WorldWideScience

Sample records for landmark genome scanning

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

    Directory of Open Access Journals (Sweden)

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

    2010-07-01

    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

  2. Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis.

    Science.gov (United States)

    Costello, Joseph F; Hong, Chibo; Plass, Christoph; Smiraglia, Dominic J

    2009-01-01

    Restriction landmark genomic scanning (RLGS) is a method that provides a quantitative genetic and epigenetic (cytosine methylation) assessment of thousands of CpG islands in a single gel without prior knowledge of gene sequence. The method is based on two-dimensional separation of radiolabeled genomic DNA into nearly 2,000 discrete fragments that have a high probability of containing gene sequences. Genomic DNA is digested with an infrequently cutting restriction enzyme, such as NotI or AscI, radiolabeled at the cleaved ends, digested with a second restriction enzyme, and then electrophoresed through a narrow, 60-cm-long agarose tube-shaped gel. The DNA in the tube gel is then digested by a third, more frequently cutting restriction enzyme and electrophoresed, in a direction perpendicular to the first separation, through a 5% nondenaturing polyacrylamide gel, and the gel is autoradiographed. Radiolabeled NotI or AscI sites are frequently used as "landmarks" because NotI or AscI cannot cleave methylated sites and since an estimated 89% and 83% of the recognition sites, respectively, are found within CpG islands. Using a methylation-sensitive enzyme, the technique has been termed RLGS-M. The resulting RLGS profile displays both the copy number and methylation status of the CpG islands. Integrated with high-resolution gene copy-number analyses, RLGS enables one to define genetic or epigenetic alteration in cells. These profiles are highly reproducible and are therefore amenable to inter- and intraindividual DNA sample comparisons. RLGS was the first of many technologies to allow large-scale DNA methylation analysis of CpG islands. PMID:18987812

  3. Fully automatic detection of corresponding anatomical landmarks in volume scans of different respiratory state

    International Nuclear Information System (INIS)

    A method is described which provides fully automatic detection of corresponding anatomical landmarks in volume scans taken at different respiratory states. The resulting control points are needed for creating a volumetric deformation model for motion compensation in radiotherapy. Prior to treatment two CT volumes are taken, one scan during inhalation, one during exhalation. These scans and the detected control point pairs are taken as input for creating the four-dimensional model by using thin-plate splines

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

    OpenAIRE

    Ritter, Martin

    2007-01-01

    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 t...

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

    OpenAIRE

    Blundell, R.; A.E. Felice

    2006-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Ritter, M.

    2007-04-27

    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.)

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

    International Nuclear Information System (INIS)

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

  8. Genome-Wide Scan Reveals Mutation Associated with Melanoma

    Science.gov (United States)

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

  9. Genome scans and microarrays: converging on genes for schizophrenia?

    OpenAIRE

    Williams, Nigel M.; O'Donovan, Michael C.; Owen, Michael J.

    2002-01-01

    Systematic genome-wide scans to date have shown that genes of major effect are not common causes of schizophrenia, but independent linkage studies looking for schizophrenia susceptibility genes are converging on a number of key chromosomal locations. Microarray expression analysis may identify new candidate genes and pathways, and a number of intriguing preliminary findings have already been reported.

  10. Enhancer scanning to locate regulatory regions in genomic loci

    Science.gov (United States)

    Buckley, Melissa; Gjyshi, Anxhela; Mendoza-Fandiño, Gustavo; Baskin, Rebekah; Carvalho, Renato S.; Carvalho, Marcelo A.; Woods, Nicholas T.; Monteiro, Alvaro N.A.

    2016-01-01

    The present protocol provides a rapid, streamlined and scalable strategy to systematically scan genomic regions for the presence of transcriptional regulatory regions active in a specific cell type. It creates genomic tiles spanning a region of interest that are subsequently cloned by recombination into a luciferase reporter vector containing the Simian Virus 40 promoter. Tiling clones are transfected into specific cell types to test for the presence of transcriptional regulatory regions. The protocol includes testing of different SNP (single nucleotide polymorphism) alleles to determine their effect on regulatory activity. This procedure provides a systematic framework to identify candidate functional SNPs within a locus during functional analysis of genome-wide association studies. This protocol adapts and combines previous well-established molecular biology methods to provide a streamlined strategy, based on automated primer design and recombinational cloning to rapidly go from a genomic locus to a set of candidate functional SNPs in eight weeks. PMID:26658467

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

    Directory of Open Access Journals (Sweden)

    Mei Lingling

    2011-11-01

    Full Text Available Abstract Background To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance. Results Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA. Conclusions AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.

  12. Improved Detection of Landmarks on 3D Human Face Data

    OpenAIRE

    Shu LIANG; Wu, Jia; Weinberg, Seth M; Shapiro, Linda G

    2013-01-01

    Craniofacial researchers make heavy use of established facial landmarks in their morphometric analyses. For studies on very large facial image datasets, the standard approach of manual landmarking is very labor intensive. With the goal of producing 20 established landmarks, we have developed a geometric methodology that can automatically locate 10 established landmark points and 7 other supporting points on human 3D facial scans. Then, to improve accuracy and produce all 20 landmarks, a defor...

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

    Science.gov (United States)

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

    2013-02-01

    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.

  14. Detecting positive selection from genome scans of linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    Rogers Alan R

    2010-01-01

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

  15. Genome-wide scan for loci of Asperger syndrome.

    Science.gov (United States)

    Ylisaukko-oja, T; Nieminen-von Wendt, T; Kempas, E; Sarenius, S; Varilo, T; von Wendt, L; Peltonen, L; Järvelä, I

    2004-02-01

    Asperger syndrome (AS), characterised by inadequate social interaction, lack of empathy and a dependence of routines and rituals, is classified as belonging to the autism spectrum disorders (DSM-IV and ICD-10). Although the prevalence of AS has been estimated to range from 0.3 up to 48.4 per 10 000, the phenotype still remains relatively unrecognised by clinicians. Several reports, including the original description by Hans Asperger (1944), have suggested that AS has a strong genetic component. Here, we have performed a genome-wide scan on Finnish families ascertained for AS with a strictly defined phenotype. In the initial scan, Z(max)>1.5 was observed on nine chromosomal regions, 1q21-22, 3p14-24, 3q25-27, 4p14, 4q32, 6p25, 6q16, 13q31-33 and 18p11. In the fine mapping stage, the highest two-point LOD scores were observed on chromosomes 1q21-22 (D1S484, Z(max dom)=3.58), 3p14-24 (D3S2432, Z(max dom)=2.50) and 13q31-33 (D13S793, Z(max dom)=1.59). The loci on 1q21-22 and 3p14-24 overlap with previously published autism susceptibility loci, and the loci on 1q21-22 and 13q31-33 overlap with the reported schizophrenia susceptibility loci. The present study is the first genome-wide screen in AS and therefore replication data sets are needed to evaluate further the significance of the AS-loci identified here. PMID:14966474

  16. A genome scan for positive selection in thoroughbred horses.

    Science.gov (United States)

    Gu, Jingjing; Orr, Nick; Park, Stephen D; Katz, Lisa M; Sulimova, Galina; MacHugh, David E; Hill, Emmeline W

    2009-01-01

    Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1) deviations from expected heterozygosity (Ewens-Watterson test) in Thoroughbred (n = 112) and (2) global differentiation among four geographically diverse horse populations (F(ST)). We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; Phorses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1), ACTA1 (actin, alpha 1, skeletal muscle), ACTN2 (actinin, alpha 2), ADHFE1 (alcohol dehydrogenase, iron containing, 1), MTFR1 (mitochondrial fission regulator 1), PDK4 (pyruvate dehydrogenase kinase, isozyme 4) and TNC (tenascin C). Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes within the complex molecular networks underlying obesity and its consequential pathologies, such as type 2 diabetes. Therefore, we propose Thoroughbred as a novel in vivo large animal model for understanding molecular protection against metabolic disease. PMID:19503617

  17. Genome scan for linkage to Gilles de la Tourette syndrome

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-09-01

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

  18. An automated annotation tool for genomic DNA sequences using GeneScan and BLAST

    Indian Academy of Sciences (India)

    Andrew M. Lynn; Chakresh Kumar Jain; K. Kosalai; Pranjan Barman; Nupur Thakur; Harish Batra; Alok Bhattacharya

    2001-04-01

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated annotation of genome DNA sequences.

  19. 3D facial landmarks

    DEFF Research Database (Denmark)

    Fagertun, Jens; Harder, Stine; Rosengren, Anders; Moeller, Christian; Werge, Thomas; Paulsen, Rasmus R; Hansen, Thomas

    2014-01-01

    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 mini...

  20. Genome scanning for segments shared identical by descent among distant relatives in isolated populations.

    OpenAIRE

    Durham, L K; Feingold, E

    1997-01-01

    In this paper, we address some of the statistical issues concerning false-positive rates that arise when the whole genome, or a portion thereof, is scanned in distantly related individuals, to search for a disease locus. We derive a method for correcting false-positive probabilities for the large number of comparisons that are performed when scanning a large portion of the genome. We consider both the idealized situation of a dense set of fully informative markers and the more realistic data-...

  1. Landmarks in Hybrid Planning

    Directory of Open Access Journals (Sweden)

    Mohamed Elkawkagy

    2013-11-01

    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.

  2. BasemapLandmarks_CEMETERY

    Data.gov (United States)

    Vermont Center for Geographic Information — The BasemapLandmarks_CEMETERY point layer contains cemeteries in the state of Vermont. The data is based on VTrans Town Highway Maps. Some points have been moved to...

  3. Landmarks in Linoleum

    Science.gov (United States)

    Skophammer, Karen

    2010-01-01

    This printmaking unit will get students excited about geography and history. In this article, the author describes how her eighth-grade students created a report and a linoleum print of a famous "landmark."

  4. BasemapLandmarks_GEONAME

    Data.gov (United States)

    Vermont Center for Geographic Information — BasemapLandmarks_GEONAME is derived from the US Geological Survey's National Geographic Names Database (GNIS). The data were obtained by VCGI for distribution.

  5. A Genome Scan for Selection Signatures in Pigs

    OpenAIRE

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

    2015-01-01

    Identifying signatures of selection can provide a straightforward insight into the mechanism of artificial selection and further uncover the causal genes related to the phenotypic variation. Based on Illumina Porcine60KSNP chip data, four complementary methods, Long-Range Haplotype (LRH), Tajima’s D, Cross Population Extend Haplotype Homozygosity Test (XPEHH) and FST, were implemented in this study to detect the selection signatures in the whole genome of one typical Chinese indigenous breed,...

  6. Genome-wide scans for loci under selection in humans

    OpenAIRE

    Ronald James; Akey Joshua M

    2005-01-01

    Abstract Natural selection, which can be defined as the differential contribution of genetic variants to future generations, is the driving force of Darwinian evolution. Identifying regions of the human genome that have been targets of natural selection is an important step in clarifying human evolutionary history and understanding how genetic variation results in phenotypic diversity, it may also facilitate the search for complex disease genes. Technological advances in high-throughput DNA s...

  7. A Genome Scan for Positive Selection in Thoroughbred Horses

    OpenAIRE

    Gu, Jingjing; Orr, Nick; Park, Stephen D; Katz, Lisa M; Sulimova, Galina; MacHugh, David E.; Hill, Emmeline W

    2009-01-01

    Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed...

  8. A genome scan for selection signatures in pigs.

    Science.gov (United States)

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

    2015-01-01

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

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

    OpenAIRE

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

    1999-01-01

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

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

    Indian Academy of Sciences (India)

    Gautam Aggarwal; Ramakrishna Ramaswamy

    2002-02-01

    We compare the annotation of three complete genomes using the ab initio methods of gene identification GeneScan and GLIMMER. The annotation given in GenBank, the standard against which these are compared, has been made using GeneMark. We find a number of novel genes which are predicted by both methods used here, as well as a number of genes that are predicted by GeneMark, but are not identified by either of the nonconsensus methods that we have used. The three organisms studied here are all prokaryotic species with fairly compact genomes. The Fourier measure forms the basis for an efficient non-consensus method for gene prediction, and the algorithm GeneScan exploits this measure. We have bench-marked this program as well as GLIMMER using 3 complete prokaryotic genomes. An effort has also been made to study the limitations of these techniques for complete genome analysis. GeneScan and GLIMMER are of comparable accuracy insofar as gene-identification is concerned, with sensitivities and specificities typically greater than 0.9. The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a significant number of cases, similar results are provided by the two techniques. This suggests that there could be some as-yet unidentified additional genes in these three genomes, and also that some of the putative identifications made hitherto might require re-evaluation. All these cases are discussed in detail.

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

    OpenAIRE

    Shi Haijiang; Lee Sophia SF; Wu Long; Sun Lei; Bull Shelley B

    2005-01-01

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    . Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477-91). The latter was recently established when a causative coronavirus (SARS......-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399-404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total...

  13. A Genome-wide Pleiotropy Scan for Prostate Cancer Risk

    DEFF Research Database (Denmark)

    Panagiotou, Orestis A; Travis, Ruth C

    2015-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Børglum Anders D

    2011-07-01

    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.

  15. Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan

    Science.gov (United States)

    Aluminum (Al) toxicity is an important limitation to food security in the tropical and subtropical regions. High Al saturation in acid soils limits root development and its ability to uptake water and nutrients. In this study, we present a genome scan for Al tolerance loci with over 50,000 GBS-based...

  16. Genome-wide scans using archived neonatal dried blood spot samples

    Directory of Open Access Journals (Sweden)

    Wiuf Carsten

    2009-07-01

    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.

  17. Genome-wide scans using archived neonatal dried blood spot samples

    DEFF Research Database (Denmark)

    Hollegaard, Mads; Grauholm, Jonas

    2009-01-01

    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.

  18. A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea.

    Science.gov (United States)

    Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-01-01

    We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23-47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea. PMID:26058368

  19. Ordered Landmarks in Planning

    CERN Document Server

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

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

  1. Whole-Genome Linkage and Association Scan in Primary, Nonsyndromic Vesicoureteric Reflux

    OpenAIRE

    Cordell, Heather J.; Darlay, Rebecca; Charoen, Pimphen; Stewart, Aisling; Gullett, Ambrose M.; Lambert, Heather J; Malcolm, Sue; Feather, Sally A.; Goodship, Timothy H. J.; Woolf, Adrian S; Kenda, Rajko B.; Goodship, Judith A

    2010-01-01

    Primary vesicoureteric reflux accounts for approximately 10% of kidney failure requiring dialysis or transplantation, and sibling studies suggest a large genetic component. Here, we report a whole-genome linkage and association scan in primary, nonsyndromic vesicoureteric reflux and reflux nephropathy. We used linkage and family-based association approaches to analyze 320 white families (661 affected individuals, generally from families with two affected siblings) from two populations (United...

  2. Autosomal genomic scan for loci linked to obesity and energy metabolism in Pima Indians.

    OpenAIRE

    Norman, R A; Tataranni, P A; Pratley, R; Thompson, D B; Hanson, R L; Prochazka, M; Baier, L; Ehm, M G; Sakul, H.; Foroud, T; Garvey, W. T.; Burns, D; Knowler, W. C.; Bennett, P. H.; Bogardus, C

    1998-01-01

    An autosomal genomic scan to search for linkage to obesity and energy metabolism was completed in Pima Indians, a population prone to obesity. Obesity was assessed by percent body fat (by hydrodensitometry) and fat distribution (the ratio of waist circumference to thigh circumference). Energy metabolism was measured in a respiratory chamber as 24-h metabolic rate, sleeping metabolic rate, and 24-h respiratory quotient (24RQ), an indicator of the ratio of carbohydrate oxidation to fat oxidatio...

  3. Enhancing Planning Heuristic with Landmarks

    OpenAIRE

    Jingjing Zhao; Dayou Liu; Yongming Yang

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

  5. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits.

    Science.gov (United States)

    Imumorin, Ikhide G; Kim, Eun-Hee; Lee, Yun-Mi; De Koning, Dirk-Jan; van Arendonk, Johan A; De Donato, Marcos; Taylor, Jeremy F; Kim, Jong-Joo

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus?×?Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0-9?cM; genomic region of 5.0-10.8?Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4???5.1% of each trait's phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits. PMID:22303340

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

    OpenAIRE

    Jaquiéry, Julie; Stoeckel, Solenn; Nouhaud, Pierre; Mieuzet, Lucie; Mahéo, Frédérique; Legeai, Fabrice; Bernard, N; Bonvoisin, Antoine; Vitalis, Renaud; Simon, Jean-Christophe

    2012-01-01

    A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome-wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a spe...

  7. Independent genome-wide scans identify a chromosome 18 quantitative-trait locus influencing dyslexia.

    Science.gov (United States)

    Fisher, Simon E; Francks, Clyde; Marlow, Angela J; MacPhie, I Laurence; Newbury, Dianne F; Cardon, Lon R; Ishikawa-Brush, Yumiko; Richardson, Alex J; Talcott, Joel B; Gayán, Javier; Olson, Richard K; Pennington, Bruce F; Smith, Shelley D; DeFries, John C; Stein, John F; Monaco, Anthony P

    2002-01-01

    Developmental dyslexia is defined as a specific and significant impairment in reading ability that cannot be explained by deficits in intelligence, learning opportunity, motivation or sensory acuity. It is one of the most frequently diagnosed disorders in childhood, representing a major educational and social problem. It is well established that dyslexia is a significantly heritable trait with a neurobiological basis. The etiological mechanisms remain elusive, however, despite being the focus of intensive multidisciplinary research. All attempts to map quantitative-trait loci (QTLs) influencing dyslexia susceptibility have targeted specific chromosomal regions, so that inferences regarding genetic etiology have been made on the basis of very limited information. Here we present the first two complete QTL-based genome-wide scans for this trait, in large samples of families from the United Kingdom and United States. Using single-point analysis, linkage to marker D18S53 was independently identified as being one of the most significant results of the genome in each scan (Pprocessing also showed linkage at this locus. We replicated linkage to 18p11.2 in a third independent sample of families (from the UK), in which the strongest evidence came from a phoneme-awareness measure (most significant P value=0.00004). A combined analysis of all UK families confirmed that this newly discovered 18p QTL is probably a general risk factor for dyslexia, influencing several reading-related processes. This is the first report of QTL-based genome-wide scanning for a human cognitive trait. PMID:11743577

  8. Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.

    Science.gov (United States)

    Gautier, Mathieu

    2015-12-01

    In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier.inra.fr/CBGP/software/baypass/. PMID:26482796

  9. Genome Scan Meta-Analysis of Schizophrenia and Bipolar Disorder, Part III: Bipolar Disorder

    Science.gov (United States)

    Segurado, Ricardo; Detera-Wadleigh, Sevilla D.; Levinson, Douglas F.; Lewis, Cathryn M.; Gill, Michael; Nurnberger, Jr., John I.; Craddock, Nick; DePaulo, J. Raymond; Baron, Miron; Gershon, Elliot S.; Ekholm, Jenny; Cichon, Sven; Turecki, Gustavo; Claes, Stephan; Kelsoe, John R.; Schofield, Peter R.; Badenhop, Renee F.; Morissette, J.; Coon, Hilary; Blackwood, Douglas; McInnes, L. Alison; Foroud, Tatiana; Edenberg, Howard J.; Reich, Theodore; Rice, John P.; Goate, Alison; McInnis, Melvin G.; McMahon, Francis J.; Badner, Judith A.; Goldin, Lynn R.; Bennett, Phil; Willour, Virginia L.; Zandi, Peter P.; Liu, Jianjun; Gilliam, Conrad; Juo, Suh-Hang; Berrettini, Wade H.; Yoshikawa, Takeo; Peltonen, Leena; Lönnqvist, Jouko; Nöthen, Markus M.; Schumacher, Johannes; Windemuth, Christine; Rietschel, Marcella; Propping, Peter; Maier, Wolfgang; Alda, Martin; Grof, Paul; Rouleau, Guy A.; Del-Favero, Jurgen; Van Broeckhoven, Christine; Mendlewicz, Julien; Adolfsson, Rolf; Spence, M. Anne; Luebbert, Hermann; Adams, Linda J.; Donald, Jennifer A.; Mitchell, Philip B.; Barden, Nicholas; Shink, Eric; Byerley, William; Muir, Walter; Visscher, Peter M.; Macgregor, Stuart; Gurling, Hugh; Kalsi, Gursharan; McQuillin, Andrew; Escamilla, Michael A.; Reus, Victor I.; Leon, Pedro; Freimer, Nelson B.; Ewald, Henrik; Kruse, Torben A.; Mors, Ole; Radhakrishna, Uppala; Blouin, Jean-Louis; Antonarakis, Stylianos E.; Akarsu, Nurten

    2003-01-01

    Genome scans of bipolar disorder (BPD) have not produced consistent evidence for linkage. The rank-based genome scan meta-analysis (GSMA) method was applied to 18 BPD genome scan data sets in an effort to identify regions with significant support for linkage in the combined data. The two primary analyses considered available linkage data for “very narrow” (i.e., BP-I and schizoaffective disorder–BP) and “narrow” (i.e., adding BP-II disorder) disease models, with the ranks weighted for sample size. A “broad” model (i.e., adding recurrent major depression) and unweighted analyses were also performed. No region achieved genomewide statistical significance by several simulation-based criteria. The most significant P values (<.01) were observed on chromosomes 9p22.3-21.1 (very narrow), 10q11.21-22.1 (very narrow), and 14q24.1-32.12 (narrow). Nominally significant P values were observed in adjacent bins on chromosomes 9p and 18p-q, across all three disease models on chromosomes 14q and 18p-q, and across two models on chromosome 8q. Relatively few BPD pedigrees have been studied under narrow disease models relative to the schizophrenia GSMA data set, which produced more significant results. There was no overlap of the highest-ranked regions for the two disorders. The present results for the very narrow model are promising but suggest that more and larger data sets are needed. Alternatively, linkage might be detected in certain populations or subsets of pedigrees. The narrow and broad data sets had considerable power, according to simulation studies, but did not produce more highly significant evidence for linkage. We note that meta-analysis can sometimes provide support for linkage but cannot disprove linkage in any candidate region. PMID:12802785

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

    Science.gov (United States)

    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

    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

  11. Whole-genome scan identifies quantitative trait loci for chronic pastern dermatitis in German draft horses.

    Science.gov (United States)

    Mittmann, E Henrike; Mömke, Stefanie; Distl, Ottmar

    2010-02-01

    Chronic pastern dermatitis (CPD), also known as chronic progressive lymphedema (CPL), is a skin disease that affects draft horses. This disease causes painful lower-leg swelling, nodule formation, and skin ulceration, interfering with movement. The aim of this whole-genome scan was to identify quantitative trait loci (QTL) for CPD in German draft horses. We recorded clinical data for CPD in 917 German draft horses and collected blood samples from these horses. Of these 917 horses, 31 paternal half-sib families comprising 378 horses from the breeds Rhenish German, Schleswig, Saxon-Thuringian, and South German were chosen for genotyping. Each half-sib family was constituted by only one draft horse breed. Genotyping was done for 318 polymorphic microsatellites evenly distributed on all equine autosomes and the X chromosome with a mean distance of 7.5 Mb. An across-breed multipoint linkage analysis revealed chromosome-wide significant QTL on horse chromosomes (ECA) 1, 9, 16, and 17. Analyses by breed confirmed the QTL on ECA1 in South German and the QTL on ECA9, 16, and 17 in Saxon-Thuringian draft horses. For the Rhenish German and Schleswig draft horses, additional QTL on ECA4 and 10 and for the South German draft horses an additional QTL on ECA7 were found. This is the first whole-genome scan for CPD in draft horses and it is an important step toward the identification of candidate genes. PMID:20039044

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

    Directory of Open Access Journals (Sweden)

    Gut Ivo

    2009-11-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Regan Kelly R

    2010-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Guimarães Simone EF

    2010-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Gasser Thomas

    2007-07-01

    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.

  16. Identifying genomic regions for fine-mapping using genome scan meta-analysis (GSMA) to identify the minimum regions of maximum significance (MRMS) across populations

    OpenAIRE

    Maher Brion S; Goldstein Toby H; Cooper Margaret E; Marazita Mary L

    2005-01-01

    Abstract In order to detect linkage of the simulated complex disease Kofendrerd Personality Disorder across studies from multiple populations, we performed a genome scan meta-analysis (GSMA). Using the 7-cM microsatellite map, nonparametric multipoint linkage analyses were performed separately on each of the four simulated populations independently to determine p-values. The genome of each population was divided into 20-cM bin regions, and each bin was rank-ordered based on the most significa...

  17. Landmarks GIScience for intelligent services

    CERN Document Server

    Richter, Kai-Florian

    2014-01-01

    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

  18. Reconciling Landmarks and Level Sets

    OpenAIRE

    Maurel, Pierre; Keriven, Renaud; Faugeras, Olivier

    2006-01-01

    Shape warping is a key problem in statistical shape analysis. This paper proposes a framework for geometric shape warping based on both shape distances and landmarks. Our method is compatible with implicit representations and a matching between shape surfaces is provided at no additional cost. It is, to our knowledge, the rst time that landmarks and shape distances are reconciled in a pure geometric level set framework. The feasibility of the method is demonstrated with two- and three-dimensi...

  19. TESS3: fast inference of spatial population structure and genome scans for selection.

    Science.gov (United States)

    Caye, Kevin; Deist, Timo M; Martins, Helena; Michel, Olivier; François, Olivier

    2016-03-01

    Geography and landscape are important determinants of genetic variation in natural populations, and several ancestry estimation methods have been proposed to investigate population structure using genetic and geographic data simultaneously. Those approaches are often based on computer-intensive stochastic simulations and do not scale with the dimensions of the data sets generated by high-throughput sequencing technologies. There is a growing demand for faster algorithms able to analyse genomewide patterns of population genetic variation in their geographic context. In this study, we present TESS3, a major update of the spatial ancestry estimation program TESS. By combining matrix factorization and spatial statistical methods, TESS3 provides estimates of ancestry coefficients with accuracy comparable to TESS and with run-times much faster than the Bayesian version. In addition, the TESS3 program can be used to perform genome scans for selection, and separate adaptive from nonadaptive genetic variation using ancestral allele frequency differentiation tests. The main features of TESS3 are illustrated using simulated data and analysing genomic data from European lines of the plant species Arabidopsis thaliana. PMID:26417651

  20. Whole genome scan to detect quantitative trait loci for bovine milk protein composition.

    Science.gov (United States)

    Schopen, G C B; Koks, P D; van Arendonk, J A M; Bovenhuis, H; Visker, M H P W

    2009-08-01

    The objective of this study was to perform a whole genome scan to detect quantitative trait loci (QTL) for milk protein composition in 849 Holstein-Friesian cows originating from seven sires. One morning milk sample was analysed for the major milk proteins using capillary zone electrophoresis. A genetic map was constructed with 1341 single nucleotide polymorphisms, covering 2829 centimorgans (cM) and 95% of the cattle genome. The chromosomal regions most significantly related to milk protein composition (P(genome) casein, alpha(S2)-casein, beta-casein and kappa-casein. The QTL on BTA11 was found at 124 cM, and affected beta-lactoglobulin, and the QTL on BTA14 was found at 0 cM, and affected protein percentage. The proportion of phenotypic variance explained by the QTL was 3.6% for beta-casein and 7.9% for kappa-casein on BTA6, 28.3% for beta-lactoglobulin on BTA11, and 8.6% for protein percentage on BTA14. The QTL affecting alpha(S2)-casein on BTA6 and 17 showed a significant interaction. We investigated the extent to which the detected QTL affecting milk protein composition could be explained by known polymorphisms in beta-casein, kappa-casein, beta-lactoglobulin and DGAT1 genes. Correction for these polymorphisms decreased the proportion of phenotypic variance explained by the QTL previously found on BTA6, 11 and 14. Thus, several significant QTL affecting milk protein composition were found, of which some QTL could partially be explained by polymorphisms in milk protein genes. PMID:19397519

  1. Collaborative regression-based anatomical landmark detection

    Science.gov (United States)

    Gao, Yaozong; Shen, Dinggang

    2015-12-01

    Anatomical landmark detection plays an important role in medical image analysis, e.g. for registration, segmentation and quantitative analysis. Among the various existing methods for landmark detection, regression-based methods have recently attracted much attention due to their robustness and efficiency. In these methods, landmarks are localised through voting from all image voxels, which is completely different from the classification-based methods that use voxel-wise classification to detect landmarks. Despite their robustness, the accuracy of regression-based landmark detection methods is often limited due to (1) the inclusion of uninformative image voxels in the voting procedure, and (2) the lack of effective ways to incorporate inter-landmark spatial dependency into the detection step. In this paper, we propose a collaborative landmark detection framework to address these limitations. The concept of collaboration is reflected in two aspects. (1) Multi-resolution collaboration. A multi-resolution strategy is proposed to hierarchically localise landmarks by gradually excluding uninformative votes from faraway voxels. Moreover, for informative voxels near the landmark, a spherical sampling strategy is also designed at the training stage to improve their prediction accuracy. (2) Inter-landmark collaboration. A confidence-based landmark detection strategy is proposed to improve the detection accuracy of ‘difficult-to-detect’ landmarks by using spatial guidance from ‘easy-to-detect’ landmarks. To evaluate our method, we conducted experiments extensively on three datasets for detecting prostate landmarks and head & neck landmarks in computed tomography images, and also dental landmarks in cone beam computed tomography images. The results show the effectiveness of our collaborative landmark detection framework in improving landmark detection accuracy, compared to other state-of-the-art methods.

  2. Genome-wide association scan for five major dimensions of personality

    Science.gov (United States)

    Terracciano, Antonio; Sanna, Serena; Uda, Manuela; Deiana, Barbara; Usala, Gianluca; Busonero, Fabio; Maschio, Andrea; Scally, Matthew; Patriciu, Nicholas; Chen, Wei-Min; Distel, Marijn A; Slagboom, Eline P; Boomsma, Dorret I; Villafuerte, Sandra; ?liwerska, El?bieta; Burmeister, Margit; Amin, Najaf; Janssens, A. Cecile J.W.; van Duijn, Cornelia M.; Schlessinger, David; Abecasis, Gonçalo R.; Costa, Paul T.

    2008-01-01

    Personality traits are summarized by five broad dimensions with pervasive influences on major life outcomes, strong links to psychiatric disorders, and clear heritable components. To identify genetic variants associated with each of the five dimensions of personality we performed a genome wide association (GWA) scan of 3,972 individuals from a genetically isolated population within Sardinia, Italy. Based on analyses of 362,129 single nucleotide polymorphisms (SNPs) we found several strong signals within or near genes previously implicated in psychiatric disorders. They include the association of Neuroticism with SNAP25 (rs362584, P = 5 × 10?5), Extraversion with BDNF and two cadherin genes (CDH13 and CDH23; Ps < 5 × 10?5), Openness with CNTNAP2 (rs10251794, P = 3 × 10?5), Agreeableness with CLOCK (rs6832769, P = 9 × 10?6), and Conscientiousness with DYRK1A (rs2835731, P = 3 × 10?5). Effect sizes were small (less than 1% of variance), and most failed to replicate in the follow-up independent samples (N up to 3,903), though the association between Agreeableness and CLOCK was supported in two of three replication samples (overall P = 2 × 10?5). We infer that a large number of loci may influence personality traits and disorders, requiring larger sample sizes for the GWA approach to identify significant genetic variants. PMID:18957941

  3. A quantitative trait locus genome scan for porcine muscle fiber traits reveals overdominance and epistasis.

    Science.gov (United States)

    Estellé, J; Gil, F; Vázquez, J M; Latorre, R; Ramírez, G; Barragán, M C; Folch, J M; Noguera, J L; Toro, M A; Pérez-Enciso, M

    2008-12-01

    Muscle histochemical characteristics are decisive determinants of meat quality. The relative percentage and diameters of the different muscular fiber types influence crucial aspects of meat such as color, tenderness, and ultimate pH. Despite its relevance, however, the information on muscle fiber genetic architecture is scant, because histochemical muscle characterization is a laborious task. Here we report a complete QTL scan of muscle fiber traits in 160 animals from a F(2) cross between Iberian and Landrace pigs using 139 markers. We identified 20 genome regions distributed along 15 porcine chromosomes (SSC1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, and X) with direct and(or) epistatic effects. Epistasis was frequent and some interactions were highly significant. Chromosomes 10 and 11 seemed to behave as hubs; they harbored 2 individual QTL, but also 6 epistatic regions. Numerous individual QTL effects had cryptic alleles, with opposite effects to phenotypic pure breed differences. Many of the QTL identified here coincided with previous reports for these traits in the literature, and there was overlapping with potential candidate genes and previously reported meat quality QTL. PMID:18641172

  4. An autosomal genomic scan for loci linked to type 2 diabetes in northern Han Chinese.

    Science.gov (United States)

    Zhao, J Y; Xiong, M M; Huang, W; Wang, H; Zuo, J; Wu, G D; Chen, Z; Qiang, B Q; Zhang, M L; Chen, J L; Ding, W; Yuan, W T; Xu, H Y; Jin, L; Li, Y X; Sun, Q; Liu, Q Y; Boerwinkle, E; Fang, F D

    2005-03-01

    We report the results of a genome-wide scan conducted in 219 individuals from 34 large multiplex nuclear pedigrees from the northern Han Chinese population at an average resolution of about 10 cM. Nonparametric two-point and multipoint linkage analyses were performed to detect evidence of linkage with type 2 diabetes in this study. On chromosome 1 four regions showed evidence of linkage with type 2 diabetes in northern Han Chinese. Of these regions a marker D1S193 (73 cM) showed evidence of linkage (two-point nonparametric linkage 2.409), and another region (around 190 cM) was a replication of several other studies performed in different ethnic populations. Evidences of linkage have been confirmed by typing additional markers (average distance 1-5 cM) flanking these two positive regions on chromosome 1. We also found indication of linkage with type 2 diabetes on chromosomes 2, 10, 12, 18, 20, and 22 by two-point linkage analyses. PMID:15776287

  5. Whole-genome linkage and association scan in primary, nonsyndromic vesicoureteric reflux.

    Science.gov (United States)

    Cordell, Heather J; Darlay, Rebecca; Charoen, Pimphen; Stewart, Aisling; Gullett, Ambrose M; Lambert, Heather J; Malcolm, Sue; Feather, Sally A; Goodship, Timothy H J; Woolf, Adrian S; Kenda, Rajko B; Goodship, Judith A

    2010-01-01

    Primary vesicoureteric reflux accounts for approximately 10% of kidney failure requiring dialysis or transplantation, and sibling studies suggest a large genetic component. Here, we report a whole-genome linkage and association scan in primary, nonsyndromic vesicoureteric reflux and reflux nephropathy. We used linkage and family-based association approaches to analyze 320 white families (661 affected individuals, generally from families with two affected siblings) from two populations (United Kingdom and Slovenian). We found modest evidence of linkage but no clear overlap with previous studies. We tested for but did not detect association with six candidate genes (AGTR2, HNF1B, PAX2, RET, ROBO2, and UPK3A). Family-based analysis detected associations with one single-nucleotide polymorphism (SNP) in the UK families, with three SNPs in the Slovenian families, and with three SNPs in the combined families. A case-control analysis detected associations with three additional SNPs. The results of this study, which is the largest to date investigating the genetics of reflux, suggest that major loci may not exist for this common renal tract malformation within European populations. PMID:19959718

  6. Landmark Discrimination Learning in the Dog

    OpenAIRE

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

    1999-01-01

    Allocentric spatial memory was studied in dogs of varying ages and sources using a landmark discrimination task. The primary goal of this study was to develop a protocol to test landmark discrimination learning in the dog. Using a modified version of a landmark test developed for use in monkeys, we successfully trained dogs to make a spatial discrimination on the basis of the position of a visual landmark relative to two identical discriminanda. Task performance decreased, however, as the dis...

