WorldWideScience

Sample records for accurate multiple locus

  1. Identifying multiple causative genes at a single GWAS locus

    Flister, Michael J.; Tsaih, Shirng-Wern; O'Meara, Caitlin C.; Endres, Bradley; Hoffman, Matthew J.; Geurts, Aron M.; Dwinell, Melinda R.; Lazar, Jozef; Jacob, Howard J.; Moreno, Carol

    2013-01-01

    Genome-wide association studies (GWAS) are useful for nominating candidate genes, but typically are unable to establish disease causality or differentiate between the effects of variants in linkage disequilibrium (LD). Additionally, some GWAS loci might contain multiple causative variants or genes that contribute to the overall disease susceptibility at a single locus. However, the majority of current GWAS lack the statistical power to test whether multiple causative genes underlie the same l...

  2. Network-based multiple locus linkage analysis of expression traits

    Pan, Wei

    2009-01-01

    Motivation: We consider the problem of multiple locus linkage analysis for expression traits of genes in a pathway or a network. To capitalize on co-expression of functionally related genes, we propose a penalized regression method that maps multiple expression quantitative trait loci (eQTLs) for all related genes simultaneously while accounting for their shared functions as specified a priori by a gene pathway or network.

  3. Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping

    Xu Shizhong

    2011-05-01

    Full Text Available Abstract Background The Bayesian shrinkage technique has been applied to multiple quantitative trait loci (QTLs mapping to estimate the genetic effects of QTLs on quantitative traits from a very large set of possible effects including the main and epistatic effects of QTLs. Although the recently developed empirical Bayes (EB method significantly reduced computation comparing with the fully Bayesian approach, its speed and accuracy are limited by the fact that numerical optimization is required to estimate the variance components in the QTL model. Results We developed a fast empirical Bayesian LASSO (EBLASSO method for multiple QTL mapping. The fact that the EBLASSO can estimate the variance components in a closed form along with other algorithmic techniques render the EBLASSO method more efficient and accurate. Comparing with the EB method, our simulation study demonstrated that the EBLASSO method could substantially improve the computational speed and detect more QTL effects without increasing the false positive rate. Particularly, the EBLASSO algorithm running on a personal computer could easily handle a linear QTL model with more than 100,000 variables in our simulation study. Real data analysis also demonstrated that the EBLASSO method detected more reasonable effects than the EB method. Comparing with the LASSO, our simulation showed that the current version of the EBLASSO implemented in Matlab had similar speed as the LASSO implemented in Fortran, and that the EBLASSO detected the same number of true effects as the LASSO but a much smaller number of false positive effects. Conclusions The EBLASSO method can handle a large number of effects possibly including both the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTL mapping.

  4. A multiple more accurate Hardy-Littlewood-Polya inequality

    Qiliang Huang

    2012-11-01

    Full Text Available By introducing multi-parameters and conjugate exponents and using Euler-Maclaurin’s summation formula, we estimate the weight coefficient and prove a multiple more accurate Hardy-Littlewood-Polya (H-L-P inequality, which is an extension of some earlier published results. We also prove that the constant factor in the new inequality is the best possible, and obtain its equivalent forms.

  5. Accurate macroscale modelling of spatial dynamics in multiple dimensions

    Roberts, A ~J; Bunder, J ~E

    2011-01-01

    Developments in dynamical systems theory provides new support for the macroscale modelling of pdes and other microscale systems such as Lattice Boltzmann, Monte Carlo or Molecular Dynamics simulators. By systematically resolving subgrid microscale dynamics the dynamical systems approach constructs accurate closures of macroscale discretisations of the microscale system. Here we specifically explore reaction-diffusion problems in two spatial dimensions as a prototype of generic systems in multiple dimensions. Our approach unifies into one the modelling of systems by a type of finite elements, and the `equation free' macroscale modelling of microscale simulators efficiently executing only on small patches of the spatial domain. Centre manifold theory ensures that a closed model exist on the macroscale grid, is emergent, and is systematically approximated. Dividing space either into overlapping finite elements or into spatially separated small patches, the specially crafted inter-element\\slash patch coupling als...

  6. Single locus affects embryonic segment polarity and multiple aspects of an adult evolutionary novelty

    Saenko Suzanne V

    2010-08-01

    Full Text Available Abstract Background The characterization of the molecular changes that underlie the origin and diversification of morphological novelties is a key challenge in evolutionary developmental biology. The evolution of such traits is thought to rely largely on co-option of a toolkit of conserved developmental genes that typically perform multiple functions. Mutations that affect both a universal developmental process and the formation of a novelty might shed light onto the genetics of traits not represented in model systems. Here we describe three pleiotropic mutations with large effects on a novel trait, butterfly eyespots, and on a conserved stage of embryogenesis, segment polarity. Results We show that three mutations affecting eyespot size and/or colour composition in Bicyclus anynana butterflies occurred in the same locus, and that two of them are embryonic recessive lethal. Using surgical manipulations and analysis of gene expression patterns in developing wings, we demonstrate that the effects on eyespot morphology are due to changes in the epidermal response component of eyespot induction. Our analysis of morphology and of gene expression in mutant embryos shows that they have a typical segment polarity phenotype, consistent with the mutant locus encoding a negative regulator of Wingless signalling. Conclusions This study characterizes the segregation and developmental effects of alleles at a single locus that controls the morphology of a lineage-specific trait (butterfly eyespots and a conserved process (embryonic segment polarity and, specifically, the regulation of Wingless signalling. Because no gene with such function was found in the orthologous, highly syntenic genomic regions of two other lepidopterans, we hypothesize that our locus is a yet undescribed, possibly lineage-specific, negative regulator of the conserved Wnt/Wg pathway. Moreover, the fact that this locus interferes with multiple aspects of eyespot morphology and maps to a

  7. Multiple-locus variable number tandem repeat analysis for Streptococcus pneumoniae: comparison with PFGE and MLST.

    Karin E M Elberse

    Full Text Available In the era of pneumococcal conjugate vaccines, surveillance of pneumococcal disease and carriage remains of utmost importance as important changes may occur in the population. To monitor these alterations reliable genotyping methods are required for large-scale applications. We introduced a high throughput multiple-locus variable number tandem repeat analysis (MLVA and compared this method with pulsed-field gel electrophoresis (PFGE and multilocus sequence typing (MLST. The MLVA described here is based on 8 BOX loci that are amplified in two multiplex PCRs. The labeled PCR products are sized on an automated DNA sequencer to accurately determine the number of tandem repeats. The composite of the number of repeats of the BOX loci makes up a numerical profile that is used for identification and clustering. In this study, MLVA was performed on 263 carriage isolates that were previously characterized by MLST and PFGE. MLVA, MLST and PFGE (cut-off of 80% yielded 164, 120, and 87 types, respectively. The three typing methods had Simpson's diversity indices of 98.5% or higher. Congruence between MLST and MLVA was high. The Wallace of MLVA to MLST was 0.874, meaning that if two strains had the same MLVA type they had an 88% chance of having the same MLST type. Furthermore, the Wallace of MLVA to clonal complex of MLST was even higher: 99.5%. For some isolates belonging to a single MLST clonal complex although displaying different serotypes, MLVA was more discriminatory, generating groups according to serotype or serogroup. Overall, MLVA is a promising genotyping method that is easy to perform and a relatively cheap alternative to PFGE and MLST. In the companion paper published simultaneously in this issue we applied the MLVA to assess the pneumococcal population structure of isolates causing invasive disease in The Netherlands before the introduction of the 7-valent conjugate vaccine.

  8. Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer

    Bojesen, Stig E; Pooley, Karen A; Johnatty, Sharon E;

    2013-01-01

    TERT-locus SNPs and leukocyte telomere measures are reportedly associated with risks of multiple cancers. Using the Illumina custom genotyping array iCOGs, we analyzed ∼480 SNPs at the TERT locus in breast (n = 103,991), ovarian (n = 39,774) and BRCA1 mutation carrier (n = 11,705) cancer cases an...

  9. Deligne-Mumford compactification of the real multiplication locus and Teichmueller curves in genus three

    Bainbridge, Matthew; Möller, Martin

    In the moduli space M_g of genus g Riemann surfaces, consider the locus RM_O of Riemann surfaces whose Jacobians have real multiplication by the order O in a totally real number field F of degree g. If g = 2 or 3, we compute the closure of RM_O in the Deligne-Mumford compactification of M_g and the...... of the field F satisfying a strong geometry of numbers type restriction. We apply this computation to give evidence for the conjecture that there are only finitely many algebraically primitive Teichmueller curves in M_3. In particular, we prove that there are only finitely many algebraically...

  10. A multiple regression analysis for accurate background subtraction in 99Tcm-DTPA renography

    A technique for accurate background subtraction in 99Tcm-DTPA renography is described. The technique is based on a multiple regression analysis of the renal curves and separate heart and soft tissue curves which together represent background activity. It is compared, in over 100 renograms, with a previously described linear regression technique. Results show that the method provides accurate background subtraction, even in very poorly functioning kidneys, thus enabling relative renal filtration and excretion to be accurately estimated. (author)

  11. Imported brucellosis in Denmark: Molecular identification and multiple-locus variable number tandem repeat analysis (MLVA) genotyping of the bacteria

    Aftab, H.; Dargis, R.; Christensen, J. J.;

    2011-01-01

    A polymerase chain reaction was used to identify Brucella species isolated from humans in Denmark. Consecutive analysis of referred bacteria and re-examination of historical isolates identified all as Brucella melitensis. Multiple-locus variable number tandem repeat analysis (MLVA) placed the iso...

  12. Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer

    Bojesen, Stig E.; Pooley, Karen A; Johnatty, Sharon E.; Beesley, Jonathan; Michailidou, Kyriaki; Tyrer, Jonathan P.; Edwards, Stacey L; Hilda A Pickett; Shen, Howard C.; Chanel E. Smart; Hillman, Kristine M.; Mai, Phuong L.; Lawrenson, Kate; Stutz, Michael D.; Lu, Yi

    2013-01-01

    TERT-locus single nucleotide polymorphisms (SNPs) and leucocyte telomere measures are reportedly associated with risks of multiple cancers. Using the iCOGs chip, we analysed ~480 TERT-locus SNPs in breast (n=103,991), ovarian (n=39,774) and BRCA1 mutation carrier (11,705) cancer cases and controls. 53,724 participants have leucocyte telomere measures. Most associations cluster into three independent peaks. Peak 1 SNP rs2736108 minor allele associates with longer telomeres (P=5.8×10−7), reduce...

  13. Identification of Multiple Alleles at the Wx Locus and Development of Single Segment Substitution Lines for the Alleles in Rice

    ZENG Rui-zhen; ZHANG Ze-min; HE Feng-hua; XI Zhang-ying; Akshay TALUKDAR; SHI Jun-qiong; QIN Li-jun; HUANG Chao-feng; ZHANG Gui-quan

    2006-01-01

    The microsatellite markers 484/485 and 484/W2R were used to identify the multiple alleles at the Wx locus in rice germplasm. Fifteen alleles were identified in 278 accessions by using microsatellite class and G-T polymorphism. Among these alleles, (CT)12-G, (CT)15-G, (CT)16-G, (CT)17-G, (CT)18-G and (CT)21-G have not been reported. Seventy-two single-segment substitution lines (SSSLs) carrying different alleles at the Wx locus were developed by using Huajingxian 74 with the (CT)11-G allele as a recipient and 20 accessions containing 12 different alleles at the Wx locus as donors. The estimated length of the substituted segments ranged from 2.2 to 77.3 cM with an average of 17.4 cM.

  14. Genotyping of Bacillus anthracis strains based on automated capillary 25-loci Multiple Locus Variable-Number Tandem Repeats Analysis

    Ciervo Alessandra

    2006-04-01

    Full Text Available Abstract Background The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR Analysis (MLVA assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary. Results Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats. Conclusion In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the

  15. Multiple-locus variable-number tandem repeat analysis for strain typing of Clostridium perfringens.

    Sawires, Youhanna S; Songer, J Glenn

    2005-10-01

    Clostridium perfringens is ubiquitous in the environment and causes diseases in man and animals, with syndromes ranging from enteritis, enterotoxemia, and sudden death to food poisoning and gas gangrene. Understanding the epidemiology of these infections and of the evolution of virulence in C. perfringens necessitate an efficient, time and cost effective strain typing method. Multiple-locus variable-number tandem repeat analysis (MLVA) has been applied to typing of other pathogens and we describe here the development of a MLVA scheme for C. perfringens. We characterized five variable tandem repeat (VNTR) loci, four of which are contained within protein encoding genes and screened 112 C. perfringens isolates to evaluate typability, reproducibility, and discriminatory power of the scheme. All the isolates were assigned a MLVA genotype and the technique has excellent reproducibility, with a numerical index of discrimination for the five VNTR loci of 0.995. Thus MLVA is an efficient tool for C. perfringens strain typing, and being PCR based makes it rapid, easy, and cost effective. In addition, it can be employed in epidemiological, ecological, and evolutionary investigations of the organism. PMID:16701582

  16. High throughput multiple locus variable number of tandem repeat analysis (MLVA) of Staphylococcus aureus from human, animal and food sources

    Daniel Sobral; Stefan Schwarz; Dominique Bergonier; Anne Brisabois; Andrea T Feßler; Gilbert, Florence B.; Kristina Kadlec; Benoit Lebeau; Fabienne Loisy-Hamon; Michaël Treilles; Christine Pourcel; Gilles Vergnaud

    2012-01-01

    Staphylococcus aureus is a major human pathogen, a relevant pathogen in veterinary medicine, and a major cause of food poisoning. Epidemiological investigation tools are needed to establish surveillance of S. aureus strains in humans, animals and food. In this study, we investigated 145 S. aureus isolates recovered from various animal species, disease conditions, food products and food poisoning events. Multiple Locus Variable Number of Tandem Repeat (VNTR) analysis (MLVA), known to be highly...

  17. Experimental Support for Multiple-Locus Complementary Sex Determination in the Parasitoid Cotesia vestalis

    de Boer, Jetske G.; Ode, Paul J.; Aaron K Rendahl; Louise E M Vet; Whitfield, James B; George E Heimpel

    2008-01-01

    Despite its fundamental role in development, sex determination is highly diverse among animals. Approximately 20% of all animals are haplodiploid, with haploid males and diploid females. Haplodiploid species exhibit diverse but poorly understood mechanisms of sex determination. Some hymenopteran insect species exhibit single-locus complementary sex determination (sl-CSD), where heterozygosity at a polymorphic sex locus initiates female development. Diploid males are homozygous at the sex locu...

  18. Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus

    Chermette René

    2010-12-01

    Full Text Available Abstract Background Multiple-locus variable-number tandem repeat (VNTR analysis (MLVA is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus. Results We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8 of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89. The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST. The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France. Conclusions MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a

  19. Multiple-locus variable-number tandem-repeat analysis of Streptococcus pneumoniae and comparison with multiple loci sequence typing

    van Cuyck Hélène

    2012-10-01

    Full Text Available Abstract Background Streptococcus pneumoniae infections remain a major cause of morbidity and mortality worldwide. The diversity of pneumococci was first evidenced by serotyping of their capsular polysaccharides, responsible of virulence, resolving into more than 93 serotypes. Molecular tools have been developed to track the emergence and the spread of resistant, hyper virulent or non-vaccine type clones, particularly DNA-based methods using genetic polymorphism. Pulsed-Field Gel Electrophoresis analysis (PFGE and Multiple Loci Sequence Typing (MLST are the most frequently used genotyping techniques for S. pneumoniae. MLST is based on sequence comparison of housekeeping genes clustering isolates within sequence types. The availability of genome sequence data from different S. pneumoniae strains facilitated the search for other class of genetic markers as polymorphic DNA sequences for a Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA. This study aims at confirming the relevance of MLVA of S. pneumoniae, comparing MLST and MLVA performances when discriminating subgroups of strains belonging to the same Sequence Type (ST, and defining a restricted but universal set of MLVA markers that has at least the same discriminatory power as MLST for S. pneumoniae by applying marker sets used by different authors on 331 isolates selected in UK. Results A minimum spanning tree was built including the serotypes distribution and comparing MLVA and MLST results. 220 MLVA types were determined grouped in 10 Sequence Types (ST. MLVA differentiated ST162 in two clonal complexes. A minimal set was defined: ms 25 and ms37, ms17, ms19, ms33, ms39, and ms40 including two universal markers. The selection was based on MLVA markers with a Diversity Index >0.8 and a selection of others depending of the population tested and the aim of the study. This set of 7 MLVA markers yields strain clusters similar to those obtained by MLST. Conclusions MLVA can discriminate

  20. Multiple-Locus VNTR Analysis (MLVA) for Bacterial Strain Identification - Quarterly Progress Report for the period 7/1/00 to 10/30/00

    Dr. Paul Keim

    2000-11-07

    Multiple locus VNTR analysis (MLVA) systems are being developed for B. anthracis, Y. pestis and F. tularensis. These are high resolution DNA fingerprinting systems that will allow for molecular epidemiology and forensic analysis of these pathogens.

  1. Multiple-Locus VNTR Analysis (MLVA) for Bacterial Strain Identification - Quarterly Progress Report for the period 7/1/00 to 10/30/00

    Multiple locus VNTR analysis (MLVA) systems are being developed for B. anthracis, Y. pestis and F. tularensis. These are high resolution DNA fingerprinting systems that will allow for molecular epidemiology and forensic analysis of these pathogens

  2. Node Handprinting: A Scalable and Accurate Algorithm for Aligning Multiple Biological Networks.

    Radu, Alex; Charleston, Michael

    2015-07-01

    Due to recent advancements in high-throughput sequencing technologies, progressively more protein-protein interactions have been identified for a growing number of species. Subsequently, the protein-protein interaction networks for these species have been further refined. The increase in the quality and availability of these networks has in turn brought a demand for efficient methods to analyze such networks. The pairwise alignment of these networks has been moderately investigated, with numerous algorithms available, but there is very little progress in the field of multiple network alignment. Multiple alignment of networks from different organisms is ideal at finding abnormally conserved or disparate subnetworks. We present a fast and accurate algorithmic approach, Node Handprinting (NH), based on our previous work with Node Fingerprinting, which enables quick and accurate alignment of multiple networks. We also propose two new metrics for the analysis of multiple alignments, as the current metrics are not as sophisticated as their pairwise alignment counterparts. To assess the performance of NH, we use previously aligned datasets as well as protein interaction networks generated from the public database BioGRID. Our results indicate that NH compares favorably with current methodologies and is the only algorithm capable of performing the more complex alignments. PMID:25695597

  3. Using multiple survey vendors to collect health outcomes information: How accurate are the data?

    Haffer Samuel C

    2003-04-01

    Full Text Available Abstract Background To measure and assess health outcomes and quality of life at the national level, large-scale surveys using multiple vendors to gather health information is becoming the norm. This study evaluates the ability of multiple survey vendors to gather and report data collected as part of the 1998 Medicare Health Outcomes Survey (HOS. Method Four hundred randomly sampled completed mailed surveys were chosen from each of six certified vendors (N = 2397 participating in the 1998 HOS. The accuracy of the data gathered from the vendors was measured by creating a "gold standard" record for each survey and comparing it to the final record submitted by the vendor. Results Overall rates of agreement were calculated, and ranged from 97.0% to 99.8% across the vendors. Conclusion Researchers may be confident that using multiple vendors to gather health outcomes information will yield accurate data.

  4. How accurately is ncRNA aligned within whole-genome multiple alignments?

    Ruzzo Walter L

    2007-10-01

    Full Text Available Abstract Background Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated. Results We evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. In particular, we find 638 instances of chimeric and partial alignments to human noncoding RNA elements, of which at least 225 can be improved by straightforward means. As a byproduct of our procedure, we predict many novel instances of known ncRNA families that are suggested by the alignment. Conclusion MULTIZ does a fairly accurate job of aligning these genomes in these difficult regions. However, our experiments indicate that better alignments exist in some regions.

  5. Evidence for multiple alleles effecting muscling and fatness at the Ovine GDF8 locus

    Oddy V Hutton; Edwards Janelle; McCulloch Russell; Kijas James W; Lee Sang; Werf Julius

    2007-01-01

    Abstract Background The current investigation surveyed genetic polymorphism at the ovine GDF8 locus and determined its contribution to variation in muscling and fatness in sheep. Results Re-sequencing 2988 bp from a panel of 15 sires revealed a total of six SNP, none of which were located within exons of the gene. One of the identified SNP, g+6723G>A, is known to increase muscularity within the Belgian Texel. A genetic survey of 326 animals revealed that the mutation is near fixation within A...

  6. Image Capture with Synchronized Multiple-Cameras for Extraction of Accurate Geometries

    Koehl, M.; Delacourt, T.; Boutry, C.

    2016-06-01

    This paper presents a project of recording and modelling tunnels, traffic circles and roads from multiple sensors. The aim is the representation and the accurate 3D modelling of a selection of road infrastructures as dense point clouds in order to extract profiles and metrics from it. Indeed, these models will be used for the sizing of infrastructures in order to simulate exceptional convoy truck routes. The objective is to extract directly from the point clouds the heights, widths and lengths of bridges and tunnels, the diameter of gyrating and to highlight potential obstacles for a convoy. Light, mobile and fast acquisition approaches based on images and videos from a set of synchronized sensors have been tested in order to obtain useable point clouds. The presented solution is based on a combination of multiple low-cost cameras designed on an on-boarded device allowing dynamic captures. The experimental device containing GoPro Hero4 cameras has been set up and used for tests in static or mobile acquisitions. That way, various configurations have been tested by using multiple synchronized cameras. These configurations are discussed in order to highlight the best operational configuration according to the shape of the acquired objects. As the precise calibration of each sensor and its optics are major factors in the process of creation of accurate dense point clouds, and in order to reach the best quality available from such cameras, the estimation of the internal parameters of fisheye lenses of the cameras has been processed. Reference measures were also realized by using a 3D TLS (Faro Focus 3D) to allow the accuracy assessment.

  7. Multiplicative and implicative importance weighted averaging aggregation operators with accurate andness direction

    Larsen, Henrik Legind

    2009-01-01

    Weighted averaging aggregation plays a key role in utilizations of electronic data and information resources for retrieving, fusing, and extracting information and knowledge, as needed for decision making. Of particular interest for such utilizations are the weighted averaging aggregation operators.......  Two central issues in the choice of such operators are the kind of importance weighting and the andness (or conjunction degree) of the operator. We present and discuss two main kinds of importance weighting, namely multiplicative and implicative, and propose schemes for their application with two...... classes of averaging operators, namely the Power Means and the Ordered Weighted Averaging operators, each in a De Morgan dual form for increased efficacy. For each class is proposed a function for a rather accurate direct control of the andness.  Operators with the same kind of importance weighting appear...

  8. An accurate 3D inspection system using heterodyne multiple frequency phase-shifting algorithm

    Xiao, Zhenzhong; Chee, Oichoo; Asundi, Anand

    This paper presents an accurate 3D inspection system for industrial applications, which uses digital fringe projection technology. The system consists of two CCD cameras and a DLP projector. The mathematical model of the 3D inspection system with 10 distortion parameters for each camera is proposed. A heterodyne multiple frequency phase-shifting algorithm is employed for overcoming the unwrapping problem of phase functions and for a reliable unwrapping procedure. The redundant phase information is used to increase the accuracy of the 3D reconstruction. To demonstrate the effectiveness of our system, a standard sphere was used for testing. The verification test for the 3D inspection systems are based on the VDI standard 2634. The result shows the proposed system can be used for industrial quality inspection with high measurement precision.

  9. Accurate 3D shape measurement of multiple separate objects with stereo vision

    3D shape measurement has emerged as a very useful tool in numerous fields because of its wide and ever-increasing applications. In this paper, we present a passive, fast and accurate 3D shape measurement technique using stereo vision approach. The technique first employs a scale-invariant feature transform algorithm to detect point matches at a number of discrete locations despite the discontinuities in the images. Then an automated image registration algorithm is applied to find full-field point matches with subpixel accuracy. After that, the 3D shapes of the objects can be reconstructed according to the obtained point matching and the camera information. The proposed technique is capable of performing a full-field 3D shape measurement with high accuracy even in the presence of discontinuities and multiple separate regions. The validity is verified by experiments. (paper)

  10. Multiple-Resonance Local Wave Functions for Accurate Excited States in Quantum Monte Carlo.

    Zulfikri, Habiburrahman; Amovilli, Claudio; Filippi, Claudia

    2016-03-01

    We introduce a novel class of local multideterminant Jastrow-Slater wave functions for the efficient and accurate treatment of excited states in quantum Monte Carlo. The wave function is expanded as a linear combination of excitations built from multiple sets of localized orbitals that correspond to the bonding patterns of the different Lewis resonance structures of the molecule. We capitalize on the concept of orbital domains of local coupled-cluster methods, which is here applied to the active space to select the orbitals to correlate and construct the important transitions. The excitations are further grouped into classes, which are ordered in importance and can be systematically included in the Jastrow-Slater wave function to ensure a balanced description of all states of interest. We assess the performance of the proposed wave function in the calculation of vertical excitation energies and excited-state geometry optimization of retinal models whose π → π* state has a strong intramolecular charge-transfer character. We find that our multiresonance wave functions recover the reference values of the total energies of the ground and excited states with only a small number of excitations and that the same expansion can be flexibly used at very different geometries. Furthermore, significant computational saving can also be gained in the orbital optimization step by selectively mixing occupied and virtual orbitals based on spatial considerations without loss of accuracy on the excitation energy. Our multiresonance wave functions are therefore compact, accurate, and very promising for the calculation of multiple excited states of different character in large molecules. PMID:26761421

  11. Evidence for multiple alleles effecting muscling and fatness at the Ovine GDF8 locus

    Oddy V Hutton

    2007-11-01

    Full Text Available Abstract Background The current investigation surveyed genetic polymorphism at the ovine GDF8 locus and determined its contribution to variation in muscling and fatness in sheep. Results Re-sequencing 2988 bp from a panel of 15 sires revealed a total of six SNP, none of which were located within exons of the gene. One of the identified SNP, g+6723G>A, is known to increase muscularity within the Belgian Texel. A genetic survey of 326 animals revealed that the mutation is near fixation within Australian Texels and present in additional breeds including White Suffolk, Poll Dorset and Lincoln. Using a resource population comprising 15 sires and 1191 half-sib progeny with genotypic data, the effect of this and other SNP was tested against a set of 50 traits describing growth, muscling, fatness, yield, meat and eating quality. The loss of function allele (g+6723A showed significant effects on slaughter measurements of muscling and fatness. No effect was detected on objectively assessed meat quality however evidence was found for an association between g+6723G>A, decreased intramuscular fat and reduced eating quality. Haplotype analysis using flanking microsatellites was performed to search for evidence of currently unidentified mutations which might affect production traits. Four haplotypes were identified that do not carry g+6723A but which showed significant associations with muscling and fatness. Conclusion The finding that g+6723G>A is present within Australian sheep facilitated an independent evaluation into its phenotypic consequence. Testing was conducted using a separate genetic background and animals raised in different environments to the Belgian Texel in which it was first identified. The observation that the direction and size of effects for g+6723A is approximately consistent represented a robust validation of the effects of the mutation. Based on observed allele frequencies within breeds, selection for g+6723A will have the largest

  12. SNP-based analysis of the HLA locus in Japanese multiple sclerosis patients

    McElroy, JP.; Isobe, N.; Gourraud, PA; Caillier, SJ; Matsushita, T.; Kohriyama, T.; Miyamoto, K; Nakatsuji, Y; Miki, T; Hauser, SL; Oksenberg, JR; KIRA, J

    2011-01-01

    Although several major histocompatibility complex (MHC)-wide single-nucleotide polymorphism (SNP) studies have been performed in populations of European descent, none have been performed in Asian populations. The objective of this study was to identify human leukocyte antigen (HLA) loci associated with multiple sclerosis (MS) in a Japanese population genotyped for 3534 MHC region SNPs. Using a logistic regression model, two SNPs (MHC Class III SNP rs422951 in the NOTCH4 gene and MHC Class II ...

  13. Quality of life, treatment adherence, and locus of control: multiple family groups for chronic medical illnesses.

    López-Larrosa, Silvia

    2013-12-01

    The Multiple Family Groups (MFGs) approach for patients with a chronic medical illness and their families is a structured psychoeducational program that unfolds in six weekly 90-minute sessions. In the MFGs, patients and family members explore new ways to balance illness and nonillness priorities in family life (Steinglass, 1998; Steinglass, 2000 Cuadernos de Terapia Familiar, 44-45, 11; Steinglass, Ostroff, & Steinglass, 2011 Family Process, 50, 393). PMID:24329410

  14. Development and validation of a single-tube multiple-locus variable number tandem repeat analysis for Klebsiella pneumoniae.

    Antoinette A T P Brink

    Full Text Available Genotyping of Klebsiella pneumoniae is indispensable for management of nosocomial infections, monitoring of emerging strains--including extended-spectrum beta-lactamase (ESBL producers-, and general epidemiology. Such objectives require a high-resolution genotyping method with a fixed scheme that allows (1 long-term retrospective and prospective assessment, (2 objective result readout and (3 library storage for database development and exchangeable results. We have developed a multiple-locus variable number tandem repeat analysis (MLVA using a single-tube fluorescently primed multiplex PCR for 8 Variable Number Tandem Repeats (VNTRs and automated fragment size analysis. The type allocation scheme was optimized using 224 K. pneumoniae clinical isolates, which yielded 101 MLVA types. The method was compared to the gold standard multilocus sequence typing (MLST using a subset of these clinical isolates (n = 95 and found to be highly concordant, with at least as high a resolution but with considerably less hands-on time. Our results position this MLVA scheme as an appropriate, high-throughput and relatively low-cost tool for K. pneumoniae epidemiology.

  15. Diversity of Acinetobacter baumannii in four French military hospitals, as assessed by multiple locus variable number of tandem repeats analysis.

    Yolande Hauck

    Full Text Available BACKGROUND: Infections by A. calcoaceticus-A. baumannii (ACB complex isolates represent a serious threat for wounded and burn patients. Three international multidrug-resistant (MDR clones (EU clone I-III are responsible for a large proportion of nosocomial infections with A. baumannii but other emerging strains with high epidemic potential also occur. METHODOLOGY/PRINCIPAL FINDINGS: We automatized a Multiple locus variable number of tandem repeats (VNTR analysis (MLVA protocol and used it to investigate the genetic diversity of 136 ACB isolates from four military hospitals and one childrens hospital. Acinetobacter sp other than baumannii isolates represented 22.6% (31/137 with a majority being A. pittii. The genotyping protocol designed for A.baumannii was also efficient to cluster A. pittii isolates. Fifty-five percent of A. baumannii isolates belonged to the two international clones I and II, and we identified new clones which members were found in the different hospitals. Analysis of two CRISPR-cas systems helped define two clonal complexes and provided phylogenetic information to help trace back their emergence. CONCLUSIONS/SIGNIFICANCE: The increasing occurrence of A. baumannii infections in the hospital calls for measures to rapidly characterize the isolates and identify emerging clones. The automatized MLVA protocol can be the instrument for such surveys. In addition, the investigation of CRISPR/cas systems may give important keys to understand the evolution of some highly successful clonal complexes.

  16. Needs of Accurate Prompt and Delayed γ-spectrum and Multiplicity for Nuclear Reactor Designs

    Rimpault, G.; Bernard, D.; Blanchet, D.; Vaglio-Gaudard, C.; Ravaux, S.; Santamarina, A.

    The local energy photon deposit must be accounted accurately for Gen-IV fast reactors, advanced light-water nuclear reactors (Gen-III+) and the new experimental Jules Horowitz Reactor (JHR). The γ energy accounts for about 10% of the total energy released in the core of a thermal or fast reactor. The γ-energy release is much greater in the core of the reactor than in its structural sub-assemblies (such as reflector, control rod followers, dummy sub-assemblies). However, because of the propagation of γ from the core regions to the neighboring fuel-free assemblies, the contribution of γ energy to the total heating can be dominant. For reasons related to their performance, power reactors require a 7.5% (1σ) uncertainty for the energy deposition in non-fuelled zones. For the JHR material-testing reactor, a 5% (1 s) uncertainty is required in experimental positions. In order to verify the adequacy of the calculation of γ-heating, TLD and γ-fission chambers were used to derive the experimental heating values. Experimental programs were and are still conducted in different Cadarache facilities such as MASURCA (for SFR), MINERVE and EOLE (for JHR and Gen-III+ reactors). The comparison of calculated and measured γ-heating values shows an underestimation in all experimental programs indicating that for the most γ-production data from 239Pu in current nuclear-data libraries is highly suspicious.The first evaluation priority is for prompt γ-multiplicity for U and Pu fission but similar values for otheractinides such as Pu and U are also required. The nuclear data library JEFF3.1.1 contains most of the photon production data. However, there are some nuclei for which there are missing or erroneous data which need to be completed or modified. A review of the data available shows a lack of measurements for conducting serious evaluation efforts. New measurements are needed to guide new evaluation efforts which benefit from consolidated modeling techniques.

  17. Multiple-Locus Departures from Panmictic Equilibrium within and between Village Gene Pools of Amerindian Tribes at Different Stages of Agglomeration

    Smouse, Peter E.; Neel, James V.; Liu, Wanda

    1983-01-01

    A comparative analysis of departures from multiple-locus Hardy-Weinberg equilibrium is presented for a set of four tribal Indian groups (the Yanomama, Makiritare, Wapishana and Ticuna) from the lowlands of South America. These tribes span a range of agglomeration and acculturation from the most traditional, swidden horticulturalists to frontier townspeople. The small-group social organization typical of traditional horticulturalists leads to substantial departures from tribal panmixia, as man...

  18. A meta-analysis identifies adolescent idiopathic scoliosis association with LBX1 locus in multiple ethnic groups

    Londono, Douglas; Kou, Ikuyo; Johnson, Todd A;

    2014-01-01

    International Consortium for Scoliosis Genetics (ICSG). METHODS: Here, we report the first ICSG study, a meta-analysis of the LBX1 locus in six Asian and three non-Asian cohorts. RESULTS: We find significant evidence for association of this locus with AIS susceptibility in all nine cohorts. Results for seven......BACKGROUND: Adolescent idiopathic scoliosis (AIS) is a common rotational deformity of the spine that presents in children worldwide, yet its etiology is poorly understood. Recent genome-wide association studies (GWAS) have identified a few candidate risk loci. One locus near the chromosome 10q24...... major susceptibility locus for AIS in Asian and non-Hispanic white groups, and provide a platform for larger studies in additional ancestral groups....

  19. How accurately is ncRNA aligned within whole-genome multiple alignments?

    Ruzzo Walter L; Wang Adrienne X; Tompa Martin

    2007-01-01

    Abstract Background Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated. Results We evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for...

  20. Multiple inducers of the Drosophila heat shock locus 93D (hsr omega): inducer-specific patterns of the three transcripts

    1989-01-01

    The Drosophila hsr omega locus produces one of the largest and most active heat shock puffs, yet it does not encode a heat shock protein. Instead, this locus produces a distinctive set of three transcripts, all from the same start site. The largest transcript, omega 1, is limited to the nucleus and appears to have a role there. A second nuclear transcript, omega 2, is produced by alternative termination and contains the sequence found in the 5' 20-25% of omega 1 (depending on the Drosophila s...

  1. Enabling accurate photodiode detection of multiple optical traps by spatial filtering

    Ott, Dino; Reihani, S. Nader S.; Oddershede, Lene B.

    2014-09-01

    Dual and multiple beam optical tweezers allow for advanced trapping geometries beyond single traps, however, these increased manipulation capabilities, usually complicate the detection of position and force. The accuracy of position and force measurements is often compromised by crosstalk between the detected signals, this crosstalk leading to a systematic error on the measured forces and distances. In dual-beam optical trapping setups, the two traps are typically orthogonal polarized and crosstalk can be minimized by inserting polarization optics in front of the detector, however, this method is not perfect because of the de-polarization of the trapping beam introduced by the required high numerical aperture optics. Moreover, the restriction to two orthogonal polarisation states limits the number of detectable traps to two. Here, we present an easy-to-implement simple method to efficiently eliminate cross-talk in dual beam setups.1 The technique is based on spatial filtering and is highly compatible with standard back-focal-plane photodiode based detection. The reported method significantly improves the accuracy of force-distance measurements, e.g., of single molecules, hence providing much more scientific value for the experimental efforts. Furthermore, it opens the possibility for fast and simultaneous photodiode based detection of multiple holographically generated optical traps.

  2. Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics

    Pesole Graziano

    2009-09-01

    Full Text Available Abstract Background The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the annotation of newly sequenced genomes. In the context of recent findings that the number non-coding transcripts in higher organisms is likely to be much higher than previously imagined, discrimination between conserved coding and non-coding sequences is a topic of considerable interest. Additionally, it should be considered desirable to discriminate between coding and non-coding conserved sequences without recourse to the use of sequence similarity searches of protein databases as such approaches exclude the identification of novel conserved proteins without characterized homologs and may be influenced by the presence in databases of sequences which are erroneously annotated as coding. Results Here we present a machine learning-based approach for the discrimination of conserved coding sequences. Our method calculates various statistics related to the evolutionary dynamics of two aligned sequences. These features are considered by a Support Vector Machine which designates the alignment coding or non-coding with an associated probability score. Conclusion We show that our approach is both sensitive and accurate with respect to comparable methods and illustrate several situations in which it may be applied, including the identification of conserved coding regions in genome sequences and the discrimination of coding from non-coding cDNA sequences.

  3. A fast and accurate method to compute the mass return from multiple stellar populations

    Calura, F; Nipoti, C

    2013-01-01

    The mass returned to the ambient medium by aging stellar populations over cosmological times sums up to a significant fraction (20% - 30% or more) of their initial mass. This continuous mass injection plays a fundamental role in phenomena such as galaxy formation and evolution, fueling of supermassive black holes in galaxies and the consequent (negative and positive) feedback phenomena, and the origin of multiple stellar populations in globular clusters. In numerical simulations the calculation of the mass return can be time consuming, since it requires at each time step the evaluation of a convolution integral over the whole star formation history, so the computational time increases quadratically with the number of time-steps. The situation can be especially critical in hydrodynamical simulations, where different grid points are characterized by different star formation histories, and the gas cooling and heating times are shorter by orders of magnitude than the characteristic stellar lifetimes. In this pape...

  4. Accurate sound source localization in a reverberant environment using multiple acoustic sensors

    This paper introduces a new method for the estimation of sound source distance and direction using at least three microphone sensors in indoor environments. Unlike the other methods that normally use approximations in obtaining the time difference between sensors, this method exploits the existed geometrical relationships of the sensors to form an exact solution to estimating the source position. To overcome reverberation, an enhancing pre-process has been used for different sound sources with different spectra, e.g., single frequency, multiple frequencies and different noise shapes. Source direction and distances are estimated from time of sound wave travel and distances of acoustic sensors. Using the method described in this paper a level of 1° accuracy is obtained. Several experimental tests have been undertaken that verify the results. Conclusions and future work are also described

  5. Accurate and efficient Nyström volume integral equation method for the Maxwell equations for multiple 3-D scatterers

    Chen, Duan; Cai, Wei; Zinser, Brian; Cho, Min Hyung

    2016-09-01

    In this paper, we develop an accurate and efficient Nyström volume integral equation (VIE) method for the Maxwell equations for a large number of 3-D scatterers. The Cauchy Principal Values that arise from the VIE are computed accurately using a finite size exclusion volume together with explicit correction integrals consisting of removable singularities. Also, the hyper-singular integrals are computed using interpolated quadrature formulae with tensor-product quadrature nodes for cubes, spheres and cylinders, that are frequently encountered in the design of meta-materials. The resulting Nyström VIE method is shown to have high accuracy with a small number of collocation points and demonstrates p-convergence for computing the electromagnetic scattering of these objects. Numerical calculations of multiple scatterers of cubic, spherical, and cylindrical shapes validate the efficiency and accuracy of the proposed method.

  6. The tyrosinase-positive oculocutaneous albinism gene shows locus homogeneity on chromosome 15q11-q13 and evidence of multiple mutations in southern African negroids

    Kedda, M.A.; Stevens, G.; Manga, P.; Viljoen, C.; Jenkins, T.; Ramsay, M. (South African Institute for Medical Research, Johannesburg (South Africa) Univ. of Witwatersrand, Johannesburg (South Africa))

    1994-06-01

    Tyrosinase-positive oculocutaneous albinism (ty-pos OCA) is an autosomal recessive disorder of the melanin pigmentary system. South African ty-pos OCA individuals occur with two distinct phenotypes, with or without darkly pigmented patches (ephelides, or dendritic freckles) on exposed areas of the skin. These phenotypes are concordant within families, suggesting that there may be more than one mutation at the ty-pos OCA locus. Linkage studies carried out in 41 families have shown linkage between markers in the Prader-Willi/Angelman syndrome (PWS/AS) region on chromosome 15q11-q13 and ty-pos OCA. Analysis showed no obligatory crossovers between the alleles at the D15S12 locus and ty-pos OCA, suggesting that the D15S12 locus is very close to or part of the disease locus, which is postulated to be the human homologue, P, of the mouse pink-eyed dilution gene, p. Unlike caucasoid [open quotes]ty-pos OCA[close quotes] individuals, negroid ty-pos OCA individuals do not show any evidence of locus heterogeneity. Studies of allelic association between the polymorphic alleles detected at the D15S12 locus and ephelus status suggest that there was a single major mutation giving rise to ty-pos OCA without ephelides. There may, however, be two major mutations causing ty-pos OCA with ephelides, one associated with D15S12 allele 1 and the other associated with D15S12 allele 2. The two loci, GABRA5 and D15S24, flanking D15S12, are both hypervariable, and many different haplotypes were observed with the alleles at the three loci on both ty-pos OCA-associated chromosomes and [open quotes]normal[close quotes] chromosomes. No haplotype showed statistically significant association with ty-pos OCA, and thus none could be used to predict the origins of the ty-pos OCA mutations. On the basis of the D15S12 results, there is evidence for multiple ty-pos OCA mutations in southern African negroids. 31 refs., 1 fig., 3 tabs.

  7. Combining multiple regression and principal component analysis for accurate predictions for column ozone in Peninsular Malaysia

    Rajab, Jasim M.; MatJafri, M. Z.; Lim, H. S.

    2013-06-01

    This study encompasses columnar ozone modelling in the peninsular Malaysia. Data of eight atmospheric parameters [air surface temperature (AST), carbon monoxide (CO), methane (CH4), water vapour (H2Ovapour), skin surface temperature (SSKT), atmosphere temperature (AT), relative humidity (RH), and mean surface pressure (MSP)] data set, retrieved from NASA's Atmospheric Infrared Sounder (AIRS), for the entire period (2003-2008) was employed to develop models to predict the value of columnar ozone (O3) in study area. The combined method, which is based on using both multiple regressions combined with principal component analysis (PCA) modelling, was used to predict columnar ozone. This combined approach was utilized to improve the prediction accuracy of columnar ozone. Separate analysis was carried out for north east monsoon (NEM) and south west monsoon (SWM) seasons. The O3 was negatively correlated with CH4, H2Ovapour, RH, and MSP, whereas it was positively correlated with CO, AST, SSKT, and AT during both the NEM and SWM season periods. Multiple regression analysis was used to fit the columnar ozone data using the atmospheric parameter's variables as predictors. A variable selection method based on high loading of varimax rotated principal components was used to acquire subsets of the predictor variables to be comprised in the linear regression model of the atmospheric parameter's variables. It was found that the increase in columnar O3 value is associated with an increase in the values of AST, SSKT, AT, and CO and with a drop in the levels of CH4, H2Ovapour, RH, and MSP. The result of fitting the best models for the columnar O3 value using eight of the independent variables gave about the same values of the R (≈0.93) and R2 (≈0.86) for both the NEM and SWM seasons. The common variables that appeared in both regression equations were SSKT, CH4 and RH, and the principal precursor of the columnar O3 value in both the NEM and SWM seasons was SSKT.

  8. SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing.

    Guo, Xiaoge; Lehner, Kevin; O'Connell, Karen; Zhang, Jenny; Dave, Sandeep S; Jinks-Robertson, Sue

    2015-12-01

    Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses. PMID:26497143

  9. Genetic stability of Brucella abortus isolates from an outbreak by multiple-locus variable-number tandem repeat analysis (MLVA16)

    Dorneles, Elaine Maria S.; Santana, Jordana A; Telma M. Alves; Pauletti, Rebeca B; Mol, Juliana Pinto da Silva; Marcos B. Heinemann; Andrey P. Lage

    2014-01-01

    Abstract Background Brucellosis caused by Brucella abortus is one of the most important zoonoses in the world. Multiple-locus variable-number tandem repeat analysis (MLVA16) has been shown be a useful tool to epidemiological traceback studies in B. abortus infection. Thus, the present study aimed (i) to evaluate the genetic diversity of B. abortus isolates from a brucellosis outbreak, and (ii) to investigate the in vivo stability of the MLVA16 markers. Results Three-hundred and seventy-five c...

  10. Use of multiple-locus variable-number tandem-repeats analysis (MLVA) typing to characterize Salmonella Typhimurium DT41 broiler breeder infections

    Litrup, E.; Christensen, H.; Nordentoft, Steen;

    2010-01-01

    To characterize isolates of Salmonella Typhimurium DT41 obtained from infected flocks of broiler breeders by multiple-locus variable-number tandem-repeats analysis (MLVA) and compare results with a diverse strain collection from Germany and United Kingdom and isolates from Danish patients. A total......41 seems to be ubiquitous in the wild fauna which might represent a risk factor for poultry. Transmission from Danish broilers to humans was not demonstrated, neither was the transmission from rearing farms to broiler breeder farms. Sources of infection at broiler breeder farm level remained...

  11. Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol.

    Roman, Tamara S; Marvelle, Amanda F; Fogarty, Marie P; Vadlamudi, Swarooparani; Gonzalez, Arlene J; Buchkovich, Martin L; Huyghe, Jeroen R; Fuchsberger, Christian; Jackson, Anne U; Wu, Ying; Civelek, Mete; Lusis, Aldons J; Gaulton, Kyle J; Sethupathy, Praveen; Kangas, Antti J; Soininen, Pasi; Ala-Korpela, Mika; Kuusisto, Johanna; Collins, Francis S; Laakso, Markku; Boehnke, Michael; Mohlke, Karen L

    2015-12-01

    Genome-wide association studies (GWASs) have identified more than 150 loci associated with blood lipid and cholesterol levels; however, the functional and molecular mechanisms for many associations are unknown. We examined the functional regulatory effects of candidate variants at the GALNT2 locus associated with high-density lipoprotein cholesterol (HDL-C). Fine-mapping and conditional analyses in the METSIM study identified a single locus harboring 25 noncoding variants (r(2) > 0.7 with the lead GWAS variants) strongly associated with total cholesterol in medium-sized HDL (e.g., rs17315646, p = 3.5 × 10(-12)). We used luciferase reporter assays in HepG2 cells to test all 25 variants for allelic differences in regulatory enhancer activity. rs2281721 showed allelic differences in transcriptional activity (75-fold [T] versus 27-fold [C] more than the empty-vector control), as did a separate 780-bp segment containing rs4846913, rs2144300, and rs6143660 (49-fold [AT(-) haplotype] versus 16-fold [CC(+) haplotype] more). Using electrophoretic mobility shift assays, we observed differential CEBPB binding to rs4846913, and we confirmed this binding in a native chromatin context by performing chromatin-immunoprecipitation (ChIP) assays in HepG2 and Huh-7 cell lines of differing genotypes. Additionally, sequence reads in HepG2 DNase-I-hypersensitivity and CEBPB ChIP-seq signals spanning rs4846913 showed significant allelic imbalance. Allelic-expression-imbalance assays performed with RNA from primary human hepatocyte samples and expression-quantitative-trait-locus (eQTL) data in human subcutaneous adipose tissue samples confirmed that alleles associated with increased HDL-C are associated with a modest increase in GALNT2 expression. Together, these data suggest that at least rs4846913 and rs2281721 play key roles in influencing GALNT2 expression at this HDL-C locus. PMID:26637976

  12. Evolutionary changes in gene expression, coding sequence and copy-number at the Cyp6g1 locus contribute to resistance to multiple insecticides in Drosophila.

    Thomas W R Harrop

    Full Text Available Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However, it is not known whether the ability of the CYP6G1 enzyme to provide resistance to multiple insecticides evolved recently in D. melanogaster or if this function is present in all Drosophila species. Here we show that duplication of the Cyp6g1 gene occurred at least four times during the evolution of different Drosophila species, and the ability of CYP6G1 to confer resistance to multiple insecticides exists in D. melanogaster and D. simulans but not in Drosophila willistoni or Drosophila virilis. In D. virilis, which has multiple copies of Cyp6g1, one copy confers resistance to DDT and another to nitenpyram, suggesting that the divergence of protein sequence between copies subsequent to the duplication affected the activity of the enzyme. All orthologs tested conferred resistance to one or more insecticides, suggesting that CYP6G1 had the capacity to provide resistance to anthropogenic chemicals before they existed. Finally, we show that expression of Cyp6g1 in the Malpighian tubules, which contributes to DDT resistance in D. melanogaster, is specific to the D. melanogaster-D. simulans lineage. Our results suggest that a combination of gene duplication, regulatory changes and protein coding changes has taken place at the Cyp6g1 locus during evolution and this locus may play a role in providing resistance to different environmental toxins in different Drosophila species.

  13. Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes.

    Small, Kerrin S; Hedman, Asa K; Grundberg, Elin; Nica, Alexandra C; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Shin, So-Youn; Richards, Hannah B; Soranzo, Nicole; Ahmadi, Kourosh R; Lindgren, Cecilia M; Stefansson, Kari; Dermitzakis, Emmanouil T; Deloukas, Panos; Spector, Timothy D; McCarthy, Mark I

    2011-06-01

    Genome-wide association studies have identified many genetic variants associated with complex traits. However, at only a minority of loci have the molecular mechanisms mediating these associations been characterized. In parallel, whereas cis regulatory patterns of gene expression have been extensively explored, the identification of trans regulatory effects in humans has attracted less attention. Here we show that the type 2 diabetes and high-density lipoprotein cholesterol-associated cis-acting expression quantitative trait locus (eQTL) of the maternally expressed transcription factor KLF14 acts as a master trans regulator of adipose gene expression. Expression levels of genes regulated by this trans-eQTL are highly correlated with concurrently measured metabolic traits, and a subset of the trans-regulated genes harbor variants directly associated with metabolic phenotypes. This trans-eQTL network provides a mechanistic understanding of the effect of the KLF14 locus on metabolic disease risk and offers a potential model for other complex traits. PMID:21572415

  14. Genetic stability of Brucella abortus S19 and RB51 vaccine strains by multiple locus variable number tandem repeat analysis (MLVA16).

    Dorneles, Elaine Maria Seles; de Faria, Ana Paula Paiva; Pauletti, Rebeca Barbosa; Santana, Jordana Almeida; Caldeira, George Afonso Vítor; Heinemann, Marcos Bryan; Titze-de-Almeida, Ricardo; Lage, Andrey Pereira

    2013-10-01

    The aims of the present study were (i) to assess the in vitro genetic stability of S19 and RB51 Brucella abortus vaccines strains and (ii) to evaluate the ability of multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) as a tool to be used in the quality control of live vaccines against brucellosis. Sixty-three batches of commercial S19 (n=53) and RB51 (n=10) vaccines, produced between 2006 and 2009, were used in this study. S19 and RB51 vaccines were obtained from, respectively, seven and two different manufacturers. Ten in vitro serial passages were performed on reference strains and on selected batches of commercial vaccines. All batches, reference strains and strains of serial passages were typed by the MLVA16. The results demonstrated that B. abortus S19 and RB51 vaccine strains are genetically stable and very homogeneous in their respective groups. Anyway, batches of S19 from one manufacturer and batches of RB51 from another presented genotypes distincts from the reference vaccine strains. In both cases, differences were found on locus Bruce07, which had addition of one repeat unit in the case of S19 batches and the deletion of one repeat unit in the case of RB51 batches. In summary, MLVA16 proved to be a molecular tool capable of discriminating small genomic variations and should be included in in vitro official tests. PMID:23933375

  15. Multiple-locus variable-number tandem repeat analysis (MLVA) of Leptospira interrogans serovar Pomona from Argentina reveals four new genotypes.

    Pavan, María Elisa; Cairó, Fabián; Brihuega, Bibiana; Samartino, Luis

    2008-01-01

    Outbreaks of leptospirosis occur regularly in Argentina, but little is known about their epidemiological relationships. We have analyzed the genetic diversity of a collection of 16 strains of Leptospira interrogans serovar Pomona isolated from animals and humans in Argentina during the past 45 years. Genotyping was performed by multiple-locus variable-number tandem repeat analysis (MLVA) using the loci VNTR4, VNTR7, VNTR9, VNTR10, VNTR19, VNTR23 and VNTR31, as described by Majed et al. [Identification of variable-number tandem-repeat loci in Leptospira interrogans sensu stricto. J Clin Microbiol 2005;43:539-45]. Clustering analysis revealed four new distinct MLVA genotypes, with a dominant one. Strains with this genotype were consistently isolated since 1960 to the present, mainly from cows and pigs, but also from humans, representing 75% of the total strains studied. These strains coexisted temporally and geographically with isolates presenting the other new genotypes. VNTR4 locus, with four different alleles, presented the highest diversity between the VNTR loci analyzed. MLVA patterns obtained will be useful for future diagnostic and epidemiological tracing analysis. PMID:17531318

  16. Development and comparison of a generic multiple-locus variable-number tandem repeat analysis with PFGE for typing of Salmonella entericasubsp. enterica

    Kjeldsen, Marianne Kirstine; Torpdahl, Mia; Pedersen, Karl; Nielsen, Eva Møller

    2015-01-01

    -related strains. Conclusions The technique showed a high discriminatory power within most serotypes comparable with or better than that of PFGE. Significance and impact of the Study This MLVA assay makes it possible to use a single typing method for Salmonella surveillance and outbreak investigations. This allows......Aims Salmonella enterica subsp. enterica causes salmonellosis in humans and animals. Serovar specific multiple-locus variable-number tandem repeat analysis (MLVA) is widely used for Salmonella surveillance; however, isolates have to be serotyped prior to MLVA typing and only the most common...... serovars can be typed. We developed a MLVA scheme for high discriminatory typing of Salmonella. Methods and Results Sixty-six unique VNTRs were investigated and the polymorphisms of seven promising VNTRs were evaluated with a panel 163 diverse isolates of 14 serotypes of significance for human health. Five...

  17. The vincamine derivative vindeburnol provides benefit in a mouse model of multiple sclerosis: effects on the Locus coeruleus.

