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Sample records for admixture linkage disequilibrium

  1. Bayesian estimates of linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    Abad-Grau María M

    2007-06-01

    Full Text Available Abstract Background The maximum likelihood estimator of D' – a standard measure of linkage disequilibrium – is biased toward disequilibrium, and the bias is particularly evident in small samples and rare haplotypes. Results This paper proposes a Bayesian estimation of D' to address this problem. The reduction of the bias is achieved by using a prior distribution on the pair-wise associations between single nucleotide polymorphisms (SNPs that increases the likelihood of equilibrium with increasing physical distances between pairs of SNPs. We show how to compute the Bayesian estimate using a stochastic estimation based on MCMC methods, and also propose a numerical approximation to the Bayesian estimates that can be used to estimate patterns of LD in large datasets of SNPs. Conclusion Our Bayesian estimator of D' corrects the bias toward disequilibrium that affects the maximum likelihood estimator. A consequence of this feature is a more objective view about the extent of linkage disequilibrium in the human genome, and a more realistic number of tagging SNPs to fully exploit the power of genome wide association studies.

  2. Effects of Worldwide Population Subdivision on ALDH2 Linkage Disequilibrium

    OpenAIRE

    Peterson, Raymond J.; Goldman, David; Long, Jeffrey C.

    1999-01-01

    The effect of human population subdivision on linkage disequilibrium has previously been studied for unlinked genes. However, no study has focused on closely linked polymorphisms or formally partitioned linkage disequilibrium within and among worldwide populations. With an emphasis on population subdivision, the goal of this paper is to investigate the causes of linkage disequilibrium in ALDH2, the gene that encodes aldehyde dehydrogenase 2. Haplotypes for 756 people from 17 populations acros...

  3. Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

    Directory of Open Access Journals (Sweden)

    Raphaël Mourad

    Full Text Available Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

  4. Linkage disequilibrium and association mapping of drought ...

    African Journals Online (AJOL)

    Drought stress is a major abiotic stress that limits crop production. Molecular association mapping techniques through linkage disequilibrium (LD) can be effectively used to tag genomic regions involved in drought stress tolerance. With the association mapping approach, 90 genotypes of cotton Gossypium hirsutum, from ...

  5. Linkage disequilibrium and demographic history of the isolated population of the Faroe Islands

    DEFF Research Database (Denmark)

    Jorgensen, Tove H; Degn, Birte; Wang, August G

    2002-01-01

    The isolated population of the Faroe Islands has a history of recent expansion after being limited to a small size for centuries. Such an isolated population may be ideal for linkage disequilibrium mapping of disease genes if linkage disequilibrium (LD) extends over large regions. Analyses of 18 ...

  6. A comparison of genetic map distance and linkage disequilibrium between 15 polymorphic dinucleotide repeat loci in two populations

    Energy Technology Data Exchange (ETDEWEB)

    Urbanek, M.; Goldman, D.; Long, J.C. [Lab. of Neurogenetics, Rockville, MD (United States)

    1994-09-01

    Linkage disequilibrium has recently been used to map the diastrophic dysplasia gene in a Finnish sample. One advantage of this method is that the large pedigrees required by some other methods are unnecessary. Another advantage is that linkage disequilibrium mapping capitalizes on the cumulative history of recombination events, rather than those occurring within the sampled individuals. A potential limitation of linkage disequilibrium mapping is that linkage equilibrium is likely to prevail in all but the most isolated populations, e.g., those which have recently experienced founder effects or severe population bottlenecks. In order to test the method`s generality, we examined patterns of linkage disequilibrium between pairs of loci within a known genetic map. Two populations were analyzed. The first population, Navajo Indians (N=45), is an isolate that experienced a severe bottleneck in the 1860`s. The second population, Maryland Caucasians (N=45), is cosmopolitan. We expected the Navajo sample to display more linkage disequilibrium than the Caucasian sample, and possibly that the Navajo disequilibrium pattern would reflect the genetic map. Linkage disequilibrium coefficients were estimated between pairs of alleles at different loci using maximum likelihood. The genetic isolate structure of Navajo Indians is confirmed by the DNA typings. Heterozygosity is lower than in the Caucasians, and fewer different alleles are observed. However, a relationship between genetic map distance and linkage disequilibrium could be discerned in neither the Navajo nor the Maryland samples. Slightly more linkage disequilibrium was observed in the Navajos, but both data sets were characterized by very low disequilibrium levels. We tentatively conclude that linkage disequilibrium mapping with dinucleotide repeats will only be useful with close linkage between markers and diseases, even in very isolated populations.

  7. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

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    Smith Oscar

    2002-10-01

    Full Text Available Abstract Background Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. Results We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp, but rare in coding regions. A small number (2–8 of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. Conclusions No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.

  8. Effect of Linkage Disequilibrium on the Identification of Functional Variants

    Science.gov (United States)

    Thomas, Alun; Abel, Haley J; Di, Yanming; Faye, Laura L; Jin, Jing; Liu, Jin; Wu, Zheyan; Paterson, Andrew D

    2011-01-01

    We summarize the contributions of Group 9 of Genetic Analysis Workshop 17. This group addressed the problems of linkage disequilibrium and other longer range forms of allelic association when evaluating the effects of genotypes on phenotypes. Issues raised by long-range associations, whether a result of selection, stratification, possible technical errors, or chance, were less expected but proved to be important. Most contributors focused on regression methods of various types to illustrate problematic issues or to develop adaptations for dealing with high-density genotype assays. Study design was also considered, as was graphical modeling. Although no method emerged as uniformly successful, most succeeded in reducing false-positive results either by considering clusters of loci within genes or by applying smoothing metrics that required results from adjacent loci to be similar. Two unexpected results that questioned our assumptions of what is required to model linkage disequilibrium were observed. The first was that correlations between loci separated by large genetic distances can greatly inflate single-locus test statistics, and, whether the result of selection, stratification, possible technical errors, or chance, these correlations seem overabundant. The second unexpected result was that applying principal components analysis to genome-wide genotype data can apparently control not only for population structure but also for linkage disequilibrium. PMID:22128051

  9. Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P; Lund, M S

    2009-01-01

    disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...... the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However...

  10. The score statistic of the LD-lod analysis: detecting linkage adaptive to linkage disequilibrium.

    Science.gov (United States)

    Huang, J; Jiang, Y

    2001-01-01

    We study the properties of a modified lod score method for testing linkage that incorporates linkage disequilibrium (LD-lod). By examination of its score statistic, we show that the LD-lod score method adaptively combines two sources of information: (a) the IBD sharing score which is informative for linkage regardless of the existence of LD and (b) the contrast between allele-specific IBD sharing scores which is informative for linkage only in the presence of LD. We also consider the connection between the LD-lod score method and the transmission-disequilibrium test (TDT) for triad data and the mean test for affected sib pair (ASP) data. We show that, for triad data, the recessive LD-lod test is asymptotically equivalent to the TDT; and for ASP data, it is an adaptive combination of the TDT and the ASP mean test. We demonstrate that the LD-lod score method has relatively good statistical efficiency in comparison with the ASP mean test and the TDT for a broad range of LD and the genetic models considered in this report. Therefore, the LD-lod score method is an interesting approach for detecting linkage when the extent of LD is unknown, such as in a genome-wide screen with a dense set of genetic markers. Copyright 2001 S. Karger AG, Basel

  11. Localizing genes using linkage disequilibrium in plants: integrating ...

    African Journals Online (AJOL)

    GREGO

    2007-03-19

    Mar 19, 2007 ... Localizing genes using linkage disequilibrium in plants: integrating lessons ... reduce that association as a function of the marker distance from the QTL. ..... the gene locus enhanced the resolution power of asso- ciation tests .... agents, such as insects, birds, water and wind, so mating is determined by a ...

  12. Whole genome study of linkage disequilibrium in Sahiwal cattle

    African Journals Online (AJOL)

    Esnart Mukumbo

    2017-12-30

    Dec 30, 2017 ... 500,968 SNPs comprising 2518.1 Mb of the genome, were used for the LD estimation. The minior ..... on a high density SNP panel. BMC Genom. ... Linkage disequilibrium and the mapping of complex human traits. Trend.

  13. Detection of QTL for Carcass Quality on Chromosome 6 by Exploiting Linkage and Linkage Disequilibrium in Hanwoo

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    J.-H. Lee

    2012-01-01

    Full Text Available The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area (LMA, and marbling score (Marb, respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp with the most significant evidence for linkage (p<10−5. Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.

  14. Genome scan for linkage to asthma using a linkage disequilibrium-lod score test.

    Science.gov (United States)

    Jiang, Y; Slager, S L; Huang, J

    2001-01-01

    We report a genome-wide linkage study of asthma on the German and Collaborative Study on the Genetics of Asthma (CSGA) data. Using a combined linkage and linkage disequilibrium test and the nonparametric linkage score, we identified 13 markers from the German data, 1 marker from the African American (CSGA) data, and 7 markers from the Caucasian (CSGA) data in which the p-values ranged between 0.0001 and 0.0100. From our analysis and taking into account previous published linkage studies of asthma, we suggest that three regions in chromosome 5 (around D5S418, D5S644, and D5S422), one region in chromosome 6 (around three neighboring markers D6S1281, D6S291, and D6S1019), one region in chromosome 11 (around D11S2362), and two regions in chromosome 12 (around D12S351 and D12S324) especially merit further investigation.

  15. Genotyping of PCR-based polymorphisms and linkage-disequilibrium analysis at the NF1 locus

    Energy Technology Data Exchange (ETDEWEB)

    Purandare, S.M.; Viskochil, D.H.; Cawthon, R. [Univ. of Utah, Salt Lake City, UT (United States)] [and others

    1996-07-01

    Six polymorphism across the NF1 gene have been adapted for genotyping through application of PCR-based assays. Three exon-based polymorphisms - at positions 702, 2034, and 10647 in the NF1 cDNA - were genotyped by mutagenically separated PCR (MS-PCR). A fourth polymorphism, DV1.9, is an L1 insertion element in intron 30, and the other two polymorphisms, GXAlu and EVI-20, are short tandem repeats in intron 27b. All the polymorphisms were evaluated in a cohort of 110 CEPH individuals who previously had been analyzed by use of eight RFLPs at the NF1 locus. Pairwise linkage-disequilibrium analyses with the six PCR-based polymorphisms and their flanking markers demonstrated disequilibrium between all tested loci. Genotypes of the four diallelic polymorphisms (702, 2034, 10647, and DV1.9) were also evaluated in cohorts from the CEPH, African, and Japanese populations. The CEPH and Japanese cohorts showed similar heterozygosities and linkage-disequilibrium coefficients. The African cohort showed a higher degree of heterozygosity and lower linkage-disequilibrium values, compared with the CEPH and Japanese cohorts. 36 refs., 2 figs., 3 tabs.

  16. Linkage disequilibrium and association mapping.

    Science.gov (United States)

    Weir, B S

    2008-01-01

    Linkage disequilibrium refers to the association between alleles at different loci. The standard definition applies to two alleles in the same gamete, and it can be regarded as the covariance of indicator variables for the states of those two alleles. The corresponding correlation coefficient rho is the parameter that arises naturally in discussions of tests of association between markers and genetic diseases. A general treatment of association tests makes use of the additive and nonadditive components of variance for the disease gene. In almost all expressions that describe the behavior of association tests, additive variance components are modified by the squared correlation coefficient rho2 and the nonadditive variance components by rho4, suggesting that nonadditive components have less influence than additive components on association tests.

  17. Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

    Science.gov (United States)

    S. Kumar; Craig Echt; P.L. Wilcox; T.E. Richardson

    2004-01-01

    Linkage analysis is commonly uscd to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to...

  18. Haplotype analysis and linkage disequilibrium for DGAT1

    OpenAIRE

    Strucken, Eva M.; Rahmatalla, Siham; De Koning, Dirk-Jan; Brockmann, Gudrun A.

    2010-01-01

    This study focused on haplotype effects and linkage disequilibrium (LD) for the K232A locus and the promoter VNTR in the DGAT1 gene. Analyses were carried out in three German Holstein Frisian populations (including 492, 305, and 518 animals) for milk yield, milk fat and protein yield, and milk fat and protein content. We found that effects of the promoter VNTR were not significant and explain only a small amount of the variation of the QTL on BTA14. Haplotype effects were less significant tha...

  19. Linkage Disequilibrium between STRPs and SNPs across the Human Genome

    OpenAIRE

    Payseur, Bret A.; Place, Michael; Weber, James L.

    2008-01-01

    Patterns of linkage disequilibrium (LD) reveal the action of evolutionary processes and provide crucial information for association mapping of disease genes. Although recent studies have described the landscape of LD among single nucleotide polymorphisms (SNPs) from across the human genome, associations involving other classes of molecular variation remain poorly understood. In addition to recombination and population history, mutation rate and process are expected to shape LD. To test this i...

  20. Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium.

    Science.gov (United States)

    Dapper, Amy L; Payseur, Bret A

    2018-02-01

    In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines

    Science.gov (United States)

    Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan

    2018-01-01

    The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13–0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24–0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens. PMID:29425208

  2. Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines.

    Science.gov (United States)

    Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan; Lee, Jun-Heon

    2018-01-01

    The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13-0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24-0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens.

  3. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data.

    Science.gov (United States)

    Mdladla, K; Dzomba, E F; Huson, H J; Muchadeyi, F C

    2016-08-01

    The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)  = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of 100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in genetic studies of these populations. © 2016 Stichting International Foundation for Animal Genetics.

  4. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

    Science.gov (United States)

    Signatures of selection are regions in the genome that have been preferentially maintained because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium patterns. The varLD methodol...

  5. Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon

    Science.gov (United States)

    The wide phenotypic diversity, in melon fruits, is the result of consumer preferences combined with genotype fitness to the different agro-climatic zones. There is no sufficient information with respect to the extent of genetic divergence, population structure and linkage disequilibrium (LD) in mel...

  6. Characterization of genetic diversity and linkage disequilibrium of ZmLOX4 and ZmLOX5 loci in maize.

    Directory of Open Access Journals (Sweden)

    Gerald N De La Fuente

    Full Text Available Maize (Zea mays L. lipoxygenases (ZmLOXs are well recognized as important players in plant defense against pathogens, especially in cross kingdom lipid communication with pathogenic fungi. This study is among the first to investigate genetic diversity at important gene paralogs ZmLOX4 and ZmLOX5. Sequencing of these genes in 400 diverse maize lines showed little genetic diversity and low linkage disequilibrium in the two genes. Importantly, we identified one inbred line in which ZmLOX5 has a disrupted open reading frame, a line missing ZmLOX5, and five lines with a duplication of ZmLOX5. Tajima's D test suggests that both ZmLOX4 and ZmLOX5 have been under neutral selection. Further investigation of haplotype data revealed that within the ZmLOX family members only ZmLOX12, a monocot specific ZmLOX, showed strong linkage disequilibrium that extends further than expected in maize. Linkage disequilibrium patterns at these loci of interest are crucial for future candidate gene association mapping studies. ZmLOX4 and ZmLOX5 mutations and copy number variants are under further investigation for crop improvement.

  7. Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data

    Science.gov (United States)

    Hernández-Lemus, Enrique; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Fernández-López, J. Carlos; Hidalgo-Miranda, Alfredo; Jiménez-Sánchez, Gerardo

    2008-02-01

    The statistical study of large scale genomic data has turned out to be a very important tool in population genetics. Quantitative methods are essential to understand and implement association studies in the biomedical and health sciences. Nevertheless, the characterization of recently admixed populations has been an elusive problem due to the presence of a number of complex phenomena. For example, linkage disequilibrium structures are thought to be more complex than their non-recently admixed population counterparts, presenting the so-called ancestry blocks, admixed regions that are not yet smoothed by the effect of genetic recombination. In order to distinguish characteristic features for various populations we have implemented several methods, some of them borrowed or adapted from the analysis of nonlinear time series in statistical physics and quantitative physiology. We calculate the main fractal dimensions (Kolmogorov's capacity, information dimension and correlation dimension, usually named, D0, D1 and D2). We also have made detrended fluctuation analysis and information based similarity index calculations for the probability distribution of correlations of linkage disequilibrium coefficient of six recently admixed (mestizo) populations within the Mexican Genome Diversity Project [1] and for the non-recently admixed populations in the International HapMap Project [2]. Nonlinear correlations showed up as a consequence of internal structure within the haplotype distributions. The analysis of these correlations as well as the scope and limitations of these procedures within the biomedical sciences are discussed.

  8. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo

    Directory of Open Access Journals (Sweden)

    Yi Li

    2015-07-01

    Full Text Available The efficiency of genome-wide association analysis (GWAS depends on power of detection for quantitative trait loci (QTL and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM, a combined linkage and linkage disequilibrium analysis (LDLA and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT, yearling weight (YWT, carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area, and marbling score (Marb. Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX] may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

  9. Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars

    NARCIS (Netherlands)

    Kraakman, A.T.W.; Martinez, F.; Mussiraliev, B.; Eeuwijk, van F.A.; Niks, R.E.

    2006-01-01

    A set of 148 modern spring barley cultivars was explored for the extent of linkage disequilibrium (LD) between genes governing traits and nearby marker alleles. Associations of agronomically relevant traits (days to heading, plant height), resistance traits (leaf rust, barley yellow dwarf virus

  10. Genomewide Linkage Disequilibrium Mapping of Severe Bipolar Disorder in a Population Isolate

    Science.gov (United States)

    Ophoff, Roel A.; Escamilla, Michael A.; Service, Susan K.; Spesny, Mitzi; Meshi, Dar B.; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L.; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C.; Dong, Penny; Leon, Pedro E.; Reus, Victor I.; Sandkuijl, Lodewijk A.; Freimer, Nelson B.

    2002-01-01

    Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601

  11. Nucleotide diversity and linkage disequilibrium in five Lolium perenne genes with putative role in shoot branching

    DEFF Research Database (Denmark)

    Brazauskas, Gintaras; Pašakinskienė, Izolda; Asp, Torben

    2010-01-01

    Knowledge on nucleotide diversity and linkage disequilibrium (LD) patterns is prerequisite for association analyses. However, little is known about the nucleotide diversity in the evolutionary important ryegrass shoot morphology genes. Five candidate genes, LpIAA1, LpRUB1, LpBRI1, LpSHOOT1 and Lp...

  12. Genomic polymorphism, recombination, and linkage disequilibrium in human major histocompatibility complex-encoded antigen-processing genes.

    Science.gov (United States)

    van Endert, P M; Lopez, M T; Patel, S D; Monaco, J J; McDevitt, H O

    1992-01-01

    Recently, two subunits of a large cytosolic protease and two putative peptide transporter proteins were found to be encoded by genes within the class II region of the major histocompatibility complex (MHC). These genes have been suggested to be involved in the processing of antigenic proteins for presentation by MHC class I molecules. Because of the high degree of polymorphism in MHC genes, and previous evidence for both functional and polypeptide sequence polymorphism in the proteins encoded by the antigen-processing genes, we tested DNA from 27 consanguineous human cell lines for genomic polymorphism by restriction fragment length polymorphism (RFLP) analysis. These studies demonstrate a strong linkage disequilibrium between TAP1 and LMP2 RFLPs. Moreover, RFLPs, as well as a polymorphic stop codon in the telomeric TAP2 gene, appear to be in linkage disequilibrium with HLA-DR alleles and RFLPs in the HLA-DO gene. A high rate of recombination, however, seems to occur in the center of the complex, between the TAP1 and TAP2 genes. Images PMID:1360671

  13. Data on genotypic distribution and linkage disequilibrium of several ANRIL polymorphisms in hemodialysis patients

    Directory of Open Access Journals (Sweden)

    A. Arbiol-Roca

    2017-04-01

    Full Text Available A long non-coding RNA called ANRIL located on chromosome 9p21.3 has been identified as a novel genetic factor associated with cardiovascular disease. Investigation of several single nucleotide polymorphisms (SNPs of Noncoding Antisense RNA in the INK4 Locus (ANRIL gene are of particular interest. This article reports data related to the research article entitled: “Association of ANRIL gene polymorphisms with major adverse cardiovascular events in hemodialysis patients” (Arbiol-Roca et al. [1]. Data presented show the genotypic distribution of four selected ANRIL SNPs: rs10757278, rs4977574, rs10757274 and rs6475606 in a cohort constituted by 284 hemodialysis patients. This article analyzes the Hardy-Weinberg disequilibrium of each studied SNP, and the linkage disequilibrium between them.

  14. Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone

    Czech Academy of Sciences Publication Activity Database

    Wang, L.; Luzynski, K.; Pool, J. E.; Janoušek, V.; Dufková, Petra; Vyskočilová, Martina; Teeter, K. C.; Nachman, M. W.; Munclinger, P.; Macholán, Miloš; Piálek, Jaroslav; Tucker, P. K.

    2011-01-01

    Roč. 20, č. 14 (2011), s. 2985-3000 ISSN 0962-1083 R&D Projects: GA ČR GA206/08/0640 Grant - others:NSF(US) DEB0746560 Institutional research plan: CEZ:AV0Z60930519; CEZ:AV0Z50450515 Keywords : house mouse * hybrid zones * linkage disequilibrium * SNP markers Subject RIV: EG - Zoology Impact factor: 5.522, year: 2011

  15. Exploiting linkage disequilibrium in statistical modelling in quantitative genomics

    DEFF Research Database (Denmark)

    Wang, Lei

    Alleles at two loci are said to be in linkage disequilibrium (LD) when they are correlated or statistically dependent. Genomic prediction and gene mapping rely on the existence of LD between gentic markers and causul variants of complex traits. In the first part of the thesis, a novel method...... to quantify and visualize local variation in LD along chromosomes in describet, and applied to characterize LD patters at the local and genome-wide scale in three Danish pig breeds. In the second part, different ways of taking LD into account in genomic prediction models are studied. One approach is to use...... the recently proposed antedependence models, which treat neighbouring marker effects as correlated; another approach involves use of haplotype block information derived using the program Beagle. The overall conclusion is that taking LD information into account in genomic prediction models potentially improves...

