders of living mammals
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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
Role of Dentate Gyrus in Aligning Internal Spatial Map to External Landmark
Humans and animals form internal representations of external space based on their own body movement (dead reckoning) as well as external landmarks. It is poorly understood, however, how different types of information are integrated to form a unified representation of external space. To examine the role of dentate gyrus (DG) in this process, we�
Lee, Jong Won; Kim, Woon Ryoung; Sun, Woong; Jung, Min Whan
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
Meta-analysis of genome-wide scans for total body BMD in children and adults reveals allelic heterogeneity and age-specific effects at the WNT16 locus.
To identify genetic loci influencing bone accrual, we performed a genome-wide association scan for total-body bone mineral density (TB-BMD) variation in 2,660 children of different ethnicities. We discovered variants in 7q31.31 associated with BMD measurements, with the lowest P = 4.1 � 10(-11) observed for rs917727 with minor allele frequency of 0.37. We sought replication for all SNPs located � 500 kb from rs917727 in 11,052 additional individuals from five independent studies including children and adults, together with de novo genotyping of rs3801387 (in perfect linkage disequilibrium (LD) with rs917727) in 1,014 mothers of children from the discovery cohort. The top signal mapping in the surroundings of WNT16 was replicated across studies with a meta-analysis P = 2.6 � 10(-31) and an effect size explaining between 0.6%-1.8% of TB-BMD variance. Conditional analyses on this signal revealed a secondary signal for total body BMD (P = 1.42 � 10(-10)) for rs4609139 and mapping to C7orf58. We also examined the genomic region for association with skull BMD to test if the associations were independent of skeletal loading. We identified two signals influencing skull BMD variation, including rs917727 (P = 1.9 � 10(-16)) and rs7801723 (P = 8.9 � 10(-28)), also mapping to C7orf58 (r(2) = 0.50 with rs4609139). Wnt16 knockout (KO) mice with reduced total body BMD and gene expression profiles in human bone biopsies support a role of C7orf58 and WNT16 on the BMD phenotypes observed at the human population level. In summary, we detected two independent signals influencing total body and skull BMD variation in children and adults, thus demonstrating the presence of allelic heterogeneity at the WNT16 locus. One of the skull BMD signals mapping to C7orf58 is mostly driven by children, suggesting temporal determination on peak bone mass acquisition. Our life-course approach postulates that these genetic effects influencing peak bone mass accrual may impact the risk of osteoporosis later in life. PMID:22792070
Medina-Gomez, Carolina; Kemp, John P; Estrada, Karol; Eriksson, Joel; Liu, Jeff; Reppe, Sjur; Evans, David M; Heppe, Denise H M; Vandenput, Liesbeth; Herrera, Lizbeth; Ring, Susan M; Kruithof, Claudia J; Timpson, Nicholas J; Zillikens, M Carola; Olstad, Ole K; Zheng, Hou-Feng; Richards, J Brent; St Pourcain, Beate; Hofman, Albert; Jaddoe, Vincent W V; Smith, George Davey; Lorentzon, Mattias; Gautvik, Kaare M; Uitterlinden, Andr� G; Brommage, Robert; Ohlsson, Claes; Tobias, Jonathan H; Rivadeneira, Fernando
Genome scanning for linkage: An overview
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Several different methods for linkage analysis are shown to arise from a single likelihood function L for the observed allele-sharing data at multiple markers in a chromosomal region. These include classical parametric lod-score methods, nonparametric or {open_quotes}model-free{close_quotes} affected-pedigree-member (APM) methods, and the Gaussian process method. Setting the methods in the context of the likelihood function L clarifies their underlying assumptions. A test statistic derived from L, the efficient score statistic, is introduced. It is asymptotically equivalent to the lod score, but it can be easier to compute when the penetrances and frequencies of alleles of the trait gene are not known. APM test statistics and the Gaussian lod score are shown to be special cases of efficient score statistics. This unified framework facilitates exploration of a range of models for the effects of a putative trait-predisposing gene, and it facilitates sensitivity analyses to examine the consequences of model misspecification. 25 refs., 1 fig., 3 tabs.
Whittemore, A.S. [Stanford Univ. School of Medicine, CA (United States)
Evaluation of soft tissue thicknesses of facial midline landmarks before and after puberty
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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
International Nuclear Information System (INIS)
This Atlas comes from a collection of 200 slides distributed by the ACOMEN. After covering the essentials of normal and pathological bone histology and physiology, the principles and technique of bone scans and normal aspects are presented. Comprehensive chapters of images illustrating the contribution of Nuclear medicine to osteoarticular pathology follow. At the end, a large section is devoted to pitfalls and artifacts. Even though this volume may be incomplete, it merits its existence; it constitutes a reference that everyone of us will be able to ase to improve his experience
Proper name retrieval in temporal lobe epilepsy: naming of famous faces and landmarks.
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
Reliability of Bony Anatomic Landmark Asymmetry Assessment in the Lumbopelvic Region: Application to Osteopathic Medical Education
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The objective of this review is to establish the current state of knowledge on the reliability of clinical assessment of asymmetry in the lumbar spine and pelvis. To search the literature, the authors consulted the databases of MEDLINE, CINAHL, AMED, MANTIS, Academic Search Complete, and Web of Knowledge using different combinations of the following keywords: palpation, asymmetry, inter- or intraex-aminer reliability, tissue texture, assessment, and anatomic landmark. Of the 23 studies identi...
A framework for automated landmark recognition in community contributed image corpora
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Any large library of information requires efficient ways to organise it and methods that allow people to access information efficiently and collections of digital images are no exception. Automatically creating high-level semantic tags based on image content is difficult, if not impossible to achieve accurately. In this thesis a framework is presented that allows for the automatic creation of rich and accurate tags for images with landmarks as the main object. This framework uses state of the...
Hughes, Mark
Knee joint secondary motion accuracy improved by quaternion-based optimizer with bony landmark constraints.
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
Opacification of tympanic membrane: As an anatomic landmark of oto-radiology
Energy Technology Data Exchange (ETDEWEB)
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.
Park, Jae Hyung [Seoul National University College of Medicine, Seoul (Korea, Republic of)
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.
The eminent German pathologist Siegfried Oberndorfer (1876-1944 and his landmark work on carcinoid tumors
Directory of Open Access Journals (Sweden)
Full Text Available
Siegfried Oberndorfer has a distinct place in the Pantheon of pathology as a century ago he described a new neoplastic entity in small bowel and coined first the term �carcinoid�. His research stands as a classical landmark in the understanding of carcinoid tumors.
Keywords Siegfried Oberndorfer, carcinoid tumors, small intestine
Ann Gastroenterol 2011; 24 (2: 98-100
Gregory Tsoucalas
AttentiRobot: A Visual Attention-based Landmark Selection Approach for Mobile Robot Navigation
Digital Repository Infrastructure Vision for European Research (DRIVER)
Visual attention refers to the ability of a vision system to rapidly detect visually salient locations in a given scene. On the other hand, the selection of robust visual landmarks of an environment represents a cornerstone of reliable vision-based robot navigation systems. Indeed, can salient scene locations provided by visual attention be useful for robot navigation ? This work investigates the potential and effectiveness of the visual attention mechanism to provide pre-attentive scene info...
Ouerhani, Nabil; Hu?gli, Heinz; Gruener, G.; Codourey, A.
A Visual Attention-Based Approach for Automatic Landmark Selection and Recognition
Digital Repository Infrastructure Vision for European Research (DRIVER)
Visual attention refers to the ability of a vision system to rapidly detect visually salient locations in a given scene. On the other hand, the selection of robust visual landmarks of an environment represents a cornerstone of reliable vision-based robot navigation systems. Indeed, can salient scene locations provided by visual attention be useful for robot navigation? This work investigates the potential and effectiveness of the visual attention mechanism to provide pre-attentive scene infor...
Ouerhani, Nabil; Hu?gli, Heinz; Gruener, G.; Codourey, A.
Information Geometry for Landmark Shape Analysis: Unifying Shape Representation and Deformation
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Shape matching plays a prominent role in the comparison of similar structures. We present a unifying framework for shape matching that uses mixture models to couple both the shape representation and deformation. The theoretical foundation is drawn from information geometry wherein information matrices are used to establish intrinsic distances between parametric densities. When a parameterized probability density function is used to represent a landmark-based shape, the modes of deformation ar...
Peter, Adrian M.; Rangarajan, Anand
Comparison of landmark-based and automatic methods for cortical surface registration
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Group analysis of structure or function in cerebral cortex typically involves as a first step the alignment of the cortices. A surface based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed ...
Pantazis, Dimitrios; Joshi, Anand; Jiang, Jintao; Shattuck, David; Bernstein, Lynne E.; Damasio, Hanna; Leahy, Richard M.
Anatomical Landmarks for Safe Elevation of the Deep Inferior Epigastric Perforator Flap: A Cadaveric Study
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Background: Breast reconstruction techniques have focused increasingly on using autologous tissue, with emphasis being placed on employing muscle sparing adipocutaneous flaps to reduce abdominal wall complications such as hernias, bulges, weakness, and length of hospital stay. The result has been the emergence of the deep inferior epigastric perforator (DIEP) flap for breast reconstruction. Isolating perforator vessels challenges most surgeons. We describe surface anatomical landmarks to pred...
Chowdhry, Saeed; Hazani, Ron; Collis, Philip; Wilhelmi, Bradon J.
The effect of providing a USB syllabus on resident reading of landmark articles
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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...
Mayy Chahla; Michael Eberlein; Scott Wright
Describing Wing Geometry of Aedes Aegypti Using Landmark-Based Geometric Morphometrics
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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
MR-guided stereotactic neurosurgery-comparison of fiducial-based and anatomical landmark transformation approaches
Energy Technology Data Exchange (ETDEWEB)
For application in magnetic resonance (MR) guided stereotactic neurosurgery, two methods for transformation of MR-image coordinates in stereotactic, frame-based coordinates exist: the direct stereotactic fiducial-based transformation method and the indirect anatomical landmark method. In contrast to direct stereotactic MR transformation, indirect transformation is based on anatomical landmark coregistration of stereotactic computerized tomography and non-stereotactic MR images. In a patient study, both transformation methods have been investigated with visual inspection and mutual information analysis. Comparison was done for our standard imaging protocol, including t2-weighted spin-echo as well as contrast enhanced t1-weighted gradient-echo imaging. For t2-weighted spin-echo imaging, both methods showed almost similar and satisfying performance with a small, but significant advantage for fiducial-based transformation. In contrast, for t1-weighted gradient-echo imaging with more geometric distortions due to field inhomogenities and gradient nonlinearity than t2-weighted spin-echo imaging, mainly caused by a reduced bandwidth per pixel, anatomical landmark transformation delivered markedly better results. Here, fiducial-based transformation yielded results which are intolerable for stereotactic neurosurgery. Mean Euclidian distances between both transformation methods were 0.96 mm for t2-weighted spin-echo and 1.67 mm for t1-weighted gradient-echo imaging. Maximum deviations were 1.72 mm and 3.06 mm, respectively.
Hunsche, S [Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne (Germany); Sauner, D [Institute for Diagnostic and Interventional Radiology, Friedrich-Schiller-University of Jena, Jena (Germany); Maarouf, M [Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne (Germany); Hoevels, M [Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne (Germany); Luyken, K [Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne (Germany); Schulte, O [Department of Radiology, University of Cologne, Cologne (Germany); Lackner, K [Department of Radiology, University of Cologne, Cologne (Germany); Sturm, V [Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne (Germany); Treuer, H [Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne (Germany)
Precise visual navigation using multi-stereo vision and landmark matching
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
A new automatic landmark extraction framework on ultrasound images of femoral condyles
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, Agn�s; Nakib, Amir; Petit, Eric; Leitner, Fran�ois
Endoscopic Orientation of the Parasellar Region in Sphenoid Sinus with Ill-Defined Bony Landmarks: An Anatomic Study
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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 lengt...