    Polak, Paul E; Kalinin, Sergey; Braun, David; Sharp, Anthony; Lin, Shao X; Feinstein, Douglas L

    2012-04-01

    The endogenous neurotransmitter noradrenaline (NA) plays several roles in maintaining brain homeostasis, including exerting anti-inflammatory and neuroprotective effects. The primary source of NA in the CNS are tyrosine hydroxylase (TH)-positive neurons located in the Locus coeruleus (LC) which send projections throughout the brain and spinal cord. We recently demonstrated that dysregulation of the LC:Noradrenergic system occurs in experimental autoimmune encephalomyelitis as well as in MS patients, associated with damage occurring to LC neurons. Vindeburnol, a structural analog of the cerebral vasodilator vincamine, was previously reported to increase TH expression and activity in LC neurons. Female C57BL/6 mice were immunized with myelin oligodendrocyte glycoprotein (MOG)(35-55) peptide, and treated with vindeburnol at the first appearance of clinical signs. Clinical signs continued to increase for about 1 week, at which point mice in the vehicle group continued to worsen while vindeburnol-treated mice showed improvement. Pro-inflammatory cytokine production from splenic T cells was not reduced by vindeburnol suggesting primarily central actions of treatment. In the cerebellum, vindeburnol decreased astrocyte activation and reduced the number of demyelinated regions. Vindeburnol reduced astrocyte activation in the LC, reduced TH+ neuronal hypertrophy, increased expression of several genes involved in LC survival and maturation, and increased NA levels in the spinal cord. These results suggest that treatments with drugs such as vindeburnol which target LC survival or function could be of benefit in MS patients. PMID:22288774

  18. Eomesodermin promotes interferon-γ expression and binds to multiple conserved noncoding sequences across the Ifng locus in mouse thymoma cell lines.

    Fukuoka, Natsuki; Harada, Misuzu; Nishida, Ai; Ito, Yuko; Shiota, Hideki; Kataoka, Takao

    2016-02-01

    The T-box transcription factors T-bet and eomesodermin (Eomes) have been shown to regulate the lineage-specific expression of interferon-γ (IFN-γ). However, in contrast to T-bet, the role of Eomes in the expression of IFN-γ remains unclear. In this study, we investigated the Eomes-dependent expression of IFN-γ in the mouse thymoma BW5147 and EL4 cells, which do not express T-bet or Eomes. The ectopic expression of Eomes induced BW5147 and EL4 cells to produce IFN-γ in response to phorbol 12-myristate 13-acetate (PMA) and ionomycin (IM). In BW5147 cells, Eomes augmented luciferase activity driven by the Ifng promoter encoding from -2500 to +113 bp; however, it was not increased by a stimulation with PMA and IM. A chromatin immunoprecipitation assay showed that Eomes bound to the Ifng promoter and conserved noncoding sequence (CNS) -22 kb across the Ifng locus with high efficacy in BW5147 cells. Moreover, Eomes increased permissive histone modifications in the Ifng promoter and multiple CNSs. The stimulation with PMA and IM greatly augmented Eomes binding to CNS-54, CNS-34, CNS+19 and CNS+30, which was inhibited by FK506. These results indicated that Eomes bound to the Ifng promoter and multiple CNSs in stimulation-dependent and stimulation-independent manners. PMID:26749212

  19. Ces locus embedded proteins control the non-ribosomal synthesis of the cereulide toxin in emetic Bacillus cereus on multiple levels

    Lücking, Genia; Frenzel, Elrike; Rütschle, Andrea; Marxen, Sandra; Stark, Timo D.; Hofmann, Thomas; Scherer, Siegfried; Ehling-Schulz, Monika

    2015-01-01

    The emetic toxin cereulide produced by Bacillus cereus is synthesized by the modular enzyme complex Ces that is encoded on a pXO1-like megaplasmid. To decipher the role of the genes adjacent to the structural genes cesA/cesB, coding for the non-ribosomal peptide synthetase (NRPS), gene inactivation- and overexpression mutants of the emetic strain F4810/72 were constructed and their impact on cereulide biosynthesis was assessed. The hydrolase CesH turned out to be a part of the complex regulatory network controlling cereulide synthesis on a transcriptional level, while the ABC transporter CesCD was found to be essential for post-translational control of cereulide synthesis. Using a gene inactivation approach, we show that the NRPS activating function of the phosphopantetheinyl transferase (PPtase) embedded in the ces locus was complemented by a chromosomally encoded Sfp-like PPtase, representing an interesting example for the functional interaction between a plasmid encoded NRPS and a chromosomally encoded activation enzyme. In summary, our results highlight the complexity of cereulide biosynthesis and reveal multiple levels of toxin formation control. ces operon internal genes were shown to play a pivotal role by acting at different levels of toxin production, thus complementing the action of the chromosomal key transcriptional regulators AbrB and CodY. PMID:26528255

  20. Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer.

    Shi, Jiajun; Zhang, Yanfeng; Zheng, Wei; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Lush, Michael; Milne, Roger L; Shu, Xiao-Ou; Beesley, Jonathan; Kar, Siddhartha; Andrulis, Irene L; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W; Zhao, Zhiguo; Guo, Xingyi; Benitez, Javier; Beeghly-Fadiel, Alicia; Blot, William; Bogdanova, Natalia V; Bojesen, Stig E; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J; Cox, Angela; Cross, Simon S; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dork, Thilo; Fasching, Peter A; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G; Grip, Mervi; Guenel, Pascal; Haiman, Christopher A; Hamann, Ute; Hartman, Mikael; Miao, Hui; Hollestelle, Antoinette; Hopper, John L; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Torres, Diana; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A; Kosma, Veli-Matti; Lambrechts, Diether; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Le Marchand, Loic; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L; Nevanlinna, Heli; Nord, Silje; Børresen-Dale, Anne-Lise; Olson, Janet E; Orr, Nick; van den Ouweland, Ans M W; Peterlongo, Paolo; Choudary Putti, Thomas; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J; Schmidt, Marjanka K; Schmutzler, Rita K; Shen, Chen-Yang; Hou, Ming-Feng; Shrubsole, Matha J; Southey, Melissa C; Swerdlow, Anthony; Hwang Teo, Soo; Thienpont, Bernard; Toland, Amanda E; Tollenaar, Robert A E M; Tomlinson, Ian; Truong, Therese; Tseng, Chiu-Chen; Wen, Wanqing; Winqvist, Robert; Wu, Anna H; Har Yip, Cheng; Zamora, Pilar M; Zheng, Ying; Floris, Giuseppe; Cheng, Ching-Yu; Hooning, Maartje J; Martens, John W M; Seynaeve, Caroline; Kristensen, Vessela N; Hall, Per; Pharoah, Paul D P; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M; Antoniou, Antonis C; Easton, Douglas F; Cai, Qiuyin; Long, Jirong

    2016-09-15

    Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2)  = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry. PMID:27087578

  1. Locus of control and prenatal depression

    Richardson, Amber; Field, Tiffany; Newton, Rae; Bendell, Debra

    2012-01-01

    Prenatal depression is a significant predictor of postpartum depression and is detrimental to fetal development. Locus of control was examined in this study as a potential predictor of prenatal depression. 133 rural pregnant women recruited from obstetricians’ offices completed the Levenson Scale on Locus of Control and the Edinburgh Postnatal Depression Scale. Multiple regression analysis indicated that after controlling for previous or current mental health problems, the External Locus of C...

  2. Genotyping of Brucella melitensis strains from dromedary camels (Camelus dromedarius) from the United Arab Emirates with multiple-locus variable-number tandem repeat analysis.

    Gyuranecz, Miklós; Wernery, Ulli; Kreizinger, Zsuzsa; Juhász, Judit; Felde, Orsolya; Nagy, Péter

    2016-04-15

    Camel brucellosis is a widespread zoonotic disease in camel-rearing countries caused by Brucella melitensis and Brucella abortus. The aim of this study was the first genetic analysis of B. melitensis strains isolated from dromedary camels (Camelus dromedarius) using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA 16 and its MLVA 8 and MLVA11 subsets were used to determine the genotypes of 15 B. melitensis isolates from dromedary camels (11 strains) and other host species (4 strains) from the United Arab Emirates and the results were then compared to B. melitensis MLVA genotypes from other parts of the world. Five, including two novel genotypes were identified with MLVA 8. MLVA 16 further discriminated these five genotypes to ten variants. The eleven camel isolates clustered into four main genetic groups within the East-Mediterranean and African clades and this clustering correlated with the geographic origin of the hosts (United Arab Emirates, Kingdom of Saudi Arabia and Sudan) and the date of their isolation. The camel strains were also genetically related to strains isolated from wild and domestic ruminants from their close habitat or from other parts of the world. Although limited number of strains were analysed, based on our data imported animals from foreign countries, local small ruminants and wildlife species are hypothesized to be the main sources of camel brucellosis in the United Arab Emirates. MLVA was successfully applied to determine the epidemiological links between the different camel B. melitensis infections in the United Arab Emirates and it can be a beneficial tool in future disease control programs. PMID:27016751

  3. Establishment of Multiple Locus Variable-number Tandem Repeat Analysis Assay for Genotyping of Borrelia burgdorferi sensu lato Detected in China

    ZHOU Xin; HOU Xue Xia; GENG Zhen; ZHAO Rui; WAN Kang Lin; HAO Qin

    2014-01-01

    Objective Human Lyme Borreliosis (LB), which is caused by Borrelia burgdorferi sensu lato (B. burgdorferi), has been identified as a major arthropod-borne infectious disease in China. We aimed to develop a multiple locus variable-number tandem repeat (VNTR) analysis (MLVA) assay for the genotyping of Borrelia burgdorferi strains detected in China. Methods B. garinii PBi complete 904.246 kb chromosome and two plasmids (cp26 and lp54) were screened by using Tandem Repeats Finder program for getting potential VNTR loci, the potential VNTR loci were analyzed and identified with PCR and the VNTR loci data were analyzed and MLVA clustering tree were constrcted by using the categorical coefficient and the unweighted pair-group method with arithmetic means (UPGMA). Results We identified 5 new VNTR loci through analyzing 47 potential VNTR loci. We used the MLVA protocol to analyse 101 B. burgdorferi strains detected in China and finally identified 51 unique genotypes in 4 major clusters including B. burgdorferi sensu stricto (B.b.s.s), B. garinii, B. afzelii, and B. valaisiana, consistent with the current MLSA phylogeny studies. The allele numbers of VNTR-1, VNTR-2, VNTR-3, VNTR-4, and VNTR-5 were 7, 3, 9, 7, and 6. The Hunter-Gaston index (HGI) of five VNTR loci were 0.79, 0.22, 0.77, 0.71, and 0.67, respectively. The combined HGI of five VNTR loci was 0.96. Clustering of the strains of Xinjiang, Inner Mongolia and Heilongjiang was confirmed, and this situation was consistent with the close geographical distribution of those provinces. Conclusion The MLVA protocol esytablished in this study is easy and can show strains’ phylogenetic relationships to distinguish the strains of Borrelia species. It is useful for further phylogenetic and epidemiological analyses of Borrelia strains.

  4. Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis

    Alcina, Antonio; Fedetz, Maria; Fernández, Óscar; Saiz, Albert; Izquierdo, Guillermo; Lucas, Miguel; Leyva, Laura; García-León, Juan-Antonio; Abad-Grau, María del Mar; Alloza, Iraide; Antigüedad, Alfredo; Garcia-Barcina, María J; Vandenbroeck, Koen; Varadé, Jezabel; de la Hera, Belén; Arroyo, Rafael; Comabella, Manuel; Montalban, Xavier; Petit-Marty, Natalia; Navarro, Arcadi; Otaegui, David; Olascoaga, Javier; Blanco, Yolanda; Urcelay, Elena; Matesanz, Fuencisla

    2013-01-01

    Background and aim Several studies have highlighted the association of the 12q13.3–12q14.1 region with coeliac disease, type 1 diabetes, rheumatoid arthritis and multiple sclerosis (MS); however, the causal variants underlying diseases are still unclear. The authors sought to identify the functional variant of this region associated with MS. Methods Tag-single nucleotide polymorphism (SNP) analysis of the associated region encoding 15 genes was performed in 2876 MS patients and 2910 healthy Caucasian controls together with expression regulation analyses. Results rs6581155, which tagged 18 variants within a region where 9 genes map, was sufficient to model the association. This SNP was in total linkage disequilibrium (LD) with other polymorphisms that associated with the expression levels of FAM119B, AVIL, TSFM, TSPAN31 and CYP27B1 genes in different expression quantitative trait loci studies. Functional annotations from Encyclopedia of DNA Elements (ENCODE) showed that six out of these rs6581155-tagged-SNPs were located in regions with regulatory potential and only one of them, rs10877013, exhibited allele-dependent (ratio A/G=9.5-fold) and orientation-dependent (forward/reverse=2.7-fold) enhancer activity as determined by luciferase reporter assays. This enhancer is located in a region where a long-range chromatin interaction among the promoters and promoter-enhancer of several genes has been described, possibly affecting their expression simultaneously. Conclusions This study determines a functional variant which alters the enhancer activity of a regulatory element in the locus affecting the expression of several genes and explains the association of the 12q13.3–12q14.1 region with MS. PMID:23160276

  5. The Development of Multiple-Choice Items Consistent with the AP Chemistry Curriculum Framework to More Accurately Assess Deeper Understanding

    Domyancich, John M.

    2014-01-01

    Multiple-choice questions are an important part of large-scale summative assessments, such as the advanced placement (AP) chemistry exam. However, past AP chemistry exam items often lacked the ability to test conceptual understanding and higher-order cognitive skills. The redesigned AP chemistry exam shows a distinctive shift in item types toward…

  6. Accurate determination of electronic transport properties of silicon wafers by nonlinear photocarrier radiometry with multiple pump beam sizes

    Wang, Qian [Institute of Optics and Electronics, Chinese Academy of Sciences, P. O. Box 350, Shuangliu, Chengdu 610209 (China); University of the Chinese Academy of Sciences, Beijing 100039 (China); Li, Bincheng, E-mail: bcli@uestc.ac.cn [Institute of Optics and Electronics, Chinese Academy of Sciences, P. O. Box 350, Shuangliu, Chengdu 610209 (China); School of Optoelectronic Information, University of Electronic Science and Technology of China, Chengdu 610054 (China)

    2015-12-07

    In this paper, photocarrier radiometry (PCR) technique with multiple pump beam sizes is employed to determine simultaneously the electronic transport parameters (the carrier lifetime, the carrier diffusion coefficient, and the front surface recombination velocity) of silicon wafers. By employing the multiple pump beam sizes, the influence of instrumental frequency response on the multi-parameter estimation is totally eliminated. A nonlinear PCR model is developed to interpret the PCR signal. Theoretical simulations are performed to investigate the uncertainties of the estimated parameter values by investigating the dependence of a mean square variance on the corresponding transport parameters and compared to that obtained by the conventional frequency-scan method, in which only the frequency dependences of the PCR amplitude and phase are recorded at single pump beam size. Simulation results show that the proposed multiple-pump-beam-size method can improve significantly the accuracy of the determination of the electronic transport parameters. Comparative experiments with a p-type silicon wafer with resistivity 0.1–0.2 Ω·cm are performed, and the electronic transport properties are determined simultaneously. The estimated uncertainties of the carrier lifetime, diffusion coefficient, and front surface recombination velocity are approximately ±10.7%, ±8.6%, and ±35.4% by the proposed multiple-pump-beam-size method, which is much improved than ±15.9%, ±29.1%, and >±50% by the conventional frequency-scan method. The transport parameters determined by the proposed multiple-pump-beam-size PCR method are in good agreement with that obtained by a steady-state PCR imaging technique.

  7. An accurate and useful tool in multiple myeloma for disease management: Technetium 99m-Sestamibi scintigraphy

    Aim: To demonstrate Technetium-99m-Sestamibi is useful tool in patients with multiple myeloma, as its increased uptake indicate myeloma activity. We propose Tc-Sestamibi scintigraphy is sign of myeloma bone disease related to gammopathies. Material and Method: we have enrolled 20 pts. affected by multiple myeloma and we have performed whole body scans after administration of 740 MBq of 99mTc-Sestamibi. Results: 16 pts. showed a negative scan; 4 pts. showed a low increased uptake of the tracer. The uptake is strictly correlated to the clinical variables. In follow-up chemotherapy treatment the 4 pts. shows a negativeness of uptake. X-Ray shows negative results in all the pts. Conclusions: This method by 99mTc-Sestamibi whole body scintigraphy indicate disease activity in bone marrow, with high sensitivity and specificity and is a very useful tool in myeloma bone disease management

  8. A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations.

    Navidi, W.; Arnheim, N; Waterman, M S

    1992-01-01

    A multiple-tubes procedure is described for using PCR to determine the genotype of a very small DNA sample. The procedure involves dividing the sample among several tubes, then amplifying and typing the contents of each tube separately. The results are analyzed by a statistical procedure which determines whether a genotype can be conclusively assigned to the DNA sample. Simulation studies show that this procedure usually gives correct results even when the number of double-stranded fragments ...

  9. Traveled Distance Is a Sensitive and Accurate Marker of Motor Dysfunction in a Mouse Model of Multiple Sclerosis

    Takemiya, Takako; Takeuchi, Chisen

    2013-01-01

    Multiple sclerosis (MS) is a common central nervous system disease associated with progressive physical impairment. To study the mechanisms of the disease, we used experimental autoimmune encephalomyelitis (EAE), an animal model of MS. EAE is induced by myelin oligodendrocyte glycoprotein35–55 peptide, and the severity of paralysis in the disease is generally measured using the EAE score. Here, we compared EAE scores and traveled distance using the open-field test for an assessment of EAE pro...

  10. Performance Analysis of Daubechies Wavelet and Differential Pulse Code Modulation Based Multiple Neural Networks Approach for Accurate Compression of Images

    S.Sridhar

    2013-09-01

    Full Text Available Large Images in general contain huge quantity of data demanding the invention of highly efficient hybrid methods of image compression systems involving various hybrid techniques. We proposed and implemented a Daubechies wavelet transform and Differential Pulse Code Modulation (DPCM based multiple neural network hybrid model for image encoding and decoding operations combining the advantages of wavelets, neural networks and DPCM because, wavelet transforms are set of mathematical functions that established their viability in the areas of image compression owing to the computational simplicity involved in their implementation, Artificial neural networks can generalize inputs even on untrained data owing to their massive parallel architectures and Differential Pulse Code Modulation reduces redundancy based on the predicted sample values. Initially the input image is subjected to two level decomposition using Daubechies family wavelet filters generating high-scale low frequency approximation coefficients A2 and high frequency detail coefficients H2, V2, D2, H1, V1 and, D1 of multiple resolutions resembling different frequency bands. Scalar quantization and Huffman encoding schemes are used for compressing different sub bands based on their statistical properties i.e the low frequency band approximation coefficients are compressed by the DPCM while the high frequency band coefficients are compressed with neural networks. Empirical analysis and objective fidelity metrics calculation is performed and tabulated for analysis.

  11. Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA

    Sintchenko Vitali

    2012-03-01

    Full Text Available Abstract Background Prospective typing of Salmonella enterica serovar Typhimurium (STM by multiple-locus variable-number tandem-repeat analysis (MLVA can assist in identifying clusters of STM cases that might otherwise have gone unrecognised, as well as sources of sporadic and outbreak cases. This paper describes the dynamics of human STM infection in a prospective study of STM MLVA typing for public health surveillance. Methods During a three-year period between August 2007 and September 2010 all confirmed STM isolates were fingerprinted using MLVA as part of the New South Wales (NSW state public health surveillance program. Results A total of 4,920 STM isolates were typed and a subset of 4,377 human isolates was included in the analysis. The STM spectrum was dominated by a small number of phage types, including DT170 (44.6% of all isolates, DT135 (13.9%, DT9 (10.8%, DT44 (4.5% and DT126 (4.5%. There was a difference in the discriminatory power of MLVA types within endemic phage types: Simpson's index of diversity ranged from 0.109 and 0.113 for DTs 9 and 135 to 0.172 and 0.269 for DTs 170 and 44, respectively. 66 distinct STM clusters were observed ranging in size from 5 to 180 cases and in duration from 4 weeks to 25 weeks. 43 clusters had novel MLVA types and 23 represented recurrences of previously recorded MLVA types. The diversity of the STM population remained relatively constant over time. The gradual increase in the number of STM cases during the study was not related to significant changes in the number of clusters or their size. 667 different MLVA types or patterns were observed. Conclusions Prospective MLVA typing of STM allows the detection of community outbreaks and demonstrates the sustained level of STM diversity that accompanies the increasing incidence of human STM infections. The monitoring of novel and persistent MLVA types offers a new benchmark for STM surveillance. A part of this study was presented at the MEEGID

  12. FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes.

    Kirchmair, Johannes; Williamson, Mark J; Afzal, Avid M; Tyzack, Jonathan D; Choy, Alison P K; Howlett, Andrew; Rydberg, Patrik; Glen, Robert C

    2013-11-25

    FAst MEtabolizer (FAME) is a fast and accurate predictor of sites of metabolism (SoMs). It is based on a collection of random forest models trained on diverse chemical data sets of more than 20 000 molecules annotated with their experimentally determined SoMs. Using a comprehensive set of available data, FAME aims to assess metabolic processes from a holistic point of view. It is not limited to a specific enzyme family or species. Besides a global model, dedicated models are available for human, rat, and dog metabolism; specific prediction of phase I and II metabolism is also supported. FAME is able to identify at least one known SoM among the top-1, top-2, and top-3 highest ranked atom positions in up to 71%, 81%, and 87% of all cases tested, respectively. These prediction rates are comparable to or better than SoM predictors focused on specific enzyme families (such as cytochrome P450s), despite the fact that FAME uses only seven chemical descriptors. FAME covers a very broad chemical space, which together with its inter- and extrapolation power makes it applicable to a wide range of chemicals. Predictions take less than 2.5 s per molecule in batch mode on an Ultrabook. Results are visualized using Jmol, with the most likely SoMs highlighted. PMID:24219364

  13. A non-contact method based on multiple signal classification algorithm to reduce the measurement time for accurately heart rate detection

    Bechet, P.; Mitran, R.; Munteanu, M.

    2013-08-01

    Non-contact methods for the assessment of vital signs are of great interest for specialists due to the benefits obtained in both medical and special applications, such as those for surveillance, monitoring, and search and rescue. This paper investigates the possibility of implementing a digital processing algorithm based on the MUSIC (Multiple Signal Classification) parametric spectral estimation in order to reduce the observation time needed to accurately measure the heart rate. It demonstrates that, by proper dimensioning the signal subspace, the MUSIC algorithm can be optimized in order to accurately assess the heart rate during an 8-28 s time interval. The validation of the processing algorithm performance was achieved by minimizing the mean error of the heart rate after performing simultaneous comparative measurements on several subjects. In order to calculate the error the reference value of heart rate was measured using a classic measurement system through direct contact.

  14. A mathematical framework for combining decisions of multiple experts toward accurate and remote diagnosis of malaria using tele-microscopy.

    Sam Mavandadi

    Full Text Available We propose a methodology for digitally fusing diagnostic decisions made by multiple medical experts in order to improve accuracy of diagnosis. Toward this goal, we report an experimental study involving nine experts, where each one was given more than 8,000 digital microscopic images of individual human red blood cells and asked to identify malaria infected cells. The results of this experiment reveal that even highly trained medical experts are not always self-consistent in their diagnostic decisions and that there exists a fair level of disagreement among experts, even for binary decisions (i.e., infected vs. uninfected. To tackle this general medical diagnosis problem, we propose a probabilistic algorithm to fuse the decisions made by trained medical experts to robustly achieve higher levels of accuracy when compared to individual experts making such decisions. By modelling the decisions of experts as a three component mixture model and solving for the underlying parameters using the Expectation Maximisation algorithm, we demonstrate the efficacy of our approach which significantly improves the overall diagnostic accuracy of malaria infected cells. Additionally, we present a mathematical framework for performing 'slide-level' diagnosis by using individual 'cell-level' diagnosis data, shedding more light on the statistical rules that should govern the routine practice in examination of e.g., thin blood smear samples. This framework could be generalized for various other tele-pathology needs, and can be used by trained experts within an efficient tele-medicine platform.

  15. A mathematical framework for combining decisions of multiple experts toward accurate and remote diagnosis of malaria using tele-microscopy.

    Mavandadi, Sam; Feng, Steve; Yu, Frank; Dimitrov, Stoyan; Nielsen-Saines, Karin; Prescott, William R; Ozcan, Aydogan

    2012-01-01

    We propose a methodology for digitally fusing diagnostic decisions made by multiple medical experts in order to improve accuracy of diagnosis. Toward this goal, we report an experimental study involving nine experts, where each one was given more than 8,000 digital microscopic images of individual human red blood cells and asked to identify malaria infected cells. The results of this experiment reveal that even highly trained medical experts are not always self-consistent in their diagnostic decisions and that there exists a fair level of disagreement among experts, even for binary decisions (i.e., infected vs. uninfected). To tackle this general medical diagnosis problem, we propose a probabilistic algorithm to fuse the decisions made by trained medical experts to robustly achieve higher levels of accuracy when compared to individual experts making such decisions. By modelling the decisions of experts as a three component mixture model and solving for the underlying parameters using the Expectation Maximisation algorithm, we demonstrate the efficacy of our approach which significantly improves the overall diagnostic accuracy of malaria infected cells. Additionally, we present a mathematical framework for performing 'slide-level' diagnosis by using individual 'cell-level' diagnosis data, shedding more light on the statistical rules that should govern the routine practice in examination of e.g., thin blood smear samples. This framework could be generalized for various other tele-pathology needs, and can be used by trained experts within an efficient tele-medicine platform. PMID:23071544

  16. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    Kapil, V.; VandeVondele, J.; Ceriotti, M.

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  17. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    Kapil, V.; Ceriotti, M., E-mail: michele.ceriotti@epfl.ch [Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland); VandeVondele, J., E-mail: joost.vandevondele@mat.ethz.ch [Department of Materials, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich (Switzerland)

    2016-02-07

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  18. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats

  19. Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

    Field, Helen I; Scollen, Serena A; Luccarini, Craig; Baynes, Caroline; Morrison, Jonathan; Dunning, Alison M; Easton, Douglas F; Pharoah, Paul DP

    2009-01-01

    Background In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once. Implementation We created Seq4SNPs, a web-based, walk-away software that can process one to several hundred SNPs given rs numbers as input. It outputs a file of fully annotated sequences formatted for one of three proprietary design softwares: TaqMan's Primer-By-Design FileBuilder, Sequenom's iPLEX or SNPstream's Autoprimer, as well as unannotated fasta sequences. We found genotyping assays to be inhibited by repetitive sequences or the presence of additional variations flanking the SNP under test, and in multiplexes, repetitive sequence flanking one SNP adversely affects multiple assays. Assay design software programs avoid such regions if the input sequences are appropriately annotated, so we used Seq4SNPs to provide suitably annotated input sequences, and improved our genotyping success rate. Adjacent SNPs can also be avoided, by annotating sequences used as input for primer design. Conclusion The accuracy of annotation by Seq4SNPs is significantly better than manual annotation (P < 1e-5). Using Seq4SNPs to incorporate all annotation for additional SNPs and repetitive elements into sequences, for genotyping assay designer software, minimizes assay failure at the design stage, reducing the cost of genotyping. Seq4SNPs provides a rapid route for replacement of poor test SNP sequences. We routinely use this software for assay sequence preparation. Seq4SNPs is available as a service at and , currently for human SNPs, but easily extended to include any species in dbSNP. PMID:19523221

  20. Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants.

    Juran, Brian D; Hirschfield, Gideon M; Invernizzi, Pietro; Atkinson, Elizabeth J; Li, Yafang; Xie, Gang; Kosoy, Roman; Ransom, Michael; Sun, Ye; Bianchi, Ilaria; Schlicht, Erik M; Lleo, Ana; Coltescu, Catalina; Bernuzzi, Francesca; Podda, Mauro; Lammert, Craig; Shigeta, Russell; Chan, Landon L; Balschun, Tobias; Marconi, Maurizio; Cusi, Daniele; Heathcote, E Jenny; Mason, Andrew L; Myers, Robert P; Milkiewicz, Piotr; Odin, Joseph A; Luketic, Velimir A; Bacon, Bruce R; Bodenheimer, Henry C; Liakina, Valentina; Vincent, Catherine; Levy, Cynthia; Franke, Andre; Gregersen, Peter K; Bossa, Fabrizio; Gershwin, M Eric; deAndrade, Mariza; Amos, Christopher I; Lazaridis, Konstantinos N; Seldin, Michael F; Siminovitch, Katherine A

    2012-12-01

    To further characterize the genetic basis of primary biliary cirrhosis (PBC), we genotyped 2426 PBC patients and 5731 unaffected controls from three independent cohorts using a single nucleotide polymorphism (SNP) array (Immunochip) enriched for autoimmune disease risk loci. Meta-analysis of the genotype data sets identified a novel disease-associated locus near the TNFSF11 gene at 13q14, provided evidence for association at six additional immune-related loci not previously implicated in PBC and confirmed associations at 19 of 22 established risk loci. Results of conditional analyses also provided evidence for multiple independent association signals at four risk loci, with haplotype analyses suggesting independent SNP effects at the 2q32 and 16p13 loci, but complex haplotype driven effects at the 3q25 and 6p21 loci. By imputing classical HLA alleles from this data set, four class II alleles independently contributing to the association signal from this region were identified. Imputation of genotypes at the non-HLA loci also provided additional associations, but none with stronger effects than the genotyped variants. An epistatic interaction between the IL12RB2 risk locus at 1p31and the IRF5 risk locus at 7q32 was also identified and suggests a complementary effect of these loci in predisposing to disease. These data expand the repertoire of genes with potential roles in PBC pathogenesis that need to be explored by follow-up biological studies. PMID:22936693

  1. Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark

    de Knegt, Leonardo; Pires, Sara Monteiro; Löfström, Charlotta;

    2016-01-01

    Salmonella is an important cause of bacterial foodborne infections in Denmark. To identify the main animal-food sources of human salmonellosis, risk managers have relied on a routine application of a microbial subtyping-based source attribution model since 1995. In 2013, multiple locus variable...... number tandem repeat analysis (MLVA) substituted phage typing as the subtyping method for surveillance of S. Enteritidis and S. Typhimurium isolated from animals, food, and humans in Denmark. The purpose of this study was to develop a modeling approach applying a combination of serovars, MLVA types...

  2. A genetic map of chromosome 20q12-q13.1: Multiple highly polymorphic microsatellite and RFLP markers linked to the maturity-onset diabetes of the young (MODY) locus

    Rothschild, Cynthia B.; Akots, Gita; Hayworth, Rosa; Pettenati, Mark J.; Rao, P. Nagesh; Wood, Patricia; Stolz, Frank-Michael; Hansmann, Ingo; Serino, Kristina; Keith, Tim P.; Fajans, Stefan S.; Bowden, Donald W.

    1993-01-01

    Multiple highly polymorphic markers have been used to construct a genetic map of the q12-q13.1 region of chromosome 20 and to map the location of the maturity-onset diabetes of the young (MODY) locus. The genetic map encompasses 23 cM and includes 11 loci with PIC values >.50, seven of which have PICs >.70. New dinucleotide repeat polymorphisms associated with the D20S17, PPGB, and ADA loci have been identified and mapped. The dinucleotide repeat polymorphisms have increased the PIC of the AD...

  3. The tyrosinase-positive oculocutaneous albinism gene shows locus homogeneity on chromosome 15q11-q13 and evidence of multiple mutations in southern African negroids.

    Kedda, M.A.; Stevens, G; Manga, P; Viljoen, C.; Jenkins, T; Ramsay, M.

    1994-01-01

    Tyrosinase-positive oculocutaneous albinism (ty-pos OCA) is an autosomal recessive disorder of the melanin pigmentary system. South African ty-pos OCA individuals occur with two distinct phenotypes, with or without darkly pigmented patches (ephelides, or dendritic freckles) on exposed areas of the skin. These phenotypes are concordant within families, suggesting that there may be more than one mutation at the ty-pos OCA locus. Linkage studies carried out in 41 families have shown linkage betw...

  4. 中山地区临床分离株铜绿假单胞菌MLVA分型初步研究%Study of multiple-locus variant-repeat analysis to differentiate Pseudomonas aeruginosa isolates in Zhongshan

    王娟; 张秀明; 兰海丽; 孙各琴; 卢兰芬; 冯雪琴; 李飞; 唐国芳

    2012-01-01

    目的 建立铜绿假单胞菌的多位点可变数目串联重复序列(multiple locus variable number of tandem repeats analysis,MLVA)基因分型技术,初步用于耐药监测和院内感染的监测. 方法 选择11个位点对50株临床分离菌株进行PCR扩增和凝胶电泳,用R 2.14.1软件进行聚类分析.SPSS13.0统计软件进行统计分析. 结果 11个位点中,ms216多态性最低,为0.619,ms212多态性最高,为0.838.50株铜绿假单胞菌被分为4大基因群,且均为单菌株基因型.前9个位点与11个位点的组合对菌株的分辨能力相同(HGDI=1.0000);前7个位点与前8个位点组合的分辨能力相同(HGDI=0.9984,成簇率为4.0%);前5个位点与前6个位点组合的分辨能力相同(HGDI-0.9935,成簇率为10.0%). 结论 前5个VNTR位点组合有良好分辨能力,可用于大规模分子流行病学调查;前7个VNTR位点具有更高的分辨能力,可用于精确分析.%Objective Multiple-locus variable-number tandem repeat analysis (MLVA) was used to analyze the relationship between strains of Pseudomonas aeruginosa in order to determine the source of outbreaks and implement effective control measures to prevent its spread. Methods This study examined 50 P. aeruginosa isolates. MLVA analysis of eleven loci was performed. R 2. 14. 1 software was used for phylogenetic and cluster analysis. Statistical associations were generated by SPSS 13. 0. Results All the loci indicated had good allelic diversity. The lowest discriminative locus was ms216 (h = 0. 619), and the highest discriminative locus was ms212 (h = 0. 838). The strains were divided into four groups. All of these strains had a unique genotype. The 9-locus set produced an HGDI value of 1, which was the same as that for the 11-locus set. The top 8 loci produced an HGDI value of 0. 9984 with a clustering rate of 4. 0%. The HGDI and clustering rate of the top 7 loci were the same as those for the 8 loci. The top 6 loci produced an HGDI value of 0

  5. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-01

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. PMID:27106060

  6. An in vivo cis-regulatory screen at the type 2 diabetes associated TCF7L2 locus identifies multiple tissue-specific enhancers.

    Daniel Savic

    Full Text Available Genome-wide association studies (GWAS have repeatedly shown an association between non-coding variants in the TCF7L2 locus and risk for type 2 diabetes (T2D, implicating a role for cis-regulatory variation within this locus in disease etiology. Supporting this hypothesis, we previously localized complex regulatory activity to the TCF7L2 T2D-associated interval using an in vivo bacterial artificial chromosome (BAC enhancer-trapping reporter strategy. To follow-up on this broad initial survey of the TCF7L2 regulatory landscape, we performed a fine-mapping enhancer scan using in vivo mouse transgenic reporter assays. We functionally interrogated approximately 50% of the sequences within the T2D-associated interval, utilizing sequence conservation within this 92-kb interval to determine the regulatory potential of all evolutionary conserved sequences that exhibited conservation to the non-eutherian mammal opossum. Included in this study was a detailed functional interrogation of sequences spanning both protective and risk alleles of single nucleotide polymorphism (SNP rs7903146, which has exhibited allele-specific enhancer function in pancreatic beta cells. Using these assays, we identified nine segments regulating various aspects of the TCF7L2 expression profile and that constitute nearly 70% of the sequences tested. These results highlight the regulatory complexity of this interval and support the notion that a TCF7L2 cis-regulatory disruption leads to T2D predisposition.

  7. Translocations affecting human immunoglobulin heavy chain locus

    Sklyar I. V.

    2014-03-01

    Full Text Available Translocations involving human immunoglobulin heavy chain (IGH locus are implicated in different leukaemias and lymphomas, including multiple myeloma, mantle cell lymphoma, Burkitt’s lymphoma and diffuse large B cell lymphoma. We have analysed published data and identified eleven breakpoint cluster regions (bcr related to these cancers within the IgH locus. These ~1 kbp bcrs are specific for one or several types of blood cancer. Our findings could help devise PCR-based assays to detect cancer-related translocations, to identify the mechanisms of translocations and to help in the research of potential translocation partners of the immunoglobulin locus at different stages of B-cell differentiation.

  8. DEVELOPMENT OF A MULTIPLE-LOCUS VARIABLE NUMBER OF TANDEM REPEAT ANALYSIS (MLVA FOR HELICOBACTER PYLORI AND ITS APPLICATION TO HELICOBACTER PYLORI ISOLATES FROM ROSTOV REGION,RUSSIA

    Sorokin VM

    2012-09-01

    Full Text Available Stomach infection with Helicobacter pylori (H. pylori is the second most common infectious disease of humans. The severe pathological consequences of this infection include gastric and duodenal ulcer disease, the development of gastric mucosal atrophy, gastric carcinoma, and, more rarely, malignant tumors of the lymphoma. H. pylori infections cause very high morbidity and mortality and are of particular concern in developing countries, where H. pylori prevalences as high as 90% have been reported. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-Locus of Variable number of tandem repeat Analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori isolates in Russia. MLVA of 4 VNTR loci with high discrimination power based on 10 candidates were performed on a collection of 22 strains of H. pylori which originated from Rostov region of Russia. This method provides a starting point on which improvements to the method and comparisons to other techniques can be made.

  9. Genotyping analysis of Helicobacter pylori using multiple-locus variable-number tandem-repeats analysis in five regions of China and Japan

    Zhang Jinyong

    2011-09-01

    Full Text Available Abstract Background H. pylori (Helicobacter pylori is the major causative agent of chronic active gastritis. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. Its long term colonization of the stomach caused different clinical outcomes, which may relate to the high degree of genetic variation of H. pylori. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-locus of variable number of tandem repeat analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori from different districts and ethnic groups of China. Results MLVA of 12 VNTR loci with high discrimination power based on 30 candidates were performed on a collection of 202 strains of H. pylori which originated from five regions of China and Japan. Phylogenetic tree was constructed using MLVA profiles. 12 VNTR loci presented with high various polymorphisms, and the results demonstrated very close relationships between genotypes and ethnic groups. Conclusions This study used MLVA methodology providing a new perspective on the ethnic groups and distribution characteristics of H. pylori.

  10. The Locus analytical framework for indoor localization and tracking applications

    Segou, Olga E.; Thomopoulos, Stelios C. A.

    2015-05-01

    Obtaining location information can be of paramount importance in the context of pervasive and context-aware computing applications. Many systems have been proposed to date, e.g. GPS that has been proven to offer satisfying results in outdoor areas. The increased effect of large and small scale fading in indoor environments, however, makes localization a challenge. This is particularly reflected in the multitude of different systems that have been proposed in the context of indoor localization (e.g. RADAR, Cricket etc). The performance of such systems is often validated on vastly different test beds and conditions, making performance comparisons difficult and often irrelevant. The Locus analytical framework incorporates algorithms from multiple disciplines such as channel modeling, non-uniform random number generation, computational geometry, localization, tracking and probabilistic modeling etc. in order to provide: (a) fast and accurate signal propagation simulation, (b) fast experimentation with localization and tracking algorithms and (c) an in-depth analysis methodology for estimating the performance limits of any Received Signal Strength localization system. Simulation results for the well-known Fingerprinting and Trilateration algorithms are herein presented and validated with experimental data collected in real conditions using IEEE 802.15.4 ZigBee modules. The analysis shows that the Locus framework accurately predicts the underlying distribution of the localization error and produces further estimates of the system's performance limitations (in a best-case/worst-case scenario basis).

  11. Evolutionary Changes in Gene Expression, Coding Sequence and Copy-Number at the Cyp6g1 Locus Contribute to Resistance to Multiple Insecticides in Drosophila

    Harrop, Thomas W. R.; Tamar Sztal; Christopher Lumb; Good, Robert T.; Daborn, Phillip J.; Philip Batterham; Henry Chung

    2014-01-01

    Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However...

  12. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types

    Doherty, Kimberly R., E-mail: kimberly.doherty@quintiles.com; Talbert, Dominique R.; Trusk, Patricia B.; Moran, Diarmuid M.; Shell, Scott A.; Bacus, Sarah

    2015-05-15

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability. - Highlights: • 24 drugs were tested for cardiac liability using an in vitro multi-parameter screen. • Changes in beating activity were the most sensitive in predicting cardiac risk. • Structural effects add in

  13. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability. - Highlights: • 24 drugs were tested for cardiac liability using an in vitro multi-parameter screen. • Changes in beating activity were the most sensitive in predicting cardiac risk. • Structural effects add in

  14. Statistical evaluation of multiple-locus linkage data in experimental species and its relevance to human studies: Application to nonobese diabetic (NOD) mouse and human insulin-dependent diabetes mellitus (IDDM)

    Risch, N. (Yale Univ. School of Medicine, New Haven, CT (United States)); Ghosh, S.; Todd, J.A.

    1993-09-01

    Common, familial human disorders generally do not follow Mendelian inheritance patterns, presumably because multiple loci are involved in disease susceptibility. One approach to mapping genes for such traits in humans is to first study an analogous form in an animal model, such as mouse, by using inbred strains and backcross experiments. Here the authors describe methodology for analyzing multiple-locus linkage data from such experimental backcrosses, particularly in light of multilocus genetic models, including the effects of epistasis. They illustrate these methods by using data from backcrosses involving nonobese diabetic mouse, which serves as an animal model for human insulin-dependent diabetes mellitus. They show that it is likely that a minimum of nine loci contribute to susceptibility, with strong epistasis effects among these loci. Three of the loci actually confer a protective effect in the homozygote, compared with the heterozygote. Further, they discuss the relevance of these studies for analogous studies of the human form of the trait. Specifically, they show that the magnitude of the gene effect in the experimental backcross is likely to correlate only weakly, at best, with the expected magnitude of effect for a human form, because in humans the gene effect will depend more heavily on disease allele frequencies than on the observed penetrance ratios; such allele frequencies are unpredictable. Hence, the major benefit from animal studies may be a better understanding of the disease process itself, rather than identification of cells through comparison mapping in humans by using regions of homology. 12 refs., 7 tabs.

  15. Anatomically standardised 99mTc-ECD brain perfusion SPET allows accurate differentiation between healthy volunteers, multiple system atrophy and idiopathic Parkinson's disease

    The clinical differentiation between typical idiopathic Parkinson's disease (IPD) and atypical parkinsonian disorders such as multiple system atrophy (MSA) is complicated by the presence of signs and symptoms common to both forms. The goal of this study was to re-evaluate the contribution of brain perfusion single-photon emission tomography (SPET) with anatomical standardisation and automated analysis in the differentiation of IPD and MSA. This was achieved by discriminant analysis in comparison with a large set of age- and gender-matched healthy volunteers. Technetium-99m ethyl cysteinate dimer SPET was performed on 140 subjects: 81 IPD patients (age 62.6±10.2 years; disease duration 11.0±6.4 years; 50 males/31 females), 15 MSA patients (61.5±9.2 years; disease duration 3.0±2.2 years; 9 males/6 females) and 44 age- and gender-matched healthy volunteers (age 59.2±11.9 years; 27 males/17 females). Patients were matched for severity (Hoehn and Yahr stage). Automated predefined volume of interest (VOI) analysis was carried out after anatomical standardisation. Stepwise discriminant analysis with cross-validation using the leave-one-out method was used to determine the subgroup of variables giving the highest accuracy for this differential diagnosis. Between MSA and IPD, the only regions with highly significant differences in uptake after Bonferroni correction were the putamen VOIs. Comparing MSA versus normals and IPD, with putamen VOI values as discriminating variables, cross-validated performance showed correct classification of MSA patients with a sensitivity of 73.3%, a specificity of 84% and an accuracy of 83.6%. Additional input from the right caudate head and the left prefrontal and left mesial temporal cortex allowed 100% discrimination even after cross-validation. Discrimination between the IPD group alone and healthy volunteers was accurate in 94% of the cases after cross-validation, with a sensitivity of 91.4% and a specificity of 100%. The three

  16. Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by Multiple-locus variable number of tandem repeat analysis (MLVA).

    Bergonier, Dominique; Sobral, Daniel; Feßler, Andrea T; Jacquet, Eric; Gilbert, Florence B; Schwarz, Stefan; Treilles, Michaël; Bouloc, Philippe; Pourcel, Christine; Vergnaud, Gilles

    2014-01-01

    Staphylococcus aureus is one of the main etiological agents of mastitis in ruminants. In the present retrospective study, we evaluated the potential interest of a previously described automated multiple loci Variable Number of Tandem Repeats (VNTR) Assay (MLVA) comprising 16 loci as a first line tool to investigate the population structure of S. aureus from mastitis. We determined the genetic diversity of S. aureus strains from cases of clinical and subclinical mastitis in dairy cattle (n = 118, of which 16 were methicillin-resistant), sheep (n = 18) and goats (n = 16). The 152 strains could be subdivided into 115 MLVA genotypes (including 14 genotypes for the ovine strains and 15 genotypes for the caprine strains). This corresponds to a discriminatory index (D) value of 0.9936. Comparison with published MLVA data obtained using the same protocol applied to strains from diverse human and animal origins revealed a low number (8.5%) of human-related MLVA genotypes among the present collection. Eighteen percent of the S. aureus mastitis collection belonged to clonal complexes apparently not associated with other pathological conditions. Some of them displayed a relatively low level of diversity in agreement with a restricted ecological niche. These findings provide arguments suggesting that specific S. aureus lineages particularly adapted to ruminant mammary glands have emerged and that MLVA is a convenient tool to provide a broad overview of the population, owing to the availability via internet of databases compiling published MLVA genotypes. PMID:25315988

  17. The LOCUS interface to the MFE database

    The MFE database now consists of over 900 shots from TFTR, PDX, PLT, T-10, JT-60, TEXT, JET and ASDEX. A variety of discharge conditions is represented, ranging from single time slice Ohmic discharges to multiple time-slice auxiliary heated discharges. Included with most datasets is a reference that describes the experiment being performed when the data was taken. The MFE database is currently implemented under INGRES on a VAX that is on Internet. LOCUS, a database utility, developed at the Princeton Plasma Physics Laboratory is now available as an interface to the database. The LOCUS front end provides a graphic interface to the database from any generic graphics terminal that supports Tektronix 4010 emulation. It provides a variety of procedures for extracting, manipulating and graphing data from the MFE database. In order to demonstrate the capabilities of the LOCUS interface, the authors examine, in detail, one of the recently added JET, H-mode discharges. In this example, they address some new concepts such as monitor functions, which have been introduced in order to help users more fully understand the multiple time-slice datasets. They also describe some of the more advanced techniques available in LOCUS for data access and manipulation. Specific areas of interest that are discussed are searching for and retrieving datasets, graphics, data fitting, and linear regression analysis

  18. Genomic analysis of ERVWE2 locus in patients with Multiple sclerosis: absence of genetic association but potential role of Human Endogenous retrovirus type W elements in molecular mimicry with myelin antigen.

    CamilaMaltaRomano

    2013-06-01

    Full Text Available Human endogenous retroviruses (HERVs arise from ancient infections of the host germline cells by exogenous retroviruses, constituting 8% of the human genome. Elevated level of envelope transcripts from HERVs-W has been detected in CSF, plasma and brain tissues from patients with Multiple Sclerosis (MS, most of them from Xq22.3, 15q21.3 and 6q21 chromosomes. However, since the locus Xq22.3 (ERVWE2 lack the 5' LTR promoter and the putative protein should be truncated due to a stop codon, we investigated the ERVWE2 genomic loci from 84 individuals, including MS patients with active HERV-W expression detected in PBMC. In addition, an automated search for promoter sequences in 20kb nearby region of ERVWE2 reference sequence was performed. Several putative binding sites for cellular cofactors and enhancers were found, suggesting that transcription may occur via alternative promoters. However, ERVWE2 DNA sequencing of MS and healthy individuals revealed that all of them harbor a stop codon at site 39, undermining the expression of a full-length protein. Finally, since plaque formation in CNS of MS patients is attributed to immunological mechanisms triggered by autoimmune attack against myelin, we also investigated the level of similarity between envelope protein and myelin oligodendrocyte glycoprotein (MOG. Comparison of the MOG to the envelope identified five retroviral regions similar to the Ig-like domain of MOG. Interestingly, one of them includes T and B cell epitopes, capable to induce T effector functions and circulating Abs in rats. In sum, although no DNA substitutions that would link ERVWE2 to the MS pathogeny was found, the similarity between the envelope protein to MOG extends the idea that ERVEW2 may be involved on the immunopathogenesis of MS, maybe facilitating the MOG recognizing by the immune system. Although awaiting experimental evidences, the data presented here may expand the scope of the endogenous retroviruses involvement on MS

  19. An improved energy-range relationship for high-energy electron beams based on multiple accurate experimental and Monte Carlo data sets

    A theoretically based analytical energy-range relationship has been developed and calibrated against well established experimental and Monte Carlo calculated energy-range data. Only published experimental data with a clear statement of accuracy and method of evaluation have been used. Besides published experimental range data for different uniform media, new accurate experimental data on the practical range of high-energy electron beams in water for the energy range 10-50 MeV from accurately calibrated racetrack microtrons have been used. Largely due to the simultaneous pooling of accurate experimental and Monte Carlo data for different materials, the fit has resulted in an increased accuracy of the resultant energy-range relationship, particularly at high energies. Up to date Monte Carlo data from the latest versions of the codes ITS3 and EGS4 for absorbers of atomic numbers between four and 92 (Be, C, H2O, PMMA, Al, Cu, Ag, Pb and U) and incident electron energies between 1 and 100 MeV have been used as a complement where experimental data are sparse or missing. The standard deviation of the experimental data relative to the new relation is slightly larger than that of the Monte Carlo data. This is partly due to the fact that theoretically based stopping and scattering cross-sections are used both to account for the material dependence of the analytical energy-range formula and to calculate ranges with the Monte Carlo programs. For water the deviation from the traditional energy-range relation of ICRU Report 35 is only 0.5% at 20 MeV but as high as - 2.2% at 50 MeV. An improved method for divergence and ionization correction in high-energy electron beams has also been developed to enable use of a wider range of experimental results. (Author)

  20. Global cDNA Amplification Combined with Real-Time RT–PCR: Accurate Quantification of Multiple Human Potassium Channel Genes at the Single Cell Level

    Al-Taher, A.; Bashein, A.; Nolan, T.; Hollingsworth, M.; Brady, G

    2000-01-01

    We have developed a sensitive quantitative RT–PCR procedure suitable for the analysis of small samples, including single cells, and have used it to measure levels of potassium channel mRNAs in a panel of human tissues and small numbers of cells grown in culture. The method involves an initial global amplification of cDNA derived from all added polyadenylated mRNA followed by quantitative RT–PCR of individual genes using specific primers. In order to facilitate rapid and accurate processing of...

  1. Application of multiple-locus variable-number tandem repeat analysis(MLVA) for molecular typing of Leptospira interrogans serogroup Icterohaemorrhagiae%黄疸出血群钩端螺旋体MLVA分型研究

    张翠彩; 聂一新; 李秀文; 崔志刚; 郭宗琪; 顾黎莉; 徐建民; 吴子贵; 蒋秀高

    2009-01-01

    目的 初步探讨MLVA(multiple-locus variable-number tandem-repeat analysis)技术在黄疸出血群钩端螺旋体基因分型中的应用.方法 选取7个VNTR位点,对我国致病性钩端螺旋体黄疸出血群菌株提取基因组DNA,采用PCR扩增和琼脂糖凝胶电泳技术检测,应用BioNumerics(Ver-sion4.0)软件进行聚类分析.结果 共对117株钩端螺旋体的7个VNTR位点进行了检测,聚类分析分为3个群(A群、B群、C群)28种基因型,其中A群占11.97%(14/117)、B群占0.85%(1/117)、c群占87.18%(102/117);多态性指数介于0.0831与0.8005之间;MLVA基因型存在明显的地域性.结论 MLVA分型技术可初步对钩端螺旋体进行遗传学分类鉴定,应用该技术,将在钩体病分子流行病学研究中发挥重要的作用.%Objective To establish the method of multiple loci VNTR(variable numbers tandem-repeats) analysis (MLVA) for genotyping Leptospira interrogans serogroup ieterohaemorrhagiae . Methods Seven VNTR loci were chosen for genotyping 117 strains of L. interrogans serogroup Icterohaemorrhagiae by PCR-electrophoresis-based VNTR analysis and the results were analyzed by software BioNumerics( Version 4.0). Results One hundred and seventeen isolates of L. interrogans serogroup Icterohaemorrhagiae detec-ted with 7 VNTR loci were classified into three clusters(A,B,C), twenty-eight types were found, type A 11.97% (14/117), type B 0.85% (1/1 17), type C 87.18% (102/117). Diversity Indexes for the loci varied between 0.0831 and 0.8005. Clinical strains isolated from the same geographic area and belonging to the same serogroup shared a common VNTR pattern. Conclusion MLVA could be used to classify and identify Leptospira interrogans preliminarily. With the improvement of technology, this rapid and easy method should greatly contribute to a better knowledge of the epidemiology of Leptospira.

  2. The effect of multiple primer-template mismatches on quantitative PCR accuracy and development of a multi-primer set assay for accurate quantification of pcrA gene sequence variants.

    Ledeker, Brett M; De Long, Susan K

    2013-09-01

    Quantitative PCR (qPCR) is a critical tool for quantifying the abundance of specific organisms and the level or expression of target genes in medically and environmentally relevant systems. However, often the power of this tool has been limited because primer-template mismatches, due to sequence variations of targeted genes, can lead to inaccuracies in measured gene quantities, detection failures, and spurious conclusions. Currently available primer design guidelines for qPCR were developed for pure culture applications, and available primer design strategies for mixed cultures were developed for detection rather than accurate quantification. Furthermore, past studies examining the impact of mismatches have focused only on single mismatches while instances of multiple mismatches are common. There are currently no appropriate solutions to overcome the challenges posed by sequence variations. Here, we report results that provide a comprehensive, quantitative understanding of the impact of multiple primer-template mismatches on qPCR accuracy and demonstrate a multi-primer set approach to accurately quantify a model gene pcrA (encoding perchlorate reductase) that has substantial sequence variation. Results showed that for multiple mismatches (up to 3 mismatches) in primer regions where mismatches were previously considered tolerable (middle and 5' end), quantification accuracies could be as low as ~0.1%. Furthermore, tests were run using a published pcrA primer set with mixtures of genomic DNA from strains known to harbor the target gene, and for some mixtures quantification accuracy was as low as ~0.8% or was non-detect. To overcome these limitations, a multiple primer set assay including minimal degeneracies was developed for pcrA genes. This assay resulted in nearly 100% accurate detection for all mixed microbial communities tested. The multi-primer set approach demonstrated herein can be broadly applied to other genes with known sequences. PMID:23806694

  3. A gene locus for targeted ectopic gene integration in Zymoseptoria tritici.

    Kilaru, S; Schuster, M; Latz, M; Das Gupta, S; Steinberg, N; Fones, H; Gurr, S J; Talbot, N J; Steinberg, G

    2015-06-01

    Understanding the cellular organization and biology of fungal pathogens requires accurate methods for genomic integration of mutant alleles or fluorescent fusion-protein constructs. In Zymoseptoria tritici, this can be achieved by integrating of plasmid DNA randomly into the genome of this wheat pathogen. However, untargeted ectopic integration carries the risk of unwanted side effects, such as altered gene expression, due to targeting regulatory elements, or gene disruption following integration into protein-coding regions of the genome. Here, we establish the succinate dehydrogenase (sdi1) locus as a single "soft-landing" site for targeted ectopic integration of genetic constructs by using a carboxin-resistant sdi1(R) allele, carrying the point-mutation H267L. We use various green and red fluorescent fusion constructs and show that 97% of all transformants integrate correctly into the sdi1 locus as single copies. We also demonstrate that such integration does not affect the pathogenicity of Z. tritici, and thus the sdi1 locus is a useful tool for virulence analysis in genetically modified Z. tritici strains. Furthermore, we have developed a vector which facilitates yeast recombination cloning and thus allows assembly of multiple overlapping DNA fragments in a single cloning step for high throughput vector and strain generation. PMID:26092798

  4. A gene locus for targeted ectopic gene integration in Zymoseptoria tritici☆

    Kilaru, S.; Schuster, M.; Latz, M.; Das Gupta, S.; Steinberg, N.; Fones, H.; Gurr, S.J.; Talbot, N.J.; Steinberg, G.

