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

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

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

2010-07-01

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Detection of New Genomic Landmarks in the Maltese Goat Using Rapd PCR  

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Since no information of the Maltese goat genome is available, RAPD technique has been used to identify a number of DNA landmarks. Genome Landmarks have been obtained from the DNA of 66 Maltese goats which were studied with Random Amplification of Polymorphic DNA (RAPD). Eleven (11) reproducible RAPD polymorphic zones were identified. For sequencing, the RAPD zones were cloned into the Puc 18 vector utilising E. coli and then sequenced using both the forward (universal) and reverse prim...

Blundell, R.; Felice, A. E.

2006-01-01

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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

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Comparative genome mapping with mobile physical map landmarks.  

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We describe a method for comparative macrorestriction mapping of the chromosomes of Escherichia coli strains. In this method, a series of physically tagged E. coli K-12 alleles serve as mobile landmarks for mapping DNAs from other strains. This technique revealed evidence of strain-specific chromosomal additions or deletions in a pathogenic isolate and can be applied to most strains, yielding information on genealogy as well as virulence. In theory, the same strategy can be used to map and co...

Bloch, C. A.; Rode, C. K.; Obreque, V.; Russell, K. Y.

1994-01-01

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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

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Scanning the human genome at kilobase resolution  

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Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ...

Chen, Jun; Kim, Yeong C.; Jung, Yong-chul; Xuan, Zhenyu; Dworkin, Geoff; Zhang, Yanming; Zhang, Michael Q.; Wang, San Ming

2008-01-01

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Clinical applications of Genome Polymorphism Scans  

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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 cli...

Weber James L

2006-01-01

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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.

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Genome-Wide Scan Reveals Mutation Associated with Melanoma  

Science.gov (United States)

... 2012 Genome-Wide Scan Reveals Mutation Associated with Melanoma A team of international researchers supported by the ... when they divide and grow uncontrollably, develop into melanoma. Also, MITF activity is known to be amplified ...

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Genome-wide DNA polymorphism analyses using VariScan  

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Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Vilella Albert J

2006-09-01

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

Science.gov (United States)

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

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

2013-02-01

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Landmarks in Hybrid Planning  

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Although planning techniques achieved a significant progress during recent years, solving many planning problem still difficult even for modern planners. In this paper, we will adopt landmark concept to hybrid planning setting - a method that combines reasoning about procedural knowledge and causalities. Land-marks are a well-known concept in the realm of classical planning. Recently, they have been adapted to hierarchical approaches. Such landmarks can be extracted in a pre-processing step f...

Mohamed Elkawkagy; Heba Elbeh

2013-01-01

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

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In order to take into account the complex genomic distribution of SNP variations when identifying chromosomal regions with significant SNP effects, a single nucleotide polymorphism (SNP) association scan statistic was developed. To address the computational needs of genome wide association (GWA) studies, a fast Java application, which combines single-locus SNP tests and a scan statistic for identifying chromosomal regions with significant clusters of significant SNP effects, was developed and...

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

2009-01-01

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

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

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

2003-01-01

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Landmarks in Hybrid Planning  

Directory of Open Access Journals (Sweden)

Full Text Available Although planning techniques achieved a significant progress during recent years, solving many planning problem still difficult even for modern planners. In this paper, we will adopt landmark concept to hybrid planning setting - a method that combines reasoning about procedural knowledge and causalities. Land-marks are a well-known concept in the realm of classical planning. Recently, they have been adapted to hierarchical approaches. Such landmarks can be extracted in a pre-processing step from a declarative hierarchical planning domain and problem description. It was shown how this technique allows for a considerable reduction of the search space by eliminating futile plan development options before the actual planning. Therefore, we will present a new approach to in¬tegrate landmark pre-processing technique in the context of hierarchical planning with landmark technique in the classical planning. This integration allows to incorporate the ability of using extracted landmark tasks from hierarchical domain knowledge in the form of HTN and using landmark literals from classical planning. To this end, we will construct a transformation technique to transform the hybrid planning domain into a classical domain model. The method¬ologies in this paper have been implemented successfully, and we will present some experimental results that give evidence for the consid-erable performance increase gained through planning system.

Mohamed Elkawkagy

2013-11-01

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

Science.gov (United States)

In order to take into account the complex genomic distribution of SNP variations when identifying chromosomal regions with significant SNP effects, a single nucleotide polymorphism (SNP) association scan statistic was developed. To address the computational needs of genome wide association (GWA) studies, a fast Java application, which combines single-locus SNP tests and a scan statistic for identifying chromosomal regions with significant clusters of significant SNP effects, was developed and implemented. To illustrate this application, SNP associations were analyzed in a pharmacogenomic study of the blood pressure lowering effect of thiazide-diuretics (N=195) using the Affymetrix Human Mapping 100K Set. 55,335 tagSNPs (pair-wise linkage disequilibrium R2<0.5) were selected to reduce the frequency correlation between SNPs. A typical workstation can complete the whole genome scan including 10,000 permutation tests within 3 hours. The most significant regions locate on chromosome 3, 6, 13 and 16, two of which contain candidate genes that may be involved in the underlying drug response mechanism. The computational performance of ChromoScan-GWA and its scalability were tested with up to 1,000,000 SNPs and up to 4,000 subjects. Using 10,000 permutations, the computation time grew linearly in these datasets. This scan statistic application provides a robust statistical and computational foundation for identifying genomic regions associated with disease and provides a method to compare GWA results even across different platforms. PMID:20161066

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

2009-01-01

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

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

Børglum Anders D

2011-07-01

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A Genome-wide Pleiotropy Scan for Prostate Cancer Risk  

DEFF Research Database (Denmark)

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

Panagiotou, Orestis A; Travis, Ruth C

2014-01-01

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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

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

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

Görg Tilman; Dempfle Astrid; Geller Frank

2003-01-01

 
 
 
 
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Pooled association genome scanning: Validation and use to identify addiction vulnerability loci in two samples  

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Association genome scanning is of increasing interest for identifying the chromosomal regions that contain gene variants that contribute to vulnerability to complex disorders, including addictions. To improve the power and feasibility of this approach, we have validated “10k” microarray-based allelic frequency assessments in pooled DNA samples and have used this approach to seek allelic frequency differences between heavy polysubstance abusers and well characterized control individuals. T...

Liu, Qing-rong; Drgon, Tomas; Walther, Donna; Johnson, Catherine; Poleskaya, Oxanna; Hess, Judith; Uhl, George R.

2005-01-01

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

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

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

2013-01-01

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

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A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromo...

Georges, Anouk; Cambisano, Nadine; Ahariz, Nai?ma; Karim, Latifa; Georges, Michel

2013-01-01

24

Genome scan of Diabrotica virgifera virgifera for genetic variation associated with crop rotation tolerance  

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Crop rotation has been a valuable technique for control of Diabrotica virgifera virgifera for almost a century. However, during the last two decades, crop rotation has ceased to be effective in an expanding area of the US corn belt. This failure appears to be due to a change in the insect's oviposition behaviour, which, in all probability, has an underlying genetic basis. A preliminary genome scan using 253 amplified fragment-length polymorphism (AFLP) markers sought to identify genetic varia...

Miller, N. J.; Ciosi, M.; Sappington, T. W.; Ratcliffe, S. T.; Spencer, J. L.; Guillemaud, T.

2007-01-01

25

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

Science.gov (United States)

AFLP-based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection owing to the difficulties of obtaining DNA sequences from AFLP fragments. Here, we combine classical AFLP outlier detection with 454 sequencing of AFLP fragments to obtain sequences from outlier loci. We applied this approach to the study of resistance to Bacillus thuringiensis israelensis (Bti) toxins in the dengue vector Aedes aegypti. A genome scan of Bti-resistant and Bti-susceptible A. aegypti laboratory strains was performed based on 432 AFLP markers. Fourteen outliers were detected using two different population genetic algorithms. Out of these, 11 were successfully sequenced. Three contained transposable elements (TEs) sequences, and the 10 outliers that could be mapped at a unique location in the reference genome were located on different supercontigs. One outlier was in the vicinity of a gene coding for an aminopeptidase potentially involved in Bti toxin-binding. Patterns of sequence variability of this gene showed significant deviation from neutrality in the resistant strain but not in the susceptible strain, even after taking into account the known demographic history of the selected strain. This gene is a promising candidate for future functional analysis. PMID:22348648

Paris, Margot; Despres, Laurence

2012-04-01

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

DEFF Research Database (Denmark)

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

Hollegaard, Mads V; Grove, Jakob

2011-01-01

27

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)

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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

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Prostate cancer is the most common non-skin cancer and the second leading cause of cancer related mortality for men in the United States. There is strong empirical and epidemiological evidence supporting a stronger role of genetics in early-onset prostate cancer. We performed a genome-wide association scan for early-onset prostate cancer. Novel aspects of this study include the focus on early-onset disease (defined as men with prostate cancer diagnosed before age 56 years) and use of publical...

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

2014-01-01

30

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

Directory of Open Access Journals (Sweden)

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

Gut Ivo

2009-11-01

31

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

Science.gov (United States)

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

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

2014-01-01

32

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

Directory of Open Access Journals (Sweden)

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

Gasser Thomas

2007-07-01

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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.

2011-01-01

34

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Systemic sclerosis (SSc) is an orphan, complex, inflammatory disease affecting the immune system and connective tissue. SSc stands out as a severely incapacitating and life-threatening inflammatory rheumatic disease, with a largely unknown pathogenesis. We have designed a two-stage genome-wide association study of SSc using case-control samples from France, Italy, Germany, and Northern Europe. The initial genome-wide scan was conducted in a French post quality-control sample of 564 cases and ...

Cusi, Daniele Maria; Salvi, Erika

2011-01-01

35

A Genome Scan Conducted in a Multigenerational Pedigree with Convergent Strabismus Supports a Complex Genetic Determinism  

Science.gov (United States)

A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromosome regions with near-suggestive evidence for linkage, respectively on chromosomes 8 and 18. The chromosome 8 linkage implied a penetrance of 0.80 and a rate of phenocopy of 0.11, while the chromosome 18 linkage implied a penetrance of 0.64 and a rate of phenocopy of 0. Our analysis excludes a simple genetic determinism of strabismus in this pedigree. PMID:24376720

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

2013-01-01

36

Multilocus and interaction-based genome scan for alcoholism risk factors in Caucasian Americans: the COGA study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract In this paper, we applied the nonparametric linkage regression approach to the Caucasian genome scan data from the Collaborative Study on the Genetics of Alcoholism to search for regions of the genome that exhibit evidence for linkage to putative alcoholism-predisposing genes. The multipoint single-locus model identified four regions of the genome with LOD scores greater than one. These regions were on 7p near D7S1790 (LOD = 1.31), two regions on 7q near D7S1870 (LOD = 1.15...

Langefeld Carl D; Mark, Brown W.; Williams Adrienne H

2005-01-01

37

Automatic localization of retinal landmarks.  

Science.gov (United States)

Retinal landmark detection is a key step in retinal screening and computer-aided diagnosis for different types of eye diseases, such as glaucomma, age-related macular degeneration(AMD) and diabetic retinopathy. In this paper, we propose a semantic image transformation(SIT) approach for retinal representation and automatic landmark detection. The proposed SIT characterizes the local statistics of a fundus image and boosts the intrinsic retinal structures, such as optic disc(OD), macula. We propose our salient OD and macular models based on SIT for retinal landmark detection. Experiments on 5928 images show that our method achieves an accuracy of 99.44% in the detection of OD and an accuracy of 93.49% in the detection of macula, while having an accuracy of 97.33% for left and right eye classification. The proposed SIT can automatically detect the retinal landmarks and be useful for further eye-disease screening and diagnosis. PMID:23367039

Cheng, Xiangang; Wong, Damon Wing Kee; Liu, Jiang; Lee, Beng-Hai; Tan, Ngan Meng; Zhang, Jielin; Cheng, Ching Yu; Cheung, Gemmy; Wong, Tien Yin

2012-01-01

38

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

39

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

DEFF Research Database (Denmark)

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

Webb, BT; van den Oord, E

2007-01-01

40

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

Science.gov (United States)

Genome scan-based tests for selection are directly applicable to natural populations to study the genetic and evolutionary mechanisms behind phenotypic differentiation. We conducted AFLP genome scans in three distinct geographic colour morphs of the cichlid fish Tropheus moorii to assess whether the extant, allopatric colour pattern differentiation can be explained by drift and to identify markers mapping to genomic regions possibly involved in colour patterning. The tested morphs occupy adjacent shore sections in southern Lake Tanganyika and are separated from each other by major habitat barriers. The genome scans revealed significant genetic structure between morphs, but a very low proportion of loci fixed for alternative AFLP alleles in different morphs. This high level of polymorphism within morphs suggested that colour pattern differentiation did not result exclusively from neutral processes. Outlier detection methods identified six loci with excess differentiation in the comparison between a bluish and a yellow-blotch morph and five different outlier loci in comparisons of each of these morphs with a red morph. As population expansions and the genetic structure of Tropheus make the outlier approach prone to false-positive signals of selection, we examined the correlation between outlier locus alleles and colour phenotypes in a genetic and phenotypic cline between two morphs. Distributions of allele frequencies at one outlier locus were indeed consistent with linkage to a colour locus. Despite the challenges posed by population structure and demography, our results encourage the cautious application of genome scans to studies of divergent selection in subdivided and recently expanded populations. PMID:22625655

Mattersdorfer, Karin; Koblmüller, Stephan; Sefc, Kristina M

2012-07-01

 
 
 
 
41

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

Directory of Open Access Journals (Sweden)

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

Niu Xiao-Yan

2010-06-01

42

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

Science.gov (United States)

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

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

2013-01-01

43

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 depos...

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

2012-01-01

44

Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have investigated whether regions of the genome showing signs of positive selection in scans based on haplotype structure also show evidence of positive selection when sequence-based tests are applied, whether the target of selection can be localized more precisely, and whether such extra evidence can lead to increased biological insights. We used two tools: simulations under neutrality or selection, and experimental investigation of two regions identified by the HapMap2 project as putativ...

Hu, Min; Ayub, Qasim; Guerra-assunc?a?o, Jose? Afonso; Long, Quan; Ning, Zemin; Huang, Ni; Romero, Irene Gallego; Mamanova, Lira; Akan, Pelin; Liu, Xin; Coffey, Alison J.; Turner, Daniel J.; Swerdlow, Harold; Burton, John; Quail, Michael A.

2011-01-01

45

A genome wide linkage scan reveals CD53 as an important regulator of innate TNF-alpha levels.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Abstract Cytokines are major immune system regulators. Previously, innate cytokine profiles determined by LPS stimulation were shown to be highly heritable. To identify regulating genes in innate immunity we analyzed data from a genome wide linkage scan using microsatellites in osteoarthritis patients (The GARP study) and their innate cytokine data on IL-1?, IL-1Ra, IL-10 and TNF?. A confirmation cohort consisted of the Leiden 85-Plus study. In this study, a linkag...

2010-01-01

46

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

Directory of Open Access Journals (Sweden)

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

David Jean-Philippe

2009-11-01

47

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

48

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

49

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

Science.gov (United States)

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. PMID:21612662

2011-01-01

50

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

51

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.)

52

Dynamic prediction by landmarking in competing risks.  

Science.gov (United States)

We propose an extension of the landmark model for ordinary survival data as a new approach to the problem of dynamic prediction in competing risks with time-dependent covariates. We fix a set of landmark time points tLM within the follow-up interval. For each of these landmark time points tLM , we create a landmark data set by selecting individuals at risk at tLM ; we fix the value of the time-dependent covariate in each landmark data set at tLM . We assume Cox proportional hazard models for the cause-specific hazards and consider smoothing the (possibly) time-dependent effect of the covariate for the different landmark data sets. Fitting this model is possible within the standard statistical software. We illustrate the features of the landmark modelling on a real data set on bone marrow transplantation. PMID:23086627

Nicolaie, M A; van Houwelingen, J C; de Witte, T M; Putter, H

2013-05-30

53

A genome-wide scan in 301 families with sibling-pairs diagnosed with schizophrenia of schizoaffective disorder suggests linkage to chromosomes 2pcen and 10p14  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In recent years genome-wide scans and association studies for schizophrenia susceptibility genes have been published. Some have yielded significant positive findings, but there is disagreement between studies concerning their location. No mutation in any gene has yet been found. Since schizophrenia is a complex disorder, a study with sufficient power to detect a locus with small or moderate gene effect is necessary. We have thus conducted a genome-wide scan of 382 sibling pairs each with a di...

Delisi, Le; Shaw, Sh; Crow, Tj; Shields, G.; Smith, Ab; Larach, Vw; Wellman, N.; Loftus, J.; Nathankumar, B.; Razi, K.; Stewart, J.; Comazzi, M.; Vita, A.; Sherrington, R.; Heffner, T.

2001-01-01

54

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

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA and total number of piglets born (TNB in a three generation Iberian by Meishan F2 intercross. Results The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P SSC17 (P P P P P Conclusions The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17, dominant and epistatic QTL in an Iberian × Meishan F2 intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

Bidanel Jean P

2009-12-01

55

Genome scans detect consistent divergent selection among subtidal vs. intertidal populations of the marine angiosperm Zostera marina.  

Science.gov (United States)

Genome scans are a powerful tool to detect natural selection in natural populations among a larger sample of marker loci. We used replicated habitat comparisons to search for consistent signals of selection among contrasting populations of the seagrass Zostera marina, a marine flowering plant with important ecological functions. We compared two different habitat types in the North Frisian Wadden Sea, either permanently submerged (subtidal) or subjected to aerial exposure (intertidal). In three independent population pairs, each consisting of one tidal creek and one tidal flat population each, we carried out a genome scan with 14 expressed sequence tag (EST)-derived microsatellites situated in 5'- or 3'-untranslated regions of putative genes, in addition to 11 anonymous genomic microsatellites. By using two approaches for outlier identification, one anonymous and two EST-derived microsatellites showed population differentiation patterns not consistent with neutrality. These microsatellites were detected in several parallel population comparisons, suggesting that they are under diverging selection. One of these loci is linked to a putative nodulin gene, which is responsible for water channelling across cellular membranes, suggesting a functional link of the observed genetic divergence with habitat characteristics. PMID:17986196

Oetjen, Katharina; Reusch, Thorsten B H

2007-12-01

56

A Genome-Wide Scan of Selective Sweeps and Association Mapping of Fruit Traits Using Microsatellite Markers in Watermelon.  

Science.gov (United States)

Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5' untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness. PMID:25425675

Reddy, Umesh K; Abburi, Lavanya; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Cantrell, Robert; Vajja, Venkata Gopinath; Reddy, Rishi; Tomason, Yan R; Levi, Amnon; Wehner, Todd C; Nimmakayala, Padma

2014-11-25

57

A genome scan to identify quantitative trait loci affecting economically important traits in a US Holstein population.  

Science.gov (United States)

Quantitative trait loci affecting economically important traits were studied for eight large US Holstein grandsire families by using the granddaughter design. A total of 155 microsatellite markers located throughout the bovine genome were selected for the scan. The data analyzed include genotypes for 50 markers not previously reported. Results analyses of 105 marker genotypes reported previously were updated. Effects of marker alleles were analyzed for 38 traits including traits for milk production, somatic cell score, productive life, conformation, calving ease, and 16 canonical traits derived from conformation and production traits. Permutation tests were used to calculate empirical traitwise error rates. A traitwise critical value of P = 0.1 was used to determine significance. Ten putative quantitative trait loci associated with seven of the new markers were identified within specific families. One marker on chromosome 14 was associated with differences in fat yield, fat percentage, and a canonical production trait in two families. Markers on chromosomes 18 and 22 were associated with differences in rump angle in the same family. Markers were associated with differences in udder depth and fore udder attachment on chromosomes 16 and 20, respectively. One marker on chromosome 27 was associated with a difference in the dairy capacity composite index, and another marker on chromosome 13 was associated with a difference in a canonical conformation trait. These additional markers complete our genome scan to identify quantitative trait loci affecting economically important traits in a selected commercial Holstein population. The quantitative trait loci identified in this genome scan may be useful for marker-assisted selection to increase the rate of genetic improvement on traits such as disease resistance and conformation traits associated with fitness while accelerating genetic improvement for production. PMID:11768096

Ashwell, M S; Van Tassell, C P; Sonstegard, T S

2001-11-01

58

A Genomic Scan for Selection Reveals Candidates for Genes Involved in the Evolution of Cultivated Sunflower (Helianthus annuus)[W  

Science.gov (United States)

Genomic scans for selection are a useful tool for identifying genes underlying phenotypic transitions. In this article, we describe the results of a genome scan designed to identify candidates for genes targeted by selection during the evolution of cultivated sunflower. This work involved screening 492 loci derived from ESTs on a large panel of wild, primitive (i.e., landrace), and improved sunflower (Helianthus annuus) lines. This sampling strategy allowed us to identify candidates for selectively important genes and investigate the likely timing of selection. Thirty-six genes showed evidence of selection during either domestication or improvement based on multiple criteria, and a sequence-based test of selection on a subset of these loci confirmed this result. In view of what is known about the structure of linkage disequilibrium across the sunflower genome, these genes are themselves likely to have been targeted by selection, rather than being merely linked to the actual targets. While the selection candidates showed a broad range of putative functions, they were enriched for genes involved in amino acid synthesis and protein catabolism. Given that a similar pattern has been detected in maize (Zea mays), this finding suggests that selection on amino acid composition may be a general feature of the evolution of crop plants. In terms of genomic locations, the selection candidates were significantly clustered near quantitative trait loci (QTL) that contribute to phenotypic differences between wild and cultivated sunflower, and specific instances of QTL colocalization provide some clues as to the roles that these genes may have played during sunflower evolution. PMID:19017747

Chapman, Mark A.; Pashley, Catherine H.; Wenzler, Jessica; Hvala, John; Tang, Shunxue; Knapp, Steven J.; Burke, John M.

2008-01-01

59

A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus).  

Science.gov (United States)

Genomic scans for selection are a useful tool for identifying genes underlying phenotypic transitions. In this article, we describe the results of a genome scan designed to identify candidates for genes targeted by selection during the evolution of cultivated sunflower. This work involved screening 492 loci derived from ESTs on a large panel of wild, primitive (i.e., landrace), and improved sunflower (Helianthus annuus) lines. This sampling strategy allowed us to identify candidates for selectively important genes and investigate the likely timing of selection. Thirty-six genes showed evidence of selection during either domestication or improvement based on multiple criteria, and a sequence-based test of selection on a subset of these loci confirmed this result. In view of what is known about the structure of linkage disequilibrium across the sunflower genome, these genes are themselves likely to have been targeted by selection, rather than being merely linked to the actual targets. While the selection candidates showed a broad range of putative functions, they were enriched for genes involved in amino acid synthesis and protein catabolism. Given that a similar pattern has been detected in maize (Zea mays), this finding suggests that selection on amino acid composition may be a general feature of the evolution of crop plants. In terms of genomic locations, the selection candidates were significantly clustered near quantitative trait loci (QTL) that contribute to phenotypic differences between wild and cultivated sunflower, and specific instances of QTL colocalization provide some clues as to the roles that these genes may have played during sunflower evolution. PMID:19017747

Chapman, Mark A; Pashley, Catherine H; Wenzler, Jessica; Hvala, John; Tang, Shunxue; Knapp, Steven J; Burke, John M

2008-11-01

60

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2010-01-01

 
 
 
 
61

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

1996-01-01

62

Landmark navigation rule, a new navigation device.  

Science.gov (United States)

Two new methods of landmark navigation were recently presented. The landmarks are assumed to be within sight of the navigator but with unknown positions. Both methods require computations which are time consuming when a computer is not available. This correspondence presents the concept of a new navigation device called 'landmark navigation rule' which eliminates all the computation effort required in both new methods. The device is simple in construction, lightweight, and consumes no power.

Hung, J. C.; Bennett, J. E.