  7. 75 FR 69120 - National Natural Landmark Designations

    Science.gov (United States)

    2010-11-10

    ... National Natural Landmark Designations AGENCY: National Park Service, Department of the Interior. ACTION: Public Notice of National Natural Landmark Designations. SUMMARY: On January 16, 2009, then Secretary of the Interior Dirk Kempthorne designated the following National Natural Landmarks: Big Bone Lick,...

  8. Acquistion of Structural versus Object Landmark Knowledge

    Science.gov (United States)

    Stankiewicz, Brian J.; Kalia, Amy A.

    2007-01-01

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

  9. 23 CFR 750.710 - Landmark signs.

    Science.gov (United States)

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Landmark signs. 750.710 Section 750.710 Highways FEDERAL... Outdoor Advertising Control § 750.710 Landmark signs. (a) 23 U.S.C. 131(c) permits the existence of signs... Secretary, to be landmark signs, including signs on farm structures or natural surfaces, of historic...

  10. 36 CFR 62.6 - Natural landmark monitoring.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Natural landmark monitoring... INTERIOR NATIONAL NATURAL LANDMARKS PROGRAM § 62.6 Natural landmark monitoring. (a) Owner contact. The... landmarks to determine whether the landmarks retain the values that qualified them for landmark...

  11. 3D facial landmarks: Inter-operator variability of manual annotation

    DEFF Research Database (Denmark)

    Fagertun, Jens; Harder, Stine

    2014-01-01

    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.

  12. 3D facial landmarks : Inter-operator variability of manual annotation

    DEFF Research Database (Denmark)

    Fagertun, Jens; Harder, Stine

    2014-01-01

    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.

  13. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features

    Science.gov (United States)

    Adhikari, Kaustubh; Fontanil, Tania; Cal, Santiago; Mendoza-Revilla, Javier; Fuentes-Guajardo, Macarena; Chacón-Duque, Juan-Camilo; Al-Saadi, Farah; Johansson, Jeanette A.; Quinto-Sanchez, Mirsha; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Barquera Lozano, Rodrigo; Macín Pérez, Gastón; Gómez-Valdés, Jorge; Villamil-Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C.; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Gonzalez-José, Rolando; Headon, Denis; López-Otín, Carlos; Tobin, Desmond J.; Balding, David; Ruiz-Linares, Andrés

    2016-01-01

    We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10−8 to 3 × 10−119), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair. PMID:26926045

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

    Directory of Open Access Journals (Sweden)

    Scherer Stephen W

    2011-05-01

    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.

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

    Science.gov (United States)

    Lotterhos, Katie E; Whitlock, Michael C

    2015-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Rosalia Leonardi

    2009-01-01

    Full Text Available Several efforts have been made to completely automate cephalometric analysis by automatic landmark search. However, accuracy obtained was worse than manual identification in every study. The analogue-to-digital conversion of X-ray has been claimed to be the main problem. Therefore the aim of this investigation was to evaluate the accuracy of the Cellular Neural Networks approach for automatic location of cephalometric landmarks on softcopy of direct digital cephalometric X-rays. Forty-one, direct-digital lateral cephalometric radiographs were obtained by a Siemens Orthophos DS Ceph and were used in this study and 10 landmarks (N, A Point, Ba, Po, Pt, B Point, Pg, PM, UIE, LIE were the object of automatic landmark identification. The mean errors and standard deviations from the best estimate of cephalometric points were calculated for each landmark. Differences in the mean errors of automatic and manual landmarking were compared with a 1-way analysis of variance. The analyses indicated that the differences were very small, and they were found at most within 0.59?mm. Furthermore, only few of these differences were statistically significant, but differences were so small to be in most instances clinically meaningless. Therefore the use of X-ray files with respect to scanned X-ray improved landmark accuracy of automatic detection. Investigations on softcopy of digital cephalometric X-rays, to search more landmarks in order to enable a complete automatic cephalometric analysis, are strongly encouraged.

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Bidanel Jean P

    2009-12-01

    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.

  20. An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error

    DEFF Research Database (Denmark)

    Abbott, Diana; Li, Yi-Ju

    2012-01-01

    To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites.

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

    Science.gov (United States)

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

    2011-01-01

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

  2. A genome-wide linkage and association scan reveals novel loci for autism

    OpenAIRE

    Weiss, LA; Arking, DE; Daly, MJ; Chakravarti, A.

    2009-01-01

    Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success. Genome-wide association studies using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits. Consequently, we initiated a linkage and association mapping study using half a million genome-wide single nucleo...

  3. A GENOME-WIDE LINKAGE AND ASSOCIATION SCAN REVEALS NOVEL LOCI FOR AUTISM

    OpenAIRE

    Weiss, Lauren A.; Arking, Dan E

    2009-01-01

    Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success 1. Genome-wide association studies (GWAS) using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits (http://www.genome.gov/26525384). Consequently, we initiated a linkage and association mapping study usin...

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

    OpenAIRE

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

    2009-01-01

    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 ...

  5. Retrosplenial cortex codes for permanent landmarks.

    OpenAIRE

    Auger, S. D.; Mullally, S. L.; Maguire, E. A.

    2012-01-01

    Landmarks are critical components of our internal representation of the environment, yet their specific properties are rarely studied, and little is known about how they are processed in the brain. Here we characterised a large set of landmarks along a range of features that included size, visual salience, navigational utility, and permanence. When human participants viewed images of these single landmarks during functional magnetic resonance imaging (fMRI), parahippocampal cortex (PHC) and r...

  6. Neurocognitive development of memory for landmarks

    OpenAIRE

    van Ekert, Janneke; Wegman, Joost; Janzen, Gabriele

    2015-01-01

    The capacity to detect landmarks in the environment and to associate each landmark with its spatial context is a fundamental operation for navigation, especially when the context is relevant for successful navigation. Recent evidence suggests robust age-related improvements in contextual memory. The current study investigated the effect of spatial context on landmark recognition memory in children and adolescents. Participants, ages 8–18, watched a video depicting a route through a virtual en...

  7. Anatomic Landmarks for the First Dorsal Compartment

    OpenAIRE

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

    2009-01-01

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

  8. Desert Ants Learn Vibration and Magnetic Landmarks

    OpenAIRE

    Buehlmann, Cornelia; Hansson, Bill S.; Knaden, Markus

    2012-01-01

    The desert ants Cataglyphis navigate not only by path integration but also by using visual and olfactory landmarks to pinpoint the nest entrance. Here we show that Cataglyphis noda can additionally use magnetic and vibrational landmarks as nest-defining cues. The magnetic field may typically provide directional rather than positional information, and vibrational signals so far have been shown to be involved in social behavior. Thus it remains questionable if magnetic and vibration landmarks a...

  9. Autonomous Robot Navigation based on Visual Landmarks

    DEFF Research Database (Denmark)

    Livatino, Salvatore

    2005-01-01

    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...... 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...... system can automatically learn and store visual landmarks, and later recognize these landmarks from arbitrary positions and thus estimate robot position and heading....

  10. A genome-wide scan of selective sweeps and association mapping of fruit traits using microsatellite markers in watermelon.

    Science.gov (United States)

    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

    2015-01-01

    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

  11. An autosomal genomic scan for loci linked to type II diabetes mellitus and body-mass index in Pima Indians.

    OpenAIRE

    Hanson, R L; Ehm, M G; Pettitt, D J; Prochazka, M; Thompson, D B; Timberlake, D.; Foroud, T; Kobes, S; Baier, L; Burns, D K; Almasy, L; Blangero, J.; Garvey, W. T.; Bennett, P. H.; Knowler, W. C.

    1998-01-01

    Genetic factors influence the development of type II diabetes mellitus, but genetic loci for the most common forms of diabetes have not been identified. A genomic scan was conducted to identify loci linked to diabetes and body-mass index (BMI) in Pima Indians, a Native American population with a high prevalence of type II diabetes. Among 264 nuclear families containing 966 siblings, 516 autosomal markers with a median distance between adjacent markers of 6.4 cM were genotyped. Variance-compon...

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

    International Nuclear Information System (INIS)

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

  13. 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 on the skull. (N.K.)

  14. A genome-wide scan for breast cancer risk haplotypes among African American women.

    Science.gov (United States)

    Song, Chi; Chen, Gary K; Millikan, Robert C; Ambrosone, Christine B; John, Esther M; Bernstein, Leslie; Zheng, Wei; Hu, Jennifer J; Ziegler, Regina G; Nyante, Sarah; Bandera, Elisa V; Ingles, Sue A; Press, Michael F; Deming, Sandra L; Rodriguez-Gil, Jorge L; Chanock, Stephen J; Wan, Peggy; Sheng, Xin; Pooler, Loreall C; Van Den Berg, David J; Le Marchand, Loic; Kolonel, Laurence N; Henderson, Brian E; Haiman, Chris A; Stram, Daniel O

    2013-01-01

    Genome-wide association studies (GWAS) simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP) have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyzed the haplotype effects for breast cancer risk among 5,761 African American women (3,016 cases and 2,745 controls) using a sliding window approach on the genome-wide scale. Three regions on chromosomes 1, 4 and 18 exhibited moderate haplotype effects. Furthermore, among 21 breast cancer susceptibility loci previously established in European populations, 10p15 and 14q24 are likely to harbor novel haplotype effects. We also proposed a heuristic of determining the significance level and the effective number of independent tests by the permutation analysis on chromosome 22 data. It suggests that the effective number was approximately half of the total (7,794 out of 15,645), thus the half number could serve as a quick reference to evaluating genome-wide significance if a similar sliding window approach of haplotype analysis is adopted in similar populations using similar genotype density. PMID:23468962

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

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa; Jensen, Anja Tatiana Ramstedt; 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

    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...

  16. 3D facial landmarks: Inter-operator variability of manual annotation

    DEFF Research Database (Denmark)

    Fagertun, Jens; Harder, Stine; Rosengren, Anders; Møller, Christian; Werge, Thomas; Paulsen, Rasmus Reinhold; Hansen, Thomas Fritz

    2014-01-01

    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......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...

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

    Directory of Open Access Journals (Sweden)

    Prasad Aparna

    2010-03-01

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

  18. Autonomous Robot Navigation based on Visual Landmarks

    DEFF Research Database (Denmark)

    Livatino, Salvatore

    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.

  19. Multiple type 2 diabetes susceptibility genes following genome-wide association scan in UK samples

    OpenAIRE

    Zeggini, Eleftheria; Weedon, Michael N.; Lindgren, Cecilia M.; Frayling, Timothy M; Elliott, Katherine S.; Lango, Hana; Timpson, Nicholas J; Perry, John R B; Rayner, Nigel W.; Freathy, Rachel M.; Barrett, Jeffrey C.; Shields, Beverley; Morris, Andrew P; Ellard, Sian; Groves, Christopher J

    2007-01-01

    The molecular mechanisms involved in the development of type 2 diabetes are poorly understood. Starting from genome-wide genotype data for 1,924 diabetic cases and 2,938 population controls generated by the Wellcome Trust Case Control Consortium, we set out to detect replicated diabetes association signals through analysis of 3,757 additional cases and 5,346 controls, and by integration of our findings with equivalent data from other international consortia. We detected diabetes susceptibilit...

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

    OpenAIRE

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

    2000-01-01

    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...

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

    OpenAIRE

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

    2005-01-01

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

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

    DEFF Research Database (Denmark)

    Kolte, Astrid Marie; Nielsen, H S; Moltke, Ida; Degn, B; Pedersen, Bjørn; Sunde, Lone E. M.; Nielsen, F C; Christiansen, O B

    2011-01-01

    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 ...

  3. Combined genome scans for body stature in 6,602 European twins

    DEFF Research Database (Denmark)

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

    2007-01-01

    Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin (http://www.genomeutwin.org) consortium consists of eight twin cohorts (Australian, Danish, Dutch, Finnish, Italian, Norwegian, Swedish, and United Kingdom) with the total resource of hundreds of thousands of twin pairs. We performed quantitative trait locu...

  4. Genome-scan for IQ discrepancy in autism: evidence for loci on chromosomes 10 and 16

    OpenAIRE

    Chapman, Nicola H; Estes, Annette; Munson, Jeff; Bernier, Raphael; Webb, Sara J.; Rothstein, Joseph H; MINSHEW, NANCY J.; Dawson, Geraldine; Schellenberg, Gerard D.; Wijsman, Ellen M

    2010-01-01

    Performance IQ (PIQ) greater than verbal IQ (VIQ) is often observed in studies of the cognitive abilities of autistic individuals. This characteristic is correlated with social and communication impairments, key parts of the autism diagnosis. We present the first genetic analyses of IQ discrepancy (PIQ–VIQ) as an autism-related phenotype. We performed genome-wide joint linkage and segregation analyses on 287 multiplex families, using a Markov chain Monte Carlo approach. Genetic data included ...

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

    DEFF Research Database (Denmark)

    Sylvester-Hvid, C.; Nielsen, Morten; Lamberth, K.; Roder, G.; Lundegaard, Claus; Worning, Peder; Thomadsen, H.; Lund, Ole; Brunak, Søren; Buus, S.

    2004-01-01

    An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly, from genomic/proteomic sequence information (Lauemoller et al., R...

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information (Lauemoller et al., Re...

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

    OpenAIRE

    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

    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...

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

    OpenAIRE

    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

    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...

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

    DEFF Research Database (Denmark)

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

    2005-01-01

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

  10. NotI genome scanning to identify unknown cancer associated genes in major human epithelial malignancies

    OpenAIRE

    Haraldson, Klas

    2010-01-01

    Epithelial cancers cause many deaths every year. Changes in the genes of human chromosome 3 are particularly common in epithelial cancers in several organs. Alterations in DNA methylation is one of the best known epigenetic changes in cancer. The abnormal epigenetic landscape of the cancer cell is characterized by a massive genomic hypomethylation and hypermethylation of CpG islands in the promoter regions of tumor suppressor genes. Microarrays is a powerful tool for stu...

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    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 ski...

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

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa; Jensen, Anja Tatiana Ramstedt; 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

    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 multiplici...

  13. A genome-wide scan for tying-up syndrome in Japanese Thoroughbreds.

    Science.gov (United States)

    Tozaki, T; Hirota, K; Sugita, S; Ishida, N; Miyake, T; Oki, H; Hasegawa, T

    2010-12-01

    Tying-up syndrome, also known as recurrent exertional rhabdomyolysis in Thoroughbreds, is a common muscle disorder for racehorses. In this study, we performed a multipoint linkage analysis using LOKI based on the Bayesian Markov chain Monte Carlo method using 5 half-sib families (51 affected and 277 nonaffected horses in total), and a genome-wide association study (GWAS) using microsatellites (144 affected and 144 nonaffected horses) to map candidate regions for tying-up syndrome in Japanese Thoroughbreds. The linkage analysis identified one strong L-score (82.45) between the loci UCDEQ411 and COR058 (24.9-27.9 Mb) on ECA12. The GWAS identified two suggestive genomic regions on ECA12 (24.9-27.8 Mb) and ECA20 (29.3-33.5 Mb). Based on both results, the genomic region between UCDEQ411 and TKY499 (24.9-27.8 Mb) on ECA12 was the most significant and was considered as a candidate region for tying-up syndrome in Japanese Thoroughbreds. PMID:21070280

  14. LARGE AREA LANDMARKS - DYNAMAP V.12.2

    Science.gov (United States)

    GDT Large Area Landmarks represents common landmark areas within United States including military areas, prisons, educational institutions, amusement centers, government centers, sport centers, golf courses, and cemeteries.

  15. Identifying genomic regions for fine-mapping using genome scan meta-analysis (GSMA) to identify the minimum regions of maximum significance (MRMS) across populations.

    Science.gov (United States)

    Cooper, Margaret E; Goldstein, Toby H; Maher, Brion S; Marazita, Mary L

    2005-01-01

    In order to detect linkage of the simulated complex disease Kofendrerd Personality Disorder across studies from multiple populations, we performed a genome scan meta-analysis (GSMA). Using the 7-cM microsatellite map, nonparametric multipoint linkage analyses were performed separately on each of the four simulated populations independently to determine p-values. The genome of each population was divided into 20-cM bin regions, and each bin was rank-ordered based on the most significant linkage p-value for that population in that region. The bin ranks were then averaged across all four studies to determine the most significant 20-cM regions over all studies. Statistical significance of the averaged bin ranks was determined from a normal distribution of randomly assigned rank averages. To narrow the region of interest for fine-mapping, the meta-analysis was repeated two additional times, with each of the 20-cM bins offset by 7 cM and 13 cM, respectively, creating regions of overlap with the original method. The 6-7 cM shared regions, where the highest averaged 20-cM bins from each of the three offsets overlap, designated the minimum region of maximum significance (MRMS). Application of the GSMA-MRMS method revealed genome wide significance (p-values refer to the average rank assigned to the bin) at regions including or adjacent to all of the simulated disease loci: chromosome 1 (p value value value < 0.05 for 7-14 cM, the region adjacent to D4). This GSMA analysis approach demonstrates the power of linkage meta-analysis to detect multiple genes simultaneously for a complex disorder. The MRMS method enhances this powerful tool to focus on more localized regions of linkage. PMID:16451653

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

    LENUS (Irish Health Repository)

    Anney, Richard

    2010-10-15

    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.

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

    Science.gov (United States)

    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

    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

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

    Directory of Open Access Journals (Sweden)

    Wang Xiaojing

    2012-12-01

    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.

  19. A Genome-Wide Scan of Ashkenazi Jewish Crohn's Disease Suggests Novel Susceptibility Loci

    Science.gov (United States)

    Kenny, Eimear E.; Pe'er, Itsik; Karban, Amir; Ozelius, Laurie; Mitchell, Adele A.; Ng, Sok Meng; Erazo, Monica; Ostrer, Harry; Abraham, Clara; Abreu, Maria T.; Atzmon, Gil; Barzilai, Nir; Brant, Steven R.; Bressman, Susan; Burns, Edward R.; Chowers, Yehuda; Clark, Lorraine N.; Darvasi, Ariel; Doheny, Dana; Duerr, Richard H.; Eliakim, Rami; Giladi, Nir; Gregersen, Peter K.; Hakonarson, Hakon; Jones, Michelle R.; Marder, Karen; McGovern, Dermot P. B.; Mulle, Jennifer; Orr-Urtreger, Avi; Proctor, Deborah D.; Pulver, Ann; Rotter, Jerome I.; Silverberg, Mark S.; Ullman, Thomas; Warren, Stephen T.; Waterman, Matti; Zhang, Wei; Bergman, Aviv; Mayer, Lloyd; Katz, Seymour; Desnick, Robert J.; Cho, Judy H.; Peter, Inga

    2012-01-01

    Crohn's disease (CD) is a complex disorder resulting from the interaction of intestinal microbiota with the host immune system in genetically susceptible individuals. The largest meta-analysis of genome-wide association to date identified 71 CD–susceptibility loci in individuals of European ancestry. An important epidemiological feature of CD is that it is 2–4 times more prevalent among individuals of Ashkenazi Jewish (AJ) descent compared to non-Jewish Europeans (NJ). To explore genetic variation associated with CD in AJs, we conducted a genome-wide association study (GWAS) by combining raw genotype data across 10 AJ cohorts consisting of 907 cases and 2,345 controls in the discovery stage, followed up by a replication study in 971 cases and 2,124 controls. We confirmed genome-wide significant associations of 9 known CD loci in AJs and replicated 3 additional loci with strong signal (p<5×10−6). Novel signals detected among AJs were mapped to chromosomes 5q21.1 (rs7705924, combined p = 2×10−8; combined odds ratio OR = 1.48), 2p15 (rs6545946, p = 7×10−9; OR = 1.16), 8q21.11 (rs12677663, p = 2×10−8; OR = 1.15), 10q26.3 (rs10734105, p = 3×10−8; OR = 1.27), and 11q12.1 (rs11229030, p = 8×10−9; OR = 1.15), implicating biologically plausible candidate genes, including RPL7, CPAMD8, PRG2, and PRG3. In all, the 16 replicated and newly discovered loci, in addition to the three coding NOD2 variants, accounted for 11.2% of the total genetic variance for CD risk in the AJ population. This study demonstrates the complementary value of genetic studies in the Ashkenazim. PMID:22412388

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

    DEFF Research Database (Denmark)

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

    2005-01-01

    Since the divergence of humans and chimpanzees about 5 million years ago, these species have undergone a remarkable evolution with drastic divergence in anatomy and cognitive abilities. At the molecular level, despite the small overall magnitude of DNA sequence divergence, we might expect such...... evolutionary changes to leave a noticeable signature throughout the genome. We here compare 13,731 annotated genes from humans to their chimpanzee orthologs to identify genes that show evidence of positive selection. Many of the genes that present a signature of positive selection tend to be involved in...... sensory perception or immune defenses. However, the group of genes that show the strongest evidence for positive selection also includes a surprising number of genes involved in tumor suppression and apoptosis, and of genes involved in spermatogenesis. We hypothesize that positive selection in some of...

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

    DEFF Research Database (Denmark)

    Kolte, Astrid Marie; Nielsen, H S

    2011-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Velculescu Victor E

    2008-04-01

    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.

  3. Genomic alterations in oral squamous cell carcinoma cell lines detected by two-dimensional gel analysis.

    Science.gov (United States)

    Yamamoto, K; Konishi, N; Inui, T; Kitahori, Y; Hiasa, Y; Kirita, T; Sugimura, M

    1998-11-01

    To initially analyze the genomic abnormalities in human oral squamous cell carcinoma, DNA extracted from each of four oral carcinoma cell lines (Ca9-22, HO-1-u-1, HSC-2, KB) was examined using restriction landmark genomic scanning (RLGS), a method especially conducive to detection of amplifications and rearrangements of genomic DNA. Isolated cell line and normal oral epithial DNAs were sequentially cleaved with specific restriction enzymes, radiolabelled and separated in two-dimensional gel electrophoreses. Thirteen distinct fragments were commonly amplified in the oral cancer cell lines, six of which were evident in all samples. These results suggest genetic alterations characteristic of oral squamous cell carcinogenesis. PMID:9930363

  4. 23 CFR 750.710 - Landmark signs.

    Science.gov (United States)

    2010-04-01

    ...RIGHT-OF-WAY AND ENVIRONMENT HIGHWAY BEAUTIFICATION Outdoor Advertising Control § 750.710 Landmark signs. (a) 23...is permitted. Substantial change in size, lighting, or message content will terminate its exempt...

  5. A genome-wide sib-pair scan for quantitative language traits reveals linkage to chromosomes 10 and 13

    Science.gov (United States)

    Evans, P. D.; Mueller, K. L.; Gamazon, E. R.; Cox, N. J.; Tomblin, J. B.

    2016-01-01

    Although there is considerable evidence that individual differences in language development are highly heritable, there have been few genome-wide scans to locate genes associated with the trait. Previous analyses of language impairment have yielded replicable evidence for linkage to regions on chromosomes 16q, 19q, 13q (within lab) and at 13q (between labs). Here we report the first linkage study to screen the continuum of language ability, from normal to disordered, as found in the general population. 383 children from 147 sib-ships (214 sib-pairs) were genotyped on the Illumina® Linkage IVb Marker Panel using three composite language-related phenotypes and a measure of phonological memory (PM). Two regions (10q23.33; 13q33.3) yielded genome-wide significant peaks for linkage with PM. A peak suggestive of linkage was also found at 17q12 for the overall language composite. This study presents two novel genetic loci for the study of language development and disorders, but fails to replicate findings by previous groups. Possible reasons for this are discussed. PMID:25997078

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

    Science.gov (United States)

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

    2009-08-01

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

  7. Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture.

    Science.gov (United States)

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

    2014-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Cordell Heather J

    2007-12-01

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

  9. Landmark perception planning for mobile robot localization

    OpenAIRE

    Armingol, José M.; Moreno, Luis; Escalera, Arturo de la; Salichs, Miguel A.

    1998-01-01

    This paper presents a fuzzy perception planner that takes into account the time cost, the suitability of every landmark detection and the different uncertainties the robot encounters along its path for mobile robot localization. The sensor used is a camera with a motorized zoom on a pan & tilt platform and the artificial landmarks are circles detected through normalized grayscale correlation. An Extended Kalman Filter is used to correct the position and orientation of the vehicle. The resulti...

  10. GENOME MAPPING

    Science.gov (United States)

    Genome maps can be thought of much like road maps except that, instead of traversing across land, they traverse across the chromosomes of an organism. Genetic markers serve as `landmarks¿ along the chromosome and provide researchers information as to how close they may be to a gene or region of int...

  11. 36 CFR 62.8 - Natural landmark designation removal.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Natural landmark designation... INTERIOR NATIONAL NATURAL LANDMARKS PROGRAM § 62.8 Natural landmark designation removal. (a) Criteria for removal. (1) Except as provided in paragraph (f) of this section, national natural landmark designation...

  12. 36 CFR 65.6 - Recognition of National Historic Landmarks.

    Science.gov (United States)

    2010-07-01

    ... Historic Landmarks. 65.6 Section 65.6 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL HISTORIC LANDMARKS PROGRAM § 65.6 Recognition of National Historic Landmarks. (a) Following designation of a property by the Secretary as a National Historic Landmark, the...

  13. 36 CFR 65.4 - National Historic Landmark criteria.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false National Historic Landmark... INTERIOR NATIONAL HISTORIC LANDMARKS PROGRAM § 65.4 National Historic Landmark criteria. The criteria applied to evaluate properties for possible designation as National Historic Landmarks or...

  14. 36 CFR 65.7 - Monitoring National Historic Landmarks.

    Science.gov (United States)

    2010-07-01

    ... Landmarks. 65.7 Section 65.7 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL HISTORIC LANDMARKS PROGRAM § 65.7 Monitoring National Historic Landmarks. (a) NPS maintains a continuing relationship with the owners of National Historic Landmarks. Periodic...

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

    Science.gov (United States)

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

    2009-01-01

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

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

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D

    2014-01-01

    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.

  17. Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D

    2014-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Bumstead Nat

    2005-09-01

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

  19. A genome scan for candidate genes involved in the adaptation of turbot (Scophthalmus maximus).

    Science.gov (United States)

    Vilas, Román; Vandamme, Sara G; Vera, Manuel; Bouza, Carmen; Maes, Gregory E; Volckaert, Filip A M; Martínez, Paulino

    2015-10-01

    Partitioning phenotypic variance in genotypic and environmental variance may benefit from the population genomic assignment of genes putatively involved in adaptation. We analyzed a total of 256 markers (120 microsatellites and 136 Single Nucleotide Polymorphisms - SNPs), several of them associated to Quantitative Trait Loci (QTL) for growth and resistance to pathologies, with the aim to identify potential adaptive variation in turbot Scophthalmus maximus L. The study area in the Northeastern Atlantic Ocean, from Iberian Peninsula to the Baltic Sea, involves a gradual change in temperature and an abrupt change in salinity conditions. We detected 27 candidate loci putatively under selection. At least four of the five SNPs identified as outliers are located within genes coding for ribosomal proteins or directly related with the production of cellular proteins. One of the detected outliers, previously identified as part of a QTL for growth, is a microsatellite linked to a gene coding for a growth factor receptor. A similar set of outliers was detected when natural populations were compared with a sample subjected to strong artificial selection for growth along four generations. The observed association between FST outliers and growth-related QTL supports the hypothesis of changes in growth as an adaptation to differences in temperature and salinity conditions. However, further work is needed to confirm this hypothesis. PMID:25959584

  20. Optimization of Landmark Selection for Cortical Surface Registration

    OpenAIRE

    Joshi, Anand,; Pantazis, Dimitrios; Damasio, Hanna; Shattuck, David; Li, Quanzheng; Leahy, Richard

    2009-01-01

    Manually labeled landmark sets are often required as inputs for landmark-based image registration. Identifying an optimal subset of landmarks from a training dataset may be useful in reducing the labor intensive task of manual labeling. In this paper, we present a new problem and a method to solve it: given a set of N landmarks, find the k(< N) best landmarks such that aligning these k landmarks that produce the best overall alignment of all N landmarks. The resulting procedure allows us to s...

  1. Automatic Landmark Identification in Mars Orbital Imagery

    Science.gov (United States)

    Wagstaff, K. L.; Panetta, J.; Greeley, R.; Schorghofer, N.; Bunte, M.; Hoffer, M. P.; Ansar, A.

    2008-12-01

    We have developed new methods for automatically identifying landmarks such as craters, gullies, dark slope streaks, and dust devil tracks in remote sensing imagery. These methods are based on statistical measures of local terrain salience. The salience of a region is defined as the degree to which it differs from its surrounding context. We use pixel intensity histograms to represent each candidate region, and we compute salience in one of two ways. The first method calculates the Kullback-Leibler divergence between the region's histogram and a larger enclosing region. The second method calculates the entropy of the region's histogram independently. The KL-divergence approach is useful for detecting unusual landmarks, while the entropy approach detects high-contrast features such as ridges and crater edges. We have automatically identified landmarks in several Mars surface images collected from orbit (MOC and THEMIS data) and evaluated them against manual annotations of dark slope streaks and dust devil tracks. We have also trained a landmark machine classifier that can assign new landmarks to one of several categories. In an evaluation on dark slope streaks, dust devil tracks, and craters, the classifier achieved an accuracy of 93%. Further, because detections are made based on a generic notion of salience, they are not restricted to known landmark types. It is possible to identify landmarks that do not fit into any existing category as novel features, enabling scientific advances that otherwise rely on serendipity to bring them to light. Automated landmark identification can be useful both onboard a remote spacecraft and in ground-based processing on the Earth. In an onboard setting, salient landmarks can be detected and catalogued as they are observed, providing a highly compressed summary of the region under study (e.g., "five craters, two gullies, and 37 sand dunes" along with their locations). On the ground, gigabyte archives of past images can be analyzed and annotated with meta-data indicating the existence and location of different landmark types. These annotations can enable a content-based search facility that will permit the easy retrieval of images that contain a specific feature of interest.

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

    Directory of Open Access Journals (Sweden)

    Chan Juliana CN

    2010-02-01

    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.

  3. 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...