    2015-01-01

    Understanding the cellular organization and biology of fungal pathogens requires accurate methods for genomic integration of mutant alleles or fluorescent fusion-protein constructs. In Zymoseptoria tritici, this can be achieved by integrating of plasmid DNA randomly into the genome of this wheat pathogen. However, untargeted ectopic integration carries the risk of unwanted side effects, such as altered gene expression, due to targeting regulatory elements, or gene disruption following integration into protein-coding regions of the genome. Here, we establish the succinate dehydrogenase (sdi1) locus as a single “soft-landing” site for targeted ectopic integration of genetic constructs by using a carboxin-resistant sdi1R allele, carrying the point-mutation H267L. We use various green and red fluorescent fusion constructs and show that 97% of all transformants integrate correctly into the sdi1 locus as single copies. We also demonstrate that such integration does not affect the pathogenicity of Z. tritici, and thus the sdi1 locus is a useful tool for virulence analysis in genetically modified Z. tritici strains. Furthermore, we have developed a vector which facilitates yeast recombination cloning and thus allows assembly of multiple overlapping DNA fragments in a single cloning step for high throughput vector and strain generation. PMID:26092798

  5. Accurate temperature measurements in flames with high spatial resolution using Stokes Raman scattering from nitrogen in a multiple-pass cell.

    Utsav, K C; Varghese, Philip L

    2013-07-10

    A multiple-pass cell is aligned to focus light at two regions at the center of the cell. The two "points" are separated by 2.0 mm. Each probe region is 200 μm×300 μm. The cell is used to amplify spontaneous Raman scattering from a CH4-air laminar flame. The signal gain is 20, and the improvement in signal-to-noise ratio varies according to the number of laser pulses used for signal acquisition. The temperature is inferred by curve fitting high-resolution spectra of the Stokes signal from N2. The model accounts for details, such as the angular dependence of Raman scattering, the presence of a rare isotope of N2 in air, anharmonic oscillator terms in the vibrational polarizability matrix elements, and the dependence of Herman-Wallis factors on the vibrational level. The apparatus function is modeled using a new line shape function that is the convolution of a trapezoid function and a Lorentzian. The uncertainty in the value of temperature arising from noise, the uncertainty in the model input parameters, and various approximations in the theory have been characterized. We estimate that the uncertainty in our measurement of flame temperature in the least noisy data is ±9 K. PMID:23852217

  6. A Locus Example

    Gheorghe Sorta

    2010-05-01

    Full Text Available In the present paper I set out to exemplify the way in which GeoGebra can be used to solve a classic locus problem, namely the loci of the centers of symmetry of a rectangle with two vertices on one of the lines of a given triangle and the other two vertices on the other two lines. I will describe the way in which I created the GeoGebra file and then present two mathematical solutions: a synthetic (elementary one and one using Cartesian coordinates.

  7. A Locus Example

    Gheorghe Sorta

    2010-01-01

    In the present paper I set out to exemplify the way in which GeoGebra can be used to solve a classic locus problem, namely the loci of the centers of symmetry of a rectangle with two vertices on one of the lines of a given triangle and the other two vertices on the other two lines. I will describe the way in which I created the GeoGebra file and then present two mathematical solutions: a synthetic (elementary) one and one using Cartesian coordinates.

  8. Human locus coeruleus neurons express the GABAA receptor γ2 subunit gene and produce benzodiazepine binding

    Hellsten, Kati S.; Sinkkonen, Saku T.; Hyde, Thomas M.; Kleinman, Joel E.; Särkioja, Terttu; Maksimow, Anu; Uusi-Oukari, Mikko; Korpi, Esa R.

    2010-01-01

    Noradrenergic neurons of the locus coeruleus project throughout the cerebral cortex and multiple subcortical structures. Alterations in the locus coeruleus firing are associated with vigilance states and with fear and anxiety disorders. Brain ionotropic type A receptors for γ-aminobutyric acid (GABA) serve as targets for anxiolytic and sedative drugs, and play an essential regulatory role in the locus coeruleus. GABAA receptors are composed of a variable array of subunits forming heteropentam...

  9. The GNAS locus and pseudohypoparathyroidism.

    Bastepe, Murat

    2008-01-01

    . Mutations identified in different forms of PHP-Ib thus point to different cis-acting elements that are apparently required for the proper imprinting of the GNAS locus. Most sporadic PHP-Ib cases also have imprinting abnormalities of GNAS that involve multiple DMRs, but the genetic lesion(s) responsible for these imprinting abnormalities remain to be discovered. PMID:18372789

  10. A Complete Enumeration and Classification of Two-Locus Disease Models

    Li, W; Li, Wentian; Reich, Jens

    1999-01-01

    There are 512 two-locus, two-allele, two-phenotype, fully-penetrant disease models. Using the permutation between two alleles, between two loci, and between being affected and unaffected, one model can be considered to be equivalent to another model under the corresponding permutation. These permutations greatly reduce the number of two-locus models in the analysis of complex diseases. This paper determines the number of non-redundant two-locus models (which can be 102, 100, 96, 51, 50, or 48, depending on which permutations are used, and depending on whether zero-locus and single-locus models are excluded). Whenever possible, these non-redundant two-locus models are classified by their property. Besides the familiar features of multiplicative models (logical AND), heterogeneity models (logical OR), and threshold models, new classifications are added or expanded: modifying-effect models, logical XOR models, interference and negative interference models (neither dominant nor recessive), conditionally dominant/...

  11. Absence of single-locus complementary sex determination in the braconid wasps Asobara tabida and Alysia manducator

    Beukeboom, Leo W.; Ellers, Jacintha; van Alphen, Jacques J.M

    2000-01-01

    In species with single-locus complementary sex determination (sl-CSD), sex is determined by multiple alleles at a single locus. In the haplodiploid Hymenoptera, sl-CSD results in females, if individuals are heterozygous at the sex locus, and in males, if individuals are hemizygous (haploid males) or homozygous (diploid males). Several hymenopteran species have been shown to have sl-CSD, but in several others sl-CSD is absent and the phylogenetic distribution remains unclear. In the family Bra...

  12. Hysteresis zone or locus - Aerodynamic of bulbous based bodies at low speeds

    Covert, E. E.

    1979-01-01

    Experimental data are presented which seem to suggest that a well-defined hysteresis locus on bulbous based bodies at low speeds does not exist. Instead, if the experiment is repeated several times, the entire hysteresis region seems to fill with data rather than trace out a specific hysteresis locus. Data obtained on an oscillating model even at low reduced frequencies may be well defined but when applied to arbitrary motion lead to less accurate results than desired.

  13. Locus of Control and Interpersonal Attraction.

    Fagan, M. Michael

    1980-01-01

    The role of locus of control in interpersonal attraction was examined by administering 1) the Nowicki-Strickland Locus of Control Scale and 2) a sociometric test of friendship to 200 eighth graders. (CM)

  14. Job Stress and Locus of Control in Teachers: Comparisons between Samples from the United States and Zimbabwe

    Crothers, Laura M.; Kanyongo, Gibbs Y.; Kolbert, Jered B.; Lipinski, John; Kachmar, Steven P.; Koch, Gary D.

    2010-01-01

    This study examines the relationship between educators' locus of control and job stress using samples from the US and Zimbabwe. Multiple regression analyses are used to identify significant relationships in the US sample between teachers' external locus of control and the severity of the job stress that they experience, coupled with the perceived…

  15. Locus-specific ribosomal RNA gene silencing in nucleolar dominance.

    Michelle S Lewis

    Full Text Available The silencing of one parental set of rRNA genes in a genetic hybrid is an epigenetic phenomenon known as nucleolar dominance. We showed previously that silencing is restricted to the nucleolus organizer regions (NORs, the loci where rRNA genes are tandemly arrayed, and does not spread to or from neighboring protein-coding genes. One hypothesis is that nucleolar dominance is the net result of hundreds of silencing events acting one rRNA gene at a time. A prediction of this hypothesis is that rRNA gene silencing should occur independent of chromosomal location. An alternative hypothesis is that the regulatory unit in nucleolar dominance is the NOR, rather than each individual rRNA gene, in which case NOR localization may be essential for rRNA gene silencing. To test these alternative hypotheses, we examined the fates of rRNA transgenes integrated at ectopic locations. The transgenes were accurately transcribed in all independent transgenic Arabidopsis thaliana lines tested, indicating that NOR localization is not required for rRNA gene expression. Upon crossing the transgenic A. thaliana lines as ovule parents with A. lyrata to form F1 hybrids, a new system for the study of nucleolar dominance, the endogenous rRNA genes located within the A. thaliana NORs are silenced. However, rRNA transgenes escaped silencing in multiple independent hybrids. Collectively, our data suggest that rRNA gene activation can occur in a gene-autonomous fashion, independent of chromosomal location, whereas rRNA gene silencing in nucleolar dominance is locus-dependent.

  16. Cognitive functioning correlates of self-esteem and health locus of control in schizophrenia

    Wang CS

    2013-10-01

    Full Text Available Chien-Shu Wang,1 Jo Yung-Wei Wu,2 Wei-Chung Chang,3 Shu-Ping Chuang1 1Department of Psychiatry, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan; 2Institute of Allied Health Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; 3Hsin-Jia Psychotherapy Clinic, Taitung County, Taiwan Aim: The study aimed to investigate the relationship among sociodemographic factors, neurocognitive factors, self-esteem, and health locus of control in patients diagnosed with schizophrenia. We examined the self-esteem, internal health locus of control, and external health locus of control through sociodemographic and neurocognitive factors. Methods: Forty-six schizophrenic patients and 31 healthy residents from the community or hospital were recruited as the control group. All subjects participated in the self-esteem questionnaire, health locus of control questionnaire, and a series of neuropychological measures. Results: Multiple regression analysis revealed that inhibition of attention and external health locus of control were predictors for self-esteem (r=−0.30, P<0.05; r=0.41, P<0.01; inhibition of attention and external health locus of control were contributors for internal health locus of control (r=−0.43, P<0.01; r=0.61, P<0.001; and education was related to external health locus of control (r=−0.31, P<0.05. Conclusion: The current study integrated background characteristics and cognitive function to better understand the impact of self-esteem and health locus of control in schizophrenia. The findings indicated that inhibition of attention, external health locus of control, and education contributed to self-esteem, internal health locus of control and external health locus of control. However, the overall predicted variance accounted for by these predictors was small; thus, further research is necessary to examine imperative variables related with self-esteem and health locus of control in

  17. Locus-specific view of flax domestication history

    Fu, Yong-Bi; Diederichsen, Axel; Allaby, Robin G.

    2012-01-01

    Crop domestication has been inferred genetically from neutral markers and increasingly from specific domestication-associated loci. However, some crops are utilized for multiple purposes that may or may not be reflected in a single domestication-associated locus. One such example is cultivated flax (Linum usitatissimum L.), the earliest oil and fiber crop, for which domestication history remains poorly understood. Oil composition of cultivated flax and pale flax (L. bienne Mill.) indicates th...

  18. A Pattern Discovery-Based Method for Detecting Multi-Locus Genetic Association

    Li, Zhong; Floratos, Aris; Wang, David; Califano, Andrea

    2007-01-01

    Methods to effectively detect multi-locus genetic association are becoming increasingly relevant in the genetic dissection of complex trait in humans. Current approaches typically consider a limited number of hypotheses, most of which are related to the effect of a single locus or of a relatively small number of neighboring loci on a chromosomal region. We have developed a novel method that is specifically designed to detect genetic association involving multiple disease-susceptibility loci, ...

  19. The discovery of an Est locus related to the origin, evolution and classification of Asian rice

    WANGXiangkun; CAIHongwei; LIZhichao; CHENGKansheng; ZHANGYaozhong

    1992-01-01

    In the isozyme studies concerning the origin and evolution of Asian rice, Morishima(1990) pointed out that, so far, there have been about 20 isozyme loci related to the differentiation of indica and japonica. In 1990, we discovered another Est locus related to the origin, evolution and classification of Asian rive. Genetic studies revealed that there were 5 multiple alleles on this locus represented 4 isozyme bands,

  20. Two-stage two-locus models in genome-wide association.

    David M Evans

    2006-09-01

    Full Text Available Studies in model organisms suggest that epistasis may play an important role in the etiology of complex diseases and traits in humans. With the era of large-scale genome-wide association studies fast approaching, it is important to quantify whether it will be possible to detect interacting loci using realistic sample sizes in humans and to what extent undetected epistasis will adversely affect power to detect association when single-locus approaches are employed. We therefore investigated the power to detect association for an extensive range of two-locus quantitative trait models that incorporated varying degrees of epistasis. We compared the power to detect association using a single-locus model that ignored interaction effects, a full two-locus model that allowed for interactions, and, most important, two two-stage strategies whereby a subset of loci initially identified using single-locus tests were analyzed using the full two-locus model. Despite the penalty introduced by multiple testing, fitting the full two-locus model performed better than single-locus tests for many of the situations considered, particularly when compared with attempts to detect both individual loci. Using a two-stage strategy reduced the computational burden associated with performing an exhaustive two-locus search across the genome but was not as powerful as the exhaustive search when loci interacted. Two-stage approaches also increased the risk of missing interacting loci that contributed little effect at the margins. Based on our extensive simulations, our results suggest that an exhaustive search involving all pairwise combinations of markers across the genome might provide a useful complement to single-locus scans in identifying interacting loci that contribute to moderate proportions of the phenotypic variance.

  1. Tuning of Synchronous-Frame PI Current Controllers in Grid-Connected Converters Operating at a Low Sampling Rate by MIMO Root Locus

    Fernandez, Francisco Daniel Freijedo; Vidal, Ana; Yepes, Alejandro G.;

    2015-01-01

    state-space. Subsequently, the characteristic polynomial of the closed-loop system is obtained and a computer-aided parametric analysis is performed to calculate the MIMO root locus as a function of the control gain. By its inspection, it is possible to identify the gain which minimizes the current......Current controller performance is key in gridconnected power converters for renewable energy applications. In this context, a challenging scenario is arising in multi-MW wind turbines, where sampling and switching frequencies tend to be lower and lower as power ratings increase. This strongly...... affects achievable control time constant. With this perspective, this paper presents a systematic procedure for accurate dynamics assessment and tuning of synchronous-frame PI current controllers, which is based on linear control for multiple input multiple output (MIMO) systems. The dominant eigenvalues...

  2. Development of a novel strategy for fungal transformation based on a mutant locus conferring carboxin-resistance in Magnaporthe oryzae.

    Guo, Min; Zhu, Xiaolei; Li, Hongxia; Tan, Leyong; Pan, Yuemin

    2016-12-01

    The accurate manipulation of genomic integration of mutant alleles or fluorescent fusion-protein constructs is necessary for understanding of pathogenic mechanism of Magnaporthe oryzae. Recently, this can be achieved by integrating of exogenous DNA randomly into genome of this pathogen, but ectopic integration may result in alteration of gene expression or gene disruption due to unpredictable position effects and/or disruption of protein-coding regions. In this study, we establish a novel strategy for locus-specific integration of exogenous DNA via carboxin-resistance reconstitution by a point-mutation (H245L) on succinate dehydrogenase subunit Mosdi1. Independent transformants derived from the same reconstitution construct showed consistent fluorescent signal and undiversified phenotypes, including hyphae growth, conidiation and pathogenicity, in M. oryzae. Meanwhile, 96 % of all transformants integrate correctly into the Mosdi1 locus as a single copy. Furthermore, we provide a vector carrying yeast recombination cassette and thus allow assembly of multiple overlapping DNA fragments by yeast in vivo recombination for gene complementation and protein localization assay. PMID:27558019

  3. The X-linked F cell production locus: Genetic mapping and role in fetal hemoglobin production

    Chang, Y.C.; Smith, K.D.; Moore, R.D. [John Hopkins Univ., Baltimore, MD (United States)] [and others

    1994-09-01

    Postnatal fetal hemoglobin (Hb F) production is confined to a subset of erythocytes termed F-cells. There is a 10-20 fold variation in F-cell production in sickle cell disease (SCD) and normal individuals. Most of the variation in F-cell production has been attributed to a diallelic (High, Low) X-linked gene, the F-cell production (FCP) locus that we recently mapped to Xp22.2-22.3 (LOD=4.56, theta=0.04). Using multiple regression analysis in 262 Jamaican SCD patients we determined the relative contribution of the FCP locus and other variables previously associated with variation in Hb F level (gender, age, beta-globin haplotypes, number of alpha-globin genes and the FCP locus phenotypes). When the FCP locus is in the regression model, the FCP locus alone accounts for approximately 40% of the variation in Hb F level while the contribution of age, alpha-globin gene number, and beta-globin haplotypes was insignificant. When individuals with High FCP allele are removed from the analysis, the beta globin haplotype now contribute to >10% of the Hb F variation. We conclude that the X-linked FCP locus is the major determinant of all known variables in Hb F production. Using 4 highly polymorphic dinucleotide repeat markers that we identified from cosmids in Xp22.2-22.3, have localized the FCP locus to a 1 Mb minimal candidate region between DXS143 and DXS410.

  4. Accurate Finite Difference Algorithms

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  5. Estimating linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations.

    Luo, Z. W.; Suhai, S.

    1999-01-01

    Positional cloning of gene(s) underlying a complex trait requires a high-resolution linkage map between the trait locus and genetic marker loci. Recent research has shown that this may be achieved through appropriately modeling and screening linkage disequilibrium between the candidate marker locus and the major trait locus. A quantitative genetics model was developed in the present study to estimate the coefficient of linkage disequilibrium between a polymorphic genetic marker locus and a lo...

  6. Multiple-genome comparison reveals new loci for Mycobacterium species identification.

    Dai, Jianli; Chen, Yuansha; Dean, Susan; Morris, J Glenn; Salfinger, Max; Johnson, Judith A

    2011-01-01

    To identify loci useful for species identification and to enhance our understanding of the population structure and genetic variability of the genus Mycobacterium, we conducted a multiple-genome comparison of a total of 27 sequenced genomes in the suborder of Corynebacterineae (18 from the Mycobacterium genus, 7 from the Corynebacterium genus, 1 each from the Nocardia and Rhodococcus genera). Our study revealed 26 informative loci for species identification in Mycobacterium. The sequences from these loci were used in a phylogenetic analysis to infer the evolutionary relations of the 18 mycobacterial genomes. Among the loci that we identified, rpoBC, dnaK, and hsp65 were amplified from 29 ATCC reference strains and 17 clinical isolates and sequenced. The phylogenetic trees generated from these loci show similar topologies. The newly identified dnaK locus is more discriminatory and more robust than the widely used hsp65 locus. The length-variable rpoBC locus is the first intergenic locus between two protein-encoding genes being used for mycobacterial species identification. A multilocus sequence analysis system including the rpoBC, dnaK, and hsp65 loci is a robust tool for accurate identification of Mycobacterium species. PMID:21048007

  7. Homological projective duality for linear systems with base locus

    Carocci, Francesca; Turcinovic, Zak

    2015-01-01

    We show how blowing up varieties in base loci of linear systems gives a procedure for creating new homological projective duals from old. Starting with a HP dual pair $X,Y$ and smooth orthogonal linear sections $X_L,Y_L$, we prove that the blowup of $X$ in $X_L$ is naturally HP dual to $Y_L$. The result does not need $Y$ to exist as a variety, i.e. it may be "noncommutative". We extend the result to the case where the base locus $X_L$ is a multiple of a smooth variety and the universal hyperp...

  8. Primary structure and transcription of an amplified genetic locus: the CUP1 locus of yeast.

    Karin, M; Najarian, R; Haslinger, A; Valenzuela, P; Welch, J; Fogel, S

    1984-01-01

    Copper resistance in yeast is controlled by the CUP1 locus. The level of resistance is proportional to the copy number of this locus, which can be found in up to 15 tandemly iterated copies. To elucidate the molecular mechanisms controlling the amplification and expression of the CUP1, locus, we determined its full nucleotide sequence. We have also identified and mapped two transcription units within the basic amplification unit of CUP1 in laboratory yeast strains. One of those transcription ...

  9. Genetic mapping of the ecotropic virus-inducing locus Akv-2 of the AKR mouse

    1980-01-01

    A combination of somatic cell hybridization and standard mendelian breeding techniques was used to map the AKR ecotropic virus inducibility locus Akv-2 to the centromeric end of chromosome 16. This assignment of Akv-2 further emphasizes the endogenous ecotropic retroviruses are inserted at multiple sites in mouse chromosomes.

  10. Effects of Students\\' Characteristics and Locus of Control on Their Satisfaction with Online Distance Education Experience

    Cui, Guoqiang

    2013-01-01

    Online learners bring varied learning experiences depending on their different personal characteristics and traits. This descriptive and correlational study explored students\\' online satisfaction in relation to their locus of control orientation and their personal characteristics including gender, age, ethnicity, and online learning experiences. Responses were collected from students in an online course at Virginia Tech. Descriptive statistics, Pearson correlations and Multiple Linear Regres...

  11. Application of multi-locus analytical methods to identify interacting loci in case-control studies.

    Vermeulen, S.; Heijer, M. den; Sham, P.; Knight, J.

    2007-01-01

    To identify interacting loci in genetic epidemiological studies the application of multi-locus methods of analysis is warranted. Several more advanced classification methods have been developed in the past years, including multiple logistic regression, sum statistics, logic regression, and the multi

  12. Developing Customer Relationship Strategies Via An Analysis Of Buying Center Network Locus Of Influence And Information Processing

    Johnston, W J; Page, T J

    1990-01-01

    This paper examines a method for analyzing buying center locus of influence and information processing. Buying centers in 70 industrial organizations are studied for the impact of organizational structure and specific purchase situation attributes including BUYCLASS. The methodology uses structural equations with multiple measures to test the hypothesized relationships. The results indicate the locus of influence and the information processing of buying center networks in customer organizatio...

  13. Culture, gender and locus of control

    Ottsen, Christina Lundsgaard; Johannessen, Kim Berg; Berntsen, Dorthe

    The current study is a cross-cultural comparison between the Middle East and Scandinavia. Two societies that offer a unique opportunity to examine gender differences in personal goals and how goals are affected by locus of control.......The current study is a cross-cultural comparison between the Middle East and Scandinavia. Two societies that offer a unique opportunity to examine gender differences in personal goals and how goals are affected by locus of control....

  14. Large registry analysis to accurately define second malignancy rates and risks in a well-characterized cohort of 744 consecutive multiple myeloma patients followed-up for 25 years.

    Engelhardt, Monika; Ihorst, Gabriele; Landgren, Ola; Pantic, Milena; Reinhardt, Heike; Waldschmidt, Johannes; May, Annette M; Schumacher, Martin; Kleber, Martina; Wäsch, Ralph

    2015-10-01

    Additional malignancies in multiple myeloma patients after first-line and maintenance treatment have been observed, questioning whether specific risks exist. Second primary malignancies have also gained attention since randomized data showed associations to newer drugs. We have conducted this large registry analysis in 744 consecutive patients and analyzed: 1) frequency and onset of additional malignancies; and 2) second primary malignancy- and myeloma-specific risks. We assessed the frequency of additional malignancies in terms of host-, myeloma- and treatment-specific characteristics. To compare these risks, we estimated cumulative incidence rates for second malignancies and myeloma with Fine and Gray regression models taking into account competing risks. Additional malignancies were found in 118 patients: prior or synchronous malignancies in 63% and subsequent in 37%. Cumulative incidence rates for second malignancies were increased in IgG-myeloma and decreased in bortezomib-treated patients (P<0.05). Cumulative incidence rates for myeloma death were increased with higher stage and age, but decreased in IgG-subtypes and due to anti-myeloma treatment (P<0.05). Cytogenetics in patients acquiring second primary malignancies were predominantly favorable, suggesting that indolent myeloma and long disease latency may allow the manifestation of additional malignancies. An assessment of the Surveillance, Epidemiology, and End Result Program of the National Cancer Institute and our data with long-term follow up of 25 years confirmed a prevalence of second malignancy of 10% at 25 years, whereas death from myeloma decreased from 90% to 83%, respectively. Our important findings widen our knowledge of second malignancies and show that they are of increasing relevance as the prognosis in myeloma improves and mortality rates decrease. PMID:26160877

  15. Three-locus and four-locus QTL interactions influence mouse insulin-like growth factor-I.

    Hanlon, Philip; Lorenz, William Andrew; Shao, Zhihong; Harper, James M; Galecki, Andrzej T; Miller, Richard A; Burke, David T

    2006-06-16

    A previous analysis of serum insulin-like growth factor I (IGF-I) levels in a mouse population (n = 961) derived from a cross of (BALB/cJ x C57BL/6J) F1 females and (C3H/HeJ x DBA/2J) F1 males documented quantitative trait loci (QTL) on chromosomes 1, 10, and 17. We employed a newly developed, random walk-based method to search for three- and four-way allelic combinations that might influence IGF-I levels through nonadditive (conditional or epistatic) interactions among 185 genotyped biallelic loci and with significance defined by experiment-wide permutation (P genetic interactions. In two cases, the four-allele combinations were associated with animals having high levels of IGF-I, and, in the third case, a four-allele combination was associated with animals having low IGF-I levels. The multiple-locus genome scan algorithm revealed new IGF-I QTL on chromosomes 2, 4, 5, 7, 8, and 12 that had not been detected in the single-locus genome search and showed that levels of this hormone can be regulated by complex, nonadditive interactions among multiple loci. The analysis method can detect multilocus interactions in a genome scan experiment and may provide new ways to explore the genetic architecture of complex physiological phenotypes. PMID:16782841

  16. Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses

    Limwongse Chanin; Sinsomros Saravudh; Piroonratana Theera; Assawamakin Anunchai; Wongseree Waranyu; Chaiyaratana Nachol

    2009-01-01

    Abstract Background Purely epistatic multi-locus interactions cannot generally be detected via single-locus analysis in case-control studies of complex diseases. Recently, many two-locus and multi-locus analysis techniques have been shown to be promising for the epistasis detection. However, exhaustive multi-locus analysis requires prohibitively large computational efforts when problems involve large-scale or genome-wide data. Furthermore, there is no explicit proof that a combination of mult...

  17. Linkage disequilibrium between incompatibility locus region genes in the plant Arabidopsis lyrata

    Hagenblad, Jenny; Bechsgaard, Jesper Smærup; Charlesworth, Deborah

    2006-01-01

    We have studied diversity in Arabidopsis lyrata of sequences orthologous to the ARK3 gene of A. thaliana. Our main goal was to test for recombination in the S-locus region. In A. thaliana, the single-copy ARK3 gene is closely linked to the non-functional copies of the self-incompatibility loci, and...... the ortholog in A. lyrata (a self-incompatible species) is in the homologous genome region and is known as Aly8. It is thus of interest to test whether Aly8 sequence diversity is elevated due to close linkage to the highly polymorphic incompatibility locus, as is theoretically predicted. However, Aly8...... linked to the incompatibility locus, one being a pseudogene. We determined the phase of multiple haplotypes in families of plants from Icelandic and other populations. Different Aly8 sequence types are associated with different SRK alleles, while haplotypes with the same SRK sequences tend to have the...

  18. Association of Five SNPs at the PARK16 locus as a Susceptibility Locus with Parkinson's Disease for Forensic Application

    CUI Hong-gang; TIAN Xiao-fei; LUO Xiao-guang; LI Feng-rui; ZHU Lan-hui; ZHOU Yi-shu; REN Yan

    2013-01-01

    To investigate the association of five SNPs (rs823083,rs708723,rs4951261,rs823076 and rs16856110) at the PARK16 locus with Parkinson's disease (PD),and to potentiate its forensic application.The genomic DNAs of 215 PD patients and 212 matched controls from the northern Han Chinese population were amplified in two independent PCR systems and subsequently genotyped by digestion with the three endonucleases (Hinf Ⅰ,Nco Ⅰ and Msp Ⅰ).The genetic parameters and association studies were carried out with SPSS 13.0,Haploview version 4.2 and PLINK 1.07 sofiwares.We detected accurately all genotypes in the five SNPs with multiplex PCR-RFLP and mismatched multiplex PCR-RFLP techniques.The genotypes of four SNPs,except for rs823083,were in Hardy-Weinberg equilibrium.The four SNPs,rs16856110,rs4951261,rs708723 and rs823076,which were in linkage equilibrium,should not be associated with PD (P-values ranging from 0.077 to 0.544).The SNPs investigated at the PARK16 locus were not found to be involved in PD-associated blocks in the northern Han Chinese population.The allele distributions of rs708723,rs4951261,rs823076 and rs16856110 in the northern Han Chinese population can be highly polymorphic,which can be applied to genetic analvsis and forensic practices.

  19. Distributed Unit Testing: supporting multiple platforms accurately and efficiently

    Francisco José GARCÍA-PEÑALVO; Santos, Pablo

    2006-01-01

    Testing is the most basic way to check the evolution of a software project. A strong test suite helps development team assuring that a certain minimum is always kept. Release after release software must pass a test group, large enough to check, at least, the most common use cases. Results will numerically show project s progress. Depending on the project testing could be done on different platforms under various operating systems. Forcing race conditions and heavy load is also a desired featu...

  20. Identification of the Modifier of Min 2 (Mom2) Locus, a New Mutation That Influences Apc-Induced Intestinal Neoplasia

    Silverman, Karen A.; Koratkar, Revati; Linda D. Siracusa; Buchberg, Arthur M.

    2002-01-01

    Min (Multiple intestinal neoplasia) mice carry a dominant mutation in the adenomatous polyposis coli (Apc) gene and develop multiple adenomas throughout their intestinal tract (Moser et al. 1990; Su et al. 1992). Polyp multiplicity in Min mice is greatly influenced by genetic background. A modifier locus, Mom1 (Modifier of Min 1), was identified and localized to distal mouse chromosome 4 (Moser et al. 1992; Dietrich et al. 1993), and accounts for some of the genetic variance in polyp multipli...

  1. #614411 GLYCEROL QUANTITATIVE TRAIT LOCUS; GLYCQTL [OMIM

    Full Text Available FIELD NO 614411 FIELD TI #614411 GLYCEROL QUANTITATIVE TRAIT LOCUS; GLYCQTL ;;GLYCEROL RELEASE D ... 07) screened 178 Spanish individuals, including 37 lean ... and 90 obese (see 606641) nondiabetics and 14 lean ... significant difference in its distribution between lean ... and obese individuals or between diabetics and non ...

  2. Locus of Equity and Brand Extension

    S.M.J. van Osselaer (Stijn); J.W. Alba (Joseph)

    2003-01-01

    textabstractPrevailing wisdom assumes that brand equity increases when a brand touts its desirable attributes. We report conditions under which the use of attribute information to promote a product can shift the locus of equity from brand to attribute, thereby reducing the attractiveness of extensio

  3. Genetic Analysis of the Hairy Locus in DROSOPHILA MELANOGASTER

    Ingham, P W; Pinchin, S M; Howard, K.R.; Ish-Horowicz, D.

    1985-01-01

    Mutations of the hairy locus in Drosophila may affect both adult chaeta differentiation and embryonic segmentation. In an effort to understand this phenotypic complexity, we have analyzed 30 mutant alleles of the locus. We find that the alleles fall into four groups according to their complementation properties, suggesting a structurally complex locus in which two distinct functions share a common coding region.

  4. Locus of Control and Psychological Distress among the Aged.

    Hale, W. Daniel; And Others

    1986-01-01

    Examined relationship between locus of control and self-reported psychopathology in 139 residents of retirement complex. Correlation coefficients computed for locus of control and each of nine symptom dimensions of the Brief Symptom Inventory indicated that locus of control was correlated with self-reported psychopatholgoy for older women but not…

  5. Self-Esteem, Locus of Control, and Student Achievement.

    Sterbin, Allan; Rakow, Ernest

    The direct effects of locus of control and self-esteem on standardized test scores were studied. The relationships among the standardized test scores and measures of locus of control and self-esteem for 12,260 students from the National Education Longitudinal Study 1994 database were examined, using the same definition of locus of control and…

  6. Lab on a chip genotyping for Brucella spp. based on 15-loci multi locus VNTR analysis

    Marianelli Cinzia

    2009-04-01

    Full Text Available Abstract Background Brucellosis is an important zoonosis caused by the genus Brucella. In addition Brucella represents potential biological warfare agents due to the high contagious rates for humans and animals. Therefore, the strain typing epidemiological tool may be crucial for tracing back source of infection in outbreaks and discriminating naturally occurring outbreaks versus bioterroristic event. A Multiple Locus Variable-number tandem repeats (VNTR Analysis (MLVA assay based on 15 polymorphic markers was previously described. The obtained MLVA band profiles may be resolved by techniques ranging from low cost manual agarose gels to the more expensive capillary electrophoresis sequencing. In this paper a rapid, accurate and reproducible system, based on the Lab on a chip technology was set up for Brucella spp. genotyping. Results Seventeen DNA samples of Brucella strains isolated in Sicily, previously genotyped, and twelve DNA samples, provided by MLVA Brucella VNTR ring trial, were analyzed by MLVA-15 on Agilent 2100. The DNA fragment sizes produced by Agilent, compared with those expected, showed discrepancies; therefore, in order to assign the correct alleles to the Agilent DNA fragment sizes, a conversion table was produced. In order to validate the system twelve unknown DNA samples were analyzed by this method obtaining a full concordance with the VNTR ring trial results. Conclusion In this paper we described a rapid and specific detection method for the characterization of Brucella isolates. The comparison of the MLVA typing data produced by Agilent system with the data obtained by standard sequencing or ethidium bromide slab gel electrophoresis showed a general concordance of the results. Therefore this platform represents a fair compromise among costs, speed and specificity compared to any conventional molecular typing technique.

  7. Genetic Analysis of Mating Locus Linked Mutations in CHLAMYDOMONAS REINHARDII

    Galloway, R. E.; Goodenough, U. W.

    1985-01-01

    The mating-type (mt) locus of Chlamydomonas reinhardii has been analyzed using four mutant strains (imp-1, imp-10, imp-11 and imp-12). All have been shown, or are shown here, to carry mutations linked to either the plus (mt+) or the minus (mt-) locus, and their behavior in complementation tests has allowed us to define several distinct functions for each locus. Specifically, we propose that the mt+ locus contains the following genes or regulatory elements: a locus designated sfu, which is n...

  8. Epigenetic Regulation of Individual Modules of the immunoglobulin heavy chain locus 3' Regulatory Region.

    Birshtein, Barbara K

    2014-01-01

    The Igh locus undergoes an amazing array of DNA rearrangements and modifications during B cell development. During early stages, the variable region gene is constructed from constituent variable (V), diversity (D), and joining (J) segments (VDJ joining). B cells that successfully express an antibody can be activated, leading to somatic hypermutation (SHM) focused on the variable region, and class switch recombination (CSR), which substitutes downstream constant region genes for the originally used Cμ constant region gene. Many investigators, ourselves included, have sought to understand how these processes specifically target the Igh locus and avoid other loci and potential deleterious consequences of malignant transformation. Our laboratory has concentrated on a complex regulatory region (RR) that is located downstream of Cα, the most 3' of the Igh constant region genes. The ~40 kb 3' RR, which is predicted to serve as a downstream major regulator of the Igh locus, contains two distinct segments: an ~28 kb region comprising four enhancers, and an adjacent ~12 kb region containing multiple CTCF and Pax5 binding sites. Analysis of targeted mutations in mice by a number of investigators has concluded that the entire 3' RR enhancer region is essential for SHM and CSR (but not for VDJ joining) and for high levels of expression of multiple isotypes. The CTCF/Pax5 binding region is a candidate for influencing VDJ joining early in B cell development and serving as a potential insulator of the Igh locus. Components of the 3' RR are subject to a variety of epigenetic changes during B cell development, i.e., DNAse I hypersensitivity, histone modifications, and DNA methylation, in association with transcription factor binding. I propose that these changes provide a foundation by which regulatory elements in modules of the 3' RR function by interacting with each other and with target sequences of the Igh locus. PMID:24795714

  9. Genomic approaches uncover increasing complexities in the regulatory landscape at the human SCL (TAL1) locus

    Dhami, P.; Bruce, A. W.; Jim, J.H.; Dillon, S. C.; Hall, A; Cooper, J. L.; Bonhoure, N.; Chiang, K.; Ellis, P D; Langford, C; Andrews, R.M.; Vetrie, D

    2010-01-01

    The SCL (TAL1) transcription factor is a critical regulator of haematopoiesis and its expression is tightly controlled by multiple cis-acting regulatory elements. To elaborate further the DNA elements which control its regulation, we used genomic tiling microarrays covering 256 kb of the human SCL locus to perform a concerted analysis of chromatin structure and binding of regulatory proteins in human haematopoietic cell lines. This approach allowed us to characterise further or redefine known...

  10. mlstdbNet – distributed multi-locus sequence typing (MLST) databases

    Maiden Martin CJ; Chan Man-Suen; Jolley Keith A

    2004-01-01

    Abstract Background Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet. Results The software enables multiple isolate databases to query a single profiles database that contains allelic profile and sequence definitions. This separation...

  11. Towards accurate emergency response behavior

    Nuclear reactor operator emergency response behavior has persisted as a training problem through lack of information. The industry needs an accurate definition of operator behavior in adverse stress conditions, and training methods which will produce the desired behavior. Newly assembled information from fifty years of research into human behavior in both high and low stress provides a more accurate definition of appropriate operator response, and supports training methods which will produce the needed control room behavior. The research indicates that operator response in emergencies is divided into two modes, conditioned behavior and knowledge based behavior. Methods which assure accurate conditioned behavior, and provide for the recovery of knowledge based behavior, are described in detail

  12. The algebraic locus of Feynman integrals

    Kol, Barak

    2016-01-01

    In the Symmetries of Feynman Integrals (SFI) approach, a diagram's parameter space is foliated by orbits of a Lie group associated with the diagram. SFI is related to the important methods of Integrations By Parts and of Differential Equations. It is shown that sometimes there exist a locus in parameter space where the set of SFI differential equations degenerates into an algebraic equation, thereby enabling a solution in terms of integrals associated with degenerations of the diagram. This is demonstrated by the two-loop vacuum diagram, where the algebraic locus can be interpreted as a threshold phenomenon and is given by the zeros of the Baikov polynomial. In addition, the symmetry group is interpreted geometrically as linear transformations of loop currents which preserve the subspace of squared currents within the space of quadratics in loop currents.

  13. Autism, fever, epigenetics and the locus coeruleus

    Mehler, Mark F.; Purpura, Dominick P.

    2008-01-01

    Some children with autism spectrum disorders (ASD) exhibit improved behaviors and enhanced communication during febrile episodes. We hypothesize that febrigenesis and the behavioral-state changes associated with fever in autism depend upon selective normalization of key components of a functionally impaired locus coeruleus-noradrenergic (LC-NA) system. We posit that autistic behaviors result from developmental dysregulation of LC-NA system specification and neural network deployment and modul...

  14. Credit Card Misuse, Money Attitudes, and Compulsive Buying Behaviors: A Comparison of Internal and External Locus of Control (LOC) Consumers

    Watson, Stevie

    2009-01-01

    This study examined attitudinal and behavioral differences between internal and external locus of control (LOC) consumers on credit card misuse, the importance of money, and compulsive buying. Using multiple analysis of variance and separate analyses of variance, internal LOC consumers were found to have lower scores on credit card misuse and…

  15. Bipolar disorder: Evidence for a major locus

    Spence, M.A.; Flodman, P.L. [Univ. of California, Irvine, CA (United States); Sadovnick, A.D.; Ameli, H. [Univ. of British Columbia, Vancouver (Canada)] [and others

    1995-10-09

    Complex segregation analyses were conducted on families of bipolar I and bipolar II probands to delineate the mode of inheritance. The probands were ascertained from consecutive referrals to the Mood Disorder Service, University Hospital, University of British Columbia and diagnosed by DSM-III-R and Research Diagnostic Criteria. Data were available on over 1,500 first-degree relatives of the 186 Caucasian probands. The purpose of the analyses was to determine if, after correcting for age and birth cohort, there was evidence for a single major locus. Five models were fit to the data using the statistical package SAGE: (1) dominant, (2) recessive, (3) arbitrary mendelian inheritance, (4) environmental, and (5) no major effects. A single dominant, mendelian major locus was the best fitting of these models for the sample of bipolar I and II probands when only bipolar relatives were defined as affected (polygenic inheritance could not be tested). Adding recurrent major depression to the diagnosis {open_quotes}affected{close_quotes} for relatives reduced the evidence for a major locus effect. Our findings support the undertaking of linkage studies and are consistent with the analyses of the National Institutes of Mental Health (NIMH) Collaborative Study data by Rice et al. and Blangero and Elston. 39 refs., 4 tabs.

  16. Determining the bistability parameter ranges of artificially induced lac operon using the root locus method.

    Avcu, N; Alyürük, H; Demir, G K; Pekergin, F; Cavas, L; Güzeliş, C

    2015-06-01

    This paper employs the root locus method to conduct a detailed investigation of the parameter regions that ensure bistability in a well-studied gene regulatory network namely, lac operon of Escherichia coli (E. coli). In contrast to previous works, the parametric bistability conditions observed in this study constitute a complete set of necessary and sufficient conditions. These conditions were derived by applying the root locus method to the polynomial equilibrium equation of the lac operon model to determine the parameter values yielding the multiple real roots necessary for bistability. The lac operon model used was defined as an ordinary differential equation system in a state equation form with a rational right hand side, and it was compatible with the Hill and Michaelis-Menten approaches of enzyme kinetics used to describe biochemical reactions that govern lactose metabolism. The developed root locus method can be used to study the steady-state behavior of any type of convergent biological system model based on mass action kinetics. This method provides a solution to the problem of analyzing gene regulatory networks under parameter uncertainties because the root locus method considers the model parameters as variable, rather than fixed. The obtained bistability ranges for the lac operon model parameters have the potential to elucidate the appearance of bistability for E. coli cells in in vivo experiments, and they could also be used to design robust hysteretic switches in synthetic biology. PMID:25864166

  17. Accurate determination of antenna directivity

    Dich, Mikael

    1997-01-01

    The derivation of a formula for accurate estimation of the total radiated power from a transmitting antenna for which the radiated power density is known in a finite number of points on the far-field sphere is presented. The main application of the formula is determination of directivity from power...

  18. The fester locus in Botryllus schlosseri experiences selection

    Nydam Marie L

    2012-12-01

    Full Text Available Abstract Background Allorecognition, the ability of an organism to distinguish self from non-self, occurs throughout the entire tree of life. Despite the prevalence and importance of allorecognition systems, the genetic basis of allorecognition has rarely been characterized outside the well-known MHC (Major Histocompatibility Complex in vertebrates and SI (Self-Incompatibility in plants. Where loci have been identified, their evolutionary history is an open question. We have previously identified the genes involved in self/non-self recognition in the colonial ascidian Botryllus schlosseri, and we can now begin to investigate their evolution. In B. schlosseri, colonies sharing 1 or more alleles of a gene called FuHC (Fusion Histocompatibility will fuse. Protein products of a locus called fester, located ~300 kb from FuHC, have been shown to play multiple roles in the histocompatibility reaction, as activating and/or inhibitory receptors. We test whether the proteins encoded by this locus are evolving neutrally or are experiencing balancing, directional, or purifying selection. Results Nearly all of the variation in the fester locus resides within populations. The 13 housekeeping genes (12 nuclear genes and mitochondrial cytochrome oxidase I have substantially more structure among populations within groups and among groups than fester. All polymorphism statistics (Tajima's D, Fu and Li's D* and F* are significantly negative for the East Coast A-type alleles, and Fu and Li's F* statistic is significantly negative for the West Coast A-type alleles. These results are likely due to selection rather than demography, given that 10 of the housekeeping loci have no populations with significant values for any of the polymorphism statistics. The majority of codons in the fester proteins have ω values 95% posterior probability of ω values > 1. Conclusion Fester proteins are evolving non-neutrally. The polymorphism statistics are consistent with either

  19. Structure and genotypic plasticity of the Campylobacter fetus sap locus.

    Tu, Zheng-Chao; Wassenaar, Trudy M; Thompson, Stuart A; Blaser, Martin J

    2003-05-01

    The Campylobacter fetus surface layer proteins (SLPs), encoded by five to nine sapA homologues, are major virulence factors. To characterize the sapA homologues further, a 65.9 kb C. fetus genomic region encompassing the sap locus from wild-type strain 23D was completely sequenced and analysed; 44 predicted open reading frames (ORFs) were recognized. The 53.8 kb sap locus contained eight complete and one partial sapA homologues, varying from 2769 to 3879 bp, sharing conserved 553-2622 bp 5' regions, with partial sharing of 5' and 3' non-coding regions. All eight sapA homologues were expressed in Escherichia coli as antigenic proteins and reattached to the surface of SLP- strain 23B, indicating their conserved function. Analysis of the sap homologues indicated three phylogenetic groups. Promoter-specific polymerase chain reactions (PCRs) and sapA homologue-specific reverse transcription (RT)-PCRs showed that the unique sapA promoter can potentially express all eight sapA homologues. Reciprocal DNA recombination based on the 5' conserved regions can involve each of the eight sapA homologues, with frequencies from 10(-1) to 10(-3). Intragenic recombination between sapA7 and sapAp8, mediated by their conserved regions with a 10(-1)-10(-2) frequency, allows the formation of new sap homologues. As divergent SLP C-termini possess multiple antigenic sites, their reciprocal recombination behind the unique sap promoter leads to continuing antigenic variation. PMID:12694614

  20. Accurately bearing measurement in non-cooperative passive location system

    The system of non-cooperative passive location based on array is proposed. In the system, target is detected by beamforming and Doppler matched filtering; and bearing is measured by a long-base-ling interferometer which is composed of long distance sub-arrays. For the interferometer with long-base-line, the bearing is measured accurately but ambiguously. To realize unambiguous accurately bearing measurement, beam width and multiple constraint adoptive beamforming technique is used to resolve azimuth ambiguous. Theory and simulation result shows this method is effective to realize accurately bearing measurement in no-cooperate passive location system. (authors)

  1. High Frequency QRS ECG Accurately Detects Cardiomyopathy

    Schlegel, Todd T.; Arenare, Brian; Poulin, Gregory; Moser, Daniel R.; Delgado, Reynolds

    2005-01-01

    RAZ scoring is a simple, accurate and inexpensive screening technique for cardiomyopathy. Although HF QRS ECG is highly sensitive for cardiomyopathy, its specificity may be compromised in patients with cardiac pathologies other than cardiomyopathy, such as uncomplicated coronary artery disease or multiple coronary disease risk factors. Further studies are required to determine whether HF QRS might be useful for monitoring cardiomyopathy severity or the efficacy of therapy in a longitudinal fashion.

  2. An empirical assessment of the construct "work locus of control"

    Allan Maram

    1998-06-01

    Full Text Available This study is concerned with the domain specificity of the locus of control construct within the workplace. The research investigated whether Specter's (1988 work locus of control scale, a work centred conceptualisation of Rotter's (1966 locus of control measure/ demonstrated evidence of criterion - related validity. This was done by assessing its relationship to leader-member exchange and organisational commitment. The results indicated that work locus of control correlated with both leader-member exchange and organisational commitment and that leadermember exchange acted as a mediator of the relationship between work locus of control and organisational commitment. This is consistent with results from a similar study undertaken by Kinicki & Vecchio (1994 who employed Rotter's (1966 general locus of control measure. The current research demonstrated stronger relationship than Kinicki & Vecchio's (1994 study, which suggests that Specter's (1988 domain specific scale may predict work behaviour more precisely than Rotter's (1966 more general measure.

  3. Locus of control and online learning

    Suretha Esterhuysen

    2004-10-01

    Full Text Available The integration of online learning in university courses is considered to be both inevitable and necessary. Thus there is an increasing need to raise awareness among educators and course designers about the critical issues impacting on online learning. The aim of this study, therefore, was to assess the differences between two groups of first-year Business Sciences learners (online and conventional learners in terms of biographic and demographic characteristics and locus of control. The study population consisted of 586 first-year learners of whom 185 completed the Locus of Control Inventory (LCI. The results show that the two groups of learners do not differ statistically significantly from each other with respect to locus of control. The findings and their implications are also discussed. Opsomming Die integrasie van aanlyn-leer in universiteitskursusse word beskou as sowel onafwendbaar as noodsaaklik. Daar is dus ’n toenemende behoefte om bewustheid onder opvoedkundiges en kursusontwerpers te kweek oor die kritiese aspekte wat ’n impak op aanlyn-leer het (Morgan, 1996. Daarom was die doel van hierdie ondersoek om die verskille tussen twee groepe eerstejaarleerders in Bestuurs- en Ekonomiese Wetenskap (aanlyn en konvensionele leerders te bepaal ten opsigte van biografiese en demografiese eienskappe en lokus van beheer. Die populasie het bestaan uit 586 eerstejaarleerders waarvan 185 die Lokus van Beheer Vraelys voltooi het. Die resultate toon dat die twee groepe leerders nie statisties beduidend van mekaar verskil het met betrekking tot lokus van beheer nie. Die bevindinge en implikasies word ook bespreek.

  4. Reinforcement of genetic coherence in a two-locus model

    Steiner Wilfried; Gregorius Hans-Rolf

    2001-01-01

    Abstract Background In order to maintain populations as units of reproduction and thus enable anagenetic evolution, genetic factors must exist which prevent continuing reproductive separation or enhance reproductive contact. This evolutionary principle is called genetic coherence and it marks the often ignored counterpart of cladistic evolution. Possibilities of the evolution of genetic coherence are studied with the help of a two-locus model with two alleles at each locus. The locus at which...

  5. Cut Locus Construction using Deformable Simplicial Complexes

    Misztal, Marek Krzysztof; Bærentzen, Jakob Andreas; Anton, François;

    2011-01-01

    In this paper we present a method for appproximating cut loci for a given point p on Riemannian 2D manifolds, closely related to the notion of Voronoi diagrams. Our method finds the cut locus by advecting a front of points equally distant from p along the geodesics originating at p and finding the...... lines of self-intersections of the front in the parametric space. This becomes possible by using the deformable simplicial complexes (DSC, [1]) method for deformable interface tracking. DSC provide a simple collision detection mechanism, allows for interface topology control, and does not require the...

  6. Accurate shear measurement with faint sources

    Zhang, Jun; Foucaud, Sebastien [Center for Astronomy and Astrophysics, Department of Physics and Astronomy, Shanghai Jiao Tong University, 955 Jianchuan road, Shanghai, 200240 (China); Luo, Wentao, E-mail: betajzhang@sjtu.edu.cn, E-mail: walt@shao.ac.cn, E-mail: foucaud@sjtu.edu.cn [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Nandan Road 80, Shanghai, 200030 (China)

    2015-01-01

    For cosmic shear to become an accurate cosmological probe, systematic errors in the shear measurement method must be unambiguously identified and corrected for. Previous work of this series has demonstrated that cosmic shears can be measured accurately in Fourier space in the presence of background noise and finite pixel size, without assumptions on the morphologies of galaxy and PSF. The remaining major source of error is source Poisson noise, due to the finiteness of source photon number. This problem is particularly important for faint galaxies in space-based weak lensing measurements, and for ground-based images of short exposure times. In this work, we propose a simple and rigorous way of removing the shear bias from the source Poisson noise. Our noise treatment can be generalized for images made of multiple exposures through MultiDrizzle. This is demonstrated with the SDSS and COSMOS/ACS data. With a large ensemble of mock galaxy images of unrestricted morphologies, we show that our shear measurement method can achieve sub-percent level accuracy even for images of signal-to-noise ratio less than 5 in general, making it the most promising technique for cosmic shear measurement in the ongoing and upcoming large scale galaxy surveys.

  7. Potentially non-klt locus and its applications

    Choi, Sung Rak; Park, Jinhyung

    2014-01-01

    We introduce the notion of potentially klt pairs for normal projective varieties with pseudoeffective anticanonical divisor. The potentially non-klt locus is a subset of $X$ which is birationally transformed precisely into the non-klt locus on a $-K_X$-minimal model of $X$. We prove basic properties of potentially non-klt locus in comparison with those of classical non-klt locus. As applications, we give a new characterization of varieties of Fano type, and we also improve results on the rati...

  8. Allelic association at the D14S43 locus in early onset Alzheimer`s disease

    Brice, A.; Tardieu, S.; Campion, D.; Martinez, M. [and others

    1995-04-24

    The D14S43 marker is closely linked to the major gene for early onset autosomal dominant Alzheimer`s disease on chromosome 14. Allelic frequencies at the D14S43 locus were compared in 113 familial and isolated cases of early onset Alzheimer`s disease (<60 years of age at onset) (EOAD) and 109 unaffected individuals of the same geographic origin. Allele 7 was significantly (P = 0.033) more frequent in type 1 EOAD patients (13.2%), defined by the presence of at least another first degree relative with EOAD, than in controls (4.1%). Since an autosomal dominant gene is probably responsible for type 1 patients, allelic association may reflect linkage disequilibrium at the D14S43 locus. This would mean that some patients share a common ancestral mutation. However, since multiple tests were carried out, this result must be interpreted with caution, and needs confirmation in an independent sample. 16 refs., 2 tabs.

  9. The Levels of Conceptual Understanding in Statistics (LOCUS Project: Results of the Pilot Study

    Douglas Whitaker

    2015-07-01

    Full Text Available The Levels of Conceptual Understanding in Statistics (LOCUS project (NSF DRL-111868 has created assessments that measure conceptual (rather than procedural understanding of statistics as outlined in GAISE Framework (Franklin et al., 2007, Guidelines for Assessment and Instruction in Statistics Education, American Statistical Association. Here we provide a brief overview of the LOCUS project and present results from multiple-choice items on the pilot administration of the assessments with data collected from over 3400 students in grades 6-12 across six states. These results help illustrate students’ understanding of statistical topics prior to the implementation of the Common Core State Standards. Using the four components of the statistical problem-solving process outlined in the GAISE Framework, middle and high school students tended to perform better on questions assessing Formulate Questions and Collect Data; both groups also tended to perform relatively worse on the Analyze Data questions.