Delivering high-resolution landmarks using inkjet micropatterning for spatial monitoring of leaf expansion
Directory of Open Access Journals (Sweden)
Full Text Available Abstract Background Inkjet micropatterning is a versatile deposition technique with broad applications in numerous fields. However, its application in plant science is largely unexplored. Leaf expansion is one of the most important parameters in the field of plant science and many methods have been developed to examine differential expansion rates of different parts of the leaf lamina. Among them, methods based on the tracking of natural landmarks through digital imaging require a complicated setup in which the leaf must remain fixed and under tension. Furthermore, the resolution is limited to that of the natural landmarks, which are often difficult to find, particularly in young leaves. To study the fine scale expansion dynamics of the leaf lamina using artificial landmarks it is necessary to place small, noninvasive marks on a leaf surface and then recover the location of those marks after a period of time. Results To monitor leaf expansion in two dimensions, at very fine scales, we used a custom designed inkjet micropatterning system to print a grid composed of c. 0.19 mm2 cells on small developing leaves of ivy (Hedera helix using 40 ?m dots at a spacing of c. 91 ?m. The leaves in different growing stages were imaged under magnification to extract the coordinates of the marks which were then used in subsequent computer-assisted leaf expansion analyses. As an example we obtained quantified global and local expansion information and created expansion maps over the entire leaf surface. The results reveal a striking pattern of fine-scale expansion differences over short periods of time. In these experiments, the base of the leaf is a "cold spot" for expansion, while the leaf sinuses are "hot spots" for expansion. We have also measured a strong shading effect on leaf expansion. We discuss the features required to build an inkjet printing apparatus optimized for use in plant science, which will further maximize the range of tissues that can be printed at these scales. Conclusions To apply inkjet micropatterning to plant studies, we have successfully delivered landmarks on ivy leaf surfaces and achieved high-resolution, two-dimensional monitoring of leaf expansion at different growing stages. The measurement is capable of reliably identifying the fine scale changes during plant growth. As well as delivering landmarks, this technology may be used to deliver microscale targeted biological components such as growth hormones, and possibly be used to pattern sensors directly on the leaves.
Cronk Quentin CB
Insect navigation en route to the goal: multiple strategies for the use of landmarks
There are at least four distinct ways in which familiar landmarks aid an insect on its trips between nest and foraging site. Recognising scenes: when bees are displaced unexpectedly from their hive to one of several familiar locations, they are able to head in the direction of home as though they had previously linked an appropriate directional vector to a view of the scene at the release site. Biased detours: ants recognise familiar landmarks en route and will correct their path by steering consistently to the left or to the right around them. Aiming at beacons: bees and ants also guide their path by approaching familiar landmarks lying on or close to the direct line between start and finish. Simulations suggest that such mechanisms acting together may suffice to account for the routes taken by desert ants through a landmark-strewn environment: the stereotyped trajectories of individual ants can be modelled by a weighted combination of dead reckoning, biased detours and beacon-aiming. These mechanisms guide an insect sufficiently close to an inconspicuous goal for image matching to be successfully employed to locate it. Insects then move until their current retinal image matches a stored view of the surrounding panorama seen from a vantage point close to the goal. Bees and wasps perform learning flights on their first departure from a site to which they will return. These flights seem to be designed to pick up the information needed for several navigational strategies. Thus, a large portion of the learning flight of a bee leaving a feeder tends to be spent close to the feeder so aiding the acquisition of a view from that vantage point, as is needed for image matching. Bees and social wasps also tend to inspect their surroundings while facing along preferred directions and to adopt similar bearings before landing, thereby making it easy to employ retinotopically stored patterns in image matching. Aiming at beacons, in contrast, requires a landmark to be familiar to the frontal retina. Objects tend to be viewed frontally while the insect circles through arcs centred on the goal. This procedure may help insects to pick out those objects close to the goal that are best suited for guiding later returns. PMID:9317693
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.
Germ�n, Robledo; Guillermo, Seijo.
Characterization of the Arachis (Leguminosae D genome using fluorescence in situ hybridization (FISH chromosome markers and total genome DNA hybridization
Directory of Open Access Journals (Sweden)
Full Text Available Chromosome markers were developed for Arachis glandulifera using fluorescence in situ hybridization (FISH of the 5S and 45S rRNA genes and heterochromatic 4'-6-diamidino-2-phenylindole (DAPI positive bands. We used chromosome landmarks identified by these markers to construct the first Arachis species ideogram in which all the homologous chromosomes were precisely identified. The comparison of this ideogram with those published for other Arachis species revealed very poor homeologies with all A and B genome taxa, supporting the special genome constitution (D genome of A. glandulifera. Genomic affinities were further investigated by dot blot hybridization of biotinylated A. glandulifera total DNA to DNA from several Arachis species, the results indicating that the D genome is positioned between the A and B genomes.
Germ�n Robledo
Are There Rearrangement Hotspots in the Human Genome?
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In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced the fragile breakage model (FBM), pos...
Alekseyev, Max A.; Pevzner, Pavel A.
RNIE: genome-wide prediction of bacterial intrinsic terminators
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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
Automated positioning of scan planes and navigator tracker locations in MRI liver scanning
International Nuclear Information System (INIS)
This report presents a new method for automatic scan prescription planning of both the scan planes and Navigator Tracker locations in MRI liver scanning. A 3D dataset acquired using a fast T1 sequence is preprocessed and converted to 2D projection images to avoid the need for complicated and time-consuming 3D segmentation. A 2D active shape model (ASM) is applied to the 2D coronal projection data, and the external shape of the liver dataset is initially extracted based on a rough estimate of the inferior edge of the liver from the 2D projection dataset. The scan plane locations are determined from the inferior and superior edges of the shape model. Navigator Tracker, which is used for motion-compensated MR abdominal MR scanning, establishes the location by selecting one of the landmarks in the ASM. Datasets obtained from 38 volunteers were tested. Good results were obtained, suggesting that this method may prove to be useful for clinical diagnosis. (author)
International Nuclear Information System (INIS)
In the post-genomic era, many new approaches to clarify the function of genome sequencing results are emerging, and the structural genomics, a genomic based structural studies on biological macromolecules, proteins, is one of the major fields. The international structural genomics organization (ISGO) is now under constructing based on Airlie agreement of April 2001 in Virginia. (author)
CAT scan - arm; Computed axial tomography scan - arm; Computed tomography scan - arm; CT scan - arm ... together. You must be still during the exam. Movement can cause blurred images. You may be told ...
CAT scan - sinus; Computed axial tomography scan - sinus; Computed tomography scan - sinus; CT scan - sinus ... polyps The cause of repeated bloody noses ( epistaxis ) Sinus infection or sinusitis or a sinus infection This ...
Multifeature landmark-free active appearance models: application to prostate MRI segmentation.
Active shape models (ASMs) and active appearance models (AAMs) are popular approaches for medical image segmentation that use shape information to drive the segmentation process. Both approaches rely on image derived landmarks (specified either manually or automatically) to define the object's shape, which require accurate triangulation and alignment. An alternative approach to modeling shape is the levelset representation, defined as a set of signed distances to the object's surface. In addition, using multiple image derived attributes (IDAs) such as gradient information has previously shown to offer improved segmentation results when applied to ASMs, yet little work has been done exploring IDAs in the context of AAMs. In this work, we present a novel AAM methodology that utilizes the levelset implementation to overcome the issues relating to specifying landmarks, and locates the object of interest in a new image using a registration based scheme. Additionally, the framework allows for incorporation of multiple IDAs. Our multifeature landmark-free AAM (MFLAAM) utilizes an efficient, intuitive, and accurate algorithm for identifying those IDAs that will offer the most accurate segmentations. In this paper, we evaluate our MFLAAM scheme for the problem of prostate segmentation from T2-w MRI volumes. On a cohort of 108 studies, the levelset MFLAAM yielded a mean Dice accuracy of 88% � 5%, and a mean surface error of 1.5 mm �.8 mm with a segmentation time of 150/s per volume. In comparison, a state of the art AAM yielded mean Dice and surface error values of 86% � 9% and 1.6 mm � 1.0 mm, respectively. The differences with respect to our levelset-based MFLAAM model are statistically significant . In addition, our results were in most cases superior to several recent state of the art prostate MRI segmentation methods. PMID:22665505
Toth, Robert; Madabhushi, Anant
Anatomical landmarks for safe elevation of the deep inferior epigastric perforator flap: a cadaveric study.
Background: Breast reconstruction techniques have focused increasingly on using autologous tissue, with emphasis being placed on employing muscle sparing adipocutaneous flaps to reduce abdominal wall complications such as hernias, bulges, weakness, and length of hospital stay. The result has been the emergence of the deep inferior epigastric perforator (DIEP) flap for breast reconstruction. Isolating perforator vessels challenges most surgeons. We describe surface anatomical landmarks to predict the location of the deep inferior epigastric artery (DIEA) and its perforators to aid in the efficient elevation of this flap. Methods: Ten fresh hemi-abdomens were dissected with loupe magnification. The DIEA and its perforators were identified, and measurements in relation to the rectus muscle, xiphoid, umbilicus, and pubis were taken. Statistical analysis was undertaken to determine distance ratios to account for variance in patient size. Results: Average distance from the xiphoid to umbilicus was 18.2 +/- 1.27 cm. The distance from the umbilicus to pubis was 14.9 +/- 2.3 cm. The vertical distance from the umbilicus to the DRJ (DIEA rtctus junction) was 10.45 +/- 1.58 cm, and the vertical distance from the level of the umbilicus to where the first DIEA perforator traverses the RAM was 7.4 +/- 1.64 cm. The distance between the umbilicus and the DRJ is approximately 0.7 times the distance between the umbilicus and the pubic symphysis. The distance between the umbilicus and the first perforator is approximately 0.5 times the distance between the umbilicus and the pubic symphysis. Conclusions: Knowledge of anatomical landmarks can aid the surgeon in more efficiently harvesting the DIEP flap. Surface landmarks along the abdominal midline coupled with normalizing ratios can aid surgeons in predicting the location of the DIEA and its first perforator. The DIEA crosses the rectus at approximately two thirds of the distance between the umbilicus and pubis, and the first perforator can reliably be located at one half of this distance. PMID:20523907
Chowdhry, Saeed; Hazani, Ron; Collis, Philip; Wilhelmi, Bradon J
A New 2D Corner Detector for Extracting Landmarks from Brain MR Images
Digital Repository Infrastructure Vision for European Research (DRIVER)
Point-based registration of images strongly depends on the extraction of suitable landmarks. Recently, various 2D operators have been proposed for the detection of corner points but most of them are not effective for medical images that need a high accuracy. In this paper we have proposed a new automatic corner detector based on the covariance between the small region of support around a central pixel and its rotated one. The main goal of this paper is medical images so we especially focus on...
Mohammadi, Gelareh; Fatemizadeh, Emad
A Robot Indoor Position and Orientation Method based on 2D Barcode Landmark
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A method for robot indoor automatic positioning and orientating based on two-dimensional (2D) barcode landmark is proposed.