  4. Reproducibility of the sella turcica landmark in three dimensions using a sella turcica-specific reference system

    Energy Technology Data Exchange (ETDEWEB)

    Pittayapat, Pisha; Jacobs, Reinhilde [University Hospitals Leuven, University of Leuven, Leuven (Belgium); Odri, Guillaume A. [Service de Chirurgie Orthopedique et Traumatologique, Centre Hospitalier Regional d' Orleans, Orleans Cedex2 (France); De Faria Vasconcelos, Karla [Dept. of Oral Diagnosis, Division of Oral Radiology, Piracicaba Dental School, University of Campinas, Sao Paulo (Brazil); Willems, Guy [Dept. of Oral Health Sciences, Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, University of Leuven, Leuven (Belgium); Olszewski, Raphael [Dept. of Oral and Maxillofacial Surgery, Cliniques Universitaires Saint Luc, Universite Catholique de Louvain, Brussels (Belgium)

    2015-03-15

    This study was performed to assess the reproducibility of identifying the sella turcica landmark in a three-dimensional (3D) model by using a new sella-specific landmark reference system. Thirty-two cone-beam computed tomographic scans (3D Accuitomo 170, J. Morita, Kyoto, Japan) were retrospectively collected. The 3D data were exported into the Digital Imaging and Communications in Medicine standard and then imported into the Maxilim software (Medicim NV, Sint-Niklaas, Belgium) to create 3D surface models. Five observers identified four osseous landmarks in order to create the reference frame and then identified two sella landmarks. The x, y, and z coordinates of each landmark were exported. The observations were repeated after four weeks. Statistical analysis was performed using the multiple paired t-test with Bonferroni correction (intraobserver precision: p<0.005, interobserver precision: p<0.0011). The intraobserver mean precision of all landmarks was <1 mm. Significant differences were found when comparing the intraobserver precision of each observer (p<0.005). For the sella landmarks, the intraobserver mean precision ranged from 0.43±0.34 mm to 0.51±0.46 mm. The intraobserver reproducibility was generally good. The overall interobserver mean precision was <1 mm. Significant differences between each pair of observers for all anatomical landmarks were found (p<0.0011). The interobserver reproducibility of sella landmarks was good, with >50% precision in locating the landmark within 1 mm. A newly developed reference system offers high precision and reproducibility for sella turcica identification in a 3D model without being based on two-dimensional images derived from 3D data.

  5. Reproducibility of the sella turcica landmark in three dimensions using a sella turcica-specific reference system

    International Nuclear Information System (INIS)

    This study was performed to assess the reproducibility of identifying the sella turcica landmark in a three-dimensional (3D) model by using a new sella-specific landmark reference system. Thirty-two cone-beam computed tomographic scans (3D Accuitomo 170, J. Morita, Kyoto, Japan) were retrospectively collected. The 3D data were exported into the Digital Imaging and Communications in Medicine standard and then imported into the Maxilim software (Medicim NV, Sint-Niklaas, Belgium) to create 3D surface models. Five observers identified four osseous landmarks in order to create the reference frame and then identified two sella landmarks. The x, y, and z coordinates of each landmark were exported. The observations were repeated after four weeks. Statistical analysis was performed using the multiple paired t-test with Bonferroni correction (intraobserver precision: p<0.005, interobserver precision: p<0.0011). The intraobserver mean precision of all landmarks was <1 mm. Significant differences were found when comparing the intraobserver precision of each observer (p<0.005). For the sella landmarks, the intraobserver mean precision ranged from 0.43±0.34 mm to 0.51±0.46 mm. The intraobserver reproducibility was generally good. The overall interobserver mean precision was <1 mm. Significant differences between each pair of observers for all anatomical landmarks were found (p<0.0011). The interobserver reproducibility of sella landmarks was good, with >50% precision in locating the landmark within 1 mm. A newly developed reference system offers high precision and reproducibility for sella turcica identification in a 3D model without being based on two-dimensional images derived from 3D data.

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-09-15

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

  8. Pooled genome linkage scan of aggressive prostate cancer: results from the International Consortium for Prostate Cancer Genetics.

    Science.gov (United States)

    Schaid, Daniel J; McDonnell, Shannon K; Zarfas, Katherine E; Cunningham, Julie M; Hebbring, Scott; Thibodeau, Stephen N; Eeles, Rosalind A; Easton, Douglas F; Foulkes, William D; Simard, Jacques; Giles, Graham G; Hopper, John L; Mahle, Lovise; Moller, Pal; Badzioch, Michael; Bishop, D Timothy; Evans, Chris; Edwards, Steve; Meitz, Julia; Bullock, Sarah; Hope, Questa; Guy, Michelle; Hsieh, Chih-lin; Halpern, Jerry; Balise, Raymond R; Oakley-Girvan, Ingrid; Whittemore, Alice S; Xu, Jianfeng; Dimitrov, Latchezar; Chang, Bao-Li; Adams, Tamara S; Turner, Aubrey R; Meyers, Deborah A; Friedrichsen, Danielle M; Deutsch, Kerry; Kolb, Suzanne; Janer, Marta; Hood, Leroy; Ostrander, Elaine A; Stanford, Janet L; Ewing, Charles M; Gielzak, Marta; Isaacs, Sarah D; Walsh, Patrick C; Wiley, Kathleen E; Isaacs, William B; Lange, Ethan M; Ho, Lindsey A; Beebe-Dimmer, Jennifer L; Wood, David P; Cooney, Kathleen A; Seminara, Daniela; Ikonen, Tarja; Baffoe-Bonnie, Agnes; Fredriksson, Henna; Matikainen, Mika P; Tammela, Teuvo L J; Bailey-Wilson, Joan; Schleutker, Johanna; Maier, Christiane; Herkommer, Kathleen; Hoegel, Josef J; Vogel, Walther; Paiss, Thomas; Wiklund, Fredrik; Emanuelsson, Monica; Stenman, Elisabeth; Jonsson, Björn-Anders; Grönberg, Henrik; Camp, Nicola J; Farnham, James; Cannon-Albright, Lisa A; Catalona, William J; Suarez, Brian K; Roehl, Kimberly A

    2006-11-01

    While it is widely appreciated that prostate cancers vary substantially in their propensity to progress to a life-threatening stage, the molecular events responsible for this progression have not been identified. Understanding these molecular mechanisms could provide important prognostic information relevant to more effective clinical management of this heterogeneous cancer. Hence, through genetic linkage analyses, we examined the hypothesis that the tendency to develop aggressive prostate cancer may have an important genetic component. Starting with 1,233 familial prostate cancer families with genome scan data available from the International Consortium for Prostate Cancer Genetics, we selected those that had at least three members with the phenotype of clinically aggressive prostate cancer, as defined by either high tumor grade and/or stage, resulting in 166 pedigrees (13%). Genome-wide linkage data were then pooled to perform a combined linkage analysis for these families. Linkage signals reaching a suggestive level of significance were found on chromosomes 6p22.3 (LOD = 3.0), 11q14.1-14.3 (LOD = 2.4), and 20p11.21-q11.21 (LOD = 2.5). For chromosome 11, stronger evidence of linkage (LOD = 3.3) was observed among pedigrees with an average at diagnosis of 65 years or younger. Other chromosomes that showed evidence for heterogeneity in linkage across strata were chromosome 7, with the strongest linkage signal among pedigrees without male-to-male disease transmission (7q21.11, LOD = 4.1), and chromosome 21, with the strongest linkage signal among pedigrees that had African American ancestry (21q22.13-22.3; LOD = 3.2). Our findings suggest several regions that may contain genes which, when mutated, predispose men to develop a more aggressive prostate cancer phenotype. This provides a basis for attempts to identify these genes, with potential clinical utility for men with aggressive prostate cancer and their relatives. PMID:16932970

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-03-01

    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.

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

    Science.gov (United States)

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

    2014-11-01

    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

  11. Impact of different anatomical landmarks on registration in imaging-guided radiation for lung cancer

    International Nuclear Information System (INIS)

    Objective: To evaluate the impact of different anatomical landmarks on registration in imaging-guided radiation (IGRT) for lung cancer. Methods: For 20 patients with non-small cell lung cancer receiving stereotactic body radiotherapy (SBRT) in Fudan University Cancer Hospital, 100 frames of kilo-voltage cone-beam computed tomography scanning were evaluated in this study. The spine, carina and tumor were selected as landmarks for registration, respectively. Results of registration using different landmarks were documented and compared. Results: The average set-up errors in the left-right, superior inferior and anterior-posterior directions were -0.08 cm ±0.32 cm, -0.16 cm ±0.45 cm and 0.06 cm ±0.23 cm with the spine for registration; 0.06 cm ±0.34 cm, -0.13 cm ±0.45 cm and -0.02 cm±0.23 cm with the carina; and -0.17 cm ±0.25 cm, 0.03 cm ±0.47 cm and 0.15 cm ±0.38 cm with tumor. The registration results between using the carina and tumor as landmarks were statistically significant different (q=4.61, P=0.002; q = 2.23 , P=0.118; q=3.44, P=0.017). The registration results were equal when using the spine and tumor as landmarks (q =1.85, P = 0.195; q = 2.54, P = 0.075; q = 1.89, P=0.185), as well as using the carina and tumor as landmarks (q=2.76, P=0.054; q=0.31, P=0.826; q=1.55, P=0.276). Conclusions: For early stage lung cancer, the spine and tumor can be used equally as registration landmarks in imaging-guided SBRT. The carina is not suggested for its poor reproducible position. (authors)

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

    Science.gov (United States)

    Xu, Jiawu; Chu, Ka Hou

    2012-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Schunke Anja C

    2012-04-01

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

  14. 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 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

  15. Automated landmark-guided deformable image registration

    Science.gov (United States)

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

    2015-01-01

    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.

  16. Landmark papers on photorefractive nonlinear optics

    CERN Document Server

    Yeh, Pochi

    1995-01-01

    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.

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

    OpenAIRE

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

    2012-01-01

    Abstract Background Interest in the placing of landmarks and subsequent morphometric analyses of shape for 3D data has increased with the increasing accessibility of computed tomography (CT) scanners. However, current computer programs for this task suffer from various practical drawbacks. We present here a free software tool that overcomes many of these problems. Results The TINA Manual Landmarking Tool was developed for the digitization of 3D data sets. It enables the generation of a modifi...

  18. 36 CFR 62.7 - Natural landmark modifications.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Natural landmark... INTERIOR NATIONAL NATURAL LANDMARKS PROGRAM § 62.7 Natural landmark modifications. (a) Determination of need for modifications. After designation, the modification of the boundaries of a natural...

  19. Ultrasound of the elbow: A systematic approach using bony landmarks

    International Nuclear Information System (INIS)

    The use of bony landmarks can be helpful in performing an ultrasound study of the elbow. We discuss bony landmarks that can be used for evaluation of the common extensor tendon, ulnar collateral ligament and common flexor tendon, coronoid and olecranon fossa, ulnar nerve, and biceps tendon. We discuss bony landmarks for each of these structures.

  20. Using local symmetry for landmark selection

    OpenAIRE

    Kootstra, Geert; de Jong, Sjoerd; Schomaker, Lambert R. B.

    2009-01-01

    Most visual Simultaneous Localization And Mapping (SLAM) methods use interest points as landmarks in their maps of the environment. Often the interest points are detected using contrast features, for instance those of the Scale Invariant Feature Transform (SIFT). The SIFT interest points, however, have problems with stability, and noise robustness. Taking our inspiration from human vision, we therefore propose the use of local symmetry to select interest points. Our method, the MUlti-scale Sy...

  1. Mapped Landmark Algorithm for Precision Landing

    Science.gov (United States)

    Johnson, Andrew; Ansar, Adnan; Matthies, Larry

    2007-01-01

    A report discusses a computer vision algorithm for position estimation to enable precision landing during planetary descent. The Descent Image Motion Estimation System for the Mars Exploration Rovers has been used as a starting point for creating code for precision, terrain-relative navigation during planetary landing. The algorithm is designed to be general because it handles images taken at different scales and resolutions relative to the map, and can produce mapped landmark matches for any planetary terrain of sufficient texture. These matches provide a measurement of horizontal position relative to a known landing site specified on the surface map. Multiple mapped landmarks generated per image allow for automatic detection and elimination of bad matches. Attitude and position can be generated from each image; this image-based attitude measurement can be used by the onboard navigation filter to improve the attitude estimate, which will improve the position estimates. The algorithm uses normalized correlation of grayscale images, producing precise, sub-pixel images. The algorithm has been broken into two sub-algorithms: (1) FFT Map Matching (see figure), which matches a single large template by correlation in the frequency domain, and (2) Mapped Landmark Refinement, which matches many small templates by correlation in the spatial domain. Each relies on feature selection, the homography transform, and 3D image correlation. The algorithm is implemented in C++ and is rated at Technology Readiness Level (TRL) 4.

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

    International Nuclear Information System (INIS)

    Purpose: To quantitatively compare a scanning liquid ion chamber electronic portal imaging device (SLIC-EPID) and an amorphous silicon flat panel (aSi) EPID with portal film in clinical applications using measures of landmark visibility and treatment review accuracy. Methods and Materials: Six radiation oncologists viewed 39 electronic portal images (EPIs) from the SLIC-EPID, 36 EPIs from the aSi-EPID, and portal films of each of these treatment fields. The physicians rated the clarity of anatomic landmarks in the portal images, and the scores were compared between EPID and film. Nine hundred portal image reviews were performed. EPID and film portal images were acquired with known setup errors in either phantom or cadaver treatments. Physicians identified the errors visually in portal films and with computerized analysis for EPID. Results: There were no statistically significant (p<0.05) differences between film and SLIC-EPID in ratings of landmark clarity. Eleven of 12 landmarks were more visible in aSi-EPID than in film. Translational setup errors were identified with an average accuracy of 2.5 mm in film, compared to 1.5 mm with SLIC-EPID and 1.3 mm with aSi-EPID. Conclusions: Both EPIDs are clinically viable replacements for film, but aSi-EPID represents a significant advancement in image quality over film

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

    Directory of Open Access Journals (Sweden)

    Zhang Hui

    2012-12-01

    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.

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

    OpenAIRE

    Marazita, Mary L; Jeffrey C Murray; 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; de Winter, Robin

    2004-01-01

    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...

  5. Planning of landmark recognition of autonomous mobile robot (PLAS)

    Energy Technology Data Exchange (ETDEWEB)

    Abe, Y.; Sakamoto, S. [Shinryo Corp., Tokyo (Japan); Fukuda, T.; Arai, F.; Ito, S. [Nagoya University, Nagoya (Japan)

    2000-05-25

    We have developed a novel nevigation system for autonomous mobile robots called the Planning of Landmark Sensing (PLAS) system which takes into account realistic environmental conditions. When a robot moves, the robot usually resets the accumulated position errors in its navigation model by sensing a landmark. In our previous work, these errors were estimated based on robot models, and a Kalman Filter was used to reset the errors after the landmark was sensed. In this method, only the spatial relation of the robot and the landmark was considered to influence the observation noise of the Kalman Filter. But, environmental conditions, like the lighting of the room, are likely to cause the misrecognition of a landmark. Therefore, we have incorporated environmental conditions into the model of the observation noise. This helps our system to recognize the possibility of a misrecognition in bad sensing environments. As a result, our navigation system allows robots to navigate precisely, even in environments not optimal for landmark sensing. (author)

  6. Landmark experiments in twentieth-century physics

    CERN Document Server

    Trigg, George L

    2011-01-01

    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

  7. Detection of natural landmarks through multiscale opponent features

    OpenAIRE

    Todt, Eduardo; Torras Genís, Carme

    2000-01-01

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

  8. Using landmarks to support older people in navigation

    OpenAIRE

    Goodman, J.; Gray, P.D.G.; Khammampad, K.; Brewster, S.

    2004-01-01

    Although landmarks are an integral aspect of navigation, they have rarely been used within electronic navigation aids. This paper describes the design of a pedestrian navigation aid for a handheld computer, which guides the user along a route using photographs of landmarks, together with audio and text instructions that reference these landmarks. This aid was designed with older users in mind who often find their mobility hampered by declines in sensory, cognitive and motor abilities. It was ...

  9. Facial Landmarks Localization Estimation by Cascaded Boosted Regression

    OpenAIRE

    Chevallier, Louis; Vigouroux, Jean-Ronan; Goguey, Alix; Ozerov, Alexey

    2013-01-01

    Accurate detection of facial landmarks is very important for many applications like face recognition or analysis. In this paper we describe an efficient detector of facial landmarks based on a cascade of boosted regressors of arbitrary number of levels. We define as many regressors as landmarks and we train them separately. We describe how the training is conducted for the series of regressors by supplying training samples centered on the predictions of the previous levels. We employ gradient...

  10. Combining Path Integration and Remembered Landmarks When Navigating without Vision

    OpenAIRE

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

    2013-01-01

    This study investigated the interaction between remembered landmark and path integration strategies for estimating current location when walking in an environment without vision. We asked whether observers navigating without vision only rely on path integration information to judge their location, or whether remembered landmarks also influence judgments. Participants estimated their location in a hallway after viewing a target (remembered landmark cue) and then walking blindfolded to the same...

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

    Science.gov (United States)

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

    2014-01-01

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

  12. Genome-Wide Scan of Gastrointestinal Nematode Resistance in Closed Angus Population Selected for Minimized Influence of MHC

    Science.gov (United States)

    Kim, Eui-Soo; Sonstegard, Tad S.; da Silva, Marcos V. G. B.; Gasbarre, Louis C.; Van Tassell, Curtis P.

    2015-01-01

    Genetic markers associated with parasite indicator traits are ideal targets for study of marker assisted selection aimed at controlling infections that reduce herd use of anthelminthics. For this study, we collected gastrointestinal (GI) nematode fecal egg count (FEC) data from post-weaning animals of an Angus resource population challenged to a 26 week natural exposure on pasture. In all, data from 487 animals was collected over a 16 year period between 1992 and 2007, most of which were selected for a specific DRB1 allele to reduce the influence of potential allelic variant effects of the MHC locus. A genome-wide association study (GWAS) based on BovineSNP50 genotypes revealed six genomic regions located on bovine Chromosomes 3, 5, 8, 15 and 27; which were significantly associated (-log10 p=4.3) with Box-Cox transformed mean FEC (BC-MFEC). DAVID analysis of the genes within the significant genomic regions suggested a correlation between our results and annotation for genes involved in inflammatory response to infection. Furthermore, ROH and selection signature analyses provided strong evidence that the genomic regions associated BC-MFEC have not been affected by local autozygosity or recent experimental selection. These findings provide useful information for parasite resistance prediction for young grazing cattle and suggest new candidate gene targets for development of disease-modifying therapies or future studies of host response to GI parasite infection. PMID:25803687

  13. Anatomical landmarks accurately determine interfractional lymph node shifts during radiotherapy of lung cancer patients

    International Nuclear Information System (INIS)

    Background and purpose: Low contrast in the cone-beam computed tomography (CBCT) scans hampers fast online evaluation of interfractional changes in the lymph node position on a daily basis. In this study we have investigated whether high-contrast anatomical landmarks in the vicinity of the nodes may be used as surrogates for the lymph node positions. Materials and methods: Forty lung cancer patients were treated with an online CBCT-based setup strategy involving soft-tissue match on the primary tumor. One hundred and sixteen lymph nodes were delineated separately on the planning-CT scans and categorized according to the lymph node stations. Five anatomical landmarks were selected as surrogate structures and assigned to the individual nodes. In addition, the carina was delineated. Registrations between the planning-CT and the daily CBCTs were performed retrospectively and positional deviations between the nodes and the surrogate structures or the carina were registered. Results: The mean displacement between lymph nodes and surrogate structures was 1.6 mm with systematic/random errors of 0.7/0.7 mm, significantly smaller than the mean displacement between nodes and the carina. Conclusions: The position of the lymph nodes can be evaluated using selected anatomical landmarks on a daily basis using CBCT

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

    International Nuclear Information System (INIS)

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

  15. 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)

    Yue Gen

    2006-10-01

    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.

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

    OpenAIRE

    Sjögren, Marketa

    2008-01-01

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

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

    DEFF Research Database (Denmark)

    Kolte, Astrid Marie; Nielsen, Henriette Svarre; Moltke, Ida; Degn, B.; Pedersen, B.; Sunde, L.; Nielsen, Finn Cilius; Christiansen, Ole B

    2011-01-01

    Previously, siblings of patients with idiopathic recurrent miscarriage (IRM) have been shown to have a higher risk of miscarriage. This study is comprised of two parts: 1) an epidemiological part, in which we introduce data on the frequency of miscarriage among 268 siblings of 244 patients with IRM and 2) a genetic part presenting data from a genome-wide linkage study of 38 affected sib-pairs with IRM. All IRM patients (probands) had experienced =3 miscarriages and affected siblings =2 miscarria...

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

    OpenAIRE

    Huang, Xinxiang; XU, HUAXI; Sun, Xiaosong; Ohkusu, Kiyofumi; Kawamura, Yoshiaki; Ezaki, Takayuki

    2007-01-01

    Salmonella enterica serovar Typhi is a human enteroinvasive pathogen that can overcome the stress caused by the high osmolarity of the human small intestine and cause systemic infection. To investigate the global transcriptional regulations of S. enterica serovar Typhi exposed to a hyperosmotic environment, a genomic oligo-DNA microarray containing 4474 Salmonella genes was prepared. A wild strain of S. enterica serovar Typhi GIFU10007 was grown in LB medium containing 50 mM NaCl to simulate ...

  19. 32 CFR 644.317 - Preserving historic landmarks and properties.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 4 2010-07-01 2010-07-01 true Preserving historic landmarks and properties. 644.317 Section 644.317 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) REAL PROPERTY REAL ESTATE HANDBOOK Disposal § 644.317 Preserving historic landmarks...

  20. 36 CFR 65.5 - Designation of National Historic Landmarks.

    Science.gov (United States)

    2010-07-01

    ... criteria but which do meet the National Register criteria for evaluation in 36 CFR part 60 or determine... Historic Landmarks. 65.5 Section 65.5 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL HISTORIC LANDMARKS PROGRAM § 65.5 Designation of National Historic...

  1. 75 FR 49520 - Landmarks Committee of the National Park System Advisory Board Meeting

    Science.gov (United States)

    2010-08-13

    ...of the Landmarks Committee are: Mr. Ronald...Historic Landmarks nominations, amendments to...and its Landmarks Committee may consider the following nominations: Nominations Delaware...HISTORIC DISTRICT, Independence, MO...

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

    Science.gov (United States)

    Llamas, José M.; Cibrián, Rosa; Gandia, José L.; Paredes, Vanessa

    2012-01-01

    Objectives: Cone Beam Computerized Tomography (CBCT) allows the possibility of modifying some of the diagnostic tools used in orthodontics, such as cephalometry. The first step must be to study the characteristics of these devices in terms of accuracy and reliability of the most commonly used landmarks. The aims were 1- To assess intra and inter-observer reliability in the location of anatomical landmarks belonging to hard tissues of the skull in images taken with a CBCT device, 2- To determine which of those landmarks are more vs. less reliable and 3- To introduce planes of reference so as to create cephalometric analyses appropriated to the 3D reality. Study design: Fifteen patients who had a CBCT (i-CAT®) as a diagnostic register were selected. To assess the reproducibility on landmark location and the differences in the measurements of two observers at different times, 41 landmarks were defined on the three spatial axes (X,Y,Z) and located. 3.690 measurements were taken and, as each determination has 3 coordinates, 11.070 data were processed with SPSS® statistical package. To discover the reproducibility of the method on landmark location, an ANOVA was undertaken using two variation factors: time (t1, t2 and t3) and observer (Ob1 and Ob2) for each axis (X, Y and Z) and landmark. The order of the CBCT scans submitted to the observers (Ob1, Ob2) at t1, t2, and t3, were different and randomly allocated. Multiple comparisons were undertaken using the Bonferroni test. The intra- and inter-examiner ICC´s were calculated. Results: Intra- and inter-examiner reliability was high, both being ICC ? 0.99, with the best frequency on axis Z. Conclusions: The most reliable landmarks were: Nasion, Sella, Basion, left Porion, point A, anterior nasal spine, Pogonion, Gnathion, Menton, frontozygomatic sutures, first lower molars and upper and lower incisors. Those with less reliability were the supraorbitals, right zygion and posterior nasal spine. Key words:Cone Beam Computed Tomography, cephalometry, landmark, orthodontics, reliability. PMID:22322503

  3. A genome scan for eye color in 502 twin families: most variation is due to a QTL on chromosome 15q.

    Science.gov (United States)

    Zhu, Gu; Evans, David M; Duffy, David L; Montgomery, Grant W; Medland, Sarah E; Gillespie, Nathan A; Ewen, Kelly R; Jewell, Mary; Liew, Yew Wah; Hayward, Nicholas K; Sturm, Richard A; Trent, Jeffrey M; Martin, Nicholas G

    2004-04-01

    We have rated eye color on a 3-point scale (1 = blue/grey, 2 = hazel/green, 3 = brown) in 502 twin families and carried out a 5-10 cM genome scan (400-757 markers). We analyzed eye color as a threshold trait and performed multipoint sib pair linkage analysis using variance components analysis in Mx. A lod of 19.2 was found at the marker D15S1002, less than 1 cM from OCA2, which has been previously implicated in eye color variation. We estimate that 74% of variance in eye color liability is due to this QTL and a further 18% due to polygenic effects. However, a large shoulder on this peak suggests that other loci affecting eye color may be telomeric of OCA2 and inflating the QTL estimate. No other peaks reached genome-wide significance, although lods > 2 were seen on 5p and 14q and lods >1 were additionally seen on chromosomes 2, 3, 6, 7, 8, 9, 17 and 18. Most of these secondary peaks were reduced or eliminated when we repeated the scan as a two locus analysis with the 15q linkage included, although this does not necessarily exclude them as false positives. We also estimated the interaction between the 15q QTL and the other marker locus but there was only minor evidence for additive x additive epistasis. Elaborating the analysis to the full two-locus model including non-additive main effects and interactions did not strengthen the evidence for epistasis. We conclude that most variation in eye color in Europeans is due to polymorphism in OCA2 but that there may be modifiers at several other loci. PMID:15169604

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

    DEFF Research Database (Denmark)

    Kolte, Astrid Marie; Nielsen, H S

    2011-01-01

    Previously, siblings of patients with idiopathic recurrent miscarriage (IRM) have been shown to have a higher risk of miscarriage. This study is comprised of two parts: 1) an epidemiological part, in which we introduce data on the frequency of miscarriage among 268 siblings of 244 patients with IRM and 2) a genetic part presenting data from a genome-wide linkage study of 38 affected sib-pairs with IRM. All IRM patients (probands) had experienced ?3 miscarriages and affected siblings ?2 miscarriages. The sib-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 sib-pairs. Maximum LOD scores were identified in four occurrences: for rs10514716 (3p14.2) when analysing sister-pairs only; for rs10511668 (9p22.1) and rs341048 (11q13.4) when only analysing families where the probands have had ?4 miscarriages; and for rs10485275 (6q16.3) when analyzing one sib-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 sib-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.

  5. Content-Based Visual Landmark Search via Multimodal Hypergraph Learning.

    Science.gov (United States)

    Zhu, Lei; Shen, Jialie; Jin, Hai; Zheng, Ran; Xie, Liang

    2015-12-01

    While content-based landmark image search has recently received a lot of attention and became a very active domain, it still remains a challenging problem. Among the various reasons, high diverse visual content is the most significant one. It is common that for the same landmark, images with a wide range of visual appearances can be found from different sources and different landmarks may share very similar sets of images. As a consequence, it is very hard to accurately estimate the similarities between the landmarks purely based on single type of visual feature. Moreover, the relationships between landmark images can be very complex and how to develop an effective modeling scheme to characterize the associations still remains an open question. Motivated by these concerns, we propose multimodal hypergraph (MMHG) to characterize the complex associations between landmark images. In MMHG, images are modeled as independent vertices and hyperedges contain several vertices corresponding to particular views. Multiple hypergraphs are firstly constructed independently based on different visual modalities to describe the hidden high-order relations from different aspects. Then, they are integrated together to involve discriminative information from heterogeneous sources. We also propose a novel content-based visual landmark search system based on MMHG to facilitate effective search. Distinguished from the existing approaches, we design a unified computational module to support query-specific combination weight learning. An extensive experiment study on a large-scale test collection demonstrates the effectiveness of our scheme over state-of-the-art approaches. PMID:25576590

  6. DETEKSI LANDMARK CITRA WAJAH DENGAN EXTRAKSI FITUR GABOR ANALISA FUZZY

    Directory of Open Access Journals (Sweden)

    Resmana Lim

    2003-01-01

    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.

  7. Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function

    Science.gov (United States)

    Puffenberger, Erik G.; Hu-Lince, Diane; Parod, Jennifer M.; Craig, David W.; Dobrin, Seth E.; Conway, Andrew R.; Donarum, Elizabeth A.; Strauss, Kevin A.; Dunckley, Travis; Cardenas, Javier F.; Melmed, Kara R.; Wright, Courtney A.; Liang, Winnie; Stafford, Phillip; Flynn, C. Robert; Morton, D. Holmes; Stephan, Dietrich A.

    2004-01-01

    We have identified a lethal phenotype characterized by sudden infant death (from cardiac and respiratory arrest) with dysgenesis of the testes in males [Online Mendelian Inheritance in Man (OMIM) accession no. 608800]. Twenty-one affected individuals with this autosomal recessive syndrome were ascertained in nine separate sibships among the Old Order Amish. High-density single-nucleotide polymorphism (SNP) genotyping arrays containing 11,555 single-nucleotide polymorphisms evenly distributed across the human genome were used to map the disease locus. A genome-wide autozygosity scan localized the disease gene to a 3.6-Mb interval on chromosome 6q22.1-q22.31. This interval contained 27 genes, including two testis-specific Y-like genes (TSPYL and TSPYL4) of unknown function. Sequence analysis of the TSPYL gene in affected individuals identified a homozygous frameshift mutation (457_458insG) at codon 153, resulting in truncation of translation at codon 169. Truncation leads to loss of a peptide domain with strong homology to the nucleosome assembly protein family. GFP-fusion expression constructs were constructed and illustrated loss of nuclear localization of truncated TSPYL, suggesting loss of a nuclear localization patch in addition to loss of the nucleosome assembly domain. These results shed light on the pathogenesis of a disorder of sexual differentiation and brainstem-mediated sudden death, as well as give insight into a mechanism of transcriptional regulation. PMID:15273283

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

    Science.gov (United States)

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

    2012-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Conord Cyrille

    2009-12-01

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

  10. An image processing system for locating craniofacial landmarks

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    Takayuki Ezaki

    2007-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Gray Joanna

    2010-11-01

    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.

  13. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective.

    Science.gov (United States)

    Foll, Matthieu; Gaggiotti, Oscar

    2008-10-01

    Identifying loci under natural selection from genomic surveys is of great interest in different research areas. Commonly used methods to separate neutral effects from adaptive effects are based on locus-specific population differentiation coefficients to identify outliers. Here we extend such an approach to estimate directly the probability that each locus is subject to selection using a Bayesian method. We also extend it to allow the use of dominant markers like AFLPs. It has been shown that this model is robust to complex demographic scenarios for neutral genetic differentiation. Here we show that the inclusion of isolated populations that underwent a strong bottleneck can lead to a high rate of false positives. Nevertheless, we demonstrate that it is possible to avoid them by carefully choosing the populations that should be included in the analysis. We analyze two previously published data sets: a human data set of codominant markers and a Littorina saxatilis data set of dominant markers. We also perform a detailed sensitivity study to compare the power of the method using amplified fragment length polymorphism (AFLP), SNP, and microsatellite markers. The method has been implemented in a new software available at our website (http://www-leca.ujf-grenoble.fr/logiciels.htm). PMID:18780740

  14. Some historical landmarks in nuclear and radiochemistry

    International Nuclear Information System (INIS)

    The study of conduction of electricity through evacuated tubes led to the discovery of cathode rays by Plucker in 1858. No outstanding results were produced in the study of these rays until 1895-1896 when incisive minds of Roentgen and Thomson led, respectively, to the Nobel prize winning discoveries of x-rays and electron. Fortutious linking of phosphorescence with x-ray emission led Becquerel to discover uranic rays and his colleagues M. Curie an P. Curie to their research on radiation phenomenon. A gigantic forward wave of human knowledge ensued from these discoveries. The postulation of nuclear atom by Rutherford was an important landmark in this forward movement. Rutherford and Soddy postulated that the spontaneous emission of radiations (? and ?) by atoms is accompanied by chemical changes. Subsequent studies by Rutherford and his colleagues in England, Curie-Joliot team in France, Fermi et al. in Italy and Hahn et al. in Germany established transmutation of atomic nuclei by nuclear radiations (? and n). This article is an attempt to pay a humble tribute to the pioneers who opened the gates to the world of nuclear sciences. (author). 135 refs., 1 fig

  15. Pterion: An anatomical variation and surgical landmark

    Directory of Open Access Journals (Sweden)

    Prashant E Natekar

    2011-01-01

    Full Text Available Introduction : The frontal and the parietal bones superiorly and the greater wing of the sphenoid and the squamous temporal inferiorly of one side meet at an H-shaped sutural junction termed the pterion. This is an important anatomical and anthropological landmark as it overlies both the anterior branch of middle meningeal artery and the lateral fissure of the cerebral hemisphere. The knowledge of sutural joints between frontal, parietal, sphenoid and temporal bones at pterion is clinically, radiologically and surgically important during surgical interventions involving burr hole surgeries. Materials and Methods : Study performed on 150 dry temporal bones. The pterion, and its sutural articulations with frontal, parietal, sphenoid and temporal bones and also anatomical variations, if any, were studied. Results : Four types of pterion, i.e. sphenoparietal, frontotemporal, stellate and epipteric, were observed. Conclusions : The knowledge of the variations of pterion and its surgical anatomy, in Indian population are important for surgeons operating in the fieldThe present study will also contribute additional information of skull bone fractures in infancy and early childhood, which may be associated with large intersutural bones giving false appearance of fracture radiologically and also during surgical interventions involving burr hole surgeries, as their extensions may lead to continuation of fracture lines.

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

    Directory of Open Access Journals (Sweden)

    Shong Huang

    2013-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-06-19

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

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

    International Nuclear Information System (INIS)

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

  19. Indoor Localization System based on Artificial Landmarks and Monocular Vision

    OpenAIRE

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

    2012-01-01

    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...

  20. Landmarking the Brain for Geometric Morphometric Analysis: An Error Study

    OpenAIRE

    Chollet, Madeleine B.; ALDRIDGE, KRISTINA; Pangborn, Nicole; Weinberg, Seth M; DeLeon, Valerie B.