1972-01-01

63

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

Science.gov (United States)

Identification of loci with adaptive importance is a key step to understand the speciation process in natural populations, because those loci are responsible for phenotypic variation that affects fitness in different environments. We conducted an AFLP genome scan in populations of ocellated lizards (Lacerta lepida) to search for candidate loci influenced by selection along an environmental gradient in the Iberian Peninsula. This gradient is strongly influenced by climatic variables, and two subspecies can be recognized at the opposite extremes: L. lepida iberica in the northwest and L. lepida nevadensis in the southeast. Both subspecies show substantial morphological differences that may be involved in their local adaptation to the climatic extremes. To investigate how the use of a particular outlier detection method can influence the results, a frequentist method, DFDIST, and a Bayesian method, BayeScan, were used to search for outliers influenced by selection. Additionally, the spatial analysis method was used to test for associations of AFLP marker band frequencies with 54 climatic variables by logistic regression. Results obtained with each method highlight differences in their sensitivity. DFDIST and BayeScan detected a similar proportion of outliers (3-4%), but only a few loci were simultaneously detected by both methods. Several loci detected as outliers were also associated with temperature, insolation or precipitation according to spatial analysis method. These results are in accordance with reported data in the literature about morphological and life-history variation of L. lepida subspecies along the environmental gradient. PMID:21091562

Nunes, Vera L; Beaumont, Mark A; Butlin, Roger K; Paulo, Octávio S

2011-01-01

64

A landmark-based 3D calibration strategy for SPM  

Science.gov (United States)

We present a new method for the complete three-dimensional (3D) calibration of scanning probe microscopes (SPM) and other high-resolution microscopes, e.g., scanning electron microscopes (SEM) and confocal laser scanning microscopes (CLSM), by applying a 3D micrometre-sized reference structure with the shape of a cascade slope-step pyramid. The 3D reference structure was produced by focused ion beam induced metal deposition. In contrast to pitch featured calibration procedures that require separate lateral and vertical reference standards such as gratings and step height structures, the new method includes the use of landmarks, which are well established in calibration and measurement tasks on a larger scale. However, the landmarks applied to the new 3D reference structures are of sub-micrometre size, the so-called 'nanomarkers'. The nanomarker coordinates are used for a geometrical calibration of the scanning process of SPM as well as of other instrument types such as SEM and CLSM. For that purpose, a parameter estimation routine involving three scale factors and three coupling factors has been developed that allows lateral and vertical calibration in only one sampling step. With this new calibration strategy, we are able to detect deviations of SPM lateral scaling errors as well as coupling effects causing, e.g., a lateral coordinate shift depending on the measured height position of the probe.

Ritter, Martin; Dziomba, Thorsten; Kranzmann, Axel; Koenders, Ludger

2007-02-01

65

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

66

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

67

Genome-wide association scans for secondary traits using case-control samples  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Genome-wide association studies (GWAS) require considerable investment, so researchers often study multiple traits collected on the same set of subjects to maximize return. However, many GWAS have adopted a case-control design; improperly accounting for case-control ascertainment can lead to biased estimates of association between markers and secondary traits. We show that under the null hypothesis of no marker-secondary trait association, naïve analyses that ignore ascertainment or stratify...

Monsees, Genevieve M.; Tamimi, Rulla M.; Kraft, Peter

2009-01-01

68

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 selectio...

Gf, Teacher Amber; André Carl; Merilä Juha; Wheat Christopher W

2012-01-01

69

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

70

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

71

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

Science.gov (United States)

Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We resequenced some of the positively selected sites (PSSs), within the positively selected genes, and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment. PMID:23246795

Sun, Yan-Bo; Zhou, Wei-Ping; Liu, He-Qun; Irwin, David M; Shen, Yong-Yi; Zhang, Ya-Ping

2013-01-01

72

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

Science.gov (United States)

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

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

73

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

74

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2009-01-01

75

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

76

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

2010-01-01

77

Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm.  

Science.gov (United States)

For all known major apple scab resistance genes except Vr, molecular markers have been published. However, the precise position of some of these genes, in the apple genome, remains to be identified. Knowledge about the relative position of apple scab resistance genes is necessary to preliminarily evaluate the probability of success of their pyramidization. Pyramidization of different resistance genes into the same genotype is a reliable way to create cultivars with durable apple scab resistance. Applying the genome scanning approach (GSA), we identified the linkage group of the scab resistance gene Vm, derived from Malus micromalus, and we found a new molecular marker tightly associated with the gene. The simple sequence repeat Hi07h02, previously mapped on linkage group 17, cosegregates with the Vm gene (no recombinants in the 95 plants tested). The already published sequence-characterized amplified region Vm marker OPB12(687) was found to be linked at about 5 cM from the resistance gene and, therefore, this marker also maps on linkage group 17 of apple. This is the first report of the discovery of a major apple scab resistance gene on linkage group 17. The advantages of using GSA for the identification of molecular markers for qualitative traits are discussed. PMID:16094431

Patocchi, A; Walser, M; Tartarini, S; Broggini, G A L; Gennari, F; Sansavini, S; Gessler, C

2005-08-01

78

A sensitive scanning technology for low frequency nuclear point mutations in human genomic DNA  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Knowledge of the kinds and numbers of nuclear point mutations in human tissues is essential to the understanding of the mutation mechanisms underlying genetic diseases. However, nuclear point mutant fractions in normal humans are so low that few methods exist to measure them. We have now developed a means to scan for point mutations in 100 bp nuclear single copy sequences at mutant fractions as low as 10–6. Beginning with about 108 human cells we first enrich for the desired nuclear sequenc...

Li-sucholeiki, Xiao-cheng; Thilly, William G.

2000-01-01

79

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

Directory of Open Access Journals (Sweden)

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

Wang Xiaojing

2012-12-01

80

Teaching and work productivity: recovering landmarks founders  

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Full Text Available In this paper, we aim to make a rescue of some historical landmarks founders productivity at work and in education to better understand the logic legitimizes reaching the core of the teaching activity. The advance of the criteria on the productive worker training has its first expressions in the 1940s, even during the dictatorship of the Estado Novo. Firstly, we make a brief presentation of the concept of productivity; after that, some of its founders landmarks in the history of the country are shown, and, lastly, there is a presentation of the particularity of one of these landmarks: the presence of CBAI (Brazilian-American Commission of Industrial Education .

Maria Ciavatta

2013-09-01

 
 
 
 
81

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

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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

82

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

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

Velculescu Victor E

2008-04-01

83

Challenges and pitfalls in the characterization of anonymous outlier AFLP markers in non-model species: lessons from an ocellated lizard genome scan.  

Science.gov (United States)

In the last few years, dozens of studies have documented the detection of loci influenced by selection from genome scans in a wide range of non-model species. Many of those studies used amplified fragment length polymorphism (AFLP) markers, which became popular for being easily applicable to any organism. However, because they are anonymous markers, AFLPs impose many challenges for their isolation and identification. Most recent AFLP genome scans used capillary electrophoresis (CE), which adds even more obstacles to the isolation of bands with a specific size for sequencing. These caveats might explain the extremely low number of studies that moved from the detection of outlier AFLP markers to their actual isolation and characterization. We document our efforts to characterize a set of outlier AFLP markers from a previous genome scan with CE in ocellated lizards (Lacerta lepida). Seven outliers were successfully isolated, cloned and sequenced. Their sequences are noncoding and show internal indels or polymorphic repetitive elements (microsatellites). Three outliers were converted into codominant markers by using specific internal primers to sequence and screen population variability from undigested DNA. Amplification in closely related lizard species was also achieved, revealing remarkable interspecific conservation in outlier loci sequences. We stress the importance of following up AFLP genome scans to validate selection signatures of outlier loci, but also report the main challenges and pitfalls that may be faced during the process. PMID:22892639

Nunes, V L; Beaumont, M A; Butlin, R K; Paulo, O S

2012-12-01

84

A GENOME-WIDE SCAN FOR QTL AFFECTING CARCASS TRAITS AT CONSTANT FAT DEPTH IN A HEREFORD X COMPOSITE DOUBLE BACKCROSS POPULATION  

Science.gov (United States)

A genome-wide scan for chromosomal regions influencing carcass traits was conducted spanning 2.497 Morgans on 29 bovine autosomes using 170 microsatellite markers. There were 151 progeny from a single Hereford x composite bull produced by backcross matings to both Hereford and composite dams. Cattl...

85

Landmarks selection in street map design  

Science.gov (United States)

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

Kao, C. J.

2014-02-01

86

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

87

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 = 1.9x10(-11)) and MSRA (WC, P = 8.9x10(-9)). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8)). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity. PMID:19557161

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; 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; Hugh Watkins; 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, Mark I

2009-06-01

88

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

Science.gov (United States)

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. PMID:24948693

Ocholla, Harold; Preston, Mark D.; Mipando, Mwapatsa; Jensen, Anja T. R.; Campino, Susana; MacInnis, Bronwyn; Alcock, Daniel; Terlouw, Anja; Zongo, Issaka; Oudraogo, Jean-Bosco; Djimde, Abdoulaye A.; Assefa, Samuel; Doumbo, Ogobara K.; Borrmann, Steffen; Nzila, Alexis; Marsh, Kevin; Fairhurst, Rick M.; Nosten, Francois; Anderson, Tim J. C.; Kwiatkowski, Dominic P.; Craig, Alister; Clark, Taane G.; Montgomery, Jacqui

2014-01-01

89

Automatic computerized radiographic identification of cephalometric landmarks.  

Science.gov (United States)

Computerized cephalometric analysis currently requires manual identification of landmark locations. This process is time-consuming and limited in accuracy. The purpose of this study was to develop and test a novel method for automatic computer identification of cephalometric landmarks. Spatial spectroscopy (SS) is a computerized method that identifies image structure on the basis of a convolution of the image with a set of filters followed by a decision method using statistical pattern recognition techniques. By this method, characteristic features are used to recognize anatomic structures. This study compared manual identification on a computer monitor and the SS automatic method for landmark identification on minimum resolution images (0.16 cm2 per pixel). Minimum resolution (defined as the lowest resolution at which a cephalometric structure could be identified) was used to reduce computational time and memory requirements during this development stage of the SS method. Fifteen landmarks were selected on a set of 14 test images. The results showed no statistical difference (p > 0.05) in mean landmark identification errors between manual identification on the computer display and automatic identification using SS. We conclude that SS shows potential for the automatic detection of landmarks, which is an important step in the development of a completely automatic cephalometric analysis. PMID:9484208

Rudolph, D J; Sinclair, P M; Coggins, J M

1998-02-01

90

Genome-wide linkage scan for factors of metabolic syndrome in a Chinese population  

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Full Text Available Abstract Background Shared genetic factors may contribute to the phenotypic clustering of different components of the metabolic syndrome (MES. This study aims to identify genetic loci that contribute to individual or multiple factors related to MES. Results We studied 478 normoglycemic subjects ascertained through 163 families participating in the Hong Kong Family Diabetes Study. Factor analysis on 15 MES-related traits yielded 6 factors including adiposity factor (body mass index, waist and hip circumferences, insulin factor (fasting insulin and insulin AUC during OGTT, glucose factor (fasting glucose and glucose AUC during OGTT, TC-LDLC factor (total cholesterol and LDL-cholesterol, blood pressure factor (systolic and diastolic blood pressure and TG-HDLC factor (triglycerides and HDL-cholesterol. Genome-wide linkage analyses were performed on these factors using variance component approach. Suggestive evidence for linkage (LOD = 1.24 - 2.46 were observed for adiposity factor (chromosome 1 at 187 cM, chromosome 9 at 34 cM and chromosome 17 at 10 cM, insulin factor (chromosome 2 at 128 cM, chromosome 5 at 21 cM and chromosome 12 at 7 cM, glucose factor (chromosome 7 at 155 cM, TC-LDLC factor (chromosome 7 at 151 cM and chromosome 13 at 15 cM and TG-HDLC factor (chromosome 7 at 155 cM. Conclusions In summary, our findings suggest the presence of susceptibility loci that influence either single (chromosomes 1, 2, 5, 9, 12, 13 and 17 or multiple factors (chromosome 7 for MES in Hong Kong Chinese without diabetes.

Chan Juliana CN

2010-02-01

91

A genome-wide admixture scan for ancestry-linked genes predisposing to sarcoidosis in African-Americans.  

Science.gov (United States)

Genome-wide linkage and association studies have uncovered variants associated with sarcoidosis, a multiorgan granulomatous inflammatory disease. African ancestry may influence disease pathogenesis, as African-Americans are more commonly affected by sarcoidosis. Therefore, we conducted the first sarcoidosis genome-wide ancestry scan using a map of 1384 highly ancestry-informative single-nucleotide polymorphisms genotyped on 1357 sarcoidosis cases and 703 unaffected controls self-identified as African-American. The most significant ancestry association was at marker rs11966463 on chromosome 6p22.3 (ancestry association risk ratio (aRR)=1.90; P=0.0002). When we restricted the analysis to biopsy-confirmed cases, the aRR for this marker increased to 2.01; P=0.00007. Among the eight other markers that demonstrated suggestive ancestry associations with sarcoidosis were rs1462906 on chromosome 8p12, which had the most significant association with European ancestry (aRR=0.65; P=0.002), and markers on chromosomes 5p13 (aRR=1.46; P=0.005) and 5q31 (aRR=0.67; P=0.005), which correspond to regions we previously identified through sib-pair linkage analyses. Overall, the most significant ancestry association for Scadding stage IV cases was to marker rs7919137 on chromosome 10p11.22 (aRR=0.27; P=2 × 10(-5)), a region not associated with disease susceptibility. In summary, through admixture mapping of sarcoidosis we have confirmed previous genetic linkages and identified several novel putative candidate loci for sarcoidosis. PMID:21179114

Rybicki, B A; Levin, A M; McKeigue, P; Datta, I; Gray-McGuire, C; Colombo, M; Reich, D; Burke, R R; Iannuzzi, M C

2011-03-01

92

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

93

A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs.  

Science.gov (United States)

Quantitative trait loci for reproductive traits in a three-generation resource population of a cross between low-indexing pigs from a control line and high-indexing pigs from a line selected 10 generations for increased index of ovulation rate and embryonic survival are reported. Phenotypic data were collected in F2 females for birth weight (BWT, n = 428), weaning weight (WWT, n = 405), age at puberty (AP, n = 295), ovulation rate (OR, n = 423), number of fully formed pigs (FF, n = 370), number of pigs born alive (NBA, n = 370), number of mummified pigs (MUM, n = 370), and number of stillborn pigs (NSB, n = 370). Grandparent, F1, and F2 animals were genotyped for 151 microsatellite markers. Sixteen putative QTL (P < 0.10) for reproductive traits were identified in previous analyses of these data with single QTL line-cross models. Data were reanalyzed with multiple QTL models, including imprinting effects. Data also were analyzed with half-sib models. Permutation was used to establish genome-wide significance levels ( = 0.01, 0.05, and 0.10). Thirty-one putative QTL for reproductive traits and two QTL for birth weight were identified (P < 0.10). One Mendelian QTL for FF (P < 0.05), one for NBA (P < 0.05), three for NSB (P < 0.05), three for NN (P < 0.05), seven for AP (P < 0.10), five for MUM (P < 0.10), and one for BWT (P < 0.10) were found. Partial imprinting of QTL affecting OR (P < 0.01), BWT (P < 0.05), and MUM (P < 0.05) was detected. There were four paternally expressed QTL for NN (P < 0.10) and one each for AP (P < 0.05) and MUM (P < 0.10). Maternally expressed QTL affecting NSB (P < 0.10), NN (P < 0.10), and MUM (P < 0.10) were detected. No QTL were detected with half-sib analyses. Multiple QTL models with imprinting effects are more appropriate for analyzing F2 data than single Mendelian QTL line-cross models. PMID:15537760

Holl, J W; Cassady, J P; Pomp, D; Johnson, R K

2004-12-01

94

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

2014-01-01

95

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

Science.gov (United States)

Systemic sclerosis (SSc) is an orphan, complex, inflammatory disease affecting the immune system and connective tissue. SSc stands out as a severely incapacitating and life-threatening inflammatory rheumatic disease, with a largely unknown pathogenesis. We have designed a two-stage genome-wide association study of SSc using case-control samples from France, Italy, Germany, and Northern Europe. The initial genome-wide scan was conducted in a French post quality-control sample of 564 cases and 1,776 controls, using almost 500 K SNPs. Two SNPs from the MHC region, together with the 6 loci outside MHC having at least one SNP with a P<10?5 were selected for follow-up analysis. These markers were genotyped in a post-QC replication sample of 1,682 SSc cases and 3,926 controls. The three top SNPs are in strong linkage disequilibrium and located on 6p21, in the HLA-DQB1 gene: rs9275224, P?=?9.18×10?8, OR?=?0.69, 95% CI [0.60–0.79]; rs6457617, P?=?1.14×10?7 and rs9275245, P?=?1.39×10?7. Within the MHC region, the next most associated SNP (rs3130573, P?=?1.86×10?5, OR?=?1.36 [1.18–1.56]) is located in the PSORS1C1 gene. Outside the MHC region, our GWAS analysis revealed 7 top SNPs (P<10?5) that spanned 6 independent genomic regions. Follow-up of the 17 top SNPs in an independent sample of 1,682 SSc and 3,926 controls showed associations at PSORS1C1 (overall P?=?5.70×10?10, OR:1.25), TNIP1 (P?=?4.68×10?9, OR:1.31), and RHOB loci (P?=?3.17×10?6, OR:1.21). Because of its biological relevance, and previous reports of genetic association at this locus with connective tissue disorders, we investigated TNIP1 expression. A markedly reduced expression of the TNIP1 gene and also its protein product were observed both in lesional skin tissue and in cultured dermal fibroblasts from SSc patients. Furthermore, TNIP1 showed in vitro inhibitory effects on inflammatory cytokine-induced collagen production. The genetic signal of association with TNIP1 variants, together with tissular and cellular investigations, suggests that this pathway has a critical role in regulating autoimmunity and SSc pathogenesis. PMID:21750679

Allanore, Yannick; Saad, Mohamad; Dieudé, Philippe; Avouac, Jérôme; Distler, Jorg H. W.; Amouyel, Philippe; Matucci-Cerinic, Marco; Riemekasten, Gabriella; Airo, Paolo; Melchers, Inga; Hachulla, Eric; Cusi, Daniele; Wichmann, H.-Erich; Wipff, Julien; Lambert, Jean-Charles; Hunzelmann, Nicolas; Tiev, Kiet; Caramaschi, Paola; Diot, Elisabeth; Kowal-Bielecka, Otylia; Valentini, Gabriele; Mouthon, Luc; Czirják, László; Damjanov, Nemanja; Salvi, Erika; Conti, Costanza; Müller, Martina; Müller-Ladner, Ulf; Riccieri, Valeria; Ruiz, Barbara; Cracowski, Jean-Luc; Letenneur, Luc; Dupuy, Anne Marie; Meyer, Oliver; Kahan, André; Munnich, Arnold; Boileau, Catherine; Martinez, Maria

2011-01-01

96

Loci for regulation of bone mineral density in men and women identified by genome wide linkage scan: the FAMOS study.  

Science.gov (United States)

Osteoporosis is a common disease with a strong genetic component, characterized by reduced bone mass and an increased risk of fracture. Bone mineral density (BMD) is a highly heritable trait and a key determinant of osteoporotic fracture risk, but the genes responsible are incompletely defined. Here, we identified quantitative trait loci (QTL) for regulation of BMD by a genome wide scan involving 3691 individuals from 715 families, who were selected because of reduced BMD values at the lumbar spine (LS-BMD) or femoral neck (FN-BMD) in probands. Linkage analysis was conducted in the study group as a whole with correction for age, gender, weight and height. Further analyses were conducted for men and women separately to identify gender-specific QTL and for those under and over the age of 50 years to distinguish QTL for peak bone mass from those that influence bone mass in older people. No regions of suggestive or significant linkage were identified when data from all subjects were analyzed together. On subgroup analysis, however, we identified a significant QTL for FN-BMD on chromosome 10q21 (LOD score +4.42; men 50 years) and 20q13 (LOD score +3.20; women 4q25, 7p14, 16p13 and 16q23. This study provides evidence for gender-specific, site-specific and age-specific QTL, which regulate BMD in humans, and illustrates the importance of conducting subgroup analysis to detect these loci. PMID:15746152

Ralston, Stuart H; Galwey, Nick; MacKay, Ian; Albagha, Omar M E; Cardon, Lon; Compston, Juliet E; Cooper, Cyrus; Duncan, Emma; Keen, Richard; Langdahl, Bente; McLellan, Alastair; O'Riordan, Jeffrey; Pols, Huibert A; Reid, David M; Uitterlinden, Andre G; Wass, John; Bennett, Simon T

2005-04-01

97

Anatomic Landmarks Versus Fiducials for Volume-Staged Gamma Knife Radiosurgery for Large Arteriovenous Malformations  

International Nuclear Information System (INIS)

Purpose: The purpose of this investigation was to compare the accuracy of using internal anatomic landmarks instead of surgically implanted fiducials in the image registration process for volume-staged gamma knife (GK) radiosurgery for large arteriovenous malformations. Methods and Materials: We studied 9 patients who had undergone 10 staged GK sessions for large arteriovenous malformations. Each patient had fiducials surgically implanted in the outer table of the skull at the first GK treatment. These markers were imaged on orthogonal radiographs, which were scanned into the GK planning system. For the same patients, 8-10 pairs of internal landmarks were retrospectively identified on the three-dimensional time-of-flight magnetic resonance imaging studies that had been obtained for treatment. The coordinate transformation between the stereotactic frame space for subsequent treatment sessions was then determined by point matching, using four surgically embedded fiducials and then using four pairs of internal anatomic landmarks. In both cases, the transformation was ascertained by minimizing the chi-square difference between the actual and the transformed coordinates. Both transformations were then evaluated using the remaining four to six pairs of internal landmarks as the test points. Results: Averaged over all treatment sessions, the root mean square discrepancy between the coordinates of the transformed and actual test points was 1.2 ± 0.2 mm using internal landmars was 1.2 ± 0.2 mm using internal landmarks and 1.7 ± 0.4 mm using the surgically implanted fiducials. Conclusion: The results of this study have shown that using internal landmarks to determine the coordinate transformation between subsequent magnetic resonance imaging scans for volume-staged GK arteriovenous malformation treatment sessions is as accurate as using surgically implanted fiducials and avoids an invasive procedure

98

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

Science.gov (United States)

A genome scan was performed on 164 Dutch affected sib pairs (ASPs) with attention-deficit/hyperactivity disorder (ADHD). All subjects were white and of Dutch descent and were phenotyped according to criteria set out in the Diagnostic and Statistical Manual Of Mental Disorders, 4th edition. Initially, a narrow phenotype was defined, in which all the sib pairs met the full ADHD criteria (117 ASPs). In a broad phenotype, additional sib pairs were included, in which one child had an autistic-spectrum disorder but also met the full ADHD criteria (164 ASPs). A set of 402 polymorphic microsatellite markers with an average intermarker distance of 10 cM was genotyped and analyzed using the Mapmaker/sibs program. Regions with multipoint maximum likelihood scores (MLSs) >1.5 in both phenotypes were fine mapped with additional markers. This genome scan indicated several regions of interest, two of which showed suggestive evidence for linkage. The most promising chromosome region was located at 15q, with an MLS of 3.54 under the broad phenotype definition. This region was previously implicated in reading disability and autism. In addition, MLSs of 3.04 and 2.05 were found for chromosome regions 7p and 9q in the narrow phenotype. Except for a region on chromosome 5, no overlap was found with regions mentioned in the only other independent genome scan in ADHD reported to date. PMID:12679898

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

2003-05-01

99

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

100

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

 
 
 
 
101

Landmark matching via large deformation diffeomorphisms.  

Science.gov (United States)

This paper describes the generation of large deformation diffeomorphisms phi:Omega=[0,1]3Omega for landmark matching generated as solutions to the transport equation dphi(x,t)/dt=nu(phi(x,t),t),epsilon[0,1] and phi(x,0)=x, with the image map defined as phi(.,1) and therefore controlled via the velocity field nu(.,t),epsilon[0,1]. Imagery are assumed characterized via sets of landmarks {xn, yn, n=1, 2, ..., N}. The optimal diffeomorphic match is constructed to minimize a running smoothness cost parallelLnu parallel2 associated with a linear differential operator L on the velocity field generating the diffeomorphism while simultaneously minimizing the matching end point condition of the landmarks. Both inexact and exact landmark matching is studied here. Given noisy landmarks xn matched to yn measured with error covariances Sigman, then the matching problem is solved generating the optimal diffeomorphism phi;(x,1)=integral0(1)nu(phi(x,t),t)dt+x where nu(.)=argmin(nu.)integral1(0) integralOmega parallelLnu(x,t) parallel2dxdt +Sigman=1N[yn-phi(xn,1)] TSigman(-1)[yn-phi(xn,1)]. Conditions for the existence of solutions in the space of diffeomorphisms are established, with a gradient algorithm provided for generating the optimal flow solving the minimum problem. Results on matching two-dimensional (2-D) and three-dimensional (3-D) imagery are presented in the macaque monkey. PMID:18262973

Joshi, S C; Miller, M I

2000-01-01

102

Landmark Constrained Non-parametric Image Registration with Isotropic Tolerances  

Science.gov (United States)

The incorporation of additional user knowledge into a nonrigid registration process is a promising topic in modern registration schemes. The combination of intensity based registration and some interactively chosen landmark pairs is a major approach in this direction. There exist different possibilities to incorporate landmark pairs into a variational non-parametric registration framework. As the interactive localization of point landmarks is always prone to errors, a demand for precise landmark matching is bound to fail. Here, the treatment of the distances of corresponding landmarks as penalties within a constrained optimization problem offers the possibility to control the quality of the matching of each landmark pair individually. More precisely, we introduce inequality constraints, which allow for a sphere-like tolerance around each landmark. We illustrate the performance of this new approach for artificial 2D images as well as for the challenging registration of preoperative CT data to intra-operative 3D ultrasound data of the liver.