  16. MICA diversity and linkage disequilibrium with HLA-B alleles in renal-transplant candidates in southern Brazil.

    Science.gov (United States)

    Yamakawa, Roger Haruki; Saito, Patrícia Keiko; Gelmini, Geórgia Fernanda; da Silva, José Samuel; Bicalho, Maria da Graça; Borelli, Sueli Donizete

    2017-01-01

    The major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located centromerically to the human leukocyte antigen (HLA)-B. The short distance between these loci in the MHC indicates the presence of linkage disequilibrium (LD). Similarly to the HLA, the MICA is highly polymorphic, and this polymorphism has not been well documented in different populations. In this study, we estimated the allelic frequencies of MICA and the linkage disequilibrium with HLA-B alleles in 346 renal-transplant candidates in southern Brazil. MICA and HLA were typed using the polymerase chain reaction-sequence-specific primer method (PCR-SSO), combined with the Luminex technology. A total of 19 MICA allele groups were identified. The most frequent allele groups were MICA*008 (21.6%), MICA*002 (17.0%) and MICA*004 (14.8%). The most common haplotypes were MICA*009-B*51 (7.8%), MICA*004-B*44 (6.06%) and MICA*002-B*35 (5.63%). As expected from the proximity of the MICA and HLA-B loci, most haplotypes showed strong LD. Renal patients and healthy subjects in the same region of Brazil showed statistically significant differences in their MICA polymorphisms. The MICA*027 allele group was more frequent in renal patients (Pc = 0.018, OR: 3.421, 95% CI: 1.516-7.722), while the MICA*019 allele group was more frequent in healthy subjects (Pc = 0.001, OR: 0.027, 95% CI: 0.002-0.469). This study provided information on the distribution of MICA polymorphisms and linkage disequilibrium with HLA-B alleles in Brazilian renal-transplant candidates. This information should help to determine the mechanisms of susceptibility to different diseases in patients with chronic kidney disease, and to elucidate the mechanisms involved in allograft rejection associated with MICA polymorphisms in a Brazilian population.

  17. A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.

    Science.gov (United States)

    Kling, Daniel; Tillmar, Andreas; Egeland, Thore; Mostad, Petter

    2015-09-01

    Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se ). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

  18. Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

    Directory of Open Access Journals (Sweden)

    Mahmood Gholami

    Full Text Available An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red, genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10. We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.

  19. Evolution of zygotic linkage disequilibrium in a finite local population.

    Directory of Open Access Journals (Sweden)

    Xin-Sheng Hu

    Full Text Available One crucial feature of zygotic linkage disequilibrium (LD analysis is its direct use of diploid genotyping data, irrespective of the type of mating system. Previous theories from an evolutionary perspective mainly focus on gametic LD, but the equivalent development for zygotic LD is not available. Here I study the evolution of zygotic LD and the covariances between gametic and zygotic LDs or between distinct zygotic LDs in a finite local population under constant immigration from a continent population. I derive the analytical theory under genetic hitchhiking effects or in a neutral process. Results indicate that zygotic LDs (diploid level are more informative than gametic LD (haploid level in indicating the effects of different evolutionary forces. Zygotic LDs may be greater than or comparable to gametic LD under the epistatic selection process, but smaller than gametic LD under the non epistatic selection process. The covariances between gametic and zygotic LDs are strongly affected by the mating system, linkage distance, and genetic drift effects, but weakly affected by seed and pollen flow and natural selection. The covariances between different zygotic LDs are generally robust to the effects of gene flow, selection, and linkage distance, but sensitive to the effects of genetic drift and mating system. Consistent patterns exist for the covariances between the zygotic LDs for the two-locus genotypes with one common genotype at one locus or without any common genotype at each locus. The results highlight that zygotic LDs can be applied to detecting natural population history.

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

    Energy Technology Data Exchange (ETDEWEB)

    Grice, D.E.; Gelernter, J. [Veterans Administration Connecticut Healthcare System, West Haven, CT (United States); Leckman, J.F.; Pauls, D.L. [Yale Univ. School of Medicine, New Haven, CT (United States)] [and others

    1996-09-01

    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 compared with the other common alleles in this DRD4 polymorphic system. We studied 64 family trios (consisting of an affected person and two parents, at least one heterozygous for DRD4*7R), including 12 nuclear family trios and 52 trios from four large TS kindreds. The DRD4*7R allele was transmitted significantly more frequently than expected ({chi}{sup 2}{sub TDT} ranging from 8.47 [P < .004] to 10.80 [P = .001], depending on breadth of disease definition and inclusion or exclusion of inferred genotypes). Confirmation of this finding will depend on either replication in other samples or the identification of a transmitted functional mutation within this sample. 56 refs., 2 figs., 3 tabs.

  1. Linkage disequilibrium between human leukocyte antigen (HLA) class II and HLA-G--possible implications for human reproduction and autoimmune disease

    DEFF Research Database (Denmark)

    Hviid, Thomas Vauvert F; Christiansen, Ole B

    2005-01-01

    ). We found a significant linkage disequilibrium between HLA-DR3 and HLA-G*010102 in both the RSA and control populations. For all four studied HLA loci, the alleles in the haplotype HLA-DRB1*03.DQA1*05.DQB1*02.G*010102 was in clear linkage disequilibrium. This HLA haplotype has repeatedly been...... associated with different autoimmune diseases but also with RSA. The G*010102 allele includes a 14-bp sequence polymorphism in the 3' untranslated region of the gene, which has been associated with differences in HLA-G mRNA alternative splicing and stability. This 14-bp polymorphism has also been associated...... with RSA, pre-eclampsia, and outcome of in vitro fertilization. Implications of HLA polymorphism--and other polymorphic genes in the MHC for pregnancy outcome--and for autoimmune diseases during pregnancy are discussed....

  2. Linkage disequilibrium in wild mice.

    Directory of Open Access Journals (Sweden)

    Cathy C Laurie

    2007-08-01

    Full Text Available Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci for complex traits related to human disease. Hundreds of these loci have been detected, but only a small number of the underlying causative genes have been identified. The main difficulty is the extensive linkage disequilibrium (LD in intercross progeny and the slow process of fine-scale mapping by traditional methods. Recently, new approaches have been introduced, such as association studies with inbred lines and multigenerational crosses. These approaches are very useful for interval reduction, but generally do not provide single-gene resolution because of strong LD extending over one to several megabases. Here, we investigate the genetic structure of a natural population of mice in Arizona to determine its suitability for fine-scale LD mapping and association studies. There are three main findings: (1 Arizona mice have a high level of genetic variation, which includes a large fraction of the sequence variation present in classical strains of laboratory mice; (2 they show clear evidence of local inbreeding but appear to lack stable population structure across the study area; and (3 LD decays with distance at a rate similar to human populations, which is considerably more rapid than in laboratory populations of mice. Strong associations in Arizona mice are limited primarily to markers less than 100 kb apart, which provides the possibility of fine-scale association mapping at the level of one or a few genes. Although other considerations, such as sample size requirements and marker discovery, are serious issues in the implementation of association studies, the genetic variation and LD results indicate that wild mice could provide a useful tool for identifying genes that cause variation in complex traits.

  3. Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae).

    Science.gov (United States)

    Moraes, M A; Kubota, T Y K; Silva, E C B; Silva, A M; Cambuim, J; Moraes, M L T; Furlani Junior, E; Sebbenn, A M

    2016-07-29

    Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations.

  4. Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.

    Science.gov (United States)

    Wall, Jeffrey D; Stevison, Laurie S

    2016-08-09

    With recent advances in DNA sequencing technologies, it has become increasingly easy to use whole-genome sequencing of unrelated individuals to assay patterns of linkage disequilibrium (LD) across the genome. One type of analysis that is commonly performed is to estimate local recombination rates and identify recombination hotspots from patterns of LD. One method for detecting recombination hotspots, LDhot, has been used in a handful of species to further our understanding of the basic biology of recombination. For the most part, the effectiveness of this method (e.g., power and false positive rate) is unknown. In this study, we run extensive simulations to compare the effectiveness of three different implementations of LDhot. We find large differences in the power and false positive rates of these different approaches, as well as a strong sensitivity to the window size used (with smaller window sizes leading to more accurate estimation of hotspot locations). We also compared our LDhot simulation results with comparable simulation results obtained from a Bayesian maximum-likelihood approach for identifying hotspots. Surprisingly, we found that the latter computationally intensive approach had substantially lower power over the parameter values considered in our simulations. Copyright © 2016 Wall and Stevison.

  5. Linkage disequilibrium in HLA cannot be explained by selective recombination.

    Science.gov (United States)

    Termijtelen, A; D'Amaro, J; van Rood, J J; Schreuder, G M

    1995-11-01

    Some combinations of HLA-A, -B and -DR antigens occur more frequently than would be expected from their gene frequencies in the population. This phenomenon, referred to as Linkage Disequilibrium (LD) has been the origin of many speculations. One hypothesis to explain LD is that some haplotypes are protected from recombination. A second hypothesis is that these HLA antigens preferentially recombine after cross-over to create an LD haplotype. We tested these 2 hypotheses: from a pool of over 10,000 families typed in our department, we analyzed 126 families in which HLA-A:B or B:DR recombinant offspring was documented. To overcome a possible bias in our material, we used the non-recombined haplotypes from the same 126 families as a control group. Our results show that the number of cross-overs through LD haplotypes is not significantly lower then would be expected if recombination occurred randomly. Also the number of LD haplotypes created upon recombination was not significantly increased.

  6. Transmission/disequilibrium tests incorporating unaffected offspring.

    Directory of Open Access Journals (Sweden)

    Qinyu Wei

    Full Text Available We propose a new method for family-based tests of association and linkage called transmission/disequilibrium tests incorporating unaffected offspring (TDTU. This new approach, constructed based on transmission/disequilibrium tests for quantitative traits (QTDT, provides a natural extension of the transmission/disequilibrium test (TDT to utilize transmission information from heterozygous parents to their unaffected offspring as well as the affected offspring from ascertained nuclear families. TDTU can be used in various study designs and can accommodate all types of independent nuclear families with at least one affected offspring. When the study sample contains only case-parent trios, the TDTU is equivalent to TDT. Informative-transmission disequilibrium test (i-TDT and generalized disequilibrium test(GDT are another two methods that can use information of both unaffected offspring and affected offspring. In contract to i-TDT and GDT, the test statistic of TDTU is simpler and more explicit, and can be implemented more easily. Through computer simulations, we demonstrate that power of the TDTU is slightly higher compared to i-TDT and GDT. All the three methods are more powerful than method that uses affected offspring only, suggesting that unaffected siblings also provide information about linkage and association.

  7. Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

    Science.gov (United States)

    2014-01-01

    Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These

  8. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach.

    Science.gov (United States)

    Fariello, María Inés; Boitard, Simon; Mercier, Sabine; Robelin, David; Faraut, Thomas; Arnould, Cécile; Recoquillay, Julien; Bouchez, Olivier; Salin, Gérald; Dehais, Patrice; Gourichon, David; Leroux, Sophie; Pitel, Frédérique; Leterrier, Christine; SanCristobal, Magali

    2017-07-01

    Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium in genome scans for selection, cumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal. Using computer simulations, we demonstrate that this approach detects selection with higher power than several state-of-the-art single-marker, windowing or haplotype-based approaches. We illustrate this on two benchmark data sets including individual genotypes, for which we obtain similar results with the local score and one haplotype-based approach. Finally, we apply the local score approach to Pool-Seq data obtained from a divergent selection experiment on behaviour in quail and obtain precise and biologically coherent selection signals: while competing methods fail to highlight any clear selection signature, our method detects several regions involving genes known to act on social responsiveness or autistic traits. Although we focus here on the detection of positive selection from multiple population data, the local score approach is general and can be applied to other genome scans for selection or other genomewide analyses such as GWAS. © 2017 John Wiley & Sons Ltd.

  9. Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers.

    Science.gov (United States)

    Zhang, Yu; Yan, Haidong; Jiang, Xiaomei; Wang, Xiaoli; Huang, Linkai; Xu, Bin; Zhang, Xinquan; Zhang, Lexin

    2016-01-01

    To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass ( Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. In this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei's gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r 2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 ( P  < 0.01). The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.

  10. Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel.

    Science.gov (United States)

    Houle, David; Márquez, Eladio J

    2015-06-10

    We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r(2) ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses or discordance between genotype and karyotype. Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines. Copyright © 2015 Houle and Márquez.

  11. GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs

    Directory of Open Access Journals (Sweden)

    Broxholme John

    2009-10-01

    Full Text Available Abstract Background A number of tools for the examination of linkage disequilibrium (LD patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500 kb. We have developed a web-based query tool (GLIDERS: Genome-wide LInkage DisEquilibrium Repository and Search engine that enables the retrieval of pairwise associations with r2 ≥ 0.3 across the human genome for any SNP genotyped within HapMap phase 2 and 3, regardless of distance between the markers. Description GLIDERS is an easy to use web tool that only requires the user to enter rs numbers of SNPs they want to retrieve genome-wide LD for (both nearby and long-range. The intuitive web interface handles both manual entry of SNP IDs as well as allowing users to upload files of SNP IDs. The user can limit the resulting inter SNP associations with easy to use menu options. These include MAF limit (5-45%, distance limits between SNPs (minimum and maximum, r2 (0.3 to 1, HapMap population sample (CEU, YRI and JPT+CHB combined and HapMap build/release. All resulting genome-wide inter-SNP associations are displayed on a single output page, which has a link to a downloadable tab delimited text file. Conclusion GLIDERS is a quick and easy way to retrieve genome-wide inter-SNP associations and to explore LD patterns for any number of SNPs of interest. GLIDERS can be useful in identifying SNPs with long-range LD. This can highlight mis-mapping or other potential association signal localisation problems.

  12. Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.

    Science.gov (United States)

    Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R; Morton, Newton E

    2004-12-28

    Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.

  13. Linkage disequilibrium in the insulin gene region: Size variation at the 5{prime} flanking polymorphism and bimodality among {open_quotes}Class I{close_quotes} alleles

    Energy Technology Data Exchange (ETDEWEB)

    McGinnis, R.E.; Spielman, R.S. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States)

    1994-09-01

    The 5{prime} flanking polymorphism (5{prime}FP), a hypervariable region at the 5{prime} end of the insulin gene, has {open_quotes}class 1{close_quotes} alleles (650-900 bp long) that are in positive linkage disequilibrium with insulin-dependent diabetes mellitus (IDDM). The authors report that precise sizing of the 5{prime}FP yields a bimodal frequency distribution of class 1 allele lengths. Class 1 alleles belonging to the lower component (650-750 bp) of the bimodal distribution were somewhat more highly associated with IDDM than were alleles from the upper component (760-900 bp), but the difference was not statistically significant. They also examined 5{prime}FP length variation in relation to allelic variation at nearby polymorphisms. At biallelic RFLPs on both sides of the 5{prime}FP, they found that one allele exhibits near-total association with the upper component of the 5FP class 1 distribution. Such associations represent a little-known but potentially wide-spread form of linkage disequilibrium. In this type of disequilibrium, a flanking allele has near-complete association with a single mode of VNTR alleles whose lengths represent consecutive numbers of tandem repeats (CNTR). Such extreme disequilibrium between a CNTR mode and flanking alleles may originate and persist because length mutations at some VNTR loci usually add or delete only one or two repeat units. 22 refs., 5 figs., 6 tabs.

  14. Characterization of Linkage Disequilibrium and Population Structure in a Mungbean Diversity Panel

    Directory of Open Access Journals (Sweden)

    Thomas J. Noble

    2018-01-01

    Full Text Available Mungbean [Vigna radiata (L. R. Wilczek var. radiata] is an important grain legume globally, providing a high-quality plant protein source largely produced and consumed in South and East Asia. This study aimed to characterize a mungbean diversity panel consisting of 466 cultivated accessions and demonstrate its utility by conducting a pilot genome-wide association study of seed coat color. In addition 16 wild accessions were genotyped for comparison and in total over 22,000 polymorphic genome-wide SNPs were identified and used to analyze the genetic diversity, population structure, linkage disequilibrium (LD of mungbean. Polymorphism was lower in the cultivated accessions in comparison to the wild accessions, with average polymorphism information content values 0.174, versus 0.305 in wild mungbean. LD decayed in ∼100 kb in cultivated lines, a distance higher than the linkage decay of ∼60 kb estimated in wild mungbean. Four distinct subgroups were identified within the cultivated lines, which broadly corresponded to geographic origin and seed characteristics. In a pilot genome-wide association mapping study of seed coat color, five genomic regions associated were identified, two of which were close to seed coat color genes in other species. This mungbean diversity panel constitutes a valuable resource for genetic dissection of important agronomical traits to accelerate mungbean breeding.

  15. Linkage disequilibrium between STRPs and SNPs across the human genome.

    Science.gov (United States)

    Payseur, Bret A; Place, Michael; Weber, James L

    2008-05-01

    Patterns of linkage disequilibrium (LD) reveal the action of evolutionary processes and provide crucial information for association mapping of disease genes. Although recent studies have described the landscape of LD among single nucleotide polymorphisms (SNPs) from across the human genome, associations involving other classes of molecular variation remain poorly understood. In addition to recombination and population history, mutation rate and process are expected to shape LD. To test this idea, we measured associations between short-tandem-repeat polymorphisms (STRPs), which can mutate rapidly and recurrently, and SNPs in 721 regions across the human genome. We directly compared STRP-SNP LD with SNP-SNP LD from the same genomic regions in the human HapMap populations. The intensity of STRP-SNP LD, measured by the average of D', was reduced, consistent with the action of recurrent mutation. Nevertheless, a higher fraction of STRP-SNP pairs than SNP-SNP pairs showed significant LD, on both short (up to 50 kb) and long (cM) scales. These results reveal the substantial effects of mutational processes on LD at STRPs and provide important measures of the potential of STRPs for association mapping of disease genes.

  16. Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks

    OpenAIRE

    Zhao, Huiying; Nyholt, Dale R.; Yang, Yuanhao; Wang, Jihua; Yang, Yuedong

    2017-01-01

    Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous...

  17. A tetranucleotide repeat (D4S1652) is linked to facioscapulohumeral dystrophy and shows no linkage disequilibrium with the disease

    Energy Technology Data Exchange (ETDEWEB)

    Mathews, K.D.; Bailey, H.L.; Mills, K.A. [and others

    1994-09-01

    Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant dystrophy which is associated with a deletion in a subtelomeric repeat element on 4q35. The gene has not yet been identified. The probe detecting this deletion (D4F104S1) is not chromosome 4-specific, and at least one large family has been identified which is not linked to chromosome 4. Thus, persymptomatic/prenatal diagnosis can only be provided to families that are proven to be chromosome 4-linked or where a new mutation is demonstrated. The markers available to demonstrate linkage to chromosome 4, D4S139, D4S163, and D4F35S1, are VNTRs. We have used D4S1652, a tetranucleotide repeat recently identified by the Cooperative Human Linkage Center, in our FSHD families. We found it is completely linked to the 4q35 VNTRs and to the disease phenotype. Physical mapping, using radiation hybrids and somatic cell hybrids, places D4S1652 between D4S139, an interval of approximately 1 Mb. We have used D4S1652 to look for linkage disequilibrium in our FSHD patient population. This result is of interest because of our hypothesis that the deletion in the subtelomeric repeat element alters transcription of a more proximal gene through a position effect. Previously available markers have been unsatisfactory for this experiment because of difficulty comparing numerous VNTR alleles across families. We observed 4, easily distinguished, D4S1652 alleles in our families. We studied 14 chromosomes associated with disease phenotype and 55 chromosomes from nontransmitting parents. We found no evidence for linkage disequilibrium ({chi}{sup 2}=1.313, nonsignificant). This result will need confirmation with a larger patient population, but is consistent with the clinical observation that there is a high rate of a new mutation in this disorder.

  18. Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.

    Directory of Open Access Journals (Sweden)

    John A Sved

    Full Text Available There is a substantial literature on the use of linkage disequilibrium (LD to estimate effective population size using unlinked loci. The Ne estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite loci. The 'Burrows composite index' is introduced in a novel way with a 'composite haplotype table'. We show that in a sample of diploid size S, the mean value of x2 or r2 from the composite haplotype table is biased by a factor of 1-1/(2S-12, rather than the usual factor 1+1/(2S-1 for a conventional haplotype table. But analysis of population data using these formulae leads to Ne estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low Ne estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to r2, and find that this factor leads to a bias in the Ne estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered r2 with lower variance than the original r2, and one that is also insensitive to null alleles. The resulting formulae are used to provide Ne estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent Ne expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated Ne values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.

  19. Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.

    Science.gov (United States)

    Sved, John A; Cameron, Emilie C; Gilchrist, A Stuart

    2013-01-01

    There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The Ne estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The 'Burrows composite index' is introduced in a novel way with a 'composite haplotype table'. We show that in a sample of diploid size S, the mean value of x2 or r2 from the composite haplotype table is biased by a factor of 1-1/(2S-1)2, rather than the usual factor 1+1/(2S-1) for a conventional haplotype table. But analysis of population data using these formulae leads to Ne estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low Ne estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to r2, and find that this factor leads to a bias in the Ne estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered r2 with lower variance than the original r2, and one that is also insensitive to null alleles. The resulting formulae are used to provide Ne estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent Ne expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated Ne values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.

  20. Evidence, from family studies, for linkage disequilibrium between TGFA and a gene for nonsyndromic cleft lip with or without cleft palate

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Hongshu; Lee, A.; Gasser, D.L. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States); Sassani, R.; Bartlett, S.P. [Children`s Hospital of Philadelphia, PA (United States); Buetow, K.H. [Fox Chase Cancer Center, Philadelphia, PA (United States); Hecht, J.T. [Univ. of Texas Medical School, Houston, TX (United States); Malcolm, S.; Winter, R.M.; Vintiner, G.M. [Univ. of London (United Kingdom)

    1994-11-01

    The inheritance of alleles of the transforming growth factor alpha (TGFA) locus has been studied in families affected with cleft lip with or without cleft palate (CL/P), by using the transmission/disequilibrium test described by Spielman and colleagues. Only heterozygous parents with an affected child can be included in this test, but within such families a significantly greater frequency of C2 alleles were transmitted to affected children than would be expected by chance. There was no evidence that the total number of C2 alleles transmitted to affected and unaffected children differed significantly from random segregation. These data provide evidence from within families that a gene for susceptibility to CL/P is in significant linkage disequilibrium with the C2 allele of the TGFA locus. 30 refs., 1 fig., 2 tabs.