    2014-01-01

    Neuroanatomic phenotypes are often assessed using volumetric analysis. Although powerful and versatile, this approach is limited in that it is unable to quantify changes in shape, to describe how regions are interrelated, or to determine whether changes in size are global or local. Statistical shape analysis using coordinate data from biologically relevant landmarks is the preferred method for testing these aspects of phenotype. To date, approximately fifty landmarks have been used to study b...

  1. A Novel Hybrid Approach for Cephalometric Landmark Detection

    OpenAIRE

    Majd, Mahshid; Shoeleh, Farzaneh

    2015-01-01

    Cephalometric analysis has an important role in dentistry and especially in orthodontics as a treatment planning tool to gauge the size and special relationships of the teeth, jaws and cranium. The first step of using such analyses is localizing some important landmarks known as cephalometric landmarks on craniofacial in x-ray image. The past decade has seen a growing interest in automating this process. In this paper, a novel hybrid approach is proposed for automatic detect...

  2. Detection of point landmarks in multidimensional tensor data?

    OpenAIRE

    Ruiz-Alzola, J.; Kikinis, R; Westin, C.-F.

    2001-01-01

    This paper describes a unified approach to the detection of point landmarks—whose neighborhoods convey discriminant information—including multidimensional scalar, vector, and higher-order tensor data. The method is based on the interpretation of generalized correlation matrices derived from the gradient of tensor functions, a probabilistic interpretation of point landmarks, and the application of tensor algebra. Results on both synthetic and real tensor data are presented.

  3. Visually-Guided Robot Navigation: From Artificial To Natural Landmarks

    OpenAIRE

    Celaya, Enric; Albarral García, José Luís; Jiménez Schlegl, Pablo; Torras, Carme

    2007-01-01

    Landmark-based navigation in unknown unstructured environments is far from solved. The bottleneck nowadays seems to be the fast detection of reliable visual references in the image stream as the robot moves. In our research, we have decoupled the navigation issues from this visual bottleneck, by first using artificial landmarks that could be easily detected and identified. Once we had a navigation system working, we developed a strategy to detect and track salient regions along image streams ...

  4. Potentiation and overshadowing between landmarks and environmental geometric cues

    OpenAIRE

    Horne, Murray R; PEARCE, JOHN M.

    2011-01-01

    Rats were required in three experiments to find one of two submerged platforms that were situated in diagonally opposite corners of a rectangular, grey swimming pool. The same corners were used throughout each experiment. Experimental groups were trained with landmarks, comprising A4 cards attached to the walls, located in the corners containing the platforms. For the control groups, the landmarks were situated in the corners containing the platforms for half the trials, and in the other corn...

  5. A new method to validate thoracic CT-CT deformable image registration using auto-segmented 3D anatomical landmarks

    DEFF Research Database (Denmark)

    Nielsen, Martin S; Østergaard, Lasse R; Carl, Jesper

    2015-01-01

    BACKGROUND: Deformable image registrations are prone to errors in aligning reliable anatomically features. Consequently, identification of registration inaccuracies is important. Particularly thoracic three-dimensional (3D) computed tomography (CT)-CT image registration is challenging due to lack of contrast in lung tissue. This study aims for validation of thoracic CT-CT image registration using auto-segmented anatomically landmarks. MATERIAL AND METHODS: Five lymphoma patients were CT scanned ...

  6. Landmark Detection in Orbital Images Using Salience Histograms

    Science.gov (United States)

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

    2010-01-01

    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.

  7. Measure of Landmark Semantic Salience through Geosocial Data Streams

    Directory of Open Access Journals (Sweden)

    Teriitutea Quesnot

    2014-12-01

    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.

  8. 36 CFR 62.4 - Natural landmark designation and recognition process.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Natural landmark designation..., DEPARTMENT OF THE INTERIOR NATIONAL NATURAL LANDMARKS PROGRAM § 62.4 Natural landmark designation and recognition process. (a) Identification. Potential national natural landmarks are identified in the...

  9. Visual Homing in the Absence of Feature-Based Landmark Information

    Science.gov (United States)

    Gillner, Sabine; Weiss, Anja M.; Mallot, Hanspeter A.

    2008-01-01

    Despite that fact that landmarks play a prominent role in human navigation, experimental evidence on how landmarks are selected and defined by human navigators remains elusive. Indeed, the concept of a "landmark" is itself not entirely clear. In everyday language, the term landmark refers to salient, distinguishable, and usually nameable objects,…

  10. Visual Homing in the Absence of Feature-Based Landmark Information

    Science.gov (United States)

    Gillner, Sabine; Weiss, Anja M.; Mallot, Hanspeter A.

    2008-01-01

    Despite that fact that landmarks play a prominent role in human navigation, experimental evidence on how landmarks are selected and defined by human navigators remains elusive. Indeed, the concept of a "landmark" is itself not entirely clear. In everyday language, the term landmark refers to salient, distinguishable, and usually nameable objects,…

  11. A new method to validate thoracic CT-CT deformable image registration using auto-segmented 3D anatomical landmarks

    DEFF Research Database (Denmark)

    Nielsen, Martin S; Østergaard, Lasse R

    2015-01-01

    BACKGROUND: Deformable image registrations are prone to errors in aligning reliable anatomically features. Consequently, identification of registration inaccuracies is important. Particularly thoracic three-dimensional (3D) computed tomography (CT)-CT image registration is challenging due to lack of contrast in lung tissue. This study aims for validation of thoracic CT-CT image registration using auto-segmented anatomically landmarks. MATERIAL AND METHODS: Five lymphoma patients were CT scanned three times within a period of 18 months, with the initial CT defined as the reference scan. For each patient the two successive CT scans were registered to the reference CT using three different image registration algorithms (Demons, B-spline and Affine). The image registrations were evaluated using auto-segmented anatomical landmarks (bronchial branch points) and Dice Similarity Coefficients (DSC). Deviation of corresponding bronchial landmarks were used to quantify inaccuracies in respect of both misalignment and geometric location within lungs. RESULTS: The median bronchial branch point deviations were 1.6, 1.1 and 4.2 (mm) for the three tested algorithms (Demons, B-spline and Affine). The maximum deviations (> 15 mm) were found within both Demons and B-spline image registrations. In the upper part of the lungs the median deviation of 1.7 (mm) was significantly different (p 15 mm in both Demons and B-spline deformable algorithms.

  12. Genome-wide linkage scan for prostate cancer susceptibility genes in men with aggressive disease: significant evidence for linkage at chromosome 15q12.

    Science.gov (United States)

    Lange, Ethan M; Ho, Lindsey A; Beebe-Dimmer, Jennifer L; Wang, Yunfei; Gillanders, Elizabeth M; Trent, Jeffrey M; Lange, Leslie A; Wood, David P; Cooney, Kathleen A

    2006-05-01

    Epidemiological and twin studies have consistently demonstrated a strong genetic component to prostate cancer (PCa) susceptibility. To date, numerous linkage studies have been performed to identify chromosomal regions containing PCa susceptibility genes. Unfortunately, results from these studies have failed to form any obvious consensus regarding which regions are most likely to contain genes that may contribute to PCa predisposition. One plausible explanation for the difficulty in mapping susceptibility loci is the existence of considerable heterogeneity in the phenotype of PCa, with significant variation in clinical stage and grade of disease even among family members. To address this issue, we performed a genome-wide linkage scan on 71 informative families with two or more men with aggressive PCa. When only men with aggressive PCa were coded as affected, statistically significant evidence for linkage at chromosome 15q12 was detected (LOD=3.49; genome-wide p=0.005). Furthermore, the evidence for linkage increased when analyses were restricted to Caucasian-American pedigrees (n=65; LOD=4.05) and pedigrees with two confirmed aggressive cases (n=42, LOD=4.76). Interestingly, a 1-LOD support interval about our peak at 15q12 overlaps a region of suggestive linkage, 15q11, identified by a recent linkage study on 1,233 PCa families by the International Consortium for Prostate Cancer Genetics. Using a more rigid definition of PCa in linkage studies will result in a severe reduction in sample sizes available for study, but may ultimately prove to increase statistical power to detect susceptibility genes for this multigenic trait. PMID:16508751

  13. Ligands of thermophilic ABC transporters encoded in a newly sequenced genomic region of Thermotoga maritima MSB8 screened by differential scanning fluorimetry.

    Science.gov (United States)

    Boucher, Nathalie; Noll, Kenneth M

    2011-09-01

    The chromosome of Thermotoga maritima strain MSB8 was found to have an 8,870-bp region that is not present in its published sequence. The isolate that was sequenced by The Institute for Genomic Research (TIGR) in 1999 is apparently a laboratory variant of the isolate deposited at the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSM 3109) in 1986. This newly sequenced region from the DSMZ culture was located between TM1848 (cbp, cellobiose phosphorylase) and TM1847 (the 3' end of a truncated ROK regulator). The new region contained seven genes: a beta glucosidase gene (bglA), three trehalose ABC transporter genes (treEFG), three xylose ABC transporter genes (xylE2F2K2), and the 5' end of a gene encoding the ROK regulator TM1847. We present a new differential scanning fluorimetry method using a low pH that was necessary to screen potential ligands of these exceptionally thermostable periplasmic substrate-binding proteins. This method showed that trehalose, sucrose, and glucose stabilized TreE, and their binding was confirmed by measuring changes in intrinsic fluorescence upon ligand binding. Binding constants of 0.024 ?M, 0.300 ?M, and 56.78 ?M at 60°C, respectively, were measured. XylE2 ligands were similarly determined and xylose, glucose, and fucose bound with K(d) (dissociation constant) values of 0.042 ?M, 0.059 ?M, and 1.436 ?M, respectively. Since there is no discernible phenotypic difference between the TIGR isolate and the DSMZ isolate despite the variance in their genomes, we propose that they be called genomovars: T. maritima MSB8 genomovar TIGR and T. maritima MSB8 genomovar DSM 3109, respectively. PMID:21764944

  14. Genome-Wide Scan for Visceral Leishmaniasis in Mixed-Breed Dogs Identifies Candidate Genes Involved in T Helper Cells and Macrophage Signaling.

    Science.gov (United States)

    Utsunomiya, Yuri T; Ribeiro, Érica S; Quintal, Amanda P N; Sangalli, Juliano R; Gazola, Valquiria R; Paula, Henrique B; Trinconi, Cristiana M; Lima, Valéria M F; Perri, Silvia H V; Taylor, Jeremy F; Schnabel, Robert D; Sonstegard, Tad S; Garcia, José F; Nunes, Cáris M

    2015-01-01

    We conducted a genome-wide scan for visceral leishmaniasis in mixed-breed dogs from a highly endemic area in Brazil using 149,648 single nucleotide polymorphism (SNP) markers genotyped in 20 cases and 28 controls. Using a mixed model approach, we found two candidate loci on canine autosomes 1 and 2. The positional association on chromosome 2 mapped to a predicted DNAse sensitive site in CD14+ monocytes that serve as a cis-regulatory element for the expression of interleukin alpha receptors 2 (IL2RA) and 15 (IL15RA). Both interleukins were previously found to lead to protective T helper 1 cell (Th1) response against Leishmania spp. in humans and mice. The associated marker on chromosome 1 was located between two predicted transcription factor binding sites regulating the expression of the transducin-like enhancer of split 1 gene (TLE1), an important player in Notch signaling. This pathway is critical for macrophage activity and CD4+ T cell differentiation into Th1 and T helper 2. Together, these findings suggest that the human and mouse model for protective response against Leishmania spp., which involves Th1 and macrophage modulation by interleukins 2, 15, gamma interferon and Notch signaling, may also hold for the canine model. PMID:26348501

  15. Shared clonal cytogenetic abnormalities in aberrant mast cells and leukemic myeloid blasts detected by single nucleotide polymorphism microarray-based whole-genome scanning.

    Science.gov (United States)

    Frederiksen, John K; Shao, Lina; Bixby, Dale L; Ross, Charles W

    2016-04-01

    Systemic mastocytosis (SM) is characterized by a clonal proliferation of aberrant mast cells within extracutaneous sites. In a subset of SM cases, a second associated hematologic non-mast cell disease (AHNMD) is also present, usually of myeloid origin. Polymerase chain reaction and targeted fluorescence in situ hybridization studies have provided evidence that, in at least some cases, the aberrant mast cells are related clonally to the neoplastic cells of the AHNMD. In this work, a single nucleotide polymorphism microarray (SNP-A) was used to characterize the cytogenetics of the aberrant mast cells from a patient with acute myeloid leukemia and concomitant mast cell leukemia associated with a KIT D816A mutation. The results demonstrate the presence of shared cytogenetic abnormalities between the mast cells and myeloid blasts, as well as additional abnormalities within mast cells (copy-neutral loss of heterozygosity) not detectable by routine karyotypic analysis. To our knowledge, this work represents the first application of SNP-A whole-genome scanning to the detection of shared cytogenetic abnormalities between the two components of a case of SM-AHNMD. The findings provide additional evidence of a frequent clonal link between aberrant mast cells and cells of myeloid AHNMDs, and also highlight the importance of direct sequencing for identifying uncommon activating KIT mutations. © 2016 Wiley Periodicals, Inc. PMID:26865278

  16. 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 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

  17. The reliability of tablet computers in depicting maxillofacial radiographic landmarks

    International Nuclear Information System (INIS)

    This study was performed to evaluate the reliability of the identification of anatomical landmarks in panoramic and lateral cephalometric radiographs on a standard medical grade picture archiving communication system (PACS) monitor and a tablet computer (iPad 5). A total of 1000 radiographs, including 500 panoramic and 500 lateral cephalometric radiographs, were retrieved from the de-identified dataset of the archive of the Section of Oral and Maxillofacial Radiology of the University Of Connecticut School Of Dental Medicine. Major radiographic anatomical landmarks were independently reviewed by two examiners on both displays. The examiners initially reviewed ten panoramic and ten lateral cephalometric radiographs using each imaging system, in order to verify interoperator agreement in landmark identification. The images were scored on a four-point scale reflecting the diagnostic image quality and exposure level of the images. Statistical analysis showed no significant difference between the two displays regarding the visibility and clarity of the landmarks in either the panoramic or cephalometric radiographs. Tablet computers can reliably show anatomical landmarks in panoramic and lateral cephalometric radiographs

  18. The reliability of tablet computers in depicting maxillofacial radiographic landmarks

    Energy Technology Data Exchange (ETDEWEB)

    Tadinada, Aditya; Mahdian, Mina; Sheth, Sonam; Chandhoke, Taranpreet K.; Gopalakrishna, Aadarsh; Potluri, Anitha; Yadav, Sumit [University of Connecticut School of Dental Medicine, Farmington (United States)

    2015-09-15

    This study was performed to evaluate the reliability of the identification of anatomical landmarks in panoramic and lateral cephalometric radiographs on a standard medical grade picture archiving communication system (PACS) monitor and a tablet computer (iPad 5). A total of 1000 radiographs, including 500 panoramic and 500 lateral cephalometric radiographs, were retrieved from the de-identified dataset of the archive of the Section of Oral and Maxillofacial Radiology of the University Of Connecticut School Of Dental Medicine. Major radiographic anatomical landmarks were independently reviewed by two examiners on both displays. The examiners initially reviewed ten panoramic and ten lateral cephalometric radiographs using each imaging system, in order to verify interoperator agreement in landmark identification. The images were scored on a four-point scale reflecting the diagnostic image quality and exposure level of the images. Statistical analysis showed no significant difference between the two displays regarding the visibility and clarity of the landmarks in either the panoramic or cephalometric radiographs. Tablet computers can reliably show anatomical landmarks in panoramic and lateral cephalometric radiographs.

  19. Landmark learning by the Ozark zigzag salamander Plethodon angusticlavius

    Directory of Open Access Journals (Sweden)

    Adam L. CRANE, Alicia MATHIS

    2011-08-01

    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].

  20. An Islet-Targeted Genome-Wide Association Scan Identifies Novel Genes Implicated in Cytokine-Mediated Islet Stress in Type 2 Diabetes.

    Science.gov (United States)

    Sharma, Poonam R; Mackey, Aaron J; Dejene, Eden A; Ramadan, James W; Langefeld, Carl D; Palmer, Nicholette D; Taylor, Kent D; Wagenknecht, Lynne E; Watanabe, Richard M; Rich, Stephen S; Nunemaker, Craig S

    2015-09-01

    Genome-wide association studies in human type 2 diabetes (T2D) have renewed interest in the pancreatic islet as a contributor to T2D risk. Chronic low-grade inflammation resulting from obesity is a risk factor for T2D and a possible trigger of ?-cell failure. In this study, microarray data were collected from mouse islets after overnight treatment with cytokines at concentrations consistent with the chronic low-grade inflammation in T2D. Genes with a cytokine-induced change of >2-fold were then examined for associations between single nucleotide polymorphisms and the acute insulin response to glucose (AIRg) using data from the Genetics Underlying Diabetes in Hispanics (GUARDIAN) Consortium. Significant evidence of association was found between AIRg and single nucleotide polymorphisms in Arap3 (5q31.3), F13a1 (6p25.3), Klhl6 (3q27.1), Nid1 (1q42.3), Pamr1 (11p13), Ripk2 (8q21.3), and Steap4 (7q21.12). To assess the potential relevance to islet function, mouse islets were exposed to conditions modeling low-grade inflammation, mitochondrial stress, endoplasmic reticulum (ER) stress, glucotoxicity, and lipotoxicity. RT-PCR revealed that one or more forms of stress significantly altered expression levels of all genes except Arap3. Thapsigargin-induced ER stress up-regulated both Pamr1 and Klhl6. Three genes confirmed microarray predictions of significant cytokine sensitivity: F13a1 was down-regulated 3.3-fold by cytokines, Ripk2 was up-regulated 1.5- to 3-fold by all stressors, and Steap4 was profoundly cytokine sensitive (167-fold up-regulation). Three genes were thus closely associated with low-grade inflammation in murine islets and also with a marker for islet function (AIRg) in a diabetes-prone human population. This islet-targeted genome-wide association scan identified several previously unrecognized candidate genes related to islet dysfunction during the development of T2D. PMID:26018251

  1. Adaptive Landmark-Based Navigation System Using Learning Techniques

    DEFF Research Database (Denmark)

    Zeidan, Bassel; Dasgupta, Sakyasingha

    2014-01-01

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

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

    Science.gov (United States)

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

    2012-07-01

    We report on a complete genome scan for quantitative trait loci (QTL) affecting milk protein percentage (PP) in the Italian Holstein-Friesian cattle population, applying a selective DNA pooling strategy in a daughter design. Ten Holstein-Friesian sires were chosen, and for each sire, about 200 daughters, each from the high and low tails of estimated breeding value for PP, were used to construct milk DNA pools. Sires and pools were genotyped for 181 dinucleotide microsatellites covering all cattle autosomes. Sire marker allele frequencies in the pools were obtained by shadow correction of peak height in the electropherograms. After quality control, pool data from eight sires were used for all subsequent analyses. The QTL heterozygosity estimate was lower than that of similar studies in other cattle populations. Multiple marker mapping identified 19 QTL located on 14 chromosomes (BTA1, 2, 3, 4, 5, 6, 8, 9, 12, 14, 17, 20, 23 and 27). The sires were also genotyped for seven polymorphic sites in six candidate genes (ABCG2, SPP1, casein kappa, DGAT1, GHR and PRLR) located within QTL regions of BTA6, 14 and 20 found in this study. The results confirmed or excluded the involvement of some of the analysed markers as the causative polymorphic sites of the identified QTL. The QTL identified, combined with genotype data of these candidate genes, will help to identify other quantitative trait genes and clarify the complex QTL patterns observed for a few chromosomes. Overall, the results are consistent with the Italian Holstein population having been under long-term selection for high PP. PMID:22742505

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

    Science.gov (United States)

    Hund, Alycia M.

    2010-01-01

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

  4. 36 CFR 62.5 - Natural landmark criteria.

    Science.gov (United States)

    2010-07-01

    ... a specific type of natural feature are the main basis for selection and are described in the... history; and fossil evidence of biological evolution. Because the general character of natural diversity... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Natural landmark criteria....

  5. An Adaptive Algorithm for Finding Frequent Sets in Landmark Windows

    DEFF Research Database (Denmark)

    Dang, Xuan-Hong; Ong, Kok-Leong; Lee, Vincent

    2012-01-01

    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.

  6. Landmark Finding Algorithms for Indoor Autonomous Mobile Robot Localization

    Directory of Open Access Journals (Sweden)

    L. To?th

    2015-12-01

    Full Text Available This contribution is oriented to ways of computer vision algorithms for mobile robot localization in internal and external agricultural environment. The main aim of this work was to design, create, verify and evaluate speed and functionality of computer vision localization algorithm. An input colour camera data and depth data were captured by MS® Kinect sensor that was mounted on 6-wheel-drive mobile robot chassis. The design of the localization algorithm was focused to the most significant blobs and points (landmarks on the colour picture. Actual coordinates of autonomous mobile robot were calculated out from measured distances (depth sensor and calculated angles (RGB camera with respect to landmark points. Time measurement script was used to compare the speed of landmark finding algorithm for localization in case of one and more landmarks on picture. The main source code was written in MS Visual studio C# programming language with Microsoft.Kinect.1.7.dll on Windows based PC. Algorithms described in this article were created for a future development of an autonomous agronomical m obile robot localization and control.

  7. The Landmark Decision that Faded into Historical Obscurity

    Science.gov (United States)

    Nance, Molly

    2007-01-01

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

  8. On-line SLAM using clustered landmarks with omnidirectional vision

    Scientific Electronic Library Online (English)

    Jun, Okamoto Jr.; Vitor Campanholo, Guizilini.

    2010-12-01

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

  9. Landmark analysis of clear and conversational speaking styles

    Science.gov (United States)

    Boyce, Suzanne; Bradlow, Ann; MacAuslan, Joel

    2005-09-01

    Speakers appear to adjust speech production according to tradeoffs between intelligibility and economy of effort [Lindblom (1992)]. Recently, there has been much interest in investigation of differences between the clear style of speech addressed to disadvantaged listeners (non-native speakers, hearing impaired listeners, etc.) and ordinary, or conversational speaking style. Clear speech has been shown to be more intelligible across a wide range of listener types [Bradlow et al., (2002); Bradlow et al., (2003)], but the full range of parameters of variation remain undetermined. Recently also, the use of abrupt changes in the speech signal, i.e., acoustic landmarks, as an organizing principle for speech recognition has garnered attention [Espy-Wilson (2005)]. Using a landmark analysis procedure based on that of Stevens (1991) and Liu (1995), we present evidence that clear and conversational speaking styles can be distinguished in terms of the distribution of particular clusters of landmarks, corresponding very roughly to syllable-sized units. The implications of this differential distribution of landmarks across speaking styles for the organization of speech production will be discussed.

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

    Science.gov (United States)

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

    2008-03-01

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

  11. Two methods for locating feducial points on three-dimensional scans of the human face

    Science.gov (United States)

    Corner, Brian D.; Li, Peng; Beecher, Robert M.; Paquette, Steven

    2002-03-01

    The objects captured with three-dimensional scanners are, by themselves, of limited value. The real power of 3D scanning emerges as applications derive useful information from the point clouds. Extracting measurements from 3D human body scans is an important capability for those interested in clothing and equipment design, human factors evaluation, and web commerce, among other applications. In order to be practical, measurement extraction functions must be fast, accurate, and reliable. Automation is critical for processing the large numbers of scans envisioned by most developers. In this paper we report two functions for identifying feducial points (landmarks) on the human face. First, we used a template-matching approach where a predefined template of 34 face landmarks is matched to a head scan using a small subset of the template landmarks. Once the template is in place, interrogating local surface geometry refines landmark location. This approach allows us to locate a large number of landmarks quickly, and, more importantly, it allows us to place important but hard to locate landmarks. In our second approach, we used image-processing methods to locate a small blue dot that has been positioned on the face prior to scanning.

  12. Landmark NIH Study Shows Intensive Blood Pressure Management May Save Lives

    Science.gov (United States)

    ... News Releases News Release Friday, September 11, 2015 Landmark NIH study shows intensive blood pressure management may ... is according to the initial results of a landmark clinical trial sponsored by the National Institutes of ...

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

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

    2014-01-01

    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, overs...

  15. Evidence consistent with the multiple-bearings hypothesis from human virtual landmark-based navigation

    OpenAIRE

    Forloines, Martha R.; Bodily, Kent D.; Sturz, Bradley R.

    2015-01-01

    One approach to explaining the conditions under which additional landmarks will be learned or ignored relates to the nature of the information provided by the landmarks (i.e., distance versus bearings). In the current experiment, we tested the ability of such an approach to explain the search behavior of human participants in a virtual landmark-based navigation task by manipulating whether landmarks provided stable distance, stable direction, or both stable distance and stable direction infor...

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

    OpenAIRE

    Suriyampola, Piyumika S.; Eason, Perri K.

    2014-01-01

    Few studies have examined how landmarks affect territories' fundamental characteristics. In this field study, we investigated effects of landmarks on territory size, shape and location in a cichlid fish (Amatitlania siquia). We provided cans as breeding sites and used plastic plants as landmarks. During 10 min trials, we recorded locations where residents chased intruders and used those locations to outline and measure the territory. In two experiments, we observed pairs without landmarks and...

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

    OpenAIRE

    Beugnon Guy; Wystrach Antoine; Cheng Ken

    2011-01-01

    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 pr...

  18. Application of Soft Tissue Artifact Compensation Using Displacement Dependency between Anatomical Landmarks and Skin Markers

    OpenAIRE

    Taebeum Ryu

    2012-01-01

    Soft tissue artifact is known to be one of the main sources of errors in motion analysis by means of stereophotogrammetry. Among many approaches to reduce such errors, one is to estimate the position of anatomical landmarks during a motion with joint angle or displacement of skin markers, which is the so-called compensation method of anatomical landmarks. The position of anatomical landmarks was modeled from the data of the so-called dynamic calibration, in which anatomical landmark positions...

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

    Science.gov (United States)

    Hund, Alycia M.; Naroleski, Amber R.

    2008-01-01

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

  20. 76 FR 55701 - Landmarks Committee of the National Park System Advisory Board Meeting

    Science.gov (United States)

    2011-09-08

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... Federal Advisory Committee Act , that a meeting of the Landmarks Committee of the National Park System... Landmarks Program, National Park Service; 1849 C Street, NW., (2280), Washington, DC 20240; Telephone...

  1. 76 FR 60079 - Landmarks Committee of the National Park System Advisory Board Meeting

    Science.gov (United States)

    2011-09-28

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... Federal Advisory Committee Act , that a meeting of the Landmarks Committee of the National Park System... Landmarks Program, National Park Service; 1849 C Street, NW., (2280); Washington, DC 20240; Telephone...

  2. 36 CFR 65.8 - Alteration of National Historic Landmark boundaries.

    Science.gov (United States)

    2010-07-01

    ... Historic Landmark boundaries. 65.8 Section 65.8 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL HISTORIC LANDMARKS PROGRAM § 65.8 Alteration of National Historic Landmark boundaries. (a) Two justifications exist for enlarging the boundary of a National...

  3. 36 CFR 800.10 - Special requirements for protecting National Historic Landmarks.

    Science.gov (United States)

    2010-07-01

    ... protecting National Historic Landmarks. 800.10 Section 800.10 Parks, Forests, and Public Property ADVISORY... Special requirements for protecting National Historic Landmarks. (a) Statutory requirement. Section 110(f... and actions as may be necessary to minimize harm to any National Historic Landmark that may...

  4. 78 FR 13377 - Landmarks Committee of the National Park System Advisory Board Meeting

    Science.gov (United States)

    2013-02-27

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... Landmarks Committee of the National Park System Advisory Board will be held beginning at 1:00 p.m. on April... National Park System Advisory Board and its Landmarks Committee may consider the following...

  5. 76 FR 15338 - Landmarks Committee of the National Park System Advisory Board Meeting

    Science.gov (United States)

    2011-03-21

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... with the Federal Advisory Committee Act , that a meeting of the Landmarks Committee of the National... Henry, National Historic Landmarks Program, National Park Service; 1849 C Street, NW. (2280);...

  6. 77 FR 44670 - Information Collection Activities: National Historic Landmarks (NHL) Condition Survey

    Science.gov (United States)

    2012-07-30

    ... National Park Service Information Collection Activities: National Historic Landmarks (NHL) Condition Survey....gov (email). Please reference Information Collection 1024-NEW, National Historic Landmarks (NHL... Historic Landmarks Program, 1201 Eye St. NW., Washington, DC 20005. You may send an email to...

  7. 77 FR 53230 - Landmarks Committee of the National Park System Advisory Board Meeting

    Science.gov (United States)

    2012-08-31

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... with the Federal Advisory Committee Act, 5 U.S.C. Appendix (1988), that a meeting of the Landmarks... Park System Advisory Board and its Landmarks Committee may consider the following nominations:...

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

    Science.gov (United States)

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

    2013-09-01

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

  9. Cephalometric landmark variability among orthodontists and dentomaxillofacial radiologists: a comparative study

    Science.gov (United States)

    Morosolli, Aline; Pittayapat, Pisha; Bolstad, Napat; Ferreira, Afonso P.; Jacobs, Reinhilde

    2015-01-01

    Purpose The aim this study was to compare the accuracy of orthodontists and dentomaxillofacial radiologists in identifying 17 commonly used cephalometric landmarks, and to determine the extent of variability associated with each of those landmarks. Materials and Methods Twenty digital lateral cephalometric radiographs were evaluated by two groups of dental specialists, and 17 cephalometric landmarks were identified. The x and y coordinates of each landmark were recorded. The mean value for each landmark was considered the best estimate and used as the standard. Variation in measurements of the distance between landmarks and measurements of the angles associated with certain landmarks was also assessed by a subset of two observers, and intraobserver and interobserver agreement were evaluated. Results Intraclass correlation coefficients were excellent for intraobserver agreement, but only good for interobserver agreement. The least reliable landmark for orthodontists was the gnathion (Gn) point (standard deviation [SD], 5.92 mm), while the orbitale (Or) was the least reliable landmark (SD, 4.41 mm) for dentomaxillofacial radiologists. Furthermore, the condylion (Co)-Gn plane was the least consistent (SD, 4.43 mm). Conclusion We established that some landmarks were not as reproducible as others, both horizontally and vertically. The most consistently identified landmark in both groups was the lower incisor border, while the least reliable points were Co, Gn, Or, and the anterior nasal spine. Overall, a lower level of reproducibility in the identification of cephalometric landmarks was observed among orthodontists. PMID:26730368

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

    Directory of Open Access Journals (Sweden)

    Yanagihara Kazuyoshi

    2009-06-01

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

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

    International Nuclear Information System (INIS)

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

  12. 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 ...

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

    Science.gov (United States)

    Ghimire, Deepak; Lee, Joonwhoan

    2014-01-01

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

  14. Optimization and evaluation of landmark-based image correlation

    International Nuclear Information System (INIS)

    Image correlation methods enable the complementary use of information from different medical images of a patient. There is a need for correlation techniques requiring no preparation in advance. The authors have developed two correlation methods, both based on three or more anatomical or artificial landmarks, to be defined in corresponding image data sets. These methods have been evaluated with phantom data as well as with patient data. The authors have improved these correlation methods by using more landmarks and special selection criteria. They are applicable to all medical tomograms and to x-ray pictures taken under stereotactical conditions. The results obtained have error ranges in the order of the three-dimensional image resolution. (author)

  15. Adaptive Landmark-Based Navigation System Using Learning Techniques

    DEFF Research Database (Denmark)

    Zeidan, Bassel; Dasgupta, Sakyasingha; Wörgötter, Florentin; Manoonpong, Poramate

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

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

    Directory of Open Access Journals (Sweden)

    Beugnon Guy

    2011-08-01

    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.

  17. Effects of landmark distance and stability on accuracy of reward relocation.

    Science.gov (United States)

    Pritchard, David J; Hurly, T Andrew; Healy, Susan D

    2015-11-01

    Although small-scale navigation is well studied in a wide range of species, much of what is known about landmark use by vertebrates is based on laboratory experiments. To investigate how vertebrates in the wild use landmarks, we trained wild male rufous hummingbirds to feed from a flower that was placed in a constant spatial relationship with two artificial landmarks. In the first experiment, the landmarks and flower were 0.25, 0.5 or 1 m apart and we always moved them 3-4 m after each visit by the bird. In the second experiment, the landmarks and flower were always 0.25 m apart and we moved them either 1 or 0.25 m between trials. In tests, in which we removed the flower, the hummingbirds stopped closer to the predicted flower location when the landmarks had been closer to the flower during training. However, while the distance that the birds stopped from the landmarks and predicted flower location was unaffected by the distance that the landmarks moved between trials, the birds directed their search nearer to the predicted direction of the flower, relative to the landmarks, when the landmarks and flower were more stable in the environment. In the field, then, landmarks alone were sufficient for the birds to determine the distance of a reward but not its direction. PMID:26198691

  18. Associative basis of landmark learning and integration in vertebrates

    OpenAIRE

    Kenneth J. Leising; Aaron P. Blaisdell

    2009-01-01

    Early work on spatial navigation evaluated what stimuli (kinesthetic or extra-maze) support small-scale navigation and the nature of the underlying learning (place versus response) process. Contemporary research has focused primarily on how cues interact to determine spatial search. This review covers three general findings from research on landmark-based spatial search in vertebrates. First, pigeons and rats encode simple spatial maps in both open-field and touchscreen environments. Second, ...