Papenberg, Nils; Olesch, Janine; Lange, Thomas; Schlag, Peter M.; Fischer, Bernd

103

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

Directory of Open Access Journals (Sweden)

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

Zhang Hui

2012-12-01

104

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

105

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

End stage renal disease (ESRD) has a four times higher incidence in African Americans compared to European Americans. This led to the hypothesis that susceptibility alleles for ESRD have a higher frequency in West African than European gene pool. We performed a genome-wide admixture scan in 1,372 ESRD cases and 806 controls and demonstrated a highly significant association between excess African ancestry and non-diabetic ESRD (LOD 5.70) but not diabetic ESRD (LOD 0.47) on chromosome 22q12. Ea...

Linda Kao, Wh; Klag, Michael J.; Meoni, Lucy A.; Reich, David; Berthier-schaad, Yvette; Li, Man; Coresh, Josef; Patterson, Nick; Tandon, Arti; Powe, Neil R.; Fink, Nancy E.; Sadler, John H.; Weir, Matthew R.; Abboud, Hanna E.; Adler, Sharon

2008-01-01

106

Investigation of susceptibility loci identified in the UK rheumatoid arthritis whole-genome scan in a further series of 217 UK affected sibling pairs.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

OBJECTIVE: A previous whole-genome scan (WGS) of 182 UK rheumatoid arthritis (RA) affected sibling pair (ASP) families suggested linkage to HLA and 11 other chromosome regions. Replication of such findings in an independent cohort can help to distinguish true linkages from false-positive linkages. Since RA is a heterogeneous disease, some loci may be linked only in subsets of patients. Thus, the aim of this study was to investigate in an additional set of RA ASP families linkage to regions sh...

Eyre, S.; Barton, A.; Shephard, N.; Hinks, A.; Brintnell, W.; Mackay, K.; Silman, A.; Ollier, W.; Wordsworth, P.; John, S.; Worthington, J.

2004-01-01

107

A Whole-Genome Scan in 164 Dutch Sib Pairs with Attention-Deficit/Hyperactivity Disorder: Suggestive Evidence for Linkage on Chromosomes 7p and 15q  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A genome scan was performed on 164 Dutch affected sib pairs (ASPs) with attention-deficit/hyperactivity disorder (ADHD). All subjects were white and of Dutch descent and were phenotyped according to criteria set out in the Diagnostic and Statistical Manual Of Mental Disorders, 4th edition. Initially, a narrow phenotype was defined, in which all the sib pairs met the full ADHD criteria (117 ASPs). In a broad phenotype, additional sib pairs were included, in which one child had an autistic-spec...

Bakker, S. C.; Meulen, E. M.; Buitelaar, J. K.; Sandkuijl, L. A.; Pauls, D. L.; Monsuur, A. J.; Slot, R. Van?‘t; Minderaa, R. B.; Gunning, W. B.; Pearson, P. L.; Sinke, R. J.

2003-01-01

108

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

109

Important anatomical landmarks in the lateral nasal wall.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

OBJECTIVES The study aimed to investigate the anatomy of the lateral nasal wall to provide a set of measurements among some important anatomical landmarks and to reveal the relationship between them. METHODS Fifty half heads were dissected to determine the distances between important landmarks in the lateral nasal wall for endoscopic sinus surgery. Landmarks were measured with an electronic caliper. This study was carried out between De...

Donmez, Baris O.; Agirdir, Bulent V.; Sindel, Muzaffer M.

2005-01-01

110

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

Directory of Open Access Journals (Sweden)

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

Xiaohong W. Gao

2007-01-01

111

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

112

Longwall automation - an ACARP Landmark Project  

Energy Technology Data Exchange (ETDEWEB)

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

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

2002-07-01

113

Landmark experiments in twentieth-century physics  

CERN Document Server

Physics is very much an experimental science, but too often, students at the undergraduate level are not exposed to the reality of experimental physics ? i.e., what was done in a given experiment, why it was done, the background of physics against which the experiment was carried out and the changes in theory and knowledge that resulted. In this hook, the author helps to remedy the situation by presenting a variety of ""landmark"" experiments that have brought about significant alterations in our ideas about some aspect of nature. Among these scientific milestones are discoveries about the wa

Trigg, George L

2013-01-01

114

Active shape models incorporating isolated landmarks for medical image annotation  

Science.gov (United States)

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

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

2014-03-01

115

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

116

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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.

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

2011-01-01

117

A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Warfarin dosing is correlated with polymorphisms in vitamin K epoxide reductase complex 1 (VKORC1) and the cytochrome P450 2C9 (CYP2C9) genes. Recently, the FDA revised warfarin labeling to raise physician awareness about these genetic effects. Randomized clinical trials are underway to test genetically based dosing algorithms. It is thus important to determine whether common single nucleotide polymorphisms (SNPs) in other gene(s) have a large effect on warfarin dosing. A retrospective genome...

Cooper, Gregory M.; Johnson, Julie A.; Langaee, Taimour Y.; Feng, Hua; Stanaway, Ian B.; Schwarz, Ute I.; Ritchie, Marylyn D.; Stein, C. Michael; Roden, Dan M.; Smith, Joshua D.; Veenstra, David L.; Rettie, Allan E.; Rieder, Mark J.

2008-01-01

118

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140?dph, respectively. The majority of these QTLs were sex-specific. One major QTL for gro...

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

2014-01-01

119

Genome-Wide Scan for Signatures of Human Population Differentiation and Their Relationship with Natural Selection, Functional Pathways and Diseases  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was...

Amato, Roberto; Pinelli, Michele; Monticelli, Antonella; Marino, Davide; Miele, Gennaro; Cocozza, Sergio

2009-01-01

120

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2006-01-01

 
 
 
 
121

View-based navigation in insects: how wood ants (Formica rufa L.) look at and are guided by extended landmarks.  

Science.gov (United States)

Bees, wasps and ants learn landmarks as views from particular vantage points, storing the retinal positions of landmark edges. By moving so as to minimise the difference between their stored and current view, they can return to the vantage point from which a view was taken. We have examined what wood ants learn about a laterally placed, extended landmark, a wall, while walking parallel to it to reach a feeder and how they use this stored information to guide their path. Manipulation of the height of the wall and the ant's starting distance from it reveals that ants maintain a desired distance from the wall by keeping the image of the top of the wall at a particular retinal elevation. Ants can thus employ image matching both for returning to a place and for following a fixed route. Unlike many flying insects, an ant's direction of motion while walking is always along its longitudinal body axis and, perhaps for this reason, it favours its frontal retina for viewing discrete landmarks. We find that ants also use their frontal retina for viewing a laterally placed wall. On a coarse scale, the ant's path along the wall is straight, but on a finer scale it is roughly sinusoidal, allowing the ant to scan the surrounding landscape with its frontal retina. The ant's side-to-side scanning means that the wall is viewed with its frontal retina for phases of the scanning cycle throughout its trajectory. Details of the scanning pattern depend on the scene. Ants scan further to the side that is empty of the wall than to the side containing the wall, and they scan further into the wall side when the wall is of a lower apparent height. We conclude that frontal retina is employed for image storage and for path control. PMID:12124373

Graham, Paul; Collett, Thomas S

2002-08-01

122

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci affecting serum glucose and insulin levels and response to glucose stress in an F16 Advan...

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

2011-01-01

123

Genome-wide scan for type 1 diabetic nephropathy in the Finnish population reveals suggestive linkage to a single locus on chromosome 3q.  

Science.gov (United States)

Diabetic nephropathy (DN) is the primary cause of morbidity and mortality in patients with type 1 as well as type 2 diabetes, and accounts for 40% of end-stage renal disease in the Western world. Familial clustering of DN suggests importance of genetic factors in the development of the disease. In the present study, we performed a two-stage genome-wide scan to search for chromosomal loci containing susceptibility genes for nephropathy in patients with type 1 diabetes. In total, 83 discordant sib pairs (DSPs), sibs concordant for type 1 diabetes but discordant for nephropathy, were collected from Finland, a homogeneous population with one of the highest incidences of type 1 diabetes. To map loci for DN, we applied DSP analysis to detect linkage. In the initial scan, 73 DSPs were typed using 900 markers with an average intermarker distance of approximately 4 cM. Multipoint DSP analysis identified five chromosome regions (3q, 4p, 9q, 16q, and 22p) with maximum logarithm of odds (LOD) score (MLS) >or=1.0 (corresponding to a nominal P-value genome-wide significance of 5%. However, one locus on 3q reached suggestive linkage with MLS of 2.67 (P=4.4 x 10(-4)). These results, together with data from others, suggest that the locus on 3q most likely has a susceptibility gene for DN. PMID:17021601

Osterholm, A-M; He, B; Pitkaniemi, J; Albinsson, L; Berg, T; Sarti, C; Tuomilehto, J; Tryggvason, K

2007-01-01

124

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

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

N. Ivalú Cacho

2013-07-01

125

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

126

DETEKSI LANDMARK CITRA WAJAH DENGAN EXTRAKSI FITUR GABOR ANALISA FUZZY  

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

Resmana Lim

2003-01-01

127

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

128

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

129

Landmarks and ant search strategies after interrupted tandem runs.  

Science.gov (United States)

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

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

2014-03-15

130

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

Science.gov (United States)

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

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

2014-01-01

131

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

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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

132

Personal genomics services: whose genomes?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States,...

Gurwitz, David; Bregman-eschet, Yael

2009-01-01

133

36 CFR 62.7 - Natural landmark modifications.  

Science.gov (United States)

...appropriate. For example...better documentation of the...e) Minor technical corrections...proposed minor technical boundary...changes in documentation, as described...is a minor technical correction to landmark documentation that...

2010-07-01

134

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

135

3D face analysis : landmarking, expression recognition and beyond  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Zhao, Xi

2010-01-01

136

DETEKSI LANDMARK CITRA WAJAH DENGAN EXTRAKSI FITUR GABOR ANALISA FUZZY  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper proposes a method that automatically finds human faces as well as its landmark points in color images based on a fuzzy analysis. The proposed approach first uses color information to detect face candidate regions and then uses a fuzzy analysis of the color, shape, symmetry and interior facial features. A deformable Gabor wavelet graph matching is used to locate the facial landmark points describing the face. The latter allows for size and orientation variation since the search for ...

Resmana Lim

2003-01-01

137

Aplicación bioantropológica para manipulación de landmarks faciales en 2D  

Digital Repository Infrastructure Vision for European Research (DRIVER)

La obtención de coordenadas de landmarks en 2 y 3D de modo automatizado y en bases de datos masivas se encuentra en un estado incipiente, a causa de las dificultades técnicas, económicas y operativas que se presentan: debe contarse con dispositivos caros, o no portátiles, capaces de tomar puntos sobre los objetos bajo estudio, y el proceso de landmarking suele ser hecho en forma manual por operadores entrenados, con el consiguiente costo en tiempo y riesgo de errores operativos. En est...

Cintas, Celia; Quinto Sa?nchez, Mirsha; Defosse?, Nahuel; Delrieux, Claudio; Gonza?lez Jose?, Rolando

2014-01-01

138

Indoor Localization System based on Artificial Landmarks and Monocular Vision  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper presents a visual localization approach well suited for the domestic and industrial environments due to its ability to provide an accurate, reliable and robust pose estimation.The mobile robot is equipped with a single camera to update their pose whenever a landmark is available on the field of view.The innovation presented by this research focus, especially, on the artificial landmark that has the ability to detect the presence of the robot, sinceboth entities communicates with ea...

Costa, Paulo G.; Paulo Moreira, A.; Pinto, Andry Maykol G.

2012-01-01

139

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

Science.gov (United States)

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

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

2010-12-01

140

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

 
 
 
 
141

Indoor Localization System based on Artificial Landmarks and Monocular Vision  

Directory of Open Access Journals (Sweden)

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

Paulo G. Costa

2012-12-01

142

Landmark Detection in Orbital Images Using Salience Histograms  

Science.gov (United States)

NASA's planetary missions have collected, and continue to collect, massive volumes of orbital imagery. The volume is such that it is difficult to manually review all of the data and determine its significance. As a result, images are indexed and searchable by location and date but generally not by their content. A new automated method analyzes images and identifies "landmarks," or visually salient features such as gullies, craters, dust devil tracks, and the like. This technique uses a statistical measure of salience derived from information theory, so it is not associated with any specific landmark type. It identifies regions that are unusual or that stand out from their surroundings, so the resulting landmarks are context-sensitive areas that can be used to recognize the same area when it is encountered again. A machine learning classifier is used to identify the type of each discovered landmark. Using a specified window size, an intensity histogram is computed for each such window within the larger image (sliding the window across the image). Next, a salience map is computed that specifies, for each pixel, the salience of the window centered at that pixel. The salience map is thresholded to identify landmark contours (polygons) using the upper quartile of salience values. Descriptive attributes are extracted for each landmark polygon: size, perimeter, mean intensity, standard deviation of intensity, and shape features derived from an ellipse fit.

Wagstaff, Kiri L.; Panetta, Julian; Schorghofer, Norbert; Greeley, Ronald; PendletonHoffer, Mary; bunte, Melissa

2010-01-01

143

Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci  

Science.gov (United States)

We report the results of a meta-analysis of genome-wide association scans for multiple sclerosis (MS) susceptibility that includes 2,624 subjects with MS and 7,220 control subjects. Replication in an independent set of 2,215 subjects with MS and 2,116 control subjects validates new MS susceptibility loci at TNFRSF1A (combined P = 1.59 × 10?11), IRF8 (P = 3.73 × 10?9) and CD6 (P = 3.79 × 10?9). TNFRSF1A harbors two independent susceptibility alleles: rs1800693 is a common variant with modest effect (odds ratio = 1.2), whereas rs4149584 is a nonsynonymous coding polymorphism of low frequency but with stronger effect (allele frequency = 0.02; odds ratio = 1.6). We also report that the susceptibility allele near IRF8, which encodes a transcription factor known to function in type I interferon signaling, is associated with higher mRNA expression of interferon-response pathway genes in subjects with MS. PMID:19525953

De Jager, Philip L; Jia, Xiaoming; Wang, Joanne; de Bakker, Paul I W; Ottoboni, Linda; Aggarwal, Neelum T; Piccio, Laura; Raychaudhuri, Soumya; Tran, Dong; Aubin, Cristin; Briskin, Rebeccah; Romano, Susan; Baranzini, Sergio E; McCauley, Jacob L; Pericak-Vance, Margaret A; Haines, Jonathan L; Gibson, Rachel A; Naeglin, Yvonne; Uitdehaag, Bernard; Matthews, Paul M; Kappos, Ludwig; Polman, Chris; McArdle, Wendy L; Strachan, David P; Evans, Denis; Cross, Anne H; Daly, Mark J; Compston, Alastair; Sawcer, Stephen J; Weiner, Howard L; Hauser, Stephen L; Hafler, David A; Oksenberg, Jorge R

2009-01-01

144

A physical map of the human genome.  

Science.gov (United States)

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map. PMID:11237014

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

2001-02-15

145

A physical map of the human genome  

Energy Technology Data Exchange (ETDEWEB)

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

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

2001-01-01

146

Algorithms for Automatic and Robust Registration of 3D Head Scans  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Two methods for registering laser-scans of human heads and transforming them to a new semantically consistent topology defined by a user-provided template mesh are described. Both algorithms are stated within the Iterative Closest Point framework. The first method is based on finding landmark correspondences by iteratively registering the vicinity of a landmark with a re-weighted error function. Thin-plate spline interpolation is then used to deform the template mesh and finally the scan is r...

Peter Eisert; Schneider, David C.

2010-01-01

147

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

Science.gov (United States)

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

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

2005-11-01

148

Landmark learning by the Ozark zigzag salamander Plethodon angusticlavius  

Directory of Open Access Journals (Sweden)

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

Adam L. CRANE, Alicia MATHIS

2011-08-01

149

Discriminative BoW framework for mobile landmark recognition.  

Science.gov (United States)

This paper proposes a new soft bag-of-words (BoW) method for mobile landmark recognition based on discriminative learning of image patches. Conventional BoW methods often consider the patches/regions in the images as equally important for learning. Amongst the few existing works that consider the discriminative information of the patches, they mainly focus on selecting the representative patches for training, and discard the others. This binary hard selection approach results in underutilization of the information available, as some discarded patches may still contain useful discriminative information. Further, not all the selected patches will contribute equally to the learning process. In view of this, this paper presents a new discriminative soft BoW approach for mobile landmark recognition. The main contribution of the method is that the representative and discriminative information of the landmark is learned at three levels: patches, images, and codewords. The patch discriminative information for each landmark is first learned and incorporated through vector quantization to generate soft BoW histograms. Coupled with the learned representative information of the images and codewords, these histograms are used to train an ensemble of classifiers using fuzzy support vector machine. Experimental results on two different datasets show that the proposed method is effective in mobile landmark recognition. PMID:23846513

Chen, Tao; Yap, Kim-Hui

2014-05-01

150

A high-density genome scan detects evidence for a bipolar-disorder susceptibility locus on 13q32 and other potential loci on 1q32 and 18p11.2  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Bipolar disorder is a severe mental illness characterized by mood swings of elation and depression. Family, twin, and adoption studies suggest a complex genetic etiology that may involve multiple susceptibility genes and an environmental component. To identify chromosomal loci contributing to vulnerability, we have conducted a genome-wide scan on ?396 individuals from 22 multiplex pedigrees by using 607 microsatellite markers. Multipoint nonparametric analysis detected the strongest evidenc...

Detera-wadleigh, Sevilla D.; Badner, Judith A.; Berrettini, Wade H.; Yoshikawa, Takeo; Goldin, Lynn R.; Turner, Gordon; Rollins, Denise Y.; Moses, Tracy; Sanders, Alan R.; Karkera, Jayaprakash D.; Esterling, Lisa E.; Zeng, Jin; Ferraro, Thomas N.; Guroff, Juliet J.; Kazuba, Diane

1999-01-01

151

Mapping genomic deletions down to the base: a quantitative copy number scanning approach used to characterise and clone the breakpoints of a recurrent 7p14.2p15.3 deletion.  

Science.gov (United States)

With the recent advances in genomic research, it has become apparent that a substantial part of human malformation and mental retardation is caused by imbalances in genomic content. Thus, there is an increasing need for versatile methods allowing a detailed mapping and cloning of the actual rearrangements. We have combined the flexibility of real-time quantitative PCR with the knowledge of human genome sequence to perform a copy number scanning in three patients known to harbour a deletion in the 7p14p15 locus. In two of the patients the actual breakpoints were cloned and sequenced, whereas the breakpoint of the third patient was mapped to a region previously predicted to be prone for rearrangements. One patient also harboured an inversion in connection with the deletion that disrupted the HDAC9 gene. All three patients showed clinical characteristics reminiscent of the hand-foot-genital syndrome and were deleted for the entire HOXA cluster. Two patients were also deleted for DFNA5, a gene implicated in dominant nonsyndromic hearing impairment, but neither patient showed signs of reduced hearing capabilities. The described copy number scanning approach is largely independent of the genomic locus and may be a valuable tool for characterising a large spectrum of deletions. PMID:15378350

Dunø, Morten; Hove, Hanne; Kirchhoff, Maria; Devriendt, Koenraad; Schwartz, Marianne

2004-11-01

152

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

153

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

154

Pontos referenciais nos acessos cranianos Landmarks to the cranial approaches  

Directory of Open Access Journals (Sweden)

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

Sebastião Gusmão

2003-06-01

155

Three-dimensional Anatomical Analysis of Surgical Landmarks for the Middle Cranial Fossa Approach.  

Science.gov (United States)

This study describes the microsurgical anatomy of the middle cranial fossa approach using temporal bone three-dimensional (3D) computed tomography (CT) reconstruction, which should contribute to determining the drilling point for the internal auditory meatus (IAM) when bony landmarks are absent. Thirty temporal bone CT scans were reviewed retrospectively. We measured the shortest and longest distances to IAM from the petrous ridge, and measured the angle between the facial nerve and various labyrinth structures. Three-dimensional reconstructed images were obtained using high-resolution axial temporal bone CT (0.7-mm-thick slices, FOV 90 × 90, KVp 120, 305 mA, width 2,800, and level 800). The mean shortest and longest distances to IAM from the petrous ridge were 5.22 and 10.1 mm, respectively. The mean distance to the IAM from the cochlea was 9.91 mm. The mean angle between the IAM and superior semicircular canal was 47.21°, which was more acute than previously reported. The mean angle between the IAM and geniculate ganglion (GG) and external auditory canal was 113.8°, and the mean distance from the GG to the IAM was 15.44 mm. Understanding the 3D relationships among the microsurgical structures will help to decide the drilling point for the IAM when bony landmarks are absent. A preoperative evaluation might be useful for preserving important neurovascular structures while approaching the middle fossa. PMID:25032122

Choi, Bong Jin; Kim, Min Ju; Chang, Ki-Hong; Yeo, Sang Won; Jun, Beom Cho

2014-09-01

156

Identifying landmark articles for advancing the practice of geriatrics.  

Science.gov (United States)

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

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

2014-11-01

157

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

158

CT Scan (CAT Scan)  

Science.gov (United States)

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

2008-08-20

159

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

Directory of Open Access Journals (Sweden)

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

Babak Nassersharif

2012-09-01

160

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

 
 
 
 
161

CAT Scan  

Medline Plus

Full Text Available CT Scan Introduction A Computed Axial Tomography Scan or CT scan is a test that provides very clear pictures of structures inside ... the benefits and risks of this scan. Test A CT scan uses x-ray technology and sophisticated computers to come up with the final pictures. The ...

162

Pontos referenciais nos acessos cranianos / Landmarks to the cranial approaches  

Scientific Electronic Library Online (English)

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

Sebastião, Gusmão; Roberto Leal, Silveira; Aluízio, Arantes.

2003-06-01

163

CAT Scan  

Medline Plus

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

164

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 ...

165

Visual landmarks facilitate rodent spatial navigation in virtual reality environments  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Because many different sensory modalities contribute to spatial learning in rodents, it has been difficult to determine whether spatial navigation can be guided solely by visual cues. Rodents moving within physical environments with visual cues engage a variety of nonvisual sensory systems that cannot be easily inhibited without lesioning brain areas. Virtual reality offers a unique approach to ask whether visual landmark cues alone are sufficient to improve performance in a spatial task. We ...

Youngstrom, Isaac A.; Strowbridge, Ben W.

2012-01-01

166

Combining Speedup techniques based on Landmarks and Containers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 whic...

Kalpana, R.; Thambidurai, Dr P.

2010-01-01

167

Design Guidelines for Landmarks to Support Navigation in Virtual Environments  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

168

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

169

Snapshot memories and landmark guidance in wood ants.  

Science.gov (United States)

Insects are thought to pinpoint a place by using memorized "snapshots," i.e., two-dimensional retinotopic views of the surrounding landmarks recorded when at the place (reviewed in ). Insects then reach the place by moving until their current view matches their snapshot. To determine when snapshots are recalled, and how differences between view and snapshot are translated into appropriate movements, we analyzed the approaches of wood ants to a feeding site that was located in the center of an array of two or three cylinders. In ants, contrary to flying hymenopterans, body orientation and direction of travel are collinear, so that an ant approaching an object always looks at it with frontal visual field. On their way to a food site, ants fixated and approached a cylinder predominantly when its angular size was smaller than when viewed from the food site. This finding implies that ants store snapshots at this place while fixating landmarks with frontal retina, so simplifying the later alignment of snapshots with their current view. It also means that ants recall snapshots well in advance of reaching the place. Although snapshots are centered on a landmark, we show that they extend at least 120 degrees into the periphery. PMID:13678592

Durier, Virginie; Graham, Paul; Collett, Thomas S

2003-09-16

170

Quality-Aware Estimation of Facial Landmarks in Video Sequences  

DEFF Research Database (Denmark)

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

Haque, Mohammad Ahsanul; Nasrollahi, Kamal

2015-01-01

171

Landmark-based robot navigation enhanced with color interest operators  

Science.gov (United States)

The most important and fascinating ability of natural vision systems is that they spend most of their time on interesting portions of their input, that is, on those aspects of an image which inform the task at hand. This helps a great deal in estimating the location of the system even under dynamic environmental conditions to which systems are subjected to in everyday life. We propose a model that incorporates such ability in robots. Landmark-based approach to robot navigation requires what we define as 'interest operators' to estimate the utility of a particular image region as an effective representative. We have chosen color as the distinguishing characteristic for landmarks. We present a color interest operator consisting of a weighted combination of heuristic scores which thereby selects those image regions or landmarks likely to be found again, even under a different viewing and/or different illumination conditions. The salient regions yield a robust representation for the recognition of a scene. The ability to reproduce regions selected by the operator can be of great help in eliminating environmental uncertainties. We also incorporate a novel color object algorithm, which surpasses all currently available algorithms in speed, robustness and performance to further quicken the response of the navigating robot.

Jagannathan, Hemanth; Narayana Bhaskar, P.