  1. Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass

    DEFF Research Database (Denmark)

    Brazauskas, Gintaras; Lenk, Ingo; Pedersen, Morten Greve

    2011-01-01

    Perennial ryegrass (Lolium perenne L.) is a highly valued temperate climate grass species grown as forage crop and for amenity uses. Due to its outbreeding nature and recent domestication, a high degree of genetic diversity is expected among cultivars. The aim of this study was to assess the extent...... of linkage disequilibrium (LD) within European elite germplasm and to evaluate the appropriate methodology for genetic association mapping in perennial ryegrass. A high level of genetic diversity was observed in a set of 380 perennial ryegrass elite genotypes when genotyped with 40 SSRs and 2 STS markers...... and occurred within 0.4 cM across European varieties, when population structure was taken into consideration. However, an extended LD of up to 6.6 cM was detected within the variety Aberdart. High genetic diversity and rapid LD decay provide means for high resolution association mapping in elite materials...

  2. Construction of the model for the Genetic Analysis Workshop 14 simulated data: genotype-phenotype relationships, gene interaction, linkage, association, disequilibrium, and ascertainment effects for a complex phenotype.

    Science.gov (United States)

    Greenberg, David A; Zhang, Junying; Shmulewitz, Dvora; Strug, Lisa J; Zimmerman, Regina; Singh, Veena; Marathe, Sudhir

    2005-12-30

    The Genetic Analysis Workshop 14 simulated dataset was designed 1) To test the ability to find genes related to a complex disease (such as alcoholism). Such a disease may be given a variety of definitions by different investigators, have associated endophenotypes that are common in the general population, and is likely to be not one disease but a heterogeneous collection of clinically similar, but genetically distinct, entities. 2) To observe the effect on genetic analysis and gene discovery of a complex set of gene x gene interactions. 3) To allow comparison of microsatellite vs. large-scale single-nucleotide polymorphism (SNP) data. 4) To allow testing of association to identify the disease gene and the effect of moderate marker x marker linkage disequilibrium. 5) To observe the effect of different ascertainment/disease definition schemes on the analysis. Data was distributed in two forms. Data distributed to participants contained about 1,000 SNPs and 400 microsatellite markers. Internet-obtainable data consisted of a finer 10,000 SNP map, which also contained data on controls. While disease characteristics and parameters were constant, four "studies" used varying ascertainment schemes based on differing beliefs about disease characteristics. One of the studies contained multiplex two- and three-generation pedigrees with at least four affected members. The simulated disease was a psychiatric condition with many associated behaviors (endophenotypes), almost all of which were genetic in origin. The underlying disease model contained four major genes and two modifier genes. The four major genes interacted with each other to produce three different phenotypes, which were themselves heterogeneous. The population parameters were calibrated so that the major genes could be discovered by linkage analysis in most datasets. The association evidence was more difficult to calibrate but was designed to find statistically significant association in 50% of datasets. We also

  3. The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits

    Directory of Open Access Journals (Sweden)

    Uleberg Eivind

    2011-05-01

    Full Text Available Abstract Background Genetically, SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium (CLD test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets. Methods The CLD test consists of two steps i.e. analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution, the best SNP is in greater LD with the QTL than the second best, while under the alternative-CLD-hypothesis, the best SNP is alike-in-state with the QTL. To find a significance threshold, the test was also performed on data excluding the causative SNP. The 5th, 10th and 50th highest TCLD value from 1000 replicated analyses were used to control the type-I-error rate of the test at p = 0.005, p = 0.01 and p = 0.05, respectively. Results In a situation where the QTL explained 48% of the phenotypic variance analysis I detected a QTL in 994 replicates (p = 0.001, where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis, 714 replicates detected evidence of a QTL (p = 0.001. In analysis II, the CLD test confirmed 280 causative SNP from 1000 simulations (p = 0.05, i.e. power was 28%. When the effect of the QTL was reduced by doubling the error variance, the power of the test reduced relatively little to 23%. When sequence data were used, the power of the test reduced to 16%. All SNP that were confirmed by the CLD test were positioned in the correct QTL position. Conclusions The CLD test can provide evidence for a causative SNP, but its power may be low in situations

  4. Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica.

    Directory of Open Access Journals (Sweden)

    Shui-Lian He

    Full Text Available Foxtail millet (Setaria italica (L. Beauv is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1 in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

  5. Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).

    Science.gov (United States)

    He, Shui-Lian; Yang, Yang; Morrell, Peter L; Yi, Ting-Shuang

    2015-01-01

    Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

  6. Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

    Directory of Open Access Journals (Sweden)

    Meuwissen Theo HE

    2007-04-01

    Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

  7. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes.

    Science.gov (United States)

    Long, Ji-Rong; Zhao, Lan-Juan; Liu, Peng-Yuan; Lu, Yan; Dvornyk, Volodymyr; Shen, Hui; Liu, Yong-Jun; Zhang, Yuan-Yuan; Xiong, Dong-Hai; Xiao, Peng; Deng, Hong-Wen

    2004-05-24

    The adequacy of association studies for complex diseases depends critically on the existence of linkage disequilibrium (LD) between functional alleles and surrounding SNP markers. We examined the patterns of LD and haplotype distribution in eight candidate genes for osteoporosis and/or obesity using 31 SNPs in 1,873 subjects. These eight genes are apolipoprotein E (APOE), type I collagen alpha1 (COL1A1), estrogen receptor-alpha (ER-alpha), leptin receptor (LEPR), parathyroid hormone (PTH)/PTH-related peptide receptor type 1 (PTHR1), transforming growth factor-beta1 (TGF-beta1), uncoupling protein 3 (UCP3), and vitamin D (1,25-dihydroxyvitamin D3) receptor (VDR). Yin yang haplotypes, two high-frequency haplotypes composed of completely mismatching SNP alleles, were examined. To quantify LD patterns, two common measures of LD, D' and r2, were calculated for the SNPs within the genes. The haplotype distribution varied in the different genes. Yin yang haplotypes were observed only in PTHR1 and UCP3. D' ranged from 0.020 to 1.000 with the average of 0.475, whereas the average r2 was 0.158 (ranging from 0.000 to 0.883). A decay of LD was observed as the intermarker distance increased, however, there was a great difference in LD characteristics of different genes or even in different regions within gene. The differences in haplotype distributions and LD patterns among the genes underscore the importance of characterizing genomic regions of interest prior to association studies.

  8. Genetic admixture and population substructure in Guanacaste Costa Rica.

    Directory of Open Access Journals (Sweden)

    Zhaoming Wang

    2010-10-01

    Full Text Available The population of Costa Rica (CR represents an admixture of major continental populations. An investigation of the CR population structure would provide an important foundation for mapping genetic variants underlying common diseases and traits. We conducted an analysis of 1,301 women from the Guanacaste region of CR using 27,904 single nucleotide polymorphisms (SNPs genotyped on a custom Illumina InfiniumII iSelect chip. The program STRUCTURE was used to compare the CR Guanacaste sample with four continental reference samples, including HapMap Europeans (CEU, East Asians (JPT+CHB, West African Yoruba (YRI, as well as Native Americans (NA from the Illumina iControl database. Our results show that the CR Guanacaste sample comprises a three-way admixture estimated to be 43% European, 38% Native American and 15% West African. An estimated 4% residual Asian ancestry may be within the error range. Results from principal components analysis reveal a correlation between genetic and geographic distance. The magnitude of linkage disequilibrium (LD measured by the number of tagging SNPs required to cover the same region in the genome in the CR Guanacaste sample appeared to be weaker than that observed in CEU, JPT+CHB and NA reference samples but stronger than that of the HapMap YRI sample. Based on the clustering pattern observed in both STRUCTURE and principal components analysis, two subpopulations were identified that differ by approximately 20% in LD block size averaged over all LD blocks identified by Haploview. We also show in a simulated association study conducted within the two subpopulations, that the failure to account for population stratification (PS could lead to a noticeable inflation in the false positive rate. However, we further demonstrate that existing PS adjustment approaches can reduce the inflation to an acceptable level for gene discovery.

  9. Linkage disequilibrium of evolutionarily conserved regions in the human genome

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    Johnson Todd A

    2006-12-01

    Full Text Available Abstract Background The strong linkage disequilibrium (LD recently found in genic or exonic regions of the human genome demonstrated that LD can be increased by evolutionary mechanisms that select for functionally important loci. This suggests that LD might be stronger in regions conserved among species than in non-conserved regions, since regions exposed to natural selection tend to be conserved. To assess this hypothesis, we used genome-wide polymorphism data from the HapMap project and investigated LD within DNA sequences conserved between the human and mouse genomes. Results Unexpectedly, we observed that LD was significantly weaker in conserved regions than in non-conserved regions. To investigate why, we examined sequence features that may distort the relationship between LD and conserved regions. We found that interspersed repeats, and not other sequence features, were associated with the weak LD tendency in conserved regions. To appropriately understand the relationship between LD and conserved regions, we removed the effect of repetitive elements and found that the high degree of sequence conservation was strongly associated with strong LD in coding regions but not with that in non-coding regions. Conclusion Our work demonstrates that the degree of sequence conservation does not simply increase LD as predicted by the hypothesis. Rather, it implies that purifying selection changes the polymorphic patterns of coding sequences but has little influence on the patterns of functional units such as regulatory elements present in non-coding regions, since the former are generally restricted by the constraint of maintaining a functional protein product across multiple exons while the latter may exist more as individually isolated units.

  10. Lack of concordance and linkage disequilibrium among brothers for androgenetic alopecia and CAG/GGC haplotypes of the androgen receptor gene in Mexican families.

    Science.gov (United States)

    Arteaga-Vázquez, Jazmín; López-Hernández, María A; Svyryd, Yevgeniya; Mutchinick, Osvaldo M

    2015-12-01

    Androgenetic alopecia (AGA) or common baldness is the most prevalent form of hair loss in males. Familial predisposition has been recognized, and heritability estimated in monozygotic twins suggests an important genetic predisposition. Several studies indicate that the numbers of CAG/GGC repeats in exon 1 of the androgen receptor gene (AR) maybe associated with AGA susceptibility. To investigate a possible correlation between AR CAG/GGC haplotypes and the presence or not of alopecia in sibships with two or more brothers among them at least one of them has AGA. Thirty-two trios including an alopecic man, one brother alopecic or not, and their mother were enrolled. Sanger sequencing of the exon 1 of the AR gene was conducted to ascertain the number of CAG/GGC repeats in each individual. Heterozygous mother for the CAG/GGC haplotypes was an inclusion criterion to analyze the segregation haplotype patterns in the family. Concordance for the number of repeats and AGA among brothers was evaluated using kappa coefficient and the probability of association in the presence of genetic linkage between CAG and GGC repeats and AGA estimated by means of the family-based association test (FBAT). The median for the CAG and GGC repeats in the AR is similar to that reported in other populations. The CAG/GGC haplotypes were less polymorphic than that reported in other studies, especially due to the GGC number of repeats found. Kappa coefficient resulted in a concordance of 37.3% (IC 95%, 5.0-69.0%) for the AGA phenotype and identical CAG/GGC haplotypes. There was no evidence of linkage disequilibrium. Our results do not confirm a possible correlation or linkage disequilibrium between the CAG/GGC haplotypes of the AR gene and androgenetic alopecia in Mexican brothers. © 2015 Wiley Periodicals, Inc.

  11. Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers

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    Geiger Dan

    2010-10-01

    Full Text Available Abstract Background The question of a genetic contribution to the higher prevalence and incidence of end stage kidney disease (ESKD among African Americans (AA remained unresolved, until recent findings using admixture mapping pointed to the association of a genomic locus on chromosome 22 with this disease phenotype. In the current study we utilize this example to demonstrate the utility of applying a multi-step admixture mapping approach. Methods A multi-step case only admixture mapping study, consisted of the following steps was designed: 1 Assembly of the sample dataset (ESKD AA; 2 Design of the estimated mutual information ancestry informative markers (n = 2016 screening panel 3; Genotyping the sample set whose size was determined by a power analysis (n = 576 appropriate for the initial screening panel; 4 Inference of local ancestry for each individual and identification of regions with increased AA ancestry using two different ancestry inference statistical approaches; 5 Enrichment of the initial screening panel; 6 Power analysis of the enriched panel 7 Genotyping of additional samples. 8 Re-analysis of the genotyping results to identify a genetic risk locus. Results The initial screening phase yielded a significant peak using the ADMIXMAP ancestry inference program applying case only statistics. Subgroup analysis of 299 ESKD patients with no history of diabetes yielded peaks using both the ANCESTRYMAP and ADMIXMAP ancestry inference programs. The significant peak was found on chromosome 22. Genotyping of additional ancestry informative markers on chromosome 22 that took into account linkage disequilibrium in the ancestral populations, and the addition of samples increased the statistical significance of the finding. Conclusions A multi-step admixture mapping analysis of AA ESKD patients replicated the finding of a candidate risk locus on chromosome 22, contributing to the heightened susceptibility of African Americans to develop non

  12. Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method.

    Directory of Open Access Journals (Sweden)

    Emile R Chimusa

    Full Text Available Admixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes. We applied this approach to a complex, uniquely admixed South African population. Using genome-wide SNP data from over 764 individuals, we accurately estimate the genetic contributions from the best ancestral populations: isiXhosa [Formula: see text], ‡Khomani SAN [Formula: see text], European [Formula: see text], Indian [Formula: see text], and Chinese [Formula: see text]. We also demonstrate that the ancestral allele frequency differences correlate with increased linkage disequilibrium in the South African population, which originates from admixture events rather than population bottlenecks.The collective term for people of mixed ancestry in southern Africa is "Coloured," and this is officially recognized in South

  13. Extent and distribution of linkage disequilibrium in the Old Order Amish.

    Science.gov (United States)

    Van Hout, Cristopher V; Levin, Albert M; Rampersaud, Evadnie; Shen, Haiqing; O'Connell, Jeffrey R; Mitchell, Braxton D; Shuldiner, Alan R; Douglas, Julie A

    2010-02-01

    Knowledge of the extent and distribution of linkage disequilibrium (LD) is critical to the design and interpretation of gene mapping studies. Because the demographic history of each population varies and is often not accurately known, it is necessary to empirically evaluate LD on a population-specific basis. Here we present the first genome-wide survey of LD in the Old Order Amish (OOA) of Lancaster County Pennsylvania, a closed population derived from a modest number of founders. Specifically, we present a comparison of LD between OOA individuals and US Utah participants in the International HapMap project (abbreviated CEU) using a high-density single nucleotide polymorphism (SNP) map. Overall, the allele (and haplotype) frequency distributions and LD profiles were remarkably similar between these two populations. For example, the median absolute allele frequency difference for autosomal SNPs was 0.05, with an inter-quartile range of 0.02-0.09, and for autosomal SNPs 10-20 kb apart with common alleles (minor allele frequency > or =0.05), the LD measure r(2) was at least 0.8 for 15 and 14% of SNP pairs in the OOA and CEU, respectively. Moreover, tag SNPs selected from the HapMap CEU sample captured a substantial portion of the common variation in the OOA ( approximately 88%) at r(2) > or =0.8. These results suggest that the OOA and CEU may share similar LD profiles for other common but untyped SNPs. Thus, in the context of the common variant-common disease hypothesis, genetic variants discovered in gene mapping studies in the OOA may generalize to other populations. 2009 Wiley-Liss, Inc.

  14. LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs

    Directory of Open Access Journals (Sweden)

    Cheng Yu-Huei

    2009-06-01

    Full Text Available Abstract Background Linkage disequilibrium (LD mapping is commonly used to evaluate markers for genome-wide association studies. Most types of LD software focus strictly on LD analysis and visualization, but lack supporting services for genotyping. Results We developed a freeware called LD2SNPing, which provides a complete package of mining tools for genotyping and LD analysis environments. The software provides SNP ID- and gene-centric online retrievals for SNP information and tag SNP selection from dbSNP/NCBI and HapMap, respectively. Restriction fragment length polymorphism (RFLP enzyme information for SNP genotype is available to all SNP IDs and tag SNPs. Single and multiple SNP inputs are possible in order to perform LD analysis by online retrieval from HapMap and NCBI. An LD statistics section provides D, D', r2, δQ, ρ, and the P values of the Hardy-Weinberg Equilibrium for each SNP marker, and Chi-square and likelihood-ratio tests for the pair-wise association of two SNPs in LD calculation. Finally, 2D and 3D plots, as well as plain-text output of the results, can be selected. Conclusion LD2SNPing thus provides a novel visualization environment for multiple SNP input, which facilitates SNP association studies. The software, user manual, and tutorial are freely available at http://bio.kuas.edu.tw/LD2NPing.

  15. HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703

    DEFF Research Database (Denmark)

    Matthews, Philippa C; Adland, Emily; Listgarten, Jennifer

    2011-01-01

    -clade-infected subjects. We present evidence that HLA-A*7401 operates an effect that is independent of HLA-B*5703, with which it is in linkage disequilibrium in some populations, to mediate lowered viremia. We describe a novel statistical approach to detecting additive effects between class I alleles in control of HIV-1...... epitopes appear immunodominant. We identify eight novel putative HLA-A*7401-restricted epitopes, of which three have been defined to the optimal epitope. In common with HLA-B alleles linked with slow progression, viremic control through an HLA-A*7401-restricted response appears to be associated...... with the selection of escape mutants within Gag epitopes that reduce viral replicative capacity. These studies highlight the potentially important contribution of an HLA-A allele to immune control of HIV infection, which may have been concealed by a stronger effect mediated by an HLA-B allele with which...

  16. [The genotype-based haplotype relative risk and transmission disequilibrium test analyses of familial febrile convulsions].

    Science.gov (United States)

    Qi, Y; Wu, X; Guo, Z; Zhang, J; Pan, H; Li, M; Bao, X; Peng, J; Zou, L; Lin, Q

    1999-10-01

    To confirm the linkage of familial febrile convulsions to the short arm of chromosome 6(6p) or the long arm of chromosome 8(8q). The authors finished genotyping of Pst I locus on the coding region of heat shock protein (HSP) 70, 5'untranslated region of HSP70-1, 3' untranslated region of HSP70-2, D8S84 and D8S85. The data were processed by the genotype-based haplotype relative risk(GHRR) and transmission disequilibrium test(TDT) methods in PPAP. Some signs of association and disequilibrium between D8S85 and FC were shown by GHRR and TDT. A suspect linkage of familial febrile convulsions to the long arm of chromosome 8 has been proposed.

  17. Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Ganal Martin W

    2006-01-01

    Full Text Available Abstract Background The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles, Principal Coordinate Analysis (PCoA, and analysis of genome-wide linkage disequilibrium. Results A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i geographical regions and (ii agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD was estimated as squared correlation of allele frequencies (r2. The values of LD for barley were comparable to other plant species (conifers, poplar, maize. The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P 0.80 provided higher LD values as compared to 19 low polymorphic loci (PIC Conclusion A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing

  18. A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents.

    Science.gov (United States)

    Wei, Yi-Liang; Wei, Li; Zhao, Lei; Sun, Qi-Fan; Jiang, Li; Zhang, Tao; Liu, Hai-Bo; Chen, Jian-Gang; Ye, Jian; Hu, Lan; Li, Cai-Xia

    2016-01-01

    A single-tube multiplex assay of a small set of ancestry-informative markers (AIMs) for effectively estimating individual ancestry and admixture is an ideal forensic tool to trace the population origin of an unknown DNA sample. We present a newly developed 27-plex single nucleotide polymorphism (SNP) panel with highly robust and balanced differential power to perfectly assign individuals to African, European, and East Asian ancestries. Evaluating 968 previously described intercontinental AIMs from three HapMap population genotyping datasets (Yoruban in Ibadan, Nigeria (YRI); Utah residents with Northern and Western European ancestry from the Centre de'Etude du Polymorphism Humain (CEPH) collection (CEU); and Han Chinese in Beijing, China (CHB)), the best set of markers was selected on the basis of Hardy-Weinberg equilibrium (p > 0.00001), population-specific allele frequency (two of three δ values >0.5), according to linkage disequilibrium (r (2) ancestry of the 11 populations in the HapMap project. Then, we tested the 27-plex SNP assay with 1164 individuals from 17 additional populations. The results demonstrated that the SNP panel was successful for ancestry inference of individuals with African, European, and East Asian ancestry. Furthermore, the system performed well when inferring the admixture of Eurasians (EUR/EAS) after analyzing admixed populations from Xinjiang (Central Asian) as follows: Tajik (68:27), Uyghur (49:46), Kirgiz (40:57), and Kazak (36:60). For individual analyses, we interpreted each sample with a three-ancestry component percentage and a population match probability sequence. This multiplex assay is a convenient and cost-effective tool to assist in criminal investigations, as well as to correct for the effects of population stratification for case-control studies.

  19. Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers.

    Science.gov (United States)

    Hao, Chenyang; Wang, Lanfen; Ge, Hongmei; Dong, Yuchen; Zhang, Xueyong

    2011-02-18

    Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of varieties displayed a wider average LD decay across the whole genome for locus pairs with r(2)>0.05 (Pvarieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5 ∼ 25 cM) compared to landraces (<5 ∼ 15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources.

  20. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

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    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  1. Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L. germplasm

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    Fricano Agostino

    2012-03-01

    Full Text Available Abstract Background The goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD in seven genomic regions using simple sequence repeat (SSR markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome. Results A genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2. The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure. Conclusions A global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.

  2. Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design.