Guoyu Lin; Xu Chen 2011-01-01
Guoyu Lin; Xu Chen
A Bony Landmark �RAI Triangle� to Prevent �Misplaced and Misdirected� Medial Cut in SSRO
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�Rai triangle�, a new anatomic landmark on the medial surface of the ramus of the mandible which when identified and taken into consideration, may have a definite advantage. This is especially in terms of performing the medial horizontal cut which is an important and integral part of the sagittal split ramus osteotomy so as to avoid a bad split. The objective of this article is to propose an easily identifiable bony land mark, which is closely related to lingula of mandible that may ease ...
Undecidability and temporal logic: some landmarks from Turing to the present
DEFF Research Database (Denmark)
This is a selective survey and discussion of some of the landmark undecidability results in temporal logic, beginning with Turing's undecidability of the Halting problem which, in retrospect, can be regarded as the historically first undecidability result for a suitable temporal logic over configuration graphs of Turing machines. I will discuss some of the natural habitats of undecidable temporal logics, such as first-order, interval-based and real time temporal logics, as well as some extensions that often lead to undecidability, such as two-dimensional temporal logics and temporal-epistemic logics.
Goranko, Valentin
Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape
Directory of Open Access Journals (Sweden)
Full Text Available Abstract Background Universally accepted landmark stages are necessary to highlight key events in plant reproductive development and to facilitate comparisons among species. Domestication and selection of tomato resulted in many varieties that differ in fruit shape and size. This diversity is useful to unravel underlying molecular and developmental mechanisms that control organ morphology and patterning. The tomato fruit shape gene SUN controls fruit elongation. The most dramatic effect of SUN on fruit shape occurs after pollination and fertilization although a detailed investigation into the timing of the fruit shape change as well as gene expression profiles during critical developmental stages has not been conducted. Results We provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new floral and fruit landmarks to present a framework for tomato developmental studies. In addition, gene expression profiles of three key stages in floral and fruit development are presented, namely floral buds 10 days before anthesis (floral landmark 7, anthesis-stage flowers (floral landmark 10 and fruit landmark 1, and 5 days post anthesis fruit (fruit landmark 3. To demonstrate the utility of the landmarks, we characterize the tomato shape gene SUN in fruit development. SUN controls fruit shape predominantly after fertilization and its effect reaches a maximum at 8 days post-anthesis coinciding with fruit landmark 4 representing the globular embryo stage of seed development. The expression profiles of the NILs that differ at sun show that only 34 genes were differentially expressed and most of them at a less than 2-fold difference. Conclusion The landmarks for flower and fruit development in tomato were outlined and integrated with the effect of SUN on fruit shape. Although we did not identify many genes differentially expressed in the NILs that differ at the sun locus, higher or lower transcript levels for many genes involved in phytohormone biosynthesis or signaling as well as organ identity and patterning of tomato fruit were found between developmental time points.
Li Dongmei
Structured light scanning to evaluate three-dimensional anthropometry in HIV facial lipoatrophy
Digital Repository Infrastructure Vision for European Research (DRIVER)
The psychological and social impact of the lipodystrophy syndrome on HIV-infected individuals may be quite considerable and adversely affect their quality of life. Currently no validated assessment tool for facial lipoatrophy is available. The main objective of this paper is to evaluate the reliability of interactive anthropometric landmark localization based on digitized 3D facial images. By comparing both computed tomography (CT) and structured light scanning we try to demonstrate that surf...
Purificaci�n Gacto-S�nchez; Fernando Lobo-Bail�n; Cristina Su�rez; Tom�s G�mez- C�a
Automatic X-ray landmark detection and shape segmentation via data-driven joint estimation of image displacements.
In this paper, we propose a new method for fully-automatic landmark detection and shape segmentation in X-ray images. To detect landmarks, we estimate the displacements from some randomly sampled image patches to the (unknown) landmark positions, and then we integrate these predictions via a voting scheme. Our key contribution is a new algorithm for estimating these displacements. Different from other methods where each image patch independently predicts its displacement, we jointly estimate the displacements from all patches together in a data driven way, by considering not only the training data but also geometric constraints on the test image. The displacements estimation is formulated as a convex optimization problem that can be solved efficiently. Finally, we use the sparse shape composition model as the a priori information to regularize the landmark positions and thus generate the segmented shape contour. We validate our method on X-ray image datasets of three different anatomical structures: complete femur, proximal femur and pelvis. Experiments show that our method is accurate and robust in landmark detection, and, combined with the shape model, gives a better or comparable performance in shape segmentation compared to state-of-the art methods. Finally, a preliminary study using CT data shows the extensibility of our method to 3D data. PMID:24561486
Chen, C; Xie, W; Franke, J; Grutzner, P A; Nolte, L-P; Zheng, G
Extracci�n de puntos caracter�sticos del rostro para medidas antropom�tricas Face landmarks extraction for anthropometric measures
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Full Text Available En este documento se propone una t�cnica para la extracci�n de 22 puntos caracter�sticos del rostro, orientada a aplicaciones de antropometr�a. La t�cnica se fundamenta en la transformada wavelets-Gabor y el uso del algoritmo EBGM (del t�rmino en ingl�s: Elastic Bunch Graph Matching. Este �ltimo algoritmo fue modificado para que los puntos extra�dos correspondan a puntos caracter�sticos del rostro, los cuales se utilizan com�nmente en medidas antropom�tricas faciales. Las modificaciones consisten en un conjunto de restricciones geom�tricas para ajustar inicialmente la ubicaci�n de los centros de b�squeda, y posteriormente para la definici�n de la regi�n de esta b�squeda. Los resultados mostraron que los puntos centrales del rostro presentan errores de ubicaci�n inferiores al mil�metro, lo cual es consistente con las medidas en antropometr�a 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 Gonz�lez
A Sensor Network Data Compression Algorithm Based on Suboptimal Clustering and Virtual Landmark Routing Within Clusters
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Full Text Available A kind of data compression algorithm for sensor networks based on suboptimal clustering and virtual landmark routing within clusters is proposed in this paper. Firstly, temporal redundancy existing in data obtained by the same node in sequential instants can be eliminated. Then sensor networks nodes will be clustered. Virtual node landmarks in clusters can be established based on cluster heads. Routing in clusters can be realized by combining a greedy algorithm and a flooding algorithm. Thirdly, a global structure tree based on cluster heads will be established. During the course of data transmissions from nodes to cluster heads and from cluster heads to sink, the spatial redundancy existing in the data will be eliminated. Only part of the raw data needs to be transmitted from nodes to sink, and all raw data can be recovered in the sink based on a compression code and part of the raw data. Consequently, node energy can be saved, largely because transmission of redundant data can be avoided. As a result the overall performance of the sensor network can obviously be improved.
Shengqiang Li
Extracci�n de puntos caracter�sticos del rostro para medidas antropom�tricas / Face landmarks extraction for anthropometric measures
Scientific Electronic Library Online (English)
Full Text Available SciELO Colombia | Language: Spanish Abstract in spanish En este documento se propone una t�cnica para la extracci�n de 22 puntos caracter�sticos del rostro, orientada a aplicaciones de antropometr�a. La t�cnica se fundamenta en la transformada wavelets-Gabor y el uso del algoritmo EBGM (del t�rmino en ingl�s: Elastic Bunch Graph Matching). Este �ltimo al [...] goritmo fue modificado para que los puntos extra�dos correspondan a puntos caracter�sticos del rostro, los cuales se utilizan com�nmente en medidas antropom�tricas faciales. Las modificaciones consisten en un conjunto de restricciones geom�tricas para ajustar inicialmente la ubicaci�n de los centros de b�squeda, y posteriormente para la definici�n de la regi�n de esta b�squeda. Los resultados mostraron que los puntos centrales del rostro presentan errores de ubicaci�n inferiores al mil�metro, lo cual es consistente con las medidas en antropometr�a facial directa. Abstract in english In this research, a technique for the extraction of a 22 face landmarks set oriented to anthropometry applications has been proposed. The technique is based on wavelets Gabor transformation and the Elastic Bunch Graph Matching (EBGM) algorithm. The EBGM algorithm was modified so that the extracted p [...] oints correspond to face landmarks which are commonly used in face anthropometric measures. Modifications were: some geometric restrictions to initially fit the centers location of the region search, and later for the definition of the region. Results show that the face central points present location errors smaller than a millimeter, which is consistent with the measures in direct face anthropometry.
Alejandro, Gonz�lez; Flavio, Prieto.
Rats with lesions of the vestibular system require a visual landmark for spatial navigation.
The role of the vestibular system in acquisition and performance of a spatial navigation task was examined in rats. Male Long-Evans rats received sham or bilateral sodium arsanilate-induced vestibular lesions. After postoperative recovery, under partial water-deprivation, rats were trained (16 trials/day) to find a water reward in one corner of a black square enclosure. A cue card fixed to one wall of the enclosure served as a stable landmark cue. The orientation of the rat at the start of each trial was pseudo-randomized such that the task could not be solved by an egocentric response strategy. Rats with vestibular lesions acquired the task in fewer trials than the sham treated control rats. Vestibular lesions did not influence the motivation or motor function necessary to perform the task. Performance of sham rats was maintained during probe trials in which the cue card was removed from the enclosure, while lesioned rats were markedly impaired. Rotation of the cue card (+/-90 degrees ) caused an equivalent shift in corner choice behavior of the lesioned rats. However, sham rats often disregarded the rotated cue card and made place responses. These results suggest that the vestibular lesions disrupt idiothetic navigation or path integration and render navigational behavior critically dependent upon external landmarks. These results are consistent with the navigational abilities of humans with bilateral vestibular dysfunction. PMID:11755687
Stackman, Robert W; Herbert, Aaron M
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
Interactions between idiothetic cues and external landmarks in the control of place cells and head direction cells.
Two types of neurons in the rat brain have been proposed to participate in spatial learning and navigation: place cells, which fire selectively in specific locations of an environment and which may constitute key elements of cognitive maps, and head direction cells, which fire selectively when the rat's head is pointed in a specific direction and which may serve as an internal compass to orient the cognitive map. The spatially and directionally selective properties of these cells arise from a complex interaction between input from external landmarks and from idiothetic cues; however, the exact nature of this interaction is poorly understood. To address this issue, directional information from visual landmarks was placed in direct conflict with directional information from idiothetic cues. When the mismatch between the two sources of information was small (45 degrees), the visual landmarks had robust control over the firing properties of place cells; when the mismatch was larger, however, the firing fields of the place cells were altered radically, and the hippocampus formed a new representation of the environment. Similarly, the visual cues had control over the firing properties of head direction cells when the mismatch was small (45 degrees), but the idiothetic input usually predominated over the visual landmarks when the mismatch was larger. Under some conditions, when the visual landmarks predominated after a large mismatch, there was always a delay before the visual cues exerted their control over head direction cells. These results support recent models proposing that prewired intrinsic connections enable idiothetic cues to serve as the primary drive on place cells and head direction cells, whereas modifiable extrinsic connections mediate a learned, secondary influence of visual landmarks. PMID:9658061
Knierim, J J; Kudrimoti, H S; McNaughton, B L
Reliability of Determination of Bony Landmarks of the Distal Femur on MR Images and MRI-Based 3D Models
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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 he...
... from the NHLBI on Twitter. What Is a Nuclear Heart Scan? A nuclear heart scan is a test that provides important ... use it to create pictures of your heart. Nuclear heart scans are used for three main purposes: ...
An RBC nuclear scan uses small amounts of radioactive material to mark (tag) red blood cells (RBCs). Your body is then ... radiation -- it does not give off radiation. Most nuclear scans (including an RBC scan) are not recommended ...