2000-06-01

172

Neural Network Based Sensory Fusion for Landmark Detection  

Science.gov (United States)

NASA is planning to send numerous unmanned planetary missions to explore the space. This requires autonomous robotic vehicles which can navigate in an unstructured, unknown, and uncertain environment. Landmark based navigation is a new area of research which differs from the traditional goal-oriented navigation, where a mobile robot starts from an initial point and reaches a destination in accordance with a pre-planned path. The landmark based navigation has the advantage of allowing the robot to find its way without communication with the mission control station and without exact knowledge of its coordinates. Current algorithms based on landmark navigation however pose several constraints. First, they require large memories to store the images. Second, the task of comparing the images using traditional methods is computationally intensive and consequently real-time implementation is difficult. The method proposed here consists of three stages, First stage utilizes a heuristic-based algorithm to identify significant objects. The second stage utilizes a neural network (NN) to efficiently classify images of the identified objects. The third stage combines distance information with the classification results of neural networks for efficient and intelligent navigation.

Kumbla, Kishan -K.; Akbarzadeh, Mohammad R.

1997-01-01

173

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

174

Automatic facial expression tracking for 4D range scans  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper presents a fully automatic approach of spatio-temporal facial expression tracking for 4D range scans without any manual interventions (such as specifying landmarks). The approach consists of three steps: rigid registration, facial model reconstruction, and facial expression tracking. A Scaling Iterative Closest Points (SICP) algorithm is introduced to compute the optimal rigid registration between a template facial model and a range scan with consideration of the scale problem. A d...

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

2010-01-01

175

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

Science.gov (United States)

Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci that affect serum glucose and insulin levels and response to glucose stress in an F(16) Advanced Intercross Line of the LG/J and SM/J intercross (Wustl:LG,SM-G16). Half of each sibship was fed a high-fat diet and half was fed a relatively low-fat diet. Context-dependent genetic (additive and dominance) and epigenetic (parent-of-origin imprinting) effects were characterized by partitioning animals into sex, diet, and sex-by-diet cohorts. We found that different cohorts often have unique genetic effects at the same loci, and that genetic signals can be masked or erroneously assigned to specific cohorts if they are not considered individually. Our data demonstrate that the effects of genes on complex trait variation are highly context-dependent and that the same genomic sequence can affect traits differently depending on an individual's sex and/or dietary environment. Our results have important implications for studies of complex traits in humans. PMID:21210123

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

2011-04-01

176

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

Science.gov (United States)

Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci affecting serum glucose and insulin levels and response to glucose stress in an F16 Advanced Intercross Line of the LG/J and SM/J intercross (Wustl:LG, SM-G16). Half of each sibship was fed a high-fat diet and half was fed a relatively low-fat diet. Context-dependent genetic (additive and dominance) and epigenetic (parent-of-origin imprinting) effects were characterized by partitioning animals into sex, diet, and sex-by-diet cohorts. We find that different cohorts often have unique genetic effects at the same loci, and that genetic signals can be masked or erroneously assigned to specific cohorts if they are not considered individually. Our data demonstrate that the effects of genes on complex trait variation are highly context dependent, and that the same genomic sequence can affect traits differently depending on an individual’s sex and/or dietary environment. Our results have important implications for studies of complex traits in humans. PMID:21210123

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

2013-01-01

177

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.

178

Automatic corpus callosum segmentation for standardized MR brain scanning  

Science.gov (United States)

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

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

2007-03-01

179

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

180

Genome scan linkage analysis comparing microsatellites and single-nucleotide polymorphisms markers for two measures of alcoholism in chromosomes 1, 4, and 7  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background We analyzed 143 pedigrees (364 nuclear families) in the Collaborative Study on the Genetics of Alcoholism (COGA) data provided to the participants in the Genetic Analysis Workshop 14 (GAW14) with the goal of comparing results obtained from genome linkage analysis using microsatellite and with results obtained using SNP markers for two measures of alcoholism (maximum number of drinks -MAXDRINK and an electrophysiological measure from EEG -TTTH1). First, we ...

Yuan Ao; Zhou Jie; Adeyemo Adebowale; Chen Guanjie; Chen Yuanxiu; Rotimi Charles

2005-01-01

 
 
 
 
181

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

182

Global Nature of Dynamic Protein-Chromatin Interactions In Vivo: Three-Dimensional Genome Scanning and Dynamic Interaction Networks of Chromatin Proteins  

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Genome structure and gene expression depend on a multitude of chromatin-binding proteins. The binding properties of these proteins to native chromatin in intact cells are largely unknown. Here, we describe an approach based on combined in vivo photobleaching microscopy and kinetic modeling to analyze globally the dynamics of binding of chromatin-associated proteins in living cells. We have quantitatively determined basic biophysical properties, such as off rate constants, residence time, and ...

Phair, Robert D.; Scaffidi, Paola; Elbi, Cem; Vecerova?, Jaromi?ra; Dey, Anup; Ozato, Keiko; Brown, David T.; Hager, Gordon; Bustin, Michael; Misteli, Tom

2004-01-01

183

Landmark-based Geodesic Computation for Heuristically Driven Path Planning  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper presents a new method to quickly extract geodesic paths on images and 3D meshes. We use a heuristic to drive the front propagation procedure of the classical Fast Marching. This results in a modification of the Fast Marching algorithm that is similar to the A$^*$ algorithm used in artificial intelligence. In order to find very quickly geodesic paths between any given couples of points, we advocate for the initial computation of distance maps to a set of landmark points and make use...

Peyre?, Gabriel; Cohen, Laurent D.

2006-01-01

184

CAT Scans  

Science.gov (United States)

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

2007-07-16

185

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  

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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

186

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

Science.gov (United States)

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

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

2012-11-01

187

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

Science.gov (United States)

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

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

2012-01-01

188

Genome-wide Scan and Fine-Mapping Linkage Study of Androgenetic Alopecia Reveals a Locus on Chromosome 3q26  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Androgenetic alopecia (AGA, male pattern baldness) is the most common form of hair loss. The origin of AGA is genetic, with the X chromosome located androgen receptor gene (AR) being the only risk gene identified to date. We present the results of a genome-wide linkage study of 95 families and linkage fine mapping of the 3q21-q29, 11q14-q25, 18p11-q23, and 19p13-q13 regions in an extended sample of 125 families of German descent. The locus with strongest evidence for linkage was mapped to 3q2...

Hillmer, Axel M.; Flaquer, Antonia; Hanneken, Sandra; Eigelshoven, Sibylle; Kortu?m, Anne-katrin; Brockschmidt, Felix F.; Golla, Astrid; Metzen, Christine; Thiele, Holger; Kolberg, Susanne; Reinartz, Roman; Betz, Regina C.; Ruzicka, Thomas; Hennies, Hans Christian; Kruse, Roland

2008-01-01

189

A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Much of the variation in inherited risk of colorectal cancer (CRC) is probably due to combinations of common low risk variants. We conducted a genome-wide association study of 550,000 tag SNPs in 930 familial colorectal tumor cases and 960 controls. The most strongly associated SNP (P = 1.72 x 10(-7), allelic test) was rs6983267 at 8q24.21. To validate this finding, we genotyped rs6983267 in three additional CRC case-control series (4,361 affected individuals and 3,752 controls; 1,901 affecte...

Tomlinson, I.; Webb, E.; Carvajal-carmona, L.; Broderick, P.; Kemp, Z.; Spain, S.; Penegar, S.; Chandler, I.; Gorman, M.; Wood, W.; Barclay, E.; Lubbe, S.; Martin, L.; Sellick, G.; Jaeger, E.

2007-01-01

190

3D BSM for face segmentation and landmarks detection  

Science.gov (United States)

An extension of Bayesian Shape Models (BSM) to 3D space is presented. The extension is based on the inclusion of shape information into the fitting functions. Shape information consists of 3D shape descriptors they are derived from curvature, and were selected by considering the relevance of the feature. We also introduce the use of functions to define the separation of face regions. In order to extract the features, the 3D BSM is deformed iteratively by looking for the vertices that best match the shape, by using a point model distribution obtained from train dataset. As result of the fitting process, a 3D face model oriented in frontal position and segmented in 48 regions is obtained, over this model 15 landmarks are extracted. The 3D BSM was trained with 150 3D face models from two different databases, and evaluated using a leave-one-out scheme. The model segmentation and the landmark location were compared against a ground truth segmentation and point location. From this comparison it is possible to affirm that the proposed system has an accuracy of approximately one millimeter, and the orientation of the models in frontal position has an average error of more or less 1.5 degrees.

Salazar, Augusto E.; Prieto, Flavio A.

2010-02-01

191

The use of radial symmetry to localize retinal landmarks.  

Science.gov (United States)

Locating the optic disc center and the fovea in digital fundus images is surprisingly difficult due to the variation range in color and contrast and the possible presence of pathologies creating bright spots or changing the appearance of retinal landmarks. These reasons make it difficult to find good templates of optic disc and fovea shape and color for pattern matching. In this paper we propose radial symmetry as the principal cue to locate both optic disc and macula centers. Centers of bright and dark circularly symmetrical regions with arbitrary radii, can be found robustly against changes in brightness and contrast by using the Fast Radial Symmetry transform. Detectors based on this transform coupled with a weak hypothesis on vessel density (optic disc intersects large vessels while the fovea lies in an avascular region), can provide a fast location of both OD and macula with accuracy similar or better than state-of-the-art methods. The approach has been chosen as the default technique for fast localization of the two landmarks in the VAMPIRE software suite. PMID:23886574

Giachetti, A; Ballerini, L; Trucco, E; Wilson, P J

2013-01-01

192

Learned predictiveness training modulates biases towards using boundary or landmark cues during navigation.  

Science.gov (United States)

A number of navigational theories state that learning about landmark information should not interfere with learning about shape information provided by the boundary walls of an environment. A common test of such theories has been to assess whether landmark information will overshadow, or restrict, learning about shape information. Whilst a number of studies have shown that landmarks are not able to overshadow learning about shape information, some have shown that landmarks can, in fact, overshadow learning about shape information. Given the continued importance of theories that grant the shape information that is provided by the boundary of an environment a special status during learning, the experiments presented here were designed to assess whether the relative salience of shape and landmark information could account for the discrepant results of overshadowing studies. In Experiment 1, participants were first trained that either the landmarks within an arena (landmark-relevant), or the shape information provided by the boundary walls of an arena (shape-relevant), were relevant to finding a hidden goal. In a subsequent stage, when novel landmark and shape information were made relevant to finding the hidden goal, landmarks dominated behaviour for those given landmark-relevant training, whereas shape information dominated behaviour for those given shape-relevant training. Experiment 2, which was conducted without prior relevance training, revealed that the landmark cues, unconditionally, dominated behaviour in our task. The results of the present experiments, and the conflicting results from previous overshadowing experiments, are explained in terms of associative models that incorporate an attention variant. PMID:25409751

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

2014-11-20

193

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

Science.gov (United States)

Elucidating the genetic architecture of preeclampsia is a major goal in obstetric medicine. We have performed a genome-wide association study (GWAS) for preeclampsia in unrelated Australian individuals of Caucasian ancestry using the Illumina OmniExpress-12 BeadChip to successfully genotype 648,175 SNPs in 538 preeclampsia cases and 540 normal pregnancy controls. Two SNP associations (rs7579169, p?=?3.58×10(-7), OR?=?1.57; rs12711941, p?=?4.26×10(-7), OR?=?1.56) satisfied our genome-wide significance threshold (modified Bonferroni p0.92). We attempted to provide evidence of a putative regulatory role for these SNPs using bioinformatic analyses and found that they all reside within regions of low sequence conservation and/or low complexity, suggesting functional importance is low. We also explored the mRNA expression in decidua of genes ±500 kb of INHBB and found a nominally significant correlation between a transcript encoded by the EPB41L5 gene, ?250 kb centromeric to INHBB, and preeclampsia (p?=?0.03). We were unable to replicate the associations shown by the significant GWAS SNPs in case-control cohorts from Norway and Finland, leading us to conclude that it is more likely that these SNPs are in LD with as yet unidentified causal variant(s). PMID:22432041

Johnson, Matthew P; Brennecke, Shaun P; East, Christine E; Göring, Harald H H; Kent, Jack W; Dyer, Thomas D; Said, Joanne M; Roten, Linda T; Iversen, Ann-Charlotte; Abraham, Lawrence J; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Kivinen, Katja; Pouta, Anneli; Laivuori, Hannele; Austgulen, Rigmor; Blangero, John; Moses, Eric K

2012-01-01

194

First genome-wide association scan on neurophysiological endophenotypes points to trans-regulation effects on SLC2A3 in dyslexic children.  

Science.gov (United States)

Dyslexia is one of the most common learning disorders affecting about 5% of all school-aged children. It has been shown that event-related potential measurements reveal differences between dyslexic children and age-matched controls. This holds particularly true for mismatch negativity (MMN), which reflects automatic speech deviance processing and is altered in dyslexic children. We performed a whole-genome association analysis in 200 dyslexic children, focusing on MMN measurements. We identified rs4234898, a marker located on chromosome 4q32.1, to be significantly associated with the late MMN component. This association could be replicated in an independent second sample of 186 dyslexic children, reaching genome-wide significance in the combined sample (P = 5.14e-08). We also found an association between the late MMN component and a two-marker haplotype of rs4234898 and rs11100040, one of its neighboring single nucleotide polymorphisms (SNPs). In the combined sample, this marker combination withstands correction for multiple testing (P = 6.71e-08). Both SNPs lie in a region devoid of any protein-coding genes; however, they both show significant association with mRNA-expression levels of SLC2A3 on chromosome 12, the predominant facilitative glucose transporter in neurons. Our results suggest a possible trans-regulation effect on SLC2A3, which might lead to glucose deficits in dyslexic children and could explain their attenuated MMN in passive listening tasks. PMID:19786962

Roeske, D; Ludwig, K U; Neuhoff, N; Becker, J; Bartling, J; Bruder, J; Brockschmidt, F F; Warnke, A; Remschmidt, H; Hoffmann, P; Müller-Myhsok, B; Nöthen, M M; Schulte-Körne, G

2011-01-01

195

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

196

Reorientation in the Real World: The Development of Landmark Use and Integration in a Natural Environment  

Science.gov (United States)

An influential series of studies have argued that young children are unable to use landmark information to reorient. However, these studies have used artificial experimental environments that may lead to an underestimation of the children's ability. We tested whether young children could reorient using landmarks in an ecologically valid setting.…

Smith, Alastair D.; Gilchrist, Iain D.; Cater, Kirsten; Ikram, Naimah; Nott, Kylie; Hood, Bruce M.

2008-01-01

197

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

Directory of Open Access Journals (Sweden)

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

Hampe O Baszio S

2010-06-01

198

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 < 0.05; P = 6.75 × 10(-7) from the meta-analysis). Consistent with studies of mood disorders, individual common genetic variants did not have any strong effect on job-related exhaustion. However, the nominally significant signals from the allelic variant of UST in four separate samples suggest that this variant might be a weak risk factor for job-related exhaustion. Together with the previously reported associations of other dermatan/chondroitin sulfate genes with mood disorders, these results indicate a potential molecular pathway for stress-related traits and mark a candidate region for further studies of job-related and general exhaustion. 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

199

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

200

A Robot Indoor Position and Orientation Method based on 2D Barcode Landmark  

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Full Text Available A method for robot indoor automatic positioning and orientating based on two-dimensional (2D barcode landmark is proposed. By using the scheme of the 2D barcode for reference, a special landmark is designed which is convenient to operate and easy to recognize, contain coordinates of their absolute positions and have some ability to automatically correct errors. Landmarks are placed over the “ceiling” and photographed by a camera mounted on the robot with its optical axis vertical to the ceiling plane. The coordinates and angle of the landmark is acquired through image segmentation, contour extracting, characteristic curves matching and landmark properties identifying, and then the robot’s current absolute position and heading angle is computed. The experiments proved the effectiveness of the method and shows that the method can meet accuracy requirements of indoor position and orientation.

Guoyu Lin

2011-06-01

 
 
 
 
201

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

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

Ma Junwu

2008-10-01

202

Bone scan  

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A bone scan is an imaging test that shows areas of increased or decreased bone turnover ( metabolism ). ... have taken up less of the radioactive material. Bone scan findings must be compared with other imaging studies, in addition to clinical information. Your health ...

203

CAT Scan  

Medline Plus

Full Text Available ... of this scan. Test A CT scan uses x-ray technology and sophisticated computers to come up with ... patient is taking Glucophage® (metformin), a diabetic medication. X-rays are used during this procedure. The amount of ...

204

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

205

Microbial Genomics  

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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.

206

CAT Scan  

Medline Plus

Full Text Available ... pictures. The CT scan machine looks like a giant donut and the “gantry” is its hole. CT ... It is an iodine-based dye. However, some people have allergies to the iodine dye used in ...

207

Landmark-Based 3D Elastic Registration of Pre- and Postoperative Liver CT Data  

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The qualitative and quantitative comparison of pre- and postoperative image data is an important possibility to validate computer assisted surgical procedures. Due to deformations after surgery a non-rigid registration scheme is a prerequisite for a precise comparison. Interactive landmark-based schemes are a suitable approach. Incorporation of a priori knowledge about the anatomical structures to be registered may help to reduce interaction time and improve accuracy. Concerning pre- and postoperative CT data of oncological liver resections the intrahepatic vessels are suitable anatomical structures. In addition to using landmarks at vessel branchings, we here introduce quasi landmarks at vessel segments with anisotropic localization precision. An experimental comparison of interpolating thin-plate splines (TPS) and Gaussian elastic body splines (GEBS) as well as approximating GEBS on both types of landmarks is performed.

Lange, Thomas; Wörz, Stefan; Rohr, Karl; Schlag, Peter M.

208

Landmark discrimination learning in the dog: effects of age, an antioxidant fortified food, and cognitive strategy.  

Science.gov (United States)

The landmark discrimination learning test can be used to assess the ability to utilize allocentric spatial information to locate targets. The present experiments examined the role of various factors on performance of a landmark discrimination learning task in beagle dogs. Experiments 1 and 2 looked at the effects of age and food composition. Experiments 3 and 4 were aimed at characterizing the cognitive strategies used in performance on this task and in long-term retention. Cognitively equivalent groups of old and young dogs were placed into either a test group maintained on food enriched with a broad-spectrum of antioxidants and mitochondrial cofactors, or a control group maintained on a complete and balanced food formulated for adult dogs. Following a wash-in period, the dogs were tested on a series of problems, in which reward was obtained when the animal responded selectively to the object closest to a thin wooden block, which served as a landmark. In Experiment 1, dogs were first trained to respond to a landmark placed directly on top of coaster, landmark 0 (L0). In the next phase of testing, the landmark was moved at successively greater distances (1, 4 or 10 cm) away from the reward object. Learning varied as a function of age group, food group, and task. The young dogs learned all of the tasks more quickly than the old dogs. The aged dogs on the enriched food learned L0 significantly more rapidly than aged dogs on control food. A higher proportion of dogs on the enriched food learned the task, when the distance was increased to 1cm. Experiment 2 showed that accuracy decreased with increased distance between the reward object and landmark, and this effect was greater in old animals. Experiment 3 showed stability of performance, despite using a novel landmark, and new locations, indicating that dogs learned the landmark concept. Experiment 4 found age impaired long-term retention of the landmark task. These results indicate that allocentric spatial learning is impaired in an age-dependent manner in dogs, and that age also affects performance when the distance between the landmark and target is increased. In addition, these results both support a role of oxidative damage in the development of age-associated cognitive dysfunction and indicate that short-term administration of a food enriched with supplemental antioxidants and mitochondrial cofactors can partially reverse the deleterious effects of aging on cognition. PMID:12479842

Milgram, Norton W; Head, E; Muggenburg, B; Holowachuk, D; Murphey, H; Estrada, J; Ikeda-Douglas, C J; Zicker, S C; Cotman, C W

2002-10-01

209

Development of a New Software for Automatic Anatomical landmark Detection in Cephalometric X-ray Images  

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Full Text Available Background & Objectives: As a routine clinical procedure in orthodontics, there are many geometrical calcula-tions usually taken place on the lateral x-ray images of the head in order to develop an appropriate treatment plan. This is currently done manually by the expert radiologists and/or orthodontists. It can take an experi-enced orthodontist up to thirty minutes to analyze one x-ray image and the results are still influenced by both subjective and objective errors. Here a new software for automatic anatomical landmark detection in cepha-lometric x-ray images is presented. The software extracts ten commonly used main landmarks. Methods and Materials: In this research, a combination of various image processing techniques including Template Matching, Edge Walking, and Shape Registration is employed to develop an automatic cephalomet-ric landmark detection algorithm within the x-ray images of the head. Ten essential and commonly used landmarks were selected as the target points. Results: The accuracy of the automatic landmark detection algorithm was evaluated with comparing the re-sults obtained by the automatic algorithm to those manually identified by an expert orthodontist on a data base of 10 x-ray images. The statistical analysis showed that 92% of the landmarks were determined accurately within an acceptable region of 4 millimeters from the points an expert had defined.. Conclusions: A MATLAB-based software was developed accordingly to help an orthodontist automatically identify the most commonly used 10 main cephalometric landmarks. The method can be extended for more landmarks in the future.

S. Nooranian

2005-08-01

210

Quantified relationships of the radial nerve with the radial groove and selected humeral landmarks  

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Anatomical relationships between the radial nerve, the deltoid muscle insertions and several bony landmarks have been investigated to assess the feasibility of surgical transfer of the deltoid transfer during humeral osteotomy. Eleven embalmed human specimens were dissected. Each specimen included the whole thorax, both shoulders and upper limbs. Spatial position of the radial nerve along the radial groove, the deltoid muscle, and several anatomical landmarks was digitised using a three-dimen...

Sint Jan, Serge; Nguyen, D.; Rooze, Marcel

2008-01-01

211

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

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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

212

Reproducibility and repeatability of upper limb landmarks palpation for junior operators  

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In human motion analysis, bone motions are usually expressed relatively to anatomical reference frames. The anatomical reference frames are constructed thanks to the localization of bony landmarks during a static phase prior to the acquisitions. These landmarks are identified by means of palpation. Accurate comparison between subjects and studies implies good reproducibility and repeatability of the palpation process. However, all investigators don’t have a long expe...

Schwartz, Ce?dric; Fedrigo, Tatiana; Bruls, Olivier; Cescotto, Serge; Denoe?l, Vincent; Croisier, Jean-louis; Forthomme, Be?ne?dicte

2011-01-01

213

Color Atlas of Skeletal landmark definitions. Guidelines for reproducible manual and virtual palpations.  

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This book defines the location of anatomic landmarks by means of two palpation protocols: manual palpation, which allows spatial location of landmarks using hands combined or not with threedimensional (3D) digitizing, and virtual palpation on 3D computer models obtained, for example, from medical imaging. These protocols can be used independently or in combination. Manual palpation is used clinically for variouspurposes:• Identification of painful areas• Positioning of particular pieces o...

Sint Jan, Serge

2007-01-01

214

Learning Compact Visual Descriptors for Low Bit Rate Mobile Landmark Search  

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Coming with the ever growing computational power of mobile devices, mobile visual search have undergone an evolution in techniques and applications. A significant trend is low bit rate visual search, where compact visual descriptors are extracted directly over a mobile and delivered as queries rather than raw images to reduce the query transmission latency. In this article, we introduce our work on low bit rate mobile landmark search, in which a compact yet discriminative landmark image descr...

Duan, Ling-yu Peking University; Chen, Jie Peking University; Ji, Rongrong Peking University; Huang, Tiejun Peking University; Gao, Wen Peking University

2013-01-01

215

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

216

Experimental comparison of landmark-based methods for 3D elastic registration of pre- and postoperative liver CT data  

Science.gov (United States)

The qualitative and quantitative comparison of pre- and postoperative image data is an important possibility to validate surgical procedures, in particular, if computer assisted planning and/or navigation is performed. Due to deformations after surgery, partially caused by the removal of tissue, a non-rigid registration scheme is a prerequisite for a precise comparison. Interactive landmark-based schemes are a suitable approach, if high accuracy and reliability is difficult to achieve by automatic registration approaches. Incorporation of a priori knowledge about the anatomical structures to be registered may help to reduce interaction time and improve accuracy. Concerning pre- and postoperative CT data of oncological liver resections the intrahepatic vessels are suitable anatomical structures. In addition to using branching landmarks for registration, we here introduce quasi landmarks at vessel segments with high localization precision perpendicular to the vessels and low precision along the vessels. A comparison of interpolating thin-plate splines (TPS), interpolating Gaussian elastic body splines (GEBS) and approximating GEBS on landmarks at vessel branchings as well as approximating GEBS on the introduced vessel segment landmarks is performed. It turns out that the segment landmarks provide registration accuracies as good as branching landmarks and can improve accuracy if combined with branching landmarks. For a low number of landmarks segment landmarks are even superior.

Lange, Thomas; Wörz, Stefan; Rohr, Karl; Schlag, Peter M.

2009-02-01

217

Automatic 3D facial model and texture reconstruction from range scans  

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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

218

Renal scan  

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... care provider will place a tight band or blood pressure cuff on your upper arm. This creates pressure and helps your arm veins become bigger. The inner elbow is scrubbed ... through your blood. The kidneys are scanned a short time later. ...