  10. Causes and Consequences of Multi-Locus Imprinting Disturbances in Humans.

    Sanchez-Delgado, Marta; Riccio, Andrea; Eggermann, Thomas; Maher, Eamonn R; Lapunzina, Pablo; Mackay, Deborah; Monk, David

    2016-07-01

    Eight syndromes are associated with the loss of methylation at specific imprinted loci. There has been increasing evidence that these methylation defects in patients are not isolated events occurring at a given disease-associated locus but that some of these patients may have multi-locus imprinting disturbances (MLID) affecting additional imprinted regions. With the recent advances in technology, methylation profiling has revealed that imprinted loci represent only a small fraction of the methylation differences observed between the gametes. To figure out how imprinting anomalies occur at multiple imprinted domains, we have to understand the interplay between DNA methylation and histone modifications in the process of selective imprint protection during pre-implantation reprogramming, which, if disrupted, leads to these complex imprinting disorders (IDs). PMID:27235113

  11. Molecular analysis of mutants of the Neurospora adenylosuccinate synthetase locus

    A. Wiest; A. J. McCarthy; R. Schnittker; K. McCluskey

    2012-08-01

    The ad-8 gene of Neurospora crassa, in addition to being used for the study of purine biology, has been extensively studied as a model for gene structure, mutagenesis and intralocus recombination. Because of this there is an extensive collection of well-characterized N. crassa ad-8 mutants in the Fungal Genetics Stock Center collection. Among these are spontaneous mutants and mutants induced with X-ray, UV or chemical mutagens. The specific lesions in these mutants have been genetically mapped at high resolution. We have sequenced the ad-8 locus from 13 of these mutants and identified the molecular nature of the mutation in each strain. We compare the historical fine-structure map to the DNA and amino acid sequence of each allele. The placement of the individual lesions in the fine-structure map was more accurate at the 5′ end of the gene and no mutants were identified in the 3′ untranslated region of this gene. We additionally analysed ad-8+ alleles in 18 N. crassa strains subjected to whole-genome sequence analysis and describe the variability among Neurospora strains and among fungi and other organisms.

  12. Lep-MAP: fast and accurate linkage map construction for large SNP datasets

    Rastas, Pasi; Paulin, Lars; Hanski, Ilkka; Lehtonen, Rainer; Auvinen, Petri

    2013-01-01

    Motivation: Current high-throughput sequencing technologies allow cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for hundreds of samples. However, the tools that are currently available for constructing linkage maps are not well suited for large datasets. Linkage maps of large datasets would be helpful in de novo genome assembly by facilitating comprehensive genome validation and refinement by enabling chimeric scaffold detection, as well as in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other complex genomic data analyses. Results: We describe a novel tool, called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP data. Lep-MAP is fast and memory efficient and largely automated, requiring minimal user interaction. It uses simultaneously data on multiple outbred families and can increase linkage map accuracy by taking into account achiasmatic meiosis, a special feature of Lepidoptera and some other taxa with no recombination in one sex (no recombination in females in Lepidoptera). We demonstrate that Lep-MAP outperforms other methods on real and simulated data. We construct a genome-wide linkage map of the Glanville fritillary butterfly (Melitaea cinxia) with over 40 000 SNPs. The data were generated with a novel in-house SOLiD restriction site-associated DNA tag sequencing protocol, which is described in the online supplementary material. Availability and implementation: Java source code under GNU general public license with the compiled classes and the datasets are available from http://sourceforge.net/users/lep-map. Contact: pasi.rastas@helsinki.fi Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24078685

  13. Accurate ab initio spin densities

    Boguslawski, Katharina; Legeza, Örs; Reiher, Markus

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...

  14. Accurate Modeling of Advanced Reflectarrays

    Zhou, Min

    of the incident field, the choice of basis functions, and the technique to calculate the far-field. Based on accurate reference measurements of two offset reflectarrays carried out at the DTU-ESA Spherical NearField Antenna Test Facility, it was concluded that the three latter factors are particularly important...... to the conventional phase-only optimization technique (POT), the geometrical parameters of the array elements are directly optimized to fulfill the far-field requirements, thus maintaining a direct relation between optimization goals and optimization variables. As a result, better designs can be obtained compared...... using the GDOT to demonstrate its capabilities. To verify the accuracy of the GDOT, two offset contoured beam reflectarrays that radiate a high-gain beam on a European coverage have been designed and manufactured, and subsequently measured at the DTU-ESA Spherical Near-Field Antenna Test Facility...

  15. Accurate thickness measurement of graphene

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  16. Multimodal Spatial Calibration for Accurately Registering EEG Sensor Positions

    Jianhua Zhang

    2014-01-01

    Full Text Available This paper proposes a fast and accurate calibration method to calibrate multiple multimodal sensors using a novel photogrammetry system for fast localization of EEG sensors. The EEG sensors are placed on human head and multimodal sensors are installed around the head to simultaneously obtain all EEG sensor positions. A multiple views’ calibration process is implemented to obtain the transformations of multiple views. We first develop an efficient local repair algorithm to improve the depth map, and then a special calibration body is designed. Based on them, accurate and robust calibration results can be achieved. We evaluate the proposed method by corners of a chessboard calibration plate. Experimental results demonstrate that the proposed method can achieve good performance, which can be further applied to EEG source localization applications on human brain.

  17. Evaluation of High-Throughput Genomic Assays for the Fc Gamma Receptor Locus.

    Chantal E Hargreaves

    Full Text Available Cancer immunotherapy has been revolutionised by the use monoclonal antibodies (mAb that function through their interaction with Fc gamma receptors (FcγRs. The low-affinity FcγR genes are highly homologous, map to a complex locus at 1p23 and harbour single nucleotide polymorphisms (SNPs and copy number variation (CNV that can impact on receptor function and response to therapeutic mAbs. This complexity can hinder accurate characterisation of the locus. We therefore evaluated and optimised a suite of assays for the genomic analysis of the FcγR locus amenable to peripheral blood mononuclear cells and formalin-fixed paraffin-embedded (FFPE material that can be employed in a high-throughput manner. Assessment of TaqMan genotyping for FCGR2A-131H/R, FCGR3A-158F/V and FCGR2B-232I/T SNPs demonstrated the need for additional methods to discriminate genotypes for the FCGR3A-158F/V and FCGR2B-232I/T SNPs due to sequence homology and CNV in the region. A multiplex ligation-dependent probe amplification assay provided high quality SNP and CNV data in PBMC cases, but there was greater data variability in FFPE material in a manner that was predicted by the BIOMED-2 multiplex PCR protocol. In conclusion, we have evaluated a suite of assays for the genomic analysis of the FcγR locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of FcγR genetics in predicting response to antibody therapeutics.

  18. Personality and Locus of Control among School Children

    Pandya, Archana A.; Jogsan, Yogesh A.

    2013-01-01

    The main purpose of this investigation is to find out the sex differences in personality traits and locus of control among school children. A total 60 children (30 boys and 30 girls) were taken as a sample. The research tool for personality, children personality questionnaire was used, which was made by Cattell and Porter. Locus of control was…

  19. 40 CFR 798.5200 - Mouse visible specific locus test.

    2010-07-01

    ... specific locus mutation is a genetic change that alters factors responsible for coat color and other... the three tests, the visible specific locus test has been most widely used in assessing genetic hazard... test species. (5) Test report. In addition to the reporting requirements as specified under 40 CFR...

  20. Genetic mapping of the Salmonella typhimurium pepB locus.

    Green, L; Miller, C G

    1980-01-01

    Transposon technology has been used to map the pepB locus of Salmonella typhimurium. This locus is cotransducible by phage P22 with glyA and strB at min 56 on the Salmonella genetic map. The gene order is strB pepB glyA.

  1. Turkish population data on the short tandem repeat locus TPOX

    Vural, B; Poda, M; Atlioglu, E;

    1998-01-01

    Allele and genotype frequencies were determined for the STR (short tandem repeat) locus TPOX in a random Turkish population sample of 200 individuals.......Allele and genotype frequencies were determined for the STR (short tandem repeat) locus TPOX in a random Turkish population sample of 200 individuals....

  2. Reevaluating the Serotype II Capsular Locus of Streptococcus agalactiae▿

    Martins, E. R.; Melo-Cristino, J.; Ramirez, M.

    2007-01-01

    We report a novel sequence of the serotype II capsular locus of group B streptococcus that resolves inconsistencies among the results of various groups and the sequence in GenBank. This locus was found in diverse lineages and presents genes consistent with the complete synthesis of the type II polysaccharide.

  3. Locus of Control and Protection of Consumer Rights

    Ivan Krastev

    2012-10-01

    Full Text Available This paper examines the influence of locus of control on the consumer behavior. Theoretical supposition is proven by analyzing empirical data from a study of 287 students. The methods assessed the capacity for defending personal and consumer rights, as well as the type of locus of control.

  4. Is this Red Spot the Blue Spot (locus ceruleum)?

    Choe, Won Sick; Lee, Yu Kyung; Lee, Min Kyung; Hwang, Kyung Hoon [Gachon University Gil Hospital, Incheon (Korea, Republic of)

    2010-06-15

    The authors report brain images of 18F-FDG-PET in a case of schizophrenia. The images showed strikingly increased bilateral uptake in the locus ceruleum. The locus ceruleum is called the blue spot and known to be a center of the norepinephrinergic system.

  5. Joint linkage of multiple loci for a complex disorder.

    MacLean, C J; Sham, P. C.; Kendler, K S

    1993-01-01

    Many investigators who have been searching for linkage to complex diseases have by now accumulated a drawer full of negative results. If disease is actually caused by genes at several loci, these data might contain multiple-locus system (MLS) information that the investigator does not realize. Trying to obtain this information formally, through the MLS likelihood, leads to severe computational and statistical difficulties. Therefore, we propose a scheme of inference based on single-locus (SL)...

  6. Rapid multi-locus sequence typing using microfluidic biochips.

    Timothy D Read

    Full Text Available BACKGROUND: Multiple locus sequence typing (MLST has become a central genotyping strategy for analysis of bacterial populations. The scheme involves de novo sequencing of 6-8 housekeeping loci to assign unique sequence types. In this work we adapted MLST to a rapid microfluidics platform in order to enhance speed and reduce laboratory labor time. METHODOLOGY/PRINCIPAL FINDINGS: Using two integrated microfluidic devices, DNA was purified from 100 Bacillus cereus soil isolates, used as a template for multiplex amplification of 7 loci and sequenced on forward and reverse strands. The time on instrument from loading genomic DNA to generation of electropherograms was only 1.5 hours. We obtained full-length sequence of all seven MLST alleles from 84 representing 46 different Sequence Types. At least one allele could be sequenced from a further 15 strains. The nucleotide diversity of B. cereus isolated in this study from one location in Rockville, Maryland (0.04 substitutions per site was found to be as great as the global collection of isolates. CONCLUSIONS/SIGNIFICANCE: Biogeographical investigation of pathogens is only one of a panoply of possible applications of microfluidics based MLST; others include microbiologic forensics, biothreat identification, and rapid characterization of human clinical samples.

  7. Peripheral and central locus of a nonspeech phonetic context effect

    Sullivan, Sarah C.; Lotto, Andrew J.

    2002-05-01

    Previous work has demonstrated that nonspeech sounds with the appropriate spectral characteristics can affect the identification of speech sounds [Lotto and Kluender, Percept. Psychophys. 60, 602-619 (1998)]. It has been proposed that these spectral context effects are due to interactions in the peripheral auditory system. For example, they could be the result of masking at the auditory nerve or of auditory enhancement effects that have been demonstrated to be monaural [Summerfield and Assmann, Percept. Psychophys. 45, 529-536 (1989)]. To examine the locus of the context effect, synthesized syllables varying from /da/ to /ga/ were preceded by single-formant stimuli that mimicked the third formant of the syllables /al/ and /ar/. The nonspeech stimulus was presented either to the same or opposite ear as the target speech stimulus. Subjects speech identifications were shifted as a function of context in predicted directions for both presentation conditions. However, the size of the shift was smaller when the context was in the ear contralateral to the target syllable. These results agree well with similar results for speech contexts. The data suggest that the context effects occur at multiple levels of the auditory system and are not simply examples of masking or auditory enhancement.

  8. Sign Stability via Root Locus Analysis

    Gibson, Travis E

    2015-01-01

    With the rise of network science old topics in ecology and economics are resurfacing. One such topic is structural stability (often referred to as qualitative stability or sign stability). A system is deemed structurally stable if the system remains stable for all possible parameter variations so long as the parameters do not change sign. This type of stability analysis is appealing when studying real systems as the underlying stability result only requires the scientist or engineer to know the sign of the parameters in the model and not the specific values. The necessary and sufficient conditions for qualitative stability however are opaque. In order to shed light on those conditions root locus analysis is employed. This technique allows us to illustrate the necessary conditions for qualitative stability.

  9. Identifying a novel locus for psoriatic arthritis.

    Budu-Aggrey, Ashley; Bowes, John; Barton, Anne

    2016-01-01

    A number of studies have identified genetic risk loci for PsA, the majority of which also confer risk for psoriasis. The stronger heritability of PsA in comparison with psoriasis suggests that there should be risk loci that are specific for PsA. Identifying such loci could potentially inform therapy development to provide more effective treatments for PsA patients, especially with a considerable proportion being non-responsive to current therapies. Evidence of a PsA-specific locus has been previously found at HLA-B27 within the MHC region. A recent study has provided evidence of non-HLA risk loci that are specific for PsA at IL23R, PTPN22 and on chromosome 5q31. Functional characterization of these loci will provide further understanding of the pathways underlying PsA, and enable us to apply genetic findings for patient benefit. PMID:26255310

  10. Locus of Control Orientation: Parents, Peers, and Place.

    Ahlin, Eileen M; Lobo Antunes, Maria João

    2015-09-01

    An internal locus of control contributes to positive youth outcomes such as a general well-being and academic success, while also serving as a protective factor against exposure to community violence and reducing negative behaviors like violence. Despite these benefits, very little is known about antecedents of an internal locus of control orientation. Without an understanding of what factors contribute to the development of an internal locus of control, it is not clear how to best encourage its formation. This study uses data from the Project on Human Development in Chicago Neighborhoods to examine whether various mesosystem variables (family management strategies, peer interactions, neighborhood context, and individual-level characteristics) are associated with an internal locus of control orientation among 1,076 youth ages 9-19 living in 78 Chicago neighborhoods. Study participants were Hispanic (46 %), African American (34 %), and White (15 %), and 50 % were female. The findings suggest that, while most levels of the mesosystem influence locus of control orientation, family management strategies are more prominent determinants of an internal locus of control than peers, neighborhood context, or individual characteristics. Parental supervision over the time a youth spends at home and family socioeconomic status are consistent predictors of an internal locus of control, while harsh discipline is associated with an external locus of control. The discussion examines the import of various parenting techniques in shaping an internal locus of control and considers future avenues for research to further unpack how antecedents of locus of control can vary across youth. PMID:25617000

  11. Escala de Locus de controle ELCO/TELEBRÁS Scale of Locus of control - ELCO

    Luiz Pasquali

    1998-01-01

    Full Text Available Com base na teoria de Rotter e Escala de Levenson foi elaborada uma escala de Locus de Controle Organizacional (ELCO, composta por 28 itens. A escala foi validada com uma amostra de 350 empregados do Sistema Telebrás. Verificou-se a presença dos 2 fatores previstos na teoria, a saber: internalidade e externalidade, aparecendo a escala de externalidade, com 18 itens, bem estruturada (alfa = 0.81 e a de internalidade, com 10 itens, deixando a desejar no que se refere à consistência interna (alfa = 0.66. Com os dados desta pesquisa foi feita também análise do Locus de Controle desses mesmos empregados. A constatação mais saliente foi a de que o nível de internalidade caiu com o aumento do nível escolar e o aumento da experiência profissional desses mesmos empregados. Estes resultados surpreendentes foram interpretados em termos da situação típica da empresa, que está passando por um período de transição, a saber: a passagem da condição de empresa estatal para empresa privada, o que seria motivo da perda de confiança dos empregados na própria competência, particularmente por parte daqueles com maior competência intelectual e maior experiência profissional. Fez-se igualmente reparos na qualidade psicométrica da escala e da própria teoria do Locus de controle, no sentido de que esta precisa ser melhor axiomatizada para possibilitar a elaboração de escalas mais precisas para a medida dos construtos que propõe.A scale with 28 items, the Organizational Locus of Control (ELCO, was built based on Rotter’s theory and Levenson’s scale. ELCO was validated on a sample of 350 employees of Telebrás, a governmental firm in Brazil. As foreseen from the theory, a principal-axis factoring showed the presence of the expected two factors, namely internal and external locus of control. The external locus of control factor, composed of 18 items, showed good internal consistency (alpha =.81 whereas the internal factor, with 10 items

  12. Isolation of a Second S-Locus-Related Cdna from Brassica Oleracea: Genetic Relationships between the S Locus and Two Related Loci

    Boyes, D. C.; Chen, C. H.; Tantikanjana, T.; Esch, J. J.; Nasrallah, J B

    1991-01-01

    Self-incompatibility in Brassica oleracea is controlled by the highly polymorphic S locus. Isolation and subsequent characterization of the S-locus-glycoprotein (SLG) gene, which encodes the S-locus-specific glycoprotein (SLSG), has revealed the presence of a self-incompatibility multigene family. One of these S-locus-related genes, SLR1, has been shown to be expressed. In this study we present the isolation and preliminary characterization of a second expressed S-locus-related sequence, SLR2...

  13. A More Accurate Fourier Transform

    Courtney, Elya

    2015-01-01

    Fourier transform methods are used to analyze functions and data sets to provide frequencies, amplitudes, and phases of underlying oscillatory components. Fast Fourier transform (FFT) methods offer speed advantages over evaluation of explicit integrals (EI) that define Fourier transforms. This paper compares frequency, amplitude, and phase accuracy of the two methods for well resolved peaks over a wide array of data sets including cosine series with and without random noise and a variety of physical data sets, including atmospheric $\\mathrm{CO_2}$ concentrations, tides, temperatures, sound waveforms, and atomic spectra. The FFT uses MIT's FFTW3 library. The EI method uses the rectangle method to compute the areas under the curve via complex math. Results support the hypothesis that EI methods are more accurate than FFT methods. Errors range from 5 to 10 times higher when determining peak frequency by FFT, 1.4 to 60 times higher for peak amplitude, and 6 to 10 times higher for phase under a peak. The ability t...

  14. The flamenco locus controls the gypsy and ZAM retroviruses and is required for Drosophila oogenesis.

    Mével-Ninio, Maryvonne; Pelisson, Alain; Kinder, Jennifer; Campos, Ana Regina; Bucheton, Alain

    2007-04-01

    In Drosophila, the as yet uncloned heterochromatic locus flamenco (flam) controls mobilization of the endogenous retrovirus gypsy through the repeat-associated small interfering (rasi) RNA silencing pathway. Restrictive alleles (flamR) downregulate accumulation of gypsy transcripts in the somatic follicular epithelium of the ovary. In contrast, permissive alleles (flamP) are unable to repress gypsy. DIP1, the closest transcription unit to a flam-insertional mutation, was considered as a good candidate to be a gypsy regulator, since it encodes a dsRNA-binding protein. To further characterize the locus we analyzed P-induced flam mutants and generated new mutations by transposon mobilization. We show that flam is required somatically for morphogenesis of the follicular epithelium, the tissue where gypsy is repressed. This developmental activity is necessary to control gypsy and another retroelement, ZAM. We also show that flam is not DIP1, as none of the new permissive mutants affect the DIP1 coding sequence. In addition, two deletions removing DIP1 coding sequences do not affect any of the flamenco functions. Our results suggest that flamenco extends proximally to DIP1, spanning >130 kb of transposon-rich heterochromatin. We propose a model explaining the multiple functions of this large heterochromatic locus. PMID:17277359

  15. Molecular analysis of intragenic recombination at the tryptophan synthetase locus in Neurospora crassa

    A. Wiest; D. Barchers; M. Eaton; R. Henderson; R. Schnittker; K. Mccluskey

    2013-12-01

    Fifteen different classically generated and mapped mutations at the tryptophan synthetase locus in Neurospora crassa have been characterized to the level of the primary sequence of the gene. This sequence analysis has demonstrated that intragenic recombination is accurate to order mutations within one open reading frame. While classic genetic analysis correctly ordered the mutations, the position of mutations characterized by gene sequence analysis was more accurate. A leaky mutation was found to have a wild-type primary sequence. The presence of unique polymorphisms in the primary sequence of the trp-3 gene from strain 861 confirms that it has a unique history relative to the other strains studied. Most strains that were previously shown to be immunologically nonreactive with antibody preparations raised against tryptophan synthetase protein were shown to have nonsense mutations. This work defines 14 alleles of the N. crassa trp-3 gene.

  16. Low Cost Upper Atmosphere Sounder (LOCUS)

    Gerber, Daniel; Swinyard, Bruce M.; Ellison, Brian N.; Aylward, Alan D.; Aruliah, Anasuya; Plane, John M. C.; Feng, Wuhu; Saunders, Christopher; Friend, Jonathan; Bird, Rachel; Linfield, Edmund H.; Davies, A. Giles; Parkes, Steve

    2014-05-01

    near future. We describe the current instrument configuration of LOCUS, and give a first preview of the expected science return such a mission would yield. The LOCUS instrument concept calls for four spectral bands, a first band at 4.7 THz to target atomic oxygen (O), a second band at 3.5 THz to target hydroxyl (OH), a third band at 1.1 THz to cover several diatomic species (NO, CO, O3, H2O) and finally a fourth band at 0.8 THz to retrieve pointing information from molecular oxygen (O2). LOCUS would be the first satellite instrument to measure atomic oxygen on a global scale with a precision that will allow the retrieval of the global O distribution. It would also be the first time that annual and diurnal changes in O are measured. This will be a significant step forward in understanding the chemistry and dynamics of the MLT. Current indications (derived from CRISTA measurement) lead us to believe that current models only give a poor representation of upper atmospheric O. The secondary target species can help us to address additional scientific questions related to both Climate (distribution of climate relevant gases, highly geared cooling of the MLT in response to Climate change, increased occurrence of Polar Mesospheric Clouds (PMC), etc) and Space Weather (precipitation of electrically charged particles and impact on NOx chemistry, fluctuations of solar Lyman-alpha flux through shown in the the distribution of photochemically active species, etc).

  17. Epigenetic regulation of individual modules of the immunoglobulin heavy chain locus 3’ regulatory region (3’ RR

    Barbara K Birshtein

    2014-04-01

    Full Text Available The Igh locus undergoes an amazing array of DNA rearrangements and modifications during B cell development. During early stages, the variable region gene is constructed from constituent variable (V, diversity (D and joining (J segments (VDJ joining. B cells that successfully express an antibody can be activated, leading to somatic hypermutation (SHM focused on the variable region, and class switch recombination (CSR, which substitutes downstream constant region genes for the originally used Cμ constant region gene. Many investigators, ourselves included, have sought to understand how these processes specifically target the Igh locus and avoid other loci and potential deleterious consequences of malignant transformation. Our laboratory has concentrated on a complex regulatory region (RR that is located downstream of Cα, the most 3’ of the Igh constant region genes. The ~40 kb 3’ RR, which is predicted to serve as a downstream major regulator of the Igh locus, contains two distinct segments: an ~28 kb region of four enhancers and an adjacent ~12 kb region containing multiple CTCF and Pax5 binding sites. Analysis of targeted mutations in mice by a number of investigators has concluded that the entire 3’ RR enhancer region is essential for SHM and CSR (but not for VDJ joining and for high levels of expression of multiple isotypes. The CTCF/Pax5 binding region is a candidate for influencing VDJ joining early in B cell development and serving as a potential insulator of the Igh locus. Components of the 3’ RR are subject to a variety of epigenetic changes during B cell development, i.e., DNAse I hypersensitivity, histone modifications and DNA methylation, in association with transcription factor binding. We propose that these changes provide a foundation by which regulatory elements in modules of the 3’ RR function by interacting with each other and with target sequences of the Igh locus.

  18. Viral Load and a Locus on Chromosome 11 Affect the Late Clinical Disease Caused by Theiler’s Virus

    Aubagnac, Stéphanie; Brahic, Michel; Bureau, Jean-François

    1999-01-01

    Theiler’s virus causes a persistent infection and a demyelinating disease of mice which is a model for multiple sclerosis. Susceptibility to viral persistence maps to several loci, including the interferon gamma locus. Inactivating the gene coding for the interferon gamma receptor makes 129/Sv mice susceptible to persistent infection and clinical disease, whereas inactivating the interferon gamma gene makes C57BL/6 mice susceptible to persistent infection but not to clinical disease. This dif...

  19. Developmental endothelial locus-1 (Del-1) is a homeostatic factor in the central nervous system limiting neuroinflammation and demyelination

    Choi, E.Y.; Lim, J-H; Neuwirth, A.; Economopoulou, M; Chatzigeorgiou, A; Chung, K-J; Bittner, S.; Lee, S-H; Langer, H; Samus, M; Kim, H.; Cho, G-S; Ziemssen, T; Bdeir, K; Chavakis, E

    2014-01-01

    Inflammation in the central nervous system (CNS) and disruption of its immune privilege are major contributors to the pathogenesis of multiple sclerosis (MS) and of its rodent counterpart, experimental autoimmune encephalomyelitis (EAE). We have previously identified developmental endothelial locus-1 (Del-1) as an endogenous anti-inflammatory factor, which inhibits integrin-dependent leukocyte adhesion. Here we show that Del-1 contributes to the immune privilege status of the CNS. Intriguingl...

  20. Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology

    Shi-Bo Wang; Jian-Ying Feng; Wen-Long Ren; Bo Huang; Ling Zhou; Yang-Jun Wen; Jin Zhang; Jim M Dunwell; Shizhong Xu; Yuan-Ming Zhang

    2016-01-01

    Genome-wide association studies (GWAS) have been widely used in genetic dissection of complex traits. However, common methods are all based on a fixed-SNP-effect mixed linear model (MLM) and single marker analysis, such as efficient mixed model analysis (EMMA). These methods require Bonferroni correction for multiple tests, which often is too conservative when the number of markers is extremely large. To address this concern, we proposed a random-SNP-effect MLM (RMLM) and a multi-locus RMLM (...

  1. Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data

    Goddard Mike E

    2004-05-01

    Full Text Available Abstract A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.

  2. 38 CFR 4.46 - Accurate measurement.

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  3. Relationship among Dimensions of Family Communication Patterns and Locus of

    Mohammad Hassan Anvari

    2014-05-01

    Full Text Available Background: This study was done to examine the relationship of self-efficacy with dimensions of family communication patterns and locus of control. Materials and Methods: The population of this study was all Isfahan University students in the 2010-2011 academic years. Two hundred seventy nine students from various faculties of the university selected by cluster sampling method. In this descriptive study were used from the revised scale of dimensions of family communication patterns, locus of control questionnaire and general self-efficacy scale. Results: Results showed that the dialogue orientation, locus of control and conformity orientation have a significant correlation with self-efficacy (p<0.01. In addition dialogue orientation, locus of control and conformity orientation predicted 13%, 7%, 2% of selfefficacy, respectively. Conclusion: Dialogue orientation in family is the most important predictor of students' self-efficacy.

  4. Familial migraine: Exclusion of the susceptibility gene from the reported locus of familial hemiplegic migraine on 19p

    Hovatta, I.; Peltonen, L. [National Public Health Institute, Helsinki (Finland); Kallela, M.; Faerkkilae, M. [Helsinki Univ. Central Hospital (Finland)

    1994-10-01

    Genetic isolates are highly useful in analyses of the molecular background of complex diseases since the enrichment of a limited number of predisposing genes can be predicted in representative families or in specific geographical regions. It has been suggested that the pathophysiology and etiology of familial hemiplegic migraine (FHM) and typical migraine with aura are most probably the same. Recent assignment of FHM locus to chromosome 19p in two French families makes it now possible to test this hypothesis. We report here linkage data on four families with multiple cases of migraine disorder originating from the genetically isolated population of Finland. We were interested to discover whether the migraine in these families would also show linkage to the markers on 19p. We could exclude a region of 50 cM, flanking the reported FHM locus, as a site of migraine locus in our four families. It seems evident that locus heterogeneity exists between different diagnostic classes of migraine spectrum of diseases and also between different ethnic groups. 10 refs., 2 figs., 1 tab.

  5. Epigenetic history of an Arabidopsis trans-silencer locus and a test for relay of trans-silencing activity

    von Arnim Albrecht G

    2002-12-01

    Full Text Available Abstract Background Meiotically heritable epimutations affecting transgene expression are not well understood, even and in particular in the plant model species, Arabidopsis thaliana. The Arabidopsis trans-silencer locus, C73, which encodes a fusion protein between the repressor of photomorphogenesis, COP1, and green fluorescent protein (GFP-COP1, heritably modifies the expression pattern and cop1-like cosuppression phenotypes of multiple GFP-COP1 target loci by transcriptional gene silencing. Results Here we describe three additional features of trans-silencing by the C73 locus. First, the silencing phenotype of C73 and of similar complex loci was acquired epigenetically over the course of no more than two plant generations via a stage resembling posttranscriptional silencing. Second, imprints imposed by the C73 locus were maintained heritably for at least five generations in the absence of the silencer with only sporadic spontaneous reversion. Third, the pairing of two other GFP-COP1 transgene loci, L91 and E82, showed an increased tendency for epigenetic modification when L91 carried an epigenetic imprint from C73, but not when E82 bore the imprint. Conclusions The latter data suggest a transfer of trans-silencing activity from one transgene locus, C73, to another, namely L91. These results extend our operational understanding of interactions among transgenes in Arabidopsis.

  6. Genetics of Serum Resistance in Neisseria gonorrhoeae: The sac-1 Genetic Locus

    Cannon, Janne G.; Lee, Terrence J.; Guymon, Lawrence F.; Sparling, P. Frederick

    1981-01-01

    A genetic locus affecting susceptibility to the bactericidal activity of normal human serum has been designated sac-1. This locus was shown to be closely linked to, but not identical with, a second locus (designated nmp-2) that affects protein 1 of the outer membrane. The sac-1 locus could be linked to known antibiotic resistance markers on the gonococcal chromosome by genetic transformation.

  7. Genetic and physical mapping of the mouse Ulnaless locus

    Peichel, C. L.; Abbott, C M; Vogt, T F

    1996-01-01

    The mouse Ulnaless locus is a semidominant mutation which displays defects in patterning along the proximal-distal and anterior-posterior axes of all four limbs. The first Ulnaless homozygotes have been generated, and they display a similar, though slightly more severe, limb phenotype than the heterozygotes. To create a refined genetic map of the Ulnaless region using molecular markers, four backcrosses segregating Ulnaless were established. A 0.4-cM interval containing the Ulnaless locus has...

  8. Characterization of the spv Locus in Salmonella enterica Serovar Arizona

    Libby, Stephen J.; Lesnick, Marc; Hasegawa, Patricia; Kurth, Michael; Belcher, Christopher; Fierer, Joshua; Guiney, Donald G.

    2002-01-01

    Salmonella enterica serovar Arizona (S. enterica subspecies IIIa) is a common Salmonella isolate from reptiles and can cause serious systemic disease in humans. The spv virulence locus, found on large plasmids in Salmonella subspecies I serovars associated with severe infections, was confirmed to be located on the chromosome of serovar Arizona. Sequence analysis revealed that the serovar Arizona spv locus contains homologues of spvRABC but lacks the spvD gene and contains a frameshift in spvA...

  9. Identification of Potentially Pathogenic Variants in the Posterior Polymorphous Corneal Dystrophy 1 Locus

    Le, Derek J.; Chung, Duk-Won D.; Frausto, Ricardo F.; Kim, Michelle J.; Aldave, Anthony J.

    2016-01-01

    Posterior polymorphous corneal dystrophy 1 (PPCD1) is a genetic disorder that affects corneal endothelial cell function and leads to loss of visual acuity. PPCD1 has been linked to a locus on chromosome 20 in multiple families; however, Sanger sequencing of protein-coding genes in the consensus region failed to identify any causative missense mutations. In this study, custom capture probes were utilized for targeted next-generation sequencing of the linked region in a previously reported family with PPCD1. Variants were detected through two bioinformatics pipelines and filtered according to multiple criteria. Additionally, a high-resolution microarray was used to detect copy number variations. No non-synonymous variants in the protein-coding region of annotated genes were identified. However, 12 single nucleotide variants in 10 genes, and 9 indels in 7 genes met the filtering criteria and were considered candidate variants for PPCD1. Eleven single nucleotide variants were confirmed by Sanger sequencing, including 2 synonymous variants and 9 non-coding variants, in 9 genes. One microdeletion was detected in an intron of OVOL2 by microarray but was subsequently not identified by PCR. Using a comprehensive next-generation sequencing approach, a total of 16 genes containing single nucleotide variants or indels that segregated with the affected phenotype in an affected family previously mapped to the PPCD1 locus were identified. Screening of these candidate genes in other families previously mapped to the PPCD1 locus will likely result in the identification of the genetic basis of PPCD1. PMID:27355326

  10. [Health locus of control of patients in disease management programmes].

    Schnee, M; Grikscheit, F

    2013-06-01

    Health locus of control beliefs plays a major role in improving self-management skills of the chronically ill - a main goal in disease management programmes (DMP). This study aims at characterising participants in disease management regarding their health locus of control. Data are based on 4 cross-sectional postal surveys between spring and autumn of 2006 and 2007 within the Health Care Monitor of the Bertelsmann Foundation. Among the 6 285 respondents, 1 266 are chronically ill and not enrolled in a DMP and 327 are participating in a DMP. A high internal locus of control (HLC) occurs significantly less often in DMP patients than in normal chronically ill patients (and healthy people) controlling for age, gender and social class. With increasing age, a high internal locus of control is also significantly less likely. When comparing healthy people, the chronically ill and the DMP participants a social gradient of a high internal locus of control belief can be observed. The weaker internal and higher doctor-related external locus of control of DMP participants should be carefully observed by the physician when trying to strengthen the patients' self-management skills. Evaluators of DMP should take into account the different baselines of DMP patients and relevant control groups and incorporate these differences into the evaluation. PMID:22864845

  11. Searching for a major locus for male pattern baldness (MPB)

    Anker, R.; Eisen, A.Z.; Donis-Keller, H. [Washington Univ. School of Medicine, St. Louis, MO (United States)

    1994-09-01

    Male pattern baldness (MPB) is a common trait in post-pubertal males. Approximately 50% of adult males present some degree of MPB by age 50. According to the classification provided by Hamilton in 1951 and modified by Norwood in 1975, the trait itself is a continuum that ranges from mild (Type I) to severe (Type VII) cases. In addition, there is extensive variability for the age of onset. The role of androgens in allowing the expression of this trait in males has been well established. This phenotype is uncommonly expressed in females. The high prevalence of the trait, the distribution of MPB as a continuous trait, and several non-allelic mutations identified in the mouse capable of affecting hair pattern, suggest that MPB is genetically heterogeneous. In order to reduce the probability of multiple non-allelic MPB genes within a pedigree, we selected 9 families in which MPB appears to segregate exclusively through the paternal lineage as compared to bilineal pedigrees. There are 32 males expressing this phenotype and females are treated as phenotype unknown. In general, affected individuals expressed the trait before 30 years of age with a severity of at least Type III or IV. We assumed an autosomal dominant model, with a gene frequency of 1/20 for the affected allele, and 90% penetrance. Simulation studies using the SLINK program with these pedigrees showed that these families would be sufficient to detect linkage under the assumption of a single major locus. If heterogeneity is present, the current resource does not have sufficient power to detect linkage at a statistically significant level, although candidate regions of the genome could be identified for further studies with additional pedigrees. Using 53 highly informative microsatellite markers, and a subset of 7 families, we have screened 30% of the genome. This search included several regions where candidate genes for MPB are located.

  12. Linkage disequilibrium between an allele at the dopamine D4 receptor locus and Tourette syndrome, by the transmission-disequilibrium test.

    Grice, D. E.; Leckman, J. F.; Pauls, D L; Kurlan, R.; Kidd, K K; Pakstis, A.J.; Chang, F. M.; Buxbaum, J. D.; Cohen, D. J.; Gelernter, J.

    1996-01-01

    Dopaminergic abnormalities are implicated in the pathogenesis of Tourette syndrome (TS) and chronic multiple tics. We used the transmission-disequilibrium test (TDT) method to test for linkage disequilibrium between a specific allele (the seven-repeat allele (DRD4*7R) of the exon 3 VNTR polymorphic site) at the D4 dopamine receptor locus (DRD4) and expression of chronic multiple tics and TS. This particular allele had been shown in functional studies to have different binding properties compa...

  13. Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation.

    Kamm, John A; Spence, Jeffrey P; Chan, Jeffrey; Song, Yun S

    2016-07-01

    Two-locus sampling probabilities have played a central role in devising an efficient composite-likelihood method for estimating fine-scale recombination rates. Due to mathematical and computational challenges, these sampling probabilities are typically computed under the unrealistic assumption of a constant population size, and simulation studies have shown that resulting recombination rate estimates can be severely biased in certain cases of historical population size changes. To alleviate this problem, we develop here new methods to compute the sampling probability for variable population size functions that are piecewise constant. Our main theoretical result, implemented in a new software package called LDpop, is a novel formula for the sampling probability that can be evaluated by numerically exponentiating a large but sparse matrix. This formula can handle moderate sample sizes ([Formula: see text]) and demographic size histories with a large number of epochs ([Formula: see text]). In addition, LDpop implements an approximate formula for the sampling probability that is reasonably accurate and scales to hundreds in sample size ([Formula: see text]). Finally, LDpop includes an importance sampler for the posterior distribution of two-locus genealogies, based on a new result for the optimal proposal distribution in the variable-size setting. Using our methods, we study how a sharp population bottleneck followed by rapid growth affects the correlation between partially linked sites. Then, through an extensive simulation study, we show that accounting for population size changes under such a demographic model leads to substantial improvements in fine-scale recombination rate estimation. PMID:27182948

  14. Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19

    Ferrell Robert E

    2011-01-01

    Full Text Available Abstract Background Abdominal aortic aneurysm (AAA is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM database. Methods Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. Single marker and haplotype analyses were performed. Three genes (CEBPG, PEPD and CD22 were selected for DNA sequencing based on the association study results, and exonic regions were analyzed. Immunohistochemical staining of aortic tissue sections from AAA and control individuals was carried out for the CD22 and PEPD proteins with specific antibodies. Results Several SNPs were nominally associated with AAA (p CEBPG, peptidase D (PEPD, and CD22. Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus. DNA sequencing of the coding regions revealed no variation in CEBPG. Seven sequence variants were identified in PEPD, including three not present in the NCBI SNP (dbSNP database. Sequencing of all 14 exons of CD22 identified 20 sequence variants, five of which were in the coding region and six were in the 3'-untranslated region. Five variants were not present in dbSNP. Immunohistochemical staining for CD22 revealed protein expression in lymphocytes present in the aneurysmal aortic wall only and no detectable expression in control aorta. PEPD protein was expressed in fibroblasts and myofibroblasts in the media-adventitia border in both aneurysmal and non-aneurysmal tissue samples. Conclusions Association testing

  15. Mutation at the Human D1S80 Minisatellite Locus

    Kuppareddi Balamurugan

    2012-01-01

    Full Text Available Little is known about the general biology of minisatellites. The purpose of this study is to examine repeat mutations from the D1S80 minisatellite locus by sequence analysis to elucidate the mutational process at this locus. This is a highly polymorphic minisatellite locus, located in the subtelomeric region of chromosome 1. We have analyzed 90,000 human germline transmission events and found seven (7 mutations at this locus. The D1S80 alleles of the parentage trio, the child, mother, and the alleged father were sequenced and the origin of the mutation was determined. Using American Association of Blood Banks (AABB guidelines, we found a male mutation rate of 1.04×10-4 and a female mutation rate of 5.18×10-5 with an overall mutation rate of approximately 7.77×10-5. Also, in this study, we found that the identified mutations are in close proximity to the center of the repeat array rather than at the ends of the repeat array. Several studies have examined the mutational mechanisms of the minisatellites according to infinite allele model (IAM and the one-step stepwise mutation model (SMM. In this study, we found that this locus fits into the one-step mutation model (SMM mechanism in six out of seven instances similar to STR loci.

  16. Accurate pose estimation using single marker single camera calibration system

    Pati, Sarthak; Erat, Okan; Wang, Lejing; Weidert, Simon; Euler, Ekkehard; Navab, Nassir; Fallavollita, Pascal

    2013-03-01

    Visual marker based tracking is one of the most widely used tracking techniques in Augmented Reality (AR) applications. Generally, multiple square markers are needed to perform robust and accurate tracking. Various marker based methods for calibrating relative marker poses have already been proposed. However, the calibration accuracy of these methods relies on the order of the image sequence and pre-evaluation of pose-estimation errors, making the method offline. Several studies have shown that the accuracy of pose estimation for an individual square marker depends on camera distance and viewing angle. We propose a method to accurately model the error in the estimated pose and translation of a camera using a single marker via an online method based on the Scaled Unscented Transform (SUT). Thus, the pose estimation for each marker can be estimated with highly accurate calibration results independent of the order of image sequences compared to cases when this knowledge is not used. This removes the need for having multiple markers and an offline estimation system to calculate camera pose in an AR application.

  17. Genomic organization and sequence dynamics of the AvrPiz-t locus in Magnaporthe oryzae

    Ping LI; Bin BAI; Hong-yan ZHANG; Heng ZHOU; Bo ZHOU

    2012-01-01

    Plants utilize multiple layers of defense mechanisms to fight against the invasion of diverse pathogens.The R gene mediates resistance,in most cases,dependent on the co-existence of its cognate pathogen-derived avirulence (Avr) gene.The rice blast R gene Piz-t corresponds in gene-for-gene fashion to the Magnaporthe oryzae Avrgene AvrPiz-t.In this study,we determined and compared the genomic sequences surrounding the AvrPiz-t gene in both avirulent and virulent isolates,designating as AvrPiz-t-ZB15 and avrPiz-t-70-15 regions,respectively.The sequence of the AvrPiz-t-ZB15 region is 120966 bp whereas avrPiz-t-70-15 is 146292 bp in length.The extreme sequence similarity and good synteny in gene order and content along with the absence of two predicted genes in the avrPiz-t-70-15 region were observed in the predicted protein-coding regions in the AvrPiz-t locus.Nevertheless,frequent presence/absence and highly dynamic organization of transposable elements (TEs) were identified,representing the major variation of the AvrPiz-t locus between different isolates.Moreover,TEs constitute 27.3% and 43.2%of the genomic contents of the AvrPiz-t-ZB15 and avrPiz-t-70-15 regions,respectively,indicating that TEs contribute largely to the organization and evolution of AvrPiz-t locus.The findings of this study suggest that M.oryzae could benefit in an evolutionary sense from the presence of active TEs in genes conferring avirulence and provide an ability to rapidly change and thus to overcome host R genes.

  18. Analysis of the ABCA4 genomic locus in Stargardt disease

    Zernant, Jana; Xie, Yajing Angela; Ayuso, Carmen;

    2014-01-01

    was designed to find the missing disease-causing ABCA4 variation by a combination of next-generation sequencing (NGS), array-Comparative Genome Hybridization (aCGH) screening, familial segregation and in silico analyses. The entire 140 kb ABCA4 genomic locus was sequenced in 114 STGD patients with one...... once. Multimodal analysis suggested 12 new likely pathogenic intronic ABCA4 variants, some of which were specific to (isolated) ethnic groups. No copy number variation (large deletions and insertions) was detected in any patient suggesting that it is a very rare event in the ABCA4 locus. Many variants...... were excluded since they were not conserved in non-human primates, were frequent in African populations and, therefore, represented ancestral, and not disease-associated, variants. The sequence variability in the ABCA4 locus is extensive and the non-coding sequences do not harbor frequent mutations in...

  19. The Accuracy of Multiples

    Stauropoulos Antonios

    2011-01-01

    Full Text Available Problem statement: Equity valuation with the use of multiples is widely used by academics and practitioners concerning its functionality. This study aims to explore the sensitivity of three multiples in terms of accuracy. Approach: Price-to-Sales (P/S multiple, the price-to-book value of equity (P/B multiple and the Price-to-Earnings (P/E multiple are three multiples under consideration, using both current and one-year-ahead earnings forecasts. Results: Evidence of empirical results show that, the multiples P/mdfy1 and P/mnfy1 are effective in terms of accuracy, with their means being negatively biased and their medians being positively biased. Finally, current earnings are identified as more appropriate value driver for the calculation of the P/E ratio by terms of accuracy. The results can be considered as reliable owing to the large sample and the procedure followed for its selection. Conclusion: This study offers a better understanding of the valuation approach through the use of multiples, in order analysts assumption to be more carefully and properly chosen and their results to be more accurately produced.

  20. Demographic Profiling of the Locus of Control of Employees

    Keith C. D’souza; Agarwal, Upasna A.; Usha Chavali

    2013-01-01

    This study examines variations in employees’ locus of control (LOC) across the demographic variables of gender, educational background and respondents’ age. The study is based on data collected from 565 employees, using an adapted version of the Rotter Internal–External Locus of Control Scale. Based on a survey of literature, three hypotheses were formulated relating the demographic variables of gender, educational background and age with LOC. The results of this study yielded evidence ...

  1. Multiple Perspectives / Multiple Readings

    Simon Biggs

    2005-01-01

    Full Text Available People experience things from their own physical point of view. What they see is usually a function of where they are and what physical attitude they adopt relative to the subject. With augmented vision (periscopes, mirrors, remote cameras, etc we are able to see things from places where we are not present. With time-shifting technologies, such as the video recorder, we can also see things from the past; a time and a place we may never have visited.In recent artistic work I have been exploring the implications of digital technology, interactivity and internet connectivity that allow people to not so much space/time-shift their visual experience of things but rather see what happens when everybody is simultaneously able to see what everybody else can see. This is extrapolated through the remote networking of sites that are actual installation spaces; where the physical movements of viewers in the space generate multiple perspectives, linked to other similar sites at remote locations or to other viewers entering the shared data-space through a web based version of the work.This text explores the processes involved in such a practice and reflects on related questions regarding the non-singularity of being and the sense of self as linked to time and place.

  2. History of the discovery of a master locus producing piRNAs: the flamenco/COM locus in Drosophila melanogaster.

    Goriaux, Coline; Théron, Emmanuelle; Brasset, Emilie; Vaury, Chantal

    2014-01-01

    The discovery of transposable elements (TEs) in the 1950s by B. McClintock implied the existence of cellular regulatory systems controlling TE activity. The discovery of flamenco (flam) an heterochromatic locus from Drosophila melanogaster and its ability to survey several TEs such as gypsy, ZAM, and Idefix contributed to peer deeply into the mechanisms of the genetic and epigenetic regulation of TEs. flam was the first cluster producing small RNAs to be discovered long before RNAi pathways were identified in 1998. As a result of the detailed genetic analyses performed by certain laboratories and of the sophisticated genetic tools they developed, this locus has played a major role in our understanding of piRNA mediated TE repression in animals. Here we review the first discovery of this locus and retrace decades of studies that led to our current understanding of the relationship between genomes and their TE targets. PMID:25136352

  3. History of the discovery of a master locus producing piRNAs: the flamenco/COM locus in Drosophila melanogaster

    Coline eGoriaux

    2014-08-01

    Full Text Available The discovery of transposable elements (TEs in the 1950s by B. McClintock implied the existence of cellular regulatory systems controlling TE activity. The discovery of flam an heterochromatic locus from Drosophila melanogaster and its ability to survey several TEs such as gypsy, ZAM and Idefix contributed to peer deeply into the mechanisms of the genetic and epigenetic regulation of TEs. flam was the first cluster producing small RNAs to be discovered long before RNAi pathways were identified in 1998. As a result of the detailed genetic analyses performed by certain laboratories and of the sophisticated genetic tools they developed, this locus has played a major role in our understanding of piRNA mediated TE repression in animals. Here we review the first discovery of this locus and retrace decades of studies that led to our current understanding of the relationship between genomes and their TE targets.

  4. SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

    Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David

    2016-01-01

    We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427

  5. Global genetic architecture of an erythroid quantitative trait locus, HMIP-2.

    Menzel, Stephan; Rooks, Helen; Zelenika, Diana; Mtatiro, Siana N; Gnanakulasekaran, Akshala; Drasar, Emma; Cox, Sharon; Liu, Li; Masood, Mariam; Silver, Nicholas; Garner, Chad; Vasavda, Nisha; Howard, Jo; Makani, Julie; Adekile, Adekunle; Pace, Betty; Spector, Tim; Farrall, Martin; Lathrop, Mark; Thein, Swee Lay

    2014-11-01

    HMIP-2 is a human quantitative trait locus affecting peripheral numbers, size and hemoglobin composition of red blood cells, with a marked effect on the persistence of the fetal form of hemoglobin, HbF, in adults. The locus consists of multiple common variants in an enhancer region for MYB (chr 6q23.3), which encodes the hematopoietic transcription factor cMYB. Studying a European population cohort and four African-descended groups of patients with sickle cell anemia, we found that all share a set of two spatially separate HbF-promoting alleles at HMIP-2, termed "A" and "B." These typically occurred together ("A-B") on European chromosomes, but existed on separate homologous chromosomes in Africans. Using haplotype signatures for "A" and "B," we interrogated public population datasets. Haplotypes carrying only "A" or "B" were typical for populations in Sub-Saharan Africa. The "A-B" combination was frequent in European, Asian, and Amerindian populations. Both alleles were infrequent in tropical regions, possibly undergoing negative selection by geographical factors, as has been reported for malaria with other hematological traits. We propose that the ascertainment of worldwide distribution patterns for common, HbF-promoting alleles can aid their further genetic characterization, including the investigation of gene-environment interaction during human migration and adaptation. PMID:25069958

  6. SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees.

    Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David

    2016-03-01

    We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to species tree/gene tree discordance--and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427

  7. Clinical applications of self-esteem and locus of control to adolescent health.

    Giblin, P T; Poland, M L; Ager, J W

    1988-01-01

    Self-esteem and locus of control are two associated constructs representing, respectively, a generalized self-evaluation and an assessment of personal control. Measures representing these constructs generally rely on self-report. These measures have been applied to adolescent health as predictors and outcomes. Most studies rely on chi 3, t-test, and ANOVA analysis and report mixed results in attaining significant group comparisons on issues including contraceptive use, adolescent pregnancy, and substance abuse. Few studies employ multiple regression or discriminant function analysis assessing the relative influence or predictive accuracy and sensitivity of these measures. Studies using these analyses report limited or nonsignificant contributions of these measures to clinical issues (e.g., adolescent fatherhood, adolescent pregnancy, substance abuse, medical management) relative to variables such as patient age, social class, parental attitudes, and peer relationships. Our discussion of these results addresses the validity of self-reports of self-esteem and locus of control versus observation procedures assessing these constructs by verbal and nonverbal presentation of self, analytic procedures appropriate to clinical prediction of behavior by person and situation characteristics, and procedures to advance the clinical adoption of behavioral measures. PMID:3275604

  8. The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation.

    Bell, Charles C; Amaral, Paulo P; Kalsbeek, Anton; Magor, Graham W; Gillinder, Kevin R; Tangermann, Pierre; di Lisio, Lorena; Cheetham, Seth W; Gruhl, Franziska; Frith, Jessica; Tallack, Michael R; Ru, Ke-Lin; Crawford, Joanna; Mattick, John S; Dinger, Marcel E; Perkins, Andrew C

    2016-01-01

    Thousands of sense-antisense mRNA-lncRNA gene pairs occur in the mammalian genome. While there is usually little doubt about the function of the coding transcript, the function of the lncRNA partner is mostly untested. Here we examine the function of the homeotic Evx1-Evx1as gene locus. Expression is tightly co-regulated in posterior mesoderm of mouse embryos and in embryoid bodies. Expression of both genes is enhanced by BMP4 and WNT3A, and reduced by Activin. We generated a suite of deletions in the locus by CRISPR-Cas9 editing. We show EVX1 is a critical downstream effector of BMP4 and WNT3A with respect to patterning of posterior mesoderm. The lncRNA, Evx1as arises from alternative promoters and is difficult to fully abrogate by gene editing or siRNA approaches. Nevertheless, we were able to generate a large 2.6 kb deletion encompassing the shared promoter with Evx1 and multiple additional exons of Evx1as. This led to an identical dorsal-ventral patterning defect to that generated by micro-deletion in the DNA-binding domain of EVX1. Thus, Evx1as has no function independent of EVX1, and is therefore unlikely to act in trans. We predict many antisense lncRNAs have no specific trans function, possibly only regulating the linked coding genes in cis. PMID:27226347

  9. A review of control processes and their locus in language switching.

    Declerck, Mathieu; Philipp, Andrea M

    2015-12-01

    Language switching has been one of the main tasks to investigate language control, a process that restricts bilingual language processing to the target language. In the current review, we discuss the How (i.e., mechanisms) and Where (i.e., locus of these mechanisms) of language control in language switching. As regards the mechanisms of language control, we describe several empirical markers of language switching and their relation to inhibition, as a potentially important mechanism of language control. From this overview it becomes apparent that some, but not all, markers indicate the occurrence of inhibition during language switching and, thus, language control. In a second part, we turn to the potential locus of language control and the role of different processing stages (concept level, lemma level, phonology, orthography, and outside language processing). Previous studies provide evidence for the employment of several of these processing stages during language control so that either a complex control mechanism involving different processing stages and/or multiple loci of language control have to be assumed. Based on the discussed results, several established and new theoretical avenues are considered. PMID:25917142

  10. Rana grylio virus TK and DUT gene locus could be simultaneously used for foreign gene expression.

    Huang, Xing; Fang, Jin; Chen, Zhongyuan; Zhang, Qiya

    2016-03-01

    Ranaviruses (family Iridoviridae, genus Ranavirus) have been recognized as emerging infectious pathogens and caused a great loss to the global biodiversity. Thymidine kinase (TK) and deoxyuridine triphosphatase (dUTPase, DUT, encoded by ORF 67R) are ubiquitous, existing in iridoviruses and other organisms. Previous studies showed that TK and DUT could be individually knocked out without impeding viral replication. In this study, we tried to insert two fluorescence genes into the above loci. We started with Δ67R-RGV, a recently generated recombinant Rana grylio virus (RGV) with the whole DUT replaced by enhanced green fluorescence protein (EGFP) gene. Then, a red fluorescence protein (RFP) gene initiated by RGV immediate-early (IE) ICP18 gene promoter was inserted into TK locus through homologous recombination. A novel recombinant virus, ΔDUT, TK-RGV, was generated by nine successive rounds of plaque isolation using RFP selection. All of the plaques produced by this recombinant virus could emit both green and red fluorescence. Furthermore, one-step and multiple-step growth curves of ΔDUT, TK-RGV were similar to those of wt-RGV and Δ67R-RGV. In conclusion, a novel dual-fluorescence labeled recombinant iridovirus in which DUT and TK gene locus were simultaneously used for foreign gene expression was constructed. PMID:26806670

  11. A multi locus variable number of tandem repeat analysis (MLVA scheme for Streptococcus agalactiae genotyping

    Mereghetti Laurent

    2011-07-01

    Full Text Available Abstract Background Multilocus sequence typing (MLST is currently the reference method for genotyping Streptococcus agalactiae strains, the leading cause of infectious disease in newborns and a major cause of disease in immunocompromised children and adults. We describe here a genotyping method based on multiple locus variable number of tandem repeat (VNTR analysis (MLVA applied to a population of S. agalactiae strains of various origins characterized by MLST and serotyping. Results We studied a collection of 186 strains isolated from humans and cattle and three reference strains (A909, NEM316 and 2603 V/R. Among 34 VNTRs, 6 polymorphic VNTRs loci were selected for use in genotyping of the bacterial population. The MLVA profile consists of a series of allele numbers, corresponding to the number of repeats at each VNTR locus. 98 MLVA genotypes were obtained compared to 51 sequences types generated by MLST. The MLVA scheme generated clusters which corresponded well to the main clonal complexes obtained by MLST. However it provided a higher discriminatory power. The diversity index obtained with MLVA was 0.960 compared to 0.881 with MLST for this population of strains. Conclusions The MLVA scheme proposed here is a rapid, cheap and easy genotyping method generating results suitable for exchange and comparison between different laboratories and for the epidemiologic surveillance of S. agalactiae and analyses of outbreaks.