    Science.gov (United States)

    Vitart, Veronique; Carothers, Andrew D; Hayward, Caroline; Teague, Peter; Hastie, Nicholas D; Campbell, Harry; Wright, Alan F

    2005-05-01

    Few studies have investigated genetic differentiation within nonisolate European populations, despite the initiation of large national sample collections such as U.K. Biobank. Here, we used short tandem repeat markers to explore fine-scale genetic structure and to examine the extent of linkage disequilibrium (LD) within national subpopulations. We studied 955 unrelated individuals of local ancestry from nine Scottish rural regions and the urban center of Edinburgh, as well as 96 unrelated individuals from the general U.K. population. Despite little overall differentiation on the basis of allele frequencies, there were clear differences among subpopulations in the extent of pairwise LD, measured between a subset of X-linked markers, that reflected presumed differences in the depths of the underlying genealogies within these subpopulations. Therefore, there are strategic advantages in studying rural subpopulations, in terms of increased power and reduced cost, that are lost by sampling across regions or within urban populations. Similar rural-urban contrasts are likely to exist in many other populations with stable rural subpopulations, which could influence the design of genetic association studies and national biobank data collections.

  3. Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L. Improved by Accounting for Linkage Disequilibrium

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    Guillaume P. Ramstein

    2016-04-01

    Full Text Available Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.

  4. Species discrimination, population structure and linkage disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis using SSR markers.

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    Shanmugapriya Arumugasundaram

    Full Text Available Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r(2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r(2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims.

  5. Linear models for joint association and linkage QTL mapping

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    Fernando Rohan L

    2009-09-01

    Full Text Available Abstract Background Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure. Results We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided. Conclusion The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward.

  6. Linkage disequilibrium with HLA-DRB1-DQB1 haplotypes explains the association of TNF-308G>A variant with type 1 diabetes in a Brazilian cohort.

    Science.gov (United States)

    Patente, Thiago A; Monteiro, Maria B; Vieira, Suzana M; Rossi da Silva, Maria E; Nery, Márcia; Queiroz, Márcia; Azevedo, Mirela J; Canani, Luis H; Parisi, Maria C; Pavin, Elizabeth J; Mainardi, Débora; Javor, Juraj; Velho, Gilberto; Coimbra, Cássio N; Corrêa-Giannella, Maria Lúcia

    2015-08-15

    A functional variant in the promoter region of the gene encoding tumor necrosis factor (TNF; rs1800629, -308G>A) showed to confer susceptibility to T1D. However, TNF rs1800629 was found, in several populations, to be in linkage disequilibrium with HLA susceptibility haplotypes to T1D. We evaluated the association of TNF rs1800629 with T1D in a cohort of Brazilian subjects, and assessed the impact of HLA susceptibility haplotypes in this association. 659 subjects with T1D and 539 control subjects were genotyped for TNF-308G>A variant. HLA-DRB1 and HLA-DQB1 genes were genotyped in a subset of 313 subjects with T1D and 139 control subjects. Associations with T1D were observed for the A-allele of rs1800629 (OR 1.69, 95% CI 1.33-2.15, p<0.0001, in a codominant model) and for 3 HLA haplotypes: DRB1*03:01-DQB1*02:01 (OR 5.37, 95% CI 3.23-8.59, p<0.0001), DRB1*04:01-DQB1*03:02 (OR 2.95, 95% CI 1.21-7.21, p=0.01) and DRB1*04:02-DQB1*03:02 (OR 2.14, 95% CI 1.02-4.50, p=0.04). Linkage disequilibrium was observed between TNF rs1800629 and HLA-DRB1 and HLA-DQB1 alleles. In a stepwise regression analysis HLA haplotypes, but not TNF rs1800629, remained independently associated with T1D. Our results do not support an independent effect of allelic variations of TNF in the genetic susceptibility to T1D. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Linkage disequilibrium at the APA insecticidal seed protein locus of common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Blair, Matthew W; Prieto, Sergio; Díaz, Lucy M; Buendía, Héctor F; Cardona, César

    2010-04-29

    An interesting seed protein family with a role in preventing insect herbivory is the multi-gene, APA family encoding the alpha-amylase inhibitor, phytohemagglutinin and arcelin proteins of common bean (Phaseolus vulgaris). Variability for this gene family exists and has been exploited to breed for insect resistance. For example, the arcelin locus has been successfully transferred from wild to cultivated common bean genotypes to provide resistance against the bruchid species Zabrotes subfasciatus although the process has been hampered by a lack of genetic tools for and understanding about the locus. In this study, we analyzed linkage disequilibrium (LD) between microsatellite markers at the APA locus and bruchid resistance in a germplasm survey of 105 resistant and susceptible genotypes and compared this with LD in other parts of the genome. Microsatellite allele diversity was found to vary with each of the eight APA-linked markers analyzed, and two markers within the APA locus were found to be diagnostic for bruchid resistance or susceptibility and for the different arcelin alleles inherited from the wild accessions. Arc1 was found to provide higher levels of resistance than Arc5 and the markers in the APA locus were highly associated with resistance showing that introgression of this gene-family from wild beans provides resistance in cultivated beans. LD around the APA locus was found to be intermediate compared to other regions of the genome and the highest LD was found within the APA locus itself for example between the markers PV-atct001 and PV-ag004. We found the APA locus to be an important genetic determinant of bruchid resistance and also found that LD existed mostly within the APA locus but not beyond it. Moderate LD was also found for some other regions of the genome perhaps related to domestication genes. The LD pattern may reflect the introgression of arcelin from the wild into the cultivated background through breeding. LD and association studies for

  8. Multiple linear combination (MLC) regression tests for common variants adapted to linkage disequilibrium structure.

    Science.gov (United States)

    Yoo, Yun Joo; Sun, Lei; Poirier, Julia G; Paterson, Andrew D; Bull, Shelley B

    2017-02-01

    By jointly analyzing multiple variants within a gene, instead of one at a time, gene-based multiple regression can improve power, robustness, and interpretation in genetic association analysis. We investigate multiple linear combination (MLC) test statistics for analysis of common variants under realistic trait models with linkage disequilibrium (LD) based on HapMap Asian haplotypes. MLC is a directional test that exploits LD structure in a gene to construct clusters of closely correlated variants recoded such that the majority of pairwise correlations are positive. It combines variant effects within the same cluster linearly, and aggregates cluster-specific effects in a quadratic sum of squares and cross-products, producing a test statistic with reduced degrees of freedom (df) equal to the number of clusters. By simulation studies of 1000 genes from across the genome, we demonstrate that MLC is a well-powered and robust choice among existing methods across a broad range of gene structures. Compared to minimum P-value, variance-component, and principal-component methods, the mean power of MLC is never much lower than that of other methods, and can be higher, particularly with multiple causal variants. Moreover, the variation in gene-specific MLC test size and power across 1000 genes is less than that of other methods, suggesting it is a complementary approach for discovery in genome-wide analysis. The cluster construction of the MLC test statistics helps reveal within-gene LD structure, allowing interpretation of clustered variants as haplotypic effects, while multiple regression helps to distinguish direct and indirect associations. © 2016 The Authors Genetic Epidemiology Published by Wiley Periodicals, Inc.

  9. CYP21A2 polymorphisms in patients with autoimmune Addison's disease, and linkage disequilibrium to HLA risk alleles.

    Science.gov (United States)

    Brønstad, Ingeborg; Skinningsrud, Beate; Bratland, Eirik; Løvås, Kristian; Undlien, Dag; Sverre Husebye, Eystein; Wolff, Anette Susanne Bøe

    2014-12-01

    Steroid 21-hydroxylase, encoded by CYP21A2, is the major autoantigen in autoimmune Addison's disease (AAD). CYP21A2 is located in the region of the HLA complex on chromosome 6p21.3, which harbours several risk alleles for AAD. The objective was to investigate whether CYP21A2 gene variants confer risk of AAD independently of other risk alleles in the HLA loci. DNA samples from 381 Norwegian patients with AAD and 340 healthy controls (HC) previously genotyped for the HLA-A, -B, -DRB1, and -DQB1 and MICA loci were used for genotyping of CYP21A2. Genotyping of CYP21A2 was carried out by direct sequencing. Linkage of CYP21A2 to the HLA loci was assessed using UNPHASED version 3.0.10 and PHASE version 2.1. Heterozygotes of the single-nucleotide polymorphisms (SNPs) rs397515394, rs6467, rs6474, rs76565726 and rs6473 were detected significantly more frequently in AAD patients compared with HC (P<0.005), but all SNPs were in a linkage disequilibrium (LD) with high-risk HLA-DRB1 haplotypes. rs6472C protected against AAD (odds ratio=0.15, 95% CI (0.08-0.30), P=3.8×10(-10)). This SNP was not in an LD with HLA loci (P=0.02), but did not increase protection when considering the effect of HLA-DRB1 alleles. Mutations causing congenital adrenal hyperplasia were found in heterozygosity in <1.5% of the cases in both groups. Genetic variants of CYP21A2 associated to AAD are in LD with the main AAD risk locus HLA-DRB1, and CYP21A2 does not constitute an independent susceptibility locus. © 2014 European Society of Endocrinology.

  10. The Transmission Disequilibrium/Heterogeneity Test with Parental-Genotype Reconstruction for Refined Genetic Mapping of Complex Diseases

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    Jing Han

    2012-01-01

    Full Text Available In linkage analysis for mapping genetic diseases, the transmission/disequilibrium test (TDT uses the linkage disequilibrium (LD between some marker and trait loci for precise genetic mapping while avoiding confounding due to population stratification. The sib-TDT (S-TDT and combined-TDT (C-TDT proposed by Spielman and Ewens can combine data from families with and without parental marker genotypes (PMGs. For some families with missing PMG, the reconstruction-combined TDT (RC-TDT proposed by Knapp may be used to reconstruct missing parental genotypes from the genotypes of their offspring to increase power and to correct for potential bias. In this paper, we propose a further extension of the RC-TDT, called the reconstruction-combined transmission disequilibrium/heterogeneity (RC-TDH test, to take into account the identical-by-descent (IBD sharing information in addition to the LD information. It can effectively utilize families with missing or incomplete parental genetic marker information. An application of this proposed method to Genetic Analysis Workshop 14 (GAW14 data sets and extensive simulation studies suggest that this approach may further increase statistical power which is particularly valuable when LD is unknown and/or when some or all PMGs are not available.

  11. Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis

    Science.gov (United States)

    Song, Bao-Hua; Windsor, Aaron J.; Schmid, Karl J.; Ramos-Onsins, Sebastian; Schranz, M. Eric; Heidel, Andrew J.; Mitchell-Olds, Thomas

    2009-01-01

    Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in ∼10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have ∼45% higher recombination per kilobase than outcrossing A. lyrata. PMID:19104077

  12. Linkage disequilibrium analysis in young populations: Pseudo-vitamin D-deficiency rickets and the founder effect in French Canadians

    Energy Technology Data Exchange (ETDEWEB)

    Labuda, M.; Glorieux, F.H. [McGill Univ., Montreal (Canada); Labuda, D.; Korab-Laskowska, M. [Universite de Montreal (Canada)] [and others

    1996-09-01

    Pseudo-vitamin D-deficiency rickets (PDDR) was mapped close to D12S90 and between proximal D12S312 and distal (D12S305, D12S104) microsatellites that were subsequently found on a single YAC clone. Analysis of a complex haplotype in linkage disequilibrium (LD) with the disease discriminated among distinct founder effects in French Canadian populations in Acadia and in Charlevoix-Saguenay-Lac-Saint-Jean (Ch-SLSJ), as well as an earlier one in precolonial Europe. A simple demographic model suggested the historical age of the founder effect in Ch-SLSJ to be {approximately}12 generations. The corresponding LD data are consistent with this figure when they are analyzed within the framework of Luria-Delbruck model, which takes into account the population growth. Population sampling due to a limited number of first settlers and the rapid demographic expansion appear to have played a major role in the founding of PDDR in Ch-SLSJ and, presumably, other genetic disorders endemic to French Canada. Similarly, the founder effect in Ashkenazim, coinciding with their early settlement in medieval Poland and subsequent expansion eastward, could explain the origin of frequent genetic diseases in this population. 48 refs., 5 figs., 2 tabs.

  13. The Genetic Diversity and Structure of Linkage Disequilibrium of the MTHFR Gene in Populations of Northern Eurasia.

    Science.gov (United States)

    Trifonova, E A; Eremina, E R; Urnov, F D; Stepanov, V A

    2012-01-01

    The structure of the haplotypes and linkage disequilibrium (LD) of the methylenetetrahydrofolate reductase gene (MTHFR) in 9 population groups from Northern Eurasia and populations of the international HapMap project was investigated in the present study. The data suggest that the architecture of LD in the human genome is largely determined by the evolutionary history of populations; however, the results of phylogenetic and haplotype analyses seems to suggest that in fact there may be a common "old" mechanism for the formation of certain patterns of LD. Variability in the structure of LD and the level of diversity of MTHFRhaplotypes cause a certain set of tagSNPs with an established prognostic significance for each population. In our opinion, the results obtained in the present study are of considerable interest for understanding multiple genetic phenomena: namely, the association of interpopulation differences in the patterns of LD with structures possessing a genetic susceptibility to complex diseases, and the functional significance of the pleiotropicMTHFR gene effect. Summarizing the results of this study, a conclusion can be made that the genetic variability analysis with emphasis on the structure of LD in human populations is a powerful tool that can make a significant contribution to such areas of biomedical science as human evolutionary biology, functional genomics, genetics of complex diseases, and pharmacogenomics.

  14. Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds.

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    Hasan Alhaddad

    Full Text Available Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2 was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

  15. Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

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    Yang Ming

    2012-07-01

    Full Text Available Abstract Background MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD within this gene in Chinese indigenous breeds and Western commercial breeds. Results A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Conclusions Chinese and Western breeds have

  16. Mapping of yield, yield stability, yield adaptability and other traits in barley using linkage disequilibrium mapping and linkage analysis

    NARCIS (Netherlands)

    Kraakman, A.T.W.

    2005-01-01

    Plants is mostly done through linkage analysis. A segregating mapping population Identification and mappping of Quantitative Trait Loci (QTLs) in is created from a bi-parental cross and linkages between trait values and mapped markers reveal the positions ofQTLs. In

  17. Geographic stratification of linkage disequilibrium: a worldwide population study in a region of chromosome 22

    Directory of Open Access Journals (Sweden)

    González-Neira Anna

    2004-11-01

    Full Text Available Abstract Recent studies of haplotype diversity in a number of genomic regions have suggested that long stretches of DNA are preserved in the same chromosome, with little evidence of recombination events. The knowledge of the extent and strength of these haplotypes could become a powerful tool for future genetic analysis of complex traits. Different patterns of linkage disequilibrium (LD have been found when comparing individuals of African and European descent, but there is scarce knowledge about the worldwide population stratification. Thus, the study of haplotype composition and the pattern of LD from a global perspective are relevant for elucidating their geographical stratification, as it may have implications in the future analysis of complex traits. We have typed 12 single nucleotide polymorphisms in a chromosome 22 region--previously described as having high LD levels in European populations -- in 39 different world populations. Haplotype structure has a clear continental structure with marked heterogeneity within some continents (Africa, America. The pattern of LD among neighbouring markers exhibits a strong clustering of all East Asian populations on the one hand and of Western Eurasian populations (including Europe on the other, revealing only two major LD patterns, but with some very specific outliers due to specific demographic histories. Moreover, it should be taken into account that African populations are highly heterogeneous. The present results support the existence of a wide (but not total communality in LD patterns in human populations from different continental regions, despite differences in their demographic histories, as population factors seem to be less relevant compared with genomic forces in shaping the patterns of LD.

  18. Mapping of yield, yield stability, yield adaptability and other traits in barley using linkage disequilibrium mapping and linkage analysis

    OpenAIRE

    Kraakman, A.T.W.

    2005-01-01

    Plants is mostly done through linkage analysis. A segregating mapping population Identification and mappping of Quantitative Trait Loci (QTLs) in is created from a bi-parental cross and linkages between trait values and mapped markers reveal the positions ofQTLs. Inthisstudyweexploredlinkagedisequilibrium(LD)mappingof traits in a set of modernbarleycultivars. LDbetweenmolecularmarkerswasfoundup to a distance of 10 centimorgan,whichislargecomparedtootherspecies.Thelarge distancemightbeinducedb...

  19. Sexual antagonism and meiotic drive cause stable linkage disequilibrium and favour reduced recombination on the X chromosome.

    Science.gov (United States)

    Rydzewski, W T; Carioscia, S A; Liévano, G; Lynch, V D; Patten, M M

    2016-06-01

    Sexual antagonism and meiotic drive are sex-specific evolutionary forces with the potential to shape genomic architecture. Previous theory has found that pairing two sexually antagonistic loci or combining sexual antagonism with meiotic drive at linked autosomal loci augments genetic variation, produces stable linkage disequilibrium (LD) and favours reduced recombination. However, the influence of these two forces has not been examined on the X chromosome, which is thought to be enriched for sexual antagonism and meiotic drive. We investigate the evolution of the X chromosome under both sexual antagonism and meiotic drive with two models: in one, both loci experience sexual antagonism; in the other, we pair a meiotic drive locus with a sexually antagonistic locus. We find that LD arises between the two loci in both models, even when the two loci freely recombine in females and that driving haplotypes will be enriched for male-beneficial alleles, further skewing sex ratios in these populations. We introduce a new measure of LD, Dz', which accounts for population allele frequencies and is appropriate for instances where these are sex specific. Both models demonstrate that natural selection favours modifiers that reduce the recombination rate. These results inform observed patterns of congealment found on driving X chromosomes and have implications for patterns of natural variation and the evolution of recombination rates on the X chromosome. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  20. Combining information from linkage and association mapping for next-generation sequencing longitudinal family data.

    Science.gov (United States)

    Balliu, Brunilda; Uh, Hae-Won; Tsonaka, Roula; Boehringer, Stefan; Helmer, Quinta; Houwing-Duistermaat, Jeanine J

    2014-01-01

    In this analysis, we investigate the contributions that linkage-based methods, such as identical-by-descent mapping, can make to association mapping to identify rare variants in next-generation sequencing data. First, we identify regions in which cases share more segments identical-by-descent around a putative causal variant than do controls. Second, we use a two-stage mixed-effect model approach to summarize the single-nucleotide polymorphism data within each region and include them as covariates in the model for the phenotype. We assess the impact of linkage disequilibrium in determining identical-by-descent states between individuals by using markers with and without linkage disequilibrium for the first part and the impact of imputation in testing for association by using imputed genome-wide association studies or raw sequence markers for the second part. We apply the method to next-generation sequencing longitudinal family data from Genetic Association Workshop 18 and identify a significant region at chromosome 3: 40249244-41025167 (p-value = 2.3 × 10(-3)).

  1. Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies.

    Science.gov (United States)

    Xu, P; Wu, X; Wang, B; Luo, J; Liu, Y; Ehlers, J D; Close, T J; Roberts, P A; Lu, Z; Wang, S; Li, G

    2012-07-01

    Association mapping of important traits of crop plants relies on first understanding the extent and patterns of linkage disequilibrium (LD) in the particular germplasm being investigated. We characterize here the genetic diversity, population structure and genome wide LD patterns in a set of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm from China. A diverse collection of 99 asparagus bean and normal cowpea accessions were genotyped with 1127 expressed sequence tag-derived single nucleotide polymorphism markers (SNPs). The proportion of polymorphic SNPs across the collection was relatively low (39%), with an average number of SNPs per locus of 1.33. Bayesian population structure analysis indicated two subdivisions within the collection sampled that generally represented the 'standard vegetable' type (subgroup SV) and the 'non-standard vegetable' type (subgroup NSV), respectively. Level of LD (r(2)) was higher and extent of LD persisted longer in subgroup SV than in subgroup NSV, whereas LD decayed rapidly (0-2 cM) in both subgroups. LD decay distance varied among chromosomes, with the longest (≈ 5 cM) five times longer than the shortest (≈ 1 cM). Partitioning of LD variance into within- and between-subgroup components coupled with comparative LD decay analysis suggested that linkage group 5, 7 and 10 may have undergone the most intensive epistatic selection toward traits favorable for vegetable use. This work provides a first population genetic insight into domestication history of asparagus bean and demonstrates the feasibility of mapping complex traits by genome wide association study in asparagus bean using a currently available cowpea SNPs marker platform.

  2. Extent of linkage disequilibrium and effective population size in four South African Sanga cattle breeds

    Directory of Open Access Journals (Sweden)

    Sithembile Olga Makina

    2015-12-01

    Full Text Available Knowledge on the extent of linkage disequilibrium (LD in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies. This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne for four Sanga cattle breeds in South Africa including the Afrikaner (n=44, Nguni (n=54, Drakensberger (n=47 and Bonsmara breeds (n=46, using Angus (n=31 and Holstein (n=29 as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21 and Holstein (0.21 and up to 100 kb in Afrikaner (0.20. This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2 ≥ 0.20 would require about 30,000 -50,000 SNPs. However, r2 ≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for genome-wide association studies in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne=95 (Nguni, Ne=87 (Drakensberger, Ne=77 (Bonsmara and Ne=41 (Afrikaner. Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

  3. A new method of linkage analysis using LOD scores for quantitative traits supports linkage of monoamine oxidase activity to D17S250 in the Collaborative Study on the Genetics of Alcoholism pedigrees.