219

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)

220

Bone scans  

International Nuclear Information System (INIS)

Oftentimes, in managing podiatric complaints, clinical and conventional radiographic techniques are insufficient in determining a patient's problem. This is especially true in the early stages of bone infection. Bone scanning or imaging can provide additional information in the diagnosis of the disorder. However, bone scans are not specific and must be correlated with clinical, radiographic, and laboratory evaluation. In other words, bone scanning does not provide the diagnosis but is an important bit of information aiding in the process of diagnosis. The more useful radionuclides in skeletal imaging are technetium phosphate complexes and gallium citrate. These compounds are administered intravenously and are detected at specific time intervals postinjection by a rectilinear scanner with minification is used and the entire skeleton can be imaged from head to toe. Minification allows visualization of the entire skeleton in a single image. A gamma camera can concentrate on an isolated area. However, it requires multiple views to complete the whole skeletal image. Recent advances have allowed computer augmentation of the data received from radionucleotide imaging. The purpose of this chapter is to present the current radionuclides clinically useful in podiatric patients

 
 
 
 
221

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

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Full Text Available 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 surface scanning shows a higher sensitivity in measuring facial reference points. Besides, we evaluate the reproducibility of facial 3D white-light scans. Three HIVpositive men attending our plastic surgery outpatient clinic for treatment of facial lipodystrophy were enrolled in the study. Localization of anthropometric landmarks measurements was performed on the patients. All patients underwent a facial CT and a facial white-light scanning on the same day. The inter-landmark distances measured on facial models developed from CT aided with VirSSPA 3D software and structured light scanning were compared to the real human models. We found that facial distances measured in the CT 3D reconstruction showed a mean error margin of 0.357 cm from the real distances measured on patients. On the contrary, mean error margin with the white-light scanning was of 0.096 cm. In both cases, measurements were found to be statistically significant (P<0.05. When compared to CT reconstructions, white-light surface scanning offers a more accurate landmark localization as well as reliable reconstructions of up to less than the tenth of a millimetre as average when compared to real measurements on facial human models.

Tomás Gómez- Cía

2011-11-01

222

Simplifying subclavian vein cannulation using innovative landmarks: a radiologic, anatomic, and clinical study.  

Science.gov (United States)

The objective of this study was to investigate novel and optimal landmarks for subclavian vein (SV) cannulation. We conducted the study in three phases: (a) Various possible markers for SV cannulation were evaluated by anatomic measurements in patients from intensive care unit and the course of SV was evaluated by radiologic means; (b) Results acquired by the two means were compared and adjusted, then innovative landmarks and a new approach for SV cannulation was proposed; (c) The efficacy of new approach for SV cannulation was compared with that of a traditional one by a prospective, randomized, controlled study. Point A (the junction of the lateral border of sternocleidomastoideus clavicular head and inferior border of clavicle), point B (a point on the lower border of clavicle just above the middle of the line joining the coracoid process and midline of the body), and point D (where SV crosses the inferior border of clavicle) were close in proximity. Points A and B could be considered as innovative landmarks for SV cannulation. Beginners using the new method had significantly higher success rate (86.9% vs. 70.2%, p = 0.008); the time consumed by new method was significant shorter than that by traditional one (5.9 vs. 10.4 min, p = 0.001). Points A and B could be considered as landmarks for identifying puncture site for SV cannulation. Beginners using innovative landmarks for SV cannulation could significantly reduce operation time and increase success rate. PMID:22561227

Hu, Bin; Hu, Mei; Wang, Yan; Wang, Dao Wen

2012-01-01

223

The Architectural Features and Prevalence of Contemporary Landmarks in Kaunas City  

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

Almantas Bružas

2011-03-01

224

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

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

Nihat Y?lmaz

2006-06-01

225

EXPLOITING 3D ULTRASOUND FOR FETAL DIAGNOSTIC PURPOSE THROUGH FACIAL LANDMARKING  

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Full Text Available In the last decade, three-dimensional landmarking has gained attention for different applications, such as face recognition for both identification of suspects and authentication, facial expression recognition, corrective and aesthetic surgery, syndrome study and diagnosis. This work focuses on the last one by proposing a geometrically-based landmark extraction algorithm aimed at diagnosing syndromes on babies before their birth. Pivotal role in this activity is the support provided by physicians and 3D ultrasound tools for working on real faces. In particular, the landmarking algorithm here proposed only relies on descriptors coming from Differential Geometry (Gaussian, mean, and principal curvatures, derivatives, coefficients of first and second fundamental forms, Shape and Curvedness indexes and is tested on nine facial point clouds referred to nine babies taken by a three-dimensional ultrasound tool at different weeks' gestation. The results obtained, validated with the support of four practitioners, show that the localization is quite accurate. All errors lie in the range between 0 and 3.5 mm and the mean distance for each shell is in the range between 0.6 and 1.6 mm. The landmarks showing the highest errors are the ones belonging to the mouth region. Instead, the most precise landmark is the pronasal, on the nose tip, with a mean distance of 0.55 mm. Relying on current literature, this study is something missing in the state-of-the-art of the field, as present facial studies on 3D ultrasound do not work on automatic landmarking yet.

Enrico Vezzetti

2014-06-01

226

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

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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

227

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome  

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CpG islands (CGIs) are vertebrate genomic landmarks that encompass the promoters of most genes and often lack DNA methylation. Querying their apparent importance, the number of CGIs is reported to vary widely in different species and many do not co-localise with annotated promoters. We set out to quantify the number of CGIs in mouse and human genomes using CXXC Affinity Purification plus deep sequencing (CAP-seq). We also asked whether CGIs not associated with annotated transcripts share prop...

Illingworth, Robert S.; Gruenewald-schneider, Ulrike; Webb, Shaun; Kerr, Alastair R. W.; James, Keith D.; Turner, Daniel J.; Smith, Colin; Harrison, David J.; Andrews, Robert; Bird, Adrian P.

2010-01-01

228

Are There Rearrangement Hotspots in the Human Genome?  

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In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced the fragile breakage model (FBM), pos...

Alekseyev, Max A.; Pevzner, Pavel A.

2007-01-01

229

Navigation in wood ants Formica japonica: context dependent use of landmarks.  

Science.gov (United States)

Wood ants Formica japonica can steer their outbound (foraging) and inbound (homing) courses without using celestial compass information, by relying exclusively on landmark cues. This is shown by training ants to run back and forth between the nest and an artificial feeder, and later displacing the trained ants either from the nest (when starting their foraging runs: outbound full-vector ants) or from the feeder (when starting their home runs: inbound full-vector ants) to various nearby release sites. In addition, ants that have already completed their foraging and homing runs are displaced after arrival either at the feeder (outbound zero-vector ants) or at the nest (inbound zero-vector ants), respectively, to the very same release sites. Upon release, the full-vector ants steer their straight courses by referring to panoramic landmark cues, while the zero-vector ants presented with the very same visual scenery immediately search for local landmark cues defining their final goal. Hence, it depends on the context, in this case on the state of the forager's round-trip cycle, what visual cues are picked out from a given set of landmarks and used for navigation. PMID:15326219

Fukushi, Tsukasa; Wehner, Rüdiger

2004-09-01

230

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

231

Reproducibility of Acetabular Landmarks and a Standardized Coordinate System Obtained from 3D Hip Ultrasound.  

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Two-dimensional (2D) ultrasound detection of developmental dysplasia of the hip (DDH) is limited by variation in acetabular appearance and alpha angle measurements, which change with position of the ultrasound probe. Three-dimensional (3D) ultrasound captures the entire acetabular shape, and a reproducible "standard central plane" may be generated, from two landmarks located on opposite ends of the acetabulum, for measurement of alpha angle and other indices. Two users identified landmarks on 51 3D ultrasounds, with ranging severity of disease, and inter- and intra-observer reproducibility of landmark and "standard plane" locations was compared; landmarks were chosen within 2 mm, and the "standard plane" rotation was reproducible within 10° between observers. We observed no difference in variability between alpha angles measured on the "standard plane" in comparison with 2D ultrasound. Applications of the standardized 3D ultrasound central plane will be to fuse serial ultrasounds for follow-up and development of new indices of 3D deformity. PMID:25394808

Mabee, Myles; Dulai, Sukhdeep; Thompson, Richard B; Jaremko, Jacob L

2014-11-13

232

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.)

233

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

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

Knaden Markus

2009-02-01

234

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 - ... head and face Stroke or bleeding in the brain A cranial CT may also be done to look for the ...

235

The Accuracy of the New Landmark Using Respiratory Jugular Venodilation and Direct Palpation in Right Internal Jugular Vein Access  

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Background Although ultrasonography is recommended in internal jugular vein (IJV) catheterization, the landmark-guided technique should still be considered. The central landmark using the two heads of the sternocleidomastoid muscle is widely used, but it is inaccurate for IJV access. As an alternative landmark, we investigated the accuracy of the new landmark determined by inspection of the respiratory jugular venodilation and direct IJV palpation in right IJV access by ultrasonography. Methods and Findings Thirty patients were enrolled. After induction of anesthesia, the central landmark was marked at the cricoid cartilage level (M1) and the alternative landmark determined by inspection of the respiratory jugular venodilation and direct palpation of IJV was also marked at the same level (M2). Using ultrasonography, the location of IJV was identified (M3) and the distance between M1 and M3 as well as between M2 and M3 were measured. The median (interquartile range) distance between the M2 and M3 was 3.5 (2.0–6.0) mm, compared to 17.5 (12.8–21.3) mm between M1 and M3. (P<0.001) The dispersion of distances between M2 and M3 was significantly smaller than between M1 and M3. (P<0.001) The visibility of respiratory jugular venodilation was associated with CVP more than 4 mmHg. Limitations of the present study are that the inter-observer variability was not investigated and that the visibility of the alternative landmark can be limited to right IJV in adults. Conclusion The alternative landmark may allow shorter distance for the right side IJV access than the central landmark and can offer advantages in right IJV catheterization when ultrasound device is unavailable. Trial Registration Clinical Research Informational Service KCT0000812 PMID:25050554

Seo, Hyungseok; Jang, Dong-Min; Yi, Jung-Min; Min, Hong-Gi; Hwang, Jai-Hyun

2014-01-01

236

Modeling and matching of landmarks for automation of Mars Rover localization  

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

Wang, Jue

237

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)

238

Landmark-free statistical analysis of the shape of plant leaves.  

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The shapes of plant leaves are important features to biologists, as they can help in distinguishing plant species, measuring their health, analyzing their growth patterns, and understanding relations between various species. Most of the methods that have been developed in the past focus on comparing the shape of individual leaves using either descriptors or finite sets of landmarks. However, descriptor-based representations are not invertible and thus it is often hard to map descriptor variability into shape variability. On the other hand, landmark-based techniques require automatic detection and registration of the landmarks, which is very challenging in the case of plant leaves that exhibit high variability within and across species. In this paper, we propose a statistical model based on the Squared Root Velocity Function (SRVF) representation and the Riemannian elastic metric of Srivastava et al. (2011) to model the observed continuous variability in the shape of plant leaves. We treat plant species as random variables on a non-linear shape manifold and thus statistical summaries, such as means and covariances, can be computed. One can then study the principal modes of variations and characterize the observed shapes using probability density models, such as Gaussians or Mixture of Gaussians. We demonstrate the usage of such statistical model for (1) efficient classification of individual leaves, (2) the exploration of the space of plant leaf shapes, which is important in the study of population-specific variations, and (3) comparing entire plant species, which is fundamental to the study of evolutionary relationships in plants. Our approach does not require descriptors or landmarks but automatically solves for the optimal registration that aligns a pair of shapes. We evaluate the performance of the proposed framework on publicly available benchmarks such as the Flavia, the Swedish, and the ImageCLEF2011 plant leaf datasets. PMID:25123432

Laga, Hamid; Kurtek, Sebastian; Srivastava, Anuj; Miklavcic, Stanley J

2014-12-21

239

Loss of Anatomical Landmarks with Eutectic Mixture of Local Anesthetic Cream for Neonatal Male Circumcision  

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We report two cases of newborns who developed marked local edema after application of a eutectic mixture of local anesthetic (EMLA) topical anesthetic cream for neonatal male circumcision (NMC). Although local edema and erythema are known potential side effects of EMLA cream, a common anesthetic used for NMC, the loss of landmarks precluding safe NMC has not previously been reported, and is described here. Although we cannot recommend an alternate local anesthetic for neonates with this react...

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

2012-01-01

240

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.)

 
 
 
 
241

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

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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

242

Using artificial landmarks to reduce the ambiguity in the environment of a mobile robot  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Robust and reliable localization is a fundamental prerequisite for many applications of mobile robots. Although there exist many solutions to the localization problem, structurally symmetrical or featureless environments can prevent different locations from being distinguishable given the data obtained with the robot’s sensors. Such ambiguities typically make localization approaches more likely to fail. In this paper, we investigate how artificial landmarks can be utilized to reduce the amb...

Meyer-delius, D.; Beinhofer, M.; Kleiner, Alexander; Burgard, W.

2011-01-01

243

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

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The objective of this review is to establish the current state of knowledge on the reliability of clinical assessment of asymmetry in the lumbar spine and pelvis. To search the literature, the authors consulted the databases of MEDLINE, CINAHL, AMED, MANTIS, Academic Search Complete, and Web of Knowledge using different combinations of the following keywords: palpation, asymmetry, inter- or intraex-aminer reliability, tissue texture, assessment, and anatomic landmark. Of the 23 studies identi...

Stovall, Bradley A.; Kumar, Shrawan

2010-01-01

244

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

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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

245

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

246

Precise visual navigation using multi-stereo vision and landmark matching  

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

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

2007-04-01

247

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

248

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

249

MR-guided stereotactic neurosurgery-comparison of fiducial-based and anatomical landmark transformation approaches  

International Nuclear Information System (INIS)

For application in magnetic resonance (MR) guided stereotactic neurosurgery, two methods for transformation of MR-image coordinates in stereotactic, frame-based coordinates exist: the direct stereotactic fiducial-based transformation method and the indirect anatomical landmark method. In contrast to direct stereotactic MR transformation, indirect transformation is based on anatomical landmark coregistration of stereotactic computerized tomography and non-stereotactic MR images. In a patient study, both transformation methods have been investigated with visual inspection and mutual information analysis. Comparison was done for our standard imaging protocol, including t2-weighted spin-echo as well as contrast enhanced t1-weighted gradient-echo imaging. For t2-weighted spin-echo imaging, both methods showed almost similar and satisfying performance with a small, but significant advantage for fiducial-based transformation. In contrast, for t1-weighted gradient-echo imaging with more geometric distortions due to field inhomogenities and gradient nonlinearity than t2-weighted spin-echo imaging, mainly caused by a reduced bandwidth per pixel, anatomical landmark transformation delivered markedly better results. Here, fiducial-based transformation yielded results which are intolerable for stereotactic neurosurgery. Mean Euclidian distances between both transformation methods were 0.96 mm for t2-weighted spin-echo and 1.67 mm for t1-weighted gradient-echo imaging. Maximum deviighted gradient-echo imaging. Maximum deviations were 1.72 mm and 3.06 mm, respectively

250

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: ...

251

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 ...

252

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

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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

253

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

Science.gov (United States)

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. PMID:25309374

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

2014-01-01

254

Genomic Testing  

Science.gov (United States)

... CDC.gov . Public Health Genomics Share Compartir Genomic Testing Fact Sheet: Identifying Opportunities to Improve Health and ... Page The Need for Reliable Information on Genetic Testing In 2008, the former Secretary's Advisory Committee on ...

255

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

Directory of Open Access Journals (Sweden)

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

Cronk Quentin CB

2011-01-01

256

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

257

Genome-wide scan identifies a copy number variable region at 3p21.1 that influences the TLR9 expression levels in IgA nephropathy patients.  

Science.gov (United States)

Immunoglobulin A nephropathy (IgAN) is a complex multifactorial disease characterized by genetic factors that influence the pathogenesis of the disease. In this context, an intriguing role could be ascribed to copy number variants (CNVs). We performed the whole-genome screening of CNVs in familial IgAN patients, their healthy relatives and healthy subjects (HSs). In the initial screening, we included 217 individuals consisting of 51 biopsy-proven familial IgAN cases and 166 healthy relatives. We identified 148 IgAN-specific aberrations, specifically 105 loss and 43 gain, using a new statistical approach that allowed us to identify aberrations that were concordant across multiple samples. Several CNVs overlapped with regions evidenced by previous genome-wide genetic studies. We focused our attention on a CNV located in chromosome 3, which contains the TLR9 gene and found that IgAN patients characterized by deteriorated renal function carried low copy number of this CNV. Moreover, the TLR9 gene expression was low and significantly correlated with the loss aberration. Conversely, IgAN patients with normal renal function had no aberration and the TLR9 mRNA was expressed at the same level as in HSs. We confirmed our data in another cohort of Greek subjects. In conclusion, here we performed the first genome-wide CNV study in IgAN identifying structural variants that could help the genetic dissection of this complex disease, and pointed out a loss aberration in the chromosome 3, which is responsible for the downregulation of TLR9 expression that, in turn, could contribute to the deterioration of the renal function in IgAN patients.European Journal of Human Genetics advance online publication, 8 October 2014; doi:10.1038/ejhg.2014.208. PMID:25293716

Sallustio, Fabio; Cox, Sharon N; Serino, Grazia; Curci, Claudia; Pesce, Francesco; De Palma, Giuseppe; Papagianni, Aikaterini; Kirmizis, Dimitrios; Falchi, Mario; Schena, Francesco P

2014-10-01

258

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.

259

Grüber's ligament as a useful landmark for the abducens nerve in the transnasal approach.  

Science.gov (United States)

OBJECT Extended endoscopic transnasal surgeries for skull base lesions have recently been performed. Some expert surgeons have attempted to remove tumors such as chordomas, meningiomas, and pituitary adenomas in the clival region using the transnasal approach and have reported abducens nerve injury as a common complication. There have been many microsurgical anatomical studies of the abducens nerve, but none of these studies has described an anatomical landmark of the abducens nerve in the transnasal approach. In this study the authors used cadaver dissections to describe Grüber's ligament as the most reliable landmark of the abducens nerve in the transnasal transclival view. METHODS The petroclival segment of the abducens nerve was dissected in the interdural space-which is also called Dorello's canal, the petroclival venous gulf, or the sphenopetroclival venous confluence-using the transnasal approach in 20 specimens obtained from 10 adult cadaveric heads. RESULTS The petroclival segment of the abducens nerve clearly crossed and attached to Grüber's ligament in the interdural space, as noted in the transnasal view. The average length of the dural porus to the intersection on the abducens nerve was 5.2 ± 1.0 mm. The length of the posterior clinoid process (PCP) to the intersection on Grüber's ligament was 6.4 ± 2.6 mm. The average width of Grüber's ligament at the midsection was 1.6 ± 0.5 mm. CONCLUSIONS Grüber's ligament is considered a useful landmark, and it is visible in most adults. Thus, surgeons can find the abducens nerve safely by visualizing inferolaterally along Grüber's ligament from the PCP. PMID:25380109

Tomio, Ryosuke; Toda, Masahiro; Sutiono, Agung Budi; Horiguchi, Takashi; Aiso, Sadakazu; Yoshida, Kazunari

2014-11-01

260

Automated annotation of landmark images using community contributed datasets and web resources  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A novel solution to the challenge of automatic image annotation is described. Given an image with GPS data of its location of capture, our system returns a semantically-rich annotation comprising tags which both identify the landmark in the image, and provide an interesting fact about it, e.g. "A view of the Eiffel Tower, which was built in 1889 for an international exhibition in Paris". This exploits visual and textual web mining in combination with content-based image analysis and natura...

Jones, Gareth J. F.; Byrne, Daragh; Hughes, Mark; O Connor, Noel E.; Salway, Andrew

2010-01-01

 
 
 
 
261

An investigation of the time course of flanker effects in the landmark task.  

Science.gov (United States)

To assess attentional, perceptual and motor contributions to pseudoneglect, the landmark task requires pointing to the subjectively shorter end of accurately pre-transected horizontal lines. We presented irrelevant flankers 317, 567 or 967 ms prior to the line transector on a touch screen and recorded reaction times, movement times, landing points and uncertainty of pointing decisions. Flankers were visible for 167 ms to exclude perceptual biases and lines disappeared upon response initiation to prevent subsequent corrections. Healthy participants showed pseudoneglect and a response bias toward the flanker. This finding is interpreted as evidence for inhibition of return and casts doubt on an attentional interpretation of previously reported flanker effects. PMID:11257284

Fischer, M H; Stumpp, T

2001-01-01

262

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

International Nuclear Information System (INIS)

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

263

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

Science.gov (United States)

We report two cases of newborns who developed marked local edema after application of a eutectic mixture of local anesthetic (EMLA) topical anesthetic cream for neonatal male circumcision (NMC). Although local edema and erythema are known potential side effects of EMLA cream, a common anesthetic used for NMC, the loss of landmarks precluding safe NMC has not previously been reported, and is described here. Although we cannot recommend an alternate local anesthetic for neonates with this reaction to EMLA, based on a review of the published data we think that serious systemic adverse events related to EMLA are extremely rare. PMID:23102766

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

2013-02-01

264

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

265

Genome-wide gene-based association study  

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Abstract Genome-wide association studies, which analyzes hundreds of thousands of single-nucleotide polymorphisms to identify disease susceptibility genes, are challenging because the work involves intensive computation and complex modeling. We propose a two-stage genome-wide association scanning procedure, consisting of a single-locus association scan for the first stage and a gene-based association scan for the second stage. Marginal effects of single-nucleotide polymorphisms are ...

Yang Hsin-Chou; Liang Yu-Jen; Chung Chia-Min; Chen Jia-Wei; Pan Wen-Harn

2009-01-01

266

Genome-wide gene-based association study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Genome-wide association studies, which analyzes hundreds of thousands of single-nucleotide polymorphisms to identify disease susceptibility genes, are challenging because the work involves intensive computation and complex modeling. We propose a two-stage genome-wide association scanning procedure, consisting of a single-locus association scan for the first stage and a gene-based association scan for the second stage. Marginal effects of single-nucleotide polymorphisms are examined by using t...

Yang, Hsin-chou; Liang, Yu-jen; Chung, Chia-min; Chen, Jia-wei; Pan, Wen-harn

2009-01-01

267

Pulmonary ventilation/perfusion scan  

Science.gov (United States)

V/Q scan; Ventilation/perfusion scan; Lung ventilation/perfusion scan ... A pulmonary ventilation/perfusion scan is actually two tests. They may be done separately or together. During the perfusion scan, a health care ...

268

Nuclear Scans (Cancer)  

Science.gov (United States)

... more References Previous Topic Mammography Next Topic Ultrasound Nuclear scans Other names include nuclear imaging , radionuclide imaging , ... to more radiation. Use of monoclonal antibodies in nuclear scans: A special type of antibody produced in ...

269

Getting a CAT Scan  

Science.gov (United States)

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

270

Thyroid Scan and Uptake  

Science.gov (United States)

Thyroid Scan and Uptake • Overview A thyroid scan is a type of nuclear medicine imaging. The radioactive iodine uptake ... use, surgery, radiotherapy or chemotherapy top of page • Preparation You may be asked to wear a gown ...

271

Abscess scan - radioactive  

Science.gov (United States)

... later. At that time, you will have a nuclear medicine scan to see if white blood cells have ... sting. Afterward, there may be some throbbing. The nuclear medicine scan is painless. It may be a little ...

272

Getting a CAT Scan  

Medline Plus

Full Text Available ... People, Places & Things That Help Feelings Q&A Movies & More Quizzes Games Kids' Medical Dictionary En Español ... Society Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) Print ...

273

Getting a CAT Scan  

Medline Plus

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

274

Coronary Calcium Scan  

Science.gov (United States)

... within the next 10 years. The coronary calcium scan may help doctors decide who within this group needs treatment. Rate This Content: Next >> March 30, 2012 Coronary Calcium Scan Clinical Trials Clinical trials are research studies that ...

275

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

276

Volume registration of interventional MRI data using needle paths and point landmarks  

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We created a method for three-dimensional registration of medical scanner image volumes to images of physical tissue sections or other volumes, and evaluated its accuracy. The method is applicable for many animal experiments, and we are applying it to evaluate interventional MRI imaging of thermal ablation and to quantify in vivo drug release from a new device for localized, controlled release. The method computes an optimum set of rigid body registration parameters by iterative minimization of the Euclidean distances between automatically generated correspondence points, along manually selected fiducial needle paths, and optional point landmarks. For numerically simulated registrations, using two needle paths over a range of needle orientations, median voxel displacement errors depended only on needle localization error when the angle between needles was at least 15 degrees. For parameters typical of our in vivo experiments, the median error was determined that the distance objective function was a useful diagnostic for predicting registration quality. To evaluate the registration quality of physical specimens, we computed the misregistration for a needle not considered during the optimization procedure. We registered an ex vivo sheep brain MR volume with another MR volume and tissue section photographs, using various combinations of needle and point landmarks. Registration error was always

Lazebnik, Roee S.; Breen, Michael S.; Lancaster, Tanya L.; Nour, Sherif G.; Lewin, Jonathan S.; Wilson, David L.