  19. Elections and landmark policies in Tanzania and Uganda

    DEFF Research Database (Denmark)

    Kjær, Anne Mette; Therkildsen, Ole

    2013-01-01

    Much of the relevant literature on Africa downplays the salience of elections for policy-making and implementation. Instead, the importance of factors such as clientelism, ethnicity, organized interest group and donor influence, is emphasized. We argue that, in addition, elections now motivate political elites to focus on policies they perceive to be able to gain votes. This is based on analyses of six landmark decisions made during the last fifteen years in the social, productive and public fin...

  20. Safe Treatment of Trigger Thumb With Longitudinal Anatomic Landmarks

    OpenAIRE

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

    2010-01-01

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

  1. Cardiac Conduction System: Delineation of Anatomic Landmarks With Multidetector CT

    OpenAIRE

    Farhood Saremi; Maria Torrone; Nooshin Yashar

    2009-01-01

    Major components of the cardiac conduction system including the sinoatrial node (SAN), atrioventricular node (AVN), the His Bundle, and the right and left bundle branches are too small to be directly visualized by multidetector CT (MDCT) given the limited spatial resolution of current scanners. However, the related anatomic landmarks and variants of this system a well as the areas with special interest to electrophysiologists can be reliably demonstrated by MDCT. Some of these structures and ...

  2. Detection of point landmarks in multidimensional tensor data☆

    Science.gov (United States)

    Ruiz-Alzola, J.; Kikinis, R.; Westin, C.-F.

    2015-01-01

    This paper describes a unified approach to the detection of point landmarks—whose neighborhoods convey discriminant information—including multidimensional scalar, vector, and higher-order tensor data. The method is based on the interpretation of generalized correlation matrices derived from the gradient of tensor functions, a probabilistic interpretation of point landmarks, and the application of tensor algebra. Results on both synthetic and real tensor data are presented. PMID:26005233

  3. On-line SLAM using clustered landmarks with omnidirectional vision

    OpenAIRE

    Jun Okamoto Jr.; Vitor Campanholo Guizilini

    2010-01-01

    The problem of SLAM (simultaneous localization and mapping) is a fundamental problem in autonomous robotics. It arises when a robot must create a map of the regions it has navigated while localizing itself on it, using results from one step to increase precision in another by eliminating errors inherent to the sensors. One common solution consists of establishing landmarks in the environment which are used as reference points for absolute localization estimates and form a sparse map that is i...

  4. Visual landmarks facilitate rodent spatial navigation in virtual reality environments

    OpenAIRE

    Youngstrom, Isaac A.; Strowbridge, Ben W.

    2012-01-01

    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 ...

  5. Color-contrast landmark detection and encoding in outdoor images

    OpenAIRE

    Todt, Eduardo; Torras Genís, Carme

    2005-01-01

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

  6. Dung beetles ignore landmarks for straight-line orientation.

    Science.gov (United States)

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

    2013-01-01

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

  7. Neural Network Based Sensory Fusion for Landmark Detection

    Science.gov (United States)

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

    1997-01-01

    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.

  8. AUTOMATIC DETECTION AND CLASSIFICATION OF RETINAL VASCULAR LANDMARKS

    Directory of Open Access Journals (Sweden)

    Hadi Hamad

    2014-06-01

    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.

  9. Quality-Aware Estimation of Facial Landmarks in Video Sequences

    DEFF Research Database (Denmark)

    Haque, Mohammad Ahsanul; Nasrollahi, Kamal

    2015-01-01

    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).

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

    International Nuclear Information System (INIS)

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

  11. New Statistical Method to Analyze Three-Dimensional Landmark Configurations Obtained with Cone-Beam CT: Basic Features and Clinical Application for Rapid Maxillary Expansion

    International Nuclear Information System (INIS)

    To describe a statistical method of three-dimensional landmark configuration data and apply it to an orthodontic data set comparing two types of rapid maxillary expansion (RME) treatments. Landmark configurations obtained from cone beam CT scans were used to represent patients in two types (please describe what were two types) of RME groups and a control group over four time points. A method using tools from persistent homology and dimensionality reduction is presented and used to identify variability between the subjects. The analysis was in agreement with previous results using conventional methods, which found significant differences between treatment groups and the control, but no distinction between the types of treatment. Additionally, it was found that second molar eruption varied considerably between the subjects, and this has not been evaluated in previous analyses. This method of analysis allows entire configurations to be considered as a whole, and does not require specific inter-landmark distances or angles to be selected. Sources of variability present themselves, without having to be individually sought after. This method is suggested as an additional tool for the analysis of landmark configuration data.

  12. New Statistical Method to Analyze Three-Dimensional Landmark Configurations Obtained with Cone-Beam CT: Basic Features and Clinical Application for Rapid Maxillary Expansion

    Energy Technology Data Exchange (ETDEWEB)

    Gamble, Jennifer; Lagravere, Manuel O.; Major, Paul W.; Heo, Giseon [University of Alberta, Edmonton (Canada)

    2012-03-15

    To describe a statistical method of three-dimensional landmark configuration data and apply it to an orthodontic data set comparing two types of rapid maxillary expansion (RME) treatments. Landmark configurations obtained from cone beam CT scans were used to represent patients in two types (please describe what were two types) of RME groups and a control group over four time points. A method using tools from persistent homology and dimensionality reduction is presented and used to identify variability between the subjects. The analysis was in agreement with previous results using conventional methods, which found significant differences between treatment groups and the control, but no distinction between the types of treatment. Additionally, it was found that second molar eruption varied considerably between the subjects, and this has not been evaluated in previous analyses. This method of analysis allows entire configurations to be considered as a whole, and does not require specific inter-landmark distances or angles to be selected. Sources of variability present themselves, without having to be individually sought after. This method is suggested as an additional tool for the analysis of landmark configuration data.

  13. CT Scans

    Science.gov (United States)

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

  14. Renal scan

    Science.gov (United States)

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

  15. Model-based automatic detection of the anterior and posterior commissures on MRI scans.

    Science.gov (United States)

    Ardekani, Babak A; Bachman, Alvin H

    2009-07-01

    The projections of the anterior and posterior commissures (AC/PC) on the mid-sagittal plane of the human brain are important landmarks in neuroimaging. They can be used, for example, during MRI scanning for acquiring the imaging sections in a standard orientation. In post-acquisition image processing, these landmarks serve to establish an anatomically-based frame of reference within the brain that can be extremely useful in designing automated image analysis algorithms such as image segmentation and registration methods. This paper presents a fully automatic model-based algorithm for AC/PC detection on MRI scans. The algorithm utilizes information from a number of model images on which the locations of the AC/PC and a reference point (the vertex of the superior pontine sulcus) are known. This information is then used to locate the landmarks on test scans by template matching. The algorithm is designed to be fast, robust, and accurate. The method is flexible in that it can be trained to work on different image contrasts, optimized for different populations, or scanning modes. To assess the effectiveness of this technique, we compared automatically and manually detected landmark locations on 84 T(1)-weighted and 42 T(2)-weighted test scans. Overall, the average Euclidean distance between automatically and manually detected landmarks was 1.1 mm. A software implementation of the algorithm is freely available online at www.nitrc.org/projects/art. PMID:19264138

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Lavoie, Caroline; Higgins, Jane; Bissonnette, Jean-Pierre [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada); Le, Lisa W. [Department of Biostatistics, Princess Margaret Hospital, Toronto, Ontario, M5G 2M9 (Canada); Sun, Alexander; Brade, Anthony; Hope, Andrew; Cho, John [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada); Bezjak, Andrea, E-mail: andrea.bezjak@rmp.uhn.on.ca [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada)

    2012-12-01

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

  18. Brain scanning

    International Nuclear Information System (INIS)

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

  19. Multifunction Digital Research Scanning System

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2013-10-01

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

  2. Statistical analysis of shape through triangulation of landmarks: A study of sexual dimorphism in hominids

    OpenAIRE

    Rao, Calyampudi R.; Suryawanshi, Shailaja

    1998-01-01

    Two objects with homologous landmarks are said to be of the same shape if the configuration of landmarks of one object can be exactly matched with that of the other by translation, rotation/reflection, and scaling. In an earlier paper, the authors proposed statistical analysis of shape by considering logarithmic differences of all possible Euclidean distances between landmarks. Tests of significance for differences in the shape of objects and methods of discrimination between populations were...

  3. From Objects to Landmarks: The Function of Visual Location Information in Spatial Navigation

    OpenAIRE

    OliverBaumann; MarkA.Bellgrove

    2012-01-01

    Landmarks play an important role in guiding navigational behavior. A host of studies in the last 15?years has demonstrated that environmental objects can act as landmarks for navigation in different ways. In this review, we propose a parsimonious four-part taxonomy for conceptualizing object location information during navigation. We begin by outlining object properties that appear to be important for a landmark to attain salience. We then systematically examine the different functions of obj...

  4. First Steps toward Location of Landmarks on X-Ray Images

    OpenAIRE

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

    2000-01-01

    We address the problem of locating some anatomical bone structures on lateral cranial X-ray images. These structures are landmarks used in orthodontic therapy. The main problem in this pattern recognition application is that the landmarks are difficult to distinguish on images even for the human expert, because of lateral projection of the X-ray process. We propose a 3 steps approach: the first step provides a statistical estimation of the landmarks, using an adaptive coordinates space; the s...

  5. All that Glitters is not Gold: Using Landmarks for Reward Shaping in FPG

    OpenAIRE

    Buffet, Olivier; Hoffmann, Joerg

    2010-01-01

    Landmarks are facts that must be true at some point in any plan. It has recently been proposed in classical planning to use landmarks for the automatic generation of heuristic functions. We herein apply this idea in probabilistic planning. We focus on the FPG tool, which derives a factored policy based on learning from samples into the state space. The rationale is that FPG's performance can be improved significantly by a trivial heuristic that counts the number of false goals; landmarks prov...

  6. "Localization Space" : a framework for localization and planning, for systems using a Sensor/Landmarks module

    OpenAIRE

    Pradalier, Cédric; Sekhavat, Sepanta

    2002-01-01

    One of the common ways of localization in robotics is the triangulation using a system composed of a sensor and some landmarks (which can be artificial or natural). This paper presents a framework, namely the Localization Space, in order to deal with problems such as the landmark placement and motion planning including the localization constraint. Based on this framework, we present general approaches to the optimal distribution of the landmarks or to the computation of reliable trajectories....

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

    OpenAIRE

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

    2014-01-01

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

  8. Evidence for a colorectal cancer susceptibility locus on chromosome 3q21-q24 from a high-density SNP genome-wide linkage scan.

    Science.gov (United States)

    Kemp, Zoe; Carvajal-Carmona, Luis; Spain, Sarah; Barclay, Ella; Gorman, Margaret; Martin, Lynn; Jaeger, Emma; Brooks, Neil; Bishop, D Timothy; Thomas, Huw; Tomlinson, Ian; Papaemmanuil, Elli; Webb, Emily; Sellick, Gabrielle S; Wood, Wendy; Evans, Gareth; Lucassen, Anneke; Maher, Eamonn R; Houlston, Richard S

    2006-10-01

    To identify a novel susceptibility gene for colorectal cancer (CRC), we conducted a genome-wide linkage analysis of 69 pedigrees segregating colorectal neoplasia in which involvement of known loci had been excluded, using a high-density single nucleotide polymorphism (SNP) array containing 10,204 markers. Multipoint linkage analyses were undertaken using both non-parametric (model-free) and parametric (model-based) methods. After the removal of SNPs in strong linkage disequilibrium, we obtained a maximum non-parametric linkage statistic of 3.40 (P=0.0003) at chromosomal region 3q21-q24. The same genomic position also yielded the highest multipoint heterogeneity LOD (HLOD) score under a dominant model (HLOD=3.10, genome-wide P=0.038) with 62% of families linked to the locus. We provide evidence for a novel CRC susceptibility gene. Further studies are needed to confirm this localization and to evaluate the contribution of this locus to disease incidence. PMID:16923799

  9. Brain scan

    International Nuclear Information System (INIS)

    Brain scanning is used to determine the presence, location, and course of neurologic disease. Tumors, cerebral infarcts, abscesses, and trauma present as areas of increased isotope uptake on the scan. In reaching a diagnosis, results of physical examination and laboratory studies should be evaluated in conjunction with the scintigraphic findings. While the scan helps detect focal neurologic disease, accurate differential diagnosis usually requires further neuroradiologic studies. (U.S.)

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

    OpenAIRE

    Hillmer, Axel M.; Flaquer, Antonia; Hanneken, Sandra; Eigelshoven, Sibylle; Kortüm, 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

    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...

  11. Ligands of Thermophilic ABC Transporters Encoded in a Newly Sequenced Genomic Region of Thermotoga maritima MSB8 Screened by Differential Scanning Fluorimetry ? †

    OpenAIRE

    Boucher, Nathalie; Noll, Kenneth M

    2011-01-01

    The chromosome of Thermotoga maritima strain MSB8 was found to have an 8,870-bp region that is not present in its published sequence. The isolate that was sequenced by The Institute for Genomic Research (TIGR) in 1999 is apparently a laboratory variant of the isolate deposited at the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSM 3109) in 1986. This newly sequenced region from the DSMZ culture was located between TM1848 (cbp, cellobiose phosphorylase) and TM1847 (the 3? end of a ...

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

    OpenAIRE

    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; De Jaeger, E (Emmanuel)

    2007-01-01

    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...

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

    International Nuclear Information System (INIS)

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

  14. Brain scanning

    International Nuclear Information System (INIS)

    The brain scan offers a simple, sensitive, and atraumatic evaluation of suspected intracranial pathological conditions. Utilizing a variety of diagnostic approaches, including new radiopharmaceuticals, the physician in nuclear medicine is frequently able to modify the technique for a particular individual problem. With proper use, the clinician may expect the scan to yield a high return of important diagnostic information. (U.S.)

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

    Science.gov (United States)

    Sutton, Jennifer E.

    2006-01-01

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

  16. Looking beyond the Boundaries: Time to Put Landmarks Back on the Cognitive Map?

    Science.gov (United States)

    Lew, Adina R.

    2011-01-01

    Since the proposal of Tolman (1948) that mammals form maplike representations of familiar environments, cognitive map theory has been at the core of debates on the fundamental mechanisms of animal learning and memory. Traditional formulations of cognitive map theory emphasize relations between landmarks and between landmarks and goal locations as…

  17. 36 CFR 13.1904 - Kennecott Mines National Historic Landmark (KNHL).

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Kennecott Mines National Historic Landmark (KNHL). 13.1904 Section 13.1904 Parks, Forests, and Public Property NATIONAL PARK SERVICE... National Park and Preserve § 13.1904 Kennecott Mines National Historic Landmark (KNHL). A map showing...

  18. 36 CFR 65.9 - Withdrawal of National Historic Landmark designation.

    Science.gov (United States)

    2010-07-01

    ... National Register criteria for evalution in 36 CFR 60.4, except if the property is redesignated on... Historic Landmark designation. 65.9 Section 65.9 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL HISTORIC LANDMARKS PROGRAM § 65.9 Withdrawal of National...

  19. 75 FR 16837 - Public Review of Draft United States Thoroughfare, Landmark, and Postal Address Data Standard

    Science.gov (United States)

    2010-04-02

    ... Address Data Standard AGENCY: Department of the Interior, U.S. Geological Survey. ACTION: Notice; request for comments on draft United States Thoroughfare, Landmark, and Postal Address Data Standard through... the draft United States Thoroughfare, Landmark, and Postal Address Data Standard. The United...

  20. Posterior belly of the digastric muscle: An important landmark for various head and neck surgeries

    Directory of Open Access Journals (Sweden)

    Vrinda Hari Ankolekar

    2015-04-01

    Conclusion: As the PBD muscle is an important surgical landmark, the present study adds to the existing knowledge about it. The present study has also included few newer landmarks, which were not given importance in the previous studies. [Arch Clin Exp Surg 2015; 4(2.000: 79-82

  1. Conservation landmarks: bureau of biological survey and national biological service

    Science.gov (United States)

    Friend, M.

    1995-01-01

    A century separates the recent development of the National Biological Service (NBS) and an early predecessor, the Bureau of Biological Survey (BBS). Both organizations were established at critical crossroads for the conservation of the nation's living biological resources and are conservation landmarks of their times. The BBS of the 192()'s was described as 'a government Bureau of the first rank, handling affairs of great scientific, educational, social, and above all, economic importance throughout the United States and its outlying possessions'' (Cameron 1929:144-145). This stature was achieved at a time of great social, economic, and ecological change. BBS had the vision to pioneer new approaches that led to enhanced understanding of the relation between people, other living things, and the environment. The NBS faces similar challenges to address the issues of the 1990's and beyond.

  2. Elections and landmark policies in Tanzania and Uganda

    DEFF Research Database (Denmark)

    Kjær, Anne Mette; Therkildsen, Ole

    2013-01-01

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

  3. FACIAL LANDMARKING LOCALIZATION FOR EMOTION RECOGNITION USING BAYESIAN SHAPE MODELS

    Directory of Open Access Journals (Sweden)

    Hernan F. Garcia

    2013-02-01

    Full Text Available This work presents a framework for emotion recognition, based in facial expression analysis using Bayesian Shape Models (BSM for facial landmarking localization. The Facial Action Coding System (FACS compliant facial feature tracking based on Bayesian Shape Model. The BSM estimate the parameters of the model with an implementation of the EM algorithm. We describe the characterization methodology from parametric model and evaluated the accuracy for feature detection and estimation of the parameters associated with facial expressions, analyzing its robustness in pose and local variations. Then, a methodology for emotion characterization is introduced to perform the recognition. The experimental results show that the proposed model can effectively detect the different facial expressions. Outperforming conventional approaches for emotion recognition obtaining high performance results in the estimation of emotion present in a determined subject. The model used and characterization methodology showed efficient to detect the emotion type in 95.6% of the cases.

  4. 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)

    Hampe O Baszio S

    2010-06-01

    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

  5. MRI Scans

    Science.gov (United States)

    Magnetic resonance imaging (MRI) uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from ...

  6. PET scan

    Science.gov (United States)

    ... and tissues are working. This is different than magnetic resonance imaging (MRI) and computed tomography (CT), which ... the scan. You will be able to drink water. If you have diabetes, your health care provider ...

  7. Scanning rheometer

    OpenAIRE

    Javier Alvarez, Nicolas; Hassager, Ole

    2015-01-01

    The present disclosure relates to a filament stretching rheometer for measuring rheological and/or mechanical properties of a sample, comprising: a pair of opposed surfaces for holding the sample therebetween; an actuator configured to provide a controlled axial displacement of at least one of said opposed surfaces; and a sample scanning unit for measuring a diameter of said sample, the sample scanning unit configured for measuring said sample diameter at an axial position controlled independ...

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

    Scientific Electronic Library Online (English)

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

    2010-12-01

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

  9. A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease.

    Science.gov (United States)

    Buch, Stephan; Schafmayer, Clemens; Völzke, Henry; Becker, Christian; Franke, Andre; von Eller-Eberstein, Huberta; Kluck, Christian; Bässmann, Ingelore; Brosch, Mario; Lammert, Frank; Miquel, Juan Francisco; Nervi, Flavio; Wittig, Michael; Rosskopf, Dieter; Timm, Birgit; Höll, Christine; Seeger, Marcus; ElSharawy, Abdou; Lu, Tim; Egberts, Jan; Fändrich, Fred; Fölsch, Ulrich R; Krawczak, Michael; Schreiber, Stefan; Nürnberg, Peter; Tepel, Jürgen; Hampe, Jochen

    2007-08-01

    With an overall prevalence of 10-20%, gallstone disease (cholelithiasis) represents one of the most frequent and economically relevant health problems of industrialized countries. We performed an association scan of >500,000 SNPs in 280 individuals with gallstones and 360 controls. A follow-up study of the 235 most significant SNPs in 1,105 affected individuals and 873 controls replicated the disease association of SNP A-1791411 in ABCG8 (allelic P value P(CCA) = 4.1 x 10(-9)), which was subsequently attributed to coding variant rs11887534 (D19H). Additional replication was achieved in 728 German (P = 2.8 x 10(-7)) and 167 Chilean subjects (P = 0.02). The overall odds ratio for D19H carriership was 2.2 (95% confidence interval: 1.8-2.6, P = 1.4 x 10(-14)) in the full German sample. Association was stronger in subjects with cholesterol gallstones (odds ratio = 3.3), suggesting that His19 might be associated with a more efficient transport of cholesterol into the bile. PMID:17632509

  10. Optimal reinforcement of training datasets in semi-supervised landmark-based segmentation

    Science.gov (United States)

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

    2015-03-01

    During the last couple of decades, the development of computerized image segmentation shifted from unsupervised to supervised methods, which made segmentation results more accurate and robust. However, the main disadvantage of supervised segmentation is a need for manual image annotation that is time-consuming and subjected to human error. To reduce the need for manual annotation, we propose a novel learning approach for training dataset reinforcement in the area of landmark-based segmentation, where newly detected landmarks are optimally combined with reference landmarks from the training dataset and therefore enriches the training process. The approach is formulated as a nonlinear optimization problem, where the solution is a vector of weighting factors that measures how reliable are the detected landmarks. The detected landmarks that are found to be more reliable are included into the training procedure with higher weighting factors, whereas the detected landmarks that are found to be less reliable are included with lower weighting factors. The approach is integrated into the landmark-based game-theoretic segmentation framework and validated against the problem of lung field segmentation from chest radiographs.

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

    International Nuclear Information System (INIS)

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

  12. Landmark constrained genus-one surface Teichmüller map applied to surface registration in medical imaging.

    Science.gov (United States)

    Lam, Ka Chun; Gu, Xianfeng; Lui, Lok Ming

    2015-10-01

    We address the registration problem of genus-one surfaces (such as vertebrae bones) with prescribed landmark constraints. The high-genus topology of the surfaces makes it challenging to obtain a unique and bijective surface mapping that matches landmarks consistently. This work proposes to tackle this registration problem using a special class of quasi-conformal maps called Teichmüller maps (T-Maps). A landmark constrained T-Map is the unique mapping between genus-1 surfaces that minimizes the maximal conformality distortion while matching the prescribed feature landmarks. Existence and uniqueness of the landmark constrained T-Map are theoretically guaranteed. This work presents an iterative algorithm to compute the T-Map. The main idea is to represent the set of diffeomorphism using the Beltrami coefficients (BC). The BC is iteratively adjusted to an optimal one, which corresponds to our desired T-Map that matches the prescribed landmarks and satisfies the periodic boundary condition on the universal covering space. Numerical experiments demonstrate the effectiveness of our proposed algorithm. The method has also been applied to register vertebrae bones with prescribed landmark points and curves, which gives accurate surface registrations. PMID:25977154

  13. Landmarks of History of Soil Science in Sri Lanka

    Science.gov (United States)

    Mapa, R.

    2012-04-01

    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

  14. Robust anatomical landmark detection with application to MR brain image registration.

    Science.gov (United States)

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

    2015-12-01

    Comparison of human brain MR images is often challenged by large inter-subject structural variability. To determine correspondences between MR brain images, most existing methods typically perform a local neighborhood search, based on certain morphological features. They are limited in two aspects: (1) pre-defined morphological features often have limited power in characterizing brain structures, thus leading to inaccurate correspondence detection, and (2) correspondence matching is often restricted within local small neighborhoods and fails to cater to images with large anatomical difference. To address these limitations, we propose a novel method to detect distinctive landmarks for effective correspondence matching. Specifically, we first annotate a group of landmarks in a large set of training MR brain images. Then, we use regression forest to simultaneously learn (1) the optimal sets of features to best characterize each landmark and (2) the non-linear mappings from the local patch appearances of image points to their 3D displacements towards each landmark. The learned regression forests are used as landmark detectors to predict the locations of these landmarks in new images. Because each detector is learned based on features that best distinguish the landmark from other points and also landmark detection is performed in the entire image domain, our method can address the limitations in conventional methods. The deformation field estimated based on the alignment of these detected landmarks can then be used as initialization for image registration. Experimental results show that our method is capable of providing good initialization even for the images with large deformation difference, thus improving registration accuracy. PMID:26433614

  15. Generalized multiresolution hierarchical shape models via automatic landmark clusterization.

    Science.gov (United States)

    Cerrolaza, Juan J; Villanueva, Arantxa; Reyes, Mauricio; Cabeza, Rafael; González Ballester, Miguel Angel; Linguraru, Marius George

    2014-01-01

    Point Distribution Models (PDM) are some of the most popular shape description techniques in medical imaging. However, to create an accurate shape model it is essential to have a representative sample of the underlying population, which is often challenging. This problem is particularly relevant as the dimensionality of the modeled structures increases, and becomes critical when dealing with complex 3D shapes. In this paper, we introduce a new generalized multiresolution hierarchical PDM (GMRH-PDM) able to efficiently address the high-dimension-low-sample-size challenge when modeling complex structures. Unlike previous approaches, our new and general framework extends hierarchical modeling to any type of structure (multi- and single-object shapes) allowing to describe efficiently the shape variability at different levels of resolution. Importantly, the configuration of the algorithm is automatized thanks to the new agglomerative landmark clustering method presented here. Our new and automatic GMRH-PDM framework performed significantly better than classical approaches, and as well as the state-of-the-art with the best manual configuration. Evaluations have been studied for two different cases, the right kidney, and a multi-object case composed of eight subcortical structures. PMID:25320775

  16. Landmark-free geometric methods in biological shape analysis.

    Science.gov (United States)

    Koehl, Patrice; Hass, Joel

    2015-12-01

    In this paper, we propose a new approach for computing a distance between two shapes embedded in three-dimensional space. We take as input a pair of triangulated genus zero surfaces that are topologically equivalent to spheres with no holes or handles, and construct a discrete conformal map f between the surfaces. The conformal map is chosen to minimize a symmetric deformation energy Esd(f) which we introduce. This measures the distance of f from an isometry, i.e. a non-distorting correspondence. We show that the energy of the minimizing map gives a well-behaved metric on the space of genus zero surfaces. In contrast to most methods in this field, our approach does not rely on any assignment of landmarks on the two surfaces. We illustrate applications of our approach to geometric morphometrics using three datasets representing the bones and teeth of primates. Experiments on these datasets show that our approach performs remarkably well both in shape recognition and in identifying evolutionary patterns, with success rates similar to, and in some cases better than, those obtained by expert observers. PMID:26631331

  17. Landmarking and feature localization in spine x-rays

    Science.gov (United States)

    Long, L. Rodney; Thoma, George R.

    2001-10-01

    The general problem of developing algorithms for the automated or computer-assisted indexing of images by structural contents is a significant research challenge. This is particularly so in the case of biomedical images, where the structures of interest are commonly irregular, overlapping, and partially occluded. Examples are the images created by digitizing film x-rays of the human cervical and lumbar spines. We have begun work toward the indexing of 17 000 such spine images for features of interest in the osteoarthritis and vertebral morphometry research communities. This work requires the segmentation of the images into vertebral structures with sufficient accuracy to distinguish pathology on the basis of shape, labeling of the segmented structures by proper anatomical name, and classification of the segmented, labeled structures into groups corresponding to high level semantic features of interest, using training data provided by biomedical experts. In this paper, we provide a technical characterization of the cervical spine images and the biomedical features of interest, describe the evolving technical approach for the segmentation and indexing problem, and provide results of algorithms to acquire basic landmark data and localization of spine regions in the images.

  18. 77 FR 44670 - Information Collection Activities: National Historic Landmarks (NHL) Condition Survey

    Science.gov (United States)

    2012-07-30

    ...regarding the condition of designated landmarks. A questionnaire will be designed and used to collect information...condition data. Regional NPS staff contributed to the design of the questionnaire that is the subject of this request. II....

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

    Science.gov (United States)

    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

    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

  20. Integrated landmark and outline-based morphometric methods efficiently distinguish species of Euglossa (Hymenoptera, Apidae, Euglossini)

    OpenAIRE

    Francoy, Tiago; Faria Franco, Fernando; Roubik, David

    2012-01-01

    Morphometric methods permit identification of insect species and are an aid for taxonomy. Quantitative wing traits were used to identify male euglossine bees. Landmark- and outline-based methods have been primarily used independently. Here, we combine the two methods using five Euglossa. Landmark-based methods correctly classified 84% and outline-based 77%, but an integrated analysis correctly classified 91% of samples. Some species presented significantly high reclassification percentages wh...

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

    OpenAIRE

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

    2013-01-01

    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 o...

  2. Parsing radiographs by integrating landmark set detection and multi-object active appearance models

    OpenAIRE

    Montillo, Albert; Song, Qi; LIU, XIAOMING; Miller, James V

    2013-01-01

    This work addresses the challenging problem of parsing 2D radiographs into salient anatomical regions such as the left and right lungs and the heart. We propose the integration of an automatic detection of a constellation of landmarks via rejection cascade classifiers and a learned geometric constellation subset detector model with a multi-object active appearance model (MO-AAM) initialized by the detected landmark constellation subset. Our main contribution is twofold. First, we propose a re...

  3. Interspecific differences in response to novel landmarks in bumblebees (Bombus sp.)

    OpenAIRE

    Goulson, Dave; Darvill, Ben; Ellis, Jon; Knight, Mairi; Hanley, Mick

    2004-01-01

    We provide evidence for interspecific differences in the behaviour of bumblebees which suggests that there may be important differences in the way that they navigate. Bumblebees commonly investigate the novel landmark presented by a human standing in open countryside. When doing so they perform a characteristic flight similar to that observed when a naïve bee first leaves the nest, suggesting that they are memorising the location of an unfamiliar landmark. We compare the frequency with which ...

  4. Vision-based Navigation Using Landmark Recognition for Unmanned Aerial Vehicles

    OpenAIRE

    Mannberg, Mikael

    2014-01-01

    This thesis describes a new approach for a vision-based positioning system for Un- manned Aerial Vehicles using a recognition method based on known, robust geo- graphic landmarks. Landmarks are used to calculate a position estimate in a global coordinate frame without requiring external signals, such as GPS. Absolute systems are of interest as they provide a redundant positioning system, allow UAVs to oper- ate when GPS-denied and can enable high-precision landings for spacecra...

  5. Effects of image enhancement on reliability of landmark identification in digital cephalometry

    Directory of Open Access Journals (Sweden)

    M Oshagh

    2013-01-01

    Full Text Available Introduction: Although digital cephalometric radiography is gaining popularity in orthodontic practice, the most important source of error in its tracing is uncertainty in landmark identification. Therefore, efforts to improve accuracy in landmark identification were directed primarily toward the improvement in image quality. One of the more useful techniques of this process involves digital image enhancement which can increase overall visual quality of image, but this does not necessarily mean a better identification of landmarks. The purpose of this study was to evaluate the effectiveness of digital image enhancements on reliability of landmark identification. Materials and Methods: Fifteen common landmarks including 10 skeletal and 5 soft tissues were selected on the cephalograms of 20 randomly selected patients, prepared in Natural Head Position (NHP. Two observers (orthodontists identified landmarks on the 20 original photostimulable phosphor (PSP digital cephalogram images and 20 enhanced digital images twice with an intervening time interval of at least 4 weeks. The x and y coordinates were further analyzed to evaluate the pattern of recording differences in horizontal and vertical directions. Reliability of landmarks identification was analyzed by paired t test. Results: There was a significant difference between original and enhanced digital images in terms of reliability of points Ar and N in vertical and horizontal dimensions, and enhanced images were significantly more reliable than original images. Identification of A point, Pogonion and Pronasal points, in vertical dimension of enhanced images was significantly more reliable than original ones. Reliability of Menton point identification in horizontal dimension was significantly more in enhanced images than original ones. Conclusion: Direct digital image enhancement by altering brightness and contrast can increase reliability of some landmark identification and this may lead to more accurate cephalometric analysis.

  6. Learning Compact Visual Descriptors for Low Bit Rate Mobile Landmark Search

    OpenAIRE

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

    2013-01-01

    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...

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

    OpenAIRE

    Fry, S. N.; Wehner, R

    2005-01-01

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

  8. A class of spline functions for landmark-based image registration

    OpenAIRE

    De Rossi, Alessandra; Cavoretto, Roberto; Allasia, Giampietro

    2012-01-01

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

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

    OpenAIRE

    Rosalia Leonardi; Daniela Giordano; Francesco Maiorana

    2009-01-01

    Several efforts have been made to completely automate cephalometric analysis by automatic landmark search. However, accuracy obtained was worse than manual identification in every study. The analogue-to-digital conversion of X-ray has been claimed to be the main problem. Therefore the aim of this investigation was to evaluate the accuracy of the Cellular Neural Networks approach for automatic location of cephalometric landmarks on softcopy of direct digital cephalometric X-rays. Forty-one, di...