    Science.gov (United States)

    Curtis, David; Knight, Jo; Sham, Pak C

    2005-09-01

    Although LOD score methods have been applied to diseases with complex modes of inheritance, linkage analysis of quantitative traits has tended to rely on non-parametric methods based on regression or variance components analysis. Here, we describe a new method for LOD score analysis of quantitative traits which does not require specification of a mode of inheritance. The technique is derived from the MFLINK method for dichotomous traits. A range of plausible transmission models is constructed, constrained to yield the correct population mean and variance for the trait but differing with respect to the contribution to the variance due to the locus under consideration. Maximized LOD scores under homogeneity and admixture are calculated, as is a model-free LOD score which compares the maximized likelihoods under admixture assuming linkage and no linkage. These LOD scores have known asymptotic distributions and hence can be used to provide a statistical test for linkage. The method has been implemented in a program called QMFLINK. It was applied to data sets simulated using a variety of transmission models and to a measure of monoamine oxidase activity in 105 pedigrees from the Collaborative Study on the Genetics of Alcoholism. With the simulated data, the results showed that the new method could detect linkage well if the true allele frequency for the trait was close to that specified. However, it performed poorly on models in which the true allele frequency was much rarer. For the Collaborative Study on the Genetics of Alcoholism data set only a modest overlap was observed between the results obtained from the new method and those obtained when the same data were analysed previously using regression and variance components analysis. Of interest is that D17S250 produced a maximized LOD score under homogeneity and admixture of 2.6 but did not indicate linkage using the previous methods. However, this region did produce evidence for linkage in a separate data set

  4. Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Horvath, Aniko; Didier, Audrey; Koenig, Jean; Exbrayat, Florence; Charmet, Gilles; Balfourier, François

    2009-11-01

    A highly polymorphic core collection of bread wheat and a more narrow-based breeding material, gathered from pedigrees of seven modern cultivars, was analysed in order to compare genetic diversity indices and linkage disequilibrium (LD) patterns along the chromosome 3B with microsatellite (SSR) and Diversity Arrays Technology markers. Five ancestral gene pools could be identified within the core collection, indicating a strong geographical structure (Northwest Europe, Southeast Europe, CIMMYT-ICARDA group, Asia, Nepal). The breeding material showed a temporal structure, corresponding to different periods of breeding programmes [old varieties (from old landraces to 1919), semi-modern varieties (1920-1959), modern varieties (1960-2006)]. Basic statistics showed a higher genetic diversity in the core collection than in the breeding material, indicating a stronger selection pressure in this latter material. More generally, the chromosome 3B had a lower diversity than the whole B-genome. LD was weak in all studied materials. Amongst geographical groups, the CIMMYT-ICARDA pool presented the longest ranged LD in contrast to Asian accessions. In the breeding material, LD increased from old cultivars to modern varieties. Genitors of seven modern cultivars were found to be different; most marker pairs in significant LD were observed amongst genitors of Alexandre and Koreli varieties, indicating an important inbreeding effect. At low genetic distances (0-5 cM), the breeding material had higher LD than the core collection, but globally the two materials had similar values in all classes. Marker pairs in significant LD are generally observed around the centromere in both arms and at distal position on the short arm of the chromosome 3B.

  5. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Cadic, Elena; Coque, Marie; Vear, Felicity; Grezes-Besset, Bruno; Pauquet, Jerôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rengel, David; Gouzy, Jerôme; Langlade, Nicolas; Mangin, Brigitte; Vincourt, Patrick

    2013-05-01

    Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.

  6. Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks.

    Science.gov (United States)

    Zhao, Huiying; Nyholt, Dale R; Yang, Yuanhao; Wang, Jihua; Yang, Yuedong

    2017-06-14

    Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous pathway-based methods have been developed. Here we propose a novel method, DGAT-path, to divide all SNPs assigned to genes in each pathway into LD blocks, and to sum the chi-square statistics of LD blocks for assessing the significance of the pathway by permutation tests. The method was proven robust with the type I error rate >1.6 times lower than other methods. Meanwhile, the method displays a higher power and is not biased by the pathway size. The applications to the GWAS summary statistics for schizophrenia and breast cancer indicate that the detected top pathways contain more genes close to associated SNPs than other methods. As a result, the method identified 17 and 12 significant pathways containing 20 and 21 novel associated genes, respectively for two diseases. The method is available online by http://sparks-lab.org/server/DGAT-path .

  7. A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer

    International Nuclear Information System (INIS)

    Middeldorp, Anneke; Wijnen, Juul T; Wezel, Tom van; Jagmohan-Changur, Shantie; Helmer, Quinta; Klift, Heleen M van der; Tops, Carli MJ; Vasen, Hans FA; Devilee, Peter; Morreau, Hans; Houwing-Duistermaat, Jeanine J

    2007-01-01

    The apparent dominant model of colorectal cancer (CRC) inheritance in several large families, without mutations in known CRC susceptibility genes, suggests the presence of so far unidentified genes with strong or moderate effect on the development of CRC. Linkage analysis could lead to identification of susceptibility genes in such families. In comparison to classical linkage analysis with multi-allelic markers, single nucleotide polymorphism (SNP) arrays have increased information content and can be processed with higher throughput. Therefore, SNP arrays can be excellent tools for linkage analysis. However, the vast number of SNPs on the SNP arrays, combined with large informative pedigrees (e.g. >35–40 bits), presents us with a computational complexity that is challenging for existing statistical packages or even exceeds their capacity. We therefore setup a procedure for linkage analysis in large pedigrees and validated the method by genotyping using SNP arrays of a colorectal cancer family with a known MLH1 germ line mutation. Quality control of the genotype data was performed in Alohomora, Mega2 and SimWalk2, with removal of uninformative SNPs, Mendelian inconsistencies and Mendelian consistent errors, respectively. Linkage disequilibrium was measured by SNPLINK and Merlin. Parametric linkage analysis using two flanking markers was performed using MENDEL. For multipoint parametric linkage analysis and haplotype analysis, SimWalk2 was used. On chromosome 3, in the MLH1-region, a LOD score of 1.9 was found by parametric linkage analysis using two flanking markers. On chromosome 11 a small region with LOD 1.1 was also detected. Upon linkage disequilibrium removal, multipoint linkage analysis yielded a LOD score of 2.1 in the MLH1 region, whereas the LOD score dropped to negative values in the region on chromosome 11. Subsequent haplotype analysis in the MLH1 region perfectly matched the mutation status of the family members. We developed a workflow for linkage

  8. Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes

    International Nuclear Information System (INIS)

    Allen-Brady, Kristina; Camp, Nicola J

    2005-01-01

    Characterization of the linkage disequilibrium (LD) structure of candidate genes is the basis for an effective association study of complex diseases such as cancer. In this study, we report the LD and haplotype architecture and tagging-single nucleotide polymorphisms (tSNPs) for five DNA repair genes: ATM, MRE11A, XRCC4, NBS1 and RAD50. The genes ATM, MRE11A, and XRCC4 were characterized using a panel of 94 unrelated female subjects (47 breast cancer cases, 47 controls) obtained from high-risk breast cancer families. A similar LD structure and tSNP analysis was performed for NBS1 and RAD50, using publicly available genotyping data. We studied a total of 61 SNPs at an average marker density of 10 kb. Using a matrix decomposition algorithm, based on principal component analysis, we captured >90% of the intragenetic variation for each gene. Our results revealed that three of the five genes did not conform to a haplotype block structure (MRE11A, RAD50 and XRCC4). Instead, the data fit a more flexible LD group paradigm, where SNPs in high LD are not required to be contiguous. Traditional haplotype blocks assume recombination is the only dynamic at work. For ATM, MRE11A and XRCC4 we repeated the analysis in cases and controls separately to determine whether LD structure was consistent across breast cancer cases and controls. No substantial difference in LD structures was found. This study suggests that appropriate SNP selection for an association study involving candidate genes should allow for both mutation and recombination, which shape the population-level genomic structure. Furthermore, LD structure characterization in either breast cancer cases or controls appears to be sufficient for future cancer studies utilizing these genes

  9. HLA class II linkage disequilibrium and haplotype evolution in the Cayapa Indians of Ecuador

    Energy Technology Data Exchange (ETDEWEB)

    Trachtenberg, E.A.; Erlich, H.A. [Roche Molecular Systems, Alameda, CA (United States); Klitz, W. [Univ. of California, Berkeley, CA (United States)] [and others

    1995-08-01

    DNA-based typing of the HLA class II loci in a sample of the Cayapa Indians of Ecuador reveals several lines of evidence that selection has operated to maintain and to diversify the existing level of polymorphism in the class II region. As has been noticed for other Native American groups, the overall level of polymorphism at the DRB1, DQA1, DQB1, and DPB1 loci is reduced relative to that found in other human populations. Nonetheless, the relative eveness in the distribution of allele frequencies at each of the four loci points to the role of balancing selection in the maintenance of the polymorphism. The DQA1 and DQB1 loci, in particular, have near-maximum departures from the neutrality model, which suggests that balancing selection has been especially strong in these cases. Several novel DQA1-DQB1 haplotypes and the discovery of a new DRB1 allele demonstrate an evolutionary tendency favoring the diversification of class II alleles and haplotypes. The recombination interval between the centromeric DPB1 locus and the other class II loci will, in the absence of other forces such as selection, reduce disequilibrium across this region. However, nearly all common alleles were found to be part of DR-DP haplotypes in strong disequilibrium, consistent with the recent action of selection acting on these haplotypes in the Cayapa. 50 refs., 3 figs., 3 tabs.

  10. Testing association and linkage using affected-sib-parent study designs.

    Science.gov (United States)

    Millstein, Joshua; Siegmund, Kimberly D; Conti, David V; Gauderman, W James

    2005-11-01

    We have developed a method for jointly testing linkage and association using data from affected sib pairs and their parents. We specify a conditional logistic regression model with two covariates, one that quantifies association (either direct association or indirect association via linkage disequilibrium), and a second that quantifies linkage. The latter covariate is computed based on expected identity-by-descend (ibd) sharing of marker alleles between siblings. In addition to a joint test of linkage and association, our general framework can be used to obtain a linkage test comparable to the mean test (Blackwelder and Elston [1985] Genet. Epidemiol. 2:85-97), and an association test comparable to the Family-Based Association Test (FBAT; Rabinowitz and Laird [2000] Hum. Hered. 50:211-223). We present simulation results demonstrating that our joint test can be more powerful than some standard tests of linkage or association. For example, with a relative risk of 2.7 per variant allele at a disease locus, the estimated power to detect a nearby marker with a modest level of LD was 58.1% by the mean test (linkage only), 69.8% by FBAT, and 82.5% by our joint test of linkage and association. Our model can also be used to obtain tests of linkage conditional on association and association conditional on linkage, which can be helpful in fine mapping. Copyright 2005 Wiley-Liss, Inc.

  11. Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

    Science.gov (United States)

    Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

    2012-08-01

    White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

  12. Linkage analysis: Inadequate for detecting susceptibility loci in complex disorders?

    Energy Technology Data Exchange (ETDEWEB)

    Field, L.L.; Nagatomi, J. [Univ. of Calgary, Alberta (Canada)

    1994-09-01

    Insulin-dependent diabetes mellitus (IDDM) may provide valuable clues about approaches to detecting susceptibility loci in other oligogenic disorders. Numerous studies have demonstrated significant association between IDDM and a VNTR in the 5{prime} flanking region of the insulin (INS) gene. Paradoxically, all attempts to demonstrate linkage of IDDM to this VNTR have failed. Lack of linkage has been attributed to insufficient marker locus information, genetic heterogeneity, or high frequency of the IDDM-predisposing allele in the general population. Tyrosine hydroxylase (TH) is located 2.7 kb from INS on the 5` side of the VNTR and shows linkage disequilibrium with INS region loci. We typed a highly polymorphic microsatellite within TH in 176 multiplex families, and performed parametric (lod score) linkage analysis using various intermediate reduced penetrance models for IDDM (including rare and common disease allele frequencies), as well as non-parametric (affected sib pair) linkage analysis. The scores significantly reject linkage for recombination values of .05 or less, excluding the entire 19 kb region containing TH, the 5{prime} VNTR, the INS gene, and IGF2 on the 3{prime} side of INS. Non-parametric linkage analysis also provided no significant evidence for linkage (mean TH allele sharing 52.5%, P=.12). These results have important implications for efforts to locate genes predisposing to complex disorders, strongly suggesting that regions which are significantly excluded by linkage methods may nevertheless contain predisposing genes readily detectable by association methods. We advocate that investigators routinely perform association analyses in addition to linkage analyses.

  13. Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium.

    Science.gov (United States)

    Schopp, Pascal; Müller, Dominik; Technow, Frank; Melchinger, Albrecht E

    2017-01-01

    Synthetics play an important role in quantitative genetic research and plant breeding, but few studies have investigated the application of genomic prediction (GP) to these populations. Synthetics are generated by intermating a small number of parents ([Formula: see text] and thereby possess unique genetic properties, which make them especially suited for systematic investigations of factors contributing to the accuracy of GP. We generated synthetics in silico from [Formula: see text]2 to 32 maize (Zea mays L.) lines taken from an ancestral population with either short- or long-range linkage disequilibrium (LD). In eight scenarios differing in relatedness of the training and prediction sets and in the types of data used to calculate the relationship matrix (QTL, SNPs, tag markers, and pedigree), we investigated the prediction accuracy (PA) of Genomic best linear unbiased prediction (GBLUP) and analyzed contributions from pedigree relationships captured by SNP markers, as well as from cosegregation and ancestral LD between QTL and SNPs. The effects of training set size [Formula: see text] and marker density were also studied. Sampling few parents ([Formula: see text]) generates substantial sample LD that carries over into synthetics through cosegregation of alleles at linked loci. For fixed [Formula: see text], [Formula: see text] influences PA most strongly. If the training and prediction set are related, using [Formula: see text] parents yields high PA regardless of ancestral LD because SNPs capture pedigree relationships and Mendelian sampling through cosegregation. As [Formula: see text] increases, ancestral LD contributes more information, while other factors contribute less due to lower frequencies of closely related individuals. For unrelated prediction sets, only ancestral LD contributes information and accuracies were poor and highly variable for [Formula: see text] due to large sample LD. For large [Formula: see text], achieving moderate accuracy requires

  14. Evidence for linkage disequilibrium in chromosome 13-linked Duchenne-like muscular dystrophy

    Energy Technology Data Exchange (ETDEWEB)

    Othmane, K.B.; Speer, M.C.; Stauffer, J. [Duke Univ. Medical Center, Durham, NC (United States)] [and others

    1995-09-01

    Duchenne-like muscular dystrophy (DLMD) is an autosomal recessive Limb Girdle muscular dystrophy (LGMD2C) characterized by late age of onset, proximal muscle weakness leading to disability, high creatine kinase values, normal intelligence and normal dystrophin in muscle biopsy. We have shown previously that three DLMD families from Tunisia are linked to chromosome 13q12. To further localize the LGMD2C gene, we have investigated seven additional families (119 individuals). Both genotyping and two-point linkage analysis were performed as described elsewhere. 7 refs., 1 fig., 1 tab.

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

    DEFF Research Database (Denmark)

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

    2006-01-01

    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 same Aly8 sequence...... the evolutionary history of these populations. Overall, the results suggest that recombination rarely occurs in the interval between the S-loci and Aly8 and that linkage to the S-loci can probably account for the observed high Aly8 diversity....

  16. Exploring linkage disequilibrium

    Czech Academy of Sciences Publication Activity Database

    Baird, Stuart J. E.

    2015-01-01

    Roč. 15, č. 5 (2015), s. 1017-1019 ISSN 1755-098X Institutional support: RVO:68081766 Keywords : bioinfomatics/phyloinfomatics * genomics /proteomics * population genetics—theoretical * population genetics—empirical Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.298, year: 2015

  17. Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds.

    Science.gov (United States)

    Kawakami, Takeshi; Mugal, Carina F; Suh, Alexander; Nater, Alexander; Burri, Reto; Smeds, Linnéa; Ellegren, Hans

    2017-08-01

    Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  18. Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences.

    Science.gov (United States)

    Haber, Marc; Doumet-Serhal, Claude; Scheib, Christiana; Xue, Yali; Danecek, Petr; Mezzavilla, Massimo; Youhanna, Sonia; Martiniano, Rui; Prado-Martinez, Javier; Szpak, Michał; Matisoo-Smith, Elizabeth; Schutkowski, Holger; Mikulski, Richard; Zalloua, Pierre; Kivisild, Toomas; Tyler-Smith, Chris

    2017-08-03

    The Canaanites inhabited the Levant region during the Bronze Age and established a culture that became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole genomes from ∼3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalog modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with recorded massive population movements in Mesopotamia during the mid-Holocene. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate that this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. disequilibrium?

    Directory of Open Access Journals (Sweden)

    J. P. L. Johnson

    2016-08-01

    τc(qs* and increasing transport rates. Model parameters are calibrated based on laboratory flume experiments that explore transport disequilibrium. The τc(qs* equation is then incorporated into a simple morphodynamic model. The evolution of τc(qs* is a negative feedback on morphologic change, while also allowing reaches to equilibrate to sediment supply at different slopes. Finally, τc(qs* is interpreted to be an important but nonunique state variable for morphodynamics, in a manner consistent with state variables such as temperature in thermodynamics.

  20. Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1 in five populations: implications for pharmacogenetic research

    Directory of Open Access Journals (Sweden)

    Sughondhabirom Atapol

    2007-10-01

    Full Text Available Abstract Background GABA transporter-1 (GAT-1; genetic locus SLC6A1 is emerging as a novel target for treatment of neuropsychiatric disorders. To understand how population differences might influence strategies for pharmacogenetic studies, we identified patterns of genetic variation and linkage disequilibrium (LD in SLC6A1 in five populations representing three continental groups. Results We resequenced 12.4 kb of SLC6A1, including the promoters, exons and flanking intronic regions in African-American, Thai, Hmong, Finnish, and European-American subjects (total n = 40. LD in SLC6A1 was examined by genotyping 16 SNPs in larger samples. Sixty-three variants were identified through resequencing. Common population-specific variants were found in African-Americans, including a novel 21-bp promoter region variable number tandem repeat (VNTR, but no such variants were found in any of the other populations studied. Low levels of LD and the absence of major LD blocks were characteristic of all five populations. African-Americans had the highest genetic diversity. European-Americans and Finns did not differ in genetic diversity or LD patterns. Although the Hmong had the highest level of LD, our results suggest that a strategy based on the use of tag SNPs would not translate to a major improvement in genotyping efficiency. Conclusion Owing to the low level of LD and presence of recombination hotspots, SLC6A1 may be an example of a problematic gene for association and haplotype tagging-based genetic studies. The 21-bp promoter region VNTR polymorphism is a putatively functional candidate allele for studies focusing on variation in GAT-1 function in the African-American population.

  1. Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study.

    Science.gov (United States)

    Bauchet, Guillaume; Grenier, Stéphane; Samson, Nicolas; Bonnet, Julien; Grivet, Laurent; Causse, Mathilde

    2017-05-01

    A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.

  2. Effects of different mineral admixtures on the properties of fresh concrete.

    Science.gov (United States)

    Khan, Sadaqat Ullah; Nuruddin, Muhammad Fadhil; Ayub, Tehmina; Shafiq, Nasir

    2014-01-01

    This paper presents a review of the properties of fresh concrete including workability, heat of hydration, setting time, bleeding, and reactivity by using mineral admixtures fly ash (FA), silica fume (SF), ground granulated blast furnace slag (GGBS), metakaolin (MK), and rice husk ash (RHA). Comparison of normal and high-strength concrete in which cement has been partially supplemented by mineral admixture has been considered. It has been concluded that mineral admixtures may be categorized into two groups: chemically active mineral admixtures and microfiller mineral admixtures. Chemically active mineral admixtures decrease workability and setting time of concrete but increase the heat of hydration and reactivity. On the other hand, microfiller mineral admixtures increase workability and setting time of concrete but decrease the heat of hydration and reactivity. In general, small particle size and higher specific surface area of mineral admixture are favourable to produce highly dense and impermeable concrete; however, they cause low workability and demand more water which may be offset by adding effective superplasticizer.

  3. Characteristics of waste forms improved by using admixtures

    International Nuclear Information System (INIS)

    Rzyski, B.M.; Suarez, A.A.

    1989-06-01

    The immobilization of nitric waste streams with ordinary Portland cement can be improved by use of some admixtures. The aim of this work was to investigated how the main characteristics of waste forms prepared with Portalnd cement pastes are modified by the addition of sulphonic naphtalene acids, lignosulphonic acids and emulsified fatty acids, which are present in some commercial admixtures. The effectiveness of the admixture in reducing the pore volume, as well as improving other parameters, depends on its chemical composition and on the amount utilized as well as the water to cement ratio and salt content. The admixture which has emulsified fatty acids in its composition shows some adverse results when the samples are immersed in water. The mechanical strenght however is some what increased even when water load is increased. (author) [pt

  4. Characteristics of waste forms improved by using admixtures

    International Nuclear Information System (INIS)

    Rzyski, B.M.; Suarez, A.A.

    1989-01-01

    The immobilization of nitric waste streams with ordinary Portland cement can be improved by use of some admixtures. The aim of this work was to investigate how the main characteristics of waste forms prepared with Portland cement pastes are modified by the addition of sulphonic naphyhalene acids, lignosulphonic acids and emulsified fatty acids, which are present in some commercial admixtures. The effectiveness of the admixtures in reducing the pore volume, as well as improving other parameters, depends on its chemical composition and on the amount utilized as well as the water to cement ratio and salt content. The admixture which has emulsified fatty acids in its composition shows some adverse results when the samples are immersed in water. The mechanical strength however is somewhat increased even when water load is increased

  5. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    Directory of Open Access Journals (Sweden)

    Khulekhani Sedwell Khanyile

    2015-02-01

    Full Text Available Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history will give valuable information to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n =146, Malawi (n =30 and Zimbabwe (n =136 were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29-0.36, was observed between SNP markers that were less than 10kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK and 0.24 (VD at SNP marker interval of 500kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population

  6. Geographic patterns of genome admixture in Latin American Mestizos.

    Directory of Open Access Journals (Sweden)

    Sijia Wang

    2008-03-01

    Full Text Available The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.

  7. Habitat Predicts Levels of Genetic Admixture in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Viranga Tilakaratna

    2017-09-01

    Full Text Available Genetic admixture can provide material for populations to adapt to local environments, and this process has played a crucial role in the domestication of plants and animals. The model yeast, Saccharomyces cerevisiae, has been domesticated multiple times for the production of wine, sake, beer, and bread, but the high rate of admixture between yeast lineages has so far been treated as a complication for population genomic analysis. Here, we make use of the low recombination rate at centromeres to investigate admixture in yeast using a classic Bayesian approach and a locus-by-locus phylogenetic approach. Using both approaches, we find that S. cerevisiae from stable oak woodland habitats are less likely to show recent genetic admixture compared with those isolated from transient habitats such as fruits, wine, or human infections. When woodland yeast strains do show recent genetic admixture, the degree of admixture is lower than in strains from other habitats. Furthermore, S. cerevisiae populations from oak woodlands are genetically isolated from each other, with only occasional migration between woodlands and local fruit habitats. Application of the phylogenetic approach suggests that there is a previously undetected population in North Africa that is the closest outgroup to the European S. cerevisiae, including the domesticated Wine population. Careful testing for admixture in S. cerevisiae leads to a better understanding of the underlying population structure of the species and will be important for understanding the selective processes underlying domestication in this economically important species.