2002-05-01

277

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

Scientific Electronic Library Online (English)

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

Alejandro, González; Flavio, Prieto.

2010-07-01

278

Surface landmarks of brachial plexus: ultrasound and magnetic resonance imaging for supraclavicular approach with anatomical correlation.  

Science.gov (United States)

The present study is able to describe a certain line, under which brachial plexus (BP) lies underneath in the supraclavicular region. A line drawn between midpoint of the sternocleidomastoid muscle to the midpoint of the clavicle was considered for BP. Surface landmarks were evaluated by applying ultrasound (US) on 30 volunteers (15 female, 15 male). Axial and sagittal views of BP were taken and distances between skin and BP were measured. Coronal magnetic resonance (MR) sections were taken from 7 volunteers according to the second line after applying two fat capsules on each line. The sonographic views were seen at the same line. Mean distances from skin were found as 16.5+/-0.7 mm for male and 14.5+/-0.5 mm for female volunteers. MR images were obtained bilaterally, which were parallel and posterior from sonographic lines. Surface landmarks, as presented in this study, are simple to accomplish and are not dependent on structural variations as external jugular vein. PMID:11516629

Apan, A; Baydar, S; Yilmaz, S; Uz, A; Tekdemir, I; Güney, S; Elhan, A; Baydar, P; Yýlmaz, S; Tekdemir, Y; Güney, P

2001-07-01

279

Electrooptical scanning of film  

Science.gov (United States)

Scan-in scan-out flying spot scanning system recognizes three different levels of transmissivity within a frame. It selectively acts on these levels either to intensify the illumination or to extend the duration of the illuminating spot to any picture element. Thus it improves the ratio of signal to tube noise in the cameras output.

Billingsley, F. C.; Volkoff, J. J.

1969-01-01

280

Urochordate genomes.  

Science.gov (United States)

Urochordates or tunicates possess a notochord, dorsal neural tube, and gill slits, features characteristic of all chordates, and thus they are a sister group of vertebrates, including humans. Urochordates consist of larvaceans, ascidians, and thaliaceans. The draft genome has been decoded in ascidians, Ciona intestinalis and C. savignyi. The C. intestinalis genome is composed of approximately 160 Mbp, similar to other invertebrate genomes, and contains approximately 16,000 protein-coding genes that represent the basic set of chordate genes without the extensive gene duplications seen in vertebrates. The C. intestinalis gene models are intensively annotated and supported by corresponding cDNAs. With the aid of two-color fluorescent in situ hybridization of BAC clones, approximately 65% of the assembled genome information has been mapped onto the 14 pairs of C. intestinalis chromosomes. In addition, a genome project is ongoing in a larvacean, Oikopleura dioica, and its genome is estimated to be 60 Mbp, with a very compacted arrangement of genes. Although the urochordate genomes have lineage-specific innovations such as horizontal acquisition of the cellulose synthase gene from bacteria and spliced-leader trans-splicing of mRNAs, applicable modern techniques have made urochordates serious contenders in the illumination of the basic principles underlying genome dynamics of vertebrates. PMID:18753780

Satoh, N; Kawashima, T; Shoguchi, E; Satou, Y

2006-01-01

 
 
 
 
281

Motion estimation in cardiac fluorescence imaging with scale-space landmarks and optical flow: a comparative study.  

Science.gov (United States)

Motion artifacts are a major disadvantage of cardiac optical mapping studies. Pixel misalignment due to contraction is a main cause of the presence of gross motion artifacts in action potential recordings. This study is focused on methods for identifying landmarks and tracking the motion of cardiac tissue for preparations in optical mapping recordings. This is a first step toward our long-term goal to implement a landmark-based image registration technique to correct for pixel misalignment in cardiac optical mapping fluorescence videos and, hence, for gross motion artifacts. Preliminary results for the registration step are presented as an initial proof of concept. The characteristics of the optical mapping images are challenging, since their lack of contrast and well-defined features impose a limitation on the techniques than can be used for landmark selection and motion tracking. This paper compares results of motion estimation of the cardiac surface with two approaches that do not rely on high-contrast features: 1) Scale-invariant feature transform (SIFT) detected "keypoints," to be used as landmarks for motion tracking, as well as 2) a classical global optical flow (OF) algorithm. Both are applied to low-contrast and low-resolution cardiac fluorescence images. We demonstrate that the performance of SIFT is superior to that of OF for pixel motion tracking in cardiac optical mapping images with simulated motion. Results for action potential recovery and action potential duration calculation after landmark-based image registration show that SIFT landmark-based registration yields superior performance in this regard as well. PMID:25350913

Rodriguez, M P; Nygren, A

2015-02-01

282

Algorithms For Automatic And Robust Registration Of 3D Head Scans  

Directory of Open Access Journals (Sweden)

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

Peter Eisert

2010-12-01

283

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

Science.gov (United States)

Rumex hastatulus is the North American endemic dioecious plant with heteromorphic sex chromosomes. It is differentiated into two chromosomal races: Texas (T) race characterised by a simple XX/XY sex chromosome system and North Carolina (NC) race with a polymorphic XX/XY1Y2 sex chromosome system. The gross karyotype morphology in NC race resembles the derived type, but chromosomal changes that occurred during its evolution are poorly understood. Our C-banding/DAPI and fluorescence in situ hybridization (FISH) experiments demonstrated that Y chromosomes of both races are enriched in DAPI-positive sequences and that the emergence of polymorphic sex chromosome system was accompanied by the break of ancestral Y chromosome and switch in the localization of 5S rDNA, from autosomes to sex chromosomes (X and Y2). Two contrasting domains were detected within North Carolina Y chromosomes: the older, highly heterochromatinised, inherited from the original Y chromosome and the younger, euchromatic, representing translocated autosomal material. The flow-cytometric DNA estimation showed ?3.5 % genome downsizing in the North Carolina race. Our results are in contradiction to earlier reports on the lack of heterochromatin within Y chromosomes of this species and enable unambiguous identification of autosomes involved in the autosome-heterosome translocation, providing useful chromosome landmarks for further studies on the karyotype and sex chromosome differentiation in this species. PMID:25394583

Grabowska-Joachimiak, Aleksandra; Kula, Adam; Ksi??czyk, Tomasz; Chojnicka, Joanna; Sliwinska, Elwira; Joachimiak, Andrzej J

2014-11-14

284

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.

285

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

Science.gov (United States)

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

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

2010-10-01

286

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.

287

Methods for determining hip and lumbosacral joint centers in a seated position from external anatomical landmarks.  

Science.gov (United States)

A global coordinate system (GCS) method is proposed to estimate hip and lumbosacral joint centers (HJC and LSJC) from at least three distances between joint center of interest and target anatomic landmarks (ALs). The distances from HJC and LSJC to relevant pelvis and femur ALs were analyzed with respect to usual pelvis and femur scaling dimensions. Forty six pelves and related pairs of femurs from a same sample of adult specimens were examined. The corresponding regression equations were obtained. These equations can be used to estimate HJC and LSJC in conditions where a very limited number of ALs are available: for example, during seated posture analysis as performed in the automotive industry. Compared to currently existing HJC and LSJC methods from ALs, the proposed method showed better results with an average error less than 11mm. PMID:25497377

Peng, Junfeng; Panda, Jules; Van Sint Jan, Serge; Wang, Xuguang

2015-01-21

288

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

289

Histology to microCT data matching using landmarks and a density biased RANSAC.  

Science.gov (United States)

The fusion of information from different medical imaging techniques plays an important role in data analysis. Despite the many proposed registration algorithms the problem of registering 2D histological images to 3D CT or MR imaging data is still largely unsolved. In this paper we propose a computationally efficient automatic approach to match 2D histological images to 3D micro Computed Tomography data. The landmark-based approach in combination with a density-driven RANSAC plane-fitting allows efficient localization of the histology images in the 3D data within less than four minutes (single-threaded MATLAB code) with an average accuracy of 0.25 mm for orrect and 2.21mm for mismatched slices. The approach managed to uccessfully localize 75% of the histology images in our database. The proposed algorithm is an important step towards solving the problem of registering 2D histology sections to 3D data fully automatically. PMID:25333124

Chicherova, Natalia; Fundana, Ketut; Müller, Bert; Cattin, Philippe C

2014-01-01

290

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

291

Scanning suprasternal echocardiography.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Scanning suprasternal echocardiography was performed in 280 patients with a variety of cardiac anomalies. By using the special suprasternal transducer on the suprasternal notch, the aortic arch, right pulmonary artery, and left atrium were recorded superoinferiorly. From this reference position various scanning techniques were made to record the main pulmonary artery, pulmonary valve, ascending aorta, aortic valve, and distal aortic arch, wherever possible. These scans made it possible to ass...

Goh, T. H.; Venables, A. W.

1980-01-01

292

Homodyne scanning holography  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have developed a modified version of a scanning holography microscope in which the Fresnel Zone Plates (FZP) are created by a homodyne rather than a heterodyne interferometer. Therefore, during the scanning the projected pattern on the specimen is frozen rather than varied as previously. In each scanning period the system produces an on-axis Fresnel hologram. The twin image problem is solved by a linear combination of at least three holograms taken with three FZPs with different phase values.

Rosen, Joseph; Indebetouw, Guy; Brooker, Gary

2006-01-01

293

Homodyne scanning holography  

Science.gov (United States)

We have developed a modified version of a scanning holography microscope in which the Fresnel Zone Plates (FZP) are created by a homodyne rather than a heterodyne interferometer. Therefore, during the scanning the projected pattern on the specimen is frozen rather than varied as previously. In each scanning period the system produces an on-axis Fresnel hologram. The twin image problem is solved by a linear combination of at least three holograms taken with three FZPs with different phase values.

Rosen, Joseph; Indebetouw, Guy; Brooker, Gary

2006-05-01

294

CT scanning in meningitis  

International Nuclear Information System (INIS)

12 pediatric cases of acute meningitis were reviewed retrospectively. Findings on CT scan were compared with the clinical course and resulting neurological sequelae. Complications detected by CT scanning include subdural effusion, empyema, hydrocephalus, cerebral atrophy, oedema and infarction. The CT scan results adequately correlated with neurological signs in most cases. Infarction was a reliable indicator of neurological sequelae. Cerebral atrophy alone, however, did not correlate well with the clinical sequelae. (author). 19 refs.; 5 figs.; 6 tabs

295

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

296

Advanced scanning probe lithography  

Science.gov (United States)

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

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

2014-08-01

297

Viral RNA polymerase scanning and the gymnastics of Sendai virus RNA synthesis  

International Nuclear Information System (INIS)

mRNA synthesis from nonsegmented negative-strand RNA virus (NNV) genomes is unique in that the genome RNA is embedded in an N protein assembly (the nucleocapsid) and the viral RNA polymerase does not dissociate from the template after release of each mRNA, but rather scans the genome RNA for the next gene-start site. A revised model for NNV RNA synthesis is presented, in which RNA polymerase scanning plays a prominent role. Polymerase scanning of the template is known to occur as the viral transcriptase negotiates gene junctions without falling off the template

298

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

299

Lung Ventilation/Perfusion Scan  

Science.gov (United States)

... NHLBI on Twitter. What Is a Lung Ventilation/Perfusion Scan? A lung ventilation/perfusion scan, or VQ scan, is a test that ... scan involves two types of scans: ventilation and perfusion. The ventilation scan shows where air flows in ...

300

A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The helical tension of chromosomal DNA is one of the epigenetic landmarks most difficult to examine experimentally. The occurrence of DNA crosslinks mediated by psoralen photobinding (PB) stands as the only suitable probe for assessing this problem. PB is affected by chromatin structure when is done to saturation; but it is mainly determined by DNA helical tension when it is done to very low hit conditions. Hence, we developed a method for genome-wide analysis of DNA helical tension based on ...

Bermu?dez, Ignacio; Garci?a-marti?nez, Jose?; Pe?rez-orti?n, Jose? E.; Roca, Joaquim

2010-01-01

 
 
 
 
301

Transverse section scanning mechanism  

International Nuclear Information System (INIS)

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

302

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.)

303

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

304

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

305

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.

306

Scanning with Iodine-125  

International Nuclear Information System (INIS)

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

307

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

308

Laser Scanning In Inspection  

Science.gov (United States)

This paper is a review of the applications of laser scanning in inspection. The reasons for the choice of a laser in flying spot scanning and the optical properties of a laser beam which are of value in a scanning instrument will be given. The many methods of scanning laser beams in both one and two dimensions will be described. The use of one dimensional laser scanners for automatic surface inspection for transmitting and reflective products will be covered in detail, with particular emphasis on light collection techniques. On-line inspection applications which will be mentioned include: photographic film web, metal strip products, paper web, glass sheet, car body paint surfaces and internal cylinder bores. Two dimensional laser scanning is employed in applications where increased resolution, increased depth of focus, and better contrast are required compared with conventional vidicon TV or solid state array cameras. Such examples as special microscope laser scanning systems and a TV compatible system for use in restricted areas of a nuclear reactor will be described. The technical and economic benefits and limitations of laser scanning video systems will be compared with conventional TV and CCD array devices.

West, Patricia; Baker, Lionel R.

1989-03-01

309

Scanning Probe Microscopy  

Science.gov (United States)

Published by the National Nanotechnology Infrastructure Network, this hour-long activity has students "simulate the function of a scanning probe microscope" by creating their own scanning probe microscope (SPM) boxes. The Teacher's Guide contains everything the instructor needs to carry out the lesson: goals and objectives, advanced preparation notes, safety considerations, materials, questions, and even variations for different classrooms. The Student Worksheet walks students through the activity by having them begin by making a prediction, giving the procedures, providing space to record observations, and asking open questions for students to respond to. This is a ready-to-use activity for classrooms looking to explore nanotechnology and scanning probe microscopes.

2009-04-14

310

Dynamic CT scanning  

International Nuclear Information System (INIS)

The improvements in CT scanning techniques towards shorter scanning times and shorter interscan periods now also allow dynamic processes to be evaluated on the basis of a temporal CT scanning sequence. The conference paper explains the results of a contrast medium study with a group of eight patients (60 ml Urovist/3 sec.), for measurements of cerebral blood flow (CBF), and cerebral blood volume (CBV). The CBV values obtained are comparable with the data produced by other methods. The CBF values are accurate in terms of the relation between grey and white cerebral matter. (orig.)

311

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

312

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

313

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

314

Skeletal Scintigraphy (Bone Scan)  

Science.gov (United States)

... www.radiologyinfo.org/en/info.cfm?pg=nuclear-pdi) . Unless your physician tells you otherwise, you may resume your normal activities after your nuclear medicine scan. If any special instructions are necessary, you will ...

315

Gallium-67 tumor scanning  

International Nuclear Information System (INIS)

Since its introduction in 1969, 67Ga has become the most widely employed tumor-scanning agent in nuclear medicine. While 67Ga is far from being the ideal tumor-scanning agent, it remains the best available isotope for this purpose. Gallium-67-citrate has been found to be of value in the staging and reevaluation of lymphomas as well as in detecting the extent and recurrence of lung tumors, breast tumors, malignant melanomas, testicular tumors, brain tumors, and malignant lesions involving the liver. In order to obtain maximum diagnostic value from gallium scanning, several technical factors have to be taken into consideration as well as an understanding of the nature of false-positive scans

316

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 ...

317

Getting a CAT Scan  

Medline Plus

Full Text Available ... More Quizzes Games Kids' Medical Dictionary En Español What Other Kids Are Reading Moving to Middle School ... that means a scanner takes computer pictures of what's going on inside your body. The scan itself ...

318

Tomographic scanning apparatus  

International Nuclear Information System (INIS)

This patent specification describes a tomographic scanning apparatus, with particular reference to the adjustable fan beam and its collimator system, together with the facility for taking a conventional x-radiograph without moving the patient. (U.K.)

319

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

320

Bone scan in pediatrics  

International Nuclear Information System (INIS)

In 1984, a survey carried out in 21 countries in Europe showed that bone scintigraphy comprised 16% of all paediatric radioisotope scans. Although the value of bone scans in paediatrics is potentially great, their quality varies greatly, and poor-quality images are giving this valuable technique a bad reputation. The handling of children requires a sensitive staff and the provision of a few simple inexpensive items of distraction. Attempting simply to scan a child between two adult patients in a busy general department is a recipe for an unhappy, uncooperative child with the probable result of poor images. The intravenous injection of isotope should be given adjacent to the gamma camera room, unless dynamic scans are required, so that the child does not associate the camera with the injection. This injection is best carried out by someone competent in paediatric venipunture; the entire procedure should be explained to the child and parent, who should remain with child throughout. It is naive to think that silence makes for a cooperative child. The sensitivity of bone-seeking radioisotope tracers and the marked improvement in gamma camera resolution has allowed the bone scanning to become an integrated technique in the assessment of children suspected of suffering from pathological bone conditions. The tracer most commonly used for routine bone scanning is 99mTc diphosphonate (MDP); other isotopes used include 99mTc colloid for bone marrow scans a9mTc colloid for bone marrow scans and 67Ga citrate and 111In white blood cells (111In WBC) for investigation of inflammatory/infective lesions

 
 
 
 
321

Josephson scanning tunneling microscopy  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2000-01-01

322

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

323

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

324

Abdominal Octoson Scan  

International Nuclear Information System (INIS)

The cocoson scan is valuable procedure in the examination of the abdominal organs, urogenital systems, and breast. The octoson was developed by Kossoff and his associates. Lt uses eight transducers on an automated scanning arm in a large water bath in order to lessen operator dependency. The authors analyzed ultrasonographic findings of octoson scans in 60 patients with abdominal lesions proven by pathology and clinical study at the Department of Radiology, Kangnam St. Mary's Hospital, Catholic University Medical College during the period of August 1984 to September 1986. The results were as follows: 1. Octoson scan brought much comfort to the patients because the transducers did not directly contact the patient. 2. Octoson scan consumed shorter time and made better image than that of any other ultrasound units in imaging of abdominal diseases, particularly in the mass lesions. The shapes and contours of the organs were less distorted. 3. Octoson scan covered many organs and systems in a single study aiding the diagnosis of the large intraabdominal mass, both kidneys, and solid organs as well as the liver and spleen at the sometime

325

Wryneck position CT scanning  

International Nuclear Information System (INIS)

For the purpose of further improvement in the CT diagnosis of skull-base and posterior fossa lesions, wryneck position CT scanning was investigated. By the lateral tilting of the patient's head, phantom and clinical study revealed that high- or low-density artifacts between petrous bones were markedly reduced using various types of CT scanners. The most appropriate angle of the lateral head tilting was assumed to be 50 - 100, and better scans were given when the scan was done parallel to Reid's baseline. A satisfactory efficacy of this method was noted in such clinical cases as trigeminal neurinoma, c-p angle meningioma, and pontine glioma. Interpetrous artifacts are caused by the beam hardening and scattering of X-rays, afterglow and crosstalk of the detectors, mastoid air cells, movements of the patients, computer overswing, and the partial-volume phenomenon. The wryneck position can reduce these artifacts by eliminating one petrous bone from the scan area. In addition, the orbit, calvarium, and tip of the middle fossa can be visualized more clearly by this method. This method is very simple and useful for use with head scanners and non-gantlytiltig body scanners which can not easily be used for coronal scans. The better visualization of the anatomical structures in the skull base and posterior fossa by wryneck-position CT scanning gives greater diagnostic ability in these areas. (author)

326

An image-based method to automatically propagate bony landmarks: application to computational spine biomechanics.  

Science.gov (United States)

In attempts to elucidate the underlying mechanisms of spinal injuries and spinal deformities, several experimental and numerical studies have been conducted to understand the biomechanical behavior of the spine. However, numerical biomechanical studies suffer from uncertainties associated with hard- and soft-tissue anatomies. Currently, these parameters are identified manually on each mesh model prior to simulations. The determination of soft connective tissues on finite element meshes can be a tedious procedure, which limits the number of models used in the numerical studies to a few instances. In order to address these limitations, an image-based method for automatic morphing of soft connective tissues has been proposed. Results showed that the proposed method is capable to accurately determine the spatial locations of predetermined bony landmarks. The present method can be used to automatically generate patient-specific models, which may be helpful in designing studies involving a large number of instances and to understand the mechanical behavior of biomechanical structures across a given population. PMID:24960066

de Oliveira, Marcelo E; Netto, Luiz M G; Kistler, Michael; Brandenberger, Daniel; Büchler, Philippe; Hasler, Carol-C

2015-11-01

327

Analysis of anatomical landmarks of the mandibular interforaminal region using CBCT in a Brazilian population  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english Aim: To evaluate the position, presence, appearance and extent of various anatomical landmarks in the mandibular interforaminal region of Brazilian patients using cone-beam computed tomography (CBCT). Methods: A total of 142 CBCT examinations were analyzed to determine the most common location of th [...] e mental foramen (MF), the presence and extent of the anterior loop (AL) of the inferior alveolar nerve, and the appearance and length of the incisive canal (IC). The presence of sexual dimorphism and differences with relation to the left and right sides were also evaluated. Results: Most of the MF (45.5%) was located below the second premolar. The AL and the IC were observed in 18.9 and 96.5% of the images respectively. The average length of AL and IC was 3.14±1.25 mm and 13.68±5.94 mm respectively. No significant differences (p>0.05) between genders or left and right sides were observed for all evaluated parameters. Conclusions: The most common location of the MF, the high rate of visualization of the IC and the occasional presence of AL in the studied Brazilian population demonstrate the importance of using three-dimensional images of the mandibular anterior region, allowing proper surgical planning and preventing injury to the neurovascular bundle.

Paloma Rodrigues, Genú; Ricardo José de Holanda, Vasconcellos; Bruna Paloma de, Oliveira; Bruna Caroline Gonçalves de, Vasconcelos; Nádia Cristina da Cruz, Delgado.

2014-12-01

328

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

329

Dynamic predicting by landmarking as an alternative for multi-state modeling: an application to acute lymphoid leukemia data  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper considers the problem of obtaining a dynamic prediction for 5-year failure free survival after bone marrow transplantation in ALL patients using data from the EBMT, the European Group for Blood and Marrow Transplantation. The paper compares the new landmark methodology as developed by the first author and the established multi-state modeling as described in a recent Tutorial in Biostatistics in Statistics in Medicine by the second author and colleagues. As expected the two approach...

Houwelingen, Hans C.; Putter, Hein

2008-01-01

330

Comparison of adhesive markers, anatomical landmarks, and surface matching in patient-to-image registration for frameless stereotaxy  

Science.gov (United States)

The application accuracy of frameless stereotaxy depends partly on the accuracy of the patient-to-image registration procedure. We compared the application accuracy of registration procedures based on anatomical landmarks, surface matching, and adhesive markers. After acquisition of a 3D-MRI volume, 30 patients were subjected to all three registration procedures. Frameless stereotaxy was performed with the STN system (Carl Zeiss, Germany). Following each registration procedure, the root-mean-squared-error (RMSE) and the target registration error (TRE) of an extra adhesive marker (target) were recorded. The first represents the goodness-of-fit of the registration procedure (not available in surface matching) while the second represents the application accuracy. The mean TRE+/- SD for each type of registration was 5.3+/- 2.1mm, 9.4+/- 6.6mm, and 3.6+/- 1.6mm (paired t-tests: pt-test: p<0.01). There was no significant correlation between the RMSE and the TRE (anatomical landmarks: R2=0.071, adhesive markers: R2=0.004). A more detailed evaluation of surface matching, using a plastic skull phantom, also could not demonstrate an improvement in application accuracy due to surface matching. In conclusion, our results indicate that adhesive markers offer the most accurate alternative to bonescrews. However, we believe anatomical landmarks to provide sufficient accuracy for many neurosurgical procedures concerning frontally located targets, reducing the need for extra preoperative imaging.

Willems, Peter W. A.; Berkelbach van der Sprenkel, Jan W.; Tulleken, Cees A. F.

2001-01-01

331

The Vesta gravity field, spin pole and rotation period, landmark positions, and ephemeris from the Dawn tracking and optical data  

Science.gov (United States)

The Vesta gravity field and related physical parameters have been precisely measured using 10-months of radiometric Doppler and range data and optical landmark tracking from the Dawn spacecraft. The gravity field, orientation parameters, landmark locations, and Vesta’s orbit are jointly estimated. The resulting spherical harmonic gravity field has a half-wavelength resolution of 42 km (degree 20). The gravitational mass uncertainty is nearly 1 part in 106. The inertial spin pole location is determined to better than 0.0001° and the uncertainty in the rotation period has been reduced by nearly a factor of 100. The combined precession and nutation of the pole of Vesta has been detected with angular rates about 70% of expected values, but not well enough to constrain the moment of inertia. The optical landmark position estimates reduce the uncertainty in the center-of-mass and center-of-figure offset to 10 m. The Vesta ephemeris uncertainty during the Dawn stay was reduced from 20 km to better than 10 m in the Earth-Vesta direction.