  12. Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution

    Ovcharenko, I; Loots, G; Giardine, B; Hou, M; Ma, J; Hardison, R; Stubbs, L; Miller, W

    2004-07-14

    Multiple sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the tba multi-aligner program for rapid identification of local sequence conservation and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short-and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multi-species comparisons of the GATA3 gene locus and the identification of elements that are conserved differently in avians than in other genomes allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://bio.cse.psu.edu/.

  13. Laboratory Building for Accurate Determination of Plutonium

    2008-01-01

    <正>The accurate determination of plutonium is one of the most important assay techniques of nuclear fuel, also the key of the chemical measurement transfer and the base of the nuclear material balance. An

  14. Heterotic trait locus (HTL mapping identifies intra-locus interactions that underlie reproductive hybrid vigor in Sorghum bicolor.

    Imri Ben-Israel

    Full Text Available Identifying intra-locus interactions underlying heterotic variation among whole-genome hybrids is a key to understanding mechanisms of heterosis and exploiting it for crop and livestock improvement. In this study, we present the development and first use of the heterotic trait locus (HTL mapping approach to associate specific intra-locus interactions with an overdominant heterotic mode of inheritance in a diallel population using Sorghum bicolor as the model. This method combines the advantages of ample genetic diversity and the possibility of studying non-additive inheritance. Furthermore, this design enables dissecting the latter to identify specific intra-locus interactions. We identified three HTLs (3.5% of loci tested with synergistic intra-locus effects on overdominant grain yield heterosis in 2 years of field trials. These loci account for 19.0% of the heterotic variation, including a significant interaction found between two of them. Moreover, analysis of one of these loci (hDPW4.1 in a consecutive F2 population confirmed a significant 21% increase in grain yield of heterozygous vs. homozygous plants in this locus. Notably, two of the three HTLs for grain yield are in synteny with previously reported overdominant quantitative trait loci for grain yield in maize. A mechanism for the reproductive heterosis found in this study is suggested, in which grain yield increase is achieved by releasing the compensatory tradeoffs between biomass and reproductive output, and between seed number and weight. These results highlight the power of analyzing a diverse set of inbreds and their hybrids for unraveling hitherto unknown allelic interactions mediating heterosis.

  15. Genome-wide association study identifies a single major locus contributing to survival into old age; the APOE locus revisited

    Deelen, Joris; Beekman, Marian; Uh, Hae-Won;

    2011-01-01

    By studying the loci which contribute to human longevity, we aim to identify mechanisms that contribute to healthy aging. To identify such loci, we performed a genome-wide association study (GWAS) comparing 403 unrelated nonagenarians from long-living families included in the Leiden Longevity Study...... nonagenarian cases from the LLS and their partners. In addition, we observed a novel association between this locus and serum levels of IGF-1 in females (P = 0.005). In conclusion, the major locus determining familial longevity up to high age as detected by GWAS was marked by rs2075650, which tags the...

  16. Metamemory in multiple sclerosis

    Claffey, Austin M

    2010-01-01

    This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University. The concept of metamemory proposes that supplementary to typically measured memory abilities, memory monitoring and control processes are used to optimise learning. Accurate memory monitoring appears to be underpinned by a range of cognitive, and possibly affective, contributions. In populations with these deficits, metamemory has been shown to be impaired. In Multiple Sclerosis (MS), only...

  17. Multiple Pregnancy

    ... Can multiple pregnancy affect my risk of postpartum depression? Having multiples might increase your risk of postpartum ... Membership For Journalists For Junior Fellows For Medical Students For Patients Contact Us Copyright Information Privacy Statement ...

  18. Multiple Myeloma

    Multiple myeloma is a cancer that begins in plasma cells, a type of white blood cell. These cells ... bones. No one knows the exact causes of multiple myeloma, but it is more common in older people ...

  19. Multiple Sclerosis

    Multiple sclerosis (MS) is a nervous system disease that affects your brain and spinal cord. It damages the ... attacks healthy cells in your body by mistake. Multiple sclerosis affects women more than men. It often begins ...

  20. Inferring relationships between pairs of individuals from locus heterozygosities

    Spinetti Isabella

    2002-11-01

    Full Text Available Abstract Background The traditional exact method for inferring relationships between individuals from genetic data is not easily applicable in all situations that may be encountered in several fields of applied genetics. This study describes an approach that gives affordable results and is easily applicable; it is based on the probabilities that two individuals share 0, 1 or both alleles at a locus identical by state. Results We show that these probabilities (zi depend on locus heterozygosity (H, and are scarcely affected by variation of the distribution of allele frequencies. This allows us to obtain empirical curves relating zi's to H for a series of common relationships, so that the likelihood ratio of a pair of relationships between any two individuals, given their genotypes at a locus, is a function of a single parameter, H. Application to large samples of mother-child and full-sib pairs shows that the statistical power of this method to infer the correct relationship is not much lower than the exact method. Analysis of a large database of STR data proves that locus heterozygosity does not vary significantly among Caucasian populations, apart from special cases, so that the likelihood ratio of the more common relationships between pairs of individuals may be obtained by looking at tabulated zi values. Conclusions A simple method is provided, which may be used by any scientist with the help of a calculator or a spreadsheet to compute the likelihood ratios of common alternative relationships between pairs of individuals.

  1. Should Farmers' Locus of Control Be Used in Extension?

    Nuthall, Peter L.

    2010-01-01

    To explore whether Farmers' Locus of Control (LOC) could be useful in agricultural extension programmes to improve managerial ability. This test records a farmer's belief in her/his control over production outcomes. A mail survey of 2300 New Zealand farmers was used to obtain a range of variables, and to measure their LOC using a question set…

  2. Job Satisfaction and Locus of Control in an Academic Setting

    Stachowiak, Bonni J.

    2010-01-01

    This study explored any relationships that existed between faculty members' locus of control and job satisfaction at a small, private, faith-based university. Two demographic variables were also analyzed in the findings: number of years teaching in higher education and tenure status. The job satisfaction instrument used was the Job in General…

  3. Significance Thresholds for Quantitative Trait Locus Mapping Under Selective Genotyping

    Manichaikul, Ani; Palmer, Abraham A.; Sen, Śaunak; Broman, Karl W.

    2007-01-01

    In the case of selective genotyping, the usual permutation test to establish statistical significance for quantitative trait locus (QTL) mapping can give inappropriate significance thresholds, especially when the phenotype distribution is skewed. A stratified permutation test should be used, with phenotypes shuffled separately within the genotyped and ungenotyped individuals.

  4. Social support, locus of control, and psychological well-being

    van der Zee, KI; Buunk, BP; Sanderman, R

    1997-01-01

    Social support seems to be positively related to psychological well-being. Studies have shown that individual differences exist in the ability to mobilize and use sources of support. The current study focused on locus of control as a personality factor that might be related to this ability, In 2 sam

  5. Locus of Control and Helplessness: Gender Differences among Bereaved Parents

    Rubinstein, Gidi

    2004-01-01

    This study investigated locus of control (LC) and hopelessness (H) among 25 pairs of bereaved parents, who lost their children in the Arab--Israeli conflict, and 25 pairs of demographically matched non-bereaved parents (mean age 53). Four of the 5 hypotheses were supported by results. LC was significantly more external and H was significantly…

  6. Alexandrov's Isodiametric Conjecture and the Cut Locus of a Surface

    Freitas, P.; Krejčiřík, David

    2015-01-01

    Roč. 67, č. 3 (2015), s. 405-417. ISSN 0040-8735 R&D Projects: GA ČR GAP203/11/0701 Institutional support: RVO:61389005 Keywords : Alexantrov's conjecture * convex surfaces * ellipsoids * cut locus * symmetrization Subject RIV: BE - Theoretical Physics Impact factor: 0.323, year: 2014

  7. Exploring Learner Autonomy: Language Learning Locus of Control in Multilinguals

    Peek, Ron

    2016-01-01

    By using data from an online language learning beliefs survey (n?=?841), defining language learning experience in terms of participants' multilingualism, and using a domain-specific language learning locus of control (LLLOC) instrument, this article examines whether more experienced language learners can also be seen as more autonomous language…

  8. Effects of "Status Sets" on Rotter's Locus of Control Scale

    Bailey, Kent G.; Davidson, Kay M.

    1978-01-01

    Subjects were given sets based on varying levels of social class to determine susceptibility of Internal-External Locus of Control Scale (I-E) scores to situationally induced frames of reference. College students (N=90) took the I-E scale twice. Present results are that the I-E scale may be subject to faking. (Author)

  9. Locus of Control of Reinforcement and Responsiveness to Social Influence.

    Doctor, Ronald M.; Marziani, A. William

    Rotter's (1966) "control of reinforcement" construct is a dimension of belief or expectancy about the locus of reinforcing consequences for behavior. A generalized disposition is represented which ascribes reinforcement contingencies to either "external" (and, hence, uncontrollable) factors or to "internal" sources in which case the individual…

  10. The Influence of Locus of Control on Student Financial Behavior

    Britt, Sonya; Cumbie, Julie A.; Bell, Mary M.

    2013-01-01

    Data on psychological influences of financial behaviors has not been well addressed in student populations, which is concerning given the high levels of general and financial stress experienced by college students. The findings of this study indicate that college students with an external locus of control exhibit the worst financial behaviors.…

  11. A New Locus Shaping Method of Quadric Aspheric Parts

    WANG Yuan-sheng; WANG He-yan; LU Gui-ying; CAI Li; PIAO Cheng-gao

    2005-01-01

    The original idea and shaping principle of locus shaping method for processing the aspheric optical parts are introduced, and the partial structure of the machine tool designed is described. The method has the advantage of high efficiency and low cost compared to the numerical control method. And it is proven that the method is feasible.

  12. Stable Base Locus Decompositions of Kontsevich Moduli Spaces

    Chen, Dawei; Coskun, Izzet

    2009-01-01

    In this paper, we determine the stable base locus decomposition of the Kontsevich moduli spaces of degree two and three stable maps to Grassmannians. This gives new examples of the decomposition for varieties with Picard rank three. We also discuss the birational models that correspond to the chambers in the decomposition.

  13. Generating clock signals for a cycle accurate, cycle reproducible FPGA based hardware accelerator

    Asaad, Sameth W.; Kapur, Mohit

    2016-01-05

    A method, system and computer program product are disclosed for generating clock signals for a cycle accurate FPGA based hardware accelerator used to simulate operations of a device-under-test (DUT). In one embodiment, the DUT includes multiple device clocks generating multiple device clock signals at multiple frequencies and at a defined frequency ratio; and the FPG hardware accelerator includes multiple accelerator clocks generating multiple accelerator clock signals to operate the FPGA hardware accelerator to simulate the operations of the DUT. In one embodiment, operations of the DUT are mapped to the FPGA hardware accelerator, and the accelerator clock signals are generated at multiple frequencies and at the defined frequency ratio of the frequencies of the multiple device clocks, to maintain cycle accuracy between the DUT and the FPGA hardware accelerator. In an embodiment, the FPGA hardware accelerator may be used to control the frequencies of the multiple device clocks.

  14. Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes

    Zhao Jun Shao; Eric Rivals; Na Zhao; Sovan Lek; Jianbo Chang; Patrick Berrebi

    2011-08-01

    The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align phylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121–96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69–10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types.

  15. Genetic Characterization of the Capsulation Locus of Haemophilus influenzae Serotype e▿

    Giufrè, Maria; Cardines, Rita; Mastrantonio, Paola; Cerquetti, Marina

    2010-01-01

    The capsulation (cap) locus of Haemophilus influenzae type e (Hie) was characterized and sequenced. No IS1016 element was found to flank the locus. The 18.2-kb locus included 14 open reading frames (ORFs), which were grouped into three functional regions. Eight new ORFs (named ecs1 to ecs8) were identified in the Hie capsule-specific region II.

  16. Development and Validation of the Health Locus of Control (HLC) Scale

    Wallston, Barbara Strudler; And Others

    1976-01-01

    The Health Locus of Control (HLC) Scale is an area-specific measure of expectancies regarding locus of control developed for prediction of health-related behavior. Two experiments show discriminant validity of the HLC in contrast with Rotter's Internal-External Locus of Control Scale. Normative data on the HLC are provided. (Author)

  17. Locus of Control, Television Viewing, and Eating Disorder Symptomatology in Young Females.

    Fouts, Gregory; Vaughan, Kimberley

    2002-01-01

    Assesses the effects of locus of control and television watching on eating disorder symptomatology in girls between the ages 10-17 years. Girls with an external locus of control had significantly greater eating disorder symptomatology. Girls who watched higher amounts of television and had an external locus of control had significantly greater…

  18. A gene locus for targeted ectopic gene integration in Zymoseptoria tritici ☆

    Kilaru, S.; Schuster, M; Latz, M.; S. Das Gupta; Steinberg, N.; Fones, H.; Gurr, S.J.; Talbot, N.J.; Steinberg, G.

    2015-01-01

    Highlights • We establish the sdi1 of Z. tritici locus for targeted integration of constructs as single copies. • Integration of constructs conveys carboxin resistance. • We provide a vector for integration of eGFP-expressing construct into the sdi1 locus. • Integration into sdi1 locus is not affecting virulence of Z. tritici.

  19. Locus of Control and Attitude toward Eating in a Female College Population.

    Groth-Marnat, Gary; Scumaker, Jack F.

    1988-01-01

    Investigated relationship between locus of control and attitude to food intake in 101 female college students. Results indicated that locus of control was unable to predict attitudes toward eating and fear of becoming overweight. Thesis that locus of control would be related to attitude toward food intake was not supported. (Author/NB)

  20. A STUDY OF LOCUS OF CONTROL AND SELF ESTEEM AMONG BOYS AND GIRLS COLLEGE STUDENTS

    Thale Arti Subhashrao

    2014-01-01

    Objective of the study was to search locus of control and self esteem among boys and girls college students. Hypothesis: Boys college students will be high Locus of Control (External Locus of Control) than girls' college's students. Second hypothesis: there will be significant difference between boys and girls college students on dimension self esteem.

  1. Reframing Student Affairs Leadership: An Analysis of Organizational Frames of Reference and Locus of Control

    Tull, Ashley; Freeman, Jerrid P.

    2011-01-01

    Examined in this study were the identified frames of reference and locus of control used by 478 student affairs administrators. Administrator responses were examined to identify frames of reference most commonly used and their preference order. Locus of control most commonly used and the relationship between frames of reference and locus of…

  2. Invariant Image Watermarking Using Accurate Zernike Moments

    Ismail A. Ismail

    2010-01-01

    Full Text Available problem statement: Digital image watermarking is the most popular method for image authentication, copyright protection and content description. Zernike moments are the most widely used moments in image processing and pattern recognition. The magnitudes of Zernike moments are rotation invariant so they can be used just as a watermark signal or be further modified to carry embedded data. The computed Zernike moments in Cartesian coordinate are not accurate due to geometrical and numerical error. Approach: In this study, we employed a robust image-watermarking algorithm using accurate Zernike moments. These moments are computed in polar coordinate, where both approximation and geometric errors are removed. Accurate Zernike moments are used in image watermarking and proved to be robust against different kind of geometric attacks. The performance of the proposed algorithm is evaluated using standard images. Results: Experimental results show that, accurate Zernike moments achieve higher degree of robustness than those approximated ones against rotation, scaling, flipping, shearing and affine transformation. Conclusion: By computing accurate Zernike moments, the embedded bits watermark can be extracted at low error rate.

  3. Multiplicity Counting

    Geist, William H. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-12-01

    This set of slides begins by giving background and a review of neutron counting; three attributes of a verification item are discussed: 240Pueff mass; α, the ratio of (α,n) neutrons to spontaneous fission neutrons; and leakage multiplication. It then takes up neutron detector systems – theory & concepts (coincidence counting, moderation, die-away time); detector systems – some important details (deadtime, corrections); introduction to multiplicity counting; multiplicity electronics and example distributions; singles, doubles, and triples from measured multiplicity distributions; and the point model: multiplicity mathematics.

  4. X-rays induce more mutations at the tk locus than at the hgprt locus in human lymphoblastoid cells

    In rodent cell systems, it has previously been noted that higher levels of gene-locus mutations are induced at autosomal loci than at X-linked loci. Generally, this has been attributed to the likelihood that the presence of alleles of essential genes on the homologous autosome permits large-scale alterations (deletion, recombination, gene conversion, etc.) in the chromosome which contains the + allele of the selectable marker, without deleterious effects to the cell. The authors found a similar result in human lymphoblastoid cells. X-rays induced two classes of mutants at the autosomal tk locus. These were differentiated by their growth rates. Both classes were induced by x-rays with linear kinetics as a function of dose; however, about 4-5 times as many slow-growing mutants appeared. Only mutants with normal growth rates were observed at the X-linked hgprt locus; the level of induced mutation was equal to the fraction of normally-growing tk mutants. They interestingly, found that ethylmethanesulfonate (EMS) also induced both classes of mutants at the tk locus, although only about 1/3 of the total were of the slow-growing variety. Molecular characterizations of a large number of these mutants have been performed and the data are presented in the paper

  5. Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus

    Fujita, Toshitsugu; Yuno, Miyuki; Fujii, Hodaka

    2016-01-01

    The clustered regularly interspaced short palindromic repeats (CRISPR) system has been adopted for a wide range of biological applications including genome editing. In some cases, dissection of genome functions requires allele-specific genome editing, but the use of CRISPR for this purpose has not been studied in detail. In this study, using the p16INK4a gene in HCT116 as a model locus, we investigated whether chromatin states, such as CpG methylation, or a single-nucleotide gap form in a target site can be exploited for allele-specific locus binding and genome editing by CRISPR in vivo. First, we showed that allele-specific locus binding and genome editing could be achieved by targeting allele-specific CpG-methylated regions, which was successful for one, but not all guide RNAs. In this regard, molecular basis underlying the success remains elusive at this stage. Next, we demonstrated that an allele-specific single-nucleotide gap form could be employed for allele-specific locus binding and genome editing by CRISPR, although it was important to avoid CRISPR tolerance of a single nucleotide mismatch brought about by mismatched base skipping. Our results provide information that might be useful for applications of CRISPR in studies of allele-specific functions in the genomes. PMID:27465215

  6. MULTIPLE OBJECTS

    A. A. Bosov

    2015-04-01

    Full Text Available Purpose. The development of complicated techniques of production and management processes, information systems, computer science, applied objects of systems theory and others requires improvement of mathematical methods, new approaches for researches of application systems. And the variety and diversity of subject systems makes necessary the development of a model that generalizes the classical sets and their development – sets of sets. Multiple objects unlike sets are constructed by multiple structures and represented by the structure and content. The aim of the work is the analysis of multiple structures, generating multiple objects, the further development of operations on these objects in application systems. Methodology. To achieve the objectives of the researches, the structure of multiple objects represents as constructive trio, consisting of media, signatures and axiomatic. Multiple object is determined by the structure and content, as well as represented by hybrid superposition, composed of sets, multi-sets, ordered sets (lists and heterogeneous sets (sequences, corteges. Findings. In this paper we study the properties and characteristics of the components of hybrid multiple objects of complex systems, proposed assessments of their complexity, shown the rules of internal and external operations on objects of implementation. We introduce the relation of arbitrary order over multiple objects, we define the description of functions and display on objects of multiple structures. Originality.In this paper we consider the development of multiple structures, generating multiple objects.Practical value. The transition from the abstract to the subject of multiple structures requires the transformation of the system and multiple objects. Transformation involves three successive stages: specification (binding to the domain, interpretation (multiple sites and particularization (goals. The proposed describe systems approach based on hybrid sets

  7. A meta-analytic examination of work and general locus of control.

    Wang, Qiang; Bowling, Nathan A; Eschleman, Kevin J

    2010-07-01

    The current meta-analysis examined the hypothesized consequences of work and general locus of control. As expected, work locus of control generally yielded stronger relationships with work-related criteria (e.g., job satisfaction, affective commitment, and burnout) than general locus of control. We also found some evidence that general locus of control yielded relatively stronger relationships with general criteria (e.g., life satisfaction, affective commitment, and burnout). Regression analysis found several unique effects for both work and general locus of control. PMID:20604595

  8. Accurate atomic data for industrial plasma applications

    Griesmann, U.; Bridges, J.M.; Roberts, J.R.; Wiese, W.L.; Fuhr, J.R. [National Inst. of Standards and Technology, Gaithersburg, MD (United States)

    1997-12-31

    Reliable branching fraction, transition probability and transition wavelength data for radiative dipole transitions of atoms and ions in plasma are important in many industrial applications. Optical plasma diagnostics and modeling of the radiation transport in electrical discharge plasmas (e.g. in electrical lighting) depend on accurate basic atomic data. NIST has an ongoing experimental research program to provide accurate atomic data for radiative transitions. The new NIST UV-vis-IR high resolution Fourier transform spectrometer has become an excellent tool for accurate and efficient measurements of numerous transition wavelengths and branching fractions in a wide wavelength range. Recently, the authors have also begun to employ photon counting techniques for very accurate measurements of branching fractions of weaker spectral lines with the intent to improve the overall accuracy for experimental branching fractions to better than 5%. They have now completed their studies of transition probabilities of Ne I and Ne II. The results agree well with recent calculations and for the first time provide reliable transition probabilities for many weak intercombination lines.

  9. More accurate picture of human body organs

    Computerized tomography and nucler magnetic resonance tomography (NMRT) are revolutionary contributions to radiodiagnosis because they allow to obtain a more accurate image of human body organs. The principles are described of both methods. Attention is mainly devoted to NMRT which has clinically only been used for three years. It does not burden the organism with ionizing radiation. (Ha)

  10. Comparative Analysis of the Orphan CRISPR2 Locus in 242 Enterococcus faecalis Strains.

    Karthik Hullahalli

    Full Text Available Clustered, Regularly Interspaced Short Palindromic Repeats and their associated Cas proteins (CRISPR-Cas provide prokaryotes with a mechanism for defense against mobile genetic elements (MGEs. A CRISPR locus is a molecular memory of MGE encounters. It contains an array of short sequences, called spacers, that generally have sequence identity to MGEs. Three different CRISPR loci have been identified among strains of the opportunistic pathogen Enterococcus faecalis. CRISPR1 and CRISPR3 are associated with the cas genes necessary for blocking MGEs, but these loci are present in only a subset of E. faecalis strains. The orphan CRISPR2 lacks cas genes and is ubiquitous in E. faecalis, although its spacer content varies from strain to strain. Because CRISPR2 is a variable locus occurring in all E. faecalis, comparative analysis of CRISPR2 sequences may provide information about the clonality of E. faecalis strains. We examined CRISPR2 sequences from 228 E. faecalis genomes in relationship to subspecies phylogenetic lineages (sequence types; STs determined by multilocus sequence typing (MLST, and to a genome phylogeny generated for a representative 71 genomes. We found that specific CRISPR2 sequences are associated with specific STs and with specific branches on the genome tree. To explore possible applications of CRISPR2 analysis, we evaluated 14 E. faecalis bloodstream isolates using CRISPR2 analysis and MLST. CRISPR2 analysis identified two groups of clonal strains among the 14 isolates, an assessment that was confirmed by MLST. CRISPR2 analysis was also used to accurately predict the ST of a subset of isolates. We conclude that CRISPR2 analysis, while not a replacement for MLST, is an inexpensive method to assess clonality among E. faecalis isolates, and can be used in conjunction with MLST to identify recombination events occurring between STs.

  11. Fine-mapping of an Arabidopsis cell death mutation locus

    2000-01-01

    An Arabidopsis cell death mutation locus was mapped to chromosome 2 between IGS1 and mi421. The YAC clone ends, CIC9A3R, CIC11C7L, CIC2G5R and RFLP marker CDs3 within this interval, were used to probe TAMU BAC library and 31 BAC clones were obtained. A BAC contig encompassing the mutation locus, which consists of T6P5, T7M23, T12A21, T8L6 and T18A18, was identified by Southern hybridization with the BAC ends as probes. 11 CAPS and 12 STS markers were developed in this region. These results will facilitate map-based cloning of the genes and sequencing of the genomic DNA in this region.

  12. The locus of microRNA-10b

    Biagioni, Francesca; Bossel Ben-Moshe, Noa; Fontemaggi, Giulia; Yarden, Yosef; Domany, Eytan; Blandino, Giovanni

    2013-01-01

    Contemporary microRNA research has led to significant advances in our understanding of the process of tumorigenesis. MicroRNAs participate in different events of a cancer cell’s life, through their ability to target hundreds of putative transcripts involved in almost every cellular function, including cell cycle, apoptosis, and differentiation. The relevance of these small molecules is even more evident in light of the emerging linkage between their expression and both prognosis and clinical outcome of many types of human cancers. This identifies microRNAs as potential therapeutic modifiers of cancer phenotypes. From this perspective, we overview here the miR-10b locus and its involvement in cancer, focusing on its role in the establishment (miR-10b*) and spreading (miR-10b) of breast cancer. We conclude that targeting the locus of microRNA 10b holds great potential for cancer treatment. PMID:23839045

  13. Cross-species identification of Mendel's I locus.

    Armstead, Ian; Donnison, Iain; Aubry, Sylvain; Harper, John; Hörtensteiner, Stefan; James, Caron; Mani, Jan; Moffet, Matt; Ougham, Helen; Roberts, Luned; Thomas, Ann; Weeden, Norman; Thomas, Howard; King, Ian

    2007-01-01

    A key gene involved in plant senescence, mutations of which partially disable chlorophyll catabolism and confer stay-green leaf and cotyledon phenotypes, has been identified in Pisum sativum, Arabidopsis thaliana, and Festuca pratensis by using classical and molecular genetics and comparative genomics. A stay-green locus in F. pratensis is syntenically equivalent to a similar stay-green locus on rice chromosome 9. Functional testing in Arabidopsis of a homolog of the rice candidate gene revealed (i) senescence-associated gene expression and (ii) a stay-green phenotype after RNA interference silencing. Genetic mapping in pea demonstrated cosegregation with the yellow/green cotyledon polymorphism (I/i) first reported by Gregor Mendel in 1866. PMID:17204643

  14. High-resolution mapping of the x-linked hypohidrotic ectodermal dysplasia (EDA) locus

    Zonana, J.; Jones, M.; Litt, M.; Kramer, P.; Browne, D.; Becker, H.W. (Oregon Health Sciences Univ., Portland, OR (United States)); Brockdorff, N.; Rastan, S. (Medical Council Clinical Research Centre, Harrow (United Kingdom)); Davies, K.P.; Clarke, A. (Univ. of Wales College of Medicine, Cardiff (United Kingdom)) (and others)

    1992-11-01

    The X-linked hypohidrotic ectodermal dysplasia (EDA) locus has been previously localized to the subchromosomal region Xq11-q21.1. The authors have extended previous linkage studies and analyzed linkage between the EDA locus and 10 marker loci, including five new loci, in 41 families. Four of the marker loci showed no recombination with the EDA locus, and six other loci were also linked to the EDA locus with recombination fractions of .009-.075. Multipoint analysis gave support to the placement of the PGK1P1 locus proximal to the EDA locus and the DXS453 and PGK1 loci distal to EDA. Further ordering of the loci could be inferred from a human-rodent somatic cell hybrid derived from an affected female with EDA and an X;9 translocation and from studies of an affected male with EDA and a submicroscopic deletion. Three of the proximal marker loci, which showed no recombination with the EDA locus, when used in combination, were informative in 92% of females. The closely linked flanking polymorphic loci DXS339 and DXS453 had heterozygosites of 72% and 76%, respectively, and when used jointly, they were doubly informative in 52% of females. The human DXS732 locus was defined by a conserved mouse probe pcos169E/4 (DXCrc169 locus) that consegregates with the mouse tabby (Ta) locus, a potential homologue to the EDA locus. The absence of recombination between EDA and the DXSA732 locus lends support to the hypothesis that the DXCrc169 locus in the mouse and the DXS732 locus in humans may contain candidate sequences for the Ta and EDA genes, respectively. 36 refs., 1 fig., 5 tabs.

  15. Generalized internal multiple imaging

    Zuberi, M. A. H.

    2014-08-05

    Internal multiples deteriorate the image when the imaging procedure assumes only single scattering, especially if the velocity model does not have sharp contrasts to reproduce such scattering in the Green’s function through forward modeling. If properly imaged, internal multiples (internally scattered energy) can enhance the seismic image. Conventionally, to image internal multiples, accurate, sharp contrasts in the velocity model are required to construct a Green’s function with all the scattered energy. As an alternative, we have developed a generalized internal multiple imaging procedure that images any order internal scattering using the background Green’s function (from the surface to each image point), constructed from a smooth velocity model, usually used for conventional imaging. For the first-order internal multiples, the approach consisted of three steps, in which we first back propagated the recorded surface seismic data using the background Green’s function, then crosscorrelated the back-propagated data with the recorded data, and finally crosscorrelated the result with the original background Green’s function. This procedure images the contribution of the recorded first-order internal multiples, and it is almost free of the single-scattering recorded energy. The cost includes one additional crosscorrelation over the conventional single-scattering imaging application. We generalized this method to image internal multiples of any order separately. The resulting images can be added to the conventional single-scattering image, obtained, e.g., from Kirchhoff or reverse-time migration, to enhance the image. Application to synthetic data with reflectors illuminated by multiple scattering (double scattering) demonstrated the effectiveness of the approach.

  16. Geographic distribution of haplotype diversity at the bovine casein locus

    Jann, Oliver; Ibeagha-Awemu, Eveline; Özbeyaz, Ceyhan; Zaragoza, Pilar; Williams, John; Ajmone-Marsan, Paolo; Lenstra, Johannes; Moazami-Goudarzi, Katy; Erhardt, Georg

    2004-01-01

    The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine b...

  17. Effect of tapentadol on neurons in the locus coeruleus

    Torres-Sanchez, Sonia; Alba-Delgado, Cristina; Llorca-Torralba, Meritxell; Mico, Juan A.; Berrocoso, Esther

    2013-01-01

    Tapentadol is a novel centrally acting drug that combines mu-opioid receptor (MOR) agonism and noradrenaline reuptake inhibition (NRI), producing analgesic effects in various painful conditions. We investigated the acute effects of tapentadol in the locus coeruleus (LC), a central nucleus regulated by the noradrenergic and opioid systems that is critical in pain modulation. In single-unit extracellular recordings of LC neurons from anaesthetized male SpragueeDawley rats, tapentado...

  18. Geography of reputation: the city as locus of business opportunity

    Glückler, Johannes

    2007-01-01

    Abstract This paper discusses the limits of current cluster theory and theorizes trans-local network externalities as an important cause for the urban agglomeration of knowledge services. A survey on management consulting firms in the metropolitan region of Frankfurt demonstrates that the benefit of co-location in the city lies in the access to reputation networks rather than in the exploitation of local value chain linkages. The city is a locus of opportunity because firms in the ...

  19. Surfeit locus gene homologs are widely distributed in invertebrate genomes.

    Armes, N; Fried, M

    1996-01-01

    The mouse Surfeit locus contains six sequence-unrelated genes (Surf-1 to -6) arranged in the tightest gene cluster so far described for mammals. The organization and juxtaposition of five of the Surfeit genes (Surf-1 to -5) are conserved between mammals and birds, and this may reflect a functional or regulatory requirement for the gene clustering. We have undertaken an evolutionary study to determine whether the Surfeit genes are conserved and clustered in invertebrate genomes. Drosophila mel...

  20. Teacher Psychological Needs, Locus of Control and Engagement

    Doménech Betoret, Fernando

    2013-01-01

    This study examines the relationships among psychological needs, locus of control and engagement in a sample of 282 Spanish secondary school teachers. Nine teacher needs were identified based on the study of Bess (1977) and on the Self-Determination Theory (Deci & Ryan, 1985, 2000, 2002). Self-report questionnaires were used to measure the construct selected for this study and their interrelationships were examined by conducting hierarchical regression analyses. An analysis of teacher respons...

  1. The discovery of the microphthalmia locus and its gene, Mitf

    Arnheiter, Heinz

    2010-01-01

    The history of the discovery of the microphthalmia locus and its gene, now called Mitf, is a testament to the triumph of serendipity. Although the first microphthalmia mutation was discovered among the descendants of a mouse that was irradiated for the purpose of mutagenesis, the mutation most likely was not radiation-induced but occurred spontaneously in one of the parents of a later breeding. Although Mitf might eventually have been identified by other molecular genetic techniques, it was f...

  2. The immunoglobulin heavy chain locus in the platypus (Ornithorhynchus anatinus).

    Gambón-Deza, F; Sánchez-Espinel, C; Magadán-Mompó, S

    2009-08-01

    Immunoglobulins loci in mammals are well known to be organized within a translocon, however their origin remains unresolved. Four of the five classes of immunoglobulins described in humans and rodents (immunoglobulins M, G, E and A-IgM, IgG, IgE and IgA) were found in marsupials and monotremes (immunoglobulin D-IgD was not found) thus showing that the genomic structure of antibodies in mammals has remained constant since its origin. We have recently described the genomic organization of the immunoglobulin heavy chain locus in reptiles (IGHM, IGHD and IGHY). These data and the characterization of the IGH locus in platypus (Ornithorhynchus anatinus), allow us to elucidate the changes that took place in this genomic region during evolution from reptile to mammal. Thus, by using available genome data, we were able to detect that platypus IGH locus contains reptilian and mammalian genes. Besides having an IGHD that is very similar to the one in reptiles and an IGHY, they also present the mammal specific antibody genes IGHG and IGHE, in addition to IGHA. We also detected a pseudogene that originated by recombination between the IGHD and the IGHM (similar to the IGHD2 found in Eublepharis macularius). The analysis of the IGH locus in platypus shows that IGHY was duplicated, firstly by evolving into IGHE and then into IGHG. The IGHA of the platypus has a complex origin, and probably arose by a process of recombination between the IGHM and the IGHY. We detected about 44 VH genes (25 were already described), most of which comprise a single group. When we compared these VH genes with those described in Anolis carolinensis, we find that there is an evolutionary relationship between the VH genes of platypus and the reptilian Group III genes. These results suggest that a fast VH turnover took place in platypus and this gave rise to a family with a high VH gene number and the disappearance of the earlier VH families. PMID:19505725

  3. Geographic distribution of haplotype diversity at the bovine casein locus.

    Moazami-Goudarzi Katy; Lenstra Johannes A; Ajmone-Marsan Paolo; Williams John L; Zaragoza Pilar; Özbeyaz Ceyhan; Ibeagha-Awemu Eveline M; Jann Oliver C; Erhardt Georg

    2004-01-01

    Abstract The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within ...

  4. The Relationship Between Locus of Control, Metacognition, and Academic Success

    Hrbáčková, Karla; Hladík, Jakub; Vávrová, Soňa

    2012-01-01

    The previous research on locus of control or metacognition suggested that they are closely related to academic performance and can be taught to students to improve their academic and non-academic success. These variables were often examined separately in order to explain and predict performance and rarely in a university setting. The integration of these variables into a common framework could provide a deeper understanding of university students' learning process. This study examined the rel...

  5. Male-pattern baldness susceptibility locus at 20p11.

    Richards, J.B.; Yuan, X.; Geller, F.; Waterworth, D.; Bataille, V.; Glass, D.; Song, K.; Waeber, G.; Vollenweider, P.; Aben, K.K.H.; Kiemeney, L.A.L.M.; Walters, B.; Soranzo, N.; Thorsteinsdottir, U.; Kong, A.; Rafnar, T.; Deloukas, P.; Sulem, P.; Stefansson, H.; Stefansson, K.; Spector, T.D.; Mooser, V.

    2008-01-01

    We conducted a genome-wide association study for androgenic alopecia in 1,125 men and identified a newly associated locus at chromosome 20p11.22, confirmed in three independent cohorts (n = 1,650; OR = 1.60, P = 1.1 x 10(-14) for rs1160312). The one man in seven who harbors risk alleles at both 20p1

  6. BUDGETARY PARTICIPATION, LOCUS OF CONTROL AND JOB SATISFACTION IN TUNISIA

    Dakhli, Anissa

    2009-01-01

    The relation between budgetary participation and job satisfaction has been examined in several accounting studies with conflicting results. The conflicting evidence may reflect the influence of contingency variables. The purpose of the present study is to examine the relationship between budgetary participation and job satisfaction, moderated by the personality variable, locus of control. In this study, Tunisian managers were selected because Tunisia provides an interesting cultural contrast ...

  7. The pgm locus and pigmentation phenotype in Yersinia pestis

    Tereza Cristina Leal-Balbino

    2006-01-01

    Full Text Available The pigmentation (pgm locus is a large unstable area of the Yersinia pestis chromosome composed of a segment of iron acquisition (HPI linked to a pigmentation segment. In this work we examined the mobility of HPI and the pigmentation segment in three Y. pestis isolates using successive subcultures on Congo red agar (CRA plates. Strain P. CE 882 was shown to be highly stable while strains P. Exu 340 and P. Peru 375 dissociated into several phenotypes, PCR analysis showing evidence of changes in the pgm locus of the derived cultures. Strains P. Exu 340 and P. Peru 375 produced previously unreported cultures positive for the pesticin/yersiniabactin outer membrane receptor (psn+ but negative for the iron-regulated protein (irp2-, suggesting the occurrence of rearrangements in this chromosomal region and either a sequential loss or the loss of separated segments. These results provide evidence that besides deletion en bloc, specific rearrangements are also involved in the deletion events for that locus.

  8. Genomic characterization of the Atlantic cod sex-locus.

    Star, Bastiaan; Tørresen, Ole K; Nederbragt, Alexander J; Jakobsen, Kjetill S; Pampoulie, Christophe; Jentoft, Sissel

    2016-01-01

    A variety of sex determination mechanisms can be observed in evolutionary divergent teleosts. Sex determination is genetic in Atlantic cod (Gadus morhua), however the genomic location or size of its sex-locus is unknown. Here, we characterize the sex-locus of Atlantic cod using whole genome sequence (WGS) data of 227 wild-caught specimens. Analyzing more than 55 million polymorphic loci, we identify 166 loci that are associated with sex. These loci are located in six distinct regions on five different linkage groups (LG) in the genome. The largest of these regions, an approximately 55 Kb region on LG11, contains the majority of genotypes that segregate closely according to a XX-XY system. Genotypes in this region can be used genetically determine sex, whereas those in the other regions are inconsistently sex-linked. The identified region on LG11 and its surrounding genes have no clear sequence homology with genes or regulatory elements associated with sex-determination or differentiation in other species. The functionality of this sex-locus therefore remains unknown. The WGS strategy used here proved adequate for detecting the small regions associated with sex in this species. Our results highlight the evolutionary flexibility in genomic architecture underlying teleost sex-determination and allow practical applications to genetically sex Atlantic cod. PMID:27499266

  9. Feedback about more accurate versus less accurate trials: differential effects on self-confidence and activation.

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-06-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected byfeedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On day 1, participants performed a golf putting task under one of two conditions: one group received feedback on the most accurate trials, whereas another group received feedback on the least accurate trials. On day 2, participants completed an anxiety questionnaire and performed a retention test. Shin conductance level, as a measure of arousal, was determined. The results indicated that feedback about more accurate trials resulted in more effective learning as well as increased self-confidence. Also, activation was a predictor of performance. PMID:22808705

  10. Multiple sclerosis

    Multiple sclerosis is the most common chronic inflammatory disease of myelin with interspersed lesions in the white matter of the central nervous system. Magnetic resonance imaging (MRI) plays a key role in the diagnosis and monitoring of white matter diseases. This article focuses on key findings in multiple sclerosis as detected by MRI. (orig.)

  11. How Accurate is inv(A)*b?

    Druinsky, Alex

    2012-01-01

    Several widely-used textbooks lead the reader to believe that solving a linear system of equations Ax = b by multiplying the vector b by a computed inverse inv(A) is inaccurate. Virtually all other textbooks on numerical analysis and numerical linear algebra advise against using computed inverses without stating whether this is accurate or not. In fact, under reasonable assumptions on how the inverse is computed, x = inv(A)*b is as accurate as the solution computed by the best backward-stable solvers. This fact is not new, but obviously obscure. We review the literature on the accuracy of this computation and present a self-contained numerical analysis of it.

  12. Accurate guitar tuning by cochlear implant musicians.

    Thomas Lu

    Full Text Available Modern cochlear implant (CI users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  13. Accurate guitar tuning by cochlear implant musicians.

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang

    2014-01-01

    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task. PMID:24651081

  14. Accurate Finite Difference Methods for Option Pricing

    Persson, Jonas

    2006-01-01

    Stock options are priced numerically using space- and time-adaptive finite difference methods. European options on one and several underlying assets are considered. These are priced with adaptive numerical algorithms including a second order method and a more accurate method. For American options we use the adaptive technique to price options on one stock with and without stochastic volatility. In all these methods emphasis is put on the control of errors to fulfill predefined tolerance level...

  15. Accurate, reproducible measurement of blood pressure.

    Campbell, N. R.; Chockalingam, A; Fodor, J. G.; McKay, D. W.

    1990-01-01

    The diagnosis of mild hypertension and the treatment of hypertension require accurate measurement of blood pressure. Blood pressure readings are altered by various factors that influence the patient, the techniques used and the accuracy of the sphygmomanometer. The variability of readings can be reduced if informed patients prepare in advance by emptying their bladder and bowel, by avoiding over-the-counter vasoactive drugs the day of measurement and by avoiding exposure to cold, caffeine con...

  16. Accurate variational forms for multiskyrmion configurations

    Jackson, A.D.; Weiss, C.; Wirzba, A.; Lande, A.

    1989-04-17

    Simple variational forms are suggested for the fields of a single skyrmion on a hypersphere, S/sub 3/(L), and of a face-centered cubic array of skyrmions in flat space, R/sub 3/. The resulting energies are accurate at the level of 0.2%. These approximate field configurations provide a useful alternative to brute-force solutions of the corresponding Euler equations.

  17. Efficient Accurate Context-Sensitive Anomaly Detection

    2007-01-01

    For program behavior-based anomaly detection, the only way to ensure accurate monitoring is to construct an efficient and precise program behavior model. A new program behavior-based anomaly detection model,called combined pushdown automaton (CPDA) model was proposed, which is based on static binary executable analysis. The CPDA model incorporates the optimized call stack walk and code instrumentation technique to gain complete context information. Thereby the proposed method can detect more attacks, while retaining good performance.

  18. Towards accurate modeling of moving contact lines

    Holmgren, Hanna

    2015-01-01

    The present thesis treats the numerical simulation of immiscible incompressible two-phase flows with moving contact lines. The conventional Navier–Stokes equations combined with a no-slip boundary condition leads to a non-integrable stress singularity at the contact line. The singularity in the model can be avoided by allowing the contact line to slip. Implementing slip conditions in an accurate way is not straight-forward and different regularization techniques exist where ad-hoc procedures ...

  19. Defining the clinical course of multiple sclerosis

    Lublin, Fred D; Reingold, Stephen C; Cohen, Jeffrey A;

    2014-01-01

    Accurate clinical course descriptions (phenotypes) of multiple sclerosis (MS) are important for communication, prognostication, design and recruitment of clinical trials, and treatment decision-making. Standardized descriptions published in 1996 based on a survey of international MS experts...

  20. Accurate phase-shift velocimetry in rock

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  1. Locus de Controle e escolha do método anticoncepcional Locus de Control y método anticonceptivo elegido Locus of Control and choice of contraceptive method

    Aline Salheb Alves

    2007-06-01

    Full Text Available Objetivou-se avaliar a relação entre o Locus de Controle e o tipo de método contraceptivo escolhido. Foi utilizada a Escala Multidimensional de Locus de Controle de Levenson e entrevistadas 191 mulheres. As usuárias de preservativo masculino apresentaram maior Internalidade do que as usuárias de injetável mensal. Quanto ao locus Externalidade Outros Poderosos, as usuárias de implante apresentavam menor externalidade do que as usuárias de preservativo masculino, laqueadura, injetável trimestral e DIU. Considerando-se o locus Externalidade Acaso, as usuárias de implante apresentaram menores escores do que as mulheres que optaram pela laqueadura, injetável trimestral e DIU. Observou-se ainda, menor Externalidade Acaso entre as usuárias de injetável mensal em relação às mulheres que fizeram opção pelo injetável trimestral.El objetivo es validar la relación entre el Locus de Control y el tipo de método anticonceptivo elegido. Fue usada la Escala Multidimensional de Locus de Control de Levenson. Fueron entrevistadas 191 mujeres. Las usuarias de condón masculino presentaron Internalidad más grande que las usuarias de inyectable mensual. Considerado el Locus Externalidad - Otro poderoso, las usuarias de implante presentaron menor externalidad de que las usuarias de condón masculino, laqueadura, inyectable trimestral y DIU. Considerado el Locus Externalidad - Quizá, las usuarias del implante presentaron menores resultados que las mujeres que eligieron por la laqueadura, inyectable trimestral y DIU. Se observo que las mujeres usuarias de inyectable mensual presentaron menor Externalidad - Quizá que las mujeres usuarias de inyectable trimestral.The purpose was to assess the relationship between locus of control and the contraceptive method chosen. It was used the Levenson's Multidimensional Locus of Control Scale and 191 women was interviewed. Users of male condoms presented greater Internality than the monthly contraceptive

  2. History of the discovery of a master locus producing piRNAs: the flamenco/COM locus in Drosophila melanogaster

    Coline, Goriaux; Théron, Emmanuelle; Brasset, Emilie; Vaury, Chantal

    2014-01-01

    The discovery of transposable elements (TEs) in the 1950s by B. McClintock implied the existence of cellular regulatory systems controlling TE activity. The discovery of flamenco (flam) an heterochromatic locus from Drosophila melanogaster and its ability to survey several TEs such as gypsy, ZAM, and Idefix contributed to peer deeply into the mechanisms of the genetic and epigenetic regulation of TEs. flam was the first cluster producing small RNAs to be discovered long before RNAi pathways w...

  3. HEALTH LOCUS OF CONTROL PERCEPTION OF ADOLESCENTS, AND ITS EFFECTS ON THEIR HEALTH BEHAVIOURS

    Ruhi Selcuk TABAK

    2006-04-01

    Full Text Available Main objective of this study is to investigate the relationships between health locus of control perceptions and health behaviours of adolescents as well as the effectiveness of lectures on health locus of control to them. The subjects of our study are 192 students in 6 groups of the 9. Grade students of a high school. Three groups of 108 students were randomly selected as the experiment group who were subjected to 4 class-hours specific lectures on health locus of control. The rest 84 students constituted the control group. A 34-item questionnaire for health behaviours and the Multidimensional Health Locus of Control Scale (MHLOC, were filled by the students before and after the lectures. The lectures on health locus of control increased the perception of internal health locus of control of adolescents while decreasing chance health locus of control. The differences between experiment and control groups in this aspect were found to be statistically significant. Internal health locus of control is the main source for the increase of responsibility and management of individuals on their health. The relations that were detected between students’ health behaviours and information solicitation and their perceptions of health locus of control showed that the students with higher internal health locus of control are more eager to be responsible and active for their health, especially, for the health behaviours such as physical exercise, smoking, tooth-brushing, medical check-ups so on. [TAF Prev Med Bull 2006; 5(2.000: 118-130

  4. Polymorphic DNA haplotypes at the phenylalanine hydroxylase (PAH) locus in European families with phenylketonuria (PKU)

    Daiger, Stephen P.; Chakraborty, Ranajit; Reed, Lori; Fekete, György; Schuler, Dezso; Berenssi, György; Nasz, Istvan; Brdička, Radim; Kamarýt, Jaromir; Pijáčková, Anna; Moore, Sharon; Sullivan, Susan; Woo, Savio L. C.

    1989-01-01

    DNA haplotype data from the phenylalanine hydroxylase (PAH) locus are available from a number of European populations as a result of RFLP testing for genetic counseling in families with phenylketonuria (PKU). We have analyzed data from Hungary and Czechoslovakia together with published data from five additional countries–Denmark, Switzerland, Scotland, Germany, and France–representing a broad geographic and ethnographic range. The data include 686 complete chromosomal haplotypes for eight RFLP sites assayed in 202 unrelated Caucasian families with PKU. Forty-six distinct RFLP haplotypes have been observed to date, 10 unique to PKU-bearing chromosomes, 12 unique to non-PKU chromosomes, and the remainder found in association with both types. Despite the large number of haplotypes observed (still much less than the theoretical maximum of 384), five haplotypes alone account for more than 76% of normal European chromosomes and four haplotypes alone account for more than 80% of PKU-bearing chromosomes. We evaluated the distribution of haplotypes and alleles within these populations and calculated pairwise disequilibrium values between RFLP sites and between these sites and a hypothetical PKU “locus.” There are statistically significant differences between European populations in the frequencies of non-PKU chromosomal haplotypes (P = .025) and PKU chromosomal haplotypes (P < < .001). Haplotype frequencies of the PKU and non-PKU chromosomes also differ significantly (P < < .001. Disequilibrium values are consistent with the PAH physical map and support the molecular evidence for multiple, independent PKU mutations in Caucasians. However, the data do not support a single geographic origin for these mutations. Within these European populations a parent carrying a PKU mutation has an average probability of greater than 86% of being heterozygous–and hence informative for linkage–at one or more PAH RFLP sites. Thus these RFLP alleles and haplotypes provide an

  5. A conserved supergene locus controls colour pattern diversity in Heliconius butterflies.

    Mathieu Joron

    2006-10-01

    Full Text Available We studied whether similar developmental genetic mechanisms are involved in both convergent and divergent evolution. Mimetic insects are known for their diversity of patterns as well as their remarkable evolutionary convergence, and they have played an important role in controversies over the respective roles of selection and constraints in adaptive evolution. Here we contrast three butterfly species, all classic examples of Müllerian mimicry. We used a genetic linkage map to show that a locus, Yb, which controls the presence of a yellow band in geographic races of Heliconius melpomene, maps precisely to the same location as the locus Cr, which has very similar phenotypic effects in its co-mimic H. erato. Furthermore, the same genomic location acts as a "supergene", determining multiple sympatric morphs in a third species, H. numata. H. numata is a species with a very different phenotypic appearance, whose many forms mimic different unrelated ithomiine butterflies in the genus Melinaea. Other unlinked colour pattern loci map to a homologous linkage group in the co-mimics H. melpomene and H. erato, but they are not involved in mimetic polymorphism in H. numata. Hence, a single region from the multilocus colour pattern architecture of H. melpomene and H. erato appears to have gained control of the entire wing-pattern variability in H. numata, presumably as a result of selection for mimetic "supergene" polymorphism without intermediates. Although we cannot at this stage confirm the homology of the loci segregating in the three species, our results imply that a conserved yet relatively unconstrained mechanism underlying pattern switching can affect mimicry in radically different ways. We also show that adaptive evolution, both convergent and diversifying, can occur by the repeated involvement of the same genomic regions.

  6. Accurate object tracking system by integrating texture and depth cues

    Chen, Ju-Chin; Lin, Yu-Hang

    2016-03-01

    A robust object tracking system that is invariant to object appearance variations and background clutter is proposed. Multiple instance learning with a boosting algorithm is applied to select discriminant texture information between the object and background data. Additionally, depth information, which is important to distinguish the object from a complicated background, is integrated. We propose two depth-based models that can compensate texture information to cope with both appearance variants and background clutter. Moreover, in order to reduce the risk of drifting problem increased for the textureless depth templates, an update mechanism is proposed to select more precise tracking results to avoid incorrect model updates. In the experiments, the robustness of the proposed system is evaluated and quantitative results are provided for performance analysis. Experimental results show that the proposed system can provide the best success rate and has more accurate tracking results than other well-known algorithms.

  7. Identifying causal variants at loci with multiple signals of association.

    Hormozdiari, Farhad; Kostem, Emrah; Kang, Eun Yong; Pasaniuc, Bogdan; Eskin, Eleazar

    2014-10-01

    Although genome-wide association studies have successfully identified thousands of risk loci for complex traits, only a handful of the biologically causal variants, responsible for association at these loci, have been successfully identified. Current statistical methods for identifying causal variants at risk loci either use the strength of the association signal in an iterative conditioning framework or estimate probabilities for variants to be causal. A main drawback of existing methods is that they rely on the simplifying assumption of a single causal variant at each risk locus, which is typically invalid at many risk loci. In this work, we propose a new statistical framework that allows for the possibility of an arbitrary number of causal variants when estimating the posterior probability of a variant being causal. A direct benefit of our approach is that we predict a set of variants for each locus that under reasonable assumptions will contain all of the true causal variants with a high confidence level (e.g., 95%) even when the locus contains multiple causal variants. We use simulations to show that our approach provides 20-50% improvement in our ability to identify the causal variants compared to the existing methods at loci harboring multiple causal variants. We validate our approach using empirical data from an expression QTL study of CHI3L2 to identify new causal variants that affect gene expression at this locus. CAVIAR is publicly available online at http://genetics.cs.ucla.edu/caviar/. PMID:25104515

  8. Multiple myeloma.

    Collins, Conor D

    2012-02-01

    Advances in the imaging and treatment of multiple myeloma have occurred over the past decade. This article summarises the current status and highlights how an understanding of both is necessary for optimum management.

  9. Cerebral fat embolism: Use of MR spectroscopy for accurate diagnosis

    Laxmi Kokatnur

    2015-01-01

    Full Text Available Cerebral fat embolism (CFE is an uncommon but serious complication following orthopedic procedures. It usually presents with altered mental status, and can be a part of fat embolism syndrome (FES if associated with cutaneous and respiratory manifestations. Because of the presence of other common factors affecting the mental status, particularly in the postoperative period, the diagnosis of CFE can be challenging. Magnetic resonance imaging (MRI of brain typically shows multiple lesions distributed predominantly in the subcortical region, which appear as hyperintense lesions on T2 and diffusion weighted images. Although the location offers a clue, the MRI findings are not specific for CFE. Watershed infarcts, hypoxic encephalopathy, disseminated infections, demyelinating disorders, diffuse axonal injury can also show similar changes on MRI of brain. The presence of fat in these hyperintense lesions, identified by MR spectroscopy as raised lipid peaks will help in accurate diagnosis of CFE. Normal brain tissue or conditions producing similar MRI changes will not show any lipid peak on MR spectroscopy. We present a case of CFE initially misdiagnosed as brain stem stroke based on clinical presentation and cranial computed tomography (CT scan, and later, MR spectroscopy elucidated the accurate diagnosis.

  10. Niche Genetic Algorithm with Accurate Optimization Performance

    LIU Jian-hua; YAN De-kun

    2005-01-01

    Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolutionary direction dynamically during evolution. After evolution, the solutions's precision can be greatly improved by means of the local searching along the recorded direction. Simulation shows that this algorithm can not only keep population diversity but also find accurate solutions. Although using this method has to take more time compared with the standard GA, it is really worth applying to some cases that have to meet a demand for high solution precision.

