WorldWideScience
1

Direct detection and isolation of restriction landmark genomic scanning (RLGS) spot DNA markers tightly linked to a specific trait by using the RLGS spot-bombing method.  

OpenAIRE

We have developed a technique for isolating DNA markers tightly linked to a target region that is based on RLGS, named RLGS spot-bombing (RLGS-SB). RLGS-SB allows us to scan the genome of higher organisms quickly and efficiently to identify loci that are linked to either a target region or gene of interest. The method was initially tested by analyzing a C57BL/6-GusS mouse congenic strain. We identified 33 variant markers out of 10,565 total loci in a 4.2-centimorgan (cM) interval surrounding ...

Okazaki, Y.; Hirose, K.; Hirotsune, S.; Okuizumi, H.; Sasaki, N.; Ohsumi, T.; Yoshiki, A.; Kusakabe, M.; Muramatsu, M.; Kawai, J.

1995-01-01

2

Arterial tree tracking from anatomical landmarks in magnetic resonance angiography scans  

Science.gov (United States)

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

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

2014-03-01

3

Restriction landmark cDNA scanning (RLCS): a novel cDNA display system using two-dimensional gel electrophoresis.  

OpenAIRE

We have developed a new method, designated restriction landmark cDNA scanning (RLCS), which displays many cDNA species quantitatively and simultaneously as two-dimensional gel spots. In this method cDNA species of uniform length were prepared for each mRNA species using restriction enzymes. After the restriction enzyme sites were radiolabeled as landmarks, the labeled fragments were subjected to high resolution two-dimensional gel electrophoresis. In analyses of cDNA samples from adult mouse ...

Suzuki, H.; Yaoi, T.; Kawai, J.; Hara, A.; Kuwajima, G.; Wantanabe, S.

1996-01-01

4

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.

2007-04-27

5

Clinical applications of Genome Polymorphism Scans  

OpenAIRE

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 ...

Weber James L

2006-01-01

6

Genome-Wide Scan Reveals Mutation Associated with Melanoma  

Science.gov (United States)

... 2000 1999 Spotlight on Research 2012 July 2012 Genome-Wide Scan Reveals Mutation Associated with Melanoma A ... out to see if a technology called whole genome sequencing would help them find other genetic risk ...

7

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.

8

A note on generalized Genome Scan Meta-Analysis statistics  

OpenAIRE

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

Feng Anne C; Koziol James A

2005-01-01

9

Uninformative polymorphisms bias genome scans for signatures of selection  

Directory of Open Access Journals (Sweden)

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

Roesti Marius

2012-06-01

10

Ranks of Genuine Associations in Whole-Genome Scans  

OpenAIRE

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.

2005-01-01

11

A note on generalized Genome Scan Meta-Analysis statistics  

Directory of Open Access Journals (Sweden)

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

Feng Anne C

2005-02-01

12

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

Science.gov (United States)

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

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

2013-02-01

13

Genome scan for linkage to Gilles de la Tourette syndrome  

Energy Technology Data Exchange (ETDEWEB)

Gilles de la Tourette Syndrome (TS) is a familial, neuropsychiatric disorder characterized by chronic, intermittent motor and vocal tics. In addition to tics, affected individuals frequently display symptoms such as attention-deficit hyperactivity disorder and/or obsessive compulsive disorder. Genetic analyses of family data have suggested that susceptibility to the disorder is most likely due to a single genetic locus with a dominant mode of transmission and reduced penetrance. In the search for genetic linkage for TS, we have collected well-characterized pedigrees with multiple affected individuals on whom extensive diagnostic evaluations have been done. The first stage of our study is to scan the genome systematically using a panel of uniformly spaced (10 to 20 cM), highly polymorphic, microsatellite markers on 5 families segregating TS. To date, 290 markers have been typed and 3,660 non-overlapping cM of the genome have been excluded for possible linkage under the assumption of genetic homogeneity. Because of the possibility of locus heterogeneity overall summed exclusion is not considered tantamount to absolute exclusion of a disease locus in that region. The results from each family are carefully evaluated and a positive lod score in a single family is followed up by typing closely linked markers. Linkage to TS was examined by two-point analysis using the following genetic model: single autosomal dominant gene with gene frequency .003 and maximum penetrance of .99. An age-of-onset correction is included using a linear function increasing from age 2 years to 21 years. A small rate of phenocopies is also incorporated into the model. Only individuals with TS or CMT according to DSM III-R criteria were regarded as affected for the purposes of this summary. Additional markers are being tested to provide coverage at 5 cM intervals. Moreover, we are currently analyzing the data non-parametrically using the Affected-Pedigree-Member Method of linkage analysis.

Barr, C.L.; Livingston, J.; Williamson, R. [and others

1994-09-01

14

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

Science.gov (United States)

An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 complex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak. PMID:18176787

Xiong, ZhaoHui; Wei, CanDong; Yang, Jian; Peng, JunPing; Xu, XingYe; Wang, Yu; Jin, Qi

2008-01-01

15

Genome scans and elusive candidate genes: detecting the variation that matters for speciation.  

Science.gov (United States)

Next-generation sequencing is providing us with vast amounts of genetic data, yet we are currently struggling in our attempts to make sense of them. In particular, it has proven difficult to link phenotypic divergence and speciation to genome level divergence. In the current issue of Molecular Ecology, Ruegg et al. () present new empirical results from two closely related bird taxa. They use a promising approach combining genome scan and candidate gene analysis. Their results suggest that we may have been looking in vain for candidate speciation genes by focusing only on genes found within genomic islands of divergence. This is because genes important in divergence and speciation may not be detected by genome scans and because features of the genomic architecture per se may have a large effect on the pattern of genome divergence. PMID:25263403

Sætre, Glenn-Peter

2014-10-01

16

Landmark Main Idea  

Science.gov (United States)

In this lesson, students will use key details to determine the main idea of informational text about landmarks. For the summative assessment, students will work in small groups to read an informational text about landmarks, fill out a Main Idea Pyramid Graphic Organizer, and then create a poster in the shape of the landmark they read about. Students will utilize the information on their graphic organizer when creating their poster.

Amanda Shipley

2012-07-23

17

Genomic scans for selective sweeps using SNP data  

OpenAIRE

Detecting selective sweeps from genomic SNP data is complicated by the intricate ascertainment schemes used to discover SNPs, and by the confounding influence of the underlying complex demographics and varying mutation and recombination rates. Current methods for detecting selective sweeps have little or no robustness to the demographic assumptions and varying recombination rates, and provide no method for correcting for ascertainment biases. Here, we present several new tests aimed at detect...

Nielsen, Rasmus; Williamson, Scott; Kim, Yuseob; Hubisz, Melissa J.; Clark, Andrew G.; Bustamante, Carlos

2005-01-01

18

Full-Genome Scan for Linkage in 50 Families Segregating the Bipolar Affective Disease Phenotype  

OpenAIRE

A genome scan of ?12-cM initial resolution was done on 50 of a set of 51 carefully ascertained unilineal multiplex families segregating the bipolar affective disorder phenotype. In addition to standard multipoint linkage analysis methods, a simultaneous-search algorithm was applied in an attempt to surmount the problem of genetic heterogeneity. The results revealed no linkage across the genome. The results exclude monogenic models and make it unlikely that two ge...

Friddle, Carl; Koskela, Rebecca; Ranade, Koustubh; Hebert, Joan; Cargill, Michele; Clark, Chris D.; Mcinnis, Melvin; Simpson, Sylvia; Mcmahon, Francis; Stine, O. Colin; Meyers, Deborah; Xu, Jianfeng; Mackinnon, Dean; Swift-scanlan, Theresa; Jamison, Kay

1999-01-01

19

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

Directory of Open Access Journals (Sweden)

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

Børglum Anders D

2011-07-01

20

A Genome Scan for Selection Signatures in Pigs  

Science.gov (United States)

Identifying signatures of selection can provide a straightforward insight into the mechanism of artificial selection and further uncover the causal genes related to the phenotypic variation. Based on Illumina Porcine60KSNP chip data, four complementary methods, Long-Range Haplotype (LRH), Tajima’s D, Cross Population Extend Haplotype Homozygosity Test (XPEHH) and FST, were implemented in this study to detect the selection signatures in the whole genome of one typical Chinese indigenous breed, Rongchang, one Chinese cultivated breed, Songliao, and two western breeds, Landrace and Yorkshire. False Discovery Rate (FDR) was implemented to control the false positive rates. In our study, a total of 159, 127, 179 and 159 candidate selection regions with average length of 0.80 Mb, 0.73 Mb, 0.78 Mb and 0.73 Mb were identified in Landrace, Rongchang, Songliao and Yorkshire, respectively, that span approximately 128.00 Mb, 92.38 Mb, 130.30 Mb and 115.40 Mb and account for approximately 3.74–5.33% of genome across all autosomes. The selection regions of 11.52 Mb shared by Landrace and Yorkshire were the longest when chosen pairs from the pool of the four breeds were examined. The overlaps between Yorkshire and Songliao, approximately 9.20 Mb, were greater than those of Yorkshire and Rongchang. Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang. Bioinformatics analysis showed that the genes/QTLs relevant to fertility, coat color, and ear morphology were found in candidate selection regions. Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds. PMID:25756180

Ma, Yunlong; Wei, Julong; Zhang, Qin; Chen, Lei; Wang, Jinyong; Liu, Jianfeng; Ding, Xiangdong

2015-01-01

21

A GENOME SCAN FOR LOCI AFFECTING PORK QUALITY IN A DUROC-LANDRACE F2 POPULATION  

Science.gov (United States)

A genome scan was conducted on 370 F2 Duroc-Landrace pigs. Microsatellite markers (n = 182) were genotyped across the entire F2 population, all F1 parents and the paternal grandparents. Breed of origin of all chromosomal segments inherited in F2 progeny were predicted using GenoProb, where genotypic...

22

Genome-wide scans using archived neonatal dried blood spot samples  

DEFF Research Database (Denmark)

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

Hollegaard, Mads; Grauholm, Jonas

2009-01-01

23

Genome-wide scans using archived neonatal dried blood spot samples  

Directory of Open Access Journals (Sweden)

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

Wiuf Carsten

2009-07-01

24

An Empirical Bayes Method for Updating Inferences in Analysis of Quantitative Trait Loci Using Information From Related Genome Scans  

OpenAIRE

Individual genome scans for quantitative trait loci (QTL) mapping often suffer from low statistical power and imprecise estimates of QTL location and effect. This lack of precision yields large confidence intervals for QTL location, which are problematic for subsequent fine mapping and positional cloning. In prioritizing areas for follow-up after an initial genome scan and in evaluating the credibility of apparent linkage signals, investigators typically examine the results of other genome sc...

Zhang, Kui; Wiener, Howard; Beasley, Mark; George, Varghese; Amos, Christopher I.; Allison, David B.

2006-01-01

25

City of Chicago Landmarks  

Science.gov (United States)

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

26

The use of sequential designs in genome scans for asthma susceptibility loci with affected sib pairs.  

Science.gov (United States)

We use optimized group sequential study designs to analyze data from two genome scans (German and CSGA) for asthma susceptibility loci with affected sib pairs from Genetic Analysis Workshop (GAW) 12. Results are compared with those from a fixed sample design and the sequential probability ratio test (SPRT). The SPRT does not reach significance at any position. Using the fixed sample design, evidence for linkage is found on chromosomes 6 and 9 in the German and on chromosome 1 in the CSGA scan. The group sequential designs identify the same regions on chromosomes 1 and 6 with a reduced sample size. PMID:11793724

Böddeker, I R; Müller, H H; Kress, R; Geller, F; Ziegler, A; Schäfer, H

2001-01-01

27

Linkage disequilibrium across two different single-nucleotide polymorphism genome scans  

OpenAIRE

Abstract 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 fo...

Warren Diane M; Dyer Thomas D; Peralta Juan; Blangero John; Almasy Laura

2005-01-01

28

A new imprinted gene cloned by a methylation-sensitive genome scanning method.  

OpenAIRE

We cloned a new imprinted gene by searching for parental-origin-specific CpG methylations using methylation-sensitive two-dimensional genome scanning method. This gene encodes a putative 51 kDa protein with significant similarity to U2 small nuclear ribonucleoprotein auxiliary factor small subunits, an essential mammalian splicing factor, and is located on mouse chromosome 11, of which maternal duplication/paternal deficiency results in a small body.

Hatada, I.; Sugama, T.; Mukai, T.

1993-01-01

29

Structural equation model-based genome scan for the metabolic syndrome  

OpenAIRE

Abstract Background The metabolic syndrome is characterized by the clustering of several traits, including obesity, hypertension, decreased levels of HDL cholesterol, and increased levels of glucose and triglycerides. Because these traits cluster, there are likely common genetic factors involved. Results We used a multivariate structural equation model (SEM) approach to scan the genome for loci involved in the metabolic syndrome. We found moderate evidence for linkage on chromosomes 2, 3, 11,...

Tiwari Hemant K; Jun Gyungah; Elston Robert C; Song Yeunjoo; Stein Catherine M; Iyengar Sudha K

2003-01-01

30

Defining the power limits of genome-wide association scan meta-analyses  

OpenAIRE

Large-scale meta-analyses of genome-wide association scans (GWAS) have been successful in discovering common risk variants with modest and small effects. The detection of lower frequency signals will undoubtedly require concerted efforts of at least similar scale. We investigate the sample size-dictated power limits of GWAS meta-analyses, in the presence and absence of modest levels of heterogeneity and across a range of different allelic architectures. We find that data combination through l...

Chapman, Kay; Ferreira, Teresa; Morris, Andrew; Asimit, Jennifer; Zeggini, Eleftheria

2011-01-01

31

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

DEFF Research Database (Denmark)

Background The search to identify disease-susceptible genes requires access to biological material from numerous well-characterized subjects. Archived residual dried blood spot (DBS) samples, also known as Guthrie cards, from national newborn screening programs may provide a DNA source for entire populations. Combined with clinical information from medical registries, DBS samples could provide a rich source for productive research. However, the amounts of DNA which can be extracted from these precious samples are minute and may be prohibitive for numerous genotypings. Previously, we demonstrated that DBS DNA can be whole-genome amplified and used for reliable genetic analysis on different platforms, including genome-wide scanning arrays. However, it remains unclear whether this approach is workable on a large sample scale. We examined the robustness of using DBS samples for whole-genome amplification following genome-wide scanning, using arrays from Illumina and Affymetrix. Results This study is based on 4,641 DBS samples from the Danish Newborn Screening Biobank, extracted for three separate genome-wide association studies. The amount of amplified DNA was significantly (P < 0.05) affected by the year of storage and storage conditions. Nine (0.2%) DBS samples failed whole-genome amplification. A total of 4,586 (98.8%) samples met our criterion of success of a genetic call-rate above 97%. The three studies used different arrays, with mean genotyping call-rates of 99.385% (Illumina Infinium Human610-Quad), 99.722% (Illumina Infinium HD HumanOmni1-Quad), and 99.206% (Affymetrix Axiom Genome-Wide CEU). We observed a concordance rate of 99.997% in the 38 methodological replications, and 99.999% in the 27 technical replications. Handling variables such as time of storage, storage conditions and type of filter paper were shown too significantly (P < 0.05) affect the genotype call-rates in some of the arrays, although the effect was minimal. Conclusion Our study indicates that archived DBS samples from the Danish Newborn Screening Biobank represent a reliable resource of DNA for whole-genome amplification and subsequent genome-wide association studies. With call-rates equivalent to high quality DNA samples, our results point to new opportunities for using the neonatal biobanks available worldwide in the hunt for genetic components of disease.

Hollegaard, Mads V; Grove, Jakob

2011-01-01

32

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 fad 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)

33

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

2004-01-01

34

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

OpenAIRE

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

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

2014-01-01

35

Ordered Landmarks in Planning  

CERN Document Server

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

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

2011-01-01

36

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

Science.gov (United States)

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

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

2013-01-01

37

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

Science.gov (United States)

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

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

2013-03-19

38

Genome scans for the contemporary response to selection in quantitative traits.  

Science.gov (United States)

Genome scans have been an important approach for discovering historical signatures of selection in both model and nonmodel species. An exciting new experimental design for genome scans is to measure the change in allele frequency before and after contemporary selection within a generation, from a single population. The most widely-used methods, however, have two major limitations: they are based on testing one locus at a time, and they only have power to uncover loci that have evolved under relatively strong selection. On the other hand, complex quantitative traits are common in nature and are caused by several loci of small effect. Selection on a quantitative trait at the phenotypic level is predicted to be accompanied by subtle allele frequency changes in many loci that covary (a polygenic soft sweep), rather than a large, single-effect allele (a selective sweep). In this issue of Molecular Ecology, Bourret et al. (2014) measure the contemporary response to natural selection across the genome in multiple cohorts of Atlantic salmon during their first year at sea. They introduce a multilocus framework based on groups of markers that covary in their genotypic distribution. While the traditional, single-locus approach did not find evidence for repeated patterns of selection, the multivariate approach found that a group of covarying SNPs was selected for in different cohorts at one site. Their multilocus framework has potential to be a more fruitful approach for uncovering the genomic basis of adaptation in quantitative traits, although caution should be applied as the framework has yet to be validated with simulated data. PMID:25208503

Lotterhos, Katie E; Schaal, Sara M

2014-09-01

39

Genome scan for human obesity and linkage to markers in 20q13.  

OpenAIRE

Obesity is a highly prevalent, multigenic trait that predicts increased morbidity and mortality. Here we report results from a genome scan based on 354 markers in 513 members of 92 nuclear families ascertained through extreme obesity and normal body weight. The average marker interval was approximately 10 cM. We examined four correlated obesity phenotypes, including the body-mass index (BMI) (both as a quantitative trait and as a discrete trait with a threshold of BMI > or /=30 kg/m2) and per...

Lee, J. H.; Reed, D. R.; Li, W. D.; Xu, W.; Joo, E. J.; Kilker, R. L.; Nanthakumar, E.; North, M.; Sakul, H.; Bell, C.; Price, R. A.

1999-01-01

40

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

Directory of Open Access Journals (Sweden)

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

Guimarães Simone EF

2010-04-01

41

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

Science.gov (United States)

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. PMID:20433753

2010-01-01

42

Genome-wide scans detect adaptation to aridity in a widespread forest tree species.  

Science.gov (United States)

Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient in southeastern Australia. Using a Bayesian analysis, we identified a suite of 94 putatively adaptive (outlying) sequence-tagged markers across the genome. Population-level allele frequencies of these outlier markers were strongly correlated with temperature and moisture availability at the site of origin, and with population differences in functional traits measured in two common gardens. Using the output from a canonical analysis of principal coordinates, we devised a metric that provides a holistic measure of genomic adaptation to aridity that could be used to guide assisted migration or genetic augmentation. PMID:24750317

Steane, Dorothy A; Potts, Brad M; McLean, Elizabeth; Prober, Suzanne M; Stock, William D; Vaillancourt, René E; Byrne, Margaret

2014-05-01

43

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

Directory of Open Access Journals (Sweden)

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

Regan Kelly R

2010-05-01

44

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

Directory of Open Access Journals (Sweden)

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

Gasser Thomas

2007-07-01

45

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

OpenAIRE

Genome-wide linkage and association studies have uncovered variants associated with sarcoidosis, a multi-organ granulomatous inflammatory disease. African ancestry may influence disease pathogenesis since African Americans are more commonly affected by sarcoidosis. Therefore, we conducted the first sarcoidosis genome-wide ancestry scan using a map of 1,384 highly ancestry informative single nucleotide polymorphisms genotyped on 1,357 sarcoidosis cases and 703 unaffected controls self-identifi...

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

2010-01-01

46

Genome-wide association scan in psoriasis: new insights into chronic inflammatory disease.  

Science.gov (United States)

Evaluation of: Liu Y, Helms C, Liao W et al. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. PLoS Genet. 4, e1000041 (2008). Genome-wide association scans have delivered on their promise of revealing susceptibility polymorphisms underlying common diseases. This comprehensive psoriasis study by Liu and colleagues reports confirmation of previously identified genes (HLA-C, IL12B and IL23R), identifies several novel psoriasis loci and is the first to report psoriatic arthritis association on a genome-wide scale. Along with other recent studies, this work gives further evidence that IL-23-mediated signaling is a key component of both psoriasis and psoriatic arthritis pathogenesis. Importantly, this study provides evidence of a single-nucleotide polymorphism (SNP), 35 kb upstream of HLA-C, which is stronger than Cw 0602 - the variant traditionally attributed to the MHC-linked psoriasis-susceptibility effect. Within this region, the authors also discovered an independent SNP with very strong predisposing effects. SNPs in the COG6 region and the USP8-TNFAIP8l3 region are among the novel psoriasis associations reported. In addition, a region showing linkage on chromosome 1q demonstrated association in the epidermal differentiation complex. Four SNPs over a 439-kb region on chromosome 4q27, where KIAA1109, ADAD1 and two cytokine-encoding genes (IL2 and IL21) reside, exhibit intriguing correlation with psoriatic arthritis, although the signal strength is moderate. These results, while still preliminary, may substantially expand our knowledge of psoriasis and psoriatic arthritis genetics, opening new avenues of chronic inflammatory disease research. PMID:20476959

Schrodi, Steven J

2008-09-01

47

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

Science.gov (United States)

A genome scan for chromosomal regions influencing body conformation traits was conducted for a population of Spanish Churra dairy sheep following a daughter design. A total of 739 ewes from 11 half-sib sire families were included in the study. The ewes were scored for the 5 linear traits used in the breeding scheme of the Churra breed to assess body conformation: stature, rear legs-rear view, foot angle, rump width, and general appearance. All the animals, including the 11 sires, were genotyped for 181 microsatellite markers evenly distributed across the 26 sheep autosomes. Using the yield deviations of the raw scores adjusted for fixed factors as phenotypic measurements, a quantitative trait loci (QTL) analysis was performed on the basis of a multi-marker regression method. Seven suggestive QTL were identified on chromosomes Ovis aries (OAR)2, OAR5, OAR16, OAR23, and OAR26, but none reached a genome-wise significance level. Putative QTL were identified for all of the traits analyzed, except for general appearance score. The suggestive QTL showing the highest test statistic influenced rear legs-rear view and was localized on OAR16, close to the growth hormone receptor coding gene, GHR. Some of the putative linkage associations reported here are consistent with previously reported QTL in cattle for similar traits. To the best of our knowledge, this study provides the first report of QTL for body conformation traits in dairy sheep; further studies will be needed to confirm and redefine the linkage associations reported herein. It is expected that future genome-wide association analyses of larger families will help identify genes underlying these putative genetic effects and provide useful markers for marker-assisted selection of such functional traits. PMID:21787947

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

2011-08-01

48

Genome-Wide Linkage Scan for Genes Influencing Plasma Triglyceride Levels in the Veterans Administration Genetic Epidemiology Study  

OpenAIRE

OBJECTIVE—Elevated plasma triglyceride concentration is a component of the insulin resistance syndrome and is commonly associated with type 2 diabetes, obesity, and coronary heart disease. The goal of our study was to perform a genome-wide linkage scan to identify genetic regions that influence variation in plasma triglyceride levels in families that are enriched with individuals with type 2 diabetes.