Konopliv, A. S.; Asmar, S. W.; Park, R. S.; Bills, B. G.; Centinello, F.; Chamberlin, A. B.; Ermakov, A.; Gaskell, R. W.; Rambaux, N.; Raymond, C. A.; Russell, C. T.; Smith, D. E.; Tricarico, P.; Zuber, M. T.

2014-09-01

332

The effect of anatomic landmark selection of the distal humerus on registration accuracy in computer-assisted elbow surgery.  

Science.gov (United States)

Incorrect selection of the flexion-extension axis of the elbow may be an important cause of failure following total elbow arthroplasty. Axis selection can be improved by locating it on a pre-operative image and registering the image to the subject intra-operatively. However, registration is dependent on the availability of anatomic landmarks that may be distorted or absent because of tumors, arthritis, dislocations, or fractures. This study determined the anatomic landmarks required to register surface data accurately to a pre-operative image of the distal humerus. Registration error for landmarks unlikely to be compromised by severe bone loss was 1.1 +/- 0.2 mm in translation and 0.4 +/- 0.1 degrees in rotation. These results suggest that a close alignment of a pre-operative image with intra-operative surface data can be achieved using only a relatively small portion of the distal humerus that is readily available to the surgeon, and unlikely to be compromised, even in the setting of significant articular bone loss. PMID:18572422

McDonald, Colin P; Beaton, Brendon J B; King, Graham J W; Peters, Terry M; Johnson, James A

2008-01-01

333

Translational genomics  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The term “Translational Genomics” reflects both title and mission of this new journal. “Translational” has traditionally been understood as “applied research” or “development”, different from or even opposed to “basic research”. Recent scientific and societal developments have triggered a re-assessment of the connotation that “translational” and “basic” are either/or activities: translational research nowadays aims at feeding the best science into applications and ...

Martin Kussmann; Jim Kaput

2014-01-01

334

Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract The power of genome-wide association studies can be improved by incorporating information from previous study findings, for example, results of genome-wide linkage analyses. Weighted false-discovery rate (FDR) control can incorporate genome-wide linkage scan results into the analysis of genome-wide association data by assigning single-nucleotide polymorphism (SNP) specific weights. Stratified FDR control can also be applied by stratifying the SNPs into high and low linkage ...

Yoo Yun; Pinnaduwage Dushanthi; Waggott Daryl; Bull Shelley B; Sun Lei

2009-01-01

335

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, Eske; Orlando, Ludovic

2015-01-19

336

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

337

An investigation on the facial midline distance to some anatomic landmarks of the jaws among people with natural dentition  

Directory of Open Access Journals (Sweden)

Full Text Available The determination of the dental midline is necessary in most dental procedures."nOne of the methods to fulfill this goal is to determine the facial midline based on the midpoints of the"nforehead, nose, upper lip and chin. However, for various reasons, this method has not always been"nproved successful. In such cases, different techniques, based on the investigations in the edentulous"npatients, have been suggested."nPurpose: The aim of this study was to investigate the conformity of some landmarks such as labial"nfrenum, incisive papilla and mid palatal suture with dental and facial midlines among people with natural"ndentition in order to obtain accurate anatomic landmarks for denture replacement."nMaterials and Methods: In this descriptive study, 96 dental students, having all their permanent teeth"nand without any orthognathic problem, were chosen. For each subject, Alginate impressions and dental"ncasts were prepared. Then, centric occlusion was recorded with a biting wax and the facial mid line was"ndetermined on the anterior part of it. The distances from the facial midline to the upper teeth midline,"nincisive papilla, labial frenum and mid palatal suture were determined with a special tool and were"nmeasured by a VERNIEH two times. In order to analyze the results, Chi- Square and t-student tests were"nused."nResults: The average of facial midline distance to the upper teeth midline, the labial frenum, the incisive"npapilla and the mid palatal suture were 0.83±0.60, 0.67±G.54, 0.83±00.63 and 0.81±0.62 mm,"nrespectively. There was no significant difference between males and females. Labial frenum showed the"nminimum distance to the facial midline, while the incisive papilla had the maximum. There was no"nsignificant difference between these anatomic landmarks, in conformity or unconformity with the facial"nmidline"nConclusion: Considering the low percentage of the subjects with complete conformity and the lack of"nsignificant differences between these three landmarks, it is suggested that there is no superiority among"nthese landmarks for the determination of facial midline. The similar distances from the facial midline to"nthe incisive papilla and upper teeth midline indicate that using incisive papilla to determine the upper"nteeth midline in edentulous patients lead to normal face.

Mosharraf R

2004-02-01

338

Genomes and evolutionary genomics of animals  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Alongside recent advances and booming applications of DNA sequencing technologies, a great number of complete genome sequences for animal species are available to researchers. Hundreds of animals have been involved in whole genome sequencing, and at least 87 non-human animal species’ complete or draft genome sequences have been published since 1998. Based on these technological advances and the subsequent accumulation of large quantity of genomic data, evolutionary genomics has become one o...

Luting Song, Wen Wang

2013-01-01

339

Atlas-driven scan planning for high-resolution micro-SPECT data acquisition based on multi-view photographs: a pilot study  

Science.gov (United States)

Highly focused Micro-SPECT scanners enable the acquisition of functional small animal data with very high-resolution. To acquire a maximum of emitted photons from a specific structure of interest and at the same time minimize the required acquisition time, typically only a small subvolume of the animal is scanned that contains the organs of interest. This Volume of Interest (VOI) can be defined manually based on photographs of the animal taken prior to SPECT scanning, for example two lateral views and a top view. In these photographs however, only the surface of the animal is visible and therefore visual estimation of the location of these organs may be difficult. In this paper, we propose a novel atlas-based technique for estimating the organ VOI for the major organs by mapping a small animal atlas to optical scout images. The user is required to outline the animal contour in one lateral view, and to mark two lateral landmarks in the top view photograph. These landmarks subsequently serve as fiducial landmarks to define a 3D Thin-Plate-Spline mapping of an anatomical mouse atlas to the photographic coordinate space. Planar projections of the mapped atlas organs on the photographs greatly facilitate the estimation of the size and position of the target organ. To validate the proposed approach, the estimated organ VOIs were compared to manually drawn organ outlines in a Micro-CT scan, which was co-registered to the scout photographs using physical landmarks. The results demonstrate a highly promising volume correspondence between the real and the estimated organ VOIs.

Baiker, Martin; Vastenhouw, Brendan; Branderhorst, Woutjan; Reiber, Johan H. C.; Beekman, Freek; Lelieveldt, Boudewijn P. F.

2009-02-01

340

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

 
 
 
 
341

Age-Stratified QTL Genome Scan Analyses for Anthropometric Measures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

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

2003-01-01

342

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

343

Autism and environmental genomics.  

Science.gov (United States)

Autism spectrum disorders (ASD) are defined by behavior and diagnosed by clinical history and observation but have no biomarkers and are presumably, etiologically and biologically heterogeneous. Given brain abnormalities and high monozygotic concordance, ASDs have been framed as neurobiologically based and highly genetic, which has shaped the research agenda and in particular criteria for choosing candidate ASD genes. Genetic studies to date have not uncovered genes of strong effect, but a move toward "genetic complexity" at the neurobiological level may not suffice, as evidence of systemic abnormalities (e.g. gastrointestinal and immune), increasing rates and less than 100% monozygotic concordance support a more inclusive reframing of autism as a multisystem disorder with genetic influence and environmental contributors. We review this evidence and also use a bioinformatic approach to explore the possibility that "environmentally responsive genes" not specifically associated with the nervous system, but potentially associated with systemic changes in autism, have not hitherto received sufficient attention in autism genetics investigations. We overlapped genes from NIEHS Environmental Genome Project, the Comparative Toxicogenomics Database, and the SeattleSNPs database of genes relevant to the human immune and inflammatory response with linkage regions identified in published autism genome scans. We identified 135 genes in overlap regions, of which 56 had never previously been studied in relation to autism and 47 had functional SNPs (in coding regions). Both our review and the bioinformatics exercise support the expansion of criteria for evaluating the relevance of genes to autism risk to include genes related to systemic impact and environmental responsiveness. This review also suggests the utility of environmental genomic resources in highlighting the potential relevance of particular genes within linkage regions. Environmental responsiveness and systems impacts consistent with system-wide findings in autism are thus supported as important considerations in identifying the numerous and complex modes of gene-environment interaction in autism. PMID:16644012

Herbert, M R; Russo, J P; Yang, S; Roohi, J; Blaxill, M; Kahler, S G; Cremer, L; Hatchwell, E

2006-09-01

344

Scanning electrochemical microscopy  

CERN Document Server

Because of its simplicity of use and quantitative results, Scanning Electrochemical Microscopy (SECM) has become an indispensable tool for the study of surface reactivity. The fast expansion of the SECM field during the last several years has been fueled by the introduction of new probes, commercially available instrumentation, and new practical applications. Scanning Electrochemical Microscopy, Second Edition offers essential background and in-depth overviews of specific applications in self-contained chapters. Recent methodological advances have greatly increased the capacity of SECM to char

Bard, Allen J

2012-01-01

345

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

ObjectiveTo evaluate the value of FibroScan in assessing liver fibrosis in chronic hepatitis B (CHB) patients with hepatocyte steatosis. MethodsFour hundred and eighteen CHB patients who had undergone liver biopsy in Shanghai Ruijin Hospital from January 2009 to December 2011 were enrolled in this study. These patients were divided into hepatocyte steatosis group (n=211) and non-hepatocyte steatosis group (n=207). FibroScan was performed in both groups on the same day. Comparisons of liver st...

Liu, Kehui

2014-01-01

346

Computed reconstruction of spatial ammonoid-shell orientation captured from digitized grinding and landmark data  

Science.gov (United States)

The internal orientation of fossil mass occurrences can be exploited as useful source of information about their primary depositional conditions. A series of studies, using different kinds of fossils, especially those with elongated shape (e.g., elongated gastropods), deal with their orientation and the subsequent reconstruction of the depositional conditions (e.g., paleocurrents and transport mechanisms). However, disk-shaped fossils like planispiral cephalopods or gastropods were used, up to now, with caution for interpreting paleocurrents. Moreover, most studies just deal with the topmost surface of such mass occurrences, due to the easier accessibility. Within this study, a new method for three-dimensional reconstruction of the internal structure of a fossil mass occurrence and the subsequent calculation of its spatial shell orientation is established. A 234 million-years-old (Carnian, Triassic) monospecific mass occurrence of the ammonoid Kasimlarceltites krystyni from the Taurus Mountains in Turkey, embedded in limestone, is used for this pilot study. Therefore, a 150×45×140 mm3 block of the ammonoid bearing limestone bed has been grinded to 70 slices, with a distance of 2 mm between each slice. By using a semi-automatic region growing algorithm of the 3D-visualization software Amira, ammonoids of a part of this mass occurrence were segmented and a 3D-model reconstructed. Landmarks, trigonometric and vector-based calculations were used to compute the diameters and the spatial orientation of each ammonoid. The spatial shell orientation was characterized by dip and dip-direction and aperture direction of the longitudinal axis, as well as by dip and azimuth of an imaginary sagittal-plane through each ammonoid. The exact spatial shell orientation was determined for a sample of 675 ammonoids, and their statistical orientation analyzed (i.e., NW/SE). The study combines classical orientation analysis with modern 3D-visualization techniques, and establishes a novel spatial orientation analyzing method, which can be adapted to any kind of abundant solid matter.

Lukeneder, Susanne; Lukeneder, Alexander; Weber, Gerhard W.

2014-03-01

347

Investigation of radon and thoron concentrations in a landmark skyscraper in Tokyo  

International Nuclear Information System (INIS)

The temporal variation of the radon concentration, and the radon and thoron concentrations every 3 months for a year were measured using two types of devices in a landmark skyscraper, the Tokyo Metropolitan Government Daiichi Building. In the measurement of temporal variation of the radon concentration using a pulse type ionization chamber, the average radon concentration was 21 ± 13 Bq m-3 (2-68 Bq m-3). The measured indoor radon concentration had a strong relationship with the operation of the mechanical ventilation system and the activities of the office workers. The radon concentration also increased together with temperature. Other environmental parameters, such as air pressure and relative humidity, were not related to the radon concentration. In the long-term measurements using a passive radon and thoron discriminative monitor, no seasonal variation was observed. The annual average concentrations of radon and thoron were 16 ± 8 and 16 ± 7 Bq m-3, respectively. There was also no relationship between the two concentrations. The annual average effective dose for office workers in this skyscraper was estimated to be 0.08 mSv y-1 for 2000 working hours per year. When considering the indoor radon exposure received from their residential dwellings using the annual mean radon concentration indoors in Japan (15.5 Bq m-3), the annual average effective dose was estimated to be 0.37 mSv y-1. This value wa 0.37 mSv y-1. This value was 31 % of the worldwide average annual effective dose. (author)

348

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

International Nuclear Information System (INIS)

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

349

[Therapy for systemic metabolic disorders based on the detection of basic corneal landmarks in childhood].  

Science.gov (United States)

Many systemic lysosomal storage disorders show basic corneal opacities already in childhood. The lysosome is a cell organelle, produced by Golgi's apparatus, that is surrounded by a membrane and contains hydrolytic enzymes that break down food molecules, especially proteins and other complex molecules. The ophthalmologist's precise diagnosis of corneal clouding at the slit-lamp may reveal the correct interpretation of the specific lysosomal storage disorder. It is very important to diagnose such diseases as soon as possible because today the development of systemic enzymatic therapies has broadened the therapeutic armamentarium for the current standard of care. The following corneal landmarks of systemic storage diseases and of the modern systemic therapy are presented: cornea verticillata in Fabry's disease, periodic infusion of alpha-galactosidase a; Kayser-Fleischer's ring in Wilson's disease, zinc, trienetin, low copper diet; multiple, punctiform crystals in cystinosis, cysteamine, Raptor RP 103(DR cysteamine) that reduces the cytotoxity in form of continous dissolving of cystine from lysosome, renal transplantation, haematopoietic stem cell transplantation; peripheral ring, but not true lipid arc, and moderate stromal haze in LCAT-deficiency, injection of recombinant enzyme or of encapsulated LCAT-secreting cells; diffuse stromal haze in mucopolysaccharidoses (MPS). Enzyme replacement therapy is currently indicated for MPS I, MPS II, and MPS VI, haematopoietic stem cell transplantation; painful, bilateral pseudo-dendritic opacities in tyrosinemia type II (eponym: Richner-Hanhart syndrome), low phenylalanine and tyrosine diet result in complete disappearance of corneal alterations with a consecutive painfree period. Strict diet during the whole life is necessary to prevent corneal recurrences and the occurrence of palmo-plantar keratoses. Such therapies can enable the patient to lead an otherwise normal life for decades. PMID:23794426

Lisch, W; Pitz, S; Geerling, G

2013-06-01

350

Evaluation of normal brain CT scan in Korean  

International Nuclear Information System (INIS)

The safety of procedure combined with wealth of information have resulted in rapid acceptance of CT as a practical and reliable neurodignostic technique. To understand the alternation in tissue density and associated displacement and distortion caused by pathologic lesion in CT, it is necessary to have clear understanding of normal anatomical landmark. For the purpose of establishing normative criteria in Korean for comparative diagnosis, 500 normal CT scan without neurologic sign were studied. The brief results are follows; 1. Among many ventricular index measured for lateral ventricle, the bifrontal CVI is more sensitive and easily determined. Ventricular size increased with age, especially after 6th decade but no difference with sex. 2. Mean width of third ventricle is 5 mm (± 0.3), more wider in male (male; 5.2 mm, female; 4.5 mm) and increased with age. 2. Mean width of fourth ventricle is 13 mm (± 1.3), without difference in age and sex. The shape of ventricle is variable form of triangle. The position of ventricle relative to Twining's line can be determined, so ratio of distance from tuberculum sellae to center of fourth ventricle to Twining's line is between 0.46-0.52. 4. Suprasellar cistern is visible in 89.7% of scan and shape of cistern is found to be pentagonal (73.3%), hexagonal (23.0%) and tetragonal (3.7%). 5. Choroid plexus can be identified in 90% and asymmetrical in 4%. 45% of identified choroid plexus can be visible on scan without contrast enhane visible on scan without contrast enhancement, and more frequently visible in older age

351

Evaluation of normal brain CT scan in Koreans  

International Nuclear Information System (INIS)

The safety of procedure combined with wealth of information have resulted in rapid acceptance of CT as a practical and reliable neurodiagnostic technique. To understand the alternation in tissue density and associated displacement and distortion caused by pathologic lesion in CT, it is necessary to have clear understanding of normal anatomical landmark. For the purpose of establishing normartive criteria in Koreans for comparative diagnosis, 500 normal CT scan without neurologic sign were studied. The brief results are follows; 1. Among many ventricular index measured for lateral ventricle, the bifrontal CVI is more sensitive and easily determined. Ventricular size increased with age, especially after 6th decade but no difference with sex. 2. Mean width of third ventricle is 5mm( ± 0.3), more wider in male (male; 5.2mm, female; 4.5mm) and increased with age. 3. Mean width of fourth ventricle is 13mm( ± 1.3), without difference in age and sex. The shape of ventricle is variable form of triangle. The position of ventricle relative to Twining's line can be determined, so ratio of distance from tuberculum sellae to center of fourth ventricle to Twining's line is between 0.46-0.52. 4. Suprasellar cistern is visible in 89.7% of scan and shape of cistern is found to be pentagonal (73.3%), hexagonal (23.0%) and tetragonal (3.7%). 5. Choroid plexus can be identified in 90% and asymetrical in 4%. 45% of identified choroid plexus can be visible on scan without contrast enhancevisible on scan without contrast enhancement, and more frequently visible in older age

352

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

353

Dialogue scanning measuring systems  

International Nuclear Information System (INIS)

The main developments of scanning measuring systems intended for mass precision processsing of films in nuclear physics problems and in related fields are reviewed. A special attention is paid to the problem of creation of dialogue systems which permit to simlify the development of control computer software

354

Scanning electron microscopy  

International Nuclear Information System (INIS)

The JSM-11 scanning electron microscope at CRNL has been used extensively for topographical studies of oxidized metals, fracture surfaces, entomological and biological specimens. A non-dispersive X-ray attachment permits the microanalysis of the surface features. Techniques for the production of electron channeling patterns have been developed. (author)

355

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

356

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

357

GenomeViz: visualizing microbial genomes  

Directory of Open Access Journals (Sweden)

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

Chakraborty Trinad

2004-12-01

358

Pathogen Evolution In Vivo: Genome Dynamics of Two Isolates Obtained 9 Years Apart from a Duodenal Ulcer Patient Infected with a Single Helicobacter pylori Strain  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The survival and microevolution of Helicobacter pylori strains in the niches of the stomach after eradication therapy have largely been unexplored. We analyzed genomic signatures for two successive isolates obtained 9 years apart from a duodenal ulcer patient who underwent eradication therapy for H. pylori. These isolates were genotyped based on 50 different parameters involving three different fingerprinting approaches and several evolutionarily significant and virulence-associated landmarks...

Prouzet-maule?on, Vale?rie; Hussain, M. Abid; Lamouliatte, Herve?; Kauser, Farhana; Me?graud, Francis; Ahmed, Niyaz

2005-01-01

359

Registration of prone and supine CT colonography scans using correlation optimized warping and canonical correlation analysis  

International Nuclear Information System (INIS)

Purpose: In computed tomographic colonography (CTC), a patient will be scanned twice--Once supine and once prone--to improve the sensitivity for polyp detection. To assist radiologists in CTC reading, in this paper we propose an automated method for colon registration from supine and prone CTC scans. Methods: We propose a new colon centerline registration method for prone and supine CTC scans using correlation optimized warping (COW) and canonical correlation analysis (CCA) based on the anatomical structure of the colon. Four anatomical salient points on the colon are first automatically distinguished. Then correlation optimized warping is applied to the segments defined by the anatomical landmarks to improve the global registration based on local correlation of segments. The COW method was modified by embedding canonical correlation analysis to allow multiple features along the colon centerline to be used in our implementation. Results: We tested the COW algorithm on a CTC data set of 39 patients with 39 polyps (19 training and 20 test cases) to verify the effectiveness of the proposed COW registration method. Experimental results on the test set show that the COW method significantly reduces the average estimation error in a polyp location between supine and prone scans by 67.6%, from 46.27±52.97 to 14.98 mm±11.41 mm, compared to the normalized distance along the colon centerline algorithm (p<0.01). Conclusions: The proposed COW algorithm is more accurate for the COW algorithm is more accurate for the colon centerline registration compared to the normalized distance along the colon centerline method and the dynamic time warping method. Comparison results showed that the feature combination of z-coordinate and curvature achieved lowest registration error compared to the other feature combinations used by COW. The proposed method is tolerant to centerline errors because anatomical landmarks help prevent the propagation of errors across the entire colon centerline.

360

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)

 
 
 
 
361

The laser scanning camera  

International Nuclear Information System (INIS)

The prototype development of a novel lenseless camera is reported which utilises a laser beam scanned in a raster by means of orthogonal vibrating mirrors to illuminate the field of view. Laser light reflected from the scene is picked up by a conveniently sited photosensitive device and used to modulate the brightness of a T.V. display scanned in synchronism with the moving laser beam, hence producing a T.V. image of the scene. The camera which needs no external lighting system can act in either a wide angle mode or by varying the size and position of the raster can be made to zoom in to view in detail any object within a 400 overall viewing angle. The resolution and performance of the camera are described and a comparison of these aspects is made with conventional T.V. cameras. (author)

362

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

Science.gov (United States)

The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and tibial bone landmarks. (1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. (2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977-0.999 for computer analysis; 0.820-0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839-0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers. PMID:19882339

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

2011-01-01

363

Energy Scan program  

Directory of Open Access Journals (Sweden)

Full Text Available Femtoscopy of two non-identical particles in heavy ion collisions enables one to study the space-time asymmetry in the particle's emission process. Theoretical studies based on EPOS model performed for collision energies from the Beam Energy Scan program in STAR allow us to investigate the dependence of source sizes and dynamics effects. Obtained information will enable us to predict the collective behaviour of femtoscopic particle's source.

Poniatowska Katarzyna M.

2014-04-01

364

Slide scanning and autofocusing  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this chapter we describe an automatic slide scanning and autofocusing system that consists of three components. First, images are captured at low magnification. This yields a panoramic view of an entire slide which allows the extraction of the positions and sizes of all particles. Then, a particle screening is carried out at medium magnification, in order to eliminate particles that are not diatom-like, i.e. debris that does not comply with pre-defined selection criteria. This method selec...

Pech-pacheco, Jose? L.; Cristo?bal Pe?rez, Gabriel

2002-01-01

365

Scanning transmission electron microscope:  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The invention relates to a scanning transmission electron microscope comprising an electron source, an electron accelerator and deflection means for directing electrons emitted by the electron source at an object to be examined, and in addition a detector for detecting electrons coming from the object and, connected to the detector, a device for processing the detected electrons so as to form an object image, wherein a beam splitter is provided for dividing the electron beam from the electron...

Brown, L.

2006-01-01

366

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.

367

Adrenal scanning in children  

International Nuclear Information System (INIS)

Adrenal scanning with 131I-Adosterol is very useful and rather non-invasive than adrenal angiography in children. It is possible to diagnose various diseases of the adrenal glands not only structural but also functional abnormalities. In patients with adrenogenital syndromes, we are able to demonstrate hyperplasia of the adrenal glands, and in patients with aldosteronism or Cushing's syndrome differential diagnosis between bilateral hyperplasia and functional adenoma of the adrenal gland can be made. (author)

368

Bone scans in neuroblastoma.  

Science.gov (United States)

Eighty-Six patients of neuroblastoma ranging in age from four months to 15 years were studied with 99m Tc-MDP for total skeletal survey over a period of seven years (1983-1990). The diagnosis of neuroblastoma was based on bone marrow examination, FNAC, lymph node biopsy, histopathology. Bone imaging was performed three hrs. after intravenous administration of 99m Tc-MDP. Out of 86 patients, 45 patients had positive bone scan showing osseous concentration in 122 sites and extraosseous concentration in 34 sites. Seven patients had liver metastases. None of these liver metastases showed concentration of MDP. Fourteen patients underwent surgery for the primary tumour at the time of bone scanning. Ten patients were studied at the time of follow up, of which four patients showed good response as bony metastases were not demonstrated on bone scintigraphy and X-rays. In conclusion, bone scan is an useful test in neuroblastoma in delineating the bony metastases and also in assessing the efficacy of chemotherapy in these patients. PMID:8500809

Bhogate, B M; Samuel, A M; Ramanathan, P

1993-03-01

369

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese 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: Ident [...] ificar 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. Abstract in english 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 t [...] he 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; Marcia Maria Ale de, Souza; Luís Carlos, Gregório; Sergio, Ajzen.