CAT scan - lumbar spine; Computed axial tomography scan - lumbar spine; Computed tomography scan - lumbar spine; CT - lower back ... stopping.) A computer creates separate images of the spine area, called slices. These images can be stored, ...
Influence of landmark and surgical variability on virtual assessment of total knee arthroplasty.
Given advances in recent years in imaging modalities and computational hardware/software, virtual analyses are increasingly valuable and practical for evaluating total knee arthroplasty (TKA). However, the influence of variabilities at each step in computational analyses on predictions of TKA performance for a population has not yet been thoroughly investigated, nor the relationship between these variabilities and expected variations in surgical practice. Understanding these influences is nevertheless essential for ensuring the clinical relevance of theoretical predictions. Here, a morphological analysis of proximal tibial resections within TKA is proposed and investigated. The goals of this analysis are to quantify the influence of variability in landmark detection on resection parameters and to evaluate this sensitivity relative to expected clinical variability in TKA resections. Results here are directly applicable to population-level computational analyses of morphological and functional TKA performance. PMID:23216047
Dai, Y; Seebeck, J; Henderson, A D; Bischoff, J E
Maximized Posteriori Attributes Selection from Facial Salient Landmarks for Face Recognition
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
Maximized Posteriori Attributes Selection from Facial Salient Landmarks for Face Recognition
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
Bony landmarks of the medial orbital wall: an anatomical study of ethmoidal foramina.
The study determines the distribution patterns of ethmoidal foramina (EF) evaluate how they are affected by gender or bilateral asymmetry, and highlights the surgical implications on the anatomical landmarks of the orbit. Two hundred and forty-nine dry orbits were assessed. The number and pattern of EF were determined and distances between the anterior lacrimal crest (ALC), anterior (AEF) middle (MEF), posterior (PEF) ethmoidal foramina and between PEF and the optic canal (OC) were measured. The patterns of EF were classified as type I (single foramen) in 4 orbits (1.6%), type II (double foramina) in 152 (61%), type III (triple foramina) in 71 (28.5%), and type IV (multiple foramina) in 22 orbits (16.4%). Two orbits were found with five EF and a single orbit with six EF. A significant gender difference was observed for ALC-AEF distance (P???0.03), in males 23.53?�?2.86 (20.67-26.39) versus females 22.51?�?3.72 (18.79-26.23) mm. Bilateral asymmetry was observed for ALC-AEF distance (P???0.01). The distances ALC-AEF and ALC-PEF varied significantly according to EF classification (P???0.03 and P???0.02). The navigation ratio from ALC-AEF, AEF-PEF, and PEF-OC, in Greek population was "23-10-4 mm". A variation in the number of EF was found, ranging from 1 to 6, with the first report of sextuple EF. Although measures were generally consistent across genders and side, there are significant differences across ethnicities. These findings suggest that surgeons must consider population differences in determining the anatomical landmarks and navigation points of the orbit. PMID:24000039
Piagkou, Maria; Skotsimara, Georgia; Dalaka, Aspasia; Kanioura, Eftychia; Korentzelou, Vasiliki; Skotsimara, Antonia; Piagkos, Giannoulis; Johnson, Elizabeth O
Germ band retraction as a landmark in glucose metabolism during Aedes aegypti embryogenesis
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Full Text Available Abstract Background The mosquito A. aegypti is vector of dengue and other viruses. New methods of vector control are needed and can be achieved by a better understanding of the life cycle of this insect. Embryogenesis is a part of A. aegypty life cycle that is poorly understood. In insects in general and in mosquitoes in particular energetic metabolism is well studied during oogenesis, when the oocyte exhibits fast growth, accumulating carbohydrates, lipids and proteins that will meet the regulatory and metabolic needs of the developing embryo. On the other hand, events related with energetic metabolism during A. aegypti embryogenesis are unknown. Results Glucose metabolism was investigated throughout Aedes aegypti (Diptera embryonic development. Both cellular blastoderm formation (CBf, 5 h after egg laying - HAE and germ band retraction (GBr, 24 HAE may be considered landmarks regarding glucose 6-phosphate (G6P destination. We observed high levels of glucose 6-phosphate dehydrogenase (G6PDH activity at the very beginning of embryogenesis, which nevertheless decreased up to 5 HAE. This activity is correlated with the need for nucleotide precursors generated by the pentose phosphate pathway (PPP, of which G6PDH is the key enzyme. We suggest the synchronism of egg metabolism with carbohydrate distribution based on the decreasing levels of phosphoenolpyruvate carboxykinase (PEPCK activity and on the elevation observed in protein content up to 24 HAE. Concomitantly, increasing levels of hexokinase (HK and pyruvate kinase (PK activity were observed, and PEPCK reached a peak around 48 HAE. Glycogen synthase kinase (GSK3 activity was also monitored and shown to be inversely correlated with glycogen distribution during embryogenesis. Conclusions The results herein support the hypothesis that glucose metabolic fate changes according to developmental embryonic stages. Germ band retraction is a moment that was characterized as a landmark in glucose metabolism during Aedes aegypti embryogenesis. Furthermore, the results also suggest a role for GSK3 in glycogen balance/distribution during morphological modifications.
Logullo Carlos
Volume registration of interventional MRI data using needle paths and point landmarks
We created a method for three-dimensional registration of medical scanner image volumes to images of physical tissue sections or other volumes, and evaluated its accuracy. The method is applicable for many animal experiments, and we are applying it to evaluate interventional MRI imaging of thermal ablation and to quantify in vivo drug release from a new device for localized, controlled release. The method computes an optimum set of rigid body registration parameters by iterative minimization of the Euclidean distances between automatically generated correspondence points, along manually selected fiducial needle paths, and optional point landmarks. For numerically simulated registrations, using two needle paths over a range of needle orientations, median voxel displacement errors depended only on needle localization error when the angle between needles was at least 15 degrees. For parameters typical of our in vivo experiments, the median error was Lazebnik, Roee S.; Breen, Michael S.; Lancaster, Tanya L.; Nour, Sherif G.; Lewin, Jonathan S.; Wilson, David L. 2002-05-01
Lazebnik, Roee S.; Breen, Michael S.; Lancaster, Tanya L.; Nour, Sherif G.; Lewin, Jonathan S.; Wilson, David L.
A study of quantitative comparisons of photographs and video images based on landmark derived feature vectors.
An abundunce of surveillance cameras highlights the necessity of identifying individuals recorded. Images captured are often unintelligible and are unable to provide irrefutable identifications by sight, and therefore a more systematic method for identification is required to address this problem. An existing database of video and photograhic images was examined, which had previously been used in a psychological research project; material consisted of 80 video (Sample 1) and 119 photograhic (Sample 2) images, though taken with different cameras. A set of 38 anthropometric landmarks were placed by hand capturing 59 ratios of inter-landmark distances to conduct within sample and between sample comparisons using normalised correlation calculations; mean absolute value between ratios, Euclidean distance and Cosine ? distance between ratios. The statistics of the two samples were examined to determine which calculation best ascertained if there were any detectable correlation differences between faces that fall under the same conditions. A comparison of each face in Sample 1 was then compared against the database of faces in Sample 2. We present pilot results showing that the Cosine ? distance equation using Z-normalised values achieved the largest separation between True Positive and True Negative faces. Having applied the Cosine ? distance equation we were then able to determine that if a match value returned is greater than 0.7, it is likely that the best match will be a True Positive allowing a decrease of database images to be verified by a human. However, a much larger sample of images requires to be tested to verify these outcomes. PMID:22277156
Kleinberg, Krista F; Siebert, J Paul
Medial calcar of proximal humeral fracture as landmark in restoration of humeral length in case of hemiarthroplasty.
Czech Academy of Sciences Publication Activity Database
Shoulder hemiarthroplastyK�d oboru RIV: FJ - Chirurgie v?. transplantologieImpakt faktor: 1.130, rok: 2012 http://library.utia.cas.cz/separaty/2013/E/smid-medial calcar of proximal humeral fracture as landmark in restoration of humeral length in case of hemiarthroplasty.pdf
Hrom�dka, R.; Kub?na, Ale� Anton�n; �m�d, Martin; Popelka, S.
Learning Your Way around Town: How Virtual Taxicab Drivers Learn to Use Both Layout and Landmark Information
By having subjects drive a virtual taxicab through a computer-rendered town, we examined how landmark and layout information interact during spatial navigation. Subject-drivers searched for passengers, and then attempted to take the most efficient route to the requested destinations (one of several target stores). Experiment 1 demonstrated that�
Newman, Ehren L.; Caplan, Jeremy B.; Kirschen, Matthew P.; Korolev, Igor O.; Sekuler, Robert; Kahana, Michael J.
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
Conventional cerebrospinal fluid scanning
International Nuclear Information System (INIS)
Conventional cerebrospinal fluid scanning (CSF scanning) today is mainly carried out in addition to computerized tomography to obtain information about liquor flow kinetics. Especially in patients with communicating obstructive hydrocephalus, CSF scanning is clinically useful for the decision for shunt surgery. In patients with intracranial cysts, CSF scanning can provide information about liquor circulation. Further indications for CSF scanning include the assessment of shunt patency especially in children, as well as the detection and localization of cerebrospinal fluid leaks. (orig.)
Anatomical landmarks and skin markers are not reliable for accurate labeling of thoracic vertebrae on MRI
Energy Technology Data Exchange (ETDEWEB)
Background: Numbering of the thoracic spine on MRI can be tedious if C2 and L5-S1 are not included and may lead to errors in lesion level. Purpose: To determine whether anatomic landmarks or external markers are reliable as an aid for accurate numbering of thoracic vertebrae on MRI. Material and Methods: Sixty-seven thoracic spine MR studies of 67 patients (30 males, 37 females, age range 18-83 years) were studied, composed of 52 consecutive MR studies and an additional 15 MRI in which vitamin E markers were placed over the skin. In the 52 thoracic MR examinations potential numbering aids such as the level of the sternal apex, pulmonary artery, aortic arch, and osseous or disc abnormalities were numbered on both cervical localizer (standard of reference) and thoracic sagittal images. The additional 15 examinations in which vitamin E markers were placed over the skin were evaluated for consistency in the level of the markers on different sequences in the same exam. Results: The sternal apex level ranged from T2 to T5 [T3 in 28/51 patients (55%), T2 in 10/51 (20%)]. The aortic arch level ranged from T2 to T4 [T4 in 18/48 (38%) and T3 in 17 (35%)]. Pulmonary artery level ranged from T4 to T6-7 disc [T5 in 20/52 patients (38%) and T6 in 14/52 (27%)]. In 3 of 12 patients who had abnormalities in a vertebral body or disc as definite point reference, the non-localizer image mislabelled the level. In 11/15 (73%) patients with vitamin E markers that were placed over the upper thoracic spine, the results showed consistency in the level of the markers in relation to the reference points or consistent inter-marker gap between the sequences. Conclusion: There are only two reliable ways to accurately define the levels if no landmarking feature is available on the magnet. The first is by including C2 in the thoracic sequence of a diagnostic quality, and the second is by using an abnormality in the discs or vertebral bodies as a point of reference
Shabshin, Nogah (Dept. of Diagnostic Imaging, Chaim Sheba Medical Center, Tel-HaShomer (Israel)), e-mail: email@example.com; Schweitzer, Mark E. (Dept. of Diagnostic Imaging, Ottawa Hospital and Univ. of Ottawa, Ottawa (Canada)); Carrino, John A. (Dept. of Radiology, Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States))
Anatomical landmarks for safer carpal tunnel decompression: an experimental cadaveric study
Background Carpal tunnel syndrome is a common presentation to surgical outpatient clinics. Treatment of carpal tunnel syndrome involves surgical division of the flexor retinaculum. Palmar and recurrent branches of the median nerve as well as the superficial palmar arch are at risk of damage. Methodology Thirteen cadavers of Sri Lankan nationality were selected. Cadavers with deformed or damaged hands were excluded. All selected cadavers were preserved with the conventional arterial method using formalin as the main preservative. Both hands of the cadavers were placed in the anatomical position and dissected carefully. We took pre- determined measurements using a vernier caliper. We hypothesized that the structures at risk during carpal tunnel decompression such as recurrent branch of the median nerve and superficial palmar arch can be protected if simple anatomical landmarks are identified. We also hypothesized that an avascular area exists in the flexor retinaculum, identification of which facilitates safe dissection with minimal intra operative bleeding. Therefore we attempted to characterize the anatomical extent of such an avascular area as well as anatomical landmarks for a safer carpal tunnel decompression. Ethical clearance was obtained for the study. Results In a majority of specimens the recurrent branch was a single trunk (n =20, 76.9%). Similarly 84.6% (n = 22) were extra ligamentous in location. Mean distance from the distal border of the TCL to the recurrent branch was 7.75 mm. Mean distance from the distal border of TCL to the superficial palmar arch was 11.48 mm. Mean length of the flexor retinaculum, as measured along the incision, was 27.00 mm. Mean proximal and distal width of the avascular area on TCL was 11.10 mm and 7.09 mm respectively. Conclusion We recommend incision along the radial border of the extended ring finger for carpal tunnel decompression. Extending the incision more than 8.16 mm proximally and 7.75 mm distally from the corresponding borders of the TCL should be avoided. Incision should be kept to a mean length of 27.0 mm, which corresponds to the length of TCL along the above axis. We also propose an avascular area along the TCL, identification of which minimizes blood loss.