Coletta, Dawn K.; Schneider, Jennifer; Hu, Shirley L.; Dyer, Thomas D.; Puppala, Sobha; Farook, Vidya S.; Arya, Rector; Lehman, Donna M.; Blangero, John; Defronzo, Ralph A.; Duggirala, Ravindranath; Jenkinson, Christopher P.

2009-01-01

49

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

Science.gov (United States)

Recent advances in population genomics have triggered great interest in the genomic landscape of divergence in taxa with 'porous' species boundaries. One important obstable of previous studies of this topic was the low genomic coverage achieved. This issue can now be overcome by the use of 'next generation' or short-read DNA-sequencing approaches capable of assaying many thousands of single nucleotide polymorphisms (SNPs) in divergent species. We have scanned the 'porous' genomes of Populus alba and Populus tremula, two ecologically divergent hybridizing forest trees, using >38,000 SNPs assayed by restriction site associated DNA (RAD) sequencing. Windowed analyses indicate great variation in genetic divergence (e.g. the proportion of fixed SNPs) between species, and these results are unlikely to be strongly biased by genomic features of the Populus trichocarpa reference genome used for SNP calling. Divergence estimates were significantly autocorrelated (P blocks, thus suggesting that allele sharing was caused by recurrent gene flow rather than shared ancestral polymorphism. A conspicuous low divergence block of three megabases was detected on chromosome XIX, recently put forward as an incipient sex chromosome in Populus, and was largely congruent with introgression of mapped microsatellites in two natural hybrid zones (N > 400). Our results help explain the origin of the 'genomic mosaic' seen in these taxa with 'porous' genomes and suggest rampant introgression or extensive among-species conservation of an incipient plant sex chromosome. RAD sequencing holds great promise for detecting patterns of divergence and gene flow in highly divergent hybridizing species. PMID:22967258

Stölting, Kai N; Nipper, Rick; Lindtke, Dorothea; Caseys, Celine; Waeber, Stephan; Castiglione, Stefano; Lexer, Christian

2013-02-01

50

Landmarks GIScience for intelligent services  

CERN Document Server

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

Richter, Kai-Florian

2014-01-01

51

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

Science.gov (United States)

High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure) exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans) separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2), shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association studies necessary to confirm the role of selection-nominated candidate genes and gene regions in adaptation to altitude. PMID:20838600

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

2010-09-01

52

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

OpenAIRE

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...

Moradi Mohammad Hossein; Nejati-Javaremi Ardeshir; Moradi-Shahrbabak Mohammad; Dodds Ken G; McEwan John C

2012-01-01

53

A computational scan for U12-dependent introns in the human genome sequence  

OpenAIRE

U12-dependent introns are found in small numbers in most eukaryotic genomes, but their scarcity makes accurate characterisation of their properties challenging. A computational search for U12-dependent introns was performed using the draft version of the human genome sequence. Human expressed sequences confirmed 404 U12-dependent introns within the human genome, a 6-fold increase over the total number of non-redundant U12-dependent introns previously identified in all genomes. Although most o...

Levine, Aaron; Durbin, Richard

2001-01-01

54

Novel approach for genome scan meta-analysis of rheumatoid arthritis: a kernel-based estimation procedure  

OpenAIRE

Abstract Genome scan meta-analysis (GSMA) can prove very useful in detecting genetic effects too small to be detected in an individual linkage study and can also lead to more consistent results. In this paper, we propose a new kernel-based estimation procedure for GSMA. Instead of estimating identity by descent between markers, as performed in interval mapping approaches, we estimated directly the nonparametric linkage score between markers using a kernel procedure. The GSMA is then extended ...

Briollais Laurent; Durrieu Gilles; Upathilake Ranodya

2007-01-01

55

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method.  

Science.gov (United States)

Although genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in 'pair' and 'transect' sampling strategies. We compared FST outlier and genetic-environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (FST or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and FST had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation and have important implications for the interpretation of genome scans based on landscape data. PMID:25648189

Lotterhos, Katie E; Whitlock, Michael C

2015-03-01

56

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

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Several statistical tests have been developed for analyzing genome-wide association data by incorporating gene pathway information in terms of gene sets. Using these methods, hundreds of gene sets are typically tested, and the tested gene sets often overlap. This overlapping greatly increases the probability of generating false positives, and the results obtained are difficult to interpret, particularly when many gene sets show statistical significance. Results We propose a flexible statistical framework to circumvent these problems. Inspired by spatial scan statistics for detecting clustering of disease occurrence in the field of epidemiology, we developed a scan statistic to extract disease-associated gene clusters from a whole gene pathway. Extracting one or a few significant gene clusters from a global pathway limits the overall false positive probability, which results in increased statistical power, and facilitates the interpretation of test results. In the present study, we applied our method to genome-wide association data for rare copy-number variations, which have been strongly implicated in common diseases. Application of our method to a simulated dataset demonstrated the high accuracy of this method in detecting disease-associated gene clusters in a whole gene pathway. Conclusions The scan statistic approach proposed here shows a high level of accuracy in detecting gene clusters in a whole gene pathway. This study has provided a sound statistical framework for analyzing genome-wide rare CNV data by incorporating topological information on the gene pathway.

Scherer Stephen W

2011-05-01

57

Genomic scan reveals loci under altitude adaptation in Tibetan and Dahe pigs.  

Science.gov (United States)

High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP) that is well adapted to the high altitude and Dahe pig (DHP) that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using FST to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP) as the low-altitude reference. Totally, we identified 12 specific selective genes (CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C, VEGFC and ADAM19) for TBP and six (OGG1, FOXM, FLT3, RTEL1, CRELD1 and RHOG) for DHP. In addition, six selective genes (VPS13A, GNA14, GDAP1, PARP8, FGF10 and ADAMTS16) were shared by the two pig breeds. Among these selective genes, three (VEGFC, FGF10 and ADAMTS9) were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes. PMID:25329542

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

2014-01-01

58

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

Science.gov (United States)

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

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

2014-12-01

59

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

DEFF Research Database (Denmark)

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

Fagertun, Jens; Harder, Stine

2014-01-01

60

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

International Nuclear Information System (INIS)

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

61

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

Directory of Open Access Journals (Sweden)

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

Avramopoulos Dimitrios

2006-06-01

62

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

OpenAIRE

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 ...

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.

2009-01-01

63

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

Directory of Open Access Journals (Sweden)

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

Law Andrew

2011-01-01

64

Genome wide scan in a Flemish inflammatory bowel disease population: support for the IBD4 locus, population heterogeneity, and epistasis  

Science.gov (United States)

Background and aims: Genome wide scans in inflammatory bowel disease (IBD) have indicated various susceptibility regions with replication of 16cen (IBD1), 12q (IBD2), 6p (IBD3), 14q11 (IBD4), and 3p21. As no linkage was previously found on IBD regions 3, 7, 12, and 16 in Flemish IBD families, a genome wide scan was performed to detect other susceptibility regions in this population. Methods: A cohort of 149 IBD affected relative pairs, all recruited from the Northern Flemish part of Belgium, were genotyped using microsatellite markers at 12 cM intervals, and analysed by Genehunter non-parametric linkage software. All families were further genotyped for the three main Crohn’s disease associated variants in the NOD2/CARD15 gene. Results: Nominal evidence for linkage was observed on chromosomes 1 (D1S197: multipoint non-parametric linkage (NPL) score 2.57, p?=?0.004; and at D1S305-D1S252: NPL 2.97, p?=?0.001), 4q (D4S406: NPL 1.95, p?=?0.03), 6q16 (D6S314: NPL 2.44, p?=?0.007), 10p12 (D10S197: NPL 2.05, p?=?0.02), 11q22 (D11S35-D11S927: NPL 1.95, p?=?0.02) 14q11-12 (D14S80: NPL 2.41, p?=?0.008), 20p12 (D20S192: NPL 2.7, p?=?0.003), and Xq (DXS990: NPL 1.70, p?=?0.04). A total of 51.4% of patients carried at least one NOD2/CARD15 variant. Furthermore, epistasis was observed between susceptibility regions 6q/10p and 20p/10p. Conclusion: Genome scanning in a Flemish IBD population found nominal evidence for linkage on 1p, 4q, 10p12, and 14q11, overlapping with other genome scan results, with linkage on 14q11-12 supporting the IBD4 locus. The results further show that epistasis is contributing to the complex model of IBD and indicate that population heterogeneity is not to be underestimated. Finally, NOD2/CARD15 is clearly implicated in the Flemish IBD population. PMID:15194648

Vermeire, S; Rutgeerts, P; Van Steen, K; Joossens, S; Claessens, G; Pierik, M; Peeters, M; Vlietinck, R

2004-01-01

65

Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex.  

Science.gov (United States)

A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome-wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a species complex of divergent host races, to explore the organization of the genomic divergence associated with host plant adaptation and ecological speciation. We analysed 390 microsatellite markers located at variable distances from predicted genes in replicate samples of sympatric populations of the pea aphid collected on alfalfa, red clover and pea, which correspond to three common host-adapted races reported in this species complex. Using a method that accounts for the hierarchical structure of our data set, we found a set of 11 outlier loci that show higher genetic differentiation between host races than expected under the null hypothesis of neutral evolution. Two of the outliers are close to olfactory receptor genes and three other nearby genes encoding salivary proteins. The remaining outliers are located in regions with genes of unknown functions, or which functions are unlikely to be involved in interactions with the host plant. This study reveals genetic signatures of divergent selection across the genome and provides an inventory of candidate genes responsible for plant specialization in the pea aphid, thereby setting the stage for future functional studies. PMID:23017212

Jaquiéry, J; Stoeckel, S; Nouhaud, P; Mieuzet, L; Mahéo, F; Legeai, F; Bernard, N; Bonvoisin, A; Vitalis, R; Simon, J-C

2012-11-01

66

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

Science.gov (United States)

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

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

2014-12-01

67

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

Directory of Open Access Journals (Sweden)

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

Prasad Aparna

2010-03-01

68

Anatomic Landmarks for the First Dorsal Compartment  

OpenAIRE

Objective: Knowledge of anatomic landmarks for the first dorsal compartment can assist clinicians with management of de Quervain's disease. The radial styloid, the scaphoid tubercle, and Lister's tubercle can be used as superficial landmarks for the first dorsal compartment. Methods: Thirty-two cadaveric wrists were dissected, and measurements were taken from the predetermined landmarks to the extensor retinaculum. The compartments were also inspected for variability of the abductor pollicis ...

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

2009-01-01

69

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

OpenAIRE

Since the divergence of humans and chimpanzees about 5 million years ago, these species have undergone a remarkable evolution with drastic divergence in anatomy and cognitive abilities. At the molecular level, despite the small overall magnitude of DNA sequence divergence, we might expect such evolutionary changes to leave a noticeable signature throughout the genome. We here compare 13,731 annotated genes from humans to their chimpanzee orthologs to identify genes that show evidence of posit...

Nielsen, Rasmus; Bustamante, Carlos; Clark, Andrew G.; Glanowski, Stephen; Sackton, Timothy B.; Hubisz, Melissa J.; Fledel-alon, Adi; Tanenbaum, David M.; Civello, Daniel; White, Thomas J.; J Sninsky, John; Adams, Mark D.; Cargill, Michele

2005-01-01

70

A genome-wide association scan on estrogen receptor -negative breast cancer  

OpenAIRE

Abstract Introduction Breast cancer is a heterogeneous disease and may be characterized on the basis of whether estrogen receptors (ER) are expressed in the tumour cells. ER status of breast cancer is important clinically, and is used both as a prognostic indicator and treatment predictor. In this study, we focused on identifying genetic markers associated with ER-negative breast cancer risk. Methods We conducted a genome-wide association analysis of 285,984 single nucleotide polymorphisms (S...

Li, Jingmei; Humphreys, Keith; Darabi, Hatef; Rosin, Gustaf; Hannelius, Ulf; Heikkinen, Tuomas; Aittomaki, Kristiina; Blomqvist, Carl; Pharoah, Paul D. P.; Dunning, Alison M.; Ahmed, Shahana; Hooning, Maartje J.; Hollestelle, Antoinette; Oldenburg, Rogier A.; Alfredsson, Lars

2010-01-01

71

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

OpenAIRE

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

2010-01-01

72

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

OpenAIRE

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

2010-01-01

73

Whole genome scan to detect quantitative trait loci for conformation and functional traits in dairy cattle  

OpenAIRE

A granddaughter design was used to locate quantitative trait loci determining conformation and functional traits in dairy cattle. In this granddaughter design, consisting of 20 Holstein Friesian grandsires and 833 sons, genotypes were determined for 277 microsatellite markers covering the whole genome. Breeding values for 27 traits, regarding conformation (18), fertility (2), birth (4), workability (2), and udder health (1), were evaluated in an across-family analysis using multimarker regres...

Schrooten, C.; Bovenhuis, H.; Coppieters, W.; Arendonk, J. A. M.

2000-01-01

74

A genome-wide scanning and fine mapping study of COGA data  

OpenAIRE

A thorough genetic mapping study was performed to identify predisposing genes for alcoholism dependence using the Collaborative Study on the Genetics of Alcoholism (COGA) data. The procedure comprised whole-genome linkage and confirmation analyses, single locus and haplotype fine mapping analyses, and gene × environment haplotype regression. Stratified analysis was considered to reduce the ethnic heterogeneity and simultaneously family-based and case-control study designs were applied to det...

Yang, Hsin-chou; Chang, Chien-ching; Chen, Chun-liang; Lin, Chin-yu; Fann, Cathy Sj

2005-01-01

75

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

OpenAIRE

To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist–hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified...

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

2009-01-01

76

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

OpenAIRE

To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N?=?38,580) informative for adult waist circumference (WC) and waist–hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identi...

Lindgren, Cecilia M.; Heid, Iris M.; Randall, Joshua C.; Lamina, Claudia; Steinthorsdottir, Valgerdur; Qi, Lu; Speliotes, Elizabeth K.; Thorleifsson, Gudmar; Willer, Cristen J.; Herrera, Blanca M.; Jackson, Anne U.; Lim, Noha; Scheet, Paul; Soranzo, Nicole; Amin, Najaf

2009-01-01

77

A Practical Subspace Approach To Landmarking  

Directory of Open Access Journals (Sweden)

Full Text Available A probabilistic, maximum aposteriori approach to finding landmarks in a face image is proposed, which provides a theoretical framework for template based landmarkers. One such landmarker, based on a likelihood ratio detector, is discussed in detail. Special attention is paid to training and implementation issues, in order to minimize storage and processing requirements. In particular a fast approximate singular value decomposition method is proposed to speed up the training process and implementation of the landmarker in the Fourier domain is presented that will speed up the search process. A subspace method for outlier correction and an iterative implementation of the landmarker are both shown to improve its accuracy. The impact of carefully tuning the many parameters of the method is illustrated. The method is extensively tested and compared with alternatives.

Gert Beumer

2010-06-01

78

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

LENUS (Irish Health Repository)

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

Anney, Richard

2010-10-15

79

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

DEFF Research Database (Denmark)

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

Nielsen, Rasmus; Bustamente, Carlos

2005-01-01

80

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

Science.gov (United States)

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

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

2010-10-15

81

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

Directory of Open Access Journals (Sweden)

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

Cordell Heather J

2007-12-01

82

A whole-genome scan for recurrent airway obstruction in Warmblood sport horses indicates two positional candidate regions.  

Science.gov (United States)

Recurrent airway obstruction (RAO), or heaves, is a naturally occurring asthma-like disease that is related to sensitisation and exposure to mouldy hay and has a familial basis with a complex mode of inheritance. A genome-wide scanning approach using two half-sibling families was taken in order to locate the chromosome regions that contribute to the inherited component of this condition in these families. Initially, a panel of 250 microsatellite markers, which were chosen as a well-spaced, polymorphic selection covering the 31 equine autosomes, was used to genotype the two half-sibling families, which comprised in total 239 Warmblood horses. Subsequently, supplementary markers were added for a total of 315 genotyped markers. Each half-sibling family is focused around a severely RAO-affected stallion, and the phenotype of each individual was assessed for RAO and related signs, namely, breathing effort at rest, breathing effort at work, coughing, and nasal discharge, using an owner-based questionnaire. Analysis using a regression method for half-sibling family structures was performed using RAO and each of the composite clinical signs separately; two chromosome regions (on ECA13 and ECA15) showed a genome-wide significant association with RAO at P RAO. Several candidate genes are located in these regions, a number of which are interleukins. These are important signalling molecules that are intricately involved in the control of the immune response and are therefore good positional candidates. PMID:19760324

Swinburne, June E; Bogle, Helen; Klukowska-Rötzler, Jolanta; Drögemüller, Michaela; Leeb, Tosso; Temperton, Elizabeth; Dolf, Gaudenz; Gerber, Vincent

2009-08-01

83

Autonomous Robot Navigation based on Visual Landmarks  

DEFF Research Database (Denmark)

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

Livatino, Salvatore

84

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

Science.gov (United States)

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

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

2013-07-01

85

Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica.  

Science.gov (United States)

Local adaptation is important in evolutionary processes and speciation. We used multiple tests to identify several candidate genes that may be involved in local adaptation from 1026 loci in 14 natural populations of Cryptomeria japonica, the most economically important forestry tree in Japan. We also studied the relationships between genotypes and environmental variables to obtain information on the selective pressures acting on individual populations. Outlier loci were mapped onto a linkage map, and the positions of loci associated with specific environmental variables are considered. The outlier loci were not randomly distributed on the linkage map; linkage group 11 was identified as a genomic island of divergence. Three loci in this region were also associated with environmental variables such as mean annual temperature, daily maximum temperature, maximum snow depth, and so on. Outlier loci identified with high significance levels will be essential for conservation purposes and for future work on molecular breeding. PMID:22929151

Tsumura, Y; Uchiyama, K; Moriguchi, Y; Ueno, S; Ihara-Ujino, T

2012-12-01

86

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

DEFF Research Database (Denmark)

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

Kolte, Astrid Marie; Nielsen, H S

2011-01-01

87

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

DEFF Research Database (Denmark)

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

Sahana, Goutam; Kadlecová, Veronika

2013-01-01

88

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

Directory of Open Access Journals (Sweden)

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

Teacher Amber GF

2012-12-01

89

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.  

Science.gov (United States)

This protocol shows how to detect putative cis-regulatory elements and regions enriched in such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat.ulb.ac.be/rsat/). The approach applies to known transcription factors, whose binding specificity is represented by position-specific scoring matrices, using the program matrix-scan. The detection of individual binding sites is known to return many false predictions. However, results can be strongly improved by estimating P value, and by searching for combinations of sites (homotypic and heterotypic models). We illustrate the detection of sites and enriched regions with a study case, the upstream sequence of the Drosophila melanogaster gene even-skipped. This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour. PMID:18802439

Turatsinze, Jean-Valery; Thomas-Chollier, Morgane; Defrance, Matthieu; van Helden, Jacques

2008-01-01

90

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

DEFF Research Database (Denmark)

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

Ocholla, Harold; Preston, Mark D

2014-01-01

91

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

Directory of Open Access Journals (Sweden)

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

Bumstead Nat

2005-09-01

92

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

Science.gov (United States)

To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N?=?38,580) informative for adult waist circumference (WC) and waist–hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P?=?1.9×10?11) and MSRA (WC, P?=?8.9×10?9). A third locus, near LYPLAL1, was associated with WHR in women only (P?=?2.6×10?8). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity. PMID:19557161

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; Nordström, Anna; Nordström, Peter; Oostra, Ben A.; Palmer, Colin N. A.; Payne, Felicity; Peden, John F.; Prokopenko, Inga; Renström, 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, André 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, Gonçalo R.; Hirschhorn, Joel N.; Loos, Ruth J. F.; Stefansson, Kari; Mohlke, Karen L.; Barroso, Inês; McCarthy for the GIANT consortium, Mark I.

2009-01-01

93

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2014-09-15

94

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

International Nuclear Information System (INIS)

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

95

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2000-03-01

96

23 CFR 750.710 - Landmark signs.  

Science.gov (United States)

...HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION RIGHT-OF-WAY AND ENVIRONMENT HIGHWAY BEAUTIFICATION Outdoor Advertising Control § 750.710 Landmark signs. (a) 23 U.S.C. 131(c) permits the existence of...

2010-04-01

97

75 FR 69120 - National Natural Landmark Designations  

Science.gov (United States)

...implications. National Natural Landmark preservation is made possible by the long- term...contains a rich fauna and significant paleontological deposits. The Chazy Fossil Reef is...Frost, Associate Director, Natural Resource Stewardship and Science....

2010-11-10

98

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

Science.gov (United States)

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

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

2014-11-01

99

Second stage of a genome scan of schizophrenia: study of five positive regions in an expanded sample.  

Science.gov (United States)

In a previous genome scan of 43 schizophrenia pedigrees, nonparametric linkage (NPL) scores with empirically derived pointwise P-values less than 0.01 were observed in two regions (chromosomes 2q12-13 and 10q23) and less than 0.05 in three regions (4q22-23, 9q22, and 11q21). Markers with a mean spacing of about 5 cM were typed in these regions in an expanded sample of 71 pedigrees, and NPL analyses carried out. No region produced significant genomewide evidence for linkage. On chromosome 10q, the empirical P-value remained at less than 0.01 for the entire sample (D10S168), evidence in the original 43 pedigrees was slightly increased, and a broad peak of positive results was observed. P-values less than 0.05 were observed on chromosomes 2q (D2S436) and 4q (D4S2623), but not on chromosomes 9q or 11q. It is concluded that this sample is most supportive of linkage on chromosome 10q, with less consistent support on chromosomes 2q and 4q. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:864-869, 2000. PMID:11121199

Mowry, B J; Ewen, K R; Nancarrow, D J; Lennon, D P; Nertney, D A; Jones, H L; O'Brien, M S; Thornley, C E; Walters, M K; Crowe, R R; Silverman, J M; Endicott, J; Sharpe, L; Hayward, N K; Gladis, M M; Foote, S J; Levinson, D F

2000-12-01

100

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

DEFF Research Database (Denmark)

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

Frayling, Timothy M; Lindgren, Cecilia M

2003-01-01

101

Genome-wide copy number scan identifies IRF6 involvement in Van der Woude syndrome in an Indian family.  