  11. How accurately can we calculate thermal systems?

    The objective was to determine how accurately simple reactor lattice integral parameters can be determined, considering user input, differences in the methods, source data and the data processing procedures and assumptions. Three simple square lattice test cases with different fuel to moderator ratios were defined. The effect of the thermal scattering models were shown to be important and much bigger than the spread in the results. Nevertheless, differences of up to 0.4% in the K-eff calculated by continuous energy Monte Carlo codes were observed even when the same source data were used. (author)

  12. Accurate diagnosis is essential for amebiasis

    2004-01-01

    @@ Amebiasis is one of the three most common causes of death from parasitic disease, and Entamoeba histolytica is the most widely distributed parasites in the world. Particularly, Entamoeba histolytica infection in the developing countries is a significant health problem in amebiasis-endemic areas with a significant impact on infant mortality[1]. In recent years a world wide increase in the number of patients with amebiasis has refocused attention on this important infection. On the other hand, improving the quality of parasitological methods and widespread use of accurate tecniques have improved our knowledge about the disease.

  13. Investigations on Accurate Analysis of Microstrip Reflectarrays

    Zhou, Min; Sørensen, S. B.; Kim, Oleksiy S.;

    2011-01-01

    An investigation on accurate analysis of microstrip reflectarrays is presented. Sources of error in reflectarray analysis are examined and solutions to these issues are proposed. The focus is on two sources of error, namely the determination of the equivalent currents to calculate the radiation...... pattern, and the inaccurate mutual coupling between array elements due to the lack of periodicity. To serve as reference, two offset reflectarray antennas have been designed, manufactured and measured at the DTUESA Spherical Near-Field Antenna Test Facility. Comparisons of simulated and measured data are...

  14. Diversity of Pol IV function is defined by mutations at the maize rmr7 locus.

    Jennifer L Stonaker

    2009-11-01

    Full Text Available Mutations affecting the heritable maintenance of epigenetic states in maize identify multiple small RNA biogenesis factors including NRPD1, the largest subunit of the presumed maize Pol IV holoenzyme. Here we show that mutations defining the required to maintain repression7 locus identify a second RNA polymerase subunit related to Arabidopsis NRPD2a, the sole second largest subunit shared between Arabidopsis Pol IV and Pol V. A phylogenetic analysis shows that, in contrast to representative eudicots, grasses have retained duplicate loci capable of producing functional NRPD2-like proteins, which is indicative of increased RNA polymerase diversity in grasses relative to eudicots. Together with comparisons of rmr7 mutant plant phenotypes and their effects on the maintenance of epigenetic states with parallel analyses of NRPD1 defects, our results imply that maize utilizes multiple functional NRPD2-like proteins. Despite the observation that RMR7/NRPD2, like NRPD1, is required for the accumulation of most siRNAs, our data indicate that different Pol IV isoforms play distinct roles in the maintenance of meiotically-heritable epigenetic information in the grasses.

  15. Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

    Erhard, Karl F.; Hollick, Jay B.

    2009-01-01

    Mutations affecting the heritable maintenance of epigenetic states in maize identify multiple small RNA biogenesis factors including NRPD1, the largest subunit of the presumed maize Pol IV holoenzyme. Here we show that mutations defining the required to maintain repression7 locus identify a second RNA polymerase subunit related to Arabidopsis NRPD2a, the sole second largest subunit shared between Arabidopsis Pol IV and Pol V. A phylogenetic analysis shows that, in contrast to representative eudicots, grasses have retained duplicate loci capable of producing functional NRPD2-like proteins, which is indicative of increased RNA polymerase diversity in grasses relative to eudicots. Together with comparisons of rmr7 mutant plant phenotypes and their effects on the maintenance of epigenetic states with parallel analyses of NRPD1 defects, our results imply that maize utilizes multiple functional NRPD2-like proteins. Despite the observation that RMR7/NRPD2, like NRPD1, is required for the accumulation of most siRNAs, our data indicate that different Pol IV isoforms play distinct roles in the maintenance of meiotically-heritable epigenetic information in the grasses. PMID:19936246

  16. Arabidopsis RRP6L1 and RRP6L2 function in FLOWERING LOCUS C silencing via regulation of antisense RNA synthesis.

    Jun-Hye Shin

    2014-09-01

    Full Text Available The exosome complex functions in RNA metabolism and transcriptional gene silencing. Here, we report that mutations of two Arabidopsis genes encoding nuclear exosome components AtRRP6L1 and AtRRP6L2, cause de-repression of the main flowering repressor FLOWERING LOCUS C (FLC and thus delay flowering in early-flowering Arabidopsis ecotypes. AtRRP6L mutations affect the expression of known FLC regulatory antisense (AS RNAs AS I and II, and cause an increase in Histone3 K4 trimethylation (H3K4me3 at FLC. AtRRP6L1 and AtRRP6L2 function redundantly in regulation of FLC and also act independently of the exosome core complex. Moreover, we discovered a novel, long non-coding, non-polyadenylated antisense transcript (ASL, for Antisense Long originating from the FLC locus in wild type plants. The AtRRP6L proteins function as the main regulators of ASL synthesis, as these mutants show little or no ASL transcript. Unlike ASI/II, ASL associates with H3K27me3 regions of FLC, suggesting that it could function in the maintenance of H3K27 trimethylation during vegetative growth. AtRRP6L mutations also affect H3K27me3 levels and nucleosome density at the FLC locus. Furthermore, AtRRP6L1 physically associates with the ASL transcript and directly interacts with the FLC locus. We propose that AtRRP6L proteins participate in the maintenance of H3K27me3 at FLC via regulating ASL. Furthermore, AtRRP6Ls might participate in multiple FLC silencing pathways by regulating diverse antisense RNAs derived from the FLC locus.

  17. Accurate radiative transfer calculations for layered media.

    Selden, Adrian C

    2016-07-01

    Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics. PMID:27409700

  18. Accurate basis set truncation for wavefunction embedding

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.

    2013-07-01

    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  19. Accurate pose estimation for forensic identification

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk

    2010-04-01

    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  20. Accurate determination of characteristic relative permeability curves

    Krause, Michael H.; Benson, Sally M.

    2015-09-01

    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  1. Rank-based characterization of pollen assemblages collected by honey bees using a multi-locus metabarcoding approach1

    Richardson, Rodney T.; Lin, Chia-Hua; Quijia, Juan O.; Riusech, Natalia S.; Goodell, Karen; Johnson, Reed M.

    2015-01-01

    Premise of the study: Difficulties inherent in microscopic pollen identification have resulted in limited implementation for large-scale studies. Metabarcoding, a relatively novel approach, could make pollen analysis less onerous; however, improved understanding of the quantitative capacity of various plant metabarcode regions and primer sets is needed to ensure that such applications are accurate and precise. Methods and Results: We applied metabarcoding, targeting the ITS2, matK, and rbcL loci, to characterize six samples of pollen collected by honey bees, Apis mellifera. Additionally, samples were analyzed by light microscopy. We found significant rank-based associations between the relative abundance of pollen types within our samples as inferred by the two methods. Conclusions: Our findings suggest metabarcoding data from plastid loci, as opposed to the ribosomal locus, are more reliable for quantitative characterization of pollen assemblages. Furthermore, multilocus metabarcoding of pollen may be more reliable than single-locus analyses, underscoring the need for discovering novel barcodes and barcode combinations optimized for molecular palynology. PMID:26649264

  2. DISTRIBUTION OF ALLELIC VARIANTS OF HEXAPLOID WHEAT GERMPLASM AT XGWM261 AND PPD-D1 LOCUS

    Sonja Petrović

    2012-12-01

    Full Text Available Traits like plant height and response to photoperiod are involved in controlling many quality characteristics that breeders look into the desired genotype. Today, climatic changes in traditional wheat growing regions cause day temperature rising and water supply shortening. Exploitation of various semi-dwarfing (Rht and photoperiod response (Ppd genes could help the implementation of wheat breeding programs, especially selection of stabile and stress adaptable varieties targeted for different environments. Microsatellite gwm261 is located on Xgwm261 locus, and it is 0.6 cM distant from Rht8 gene on 2DS chromosome, which can also include Ppd1 gen for insensitivity to photoperiod. PCR screening of Croatian and foreign wheat varieties showed prevalence of 192 bp allele at Xgwm261 locus and photoperiod insensitive allele (Ppd-D1a. The results of this research could be useful for more accurate characterization and selection of Croatian wheat cultivars and foreign ones aiming to cross and create new adaptable varieties.

  3. A comparison of alternative methods to compute conditional genotype probabilities for genetic evaluation with finite locus models

    Dekkers Jack CM

    2003-11-01

    Full Text Available Abstract An increased availability of genotypes at marker loci has prompted the development of models that include the effect of individual genes. Selection based on these models is known as marker-assisted selection (MAS. MAS is known to be efficient especially for traits that have low heritability and non-additive gene action. BLUP methodology under non-additive gene action is not feasible for large inbred or crossbred pedigrees. It is easy to incorporate non-additive gene action in a finite locus model. Under such a model, the unobservable genotypic values can be predicted using the conditional mean of the genotypic values given the data. To compute this conditional mean, conditional genotype probabilities must be computed. In this study these probabilities were computed using iterative peeling, and three Markov chain Monte Carlo (MCMC methods – scalar Gibbs, blocking Gibbs, and a sampler that combines the Elston Stewart algorithm with iterative peeling (ESIP. The performance of these four methods was assessed using simulated data. For pedigrees with loops, iterative peeling fails to provide accurate genotype probability estimates for some pedigree members. Also, computing time is exponentially related to the number of loci in the model. For MCMC methods, a linear relationship can be maintained by sampling genotypes one locus at a time. Out of the three MCMC methods considered, ESIP, performed the best while scalar Gibbs performed the worst.

  4. Intra-locus sexual conflict and sexually antagonistic genetic variation in hermaphroditic animals

    Abbott, Jessica K.

    2010-01-01

    Intra-locus sexual conflict results when sex-specific selection pressures for a given trait act against the intra-sexual genetic correlation for that trait. It has been found in a wide variety of taxa in both laboratory and natural populations, but the importance of intra-locus sexual conflict and sexually antagonistic genetic variation in hermaphroditic organisms has rarely been considered. This is not so surprising given the conceptual and theoretical association of intra-locus sexual confl...

  5. Self Esteem, Locus of Control and Multidimensional Perfectionism as the Predictors of Subjective Well Being

    Zeynep Karatas; Ozlem Tagay

    2012-01-01

    The purpose of this study is to determine whether there is a relationship between self-esteem, locus of control and multidimensional perfectionism, and the extent to which the variables of self-esteem, locus of control and multidimensional perfectionism contribute to the prediction of subjective well-being. The study was carried out with 318 final year (fourth grade) university students. Subjective Well-Being Scale, Rosenberg Self-Esteem Scale, Rotter Internal External Locus of Control Scale ...

  6. Locus of Control and Career Interest of Sophomore Accountancy Students: Basis for Employment Path

    Jovielyn Mañibo; Elna Lopez

    2014-01-01

    This academic undertaking sought to determine the relationship between the locus of control and career interest of the respondents towards their future employment. The objectives of the study were to determine the respondents’ locus of control and career interest; to find if there is a significant relationship between the respondents’ locus of control and career interest and to develop an action plan that will gauge the students’ employment success as to their chosen field. In ...

  7. Healthy habits: The connection between diet, exercise, and locus of control

    Cobb-Clark, Deborah A.; Kassenböhmer, Sonja C.; Schurer, Stefanie

    2012-01-01

    This paper analyzes the relationship between individuals' locus of control and their decisions to exercise regularly, eat well, drink moderately, and avoid tobacco. Our primary goal is to assess the relative importance of the alternative pathways that potentially link locus of control to healthy habits. We find that individuals with an internal locus of control are more likely to eat well and exercise regularly. This link cannot be explained by the extent to which they are future-orientated a...

  8. Predictors of Parental Locus of Control in Mothers of Pre- and Early-Adolescents

    Freed, Rachel D.; Tompson, Martha C.

    2011-01-01

    Parental locus of control refers to parents’ perceived power and efficacy in child-rearing situations. This study explored parental locus of control and its correlates in 160 mothers of children ages 8–14 cross-sectionally and 1 year later. Maternal depression, maternal expressed emotion, and child internalizing and externalizing behavior were examined, along with a number of sociodemographic factors. Cross-sectional analyses indicated that external parental locus of control was associated wi...

  9. Conditional probabilities of identity of genes at a locus linked to a marker

    Chevalet, Claude; GILLOIS, M.; Vu Tien Khang Bourgoin, Jacqueline

    1984-01-01

    A method is given for determining the probabilities that genes are identical by descent, at a locus linked to a marker where phenotypic data are available. For tight linkage, such conditional probabilities of identity may differ very much from unconditional ones ; they depend on the dominance relationships between alleles at the marker locus, and on the allelic frequencies. Applications discussed refer to the calculation of general two-locus descent measures, to the validation of pedigre...

  10. Prevalence of Porphyromonas gingivalis Four rag Locus Genotypes in Patients of Orthodontic Gingivitis and Periodontitis

    Liu, Yi; Zhang, Yujie; Wang, Lili; GUO, YANG; Xiao, Shuiqing

    2013-01-01

    Porphyromonas gingivalis is considered as a major etiological agent in periodontal diseases and implied to result in gingival inflammation under orthodontic appliance. rag locus is a pathogenicity island found in Porphyromonas gingivalis. Four rag locus variants are different in pathogenicity of Porphyromonas gingivalis. Moreover, there are different racial and geographic differences in distribution of rag locus genotypes. In this study, we assessed the prevalence of Porphyromonas gingivalis ...

  11. Locus of Control and Peer Relationships Among Caucasian, Hispanic, Asian, and African American Adolescents

    KANG, HS; Chang, KE; Chen, C.; Greenberger, E

    2015-01-01

    © 2013, Springer Science+Business Media New York. Past research has shown that locus of control plays an important role in a wide range of behaviors, such as academic achievement and positive social behaviors. However, little is known about whether locus of control plays the same role in minority adolescents’ peer relationships. The current study examined ethnic differences in the associations between locus of control and peer relationships in early adolescence using samples from the Early Ch...

  12. Oakleaf: an S locus-linked mutation of Primula vulgaris that affects leaf and flower development

    Cocker, Jonathan; Webster, Margaret; Li, Jinhong; Wright, Jonathan; Kaithakottil, Gemy; Swarbreck, David; Gilmartin, Philip

    2015-01-01

    •In Primula vulgaris outcrossing is promoted through reciprocal herkogamy with insect-mediated cross-pollination between pin and thrum form flowers. Development of heteromorphic flowers is coordinated by genes at the S locus. To underpin construction of a genetic map facilitating isolation of these S locus genes, we have characterised Oakleaf, a novel S locus-linked mutant phenotype. •We combine phenotypic observation of flower and leaf development, with classical genetic analysis and next-ge...

  13. A novel stroke locus identified in a northern Sweden pedigree

    Janunger, T.; Nilsson-Ardnor, S.; Wiklund, P.-G.;

    2009-01-01

    OBJECTIVES: The population of northern Sweden is characterized by reduced genetic diversity and a high incidence of stroke. We sought to reduce genetic variation further, using genealogic analysis in a set of nuclear families affected by stroke, and we subsequently performed a genome-wide scan to...... of 4.81 on chromosome 9q31-q33 was detected. Haplotype analysis identified a common 2.2-megabase interval in the chromosomal region in 4 of the nuclear families, where an overrepresentation of intracerebral hemorrhage was observed. CONCLUSIONS: We have identified a novel susceptibility locus for...... stroke. Haplotype analysis suggests that a shared genetic factor is of particular importance for intracerebral hemorrhage....

  14. Burnout, locus de control y deportistas de alto rendimiento

    Medina Mojena, Greisy; García Ucha, Francisco Enrique

    2002-01-01

    Los estudios sobre burnout comenzaron en los 70 por Freudenberg (1974) y en los 80 en el deporte. En Cuba este es de los primeros sobre el tema. Se estudiaron 40 deportistas de alto rendimiento de pesas, balonmano, baloncesto y tackewondo. Con una edad entre los 18 y 28 años y experiencia deportiva entre 5 y 16 años. Las técnicas utilizadas son una adaptación, de Garcés de Los Fayos (1999) del Maslach Burnout Inventory (1981) y un test de Locus de control. Los principales resultados c...

  15. Male-pattern baldness susceptibility locus at 20p11

    Richards, J. Brent; Yuan, Xin; Geller, Frank; Waterworth, Dawn; Bataille, Veronique; Glass, Daniel; Song, Kijoung; Waeber, Gerard; Vollenweider, Peter; Aben, Katja K. H; Lambertus A Kiemeney; Walters, Bragi; Soranzo, Nicole; Thorsteinsdottir, Unnur; Kong, Augustine

    2008-01-01

    We conducted a genome-wide association study for androgenic alopecia in 1,125 men and identified a newly associated locus at chromosome 20p11.22, confirmed in three independent cohorts (n = 1,650; OR = 1.60, P = 1.1 × 10−14 for rs1160312). The one man in seven who harbors risk alleles at both 20p11.22 and AR (encoding the androgen receptor) has a sevenfold-increased odds of androgenic alopecia (OR = 7.12, P = 3.7 × 10−15).

  16. Experimentation of Fish Swimming Based on Tracking Locomotion Locus

    Hui Yan; Yu-min Su; Liang Yang

    2008-01-01

    There are many kinds of swimming mode in the fish world, and we investigated two of them, used by cyprinids and bulltrout. In this paper we track the locomotion locus by marks in different flow velocity from 0.2 m.s-1 to 0.8 m's-1. By fit the data above we could find out the locomotion mechanism of the two kinds of fish and generate a mathematical model of fish kinematics. The cyprinid fish has a greater oscillation period and amplitude compared with the bulltrout, and the bulltrout changes velocity mainly by controlling frequency of oscillation.

  17. Accurate strand-specific quantification of viral RNA.

    Nicole E Plaskon

    Full Text Available The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR assays are increasingly being used for this purpose, but the accuracy of these assays depends on the assumption that the amount of cDNA measured during the quantitative PCR (qPCR step accurately reflects amounts of a specific viral RNA strand present in the RT reaction. To specifically test this assumption, we developed multiple ssqPCR assays for the positive-strand RNA virus o'nyong-nyong (ONNV that were based upon the most prevalent ssqPCR assay design types in the literature. We then compared various parameters of the ONNV-specific assays. We found that an assay employing standard unmodified virus-specific primers failed to discern the difference between cDNAs generated from virus specific primers and those generated through false priming. Further, we were unable to accurately measure levels of ONNV (- strand RNA with this assay when higher levels of cDNA generated from the (+ strand were present. Taken together, these results suggest that assays of this type do not accurately quantify levels of the anti-genomic strand present during RNA virus infectious cycles. However, an assay permitting the use of a tag-specific primer was able to distinguish cDNAs transcribed from ONNV (- strand RNA from other cDNAs present, thus allowing accurate quantification of the anti-genomic strand. We also report the sensitivities of two different detection strategies and chemistries, SYBR(R Green and DNA hydrolysis probes, used with our tagged ONNV-specific ssqPCR assays. Finally, we describe development, design and validation of ssqPCR assays for chikungunya virus (CHIKV, the recent cause of large outbreaks of disease in the Indian Ocean

  18. Locus of Control Effect on Creative Thinking in Secondary School Children

    AYDIN, Betül; CANEL, A.Nilgün

    2013-01-01

    The aim of this research is to explain the effects of locus of control on creative thinking at the level of high school adolescents. This research has been done among the 135 students. The Torrance Test of Creative Thinking has been used to measure the creativity. The Nowicki-Strickland Locus of Control Scale has been used to measure the locus of control. Finally, the effects of verbal flexibility, figural fluency and figural eleboration on locus of control have been examined. Key Words : Cre...

  19. Multiple myeloma

    Conventional radiography is the means generally used in the assessment of skeletal involvement in multiple myeloma. Many findings such as osteolytic lesions, fractures, and osteoporosis are characteristic of myeloma. However, it seems likely that the extent of bone destruction is sometimes underestimated by radiography. Bone scintigraphy is considered a sensitive technique for the detection of skeletal metastatic lesions, but contradictory results have been reported in multiple myeloma, and many reports indicate that bone scintigraphy is less effective than conventional radiography. This phenomenon could depend on the fact that myeloma is a bone-marrow disease; bone structure is only indirectly involved; furthermore, studies have demonstrated that myelomatous lesions induce, by osteclast activation, larger bone resorption than new bone formation. On this basis the authors proposed the evaluation of bone marrow scanning plus bone scanning in comparison to conventional diagnostic radiology for the detection of skeletal involvement in multiple myeloma

  20. Accurate Telescope Mount Positioning with MEMS Accelerometers

    Mészáros, László; Pál, András; Csépány, Gergely

    2014-01-01

    This paper describes the advantages and challenges of applying microelectromechanical accelerometer systems (MEMS accelerometers) in order to attain precise, accurate and stateless positioning of telescope mounts. This provides a completely independent method from other forms of electronic, optical, mechanical or magnetic feedback or real-time astrometry. Our goal is to reach the sub-arcminute range which is well smaller than the field-of-view of conventional imaging telescope systems. Here we present how this sub-arcminute accuracy can be achieved with very cheap MEMS sensors and we also detail how our procedures can be extended in order to attain even finer measurements. In addition, our paper discusses how can a complete system design be implemented in order to be a part of a telescope control system.

  1. Accurate estimation of indoor travel times

    Prentow, Thor Siiger; Blunck, Henrik; Stisen, Allan;

    2014-01-01

    the InTraTime method for accurately estimating indoor travel times via mining of historical and real-time indoor position traces. The method learns during operation both travel routes, travel times and their respective likelihood---both for routes traveled as well as for sub-routes thereof. InTraTime...... allows to specify temporal and other query parameters, such as time-of-day, day-of-week or the identity of the traveling individual. As input the method is designed to take generic position traces and is thus interoperable with a variety of indoor positioning systems. The method's advantages include...... a minimal-effort setup and self-improving operations due to unsupervised learning---as it is able to adapt implicitly to factors influencing indoor travel times such as elevators, rotating doors or changes in building layout. We evaluate and compare the proposed InTraTime method to indoor adaptions...

  2. Accurate sky background modelling for ESO facilities

    Full text: Ground-based measurements like e.g. high resolution spectroscopy are heavily influenced by several physical processes. Amongst others, line absorption/ emission, air glow by OH molecules, and scattering of photons within the earth's atmosphere make observations in particular from facilities like the future European extremely large telescope a challenge. Additionally, emission from unresolved extrasolar objects, the zodiacal light, the moon and even thermal emission from the telescope and the instrument contribute significantly to the broad band background over a wide wavelength range. In our talk we review these influences and give an overview on how they can be accurately modeled for increasing the overall precision of spectroscopic and imaging measurements. (author)

  3. Toward Accurate and Quantitative Comparative Metagenomics.

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  4. Accurate valence band width of diamond

    An accurate width is determined for the valence band of diamond by imaging photoelectron momentum distributions for a variety of initial- and final-state energies. The experimental result of 23.0±0.2 eV2 agrees well with first-principles quasiparticle calculations (23.0 and 22.88 eV) and significantly exceeds the local-density-functional width, 21.5±0.2 eV2. This difference quantifies effects of creating an excited hole state (with associated many-body effects) in a band measurement vs studying ground-state properties treated by local-density-functional calculations. copyright 1997 The American Physical Society

  5. Accurate Weather Forecasting for Radio Astronomy

    Maddalena, Ronald J.

    2010-01-01

    The NRAO Green Bank Telescope routinely observes at wavelengths from 3 mm to 1 m. As with all mm-wave telescopes, observing conditions depend upon the variable atmospheric water content. The site provides over 100 days/yr when opacities are low enough for good observing at 3 mm, but winds on the open-air structure reduce the time suitable for 3-mm observing where pointing is critical. Thus, to maximum productivity the observing wavelength needs to match weather conditions. For 6 years the telescope has used a dynamic scheduling system (recently upgraded; www.gb.nrao.edu/DSS) that requires accurate multi-day forecasts for winds and opacities. Since opacity forecasts are not provided by the National Weather Services (NWS), I have developed an automated system that takes available forecasts, derives forecasted opacities, and deploys the results on the web in user-friendly graphical overviews (www.gb.nrao.edu/ rmaddale/Weather). The system relies on the "North American Mesoscale" models, which are updated by the NWS every 6 hrs, have a 12 km horizontal resolution, 1 hr temporal resolution, run to 84 hrs, and have 60 vertical layers that extend to 20 km. Each forecast consists of a time series of ground conditions, cloud coverage, etc, and, most importantly, temperature, pressure, humidity as a function of height. I use the Liebe's MWP model (Radio Science, 20, 1069, 1985) to determine the absorption in each layer for each hour for 30 observing wavelengths. Radiative transfer provides, for each hour and wavelength, the total opacity and the radio brightness of the atmosphere, which contributes substantially at some wavelengths to Tsys and the observational noise. Comparisons of measured and forecasted Tsys at 22.2 and 44 GHz imply that the forecasted opacities are good to about 0.01 Nepers, which is sufficient for forecasting and accurate calibration. Reliability is high out to 2 days and degrades slowly for longer-range forecasts.

  6. Locus Reference Genomic sequences: An improved basis for describing human DNA variants

    Dalgleish, Raymond

    2010-04-15

    As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

  7. Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation.

    González, Alvaro J; Setty, Manu; Leslie, Christina S

    2015-11-01

    We carried out an integrative analysis of enhancer landscape and gene expression dynamics during hematopoietic differentiation using DNase-seq, histone mark ChIP-seq and RNA sequencing to model how the early establishment of enhancers and regulatory locus complexity govern gene expression changes at cell state transitions. We found that high-complexity genes-those with a large total number of DNase-mapped enhancers across the lineage-differ architecturally and functionally from low-complexity genes, achieve larger expression changes and are enriched for both cell type-specific and transition enhancers, which are established in hematopoietic stem and progenitor cells and maintained in one differentiated cell fate but lost in others. We then developed a quantitative model to accurately predict gene expression changes from the DNA sequence content and lineage history of active enhancers. Our method suggests a new mechanistic role for PU.1 at transition peaks during B cell specification and can be used to correct assignments of enhancers to genes. PMID:26390058

  8. Thorough investigation of a canine autoinflammatory disease (AID confirms one main risk locus and suggests a modifier locus for amyloidosis.

    Mia Olsson

    Full Text Available Autoinflammatory disease (AID manifests from the dysregulation of the innate immune system and is characterised by systemic and persistent inflammation. Clinical heterogeneity leads to patients presenting with one or a spectrum of phenotypic signs, leading to difficult diagnoses in the absence of a clear genetic cause. We used separate genome-wide SNP analyses to investigate five signs of AID (recurrent fever, arthritis, breed specific secondary dermatitis, otitis and systemic reactive amyloidosis in a canine comparative model, the pure bred Chinese Shar-Pei. Analysis of 255 DNA samples revealed a shared locus on chromosome 13 spanning two peaks of association. A three-marker haplotype based on the most significant SNP (p<2.6×10(-8 from each analysis showed that one haplotypic pair (H13-11 was present in the majority of AID individuals, implicating this as a shared risk factor for all phenotypes. We also noted that a genetic signature (F ST distinguishing the phenotypic extremes of the breed specific Chinese Shar-Pei thick and wrinkled skin, flanked the chromosome 13 AID locus; suggesting that breed development and differentiation has played a parallel role in the genetics of breed fitness. Intriguingly, a potential modifier locus for amyloidosis was revealed on chromosome 14, and an investigation of candidate genes from both this and the chromosome 13 regions revealed significant (p<0.05 renal differential expression in four genes previously implicated in kidney or immune health (AOAH, ELMO1, HAS2 and IL6. These results illustrate that phenotypic heterogeneity need not be a reflection of genetic heterogeneity, and that genetic modifiers of disease could be masked if syndromes were not first considered as individual clinical signs and then as a sum of their component parts.

  9. Characterizing the Retinoblastoma 1 Locus: a plethora of putative elements for Rb1 regulation by in silico analysis

    Mohammadreza eHajjari

    2014-01-01

    Full Text Available Limited understanding of the Rb1 locus hinders genetic and epigenetic analyses of Retinoblastoma, a childhood cancer of the nervous systems. In this study, we used in silico tools to investigate and review putative genetic and epigenetic elements of the Rb1 gene. We report transcription start sites, CpG islands, and regulatory moieties that are likely to influence transcriptional states of this gene. These might contribute genetic and epigenetic information modulating tissue-specific transcripts and expression levels of the Rb1 gene. The elements we identified include tandem repeats that reside within or next to some identified putative CpG islands near Rb1’s transcriptional start site, and that are likely to be polymorphic among individuals. Our analyses highlight the complexity of this gene and suggest opportunities and limitations for future studies of retinoblastoma, genetic counseling, and the accurate identification of patients at greater risk of developing the malignancy.

  10. CDKN2B expression and subcutaneous adipose tissue expandability: Possible influence of the 9p21 atherosclerosis locus

    Svensson, Per-Arne; Wahlstrand, Björn; Olsson, Maja [Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg (Sweden); Froguel, Philippe; Falchi, Mario [Department of Genomics of Common Disease, School of Public Health, Imperial College London (United Kingdom); Bergman, Richard N. [Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA (United States); McTernan, Philip G. [Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry (United Kingdom); Hedner, Thomas; Carlsson, Lena M.S. [Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg (Sweden); Jacobson, Peter, E-mail: peter.jacobson@medfak.gu.se [Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg (Sweden)

    2014-04-18

    Highlights: • The tumor suppressor gene CDKN2B is highly expressed in human adipose tissue. • Risk alleles at the 9p21 locus modify CDKN2B expression in a BMI-dependent fashion. • There is an inverse relationship between expression of CDKN2B and adipogenic genes. • CDKN2B expression influences to postprandial triacylglycerol clearance. • CDKN2B expression in adipose tissue is linked to markers of hepatic steatosis. - Abstract: Risk alleles within a gene desert at the 9p21 locus constitute the most prevalent genetic determinant of cardiovascular disease. Previous research has demonstrated that 9p21 risk variants influence gene expression in vascular tissues, yet the biological mechanisms by which this would mediate atherosclerosis merits further investigation. To investigate possible influences of this locus on other tissues, we explored expression patterns of 9p21-regulated genes in a panel of multiple human tissues and found that the tumor suppressor CDKN2B was highly expressed in subcutaneous adipose tissue (SAT). CDKN2B expression was regulated by obesity status, and this effect was stronger in carriers of 9p21 risk alleles. Covariation between expression of CDKN2B and genes implemented in adipogenesis was consistent with an inhibitory effect of CDKN2B on SAT proliferation. Moreover, studies of postprandial triacylglycerol clearance indicated that CDKN2B is involved in down-regulation of SAT fatty acid trafficking. CDKN2B expression in SAT correlated with indicators of ectopic fat accumulation, including markers of hepatic steatosis. Among genes regulated by 9p21 risk variants, CDKN2B appears to play a significant role in the regulation of SAT expandability, which is a strong determinant of lipotoxicity and therefore might contribute to the development of atherosclerosis.

  11. CDKN2B expression and subcutaneous adipose tissue expandability: Possible influence of the 9p21 atherosclerosis locus

    Highlights: • The tumor suppressor gene CDKN2B is highly expressed in human adipose tissue. • Risk alleles at the 9p21 locus modify CDKN2B expression in a BMI-dependent fashion. • There is an inverse relationship between expression of CDKN2B and adipogenic genes. • CDKN2B expression influences to postprandial triacylglycerol clearance. • CDKN2B expression in adipose tissue is linked to markers of hepatic steatosis. - Abstract: Risk alleles within a gene desert at the 9p21 locus constitute the most prevalent genetic determinant of cardiovascular disease. Previous research has demonstrated that 9p21 risk variants influence gene expression in vascular tissues, yet the biological mechanisms by which this would mediate atherosclerosis merits further investigation. To investigate possible influences of this locus on other tissues, we explored expression patterns of 9p21-regulated genes in a panel of multiple human tissues and found that the tumor suppressor CDKN2B was highly expressed in subcutaneous adipose tissue (SAT). CDKN2B expression was regulated by obesity status, and this effect was stronger in carriers of 9p21 risk alleles. Covariation between expression of CDKN2B and genes implemented in adipogenesis was consistent with an inhibitory effect of CDKN2B on SAT proliferation. Moreover, studies of postprandial triacylglycerol clearance indicated that CDKN2B is involved in down-regulation of SAT fatty acid trafficking. CDKN2B expression in SAT correlated with indicators of ectopic fat accumulation, including markers of hepatic steatosis. Among genes regulated by 9p21 risk variants, CDKN2B appears to play a significant role in the regulation of SAT expandability, which is a strong determinant of lipotoxicity and therefore might contribute to the development of atherosclerosis

  12. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  13. Fine mapping of the Schnyder's crystalline corneal dystrophy locus.

    Theendakara, Veena; Tromp, Gerard; Kuivaniemi, Helena; White, Peter S; Panchal, Seema; Cox, Jennifer; Winters, R Scott; Riebeling, Petra; Tost, Frank; Hoeltzenbein, Maria; Tervo, Timo M; Henn, Wolfram; Denniger, Elke; Krause, Matthias; Koksal, Murat; Kargi, Sebnem; Ugurbas, Suat H; Latvala, Terho; Shearman, Amanda M; Weiss, Jayne S

    2004-05-01

    Schnyder's crystalline corneal dystrophy (SCCD) is a rare autosomal dominant eye disease with a spectrum of clinical manifestations that may include bilateral corneal clouding, arcus lipoides, and anterior corneal crystalline cholesterol deposition. We have previously performed a genome-wide linkage analysis on two large Swede-Finn families and mapped the SCCD locus to a 16-cM interval between markers D1S2633 and D1S228 on chromosome 1p36. We have collected 11 additional families from Finland, Germany, Turkey, and USA to narrow the critical region for SCCD. Here, we have used haplotype analysis with densely spaced microsatellite markers in a total of 13 families to refine the candidate interval. A common disease haplotype was observed among the four Swede-Finn families indicating the presence of a founder effect. Recombination results from all 13 families refined the SCCD locus to 2.32 Mbp between markers D1S1160 and D1S1635. Within this interval, identity-by-state was present in all 13 families for two markers D1S244 and D1S3153, further refining the candidate region to 1.58 Mbp. PMID:15034782

  14. Allelism of Genes in the Ml-a locus

    Giese, Nanna Henriette; Jensen, Hans Peter; Jørgensen, Jørgen Helms

    1980-01-01

    Seven barley lines or varieties, each with a different gene at the Ml-a locus for resistance to Erysiphe graminis were intercrossed. Progeny testing of the F2s using two different fungal isolates per cross provided evidence that there are two or more loci in the Ml-a region. Apparent recombinants...... were also screened for recombination between the Hor1 and Hor2 loci which are situated either side of the Ml-a locus. The cross between Ricardo and Iso42R (Rupee) yielded one possible recombinant, with Ml-a3 and Ml-a(Rul) in the coupling phase; other recombinants had wild-type genes in the coupling...... phase. Iso20R, derived from Hordeum spontaneum 'H204', carrying Ml-a6, had an additional gene, in close coupling with Ml-a6, tentatively named Ml-aSp2 or Reglv, causing an intermediate infection type with isolate EmA30. It is suggested that Ml-a(Ar) in Emir and Ml-a(Rul), shown to differ from other Ml...

  15. Geographic distribution of haplotype diversity at the bovine casein locus

    Moazami-Goudarzi Katy

    2004-03-01

    Full Text Available Abstract The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine breeds in Europe was found to decrease significantly from the south to the north and from the east to the west. Such geographic patterns of cattle genetic variation at the casein locus may be a result of the domestication process of modern cattle as well as geographically differentiated natural or artificial selection. The comparison of African Bos taurus and Bos indicus breeds allowed the identification of several Bos indicus specific haplotypes (CSN1S1*C-CSN2*A2-CSN3*AI/CSN3*H that are not found in pure taurine breeds. The occurrence of such haplotypes in southern European breeds also suggests that an introgression of indicine genes into taurine breeds could have contributed to the distribution of the genetic variation observed.

  16. Cynomolgus macaque (Macaca fascicularis) immunoglobulin heavy chain locus description.

    Yu, Guo-Yun; Mate, Suzanne; Garcia, Karla; Ward, Michael D; Brueggemann, Ernst; Hall, Matthew; Kenny, Tara; Sanchez-Lockhart, Mariano; Lefranc, Marie-Paule; Palacios, Gustavo

    2016-07-01

    Cynomolgus macaques (Macaca fascicularis) have become an important animal model for biomedical research. In particular, it is the animal model of choice for the development of vaccine candidates associated with emerging dangerous pathogens. Despite their increasing importance as animal models, the cynomolgus macaque genome is not fully characterized, hindering molecular studies for this model. More importantly, the lack of knowledge about the immunoglobulin (IG) locus organization directly impacts the analysis of the humoral response in cynomolgus macaques. Recent advances in next generation sequencing (NGS) technologies to analyze IG repertoires open the opportunity to deeply characterize the humoral immune response. However, the IG locus organization for the animal is required to completely dissect IG repertoires. Here, we describe the localization and organization of the rearranging IG heavy (IGH) genes on chromosome 7 of the cynomolgus macaque draft genome. Our annotation comprises 108 functional genes which include 63 variable (IGHV), 38 diversity (IGHD), and 7 joining (IGHJ) genes. For validation, we provide RNA transcript data for most of the IGHV genes and all of the annotated IGHJ genes, as well as proteomic data to validate IGH constant genes. The description and annotation of the rearranging IGH genes for the cynomolgus macaques will significantly facilitate scientific research. This is particularly relevant to dissect the immune response during vaccination or infection with dangerous pathogens such as Ebola, Marburg and other emerging pathogens where non-human primate models play a significant role for countermeasure development. PMID:27233955

  17. Multiple Sclerosis.

    Plummer, Nancy; Michael, Nancy, Ed.

    This module on multiple sclerosis is intended for use in inservice or continuing education programs for persons who administer medications in long-term care facilities. Instructor information, including teaching suggestions, and a listing of recommended audiovisual materials and their sources appear first. The module goal and objectives are then…

  18. Multiple myeloma

    Multiple myeloma is a malignant plasma cell tumor that is thought to originate proliferation of a single clone of abnormal plasma cell resulting production of a whole monoclonal paraprotein. The authors experienced a case of multiple myeloma with severe mandibular osteolytic lesions in 46-year-old female. As a result of careful analysis of clinical, radiological, histopathological features, and laboratory findings, we diagnosed it as multiple myeloma, and the following results were obtained. 1. Main clinical symptoms were intermittent dull pain on the mandibular body area, abnormal sensation of lip and pain due to the fracture on the right clavicle. 2. Laboratory findings revealed M-spike, reversed serum albumin-globulin ratio, markedly elevated ESR and hypercalcemia. 3. Radiographically, multiple osteolytic punched-out radiolucencies were evident on the skull, zygoma, jaw bones, ribs, clavicle and upper extremities. Enlarged liver and increased uptakes on the lesional sites in RN scan were also observed. 4. Histopathologically, markedly hypercellular marrow with sheets of plasmoblasts and megakaryocytes were also observed.

  19. Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia.

    Sier-Ching Chantha

    Full Text Available Self-incompatibility (SI is the flowering plant reproductive system in which self pollen tube growth is inhibited, thereby preventing self-fertilization. SI has evolved independently in several different flowering plant lineages. In all Brassicaceae species in which the molecular basis of SI has been investigated in detail, the product of the S-locus receptor kinase (SRK gene functions as receptor in the initial step of the self pollen-rejection pathway, while that of the S-locus cysteine-rich (SCR gene functions as ligand. Here we examine the hypothesis that the S locus in the Brassicaceae genus Leavenworthia is paralogous with the S locus previously characterized in other members of the family. We also test the hypothesis that self-compatibility in this group is based on disruption of the pollen ligand-producing gene. Sequence analysis of the S-locus genes in Leavenworthia, phylogeny of S alleles, gene expression patterns, and comparative genomics analyses provide support for both hypotheses. Of special interest are two genes located in a non-S locus genomic region of Arabidopsis lyrata that exhibit domain structures, sequences, and phylogenetic histories similar to those of the S-locus genes in Leavenworthia, and that also share synteny with these genes. These A. lyrata genes resemble those comprising the A. lyrata S locus, but they do not function in self-recognition. Moreover, they appear to belong to a lineage that diverged from the ancestral Brassicaceae S-locus genes before allelic diversification at the S locus. We hypothesize that there has been neo-functionalization of these S-locus-like genes in the Leavenworthia lineage, resulting in evolution of a separate ligand-receptor system of SI. Our results also provide support for theoretical models that predict that the least constrained pathway to the evolution of self-compatibility is one involving loss of pollen gene function.

  20. ERBB3-rs2292239 as primary type 1 diabetes association locus among non-HLA genes in Chinese.

    Sun, Chengjun; Wei, Haiyan; Chen, Xiuli; Zhao, Zhuhui; Du, Hongwei; Song, Wenhui; Yang, Yu; Zhang, Miaoying; Lu, Wei; Pei, Zhou; Xi, Li; Yan, Jian; Zhi, Dijing; Cheng, Ruoqian; Luo, Feihong

    2016-09-01

    Type 1 diabetes (T1D) is an autoimmune disease that has strong contribution of genetic factors to its etiology. We aimed to assess the genetic association between non-HLA genes and T1D in a Chinese case-control cohort recruited from multiple centers consisting of 364 patients with T1D and 719 unrelated healthy children. We genotyped 55 single nucleotide polymorphisms (SNP) markers located in 16 non-HLA genes (VTCN1, PTPN22, CTLA4, SUMO4, CD274, IL2RA, INS, DHCR7, ERBB3, VDR, CYP27B1, CD69, CD276, PTPN2, UBASH3A, and IL2RB) using SNaPshot multiple single-base extension methods. After multivariate analysis and correction for multiple comparisons, we identified the SNP rs2292239 in ERBB3 gene were significantly associated with T1D. The frequency of the major G allele was significantly decreased in patients with T1D (68.8% in T1D vs 77.3% in controls, OR 0.65, 95% CI 0.53-0.79, P = 0.02), and the minor allele T was associated with an increased risk of T1D (OR 1.55, 95% CI 1.26-1.90, P = 0.02). Our haplotype analysis confirmed that rs2292239 was the primary T1D association locus in our current investigation. These results indicated that the ERBB3-rs2292239 was the primary T1D association locus among the investigated 55 SNPs in 16 non-HLA genes in Chinese Han population. PMID:27331016

  1. Multiple Sparse Representations Classification.

    Plenge, Esben; Klein, Stefan; Klein, Stefan S; Niessen, Wiro J; Meijering, Erik

    2015-01-01

    Sparse representations classification (SRC) is a powerful technique for pixelwise classification of images and it is increasingly being used for a wide variety of image analysis tasks. The method uses sparse representation and learned redundant dictionaries to classify image pixels. In this empirical study we propose to further leverage the redundancy of the learned dictionaries to achieve a more accurate classifier. In conventional SRC, each image pixel is associated with a small patch surrounding it. Using these patches, a dictionary is trained for each class in a supervised fashion. Commonly, redundant/overcomplete dictionaries are trained and image patches are sparsely represented by a linear combination of only a few of the dictionary elements. Given a set of trained dictionaries, a new patch is sparse coded using each of them, and subsequently assigned to the class whose dictionary yields the minimum residual energy. We propose a generalization of this scheme. The method, which we call multiple sparse representations classification (mSRC), is based on the observation that an overcomplete, class specific dictionary is capable of generating multiple accurate and independent estimates of a patch belonging to the class. So instead of finding a single sparse representation of a patch for each dictionary, we find multiple, and the corresponding residual energies provides an enhanced statistic which is used to improve classification. We demonstrate the efficacy of mSRC for three example applications: pixelwise classification of texture images, lumen segmentation in carotid artery magnetic resonance imaging (MRI), and bifurcation point detection in carotid artery MRI. We compare our method with conventional SRC, K-nearest neighbor, and support vector machine classifiers. The results show that mSRC outperforms SRC and the other reference methods. In addition, we present an extensive evaluation of the effect of the main mSRC parameters: patch size, dictionary size, and

  2. Fast and Provably Accurate Bilateral Filtering.

    Chaudhury, Kunal N; Dabhade, Swapnil D

    2016-06-01

    The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires O(S) operations per pixel, where S is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to O(1) per pixel for any arbitrary S . The algorithm has a simple implementation involving N+1 spatial filterings, where N is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to estimate the order N required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with the state-of-the-art methods in terms of speed and accuracy. PMID:27093722

  3. Accurate adiabatic correction in the hydrogen molecule

    Pachucki, Krzysztof, E-mail: krp@fuw.edu.pl [Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw (Poland); Komasa, Jacek, E-mail: komasa@man.poznan.pl [Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań (Poland)

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  4. Accurate fission data for nuclear safety

    Solders, A; Jokinen, A; Kolhinen, V S; Lantz, M; Mattera, A; Penttila, H; Pomp, S; Rakopoulos, V; Rinta-Antila, S

    2013-01-01

    The Accurate fission data for nuclear safety (AlFONS) project aims at high precision measurements of fission yields, using the renewed IGISOL mass separator facility in combination with a new high current light ion cyclotron at the University of Jyvaskyla. The 30 MeV proton beam will be used to create fast and thermal neutron spectra for the study of neutron induced fission yields. Thanks to a series of mass separating elements, culminating with the JYFLTRAP Penning trap, it is possible to achieve a mass resolving power in the order of a few hundred thousands. In this paper we present the experimental setup and the design of a neutron converter target for IGISOL. The goal is to have a flexible design. For studies of exotic nuclei far from stability a high neutron flux (10^12 neutrons/s) at energies 1 - 30 MeV is desired while for reactor applications neutron spectra that resembles those of thermal and fast nuclear reactors are preferred. It is also desirable to be able to produce (semi-)monoenergetic neutrons...

  5. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization

    Klau Gunnar W

    2007-07-01

    Full Text Available Abstract Background The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. Results We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP. We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. Conclusion The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

  6. Population variability complicates the accurate detection of climate change responses.

    McCain, Christy; Szewczyk, Tim; Bracy Knight, Kevin

    2016-06-01

    The rush to assess species' responses to anthropogenic climate change (CC) has underestimated the importance of interannual population variability (PV). Researchers assume sampling rigor alone will lead to an accurate detection of response regardless of the underlying population fluctuations of the species under consideration. Using population simulations across a realistic, empirically based gradient in PV, we show that moderate to high PV can lead to opposite and biased conclusions about CC responses. Between pre- and post-CC sampling bouts of modeled populations as in resurvey studies, there is: (i) A 50% probability of erroneously detecting the opposite trend in population abundance change and nearly zero probability of detecting no change. (ii) Across multiple years of sampling, it is nearly impossible to accurately detect any directional shift in population sizes with even moderate PV. (iii) There is up to 50% probability of detecting a population extirpation when the species is present, but in very low natural abundances. (iv) Under scenarios of moderate to high PV across a species' range or at the range edges, there is a bias toward erroneous detection of range shifts or contractions. Essentially, the frequency and magnitude of population peaks and troughs greatly impact the accuracy of our CC response measurements. Species with moderate to high PV (many small vertebrates, invertebrates, and annual plants) may be inaccurate 'canaries in the coal mine' for CC without pertinent demographic analyses and additional repeat sampling. Variation in PV may explain some idiosyncrasies in CC responses detected so far and urgently needs more careful consideration in design and analysis of CC responses. PMID:26725404

  7. An accurate and portable solid state neutron rem meter

    Accurately resolving the ambient neutron dose equivalent spanning the thermal to 15 MeV energy range with a single configuration and lightweight instrument is desirable. This paper presents the design of a portable, high intrinsic efficiency, and accurate neutron rem meter whose energy-dependent response is electronically adjusted to a chosen neutron dose equivalent standard. The instrument may be classified as a moderating type neutron spectrometer, based on an adaptation to the classical Bonner sphere and position sensitive long counter, which, simultaneously counts thermalized neutrons by high thermal efficiency solid state neutron detectors. The use of multiple detectors and moderator arranged along an axis of symmetry (e.g., long axis of a cylinder) with known neutron-slowing properties allows for the construction of a linear combination of responses that approximate the ambient neutron dose equivalent. Variations on the detector configuration are investigated via Monte Carlo N-Particle simulations to minimize the total instrument mass while maintaining acceptable response accuracy—a dose error less than 15% for bare 252Cf, bare AmBe, an epi-thermal and mixed monoenergetic sources is found at less than 4.5 kg moderator mass in all studied cases. A comparison of the energy dependent dose equivalent response and resultant energy dependent dose equivalent error of the present dosimeter to commercially-available portable rem meters and the prior art are presented. Finally, the present design is assessed by comparison of the simulated output resulting from applications of several known neutron sources and dose rates

  8. In depth analysis of the Sox4 gene locus that consists of sense and natural antisense transcripts.

    Ling, King-Hwa; Brautigan, Peter J; Moore, Sarah; Fraser, Rachel; Leong, Melody Pui-Yee; Leong, Jia-Wen; Zainal Abidin, Shahidee; Lee, Han-Chung; Cheah, Pike-See; Raison, Joy M; Babic, Milena; Lee, Young Kyung; Daish, Tasman; Mattiske, Deidre M; Mann, Jeffrey R; Adelson, David L; Thomas, Paul Q; Hahn, Christopher N; Scott, Hamish S

    2016-06-01

    SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene expression during post-mitotic cell differentiation within the mammalian brain. Sox4 gene locus has been previously characterized with multiple sense and overlapping natural antisense transcripts [1], [2]. Here we provide accompanying data on various analyses performed and described in Ling et al. [2]. The data include a detail description of various features found at Sox4 gene locus, additional experimental data derived from RNA-Fluorescence in situ Hybridization (RNA-FISH), Western blotting, strand-specific reverse-transcription quantitative polymerase chain reaction (RT-qPCR), gain-of-function and in situ hybridization (ISH) experiments. All the additional data provided here support the existence of an endogenous small interfering- or PIWI interacting-like small RNA known as Sox4_sir3, which origin was found within the overlapping region consisting of a sense and a natural antisense transcript known as Sox4ot1. PMID:26958646

  9. Multiple Sklerose

    Hoffmann, Sarah

    2010-01-01

    Background: Multiple Sclerosis (MS) is the most common disabling neurological disease affecting young adults and the number of chronically sick MS patients to be found in the world of employment is on the increase. Research activities in the field of MS are numerous and wide-ranging. However, precise bibliometric analyses of research on the subject of MS do not exist so far. Methods: The present dissertation employs classical bibliometric tools with novel scientometric and visualizing tec...

  10. An investigation of the HUMVWA31A locus in British Caucasians

    Drozd, M A; Archard, L; Lincoln, P J;

    1994-01-01

    A number of short tandem repeat (STR) loci are currently being examined for their usefulness as markers of identity; HUMVWA31A is one such locus. We used a high-sieving agarose technique to type 200 British Caucasians for this locus. Comparison of the resultant allele frequencies with other...

  11. The Relationship between Religious Attitudes, Locus of Control and Tendency to Substace Abuse in University Students

    Farhad Asghari

    2013-05-01

    Full Text Available Aim: The purpose of this study was the study of relationship between religious attitudes, locus of control and tendency to substance abuse among students of Guilan University. Method: The research design was correlational design. For this purpose, 340 university students of Guilan University selected through Morgan table by cluster randome sampling. Allport religious orientation, Ratter locus of control and addiction potential scale administered among selected sample. Results: The results showed significant relationship between religious attitude, locus of control and tendency to substance abuse. That is religious attitude, locus of control entered in regression model as significant predictors. Also there was significant relationship between religious attitude, and locus of control. Altogheder, results showed that people with internal religious attitude have internal locus of control and lower tendency to substance abuse. Also, people with external religious attitude have external locus of control and higher tendency to substance abuse. Conclusion: According to the results, we can conclude that religious attitude and locus of control play important role on tendency to substance abuse.

  12. Locus of Control, Attributional Style and Discipline Problems in Secondary Schools

    Tony, Tam Shui Kee

    2003-01-01

    This article presents the findings of a study hypothesizing that school discipline problems are a maladaptive response to the demand of the school environment as a result of deficits in the area of locus of control and attributional style. The findings indicate that an external orientation of locus of control and a passive pattern of attribution…

  13. Authoritarian Child Rearing, Parental Locus of Control, and the Child's Behavior Style.

    Janssens, Jan M. A. M.

    1994-01-01

    Examined relationships among childrearing, parental locus of control about childrearing, and child's behavior style. Found that parents who perceived their child's behavior as either externalizing or internalizing had a weak internal locus of control and were more authoritarian. Perceived externalizing child behavior was positively related to…

  14. An Examination of Locus of Control, Epistemological Beliefs and Metacognitive Awareness in Preservice Early Childhood Teachers

    Bedel, Emine Ferda

    2012-01-01

    This study aims to explore the locus of control, epistemological beliefs and metacognitive awareness levels of preservice early childhood education teachers and to determine the interrelations among these variables. 206 teacher candidates have been asked to fill out Rotter's Internal-External Locus of Control Scale, Central Epistemological Beliefs…

  15. DMPD: The Lps locus: genetic regulation of host responses to bacteriallipopolysaccharide. [Dynamic Macrophage Pathway CSML Database

    Full Text Available 10669111 The Lps locus: genetic regulation of host responses to bacteriallipopolysa...ccharide. Qureshi ST, Gros P, Malo D. Inflamm Res. 1999 Dec;48(12):613-20. (.png) (.svg) (.html) (.csml) Show The... Lps locus: genetic regulation of host responses to bacteriallipopolysaccharide. PubmedID 10669111 Title The

  16. Locus of control as a moderator of the relationship between influence and procedural justice

    Flinder, Sharon W.

    1991-01-01

    The present field experiment investigated the interaction between influence and locus of control in determining procedural justice and satisfaction, in a classroom situation. Perceptions of influence accounted for unique variance in procedural justice and satisfaction. The proposed moderating effects of locus of control on the influence-procedural justice and influence-satisfaction relationships were not supported. Unfortunately, the manipulation of influence was unsuc...

  17. Predictors of Parental Locus of Control in Mothers of Pre- and Early Adolescents

    Freed, Rachel D.; Tompson, Martha C.

    2011-01-01

    Parental locus of control refers to parents' perceived power and efficacy in child-rearing situations. This study explored parental locus of control and its correlates in 160 mothers of children ages 8 to 14 cross-sectionally and 1 year later. Maternal depression, maternal expressed emotion, and child internalizing and externalizing behavior were…

  18. Locus of Control and Self-Esteem in Indian and White Students.

    Martin, James C.