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In rapid frequency scan EPR with triangular scans, sufficient time must be allowed to insure that the magnetization in the x,y plane decays to baseline at the end of the scan, which typically is about 5 T2 after the spins are excited. To permit relaxation of signals excited toward the extremes of the scan the total scan time required may be much longer than 5 T2. However, with periodic, saw-tooth excitation, the slow-scan EPR spectrum can be recovered by Fourier deconvolution of data recorded...
Fiber feature map based landmark initialization for highly deformable DTI registration
This paper presents a novel pipeline for the registration of diffusion tensor images (DTI) with large pathological variations to normal controls based on the use of a novel feature map derived from white matter (WM) fiber tracts. The research presented aims towards an atlas based DTI analysis of subjects with considerable brain pathologies such as tumors or hydrocephalus. In this paper, we propose a novel feature map that is robust against variations in WM fiber tract integrity and use these feature maps to determine a landmark correspondence using a 3D point correspondence algorithm. This correspondence drives a deformation field computed using Gaussian radial basis functions(RBF). This field is employed as an initialization to a standard deformable registration method like demons. We present early preliminary results on the registration of a normal control dataset to a dataset with abnormally enlarged lateral ventricles affected by fatal demyelinating Krabbe disease. The results are analyzed based on a regional tensor matching criterion and a visual assessment of overlap of major WM fiber tracts. While further evaluation and improvements are necessary, the results presented in this paper highlight the potential of our method in handling registration of subjects with severe WM pathology.
Gupta, Aditya; Toews, Matthew; Janardhana, Ravikiran; Rathi, Yogesh; Gilmore, John; Escolar, Maria; Styner, Martin
... more References Previous Topic Mammography Next Topic Ultrasound Nuclear scans Other names include nuclear imaging , radionuclide imaging , ... to more radiation. Use of monoclonal antibodies in nuclear scans: A special type of antibody produced in ...
This report summarizes the results and knowledge of scan behavior gained in various simulation and laboratory studies. Results were obtained through various analysis techniques such as real-time viewing of the pilot's scanning behavior and quantitative analysis of scan behavior performance parameters (average dwell time, dwell percentages, instrument transition paths, dwell histograms, and entropy rate measures). Pilot scan behavior is discussed in the following areas; scanning is a subconscious conditioned activity, scanning is situation dependent, pilots' scanning pattern is centered around a home base. Scanning behavior data have been shown to be useful in determining pilot's workload, evaluating pilot's strategy and role, determining the rate of information transfer of various displays, and aiding in pilot training.
Harris, R. L., Sr.; Spady, A. A., Jr.
Comparing the Effectiveness of GPS-Enhanced Voice Guidance for Pedestrians with Metric- and Landmark-Based Instruction Sets
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; H�usler, Elisabeth; Leitinger, Sven
Homing in the wolf spider Lycosa tarantula (Araneae, Lycosidae): the role of active locomotion and visual landmarks
Previous studies on the homing of the wolf spider Lycosa tarantula have shown that it is carried out by path integration. Animals using this mechanism must measure the distance walked and the angles turned. This study aims to understand if wolf spider L. tarantula is able to estimate the walked distance in an outward path. As this information is more likely obtained by proprioceptive mechanisms, active or passive displacements have been performed. An active locomotion was found essential to estimate distances. During passive locomotion, spiders searched for their burrows near the release point while when displaced actively the inbound journey was longer than the outbound one. The possible use of visual landmarks near the burrow was also tested as a cue to complete the inbound journey. Our results did not show that L. tarantula used these visual landmarks to find the burrow. L. tarantula seems to use only proprioceptive information obtained during the outbound path to estimate the distance traveled.
Reyes-Alcubilla, Carmen; Ruiz, Miguel A.; Ortega-Escobar, Joaqu�n
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
Digital Repository Infrastructure Vision for European Research (DRIVER)
Since the completion of the Human Genome Project 10 years ago, the world has witnessed an incredible progress in human genetics and genomics.1 This progress was largely driven by the availability of better, faster and cheaper sequencing technology.2 While it took more than 10 years and more than 1 billion dollars to complete the Human Genome Project,3-5 an individual in the year 2011 can have his whole genome sequenced within a week for less than $30,000. With cheaper and faster sequencing ca...
Energy Technology Data Exchange (ETDEWEB)
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.
Bevan, J.A.
Energy Technology Data Exchange (ETDEWEB)
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.
Bevan, J.A.
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 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.
Computed reconstruction of spatial ammonoid-shell orientation captured from digitized grinding and landmark data
The internal orientation of fossil mass occurrences can be exploited as useful source of information about their primary depositional conditions. A series of studies, using different kinds of fossils, especially those with elongated shape (e.g., elongated gastropods), deal with their orientation and the subsequent reconstruction of the depositional conditions (e.g., paleocurrents and transport mechanisms). However, disk-shaped fossils like planispiral cephalopods or gastropods were used, up to now, with caution for interpreting paleocurrents. Moreover, most studies just deal with the topmost surface of such mass occurrences, due to the easier accessibility. Within this study, a new method for three-dimensional reconstruction of the internal structure of a fossil mass occurrence and the subsequent calculation of its spatial shell orientation is established. A 234 million-years-old (Carnian, Triassic) monospecific mass occurrence of the ammonoid Kasimlarceltites krystyni from the Taurus Mountains in Turkey, embedded in limestone, is used for this pilot study. Therefore, a 150�45�140 mm3 block of the ammonoid bearing limestone bed has been grinded to 70 slices, with a distance of 2 mm between each slice. By using a semi-automatic region growing algorithm of the 3D-visualization software Amira, ammonoids of a part of this mass occurrence were segmented and a 3D-model reconstructed. Landmarks, trigonometric and vector-based calculations were used to compute the diameters and the spatial orientation of each ammonoid. The spatial shell orientation was characterized by dip and dip-direction and aperture direction of the longitudinal axis, as well as by dip and azimuth of an imaginary sagittal-plane through each ammonoid. The exact spatial shell orientation was determined for a sample of 675 ammonoids, and their statistical orientation analyzed (i.e., NW/SE). The study combines classical orientation analysis with modern 3D-visualization techniques, and establishes a novel spatial orientation analyzing method, which can be adapted to any kind of abundant solid matter.
Lukeneder, Susanne; Lukeneder, Alexander; Weber, Gerhard W.
[Therapy for systemic metabolic disorders based on the detection of basic corneal landmarks in childhood].
Many systemic lysosomal storage disorders show basic corneal opacities already in childhood. The lysosome is a cell organelle, produced by Golgi's apparatus, that is surrounded by a membrane and contains hydrolytic enzymes that break down food molecules, especially proteins and other complex molecules. The ophthalmologist's precise diagnosis of corneal clouding at the slit-lamp may reveal the correct interpretation of the specific lysosomal storage disorder. It is very important to diagnose such diseases as soon as possible because today the development of systemic enzymatic therapies has broadened the therapeutic armamentarium for the current standard of care. The following corneal landmarks of systemic storage diseases and of the modern systemic therapy are presented: cornea verticillata in Fabry's disease, periodic infusion of alpha-galactosidase a; Kayser-Fleischer's ring in Wilson's disease, zinc, trienetin, low copper diet; multiple, punctiform crystals in cystinosis, cysteamine, Raptor RP 103(DR cysteamine) that reduces the cytotoxity in form of continous dissolving of cystine from lysosome, renal transplantation, haematopoietic stem cell transplantation; peripheral ring, but not true lipid arc, and moderate stromal haze in LCAT-deficiency, injection of recombinant enzyme or of encapsulated LCAT-secreting cells; diffuse stromal haze in mucopolysaccharidoses (MPS). Enzyme replacement therapy is currently indicated for MPS I, MPS II, and MPS VI, haematopoietic stem cell transplantation; painful, bilateral pseudo-dendritic opacities in tyrosinemia type II (eponym: Richner-Hanhart syndrome), low phenylalanine and tyrosine diet result in complete disappearance of corneal alterations with a consecutive painfree period. Strict diet during the whole life is necessary to prevent corneal recurrences and the occurrence of palmo-plantar keratoses. Such therapies can enable the patient to lead an otherwise normal life for decades. PMID:23794426
Lisch, W; Pitz, S; Geerling, G
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
Whole-genome shotgun assembly and comparison of human genome assemblies.
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries. The quality-trimmed reads covered the genome 5.3 times, and the inserts from which pairs of reads were obtained covered the genome 39 times. With the nearly complete human DNA sequence [National Center for Biotechnology Information (NCBI) Build 34] now available, it is possible to directly assess the quality, accuracy, and completeness of WGSA and of the first reconstructions of the human genome reported in two landmark papers in February 2001 [Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) Science 291, 1304-1351; International Human Genome Sequencing Consortium (2001) Nature 409, 860-921]. The analysis of WGSA shows 97% order and orientation agreement with NCBI Build 34, where most of the 3% of sequence out of order is due to scaffold placement problems as opposed to assembly errors within the scaffolds themselves. In addition, WGSA fills some of the remaining gaps in NCBI Build 34. The early genome sequences all covered about the same amount of the genome, but they did so in different ways. The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats. PMID:14769938
Istrail, Sorin; Sutton, Granger G; Florea, Liliana; Halpern, Aaron L; Mobarry, Clark M; Lippert, Ross; Walenz, Brian; Shatkay, Hagit; Dew, Ian; Miller, Jason R; Flanigan, Michael J; Edwards, Nathan J; Bolanos, Randall; Fasulo, Daniel; Halldorsson, Bjarni V; Hannenhalli, Sridhar; Turner, Russell; Yooseph, Shibu; Lu, Fu; Nusskern, Deborah R; Shue, Bixiong Chris; Zheng, Xiangqun Holly; Zhong, Fei; Delcher, Arthur L; Huson, Daniel H; Kravitz, Saul A; Mouchard, Laurent; Reinert, Knut; Remington, Karin A; Clark, Andrew G; Waterman, Michael S; Eichler, Evan E; Adams, Mark D; Hunkapiller, Michael W; Myers, Eugene W; Venter, J Craig
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
Radionucleotide scanning in osteomyelitis
International Nuclear Information System (INIS)
Radionucleotide bone scanning can be an excellent adjunct to the standard radiograph and clinical findings in the diagnosis of osteomyelitis. Bone scans have the ability to detect osteomyelitis far in advance of the standard radiograph. The sequential use of technetium and gallium has been useful in differentiating cellulitis and osteomyelitis. Serial scanning with technetium and gallium may be used to monitor the response of osteomyelitis to antibiotic therapy
Full Text Available ... Recipes & Cooking Staying Safe Health Problems Illnesses & Injuries Health Problems ... Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT ...