Science.gov (United States)

Summary Van der Woude syndrome (VWS) is an autosomal dominant developmental malformation presenting with bilateral lower lip pits related to cleft lip, cleft palate and other malformations. We performed a whole-genome copy number variations (CNVs) scan in an Indian family with members suffering from VWS using 2·6 million combined SNP and CNV markers. We found CNVs affecting IRF6, a known candidate gene for VWS, in all three cases, while none of the non-VWS members showed any CNVs in the IRF6 region. The duplications and deletions of the chromosomal critical region in 1q32-q41 confirm the involvement of CNVs in IRF6 in South Indian VWS patients. Molecular network analysis of these and other cleft lip/palate related module genes suggests that they are associated with cytokine-mediated signalling pathways and response to interferon-gamma mediated signalling pathways. This is a maiden study indicating the involvement of CNVs in IRF6 in causing VWS in the Indian population. PMID:25579819

Manjegowda, Dinesh S; Prasad, Manu; Veerappa, Avinash M; Ramachandra, Nallur B

2014-01-01

102

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

Science.gov (United States)

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

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

2010-11-01

103

3-D Facial Landmark Localization With Asymmetry Patterns and Shape Regression from Incomplete Local Features.  

Science.gov (United States)

We present a method for the automatic localization of facial landmarks that integrates nonrigid deformation with the ability to handle missing points. The algorithm generates sets of candidate locations from feature detectors and performs combinatorial search constrained by a flexible shape model. A key assumption of our approach is that for some landmarks there might not be an accurate candidate in the input set. This is tackled by detecting partial subsets of landmarks and inferring those that are missing, so that the probability of the flexible model is maximized. The ability of the model to work with incomplete information makes it possible to limit the number of candidates that need to be retained, drastically reducing the number of combinations to be tested with respect to the alternative of trying to always detect the complete set of landmarks. We demonstrate the accuracy of the proposed method in the face recognition grand challenge database, where we obtain average errors of approximately 3.5 mm when targeting 14 prominent facial landmarks. For the majority of these our method produces the most accurate results reported to date in this database. Handling of occlusions and surfaces with missing parts is demonstrated with tests on the Bosphorus database, where we achieve an overall error of 4.81 and 4.25 mm for data with and without occlusions, respectively. To investigate potential limits in the accuracy that could be reached, we also report experiments on a database of 144 facial scans acquired in the context of clinical research, with manual annotations performed by experts, where we obtain an overall error of 2.3 mm, with averages per landmark below 3.4 mm for all 14 targeted points and within 2 mm for half of them. The coordinates of automatically located landmarks are made available on-line. PMID:25314716

Sukno, Federico M; Waddington, John L; Whelan, Paul F

2014-10-01

104

Significant evidence for linkage to chromosome 5q13 in a genome-wide scan for asthma in an extended pedigree resource  

OpenAIRE

Asthma is a multifactorial disease with undetermined genetic factors. We performed a genome-wide scan to identify predisposition loci for asthma. The asthma phenotype consisted of physician-confirmed presence or absence of asthma symptoms. We analyzed 81 extended Utah pedigrees ranging from three to six generations, including 742 affected individuals, ranging from 2 to 40 per pedigree. We performed parametric multipoint linkage analyses with dominant and recessive models. Our analysis reveale...

Teerlink, Craig C.; Camp, Nicola J.; Bansal, Aruna; Crapo, Robert; Hughes, Dana; Kort, Edward; Rowe, Kerry; Cannon-albright, Lisa A.

2008-01-01

105

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

Science.gov (United States)

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

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

2015-04-01

106

Comprehensive genome-wide comparison of DNA and RNA level scan using microarray technology for identification of candidate cancer-related genes in the HL-60 cell line.  

Science.gov (United States)

Genome-wide scans for DNA and RNA changes in the HL-60 cell line relative to normal leukocytes were conducted. Microarray-based comparative genome hybridization (CGH) studies were performed with the Spectral Genomics Human Bacterial Artificial Chromosome (BAC) 3MB system. Transcriptional measurements of approximately 12,500 human genes were monitored using Affymetrix U95A GeneChips. In HL-60, genomic DNA amplification of the 8q24 locus, trisomy 18, and deletions at loci 5q11.2 approximately q31, 6q12, 9p21.3 approximately p22, 10p12 approximately p15, 14q22 approximately q31, 17p12 approximately p13.3, and monosomy X were detected. After obtaining locus information about the RNA transcripts from the Affymetrix database, 4368 genes were stratified both according to status of RNA expression and the DNA copy number of their designated loci. The expression level of 2326 (53.25%) of 4368 transcripts is concordant with DNA copy number. Examples of specific, highly expressed, cancer-associated genes in amplified loci include SERPINB10, MYC, TYMS, HEC, and EPB41L3, while CD14, GZMK, TCF7, FOS, MLH3, CTNNA1, IRF1, VIM, CRK, MAP3K1, STAM, MAX, SFRG5, ENC1, PURA, MNT, RASA1, GLRX, UBE2B, NR3C1, PTENP1, BS69, COPEB, SKIP, PIM2, and MIC2 represent cancer-associated genes in deleted loci with decreased expression. The complementary usage of genome-wide DNA and RNA scans should enhance the identification of candidate genes in the neoplastic process. PMID:14580768

Ulger, Celal; Toruner, Gokce A; Alkan, Mualla; Mohammed, Mansoor; Damani, Shamsha; Kang, Jason; Galante, Anthony; Aviv, Hana; Soteropoulos, Patricia; Tolias, Peter P; Schwalb, Marvin N; Dermody, James J

2003-11-01

107

Automated landmark-guided deformable image registration  

Science.gov (United States)

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

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

2015-01-01

108

VISITO Tuscany: landmark recognition for cultural heritage  

OpenAIRE

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

2011-01-01

109

Landmark papers on photorefractive nonlinear optics  

CERN Document Server

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

Yeh, Pochi

1995-01-01

110

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

Science.gov (United States)

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

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

2004-01-01

111

Bayesian landmark identification in medical images  

Science.gov (United States)

This paper presents a generic and unified method to identify a set of anatomical landmarks of interest within the medical image domains. Landmark identification is important as it provides us with: 1) initial information for registration, 2) navigation and retrieval guidance through the image data, 3) initial models for segmentation, and 4) valuable (though rough) information about the organs/structures of interest. The proposed method initially uses a supervised learning procedure and then improves itself based on the Bayes" theory. The procedure at the first step requires an expert to define a rough roadmap passing through a set of high-contrast landmarks (milestones), and eventually reaching at the structure of interest. The expert is asked to mark the milestones as desired points and a few points around them as undesired points, respectively. Then we estimate Gaussian models for the marked points by which the optimal search area for each desired landmark is determined. The search areas estimated at this step are considered as the segments of the statistical roadmap. An additional set of statistical models along with the above ones are used to form a set of rules to evaluate the points being found during the search procedure. The points that satisfy the rules will be recognized as the landmarks of interest. As the above method is being applied on a set of new patients/cases, a set of valid landmarks of interests becomes available. This new piece of information is then being used to modify the current statistical roadmap based on the Bayes' theory. We have applied the proposed method on T1-weighted brain MRI of 10 epileptic patients to find the landmarks of the hippocampus. In our experiment, six patients formed the training set, and we observed one-step iteration of the Bayesian modification. The method made no false alarms. The overall success rate (average of sensitivity and specificity) of the algorithm was 83.3% with an accuracy of 99.2%. In localizing the hippocampus, the proposed method (with almost perfect results) was 600 times faster than the mutual information registration (with poor and partly wrong results).

Siadat, Mohammad-Reza; Soltanian-Zadeh, Hamid; Fotouhi, Farshad; Elisevich, Kost

2004-05-01

112

A genome-wide linkage scan for cleft lip and cleft palate identifies a novel locus on 8p11-23.  

Science.gov (United States)

Isolated or nonsyndromic cleft lip and palate (NS CLP) is a complex disorder resulting from multiple genetic and environmental factors. NS CLP has a birth prevalence of 1 per 500 in the Philippines where large families provide an opportunity for gene localization. Genotyping of 392 microsatellite repeat markers at 10 cM intervals over the genome was performed by the Center for Inherited Disease Research (CIDR) on 220 Filipino families with 567 affected and 1,109 unaffected family members genotyped. Among the most statistically significant results from analysis of the genome-wide scan data was a 20 cM region at 8p11-23 in which markers had LODs > or =1.0. This region on 8p11-23 has not been found in any previous genome wide scan nor does it contain any of the candidate genes widely studied in CLP. Fine mapping in 8p11-23 was done in the 220 families plus an additional 51 families, using SNP markers from 10 known genes (FGFR1, NRG1, FZD3, SLC8A1, PPP3CC, EPHX2, BNIP3L, EGR3, PPP2R2A, and NAT1) within the 20 cM region of 8p11-23. Linkage and association analyses of these SNPs yield suggestive results for markers in FGFR1 (recessive multipoint HLOD 1.07) and BAG4 (recessive multipoint HLOD 1.31). PMID:17366557

Riley, B M; Schultz, R E; Cooper, M E; Goldstein-McHenry, T; Daack-Hirsch, S; Lee, K T; Dragan, E; Vieira, A R; Lidral, A C; Marazita, M L; Murray, J C

2007-04-15

113

Scanning genomic areas under selection sweep and association mapping as tools to identify horticultural important genes in watermelon  

Science.gov (United States)

Watermelon (Citrullus lanatus var. lanatus) contains 88% water, sugars, and several important health-related compounds, including lycopene, citrulline, arginine, and glutathione. The current genetic diversity study uses microsatellites with known map positions to identify genomic regions that under...

114

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

OpenAIRE

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 (P

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

2012-01-01

115

Meta-Analysis of 13 Genome Scans Reveals Multiple Cleft Lip/Palate Genes with Novel Loci on 9q21 and 2q32-35  

OpenAIRE

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

2004-01-01

116

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

OpenAIRE

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

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

2009-01-01

117

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

Directory of Open Access Journals (Sweden)

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

Moradi Mohammad Hossein

2012-02-01

118

Fast Localization of Facial Landmark Points  

OpenAIRE

The main objective of this work is to develop a method that can accurately estimate the positions of relevant facial landmarks in real-time on hardware with limited processing power, such as modern mobile devices. This is achieved with a sequence of estimators based on ensembles of regression trees. The trees use simple pixel intensity comparisons in their internal nodes and this makes them able to process image regions very fast. We test the developed system on several publ...

Markus?, Nenad; Frljak, Miroslav; Pandz?ic?, Igor S.; Ahlberg, Jo?rgen; Forchheimer, Robert

2014-01-01

119

The behavioural relevance of landmark texture for honeybee homing  

Directory of Open Access Journals (Sweden)

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

LauraDittmar

2011-04-01

120

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

2008-01-01

121

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

Directory of Open Access Journals (Sweden)

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

Yue Gen

2006-10-01

122

Genome-wide scans of genetic variants for psychophysiological endophenotypes: introduction to this special issue of Psychophysiology.  

Science.gov (United States)

This special issue addresses the heritability and molecular genetic basis of 17 putative endophenotypes involving resting EEG power, P300 event-related potential amplitude, electrodermal orienting and habituation, antisaccade eye tracking, and affective modulation of the startle eye blink. These measures were collected from approximately 4,900 twins and parents who provided DNA samples through their participation in the Minnesota Twin Family Study. Included are papers that detail the methodology followed, genome-wide association analyses of single nucleotide polymorphisms and genes, analysis of rare variants in the human exome, and a whole genome sequencing study. Also included are 11 articles by leading experts in psychophysiology and genetics that provide perspective and commentary. A final integrative report summarizes findings and addresses issues raised. This introduction provides an overview of the aims and rationale behind these studies. PMID:25387700

Iacono, William G

2014-12-01

123

Assessment of Landmark Visibility for Automated Wayfinding Route Instructions  

OpenAIRE

Landmarks are used by people in unfamiliar spatial environments as points of reference with which to construct a mental comprehension of space. Supplementing route directions with landmark knowledge therefore improves cognitive ergonomics by increasing people’s ability to use, remember and communicate routes. This research addresses the problem of incorporating landmark knowledge into automatically generated route instructions by exploring the full lifecycle of application development. Two ...

Frankland, David

2010-01-01

124

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

OpenAIRE

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

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

2014-01-01

125

Validation and detection of vessel landmarks by using anatomical knowledge  

Science.gov (United States)

The detection of anatomical landmarks is an important prerequisite to analyze medical images fully automatically. Several machine learning approaches have been proposed to parse 3D CT datasets and to determine the location of landmarks with associated uncertainty. However, it is a challenging task to incorporate high-level anatomical knowledge to improve these classification results. We propose a new approach to validate candidates for vessel bifurcation landmarks which is also applied to systematically search missed and to validate ambiguous landmarks. A knowledge base is trained providing human-readable geometric information of the vascular system, mainly vessel lengths, radii and curvature information, for validation of landmarks and to guide the search process. To analyze the bifurcation area surrounding a vessel landmark of interest, a new approach is proposed which is based on Fast Marching and incorporates anatomical information from the knowledge base. Using the proposed algorithms, an anatomical knowledge base has been generated based on 90 manually annotated CT images containing different parts of the body. To evaluate the landmark validation a set of 50 carotid datasets has been tested in combination with a state of the art landmark detector with excellent results. Beside the carotid bifurcation the algorithm is designed to handle a wide range of vascular landmarks, e.g. celiac, superior mesenteric, renal, aortic, iliac and femoral bifurcation.

Beck, Thomas; Bernhardt, Dominik; Biermann, Christina; Dillmann, Rüdiger

2010-03-01

126

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

Science.gov (United States)

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

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

2014-01-01

127

Genome-Wide Scan on Total Serum IgE Levels Identifies FCER1A as Novel Susceptibility Locus  

OpenAIRE

High levels of serum IgE are considered markers of parasite and helminth exposure. In addition, they are associated with allergic disorders, play a key role in anti-tumoral defence, and are crucial mediators of autoimmune diseases. Total IgE is a strongly heritable trait. In a genome-wide association study (GWAS), we tested 353,569 SNPs for association with serum IgE levels in 1,530 individuals from the population-based KORA S3/F3 study. Replication was performed in four independent populatio...

Weidinger, Stephan; Gieger, Christian; Rodriguez, Elke; Baurecht, Hansjoerg; Mempel, Martin; Klopp, Norman; Gohlke, Henning; Wagenpfeil, Stefan; Ollert, Markus; Ring, Johannes; Behrendt, Heidrun; Heinrich, Joachim; Novak, Natalija; Bieber, Thomas; Kraemer, Ursula

2008-01-01

128

Genome-Wide Scan for Copy Number Variation Association with Age at Onset of Alzheimer’s Disease  

Science.gov (United States)

Alzheimer’s disease (AD) is a progressive neurodegenerative disease with high prevalence, which imposes a substantial public health problem. The heritability of AD is estimated at 60–80% forecasting the potential use of genetic biomarkers for risk stratification in the future. Several large scale genome-wide association studies using high frequency variants identified 10 loci accountable for only a fraction of the estimated heritability. To find the missing heritability, systematic assessment of various mutational mechanisms needs to be performed. This copy number variation (CNV) genome-wide association study with age at onset (AAO) of AD identified 5 CNV regions that may contribute to the heritability of AAO of AD. Two CNV events are intragenic causing a deletion in CPNE4. In addition, to further study the mutational load at the 10 known susceptibility loci, CNVs overlapping with these loci were also catalogued. We identified rare small events overlapping CR1 and BIN1 in AD and normal controls with opposite CNV dosage. The CR1 events are consistent with previous reports. Larger scale studies with deeper genotyping specifically addressing CNV are needed to evaluate the significance of these findings. PMID:23202439

Szigeti, Kinga; Lal, Deepika; Li, Yanchun; Doody, Rachelle S.; Wilhelmsen, Kirk; Yan, Li; Liu, Song; Ma, Changxing

2014-01-01

129

Genome scan for cognitive trait loci of dyslexia: Rapid naming and rapid switching of letters, numbers, and colors.  

Science.gov (United States)

Dyslexia, or specific reading disability, is a common developmental disorder that affects 5-12% of school-aged children. Dyslexia and its component phenotypes, assessed categorically or quantitatively, have complex genetic bases. The ability to rapidly name letters, numbers, and colors from rows presented visually correlates strongly with reading in multiple languages and is a valid predictor of reading and spelling impairment. Performance on measures of rapid naming and switching, RAN and RAS, is stable throughout elementary school years, with slowed performance persisting in adults who still manifest dyslexia. Targeted analyses of dyslexia candidate regions have included RAN measures, but only one other genome-wide linkage study has been reported. As part of a broad effort to identify genetic contributors to dyslexia, we performed combined oligogenic segregation and linkage analyses of measures of RAN and RAS in a family-based cohort ascertained through probands with dyslexia. We obtained strong evidence for linkage of RAN letters to the DYX3 locus on chromosome 2p and RAN colors to chromosome 10q, but were unable to confirm the chromosome 6p21 linkage detected for a composite measure of RAN colors and objects in the previous genome-wide study. PMID:24807833

Rubenstein, Kevin B; Raskind, Wendy H; Berninger, Virginia W; Matsushita, Mark M; Wijsman, Ellen M

2014-06-01

130

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

Science.gov (United States)

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

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

2012-05-01

131

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

Science.gov (United States)

In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47?303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P=4.2 × 10(-11) for all the colours; P=2.3 × 10(-11) for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding. PMID:24022497

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

2014-02-01

132

Meta-Analysis of Genome-Wide Scans for Human Adult Stature Identifies Novel Loci and Associations with Measures of Skeletal Frame Size  

Science.gov (United States)

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?=?6.1×10?8 and rs910316 in TMED10, P-value?=?1.4×10?7) and two had previously been described with weak statistical support (rs10472828 in NPR3, P-value?=?3×10?7 and rs849141 in JAZF1, P-value?=?3.2×10?11). One locus (rs1182188 at GNA12) identifies the first height eQTL. We also assessed the contribution of height loci to the upper- (trunk) and lower-body (hip axis and femur) skeletal components of height. We find evidence for several loci associated with trunk length (including rs6570507 in GPR126, P-value?=?4×10?5 and rs6817306 in LCORL, P-value?=?4×10?4), hip axis length (including rs6830062 at LCORL, P-value?=?4.8×10?4 and rs4911494 at UQCC, P-value?=?1.9×10?4), and femur length (including rs710841 at PRKG2, P-value?=?2.4×10?5 and rs10946808 at HIST1H1D, P-value?=?6.4×10?6). Finally, we used conditional analyses to explore a possible differential contribution of the height loci to these different skeletal size measurements. In addition to validating four novel loci controlling adult stature, our study represents the first effort to assess the contribution of genetic loci to three skeletal components of height. Further statistical tests in larger numbers of individuals will be required to verify if the height loci affect height preferentially through these subcomponents of height. PMID:19343178

Malkina, Ida; Richards, J. Brent; Hammond, Naomi; Stolk, Lisette; Nica, Alexandra; Inouye, Michael; Hofman, Albert; Stephens, Jonathan; Wheeler, Eleanor; Arp, Pascal; Gwilliam, Rhian; Jhamai, P. Mila; Potter, Simon; Chaney, Amy; Ghori, Mohammed J. R.; Ravindrarajah, Radhi; Ermakov, Sergey; Estrada, Karol; Pols, Huibert A. P.; Williams, Frances M.; McArdle, Wendy L.; van Meurs, Joyce B.; Loos, Ruth J. F.; Dermitzakis, Emmanouil T.; Ahmadi, Kourosh R.; Hart, Deborah J.; Ouwehand, Willem H.; Wareham, Nicholas J.; Barroso, Inês; Sandhu, Manjinder S.; Strachan, David P.; Livshits, Gregory; Spector, Timothy D.; Uitterlinden, André G.; Deloukas, Panos

2009-01-01

133

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

Science.gov (United States)

Recent genome-wide (GW) scans have identified several independent loci affecting human stature, but their contribution through the different skeletal components of height is still poorly understood. We carried out a genome-wide scan in 12,611 participants, followed by replication in an additional 7,187 individuals, and identified 17 genomic regions with GW-significant association with height. Of these, two are entirely novel (rs11809207 in CATSPER4, combined P-value = 6.1x10(-8) and rs910316 in TMED10, P-value = 1.4x10(-7)) and two had previously been described with weak statistical support (rs10472828 in NPR3, P-value = 3x10(-7) and rs849141 in JAZF1, P-value = 3.2x10(-11)). One locus (rs1182188 at GNA12) identifies the first height eQTL. We also assessed the contribution of height loci to the upper- (trunk) and lower-body (hip axis and femur) skeletal components of height. We find evidence for several loci associated with trunk length (including rs6570507 in GPR126, P-value = 4x10(-5) and rs6817306 in LCORL, P-value = 4x10(-4)), hip axis length (including rs6830062 at LCORL, P-value = 4.8x10(-4) and rs4911494 at UQCC, P-value = 1.9x10(-4)), and femur length (including rs710841 at PRKG2, P-value = 2.4x10(-5) and rs10946808 at HIST1H1D, P-value = 6.4x10(-6)). Finally, we used conditional analyses to explore a possible differential contribution of the height loci to these different skeletal size measurements. In addition to validating four novel loci controlling adult stature, our study represents the first effort to assess the contribution of genetic loci to three skeletal components of height. Further statistical tests in larger numbers of individuals will be required to verify if the height loci affect height preferentially through these subcomponents of height. PMID:19343178

Soranzo, Nicole; Rivadeneira, Fernando; Chinappen-Horsley, Usha; Malkina, Ida; Richards, J Brent; Hammond, Naomi; Stolk, Lisette; Nica, Alexandra; Inouye, Michael; Hofman, Albert; Stephens, Jonathan; Wheeler, Eleanor; Arp, Pascal; Gwilliam, Rhian; Jhamai, P Mila; Potter, Simon; Chaney, Amy; Ghori, Mohammed J R; Ravindrarajah, Radhi; Ermakov, Sergey; Estrada, Karol; Pols, Huibert A P; Williams, Frances M; McArdle, Wendy L; van Meurs, Joyce B; Loos, Ruth J F; Dermitzakis, Emmanouil T; Ahmadi, Kourosh R; Hart, Deborah J; Ouwehand, Willem H; Wareham, Nicholas J; Barroso, Inês; Sandhu, Manjinder S; Strachan, David P; Livshits, Gregory; Spector, Timothy D; Uitterlinden, André G; Deloukas, Panos

2009-04-01

134

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

Directory of Open Access Journals (Sweden)

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

N. Ivalú Cacho

2013-07-01

135

A genome-wide scan in affected sib-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, Henriette Svarre

2011-01-01

136

Neural systems for landmark-based wayfinding in humans.  