  8. Habitat Predicts Levels of Genetic Admixture in Saccharomyces cerevisiae.

    Science.gov (United States)

    Tilakaratna, Viranga; Bensasson, Douda

    2017-09-07

    Genetic admixture can provide material for populations to adapt to local environments, and this process has played a crucial role in the domestication of plants and animals. The model yeast, Saccharomyces cerevisiae , has been domesticated multiple times for the production of wine, sake, beer, and bread, but the high rate of admixture between yeast lineages has so far been treated as a complication for population genomic analysis. Here, we make use of the low recombination rate at centromeres to investigate admixture in yeast using a classic Bayesian approach and a locus-by-locus phylogenetic approach. Using both approaches, we find that S. cerevisiae from stable oak woodland habitats are less likely to show recent genetic admixture compared with those isolated from transient habitats such as fruits, wine, or human infections. When woodland yeast strains do show recent genetic admixture, the degree of admixture is lower than in strains from other habitats. Furthermore, S. cerevisiae populations from oak woodlands are genetically isolated from each other, with only occasional migration between woodlands and local fruit habitats. Application of the phylogenetic approach suggests that there is a previously undetected population in North Africa that is the closest outgroup to the European S. cerevisiae , including the domesticated Wine population. Careful testing for admixture in S. cerevisiae leads to a better understanding of the underlying population structure of the species and will be important for understanding the selective processes underlying domestication in this economically important species. Copyright © 2017 Tilakaratna and Bensasson.

  9. Freezing temperature protection admixture for Portland cement concrete

    Science.gov (United States)

    1996-10-01

    A number of experimental admixtures were compared to Pozzutec 20 admixture for their ability to protect fresh concrete from freezing and for increasing the rate of cement hydration at below-freezing temperatures. The commercial accelerator and low-te...

  10. New generation pharmacogenomic tools: a SNP linkage disequilibrium Map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies.

    Science.gov (United States)

    De La Vega, Francisco M; Dailey, David; Ziegle, Janet; Williams, Julie; Madden, Dawn; Gilbert, Dennis A

    2002-06-01

    Since public and private efforts announced the first draft of the human genome last year, researchers have reported great numbers of single nucleotide polymorphisms (SNPs). We believe that the availability of well-mapped, quality SNP markers constitutes the gateway to a revolution in genetics and personalized medicine that will lead to better diagnosis and treatment of common complex disorders. A new generation of tools and public SNP resources for pharmacogenomic and genetic studies--specifically for candidate-gene, candidate-region, and whole-genome association studies--will form part of the new scientific landscape. This will only be possible through the greater accessibility of SNP resources and superior high-throughput instrumentation-assay systems that enable affordable, highly productive large-scale genetic studies. We are contributing to this effort by developing a high-quality linkage disequilibrium SNP marker map and an accompanying set of ready-to-use, validated SNP assays across every gene in the human genome. This effort incorporates both the public sequence and SNP data sources, and Celera Genomics' human genome assembly and enormous resource ofphysically mapped SNPs (approximately 4,000,000 unique records). This article discusses our approach and methodology for designing the map, choosing quality SNPs, designing and validating these assays, and obtaining population frequency ofthe polymorphisms. We also discuss an advanced, high-performance SNP assay chemisty--a new generation of the TaqMan probe-based, 5' nuclease assay-and high-throughput instrumentation-software system for large-scale genotyping. We provide the new SNP map and validation information, validated SNP assays and reagents, and instrumentation systems as a novel resource for genetic discoveries.

  11. Two-sector disequilibrium growth

    NARCIS (Netherlands)

    J.G.M. van Marrewijk (Charles); J.B.L.M. Verbeek (Jos)

    1994-01-01

    textabstractWe investigate the effects of (i) profit distribution to either laborers or capital-owners, (ii) sector-specific or efficient rationing schemes, and (iii) government consumption in a two-sector disequilibrium growth model with sluggish real wage rate adjustment (which affects capital

  12. Tamping Mortars with Stabilizing and Plasticizing Admixtures

    Science.gov (United States)

    Terlyha, Volodymir; Sobol, Khrystyna

    2012-06-01

    Boreholes cementing operations at the depth of several kilometers requires the best technology as well as the best materials. To produce the materials satisfying all the requirements concerning the tamping works is possible using the technology of dry building mixes (DBM) prepared at the factories by thorough mixing of accurately dosed components. Using of chemical admixtures allows improving some properties of these mixes. In this work the influence of mineral fillers and chemical admixtures on the properties of the fresh mixture and hardened tamping mortar was investigated. It is established that introduction of the admixture with complex action on the basis of stabilizer Walocel 15-01 and plasticizer Melflux 2651 allows obtaining the fresh mixture with high spreadability. At the same time the value of dehydration approaches to zero which favorably effects on stabilization of fresh mixture and not allows the sedimentation processes to take place. By the X-ray analysis, the positive influence of modification admixtures on the hydration processes in the tamping mortars by activating them was identified. In the result of this, the formation of hydrate phases is accelerated; these phases tightly mud the pore area of tamping stone increasing by this its strength.

  13. Uranium and radium geochemistry. Radioactive disequilibrium in natural waters

    International Nuclear Information System (INIS)

    Beaucaire, C.

    1987-09-01

    Rock-water interactions play a primary part in uranium-series disequilibrium either by different chemical behavior or by recoiling alpha emitting nuclei in solution. Three series of thermal water containing CO 2 (Vichy, Vals and Cezallier) and one from Lodeve uranium deposit are studied to define parameters (pH, Eh, pCO 2 , T,...) controlling studied nuclei. For U complexation by carbonates is in competition with redox conditions. Ra is coprecipitated by barium. For thermal waters keeping their deep characteristics there is a low disequilibriums 234 U- 238 U between 1 and 2. On the contrary important disequilibrium (up to 12) in Vichy Saint Yorre water are due to secondary remobilization. In the same way for these waters 234 U and 226 Ra are correlated. Then leaching is essential for the radioactive disequilibrium but alpha recoil of 234 Th is of secondary importance in this case [fr

  14. Behavior of passive admixture in a vortical hydrodynamic field

    Directory of Open Access Journals (Sweden)

    R.O.Bobrov

    2006-01-01

    Full Text Available The motion of passive admixture of spherical particles in the stationary hydrodynamic field of a swirling flow is studied. A spherical particle of a given mass in the hydrodynamic field of a swirling flow is located on a certain circular orbit, where the centrifugal force is compensated by the radial drag force due to the sink. This leads to the separation of the host fluid and admixture. A theory of Brownian motion of admixture in dilute solutions with a non-uniform flow is constructed.

  15. Archaic admixture in human history.

    Science.gov (United States)

    Wall, Jeffrey D; Yoshihara Caldeira Brandt, Debora

    2016-12-01

    Modern humans evolved in Southern or Eastern Africa, and spread from there across the rest of the world. As they expanded across Africa and Eurasia, they encountered other hominin groups. The extent to which modern and 'archaic' human groups interbred is an area of active research, and while we know that modern humans interbred with Neanderthals and Denisovans, there is not yet agreement on how many admixture events there were or on how much Neanderthal or Denisovan DNA can be found in contemporary genomes. Here we review what is known about archaic admixture in human history, with a focus on what has been discovered in the past 2 years. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Practical handling of AIO admixtures – Guidelines on Parenteral Nutrition, Chapter 10

    Directory of Open Access Journals (Sweden)

    Stanga, Z.

    2009-11-01

    Full Text Available All-in-one admixtures (AIO-admixtures provide safe, effective and low-risk PN (parenteral nutrition for practically all indications and applications. Water, energy (carbohydrates and lipids, amino acids, vitamins and trace elements are infused together with PN either as industrially-manufactured AIO admixtures provided as two- or three-chamber bags (shelf life usually more than 12 months completed with electrolytes and micronutrients where appropriate or as individually compounded ready-to-use AIO admixtures (compounding, usually prepared by a pharmacy on either a daily or weekly basis and stored at 2–8°C. Physico-chemical and microbial stability of an AIO admixture is essential for the safety and effectiveness of patient-specific PN, and its assurance requires specialist pharmaceutical knowledge. The stability should be documented for an application period of 24 (–48 hours. It is advisable to offer a limited selection of different PN regimes in each hospital. For reasons of drug and medication safety, PN admixtures prepared for individual patients must be correctly labelled and specifications for storage conditions must also be followed during transport. Monitoring is required where applicable. Micronutrients are usually administered separately to AIO admixtures. In case compatibility and stability have been well documented trace elements and/or combination preparations including water-soluble or water-soluble/fat soluble vitamin supplements can be added to PN admixtures under strict aseptic conditions. AIO admixtures are usually not used as vehicles for drugs (incompatibilities.

  17. Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V.

    Science.gov (United States)

    Achenbach, Ute; Paulo, Joao; Ilarionova, Evgenyia; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Gebhardt, Christiane

    2009-02-01

    The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family.

  18. A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

    Science.gov (United States)

    Tennessen, Jacob A; Bollmann, Stephanie R; Blouin, Michael S

    2017-07-05

    The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail-schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite. Copyright © 2017 Tennessen et al.

  19. Disequilibrium biosignatures over Earth history and implications for detecting exoplanet life.

    Science.gov (United States)

    Krissansen-Totton, Joshua; Olson, Stephanie; Catling, David C

    2018-01-01

    Chemical disequilibrium in planetary atmospheres has been proposed as a generalized method for detecting life on exoplanets through remote spectroscopy. Among solar system planets with substantial atmospheres, the modern Earth has the largest thermodynamic chemical disequilibrium due to the presence of life. However, how this disequilibrium changed over time and, in particular, the biogenic disequilibria maintained in the anoxic Archean or less oxic Proterozoic eons are unknown. We calculate the atmosphere-ocean disequilibrium in the Precambrian using conservative proxy- and model-based estimates of early atmospheric and oceanic compositions. We omit crustal solids because subsurface composition is not detectable on exoplanets, unlike above-surface volatiles. We find that (i) disequilibrium increased through time in step with the rise of oxygen; (ii) both the Proterozoic and Phanerozoic may have had remotely detectable biogenic disequilibria due to the coexistence of O 2 , N 2 , and liquid water; and (iii) the Archean had a biogenic disequilibrium caused by the coexistence of N 2 , CH 4 , CO 2 , and liquid water, which, for an exoplanet twin, may be remotely detectable. On the basis of this disequilibrium, we argue that the simultaneous detection of abundant CH 4 and CO 2 in a habitable exoplanet's atmosphere is a potential biosignature. Specifically, we show that methane mixing ratios greater than 10 -3 are potentially biogenic, whereas those exceeding 10 -2 are likely biogenic due to the difficulty in maintaining large abiotic methane fluxes to support high methane levels in anoxic atmospheres. Biogenicity would be strengthened by the absence of abundant CO, which should not coexist in a biological scenario.

  20. Early hydration cement Effect of admixtures superplasticizers

    Directory of Open Access Journals (Sweden)

    Puertas, F.

    2001-06-01

    Full Text Available Early hydration of portland cement with superplasticizer admixtures of different nature has been studied. These admixtures were: one based on melamine synthetic, other based on vinyl copolymer and other based on polyacrylate copolymers. The dosage of the formers were constant (1% weigth of cement and for the third, the influence of admixture dosage was also evaluated, giving dosage values among 1-0.3%. The pastes obtained were studied by conduction calorimetry, XRD and FTIR. Also the apparent fluidity was determined by "Minislump" test. The main results obtained were: a superplasticizers admixtures used, regardless of their nature and for the polycarboxilate one the dosage, retard the silicate hydration (specially, alite phase, b The ettringite formation is affected by the nature of the admixture. cA relationship between the dosage of admixture based on polycarboxilates and the time at the acceleration has been established. A lineal relation (y = 11.03 + 16.05x was obtained. From these results is possible to know, in function of dosage admixture, the time when the masive hydration products and the setting times are produced. Also the total heat releases in these reactions is independent of the nature and dosage of admixture, saying that in all cases the reactions are the same.

    En el presente trabajo se ha estudiado la hidratación inicial de un cemento portland aditivado con superplastificantes de diferente naturaleza. Dichos aditivos fueron: uno basado en melaminas sintéticas, otro en copolímeros vinilicos y otro en policarboxilatos. La dosificación de los dos primeros se fijó constante en 1% en peso con relación al cemento, mientras que para el tercero se evaluó, también, la influencia de la dosificación, tomando proporciones desde el 1% hasta el 0,3%. Las pastas obtenidas se estudiaron por: calorimetría de conducción, DRX y FTIR. También se determinó la fluidez de la pasta a través del ensayo del "Minislump ". Los

  1. Uranium series disequilibrium measurements at Mol, Belgium

    International Nuclear Information System (INIS)

    Ivanovich, M.; Wilkins, M.A.

    1985-02-01

    The contract just completed has funded two parallel uranium series disequilibrium studies and the aims of and the progress to completion of these studies are given in this report. The larger study was concerned with the measurement of uranium series disequilibrium in ground waters derived from sand layers above and below the Boom Clay formation in North East Belgium. The disequilibrium data are analysed in terms of uranium, thorium and radium isotopic geochemistries and in terms of water types and their mixing in the regional groundwater system. It is concluded that most sampled waters are mixtures of younger and older waters. No true old water end-members have been sampled. Simple considerations of the uranium isotopic data indicate that the longest residence times of the sampled waters are not much in excess of 1 to 10 x 10 3 y. Detailed mixing patterns could not be established from this limited data set particularly in the absence of more detailed modelling in conjunction with groundwater hydraulic pressure and flow direction data. (author)

  2. Study of distribution coefficients of admixtures in tellurium

    International Nuclear Information System (INIS)

    Kuchar, L.; Drapala, J.; Kuchar, L. jr.

    1986-01-01

    Limit areas of tellurium-admixture binary systems were studied and the values determined of steady-state distribution coefficients of admixtures. A second order polynomial was used to express equations of solidus and liquidus curves for Te-Se, Te-S, Te-Hg systems; the curves are graphically represented. The most effective method for preparing high-purity tellurium is zonal melting with material removal. (M.D.). 4 figs., 4 tabs., 16 refs

  3. Disequilibrium biosignatures over Earth history and implications for detecting exoplanet life

    Science.gov (United States)

    Krissansen-Totton, Joshua; Olson, Stephanie; Catling, David C.

    2018-01-01

    Chemical disequilibrium in planetary atmospheres has been proposed as a generalized method for detecting life on exoplanets through remote spectroscopy. Among solar system planets with substantial atmospheres, the modern Earth has the largest thermodynamic chemical disequilibrium due to the presence of life. However, how this disequilibrium changed over time and, in particular, the biogenic disequilibria maintained in the anoxic Archean or less oxic Proterozoic eons are unknown. We calculate the atmosphere-ocean disequilibrium in the Precambrian using conservative proxy- and model-based estimates of early atmospheric and oceanic compositions. We omit crustal solids because subsurface composition is not detectable on exoplanets, unlike above-surface volatiles. We find that (i) disequilibrium increased through time in step with the rise of oxygen; (ii) both the Proterozoic and Phanerozoic may have had remotely detectable biogenic disequilibria due to the coexistence of O2, N2, and liquid water; and (iii) the Archean had a biogenic disequilibrium caused by the coexistence of N2, CH4, CO2, and liquid water, which, for an exoplanet twin, may be remotely detectable. On the basis of this disequilibrium, we argue that the simultaneous detection of abundant CH4 and CO2 in a habitable exoplanet’s atmosphere is a potential biosignature. Specifically, we show that methane mixing ratios greater than 10−3 are potentially biogenic, whereas those exceeding 10−2 are likely biogenic due to the difficulty in maintaining large abiotic methane fluxes to support high methane levels in anoxic atmospheres. Biogenicity would be strengthened by the absence of abundant CO, which should not coexist in a biological scenario. PMID:29387792

  4. Microsatellite markers of water buffalo, Bubalus bubalis - development, characterisation and linkage disequilibrium studies

    Directory of Open Access Journals (Sweden)

    Vaidhegi R

    2009-10-01

    Full Text Available Abstract Background Microsatellite markers are highly polymorphic and widely used in genome mapping and population genetic studies in livestock species. River buffalo, Bubalus bubalis is an economically important livestock species, though only a limited number of microsatellite markers have been reported thus far in this species. Results In the present study, using two different approaches 571 microsatellite markers have been characterized for water buffalo. Of the 571 microsatellite markers, 498 were polymorphic with average heterozygosity of 0.51 on a panel of 24 unrelated buffalo. Fisher exact test was used to detect LD between the marker pairs. Among the 137550 pairs of marker combination, 14.58% pairs showed significant LD (P Conclusion The high conservation of cattle microsatellite loci in water buffalo promises the usefulness of the cattle microsatellites markers on buffalo. The polymorphic markers characterised in this study will contribute to genetic linkage and radiation hybrid mapping of water buffalo and population genetic studies.

  5. Patterns of admixture and population structure in native populations of Northwest North America.

    Directory of Open Access Journals (Sweden)

    Paul Verdu

    2014-08-01

    Full Text Available The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

  6. Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach

    Directory of Open Access Journals (Sweden)

    Heinz Ruth A

    2008-01-01

    Full Text Available Abstract Background Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs and short insertion and/or deletions (indels to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. Results A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (θ = 0.0056, as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88. Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2, with a large proportion of the inbred lines being assigned to one of them (G1. Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance. Conclusion Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop

  7. Effects of Mineral Admixtures, Water Binder Ratio and Curing on ...

    African Journals Online (AJOL)

    Suitable addition of mineral admixtures like fly ash (FA), silica fume (SF), metakaolin (MK) etc., in concrete improves strength and durability characteristics of concrete. This paper presents the laboratory investigation on the effects of mineral admixtures and water binder ratio on compressive strength is discussed. The study ...

  8. Genetic mapping of the gene for Usher syndrome: Linkage analysis in a large Samaritan kindred

    Energy Technology Data Exchange (ETDEWEB)

    Bonne-Tamir, B.; Korostishevsky, M.; Kalinsky, H.; Seroussi, E.; Beker, R.; Weiss, S. (Sackler Faculty of Medicine, Ramat-Aviv (Israel)); Godel, V. (Ichilov Hospital, Tel-Aviv (Israel))

    1994-03-01

    Usher syndrome is a group of autosomal recessive disorders associated with congenital sensorineural deafness and progressive visual loss due to retinitis pigmentosa. Sixteen members of the small inbred Samaritan isolate with autosomal recessive deafness from 59 individuals including parents and affected and nonaffected sibs were typed for markers on chromosomes 1q and 11q for which linkage has recently been established for Usher syndrome types II and I. Statistically significant linkage was observed with four markers on 11q (D11S533, D11S527, OMP, and INT2) with a maximum six-point location score of 11.61 at the D11S533 locus. Analysis of haplotypes supports the notion that the mutation arose only once in an ancestral chromosome carrying a specific haplotype. The availability of markers closely linked to the disease locus allows indirect genotype analysis and identifies all carriers of the gene within the community. Furthermore, the detection of complete linkage disequilibrium between the D11S533 marker and the Usher gene suggests that these loci are either identical or adjacent and narrows the critical region to which physical mapping efforts are currently directed. 35 refs., 2 figs., 6 tabs.

  9. Nonsyndromic cleft lip with or without cleft palate: Evidence of linkage to BCL3 in 17 multigenerational families

    Energy Technology Data Exchange (ETDEWEB)

    Stein, J.; Hecht, T. [Univ. of Texas, Houston, TX (United States); Stal, S. [Texas Children`s Hospital, Houston, TX (United States)] [and others

    1995-08-01

    Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common craniofacial developmental defect. Recent segregation analyses have suggested that major genes play a role in the etiology of CL/P. Linkage to 22 candidate genes was tested in 11 multigenerational families with CL/P, and 21 of these candidates were excluded. APOC2, 19q13.1, which is linked to the proto-oncogene BCL3, gave suggestive evidence for linkage to CL/P. The study was expanded to include a total of 39 multigenerational CL/P families. Linkage was tested in all families, using anonymous marker, D19S178, and intragenic markers in BCL3 and APOC2. Linkage was tested under two models, autosomal dominant with reduced penetrance and affecteds-only model. Both models showed evidence of heterogeneity, with 43% of families linked at zero recombination to BCL3 when marker data from BCL3 and APOC2 were included. A maximum multipoint LOD score of 7.00 at BCL3 was found among the 17 families that had posterior probabilities {ge}50% in favor of linkage. The transmission disequilibrium test provided additional evidence for linkage with the 3 allele of BCL3 more often transmitted to affected children. These results suggest that BCL3, or a nearby gene, plays a role in the etiology of CL/P in some families. 39 refs., 8 figs., 4 tabs.

  10. Mechanical characteristics of hardened concrete with different mineral admixtures: a review.

    Science.gov (United States)

    Ayub, Tehmina; Khan, Sadaqat Ullah; Memon, Fareed Ahmed

    2014-01-01

    The available literature identifies that the addition of mineral admixture as partial replacement of cement improves the microstructure of the concrete (i.e., porosity and pore size distribution) as well as increasing the mechanical characteristics such as drying shrinkage and creep, compressive strength, tensile strength, flexural strength, and modulus of elasticity; however, no single document is available in which review and comparison of the influence of the addition of these mineral admixtures on the mechanical characteristics of the hardened pozzolanic concretes are presented. In this paper, based on the reported results in the literature, mechanical characteristics of hardened concrete partially containing mineral admixtures including fly ash (FA), silica fume (SF), ground granulated blast furnace slag (GGBS), metakaolin (MK), and rice husk ash (RHA) are discussed and it is concluded that the content and particle size of mineral admixture are the parameters which significantly influence the mechanical properties of concrete. All mineral admixtures enhance the mechanical properties of concrete except FA and GGBS which do not show a significant effect on the strength of concrete at 28 days; however, gain in strength at later ages is considerable. Moreover, the comparison of the mechanical characteristics of different pozzolanic concretes suggests that RHA and SF are competitive.