    1976-01-01

    The development and relationship of two dimensions of personality, self esteem and locus of control, were examined in a study of 763 fourth, eighth, and twelfth grade Indian and white children selected from 22 Oklahoma public schools. The students were given the Coopersmith Self-Esteem Inventory and Nowicky-Strickland Locus of Control Scale during…

  19. Social Self-Efficacy, Academic Locus of Control, and Internet Addiction

    Iskender, Murat; Akin, Ahmet

    2010-01-01

    The purpose of this research is to examine the relationship of internet addiction, social self-efficacy, and academic locus of control. Participants were 311 university students who completed a questionnaire package that included the Online Cognition Scale, the Academic Locus of Control Scale, and the Perceived Social Self-efficacy Scale. The…

  20. Metacognition: As a Predictor of One's Academic Locus of Control

    Arslan, Serhat; Akin, Ahmet

    2014-01-01

    The purpose of this study is to examine the effect of metacognition on one's academic locus of control. The study's sample group consists of 451 university students enrolled in various programs at Sakarya University, Turkey. In this study, the Metacognitive Awareness Inventory and the Academic Locus of Control Scale were used. The…

  1. Adult Children of Workaholics: Self-Concept, Anxiety, Depression, and Locus of Control.

    Robinson, Bryan E.; Kelley, Lisa

    1998-01-01

    Adult children of workaholics were compared with adult children of nonworkaholics on self-concept, anxiety, depression, and external locus of control. Results indicate greater depression and external locus of control among the offspring of workaholics. Children of workaholic fathers also experienced higher anxiety. Self-concept was not related to…

  2. Locus of Semantic Interference in Picture Naming: Evidence from Dual-Task Performance

    Piai, Vitória; Roelofs, Ardi; Schriefers, Herbert

    2014-01-01

    Disagreement exists regarding the functional locus of semantic interference of distractor words in picture naming. This effect is a cornerstone of modern psycholinguistic models of word production, which assume that it arises in lexical response-selection. However, recent evidence from studies of dual-task performance suggests a locus in…

  3. Identification of a sporulation locus in cloned Bacillus subtilis deoxyribonucleic acid.

    Moran, C P; Losick, R; Sonenshein, A L

    1980-01-01

    A cloned deoxyribonucleic acid from the purA-cysA region of the Bacillus subtilis chromosome was shown to contain the spoVC locus, a gene whose product is required for sporulation. This is the first demonstration of a spo locus in cloned B. subtilis deoxyribonucleic acid.

  4. Health Locus of Control and Preventive Behaviour among Students of Music

    Spahn, Claudia; Burger, Thorsten; Hildebrandt, Horst; Seidenglanz, Karin

    2005-01-01

    The present study investigated health locus of control, preventive behaviour and previous playing-related health problems of music students; 326 students of music (58% female, mean age 22 years) filled in the Locus of Control Inventory for Illness and Health (Lohaus and Schmitt, 1989) and the Epidemiological Questionnaire for Musicians (Spahn,…

  5. Fine-Scale Mapping of the FGFR2 Breast Cancer Risk Locus

    Meyer, Kerstin B; O'Reilly, Martin; Michailidou, Kyriaki;

    2013-01-01

    The 10q26 locus in the second intron of FGFR2 is the locus most strongly associated with estrogen-receptor-positive breast cancer in genome-wide association studies. We conducted fine-scale mapping in case-control studies genotyped with a custom chip (iCOGS), comprising 41 studies (n = 89,050) of...

  6. A Study to Investigate the Relationship between Locus of Control and Academic Achievement of Students

    Gujjar, Aijaz Ahmed; Aijaz, Rukhma

    2014-01-01

    Motivation is regarded as the alpha and omega of learning. It is the heart of teaching learning process. Motivation is defined as an internal state that arouses, directs, and maintains the behavior over time. Thus motivation is the pivotal component of learning and locus of control which is one of the important factors it stems from. Locus of…

  7. Multiple myeloma

    This chapter overviews the outcome of the previous studies on multiple myeloma and its related diseases. The incidence of multiple myeloma has become frequent 20 years after A-bombing. As of 1976, it is found to be increased, depending upon bone marrow doses of 50 rad or more (based on T65DR). This is noticeable in A-bomb survivors aged 20-59 years at the time of exposure. The number of autopsy cases has been increased since 1975, and has been significantly high since 1981. Mass screening for A-bomb survivors has revealed the existence of M proteinemia characterized by findings similar to those of multiple myeloma and benign monoclonal gammopathy. There is no significant difference in the incidence of subtype of M proteinemia by distance from the hypocenter. These findings suggest that M proteinemia may be one of the delayed effects of A-bomb radiation. Otherwise, an increased incidence of M proteinemia may be attributable to the cancer-prone age in A-bomb survivors aged 30 years or less at the time of exposure. (N.K.)

  8. Multiple sclerosis

    Eleven patients with a definite diagnosis of multiple sclerosis were examined in terms of correlations between the clinical features and the results of cranial computed tomography (CT), and magnetic resonance imaging (MRI). Results: In 5 of the 11 patients, both CT and MRI demonstrated lesions consistent with a finding of multiple sclerosis. In 3 patients, only MRI demonstrated lesions. In the remaining 3 patients, neither CT nor MRI revealed any lesion in the brain. All 5 patients who showed abnormal findings on both CT and MRI had clinical signs either of cerebral or brainstem - cerebellar lesions. On the other hand, two of the 3 patients with normal CT and MRI findings had optic-nerve and spinal-cord signs. Therefore, our results suggested relatively good correlations between the clinical features, CT, and MRI. MRI revealed cerebral lesions in two of the four patients with clinical signs of only optic-nerve and spinal-cord lesions. MRI demonstrated sclerotic lesions in 3 of the 6 patients whose plaques were not detected by CT. In conclusion, MRI proved to be more helpful in the demonstration of lesions attributable to chronic multiple sclerosis. (author)

  9. Multiples waveform inversion

    Zhang, D. L.

    2013-01-01

    To increase the illumination of the subsurface and to eliminate the dependency of FWI on the source wavelet, we propose multiples waveform inversion (MWI) that transforms each hydrophone into a virtual point source with a time history equal to that of the recorded data. These virtual sources are used to numerically generate downgoing wavefields that are correlated with the backprojected surface-related multiples to give the migration image. Since the recorded data are treated as the virtual sources, knowledge of the source wavelet is not required, and the subsurface illumination is greatly enhanced because the entire free surface acts as an extended source compared to the radiation pattern of a traditional point source. Numerical tests on the Marmousi2 model show that the convergence rate and the spatial resolution of MWI is, respectively, faster and more accurate then FWI. The potential pitfall with this method is that the multiples undergo more than one roundtrip to the surface, which increases attenuation and reduces spatial resolution. This can lead to less resolved tomograms compared to conventional FWI. The possible solution is to combine both FWI and MWI in inverting for the subsurface velocity distribution.

  10. Multiple myeloma: 45 cases

    We evaluated 45 cases of multiple myelomas retrospectively confirmed in Severance Hospital from the period of 1983-1989. In order to assess the radiologic features of the multiple myeloma and to assist in possible early diagnosis and treatment. The result were as follows: 1. IgG(41%) was the most common immunoglobulin type secreted followed by light chain(36%). IgA(19%) and IgD(2%). Two percent of the patients had non-secretory type. 89% of patients were in their stage III of the disease. 2. Among the 45 patients, 96% had abnormal plain radiographic findings with average number of 4.5 lesions. Common sites were the spine, rib, skull, pelvis, and humerus in descending orders. The findings were localized or diffuse osteolytic bone destruction(85%). osteoporosis(49%), pathologic fracture and endosteal scalloping(55%). Osteoporosis was more prominent in stage III than stage II. 3. Both plain X-ray and radioisotope study was available for comparison in 28 patients. Concordance between the two studies were 44%, lesions detected only on plain X-ray film were 51%, and lesions detected only on the radioisotope were 5%. The plain radiography was able to detect only 54% of bone lesions confirmed by bone marrow biopsy. With the above results, accurate evaluation of bone lesions in multiple myeloma may be difficult with radiologic studies only. But familiarity with these radiologic findings of the this disease entity is necessary for early suspicion of the disease, thus for early diagnosis and treatment

  11. Towards a more accurate concept of fuels

    Full text: The introduction of LEU in Atucha and the approval of CARA show an advancement of the Argentine power stations fuels, which stimulate and show a direction to follow. In the first case, the use of enriched U fuel relax an important restriction related to neutronic economy; that means that it is possible to design less penalized fuels using more Zry. The second case allows a decrease in the lineal power of the rods, enabling a better performance of the fuel in normal and also in accident conditions. In this work we wish to emphasize this last point, trying to find a design in which the surface power of the rod is diminished. Hence, in accident conditions owing to lack of coolant, the cladding tube will not reach temperatures that will produce oxidation, with the corresponding H2 formation and with plasticity enough to form blisters, which will obstruct the reflooding and hydration that will produce fragility and rupture of the cladding tube, with the corresponding radioactive material dispersion. This work is oriented to find rods designs with quasi rectangular geometry to lower the surface power of the rods, in order to obtain a lower central temperature of the rod. Thus, critical temperatures will not be reached in case of lack of coolant. This design is becoming a reality after PPFAE's efforts in search of cladding tubes fabrication with different circumferential values, rectangular in particular. This geometry, with an appropriate pellet design, can minimize the pellet-cladding interaction and, through the accurate width election, non rectified pellets could be used. This means an important economy in pellets production, as well as an advance in the fabrication of fuels in gloves box and hot cells in the future. The sequence to determine critical geometrical parameters is described and some rod dispositions are explored

  12. Accurate orbit propagation with planetary close encounters

    Baù, Giulio; Milani Comparetti, Andrea; Guerra, Francesca

    2015-08-01

    We tackle the problem of accurately propagating the motion of those small bodies that undergo close approaches with a planet. The literature is lacking on this topic and the reliability of the numerical results is not sufficiently discussed. The high-frequency components of the perturbation generated by a close encounter makes the propagation particularly challenging both from the point of view of the dynamical stability of the formulation and the numerical stability of the integrator. In our approach a fixed step-size and order multistep integrator is combined with a regularized formulation of the perturbed two-body problem. When the propagated object enters the region of influence of a celestial body, the latter becomes the new primary body of attraction. Moreover, the formulation and the step-size will also be changed if necessary. We present: 1) the restarter procedure applied to the multistep integrator whenever the primary body is changed; 2) new analytical formulae for setting the step-size (given the order of the multistep, formulation and initial osculating orbit) in order to control the accumulation of the local truncation error and guarantee the numerical stability during the propagation; 3) a new definition of the region of influence in the phase space. We test the propagator with some real asteroids subject to the gravitational attraction of the planets, the Yarkovsky and relativistic perturbations. Our goal is to show that the proposed approach improves the performance of both the propagator implemented in the OrbFit software package (which is currently used by the NEODyS service) and of the propagator represented by a variable step-size and order multistep method combined with Cowell's formulation (i.e. direct integration of position and velocity in either the physical or a fictitious time).

  13. Accurate paleointensities - the multi-method approach

    de Groot, Lennart

    2016-04-01

    The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.

  14. Towards Accurate Application Characterization for Exascale (APEX)

    Hammond, Simon David [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    Sandia National Laboratories has been engaged in hardware and software codesign activities for a number of years, indeed, it might be argued that prototyping of clusters as far back as the CPLANT machines and many large capability resources including ASCI Red and RedStorm were examples of codesigned solutions. As the research supporting our codesign activities has moved closer to investigating on-node runtime behavior a nature hunger has grown for detailed analysis of both hardware and algorithm performance from the perspective of low-level operations. The Application Characterization for Exascale (APEX) LDRD was a project concieved of addressing some of these concerns. Primarily the research was to intended to focus on generating accurate and reproducible low-level performance metrics using tools that could scale to production-class code bases. Along side this research was an advocacy and analysis role associated with evaluating tools for production use, working with leading industry vendors to develop and refine solutions required by our code teams and to directly engage with production code developers to form a context for the application analysis and a bridge to the research community within Sandia. On each of these accounts significant progress has been made, particularly, as this report will cover, in the low-level analysis of operations for important classes of algorithms. This report summarizes the development of a collection of tools under the APEX research program and leaves to other SAND and L2 milestone reports the description of codesign progress with Sandia’s production users/developers.

  15. Accurate hydrocarbon estimates attained with radioactive isotope

    To make accurate economic evaluations of new discoveries, an oil company needs to know how much gas and oil a reservoir contains. The porous rocks of these reservoirs are not completely filled with gas or oil, but contain a mixture of gas, oil and water. It is extremely important to know what volume percentage of this water--called connate water--is contained in the reservoir rock. The percentage of connate water can be calculated from electrical resistivity measurements made downhole. The accuracy of this method can be improved if a pure sample of connate water can be analyzed or if the chemistry of the water can be determined by conventional logging methods. Because of the similarity of the mud filtrate--the water in a water-based drilling fluid--and the connate water, this is not always possible. If the oil company cannot distinguish between connate water and mud filtrate, its oil-in-place calculations could be incorrect by ten percent or more. It is clear that unless an oil company can be sure that a sample of connate water is pure, or at the very least knows exactly how much mud filtrate it contains, its assessment of the reservoir's water content--and consequently its oil or gas content--will be distorted. The oil companies have opted for the Repeat Formation Tester (RFT) method. Label the drilling fluid with small doses of tritium--a radioactive isotope of hydrogen--and it will be easy to detect and quantify in the sample

  16. Fast, accurate standardless XRF analysis with IQ+

    Full text: Due to both chemical and physical effects, the most accurate XRF data are derived from calibrations set up using in-type standards, necessitating some prior knowledge of the samples being analysed. Whilst this is often the case for routine samples, particularly in production control, for completely unknown samples the identification and availability of in-type standards can be problematic. Under these circumstances standardless analysis can offer a viable solution. Successful analysis of completely unknown samples requires a complete chemical overview of the speciemen together with the flexibility of a fundamental parameters (FP) algorithm to handle wide-ranging compositions. Although FP algorithms are improving all the time, most still require set-up samples to define the spectrometer response to a particular element. Whilst such materials may be referred to as standards, the emphasis in this kind of analysis is that only a single calibration point is required per element and that the standard chosen does not have to be in-type. The high sensitivities of modern XRF spectrometers, together with recent developments in detector counting electronics that possess a large dynamic range and high-speed data processing capacity bring significant advances to fast, standardless analysis. Illustrated with a tantalite-columbite heavy-mineral concentrate grading use-case, this paper will present the philosophy behind the semi-quantitative IQ+ software and the required hardware. This combination can give a rapid scan-based overview and quantification of the sample in less than two minutes, together with the ability to define channels for specific elements of interest where higher accuracy and lower levels of quantification are required. The accuracy, precision and limitations of standardless analysis will be assessed using certified reference materials of widely differing chemical and physical composition. Copyright (2002) Australian X-ray Analytical Association Inc

  17. Polarimetry with multiple mirror telescopes

    West, S. C.

    1986-01-01

    The polarizations of multiple mirror telescopes are calculated using Mueller calculus. It is found that the Multiple Mirror Telescope (MMT) produces a constant depolarization that is a function of wavelength and independent of sky position. The efficiency and crosstalk are modeled and experimentally verified. The two- and four-mirror new generation telescopes are found to produce sinusoidal depolarization for which an accurate interpretation of the incident Stokes vector requires inverse matrix calculations. Finally, the depolarization of f/1 paraboloids is calculated and found to be less than 0.1 percent at 3000 A.

  18. Identifying growth hormone-regulated enhancers in the Igf1 locus.

    Alzhanov, Damir; Mukherjee, Aditi; Rotwein, Peter

    2015-11-01

    Growth hormone (GH) plays a central role in regulating somatic growth and in controlling multiple physiological processes in humans and other vertebrates. A key agent in many GH actions is the secreted peptide, IGF-I. As established previously, GH stimulates IGF-I gene expression via the Stat5b transcription factor, leading to production of IGF-I mRNAs and proteins. However, the precise mechanisms by which GH-activated Stat5b promotes IGF-I gene transcription have not been defined. Unlike other GH-regulated genes, there are no Stat5b sites near either of the two IGF-I gene promoters. Although dispersed GH-activated Stat5b binding elements have been mapped in rodent Igf1 gene chromatin, it is unknown how these distal sites might function as potential transcriptional enhancers. Here we have addressed mechanisms of regulation of IGF-I gene transcription by GH by generating cell lines in which the rat Igf1 chromosomal locus has been incorporated into the mouse genome. Using these cells we find that physiological levels of GH rapidly and potently activate Igf1 gene transcription while stimulating physical interactions in chromatin between inducible Stat5b-binding elements and the Igf1 promoters. We have thus developed a robust experimental platform for elucidating how dispersed transcriptional enhancers control Igf1 gene expression under different biological conditions. PMID:26330488

  19. A mutagenesis-derived broad-spectrum disease resistance locus in wheat.

    Campbell, Jackie; Zhang, Hongtao; Giroux, Michael J; Feiz, Leila; Jin, Yue; Wang, Meinan; Chen, Xianming; Huang, Li

    2012-07-01

    Wheat leaf rust, stem rust, stripe rust, and powdery mildew caused by the fungal pathogens Puccinia triticina, P. graminis f. sp. tritici, P. striiformis f. sp. tritici, and Blumeria graminis f. sp. tritici, respectively, are destructive diseases of wheat worldwide. Breeding durable disease resistance cultivars rely largely on continually introgressing new resistance genes, especially the genes with different defense mechanisms, into adapted varieties. Here, we describe a new resistance gene obtained by mutagenesis. The mutant, MNR220 (mutagenesis-derived new resistance), enhances resistance to three rusts and powdery mildew, with the characteristics of delayed disease development at the seedling stage and completed resistance at the adult plant stage. Genetic analysis demonstrated that the resistance in MNR220 is conferred by a single semidominant gene mapped on the short arm of chromosome 2B. Gene expression profiling of several pathogenesis-related genes indicated that MNR220 has an elevated and rapid pathogen-induced response. In addition to its potential use in breeding for resistance to multiple diseases, high-resolution mapping and cloning of the disease resistance locus in MNR220 may lead to a better understanding of the regulation of defense responses in wheat. PMID:22446929

  20. Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast

    Thierry, Agnès; Khanna, Varun; Dujon, Bernard

    2016-01-01

    Gene amplification has been observed in different organisms in response to environmental constraints, such as limited nutrients or exposure to a variety of toxic compounds, conferring them with specific phenotypic adaptations via increased expression levels. However, the presence of multiple gene copies in natural genomes has generally not been found in the absence of specific functional selection. Here, we show that the massive amplification of a chromosomal locus (up to 880 copies per cell) occurs in the absence of any direct selection, and is associated with low-order amplifications of flanking segments in complex chromosomal alterations. These results were obtained from mutants with restored phenotypes that spontaneously appeared from genetically engineered strains of the yeast Saccharomyces cerevisiae suffering from severe fitness reduction. Grossly extended chromosomes (macrotene) were formed, with complex structural alterations but sufficient stability to propagate unchanged over successive generations. Their detailed molecular analysis, including complete genome sequencing, identification of sequence breakpoints, and comparisons between mutants, revealed novel mechanisms causing their formation, whose combined action underlies the astonishing dynamics of eukaryotic chromosomes and their consequences. PMID:26945028

  1. mlstdbNet – distributed multi-locus sequence typing (MLST databases

    Maiden Martin CJ

    2004-07-01

    Full Text Available Abstract Background Multi-locus sequence typing (MLST is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet. Results The software enables multiple isolate databases to query a single profiles database that contains allelic profile and sequence definitions. This separation enables isolate databases to be established by individual laboratories, each customised to the needs of the particular project and with appropriate access restrictions, while maintaining the benefits of a single definitive source of profile and sequence information. Databases are described by an XML file that is parsed by a Perl CGI script. The software offers a large number of ways to query the databases and to further break down and export the results generated. Additional features can be enabled by installing third-party (freely available tools. Conclusion Development of a distributed structure for MLST databases offers scalability and flexibility, allowing participating centres to maintain ownership of their own data, without introducing duplication and data integrity issues.

  2. The beneficial effects of meditation: contribution of the anterior cingulate and locus coeruleus

    Nancy Alker Craigmyle

    2013-10-01

    Full Text Available Abstract During fMRI studies of meditation the cortical salience detecting and executive networks become active during awareness of mind wandering, shifting and sustained attention. The anterior cingulate (AC is activated during awareness of mind wandering.The AC modulates both the peripheral sympathetic nervous system (SNS and the central locus coeruleus (LC norepinephrine systems, which form the principal neuromodulatory system, regulating in multiple ways both neuronal and non-neuronal cells to maximize adaptation in changing environments. The LC is the primary source of central norepinephrine (C-NE and nearly the exclusive source of cortical norepinephrine. Normally activated by novel or salient stimuli, the AC initially inhibits the SNS reflexively, lowering peripheral norepinephrine (P-NE and activates the LC, increasing C-NE.Moderate levels of C-NE enhance working memory through alpha 2 adrenergic receptors, while higher levels of C-NE, acting on alpha 1 and beta receptors, enhance other executive network functions such as the stopping of ongoing behavior, attentional set shifting and sustained attention. The actions of the AC on both the central and peripheral noradrenergic systems are implicated in the beneficial effects of meditation. This paper will explore some of the known functions and interrelationships of the AC, SNS and LC with respect to their possible relevance to meditation.

  3. Multiple sclerosis-associated CLEC16A controls HLA class II expression via late endosome biogenesis

    M.M. van Luijn (Marvin M.); K.L. Kreft (Karim); M.L. Jongsma (Marlieke L.); S.W. Mes (Steven); A.F. Wierenga-Wolf (Annet); M. van Meurs (Marjan); M.J. Melief; Rv. der Kant (Rik van); L. Janssen (Lennert); H. Janssen (Hans); R. Tan (Rusung); J.J. Priatel (John J.); J. Neefjes (Jacques); J.D. Laman (Jon); R.Q. Hintzen (Rogier)

    2015-01-01

    textabstractC-type lectins are key players in immune regulation by driving distinct functions of antigen-presenting cells. The C-type lectin CLEC16A gene is located at 16p13, a susceptibility locus for several autoimmune diseases, including multiple sclerosis. However, the function of this gene and

  4. Somatic cell genotoxicity at the glycophorin A locus in humans

    We have developed an assay for detecting variant erythrocytes that occur as a result of in vivo allele loss at the glycophorin A (GPA) locus on chromosome 4 in humans. This gene codes for an erythroid- specific cell surface glycoprotein, and with our assay we are able to detect rare variant erythrocytes that have lost expression of one of the two GPA alleles. Two distinctly different variant cell types are detected with this assay. One variant cell type (called N OE) is hemizygous. Our assay also detects homozygous variant erythrocytes that have lost expression of the GPA(M) allele and express the GPA(N) allele at twice the heterozygous level. The results of this assay are an enumeration of the frequency of N OE and NN variant cell types for each individual analyzed. These variant cell frequencies provide a measure of the amount of somatic cell genotoxicity that has occurred at the GPA locus. Such genotoxicity could be the result of (1) reactions of toxic chemicals to which the individual has been exposed, or (2) high energy radiation effects on erythroid precursor cells, or (3) errors in DNA replication or repair in these cells of the bone marrow. Thus, the GPA-based variant cell frequency can serve as a biodosimeter that indicates the amount of genotoxic exposure each individual has received. Because two very different kinds of variant cells are enumerated, different kinds of genotoxicity should be distinguishable. Results of the GPA somatic genotoxicity assay may also provide valuable information for cancer-risk estimation on each individual. 16 refs

  5. Role of CTCF protein in regulating FMR1 locus transcription.

    Stella Lanni

    Full Text Available Fragile X syndrome (FXS, the leading cause of inherited intellectual disability, is caused by epigenetic silencing of the FMR1 gene, through expansion and methylation of a CGG triplet repeat (methylated full mutation. An antisense transcript (FMR1-AS1, starting from both promoter and intron 2 of the FMR1 gene, was demonstrated in transcriptionally active alleles, but not in silent FXS alleles. Moreover, a DNA methylation boundary, which is lost in FXS, was recently identified upstream of the FMR1 gene. Several nuclear proteins bind to this region, like the insulator protein CTCF. Here we demonstrate for the first time that rare unmethylated full mutation (UFM alleles present the same boundary described in wild type (WT alleles and that CTCF binds to this region, as well as to the FMR1 gene promoter, exon 1 and intron 2 binding sites. Contrariwise, DNA methylation prevents CTCF binding to FXS alleles. Drug-induced CpGs demethylation does not restore this binding. CTCF knock-down experiments clearly established that CTCF does not act as insulator at the active FMR1 locus, despite the presence of a CGG expansion. CTCF depletion induces heterochromatinic histone configuration of the FMR1 locus and results in reduction of FMR1 transcription, which however is not accompanied by spreading of DNA methylation towards the FMR1 promoter. CTCF depletion is also associated with FMR1-AS1 mRNA reduction. Antisense RNA, like sense transcript, is upregulated in UFM and absent in FXS cells and its splicing is correlated to that of the FMR1-mRNA. We conclude that CTCF has a complex role in regulating FMR1 expression, probably through the organization of chromatin loops between sense/antisense transcriptional regulatory regions, as suggested by bioinformatics analysis.

  6. Identification of a new virulence locus in Agrobacterium tumefaciens that affects polysaccharide composition and plant cell attachment.

    Thomashow, M F; Karlinsey, J E; Marks, J R; Hurlbert, R. E.

    1987-01-01

    We have identified a new virulence locus in Agrobacterium tumefaciens. Strains carrying Tn5 inserts at this locus could not incite tumors on Kalanchoe daigremontiana, Nicotiana rustica, tobacco, or sunflower and had severely attenuated virulence on carrot disks. We termed the locus pscA, because the mutants that defined the locus were initially isolated as having an altered polysaccharide composition; they were nonfluorescent on media containing Leucophor or Calcofluor, indicating a defect in...

  7. Intelligences multiples

    Partoune, Christine

    2010-01-01

    La conception d’un accompagnement méthodologique dans le but de favoriser un changement de pratiques implique une référence à des modèles de l’apprentissage que l’on espère cohérents avec les finalités poursuivies. Le but de cette fiche est de présenter la théorie des intelligences multiples proposée par Howard Gardner, qui nous invite au respect et à la prise en compte des différences entre les individus dans les pratiques en matière de gouvernance.

  8. Multiple sclerosis

    Stenager, Egon; Stenager, E N; Knudsen, Lone;

    1994-01-01

    , need for structural changes in home and need for pension became greater with increasing physical handicap. No significant differences between gender were found. It is concluded that patients and relatives are under increased social strain, when multiple sclerosis progresses to a moderate handicap....... Ninety-five percent lived in own house or flat and 70 percent received disablement pension. More than half of the patients (56.4 percent) were dependent on help from close relatives, most frequently spouse. The need for help, the risk of divorce, loss of contact with relatives, difficulty in going out...

  9. Variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps biosynthetic locus in Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice

    Sonti Ramesh V

    2004-10-01

    respectively. Conclusion This is the first report of hypervariation at an lps locus between different strains of a plant pathogenic bacterium. Our results indicate that multiple HGT events have occurred at this locus in the xanthomonad group of plant pathogens.

  10. Accurate measurement of oxygen consumption in children undergoing cardiac catheterization.

    Li, Jia

    2013-01-01

    Oxygen consumption (VO(2) ) is an important part of hemodynamics using the direct Fick principle in children undergoing cardiac catheterization. Accurate measurement of VO(2) is vital. Obviously, any error in the measurement of VO(2) will translate directly into an equivalent percentage under- or overestimation of blood flows and vascular resistances. It remains common practice to estimate VO(2) values from published predictive equations. Among these, the LaFarge equation is the most commonly used equation and gives the closest estimation with the least bias and limits of agreement. However, considerable errors are introduced by the LaFarge equation, particularly in children younger than 3 years of age. Respiratory mass spectrometry remains the "state-of-the-art" method, allowing highly sensitive, rapid and simultaneous measurement of multiple gas fractions. The AMIS 2000 quadrupole respiratory mass spectrometer system has been adapted to measure VO(2) in children under mechanical ventilation with pediatric ventilators during cardiac catheterization. The small sampling rate, fast response time and long tubes make the equipment a unique and powerful tool for bedside continuous measurement of VO(2) in cardiac catheterization for both clinical and research purposes. PMID:22488802

  11. mutM, a second mutator locus in Escherichia coli that generates G.C----T.A transversions.

    Cabrera, M.; Nghiem, Y; Miller, J H

    1988-01-01

    We used strains carrying specific lacZ alleles to identify a new mutator locus in Escherichia coli which generates only G.C----T.A transversions among base substitutions. The locus, mutM, mapped near the cysE locus, which is at 81 min on the genetic map.

  12. Multiple Myeloma Overview

    ... Web version Multiple Myeloma Overview What is multiple myeloma? Multiple myeloma (say: my-a-low-ma) is a ... Do I need to be screened for multiple myeloma? Source Multiple Myeloma: Recognition and Management by ED George, R ...

  13. Prevalence of Porphyromonas gingivalis four rag locus genotypes in patients of orthodontic gingivitis and periodontitis.

    Yi Liu

    Full Text Available Porphyromonas gingivalis is considered as a major etiological agent in periodontal diseases and implied to result in gingival inflammation under orthodontic appliance. rag locus is a pathogenicity island found in Porphyromonas gingivalis. Four rag locus variants are different in pathogenicity of Porphyromonas gingivalis. Moreover, there are different racial and geographic differences in distribution of rag locus genotypes. In this study, we assessed the prevalence of Porphyromonas gingivalis and rag locus genotypes in 102 gingival crevicular fluid samples from 57 cases of gingivitis patients with orthodontic appliances, 25 cases of periodontitis patients and 20 cases of periodontally healthy people through a 16S rRNA-based PCR and a multiplex PCR. The correlations between Porphyromona.gingivalis/rag locus and clinical indices were analyzed. The prevalence of Porphyromonas gingivalis and rag locus genes in periodontitis group was the highest among three groups and higher in orthodontic gingivitis than healthy people (p<0.01. An obviously positive correlation was observed between the prevalence of Porphyromonas gingivalis/rag locus and gingival index. rag-3 and rag-4 were the predominant genotypes in the patients of orthodontic gingivitis and mild-to-moderate periodontitis in Shandong. Porphyromonas.gingivalis carrying rag-1 has the strong virulence and could be associated with severe periodontitis.

  14. Prevalence of Porphyromonas gingivalis four rag locus genotypes in patients of orthodontic gingivitis and periodontitis.

    Liu, Yi; Zhang, Yujie; Wang, Lili; Guo, Yang; Xiao, Shuiqing

    2013-01-01

    Porphyromonas gingivalis is considered as a major etiological agent in periodontal diseases and implied to result in gingival inflammation under orthodontic appliance. rag locus is a pathogenicity island found in Porphyromonas gingivalis. Four rag locus variants are different in pathogenicity of Porphyromonas gingivalis. Moreover, there are different racial and geographic differences in distribution of rag locus genotypes. In this study, we assessed the prevalence of Porphyromonas gingivalis and rag locus genotypes in 102 gingival crevicular fluid samples from 57 cases of gingivitis patients with orthodontic appliances, 25 cases of periodontitis patients and 20 cases of periodontally healthy people through a 16S rRNA-based PCR and a multiplex PCR. The correlations between Porphyromona.gingivalis/rag locus and clinical indices were analyzed. The prevalence of Porphyromonas gingivalis and rag locus genes in periodontitis group was the highest among three groups and higher in orthodontic gingivitis than healthy people (pPorphyromonas gingivalis/rag locus and gingival index. rag-3 and rag-4 were the predominant genotypes in the patients of orthodontic gingivitis and mild-to-moderate periodontitis in Shandong. Porphyromonas.gingivalis carrying rag-1 has the strong virulence and could be associated with severe periodontitis. PMID:23593379

  15. [Multiple myeloma].

    Kortüm, K M; Engelhardt, M; Rasche, L; Knop, S; Einsele, H

    2013-08-01

    Multiple myeloma (MM) is a cancer originating from terminally differentiated B lymphocytes, the plasma cells and is classified as a B cell non-Hodgkin lymphoma. As clonal plasma cells secrete immunoglobulin molecules (lacking antigenic specificity), an "M component" can incidentally be detected. Besides intact immunoglobulin molecules, free light chains can be produced. Although there is no specific treatment for monoclonal gammopathy of undetermined significance (MGUS), which is the defined as the presence of clonal bone marrow plasma cells and low levels (serum and/or urine) of the M component, it should be followed up in affected individuals. The symptoms of MM are numerous and often nonspecific. Diagnosis includes the quantification of monoclonal proteins in serum and urine, blood count, electrolytes and renal function, imaging of the skeleton and bone marrow puncture. The cornerstone of therapy includes melphalan- or cyclophosphamide-based regimens incorporating one of the "novel drugs" (i.e. bortezomib, thalidomide, or lenalidomide). PMID:23860514

  16. Assessing temporal flux of plant hormones in stored processing potatoes using high definition accurate mass spectrometry

    José Juan Ordaz-Ortiz; Sofia Foukaraki; Leon Alexander Terry

    2015-01-01

    Plant hormones are important molecules which at low concentration can regulate various physiological processes. Mass spectrometry has become a powerful technique for the quantification of multiple classes of plant hormones because of its high sensitivity and selectivity. We developed a new ultrahigh pressure liquid chromatography–full-scan high-definition accurate mass spectrometry method, for simultaneous determination of abscisic acid and four metabolites phaseic acid, dihydrophaseic acid, ...

  17. Accurate Determination of Quantity of Material in Thin Films by Rutherford Backscattering Spectrometry

    Jeynes, C.; Barradas, NP; Szilágyi, E.

    2012-01-01

    Ion beam analysis (IBA) is a cluster of techniques including Rutherford and non-Rutherford backscattering spectrometry, and particle-induced X-ray emission (PIXE). Recently, the ability to treat multiple IBA techniques (including PIXE) self-consistently has been demonstrated. The utility of IBA for accurately depth profiling thin films is critically reviewed. As an important example of IBA, three laboratories have independently measured a silicon sample implanted with a fluence of nominally 5...

  18. MRI-Based evaluation of locus and extent of neurotoxic lesions in monkeys.

    Málková, L; Lex, C K; Mishkin, M; Saunders, R C

    2001-01-01

    To minimize the variability in the extent of lesions made by injections of the excitotoxin ibotenic acid in rhesus monkeys, we developed and validated an MRI-based method to determine the efficacy of the injections soon after surgery. T2-weighted MR images were obtained 6-11 days after surgery from 17 brain hemispheres of monkeys that had received bilateral lesions of either the hippocampal formation (HF), perirhinal cortex, or parahippocampal cortex. The extent of lesion estimated from the hypersignal that appeared in and outside of the targeted area on these MR images was compared with the extent of damage assessed histologically after survival periods ranging from 120-370 days. Highly significant correlations (r values between 0.85-0.99) were found between these two measures for several regions in the medial temporal lobe. Based on this finding, lack of hypersignal in the targeted area of some Ss was followed by successful reinjection of the neurotoxin to create more complete cell loss prior to the postoperative phase of the study. We also assessed the relationship between a postoperative reduction in HF volume, measured from T1-weighted MR images, and the extent of damage determined histologically in 14 hemispheres of monkeys with bilateral excitotoxic HF lesions. The HF volume decreases sharply after surgery until 40-50 days postoperatively, after which there is only a minor further decrease. Based on this finding, we obtained T1-weighted MR images at least 44 days but in most cases close to 1 year after surgery. A highly significant positive correlation (r = 0.95, P < 0.001) was found between neuronal damage and volume reduction, with nearly complete neuronal damage (96-99%) corresponding to a volume reduction of 68-79%. These MRI-based methods thus provide an accurate in vivo evaluation of the locus and extent of neurotoxic lesions. Application of these methods can ensure that each animal in the experiment is used effectively. PMID:11530840

  19. Molecular Characterization Of The Vernalization Locus VRN1 In Perennial Ryegrass

    Asp, Torben; Byrne, Stephen; Andersen, Jeppe R;

    Vernalization, the requirement of a period of low temperature to induce transition from vegetative to reproductive state, is an important trait in grasses. The objective of this study was to identify the causative polymorphism(s) for the variation in vernalization requirement at the VRN1 locus in...... perennial ryegrass (Lolium perenne). Two allelic BAC clones of the VRN1 locus from the two genotypes Veyo and Falster with contrasting vernalization requirements were identified, sequenced, and characterized. The region surrounding the VRN1 locus in perennial ryegrass showed micro-colinearity to the...

  20. Capsulation and Gene Copy Number at the cap Locus of Haemophilus influenzae Type b

    1988-01-01

    Although more than 98% of natural isolates of Haemophilus influenzae type b carry a duplication of 17 kilobases (kb) of DNA at the chromosomal capsulation locus, only one copy is required for capsulation. In one laboratory-derived and two clinical type b strains, the capsulation locus had a single copy of this 17-kb segment, together with 1.3 kb of DNA identified as lying between the repeats of the duplicated locus. This 1.3 kb appears to be crucial for capsule production, since strains lacki...

  1. Mapping and disruption of the chpB locus in Escherichia coli.

    Masuda, Y; Ohtsubo, E

    1994-01-01

    The chpB locus is a chromosomal homolog of the pem locus, which is responsible for stable maintenance of plasmid R100 within the host cells. Like pem, chpB codes for two genes, chpBK and chpBI, encoding a growth inhibitor and a suppressor for the killing action of the ChpBK protein, respectively. Here, we determined the precise location of the chpB locus, which is linked to ileR and ppa in the order ileR-chpB-ppa, at 95.7 min on the map of Escherichia coli. We then constructed mutants with an...

  2. Locus Of Control - Predictor Of Health And Subjective Well – Being

    Svetlana Popova

    2012-01-01

    The article presents results of a study of the relationship 'locus of control - health and subjective well-being. In a heterogeneous sample (N = 239) in the stage of youth (19-30 years) shall be established: locus of control determines 11.56% of the changes in the assessment of health, changes in health contribute to 12.82% of the variation in assessment of happiness and 6.10% in the measurement of life satisfaction. Young people with an internal locus of control are healthier, happier and mo...

  3. [Illness concepts of children. Validation of a modified locus of control test in illness and health].

    Schmidt, A; Altmann-Herz, U

    1992-12-01

    We investigated the health and illness concepts of 53 healthy children aged 8 to 14 years using a modified illness and health locus of control scale (KKG, Lohaus and Schmitt, 1989) with the scales internal, external-p (powerful others) and external-c (chance). A comparison of the results with those on self-esteem (FSK 4-6), anxiety (CMAS-R) and hopelessness (HSC) scales showed a decrease in externality, but not an increase in internality, with increasing age and a correlation between self-confidence and a more internal locus of control. The influence of children's health locus of control on treatment compliance is discussed. PMID:1288033

  4. Bayesian inference of population size history from multiple loci

    Drummond Alexei J

    2008-10-01

    Full Text Available Abstract Background Effective population size (Ne is related to genetic variability and is a basic parameter in many models of population genetics. A number of methods for inferring current and past population sizes from genetic data have been developed since JFC Kingman introduced the n-coalescent in 1982. Here we present the Extended Bayesian Skyline Plot, a non-parametric Bayesian Markov chain Monte Carlo algorithm that extends a previous coalescent-based method in several ways, including the ability to analyze multiple loci. Results Through extensive simulations we show the accuracy and limitations of inferring population size as a function of the amount of data, including recovering information about evolutionary bottlenecks. We also analyzed two real data sets to demonstrate the behavior of the new method; a single gene Hepatitis C virus data set sampled from Egypt and a 10 locus Drosophila ananassae data set representing 16 different populations. Conclusion The results demonstrate the essential role of multiple loci in recovering population size dynamics. Multi-locus data from a small number of individuals can precisely recover past bottlenecks in population size which can not be characterized by analysis of a single locus. We also demonstrate that sequence data quality is important because even moderate levels of sequencing errors result in a considerable decrease in estimation accuracy for realistic levels of population genetic variability.

  5. Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization

    Li, Jinhong; Webster, Margaret; Wright, Jonathan; Cocker, Jonathan; Smith, Matthew; Badakshi, Farah; Heslop-Harrison, Pat; Gilmartin, Philip

    2015-01-01

    •Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S-linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its...

  6. Accurate phase measurements for thick spherical objects using optical quadrature microscopy

    Warger, William C., II; DiMarzio, Charles A.

    2009-02-01

    In vitro fertilization (IVF) procedures have resulted in the birth of over three million babies since 1978. Yet the live birth rate in the United States was only 34% in 2005, with 32% of the successful pregnancies resulting in multiple births. These multiple pregnancies were directly attributed to the transfer of multiple embryos to increase the probability that a single, healthy embryo was included. Current viability markers used for IVF, such as the cell number, symmetry, size, and fragmentation, are analyzed qualitatively with differential interference contrast (DIC) microscopy. However, this method is not ideal for quantitative measures beyond the 8-cell stage of development because the cells overlap and obstruct the view within and below the cluster of cells. We have developed the phase-subtraction cell-counting method that uses the combination of DIC and optical quadrature microscopy (OQM) to count the number of cells accurately in live mouse embryos beyond the 8-cell stage. We have also created a preliminary analysis to measure the cell symmetry, size, and fragmentation quantitatively by analyzing the relative dry mass from the OQM image in conjunction with the phase-subtraction count. In this paper, we will discuss the characterization of OQM with respect to measuring the phase accurately for spherical samples that are much larger than the depth of field. Once fully characterized and verified with human embryos, this methodology could provide the means for a more accurate method to score embryo viability.

  7. Automatic classification and accurate size measurement of blank mask defects

    Bhamidipati, Samir; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

    2015-07-01

    A blank mask and its preparation stages, such as cleaning or resist coating, play an important role in the eventual yield obtained by using it. Blank mask defects' impact analysis directly depends on the amount of available information such as the number of defects observed, their accurate locations and sizes. Mask usability qualification at the start of the preparation process, is crudely based on number of defects. Similarly, defect information such as size is sought to estimate eventual defect printability on the wafer. Tracking of defect characteristics, specifically size and shape, across multiple stages, can further be indicative of process related information such as cleaning or coating process efficiencies. At the first level, inspection machines address the requirement of defect characterization by detecting and reporting relevant defect information. The analysis of this information though is still largely a manual process. With advancing technology nodes and reducing half-pitch sizes, a large number of defects are observed; and the detailed knowledge associated, make manual defect review process an arduous task, in addition to adding sensitivity to human errors. Cases where defect information reported by inspection machine is not sufficient, mask shops rely on other tools. Use of CDSEM tools is one such option. However, these additional steps translate into increased costs. Calibre NxDAT based MDPAutoClassify tool provides an automated software alternative to the manual defect review process. Working on defect images generated by inspection machines, the tool extracts and reports additional information such as defect location, useful for defect avoidance[4][5]; defect size, useful in estimating defect printability; and, defect nature e.g. particle, scratch, resist void, etc., useful for process monitoring. The tool makes use of smart and elaborate post-processing algorithms to achieve this. Their elaborateness is a consequence of the variety and

  8. The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the beta subunit of casein kinase 2

    Bozzetti, M P; Massari, S; Finelli, P; Meggio, F; Pinna, L A; Boldyreff, B; Issinger, O G; Palumbo, G; Ciriaco, C; Bonaccorsi, S

    1995-01-01

    Males of Drosophila melanogaster lacking the Y chromosome-linked crystal locus show multiple meiotic alterations including chromosome disorganization and prominent crystal formation in primary spermatocytes. These alterations are due to the derepression of the X chromosome-linked Stellate sequenc...... is a major component of the crystals. Moreover, in vitro experiments have shown that this protein can interact with the catalytic alpha subunit of casein kinase 2 enzyme, altering its activity....

  9. The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the beta subunit of casein kinase 2

    Bozzetti, M P; S. Massari; Finelli, P.; Meggio, F; Pinna, L A; Boldyreff, B; O.-G. Issinger; Palumbo, G; Ciriaco, C; Bonaccorsi, S.; Pimpinelli, S.

    1995-01-01

    Males of Drosophila melanogaster lacking the Y chromosome-linked crystal locus show multiple meiotic alterations including chromosome disorganization and prominent crystal formation in primary spermatocytes. These alterations are due to the derepression of the X chromosome-linked Stellate sequences. To understand how the derepression of the Stellate elements gives rise to these abnormalities, we have expressed the protein encoded by the Stellate sequences in bacteria and produced an antibody ...

  10. Quantitative trait locus mapping can benefit from segregation distortion.

    Xu, Shizhong

    2008-12-01

    Segregation distortion is a phenomenon that has been observed in many experimental systems. How segregation distortion among markers arises and its impact on mapping studies are the focus of this work. Segregation distortion of markers can be considered to arise from segregation distortion loci (SDL). I develop a theory of segregation distortion and show that the presence of only a few SDL can cause the entire chromosome to distort from Mendelian segregation. Segregation distortion is detrimental to the power of detecting quantitative trait loci (QTL) with dominance effects, but it is not always a detriment to QTL mapping for additive effects. When segregation distortion of a locus is a random event, the SDL is beneficial to QTL mapping approximately 44% of the time. If SDL are present and ignored, power loss can be substantial. A dense marker map can be used to ameliorate the situation, and if dense marker information is incorporated, power loss is minimal. However, other situations are less benign. A method that can simultaneously map QTL and SDL is discussed, maximizing both use of mapping resources and use by agricultural and evolutionary biologists. PMID:18957707

  11. The PKU locus in man is on chromosome 12.

    Lidksy, A S; Robson, K J; Thirumalachary, C; Barker, P E; Ruddle, F H; Woo, S L

    1984-01-01

    Classical phenylketonuria (PKU) is a typical example of inborn errors in metabolism and is characterized by a complete lack of the hepatic enzyme phenylalanine hydroxylase, which normally converts phenylalanine to tyrosine. The genetic disorder causes impairment of postnatal brain development, resulting in severe mental retardation in untreated children. The disease is transmitted as an autosomal recessive trait and has a collective prevalence of about one in 10,000 among Caucasians, so that 2% of the population are carriers of the PKU trait. We have recently reported the cloning of human phenylalanine hydroxylase cDNA and that the human chromosomal phenylalanine hydroxylase gene is encoded by a unique DNA sequence. Using the human phenylalanine hydroxylase cDNA clone to analyze a clonal human/mouse hybrid cell panel by Southern hybridization, the phenylalanine hydroxylase gene has been assigned to human chromosome 12. Since the hypothesis that classical PKU is caused by structural mutations in the phenylalanine hydroxylase gene itself rather than through some transregulatory mechanisms has recently been confirmed by gene mapping, the PKU locus in man is determined to be on chromosome 12. Images Fig. 1 PMID:6547271

  12. Analysis of the pathogenicity locus in Clostridium difficile strains.

    Cohen, S H; Tang, Y J; Silva, J

    2000-02-01

    The genes for Clostridium difficile toxins A and B (tcdA and tcdB) are part of a 19.6-kb pathogenicity locus (PaLoc) that includes the genes tcdD, tcdE, and tcdC. To determine whether the C. difficile PaLoc is a stable and conserved genetic unit in toxigenic strains, a multiplex polymerase chain reaction was used to analyze 50 toxigenic, 39 nontoxigenic, and 2 toxin-defective isolates. The respective amplicons were identified for tcdA-E in the toxigenic isolates; these were absent in the nontoxigenic isolates. C. difficile P-829 lacked at least a fragment of tcdD, tcdB, tcdE, and tcdC, but tcdA was present. C. difficile 8864 had deletions in the tcdA and tcdC genes. These data suggest that the PaLoc is highly stable in toxigenic C. difficile, nontoxigenic isolates lack the unit, and isolates with a defective PaLoc can still cause clinical disease. Further studies are needed to define the role of individual genes in the pathogenesis of C. difficile-associated diarrhea. PMID:10669352

  13. The Relationship between Adjustment and Perceived Locus of Control for Female Psychiatric Inpatients.

    Youkilis, Hildreth D.; Bootzin, Richard R.

    1979-01-01

    Examines the longitudinal relationship between internal-external locus of control and adjustment using independent measures within two dissimilar treatment environments: a traditional ward and a token economy ward. Subjects were 65 female psychiatric inpatients. (CM)

  14. Internal-External Locus of Control and Labor Market Performance: Empirical Evidence Using Longitudinal Survey Data.

    Frantz, Roger S.

    1980-01-01

    Internal-external control affects hourly wages independent of other factors such as educational attainment, labor market experience, race, and collective bargaining affiliation. Internal-external locus of control is affected by labor market success, race, and city size. (Author)

  15. Vocational interests of adolescents: relationships between self-esteem and locus of control.

    Mullis, A K; Mullis, R L

    1997-12-01

    The purpose of this study was to examine relationships among scores on vocational interests, self-esteem, and locus of control for high school students. Grade and sex differences were also examined. 1364 high school students ranging in age from 14 to 19 years of age were administered the Coopersmith Self-esteem Inventory, Nowicki-Strickland Locus of Control Scale for Children, and the Strong-Campbell Interest Inventory. High school students with higher scores on self-esteem and showing an orientation toward internal locus of control expressed more interests in a variety of vocational themes than adolescents with lower scores on self-esteem and scores for external locus of control. Sex and grade differences in vocational interests of adolescents were also noted. The findings were discussed in light of theoretical and practical considerations. PMID:9461772

  16. Lexical Access and Dual-Task Performance: Determining the Locus of the Bottleneck

    Allen, Phil

    2004-01-01

    During the two years of funding for NASA Grant "NCC21325, Lexical access and dual-task performance: Determining the locus of the bottleneck," we completed three experiments involving the psychological refractory period (PRP) and word frequency.

  17. Effects of a Structured Camp Experience on Locus of Control Orientation

    Nowicki, Stephen, Jr.; Barnes, Jarvis

    1973-01-01

    Inner-city teenagers experienced a structured camp program for a week. It was predicted and found that this experience led to a change toward internality, in the locus of control orientation of these youngsters. (Authors)

  18. Social support and Job stress: Moderation role of Locus of control

    Roohangiz Karimi; Farhad Alipour

    2011-01-01

    The purpose of this study is to investigate theoretically how locus of control can moderate the relationship between social support and job stress so as to increase the effect of social support to reduce stress in the workplaces. By utilizing the proposed model the researchers explore how supervisors can increase locus of control among their employees in order to increase the effect of social support to decrease stress in the organizations. This study may help managers and human resource deve...

  19. Functional and genetic analysis of haplotypic sequence variation at the nicastrin genomic locus

    Hamilton, Gillian; Killick, Richard; Lambert, Jean-Charles; Amouyel, Philippe; Carrasquillo, Minerva M.; Pankratz, V. Shane; Neill R Graff-Radford; Dickson, Dennis W.; Petersen, Ronald C.; Younkin, Steven G.; Powell, John F.; Wade-Martins, Richard

    2012-01-01

    Nicastrin (NCSTN) is a component of the γ-secretase complex and therefore potentially a candidate risk gene for Alzheimer's disease. Here, we have developed a novel functional genomics methodology to express common locus haplotypes to assess functional differences. DNA recombination was used to engineer 5 bacterial artificial chromosomes (BACs) to each express a different haplotype of the NCSTN locus. Each NCSTN-BAC was delivered to knockout nicastrin (Ncstn−/−) cells and clonal NCSTN-BAC+/Nc...

  20. A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens.

    McDaniel, T K; Jarvis, K. G.; Donnenberg, M S; Kaper, J B

    1995-01-01

    Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli O157:H7 are intestinal pathogens that profoundly damage the microvilli and subapical cytoskeleton of epithelial cells. Here we report finding in EPEC a 35-kbp locus containing several regions implicated in formation of these lesions. DNA probes throughout this locus hybridize to E. coli O157:H7 and other pathogens of three genera that cause similar lesions but do not hybridize to avirulent members of the same species. The ...

  1. A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait

    Geroldinger, Ludwig; Bürger, Reinhard

    2014-01-01

    The consequences of spatially varying, stabilizing or directional selection on a quantitative trait in a subdivided population are studied. A deterministic two-locus two-deme model is employed to explore the effects of migration, the degree of divergent selection, and the genetic architecture, i.e., the recombination rate and ratio of locus effects, on the maintenance of genetic variation. The possible equilibrium configurations are determined as functions of the migration rate. They depend c...

  2. Transposition of Ac from the P Locus of Maize into Unreplicated Chromosomal Sites

    Chen, Jychian; Greenblatt, Irwin M.; Dellaporta, Stephen L.

    1987-01-01

    We have analyzed donor and target sites of the mobile element Activator (Ac) that are altered as a result of somatic transposition from the P locus in maize. Previous genetic analysis has indicated that the two mitotic daughter lineages which result from Ac transposition from P differ in their Ac constitution at the P locus. Both lineages, however, usually contain transposed Ac elements which map to the same genetic position. Using methylation-sensitive restriction enzymes and genomic blot a...

  3. Analysis of genes for alcoholism using two-disease-locus models

    Shete Sanjay; Wu Chih-Chieh

    2005-01-01

    Abstract Using model-based two-locus methods for mapping genes, we analyzed the family data from the Collaborative Study on the Genetics of Alcoholism. Microsatellite data from 143 families ascertained through having three or more individuals affected with alcohol dependence were used for this investigation. Four regions showing evidence for linkage were identified using single-locus models from previous investigations. We investigated the genetic linkage, pattern of disease inheritance, and ...

  4. Natural Selection Opposing Artificial Selection: A Two-Locus Deterministic Simulation

    Minvielle, Francis

    1981-01-01

    A two-locus, two-allele metric trait was submitted to artificial truncation selection and to three types of opposing natural selection (two-locus extensions of directional selection, overdominance and underdominance) by numerical simulation in a large random-mating population. Limits to selection were generally reached by generation 100. Intermediate selection plateaus were found, with minor genes, for all three modes of opposing natural selection, but they were least frequent with underdomin...

  5. Identification of the Mating-Type (MAT) Locus That Controls Sexual Reproduction of Blastomyces dermatitidis

    Li, Wenjun; Sullivan, Thomas D.; Walton, Eric; Averette, Anna Floyd; Sakthikumar, Sharadha; Cuomo, Christina A.; Klein, Bruce S.; Heitman, Joseph

    2013-01-01

    Blastomyces dermatitidis is a dimorphic fungal pathogen that primarily causes blastomycosis in the midwestern and northern United States and Canada. While the genes controlling sexual development have been known for a long time, the genes controlling sexual reproduction of B. dermatitidis (teleomorph, Ajellomyces dermatitidis) are unknown. We identified the mating-type (MAT) locus in the B. dermatitidis genome by comparative genomic approaches. The B. dermatitidis MAT locus resembles those of...

  6. Genetic and Molecular Characterization of the I Locus of Phaseolus vulgaris

    Vallejos, C. Eduardo; Astua-Monge, Gustavo; Jones, Valerie; Plyler, Tammy R.; Sakiyama, Ney S.; Mackenzie, Sally A.

    2006-01-01

    The I locus of the common bean, Phaseolus vulgaris, controls the development of four different phenotypes in response to inoculation with Bean common mosaic virus, Bean common mosaic necrosis virus, several other related potyviruses, and one comovirus. We have generated a high-resolution linkage map around this locus and have aligned it with a physical map constructed with BAC clones. These clones were obtained from a library of the cultivar “Sprite,” which carries the dominant allele at the ...

  7. A Mycobacterium tuberculosis IS6110 preferential locus (ipl) for insertion into the genome.

    Fang, Z.; Forbes, K.J.

    1997-01-01

    A 267-nucleotide Mycobacterium tuberculosis genomic sequence (ipl, the IS6110 preferential locus) which can harbor the insertion sequence IS6110 at six alternative locations has been identified in some three-quarters of the isolates tested. Only one IS6110 copy was observed at this locus in the ipl::IS6110(+)-containing isolates tested, and all insertions had the same orientation. The implications of this finding for IS6110 fingerprint typing methods is discussed in this work.

  8. Understanding the role of locus of control in consultative decision-making: a case study

    Selart, Marcus

    2005-01-01

    Purpose: The study aims at clarifying whether locus of control may act as a bias in organisational decision-making or not. Design/methodology/approach: Altogether 44 managers working at Skanska (a Swedish multinational construction company) participated in the study. They were asked to complete a booklet including a locus of control test and a couple of decision tasks. The latter were based on case scenarios reflecting strategic issues relevant for consultative/ participative decision-making....