Science.gov (United States)

Humans and animals use landmarks during wayfinding to determine where they are in the world and to guide their way to their destination. To implement this strategy, known as landmark-based piloting, a navigator must be able to: (i) identify individual landmarks, (ii) use these landmarks to determine their current position and heading, (iii) access long-term knowledge about the spatial relationships between locations and (iv) use this knowledge to plan a route to their navigational goal. Here, we review neuroimaging, neuropsychological and neurophysiological data that link the first three of these abilities to specific neural systems in the human brain. This evidence suggests that the parahippocampal place area is critical for landmark recognition, the retrosplenial/medial parietal region is centrally involved in localization and orientation, and both medial temporal lobe and retrosplenial/medial parietal lobe regions support long-term spatial knowledge. PMID:24366141

Epstein, Russell A; Vass, Lindsay K

2014-02-01

137

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

Directory of Open Access Journals (Sweden)

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

2012-01-01

138

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

DEFF Research Database (Denmark)

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

Gregersen, Vivi R; Conley, Lene N

2012-01-01

139

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

Directory of Open Access Journals (Sweden)

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

Gray Joanna

2010-11-01

140

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

Directory of Open Access Journals (Sweden)

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

Shong Huang

2013-04-01

141

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

Science.gov (United States)

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

2013-01-01

142

Chromosomes 4 and 8 Implicated in a Genome Wide SNP Linkage Scan of 762 Prostate Cancer Families Collected by the ICPCG  

Science.gov (United States)

Background In spite of intensive efforts, understanding of the genetic aspects of familial prostate cancer remains largely incomplete. In a previous microsatellite-based linkage scan of 1233 prostate cancer (PC) families, we identified suggestive evidence for linkage (i.e. LOD?1.86) at 5q12, 15q11, 17q21, 22q12, and two loci on 8p, with additional regions implicated in subsets of families defined by age at diagnosis, disease aggressiveness, or number of affected members. Methods In an attempt to replicate these findings and increase linkage resolution, we used the Illumina 6000 SNP linkage panel to perform a genome-wide linkage scan of an independent set of 762 multiplex PC families, collected by 11 ICPCG groups. Results Of the regions identified previously, modest evidence of replication was observed only on the short arm of chromosome 8, where HLOD scores of 1.63 and 3.60 were observed in the complete set of families and families with young average age at diagnosis, respectively. The most significant linkage signals found in the complete set of families were observed across a broad, 37 cM interval on 4q13-25, with LOD scores ranging from 2.02 to 2.62, increasing to 4.50 in families with older average age at diagnosis. In families with multiple cases presenting with more aggressive disease, LOD scores over 3.0 were observed at 8q24 in the vicinity of previously identified common PC risk variants, as well as MYC, an important gene in PC biology. Conclusions These results will be useful in prioritizing future susceptibility gene discovery efforts in this common cancer. PMID:21748754

Lu, Lingyi; Cancel-Tassin, Geraldine; Valeri, Antoine; Cussenot, Olivier; Lange, Ethan M.; Cooney, Kathleen A.; Farnham, James M.; Camp, Nicola J.; Cannon-Albright, Lisa A.; Tammela, Teuvo L.J.; Schleutker, Johanna; Hoegel, Josef; Herkommer, Kathleen; Maier, Christiane; Vogel, Walther; Wiklund, Fredrik; Emanuelsson, Monica; Grönberg, Henrik; Wiley, Kathleen E.; Isaacs, Sarah D.; Walsh, Patrick C.; Helfand, Brian T.; Kan, Donghui; Catalona, William J.; Stanford, Janet L.; FitzGerald, Liesel M.; Johanneson, Bo; Deutsch, Kerry; McIntosh, Laura; Ostrander, Elaine A.; Thibodeau, Stephen N.; McDonnell, Shannon K.; Hebbring, Scott; Schaid, Daniel J.; Whittemore, Alice S.; Oakley-Girvan, Ingrid; Hsieh, Chih-Lin; Powell, Isaac; Bailey-Wilson, Joan E.; Carpten, John D.; Seminara, Daniela; Zheng, S. Lilly; Xu, Jianfeng; Giles, Graham G.; Severi, Gianluca; Hopper, John L.; English, Dallas R.; Foulkes, William D.; Maehle, Lovise; Moller, Pal; Badzioch, Michael D.; Edwards, Steve; Guy, Michelle; Eeles, Ros; Easton, Douglas; Isaacs, William B.

2012-01-01

143

Personal genomics services: whose genomes?  

OpenAIRE

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

2009-01-01

144

Visual Homing in the Absence of Feature-Based Landmark Information  

Science.gov (United States)

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.

2008-01-01

145

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

International Nuclear Information System (INIS)

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

146

Automatic Evaluation of Landmarks for Image-Based Navigation Update  

Directory of Open Access Journals (Sweden)

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

Stefan Lang

2009-01-01

147

3D face analysis : landmarking, expression recognition and beyond  

OpenAIRE

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

Zhao, Xi

2010-01-01

148

Object-oriented landmark recognition for UAV-navigation  

OpenAIRE

Computer vision is an ever more important means for the navigation of UAVs. Here we propose a landmark recognition system looking for salient man-made infrastructure. An object-oriented structural system is preferred since it can utilize known properties of these objects such as part-of hierarchies, mutual geometric constraints of parts, generalization etc. The structure, available for use as landmark, will vary strongly with the region the UAV is supposed to navigate in. Clear object-oriente...

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

2010-01-01

149

Dispersion assessment in the location of facial landmarks on photographs.  

Science.gov (United States)

The morphological assessment of facial features using photographs has played an important role in forensic anthropology. The analysis of anthropometric landmarks for determining facial dimensions and angles has been considered in diverse forensic areas. Hence, the quantification of the error associated to the location of facial landmarks seems to be necessary when photographs become a key element of the forensic procedure. In this work, we statistically evaluate the inter- and intra-observer dispersions related to the facial landmark identification on photographs. In the inter-observer experiment, a set of 18 facial landmarks was provided to 39 operators. They were requested to mark only those that they could precisely place on 10 photographs with different poses (frontal, oblique, and lateral views). The frequency of landmark location was studied together with their dispersion. Regarding the intra-observer evaluation, three participants identified 13 facial points on five photographs classified in the frontal and oblique views. Each landmark location was repeated five times at intervals of at least 24 h. The frequency results reveal that glabella, nasion, subnasale, labiale superius, and pogonion obtained the highest location frequency in the three image categories. On the contrary, the lowest rate corresponds to labiale inferius and menton. Meanwhile, zygia, gonia, and gnathion were significantly more difficult to locate than other facial landmarks. They produced a significant effect on the dispersion depending on the pose of the image where they were placed, regardless of the type of observer that positioned them. In particular, zygia and gonia presented a statistically greater variation in the three image poses, while the location of gnathion is less precise in oblique view photographs. Hence, our findings suggest that the latter landmarks tend to be highly variable when determining their exact position. PMID:24878615

Campomanes-Álvarez, B R; Ibáñez, O; Navarro, F; Alemán, I; Cordón, O; Damas, S

2015-01-01

150

Measure of Landmark Semantic Salience through Geosocial Data Streams  

Directory of Open Access Journals (Sweden)

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

Teriitutea Quesnot

2014-12-01

151

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

OpenAIRE

Abstract Background Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS), which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization....

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

2009-01-01

152

CT Scan (CAT Scan)  

Science.gov (United States)

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

153

Does spatial locative comprehension predict landmark-based navigation?  

Science.gov (United States)

In the present study we investigated the role of spatial locative comprehension in learning and retrieving pathways when landmarks were available and when they were absent in a sample of typically developing 6- to 11-year-old children. Our results show that the more proficient children are in understanding spatial locatives the more they are able to learn pathways, retrieve them after a delay and represent them on a map when landmarks are present in the environment. These findings suggest that spatial language is crucial when individuals rely on sequences of landmarks to drive their navigation towards a given goal but that it is not involved when navigational representations based on the geometrical shape of the environment or the coding of body movements are sufficient for memorizing and recalling short pathways. PMID:25629814

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

2015-01-01

154

Cardiac Conduction System: Delineation of Anatomic Landmarks With Multidetector CT  

Directory of Open Access Journals (Sweden)

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

Farhood Saremi

2009-11-01

155

Combining Speedup techniques based on Landmarks and Containers  

Directory of Open Access Journals (Sweden)

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

R. KALPANA

2010-09-01

156

Adaptive Landmark-Based Navigation System Using Learning Techniques  

DEFF Research Database (Denmark)

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

Zeidan, Bassel; Dasgupta, Sakyasingha

2014-01-01

157

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

Directory of Open Access Journals (Sweden)

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

Yanagihara Kazuyoshi

2009-06-01

158

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

International Nuclear Information System (INIS)

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

159

Nuclear Scans  

Science.gov (United States)

Nuclear scans use radioactive substances to see structures and functions inside your body. They use a special ... images. Most scans take 20 to 45 minutes. Nuclear scans can help doctors diagnose many conditions, including ...

160

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

Science.gov (United States)

In our virtual environment laboratory, we focus on different topics in human spatial cognition with projects on landmark salience, route knowledge, and survey knowledge. Within this laboratory note, we provide an overview of previous, current, and future work with our virtual environment SQUARELAND. PMID:21279666

Röser, Florian; Hamburger, Kai; Knauff, Markus

2011-05-01

161

On-line SLAM using clustered landmarks with omnidirectional vision  

Scientific Electronic Library Online (English)

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

Jun, Okamoto Jr.; Vitor Campanholo, Guizilini.

2010-12-01

162

What Factors Shape "by" Ratings in Relation to Landmarks?  

Science.gov (United States)

Two experiments investigated how absolute and relative distance shape adults' and young children's ratings concerning the extent to which the term "by" describes the relation between locations. Three- and 4-year-old children and adults were asked to rate how well the word "by" described the relation between several blocks and a landmark. The…

Hund, Alycia M.

2010-01-01

163

An Adaptive Algorithm for Finding Frequent Sets in Landmark Windows  

DEFF Research Database (Denmark)

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

Dang, Xuan-Hong; Ong, Kok-Leong

2012-01-01

164

Group-wise FMRI activation detection on DICCCOL landmarks.  

Science.gov (United States)

Group-wise activation detection in task-based fMRI has been widely used because of its robustness to noises and its capacity to deal with variability of individual brains. However, current group-wise fMRI activation detection methods typically rely on the co-registration of individual brains' fMRI images, which has difficulty in dealing with the remarkable anatomic variation of different brains. As a consequence, the resulted misalignments could significantly degrade the required inter-subject correspondences, thus substantially reducing the sensitivity and specificity of group-wise fMRI activation detection. To deal with these challenges, this paper presents a novel approach to detecting group-wise fMRI activation on our recently developed and validated Dense Individualized and Common Connectivity-based Cortical Landmarks (DICCCOL). The basic idea here is that the first-level general linear model (GLM) analysis is first performed on the fMRI signal of each corresponding DICCCOL landmark in individual brain's own space, and then the estimated effect sizes of the same landmark from a group of subjects are statistically assessed with the mixed-effect model at the group level. Finally, the consistently activated DICCCOL landmarks are determined and declared in a group-wise fashion in response to external block-based stimuli. Our experimental results have demonstrated that the proposed approach can detect meaningful activations. PMID:24777386

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

2014-10-01

165

Robust Discriminative Tracking via Landmark-Based Label Propagation.  

Science.gov (United States)

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

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

2015-05-01

166

Children's Wayfinding: Response to Instructions to Use Environmental Landmarks.  

Science.gov (United States)

Examined the ability of 144 children of 6 and 12 years to respond to instructions to use environmental landmarks when leading the way. Children who were told they would lead the way did not prepare more adequately than children who were not told. Children did benefit from instructions to attend to environmental features. (RJC)

Cornell, Edward H.; And Others

1989-01-01

167

On-line SLAM using clustered landmarks with omnidirectional vision  

Directory of Open Access Journals (Sweden)

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

Jun Okamoto Jr.

2010-12-01

168

Developmental Changes in Young Children's Spatial Memory and Language in Relation to Landmarks  

Science.gov (United States)

Two experiments investigated how young children and adults understand whether objects are "by" a landmark and remember their locations. Three- and 4-year-old children and adults were asked to judge whether several blocks were "by" a landmark. The blocks were arranged so that their absolute and relative distances from the landmark varied. Later,…

Hund, Alycia M.; Naroleski, Amber R.

2008-01-01

169

Audible Signage as a Wayfinding Aid: Verbal Landmark versus Talking Signs.  

Science.gov (United States)

Comparison by 40 users of 2 technologies--Verbal Landmark and Talking Signs--that provide speech messages to hand-held receivers for blind travelers found that, on all measures, the Talking Signs system proved superior to the Verbal Landmark system. This was attributed to Verbal Landmark's more cognitively demanding technology. (DB)

Bentzen, B. L.; Mitchell, P. A.

1995-01-01

170

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

Science.gov (United States)

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

Ghimire, Deepak; Lee, Joonwhoan

2014-01-01

171

Global and local spatial landmarks: their role during foraging by Columbian ground squirrels (Spermophilus columbianus).  

Science.gov (United States)

Locating food and refuge is essential for an animal's survival. However, little is known how mammals navigate under natural conditions and cope with given environmental constraints. In a series of six experiments, I investigated landmark-based navigation in free-ranging Columbian ground squirrels (Spermophilus columbianus). Squirrels were trained individually to find a baited platform within an array of nine identical platforms and artificial landmarks set up on their territories. After animals learned the location of the food platform in the array, the position of the latter with respect to local artificial, local natural, and global landmarks was manipulated, and the animal's ability to find the food platform was tested. When only positions of local artificial landmarks were changed, squirrels located food with high accuracy. When the location of the array relative to global landmarks was altered, food-finding accuracy decreased but remained significant. In the absence of known global landmarks, the presence of a familiar route and natural local landmarks resulted in significant but not highly accurate performance. Squirrels likely relied on multiple types of cues when orienting towards a food platform. Local landmarks were used only as a secondary mechanism of navigation, and were not attended to when a familiar route and known global landmarks were present. This study provided insights into landmark use by a wild mammal in a natural situation, and it demonstrated that an array of platforms can be employed to investigate landmark-based navigation under such conditions. PMID:16163480

Vlasak, Anna N

2006-01-01

172

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

Directory of Open Access Journals (Sweden)

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

Beugnon Guy

2011-08-01

173

Age-dependent use of local and global landmarks during escape: experiments using Columbian ground squirrels.  

Science.gov (United States)

How animals utilize their space often changes during ontogeny, perhaps resulting from alternative use of orientation mechanisms. This study investigated whether landmark-based navigation mechanisms were age-dependent in Columbian ground squirrels (Spermophilus columbianus). In field tests, young (1-2 years old) and adult (3-6 years old) animals had to find an escape burrow when either local, global, or both types of landmarks were obstructed. The comparison of escape times between age groups revealed that adult squirrels found escape burrow faster than young animals if global landmarks were available. However, if only local landmarks were present, young squirrels outperformed older animals. The comparison of escape time within each age group showed that obstruction of global or local landmarks lengthened escape time of adult squirrels. In contrast, young animals had longer escapes only when local landmarks were obstructed. The results suggested that the use of different types of landmarks was age specific. PMID:17462833

Nesterova, Anna P

2007-07-01

174

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.

175

A Genome-Wide SNP Scan Reveals Novel Loci for Egg Production and Quality Traits in White Leghorn and Brown-Egg Dwarf Layers  

OpenAIRE

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

2011-01-01

176

Landmark based registration of 18F FDG PET to CT in patients with head and neck cancer: Case reports  

International Nuclear Information System (INIS)

Previous studies have suggested that 18F-FDG PET can be of assistance in the monitoring of disease activity in patients with head and neck cancer undergoing radical radiotherapy treatment. Provided that an adequate period of time elapses between radiotherapy treatment and FDG-PET scanning, this metabolic imaging modality has distinct advantages over anatomical imaging modalities such as CT or MRI which rely largely on changes in size, contrast enhancement and radiodensity of residual mass. The distinction between radiation necrosis and residual tumour is particularly difficult with these modalities. Co-registration of anatomical images from CT or MRI with metabolic images from FDG-PET in this setting may help to locate residual tumour tissue more accurately than PET alone. THE PET scan was peformed on a Siemens 951/3t R PET scanner (6.5 mm in-plane resolution). Patients were positioned supine on the bed in the radiotherapy planning mask to hold the head and neck immobile. A three-bed transmission scan was peformed followed by an intravenous injection of 370 MBq of 18F-FDG. After a 45 min uptake period, a three-bed emission scan was performed to complete the study. Contrast enhanced CT was pedormed on a Picker PQ2000 helical CT scanner. Patients were scanned supine on the bed in the radiotherapy planning mask at a resolution of 21 line pairs/cm. Landmark based registration was used to co-register the PET mages to the CT images. The algorithm uses an analytic linear lea The algorithm uses an analytic linear least-squares solution for a 12 parameter fit of at least 12 operator defined anatomical homologous landmarks in the two image volumes. Both the CT and PET scans include an area of the patient from the base of the brain to the lung apices, thus providing sufficient landmarks for the registration algorithm. We present two patients in whom FDG-PET and CT were used as tools in monitoring disease activity

177

Multifunction Digital Research Scanning System  

International Nuclear Information System (INIS)

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

178

The influence of off-screen landmarks on user orientation  

OpenAIRE

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

Korda, Amichai

2014-01-01

179

Design Guidelines for Landmarks to Support Navigation in Virtual Environments  

OpenAIRE

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

Vinson, Norman G.

2003-01-01

180

Intra-Articular Hip Injection Using Anatomic Surface Landmarks  

OpenAIRE

Intra-articular hip injection is a frequently used technique for diagnostic and therapeutic purposes and is gaining more importance for the early diagnosis of hip disease. It is commonly performed with imaging guidance such as ultrasonographic or fluoroscopic control. We describe our technique of injection of the hip using relative distances from anatomic surface landmarks, with the needle insertion point at the site of the proximal anterolateral portal for hip arthroscopy, with a posterior d...

Masoud, Mohammad A.; Said, Hatem G.

2013-01-01

181

Associative Basis of Landmark Learning and Integration in Vertebrates  

OpenAIRE

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.

2009-01-01

182

Perceptual organization and artificial attention for visual landmarks detection.  

Science.gov (United States)

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

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

2013-03-01

183

Quality-Aware Estimation of Facial Landmarks in Video Sequences  

DEFF Research Database (Denmark)

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

Haque, Mohammad Ahsanul; Nasrollahi, Kamal

2015-01-01

184

AUTOMATIC DETECTION AND CLASSIFICATION OF RETINAL VASCULAR LANDMARKS  

Directory of Open Access Journals (Sweden)

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

Hadi Hamad

2014-06-01

185

Ageing effects on path integration and landmark navigation.  

Science.gov (United States)

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

Harris, Mathew A; Wolbers, Thomas

2012-08-01

186

Dung beetles ignore landmarks for straight-line orientation.  

Science.gov (United States)

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

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

2013-01-01

187

Locating landmarks on high-dimensional free energy surfaces.  

Science.gov (United States)

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

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

2015-03-17

188

CT Scans  

Science.gov (United States)

... cross-sectional pictures of your body. Doctors use CT scans to look for Broken bones Cancers Blood clots Signs of heart disease Internal bleeding During a CT scan, you lie still on a table. The table ...

189

Microarray data mining using landmark gene-guided clustering  

Directory of Open Access Journals (Sweden)

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

Cho HyungJun

2008-02-01

190

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

International Nuclear Information System (INIS)

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

191

A Genome-Wide Linkage Scan for Cleft Lip and Cleft Palate Identifies a Novel Locus on 8p11-23  

OpenAIRE

Isolated or nonsyndromic cleft lip and palate (NS CLP) is a complex disorder resulting from multiple genetic and environmental factors. NS CLP has a birth prevalence of 1 per 500 in the Philippines where large families provide an opportunity for gene localization. Genotyping of 392 microsatellite repeat markers at 10 cM intervals over the genome was performed by the Center for Inherited Disease Research (CIDR) on 220 Filipino families with 567 affected and 1,109 unaffected family members geno...

Riley, B. M.; Schultz, R. E.; Cooper, M. E.; Goldstein-mchenry, T.; Daack-hirsch, S.; Lee, K. T.; Dragan, E.; Vieira, A. R.; Lidral, A. C.; Marazita, M. L.; Murray, J. C.

2007-01-01

192

Genome-Wide Linkage Scan to Identify Loci Associated with Type 2 Diabetes and Blood Lipid Phenotypes in the Sikh Diabetes Study  

OpenAIRE

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 familie...

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.

2011-01-01

193

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

OpenAIRE

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

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

2013-01-01

194

Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations  

OpenAIRE

Hypertension is a complex disease that affects a large proportion of adult population. Although approximately half of the inter-individual variance in blood pressure (BP) level is heritable, identification of genes responsible for its regulation has remained challenging. Genome-wide association study (GWAS) is a novel approach to search for genetic variants contributing to complex diseases. We conducted GWAS for three BP traits [systolic and diastolic blood pressure (SBP and DBP); hypertensio...

Org, Elin; Eyheramendy, Susana; Juhanson, Peeter; Gieger, Christian; Lichtner, Peter; Klopp, Norman; Veldre, Gudrun; Do?ring, Angela; Viigimaa, Margus; So?ber, Siim; Tomberg, Ka?rt; Eckstein, Gertrud; Kelgo, Piret; Rebane, Tiina; Shaw-hawkins, Sue

2009-01-01

195

Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations.  

OpenAIRE

Hypertension is a complex disease that affects a large proportion of adult population. Although approximately half of the inter-individual variance in blood pressure (BP) level is heritable, identification of genes responsible for its regulation has remained challenging. Genome-wide association study (GWAS) is a novel approach to search for genetic variants contributing to complex diseases. We conducted GWAS for three BP traits [systolic and diastolic blood pressure (SBP and DBP); hypertensio...

Org, E.; Eyheramendy, S.; Juhanson, P.; Gieger, C.; Lichtner, P.; Klopp, N.; Veldre, G.; Do?ring, A.; Viigimaa, M.; So?ber, S.; Tomberg, K.; Eckstein, G.; Kelgo, P.; Rebane, T.; Shaw-hawkins, S.

2009-01-01

196

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

Science.gov (United States)

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

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

2015-04-01

197

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

International Nuclear Information System (INIS)

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

198

A new genome scan for primary nonsyndromic vesicoureteric reflux emphasizes high genetic heterogeneity and shows linkage and association with various genes already implicated in urinary tract development  

OpenAIRE

Primary vesicoureteric reflux (VUR), the retrograde flow of urine from the bladder toward the kidneys, results from a developmental anomaly of the vesicoureteric valve mechanism, and is often associated with other urinary tract anomalies. It is the most common urological problem in children, with an estimated prevalence of 1–2%, and is a major cause of hypertension in childhood and of renal failure in childhood or adult life. We present the results of a genetic linkage and association scan ...

Darlow, J. M.; Dobson, M. G.; Darlay, R.; Molony, C. M.; Hunziker, M.; Green, A. J.; Cordell, H. J.; Puri, P.; Barton, D. E.

2013-01-01

199

The Landmark-based Meta Best-First Search Algorithm for Classical Planning.  

OpenAIRE

In this paper, we revisit the idea of splitting a planning problem into subproblems hopefully easier to solve with the help of landmark analysis. This technique initially proposed in the first approaches related to landmarks in classical planning has been outperformed by landmark-based heuristics and has not been paid much attention over the last years. We believe that it is still a promising research direction, particularly for devising distributed search algorithms that could explore differ...

Vernhes, S.; Infantes, G.; Vidal, V.

2012-01-01

200

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

OpenAIRE

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

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

2014-01-01

201

Dominance of the odometer over serial landmark learning in honeybee navigation  

Science.gov (United States)

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

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

2010-08-01

202

Members of the Arabidopsis actin gene family are widely dispersed in the genome.  