  10. 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

  11. An Effect of Landmarks on Territory Shape in a Convict Cichlid.

    Science.gov (United States)

    Mesterton-Gibbons, Mike; Dai, Yao

    2015-12-01

    We determine size, shape and location for a territory that is optimal in the sense of minimizing defense costs, when a given proportion of the boundary is landmarked and its primary benefit in terms of fitness is greater ease of detecting intruders across it. Increasing the landmarked proportion of boundary causes the optimal configuration to be smaller and more elongated, and to be located with its center further from the nest, so that the nest is closer to the landmarked boundary. These predictions accord with observations in a recent study of the convict cichlid Amatitlania siquia. Our results thus confirm the consistency of the observed behavior with the hypothesis that A. siquia designs its territory to make intruders easier to spot. Our results also lead us to conjecture that moving the landmark proportionately closer to or further away from the nest would have yielded essentially the same outcome in this study, because the optimal configuration depends only on the angle subtended by the landmark at the nest and hence only on the length of the landmark relative to its distance from the nest, as opposed to its absolute value. PMID:26621358

  12. Configurational salience of landmarks: an analysis of sketch maps using Space Syntax.

    Science.gov (United States)

    von Stülpnagel, Rul; Frankenstein, Julia

    2015-09-01

    We conducted a visibility graph analysis (a Space Syntax method) of a virtual environment to examine how the configurational salience of global and local landmarks (i.e., their relative positions in the environment) as compared to their visual salience affects the probability of their depiction on sketch maps. Participants of two experimental conditions produced sketch maps from memory after exploration with a layout map or without a map, respectively. Participants of a third condition produced sketch maps in parallel to exploration. More detailed sketch maps were produced in the third condition, but landmarks with higher configurational salience were depicted more frequently across all experimental conditions. Whereas the inclusion of global landmarks onto sketch maps was best predicted by their size, both visual salience and isovist size (i.e., the area a landmark was visible from) predicted the frequency of depiction for local landmarks. Our findings imply that people determine the relevance of landmarks not only by their visual, but even more by their configurational salience. PMID:26239756

  13. Ultrasound Guided Internal Jugular Venous Cannulation: Comparison with Land-Mark Technique

    International Nuclear Information System (INIS)

    Objective: To compare real-time ultrasonography-guided technique versus the traditional land-mark technique for internal Jugular venous cannulation. Study Design: Randomized controlled trial. Place and Duration of Study: Department of Anaesthesia, Combined Military Hospital, Rawalpindi, from September 2013 to July 2014. Methodology:Atotal of 200 patients who required internal jugular vein cannulation were randomly assigned using either real-time ultrasound-guided technique or land-mark technique. Access time, number of attempts until successful cannulation, complications and the demographics of each patient were recorded. Results:Access time was significantly less in real-time ultrasound group (34.95 ± 11.47 vs. 146.59 ± 40.20 seconds, p < 0.001). Cannulation was performed in first attempt in 99 percentage of patients in ultrasound group as compared to 89 percentage of landmark group. Complication rate was significantly higher in the land-mark group than in the ultrasound-guided group. Carotid artery puncture rate (9 percentage vs. 1 percentage) and haematoma formation (7 percentage vs. 0 percentage) were more frequent in the land-mark group than in the ultrasound-guided group. Brachial plexus irritation was also more in land-mark group (6 percentage vs. 0 percentage). Conclusion:Access time, failure rate and procedure related complications are reduced when real-time ultrasonography is used to cannulate internal Jugular vein. (author)

  14. How you get there from here: interaction of visual landmarks and path integration in human navigation.

    Science.gov (United States)

    Zhao, Mintao; Warren, William H

    2015-06-01

    How do people combine their sense of direction with their use of visual landmarks during navigation? Cue-integration theory predicts that such cues will be optimally integrated to reduce variability, whereas cue-competition theory predicts that one cue will dominate the response direction. We tested these theories by measuring both accuracy and variability in a homing task while manipulating information about path integration and visual landmarks. We found that the two cues were near-optimally integrated to reduce variability, even when landmarks were shifted up to 90°. Yet the homing direction was dominated by a single cue, which switched from landmarks to path integration when landmark shifts were greater than 90°. These findings suggest that cue integration and cue competition govern different aspects of the homing response: Cues are integrated to reduce response variability but compete to determine the response direction. The results are remarkably similar to data on animal navigation, which implies that visual landmarks reset the orientation, but not the precision, of the path-integration system. PMID:25944773

  15. Reliability and reproducibility of three-dimensional cephalometric landmarks using CBCT: a systematic review

    Scientific Electronic Library Online (English)

    Cinthia de Oliveira, LISBOA; Daniele, MASTERSON; Andréa Fonseca Jardim, MOTTA; Alexandre Trindade, MOTTA.

    2015-04-01

    Full Text Available Objective : The aim of this study was to review the reliability and reproducibility of 3D-CBCT (cone beam computed tomography) cephalometric landmark identification. Methods : Electronic databases (Pubmed, Scopus, Web of Science) were searched for papers published from 1998 to October 2014. Specifi [...] c strategies were developed for each database, with the guidance of a librarian. Two reviewers independently analyzed the titles and abstracts for inclusion. The articles that met the inclusion and exclusion criteria were selected for full-text reading, and the selected articles went through methodological quality evaluation. After the exclusion of repeated articles, the titles of the remaining ones were read and 1,328 of them were excluded. The abstracts of 173 articles were read, of which 43 were selected, read in full and submitted to the inclusion and exclusion criteria. Fourteen articles or studies with reliable methodology and reproducibility remained. The data were collected, organized into figures and analyzed for determination of the reliability and reproducibility of the three-dimensional cephalometric landmarks. Results : Overall, the landmarks on the median sagittal line and dental landmarks had the highest reliability, while the landmarks on the condyle, porion and the orbitale presented lower levels of reliability. Point S must be marked in the multiplanar views associated with visualization in 3D reconstruction. Further studies are necessary for evaluating soft tissue landmarks.

  16. 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)

  17. Femoral arterial puncture: comparison of using the inguinal crease and bony landmarks

    International Nuclear Information System (INIS)

    We tried to compare the accuracy of using bony landmarks and inguinal crease landmarks for performing femoral artery puncture and to determine an ideal puncture site. We studied ninety consecutive patients who underwent femoral arterial puncture for performing angiogram. For the evaluation of bony landmarks, the pelvis and inguinal areas were divided into 8 zones according to 7 lines that were drawn parallel to the line drawn between the anterior superior iliac spine and the pubic tubercle. For evaluation of the inguinal crease as a landmark, the 8 zones above and 4 zones below the inguinal crease were determined. The zones were divided by 11 lines drawn parallel to the inguinal crease, and the interval between each line was 1 cm. Locations of the inguinal ligament and femoral bifurcation were recorded for every patient according to the above zones, and an ideal zone for the femoral arterial puncture was decided upon. The ideal zone was considered if the locations of all of inguinal ligaments were above the zone and the least possibility to puncture was below the femoral bifurcation. On the bony landmark, the femoral bifurcations were located at zone 3 in 1 patient (1.1%), at zone 4 in 2 patients (2.2%), at zone 5 in 3 patients (3.3%), at zone 6 in 24 patients (26.7%), and at zone 7 in 44 patients (48.9%). Inguinal ligaments were at zone 1 in 2 patient (3.0%), at zone 2 in 34 patients (50.7%), at zone 3 in 25 patients (37.3%), and at zone 4 in 6 patients (8.9%). When the inguinal creases were used as a landmark, the femoral bifurcations were located at zone 4 in 4 patients (4.4%), at zone 3 in 19 patients (21.1%). at zone 2 in 30 patients (33.3%), at zone 1 in 19 patients (21.1%), at zone -1 in 13 patients (14.4%), at zone -2 in 3 patients (3.3%) and at zone -4 in 2 patients (2.2%). Inguinal ligaments were at zone 8 in 7 patients (10.4%), at zone 7 in 11 patients (16.4%), at zone 6 in 19 patients (28.4%), at zone 5 in 20 patients (29.9%), at zone 4 in 7 patients (10.4%), and at zone 3 in 3 patients (4.5%). Therefore, the best zone for femoral arterial puncture was zone 5 with using bony landmarks and zone 2 with using inguinal crease landmarks. In terms of zone 5 on the bony landmark, every locations of inguinal ligaments was above it and 84 patients (93.4%) had their femoral bifurcation below it, excluding the 6 patients who had their femoral bifurcations at zones 3, 4, and 5. Therefore, zone 5 with using the bony landmarks was a good indicator for femoral arterial puncture. In case of zone 2 on the inguinal crease landmark, although every location of the inguinal ligament was above it, 53 patients (58.8%) had their femoral bifurcation above it at zone 4, 3, and 2. So, it was not a good indicator for femoral arterial puncture. Bony landmarks are more accurate indicators for performing femoral arterial puncture than the inguinal crease landmark. Zone 5 on the bony landmark is an ideal location for femoral arterial puncture

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

    International Nuclear Information System (INIS)

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

  19. The accuracy of a designed software for automated localization of craniofacial landmarks on CBCT images

    International Nuclear Information System (INIS)

    Two-dimensional projection radiographs have been traditionally considered the modality of choice for cephalometric analysis. To overcome the shortcomings of two-dimensional images, three-dimensional computed tomography (CT) has been used to evaluate craniofacial structures. However, manual landmark detection depends on medical expertise, and the process is time-consuming. The present study was designed to produce software capable of automated localization of craniofacial landmarks on cone beam (CB) CT images based on image registration and to evaluate its accuracy. The software was designed using MATLAB programming language. The technique was a combination of feature-based (principal axes registration) and voxel similarity-based methods for image registration. A total of 8 CBCT images were selected as our reference images for creating a head atlas. Then, 20 CBCT images were randomly selected as the test images for evaluating the method. Three experts twice located 14 landmarks in all 28 CBCT images during two examinations set 6 weeks apart. The differences in the distances of coordinates of each landmark on each image between manual and automated detection methods were calculated and reported as mean errors. The combined intraclass correlation coefficient for intraobserver reliability was 0.89 and for interobserver reliability 0.87 (95% confidence interval, 0.82 to 0.93). The mean errors of all 14 landmarks were <4 mm. Additionally, 63.57% of landmarks had a mean error of <3 mm compared with manual detection (gold standard method). The accuracy of our approach for automated localization of craniofacial landmarks, which was based on combining feature-based and voxel similarity-based methods for image registration, was acceptable. Nevertheless we recommend repetition of this study using other techniques, such as intensity-based methods

  20. Personal Landmarks from the Legacy of Arthur Phelps

    Science.gov (United States)

    Lowke, John

    2013-09-01

    I have been influenced for my whole life by Art Phelps, more than by anyone else - other than my wife! I first heard of Art Phelps in 1960 when, in the middle of doing my PhD in Adelaide, South Australia, Frost and Phelps published their land-mark paper, not only on drift velocities, the subject of my PhD, but on Boltzmann analyses, which were to deliver detailed cross sections for all common gases. Later I dared to suggest to my university that one of my two external PhD examiners be Phelps, a move that led to me being accepted for a position at Westinghouse Research Laboratories in Pittsburgh for 6 years, with Phelps as my direct supervisor. Throughout this period, Phelps refused to be a co-author of any of my papers, leaving me with severe doubts as to what he thought of their quality! I list areas where insights from Phelps inspired the growth of new fruit. (1) That transverse and longitudinal electron diffusion coefficients differ, typically by a factor of two. (2) That averaging radiation absorption coefficients in electric arcs, using common weightings involving Black Body radiation, can and usually do lead to errors of orders of magnitude. (3) That CO2 laser discharges are largely controlled by electron attachment rather than by diffusion or recombination. (4) That boundary conditions for electrons at metal electrodes in arc welding, are not zero, but from an astrophysical analogy, are zero when extrapolated to one mean free path beyond the surface. (5) That the metastable vibrational states of nitrogen become an energy gain rather than a loss process for low energy electrons as occur in electrical breakdown in air, resulting in increases of the ionisation coefficient by orders of magnitude. Coupled with the detachment of electrons from negative ions by singlet delta states of metastable oxygen molecules, sustaining discharge electric fields are reduced a factor of five. Phelps worked on this problem with me until a few months before he died.

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

    OpenAIRE

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

    2014-01-01

    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...

  2. Online updating of context-aware landmark detectors for prostate localization in daily treatment CT images

    International Nuclear Information System (INIS)

    Purpose: In image guided radiation therapy, it is crucial to fast and accurately localize the prostate in the daily treatment images. To this end, the authors propose an online update scheme for landmark-guided prostate segmentation, which can fully exploit valuable patient-specific information contained in the previous treatment images and can achieve improved performance in landmark detection and prostate segmentation. Methods: To localize the prostate in the daily treatment images, the authors first automatically detect six anatomical landmarks on the prostate boundary by adopting a context-aware landmark detection method. Specifically, in this method, a two-layer regression forest is trained as a detector for each target landmark. Once all the newly detected landmarks from new treatment images are reviewed or adjusted (if necessary) by clinicians, they are further included into the training pool as new patient-specific information to update all the two-layer regression forests for the next treatment day. As more and more treatment images of the current patient are acquired, the two-layer regression forests can be continually updated by incorporating the patient-specific information into the training procedure. After all target landmarks are detected, a multiatlas random sample consensus (multiatlas RANSAC) method is used to segment the entire prostate by fusing multiple previously segmented prostates of the current patient after they are aligned to the current treatment image. Subsequently, the segmented prostate of the current treatment image is again reviewed (or even adjusted if needed) by clinicians before including it as a new shape example into the prostate shape dataset for helping localize the entire prostate in the next treatment image. Results: The experimental results on 330 images of 24 patients show the effectiveness of the authors’ proposed online update scheme in improving the accuracies of both landmark detection and prostate segmentation. Besides, compared to the other state-of-the-art prostate segmentation methods, the authors’ method achieves the best performance. Conclusions: By appropriate use of valuable patient-specific information contained in the previous treatment images, the authors’ proposed online update scheme can obtain satisfactory results for both landmark detection and prostate segmentation

  3. Online updating of context-aware landmark detectors for prostate localization in daily treatment CT images

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Xiubin [College of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210015, China and IDEA Lab, Department of Radiology and BRIC, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, North Carolina 27510 (United States); Gao, Yaozong [IDEA Lab, Department of Radiology and BRIC, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, North Carolina 27510 (United States); Shen, Dinggang, E-mail: dgshen@med.unc.edu [IDEA Lab, Department of Radiology and BRIC, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, North Carolina 27510 and Department of Brain and Cognitive Engineering, Korea University, Seoul (Korea, Republic of)

    2015-05-15

    Purpose: In image guided radiation therapy, it is crucial to fast and accurately localize the prostate in the daily treatment images. To this end, the authors propose an online update scheme for landmark-guided prostate segmentation, which can fully exploit valuable patient-specific information contained in the previous treatment images and can achieve improved performance in landmark detection and prostate segmentation. Methods: To localize the prostate in the daily treatment images, the authors first automatically detect six anatomical landmarks on the prostate boundary by adopting a context-aware landmark detection method. Specifically, in this method, a two-layer regression forest is trained as a detector for each target landmark. Once all the newly detected landmarks from new treatment images are reviewed or adjusted (if necessary) by clinicians, they are further included into the training pool as new patient-specific information to update all the two-layer regression forests for the next treatment day. As more and more treatment images of the current patient are acquired, the two-layer regression forests can be continually updated by incorporating the patient-specific information into the training procedure. After all target landmarks are detected, a multiatlas random sample consensus (multiatlas RANSAC) method is used to segment the entire prostate by fusing multiple previously segmented prostates of the current patient after they are aligned to the current treatment image. Subsequently, the segmented prostate of the current treatment image is again reviewed (or even adjusted if needed) by clinicians before including it as a new shape example into the prostate shape dataset for helping localize the entire prostate in the next treatment image. Results: The experimental results on 330 images of 24 patients show the effectiveness of the authors’ proposed online update scheme in improving the accuracies of both landmark detection and prostate segmentation. Besides, compared to the other state-of-the-art prostate segmentation methods, the authors’ method achieves the best performance. Conclusions: By appropriate use of valuable patient-specific information contained in the previous treatment images, the authors’ proposed online update scheme can obtain satisfactory results for both landmark detection and prostate segmentation.

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

    Science.gov (United States)

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

    2015-01-28

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

  5. TU-F-BRF-03: Effect of Radiation Therapy Planning Scan Registration On the Dose in Lung Cancer Patient CT Scans

    International Nuclear Information System (INIS)

    Purpose: To characterize the effect of deformable registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan. Methods: Eighteen patients who received curative doses (?60Gy, 2Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic-quality pre-therapy (4–75 days) CT scan and a treatment planning scan with an associated dose map calculated in Pinnacle were collected. To establish baseline correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pre-therapy scans were co-registered with planning scans (and associated dose maps) using the Plastimatch demons and Fraunhofer MEVIS deformable registration algorithms. Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from both registration algorithms. The absolute difference in planned dose (|?D|) between manually and automatically mapped landmark points was calculated. Using regression modeling, |?D| was modeled as a function of the distance between manually and automatically matched points (registration error, E), the dose standard deviation (SD-dose) in the eight-pixel neighborhood, and the registration algorithm used. Results: 52–92 landmark point pairs (median: 82) were identified in each patient's scans. Average |?D| across patients was 3.66Gy (range: 1.2–7.2Gy). |?D| was significantly reduced by 0.53Gy using Plastimatch demons compared with Fraunhofer MEVIS. |?D| increased significantly as a function of E (0.39Gy/mm) and SD-dose (2.23Gy/Gy). Conclusion: An average error of <4Gy in radiation dose was introduced when points were mapped between CT scan pairs using deformable registration. Dose differences following registration were significantly increased when the Fraunhofer MEVIS registration algorithm was used, spatial registration errors were larger, and dose gradient was higher (i.e., higher SD-dose). To our knowledge, this is the first study to directly compute dose errors following deformable registration of lung CT scans

  6. Conservative management of large avulsions of the lip and local landmarks.

    Science.gov (United States)

    Rhee, Samuel T; Colville, Christopher; Buchman, Steven R

    2004-01-01

    Large lip avulsion injuries that involve significant tissue loss to the lip vermilion and other local landmarks can often pose a surgical dilemma for the reconstructive surgeon. Immediate reconstruction of these injuries are frequently performed using local flaps and adjacent tissue transfer to close the defect, but these repairs frequently suffer from the unfortunate consequence of increased associated scarring and further permanent distortion of the local anatomy. We present 2 patients sustaining dog bite injuries associated with extensive traumatic tissue loss to the lip vermilion and other local landmarks. These patients were treated conservatively with excellent functional and cosmetic results. A single minor surgical revision of 1 patient's cupid's bow was performed 1 year after injury. In cases of significant traumatic avulsion involving the lip vermilion and the perioral composite soft tissue, even with injuries including delicate anatomic landmarks, healing by secondary intention can be instituted as the initial treatment of choice in younger patients, often providing optimal results. PMID:14716166

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

    Directory of Open Access Journals (Sweden)

    Nihat Y?lmaz

    2006-06-01

    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.

  8. An Efficient Ceiling-view SLAM Using Relational Constraints Between Landmarks

    Directory of Open Access Journals (Sweden)

    Hyukdoo Choi

    2014-01-01

    Full Text Available In this paper, we present a new indoor ‘simultaneous localization and mapping’ (SLAM technique based on an upward-looking ceiling camera. Adapted from our previous work [17], the proposed method employs sparsely-distributed line and point landmarks in an indoor environment to aid with data association and reduce extended Kalman filter computation as compared with earlier techniques. Further, the proposed method exploits geometric relationships between the two types of landmarks to provide added information about the environment. This geometric information is measured with an upward-looking ceiling camera and is used as a constraint in Kalman filtering. The performance of the proposed ceiling-view (CV SLAM is demonstrated through simulations and experiments. The proposed method performs localization and mapping more accurately than those methods that use the two types of landmarks without taking into account their relative geometries.

  9. Evaluation of clinically relevant landmarks of the marginal mandibular branch of the facial nerve: A three-dimensional study with application to avoiding facial nerve palsy.

    Science.gov (United States)

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

    2016-03-01

    Injury to the marginal mandibular branch of the facial nerve (MMN) during surgery often results in poor functional and cosmetic outcomes. A line two finger breadths or 2 cm inferior to the border of the mandible is commonly used in planning neck incisions to avoid injury to the MMN. The purpose was to compare the two finger breadth/2 cm landmarks in predicting MMN course, and their accuracy/reliability. Thirty-one cadaveric specimens were scanned to obtain 3D surface topography (FARO® scanner). Four independent raters pinned the inferior border of the mandible and a two finger breadth line and 2cm line below. The location of each pin was digitized (Microscribe™). A preauricular flap was raised, and MMN branches were digitized and modelled (Geomagic®/Maya®) enabling quantification of the accuracy of these landmarks. The location of the two-finger breadth line was variable, spanning 25-51 mm below the inferior border of the mandible (ICC = 0.10). The most inferior MMN branch did not pass below the two-finger breadth line in any specimen, but a narrow clearance zone (≤5 mm) was found in two. In contrast, in 7/31 specimens, the most inferior MMN branch coursed below the 2 cm line and would be at risk of injury. It was concluded that an incision two finger breadths below the inferior border of the mandible could provide safer access than the 2 cm line. After an incision has been placed using the two finger-breadth landmark, caution must be exercised during dissection as branches of the MMN may lie only a few millimeters superior to the incision. Clin. Anat. 29:151-156, 2016. © 2015 Wiley Periodicals, Inc. PMID:26096443

  10. UAV Control on the Basis of 3D Landmark Bearing-Only Observations.

    Science.gov (United States)

    Karpenko, Simon; Konovalenko, Ivan; Miller, Alexander; Miller, Boris; Nikolaev, Dmitry

    2015-01-01

    The article presents an approach to the control of a UAV on the basis of 3D landmark observations. The novelty of the work is the usage of the 3D RANSAC algorithm developed on the basis of the landmarks' position prediction with the aid of a modified Kalman-type filter. Modification of the filter based on the pseudo-measurements approach permits obtaining unbiased UAV position estimation with quadratic error characteristics. Modeling of UAV flight on the basis of the suggested algorithm shows good performance, even under significant external perturbations. PMID:26633394

  11. Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

    Science.gov (United States)

    Grocott, Timothy; Thomas, Paul; Münsterberg, Andrea E.

    2016-01-01

    Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states. PMID:26864723

  12. 16 landmarks of the mouse brain have been validated as fiducials for registration to WHS

    Directory of Open Access Journals (Sweden)

    Marina Sergejeva

    2014-02-01

    Full Text Available A standard space for describing coordinate-based knowledge about the rodent brain is urgently needed. The INCF Digital Atlasing Program has yielded an open access 3D atlas reference system for the mouse brain - Waxholm Space (WHS and a supporting Digital Atlasing Infrastructure (DAI – for sharing of multimodal data (genomic, proteomic, imaging from research groups around the world. We need convenient methods that permit researchers to register their own data to WHS. Existing automatic registration processes are rather complex. In addition, we propose an easier and faster approach: registration based on well recognizable brain landmarks (LMs or fiducials. Here we present a set of LMs validated as fiducials, as they were reliably identified • by different individuals (anatomy specialists and novice • in different MR imaging modalities (T1, T2, T2* • in various specimens • by different cutting directions • by different image resolutions. On coronal MR datasets (T1, T2, T2*, 256x256x128, 80 ?m from an adult C57BL/6J male we defined an initial set of LMs recognizable in all 3 modalities and rendered descriptions how to find them. 15 guessers identified these LMs according to the descriptions on datasets from two C57BL/6J males, visualized in ImageJ as coronal slices. The probability of finding them, mean values for x, y and z coordinates and deviations from the mean were calculated for every LM. Finally, we excluded LMs with a deviation of more than 1,5 voxels in the x and y directions in both animals and ended up with 16 potential fiducials. Their average deviations were: 1,0 (x, 0,6 (y and 1,5 (z, the probability of finding was > 95%. Further, we located these 16 LMs on the canonical WHS datasets, and presented them in the web-based atlasing tool Scalable Brain Atlas (http://scalablebrainatlas.incf.org/WHS10. WHS images have a four times higher resolution and a different inclination than ours, but despite the differences all LMs were well identifiable according to our definitions. This supports their validity as fiducials. We also evaluated “the classical” LMs, Bregma and Lambda derived from the skull 3D µCT datasets coregistered to brain MRI datasets of five mice. We found that positions of these LMs with respect to brain anatomy vary considerably between the mice. The largest distance between Bregma z-positions was 1,2 mm, and between Lambda z-positions - 1,68 mm. Thus, we cannot accept these two LMs as fiducials.

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

    Directory of Open Access Journals (Sweden)

    Elisabeth Jeannette Ploran

    2014-01-01

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

  14. Dorsolateral Striatal Lesions Impair Navigation Based on Landmark-Goal Vectors but Facilitate Spatial Learning Based on a "Cognitive Map"

    Science.gov (United States)

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

    2015-01-01

    In three experiments, the nature of the interaction between multiple memory systems in rats solving a variation of a spatial task in the water maze was investigated. Throughout training rats were able to find a submerged platform at a fixed distance and direction from an intramaze landmark by learning a landmark-goal vector. Extramaze cues were…

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

    Science.gov (United States)

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

    2014-12-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  17. Use of Geometric Properties of Landmark Arrays for Reorientation Relative to Remote Cities and Local Objects

    Science.gov (United States)

    Mou, Weimin; Nankoo, Jean-François; Zhou, Ruojing; Spetch, Marcia L.

    2014-01-01

    Five experiments investigated how human adults use landmark arrays in the immediate environment to reorient relative to the local environment and relative to remote cities. Participants learned targets' directions with the presence of a proximal 4 poles forming a rectangular shape and an array of more distal poles forming a rectangular shape. Then…

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

    Science.gov (United States)

    Micho?ski, Jakub; Glinkowski, Wojciech; Witkowski, Marcin; Sitnik, Robert

    2012-05-01

    Faulty postures, scoliosis and sagittal plane deformities should be detected as early as possible to apply preventive and treatment measures against major clinical consequences. To support documentation of the severity of deformity and diminish x-ray exposures, several solutions utilizing analysis of back surface topography data were introduced. A novel approach to automatic recognition and localization of anatomical landmarks of the human back is presented that may provide more repeatable results and speed up the whole procedure. The algorithm was designed as a two-step process involving a statistical model built upon expert knowledge and analysis of three-dimensional back surface shape data. Voronoi diagram is used to connect mean geometric relations, which provide a first approximation of the positions, with surface curvature distribution, which further guides the recognition process and gives final locations of landmarks. Positions obtained using the developed algorithms are validated with respect to accuracy of manual landmark indication by experts. Preliminary validation proved that the landmarks were localized correctly, with accuracy depending mostly on the characteristics of a given structure. It was concluded that recognition should mainly take into account the shape of the back surface, putting as little emphasis on the statistical approximation as possible.

  19. The developmental trajectory of intramaze and extramaze landmark biases in spatial navigation: An unexpected journey.

    Science.gov (United States)

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

    2015-06-01

    Adults learning to navigate to a hidden goal within an enclosed space have been found to prefer information provided by the distal cues of an environment, as opposed to proximal landmarks within the environment. Studies with children, however, have shown that 5- or 7-year-olds do not display any preference toward distal or proximal cues during navigation. This suggests that a bias toward learning about distal cues occurs somewhere between the age of 7 years and adulthood. We recruited 5- to 11-year-old children and an adult sample to explore the developmental profile of this putative change. Across a series of 3 experiments, participants were required to navigate to a hidden goal in a virtual environment, the location of which was signaled by both extramaze and intramaze landmark cues. During testing, these cues were placed into conflict to assess the search preferences of participants. Consistent with previously reported findings, adults were biased toward using extramaze information. However, analysis of the data from children, which incorporated age as a continuous variable, suggested that older children in our sample were, in fact, biased toward using the intramaze landmark in our task. These findings suggest the bias toward using distal cues in spatial navigation, frequently displayed by adults, may be a comparatively late developing trait, and one that could supersede an initial developmental preference for proximal landmarks. PMID:25844850

  20. Columbia's "Working Paper 1": Creative Analysis for the Reprograming of Landmarks

    Science.gov (United States)

    Byard, Paul S.

    1976-01-01

    "Working Paper 1" is the first publication of the Center for Advanced Research in Urban and Environmental Affairs of Columbia University's Graduate School of Architecture and Planning. It sets out the results of a year-long study made by the Center of the Christopher Street Federal Archive Building, an important landmark of New York's West…

  1. Precision landmark location for machine vision and photogrammetry finding and achieving the maximum possible accuracy

    CERN Document Server

    Gutierrez, José A

    2007-01-01

    Shows the reader how to derive theoretical limits to the precision of landmark identification in electronic imagesMATLAB® package assists the reader with applying theoretical results in real engineering systemsSteps outside the usual earth-sciences and civil-engineering base of photogrammetry to improve animation, medical imaging and robotic vision applications

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

    Science.gov (United States)

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

    2015-10-01

    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

  3. Obstacles Facing Promoting Tourism for Islamic Landmarks from the Perspective of Tour Operators in Egypt

    Directory of Open Access Journals (Sweden)

    Suzan Bakri Hassan

    2015-05-01

    Full Text Available The UNESCO launched a campaign #unite4heritage in Egypt to defeat extremism and intolerance. The message of such campaigne is peace, dialogue and unity embedded in cultural heritage. As culture and tourism are linked together, such message could be delivered through improving culture heritage tourism in Egypt. Islamic landmarks  are considered as a part of human heritage. Therefore, the purpose of this study is to identify how much tour operators in Egypt include Islamic landmarks in their programs to determine the obstacles facing promoting cultural tourism in Islamic landmarks' areas. Additionally, the study would identify positive results in the case of developing heritage tourism in Egypt. To achieve a high result, a survey approach was employed to collect data from 100 tour operators, using a completed questionnaire technique as well as a Likert Scale and statistical models in order to test and interpret the research outcomes. The research findings indicated that although tour operators in Egypt are convinced of the significance of the Islamic landmarks, there is no contradiction between creating global understanding and at the same time achieving benefit to the local community. However, there is a range of obstacles facing promoting such type of tourism in Egypt. Keywords: Culture heritage tourism, community, Egypt, Islamic civilization.

  4. Simulation of satellite landmark navigation on the base of optoelectronic image processing technique

    Science.gov (United States)

    Dyblenko, Sergey; Janschek, Klaus; Kisselev, Anton; Sultanov, Albert; Tchernykh, Valeri

    2005-06-01

    Hybrid optoelectronic landmark navigation is proposed as backup navigation for Low Earth Orbit satellite. Optoelectronic navigation can use earth observation camera, originally not assigned for navigation purposes. The concept of the landmark navigation system is based on the onboard optical correlator application for real time matching of the earth images and pre-recorded images of landmarks with known coordinates. The software model of image processing by optical correlator has been developed to test the system operation in simulated experiments and to estimate the expected performance. The hardware model of the joint transform optical correlator has been manufactured and tested. The model uses commercially available optoelectronic components and works with PC, which performs all digital processing and data flow control. As a result ofthe model testing, the feasibility ofthe system concept and the adequacy ofthe software model have been proved. The image processing system which calculates satellite attitude and position on the base of correlation peaks measurements has been used for simulation of optoelectronic satellite landmark navigation. In the series of simulated experiments the navigation accuracy was estimated in presence of image distortions and noise for earth observation mission.

  5. 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 landmarks - provided by a human expert into a non-rigid registration process. (orig.)

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

    International Nuclear Information System (INIS)

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

  7. Software Designation to Assess the Proximity of Different Facial Anatomic Landmarks to Midlines of the Mouth and Face

    Directory of Open Access Journals (Sweden)

    Moshkelgosha V

    2014-12-01

    Full Text Available Statement of Problem: Recognition and determination of facial and dental midline is important in dentistry. Currently, there are no verifiable guidelines that direct the choice of specific anatomic landmarks to determine the midline of the face or mouth. Objectives: The purpose of this study was to determine which of facial anatomic landmarks is closest to the midline of the face as well as that of the mouth. Materials and Methods: Frontal full-face digital images of 92 subjects (men and women age range: 20-30 years in smile were taken under standardized conditions; commonly used anatomic landmarks, nasion, tip of the nose, and tip of the philtrum were digitized on the images of subjects and aesthetic analyzer software used for midline analysis using Esthetic Frame. Deviations from the midlines of the face and mouth were measured for the 3 clinical landmarks; the existing dental midline was considered as the fourth landmark. The entire process of midline analysis was done by a single observer and repeated twice. Reliability analysis and 1-sample t- tests were conducted. Results: The Intra-class correlation coefficients (ICCs for reliability analysis of RFV and RCV measures made two times revealed that the reliabilities were all acceptable. The results indicated that each of the 4 landmarks deviated uniquely and significantly (P<.001 from the midlines of the face as well as mouth in both males and females. Conclusions: There was a significant difference between the mean ratios of the chosen anatomic landmarks and the midlines of the face and mouth. The hierarchy of anatomic landmarks closest to the midline of the face is: (1 midline of the commissures, (2 nasion , (3 tip of philtrum,(4 dental midline, and (5 tip ofthe nose. The closest anatomic landmarks to the mouth midline are: (1 tip of philtrum, (2 dental midline, (3 tip of nose, and (4 nasion.

  8. Modeling and matching of landmarks for automation of Mars Rover localization

    Science.gov (United States)

    Wang, Jue

    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.

  9. 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 ... scanner does not give off any radiation. Most nuclear scans (including an RBC scan) are not recommended ...

  10. Nuclear Heart Scan

    Science.gov (United States)

    ... 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: ...

  11. Coronary Calcium Scan

    Science.gov (United States)

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

  12. Heart PET scan

    Science.gov (United States)

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

  13. On landmark selection and sampling in high-dimensional data analysis

    CERN Document Server

    Belabbas, Mohamed-Ali

    2009-01-01

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

  14. Trajectory Reconstruction of the ST-9 Sounding Rocket Experiment Using IMU and Landmark Data

    Science.gov (United States)

    Park, Ryan S.; Bhaskaran, Shyam; Bordi, John J.; Cheng, Yang; Johnson, Andrew J.; Kruizinga, Gerhard L.; Lisano, Michael E.; Owen, William M.; Wolf, Aron A.