The providers of this searchable metasite have, over the years, accumulated hundreds of genomics-related bookmarks which they now share freely. The eighteen major categories at 123 genomics each contain dozens of links to bioinformatics- and genomics-related science news, research labs, databases, scientific societies, protocol guides, etc. Examples of the category headings include Microarrays, Molecular Pathways, Sequence Databases, Journals and Publications, and Diseases and Disorders. This simply designed site provides enough good resources to keep most graduate students and researchers of bioinformatics happy and well informed.
Bone scanning in otolaryngology.
Modern radionuclide bone scanning has introduced a new concept in physiologic and anatomic diagnostic imaging to general medicine. As otolaryngologists must diagnose and treat disease in relation to the bony and/or cartilaginous supporting structures of the neurocranium and upper airway, this modality should be included in the otolaryngologist's diagnostic armamentarium. It is the purpose of this manuscript to study the specific applications of bone scanning to our specialty at this time, based on clinical experience over the past three years. This thesis describes the development of bone scanning in general (history of nuclear medicine and nuclear physics; history of bone scanning in particular). General concepts in nuclear medicine are then presented; these include a discussion of nuclear semantics, principles of radioactive emmissions, the properties 99mTc as a radionuclide, and the tracer principle. On the basis of these general concepts, specific concepts in bone scanning are then brought forth. The physiology of bone and the action of the bone scan agents is presented. Further discussion considers the availability and production of the bone scan agent, patient factors, the gamma camera, the triphasic bone scan and the ultimate diagnostic principle of the bone scan. Clinical applications of bone scanning in otolaryngology are then presented in three sections. Proven areas of application include the evaluation of malignant tumors of the head and neck, the diagnosis of temporomandibular joint disorders, the diagnosis of facial fractures, the evaluation of osteomyelitis, nuclear medicine imaging of the larynx, and the assessment of systemic disease. Areas of adjunctive or supplementary value are also noted, such as diagnostic imaging of meningioma. Finally, areas of marginal value in the application of bone scanning are described. PMID:470539
Noyek, A M
Scanning scheme is more efficient than conventional scanning. Originally designed for optical radar in space vehicles, scheme may also find uses in site-surveillance security systems and in other industrial applications. It should be particularly useful when system must run on battery energy, as would be case in power outages.
Levinson, S.
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
Because genomics is an interdisciplinary science that unites biology, chemistry, physics, and mathematics, its language is diverse and includes terms not always found in dictionaries. This site from Cambridge Healthtech Institute of Massachusetts was designed to help scientists keep on top of this complex language. Loads of terms in categories such as basic genetics, functional and structural genomics, informatics, and genomic-related technology are defined here. Users can access the glossary terms either through a short index of major subject headings or by a longer alphabetically-arranged subject list. The Genomics Glossary deserves bonus points for including links to related resources in the text of its definitions. For example, within the definition of "polymerase chain reaction" are links to sites at Yale Medical School and the National Library of Medicine. In addition, links to pages on nomenclature, a bibliography of Web and print resources, and a FAQ page are available at this fantastic Website.
Chitty, Mary G.
Saltatory changes in genomic technologies have driven successive eras of discovery of loci underlying human traits. The development of complete genetic maps of the human genome in the 1980's fueled the mapping of Mendelian loci in extended kindreds for dominant traits and predominantly in consanguineous kindreds for recessive traits. Further accelerated by the acquisition of the sequence of the human genome in 2001, this first Mendelian era identified over 2800 disease loci and profoundly changed our understanding of the biology and pathophysiology of every organ system. A second era, examining the contribution of common variants to common disease, was driven by the identification of more than 10 million common variants in the human genome sequence recognition of substantial linkage disequilibrium in the human genome, and methods to rapidly and relatively inexpensively genotype 500,000 � 1,000,000 SNPs in large cohorts. This led to identification of more than 1000 loci that show robust association with diverse human traits, a number of which have also drastically changed our understanding of disease biology. We have recently entered a third era of discovery, this one driven by spectacular reductions in the cost of DNA sequencing from ?$100,000 per million bases in 1998 to less than $0.10 today on the HiSeq instrument. Coupled with our development of robust methods for selectively sequencing complete coding regions of the genome, which harbor the overwhelming majority of Mendelian loci, and analytic methods to rapidly and with high sensitivity and specificity identify variations from the reference sequence, one can now sequence ostensibly all the genes in the human genome (the exome) to high levels of completion for ?$ 700. This has provided fundamental new opportunities for identifying Mendelian loci that were previously elusive. Drs. Shrikant Mane, Kaya Bilguvar and Martin Kircher will present the efforts being made at Yale and at University of Washington to discover Mendelian loci using cutting edge genomic technologies.
Mane, Shrikant; Bilgvar, Kaya; Kircher, Martin; Mane, Shrikant
SCAN: A Systems Biology Approach to Pharmacogenomic Discovery
Genome-wide association (GWA) studies have identified thousands of genetic variants that contribute to disease and pharmacologic traits. More recently, high-throughput sequencing studies promise to provide a more complete catalog of genetic variants with roles in human phenotypic variation. Yet, characterizing the influence of functional variants on genes, RNAs, proteins, and ultimately disease or pharmacologic traits is a critical challenge for a vast majority of the implicated susceptibility loci. Here we describe SCAN, a bioinformatics resource we have developed to elucidate the functional consequences of genetic variants identified by genome-wide scans. In particular, this public resource implements a systems biology approach to pharmacogenomic discovery.
Gamazon, Eric R.; Huang, R. Stephanie; Cox, Nancy J.
Environmental scanning electron microscopy
International Nuclear Information System (INIS)
The ElectroScan environmental scanning electron microscope (ESEM) is one of the most exciting new developments in the field of Electron Microscopy. The ESEM differs from conventional Scanning Electron Microscopes (SEM) by being able to examine materials including liquids and oils in their natural state with no prior sample preparation. Accessory equipment, cooling, heating and manipulating devices allow the manipulation of samples thus making it possible for the first time to image dynamic processes such as wetting, drying, absorption, corrosion, melting, crystallisation, curing and fracturing at high magnification. Papers concerning the historical development of the ESEM are given in a bibliography at the end of this paper. 24 refs., 18 figs
International Nuclear Information System (INIS)
The improvements in CT scanning techniques towards shorter scanning times and shorter interscan periods now also allow dynamic processes to be evaluated on the basis of a temporal CT scanning sequence. The conference paper explains the results of a contrast medium study with a group of eight patients (60 ml Urovist/3 sec.), for measurements of cerebral blood flow (CBF), and cerebral blood volume (CBV). The CBV values obtained are comparable with the data produced by other methods. The CBF values are accurate in terms of the relation between grey and white cerebral matter. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.
Courteau, J.
Tomographic scanning apparatus
International Nuclear Information System (INIS)
This patent specification describes a tomographic scanning apparatus, with particular reference to the adjustable fan beam and its collimator system, together with the facility for taking a conventional x-radiograph without moving the patient. (U.K.)
Tomographic scanning apparatus
International Nuclear Information System (INIS)
This patent specification relates to a tomographic scanning apparatus using a fan beam and digital output signal, and particularly to the design of the gas-pressurized ionization detection system. (U.K.)
Tomographic scanning apparatus
International Nuclear Information System (INIS)
Details are presented of a tomographic scanning apparatus, its rotational assembly, and the control and circuit elements, with particular reference to the amplifier and multiplexing circuits enabling detector signal calibration. (U.K.)
Tomographic scanning apparatus
International Nuclear Information System (INIS)
Details are given of a tomographic scanning apparatus, with particular reference to a multiplexer slip ring means for receiving output from the detectors and enabling interfeed to the image reconstruction station. (U.K.)
Originally developed under contract for NASA by Ball Bros. Research Corporation for acquiring visual information from lunar and planetary spacecraft, system uses standard closed circuit camera connected to a device called a scan converter, which slows the stream of images to match an audio circuit, such as a telephone line. Transmitted to its destination, the image is reconverted by another scan converter and displayed on a monitor. In addition to assist scans, technique allows transmission of x-rays, nuclear scans, ultrasonic imagery, thermograms, electrocardiograms or live views of patient. Also allows conferencing and consultation among medical centers, general practitioners, specialists and disease control centers. Commercialized by Colorado Video, Inc., major employment is in business and industry for teleconferencing, cable TV news, transmission of scientific/engineering data, security, information retrieval, insurance claim adjustment, instructional programs, and remote viewing of advertising layouts, real estate, construction sites or products.
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
An analysis of anatomic landmark mobility and setup errors in radiotherapy for lung cancer
International Nuclear Information System (INIS)
Purpose: To identify visible structures in the thorax which exhibit little internal motion during irradiation and, to determine random and systematic setup deviations in lung cancer patients with the use of these structures. Methods: Ten patients with lung cancer were set up in the supine position, and aligned using lasers. No immobilization devices were used. With an electronic portal imaging device (Siemens Beam ViewPLUS), 12 sequential images (exposure 0.54 sec.; processing time 1.5 sec.) were obtained during a single fraction of radiotherapy. These 'movie loops' were generated for the A-P fields during each of 3-5 fractions. In order to determine the mobility of internal structures during each fraction, visible structures such as the trachea, carina, the upper chest wall, aortic arch, clavicle and paraspinal line were contoured manually in each image and matched with the first image of the corresponding movie loop by means of a cross-correlation algorithm. Translations in the cranial and lateral directions and in-plane rotations were determined for each structure separately. As the reference image represents a random position, relative movements were determined by comparing the translations and rotation for every image to the calculated means per movie-loop. Standard deviations of the relative movements were determined for each structure and each patient. Patient setup was evaluated for 15 patients with lung cancer. Setup was not corrected at any time during the treatment. The electronic portal images of each fraction were matched with the digitized simulator films by using a combination of the structures which had been determined to be relatively stable in the infra-fractional analysis. Results: In the infra-fractional analysis 120 to 380 matches were made per structure (a total of 1400). The standard deviation (SD) of translations in the lateral direction was small (?1 mm) for the trachea, thoracic wall, paraspinal line and aortic arch. This was also the case for the SD of the translations in the cranial direction of the clavicle, aortic arch and upper thoracic wall. The carina was found to be relatively mobile (up to 6 mm) in both directions. The SD for in-plane rotations was negligible (<0.5 deg.) for all structures. The interpatient variation was very small (SD < 0.5 mm). In a preliminary analysis of patient setup, the random errors for translations are 2.0 mm in the lateral direction and 2.4 mm in the cranial direction (1 SD). The standard deviations of systematic errors are about 3 mm in both directions. In plane rotations were found to be negligible. Conclusions: We have identified a number of structures which exhibit little internal motion in the frontal plane, and recommend that a combination of these structures be used as anatomic landmarks for setup verification during radiotherapy of thoracic tumors. Preliminary results indicate that setup errors of patients with lung cancer in our center appear to be acceptable, even though no specific immobilization devices were used
Identifying biological landmarks using a novel cell measuring image analysis tool: Cell-o-Tape
Digital Repository Infrastructure Vision for European Research (DRIVER)
Abstract Background The ability to quantify the geometry of plant organs at the cellular scale can provide novel insights into their structural organization. Hitherto manual methods of measurement provide only very low throughput and subjective solutions, and often quantitative measurements are neglected in favour of a simple cell count. Results We present a tool to count and measure individual neighbouring cells along a defined file in confocal laser scanning m...