OpenAIRE

Plant genomes are subjected to a variety of DNA turnover mechanisms that are thought to result in rapid expansion and presumable contraction of gene copy number. The evolutionary history of the 10 actin genes in Arabidopsis thaliana is well characterized and can be traced to the origin of vascular plant genomes. Knowledge about the genomic position of each actin gene may be the key to tracing landmark genomic duplication events that define plant families or genera and facilitate further mutan...

Mckinney, E. C.; Meagher, R. B.

1998-01-01

203

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

OpenAIRE

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

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

2002-01-01

204

Genome-wide scan on total serum IgE levels identifies no common variants in a healthy Chinese male population.  

Science.gov (United States)

Immunoglobulin E (IgE) provides important information on the humoral immune status, and the IgE level is routinely detected in clinical practice. There are many diseases associated with IgE, such as atopic disease, autoimmune diseases, and so on. IgE is a genetically complex trait, but comprehensive genetic assessment of the variability in serum IgE levels is lacking. Previous genome-wide association studies (GWAS) on total serum IgE levels have identified FCER1A as the susceptibility locus; however, the candidate gene association study in southern Chinese patients reported no association. Given the genetic difference in different populations, we firstly conducted this two-stage GWAS in a Chinese population of 3,495 men, including 1,999 unrelated subjects in the first stage and 1,496 independent individuals replicated in the second stage. In the first stage, we totally identified three single nucleotide polymorphisms (SNPs) which reached a P value of 1.0 × 10??. Rs17090302 on chromosome 3 and Rs28708846 on chromosome 13 are intergenic. Rs432085 from chromosome 3p28 is located in the gene CCDC50. When the two-stage data was combined, none of the SNPs reached the genome-wide significant level. Collectively, we did not identify novel loci associated with the serum IgE level in Chinese males, but we hypothesized that CCDC50 was a candidate gene in regulation on IgE level. PMID:23661040

Liao, Ming; Shi, Dianchun; Wang, Yao; Zhang, Kai; Chen, Xin; Gao, Yong; Tan, Aihua; Xuan, Qiang; Yang, Xiaobo; Hu, Yanlin; Qin, Xue; Zhang, Haiying; Mo, Zengnan

2013-08-01

205

Toward 959 nematode genomes.  

Science.gov (United States)

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

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

2012-01-01

206

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

Science.gov (United States)

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

2011-01-01

207

Quantitative trait loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan.  

Science.gov (United States)

Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata). This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL) detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax), a gonochoristic species and the Asian sea bass (Lates calcarifer) a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been submitted to GenBank under accession numbers HQ021443-HQ021749.]. PMID:21304996

Loukovitis, Dimitrios; Sarropoulou, Elena; Tsigenopoulos, Costas S; Batargias, Costas; Magoulas, Antonios; Apostolidis, Apostolos P; Chatziplis, Dimitrios; Kotoulas, Georgios

2011-01-01

208

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

Science.gov (United States)

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

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

2013-08-15

209

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

Science.gov (United States)

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

2013-08-01

210

Manual palpation of lumbo-pelvic landmarks: a validity study.  

Science.gov (United States)

Manual palpation (MP) is commonly used for the assessment of patients with neuromusculoskeletal dysfunction. During assessment of lumbo-pelvic disorders in particular, it may be used not only to explore pain and resistance in the region, but also to evaluate the symmetry and movement quality of the area. Whilst reliability of MP has been extensively investigated, its validity remains relatively under researched. The aim of this study was to explore the accuracy of MP of lumbo-pelvic bony points. Ultrasound images of three bony landmarks [4th lumbar spinous process (L4), left and right posterior superior iliac spines (PSIS)] were acquired from models (n = 3) in the prone position and the points marked with an ultra-violet (UV) pen. Nine musculoskeletal physiotherapists were asked to identify the bony landmarks using MP. Measurements (mms) were taken between the UV marks and the palpators' marks. The mean error (standard deviation) (mm) for MP of L4, LPSIS, RPSIS were 15.63 (3.89), 20.07 (4.60), 20.59 (2.79) respectively. Bland and Altman analysis gave a mean value of 0.173, with 95% limits of agreement ranging from -27.8 to 26.3. This study suggests that MP of specific lumbo-pelvic bony points has limited validity. PMID:21945296

Kilby, Julia; Heneghan, Nicola R; Maybury, Mark

2012-06-01

211

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

Science.gov (United States)

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

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

1998-06-01

212

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  

Directory of Open Access Journals (Sweden)

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

Ma Junwu

2008-10-01

213

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  

Science.gov (United States)

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. PMID:18840302

Mao, Huirong; Guo, Yuanmei; Yang, Guangcheng; Yang, Bin; Ren, Jun; Liu, Sanfeng; Ai, Huashui; Ma, Junwu; Brenig, Bertram; Huang, Lusheng

2008-01-01

214

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

Scientific Electronic Library Online (English)

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

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

2010-12-01

215

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

Science.gov (United States)

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

Sutton, Jennifer E.

2006-01-01

216

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

Science.gov (United States)

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

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

2014-04-01

217

Technical note: Quantification of neurocranial shape variation using the shortest paths connecting pairs of anatomical landmarks.  

Science.gov (United States)

Three-dimensional geometric morphometric techniques have been widely used in quantitative comparisons of craniofacial morphology in humans and nonhuman primates. However, few anatomical landmarks can actually be defined on the neurocranium. In this study, an alternative method is proposed for defining semi-landmarks on neurocranial surfaces for use in detailed analysis of cranial shape. Specifically, midsagittal, nuchal, and temporal lines were approximated using Bezier curves and equally spaced points along each of the curves were defined as semi-landmarks. The shortest paths connecting pairs of anatomical landmarks as well as semi-landmarks were then calculated in order to represent the surface morphology between landmarks using equally spaced points along the paths. To evaluate the efficacy of this method, the previously outlined technique was used in morphological analysis of sexual dimorphism in modern Japanese crania. The study sample comprised 22 specimens that were used to generate 110 anatomical semi-landmarks, which were used in geometric morphometric analysis. Although variations due to sexual dimorphism in human crania are very small, differences could be identified using the proposed landmark placement, which demonstrated the efficacy of the proposed method. PMID:23868177

Morita, Yusuke; Ogihara, Naomichi; Kanai, Takashi; Suzuki, Hiromasa

2013-08-01

218

Blocking of Spatial Learning between Enclosure Geometry and a Local Landmark  

Science.gov (United States)

In a virtual environment, blocking of spatial learning to locate an invisible target was found reciprocally between a distinctively shaped enclosure and a local landmark within its walls. The blocking effect was significantly stronger when the shape of the enclosure rather than the landmark served as the blocking cue. However, the extent to which…

Wilson, Paul N.; Alexander, Tim

2008-01-01

219

Landmark Learning in a Navigation Task Is Not Affected by the Female Rats' Estrus Cycle  

Science.gov (United States)

In two experiments rats were required to escape from a circular pool by swimming to an invisible platform that was located in the same place relative to one configuration of two landmarks (X and Y). The two landmarks were placed relatively far and equidistant from the hidden platform. Training could be either on consecutive days (Experiment 1) or…

Rodriguez, Clara A.; Aguilar, Raul; Chamizo, V. D.

2011-01-01

220

MRI Scans  

Science.gov (United States)

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 ...

221

The use of anatomical landmarks for percutaneous nephrolithotomy  

Directory of Open Access Journals (Sweden)

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

Esat Kaan Akbay

2012-06-01

222

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

Science.gov (United States)

This study investigates the development of landmark and route knowledge in complex wayfinding situations. It focuses on how children (aged 6, 8, and 10 years) and young adults (n = 79) indicate, recognize, and bind landmarks and directions in both verbal and visuo-spatial tasks after learning a virtual route. Performance in these tasks is also related to general verbal and visuo-spatial abilities as assessed by independent standardized tests (attention, working memory, perception of direction, production and comprehension of spatial terms, sentences and stories). The results first show that the quantity and quality of landmarks and directions produced and recognized by participants in both verbal and visuo-spatial tasks increased with age. In addition, an increase with age was observed in participants' selection of decisional landmarks (i.e., landmarks associated with a change of direction), as well as in their capacity to bind landmarks and directions. Our results support the view that children first acquire landmark knowledge, then route knowledge, as shown by their late developing ability to bind knowledge of directions and landmarks. Overall, the quality of verbal and visuo-spatial information in participants' spatial representations was found to vary mostly with their visuo-spatial abilities (attention and perception of directions) and not with their verbal abilities. Interestingly, however, when asked to recognize landmarks encountered during the route, participants show an increasing bias with age toward choosing a related landmark of the same category, regardless of its visual characteristics, i.e., they incorrectly choose the picture of another fountain. The discussion highlights the need for further studies to determine more precisely the role of verbal and visuo-spatial knowledge and the nature of how children learn to represent and memorize routes. PMID:25667573

Nys, Marion; Gyselinck, Valérie; Orriols, Eric; Hickmann, Maya

2014-01-01

223

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

Science.gov (United States)

This study investigates the development of landmark and route knowledge in complex wayfinding situations. It focuses on how children (aged 6, 8, and 10 years) and young adults (n = 79) indicate, recognize, and bind landmarks and directions in both verbal and visuo-spatial tasks after learning a virtual route. Performance in these tasks is also related to general verbal and visuo-spatial abilities as assessed by independent standardized tests (attention, working memory, perception of direction, production and comprehension of spatial terms, sentences and stories). The results first show that the quantity and quality of landmarks and directions produced and recognized by participants in both verbal and visuo-spatial tasks increased with age. In addition, an increase with age was observed in participants’ selection of decisional landmarks (i.e., landmarks associated with a change of direction), as well as in their capacity to bind landmarks and directions. Our results support the view that children first acquire landmark knowledge, then route knowledge, as shown by their late developing ability to bind knowledge of directions and landmarks. Overall, the quality of verbal and visuo-spatial information in participants’ spatial representations was found to vary mostly with their visuo-spatial abilities (attention and perception of directions) and not with their verbal abilities. Interestingly, however, when asked to recognize landmarks encountered during the route, participants show an increasing bias with age toward choosing a related landmark of the same category, regardless of its visual characteristics, i.e., they incorrectly choose the picture of another fountain. The discussion highlights the need for further studies to determine more precisely the role of verbal and visuo-spatial knowledge and the nature of how children learn to represent and memorize routes. PMID:25667573

Nys, Marion; Gyselinck, Valérie; Orriols, Eric; Hickmann, Maya

2015-01-01

224

Robust Mobile Robot Localization by Tracking Natural Landmarks  

Science.gov (United States)

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

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

225

Intra-articular hip injection using anatomic surface landmarks.  

Science.gov (United States)

Intra-articular hip injection is a frequently used technique for diagnostic and therapeutic purposes and is gaining more importance for the early diagnosis of hip disease. It is commonly performed with imaging guidance such as ultrasonographic or fluoroscopic control. We describe our technique of injection of the hip using relative distances from anatomic surface landmarks, with the needle insertion point at the site of the proximal anterolateral portal for hip arthroscopy, with a posterior direction of 30° and targeted toward a junctional point between 2 perpendicular lines, 1 distal from the anterior superior iliac spine and the second anterior from the tip of the greater trochanter. This technique can be used without imaging guidance in the outpatient clinic. Moreover, it minimizes the need for radiographic exposure for more critical injections, such as the injection of contrast material before conducting magnetic resonance arthrogaphy of the hip. PMID:23875141

Masoud, Mohammad A; Said, Hatem G

2013-05-01

226

Bringing history to life: simulating landmark experiments in psychology.  

Science.gov (United States)

The course in history of psychology can be challenging for students, many of whom enter it with little background in history and faced with unfamiliar names and concepts. The sheer volume of material can encourage passive memorization unless efforts are made to increase student involvement. As part of a trend toward experiential history, historians of science have begun to supplement their lectures with demonstrations of classic physics experiments as a way to bring the history of science to life. Here, the authors report on computer simulations of five landmark experiments from early experimental psychology in the areas of reaction time, span of attention, and apparent motion. The simulations are designed not only to permit hands-on replication of historically important results but also to reproduce the experimental procedures closely enough that students can gain a feel for the nature of early research and the psychological processes being studied. PMID:17152604

Boynton, David M; Smith, Laurence D

2006-05-01

227

A neural wayfinding mechanism adjusts for ambiguous landmark information.  

Science.gov (United States)

Objects along a route can serve as crucial landmarks that facilitate successful navigation. Previous functional magnetic resonance imaging (fMRI) evidence indicated that the human parahippocampal gyrus automatically distinguishes between objects placed at navigationally relevant (decision points) and irrelevant locations (non-decision points). This storage of relevant objects can provide a neural mechanism underlying successful navigation. However, only objects that actually support wayfinding need to be stored. Objects can also provide misleading information if similar objects appear at different locations along a route. An efficient mechanism needs to specifically adjust for ambiguous landmark information. We investigated this by placing identical objects twice in a virtual labyrinth at places with the same as well as with a different navigational relevance. Twenty right-handed volunteers moved through a virtual maze. They viewed the same object either at two different decision points, at two different non-decision points, or at a decision as well as at a non-decision point. Afterwards, event-related fMRI data were acquired during object recognition. Participants decided whether they had seen the objects in the maze or not. The results showed that activity in the parahippocampal gyrus was increased for objects placed at a decision and at a non-decision point as compared to objects placed at two non-decision points. However, ambiguous information resulting from the same object placed at two different decision points revealed increased activity in the right middle frontal gyrus. These findings suggest a neural wayfinding mechanism that differentiates between helpful and misleading information. PMID:20381625

Janzen, Gabriele; Jansen, Clemens

2010-08-01

228

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

Science.gov (United States)

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

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

2014-04-01

229

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

International Nuclear Information System (INIS)

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

230

Cervical spine CT scan  

Science.gov (United States)

... scan – cervical spine; Computed tomography scan – cervical spine; CT scan - cervical spine; Neck CT scan ... Risks of CT scans include: Being exposed to radiation Allergic reaction to contrast dye CT scans expose you to more radiation than ...

231

Automatic 3D facial model and texture reconstruction from range scans  

OpenAIRE

This paper presents a fully automatic approach to fitting a generic facial model to detailed range scans of human faces to reconstruct 3D facial models and textures with no manual intervention (such as specifying landmarks). A Scaling Iterative Closest Points (SICP) algorithm is introduced to compute the optimal rigid registrations between the generic model and the range scans with different sizes. And then a new template-fitting method, formulated in an optmization framework of minimizing th...

Xiang, G.; Ju, X.; Holt, P.

2010-01-01

232

Landmarks of History of Soil Science in Sri Lanka  

Science.gov (United States)

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

Mapa, R.

2012-04-01

233

Microbial Genomics  

Science.gov (United States)

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

234

The relative importance of global and local landmarks in navigation by Columbian ground squirrels (Spermophilus columbianus).  

Science.gov (United States)

In order to survive, small burrowing mammals need to remember the locations of escape burrows. Therefore, it is important to know what types of landmarks are used to aid navigation in the wild. The author tested the ability of free-ranging Columbian ground squirrels (Spermophilus columbianus) to locate escape burrows when local (e.g., vegetation pattern, local relief), global (e.g., forest edge, mountain outline), or both types of landmarks were obstructed. Results suggest that squirrels need both local and global landmarks of the environment for successful navigation, and that the upper portion of the horizon is especially important for orientation. Moreover, the lack of information from one type of landmark (local or global) cannot be completely compensated by the other type. PMID:16719591

Vlasak, Anna N

2006-05-01

235

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

Science.gov (United States)

...collect information regarding the condition of designated landmarks. A...owners or other stewards so the condition of NHLs can be monitored over time. The regional offices...assist in the collection of the condition data. Regional NPS staff...

2012-07-30

236

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

Science.gov (United States)

...EERE-BT-PET-0043] Energy Conservation Program for Consumer Products: Landmark Legal Foundation...energy conservation standards for various consumer products and certain commercial and industrial...the opportunity to comment on DOE's motivations, methodologies and conclusions in...

2013-08-16

237

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.  

Science.gov (United States)

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, André G; Brommage, Robert; Ohlsson, Claes; Tobias, Jonathan H; Rivadeneira, Fernando

2012-07-01

238

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

OpenAIRE

This report describes the piloting mechanisms employed by honey bees during their final approach to a goal. Conceptually applying a bottom-up approach, we systematically varied the position, number and appearance landmarks associated with a rewarded target location within a large, homogenous flight tent. The flight behavior measured under various conditions is well explained with visuo-motor control loops that link perceived landmarks with appropriate turning responses. This view is consisten...

Fry, S. N.; Wehner, R.

2005-01-01

239

A class of spline functions for landmark-based image registration  

OpenAIRE

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

Rossi, Alessandra; Cavoretto, Roberto; Allasia, Giampietro

2011-01-01

240

Clinically relevant landmarks of the frontotemporal branch of the facial nerve: a three-dimensional study.  

Science.gov (United States)

The frontotemporal branch of the facial nerve (FTN) is vulnerable during craniofacial surgeries due to its superficial course and variable distribution. Surface landmarks that correlate with the underlying course of the FTN can assist in surgical planning. Estimates of the course of FTN commonly rely on Pitanguy's line (PL), which utilizes variable soft-tissue landmarks. The purpose of this study was to evaluate palpable surface landmarks to predict the course and distribution of FTN using 3D modeling. Fifteen half-heads were used. In five formalin-embalmed specimens, surface topography was obtained using a FARO® scanner and landmarks corresponding to PL, porion, supraorbital notch, frontozygomatic and zygomaticotemporal sutures, and supraorbitomeatal line (SOML) and infraorbitomeatal line (IOML) were demarcated/digitized using a Microscribe™ digitizer. A preauricular flap was raised, and branches of FTN were isolated and digitized. The data were reconstructed into 3D models (Geomagic®/Maya®) to quantify landmarks. In 10 Thiel-embalmed specimens, four independent raters identified/palpated and pinned the frontozygomatic and zygomaticotemporal sutures and PL. Data were collected and analyzed using the same protocol as in the first part of the study. Landmarking of PL was inconsistent between raters and not representative of FTN distribution. The easily identifiable surface landmarks defined in this study, a line 12 mm anterior to the porion along the SOML and IOML and a line joining the zygomaticotemporal and frontozygomatic sutures, comprehensively captured the distribution of FTN. The raters found a mean of 21 ± 2 branches between the lines out of a total of 22 ± 2 branches. These landmarks may be used clinically to avoid injury to FTN. PMID:22991167

Davies, Joel C; Fattah, Adel; Ravichandiran, Mayoorendra; Agur, Anne M

2012-10-01

241

Learning Compact Visual Descriptors for Low Bit Rate Mobile Landmark Search  

OpenAIRE

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

2013-01-01

242

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

OpenAIRE

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

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

2012-01-01

243

Further evidence for visual landmark involvement in the pigeon's familiar area map  

OpenAIRE

In previous experiments suggesting that previewing visual landscapes speeds homing from familiar release sites, restricted access to olfactory cues may have artefactually encouraged homing pigeons, Columba liviato resort to visual landmark orientation. Since evidence for the role of visual landmarks in wide-ranging avian orientation is still equivocal, Braithwaite and Guilford's (1991, Proc. R. Soc. Lond. Ser. B245, 183-186) 'previewing' experiments were replicated: birds were allowed or deni...

Burt, T.; Holland, R.; Guilford, T.

1997-01-01

244

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

Science.gov (United States)

Visuospatial difficulties in Williams syndrome (WS) are well documented. Recently, research has shown that spatial difficulties in WS extend to large-scale space, particularly in coding space using an allocentric frame of reference. Typically developing (TD) children and adults predominantly rely on the use of a sequential egocentric strategy to navigate a large-scale route (retracing a sequence of left-right body turns). The aim of this study was to examine whether individuals with WS are able to employ a sequential egocentric strategy to guide learning and the retracing of a route. Forty-eight TD children, aged 5, 7, and 9 years and 18 participants with WS were examined on their ability to learn and retrace routes in two (6-turn) virtual environment mazes (with and without landmarks). The ability to successfully retrace a route following the removal of landmarks (use of sequential egocentric coding) was also examined. Although in line with TD 5-year-olds when learning a route with landmarks, individuals with WS showed significantly greater detriment when these landmarks were removed, relative to all TD groups. Moreover, the WS group made significantly more errors than all TD groups when learning a route that never contained landmarks. On a perceptual view-matching task, results revealed a high level of performance across groups, indicative of an ability to use this visual information to potentially aid navigation. These findings suggest that individuals with WS rely on landmarks to a greater extent than TD children, both for learning a route and for retracing a recently learned route. TD children, but not individuals with WS, were able to fall back on the use of a sequential egocentric strategy to navigate when landmarks were not present. Only TD children therefore coded sequential route information simultaneously with landmark information. The results are discussed in relation to known atypical cortical development and perceptual-matching abilities in WS. PMID:25762973

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

2015-01-01

245

Deficits in Landmark Navigation and Path Integration after Lesions of the Interpeduncular Nucleus  

OpenAIRE

Experiments were designed to determine the role of the interpeduncular nucleus (IPN) in three forms of navigation: beacon, landmark, and path integration. In beacon navigation, animals reach goals using cues directly associated with them, whereas in landmark navigation animals use external cues to determine a direction and distance to goals. Path integration refers to the use of self-movement cues to obtain a trajectory to a goal. IPN-lesioned rats were tested in a food-carrying task where th...

Clark, Benjamin J.; Taube, Jeffrey S.

2009-01-01

246

Nuclear Scans (Cancer)  

Science.gov (United States)

... detail further on) are: Bone scans PET scans Thyroid scans MUGA scans Gallium scans Some nuclear scans are ... 131) can be used to find and treat thyroid cancers. Gallium-67 is ... for a whole body scan. This may be called a gallium scan . Radionuclides ...