2009-02-01

370

Tandem Scanning Slit Microscope  

Science.gov (United States)

The main purpose of the (TSSM) is to confine illumination, in effect, to just the plane of focus of the specimen, also a major purpose of the tandem scanning microscopes based on pinhole field apertures. However the TSSM achieves this end by a different method, with possible advantages in both cost and performance. It can be thought of as an epiillumination tandem scanning pinhole microscope with substitution of the pinhole apertures by slits, and substitution of the beam splitter (which makes the mirror image of one field aperture coincident with the other) by an opaque mirror. This mirror is placed with an edge in the plane defined by the viewing slit and the center of the objective aperture, so that the mirror reflects light from the illuminated slit onto just one semicircle of the objective aperture, the remaining semicircle used for projecting light from the specimen to the viewing slit. The illuminated volume of the specimen is then non-intersecting with the viewable volume except where these volumes intersect at the image of the illuminated slit, only in the plane of focus. Scanning can be accomplished by reciprocally rotating the two slits and the mirror as a light weight, rigid assembly. Advantages relative to raster scanned confocal microscopes include 1) scanning in just one dimension, 2) no need for electronic sensing and display of the image, 3) production of a real time, actual color, direct optical image, without raster lines or pixel boundaries, and 4) utilization of a single, inexpensive, broadspectrum light source for reflected light and for a wide variety of flourescent dyes. Relative to the Petran/Hadraysky multiple pinhole microscope, advantages include 1) ease of fabricating slit apertures which cause no visible noise in the image, 2) ease of adjusting these apertures to optimize, for each specimen, the tradeoff between image brightness and focal plane specificity, 3) shorter effective photographic exposure times (because with a single sweep, each point in the specimen is exposed just a fraction of the total sweep time) , and 4) better out-of-focus light rejection at large distances from the plane of focus.

Baer, Stephen C.

1989-09-01

371

Acetabular orientation variability and symmetry based on CT scans of adults  

International Nuclear Information System (INIS)

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

372

Acetabular orientation variability and symmetry based on CT scans of adults  

Energy Technology Data Exchange (ETDEWEB)

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

Lubovsky, Omri; Liebergall, Meir; Khoury, Amal [Hadassah-Hebrew University Medical Center, Orthopedic Surgery Complex, Jerusalem (Israel); Peleg, Eran [Hadassah-Hebrew University Medical Center, Department of Medical Engineering, Jerusalem (Israel); Joskowicz, Leo [Hebrew University of Jerusalem, School of Engineering and Computer Science, Jerusalem (Israel)

2010-09-15

373

Translational genomics  

Directory of Open Access Journals (Sweden)

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

Martin Kussmann

2014-09-01

374

ABrowse - a customizable next-generation genome browser framework  

Directory of Open Access Journals (Sweden)

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

Kong Lei

2012-01-01

375

Ontology for Genome Comparison and Genomic Rearrangements  

Directory of Open Access Journals (Sweden)

Full Text Available 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 standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

Anil Wipat

2006-04-01

376

Scanning apparatus and method  

International Nuclear Information System (INIS)

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

377

Visualization in Scanning  

International Nuclear Information System (INIS)

Scanning is essentially a method of making the unknown known, and for the vast majority of scanning work this means making the invisible visible. Visualization is developed as a process involving a model of eye and brain function, display performance and counter performance combined with the spatial frequency components in the object scanned. The performance of a scanner or gamma camera depends in part on its display system and experiments have been performed to determine the fractional change in count-rate which can be perceived by the eye from colour, photoscan and cathode-ray tube displays, for both circular and line sources of radioactivity. For circular sources, colour and photoscan displays are capable of making 10% increases in count-rate perceptible in backgrounds ranging from 5 to 100 counts/s for sources of 1 to 4 cm diameter, whilst cathode-ray tube and black-mark displays show only 20% at best. The results for line sources are also given. In testing for the statistical significance of count-rate differences on a scan, the counts are usually compared for equal areas. On this basis the cathode-ray tube display is only able to show five standard deviations of difference whereas colour and photoscan displays show from 2.5 to 3 standard deviations, levels not usually accepted statistically as significant. It is suggested that if the eye examines the areas surrounding the area of interest then the significance of a count-rate difference may be established more a-rate difference may be established more accurately and in general will be increased, thereby accounting for the visualization of apparently 'insignificant' regions. This theory is used to predict the areas of count density which should be visually perceived in the presence of noise, and extended to consider practical display conditions, which have been described in this paper. The performance of a scanner can be considered in terms of its modulation transfer function (derived from a line spread function). Fourier analysis has been performed of simple objects, (e.g. discs, lines, etc.) so that the shape is defined in terms of fundamental and harmonic spatial frequencies. The performance of a counter and collimator for a selected object is then calculated from the MTF values and compared directly with phantom measurements. (author)

378

Radiographic scanning agent  

International Nuclear Information System (INIS)

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

379

Spinal CT scan, 1  

International Nuclear Information System (INIS)

Methods of CT of the cervical and thoracic spines were explained, and normal CT pictures of them were described. Spinal CT was evaluated in comparison with other methods in various spinal diseases. Plain CT revealed stenosis due to spondylosis or ossification of posterior longitudinal ligament and hernia of intervertebral disc. CT took an important role in the diagnosis of spinal cord tumors with calcification and destruction of the bone. CT scan in combination with other methods was also useful for the diagnosis of spinal injuries, congenital anomalies and infections. (Ueda, J.)

380

Adiponectin is associated with cardiovascular disease in male renal transplant recipients: baseline results from the LANDMARK 2 study  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Adiponectin is a major adipocyte-derived protein with insulin-sensitizing, anti-inflammatory and anti-atherogenic properties. Adiponectin levels correlate inversely with renal function and higher levels are predictive of lower cardiovascular disease (CVD in patients with normal renal function and chronic kidney disease. No data exists on the association between adiponectin and CVD in renal transplant recipients (RTR. Methods Standard biochemistry, clinical data and adiponectin were collected from 137 RTR recruited to the LANDMARK 2 study at baseline. The LANDMARK 2 study is an ongoing randomized controlled study that compares the outcome of aggressive risk factor modification for cardiovascular disease versus standard post-transplant care in renal transplant recipients with impaired glucose tolerance or diabetes mellitus. Results Mean patient age was 53.4 ± 12 years and the median post-transplantation period was 5 (0.5-31.9 years. Mean serum adiponectin level was 12.3 ± 7.1 ?g/mL. On univariate analysis, adiponectin was positively associated with female gender (P = 0.01 and serum high-density lipoprotein (HDL concentration (P Conclusion In conclusion, adiponectin is positively correlated with inflammation, dyslipidemia and abnormal glucose tolerance in RTR. Furthermore, hypoadiponectinemia correlated with increased baseline CVD in male RTR.

Mudge David

2009-10-01

 
 
 
 
381

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

Directory of Open Access Journals (Sweden)

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

Leeder J Steven

2003-09-01

382

Contour-based brain segmentation method for magnetic resonance imaging human head scans.  

Science.gov (United States)

The high-resolution magnetic resonance brain images often contain some nonbrain tissues (ie, skin, fat, muscle, neck, eye balls, etc) compared with the functional images such as positron emission tomography, single-photon emission computed tomography, and functional magnetic resonance imaging (MRI) scans, which usually contain few nonbrain tissues. Automatic segmentation of brain tissues from MRI scans remains a challenging task due to the variation in shape and size, use of different pulse sequences, overlapping signal intensities and imaging artifacts. This article presents a contour-based automatic brain segmentation method to segment the brain regions from T1-, T2-, and proton density-weighted MRI of human head scans. The proposed method consists of 2 stages. In stage 1, the brain regions in the middle slice is extracted. Many of the existing methods failed to extract brain regions in the lower and upper slices of the brain volume, where the brain appears in more than 1 connected region. To overcome this problem, in the proposed method, a landmark circle is drawn at the center of the extracted brain region of a middle slice and is likely to pass through all the brain regions in the remaining lower and upper slices irrespective of whether the brain is composed of 1 or more connected components. In stage 2, the brain regions in the remaining slices are extracted with reference to the landmark circle obtained in stage 1. The proposed method is robust to the variability of brain anatomy, image orientation, and image type, and it extracts the brain regions accurately in T1-, T2-, and proton density-weighted normal and abnormal brain images. Experimental results by applying the proposed method on 100 volumes of brain images show that the proposed method exhibits best and consistent performance than by the popular existing methods brain extraction tool, brain surface extraction, watershed algorithm, hybrid watershed algorithm, and skull stripping using graph cuts. PMID:23674005

Somasundaram, K; Kalavathi, P

2013-01-01

383

Design of an Enterobacteriaceae Pan-genome Microarray Chip  

DEFF Research Database (Denmark)

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

Lukjancenko, Oksana; Ussery, David

2010-01-01

384

Photon scanning tunneling microscopy  

Energy Technology Data Exchange (ETDEWEB)

An optical tunneling microscope is presented that operates in exactly the same way as the electron scanning tunneling microscope (ESTM). It takes advantage of evanescent fields generated by the total internal reflection (TIR) of light at the interface between materials of different optical densities. The photon scanning tunneling microscope (PSTM) employs an optically conducting probe tip to map spatial variations in the evanescent and scattered field intensity distributions adjacent to a sample surface, which forms or is placed on the TIR surface. These variations are due to the local topography, morphology, and optical activity of the surface and form the basis of imaging. Evanescent field theory is discussed and the evanescent field intensity as a function of surface-probe separation is calculated using several probe tip models. After a description of PSTM construction and operation, evanescent field intensity measurements are shown to agree with the model calculations. PSTM images of various sample surfaces demonstrate subwavelength resolution exceeding that of conventional optical microscopy, especially in the vertical dimension. Limitations and interpretation of PSTM images are discussed as well as the PSTMs applicability to other forms of surface analysis.

Reddick, R.C.; Warmack, R.J.; Chilcott, D.W.; Sharp, S.L.; Ferrell, T.L. (Health and Safety Research Division, Oak Ridge National Laboratory, Oak Ridge, TN (USA) Department of Physics and Astronomy, University of Tennessee, Knoxville, TN (USA))

1990-12-01

385

Free Motion Scanning System  

Energy Technology Data Exchange (ETDEWEB)

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

Sword, Charles K.

1998-06-18

386

Ultrafast scanning tunneling microscopy  

Energy Technology Data Exchange (ETDEWEB)

I have developed an ultrafast scanning tunneling microscope (USTM) based on uniting stroboscopic methods of ultrafast optics and scanned probe microscopy to obtain nanometer spatial resolution and sub-picosecond temporal resolution. USTM increases the achievable time resolution of a STM by more than 6 orders of magnitude; this should enable exploration of mesoscopic and nanometer size systems on time scales corresponding to the period or decay of fundamental excitations. USTM consists of a photoconductive switch with subpicosecond response time in series with the tip of a STM. An optical pulse from a modelocked laser activates the switch to create a gate for the tunneling current, while a second laser pulse on the sample initiates a dynamic process which affects the tunneling current. By sending a large sequence of identical pulse pairs and measuring the average tunnel current as a function of the relative time delay between the pulses in each pair, one can map the time evolution of the surface process. USTM was used to measure the broadband response of the STM`s atomic size tunnel barrier in frequencies from tens to hundreds of GHz. The USTM signal amplitude decays linearly with the tunnel junction conductance, so the spatial resolution of the time-resolved signal is comparable to that of a conventional STM. Geometrical capacitance of the junction does not appear to play an important role in the measurement, but a capacitive effect intimately related to tunneling contributes to the measured signals and may limit the ultimate resolution of the USTM.

Botkin, D.A. [California Univ., Berkeley, CA (United States). Dept. of Physics]|[Lawrence Berkeley Lab., CA (United States)

1995-09-01

387

The scanning laser ophthalmoscope.  

Science.gov (United States)

The imaging of the fundus of the eye poses two major technical challenges. First, it is necessary for both the illuminating and reflected beams to pass through the same aperture, the iris. In some commonly used instruments this leads to the use of levels of illumination close to the maximum tolerable by a patient. Second, in order to visualize the different structures present in the various layers of the fundus it is necessary to perform tomographic imaging. The scanning laser ophthalmoscope provides an answer to these particular problems. By scanning the fundus with a narrow laser beam most of the area of the iris is then available for the reflected light and so the intensity of the illuminating beam can be kept low, making it more acceptable for patients. The use of confocal imaging allows 3D images to be produced. In this short review the performance of the instrument will be discussed and its application to a number of clinical problems in ophthalmology considered. Finally there will be a brief description of other instrumentation currently under development. PMID:9172269

Sharp, P F; Manivannan, A

1997-05-01

388

An analysis of anatomic landmark mobility and setup errors in radiotherapy for lung cancer  

International Nuclear Information System (INIS)

Purpose: To identify visible structures in the thorax which exhibit little internal motion during irradiation and, to determine random and systematic setup deviations in lung cancer patients with the use of these structures. Methods: Ten patients with lung cancer were set up in the supine position, and aligned using lasers. No immobilization devices were used. With an electronic portal imaging device (Siemens Beam ViewPLUS), 12 sequential images (exposure 0.54 sec.; processing time 1.5 sec.) were obtained during a single fraction of radiotherapy. These 'movie loops' were generated for the A-P fields during each of 3-5 fractions. In order to determine the mobility of internal structures during each fraction, visible structures such as the trachea, carina, the upper chest wall, aortic arch, clavicle and paraspinal line were contoured manually in each image and matched with the first image of the corresponding movie loop by means of a cross-correlation algorithm. Translations in the cranial and lateral directions and in-plane rotations were determined for each structure separately. As the reference image represents a random position, relative movements were determined by comparing the translations and rotation for every image to the calculated means per movie-loop. Standard deviations of the relative movements were determined for each structure and each patient. Patient setup was evaluated for 15 patients with lung cancer. Setup was not corrected at any time dcer. Setup was not corrected at any time during the treatment. The electronic portal images of each fraction were matched with the digitized simulator films by using a combination of the structures which had been determined to be relatively stable in the infra-fractional analysis. Results: In the infra-fractional analysis 120 to 380 matches were made per structure (a total of 1400). The standard deviation (SD) of translations in the lateral direction was small (?1 mm) for the trachea, thoracic wall, paraspinal line and aortic arch. This was also the case for the SD of the translations in the cranial direction of the clavicle, aortic arch and upper thoracic wall. The carina was found to be relatively mobile (up to 6 mm) in both directions. The SD for in-plane rotations was negligible (<0.5 deg.) for all structures. The interpatient variation was very small (SD < 0.5 mm). In a preliminary analysis of patient setup, the random errors for translations are 2.0 mm in the lateral direction and 2.4 mm in the cranial direction (1 SD). The standard deviations of systematic errors are about 3 mm in both directions. In plane rotations were found to be negligible. Conclusions: We have identified a number of structures which exhibit little internal motion in the frontal plane, and recommend that a combination of these structures be used as anatomic landmarks for setup verification during radiotherapy of thoracic tumors. Preliminary results indicate that setup errors of patients with lung cancer in our center appear to be acceptable, even though no specific immobilization devices were used

389

Genome Maps, a new generation genome browser.  

Science.gov (United States)

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

390

Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after?  

Science.gov (United States)

Two rounds of whole-genome duplications are thought to have played an important role in the establishment of gene repertoires in vertebrates. These events occurred during chordate evolution after the split of the urochordate and cephalochordate lineages but before the radiation of extant gnathostomes (jawed vertebrates). During this interval, diverse agnathans (jawless fishes), including cyclostomes (hagfishes and lampreys), diverged. However, there is no solid evidence for the timing of these genome duplications in relation to the divergence of cyclostomes from the gnathostome lineage. We conducted cDNA sequencing in diverse early vertebrates for members of homeobox-containing (Dlx and ParaHox) and other gene families that would serve as landmarks for genome duplications. Including these new sequences, we performed a molecular phylogenetic census using the maximum likelihood method for 55 gene families. In most of these gene families, we detected many more gene duplications before the cyclostome-gnathostome split, than after. Many of these gene families (e.g., visual opsins, RAR, Notch) have multiple paralogs in conserved, syntenic genomic regions that must have been generated by large-scale duplication events. Taken together, this indicates that the genome duplications occurred before the cyclostome-gnathostome split. We propose that the redundancy in gene repertoires possessed by all vertebrates, including hagfishes and lampreys, was introduced primarily by genome duplications. Apart from subsequent lineage-specific modifications, these ancient genome duplication events might serve generally to distinguish vertebrates from invertebrates at the genomic level. PMID:18842688

Kuraku, Shigehiro; Meyer, Axel; Kuratani, Shigeru

2009-01-01

391

Scan mirrors relay for high resolution laser scanning systems  

Science.gov (United States)

Two dimensional beam deflection is often required in medical laser scanning systems such as OCT or confocal microscopy. Commonly two linear galvo mirrors are used for performance in terms of their large apertures and scan angles. The galvo mirrors are placed at the vicinity of entrance pupil of the scan lens with a "displacement distance" separating them. This distance limits the scan fields and/or reduces the effective aperture of the scan lens. Another option is to use a beam or pupil relay, and image one galvo mirror onto the other. However, beam (or pupil) relays are notoriously complicated, expensive and can add significant aberrations. This paper discusses a simple, all reflective, diffraction limited, color corrected, beam relay, capable of large scan angles and large deflecting mirrors. The design is based on a unique combination of an Offner configuration with a Schmidt aspheric corrector. The design is highly corrected up to large scan mirrors and large scan angles down to milliwaves of aberrations. It allows significantly larger scan field and or scan lenses with higher numerical aperture as compared with scanners using galvos separated by the displacement distance. While this relay is of exceptionally high performance, it has one element located where the beam is focused which may present a problem for high power lasers. Thus modifications of the above design are introduced where the beam is focused in mid air thus making it usable for high power systems such including laser marking and fabrication systems.

Kessler, David

2014-09-01

392

CT scans in encephalitis  

International Nuclear Information System (INIS)

Generally, CT scans reveal a decrease in the volume of the ventricular system, sylvian fissures and cortical sulci in the acute stage of encephalitis, and softening of the cerebral lobes with dilatation of the lateral ventricles and subarachnoidian dilated spaces in the chronic stage. We encountered three cases of encephalitis: mumps (case 1), herpes simplex (case 2), and syphilis (case 3). In case 1, brain edema was seen in the acute stage and brain atrophy in the chronic stage. In case 2, necrosis of the temporal pole, which is pathognomonic in herpes simplex encephalitis, was recognized. And in case 3, multiple lesions whose CT appearance was enhanced by contrast materials were found scattered over the whole brain. These lesions were diagnosed as inflammatory granuloma by histological examination. (author)

393

A Scanning Cavity Microscope  

CERN Document Server

Imaging of the optical properties of individual nanosystems beyond fluorescence can provide a wealth of information. However, the minute signals for absorption and dispersion are challenging to observe, and only specialized techniques requiring sophisticated noise rejection are available. Here we use signal enhancement in a scanning optical microcavity to demonstrate ultra-sensitive imaging. Harnessing multiple interactions of probe light with a sample within an optical resonator, we achieve a 1700-fold signal enhancement compared to diffraction-limited microscopy. We demonstrate quantitative imaging of the extinction cross section of gold nanoparticles with a sensitivity below 1 nm2, we show a method to improve spatial resolution potentially below the diffraction limit by using higher order cavity modes, and we present measurements of the birefringence and extinction contrast of gold nanorods. The demonstrated simultaneous enhancement of absorptive and dispersive signals promises intriguing potential for opt...

Mader, Matthias; Hänsch, Theodor W; Hunger, David

2014-01-01

394

Surface micromachined scanning mirrors  

DEFF Research Database (Denmark)

Both aluminum cantilever and torsional scanning mirrors have been fabricated and their static and dynamic properties are studied experimentally and theoretically. The experiments showed resonance frequencies in the range of 163 k-Hz - 632 kHz for cantilever beams with Q values between 5 and 11. Torsional mirrors showed resonance frequencies in the range of 410 kHz - 667 kHz with Q values of 10 - 17. All measurements performed at atmospheric pressure. Both types of mechanical structures were deflected electrostatically at large angles (± 5°) more than 1011 times without breaking and without any noticeable deterioration due to fatigue. A number of different light modulator arrays made up of adjacent devices was investigated and the measured performance parameters were in good agreement with calculations.

Mattsson, Kent Erik

1992-01-01

395

Telescopic horizon scanning.  

Science.gov (United States)

The problem of "distortionless" viewing with terrestrial telescopic systems (mainly "binoculars") remains problematic. The so called "globe effect" is only partially counteracted in modern designs. Theories addressing the phenomenon have never reached definitive closure. In this paper, we show that exact distortionless viewing with terrestrial telescopic systems is not possible in general, but that it is in principle possible in-very frequent in battle field and marine applications-the case of horizon scanning. However, this involves cylindrical optical elements. For opto-electronic systems, a full solution is more readily feasible. The solution involves a novel interpretation of the relevant constraints and objectives. For final design decisions, it is not necessary to rely on a corpus of psychophysical (or ergonomic) data, although one has to decide whether the instrument is intended as an extension of the eye or as a "pictorial" device. PMID:25608206

Koenderink, Jan

2014-12-20

396

Scanning Electrochemical Microscopy  

Science.gov (United States)

This review describes work done in scanning electrochemical microscopy (SECM) since 2000 with an emphasis on new applications and important trends, such as nanometer-sized tips. SECM has been adapted to investigate charge transport across liquid/liquid interfaces and to probe charge transport in thin films and membranes. It has been used in biological systems like single cells to study ion transport in channels, as well as cellular and enzyme activity. It is also a powerful and useful tool for the evaluation of the electrocatalytic activities of different materials for useful reactions, such as oxygen reduction and hydrogen oxidation. SECM has also been used as an electrochemical tool for studies of the local properties and reactivity of a wide variety of materials, including metals, insulators, and semiconductors. Finally, SECM has been combined with several other nonelectrochemical techniques, such as atomic force microscopy, to enhance and complement the information available from SECM alone.

Amemiya, Shigeru; Bard, Allen J.; Fan, Fu-Ren F.; Mirkin, Michael V.; Unwin, Patrick R.

2008-07-01

397

Scanning the periphery.  

Science.gov (United States)

Companies often face new rivals, technologies, regulations, and other environmental changes that seem to come out of left field. How can they see these changes sooner and capitalize on them? Such changes often begin as weak signals on what the authors call the periphery, or the blurry zone at the edge of an organization's vision. As with human peripheral vision, these signals are difficult to see and interpret but can be vital to success or survival. Unfortunately, most companies lack a systematic method for determining where on the periphery they should be looking, how to interpret the weak signals they see, and how to allocate limited scanning resources. This article provides such a method-a question-based framework for helping companies scan the periphery more efficiently and effectively. The framework divides questions into three categories: learning from the past (What have been our past blind spots? What instructive analogies do other industries offer? Who in the industry is skilled at picking up weak signals and acting on them?); evaluating the present (What important signals are we rationalizing away? What are our mavericks, outliers, complainers, and defectors telling us? What are our peripheral customers and competitors really thinking?); and envisioning the future (What future surprises could really hurt or help us? What emerging technologies could change the game? Is there an unthinkable scenario that might disrupt our business?). Answering these questions is a good first step toward anticipating problems or opportunities that may appear on the business horizon. The article concludes with a self-test that companies can use to assess their need and capability for peripheral vision. PMID:16299966

Day, George S; Schoemaker, Paul J H

2005-11-01

398

JGI Fungal Genomics Program  

Energy Technology Data Exchange (ETDEWEB)

Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

Grigoriev, Igor V.

2011-03-14

399

Genomic Encyclopedia of Fungi  

Energy Technology Data Exchange (ETDEWEB)

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

Grigoriev, Igor

2012-08-10

400

Recognition of dilated ventricular cavities in high resolution positron emission tomography (PET) scans using F-18 fluorodeoxyglucose (FDG)  

International Nuclear Information System (INIS)

Discrimination of the cerebral ventricles from white matter areas has not been previously possible in FDG-PET scans. With the improved resolution offered by the Neuro-PET scanner (NIH), the authors have been able to identify not only the lateral, but also the third and fourth ventricles. This has been possible not only when these CSF cavities were markedly dilated but also in cases of moderate to slight enlargement as demonstrated by CT. In a review of the scans of 56 patients, without knowledge of their clinical history or CT findings, dilated ventricles were identified in 8 cases and, in each instance, verified by CT. Metabolic rates measured in the ventricular areas of these cases were consistently between 0.3 and 1.3 mg glucose per min/100 g tissue, compared to white matter values of 2 to 4 and cortical values of 5 to 8 for the same patients. The ventricles constitute an in vivo cold spot; the measured values are above zero because of partial volume effects and errors in scatter correction. FDG-PET recognition of normal sized ventricles has not been possible due to small volumes and merging of their metabolic values with those of the surrounding white matter. Differentiation of the ventricular cavities may assist in the mapping of cerebral structures by providing additional clearly anatomical landmarks. The need for such landmarks in PET studies is critical, particularly considering the fact that vital neural centers and tracts are adjacent or in proximity to the ventricular system