French Andrew P; Wilson Michael H; Kenobi Kim; Dietrich Daniela; Vo� Ute; Ubeda-Tom�s Susana; Pridmore Tony P; Wells Darren M
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.
Digital Repository Infrastructure Vision for European Research (DRIVER)
V/SCAN� is a computerized video scanning instrument incorporating new concepts in the analysis of microscopic images, having applications to the detailed analysis and construction of chromosome karyotypes. Its primary use is for research applications in the areas of automating hybrid cell karyotyping where 150 or more chromosomes may appear, of automating prometaphase banding pattern analysis where complex banding patterns occur, and of automating fluorescence stains of chromosomal probes w...
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.
Directory of Open Access Journals (Sweden)
Full Text Available In today�s scenario due to advancement in computing power, technology, advance tools and coding techniques password cracking and finding vulnerability has become simpler. One of the most common techniques used by intruders is port scanning, by which attacker identifies running applications and makes entry in the system.In this paper the idea of random port selection is suggested to make the port scanning more difficult for intruders
Pratik Kanani
Based at the University of Leiden in the Netherlands, The Arts & Genomics Centre is interested in expanding the "public debate on (future) goals, means, possibilities and use of results of genomics, from the specific point of view of bio-genetic art." The homepage provides ample information about their most recent initiatives, which have included a symposium on food, art and science and a video on their VivoArts program, which attempts to bring together biology and various contemporary arts. Moving on, the "Research" section of the site includes project documents and proposals that deal with their representational space program and the "Imagining Genomics" initiative. The site is rounded out by a collection of links to other germane sites and online resources.
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.
Genome Maps, a new generation genome browser
Digital Repository Infrastructure Vision for European Research (DRIVER)
Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 sta...
Medina, Ignacio; Salavert, Francisco; Sanchez, Rube?n; Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaqui?n
Identification of an Amphipathic Helix Important for the Formation of Ectopic Septin Spirals and Axial Budding in Yeast Axial Landmark Protein Bud3p
Digital Repository Infrastructure Vision for European Research (DRIVER)
Correct positioning of polarity axis in response to internal or external cues is central to cellular morphogenesis and cell fate determination. In the budding yeast Saccharomyces cerevisiae, Bud3p plays a key role in the axial bud-site selection (axial budding) process in which cells assemble the new bud next to the preceding cell division site. Bud3p is thought to act as a component of a spatial landmark. However, it is not clear how Bud3p interacts with other components of the landmark, suc...
Femtosecond scanning tunneling microscope
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This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). By combining scanning tunneling microscopy with ultrafast optical techniques we have developed a novel tool to probe phenomena on atomic time and length scales. We have built and characterized an ultrafast scanning tunneling microscope in terms of temporal resolution, sensitivity and dynamic range. Using a novel photoconductive low-temperature-grown GaAs tip, we have achieved a temporal resolution of 1.5 picoseconds and a spatial resolution of 10 nanometers. This scanning tunneling microscope has both cryogenic and ultra-high vacuum capabilities, enabling the study of a wide range of important scientific problems.
Taylor, A.J.; Donati, G.P.; Rodriguez, G.; Gosnell, T.R.; Trugman, S.A.; Some, D.I.
Vector generator scan converter
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High printing speeds for graphics data are achieved with a laser printer by transmitting compressed graphics data from a main processor over an I/O channel to a vector generator scan converter which reconstructs a full graphics image for input to the laser printer through a raster data input port. The vector generator scan converter includes a microprocessor with associated microcode memory containing a microcode instruction set, a working memory for storing compressed data, vector generator hardware for drawing a full graphic image from vector parameters calculated by the microprocessor, image buffer memory for storing the reconstructed graphics image and an output scanner for reading the graphics image data and inputting the data to the printer. The vector generator scan converter eliminates the bottleneck created by the I/O channel for transmitting graphics data from the main processor to the laser printer, and increases printer speed up to thirty fold. 7 figs.
Moore, J.M.; Leighton, J.F.
Vector generator scan converter
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This patent describes high printing speeds for graphics data that are achieved with a laser printer by transmitting compressed graphics data from a main processor over an I/O (input/output) channel to a vector generator scan converter which reconstructs a full graphics image for input to the laser printer through a raster data input port. The vector generator scan converter includes a microprocessor with associated microcode memory containing a microcode instruction set, a working memory for storing compressed data, vector generator hardware for drawing a full graphic image from vector parameters calculated by the microprocessor, image buffer memory for storing the reconstructed graphics image and an output scanner for reading the graphics image data and inputting the data to the printer. The vector generator scan converter eliminates the bottleneck created by the I/O channel for transmitting graphics data from the main processor to the laser printer, and increases printer speed up to thirty fold.
Moore, J.M.; Leighton, J.F.
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.)
Robust facial landmark detection for three-dimensional face segmentation and alignment
Three-dimensional human faces have been applied in many fields, such as face animation, identity recognition, and facial plastic surgery. Segmenting and aligning 3-D faces from raw scanned data is the first vital step toward making these applications successful. However, the existence of artifacts, facial expressions, and noises poses many challenges to this problem. We propose an automatic and robust method to segment and align 3-D face surfaces by locating the nose tip and nose ridge. Taking a raw scanned surface as input, a novel feature-based moment analysis on scale spaces is presented to locate the nose tip accurately and robustly, which is then used to crop the face region. A technique called the geodesic Euclidean ratio is then developed to find the nose ridge. Each face is aligned based on the locations of nose tip and nose ridge. The proposed method is not only invariant to translations and rotations, but also robust in the presence of facial expressions and artifacts such as hair, clothing, other body parts, etc. Experimental results on two large 3-D face databases demonstrate the accuracy and robustness of the proposed method.
Wu, Hai Shan; Chen, Yan Qiu
Liver Scanning with Radiomolybdate
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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. M�tastas�s, 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)
How reliable are empirical genomic scans for selective sweeps?
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The beneficial substitution of an allele shapes patterns of genetic variation at linked sites. Thus, in principle, adaptations can be mapped by looking for the signature of directional selection in polymorphism data. In practice, such efforts are hampered by the need for an accurate characterization of the demographic history of the species and of the effects of positive selection. In an attempt to circumvent these difficulties, researchers are increasingly taking a purely empirical approach,...
Predicting a novel pathogenicity island in Helicobacter pylori by genomic barcoding
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AIM: To apply a new, integrated technique for visualizing bacterial genomes to identify novel pathogenicity islands in Helicobacter pylori (H. pylori). METHODS: A genomic barcode imaging method (converting frequency matrices to grey-scale levels) was designed to visually distinguish origin-specific genomic regions in H. pylori. The complete genome sequences of the six H. pylori strains published in the National Center for Biotechnological Information prokaryotic genome database were scanned, ...
Guo-Qing Wang; Jian-Ting Xu; Guang-Yu Xu; Yang Zhang; Fan Li; Jian Suo
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
Energy Technology Data Exchange (ETDEWEB)
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.
Binnig, G.; Rohrer, H. (IBM Research Lab., Zurich (Switzerland))
Tomographic scanning apparatus
International Nuclear Information System (INIS)
Details are given of a tomographic scanning apparatus, with particular reference to the means of adjusting the apparent gain of the signal processing means for receiving output signals from the detectors, to compensate for drift in the gain characteristics, including means for passing a reference signal. (U.K.)
Scanning bubble chamber pictures
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.
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Scanning Deep Level Transient Spectroscopy (SDLTS) is a current SEM technique for the detection of the local distribution of deep level centres in semiconductors. The contribution deals with the physical foundations of the SDLTS technique and it discusses the demands on the instrumentation. The measurement practice is described and illustrated by several experimental examples. Finally, the possibilities and limitations of SDLTS are critically reviewed.
Breitenstein, O.
Reappraisal of the anatomical landmarks of motor and premotor cortical regions for image-guided brain navigation in TMS practice.
Image-guided navigation systems dedicated to transcranial magnetic stimulation (TMS) have been recently developed and offer the possibility to visualize directly the anatomical structure to be stimulated. Performing navigated TMS requires a perfect knowledge of cortical anatomy, which is very variable between subjects. This study aimed at providing a detailed description of sulcal and gyral anatomy of motor cortical regions with special interest to the inter-individual variability of sulci. We attempted to identify the most stable structures, which can serve as anatomical landmarks for motor cortex mapping in navigated TMS practice. We analyzed the 3D reconstruction of 50 consecutive healthy adult brains (100 hemispheres). Different variants were identified regarding sulcal morphology, but several anatomical structures were found to be remarkably stable (four on dorsoventral axis and five on rostrocaudal axis). These landmarks were used to define a grid of 12 squares, which covered motor cortical regions. This grid was used to perform motor cortical mapping with navigated TMS in 12 healthy subjects from our cohort. The stereotactic coordinates (x-y-z) of the center of each of the 12 squares of the mapping grid were expressed into the standard Talairach space to determine the corresponding functional areas. We found that the regions whose stimulation produced almost constantly motor evoked potentials mainly correspond to the primary motor cortex, with rostral extension to premotor cortex and caudal extension to posterior parietal cortex. Our anatomy-based approach should facilitate the expression and the comparison of the results obtained in motor mapping studies using navigated TMS. PMID:24038518
Ahdab, Rechdi; Ayache, Samar S; Farhat, Wassim H; Mylius, Veit; Schmidt, Sein; Brugi�res, Pierre; Lefaucheur, Jean-Pascal
Navigating in small-scale space: the role of landmarks and resource monitoring in understanding saddleback tamarin travel.