247

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

Science.gov (United States)

The sphenoid sinus occupies a central location in transsphenoidal surgery (TSS). It is important to identify relevant anatomical landmarks to enter the sphenoid sinus and sellar region properly. The aim of this study was to identify anatomical landmarks and their value in single-nostril endonasal TSS. A retrospective study was performed to review 148 cases of single-nostril endonasal TSS for pituitary lesions. The structure of the nasal cavities and sphenoid sinus, the position of apertures of the sphenoid sinus and relevant arteries and the morphological characteristics of the anterior wall of the sphenoid sinus and sellar floor were observed and recorded. The important anatomical landmarks included the mucosal aperture of the sphenoid sinus, a blunt longitudinal prominence on the posterior nasal septum, the osseocartilaginous junction of the nasal septum, the ‘bow sign’ of the anterior wall of the sphenoid sinus, the osseous aperture and its relationship with the nutrient arteries, the bulge of the sellar floor and the carotid protuberance. These landmarks outlined a clear route to the sella turcica with an optimal view and lesser tissue damage. Although morphological variation may exist, the position of these landmarks was generally consistent. Locating the sphenoid sinus aperture is the gold standard to direct the surgical route of TSS. The ‘bow sign’ and the sellar bulge are critical landmarks for accurate entry into the sphenoid sinus and sella fossa, respectively. PMID:23596471

WEI, LIANG-FENG; ZHANG, JINCHAO; CHEN, HONG-JIE; WANG, RUMI

2013-01-01

248

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

Science.gov (United States)

The sphenoid sinus occupies a central location in transsphenoidal surgery (TSS). It is important to identify relevant anatomical landmarks to enter the sphenoid sinus and sellar region properly. The aim of this study was to identify anatomical landmarks and their value in single-nostril endonasal TSS. A retrospective study was performed to review 148 cases of single-nostril endonasal TSS for pituitary lesions. The structure of the nasal cavities and sphenoid sinus, the position of apertures of the sphenoid sinus and relevant arteries and the morphological characteristics of the anterior wall of the sphenoid sinus and sellar floor were observed and recorded. The important anatomical landmarks included the mucosal aperture of the sphenoid sinus, a blunt longitudinal prominence on the posterior nasal septum, the osseocartilaginous junction of the nasal septum, the 'bow sign' of the anterior wall of the sphenoid sinus, the osseous aperture and its relationship with the nutrient arteries, the bulge of the sellar floor and the carotid protuberance. These landmarks outlined a clear route to the sella turcica with an optimal view and lesser tissue damage. Although morphological variation may exist, the position of these landmarks was generally consistent. Locating the sphenoid sinus aperture is the gold standard to direct the surgical route of TSS. The 'bow sign' and the sellar bulge are critical landmarks for accurate entry into the sphenoid sinus and sella fossa, respectively. PMID:23596471

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

2013-04-01

249

Personal genomics services: whose genomes?  

Science.gov (United States)

New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below. PMID:19259127

Gurwitz, David; Bregman-Eschet, Yael

2009-07-01

250

Thyroid Scan and Uptake  

Science.gov (United States)

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

251

Genome-wide linkage scans for fasting glucose, insulin, and insulin resistance in the National Heart, Lung, and Blood Institute Family Blood Pressure Program: evidence of linkages to chromosome 7q36 and 19q13 from meta-analysis.  

Science.gov (United States)

Genome-wide linkage analyses were performed using a multipoint variance components method in eight study groups from four multicenter networks (whites and blacks in GenNet; whites, blacks, and Mexican Americans in GENOA; whites and blacks in HyperGEN; and Asians in SAPPHIRe) that comprise the National Heart, Lung, and Blood Institute Family Blood Pressure Program (FBPP), in order to identify quantitative trait loci (QTLs) influencing fasting glucose, insulin, and homeostasis model assessment of insulin resistance (HOMA-IR). These study populations were enriched with subjects who had elevated blood pressure. Participants fasting field center separately by sex within each of the eight network ethnicity groups before genetic analysis. A total of 8,664 subjects comprising 5,923 sibpairs from 4,043 families with 365 markers were available for conducting a meta-analysis using a modified Fisher's method of combining the P values from each of the eight scans. Evidence of linkages was found on chromosome 7q36 at 163 cM, with a logarithm of odds (LOD) score of 3.21 for HOMA-IR, and on chromosome 19q13 at 88 cM, with a LOD score of 3.33 for fasting glucose. We also found suggestive linkages (LOD score >/=2.2) on chromosome 7q36 at 163 cM, with LOD scores of 2.31 for fasting glucose and 2.26 for fasting insulin (versus the LOD score of 3.21 for HOMA-IR at this locus). In conclusion, QTLs were identified on chromosomes 7q36 and 19q13 for fasting glucose, insulin, and insulin resistance in large and multiple-ethnicity populations in the FBPP with good replications across several other independent studies for relevant traits. Follow-up dense mapping and association studies are warranted. PMID:15734873

An, Ping; Freedman, Barry I; Hanis, Craig L; Chen, Yii-Der I; Weder, Alan B; Schork, Nicholas J; Boerwinkle, Eric; Province, Michael A; Hsiung, Chao Agnes; Wu, Xiaodong; Quertermous, Thomas; Rao, D C

2005-03-01

252

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

Science.gov (United States)

Transcatheter aortic valve implantation (TAVI) is a minimally invasive procedure to treat severe aortic valve stenosis. As an emerging imaging technique, C-arm computed tomography (CT) plays a more and more important role in TAVI on both pre-operative surgical planning (e.g., providing 3-D valve measurements) and intra-operative guidance (e.g., determining a proper C-arm angulation). Automatic aorta segmentation and aortic valve landmark detection in a C-arm CT volume facilitate the seamless integration of C-arm CT into the TAVI workflow and improve the patient care. In this paper, we present a part-based aorta segmentation approach, which can handle structural variation of the aorta in case that the aortic arch and descending aorta are missing in the volume. The whole aorta model is split into four parts: aortic root, ascending aorta, aortic arch, and descending aorta. Discriminative learning is applied to train a detector for each part separately to exploit the rich domain knowledge embedded in an expert-annotated dataset. Eight important aortic valve landmarks (three hinges, three commissures, and two coronary ostia) are also detected automatically with an efficient hierarchical approach. Our approach is robust under all kinds of variations observed in a real clinical setting, including changes in the field-of-view, contrast agent injection, scan timing, and aortic valve regurgitation. Taking about 1.1 s to process a volume, it is also computationally efficient. Under the guidance of the automatically extracted patient-specific aorta model, the physicians can properly determine the C-arm angulation and deploy the prosthetic valve. Promising outcomes have been achieved in real clinical applications. PMID:22955891

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

2012-12-01

253

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

Directory of Open Access Journals (Sweden)

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

Elisabeth Jeannette Ploran

2014-01-01

254

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

Science.gov (United States)

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

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

2014-01-01

255

IAEA Director General welcomes landmark convention to combat nuclear terrorism  

International Nuclear Information System (INIS)

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

256

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

OpenAIRE

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

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

2013-01-01

257

A multi-subject evaluation of uncertainty in anatomical landmark location on shoulder kinematic description.  

Science.gov (United States)

An accurate assessment of shoulder kinematics is useful for understanding healthy normal and pathological mechanics. Small variability in identifying and locating anatomical landmarks (ALs) has potential to affect reported shoulder kinematics. The objectives of this study were to quantify the effect of landmark location variability on scapular and humeral kinematic descriptions for multiple subjects using probabilistic analysis methods, and to evaluate the consistency in results across multiple subjects. Data from 11 healthy subjects performing humeral elevation in the scapular plane were used to calculate Euler angles describing humeral and scapular kinematics. Probabilistic analyses were performed for each subject to simulate uncertainty in the locations of 13 upper-extremity ALs. For standard deviations of 4 mm in landmark location, the analysis predicted Euler angle envelopes between the 1 and 99 percentile bounds of up to 16.6 degrees . While absolute kinematics varied with the subject, the average 1-99% kinematic ranges for the motion were consistent across subjects and sensitivity factors showed no statistically significant differences between subjects. The description of humeral kinematics was most sensitive to the location of landmarks on the thorax, while landmarks on the scapula had the greatest effect on the description of scapular elevation. The findings of this study can provide a better understanding of kinematic variability, which can aid in making accurate clinical diagnoses and refining kinematic measurement techniques. PMID:19021031

Langenderfer, Joseph E; Rullkoetter, Paul J; Mell, Amy G; Laz, Peter J

2009-04-01

258

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

Science.gov (United States)

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

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

2015-01-28

259

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

Science.gov (United States)

Current methods for the development of pelvic finite element (FE) models generally are based upon specimen specific computed tomography (CT) data. This approach has traditionally required segmentation of CT data sets, which is time consuming and necessitates high levels of user intervention due to the complex pelvic anatomy. The purpose of this research was to develop and assess CT landmark-based semi-automated mesh morphing and mapping techniques to aid the generation and mechanical analysis of specimen-specific FE models of the pelvis without the need for segmentation. A specimen-specific pelvic FE model (source) was created using traditional segmentation methods and morphed onto a CT scan of a different (target) pelvis using a landmark-based method. The morphed model was then refined through mesh mapping by moving the nodes to the bone boundary. A second target model was created using traditional segmentation techniques. CT intensity based material properties were assigned to the morphed/mapped model and to the traditionally segmented target models. Models were analyzed to evaluate their geometric concurrency and strain patterns. Strains generated in a double-leg stance configuration were compared to experimental strain gauge data generated from the same target cadaver pelvis. CT landmark-based morphing and mapping techniques were efficiently applied to create a geometrically multifaceted specimen-specific pelvic FE model, which was similar to the traditionally segmented target model and better replicated the experimental strain results (R(2)=0.873). This study has shown that mesh morphing and mapping represents an efficient validated approach for pelvic FE model generation without the need for segmentation. PMID:25680299

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

2015-04-13

260

Arm CT scan  

Science.gov (United States)

... scan - arm; Computed axial tomography scan - arm; Computed tomography scan - arm; CT scan - arm ... DM, Roditi G. Intravascular contrast media for radiology, CT, and MRI. ... tomography. In: Adam A, Dixon AK, eds. Grainger & Allison's ...

261

Heart CT scan  

Science.gov (United States)

A computed tomography (CT) scan of the heart is an imaging method that uses x-rays to create detailed pictures of the ... scan - heart; Computed axial tomography scan - heart; Computed ... CT scan - heart; Electron beam computed tomography - heart; Agaston ...

262

Sinus CT scan  

Science.gov (United States)

... scan - sinus; Computed axial tomography scan - sinus; Computed tomography scan - sinus; CT scan - sinus ... D, Roditi G. Intravascular contrast media for radiology, CT, and MRI. ... tomography. In: Adam A, Dixon AK, eds. Grainger & Allison's ...

263

Pelvic CT scan  

Science.gov (United States)

... scan - pelvis; Computed axial tomography scan - pelvis; Computed tomography scan - pelvis; CT scan - pelvis ... chap 19. Gjelsteen AC. CT, MRI, PET, PET/CT, and ultrasound in the ... tomography. In: Grainger RC, Allison D, Adam, Dixon AK, ...

264

Shoulder CT scan  

Science.gov (United States)

... scan - shoulder; Computed axial tomography scan - shoulder; Computed tomography scan - shoulder; CT scan - shoulder ... DM, Roditi G. Intravascular contrast media for radiology, CT, and MRI. ... tomography. In: Adam A, Dixon AK, eds. Grainger & Allison's ...

265

Leg CT scan  

Science.gov (United States)

... scan - leg; Computed axial tomography scan - leg; Computed tomography scan - leg; CT scan - leg ... DM, Roditi G. Intravascular contrast media for radiology, CT, and MRI. ... tomography. In: Adam A, Dixon AK, eds. Grainger & Allison's ...

266

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

Scientific Electronic Library Online (English)

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

Germán, Robledo; Guillermo, Seijo.

267

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

Science.gov (United States)

To effectively wayfind through unfamiliar buildings, humans infer their relative position to target locations not only by interpreting geometric layouts, especially length of line of sight, but also by using background knowledge to evaluate landmarks with respect to their probable spatial relation to a target. Questionnaire results revealed that participants have consistent background knowledge about the relative position of target locations. Landmarks were rated significantly differently with respect to their spatial relation to targets. In addition, results from a forced-choice task comparing snapshots of a virtual environment revealed that background knowledge influenced wayfinding decisions. We suggest that landmarks are interpreted semantically with respect to their function and spatial relation to the target location and thereby influence wayfinding decisions. This indicates that background knowledge plays a role in wayfinding. PMID:22806666

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

2012-08-01

268

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

Directory of Open Access Journals (Sweden)

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

Nihat Y?lmaz

2006-06-01

269

Identification of an Alternate Maxillary Apical Base Landmark from Pre-existing Substitutions  

Science.gov (United States)

ABSTRACT Background: Cephalometrically the position of maxilla is usually assessed by point A, which is one of the most common cephalometric landmarks used for spatial analysis of maxilla, however in certain scenarios we require a alternative landmark. Aims: In this study a nearest alternative maxillary apical base landmark was identified for Point A substitutions given by different authors. Methods and Material: A cross sectional study was conducted on thirty (30) good quality lateral cephalograms. Only those lateral cephalograms were selected where Point A was easily identified. Landmarks: Sella (S), Nasion (N), Point A and three substitution points Y, L, X were traced. Angles formed by SN with Point A (Angle SNA) and three substitution points (Angle SNY, SNX, SNL) were measured. Correlation of angle SNA with angles SNY, SNX and SNL were derived. Statistical analysis used Results: Mean and standard deviation for Angles SNA, SNY, SNL and SNX were calculated individually for males and females. ‘T’ Test was applied to determine statistical significance for all the parameters i.e Age, Angles SNA, SNY, SNL and SNX respectively. Karl Pearson correlation coefficient was carried out to determine the statistical significant correlation for Angle SNA with SNY, SNL and SNX. Results: A mean value of 82.8° ±1.9°, 83.1° ±1.8°, 78.3° ±2.9° and 78.7° ±2.7° for Angle's SNA, SNY, SNL and SNX respectively was observed. A statistically significant correlation was observed between angles SNA & SNY, SNL, SNX & strong positive correlation was observed with angle SNY. Conclusions: We conclude that Point Y is the most nearing maxillary apical base landmark to Point A. Hence maxillary apical base landmark can be substituted by Point Y where identification of point A is not obvious. PMID:25568586

Patel, Kunal S.; Kulkarni, Narayan; Singh, Varun Pratap; Parikh, Kartik

2014-01-01

270

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

Science.gov (United States)

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

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

2007-01-01

271

Structured light scanning to evaluate three-dimensional anthropometry in HIV facial lipoatrophy  

OpenAIRE

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...

Tomás Gómez- Cía; Cristina Suárez; Fernando Lobo-Bailón; Purificación Gacto-Sánchez

2011-01-01

272

Robust 3D face landmark localization based on local coordinate coding.  

Science.gov (United States)

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

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

2014-12-01

273

Use of a Non-Navigational, Non-Verbal Landmark Task in Children  

Science.gov (United States)

Two hundred and twenty two children (104 females), 1-8 years of age and young adults, were tested for up to 25 days on five versions of a non-verbal, non-navigational landmark task that had previously been used for monkeys. In monkeys, performance on this task is severely impaired following damage to the parietal cortex. For the basic task, the…

Overman, William; Pierce, Allison; Watterson, Lucas; Coleman, Jennifer K.

2013-01-01

274

The central sulcus: an observer-independent characterization of sulcal landmarks and depth asymmetry.  

Science.gov (United States)

Studies of the central sulcus (CS) often use observer-dependent procedures to assess CS morphology and sulcal landmarks. Here, we applied a novel method combining automated sulcus reconstruction, surface parameterization, and an observer-independent depth measurement to study the CS. This facilitated the quantitative assessment of the spatial position and intersubject variability of several sulcal landmarks. Sulcal depth profiles also allowed us to develop an algorithm for the clear identification of several landmarks, including the pli de passage fronto-pariétal moyen (PPFM), first described by Broca. Using this algorithm, the PPFM was identified in the majority of sulci, but exhibited limited spatial variability. This appears to support Cunningham's theory that this landmark may be a developmental remnant, and may argue against its role as a guide to the more variable somatotopic hand area. Sulcal depth profiles were also utilized to assess the influence of sex, handedness, and age on CS morphology. These profiles revealed leftward depth asymmetry in the superior extent of the CS of male subjects and near the midpoint of the CS in female subjects. Age correlations were performed for these asymmetries, and a significant correlation was seen only in the male subgroup. PMID:18071195

Cykowski, Matthew D; Coulon, Olivier; Kochunov, Peter V; Amunts, Katrin; Lancaster, Jack L; Laird, Angela R; Glahn, David C; Fox, Peter T

2008-09-01

275

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

Directory of Open Access Journals (Sweden)

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

Leslie Marcus

2000-06-01

276

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

Science.gov (United States)

...INFORMATION: The purpose of the meeting of the Landmarks Committee...Board at a subsequent meeting at a place and time to...Mr. Ronald James, Chair Dr. James M. Allan Dr...Michael E. Stevens The meeting will be open to the...

2012-08-31

277

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

Science.gov (United States)

...INFORMATION: The purpose of the meeting of the Landmarks Committee...Board at a subsequent meeting at a place and time to...Mr. Ronald James, Chair, Dr. James M. Allan, Dr...Michael E. Stevens. The meeting will be open to the...

2011-09-28

278

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

Science.gov (United States)

...committee, with exception of the Chair, will be participating remotely at this meeting. The members of the Landmarks...are: Mr. Ronald James, Chair Dr. James M. Allan Dr. Cary...Michael E. Stevens The meeting will be open to the...

2013-02-27

279

76 FR 15338 - Landmarks Committee of the National Park System Advisory Board Meeting  

Science.gov (United States)

...INFORMATION: The purpose of the meeting of the Landmarks Committee...Board at its subsequent meeting at a place and time to...Mr. Ronald James, Chair, Dr. James M. Allan, Dr...Michael E. Stevens. The meeting will be open to the...

2011-03-21

280

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

Science.gov (United States)

...INFORMATION: The purpose of the meeting of the Landmarks Committee...Board at a subsequent meeting at a place and time to...Mr. Ronald James, Chair, Dr. James M. Allan, Dr...Michael E. Stevens. The meeting will be open to the...

2012-03-09

281

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

Science.gov (United States)

...INFORMATION: The purpose of the meeting of the Landmarks Committee...Board at a subsequent meeting at a place and time to...Belinda Faustinos, Acting Chair Dr. James M. Allan Dr...Michael E. Stevens The meeting will be open to the...

2013-11-19

282

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

Science.gov (United States)

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

2012-05-01

283

3D ultrasound-CT registration of the liver using combined landmark-intensity information  

International Nuclear Information System (INIS)

An important issue in computer-assisted surgery of the liver is a fast and reliable transfer of preoperative resection plans to the intraoperative situation. One problem is to match the planning data, derived from preoperative CT or MR images, with 3D ultrasound images of the liver, acquired during surgery. As the liver deforms significantly in the intraoperative situation non-rigid registration is necessary. This is a particularly challenging task because pre- and intraoperative image data stem from different modalities and ultrasound images are generally very noisy. One way to overcome these problems is to incorporate prior knowledge into the registration process. We propose a method of combining anatomical landmark information with a fast non-parametric intensity registration approach. Mathematically, this leads to a constrained optimization problem. As distance measure we use the normalized gradient field which allows for multimodal image registration. A qualitative and quantitative validation on clinical liver data sets of three different patients has been performed. We used the distance of dense corresponding points on vessel center lines for quantitative validation. The combined landmark and intensity approach improves the mean and percentage of point distances above 3 mm compared to rigid and thin-plate spline registration based only on landmarks. The proposed algorithm offers the possibility to incorporate additional a priori knowledge - in terms of few landma priori knowledge - in terms of few landmarks - provided by a human expert into a non-rigid registration process. (orig.)

284

The eminent German pathologist Siegfried Oberndorfer (1876-1944) and his landmark work on carcinoid tumors.  

Science.gov (United States)

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. PMID:24713679

Tsoucalas, Gregory; Karamanou, Marianna; Androutsos, George

2011-01-01

285

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

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

Ahmed Raad Al Shams

2014-01-01

286

Shape shifting: Local landmarks interfere with navigation by, and recognition of, global shape.  

Science.gov (United States)

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

2014-03-01

287

Cranial CT scan  

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Brain CT; Head CT; CT scan - skull; CT scan - head; CT scan - orbits; CT scan - sinuses; Computed tomography - cranial ... The x-rays produced by the CT scan are painless. Some people may ... hard table. Contrast given through a vein may cause a slight ...

288

Nuclear Heart Scan  

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... 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: ...

289

RBC nuclear scan  

Science.gov (United States)

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

290

Coronary Calcium Scan  

Science.gov (United States)

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

291

Genome Research  

Science.gov (United States)

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

292

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

OpenAIRE

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

Elisabeth Jeannette Ploran; Jacob Bevitt

2014-01-01

293

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

International Nuclear Information System (INIS)

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

294

A note on statistical analysis of shape through triangulation of landmarks  

OpenAIRE

In an earlier paper, the author jointly with S. Suryawanshi proposed statistical analysis of shape through triangulation of landmarks on objects. It was observed that the angles of the triangles are invariant to scaling, location, and rotation of objects. No distinction was made between an object and its reflection. The present paper provides the methodology of shape discrimination when reflection is also taken into account and makes suggestions for modifications to be made when some of the l...

Rao, C. Radhakrishna

2000-01-01

295

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

Science.gov (United States)

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

Wang, Hongsheng; Zheng, Naiqaun Nigel

2010-12-01

296

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

International Nuclear Information System (INIS)

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

297

Finding centre: ocular and fMRI investigations of bisection and landmark task performance.  

Science.gov (United States)

The line bisection task is used as a bedside test of spatial neglect patients who typically bisect lines to the right of true centre. To disambiguate the contribution of perceptual from motor biases in bisection, previous research has used the landmark task in which participants determine whether a transection mark is left or right of centre. One recent study using stimuli that reliably leads to leftward perceptual biases in healthy individuals, found that ocular judgements of centre were biased to the right of centre, whereas manual bisections were biased leftwards. Here we used behavioural measures and functional MRI in healthy individuals to investigate ocular and perceptual judgements of centre. Ocular judgements were made by having participants fixate the centre of a horizontal bar that was dark at one end and light at the other (i.e., a 'greyscale' stimulus), whereas perceptual responses were made by having participants indicate whether a transection mark on the greyscales stimuli was to the left or right of centre. Behavioural data indicated a leftward bias in the first, second and longest fixations for bisection. Moreover, greyscale orientation (i.e., dark extremity to the right or to the left), and stimulus position modulated fixations. In contrast, for the landmark task, initial fixations were attracted towards the transection mark, whereas subsequent fixations were closer to veridical centre. Imaging data showed a large bilateral network, including superior parietal and lingual cortex, that was active for bisection. The landmark task activated a predominantly right hemisphere network including superior and inferior parietal cortices. Taken together these results indicate that very different strategies and underlying neural networks are invoked by the bisection and landmark tasks. PMID:22230669

Cavézian, Céline; Valadao, Derick; Hurwitz, Marc; Saoud, Mohamed; Danckert, James

2012-02-01

298

Reliability of Bony Anatomic Landmark Asymmetry Assessment in the Lumbopelvic Region: Application to Osteopathic Medical Education  

OpenAIRE

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...

Stovall, Bradley A.; Kumar, Shrawan

2010-01-01

299

The eminent German pathologist Siegfried Oberndorfer (1876-1944) and his landmark work on carcinoid tumors  

OpenAIRE

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; Marianna Karamanou; George Androutsos

2011-01-01

300

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2010-06-15

301

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

2011-05-01

302

Landmark-based registration using a local radial basis function transformation  

OpenAIRE

In this paper we propose the use of a local image transformation involving radial basis functions for landmark-based registration of medical images. More precisely, we consider radial basis functions as nodal functions in the modified Shepard method. In this way we obtain an image transformation more accurate and stable than the one given by the global radial basis functions, as shown by numerical results.