  11. Effect of Mixing Time and Storage Condition on Characterization of Heparinoid Admixtures with Corticosteroids.

    Science.gov (United States)

    Sugiyama, Ikumi; Takahashi, Namiki; Sadzuka, Yasuyuki

    2016-01-01

    In dermatologic therapy, several external preparations formulated as ointments or creams are prescribed. And they are often admixture to improve patient compliance. In this study, we prepared admixtures of moisturizer with steroids and examined their usability and the amount of principal agent in formulations, particularly focusing on the moisturizer content. Four heparinoid semisolid formulations were selected: Hirudoid ® soft ointment 0.3% (Formulation A) and 3 generic agents [(Besoften ® oil-based cream 0.3% (Formulation B), Kuradoido ® ointment 0.3% (Formulation C), and Hepadaerm ointment 0.3% (Formulation D)], and Antebate ® ointment 0.05% (Formulation E) were used as steroids. Formulation A and B are water-in-oil emulsions, and Formulation C and D are oil-in-water emulsions. Admixtures looked like to be mixed uniformly by visual observation. In the examination of heparinoid amount, admixture A+E and B+E were mixed uniformly. On the other hand, admixture C+E was remarkable un-uniformly. It was speculated that the emulsification of formulation C was broken. The phenomenon was supported by the result of malleability. After 8 weeks storage, the heparinoid ratio in each formulation could be expressed as follows: Admixture B≥Admixture A>Admixture C=Admixture D. A suitable storage temperature was 4°C. The results of physicochemical data analysis reveal the formulations composed of water-in-oil cream, i.e., Formulation A and Formulation B, to be the optimal choices for mixing with steroid ointments. Mixing time and storage conditions may be optimized to solve pharmaceutical problems. Moreover, understanding the emulsion type and character of semisolid formulations can expand the range of formulation options.

  12. A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations.

    Directory of Open Access Journals (Sweden)

    Emile R Chimusa

    2015-03-01

    Full Text Available We report a study of genome-wide, dense SNP (∼ 900K and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region.

  13. A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations.

    Science.gov (United States)

    Chimusa, Emile R; Meintjies, Ayton; Tchanga, Milaine; Mulder, Nicola; Seoighe, Cathal; Seioghe, Cathal; Soodyall, Himla; Ramesar, Rajkumar

    2015-03-01

    We report a study of genome-wide, dense SNP (∼ 900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region.

  14. A genetic atlas of human admixture history.

    Science.gov (United States)

    Hellenthal, Garrett; Busby, George B J; Band, Gavin; Wilson, James F; Capelli, Cristian; Falush, Daniel; Myers, Simon

    2014-02-14

    Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

  15. Fine mapping of a linkage peak with integration of lipid traits identifies novel coronary artery disease genes on chromosome 5

    Directory of Open Access Journals (Sweden)

    Nolan Daniel K

    2012-02-01

    Full Text Available Abstract Background Coronary artery disease (CAD, and one of its intermediate risk factors, dyslipidemia, possess a demonstrable genetic component, although the genetic architecture is incompletely defined. We previously reported a linkage peak on chromosome 5q31-33 for early-onset CAD where the strength of evidence for linkage was increased in families with higher mean low density lipoprotein-cholesterol (LDL-C. Therefore, we sought to fine-map the peak using association mapping of LDL-C as an intermediate disease-related trait to further define the etiology of this linkage peak. The study populations consisted of 1908 individuals from the CATHGEN biorepository of patients undergoing cardiac catheterization; 254 families (N = 827 individuals from the GENECARD familial study of early-onset CAD; and 162 aorta samples harvested from deceased donors. Linkage disequilibrium-tagged SNPs were selected with an average of one SNP per 20 kb for 126.6-160.2 MB (region of highest linkage and less dense spacing (one SNP per 50 kb for the flanking regions (117.7-126.6 and 160.2-167.5 MB and genotyped on all samples using a custom Illumina array. Association analysis of each SNP with LDL-C was performed using multivariable linear regression (CATHGEN and the quantitative trait transmission disequilibrium test (QTDT; GENECARD. SNPs associated with the intermediate quantitative trait, LDL-C, were then assessed for association with CAD (i.e., a qualitative phenotype using linkage and association in the presence of linkage (APL; GENECARD and logistic regression (CATHGEN and aortas. Results We identified four genes with SNPs that showed the strongest and most consistent associations with LDL-C and CAD: EBF1, PPP2R2B, SPOCK1, and PRELID2. The most significant results for association of SNPs with LDL-C were: EBF1, rs6865969, p = 0.01; PPP2R2B, rs2125443, p = 0.005; SPOCK1, rs17600115, p = 0.003; and PRELID2, rs10074645, p = 0.0002. The most significant results for

  16. A Spatial Framework for Understanding Population Structure and Admixture.

    Science.gov (United States)

    Bradburd, Gideon S; Ralph, Peter L; Coop, Graham M

    2016-01-01

    Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.

  17. Stability investigation of total parenteral nutrition admixture prepared in a hospital pharmacy

    Directory of Open Access Journals (Sweden)

    Mirković Dušica

    2008-01-01

    Full Text Available Background/Aim. In the cases when nutrition of patients can not be orally nor enterally performed, parenteral nutrition is a method of the therapy that provides more successful and rapid recovery. In that way, hospitalization can be significantly shorter, healing costs reduced and mortality minimized. Total parenteral nutrition (TPN admixtures are the most complex systems which contain amino acids, carbohydrates, lipid emulsion, macroelectrolytes (Na+, K+, Ca2+, Mg2+, Cl-, SO42-, PO43-, oligoelements, hydro- and liposoluble vitamines, heparin, insulin and water. Concerning the mentioned complexity, special attention should be payed to physicochemical and microbiological stability of a mixture, because of interactions among components, that can be very hard to analyze. The aim of this study was to investigate the problem of stability of TPN admixtures prepared in a hospital pharmacy. Methods. Admixture TPN was aseptically prepared in laminar air - flow environment on the basis of the specified order in supplementing components and additives to basic solutions. Solutions were kept in sterile multicompartment ethylene-vinyl-acetate bags. After preparation and slow homogenization, TPN admixtures were submitted to physicochemical and microbiological stability analyses in various period of time. The assessment of physical stability of TPN admixture was done on the basis of visual inspection, determination of pH value and measuring of particle size. The investigation of sterility and pyrogenic test were performed according to Ph. Yug. V regulations. Results. Physico-chemical and microbiological analyses were applied and no significant changes in visual sense, pH value and droplet size stability of the TPN admixture were observed during the period of 60 hours. The lipid droplets were smaller in size than 5 μm, that is the most common pharmacopoeia requirement. Conclusion. The results of our study confirmed that a TPN admixture prepared in a hospital

  18. Effect of Gum Arabic karroo as a Water-Reducing Admixture in Concrete.

    Science.gov (United States)

    Mbugua, Rose; Salim, Ramadhan; Ndambuki, Julius

    2016-01-28

    Concrete is one of the most popular construction materials in the world. Chemical admixtures are ingredients added to concrete to enhance its properties. However, most chemical admixtures on the market today are expensive, thereby making them out of reach for small consumers of concrete. In Africa, use of chemical admixtures is rare despite the harsh weather conditions. In the current study, Gum from Acacia karroo (GAK) was used as a water-reducing admixture in concrete. A slump test, density and compressive strength were studied using different dosages of GAK while neat concrete was the control. Results showed that slump increased by 200% at a 2% dosage of GAK. This enabled reduction of water-to-binder (w/b) ratio from 0.61 to 0.48 for samples with a 3% dosage. Reduction in w/b resulted in increased compressive strength of 37.03% above the control after 180 days of curing for a 3% dosage. XRD studies also showed a decreased rate of hydration in the presence of GAK in concrete. It was concluded that GAK can be used in concrete as a water-reducing admixture, which is environmentally-friendly, thus producing sustainable and greener concrete.

  19. Neandertal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes.

    Science.gov (United States)

    Lohse, Konrad; Frantz, Laurent A F

    2014-04-01

    Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.

  20. Effect of Gum Arabic karroo as a Water-Reducing Admixture in Concrete

    Science.gov (United States)

    Mbugua, Rose; Salim, Ramadhan; Ndambuki, Julius

    2016-01-01

    Concrete is one of the most popular construction materials in the world. Chemical admixtures are ingredients added to concrete to enhance its properties. However, most chemical admixtures on the market today are expensive, thereby making them out of reach for small consumers of concrete. In Africa, use of chemical admixtures is rare despite the harsh weather conditions. In the current study, Gum from Acacia karroo (GAK) was used as a water-reducing admixture in concrete. A slump test, density and compressive strength were studied using different dosages of GAK while neat concrete was the control. Results showed that slump increased by 200% at a 2% dosage of GAK. This enabled reduction of water-to-binder (w/b) ratio from 0.61 to 0.48 for samples with a 3% dosage. Reduction in w/b resulted in increased compressive strength of 37.03% above the control after 180 days of curing for a 3% dosage. XRD studies also showed a decreased rate of hydration in the presence of GAK in concrete. It was concluded that GAK can be used in concrete as a water-reducing admixture, which is environmentally-friendly, thus producing sustainable and greener concrete. PMID:28787879

  1. A genetic atlas of human admixture history

    Science.gov (United States)

    Hellenthal, Garrett; Busby, George B.J.; Band, Gavin; Wilson, James F.; Capelli, Cristian

    2014-01-01

    Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed using genetic data alone and encompassing over 100 events occurring over the past 4,000 years. We identify events whose dates and participants suggest they describe genetic impacts of the Mongol Empire, Arab slave trade, Bantu expansion, first millennium CE migrations in eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations. PMID:24531965

  2. Genetic mapping of the gene for Usher syndrome: linkage analysis in a large Samaritan kindred.

    Science.gov (United States)

    Bonné-Tamir, B; Korostishevsky, M; Kalinsky, H; Seroussi, E; Beker, R; Weiss, S; Godel, V

    1994-03-01

    Usher syndrome is a group of autosomal recessive disorders associated with congenital sensorineural deafness and progressive visual loss due to retinitis pigmentosa. Sixteen members of the small inbred Samaritan isolate with autosomal recessive deafness were studied in 10 related sibships. DNA samples from 59 individuals including parents and affected and nonaffected sibs were typed for markers on chromosomes 1q and 11q for which linkage has recently been established for Usher syndrome types II and I. Statistically significant linkage was observed with four markers on 11q (D11S533, D11S527, OMP, and INT2) with a maximum six-point location score of 11.61 at the D11S533 locus. Analysis of haplotypes supports the notion that the mutation arose only once in an ancestral chromosome carrying a specific haplotype. The availability of markers closely linked to the disease locus allows indirect genotype analysis and identifies all carriers of the gene within the community. Furthermore, the detection of complete linkage disequilibrium between the D11S533 marker and the Usher gene suggests that these loci are either identical or adjacent and narrows the critical region to which physical mapping efforts are currently directed.

  3. Experimental Study on Durability Improvement of Fly Ash Concrete with Durability Improving Admixture

    OpenAIRE

    Quan, Hong-zhu; Kasami, Hideo

    2014-01-01

    In order to improve the durability of fly ash concrete, a series of experimental studies are carried out, where durability improving admixture is used to reduce drying shrinkage and improve freezing-thawing resistance. The effects of durability improving admixture, air content, water-binder ratio, and fly ash replacement ratio on the performance of fly ash concrete are discussed in this paper. The results show that by using durability improving admixture in nonair-entraining fly ash concrete,...

  4. Diffusion Decay Coefficient for Chloride Ions of Concrete Containing Mineral Admixtures

    Directory of Open Access Journals (Sweden)

    Jae-Im Park

    2016-01-01

    Full Text Available The diffusion coefficient for chloride ions and the diffusion decay coefficient for chloride ions are essential variables for a service life evaluation of concrete structures. They are influenced by water-binder ratio, exposure condition, curing temperature, cement type, and the type and use of mineral admixture. Mineral admixtures such as ground granulated blast furnace slag, fly ash, and silica fume have been increasingly used to improve resistance against chloride ions penetration in concrete structures built in an offshore environment. However, there is not enough measured data to identify the statistical properties of diffusion decay coefficient for chloride ions in concrete using mineral admixtures. This paper is aimed at evaluating the diffusion decay coefficient for chloride ions of concrete using ordinary Portland cement or blended cement. NT BUILD 492 method, an electrophoresis experiment, was used to measure the diffusion coefficient for chloride ions with ages. It was revealed from the test results that the diffusion decay coefficient for chloride ions was significantly influenced by W/B and the replacement ratio of mineral admixtures.

  5. Effect of Gum Arabic Karroo as a water-reducing admixture in cement mortar

    Directory of Open Access Journals (Sweden)

    Rose Mbugua

    2016-12-01

    Full Text Available The aim of this study was to develop Gum Acacia Karroo (GAK as set retarding-water reducing admixture in cement mortars. Retarding admixtures are used to counter effect the accelerated hydration of cement at elevated temperatures by slowing down the retarding process especially during the day when concreting work is done. However most retarding admixtures available in the market are expensive, thereby making them out of reach for small consumers of concrete in Africa are expensive and not readily available. GAK, which contains soluble sugars, was investigated as a set-retarding water reducing-admixture. Setting time was measured in cement pastes with different dosages of GAK and a commercial retarding agent (Tard CE. Compressive strength, bleeding and flow test were investigated on cement mortars with the control being cement mortar without admixture. GAK was found to increase final setting time by 6 h above control. Compressive strength increased when water cement ratio was reduced from 0.5 to 0.4. Thermogravimetric analysis revealed increased dosage of GAK reduced hydration rate.

  6. A Novel Admixture-Based Pharmacogenetic Approach to Refine Warfarin Dosing in Caribbean Hispanics.

    Directory of Open Access Journals (Sweden)

    Jorge Duconge

    Full Text Available This study is aimed at developing a novel admixture-adjusted pharmacogenomic approach to individually refine warfarin dosing in Caribbean Hispanic patients.A multiple linear regression analysis of effective warfarin doses versus relevant genotypes, admixture, clinical and demographic factors was performed in 255 patients and further validated externally in another cohort of 55 individuals.The admixture-adjusted, genotype-guided warfarin dosing refinement algorithm developed in Caribbean Hispanics showed better predictability (R2 = 0.70, MAE = 0.72mg/day than a clinical algorithm that excluded genotypes and admixture (R2 = 0.60, MAE = 0.99mg/day, and outperformed two prior pharmacogenetic algorithms in predicting effective dose in this population. For patients at the highest risk of adverse events, 45.5% of the dose predictions using the developed pharmacogenetic model resulted in ideal dose as compared with only 29% when using the clinical non-genetic algorithm (p<0.001. The admixture-driven pharmacogenetic algorithm predicted 58% of warfarin dose variance when externally validated in 55 individuals from an independent validation cohort (MAE = 0.89 mg/day, 24% mean bias.Results supported our rationale to incorporate individual's genotypes and unique admixture metrics into pharmacogenetic refinement models in order to increase predictability when expanding them to admixed populations like Caribbean Hispanics.ClinicalTrials.gov NCT01318057.

  7. Creative Activities in Music--A Genome-Wide Linkage Analysis.

    Science.gov (United States)

    Oikkonen, Jaana; Kuusi, Tuire; Peltonen, Petri; Raijas, Pirre; Ukkola-Vuoti, Liisa; Karma, Kai; Onkamo, Päivi; Järvelä, Irma

    2016-01-01

    Creative activities in music represent a complex cognitive function of the human brain, whose biological basis is largely unknown. In order to elucidate the biological background of creative activities in music we performed genome-wide linkage and linkage disequilibrium (LD) scans in musically experienced individuals characterised for self-reported composing, arranging and non-music related creativity. The participants consisted of 474 individuals from 79 families, and 103 sporadic individuals. We found promising evidence for linkage at 16p12.1-q12.1 for arranging (LOD 2.75, 120 cases), 4q22.1 for composing (LOD 2.15, 103 cases) and Xp11.23 for non-music related creativity (LOD 2.50, 259 cases). Surprisingly, statistically significant evidence for linkage was found for the opposite phenotype of creative activity in music (neither composing nor arranging; NCNA) at 18q21 (LOD 3.09, 149 cases), which contains cadherin genes like CDH7 and CDH19. The locus at 4q22.1 overlaps the previously identified region of musical aptitude, music perception and performance giving further support for this region as a candidate region for broad range of music-related traits. The other regions at 18q21 and 16p12.1-q12.1 are also adjacent to the previously identified loci with musical aptitude. Pathway analysis of the genes suggestively associated with composing suggested an overrepresentation of the cerebellar long-term depression pathway (LTD), which is a cellular model for synaptic plasticity. The LTD also includes cadherins and AMPA receptors, whose component GSG1L was linked to arranging. These results suggest that molecular pathways linked to memory and learning via LTD affect music-related creative behaviour. Musical creativity is a complex phenotype where a common background with musicality and intelligence has been proposed. Here, we implicate genetic regions affecting music-related creative behaviour, which also include genes with neuropsychiatric associations. We also propose

  8. Creative Activities in Music--A Genome-Wide Linkage Analysis.

    Directory of Open Access Journals (Sweden)

    Jaana Oikkonen

    Full Text Available Creative activities in music represent a complex cognitive function of the human brain, whose biological basis is largely unknown. In order to elucidate the biological background of creative activities in music we performed genome-wide linkage and linkage disequilibrium (LD scans in musically experienced individuals characterised for self-reported composing, arranging and non-music related creativity. The participants consisted of 474 individuals from 79 families, and 103 sporadic individuals. We found promising evidence for linkage at 16p12.1-q12.1 for arranging (LOD 2.75, 120 cases, 4q22.1 for composing (LOD 2.15, 103 cases and Xp11.23 for non-music related creativity (LOD 2.50, 259 cases. Surprisingly, statistically significant evidence for linkage was found for the opposite phenotype of creative activity in music (neither composing nor arranging; NCNA at 18q21 (LOD 3.09, 149 cases, which contains cadherin genes like CDH7 and CDH19. The locus at 4q22.1 overlaps the previously identified region of musical aptitude, music perception and performance giving further support for this region as a candidate region for broad range of music-related traits. The other regions at 18q21 and 16p12.1-q12.1 are also adjacent to the previously identified loci with musical aptitude. Pathway analysis of the genes suggestively associated with composing suggested an overrepresentation of the cerebellar long-term depression pathway (LTD, which is a cellular model for synaptic plasticity. The LTD also includes cadherins and AMPA receptors, whose component GSG1L was linked to arranging. These results suggest that molecular pathways linked to memory and learning via LTD affect music-related creative behaviour. Musical creativity is a complex phenotype where a common background with musicality and intelligence has been proposed. Here, we implicate genetic regions affecting music-related creative behaviour, which also include genes with neuropsychiatric associations. We

  9. Shrinkage Reducing Admixture for Concrete

    OpenAIRE

    ECT Team, Purdue

    2007-01-01

    Concrete shrinkage cracking is a common problem in all types of concrete structures, especially for structures and environments where the cracks are prevalent and the repercussions are most severe. A liquid shrinkage reducing admixture for concrete, developed by GRACE Construction Products and ARCO Chemical Company, that reduces significantly the shrinkage during concrete drying and potentially reduces overall cracking over time.

  10. Effects of Shrinkage Reducing Agent and Expansive Admixture on the Volume Deformation of Ultrahigh Performance Concrete

    OpenAIRE

    Anshuang, Su; Ling, Qin; Shoujie, Zhang; Jiayang, Zhang; Zhaoyu, Li

    2017-01-01

    This paper investigated the influences of shrinkage reducing agent and expansive admixture on autogenous and drying shrinkage of ultrahigh performance concrete (UHPC) containing antifoaming admixture. The shrinkage reducing agent was used at dosage of 0.5%, 1%, and 2% and the expansive admixture was used at dosage of 2% to 4% by mass of cementitious material. The results show that the air content of UHPC increases with the higher addition of shrinkage reducing agent and expansive admixtures. ...

  11. Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Mensberg, Karen-Lise Dons

    2009-01-01

    , but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943-1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pair-wise F-ST of 0.047 and 0.053). By analysing...... a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals...... nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor...

  12. The Family Investigation of Nephropathy and Diabetes (FIND): design and methods.

    Science.gov (United States)

    Knowler, William C; Coresh, Josef; Elston, Robert C; Freedman, Barry I; Iyengar, Sudha K; Kimmel, Paul L; Olson, Jane M; Plaetke, Rosemarie; Sedor, John R; Seldin, Michael F

    2005-01-01

    The Family Investigation of Nephropathy and Diabetes (FIND) is a multicenter study designed to identify genetic determinants of diabetic nephropathy. It is conducted in eight U.S. clinical centers and a coordinating center, and with four ethnic groups (European Americans, African Americans, Mexican Americans, and American Indians). Two strategies are used to localize susceptibility genes: a family-based linkage study and a case-control study using mapping by admixture linkage disequilibrium (MALD). In the family-based study, probands with diabetic nephropathy are recruited with their parents and selected siblings. Linkage analyses will be conducted to identify chromosomal regions containing genes that influence the development of diabetic nephropathy or related quantitative traits such as serum creatinine concentration, urinary albumin excretion, and plasma glucose concentrations. Regions showing evidence of linkage will be examined further with both genetic linkage and association studies to identify genes that influence diabetic nephropathy or related traits. Two types of MALD studies are being done. One is a case-control study of unrelated individuals of Mexican American heritage in which both cases and controls have diabetes, but only the case has nephropathy. The other is a case-control study of African American patients with nephropathy (cases) and their spouses (controls) unaffected by diabetes and nephropathy; offspring are genotyped when available to provide haplotype data. Identification of genes that influence susceptibility to diabetic nephropathy will lead to a better understanding of how nephropathy develops. This should eventually lead to improved treatment and prevention.