    2009-01-01

    This paper presents trajectory reconstruction of the ST-9 sounding rocket experiment using the onboard IMU data and descent imagery. The raw IMU accelerometer measurements are first converted into inertial acceleration and then used in trajectory integration. The descent images are pre-processed using a map-matching algorithm and unique landmarks for each image are created. Using the converted IMU data and descent images, the result from dead-reckoning and the kinematic-fix approaches are first compared with the GPS measurements. Then, both the IMU data and landmarks are processed together using a batch least-squares filter and the position, velocity, stochastic acceleration, and camera orientation of each image are estimated. The reconstructed trajectory is compared with the GPS data and the corresponding formal uncertainties are presented. The result shows that IMU data and descent images processed with a batch filter algorithm provide the trajectory accuracy required for pin-point landing.

  15. 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)

  16. Examining the Variations in the Results of the Hotelling T (2) Test in Case of Changing Baseline Landmarks in the Bookstein Coordinates.

    Science.gov (United States)

    Ercan, Ilker; Sigirli, Deniz; Ozkaya, Guven

    2015-06-01

    In many biological and biomedical investigations, the most effective way to analyze the forms of whole biological organs or organisms is by recording geometric locations of landmark points. If we want to compare shapes, then individuals should be translated, rotated and scaled in such a way that all of the individuals lie in a standard position and are centered. Bookstein conducted this process by choosing two landmarks as reference landmarks. Each individual is translated, rotated and scaled according to these reference landmarks. The aim of the present study was to examine the change in the p values in the case of choosing different baseline landmarks when performing the Hotelling T (2) test, which is commonly used when comparing two sample shape configurations based on Bookstein coordinates. For this purpose, the changes in the p values were investigated in shape configurations that are composed of a different number of landmarks by taking all of the possible paired landmark combinations at different variance levels and sample sizes. As a result of the present study, it was observed that with the increase in the landmark number, the number of possible baseline landmark combinations also increases and, for this reason, a substantial number of variations occur in the p values. Therefore, it is an important to decide which landmarks should be taken as reference landmarks when using the Bookstein coordinates. PMID:26199212

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

    DEFF Research Database (Denmark)

    Goranko, Valentin

    2012-01-01

    This is a selective survey and discussion of some of the landmark undecidability results in temporal logic, beginning with Turing's undecidability of the Halting problem which, in retrospect, can be regarded as the historically first undecidability result for a suitable temporal logic over configuration graphs of Turing machines. I will discuss some of the natural habitats of undecidable temporal logics, such as first-order, interval-based and real time temporal logics, as well as some extension...

  18. Institutional landmarks in Brazilian research on soil erosion: a historical overview

    OpenAIRE

    Tiago Santos Telles; Sonia Carmela Falci Dechen; Maria Fátima de Guimarães

    2013-01-01

    The problem of soil erosion in Brazil has been a focus of agricultural scientific research since the 19th century. The aim of this study was to provide a historical overview of the institutional landmarks which gave rise to the first studies in soil erosion and established the foundations of agricultural research in Brazil. The 19th century and beginning of the 20th century saw the founding of a series of institutions in Brazil, such as Botanical Gardens, executive institutions, research inst...

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

    OpenAIRE

    Mayy Chahla; Michael Eberlein; Scott Wright

    2010-01-01

    Background: The acquisition of new knowledge is a primary goal of residency training. Retrieving and retaining influential primary and secondary medical literature can be challenging for house officers. We set out to investigate the effect of a Universal Serial Bus (USB) drive loaded with landmark scientific articles on housestaff education in a pilot study. Methods: We created a USB syllabus that contains 187 primary scientific research articles. The electronic syllabus had links to the full...

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

    International Nuclear Information System (INIS)

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

  1. A note on statistical analysis of shape through triangulation of landmarks

    OpenAIRE

    Rao, C. Radhakrishna

    2000-01-01

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

  2. 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 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.)

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

    Science.gov (United States)

    Wang, Hongsheng; Zheng, Naiqaun Nigel

    2010-12-01

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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

    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.)

  5. Landmark-based registration using a local radial basis function transformation

    OpenAIRE

    Cavoretto, Roberto; De Rossi, Alessandra; Quatember, Bernhard

    2008-01-01

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

  6. A landmark-based algorithm for automatic pattern recognition and abnormality detection

    OpenAIRE

    Huzurbazar, S.; Lee, Long; Kuang, Dongyang

    2016-01-01

    We study a class of mathematical and statistical algorithms with the aim of establishing a computer-based framework for fast and reliable automatic pattern recognition and abnormality detection. Under this framework, we propose a numerical algorithm for finding group averages where an average of a group is an estimator that is said to best represent the properties of interest of that group. A novelty of the proposed landmark-based algorithm is that the algorithm tracks information of the mome...

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

    OpenAIRE

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

    2011-01-01

    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...

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

    Directory of Open Access Journals (Sweden)

    udy P. Sendaydiego

    2013-07-01

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

  9. Propagation of anatomical landmark misplacement to knee kinematics: performance of single and double calibration.

    Science.gov (United States)

    Stagni, Rita; Fantozzi, Silvia; Cappello, Angelo

    2006-10-01

    Soft tissue artefact and anatomical landmark misplacement have been recognized as the most critical sources of error in gait analysis. The double calibration method was recently proposed to compensate for soft tissue artefact in knee kinematics. This compensation method resulted very effective in the absence of anatomical landmark misplacement. The purpose of the present work was to assess the effectiveness of double calibration in reducing the effects of skin motion artefact on knee rotations and translations when anatomical landmark misplacement is present on the thigh and shank. The double calibration method was used to calculate knee kinematics of two subjects while they performed several motor tasks. The results were compared with those from conventional single calibration. The soft tissue artefact propagated to knee kinematics was quantified by simulating different misplacement errors using both single and double calibration. The double calibration method performed much better than the single calibration one in quantifying knee rotations and particularly translations, with misplacement error up to 15mm superimposed on the anatomical coordinates of the epicondyles. If misplacement errors were limited to just 5mm, the double calibration would be effective in providing kinematics accurate enough for orthopaedic biomechanic applications. PMID:16934471

  10. Tools for quantitative form description; an evaluation of different software packages for semi-landmark analysis

    Science.gov (United States)

    Houssaye, Alexandra; Herrel, Anthony; Fabre, Anne-Claire; Cornette, Raphael

    2015-01-01

    The challenging complexity of biological structures has led to the development of several methods for quantitative analyses of form. Bones are shaped by the interaction of historical (phylogenetic), structural, and functional constrains. Consequently, bone shape has been investigated intensively in an evolutionary context. Geometric morphometric approaches allow the description of the shape of an object in all of its biological complexity. However, when biological objects present only few anatomical landmarks, sliding semi-landmarks may provide good descriptors of shape. The sliding procedure, mandatory for sliding semi-landmarks, requires several steps that may be time-consuming. We here compare the time required by two different software packages (‘Edgewarp’ and ‘Morpho’) for the same sliding task, and investigate potential differences in the results and biological interpretation. ‘Morpho’ is much faster than ‘Edgewarp,’ notably as a result of the greater computational power of the ‘Morpho’ software routines and the complexity of the ‘Edgewarp’ workflow. Morphospaces obtained using both software packages are similar and provide a consistent description of the biological variability. The principal differences between the two software packages are observed in areas characterized by abrupt changes in the bone topography. In summary, both software packages perform equally well in terms of the description of biological structures, yet differ in the simplicity of the workflow and time needed to perform the analyses. PMID:26618086

  11. 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 deviations were 1.72 mm and 3.06 mm, respectively

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

    International Nuclear Information System (INIS)

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

  13. A low-cost test-bed for real-time landmark tracking

    Science.gov (United States)

    Csaszar, Ambrus; Hanan, Jay C.; Moreels, Pierre; Assad, Christopher

    2007-04-01

    A low-cost vehicle test-bed system was developed to iteratively test, refine and demonstrate navigation algorithms before attempting to transfer the algorithms to more advanced rover prototypes. The platform used here was a modified radio controlled (RC) car. A microcontroller board and onboard laptop computer allow for either autonomous or remote operation via a computer workstation. The sensors onboard the vehicle represent the types currently used on NASA-JPL rover prototypes. For dead-reckoning navigation, optical wheel encoders, a single axis gyroscope, and 2-axis accelerometer were used. An ultrasound ranger is available to calculate distance as a substitute for the stereo vision systems presently used on rovers. The prototype also carries a small laptop computer with a USB camera and wireless transmitter to send real time video to an off-board computer. A real-time user interface was implemented that combines an automatic image feature selector, tracking parameter controls, streaming video viewer, and user generated or autonomous driving commands. Using the test-bed, real-time landmark tracking was demonstrated by autonomously driving the vehicle through the JPL Mars yard. The algorithms tracked rocks as waypoints. This generated coordinates calculating relative motion and visually servoing to science targets. A limitation for the current system is serial computing-each additional landmark is tracked in order-but since each landmark is tracked independently, if transferred to appropriate parallel hardware, adding targets would not significantly diminish system speed.

  14. Surgical and topographic anatomy of the maxillary line: an important landmark for endoscopic nasal surgery.

    Science.gov (United States)

    Raikos, Athanasios; Waidyasekara, Pasan; Morrison, Amy Kathleen

    2015-01-01

    The maxillary line is an important surgical landmark in the lateral nasal cavity. We investigated its location, variation, and relation to other landmarks in 47 formalin fixed cadaveric half-heads dissected in steps. Measurements and observations were made to describe the topography of the maxillary line, maxillary line midpoint (M-point), and their relationship with surgically important structures. The mean curved length of the maxillary line was 15 mm (SD 3.5) and can be classified into three types. The M-point had a mean vertical distance of 0.8mm (SD 2.9) below the nasolacrimal sac-duct junction. It was found below, above, or on the same level as the nasolacrimal sac-duct junction in 57.4%, 38.3%, and 4.3% of specimens, respectively. In 51.1% the M-point was anterior to the nasolacrimal duct axis and 48.9% overlapping the lacrimal apparatus. The maxillary line and its M-point are useful surgical landmarks for localizing the nasolacrimal duct segments. PMID:25466929

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

    Science.gov (United States)

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

    2014-12-01

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

  16. Neural Network-Based Landmark Recognition and Navigation with IAMRs. Understanding the Principles of Thought and Behavior.

    Science.gov (United States)

    Doty, Keith L.

    1999-01-01

    Research on neural networks and hippocampal function demonstrating how mammals construct mental maps and develop navigation strategies is being used to create Intelligent Autonomous Mobile Robots (IAMRs). Such robots are able to recognize landmarks and navigate without "vision." (SK)

  17. Independent effects of geometry and landmark in a spontaneous reorientation task: a study of two species of fish.

    Science.gov (United States)

    Lee, Sang Ah; Vallortigara, Giorgio; Ruga, Vincenza; Sovrano, Valeria A

    2012-09-01

    While disoriented humans and animals use both landmarks and environmental geometry to guide their navigation, it is not clear what kinds of cognitive mechanisms underlie these behaviors. Because traditional tests of trained navigation behavior in environments containing both landmarks and geometric information may cloud our insight into the nature of these processes, the present study tested the spontaneous use of landmarks and environmental shape by two species of fish-Redtail Splitfins (Xenotoca eiseni) and Zebrafish (Danio rerio). The results suggest that while geometry is spontaneously used by both species and both sexes to compute relative position or direction, the spontaneous use of landmarks is limited to direct beaconing and complicated by attraction to features and variability across species and sex. These findings support the view that while multiple cues may ultimately guide behavior, the computation of orientation and relative positions is specified by geometric input and is independent from other navigation processes such as beaconing. PMID:22610461

  18. Reconciling landmarks and level sets: geometric shape warping and matching using generalized gradients and correspondence-augmented implicit representations

    OpenAIRE

    Maurel, Pierre; Faugeras, Olivier; Keriven, Renaud

    2006-01-01

    Shape warping is a key problem in statistical shape analysis. This paper proposes a framework for geometric shape warping based on both shape distances and landmarks. Taking advantage of the recently proposed spatially coherent flows, our method is mathematically well-posed and uses only intrinsic shape information, namely some similarity measure between shapes and the correspondence of landmarks provided on the shape surface. No extrinsic quantity is considered, neither a diffeomorphism of t...

  19. Endoscopic Orientation of the Parasellar Region in Sphenoid Sinus with Ill-Defined Bony Landmarks: An Anatomic Study

    OpenAIRE

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

    2010-01-01

    The sphenoid bony landmarks are important for endoscopic orientation in skull base surgery but show a wide range of variations. We aimed to describe an instructional model for the endoscopic parasellar anatomy in sphenoid sinuses with ill-defined bony landmarks. Five preserved injected cadaveric heads and four sides of dry skulls were studied endoscopically via transethmoid, transsphenoidal approach. The parasellar region was exposed by drilling along the maxillary nerve (V2) canal [the lengt...

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

    Directory of Open Access Journals (Sweden)

    Martin Egelhaaf

    2014-09-01

    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.

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

    OpenAIRE

    Zamora, Natalia; Llamas, José M.; Cibrián, Rosa; Gandia, José L.; Paredes, Vanessa

    2012-01-01

    Objectives: Cone Beam Computerized Tomography (CBCT) allows the possibility of modifying some of the diagnostic tools used in orthodontics, such as cephalometry. The first step must be to study the characteristics of these devices in terms of accuracy and reliability of the most commonly used landmarks. The aims were 1- To assess intra and inter-observer reliability in the location of anatomical landmarks belonging to hard tissues of the skull in images taken with a CBCT device, 2- To determi...

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

    Directory of Open Access Journals (Sweden)

    Cronk Quentin CB

    2011-01-01

    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 μm dots at a spacing of c. 91 μm. 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.

  3. Automatic categorization of anatomical landmark-local appearances based on diffeomorphic demons and spectral clustering for constructing detector ensembles.

    Science.gov (United States)

    Hanaoka, Shouhei; Masutani, Yoshitaka; Nemoto, Mitsutaka; Nomura, Yukihiro; Yoshikawa, Takeharu; Hayashi, Naoto; Ohtomo, Kuni

    2012-01-01

    A method for categorizing landmark-local appearances extracted from computed tomography (CT) datasets is presented. Anatomical landmarks in the human body inevitably have inter-individual variations that cause difficulty in automatic landmark detection processes. The goal of this study is to categorize subjects (i.e., training datasets) according to local shape variations of such a landmark so that each subgroup has less shape variation and thus the machine learning of each landmark detector is much easier. The similarity between each subject pair is measured based on the non-rigid registration result between them. These similarities are used by the spectral clustering process. After the clustering, all training datasets in each cluster, as well as synthesized intermediate images calculated from all subject-pairs in the cluster, are used to train the corresponding subgroup detector. All of these trained detectors compose a detector ensemble to detect the target landmark. Evaluation with clinical CT datasets showed great improvement in the detection performance. PMID:23286038

  4. Transabdominal ultrasound for detection of pregnancy, fetal and placental landmarks, and fetal age before Day 45 of gestation in the sheep.

    Science.gov (United States)

    Jones, Amanda K; Gately, Rachael E; McFadden, Katelyn K; Zinn, Steven A; Govoni, Kristen E; Reed, Sarah A

    2016-03-15

    Detection of pregnancy during early gestation is advantageous for flock breeding management. Transabdominal ultrasound is a practical and efficient approach for monitoring pregnancy and fetal growth in small ruminants. However, there is limited information using the transabdominal technique before Day 45 of gestation in sheep. Therefore, our objective was to determine how accurately transabdominal ultrasound could be used to detect pregnancy, to identify pregnancy landmarks, and to quantify fetal length before Day 45 in ewes. Multiparous Western White-faced ewes (n = 99) were estrus synchronized and exposed to one of four Dorset rams. The day a ewe was marked by a ram was considered Day 0 of gestation. Ewes not remarked by Day 20 were separated for ultrasonography. To detect pregnancy and landmarks, ewes were scanned three times per week between Day 26.0 ± 0.3 (mean ± standard error) and Day 40.0 ± 0.2. A single technician performed all scans in the right nonhaired abdominal pit using a real-time portable Eazi-Scan machine and a 5-MHz linear rectal transducer. All data were analyzed using the MIXED procedure in SAS (with repeated measures where appropriate). Because of rebreeding activity, 113 ultrasound periods were initiated. The specificity and positive predictive value were 100% during the entire study. The accuracy, sensitivity, and negative predictive value of ultrasound scanning were greater than 90% beginning at Day 33 ± 1. On average, pregnancy (n = 85) was detected at Day 28.7 ± 0.4 and nonpregnancy (n = 28) at Day 25.5 ± 0.6. Three early fetal losses were identified at Day 39.7 ± 0.7. In pregnant ewes (n = 82), the overall accuracy of fetal counting was 78%. The first observance of an enlarged uterus (P = 0.05) and pregnancy (P = 0.03) was detected earlier when multiple fetuses were developing compared with singletons. Placentome evagination was first observed earlier in triplets compared with twins and singletons (P = 0.02). Fetal length increased with day of gestation (P sheep. PMID:26706599

  5. Conventional cerebrospinal fluid scanning

    International Nuclear Information System (INIS)

    Conventional cerebrospinal fluid scanning (CSF scanning) today is mainly carried out in addition to computerized tomography to obtain information about liquor flow kinetics. Especially in patients with communicating obstructive hydrocephalus, CSF scanning is clinically useful for the decision for shunt surgery. In patients with intracranial cysts, CSF scanning can provide information about liquor circulation. Further indications for CSF scanning include the assessment of shunt patency especially in children, as well as the detection and localization of cerebrospinal fluid leaks. (orig.)

  6. Conventional cerebrospinal fluid scanning

    Energy Technology Data Exchange (ETDEWEB)

    Schicha, H.

    1985-06-01

    Conventional cerebrospinal fluid scanning (CSF scanning) today is mainly carried out in addition to computerized tomography to obtain information about liquor flow kinetics. Especially in patients with communicating obstructive hydrocephalus, CSF scanning is clinically useful for the decision for shunt surgery. In patients with intracranial cysts, CSF scanning can provide information about liquor circulation. Further indications for CSF scanning include the assessment of shunt patency especially in children, as well as the detection and localization of cerebrospinal fluid leaks.

  7. Genome-wide retroviral insertional tagging of genes involved in cancer in Cdkn2a-deficient mice

    DEFF Research Database (Denmark)

    Lund, Anders H; Turner, Geoffrey; Trubetskoy, Alla; Verhoeven, Els; Wientjens, Ellen; Hulsman, Danielle; Russell, Robert; DePinho, Ronald A; Lenz, Jack; van Lohuizen, Maarten

    2002-01-01

    We have used large-scale insertional mutagenesis to identify functional landmarks relevant to cancer in the recently completed mouse genome sequence. We infected Cdkn2a(-/-) mice with Moloney murine leukemia virus (MoMuLV) to screen for loci that can participate in tumorigenesis in collaboration ...

  8. 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)

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

    2014-10-01

    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

  9. Patterns of positive selection in six Mammalian genomes

    DEFF Research Database (Denmark)

    Kosiol, Carolin; Vinar, Tomás; da Fonseca, Rute R; Hubisz, Melissa J; Bustamante, Carlos D; Nielsen, Rasmus; Siepel, Adam

    2008-01-01

    Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight into the dynamics of genome evolution, the genetic basis of differences between species, and the functions of individual genes. However, previous scans have been limited in power and accuracy owing to small numbers of available genomes. Here we present the most comprehensive examination of mammalian PSGs to date, using the six high-coverage genome assemblies now available for eutherian mammals. The increased ...

  10. Efficacy and costs comparison of anatomical landmarks and ultrasonic guidance during brachial plexus block

    International Nuclear Information System (INIS)

    Objective: To compare the efficacy and costs of brachial plexus block (BPB) guided by ultrasound with that used anatomical landmarks. Methods: Eighty ASA ? or ? patients scheduled for upper extremity operation were prospectively randomized into 2 groups: Group A (n=40, BPB using anatomical landmarks) and group U (n=40, BPB guided in real time by a two-dimensional ultrasonic image). The time spent on performing the block, the onset time and duration of analgesia were measured. The proportion of successful and excellent blocks and the incidence of complications were assessed. The cost of anesthetic and the total cost of anesthesia were recorded. Results: Compared with group A, in group U the time spent on performing the block and the onset time of analgesia were significantly shorter, the duration of analgesia was significantly longer, the excellence rate of block was significantly higher (all P<0.05). 95.0% of patients in group A and 97.5% of patients in group U had a successful block (P >0.05). Four patients in group A and two patients in group U had occurred complications (P>0.05). The cost of anesthetic in group U was significantly less than in group A (P<0.01). There was no significant difference in the total cost of anesthesia between the two groups (P>0.05). Conclusion: BPB guided by ultrasound provides better block with more rapid performance and longer duration of analgesia as compared with that used anatomical landmarks. Ultrasound-guided BPB is suitable for upper extremity operation and lowers the anesthetic cost. (authors)

  11. Information geometry for landmark shape analysis: unifying shape representation and deformation.

    Science.gov (United States)

    Peter, Adrian M; Rangarajan, Anand

    2009-02-01

    Shape matching plays a prominent role in the comparison of similar structures. We present a unifying framework for shape matching that uses mixture models to couple both the shape representation and deformation. The theoretical foundation is drawn from information geometry wherein information matrices are used to establish intrinsic distances between parametric densities. When a parameterized probability density function is used to represent a landmark-based shape, the modes of deformation are automatically established through the information matrix of the density. We first show that given two shapes parameterized by Gaussian mixture models (GMMs), the well-known Fisher information matrix of the mixture model is also a Riemannian metric (actually, the Fisher-Rao Riemannian metric) and can therefore be used for computing shape geodesics. The Fisher-Rao metric has the advantage of being an intrinsic metric and invariant to reparameterization. The geodesicâcomputed using this metricâestablishes an intrinsic deformation between the shapes, thus unifying both shape representation and deformation. A fundamental drawback of the Fisher-Rao metric is that it is not available in closed form for the GMM. Consequently, shape comparisons are computationally very expensive. To address this, we develop a new Riemannian metric based on generalized \\phi-entropy measures. In sharp contrast to the Fisher-Rao metric, the new metric is available in closed form. Geodesic computations using the new metric are considerably more efficient. We validate the performance and discriminative capabilities of these new information geometry-based metrics by pairwise matching of corpus callosum shapes. We also study the deformations of fish shapes that have various topological properties. A comprehensive comparative analysis is also provided using other landmark-based distances, including the Hausdorff distance, the Procrustes metric, landmark-based diffeomorphisms, and the bending energies of the thin-plate (TPS) and Wendland splines. PMID:19110497

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

    Scientific Electronic Library Online (English)

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

    Full Text Available 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.

  13. Nuclear Scans (Cancer)

    Science.gov (United States)

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

  14. Getting a CAT Scan

    Medline Plus

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

  15. 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 ... Page Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) Print ...

  16. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Skiing, Snowboarding, Skating Crushes What's a Booger? Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A Text Size en español Obtención de ...

  17. Getting a CAT Scan

    Science.gov (United States)

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

  18. Lung PET scan

    Science.gov (United States)

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

  19. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Games Kids' Medical Dictionary En Español What Other Kids Are Reading Girls and Puberty Boys and Puberty ... Main Page Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) ...

  20. Visual scanning behavior

    Science.gov (United States)

    Harris, R. L., Sr.; Spady, A. A., Jr.

    1985-01-01

    This report summarizes the results and knowledge of scan behavior gained in various simulation and laboratory studies. Results were obtained through various analysis techniques such as real-time viewing of the pilot's scanning behavior and quantitative analysis of scan behavior performance parameters (average dwell time, dwell percentages, instrument transition paths, dwell histograms, and entropy rate measures). Pilot scan behavior is discussed in the following areas; scanning is a subconscious conditioned activity, scanning is situation dependent, pilots' scanning pattern is centered around a home base. Scanning behavior data have been shown to be useful in determining pilot's workload, evaluating pilot's strategy and role, determining the rate of information transfer of various displays, and aiding in pilot training.

  1. Brain PET scan

    Science.gov (United States)

    ... tissues are working. Other imaging tests, such as magnetic resonance imaging ( MRI ) and computed tomography ( CT ) scans ... the scan. You will be able to drink water. Tell your health care provider if: You are ...

  2. Effect of deformable registration on the dose calculated in radiation therapy planning CT scans of lung cancer patients

    International Nuclear Information System (INIS)

    Purpose: To characterize the effects of deformable image registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan. Methods: Eighteen patients who received curative doses (?60 Gy, 2 Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic-quality pretherapy (4–75 days) CT scan and a treatment planning scan with an associated dose map were collected. To establish correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pretherapy scans then were coregistered with planning scans (and associated dose maps) using the demons deformable registration algorithm and two variants of the Fraunhofer MEVIS algorithm (“Fast” and “EMPIRE10”). Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from each of the three algorithms. The Euclidean distance between manually and automatically mapped landmark points (dE) and the absolute difference in planned dose (|?D|) were calculated. Using regression modeling, |?D| was modeled as a function of dE, dose (D), dose standard deviation (SDdose) in an eight-pixel neighborhood, and the registration algorithm used. Results: Over 1400 landmark point pairs were identified, with 58–93 (median: 84) points identified per patient. Average |?D| across patients was 3.5 Gy (range: 0.9–10.6 Gy). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, with an average dE across patients of 5.2 mm (compared with >7 mm for the other two algorithms). Consequently, average |?D| was also lowest using the Fraunhofer MEVIS EMPIRE10 algorithm. |?D| increased significantly as a function of dE (0.42 Gy/mm), D (0.05 Gy/Gy), SDdose (1.4 Gy/Gy), and the algorithm used (?1 Gy). Conclusions: An average error of <4 Gy in radiation dose was introduced when points were mapped between CT scan pairs using deformable registration, with the majority of points yielding dose-mapping error <2 Gy (approximately 3% of the total prescribed dose). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, resulting in the smallest errors in mapped dose. Dose differences following registration increased significantly with increasing spatial registration errors, dose, and dose gradient (i.e., SDdose). This model provides a measurement of the uncertainty in the radiation dose when points are mapped between serial CT scans through deformable registration

  3. Effect of deformable registration on the dose calculated in radiation therapy planning CT scans of lung cancer patients

    Energy Technology Data Exchange (ETDEWEB)

    Cunliffe, Alexandra R.; Armato, Samuel G.; White, Bradley; Justusson, Julia [Department of Radiology, The University of Chicago, 5841 South Maryland Avenue, Chicago, Illinois 60637 (United States); Contee, Clay; Malik, Renuka; Al-Hallaq, Hania A., E-mail: hal-hallaq@radonc.uchicago.edu [Department of Radiation and Cellular Oncology, The University of Chicago, 5841 South Maryland Avenue, Chicago, Illinois 60637 (United States)

    2015-01-15

    Purpose: To characterize the effects of deformable image registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan. Methods: Eighteen patients who received curative doses (?60 Gy, 2 Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic-quality pretherapy (4–75 days) CT scan and a treatment planning scan with an associated dose map were collected. To establish correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pretherapy scans then were coregistered with planning scans (and associated dose maps) using the demons deformable registration algorithm and two variants of the Fraunhofer MEVIS algorithm (“Fast” and “EMPIRE10”). Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from each of the three algorithms. The Euclidean distance between manually and automatically mapped landmark points (d{sub E}) and the absolute difference in planned dose (|?D|) were calculated. Using regression modeling, |?D| was modeled as a function of d{sub E}, dose (D), dose standard deviation (SD{sub dose}) in an eight-pixel neighborhood, and the registration algorithm used. Results: Over 1400 landmark point pairs were identified, with 58–93 (median: 84) points identified per patient. Average |?D| across patients was 3.5 Gy (range: 0.9–10.6 Gy). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, with an average d{sub E} across patients of 5.2 mm (compared with >7 mm for the other two algorithms). Consequently, average |?D| was also lowest using the Fraunhofer MEVIS EMPIRE10 algorithm. |?D| increased significantly as a function of d{sub E} (0.42 Gy/mm), D (0.05 Gy/Gy), SD{sub dose} (1.4 Gy/Gy), and the algorithm used (?1 Gy). Conclusions: An average error of <4 Gy in radiation dose was introduced when points were mapped between CT scan pairs using deformable registration, with the majority of points yielding dose-mapping error <2 Gy (approximately 3% of the total prescribed dose). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, resulting in the smallest errors in mapped dose. Dose differences following registration increased significantly with increasing spatial registration errors, dose, and dose gradient (i.e., SD{sub dose}). This model provides a measurement of the uncertainty in the radiation dose when points are mapped between serial CT scans through deformable registration.

  4. Brain scanning in oligodendrogliomas

    International Nuclear Information System (INIS)

    Thirty-six brain scans and biopsies from 34 patients with histologically verified oligodendrogliomas were evaluated. Twenty-nine of the 36 scans were positive (80.6 percent) but the abnormal uptake produced by these neoplasms had no distinguishing features. The levels of endothelial proliferation-vascularity, necrosis, and mitoses were significantly different between the positive and negative scans. In the oligodendrogliomas, the relationship between histologic malignancy, detectability on scan, and prognosis remains unresolved. (U.S.)

  5. Scanning gamma camera

    International Nuclear Information System (INIS)

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

  6. 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)

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

    DEFF Research Database (Denmark)

    Goranko, Valentin

    2012-01-01

    This is a selective survey and discussion of some of the landmark undecidability results in temporal logic, beginning with Turing's undecidability of the Halting problem which, in retrospect, can be regarded as the historically first undecidability result for a suitable temporal logic over configuration graphs of Turing machines. I will discuss some of the natural habitats of undecidable temporal logics, such as first-order, interval-based and real time temporal logics, as well as some extensions that often lead to undecidability, such as two-dimensional temporal logics and temporal-epistemic logics.

  8. The Developmental Trajectory of Intramaze and Extramaze Landmark Biases in Spatial Navigation: An Unexpected Journey

    OpenAIRE

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

    2015-01-01

    Adults learning to navigate to a hidden goal within an enclosed space have been found to prefer information provided by the distal cues of an environment, as opposed to proximal landmarks within the environment. Studies with children, however, have shown that 5- or 7-year-olds do not display any preference toward distal or proximal cues during navigation. This suggests that a bias toward learning about distal cues occurs somewhere between the age of 7 years and adulthood. We recruited 5- to 1...

  9. Scanning Seismic Intrusion Detector

    Science.gov (United States)

    Lee, R. D.

    1982-01-01

    Scanning seismic intrusion detector employs array of automatically or manually scanned sensors to determine approximate location of intruder. Automatic-scanning feature enables one operator to tend system of many sensors. Typical sensors used with new system are moving-coil seismic pickups. Detector finds uses in industrial security systems.

  10. Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape

    Directory of Open Access Journals (Sweden)

    Li Dongmei

    2009-05-01

    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.

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Hsin-Chen; Wu, Chia-Hsing; Sun, Yung-Nien [Department of Computer Science and Information Engineering, National Cheng Kung University, 1 University Road, Tainan 701, Taiwan (China); Lin, Chii-Jeng [Department of Orthopedics, College of Medicine, National Cheng Kung University, 138 Sheng Li Road, Tainan 704, Taiwan (China); Wang, Chien-Kuo, E-mail: ynsun@mail.ncku.edu.t, E-mail: wale1212@gmail.co, E-mail: btmage@gmail.co, E-mail: mark@mail.ncku.edu.t, E-mail: n044206@mail.hosp.ncku.edu.t [Department of Radiology, National Cheng Kung University Hospital, 138 Sheng Li Road, Tainan 704, Taiwan (China)

    2010-11-21

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

  14. Radiographic scanning agent

    International Nuclear Information System (INIS)

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

  15. Evaluation of facial nerve and its landmarks in adult temporal bones

    Directory of Open Access Journals (Sweden)

    Saeid Soheilipour

    2010-06-01

    Full Text Available Introduction: The aim of this study was to identify variations of different segments of facial nerve in temporal bone. Materials and Methods: In this descriptive study that conducted on drilled bones in the temporal bone center of the Al-Zahra Hospital of Isfahan University of Medical Sciences, the landmarks of facial nerve in temporal bone were identified as separate variables and their distances from outer cortex of temporal bone and Henles spine and distances between different segments of nerve were recorded. Results: In the 50 temporal bones dissected, the distance between the tip of incus short process to the cortex was 14.2±1.96 mm, the distance between the facial recess from the facial nerve to the cortex was 14.5±2.58 mm, the distance between the stylomastoid foramen to the cortex was 20.6±2.49 mm, the distance between the lateral semicircular canal to the cortex was 15.9±2.31 mm and the distance between the sigmoid sinus dome to the cortex was 14.08±2.83 mm. The mean length of tympanic and mastoid segments (2nd and 3rd segments of facial nerve were 11.35±0.68 mm and 13.28±1.11mm, respectively. Conclusion: The mean lengths of segment of facial nerve and distant of landmarks from outer cortex of temporal bone are partially similar compared to those described in the western literature and text books, but different compared to eastern researches.