  9. Polymorphic DNA haplotypes at the phenlalanine hydroxylase (PAH) locus in Asian families with phenylketonuria (PKU)

    Daiger, Stephen P.; Reed, Lori; Huang, Shu-Shen; Zeng, Yi-Tao; Wang, Tao; Lo, Wilson H. Y.; Okano, Yoshiyuki; Hase, Yutaka; Fukuda, Y; Oura, Toshiaki; Tada, Keiya; Woo, Savio L. C.

    1989-01-01

    DNA polymorphisms at the phenylalanine hydroxylase (PAH) locus have proved highly efiective in linkage diagnosis of phenylketonuria (PKU) in Caucasian families. More than 10 RFLP sites have been reported within the PAH structural locus in Caucasians. With information from affected and unaffected offspring in PKU families it is often possible to reconstruct complete RFLP haplotypes in parents and to use these haplotypes to follow the segregation of PKU within families and to determine the dist...

  10. Self-esteem and locus of control of secondary school children both in England and Turkey

    PİŞKİN, Metin

    1996-01-01

    This study investigates self-esteem and locus of control in a cross-cultural context, comparing British and Turkish students. Sex differences are also considered. The relationship between academic achievement and the personality variables of self-esteem and locus of control is also examined. 
    The sample consisted of year-11 secondary school students. 190 were British and 315 were Turkish. In order to collect data, the Coopersmith Self-Esteem Inventory (SEI), the No...

  11. A re-examination of the case for a locus standi rule in public law

    Hough, Barry

    1997-01-01

    The doctrine of locus standi, or standing, determines the competence of a plaintiff to assert the matter of their complaint before the court. Since an individual lacking locus standi is an incompetent plaintiff, it follows that, in public law, government can exceed or abuse its powers with impunity provided no such "qualified" litigant seeks the intervention of the court. This appears directly in conflict with the constitutional requirement of legality. Public law is about imposing legal cont...

  12. Developmental Stability Covaries with Genome-Wide and Single-Locus Heterozygosity in House Sparrows

    Carl Vangestel; Joachim Mergeay; Deborah A Dawson; Viki Vandomme; Luc Lens

    2011-01-01

    Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to increase with genetic stress. Despite numerous studies providing empirical evidence for associations between FA and genome-wide properties such as multi-locus heterozygosity, support for single-locus effects remains scant. Here we test if, and to what extent, FA co-varies with single- and multilocus markers of genetic diversity in house sparrow (Passer domesticus) populations along an urban gradient. ...

  13. Social Work Professionals’ Emotional Intelligence, Locus Of Control And Role Efficacy: An Exploratory Study

    Singh, Sanjay K.

    2006-01-01

    The principal objective of the study was to study social work professionals psychologically. This study was conducted on a sample of 178 participants. The findings depict role efficacy to be associated positively with emotional intelligence and internal locus of control, but negatively with external locus of control. Similarly, emotional intelligence was found to be associated positively with internality, but negatively related to externality. The findings also indicated that emotional intell...

  14. Health locus of control and self-care behaviors in diabetic foot patients

    Abredari, Hamid; Bolourchifard, Fariba; Rassouli, Maryam; Nasiri, Navideh; Taher, Mohammad; Abedi, Ahmadreza

    2015-01-01

    Background: Diabetic foot affects more than 25% of diabetic patients and finally up to 20% of cases result in amputation. The most important factor resulting in severe complications or even death is lack of self-care. Health locus of control has been introduced as one of health factors and predicting factors of self-care. This research was performed for analyzing the correlation between self-care behaviors and health locus of control in diabetic foot patients. Methods: In this descriptive stu...

  15. Heterogeneous organization of the locus coeruleus projections to prefrontal and motor cortices

    Chandler, Daniel J.; Gao, Wen-Jun; WATERHOUSE, BARRY D.

    2014-01-01

    The locus coeruleus projection system in the brain is thought to exert uniform and synchronous modulatory effects on cells and circuits throughout the CNS by widespread release of its transmitter, norepinephrine. We challenge this notion by demonstrating that neurons in the locus coeruleus maintain segregated connections to brain regions with distinctly different functions. Specifically, cells that communicate with the prefrontal cortex, a region involved in cognition and executive function, ...

  16. Pure Land or Pure Mind?: Locus of Awakening and American Popular Religious Culture

    Richard K. Payne

    2015-01-01

    This essay has two sections, each with its own distinct goal, forming an interrelated whole. The first introduces “locus of awakening,” and applies it to the relative success in America of Zen and Tibetan Buddhisms, compared to Pure Land Buddhism. The explanatory power of the concept is demonstrated by also considering Soka Gakkai. The difference between popular culture treatments of Zen and Tibetan Buddhisms, and Pure Land Buddhism was the problematic leading to identifying locus of awakenin...

  17. Accurate Jones Matrix of the Practical Faraday Rotator

    王林斗; 祝昇翔; 李玉峰; 邢文烈; 魏景芝

    2003-01-01

    The Jones matrix of practical Faraday rotators is often used in the engineering calculation of non-reciprocal optical field. Nevertheless, only the approximate Jones matrix of practical Faraday rotators has been presented by now. Based on the theory of polarized light, this paper presents the accurate Jones matrix of practical Faraday rotators. In addition, an experiment has been carried out to verify the validity of the accurate Jones matrix. This matrix accurately describes the optical characteristics of practical Faraday rotators, including rotation, loss and depolarization of the polarized light. The accurate Jones matrix can be used to obtain the accurate results for the practical Faraday rotator to transform the polarized light, which paves the way for the accurate analysis and calculation of practical Faraday rotators in relevant engineering applications.

  18. Duplication of Locus Coding of Malate Dehydrogenase in Populus tomentosa Carr.

    2005-01-01

    Horizontal starch-gel electrophoresis was used to study crude enzyme extraction from young leaves of 234 clones of Populus tomentosa Carr. selected from nine provenances in North China. Ten enzyme systems were resolved. One hundred and fifty-six clones showing unusual allozyme band patterns at locus Mdh-1 were found. Three allozyme bands at locus Mdh-1 were 9:6:1 in concentration. Further studies on the electrophoretic patterns of ground mixed pollen extraction of 30 male clones selected at random from the 156 clones were conducted and it was found that allozyme bands at locus Mdh-1 were composed of two dark-stained bands and a weak band. Only one group of the malate dehydrogenase (MDH) zymogram composed of two bands was obtained from the electrophoretic segregation of pollen leachate of the same clones. A comparison of the electrophoretic patterns one another suggested that the locus Mdh-1 coding malate dehydrogenase in diploid species of P. tomentosa was duplicated. The duplicate gene locus possessed three same alleles and was located in mitochondria. The locus duplication of alleles coding malate dehydrogenase in P. tomentosa was discovered and reported for the first time.

  19. Locus of control in maltreated children: the impact of attachment and cumulative trauma

    Antonio Roazzi

    2016-01-01

    Full Text Available Abstract Up until now research studies carried out on abused children have rarely taken in consideration the impact of maltreatment on the locus of control; furthermore results concerning the distribution of attachment internal models in this population are inconclusive. In addition, no study has ever taken in consideration the differential role of attachment and time of exposure to stress in the formation of attributive styles. This research work involved 60 maltreated children and 100 controls with the purpose of evaluating the associations between their attachment and age as for their locus of control. Internal Working Models were assessed by SAT and locus of control by the Nowicki-Strickland Scale. Results highlight mainly external locus of control and disorganized and avoidant IWMs in abused children. Furthermore, age was more predictive than attachment for locus of control. By contrast, in the control group at both age taken in consideration attachment was predictive of locus of control. Results are discussed in terms of problematic symptoms associated to maltreatment.

  20. Specificity of prenatal cocaine on inhibition of locus coeruleus neurite outgrowth.

    Dey, S; Mactutus, C F; Booze, R M; Snow, D M

    2006-01-01

    Prenatal cocaine exposure induces alterations in attentional function that presumably involve locus coeruleus noradrenergic neurons and their projections. Previous reports indicate that embryonic rat locus coeruleus neurons exposed to cocaine, both in vitro and in vivo, showed in decreased cell survival and inhibition of neurite outgrowth, and that the effects were most deleterious during early gestation. The present study performed in vitro addressed the specificity of the inhibitory effects of cocaine by comparing locus coeruleus neurite formation and extension to that of dopaminergic substantia nigra neurons following exposure to a physiologically-relevant dose of cocaine (500 ng/ml, two times a day, for four days) during peak neuritogenesis. Following cocaine treatment, immunocytochemistry (anti-norepinephrine antibody to locus coeruleus; anti-tyrosine hydroxylase antibody to substantia nigra) and image analysis were performed to measure a variety of neurite outgrowth parameters. For locus coeruleus neurons, cocaine treatment decreased the 1) number of cells initiating neurites [Pcocaine for any of the parameters examined. More importantly, a significant interaction between cocaine treatment and brain region was observed [Pcocaine exposure. These data support our hypothesis that cocaine targets the noradrenergic system by negatively regulating locus coeruleus neuronal outgrowth, which likely affects pathfinding, synaptic connectivity, and ultimately attentional behavior in cocaine-exposed offspring. PMID:16483722

  1. Locus Of Control - Predictor Of Health And Subjective Well – Being

    Svetlana Popova

    2012-10-01

    Full Text Available The article presents results of a study of the relationship 'locus of control - health and subjective well-being. In a heterogeneous sample (N = 239 in the stage of youth (19-30 years shall be established: locus of control determines 11.56% of the changes in the assessment of health, changes in health contribute to 12.82% of the variation in assessment of happiness and 6.10% in the measurement of life satisfaction. Young people with an internal locus of control are healthier, happier and more satisfied with their lives than those with an external locus of control. In a study of cause - effect relationship is established that internal locus of control determines a healthier lifestyle. Inadequate health care, more severe risk factors (stress, unhealthy diet, inadequate sleep, smoking among young people with an external locus of control, outline prospects for greater vulnerability of this group of the population of the so called "Diseases of modern society." Most preferred activities of young people beneficial to their health are: walking, relaxation, hobbies and sports, and this is the way to state "flow" (activity of happiness and highlights the positive experiences in health. 

  2. Thorough investigation of a canine autoinflammatory disease (AID) confirms one main risk locus and suggests a modifier locus for amyloidosis.

    Olsson, Mia; Tintle, Linda; Kierczak, Marcin; Perloski, Michele; Tonomura, Noriko; Lundquist, Andrew; Murén, Eva; Fels, Max; Tengvall, Katarina; Pielberg, Gerli; Dufaure de Citres, Caroline; Dorso, Laetitia; Abadie, Jérôme; Hanson, Jeanette; Thomas, Anne; Leegwater, Peter; Hedhammar, Åke; Lindblad-Toh, Kerstin; Meadows, Jennifer R S

    2013-01-01

    Autoinflammatory disease (AID) manifests from the dysregulation of the innate immune system and is characterised by systemic and persistent inflammation. Clinical heterogeneity leads to patients presenting with one or a spectrum of phenotypic signs, leading to difficult diagnoses in the absence of a clear genetic cause. We used separate genome-wide SNP analyses to investigate five signs of AID (recurrent fever, arthritis, breed specific secondary dermatitis, otitis and systemic reactive amyloidosis) in a canine comparative model, the pure bred Chinese Shar-Pei. Analysis of 255 DNA samples revealed a shared locus on chromosome 13 spanning two peaks of association. A three-marker haplotype based on the most significant SNP (pELMO1, HAS2 and IL6). These results illustrate that phenotypic heterogeneity need not be a reflection of genetic heterogeneity, and that genetic modifiers of disease could be masked if syndromes were not first considered as individual clinical signs and then as a sum of their component parts. PMID:24130694

  3. Multiple System Atrophy

    ... Enhancing Diversity Find People About NINDS NINDS Multiple System Atrophy Information Page Condensed from Multiple System Atrophy ... Trials Organizations Publicaciones en Español What is Multiple System Atrophy? Multiple system atrophy (MSA) is a progressive ...

  4. Multiple Myeloma Symptoms

    ... Center Finder Home » About Multiple Myeloma » Symptoms Multiple Myeloma Symptoms Multiple myeloma symptoms may vary by patient, with the ... to be managed or prevented. The most common multiple myeloma symptoms may include: Bone pain or bone fractures ...

  5. Biomimetic Approach for Accurate, Real-Time Aerodynamic Coefficients Project

    National Aeronautics and Space Administration — Aerodynamic and structural reliability and efficiency depends critically on the ability to accurately assess the aerodynamic loads and moments for each lifting...

  6. Deletional rearrangement in the human T-cell receptor α-chain locus

    The antigen-specific receptor on the surface of mature T lymphocytes is a heterodimer consisting of polypeptides termed α and β. In the course of characterizing human T-cell tumors with an immature (CD4-, CD8-) surface phenotype, the authors detected a 2-kilobase α-related transcript. Analysis of cDNA clones corresponding to this transcript established that a genetic element (which they call TEA, for T early α) located between the α-chain variable- and joining-region genes had been spliced to the α constant region. The TEA transcript is present early in thymocyte ontogeny, and its expression declines during T-cell maturation. More important, the TEA area functions as an active site for rearrangement within the α gene locus. Blot hybridization of restriction enzyme-digested DNA with a TEA probe revealed a narrowly limited pattern of rearrangement in polyclonal thymic DNA, surprisingly different from the pattern expected for the mature α gene with its complex diversity. These DNA blots also showed that TEA is generally present in the germ-line configuration in cells expressing the γδ heterodimeric receptor and is deleted from mature (αβ-expressing) T-lymphocyte tumors and lines. Moreover, the TEA transcript lacked a long open reading frame for protein but instead possessed multiple copies of a repetitive element resembling those utilized in the heavy-chain class switch of the immunoglobulin genes. The temporal nature of the rearrangements and expression detected by TEA suggests that this recombination could mediate a transition between immature (γδ-expressing) T cells and mature (αβ-expressing) T cells

  7. Use of an endogenous plasmid locus for stable in trans complementation in Borrelia burgdorferi.

    Kasumba, Irene N; Bestor, Aaron; Tilly, Kit; Rosa, Patricia A

    2015-02-01

    Targeted mutagenesis and complementation are important tools for studying genes of unknown function in the Lyme disease spirochete Borrelia burgdorferi. A standard method of complementation is reintroduction of a wild-type copy of the targeted gene on a shuttle vector. However, shuttle vectors are present at higher copy numbers than B. burgdorferi plasmids and are potentially unstable in the absence of selection, thereby complicating analyses in the mouse-tick infectious cycle. B. burgdorferi has over 20 plasmids, with some, such as linear plasmid 25 (lp25), carrying genes required by the spirochete in vivo but relatively unstable during in vitro cultivation. We propose that complementation on an endogenous plasmid such as lp25 would overcome the copy number and in vivo stability issues of shuttle vectors. In addition, insertion of a selectable marker on lp25 could ensure its stable maintenance by spirochetes in culture. Here, we describe the construction of a multipurpose allelic-exchange vector containing a multiple-cloning site and either of two selectable markers. This suicide vector directs insertion of the complementing gene into the bbe02 locus, a site on lp25 that was previously shown to be nonessential during both in vitro and in vivo growth. We demonstrate the functional utility of this strategy by restoring infectivity to an ospC mutant through complementation at this site on lp25 and stable maintenance of the ospC gene throughout mouse infection. We conclude that this represents a convenient and widely applicable method for stable gene complementation in B. burgdorferi. PMID:25452278

  8. Development and evaluation of a multi-locus sequence typing scheme for Mycoplasma synoviae.

    Dijkman, R; Feberwee, A; Landman, W J M

    2016-08-01

    Reproducible molecular Mycoplasma synoviae typing techniques with sufficient discriminatory power may help to expand knowledge on its epidemiology and contribute to the improvement of control and eradication programmes of this mycoplasma species. The present study describes the development and validation of a novel multi-locus sequence typing (MLST) scheme for M. synoviae. Thirteen M. synoviae isolates originating from different poultry categories, farms and lesions, were subjected to whole genome sequencing. Their sequences were compared to that of M. synoviae reference strain MS53. A high number of single nucleotide polymorphisms (SNPs) indicating considerable genetic diversity were identified. SNPs were present in over 40 putative target genes for MLST of which five target genes were selected (nanA, uvrA, lepA, ruvB and ugpA) for the MLST scheme. This scheme was evaluated analysing 209 M. synoviae samples from different countries, categories of poultry, farms and lesions. Eleven clonal clusters and 76 different sequence types (STs) were obtained. Clustering occurred following geographical origin, supporting the hypothesis of regional population evolution. M. synoviae samples obtained from epidemiologically linked outbreaks often harboured the same ST. In contrast, multiple M. synoviae lineages were found in samples originating from swollen joints or oviducts from hens that produce eggs with eggshell apex abnormalities indicating that further research is needed to identify the genetic factors of M. synoviae that may explain its variations in tissue tropism and disease inducing potential. Furthermore, MLST proved to have a higher discriminatory power compared to variable lipoprotein and haemagglutinin A typing, which generated 50 different genotypes on the same database. PMID:26926568

  9. [Gene polymorphism at apoB locus and the serum lipids profile in children].

    Zhu, W; Feng, N; Wang, Y; Ye, G

    2001-09-01

    The relations of gene polymorphism at the apolipoprotein B locus and serum lipid profile in children was studied in 308 normal 7-11 year-old children, including 151 boys and 157 girls. Blood samples were collected for all subjects, and then the serum and blood clot were separated. Serum lipids, including TC, TG, LDL-C, HDL-C, apoB, apoA I and Lp(a) were detected. Genome DNA was extracted from blood clot, then apoB-Xba I gene polymorphism were tested by PCR-RFLP method. The results showed that the distribution of apoB-Xba I genotype in 308 children accorded with Hardy-Weiberg inheritance equilibrium law. The frequency of heterozygote(+/-) was 13.3%, allele(+) was 0.067. The frequency of allele(+) was closed to the internal and Japanese reports (0.033 and 0.04), but much less than the Caucasians (0.50). This showed a ethnic and population difference in the inheritance variation. The average LDL-C levels of the heterozygotes(+/-) were 2.17 mmol/L, no difference compared with homozygotes(-/-) (2.21 mmol/L, P > 0.05). There was also no difference for the genotype distribution between the hyperlipidemia group and control group, which may be the results of no enough sample size and the sample selection, and so on. On the other hand, in normal children, serum lipids controlled by many genes, the effect of a single gene might be small. More studies and analysis on the relationship between serum lipids and multiple genes in multisites should be the next step. PMID:12561593

  10. Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level

    Lu, Wenbin; Tzeng, Jung-Ying

    2016-01-01

    Genetic association analyses of rare variants in next-generation sequencing (NGS) studies are fundamentally challenging due to the presence of a very large number of candidate variants at extremely low minor allele frequencies. Recent developments often focus on pooling multiple variants to provide association analysis at the gene instead of the locus level. Nonetheless, pinpointing individual variants is a critical goal for genomic researches as such information can facilitate the precise delineation of molecular mechanisms and functions of genetic factors on diseases. Due to the extreme rarity of mutations and high-dimensionality, significances of causal variants cannot easily stand out from those of noncausal ones. Consequently, standard false-positive control procedures, such as the Bonferroni and false discovery rate (FDR), are often impractical to apply, as a majority of the causal variants can only be identified along with a few but unknown number of noncausal variants. To provide informative analysis of individual variants in large-scale sequencing studies, we propose the Adaptive False-Negative Control (AFNC) procedure that can include a large proportion of causal variants with high confidence by introducing a novel statistical inquiry to determine those variants that can be confidently dispatched as noncausal. The AFNC provides a general framework that can accommodate for a variety of models and significance tests. The procedure is computationally efficient and can adapt to the underlying proportion of causal variants and quality of significance rankings. Extensive simulation studies across a plethora of scenarios demonstrate that the AFNC is advantageous for identifying individual rare variants, whereas the Bonferroni and FDR are exceedingly over-conservative for rare variants association studies. In the analyses of the CoLaus dataset, AFNC has identified individual variants most responsible for gene-level significances. Moreover, single-variant results

  11. Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.

    Stojanov, M; Magalhaes, B; Terletsky, V; Basset, P; Prod'hom, G; Greub, G; Senn, L; Blanc, D S

    2016-02-01

    Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases. PMID:26581425

  12. Brucella 'HOOF-Prints': strain typing by multi-locus analysis of variable number tandem repeats (VNTRs

    Halling Shirley M

    2003-07-01

    Full Text Available Abstract Background Currently, there are very few tools available for subtyping Brucella isolates for epidemiological trace-back. Subtyping is difficult because of the genetic homogeneity within the genus. Sequencing of the genomes from three Brucella species has facilitated the search for DNA sequence variability. Recently, hypervariability among short tandem repeat sequences has been exploited for strain-typing of several bacterial pathogens. Results An eight-base pair tandem repeat sequence was discovered in nine genomic loci of the B. abortus genome. Eight loci were hypervariable among the three Brucella species. A PCR-based method was developed to identify the number of repeat units (alleles at each locus, generating strain-specific fingerprints. None of the loci exhibited species- or biovar-specific alleles. Sometimes, a species or biovar contained a specific allele at one or more loci, but the allele also occurred in other species or biovars. The technique successfully differentiated the type strains for all Brucella species and biovars, among unrelated B. abortus biovar 1 field isolates in cattle, and among B. abortus strains isolated from bison and elk. Isolates from the same herd or from short-term in vitro passage exhibited little or no variability in fingerprint pattern. Sometimes, isolates from an animal would have multiple alleles at a locus, possibly from mixed infections in enzootic areas, residual disease from incomplete depopulation of an infected herd or molecular evolution within the strain. Therefore, a mixed population or a pool of colonies from each animal and/or tissue was tested. Conclusion This paper describes a new method for fingerprinting Brucella isolates based on multi-locus characterization of a variable number, eight-base pair, tandem repeat. We have named this technique "HOOF-Prints" for Hypervariable Octameric Oligonucleotide Finger-Prints. The technique is highly discriminatory among Brucella species, among

  13. Quantitative Trait Locus and Brain Expression of HLA-DPA1 Offers Evidence of Shared Immune Alterations in Psychiatric Disorders.

    Morgan, Ling Z; Rollins, Brandi; Sequeira, Adolfo; Byerley, William; DeLisi, Lynn E; Schatzberg, Alan F; Barchas, Jack D; Myers, Richard M; Watson, Stanley J; Akil, Huda; Bunney, William E; Vawter, Marquis P

    2016-01-01

    Genome-wide association studies of schizophrenia encompassing the major histocompatibility locus (MHC) were highly significant following genome-wide correction. This broad region implicates many genes including the MHC complex class II. Within this interval we examined the expression of two MHC II genes (HLA-DPA1 and HLA-DRB1) in brain from individual subjects with schizophrenia (SZ), bipolar disorder (BD), major depressive disorder (MDD), and controls by differential gene expression methods. A third MHC II mRNA, CD74, was studied outside of the MHC II locus, as it interacts within the same immune complex. Exon microarrays were performed in anterior cingulate cortex (ACC) in BD compared to controls, and both HLA-DPA1 and CD74 were decreased in expression in BD. The expression of HLA-DPA1 and CD74 were both reduced in hippocampus, amygdala, and dorsolateral prefrontal cortex regions in SZ and BD compared to controls by specific qPCR assay. We found several novel HLA-DPA1 mRNA variants spanning HLA-DPA1 exons 2-3-4 as suggested by exon microarrays. The intronic rs9277341 SNP was a significant cis expression quantitative trait locus (eQTL) that was associated with the total expression of HLA-DPA1 in five brain regions. A biomarker study of MHC II mRNAs was conducted in SZ, BD, MDD, and control lymphoblastic cell lines (LCL) by qPCR assay of 87 subjects. There was significantly decreased expression of HLA-DPA1 and CD74 in BD, and trends for reductions in SZ in LCLs. The discovery of multiple splicing variants in brain for HLA-DPA1 is important as the HLA-DPA1 gene is highly conserved, there are no reported splicing variants, and the functions in brain are unknown. Future work on the function and localization of MHC Class II proteins in brain will help to understand the role of alterations in neuropsychiatric disorders. The HLA-DPA1 eQTL is located within a large linkage disequilibrium block that has an irrefutable association with schizophrenia. Future tests in a

  14. Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history.

    Cobble, Kacy R; Califf, Katy J; Stone, Nathan E; Shuey, Megan M; Birdsell, Dawn N; Colman, Rebecca E; Schupp, James M; Aziz, Maliha; Van Andel, Roger; Rocke, Tonie E; Wagner, David M; Busch, Joseph D

    2016-04-01

    Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague-related die-offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67-0.87) in all colonies. Two other DRB1 alleles appear to be trans-species polymorphisms shared with the black-tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (F ST = 0.033) than at microsatellite markers (F ST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an F ST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival. PMID:27066243

  15. Dissecting multiple sequence alignment methods : the analysis, design and development of generic multiple sequence alignment components in SeqAn

    Rausch, T.

    2010-01-01

    Multiple sequence alignments are an indispensable tool in bioinformatics. Many applications rely on accurate multiple alignments, including protein structure prediction, phylogeny and the modeling of binding sites. In this thesis we dissected and analyzed the crucial algorithms and data structures required to construct such a multiple alignment. Based upon that dissection, we present a novel graph-based multiple sequence alignment program and a new method for multi-read alignments occurring i...

  16. The 4q27 locus and prostate cancer risk

    Chronic inflammation is considered to be implicated in the development of prostate cancer. In this study we are the first to investigate a potential association between variants in an autoimmune related region on chromosome 4q27 and prostate cancer risk. This region harbors two cytokine genes IL-2 and the recently described IL-21. We genotyped six variants previously associated with autoimmune disease (namely rs13151961, rs13119723, rs17388568, rs3136534, rs6822844 and rs6840978) and one functional IL-2 promoter variant (rs2069762) for possible association with prostate cancer risk using the Australian Risk Factors for Prostate Cancer case-control Study. Overall, our results do not support an association between the seven variants at position 4q27 and prostate cancer risk. Per allele odds ratios (ORs) were not significantly different from 1 (all P-values = 0.06). However, we found suggestive evidence for a significant association between the presence of the rs13119723 variant (located in a protein of unknown function) and men with a family history of prostate cancer in first-degree relatives (P-value for interaction 0.02). The per allele OR associated with this variant was significantly higher than 1 (2.37; 95% C.I. = 1.01-5.57). We suggest that genetic variation within the chromosome 4q27 locus might be associated with prostate cancer susceptibility in men with a family history of the disease. Furthermore, our study alludes to a potential role of unknown protein KIAA1109 in conferring this risk

  17. Role of TRAV locus in low caries experience.

    Briseño-Ruiz, Jessica; Shimizu, Takehiko; Deeley, Kathleen; Dizak, Piper M; Ruff, Timothy D; Faraco, Italo M; Poletta, Fernando A; Brancher, João A; Pecharki, Giovana D; Küchler, Erika C; Tannure, Patricia N; Lips, Andrea; Vieira, Thays C S; Patir, Asli; Koruyucu, Mine; Mereb, Juan C; Resick, Judith M; Brandon, Carla A; Letra, Ariadne; Silva, Renato M; Cooper, Margaret E; Seymen, Figen; Costa, Marcelo C; Granjeiro, José M; Trevilatto, Paula C; Orioli, Iêda M; Castilla, Eduardo E; Marazita, Mary L; Vieira, Alexandre R

    2013-09-01

    Caries is the most common chronic, multifactorial disease in the world today; and little is still known about the genetic factors influencing susceptibility. Our previous genome-wide linkage scan has identified five loci related to caries susceptibility: 5q13.3, 13q31.1, 14q11.2, 14q 24.3, and Xq27. In the present study, we fine mapped the 14q11.2 locus to identify genetic contributors to caries susceptibility. Four hundred seventy-seven subjects from 72 pedigrees with similar cultural and behavioral habits and limited access to dental care living in the Philippines were studied. An additional 387 DNA samples from unrelated individuals were used to determine allele frequencies. For replication purposes, a total of 1,446 independent subjects from four different populations were analyzed based on their caries experience (low versus high). Forty-eight markers in 14q11.2 were genotyped using TaqMan chemistry. Transmission disequilibrium test was used to detect over transmission of alleles in the Filipino families, and Chi-square, Fisher's exact and logistic regression were used to test for association between low caries experience and variant alleles in the replication data sets. We finally assessed the mRNA expression of TRAV4 in the saliva of 143 study subjects. In the Filipino families, statistically significant associations were found between low caries experience and markers in TRAV4. We were able to replicate these results in the populations studied that were characteristically from underserved areas. Direct sequencing of 22 subjects carrying the associated alleles detects one missense mutation (Y30R) that is predicted to be probably damaging. Finally, we observed higher expression in children and teenagers with low caries experience, correlating with specific alleles in TRAV4. Our results suggest that TRAV4 may have a role in protecting against caries. PMID:23657505

  18. Opioid-glutamate interactions in rat locus coeruleus neurons.

    Oleskevich, S; Clements, J D; Williams, J T

    1993-09-01

    1. The effect of mu-opioids on the glutamate response was investigated in rat locus coeruleus (LC) neurons by intracellular recording in the brain slice preparation. Glutamate responses were evoked by bath application of selective glutamate agonists, glutamate iontophoresis, and stimulation of excitatory afferents. 2. The mu-opioid agonist D-Ala2-MePhe4-Gly-ol5-enkephalin (DAMGO; 1 microM) potentiated the response to bath application of N-methyl-D-aspartate (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionic acid by 91 and 142%, respectively, in slices cut in the horizontal plane. The mechanism of action of this effect was investigated under conditions that limited the DAMGO-induced hyperpolarization and improved the space clamp of the neuron through 1) addition of barium, 2) increase in extracellular potassium concentration, 3) sectioning of the LC in the coronal plane, and 4) addition of carbenoxolone. Each experimental manipulation decreased the DAMGO outward current and reduced the mu-opioid potentiation of the glutamate response. The results suggest that the mu-opioid-mediated potentiation of the glutamate response is dependent on membrane hyperpolarization. 3. Neither forskolin nor the phorbol ester 4b-phorbol 12,13-dibutyrate (PDBu) altered the glutamate-mediated inward currents. The potentiation of the glutamate response by DAMGO was not affected by PDBu. 4. The mu-opioids DAMGO and [met]5enkephalin (10 microM) did not significantly affect the NMDA receptor-mediated depolarization (mean 14%) evoked by local application of glutamate but inhibited the NMDA receptor-mediated synaptic potential (mean 25%).(ABSTRACT TRUNCATED AT 400 WORDS) PMID:7693886

  19. Fine mapping of the NRG1 Hirschsprung's disease locus.

    Clara Sze-Man Tang

    Full Text Available The primary pathology of Hirschsprung's disease (HSCR, colon aganglionosis is the absence of ganglia in variable lengths of the hindgut, resulting in functional obstruction. HSCR is attributed to a failure of migration of the enteric ganglion precursors along the developing gut. RET is a key regulator of the development of the enteric nervous system (ENS and the major HSCR-causing gene. Yet the reduced penetrance of RET DNA HSCR-associated variants together with the phenotypic variability suggest the involvement of additional genes in the disease. Through a genome-wide association study, we uncovered a ∼350 kb HSCR-associated region encompassing part of the neuregulin-1 gene (NRG1. To identify the causal NRG1 variants contributing to HSCR, we genotyped 243 SNPs variants on 343 ethnic Chinese HSCR patients and 359 controls. Genotype analysis coupled with imputation narrowed down the HSCR-associated region to 21 kb, with four of the most associated SNPs (rs10088313, rs10094655, rs4624987, and rs3884552 mapping to the NRG1 promoter. We investigated whether there was correlation between the genotype at the rs10088313 locus and the amount of NRG1 expressed in human gut tissues (40 patients and 21 controls and found differences in expression as a function of genotype. We also found significant differences in NRG1 expression levels between diseased and control individuals bearing the same rs10088313 risk genotype. This indicates that the effects of NRG1 common variants are likely to depend on other alleles or epigenetic factors present in the patients and would account for the variability in the genetic predisposition to HSCR.

  20. Clinical Clostridium difficile: clonality and pathogenicity locus diversity.

    Dingle, Kate E; Griffiths, David; Didelot, Xavier; Evans, Jessica; Vaughan, Alison; Kachrimanidou, Melina; Stoesser, Nicole; Jolley, Keith A; Golubchik, Tanya; Harding, Rosalind M; Peto, Tim E; Fawley, Warren; Walker, A Sarah; Wilcox, Mark; Crook, Derrick W

    2011-01-01

    Clostridium difficile infection (CDI) is an important cause of mortality and morbidity in healthcare settings. The major virulence determinants are large clostridial toxins, toxin A (tcdA) and toxin B (tcdB), encoded within the pathogenicity locus (PaLoc). Isolates vary in pathogenicity from hypervirulent PCR-ribotypes 027 and 078 with high mortality, to benign non-toxigenic strains carried asymptomatically. The relative pathogenicity of most toxigenic genotypes is still unclear, but may be influenced by PaLoc genetic variant. This is the largest study of C. difficile molecular epidemiology performed to date, in which a representative collection of recent isolates (n = 1290) from patients with CDI in Oxfordshire, UK, was genotyped by multilocus sequence typing. The population structure was described using NeighborNet and ClonalFrame. Sequence variation within toxin B (tcdB) and its negative regulator (tcdC), was mapped onto the population structure. The 69 Sequence Types (ST) showed evidence for homologous recombination with an effect on genetic diversification four times lower than mutation. Five previously recognised genetic groups or clades persisted, designated 1 to 5, each having a strikingly congruent association with tcdB and tcdC variants. Hypervirulent ST-11 (078) was the only member of clade 5, which was divergent from the other four clades within the MLST loci. However, it was closely related to the other clades within the tcdB and tcdC loci. ST-11 (078) may represent a divergent formerly non-toxigenic strain that acquired the PaLoc (at least) by genetic recombination. This study focused on human clinical isolates collected from a single geographic location, to achieve a uniquely high density of sampling. It sets a baseline of MLST data for future comparative studies investigating genotype virulence potential (using clinical severity data for these isolates), possible reservoirs of human CDI, and the evolutionary origins of hypervirulent strains

  1. ABI3 controls embryo degreening through Mendel's I locus.

    Delmas, Frédéric; Sankaranarayanan, Subramanian; Deb, Srijani; Widdup, Ellen; Bournonville, Céline; Bollier, Norbert; Northey, Julian G B; McCourt, Peter; Samuel, Marcus A

    2013-10-01

    Chlorophyll (chl) is essential for light capture and is the starting point that provides the energy for photosynthesis and thus plant growth. Obviously, for this reason, retention of the green chlorophyll pigment is considered a desirable crop trait. However, the presence of chlorophyll in mature seeds can be an undesirable trait that can affect seed maturation, seed oil quality, and meal quality. Occurrence of mature green seeds in oil crops such as canola and soybean due to unfavorable weather conditions during seed maturity is known to cause severe losses in revenue. One recently identified candidate that controls the chlorophyll degradation machinery is the stay-green gene, SGR1 that was mapped to Mendel's I locus responsible for cotyledon color (yellow versus green) in peas. A defect in SGR1 leads to leaf stay-green phenotypes in Arabidopsis and rice, but the role of SGR1 in seed degreening and the signaling machinery that converges on SGR1 have remained elusive. To decipher the gene regulatory network that controls degreening in Arabidopsis, we have used an embryo stay-green mutant to demonstrate that embryo degreening is achieved by the SGR family and that this whole process is regulated by the phytohormone abscisic acid (ABA) through ABSCISIC ACID INSENSITIVE 3 (ABI3); a B3 domain transcription factor that has a highly conserved and essential role in seed maturation, conferring desiccation tolerance. Misexpression of ABI3 was sufficient to rescue cold-induced green seed phenotype in Arabidopsis. This finding reveals a mechanistic role for ABI3 during seed degreening and thus targeting of this pathway could provide a solution to the green seed problem in various oil-seed crops. PMID:24043799

  2. Variants at the 9p21 locus and melanoma risk

    The influence of variants at the 9p21 locus on melanoma risk has been reported through investigation of CDKN2A variants through candidate gene approach as well as by genome wide association studies (GWAS). In the present study we genotyped, 25 SNPs that tag 273 variants on chromosome 9p21 in 837 melanoma cases and 1154 controls from Spain. Ten SNPs were selected based on previous associations, reported in GWAS, with either melanocytic nevi or melanoma risk or both. The other 15 SNPs were selected to fine map the CDKN2A gene region. All the 10 variants selected from the GWAS showed statistically significant association with melanoma risk. Statistically significant association with melanoma risk was also observed for the carriers of the variant T-allele of rs3088440 (540 C>T) at the 3’ UTR of CDKN2A gene with an OR 1.52 (95% CI 1.14-2.04). Interaction analysis between risk associated polymorphisms and previously genotyped MC1R variants, in the present study, did not show any statistically significant association. Statistical significant association was observed for the interaction between phototypes and the rs10811629 (located in intron 5 of MTAP). The strongest association was observed between the homozygous carrier of the A–allele and phototype II with an OR of 15.93 (95% CI 5.34-47.54). Our data confirmed the association of different variants at chromosome 9p21 with melanoma risk and we also found an association of a variant with skin phototypes

  3. Fast and simple epidemiological typing of Pseudomonas aeruginosa using the double-locus sequence typing (DLST) method.

    Basset, P; Blanc, D S

    2014-06-01

    Although the molecular typing of Pseudomonas aeruginosa is important to understand the local epidemiology of this opportunistic pathogen, it remains challenging. Our aim was to develop a simple typing method based on the sequencing of two highly variable loci. Single-strand sequencing of three highly variable loci (ms172, ms217, and oprD) was performed on a collection of 282 isolates recovered between 1994 and 2007 (from patients and the environment). As expected, the resolution of each locus alone [number of types (NT) = 35-64; index of discrimination (ID) = 0.816-0.964] was lower than the combination of two loci (NT = 78-97; ID = 0.966-0.971). As each pairwise combination of loci gave similar results, we selected the most robust combination with ms172 [reverse; R] and ms217 [R] to constitute the double-locus sequence typing (DLST) scheme for P. aeruginosa. This combination gave: (i) a complete genotype for 276/282 isolates (typability of 98%), (ii) 86 different types, and (iii) an ID of 0.968. Analysis of multiple isolates from the same patients or taps showed that DLST genotypes are generally stable over a period of several months. The high typability, discriminatory power, and ease of use of the proposed DLST scheme makes it a method of choice for local epidemiological analyses of P. aeruginosa. Moreover, the possibility to give unambiguous definition of types allowed to develop an Internet database ( http://www.dlst.org ) accessible by all. PMID:24326699

  4. Polymorphisms within the novel type 2 diabetes risk locus MTNR1B determine beta-cell function.

    Harald Staiger

    Full Text Available BACKGROUND: Very recently, a novel type 2 diabetes risk gene, i.e., MTNR1B, was identified and reported to affect fasting glycemia. Using our thoroughly phenotyped cohort of subjects at an increased risk for type 2 diabetes, we assessed the association of common genetic variation within the MTNR1B locus with obesity and prediabetes traits, namely impaired insulin secretion and insulin resistance. METHODOLOGY/PRINCIPAL FINDINGS: We genotyped 1,578 non-diabetic subjects, metabolically characterized by oral glucose tolerance test, for five tagging single nucleotide polymorphisms (SNPs covering 100% of common genetic variation (minor allele frequency > 0.05 within the MTNR1B locus (rs10830962, rs4753426, rs12804291, rs10830963, rs3781638. In a subgroup (N = 513, insulin sensitivity was assessed by hyperinsulinemic-euglycemic clamp, and in a further subgroup (N = 301, glucose-stimulated insulin secretion was determined by intravenous glucose tolerance test. After appropriate adjustment for confounding variables and Bonferroni correction for multiple comparisons, none of the tagging SNPs was reliably associated with measures of adiposity. SNPs rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations (p < 0.0001 and reduced OGTT- and IVGTT-induced insulin release (p < or = 0.0007 and p < or = 0.01, respectively. By contrast, SNP rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release (p<0.0001 and p < or = 0.0002, respectively. Moreover, SNP rs3781638 revealed significant association with elevated fasting- and OGTT-derived insulin sensitivity (p < or = 0.0021. None of the MTNR1B tagging SNPs altered proinsulin-to-insulin conversion. CONCLUSIONS/SIGNIFICANCE: In conclusion, common genetic variation within MTNR1B determines glucose-stimulated insulin secretion and plasma glucose concentrations. Their impact on beta

  5. Fast-forward genetics by radiation hybrids to saturate the locus regulating nuclear-cytoplasmic compatibility in Triticum.

    Bassi, Filippo M; Ghavami, Farhad; Hayden, Matthew J; Wang, Yi; Forrest, Kerrie L; Kong, Stephan; Dizon, Rhoderissa; Michalak de Jimenez, Monika K; Meinhardt, Steven W; Mergoum, Mohamed; Gu, Yong Q; Kianian, Shahryar F

    2016-08-01

    The nuclear-encoded species cytoplasm specific (scs) genes control nuclear-cytoplasmic compatibility in wheat (genus Triticum). Alloplasmic cells, which have nucleus and cytoplasm derived from different species, produce vigorous and vital organisms only when the correct version of scs is present in their nucleus. In this study, bulks of in vivo radiation hybrids segregating for the scs phenotype have been genotyped by sequencing with over 1.9 million markers. The high marker saturation obtained for a critical region of chromosome 1D allowed identification of 3318 reads that mapped in close proximity of the scs. A novel in silico approach was deployed to extend these short reads to sequences of up to 70 Kb in length and identify candidate open reading frames (ORFs). Markers were developed to anchor the short contigs containing ORFs to a radiation hybrid map of 650 individuals with resolution of 288 Kb. The region containing the scs locus was narrowed to a single Bacterial Artificial Chromosome (BAC) contig of Aegilops tauschii. Its sequencing and assembly by nano-mapping allowed rapid identification of a rhomboid gene as the only ORF existing within the refined scs locus. Resequencing of this gene from multiple germplasm sources identified a single nucleotide mutation, which gives rise to a functional amino acid change. Gene expression characterization revealed that an active copy of this rhomboid exists on all homoeologous chromosomes of wheat, and depending on the specific cytoplasm each copy is preferentially expressed. Therefore, a new methodology was applied to unique genetic stocks to rapidly identify a strong candidate gene for the control of nuclear-cytoplasmic compatibility in wheat. PMID:26915753

  6. Determining locus and periphery of optic disk in retinal images

    Norouzi Fard, Mohammad; Salehi, Alireza; Shanbeh Zadeh, Jamshid

    2008-04-01

    Diabetes can be recognized by features of retina. Automatic retina feature extraction improves the speed of diabetes diagnosis. The first step in extracting the features is to localize the optic disk. Methods with low accuracy in localizing the optic disk include area with maximum lightness or the largest area containing pixels with maximum gray levels. A more accurate method is to find the physical position of blood vessel that passes through optic disk. This paper presents a fast and accurate algorithm for localizing the optic disk. The process of localization consists of finding the target area, Optic Disk center and Optic Disk boundaries. Optic Disk boundaries are recognized by our algorithm with %90 accuracy.

  7. Children with Haemophilus influenzae type b (Hib) vaccine failure have long-term bactericidal antibodies against virulent Hib strains with multiple capsular loci.

    Townsend-Payne, Kelly; Ladhani, Shamez N; Findlow, Helen; Slack, Mary; Borrow, Ray

    2016-07-25

    Children who develop invasive Haemophilus influenzae serotype b (Hib) disease after immunisation with a highly-effective conjugate vaccine are more likely to have been infected with Hib strains possessing multiple copies of the capsulation locus. Using a recently-validated serum bactericidal antibody (SBA) assay, we tested convalescent sera from 127 Hib vaccine failure cases against clinical Hib strains expressing 1-5 copies of the capsulation locus. SBA titres correlated weakly with anti-capsular IgG antibody concentrations and there was no association between SBA geometric mean titres and number of capsulation locus copies. After infection, children with Hib vaccine failure were equally protected against Hib strains with 1-5 copies of the capsulation locus. PMID:27317452

  8. Novel algorithm for simultaneously detecting multiple vapor materials with multiple-wavelength differential absorption lidar

    Shirong Yin; Weiran Wang

    2006-01-01

    Differential absorption lidar (DIAL) has been successfully used to detect vapor material, however limited to detect single vapor using two closely spaced wavelengths. The progress in multiple-wavelength lasers motivates the need for detection and estimation algorithms that have the capability for simultaneous detection of multiple materials. In this paper, a simple and accurate algorithm is presented for simultaneously detecting and estimating multiple vapor materials with multiple-wavelength DIAL, which based on the maximum likelihood estimation (MLE) methodology. The performance of the algorithm is evaluated by simulation experiments, the results show that this algorithm can separately identify and quantify vapor material in mixtures and perform quite well.

  9. Accurate formulas for the penalty caused by interferometric crosstalk

    Rasmussen, Christian Jørgen; Liu, Fenghai; Jeppesen, Palle

    2000-01-01

    New simple formulas for the penalty caused by interferometric crosstalk in PIN receiver systems and optically preamplified receiver systems are presented. They are more accurate than existing formulas.......New simple formulas for the penalty caused by interferometric crosstalk in PIN receiver systems and optically preamplified receiver systems are presented. They are more accurate than existing formulas....

  10. A new, accurate predictive model for incident hypertension

    Völzke, Henry; Fung, Glenn; Ittermann, Till; Yu, Shipeng; Baumeister, Sebastian E; Dörr, Marcus; Lieb, Wolfgang; Völker, Uwe; Linneberg, Allan; Jørgensen, Torben; Felix, Stephan B; Rettig, Rainer; Rao, Bharat; Kroemer, Heyo K

    2013-01-01

    Data mining represents an alternative approach to identify new predictors of multifactorial diseases. This work aimed at building an accurate predictive model for incident hypertension using data mining procedures.......Data mining represents an alternative approach to identify new predictors of multifactorial diseases. This work aimed at building an accurate predictive model for incident hypertension using data mining procedures....

  11. 78 FR 34604 - Submitting Complete and Accurate Information

    2013-06-10

    ... COMMISSION 10 CFR Part 50 Submitting Complete and Accurate Information AGENCY: Nuclear Regulatory Commission... accurate information as would a licensee or an applicant for a license.'' DATES: Submit comments by August... may submit comments by any of the following methods (unless this document describes a different...

  12. Engineering the AAVS1 locus for consistent and scalable transgene expression in human iPSCs and their differentiated derivatives.

    Oceguera-Yanez, Fabian; Kim, Shin-Il; Matsumoto, Tomoko; Tan, Ghee Wan; Xiang, Long; Hatani, Takeshi; Kondo, Takayuki; Ikeya, Makoto; Yoshida, Yoshinori; Inoue, Haruhisa; Woltjen, Knut

    2016-05-15

    The potential use of induced pluripotent stem cells (iPSCs) in personalized regenerative medicine applications may be augmented by transgenics, including the expression of constitutive cell labels, differentiation reporters, or modulators of disease phenotypes. Thus, there is precedence for reproducible transgene expression amongst iPSC sub-clones with isogenic or diverse genetic backgrounds. Using virus or transposon vectors, transgene integration sites and copy numbers are difficult to control, and nearly impossible to reproduce across multiple cell lines. Moreover, randomly integrated transgenes are often subject to pleiotropic position effects as a consequence of epigenetic changes inherent in differentiation, undermining applications in iPSCs. To address this, we have adapted popular TALEN and CRISPR/Cas9 nuclease technologies in order to introduce transgenes into pre-defined loci and overcome random position effects. AAVS1 is an exemplary locus within the PPP1R12C gene that permits robust expression of CAG promoter-driven transgenes. Gene targeting controls transgene copy number such that reporter expression patterns are reproducible and scalable by ∼2-fold. Furthermore, gene expression is maintained during long-term human iPSC culture and in vitro differentiation along multiple lineages. Here, we outline our AAVS1 targeting protocol using standardized donor vectors and construction methods, as well as provide practical considerations for iPSC culture, drug selection, and genotyping. PMID:26707206

  13. EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture.

    Armengaud, Patrick; Zambaux, Kevin; Hills, Adrian; Sulpice, Ronan; Pattison, Richard J; Blatt, Michael R; Amtmann, Anna

    2009-03-01

    The root system is essential for the growth and development of plants. In addition to anchoring the plant in the ground, it is the site of uptake of water and minerals from the soil. Plant root systems show an astonishing plasticity in their architecture, which allows for optimal exploitation of diverse soil structures and conditions. The signalling pathways that enable plants to sense and respond to changes in soil conditions, in particular nutrient supply, are a topic of intensive research, and root system architecture (RSA) is an important and obvious phenotypic output. At present, the quantitative description of RSA is labour intensive and time consuming, even using the currently available software, and the lack of a fast RSA measuring tool hampers forward and quantitative genetics studies. Here, we describe EZ-Rhizo: a Windows-integrated and semi-automated computer program designed to detect and quantify multiple RSA parameters from plants growing on a solid support medium. The method is non-invasive, enabling the user to follow RSA development over time. We have successfully applied EZ-Rhizo to evaluate natural variation in RSA across 23 Arabidopsis thaliana accessions, and have identified new RSA determinants as a basis for future quantitative trait locus (QTL) analysis. PMID:19000163

  14. Analysis of the albino-locus region of the mouse. I. Orgin and viability

    Numerous specific-locus experiments designed to test the mutagenic effect of external radiation have yielded, in over 3,600,000 animals observed, altogether 119 presumed mutations involving the c locus. Of these, 55 were viable and albino (c/sup av/), 13 were viable and of various intermediate pigment types (c/sup xv/), four were subvital (c/sup as/ and c/sup xs/), seven were neonatally lethal albinos (c/sup al/), 28 prenatally lethal albinos (c/sup al/); 12 died untested. All of the prenatally lethal and at least one of the neonatally lethal c-locus mutations (c/sup al/ classes) are probably deficiencies that we have analyzed extensively in other experiments. Since absence of the locus mimics albino in phenotype, the intermediates (c/sup xv/ and c/sup xs/ groups) probably resulted from intragenic changes. The class of viable albino mutants (c/sup av/) might include, in addition to intragenic changes, some extremely small deficiencies. The effects on viability of c-locus lethals (c/sup al'/s) in heterozygous condition are not drastic enough to be perceived in stocks of mixed genetic background except in the case of the two longest known deficiencies and a few others. Analysis of the relation between radiation treatment and type of c-locus mutants obtained shows that the relative frequency of viable mutations, for each germ-cell type, is greater for low-LET than for neutron irradiation; however, the difference for any individual cell type is not significant. The majority (66.7%) of mutations derived from x- or γ-ray irradiated spermatogonia are viable, and the proportion of ''intermediates'' among these viables is similar to that among presumed spontaneous c-locus mutations

  15. Fast and accurate line scanner based on white light interferometry

    Lambelet, Patrick; Moosburger, Rudolf

    2013-04-01

    White-light interferometry is a highly accurate technology for 3D measurements. The principle is widely utilized in surface metrology instruments but rarely adopted for in-line inspection systems. The main challenges for rolling out inspection systems based on white-light interferometry to the production floor are its sensitivity to environmental vibrations and relatively long measurement times: a large quantity of data needs to be acquired and processed in order to obtain a single topographic measurement. Heliotis developed a smart-pixel CMOS camera (lock-in camera) which is specially suited for white-light interferometry. The demodulation of the interference signal is treated at the level of the pixel which typically reduces the acquisition data by one orders of magnitude. Along with the high bandwidth of the dedicated lock-in camera, vertical scan-speeds of more than 40mm/s are reachable. The high scan speed allows for the realization of inspection systems that are rugged against external vibrations as present on the production floor. For many industrial applications such as the inspection of wafer-bumps, surface of mechanical parts and solar-panel, large areas need to be measured. In this case either the instrument or the sample are displaced laterally and several measurements are stitched together. The cycle time of such a system is mostly limited by the stepping time for multiple lateral displacements. A line-scanner based on white light interferometry would eliminate most of the stepping time while maintaining robustness and accuracy. A. Olszak proposed a simple geometry to realize such a lateral scanning interferometer. We demonstrate that such inclined interferometers can benefit significantly from the fast in-pixel demodulation capabilities of the lock-in camera. One drawback of an inclined observation perspective is that its application is limited to objects with scattering surfaces. We therefore propose an alternate geometry where the incident light is

  16. Fast and accurate mock catalogue generation for low-mass galaxies

    Koda, Jun; Beutler, Florian; Kazin, Eyal; Marin, Felipe

    2015-01-01

    We present an accurate and fast framework for generating mock catalogues including low-mass halos, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realisations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate- mass galaxies in $10^{12} M_\\odot$ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k < 0.15 h/Mpc, and with only 3-per-cent error for k < 0.2 h/Mpc. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at ...

  17. Fast and accurate mock catalogue generation for low-mass galaxies

    Koda, Jun; Blake, Chris; Beutler, Florian; Kazin, Eyal; Marin, Felipe

    2016-06-01

    We present an accurate and fast framework for generating mock catalogues including low-mass haloes, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realizations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate-mass galaxies in 1012 M⊙ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k ≤ 0.15 h Mpc-1, and with only 3-per cent error for k ≤ 0.2 h Mpc-1. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at github.com/junkoda/cola_halo.

  18. Genetic locus (stmF) associated with cyclic GMP phosphodiesterase activity in Dictyostelium discoideum maps in linkage group II.

    Coukell, M. B.; Cameron, A M

    1985-01-01

    Previous attempts to map the stmF locus in Dictyostelium discoideum, by using only clone morphology as a marker, have led to equivocal results. Since strains carrying mutations at the stmF locus possess very low cyclic GMP phosphodiesterase activity, we have remapped this locus using both morphological and biochemical markers. Our results indicate that mutations producing a stable "streamer" phenotype and reduced cyclic GMP phosphodiesterase activity are located in linkage group II, probably ...

  19. Anxiety, locus of control, and coping strategies among end-stage renal disease patients undergoing maintenance hemodialysis

    Kohli, S.; Batra, P.; Aggarwal, H. K.

    2011-01-01

    End-stage kidney disease (ESKD) patients on maintenance hemodialysis (MHD) have a lot of anxiety. Anxiety and coping are associated with the locus of control; the present investigation aimed to study the state and trait anxiety, locus of control, and active and passive coping among patients on MHD. Thirty MHD patients and 30 controls were administered State–Trait Anxiety Inventory, Rotter's Locus of Control Scale, and Coping Responses Inventory. There were significantly higher scores on state...

  20. A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.

    Hongmei Jiang

    Full Text Available The advent of next-generation sequencing technologies has greatly promoted the field of metagenomics which studies genetic material recovered directly from an environment. Characterization of genomic composition of a metagenomic sample is essential for understanding the structure of the microbial community. Multiple genomes contained in a metagenomic sample can be identified and quantitated through homology searches of sequence reads with known sequences catalogued in reference databases. Traditionally, reads with multiple genomic hits are assigned to non-specific or high ranks of the taxonomy tree, thereby impacting on accurate estimates of relative abundance of multiple genomes present in a sample. Instead of assigning reads one by one to the taxonomy tree as many existing methods do, we propose a statistical framework to model the identified candidate genomes to which sequence reads have hits. After obtaining the estimated proportion of reads generated by each genome, sequence reads are assigned to the candidate genomes and the taxonomy tree based on the estimated probability by taking into account both sequence alignment scores and estimated genome abundance. The proposed method is comprehensively tested on both simulated datasets and two real datasets. It assigns reads to the low taxonomic ranks very accurately. Our statistical approach of taxonomic assignment of metagenomic reads, TAMER, is implemented in R and available at http://faculty.wcas.northwestern.edu/hji403/MetaR.htm.