Recent studies of spatial memory in wild nonhuman primates indicate that foragers may rely on a combination of navigational strategies to locate nearby and distant feeding sites. When traveling in large-scale space, tamarins are reported to encode spatial information in the form of a route-based map. However, little is known concerning how wild tamarins navigate in small-scale space (between feeding sites located at a distance of ?60?m). Therefore, we collected data on range use, diet, and the angle and distance traveled to visit sequential feeding sites in the same group of habituated Bolivian saddleback tamarins (Saguinus fuscicollis weddelli) in 2009 and 2011. For 7-8?hr a day for 54 observation days, we recorded the location of the study group at 10?min intervals using a GPS unit. We then used GIS software to map and analyze the monkeys' movements and travel paths taken between feeding sites. Our results indicate that in small-scale space the tamarins relied on multiple spatial strategies. In 31% of cases travel was route-based. In the remaining 69% of cases, however, the tamarins appeared to attend to the spatial positions of one or more near-to-site landmarks to relocate feeding sites. In doing so they approached the same feeding site from a mean of 4.5 different directions, frequently utilized different arboreal pathways, and traveled approximately 30% longer than then the straight-line distance. In addition, the monkeys' use of non-direct travel paths allowed them to monitor insect and fruit availability in areas within close proximity of currently used food patches. We conclude that the use of an integrated spatial strategy (route-based travel and attention to near-to-goal landmarks) provides tamarins with the opportunity to relocate productive feeding sites as well as monitor the availability of nearby resources in small-scale space. PMID:24038234
Garber, Paul A; Porter, Leila M
Treatment planning for resected abdominal tumors: Differences in organ position between diagnostic and radiation-planning computed tomography scans
International Nuclear Information System (INIS)
Purpose: To evaluate whether organ location, determined from preoperative diagnostic computed tomography scans (CTs), accurately reflects organ location when patients are positioned for radiation therapy. Methods and Materials: We identified patients with upper abdominal malignancies treated with surgery and/or radiation therapy. Comparisons of organ position relative to fixed bony landmarks were made among preoperative diagnostic CTs, postoperative diagnostic CTs, and radiation-planning CTs. We studied 18 patients who had CTs differing only in scanning technique, 11 patients who had CTs differing only in operative state, and 7 patients with CTs differing in both scanning technique and operative state. Results: For patients with diagnostic CTs and radiation-planning CTs that were either both preoperative or both postoperative, mean organ position, measured relative to a fixed bony landmark, ranged from 1.9 to 3.2 cm superior on radiation-planning CTs compared with diagnostic CTs (p < 0.0001). Mean organ position ranged from 0.9 to 1.7 cm posterior on radiation-planning CTs compared with diagnostic CTs (p ? 0.008). Shifts in the right-left direction were small and variable. For patients with pre- and postoperative diagnostic CTs, organ shifts were variable and not significant. Organ shifts for patients with preoperative diagnostic CTs and postoperative radiation-planning CTs were similar to shifts observed for the first group. Conclusions: Relative to bony landmarks, there are superior and posterior shifts in organ position for radiation-planning CTs compared with diagnostic CTs. These shifts should be considered during treatment planning for resected abdominal tumors
Genome cartography: charting the apicomplexan genome
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Genes reside in particular genomic contexts that can be mapped at many levels. Historically, genetic maps were used primarily to locate genes. Recent technological advances in genome sequence determination have made the analysis and comparison of whole genomes possible and increasingly tractable. If we shift our focus from gene content (the inventory of genes contained within a genome), to genome composition and organization, what do we see? This review examines what has been learned about th...
Kissinger, Jessica C.; Debarry, Jeremy
Rodent malaria parasites : genome organization & comparative genomics
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The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P. falciparum and partial genome sequences of three RMPs (Plasmodium yoelii - Chapter 3; Plasmodium berghei and Plasmodium chabaudi - Chapter 4) enabled us to expand the analysis to a genome-wide survey. By al...
Two-dimensional DNA displays for comparisons of bacterial genomes
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We have developed two whole genome-scanning techniques to aid in the discovery of polymorphisms as well as horizontally acquired genes in prokaryotic organisms. First, two-dimensional bacterial genomic display (2DBGD) was developed using restriction enzyme fragmentation to separate genomic DNA based on size, and then employing denaturing gradient gel electrophoresis (DGGE) in the second dimension to exploit differences in sequence composition. This technique was used to generate h...
Malloff Chad; Dullaghan Edie; Li Alice; Stokes Richard; Fernandez Rachel; Lam Wan
Adaptive Processing of Range Scanned Head: Synthesis of Personalized Animated Human Face Representation with Multiple-Level Radial Basis Function
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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.
Edmond C. Prakash
Mobile element scanning (ME-Scan by targeted high-throughput sequencing
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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
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
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)
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.
Technical note: a landmark-based approach to the study of the ear ossicles using ultra-high-resolution X-ray computed tomography data.
Previous study of the ear ossicles in Primates has demonstrated that they vary on both functional and phylogenetic bases. Such studies have generally employed two-dimensional linear measurements rather than three-dimensional data. The availability of Ultra- high-resolution X-ray computed tomography (UhrCT) has made it possible to accurately image the ossicles so that broadly accepted methodologies for acquiring and studying morphometric data can be applied. Using UhrCT data also allows for the ossicular chain to be studied in anatomical position, so that it is possible to consider the spatial and size relationships of all three bones. One issue impeding the morphometric study of the ear ossicles is a lack of broadly recognized landmarks. Distinguishing landmarks on the ossicles is difficult in part because there are only two areas of articulation in the ossicular chain, one of which (the malleus/incus articulation) has a complex three-dimensional form. A measurement error study is presented demonstrating that a suite of 16 landmarks can be precisely located on reconstructions of the ossicles from UhrCT data. Estimates of measurement error showed that most landmarks were highly replicable, with an average CV for associated interlandmark distances of less than 3%. The positions of these landmarks are chosen to reflect not only the overall shape of the bones in the chain and their relative positions, but also functional parameters. This study should provide a basis for further examination of the smallest bones in the body in three dimensions. PMID:21732321
Schmidt, Jodi L; Cole, Theodore M; Silcox, Mary T
International Nuclear Information System (INIS)
The principles of operation of a scanning tunnel microscope (STM) and an atomic forces scanning microscope (AFSM) widely used for studying the surface of solid bodies with atomic resolution, are described. The STM basic element is a piesoelectric scanner, where the transverse piesoeffect is used. Three versions of the piesoelectric scanner design, which can move along three coordinates, are considered. The results of studies of surfaces of graphite, silicon and hallium arsenide, as well as large molecules and biological structures using STM are given. One of the most successful STM designs is a microscope based on atomic forces. It is a tandem of two piesoceramic scanners, one of them carrying a sample and the other one - the STM point. It is a great advantage that the AFSM can be used in nanometry and tests of dielectrics
Photon scanning tunneling microscopy
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The Photon Scanning Tunneling Microscopy (PSTM) is the photon analogue of the electron Scanning Tunneling Microscope (STM). It uses the evanescent field due to the total internal reflection of a light beam in a Total Internal Reflection (TIR) prism. The sample, mounted on the base of the prism, modulates the evanescent field. A sharpened optical fiber probes this field, and the collected light is processed to generate an image of the topography and the chemical composition of the surface. We give, in this paper, a description of the microscope and discuss the influence of several parameters such as -- polarization of light, angle of incidence, shape of the end of the fiber -- on the resolution. Images of various samples -- glass samples, teflon spheres -- are presented. 8 refs., 7 figs.
Goudonnet, J.P.; Salomon, L.; De Fornel, F.; Chabrier, G. (Dijon Univ., 21 (France). Lab. de Physique du Solide); Warmack, R.J.; Ferrell, T.L. (Oak Ridge National Lab., TN (USA))
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
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)
The optical scanning technology in laser scanning and tracking system
Laser scanning and tracking technology has been widely used in many applications. For a laser scanning and tracking system, a two-dimensional scanning mirror is usually combined with a plane array detector to detect and track the object. The scanning process and quality of acquired images from the detector are two key factors and they are both correlated with the choice of scanning mode, which is a known hard problem and little has been done in the subject. Based on this deficiency, this paper analyzes and compares two common two-dimensional scan mode-continuous scan and step scan, from a theoretical point of view. As we known, the continuous scan can acquire data quickly and is easy to implement. But the acquired images may blur severely due to the fast continuous scan velocity. The step scan can produce highquality images, but it takes much longer time and is more difficult to control. Formulas are proposed in this paper to quantitatively measure the characteristics of each mode and evaluate the parameters that affect the scanning process. These results can be provided as a reference for the proper choice of scanning mode. Moreover, through analysis of imaging characteristics of the detector, an improved raster scan pattern is presented to reduce the number of dead zones and enhance the performance of the system.
Li, Shu-Ying; Zhou, Shi-Chun
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In this chapter we describe an automatic slide scanning and autofocusing system that consists of three components. First, images are captured at low magnification. This yields a panoramic view of an entire slide which allows the extraction of the positions and sizes of all particles. Then, a particle screening is carried out at medium magnification, in order to eliminate particles that are not diatom-like, i.e. debris that does not comply with pre-defined selection criteria. This method selec...
Pech-pacheco, Jose? L.; Cristo?bal Pe?rez, Gabriel
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A brief review of the state-of-the-art of scanning tunneling microscopy (STM) is presented with emphasis on materials problems. I shall discuss in particular the variety of materials, environrnents and temperatures that can be investigated. In addition to topographie studies, some examples of STM as local probe are given. It is proposed that STM be increasingly incorporated as a technique for investigation of real materials problems.
Gimzewski, J.
International Nuclear Information System (INIS)
Adrenal scanning with 131I-Adosterol is very useful and rather non-invasive than adrenal angiography in children. It is possible to diagnose various diseases of the adrenal glands not only structural but also functional abnormalities. In patients with adrenogenital syndromes, we are able to demonstrate hyperplasia of the adrenal glands, and in patients with aldosteronism or Cushing's syndrome differential diagnosis between bilateral hyperplasia and functional adenoma of the adrenal gland can be made. (author)
Energy Technology Data Exchange (ETDEWEB)
A scanning micro-sclerometer measures changes in contact stiffness and correlates these changes to characteristics of a scratch. A known force is applied to a contact junction between two bodies and a technique employing an oscillating force is used to generate the contact stiffness between the two bodies. As the two bodies slide relative to each other, the contact stiffness changes. The change is measured to characterize the scratch.
Oliver, Warren C. (Knoxville, TN); Blau, Peter J. (Oak Ridge, TN)
Energy Technology Data Exchange (ETDEWEB)
A scanning micro-sclerometer measures changes in contact stiffness and correlates these changes to characteristics of a scratch. A known force is applied to a contact junction between two bodies and a technique employing an oscillating force is used to generate the contact stiffness between the two bodies. As the two bodies slide relative to each other, the contact stiffness changes. The change is measured to characterize the scratch. 2 figs.
Oliver, W.C.; Blau, P.J.
Identifying biological landmarks using a novel cell measuring image analysis tool: Cell-o-Tape
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Full Text Available Abstract Background The ability to quantify the geometry of plant organs at the cellular scale can provide novel insights into their structural organization. Hitherto manual methods of measurement provide only very low throughput and subjective solutions, and often quantitative measurements are neglected in favour of a simple cell count. Results We present a tool to count and measure individual neighbouring cells along a defined file in confocal laser scanning microscope images. The tool allows the user to extract this generic information in a flexible and intuitive manner, and builds on the raw data to detect a significant change in cell length along the file. This facility can be used, for example, to provide an estimate of the position of transition into the elongation zone of an Arabidopsis root, traditionally a location sensitive to the subjectivity of the experimenter. Conclusions Cell-o-tape is shown to locate cell walls with a high degree of accuracy and estimate the location of the transition feature point in good agreement with human experts. The tool is an open source ImageJ/Fiji macro and is available online.
French Andrew P
International Nuclear Information System (INIS)
Eighty-six patients of neuroblastoma ranging in age from four months to 15 years were studied with 99mTc-MDP (methylene diphosphonate) for total skeletal survey over a period of seven years (1983-1990). The diagnosis of neuroblastoma as based on bone marrow examination, FNAC, lymph node biopsy, histopathology. Bone imaging was performed three hrs. after intravenous administration of 99mTc-MDP. Out of 86 patients, 45 patients had positive bone scan showing osseous concentration in 122 sites and extraosseous concentration in 34 sites. Seven patients had liver metastases. None of these liver metastases showed concentration of MDP. Fourteen patients underwent surgery for the primary tumour at the time of bone scanning. Ten patients were studied at the time of follow up, of which four patients showed good response as bony metastases were not demonstrated on bone scintigraphy and X-rays. In conclusion, bone scan is an useful test in neuroblastoma in delineating the bony metastases and also in assessing the efficacy of chemotherapy in these patients. (author). 12 refs., 2 figs., 3 tabs