  16. A Sensor Network Data Compression Algorithm Based on Suboptimal Clustering and Virtual Landmark Routing Within Clusters

    Directory of Open Access Journals (Sweden)

    Shengqiang Li

    2010-10-01

    Full Text Available A kind of data compression algorithm for sensor networks based on suboptimal clustering and virtual landmark routing within clusters is proposed in this paper. Firstly, temporal redundancy existing in data obtained by the same node in sequential instants can be eliminated. Then sensor networks nodes will be clustered. Virtual node landmarks in clusters can be established based on cluster heads. Routing in clusters can be realized by combining a greedy algorithm and a flooding algorithm. Thirdly, a global structure tree based on cluster heads will be established. During the course of data transmissions from nodes to cluster heads and from cluster heads to sink, the spatial redundancy existing in the data will be eliminated. Only part of the raw data needs to be transmitted from nodes to sink, and all raw data can be recovered in the sink based on a compression code and part of the raw data. Consequently, node energy can be saved, largely because transmission of redundant data can be avoided. As a result the overall performance of the sensor network can obviously be improved.

  17. Pressure distribution on the anatomic landmarks of the knee and the effect of kneepads.

    Science.gov (United States)

    Porter, William L; Mayton, Alan G; Moore, Susan M

    2010-12-01

    This study examines stress transmitted to anatomic landmarks of the knee (patella, combined patella tendon and tibial tubercle) while in static kneeling postures without kneepads and while wearing two kneepads commonly worn in the mining industry. Ten subjects (7 male, 3 female) simulated postures utilized in low-seam mines: kneeling in full flexion; kneeling at 90° of knee flexion; and kneeling on one knee while in one of three kneepad states (no kneepads, non-articulated kneepads, and articulated kneepads). For each posture, peak and mean pressure on the anatomic landmarks of the knee were obtained. The majority of the pressure was found to be transmitted to the knee via the combined patellar tendon and tibial tubercle rather than through the patella. While the kneepads tested decreased the maximum pressure experienced at the combined patellar tendon and tibial tubercle, peak pressures of greater than 25 psi were still experienced over structures commonly injured in mining (e.g. bursa sac - bursitis/Miner's Knee). The major conclusion of this study is that novel kneepad designs that redistribute the stresses at the knee across a greater surface area and to other regions of the leg away from key structures of the knee are needed. PMID:20554268

  18. Fusion of WiFi, Smartphone Sensors and Landmarks Using the Kalman Filter for Indoor Localization

    Directory of Open Access Journals (Sweden)

    Zhenghua Chen

    2015-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    Fry, S N; Wehner, R

    2005-10-01

    This report describes the piloting mechanisms employed by honey bees during their final approach to a goal. Conceptually applying a bottom-up approach, we systematically varied the position, number and appearance landmarks associated with a rewarded target location within a large, homogenous flight tent. The flight behavior measured under various conditions is well explained with visuo-motor control loops that link perceived landmarks with appropriate turning responses. This view is consistent with the requirement of prolonged reinforcement learning for efficient goal navigation. A simple model is able to provide a comprehensive explanation for diverse flight patterns that range from convoluted searching behavior to highly idiosyncratic approaches, depending on the experimental context. Our results challenge the prevalent notion that honey bees employ image matching for visual guidance toward a goal site. Basic visuo-motor control loops may better meet the high demands for robust and fast flight control, which could serve as a powerful bio-mimetic design principle for micro-robotic aircraft. PMID:16215221

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

    Science.gov (United States)

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

    2015-01-01

    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

  1. Visual navigation of the UAVs on the basis of 3D natural landmarks

    Science.gov (United States)

    Karpenko, Simon; Konovalenko, Ivan; Miller, Alexander; Miller, Boris; Nikolaev, Dmitry

    2015-12-01

    This work considers the tracking of the UAV (unmanned aviation vehicle) on the basis of onboard observations of natural landmarks including azimuth and elevation angles. It is assumed that UAV's cameras are able to capture the angular position of reference points and to measure the angles of the sight line. Such measurements involve the real position of UAV in implicit form, and therefore some of nonlinear filters such as Extended Kalman filter (EKF) or others must be used in order to implement these measurements for UAV control. Recently it was shown that modified pseudomeasurement method may be used to control UAV on the basis of the observation of reference points assigned along the UAV path in advance. However, the use of such set of points needs the cumbersome recognition procedure with the huge volume of on-board memory. The natural landmarks serving as such reference points which may be determined on-line can significantly reduce the on-board memory and the computational difficulties. The principal difference of this work is the usage of the 3D reference points coordinates which permits to determine the position of the UAV more precisely and thereby to guide along the path with higher accuracy which is extremely important for successful performance of the autonomous missions. The article suggests the new RANSAC for ISOMETRY algorithm and the use of recently developed estimation and control algorithms for tracking of given reference path under external perturbation and noised angular measurements.

  2. Management of Neovascular Age-related Macular Degeneration: A Review on Landmark Randomized Controlled Trials.

    Science.gov (United States)

    Agarwal, Aniruddha; Aggarwal, Kanika; Gupta, Vishali

    2016-01-01

    In the last decade, a number of prospective clinical trials with carefully designed study protocols have been conducted for the treatment of neovascular age-related macular degeneration (AMD). These landmark clinical trials such as ANCHOR and MARINA and, more recently, the Comparison of AMD Treatment Trials and VIEW studies have revolutionized the management of neovascular AMD. While AMD continues to remain a leading cause of severe visual loss worldwide, advances in pharmacotherapeutics have led to substantial improvements in the outcome of these patients. The introduction of anti-vascular endothelial growth factor agents has resulted in improvement of visual outcomes and has had a positive impact on the quality of life among elderly population. While the contemporary management of neovascular AMD has been successful in tremendously reducing the visual morbidity, the financial burden of therapy has increased exponentially. To overcome these challenges, newer pharmacologic agents are evaluated for their efficacy and safety in AMD. Ground-breaking advances in bench to bedside research have led to discovery of new pathways that appear to be viable targets for preventing visual loss in AMD. In this review, study designs and results of landmark clinical trials in AMD from the past decade have been summarized. PMID:26957836

  3. Polarised skylight and the landmark panorama provide night-active bull ants with compass information during route following.

    Science.gov (United States)

    Reid, Samuel F; Narendra, Ajay; Hemmi, Jan M; Zeil, Jochen

    2011-02-01

    Navigating animals are known to use a number of celestial and terrestrial compass cues that allow them to determine and control their direction of travel. Which of the cues dominate appears to depend on their salience. Here we show that night-active bull ants attend to both the pattern of polarised skylight and the landmark panorama in their familiar habitat. When the two directional cues are in conflict, ants choose a compromise direction. However, landmark guidance appears to be the primary mechanism of navigation used by forager ants, with those cues in the direction of heading having the greatest influence on navigation. Different colonies respond to the removal of these cues to different degrees, depending on the directional information provided by the local landmark panorama. Interestingly, other parts of the surrounding panorama also influence foraging speed and accuracy, suggesting that they too play a role in navigation. PMID:21228195

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

    Science.gov (United States)

    Rodriguez, M P; Nygren, A

    2015-02-01

    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

  5. Not only … but also: REM sleep creates and NREM Stage 2 instantiates landmark junctions in cortical memory networks.

    Science.gov (United States)

    Llewellyn, Sue; Hobson, J Allan

    2015-07-01

    This article argues both rapid eye movement (REM) and non-rapid eye movement (NREM) sleep contribute to overnight episodic memory processes but their roles differ. Episodic memory may have evolved from memory for spatial navigation in animals and humans. Equally, mnemonic navigation in world and mental space may rely on fundamentally equivalent processes. Consequently, the basic spatial network characteristics of pathways which meet at omnidirectional nodes or junctions may be conserved in episodic brain networks. A pathway is formally identified with the unidirectional, sequential phases of an episodic memory. In contrast, the function of omnidirectional junctions is not well understood. In evolutionary terms, both animals and early humans undertook tours to a series of landmark junctions, to take advantage of resources (food, water and shelter), whilst trying to avoid predators. Such tours required memory for emotionally significant landmark resource-place-danger associations and the spatial relationships amongst these landmarks. In consequence, these tours may have driven the evolution of both spatial and episodic memory. The environment is dynamic. Resource-place associations are liable to shift and new resource-rich landmarks may be discovered, these changes may require re-wiring in neural networks. To realise these changes, REM may perform an associative, emotional encoding function between memory networks, engendering an omnidirectional landmark junction which is instantiated in the cortex during NREM Stage 2. In sum, REM may preplay associated elements of past episodes (rather than replay individual episodes), to engender an unconscious representation which can be used by the animal on approach to a landmark junction in wake. PMID:25921620

  6. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines when...... and where in the organism a given gene is active. This is the epigenetic information. Genomics is the study of DNA sequences and the epigenetic information of gene regulation....

  7. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  8. Radioactively labelled scanning agent

    International Nuclear Information System (INIS)

    According to the invention, a stabilized alcohol solution of a reducing salt preparation has been developed and used for the preparation of radioactively labelled scanning agents, in particular for the liver. These scanning agents contain colloids of sup(99m)Tc and a reduction agent, e.g. SnCl2, TiCl3, CrCl2, FeCl2, etc., and, if necessary, an additional stabilizing agent. Bone scanning agents further contain a phosphate complex and lung scanning agents a macroaggregated albumin. (VJ)

  9. Scanning of bone metastases

    International Nuclear Information System (INIS)

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

  10. Algorithms For Automatic And Robust Registration Of 3D Head Scans

    Directory of Open Access Journals (Sweden)

    Peter Eisert

    2010-12-01

    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.

  11. Corrective surgery for canine patellar luxation in 75 cases (107 limbs: landmark for block recession

    Directory of Open Access Journals (Sweden)

    Mitsuhiro Isaka

    2014-05-01

    Full Text Available Canine medial patellar luxation (MPL is a very common orthopedic disease in small animals. Because the pathophysiology of this disease involves various pathways, the surgical techniques and results vary according to the veterinarian. Further, the landmark for block recession is not completely clear. We retrospectively evaluated 75 dogs (107 limbs with MPL in whom our landmark for block recession was used from July 2008 to May 2013. Information regarding the breed, age, sex, body weight, body condition score (BCS, lateral vs bilateral, pre-operative grading, surgical techniques, removal of implants, concomitance with anterior cruciate ligament (ACL rupture, re-luxation, re-operation, and rehabilitation was obtained from the medical records. The breeds were as follows: Chihuahua (n=23, Pomeranian (n=12, Yorkshire Terrier (n=9, and so on. The study group consisted of 33 males (castrated n=13 and 42 females (spayed n=21. The median age was 53.3±35.9 months (32-146 months; 13 cases were less than 12 months of age (17.3%. The pre-surgical BCSs were as follows: 1 (n=0, 2 (n=20, 3 (n=24, 4 (n=24 and 5 (n=7. The body weight was 4.51±3.48 kg (1.34-23.0 kg; 71 cases (94.7% were less than 10 kg. The MPL grades (each limb were G1 (n=1, G2 (n=18, G3 (n=78, and G4 (n=10; 32 cases were bilateral and 43 cases were unilateral (right n=27; left n=16. The specific surgical procedure (distal femoral osteotomy was 3 stifles in Chihuahuas. Concurrent with ACL rupture was 16/107 stifles (15.0% corrected with the over-the-top method or the extracapsular method in Papillons (5/6, Chihuahuas (5/23, and so on. The occurrences of re-luxation and re-operation were 3 out of 107 stifles (2.8% and 0%, respectively. In this retrospective study, we present a potentially good surgical landmark for block recession of MPL in dogs.

  12. Landmark constrained registration of high-genus surfaces applied to vestibular system morphometry.

    Science.gov (United States)

    Wen, Chengfeng; Wang, Defeng; Shi, Lin; Chu, Winnie C W; Cheng, Jack C Y; Lui, Lok Ming

    2015-09-01

    The analysis of the vestibular system (VS) is an important research topic in medical image analysis. VS is a sensory structure in the inner ear for the perception of spatial orientation. It is believed several diseases, such as the Adolescent Idiopathic Scoliosis (AIS), are due to the impairment of the VS function. The morphology of the VS is thus of great research significance. A major challenge is that the VS is a genus-3 surface. The high-genus topology of the VS poses great challenges to find accurate pointwise correspondences between the surfaces and whereby perform accurate shape analysis. In this paper, we present a method to obtain the landmark constrained diffeomorphic registration between the VS surfaces based on the quasi-conformal theory. Given a set of corresponding landmarks on the VS surfaces, a diffeomorphism between the VS surfaces that matches the features consistently can be obtained. The basic idea is to iteratively search for an admissible Beltrami coefficient, which is associated to our desired landmark matching registration. With the obtained surface registrations, vertex-wise morphometric analysis can be carried out. Two types of geometric features are used for shape comparison. One is the collection of homotopic loops on each canals of the VS, which can be used to measure the local thickness of the canals. From the homotopic loops, centerlines can be extracted. By examining the deviations of the centerlines from the best fit planes, bendings of the canals can be detected. The second geometric feature is the minimal surface enclosed by the homotopic loop. From the minimal surfaces of each homotopic loops, cross-sectional area of the canals can be evaluated. To study the local shape difference more comprehensively, a complete shape index, which is defined using the Beltrami coefficients and surface curvatures, is used. We test proposed registration method on 15 VS of normal control subjects and 12 VS of patients suffering from AIS. Experimental results show the efficacy and accuracy of the proposed algorithm to compute the VS surface registration. Shape analysis has also been carried out using the proposed geometric features and shape index, which reveals shape differences in the posterior canal between normal and diseased AIS groups. PMID:26069905

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

    Science.gov (United States)

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

    2015-06-01

    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

  14. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Snowboarding, Skating Crushes What's a Booger? Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A Text Size en español Obtención de una tomografía computada (video) CAT stands for "computerized axial tomography." Translated, that means ...

  15. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Snowboarding, Skating Crushes What's a Booger? Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A Text Size en español Obtención de una tomografía computada (video) CAT stands for "computerized axial tomography." Translated, that means ...

  16. Getting a CAT Scan

    Medline Plus

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

  17. Frequency scanning microstrip antennas

    DEFF Research Database (Denmark)

    Danielsen, Magnus; Jørgensen, Rolf

    1979-01-01

    The principles of using radiating microstrip resonators as elements in a frequency scanning antenna array are described. The resonators are cascade-coupled. This gives a scan of the main lobe due to the phase-shift in the resonator in addition to that created by the transmission line phase...

  18. Getting a CAT Scan

    Science.gov (United States)

    ... Snowboarding, Skating Crushes What's a Booger? Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A Text Size en español Obtención de una tomografía computada (video) CAT stands for "computerized axial tomography." Translated, that means ...

  19. The Royal Philanthropic Expedition of the Vaccine: a landmark in the history of public health.

    Science.gov (United States)

    Soto-Pérez-de-Celis, E

    2008-11-01

    In 1979, smallpox officially became the first disease ever to be eradicated by mankind. The global efforts to defeat this dreadful pandemic, however, started almost two centuries before. One of the most important, and sometimes forgotten, events in the fight against smallpox was the Royal Philanthropic Expedition of the Vaccine, commissioned by Charles IV of Spain to physicians Francisco Xavier Balmis y Berenguer and Jose Salvany in 1804. The aim of this expedition was to take the smallpox vaccine, discovered by Jenner, to Spain's territories in the Americas and in the Far East. After several years of vaccination in modern day Puerto Rico, Cuba, Venezuela, Ecuador, Peru, Bolivia, Chile, Mexico and the Philippines, the expedition returned to Europe. To this day, the Balmis and Salvany expedition remains a great example of international cooperation, and a landmark in the history of public health. PMID:19103818

  20. Maximized Posteriori Attributes Selection from Facial Salient Landmarks for Face Recognition

    CERN Document Server

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

    2010-01-01

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

  1. 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

  2. Global polity in adult education and UNESCO: landmarking, brokering, and framing policy

    DEFF Research Database (Denmark)

    Milana, Marcella

    2015-01-01

    Taking into account the complexity and multidimensionality of local-global interconnections, the author argues for the adoption of a global polity perspective in adult education, which is applied to study mobilization processes that occur through UNESCO. The findings point to three processes, neither within nor outside, but across geo-political borders and professional interests: ‘landmarking’, by which a shared sense of a common past in adult education is created; ‘brokering’, which helps shape a common future direction in adult education; and ‘framing’, which is used to convert ideational landscapes into material government-led actions. Both the theoretical perspectives and the analytical insights presented here could be used in analogous studies in other areas of education or with a focus on different political actors.

  3. Surgical Anatomical Landmarks of the Thoracolumbar Vertebral Column on Magnetic Resonance Imaging in Dogs.

    Science.gov (United States)

    Yeamans, C L; Haley, A; Gutierrez-Quintana, R; Penderis, J

    2016-04-01

    Magnetic resonance imaging (MRI) in veterinary medicine profoundly improved spinal cord disease investigation in canine patients. We aimed to further describe the anatomical landmarks of the thoracolumbar junction in sagittal MRI sequences. MRI studies from 90 dogs were reviewed retrospectively, representing a broad cross section of breeds and body weights. The ratio of the distance from the dorsal aspect of the vertebral canal to the dorsal aspect of the transverse process or rib articulation relative to the length of L2 vertebra was determined for T12, T13, L1 and L2 vertebrae. A statistically significant difference was noted with the transverse processes being more ventrally located than the cranial fovea costalis. The lumbar transverse processes and rib articulations dramatically varied in shape, being oval or round, respectively. The sagittal image at the level of the lateral margin of the articular facet joint proved to be the most consistent for review of these structures. PMID:26105110

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

    Science.gov (United States)

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

    2015-01-21

    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 11 mm. PMID:25497377

  5. Global polity in adult education and UNESCO: landmarking, brokering, and framing policy

    DEFF Research Database (Denmark)

    Milana, Marcella

    2015-01-01

    Taking into account the complexity and multidimensionality of local-global interconnections, the author argues for the adoption of a global polity perspective in adult education, which is applied to study mobilization processes that occur through UNESCO. The findings point to three processes......, neither within nor outside, but across geo-political borders and professional interests: ‘landmarking’, by which a shared sense of a common past in adult education is created; ‘brokering’, which helps shape a common future direction in adult education; and ‘framing’, which is used to convert ideational...... landscapes into material government-led actions. Both the theoretical perspectives and the analytical insights presented here could be used in analogous studies in other areas of education or with a focus on different political actors....

  6. 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)

  7. Evaluation and Comparison of Anatomical Landmark Detection Methods for Cephalometric X-Ray Images: A Grand Challenge.

    Science.gov (United States)

    Wang, Ching-Wei; Huang, Cheng-Ta; Hsieh, Meng-Che; Li, Chung-Hsing; Chang, Sheng-Wei; Li, Wei-Cheng; Vandaele, Rémy; Marée, Raphaël; Jodogne, Sébastien; Geurts, Pierre; Chen, Cheng; Zheng, Guoyan; Chu, Chengwen; Mirzaalian, Hengameh; Hamarneh, Ghassan; Vrtovec, Tomaz; Ibragimov, Bulat

    2015-09-01

    Cephalometric analysis is an essential clinical and research tool in orthodontics for the orthodontic analysis and treatment planning. This paper presents the evaluation of the methods submitted to the Automatic Cephalometric X-Ray Landmark Detection Challenge, held at the IEEE International Symposium on Biomedical Imaging 2014 with an on-site competition. The challenge was set to explore and compare automatic landmark detection methods in application to cephalometric X-ray images. Methods were evaluated on a common database including cephalograms of 300 patients aged six to 60 years, collected from the Dental Department, Tri-Service General Hospital, Taiwan, and manually marked anatomical landmarks as the ground truth data, generated by two experienced medical doctors. Quantitative evaluation was performed to compare the results of a representative selection of current methods submitted to the challenge. Experimental results show that three methods are able to achieve detection rates greater than 80% using the 4 mm precision range, but only one method achieves a detection rate greater than 70% using the 2 mm precision range, which is the acceptable precision range in clinical practice. The study provides insights into the performance of different landmark detection approaches under real-world conditions and highlights achievements and limitations of current image analysis techniques. PMID:25794388

  8. Laser Scanning in Forests

    Directory of Open Access Journals (Sweden)

    Håkan Olsson

    2012-09-01

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

  9. 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

  10. WE-D-9A-02: Automated Landmark-Guided CT to Cone-Beam CT Deformable Image Registration

    International Nuclear Information System (INIS)

    Purpose: The anatomical changes that occur between the simulation CT and daily cone-beam CT (CBCT) are investigated using an automated landmark-guided deformable image registration (LDIR) algorithm with simultaneous intensity correction. LDIR was designed to be accurate in the presence of tissue intensity mismatch and heavy noise contamination. Method: An auto-landmark generation algorithm was used in conjunction with a local small volume (LSV) gradient matching search engine to map corresponding landmarks between the CBCT and planning CT. The LSVs offsets were used to perform an initial deformation, generate landmarks, and correct local intensity mismatch. The landmarks act as stabilizing controlpoints in the Demons objective function. The accuracy of the LDIR algorithm was evaluated on one synthetic case with ground truth and data of ten head and neck cancer patients. The deformation vector field (DVF) accuracy was accessed using a synthetic case. The Root mean square error of the 3D canny edge (RMSECE), mutual information (MI), and feature similarity index metric (FSIM) were used to access the accuracy of LDIR on the patient data. The quality of the corresponding deformed contours was verified by an attending physician. Results: The resulting 90 percentile DVF error for the synthetic case was within 5.63mm for the original demons algorithm, 2.84mm for intensity correction alone, 2.45mm using controlpoints without intensity correction, and 1.48 mm for the LDIR algorithm. For the five patients the mean RMSECE of the original CT, Demons deformed CT, intensity corrected Demons CT, control-point stabilized deformed CT, and LDIR CT was 0.24, 0.26, 0.20, 0.20, and 0.16 respectively. Conclusion: LDIR is accurate in the presence of multimodal intensity mismatch and CBCT noise contamination. Since LDIR is GPU based it can be implemented with minimal additional strain on clinical resources. This project has been supported by a CPRIT individual investigator award RP11032

  11. Environmental scanning electron microscopy

    International Nuclear Information System (INIS)

    The ElectroScan environmental scanning electron microscope (ESEM) is one of the most exciting new developments in the field of Electron Microscopy. The ESEM differs from conventional Scanning Electron Microscopes (SEM) by being able to examine materials including liquids and oils in their natural state with no prior sample preparation. Accessory equipment, cooling, heating and manipulating devices allow the manipulation of samples thus making it possible for the first time to image dynamic processes such as wetting, drying, absorption, corrosion, melting, crystallisation, curing and fracturing at high magnification. Papers concerning the historical development of the ESEM are given in a bibliography at the end of this paper. 24 refs., 18 figs

  12. CT scanning in children

    International Nuclear Information System (INIS)

    This paper assesses clinical feasibility of, image quality of, need for sedation in, and radiation dose in pediatric studies obtained with a continuously rotating (CR) CT scanner. The authors review the body CT scans of 25 children (mean age, 2.6 y) performed on a CR Scanner (Siemens Somatom Plus) (1-sec scan time). Parameters evaluated included edge sharpness, streak artifacts, contrast enhancement, need for sedation, and imaging time. The same parameters were assessed in a control group of 25 patients examined on a conventional stop-start CT scanner (Somatom DR- H) (3-sec scan time). Internal radiation doses were determined using child-sized phantoms

  13. Prophage Genomics

    OpenAIRE

    Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brüssow, Harald

    2003-01-01

    The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage s...

  14. Pediatric CT Scans

    Science.gov (United States)

    The Radiation Epidemiology Branch and collaborators have initiated a retrospective cohort study to evaluate the relationship between radiation exposure from CT scans conducted during childhood and adolescence and the subsequent development of cancer.

  15. Shoulder MRI scan

    Science.gov (United States)

    ... finding on an x-ray or bone scan Shoulder pain and fever Decreased motion of the shoulder joint ... of the shoulder joint Shoulder instability Shoulder weakness Shoulder pain and a history of cancer Shoulder pain that ...

  16. Hepatobiliary scanning in cholecystitis

    International Nuclear Information System (INIS)

    To validate the use of sup(99m)Tc-PIPIDA in the diagnosis of biliary tract disease, 117 patients with clinical symptoms of acute cholecystitis were prospectively scanned as an initial screening test. The accuracy of the test was evaluated on the basis of surgical pathology in 59 patients. Three groups were defined: cystic duct obstruction, common duct obstruction, and normal scan. The diagnostic accuracy of the test for acute cholecystitis was 97%. Complete common duct obstruction was confirmed at surgery in 12 patients (100%). A normal scan helped to rule out acute cholecystitis. Jaundice did not influence the reliability of the method. Hepatobiliary scanning is an accurate, safe, and rapid diagnostic test for acute cholecystitis. (orig.)

  17. Abscess scan - radioactive

    Science.gov (United States)

    ... or had any of the following medical conditions, procedures, or treatments, as they can interfere with test results: Gallium (Ga) scan within the past month Hemodialysis Hyperglycemia Long-term antibiotic therapy Steroid therapy Total ...

  18. Frequency scanning microstrip antennas

    DEFF Research Database (Denmark)

    Danielsen, Magnus; JØrgensen, Rolf

    1979-01-01

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

  19. Getting a CAT Scan

    Medline Plus

    Full Text Available ... Kids for Teens Kids Home How the Body Works Puberty & Growing Up Staying Healthy Recipes & Cooking Staying ... and Puberty) Movie: Digestive System How the Body Works Main Page Getting a CAT Scan (Video) KidsHealth > ...

  20. Getting a CAT Scan

    Medline Plus

    Full Text Available ... How the Body Works Puberty & Growing Up Staying Healthy Recipes & Cooking Staying Safe Health Problems Illnesses & Injuries ... your body. The scan itself is painless. All you'll need to do is hold still for ...

  1. Slow Scan Telemedicine

    Science.gov (United States)

    1984-01-01

    Originally developed under contract for NASA by Ball Bros. Research Corporation for acquiring visual information from lunar and planetary spacecraft, system uses standard closed circuit camera connected to a device called a scan converter, which slows the stream of images to match an audio circuit, such as a telephone line. Transmitted to its destination, the image is reconverted by another scan converter and displayed on a monitor. In addition to assist scans, technique allows transmission of x-rays, nuclear scans, ultrasonic imagery, thermograms, electrocardiograms or live views of patient. Also allows conferencing and consultation among medical centers, general practitioners, specialists and disease control centers. Commercialized by Colorado Video, Inc., major employment is in business and industry for teleconferencing, cable TV news, transmission of scientific/engineering data, security, information retrieval, insurance claim adjustment, instructional programs, and remote viewing of advertising layouts, real estate, construction sites or products.

  2. Optisk scanning af spørgeskemaer

    DEFF Research Database (Denmark)

    Paulsen, Aksel

    , men processen er tidkrævende. Optisk scanning af spørgeskemaer med automatisk registrering af svar kan være et alternativ, men videre validering af metoden er nødvendig. Design: 200 patienter blev tilfældigt udvalgt fra en kohorte på 5777 patienter der tidligere havde svaret på to forskellige....../ 1000 felter= 0.370 (95% CI: 0.160-0.729), (p= 0.020)). Der var ingen statistisk forskel mellem optisk scanning (fejl/ 1000 felter= 0.046 (95% CI: 0.001-0.258)) og manuel dobbelt indtastning (p=1.000). Konklusioner: Optisk scanning er et godt alternativ til manuel dobbelt indtastning for spørgeskema med...... markeringsbokser. Det kan se ud som om der er flere fejl med automatisk aflæsning af tal end med automatisk aflæsning af markeringer i markeringsbokser. Vi havde relativt få data med automatisk aflæsning af tal i vores studie og videre studier, samt forbedringer i teknologi for optisk scanning og aflæsning af tal...

  3. 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

  4. Comparison of Two Deformable Registration Algorithms in the Presence of Radiologic Change Between Serial Lung CT Scans.

    Science.gov (United States)

    Cunliffe, Alexandra R; White, Bradley; Justusson, Julia; Straus, Christopher; Malik, Renuka; Al-Hallaq, Hania A; Armato, Samuel G

    2015-12-01

    We evaluated the image registration accuracy achieved using two deformable registration algorithms when radiation-induced normal tissue changes were present between serial computed tomography (CT) scans. Two thoracic CT scans were collected for each of 24 patients who underwent radiation therapy (RT) treatment for lung cancer, eight of whom experienced radiologically evident normal tissue damage between pre- and post-RT scan acquisition. For each patient, 100 landmark point pairs were manually placed in anatomically corresponding locations between each pre- and post-RT scan. Each post-RT scan was then registered to the pre-RT scan using (1) the Plastimatch demons algorithm and (2) the Fraunhofer MEVIS algorithm. The registration accuracy for each scan pair was evaluated by comparing the distance between landmark points that were manually placed in the post-RT scans and points that were automatically mapped from pre- to post-RT scans using the displacement vector fields output by the two registration algorithms. For both algorithms, the registration accuracy was significantly decreased when normal tissue damage was present in the post-RT scan. Using the Plastimatch algorithm, registration accuracy was 2.4 mm, on average, in the absence of radiation-induced damage and 4.6 mm, on average, in the presence of damage. When the Fraunhofer MEVIS algorithm was instead used, registration errors decreased to 1.3 mm, on average, in the absence of damage and 2.5 mm, on average, when damage was present. This work demonstrated that the presence of lung tissue changes introduced following RT treatment for lung cancer can significantly decrease the registration accuracy achieved using deformable registration. PMID:25822396

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

    Indian Academy of Sciences (India)

    Rahul Kumar; Ashima Khurana

    2014-12-01

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

  6. Cryptosporidium Parvum Genome Project

    Directory of Open Access Journals (Sweden)

    Mitchell S. Abrahamsen

    2006-04-01

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

  7. 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.)

  8. 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)

    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

    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.)

  9. Validation of automatic landmark identification for atlas-based segmentation for radiation treatment planning of the head-and-neck region

    Science.gov (United States)

    Leavens, Claudia; Vik, Torbjørn; Schulz, Heinrich; Allaire, Stéphane; Kim, John; Dawson, Laura; O'Sullivan, Brian; Breen, Stephen; Jaffray, David; Pekar, Vladimir

    2008-03-01

    Manual contouring of target volumes and organs at risk in radiation therapy is extremely time-consuming, in particular for treating the head-and-neck area, where a single patient treatment plan can take several hours to contour. As radiation treatment delivery moves towards adaptive treatment, the need for more efficient segmentation techniques will increase. We are developing a method for automatic model-based segmentation of the head and neck. This process can be broken down into three main steps: i) automatic landmark identification in the image dataset of interest, ii) automatic landmark-based initialization of deformable surface models to the patient image dataset, and iii) adaptation of the deformable models to the patient-specific anatomical boundaries of interest. In this paper, we focus on the validation of the first step of this method, quantifying the results of our automatic landmark identification method. We use an image atlas formed by applying thin-plate spline (TPS) interpolation to ten atlas datasets, using 27 manually identified landmarks in each atlas/training dataset. The principal variation modes returned by principal component analysis (PCA) of the landmark positions were used by an automatic registration algorithm, which sought the corresponding landmarks in the clinical dataset of interest using a controlled random search algorithm. Applying a run time of 60 seconds to the random search, a root mean square (rms) distance to the ground-truth landmark position of 9.5 +/- 0.6 mm was calculated for the identified landmarks. Automatic segmentation of the brain, mandible and brain stem, using the detected landmarks, is demonstrated.

  10. 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 and 67Ga citrate and 111In white blood cells (111In WBC) for investigation of inflammatory/infective lesions

  11. 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

  12. Viral DNA polymerase scanning and the gymnastics of Sendai virus RNA synthesis

    OpenAIRE

    Kolakofsky, Daniel; Le Mercier, Philippe; Iseni, Frédéric; Garcin, Dominique

    2004-01-01

    mRNA synthesis from nonsegmented negative-strand RNA virus (NNV) genomes is unique in tht 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 tra...

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

    Energy Technology Data Exchange (ETDEWEB)

    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

    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

  14. 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 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

  15. Cortical projection of the inferior choroidal point as a reliable landmark to place the corticectomy and reach the temporal horn through a middle temporal gyrus approach

    Directory of Open Access Journals (Sweden)

    Thomas Frigeri

    2014-10-01

    Full Text Available Objective To establish preoperatively the localization of the cortical projection of the inferior choroidal point (ICP and use it as a reliable landmark when approaching the temporal horn through a middle temporal gyrus access. To review relevant anatomical features regarding selective amigdalohippocampectomy (AH for treatment of mesial temporal lobe epilepsy (MTLE. Method The cortical projection of the inferior choroidal point was used in more than 300 surgeries by one authors as a reliable landmark to reach the temporal horn. In the laboratory, forty cerebral hemispheres were examined. Conclusion The cortical projection of the ICP is a reliable landmark for reaching the temporal horn.

  16. Confocal Line Scanning Sensor

    International Nuclear Information System (INIS)

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

  17. Vector generator scan converter

    Energy Technology Data Exchange (ETDEWEB)

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

    1990-01-01

    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.

  18. Vector generator scan converter

    Energy Technology Data Exchange (ETDEWEB)

    Moore, J.M.; Leighton, J.F.

    1990-04-17

    This patent describes high printing speeds for graphics data that are achieved with a laser printer by transmitting compressed graphics data from a main processor over an I/O (input/output) channel to a vector generator scan converter which reconstructs a full graphics image for input to the laser printer through a raster data input port. The vector generator scan converter includes a microprocessor with associated microcode memory containing a microcode instruction set, a working memory for storing compressed data, vector generator hardware for drawing a full graphic image from vector parameters calculated by the microprocessor, image buffer memory for storing the reconstructed graphics image and an output scanner for reading the graphics image data and inputting the data to the printer. The vector generator scan converter eliminates the bottleneck created by the I/O channel for transmitting graphics data from the main processor to the laser printer, and increases printer speed up to thirty fold.

  19. Liver Scanning with Radiomolybdate

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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