Cavoretto, Roberto; Rossi, Alessandra; Quatember, Bernhard

2011-01-01

303

Shape Shifting: Local Landmarks Interfere With Navigation by, and Recognition of, Global Shape  

OpenAIRE

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 requir...

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

2013-01-01

304

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

Directory of Open Access Journals (Sweden)

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

Martin Egelhaaf

2014-09-01

305

Role of squamosal suture as a consistent landmark for middle fossa approach craniotomy: an anatomical study.  

Science.gov (United States)

Objective?To establish a consistent surface bony landmark for a middle fossa approach (MFA) lateral craniotomy represented by the squamosal suture (SS). Methods?In 60 dried skulls, we assessed the relation between the SS and the external auditory canal (EAC). The lateral portion of the middle cranial fossa floor was also assessed for a possible relation with the anteroposterior diameter (APD) of the squama temporalis (ST). Clinically, we applied our findings on the SS in MFA for different lesions. Results?A vertical line at the EAC divided the ST into the anterior part constituting 61% of the APD (i.e., two thirds) and the posterior part forming 39% (i.e., one third). The average ST height was 35.92 mm. The SS posterior limit at the supramastoid crest was located just anterior to the external projection of the petrous ridge in 35 skulls (58%) and exactly corresponded to it in 25 skulls (42%). The APD of the ST equals on average 97% of the APD of the lateral middle cranial fossa. Optimum exposure of the middle fossa was obtained without any further craniotomy extension. Conclusion?The SS serves as a consistent natural surface bony landmark for MFA. Optimum craniotomy, two thirds anterior to the EAC and one third posterior, is obtained following SS as a landmark. PMID:25685647

Alkhalili, Kenan; Tantawy, Mohammed; Nageeb, Mohab M; Ragaee, Mohamed A; Alshyal, Gasser H; Alcindor, Dunbar S; Chen, Douglas A; Aziz, Khaled M Abdel

2015-02-01

306

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

Directory of Open Access Journals (Sweden)

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

R. Kalpana

2011-02-01

307

Landmark-driven parameter optimization for non-linear image registration  

Science.gov (United States)

Image registration is one of the most common research areas in medical image processing. It is required for example for image fusion, motion estimation, patient positioning, or generation of medical atlases. In most intensity-based registration approaches, parameters have to be determined, most commonly a parameter indicating to which extend the transformation is required to be smooth. Its optimal value depends on multiple factors like the application and the occurrence of noise in the images, and may therefore vary from case to case. Moreover, multi-scale approaches are commonly applied on registration problems and demand for further adjustment of the parameters. In this paper, we present a landmark-based approach for automatic parameter optimization in non-linear intensity-based image registration. In a first step, corresponding landmarks are automatically detected in the images to match. The landmark-based target registration error (TRE), which is shown to be a valid metric for quantifying registration accuracy, is then used to optimize the parameter choice during the registration process. The approach is evaluated for the registration of lungs based on 22 thoracic 4D CT data sets. Experiments show that the TRE can be reduced on average by 0.07 mm using automatic parameter optimization.

Schmidt-Richberg, Alexander; Werner, René; Ehrhardt, Jan; Wolf, Jan-Christoph; Handels, Heinz

2011-03-01

308

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

International Nuclear Information System (INIS)

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

309

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

Directory of Open Access Journals (Sweden)

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

udy P. Sendaydiego

2013-07-01

310

The more, the better: the use of multiple landmark configurations to solve the phylogenetic relationships in musteloids.  

Science.gov (United States)

Although the use of landmark data to study shape changes along a phylogenetic tree has become a common practice in evolutionary studies, the role of this sort of data for the inference of phylogenetic relationships remains under debate. Theoretical issues aside, the very existence of historical information in landmark data has been challenged, since phylogenetic analyses have often shown little congruence with alternative sources of evidence. However, most analyses conducted in the past were based upon a single landmark configuration, leaving it unsettled whether the incorporation of multiple configurations may improve the rather poor performance of this data source in most previous phylogenetic analyses. In the present study, we present a phylogenetic analysis of landmark data that combines information derived from several skeletal structures to derive a phylogenetic tree for musteloids. The analysis includes nine configurations representing different skeletal structures for 24 species. The resulting tree presents several notable concordances with phylogenetic hypotheses derived from molecular data. In particular, Mephitidae, Procyonidae, and Lutrinae plus the genera Martes, Mustela, Galictis, and Procyon were retrieved as monophyletic. In addition, other groupings were in agreement with molecular phylogenies or presented only minor discordances. Complementary analyses have also indicated that the results improve substantially when an increasing number of landmark configurations are included in the analysis. The results presented here thus highlight the importance of combining information from multiple structures to derive phylogenetic hypotheses from landmark data. PMID:25516268

Catalano, Santiago A; Ercoli, Marcos D; Prevosti, Francisco J

2015-03-01

311

Rapid Frequency Scan EPR  

OpenAIRE

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...

Tseitlin, Mark; Rinard, George A.; Quine, Richard W.; Eaton, Sandra S.; Eaton, Gareth R.

2011-01-01

312

Insect navigation en route to the goal: multiple strategies for the use of landmarks  

Science.gov (United States)

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

Collett

1996-01-01

313

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

Science.gov (United States)

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

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

2014-10-01

314

Genomewide Identification of Genes Under Directional Selection: Gene Transcription QST Scan in Diverging Atlantic Salmon Subpopulations  

OpenAIRE

Evolutionary genomics has benefited from methods that allow identifying evolutionarily important genomic regions on a genomewide scale, including genome scans and QTL mapping. Recently, genomewide scanning by means of microarrays has permitted assessing gene transcription differences among species or populations. However, the identification of differentially transcribed genes does not in itself suffice to measure the role of selection in driving evolutionary changes in gene transcription. Her...

Roberge, C.; Guderley, H.; Bernatchez, L.

2007-01-01

315

Identifying synonymous regulatory elements in vertebrate genomes  

OpenAIRE

Synonymous gene regulation, defined by regulatory elements driving shared temporal and/or spatial aspects of gene expression, is most probably predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identifies synonymous regulatory elements (SREs) in vertebrate genomes. Syn...

Ovcharenko, Ivan; Nobrega, Marcelo A.

2005-01-01

316

Radiopharmaceutical scanning agents  

International Nuclear Information System (INIS)

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

317

Lung PET scan  

Science.gov (United States)

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

318

Getting a CAT Scan  

Medline Plus

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

319

Getting a CAT Scan  

Science.gov (United States)

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

320

Bone density scan (image)  

Science.gov (United States)

... bone the higher the risk of fractures. A bone scan, along with a patient's medical history, is a ... and whether any preventative treatment is needed. A bone density scan has the advantage of being painless and exposing ...

321

Lumbar spine CT scan  

Science.gov (United States)

... spine; Computed axial tomography scan - lumbar spine; Computed tomography scan - lumbar spine; CT - lower back ... DM, Roditi G. Intravascular contrast media for radiology, CT, and MRI. ... tomography. In: Adam A, Dixon AK, eds. Grainger & Allison's ...

322

Heart PET scan  

Science.gov (United States)

Heart nuclear medicine scan; Heart positron emission tomography; Myocardial PET scan ... Udelson JE, Dilsizian V, Bonow RO. Nuclear cardiology. In: Bonow RO, ... . 9th ed. Philadelphia, PA: Saunders Elsevier; 2011:chap 17.

323

The Genome Sequence of Drosophila melanogaster  

Science.gov (United States)

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

Ramanujan, Krishna.

324

Atlas of duplex scanning  

International Nuclear Information System (INIS)

This book presents the first atlas devoted entirely to duplex scanning. It details the uses of this important ''up-and-coming'' diagnostic tool for vascular and general surgeons and radiologists. It also covers scanning of the extremities, as well as the carotoids. The topics also covered are correlative line drawings elaborate and clarify the excellent scan images; the principles of duplex scanning or arteries and veins, techniques, and results; pictures normal anatomy; venous thromboses, arterial occlusion, true and false aneurysms, graft stenoses

325

Exploring the origin of the D genome of oat by fluorescence in situ hybridization.  

Science.gov (United States)

Further understanding of the origin of cultivated oat would accelerate its genetic improvement. In particular, it would be useful to clarify which diploid progenitor contributed the D genome of this allohexaploid species. In this study, we demonstrate that the landmarks produced by fluorescence in situ hybridization (FISH) of species of Avena using probes derived from Avena sativa can be used to explore the origin of the D genome. Selected sets of probes were hybridized in several sequential experiments performed on exactly the same chromosome spreads, with multiple probes of cytological preparations. Probes pITS and A3-19 showed there might be a similar distribution of pITS between the Ac and D genomes. These results indicated that the Ac genome is closely related to the D genome, and that Avena canariensis (AcAc) could be the D-genome donor of cultivated oat. PMID:25478818

Luo, Xiaomei; Zhang, Haiqin; Kang, Houyang; Fan, Xing; Wang, Yi; Sha, Lina; Zhou, Yonghong

2014-09-01

326

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

Scientific Electronic Library Online (English)

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

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

327

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

2009-05-01

328

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

Science.gov (United States)

As part of the 2009 International League Against Epilepsy (ILAE) Centenary Celebration, a special symposium was dedicated to Epilepsia (100 Years of Epilepsia: Landmark Papers and Their Influence). The Associate Editors were asked to identify a particularly salient and meaningful paper in their areas of expertise. From the content areas of neuropsychology and neuropsychiatry two very interesting papers were identified using quite different ascertainment techniques. One paper addressed the problem of psychosis in temporal lobe epilepsy, whereas the other represents the first paper to appear in Epilepsia presenting quantitative assessment of cognitive status in epilepsy. These two papers are reviewed in detail and placed in historical context. PMID:20132299

Hermann, Bruce

2010-07-01

329

Baculovirus Genomics  

OpenAIRE

Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies (Hymenoptera) and one has a mosquito host (Diptera). With this information, general patterns of genome structure and gene content became apparent. Baculovirus open reading frames are tightly packed with minim...

Oers, M. M.; Vlak, J. M.

2007-01-01

330

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

331

Scanned projection radiography  

International Nuclear Information System (INIS)

Fan beam digital radiography systems are referred to by the term 'scanned projection radiography', or 'SPR'. The most familiar scanned projection radiography devices are the localization systems employed on computed tomography scanners which use the CT detector and electronics to generate a 'computed radiograph' of the anatomy. The authors discuss temporal and energy subtraction techniques, clinical applications and some pending developments in spatial resolution, signal-to-noise ratio and scan speed. (Auth.)

332

Design of an Enterobacteriaceae Pan-genome Microarray Chip  

OpenAIRE

Abstract. Microarrays are a common method for evaluating genomic content of bacterial species and comparing unsequenced bacterial genomes. This technology allows for quick scans of characteristic genes and chromosomal regions, and to search for indications of horizontal transfer. A high-density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chi...

Lukjancenko, Oksana; Ussery, David

2010-01-01

333

Advanced scanning probe lithography.  

Science.gov (United States)

The nanoscale control afforded by scanning probe microscopes has prompted the development of a wide variety of scanning-probe-based patterning methods. Some of these methods have demonstrated a high degree of robustness and patterning capabilities that are unmatched by other lithographic techniques. However, the limited throughput of scanning probe lithography has prevented its exploitation in technological applications. Here, we review the fundamentals of scanning probe lithography and its use in materials science and nanotechnology. We focus on robust methods, such as those based on thermal effects, chemical reactions and voltage-induced processes, that demonstrate a potential for applications. PMID:25091447

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

2014-08-01

334

Atlas of duplex scanning  

Energy Technology Data Exchange (ETDEWEB)

This book presents the first atlas devoted entirely to duplex scanning. It details the uses of this important ''up-and-coming'' diagnostic tool for vascular and general surgeons and radiologists. It also covers scanning of the extremities, as well as the carotoids. The topics also covered are correlative line drawings elaborate and clarify the excellent scan images; the principles of duplex scanning or arteries and veins, techniques, and results; pictures normal anatomy; venous thromboses, arterial occlusion, true and false aneurysms, graft stenoses.

Cranley, J.J.; Karkow, W.S.

1987-01-01

335

Functional genomics of tomato: opportunities and challenges in post-genome NGS era.  

Science.gov (United States)

The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies. PMID:25431420

Kumar, Rahul; Khurana, Ashima

2014-12-01

336

Facial image comparison using a 3D laser scanning system  

Science.gov (United States)

To reliably perform comparisons of facial images, it is important to position the head corresponding to the facial images available. Techniques using three or more landmark points on the face have been proposed for matching the face and camera positions to the available photographs. However, these methods can be cumbersome, and require the cooperation of the subject. 3D photographs, together with 3D modeling software, offer the possibility of flexible and reproducable positioning of the head of a person corresponding to the face and camera position of the facial images. We will present our experiences with a non-contact 3D laser-scanning system (Minolta VI-900), especially with respect to ease-of-use, reproducabilty, and performance for facial comparison applications.

Ruifrok, Arnout C.; Goos, Mirelle; Hoogeboom, Bart; Vrijdag, Derk; Bijhold, Jurrien

2003-08-01

337

New Landmark for the Endoscopic Endonasal Transsphenoidal Approach of Pituitary Surgery  

Science.gov (United States)

Objective To clarify the anatomical correlations of the sphenoid sinus with surrounding structures in the normal Korean population, and to identify surgical landmarks for safe sellar floor dissection in the anterior skull base by endoscopy and microscopy. Methods We reviewed the 196 brain magnetic resonance imaging findings showing a normal appearance, and measured the distances between anatomical landmarks. Results The mean distances from the base of the columella to the anterior wall of the sphenoid sinus and the sellar floor were 69.71±4.25 mm and 86.26±4.57 mm, respectively in the over 15 age group, and showed the smallest degree of variation among the measurements. The mean angles between the floor of the nasal cavity and the straight line connecting the base of the columella and the sellar floor were 29.45±3.25° and 24.75±4.00° in the over 15 and under 15 age groups, respectively. The mean values of both distances and angles increased with age until 15 years after which no further increases were evident. There were no significant differences in the measurements between males and females or among subjects with different degrees of pneumatization in the over 15 age group. Conclusion The distances from the base of the columella to the sellar floor and the anterior wall of the sphenoid sinus, which were consistent among individuals, could be used as a surgical indicator to investigate the sellar floor in endoscopic or microscopic transsphenoidal approaches. PMID:23826477

Kim, Young Ha; Kim, Ju Eun; Kim, Min Joo

2013-01-01

338

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

Science.gov (United States)

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

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

2015-01-01

339

Sectional Curvature in terms of the Cometric, with Applications to the Riemannian Manifolds of Landmarks  

CERN Document Server

This paper deals with the computation of sectional curvature for the manifolds of~$N$ landmarks (or feature points) in~$D$ dimensions, endowed with the Riemannian metric induced by the group action of diffeomorphisms. The inverse of the metric tensor for these manifolds (i.e.~the cometric), when written in coordinates, is such that each of its elements depends on at most~$2D$ of the~$ND$ coordinates. This makes the matrices of partial derivatives of the cometric very sparse in nature, thus suggesting solving the highly non-trivial problem of developing a formula that expresses sectional curvature in terms of the cometric and its first and second partial derivatives (we call this Mario's formula). We apply such formula to the manifolds of landmarks and in particular we fully explore the case of geodesics on which only two points have non-zero momenta and compute the sectional curvatures of 2-planes spanned by the tangents to such geodesics. The latter example gives insight to the geometry of the full manifolds...

Micheli, Mario; Mumford, David

2010-01-01

340

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

Science.gov (United States)

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

Little, J P; Adam, C J

2015-01-01

341

Optical Scanning Applications.  

Science.gov (United States)

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

Wagner, Hans

342

Knee CT scan  

Science.gov (United States)

A computed tomography (CT) scan of the knee is test that uses x-rays to make detailed images of the knee. ... A CT scan can quickly create more detailed pictures of the knee than standard x-rays. The test may be ...

343

Getting a CAT Scan  

Medline Plus

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

344

Genome Bioinformatics  

Science.gov (United States)

This no-frills UC-Santa Cruz Genome Bioinformatics Web site contains searchable "working drafts of the human genome and the mouse genome," which each represent "immense collaborative efforts" within the biomedical research community. Those who are active in genome research may find this Web site useful, especially for the multi-faceted genome browser that "provides a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more)." Users may also access Blat alignments, a table browser (provides tabular representation of the data as an alternative to the graphical display of the genome browser), downloadable versions of the data set, and more. The site also contains a helpful FAQ page and a News section that alerts the user to corrected errors, new features, etc. The extensive list of links leads to dozens of other genome databases, browsers, and related tools.

345

Resonant scanning mechanism  

Science.gov (United States)

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

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

2014-10-01

346

Assessing inhomogeneities in bacterial long genomic sequences  

Energy Technology Data Exchange (ETDEWEB)

Several complete prokaryotic and eukaryotic genomes are already at hand (S. cerevisiae, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, sp.) and many are forthcoming (e.g., E. coli, H, pylori, C. elegans). The comparative analysis of genomes generally strives to identify genes and characterize function/structure relationships inferred mostly via amino acid sequence comparisons. We describe concisely methods for comparing genomes (or long contigs) emphasizing sequence features other than gene comparisons. These center on the following measures of genomic organization and sequence heterogeneity: (i) compositional biases of short oligonucleotides; (ii) dinucleotide relative abundance distances within and between genomes; (iii) rare and frequent word (oligonucleotide) determinations and their distributional properties; (iv) r-scan statistics assessing clustering, overdispersion, or excessive evenness of various marker arrays; and (v) characterizations of repeat structures in the genome. 20 refs., 3 figs.

Karlin, S. [Stanford Univ., CA (United States)

1997-12-01

347

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

International Nuclear Information System (INIS)

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

348

123Genomics  

Science.gov (United States)

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

349

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

Science.gov (United States)

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

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

2015-03-01

350

New Approach of Estimating the Minimum Value of the Sum of Distances of the Landmarks in a Planar Shape  

Science.gov (United States)

Allometry is defined as the study of the relationship between size and shape. If we take a set of measurements of distances between points on a body, then a size variable can be regarded as a summary of the overall scale of these measurements. For example, the arithmetic mean and the geometric mean of a set of distances are both size variables. In the book of Christopher G. Small "The Statistical Theory of Shape" the main concern is linked with aspects of the data that remain after location and scale information are discounted, and the emphasis is that the statistical shape concepts have not been as prominent as the theory of inference for location and scale. Our contribution is on the estimation of the distances of the landmarks in a planar shape from the centroid of the shape defined by the landmarks. The new approach is the estimation of the sums of the distances of the landmarks of the two separate subsystems of the shape from their centroids C1 and C2, which is less or equal to the sum of the distances of all the landmarks of the shape from its centroid C.

Kllogjeria, Adrian; Kllogjeri, Qamil

2011-09-01

351

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

Science.gov (United States)

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

Hodges, John R

2006-11-01

352

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

International Nuclear Information System (INIS)

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

353

On-board landmark navigation and attitude reference parallel processor system  

Science.gov (United States)

An approach to autonomous navigation and attitude reference for earth observing spacecraft is described along with the landmark identification technique based on a sequential similarity detection algorithm (SSDA). Laboratory experiments undertaken to determine if better than one pixel accuracy in registration can be achieved consistent with onboard processor timing and capacity constraints are included. The SSDA is implemented using a multi-microprocessor system including synchronization logic and chip library. The data is processed in parallel stages, effectively reducing the time to match the small known image within a larger image as seen by the onboard image system. Shared memory is incorporated in the system to help communicate intermediate results among microprocessors. The functions include finding mean values and summation of absolute differences over the image search area. The hardware is a low power, compact unit suitable to onboard application with the flexibility to provide for different parameters depending upon the environment.

Gilbert, L. E.; Mahajan, D. T.

1978-01-01

354

Preliminary analysis to achieve a high-precision measurement of the excitation energy of the He (2p 3d) 1P doubly excited state in helium using landmark states in neon  

International Nuclear Information System (INIS)

Full text: We present the groundwork a scheme to employ both first-and third- harmonic undulator light to excite states of well-known energy in singly-excited neon and high excitation energy doubly-excited states in helium in a single scan. This simultaneous excitation superimposes the features of the two spectra, providing landmarks for accurate measurement of the helium features. We measured an excitation energy of 64.1198(14) for the He (2p 3d) 1P which differs by 5.3 meV from the value calculated initnik et al. These measurements were performed at a resolving power more than 4 times the designed operating range of the BL 6.2 R gas-phase beamline at Elettra, where the data were recorded. This induced significant technical challenges in calibrating the energy scale. Copyright (2005) Australian Institute of Physics

355

Skeletal Scintigraphy (Bone Scan)  

Science.gov (United States)

... well as a patient’s immediate response to therapeutic interventions. In fact, a skeletal scintigram or bone scan ... inform their physician or technologist if they are breastfeeding or if there is any possibility that they ...

356

The conical scan radiometer  

Science.gov (United States)

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

Prosch, T.; Hennings, D.

1982-07-01

357

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

358

Photothermal imaging scanning microscopy  

Science.gov (United States)

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

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

2006-07-11

359

Abdominal MRI scan  

Science.gov (United States)

... can be damaged. Pens, pocketknives, and eyeglasses may fly across the room. Pins, hairpins, metal zippers, and similar metallic items can distort the images. Removable dental work should be taken out just before the scan.

360

Arm MRI scan  

Science.gov (United States)

... An abnormal finding on an x-ray or bone scan Arm pain and a history of cancer Arm or wrist pain that does not get better with treatment Bone infection (osteomyelitis) Bone pain and fever Broken bone ...

361

Frequency scanning microstrip antennas  

DEFF Research Database (Denmark)

The principles of using radiating microstrip resonators as elements in a frequency scanning antenna array are described. The resonators are cascade-coupled. This gives a scan of the main lobe due to the phase-shift in the resonator in addition to that created by the transmission line phase-shift. Experimental results inX-band, in good agreement with the theory, show that it is possible to scan the main lobe an angle ofpm30degby a variation of the frequencypm300MHz, and where the 3 dB beamwidth is less than10deg. The directivity was 14.7 dB, while the gain was 8.1 dB. The efficiency might be improved by a trade-off between the efficiency and the scanning angle, or by using a better amplitude distribution.

Danielsen, Magnus; JØrgensen, Rolf

1979-01-01

362

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.)

363

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.)

364

Slow Scan Telemedicine  

Science.gov (United States)

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.

1984-01-01

365

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

Directory of Open Access Journals (Sweden)

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

2010-02-01

366

Landmark Prediction of Long Term Survival Incorporating Short Term Event Time Information.  

Science.gov (United States)

In recent years, a wide range of markers have become available as potential tools to predict risk or progression of disease. In addition to such biological and genetic markers, short term outcome information may be useful in predicting long term disease outcomes. When such information is available, it would be desirable to combine this along with predictive markers to improve the prediction of long term survival. Most existing methods for incorporating censored short term event information in predicting long term survival focus on modeling the disease process and are derived under restrictive parametric models in a multi-state survival setting. When such model assumptions fail to hold, the resulting prediction of long term outcomes may be invalid or inaccurate. When there is only a single discrete baseline covariate, a fully non-parametric estimation procedure to incorporate short term event time information has been previously proposed. However, such an approach is not feasible for settings with one or more continuous covariates due to the curse of dimensionality. In this paper, we propose to incorporate short term event time information along with multiple covariates collected up to a landmark point via a flexible varying-coefficient model. To evaluate and compare the prediction performance of the resulting landmark prediction rule, we use robust non-parametric procedures which do not require the correct specification of the proposed varying coefficient model. Simulation studies suggest that the proposed procedures perform well in finite samples. We illustrate them here using a dataset of post-dialysis patients with end-stage renal disease. PMID:23293405

Parast, Layla; Cheng, Su-Chun; Cai, Tianxi

2012-01-01

367

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

Science.gov (United States)

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

Bruner, Emiliano; Manzi, Giorgio

2007-03-01

368

ScanMaris  

OpenAIRE

Developing and Evaluating Solutions of Prevention and Monitoring Maritme Borders: The ScanMaris project is a software workshop conceived to develop and evaluate solutions of prevention and monitoring the maritime borders. It relies on tactical picture exploitation tools, known as enriched for resulting from the continuous treatment of important volumes of heterogeneous data gathered in real time and differed time. ScanMaris allow supervising the permanent evolutions traffic on a global mariti...

Morel, Michel; Glize, Pierre; Littaye, Anne; Bazin, Vale?rie; Napoli, Aldo; Alhadef, Bernard; Lebrevelec, Jacques

2007-01-01

369

V/SCAN  

OpenAIRE

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...

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

1988-01-01

370

Scanning Tunneling Microscopy  

Science.gov (United States)

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

The Concord Consortium

2011-12-11

371

Genomics Glossary  

Science.gov (United States)

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 Glen.

372

External landmark, body surface, and volume data of a mid-sized male in seated and standing postures.  

Science.gov (United States)

The purpose of this study was to acquire external landmark, undeformed surface, and volume data from a pre-screened individual representing a mid-sized male (height 174.9 cm, weight 78.6 ± 0.77 kg) in the seated and standing postures. The individual matched the 50th percentile value of 15 measures of external anthropometry from previous anthropometric studies with an average deviation of 3%. As part of a related study, a comprehensive full body medical image data set was acquired from the same individual on whom landmark data were collected. Three dimensional bone renderings from this data were used to visually verify the landmark and surface results. A total of 54 landmarks and external surface data were collected using a 7-axis digitizer. A seat buck designed in-house with removable back and seat pan panels enabled collection of undeformed surface contours of the back, buttocks, and posterior thigh. Eight metrics describing the buck positioning are provided. A repeatability study was conducted with three trials to assess intra-observer variability. Total volume and surface area of the seated model were found to be 75.8 × 10(3) cm(3) and 18.6 × 10(3) cm(2) and match the volume and surface area of the standing posture within 1%. Root mean squared error values from the repeatability study were on average 5.9 and 6.6 mm for the seated and standing postures respectively. The peak RMS error as a percentage of the centroid size of the landmark data sets were 3% for both the seated and standing trials. The data were collected as part of a global program on the development of an advanced human body model for blunt injury simulation. In addition, the reported data can be used for many diverse applications of biomechanical research such as ergonomics and morphometrics studies. PMID:22441664

Gayzik, F S; Moreno, D P; Danelson, K A; McNally, C; Klinich, K D; Stitzel, Joel D

2012-09-01

373

Human abdomen recognition using camera and force sensor in medical robot system for automatic ultrasound scan.  

Science.gov (United States)

Physicians use ultrasound scans to obtain real-time images of internal organs, because such scans are safe and inexpensive. However, people in remote areas face difficulties to be scanned due to aging society and physician's shortage. Hence, it is important to develop an autonomous robotic system to perform remote ultrasound scans. Previously, we developed a robotic system for automatic ultrasound scan focusing on human's liver. In order to make it a completely autonomous system, we present in this paper a way to autonomously localize the epigastric region as the starting position for the automatic ultrasound scan. An image processing algorithm marks the umbilicus and mammary papillae on a digital photograph of the patient's abdomen. Then, we made estimation for the location of the epigastric region using the distances between these landmarks. A supporting algorithm distinguishes rib position from epigastrium using the relationship between force and displacement. We implemented these algorithms with the automatic scanning system into an apparatus: a Mitsubishi Electric's MELFA RV-1 six axis manipulator. Tests on 14 healthy male subjects showed the apparatus located the epigastric region with a success rate of 94%. The results suggest that image recognition was effective in localizing a human body part. PMID:24110822

Bin Mustafa, Ammar Safwan; Ishii, Takashi; Matsunaga, Yoshiki; Nakadate, Ryu; Ishii, Hiroyuki; Ogawa, Kouji; Saito, Akiko; Sugawara, Motoaki; Niki, Kiyomi; Takanishi, Atsuo

2013-01-01

374

Brachypodium Genomics  

Directory of Open Access Journals (Sweden)

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

Hikmet Budak

2008-02-01

375

Population Genomics of Human Adaptation  

OpenAIRE

Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 –...

Lachance, Joseph; Tishkoff, Sarah A.

2013-01-01

376

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

International Nuclear Information System (INIS)

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

377

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2010-09-15

378

Theory of Radioisotope Scanning  

International Nuclear Information System (INIS)

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

379

Confocal Line Scanning Sensor  

International Nuclear Information System (INIS)

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

380

Confocal Line Scanning Sensor  

Energy Technology Data Exchange (ETDEWEB)

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

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

2011-08-19

381

Scanning optical densitometer  

International Nuclear Information System (INIS)

In radiology, it is necessary to analyze X-ray film for film density. This information can be used for analysis of bone density, tumor detection, or even to check for X-ray source uniformity. A scanning optical densitometer is a device that scans X-ray film for film density. In addition, the scanner relays the variable density to a host computer. A device of this type was designed and several prototypes are being built and tested. This device requires unique software which will receive the information from the scanning optical densitometer and provide meaningful displays and analysis for the user. The software will provide a full color display of the X-ray image with four user-specified density levels

382

Femtosecond scanning tunneling microscope  

Energy Technology Data Exchange (ETDEWEB)

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.

1998-11-01

383

Vector generator scan converter  

Science.gov (United States)

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 (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 hardward 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, James M. (Livermore, CA); Leighton, James F. (Livermore, CA)

1990-01-01

384

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

Directory of Open Access Journals (Sweden)

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

F. Esfandiarpour

2009-12-01

385

Tomographic scanning apparatus  

International Nuclear Information System (INIS)

A computerized tomographic scanning apparatus suitable for diagnosis and for improving target identification in stereotactic neurosurgery is described. It consists of a base, a source of penetrating energy, a detector which produces scanning signals and detector positioning means. A frame with top and bottom arms secures the detector and source to the top and bottom arms respectively. A drive mechanism rotates the frame about an axis along which the frame may also be moved. Finally, the detector may be moved relative to the bottom arm in a direction contrary to the rotation of the frame. (U.K.)

386

Arts & Genomics  

Science.gov (United States)

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

387

Listeria Genomics  

Science.gov (United States)

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

Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

388

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: shabshin@gmail.com; Schweitzer, Mark E. (Dept. of Diagnostic Imaging, Ottawa Hospital and Univ. of Ottawa, Ottawa (Canada)); Carrino, John A. (Dept. of Radiology, Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States))

2010-11-15

389

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

International Nuclear Information System (INIS)

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 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

390

Radiographic scanning agent  

International Nuclear Information System (INIS)

A stable radiographic scanning agent on a sup(99m)Tc basis has been developed. The substance contains a pertechnetate reduction agent, tin(II)-chloride, chromium(II)-chloride, or iron(II)-sulphate, as well as an organospecific carrier and ascorbic acid or a pharmacologically admissible salt or ester of ascorbic acid. (VJ)

391

Environmental Scanning Report, 1992.  

Science.gov (United States)

In response to the change in the provincial economy from natural-resource-based industries to service-oriented industries, Vancouver Community College (VCC) in British Columbia (BC) conducted an environmental scan of the social and economic trends in the college's service region that will most likely affect prospective students' educational and…

Yao, Min

392

Scanning Electron Microscope  

Science.gov (United States)

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

Science Learning Network

393

Bone scan in rheumatology  

International Nuclear Information System (INIS)

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

394

Scanning bubble chamber pictures  

CERN Multimedia

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

1974-01-01

395

Thoracic spine CT scan  

Science.gov (United States)

... spine Arthritis of the spine Tumor of the spine Other spinal injury Thoracic CT scan can also be used during or after an x-ray of the spinal cord and spinal nerve roots (myelography) or an x-ray of the disk ( ...

396

Genomic information as a behavioral health intervention: can it work?  

OpenAIRE

Individuals can now obtain their personal genomic information via direct-to-consumer genetic testing, but what, if any, impact will this have on their lifestyle and health? A recent longitudinal cohort study of individuals who underwent consumer genome scanning found minimal impacts of testing on risk-reducing lifestyle behaviors, such as diet and exercise. These results raise an important question: is personal genomic information likely to beneficially impact public health through motivation...

Bloss, Cinnamon S.; Madlensky, Lisa; Schork, Nicholas J.; Topol, Eric J.

2011-01-01

397

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

CERN Document Server

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

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

2014-01-01

398

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

Science.gov (United States)

Alu retrotransposons are the most numerous and active mobile elements in humans, causing genetic disease and creating genomic diversity. Mobile element scanning (ME-Scan) enables comprehensive and affordable identification of mobile element insertions (MEI) using targeted high-throughput sequencing of multiplexed MEI junction libraries. In a single experiment, ME-Scan identifies nearly all AluYb8 and AluYb9 elements, with high sensitivity for both rare and common insertions, in 169 individuals of diverse ancestry. ME-Scan detects heterozygous insertions in single individuals with 91% sensitivity. Insertion presence or absence states determined by ME-Scan are 95% concordant with those determined by locus-specific PCR assays. By sampling diverse populations from Africa, South Asia, and Europe, we are able to identify 5799 Alu insertions, including 2524 novel ones, some of which occur in exons. Sub-Saharan populations and a Pygmy group in particular carry numerous intermediate-frequency Alu insertions that are absent in non-African groups. There is a significant dearth of exon-interrupting insertions among common Alu polymorphisms, but the density of singleton Alu insertions is constant across exonic and nonexonic regions. In one case, a validated novel singleton Alu interrupts a protein-coding exon of FAM187B. This implies that exonic Alu insertions are generally deleterious and thus eliminated by natural selection, but not so quickly that they cannot be observed as extremely rare variants. PMID:23599355

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

2013-07-01

399

The personal genome browser: visualizing functions of genetic variants  

Science.gov (United States)

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

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

2014-01-01

400

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

Science.gov (United States)

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

Rehrl, Karl; Häusler, Elisabeth; Leitinger, Sven

401

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

Science.gov (United States)

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, Joaquín

2009-04-01

402

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

OpenAIRE

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

Michaelsen, Eckart

2012-01-01

403

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

Czech Academy of Sciences Publication Activity Database

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

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

2014-01-01

404

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

OpenAIRE

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

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

2009-01-01

405

Landmark mapping: A general method for localizing cysteine residues within a protein  

International Nuclear Information System (INIS)

The authors describe a general method to locate the positions of cysteine residues relative to the amino terminus of a protein, using a modified chemical cleavage of the polypeptide backbone at cysteine. The cleavage reaction introduces the carbon atom of 14CN into the carboxyl-terminal fragment produced at each cleavage of the polypeptide chain. Peptides containing the amino terminus of the intact protein are not labeled; all other peptides are labeled at their amino termini. Partial cleavage of a protein followed by gel electrophoresis and autoradiography identifies a ladder of unlabeled peptides that maps positions of the cysteine residues relative to the protein amino terminus. To map individual proteins present in a complex mixture, the polypeptides are cyanolated in solution with 14CN, and the modified proteins are separated by discontinuous SDS/PAGE. The gel is stained, and the desired protein is excised, cleaved at cysteine within the gel slice, and mapped in the second dimension by gel electrophoresis. These techniques are demonstrated with proteins of known sequence containing from zero to five cysteine residues. The cysteine landmark map should be particularly useful in locating protein modifications, in questions of protein similarity, and in mapping functional domains. A strategy is also presented for locating other residues in the polypeptide, for which specific cleavage methods exist

406

The tricipital aponeurosis--a reliable soft tissue landmark for humeral plating.  

Science.gov (United States)

This study aims to identify the relationship of the radial nerve as it descends across the humerus with reference to a reliable soft tissue landmark, the tricipital aponeurosis. Following cadaveric dissection of 10 adult humerii, the radial nerve was located as it crossed the lateral midsagittal point of the humeral diaphysis. A horizontal line was then subtended medially from this point to another line subtended vertically from the lateral border of the tricipital aponeurosis. The vertical distance from this intersection to the lateral apex of the aponeurosis was recorded in three positions (full flexion, 90° of flexion and full extension). The location of the radial nerve on the posterior aspect of the humeral diaphysis to the medial apex of the tricipital aponeurosis was also noted. In 90° of flexion the radial nerve at the lateral midsagittal point of the humerus was 0.9 mm proximal to the lateral apex of the tricipital aponeurosis. Flexion and extension of the elbow changed the interval to 16.3 mm (nerve proximal) in full flexion and 7.1 mm in full extension (nerve distal). On the posterior aspect of the humerus the radial nerve was 21.8 mm proximal to the medial aspect of the tricipital aponeurosis. The aponeurosis provides a reference point from which the nerve can be easily located on the lateral aspect of the humerus intraoperatively in a range of positions, whilst the medial apex provides a guide to the location of the nerve on the posterior aspect of the arm. PMID:25609275

McCann, P A; Smith, G C S; Clark, D; Amirfeyz, R

2015-01-01

407

The early history of keratoconus prior to Nottingham's landmark 1854 treatise on conical cornea: a review.  

Science.gov (United States)

In an era of scientific method, precision of nomenclature and an electronically accessible publication record, the early history of keratoconus still remains, in parts, as complex and perplexing as the disease itself. Historically, the disease has been somewhat confusingly referred to by several different terms, including hyperkeratosis, ochlodes, conical formed cornea, cornea conica, cornée conique, sugar loaf cornea, prolapses corneae, procidentia corneae, staphyloma transparent de la cornée, staphyloma pellucidum, staphyloma corneae totale conicum pellucidum, staphyloma diaphanum, keratconus and keratoconus. In his major 1854 treatise on conical cornea, John Nottingham is widely cited as the first author to succinctly define keratoconus and its associations; however, for 150 years prior to this landmark publication, others had been slowly deciphering elements of keratoconus and distilling their knowledge in a series of publications obscured by the passage of years. Uncritical re-writing of core information and references without their full verification has also led to confusion in the published literature in the 150 years since Nottingham's comprehensive description of keratoconus. In the light of the preceding limitations in the established literature, the authors conducted an historical survey, based on the analysis of original sources, to more fully establish the chronology of early descriptions of keratoconus prior to 1854, with particular focus on the works of Duddell, Taylor, Mauchart, Scarpa, Wardrop, Lyall, MacKenzie, Lawrence, Schmidt, von Ammon and Pickford. This review attempts to place the observations of these practitioners and others both in the context of contemporary ophthalmic practice and historical precedent. PMID:23414219

Grzybowski, Andrzej; McGhee, Charles N J

2013-03-01

408

Fiber feature map based landmark initialization for highly deformable DTI registration.  

Science.gov (United States)

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. PMID:24353392

Gupta, Aditya; Toews, Matthew; Janardhana, Ravikiran; Rathi, Yogesh; Gilmore, John; Escolar, Maria; Styner, Martin

2013-03-13

409

Determination of equine deep digital flexor muscle volume based on distances between anatomical landmarks.  

Science.gov (United States)

In equine medicine the use of Botox® is experimental. Dosages are determined from human treatment-protocols and limited numbers of equine studies. Determination of target-muscle volume can be helpful to extrapolate human dosages. The aim of the study was to calculate a formula enabling the estimation of the deep digital flexor muscle (DDFM) volume based on distances between anatomical landmarks. Nineteen cadaveric limbs were collected and distance A (top of olecranon to Os carpi accessorium) and B (circumference of limb) were measured. Converting mathematical formulas, C was calculated: ? × (((0.5B)/?)(2)) × A. DDFM volume was determined by water displacement. Linear Regression Analysis was used to analyse data. The line best fitting the observed points was: Ln(volume[ml])?=?-1.89 + 0.98 × Ln(value C[cm(3)]). Correlation was highest when natural logarithm was applied to both variables and was 0.97. The calculated formula enables estimating DDFM volume of a living horse. This estimated volume can be useful to apply human Botox® treatment-protocols. PMID:25264361

Hardeman, L C; van der Meij, B R; Lamers, A A H; van der Kolk, J H; Back, W; Wijnberg, I D

2014-10-01

410

Genome-wide Association Scan of Attention Deficit Hyperactivity Disorder  

OpenAIRE

Results of behavioral genetic and molecular genetic studies have converged to suggest that genes substantially contribute to the development of attention deficit/hyperactivity disorder (ADHD), a common disorder that onsets in childhood. Yet, despite numerous linkage and candidate gene studies, strongly consistent and replicable association has eluded detection. To search for ADHD susceptibility genes, we genotyped approximately 600,000 SNPs in 958 ADHD affected family trios. After cleaning th...

Neale, Benjamin M.; Su, Jessica; Anney, Richard; Franke, Barbara; Zhou, Kaixin; Maller, Julian B.; Vasquez, Alejandro Arias; Asherson, Philip; Chen, Wai; Banaschewski, Tobias; Buitelaar, Jan; Ebstein, Richard; Gill, Michael; Miranda, Ana; Oades, Robert D.

2008-01-01

411

Genome wide scan maps mutations in deadly lung cancers  

Science.gov (United States)

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

412

Age-Stratified QTL Genome Scan Analyses for Anthropometric Measures  

OpenAIRE

Abstract With the availability of longitudinal data, age-specific (stratified) or age-adjusted genetic analyses have the potential to localize different putative trait influencing loci. If age does not influence the locus-specific penetrance function within the range examined, age-stratified analyses will tend to yield comparable results for an individual trait. However, age-stratified results should vary across age strata when the locus-specific penetrance function is age dependent. In this ...

Rich Stephen S; Pierce June; Williams Adrienne H; Mark, Brown W.; Beck Stephanie R; Langefeld Carl D

2003-01-01

413

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

Science.gov (United States)

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

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

2009-02-01

414

Encouraging 5-year olds to attend to landmarks: a way to improve children's wayfinding strategies in a virtual environment  

Science.gov (United States)

Wayfinding is defined as the ability to learn and remember a route through an environment. Previous researchers have shown that young children have difficulties remembering routes. However, very few researchers have considered how to improve young children's wayfinding abilities. Therefore, we investigated ways to help children increase their wayfinding skills. In two studies, a total of 72 5-year olds were shown a route in a six turn maze in a virtual environment and were then asked to retrace this route by themselves. A unique landmark was positioned at each junction and each junction was made up of two paths: a correct path and an incorrect path. Two different strategies improved route learning performance. In Experiment 1, verbally labeling on-route junction landmarks during the first walk reduced the number of errors and the number of trials to reach a learning criterion when the children retraced the route. In Experiment 2, encouraging children to attend to on-route junction landmarks on the first walk reduced the number of errors when the route was retraced. This was the first study to show that very young children can be taught route learning skills. The implications of our results are discussed. PMID:25814960

Lingwood, Jamie; Blades, Mark; Farran, Emily K.; Courbois, Yannick; Matthews, Danielle

2015-01-01

415

Scanning electron microscope autoradiography  

International Nuclear Information System (INIS)

The technique of scanning electron microscope autoradiography (SEMA) has been adopted and developed for the location and detailed study of individual microscopic particles of radioactive ?-emitting material. Samples of particulates collected on Nuclepore filters are coated with a thin layer of liquid photographic emulsion and, after development, any active particles can be readily identified by scanning electron microscope (SEM) observation of their surrounding distribution of exposed silver grains. As well as providing the means of location, the grain distribution can be analyzed to provide estimates of both the particle activity and the energy of the emitted ?-particles. The technique is particularly well suited to the study of particles in the submicron and micron size range. A knowledge of the elemental composition of the identified active particles can also be obtained in situ by energy dispersive x-ray spectroscopy (EDS) and the use of an SEM makes the technique readily amenable to on-line image analysis. (author)

416

Scanning in Thyroid Cancer  

International Nuclear Information System (INIS)

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

417

Fluorescent thyroid scanning  

International Nuclear Information System (INIS)

This paper discusses fluorescent thyroid scanning produces images that reflect the distribution of stable iodine without injection of radioactive material. It also allows in vivo estimation of the amount of stable iodine in the thyroid. The authors report that it was only recently that certain technological advances improved image quality and the accuracy of measurements sufficiently to permit x-ray fluorescent imaging to be applied to human thyroid studies under satisfactory conditions

418

Scanning Electron Microscope - SEM  

Science.gov (United States)

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

419

IMEF gamma scanning system  

International Nuclear Information System (INIS)

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

420

Underwater laser scanning system  

Science.gov (United States)

A system is described that produces high quality images through turbid waters by means of time encoded reflected light transmitted by scattering. The system consists of a compact battery operated laser scanning unit that scans the underwater scene with the laser beam in a manner similar to a television raster. Light reflected from any object in the scene varies in accordance with the reflectance of the minute spot being illuminated. This time varying intensity (TVI) signal is transmitted through the water to a remote receiver by both scattered and unscattered light where the received signal may be stored and/or displayed. The underwater laser scanning unit can be moved freely about the field of interest by scuba diver or ROV, unencumbered by entangling umbilicals, and can send real-time images over distances of 15 to 20 attenuation lengths to observers in a shirt-sleeve environment for critical viewing on an image display monitor. This previously undescribed system was developed in the early 1970s for proof of concept tests and used technology that is now 18 or more years old. The physical principles and the experimental hardware are described and examples are given of images providing exquisite detail that were made in an experimental tank together with some images obtained in ocean trials.

Austin, Roswell W.; Duntley, Seibert Q.; Ensminger, Richard L.; Petzold, Theodore J.; Smith, Raymond C.

1991-12-01

421

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2014-01-01

422

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

Directory of Open Access Journals (Sweden)

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

Soraia Ale Souza

2009-02-01

423

Citrus Genomics  

OpenAIRE

Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The hist...

Gmitter, Fred G.; Manuel Talon

2008-01-01

424

Ontology for Genome Comparison and Genomic Rearrangements  

OpenAIRE

We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also ...

Anil Wipat; Pete Lee; Matthew Pocock; Robert Stevens; Keith Flanagan

2006-01-01

425

Rodent malaria parasites : genome organization & comparative genomics  

OpenAIRE

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...

Kooij, Taco W. A.

2006-01-01

426

Ancient genomics  

DEFF Research Database (Denmark)

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

Der Sarkissian, Clio; Allentoft, Morten E

2015-01-01

427

Ancient genomics.  

Science.gov (United States)

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

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