  13. Validation of the polysemen admixture on viability and acrosomal morphology of boar spermatozoa

    Directory of Open Access Journals (Sweden)

    Ogbuewu IP

    2007-07-01

    Full Text Available Semen were collected using artificial vagina (AV, from 5 large white boars aged 2-2.5 years twice a week for 16 weeks in each of the two seasons, early rainy (ER and late rainy (LR seasons, to determine the effects of multiple semen pool admixture on the viability and acrosomal morphology. The semen qualities studied were sperm motility, live sperm and sperm concentration, while the acrosomal parameters includes normal apical ridge (NAR, damaged apical ridge (DAR, missing apical ridge (MAR and loose apical ridge (LAC. There were no significant (P>0.05 seasonal effects. Three-boar semen admixture gave the highest percentage NAR, motility, live sperm concentration and least DAR and LAC, although these were not significantly (P>0.05 different from the 2-boar semen admixture. The result of this study suggests that 3-boar semen admixture is most suitable for use in artificial insemination program.

  14. Effects of Admixtures on the Properties of Corn Cob Ash Cement Concrete

    Directory of Open Access Journals (Sweden)

    Akeem Ayinde RAHEEM

    2010-12-01

    Full Text Available The study investigated the effects of admixtures on the properties of corn cob ash (CCA cement concrete. The workability and compressive strength of CCA cement concrete incorporated with accelerator, plasticizer and water reducing and retarding were carried out. The dosage of admixture incorporated was: 0.124litre per 15.55kg of cementitious material based on the recommendation by BS EN 934-2.The results revealed that admixtures generally improve the workability of corn cob ash cement concrete. The compressive strength obtained at 28th day for concrete without admixture (The Control was 29.82N/mm2, while for concrete with accelerator, plasticizer, and water reducing and retarding it was 32.80 N/mm2, 38.51 N/mm2 and 34.09 N/mm2 respectively. These results showed that CCA cement concrete incorporated with accelerator achieved greater strength at early ages. With plasticizer, it achieved very high strength at both young and old ages; while with water reducing and retarding it achieved greater strength at old ages alone.

  15. GeneRecon Users' Manual — A coalescent based tool for fine-scale association mapping

    DEFF Research Database (Denmark)

    Mailund, T

    2006-01-01

    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of th...

  16. A Novel Admixture-Based Pharmacogenetic Approach to Refine Warfarin Dosing in Caribbean Hispanics

    Science.gov (United States)

    Claudio-Campos, Karla; Rivera-Miranda, Giselle; Bermúdez-Bosch, Luis; Renta, Jessicca Y.; Cadilla, Carmen L.; Cruz, Iadelisse; Feliu, Juan F.; Vergara, Cunegundo; Ruaño, Gualberto

    2016-01-01

    Aim This study is aimed at developing a novel admixture-adjusted pharmacogenomic approach to individually refine warfarin dosing in Caribbean Hispanic patients. Patients & Methods A multiple linear regression analysis of effective warfarin doses versus relevant genotypes, admixture, clinical and demographic factors was performed in 255 patients and further validated externally in another cohort of 55 individuals. Results The admixture-adjusted, genotype-guided warfarin dosing refinement algorithm developed in Caribbean Hispanics showed better predictability (R2 = 0.70, MAE = 0.72mg/day) than a clinical algorithm that excluded genotypes and admixture (R2 = 0.60, MAE = 0.99mg/day), and outperformed two prior pharmacogenetic algorithms in predicting effective dose in this population. For patients at the highest risk of adverse events, 45.5% of the dose predictions using the developed pharmacogenetic model resulted in ideal dose as compared with only 29% when using the clinical non-genetic algorithm (pwarfarin dose variance when externally validated in 55 individuals from an independent validation cohort (MAE = 0.89 mg/day, 24% mean bias). Conclusions Results supported our rationale to incorporate individual’s genotypes and unique admixture metrics into pharmacogenetic refinement models in order to increase predictability when expanding them to admixed populations like Caribbean Hispanics. Trial Registration ClinicalTrials.gov NCT01318057 PMID:26745506

  17. Creative Activities in Music – A Genome-Wide Linkage Analysis

    Science.gov (United States)

    Oikkonen, Jaana; Kuusi, Tuire; Peltonen, Petri; Raijas, Pirre; Ukkola-Vuoti, Liisa; Karma, Kai; Onkamo, Päivi; Järvelä, Irma

    2016-01-01

    Creative activities in music represent a complex cognitive function of the human brain, whose biological basis is largely unknown. In order to elucidate the biological background of creative activities in music we performed genome-wide linkage and linkage disequilibrium (LD) scans in musically experienced individuals characterised for self-reported composing, arranging and non-music related creativity. The participants consisted of 474 individuals from 79 families, and 103 sporadic individuals. We found promising evidence for linkage at 16p12.1-q12.1 for arranging (LOD 2.75, 120 cases), 4q22.1 for composing (LOD 2.15, 103 cases) and Xp11.23 for non-music related creativity (LOD 2.50, 259 cases). Surprisingly, statistically significant evidence for linkage was found for the opposite phenotype of creative activity in music (neither composing nor arranging; NCNA) at 18q21 (LOD 3.09, 149 cases), which contains cadherin genes like CDH7 and CDH19. The locus at 4q22.1 overlaps the previously identified region of musical aptitude, music perception and performance giving further support for this region as a candidate region for broad range of music-related traits. The other regions at 18q21 and 16p12.1-q12.1 are also adjacent to the previously identified loci with musical aptitude. Pathway analysis of the genes suggestively associated with composing suggested an overrepresentation of the cerebellar long-term depression pathway (LTD), which is a cellular model for synaptic plasticity. The LTD also includes cadherins and AMPA receptors, whose component GSG1L was linked to arranging. These results suggest that molecular pathways linked to memory and learning via LTD affect music-related creative behaviour. Musical creativity is a complex phenotype where a common background with musicality and intelligence has been proposed. Here, we implicate genetic regions affecting music-related creative behaviour, which also include genes with neuropsychiatric associations. We also propose

  18. Techniques and methods of characterization of admixtures for the concrete

    OpenAIRE

    Palacios, M.; Sierra, C.; Puertas, F.

    2003-01-01

    Admixtures are defined as those products that are incorporated in the moment of the process of mixture of the concrete in a quantity not bigger than 5 by mass of the cement %, with relationship to the cement content in the concrete, with object of modifying the properties of the mixture in .state fresh and/or hardened. The behaviour of the admixtures depends on its chemical and ionic composition, the organic functional groups present, and the structure of the polymer and the distribution of m...

  19. Chemical evolution of the Earth: Equilibrium or disequilibrium process?

    Science.gov (United States)

    Sato, M.

    1985-01-01

    To explain the apparent chemical incompatibility of the Earth's core and mantle or the disequilibrium process, various core forming mechanisms have been proposed, i.e., rapid disequilibrium sinking of molten iron, an oxidized core or protocore materials, and meteorite contamination of the upper mantle after separation from the core. Adopting concepts used in steady state thermodynamics, a method is devised for evaluating how elements should distribute stable in the Earth's interior for the present gradients of temperature, pressure, and gravitational acceleration. Thermochemical modeling gives useful insights into the nature of chemical evolution of the Earth without overly speculative assumptions. Further work must be done to reconcile siderophile elements, rare gases, and possible light elements in the outer core.

  20. Hydration of mineral shrinkage-compensating admixture for concrete : an experimental and numerical study

    NARCIS (Netherlands)

    Chen, Wei; Brouwers, H.J.H.

    2012-01-01

    The use of shrinkage-compensating admixture in concrete has been proven to be an effective way to mitigate the shrinkage of concrete. The hydration of a shrinkage-compensating admixture in cement paste and concrete is investigated in this paper with numerical simulation and experimental study. An

  1. Uranium series disequilibrium: Concepts and applications

    International Nuclear Information System (INIS)

    Ivanovich, M.

    1994-01-01

    During the past four decades it has been recognized that natural disruption of the U and Th decay chains, resulting in the separation of parent and daughter nuclides, occurs as a consequence of geochemical processes acting in the near-surface environment. This realization has lead to a rapid growth in the application of the naturally occurring radioactive disequilibria diversifying broadly to touch upon a wide spectrum of problems in earth sciences. This paper is a brief review of the subject and addresses a number of issues concerning (1) physico-chemical processes responsible for fractionation of radionuclides in the decay series, (2) the range of observed radioactive disequilibrium in nature, (3) implications in terms of relative mobilities of U, Th, Ra and their daughters in the geosphere, and (4) examples of the application of these concepts to studies of paleoclimate, dating of old groundwaters, and rock/water interaction processes. This review concludes that the concept of radioactive disequilibrium in naturally occurring decay series is a powerful isotopic tool with applications in both terrestrial and marine environments over timescales of up to one million years. (orig.)

  2. Complex Patterns of Admixture across the Indonesian Archipelago

    Science.gov (United States)

    Hudjashov, Georgi; Karafet, Tatiana M.; Lawson, Daniel J.; Downey, Sean; Savina, Olga; Sudoyo, Herawati; Lansing, J. Stephen; Hammer, Michael F.; Cox, Murray P.

    2017-01-01

    Abstract Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups. PMID:28957506

  3. When to conduct probabilistic linkage vs. deterministic linkage? A simulation study.

    Science.gov (United States)

    Zhu, Ying; Matsuyama, Yutaka; Ohashi, Yasuo; Setoguchi, Soko

    2015-08-01

    When unique identifiers are unavailable, successful record linkage depends greatly on data quality and types of variables available. While probabilistic linkage theoretically captures more true matches than deterministic linkage by allowing imperfection in identifiers, studies have shown inconclusive results likely due to variations in data quality, implementation of linkage methodology and validation method. The simulation study aimed to understand data characteristics that affect the performance of probabilistic vs. deterministic linkage. We created ninety-six scenarios that represent real-life situations using non-unique identifiers. We systematically introduced a range of discriminative power, rate of missing and error, and file size to increase linkage patterns and difficulties. We assessed the performance difference of linkage methods using standard validity measures and computation time. Across scenarios, deterministic linkage showed advantage in PPV while probabilistic linkage showed advantage in sensitivity. Probabilistic linkage uniformly outperformed deterministic linkage as the former generated linkages with better trade-off between sensitivity and PPV regardless of data quality. However, with low rate of missing and error in data, deterministic linkage performed not significantly worse. The implementation of deterministic linkage in SAS took less than 1min, and probabilistic linkage took 2min to 2h depending on file size. Our simulation study demonstrated that the intrinsic rate of missing and error of linkage variables was key to choosing between linkage methods. In general, probabilistic linkage was a better choice, but for exceptionally good quality data (<5% error), deterministic linkage was a more resource efficient choice. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. The importance of a sub-region on chromosome 19q13.3 for prognosis of multiple myeloma patients after high-dose treatment and stem cell support: a linkage disequilibrium mapping in RAI and CD3EAP

    DEFF Research Database (Denmark)

    Vangsted, Annette Juul; Klausen, Tobias Wirenfeldt; Gimsing, Peter

    2011-01-01

    The gene RAI was originally described as an inhibitor of RelA/p65 subunit of nuclear factor ¿B (NF-¿B). Here, we analyse the association between genetic variation in the genes RAI and CD3EAP and outcome of 348 myeloma patients treated with high-dose treatment (HDT), 146 patients treated with inte......The gene RAI was originally described as an inhibitor of RelA/p65 subunit of nuclear factor ¿B (NF-¿B). Here, we analyse the association between genetic variation in the genes RAI and CD3EAP and outcome of 348 myeloma patients treated with high-dose treatment (HDT), 146 patients treated...... with interferon-a (INF-a) as maintenance treatment, 177 patients treated with thalidomide, and 74 patients treated with bortezomib at relapse and address if the effects of polymorphisms in CD3EAP and RAI are modified by a functional polymorphism in NF¿B1. By linkage disequilibrium mapping, we found that variant...... alleles of several polymorphisms in a sub-region of 19q13.3 spanning the regions RAI-intron1-1 to RAI intron1-3 and the region exon1 to exon3-6 in CD3EAP were associated with prolonged time-to-treatment failure (TTF; p¿=¿0.003) and overall survival (OS; p¿=¿0.02). Haplotype analyses revealed that none...

  5. The importance of a sub-region on chromosome 19q13.3 for prognosis of multiple myeloma patients after high-dose treatment and stem cell support: a linkage disequilibrium mapping in RAI and CD3EAP

    DEFF Research Database (Denmark)

    Vangsted, Annette J.; Klausen, Tobias Wirenfeldt; Gimsing, Peter

    2011-01-01

    The gene RAI was originally described as an inhibitor of RelA/p65 subunit of nuclear factor κB (NF–κB). Here, we analyse the association between genetic variation in the genes RAI and CD3EAP and outcome of 348 myeloma patients treated with high-dose treatment (HDT), 146 patients treated with inte......The gene RAI was originally described as an inhibitor of RelA/p65 subunit of nuclear factor κB (NF–κB). Here, we analyse the association between genetic variation in the genes RAI and CD3EAP and outcome of 348 myeloma patients treated with high-dose treatment (HDT), 146 patients treated...... with interferon-α (INF-α) as maintenance treatment, 177 patients treated with thalidomide, and 74 patients treated with bortezomib at relapse and address if the effects of polymorphisms in CD3EAP and RAI are modified by a functional polymorphism in NFКB1. By linkage disequilibrium mapping, we found that variant...... alleles of several polymorphisms in a sub-region of 19q13.3 spanning the regions RAI-intron1-1 to RAI intron1-3 and the region exon1 to exon3–6 in CD3EAP were associated with prolonged time-to-treatment failure (TTF; p = 0.003) and overall survival (OS; p = 0.02). Haplotype analyses revealed that none...

  6. Tests of fit of historically-informed models of African American Admixture.

    Science.gov (United States)

    Gross, Jessica M

    2018-02-01

    African American populations in the U.S. formed primarily by mating between Africans and Europeans over the last 500 years. To date, studies of admixture have focused on either a one-time admixture event or continuous input into the African American population from Europeans only. Our goal is to gain a better understanding of the admixture process by examining models that take into account (a) assortative mating by ancestry in the African American population, (b) continuous input from both Europeans and Africans, and (c) historically informed variation in the rate of African migration over time. We used a model-based clustering method to generate distributions of African ancestry in three samples comprised of 147 African Americans from two published sources. We used a log-likelihood method to examine the fit of four models to these distributions and used a log-likelihood ratio test to compare the relative fit of each model. The mean ancestry estimates for our datasets of 77% African/23% European to 83% African/17% European ancestry are consistent with previous studies. We find admixture models that incorporate continuous gene flow from Europeans fit significantly better than one-time event models, and that a model involving continuous gene flow from Africans and Europeans fits better than one with continuous gene flow from Europeans only for two samples. Importantly, models that involve continuous input from Africans necessitate a higher level of gene flow from Europeans than previously reported. We demonstrate that models that take into account information about the rate of African migration over the past 500 years fit observed patterns of African ancestry better than alternative models. Our approach will enrich our understanding of the admixture process in extant and past populations. © 2017 Wiley Periodicals, Inc.

  7. Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression.

    Science.gov (United States)

    Hüls, Anke; Ickstadt, Katja; Schikowski, Tamara; Krämer, Ursula

    2017-06-12

    SNPs estimated by a multivariate elastic net regression were shown to be a powerful tool to detect gene-environment interactions in scenarios of high Linkage disequilibrium and noise.

  8. Effects of lithium nitrate admixture on early-age cement hydration

    International Nuclear Information System (INIS)

    Millard, M.J.; Kurtis, K.E.

    2008-01-01

    Although the benefits of lithium admixtures for mitigation of alkali-silica reaction (ASR) have been well documented, the potential ancillary effects of lithium compounds on cement and concrete remain largely uncharacterized. To examine the effects of the most common lithium admixture - lithium nitrate - on early-age behavior, the admixture was introduced at dosages of 0% to 400% of the recommended dosage to six cements of varying composition and to a cement-fly ash blend. Behavior was examined by isothermal calorimetry and measurements of chemical shrinkage, autogenous shrinkage, and setting time. Results indicate that lithium nitrate accelerates the early hydration of most cements but may retard hydration after 24 h. In the lowest alkali cement tested, set times were shortened in the presence of lithium nitrate by 15-22%. Higher dosages appeared to increase autogenous shrinkage after 40 days. The replacement of cement by Class F fly ash at 20% by weight appeared to diminish the early acceleration effects, but later hydration retardation and autogenous shrinkage were still observed

  9. Admixture enhanced controlled low-strength material for direct underwater injection with minimal cross-contamination

    International Nuclear Information System (INIS)

    Hepworth, H.K.; Davidson, J.S.; Hooyman, J.L.

    1997-01-01

    Commercially available admixtures have been developed for placing traditional concrete products under water. This paper evaluates adapting anti-washout admixture (AWA) and high range water reducing admixture (HRWRA) products to enhance controlled low-strength materials (CLSMs) for underwater placement. A simple experimental scale model (based on dynamic and geometric similitude) of typical grout pump emplacement equipment has been developed to determine the percentage of cementing material washed out. The objective of this study was to identify proportions of admixtures and underwater CLSM emplacement procedures which would minimize the cross-contamination of the displaced water while maintaining the advantages of CLSM. Since the displaced water from radioactively contaminated systems must be subsequently treated prior to release to the environment, the amount of cross-contamination is important for cases in which cementing material could form hard sludges in a water treatment facility and contaminate the in-place CLSM stabilization medium

  10. Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture.

    Directory of Open Access Journals (Sweden)

    John E Pool

    Full Text Available Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia, while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa F(ST were found to be enriched in genomic regions of locally

  11. Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

    Science.gov (United States)

    Pool, John E.; Corbett-Detig, Russell B.; Sugino, Ryuichi P.; Stevens, Kristian A.; Cardeno, Charis M.; Crepeau, Marc W.; Duchen, Pablo; Emerson, J. J.; Saelao, Perot; Begun, David J.; Langley, Charles H.

    2012-01-01

    Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan

  12. Recycling of tailings from Korea Molybdenum Corporation as admixture for high-fluidity concrete.

    Science.gov (United States)

    Jung, Moon Young; Choi, Yun Wang; Jeong, Jae Gwon

    2011-01-01

    The main objective of this study is to develop an eco-friendly and a large recycling technique of flotation Tailings from korea (TK) from metal mines as construction materials such as admixtures for high-fluidity concrete (HFC). TK used in this study was obtained from the Korea Molybdenum Corporation in operation. TK was used as the alternative material to adjust flowability and viscosity of HFC in the form of powder agent which enables adjustment of concrete compressive strength. In this study, we have performed concrete rheological tests and concrete flowability tests to obtain the quality characteristics of TK for using as the admixture in producing HFC. The results indicated that the adequate mix ratio of cement to TK should be 8:2 (vol%). It is more effective to use the TK as admixture to control flowability, viscosity and strength of HFC than the normal concrete. It was found that TK could be recycled construction materials in bulk such as admixture for HFC, in terms of the economic and eco-friendly aspects.

  13. Experimental study on durability improvement of fly ash concrete with durability improving admixture.

    Science.gov (United States)

    Quan, Hong-zhu; Kasami, Hideo

    2014-01-01

    In order to improve the durability of fly ash concrete, a series of experimental studies are carried out, where durability improving admixture is used to reduce drying shrinkage and improve freezing-thawing resistance. The effects of durability improving admixture, air content, water-binder ratio, and fly ash replacement ratio on the performance of fly ash concrete are discussed in this paper. The results show that by using durability improving admixture in nonair-entraining fly ash concrete, the compressive strength of fly ash concrete can be improved by 10%-20%, and the drying shrinkage is reduced by 60%. Carbonation resistance of concrete is roughly proportional to water-cement ratio regardless of water-binder ratio and fly ash replacement ratio. For the specimens cured in air for 2 weeks, the freezing-thawing resistance is improved. In addition, by making use of durability improving admixture, it is easier to control the air content and make fly ash concrete into nonair-entraining one. The quality of fly ash concrete is thereby optimized.

  14. PCE and BNS admixture adsorption in sands with different composition and particle size distribution

    International Nuclear Information System (INIS)

    Alonso, M.M.; Martínez-Gaitero, R.; Gismera-Diez, S.; Puertas, F.

    2017-01-01

    The choice of a superplasticiser (SP) for concrete is of great complexity, as it is well known that properties of the end product are related to admixture and its compatibility with concrete components. Very few studies have been conducted on the compatibility between SPs and the sand of mortars and concretes, however. Practical experience has shown that sand fineness and mineralogical composition affect water demand and admixture consumption. Clay-containing sand has been found also to adsorb SPs, reducing the amount available in solution for adsorption by the cement. This study analysed the isotherms for PCE and BNS superplasticiser adsorption on four sands with different fineness and compositions commonly used to prepare mortars and concretes. BNS-based SP did not adsorb on sands, while PCE-based admixtures exhibited variable adsorption depending on different factors. The adsorption curves obtained revealed that the higher the sand fineness, the finer the particle size distribution and the higher the clay material, the greater was PCE admixture adsorption/ consumption. [es

  15. PCE and BNS admixture adsorption in sands with different composition and particle size distribution

    Directory of Open Access Journals (Sweden)

    M. M. Alonso

    2017-02-01

    Full Text Available The choice of a superplasticiser (SP for concrete is of great complexity, as it is well known that properties of the end product are related to admixture and its compatibility with concrete components. Very few studies have been conducted on the compatibility between SPs and the sand of mortars and concretes, however. Practical experience has shown that sand fineness and mineralogical composition affect water demand and admixture consumption. Clay-containing sand has been found also to adsorb SPs, reducing the amount available in solution for adsorption by the cement. This study analysed the isotherms for PCE and BNS superplasticiser adsorption on four sands with different fineness and compositions commonly used to prepare mortars and concretes. BNS-based SP did not adsorb on sands, while PCE-based admixtures exhibited variable adsorption depending on different factors. The adsorption curves obtained revealed that the higher the sand fineness, the finer the particle size distribution and the higher the clay material, the greater was PCE admixture adsorption/ consumption.

  16. A theoretical treatment of interval mapping of a disease gene using ...

    Indian Academy of Sciences (India)

    The genetic basis of the transmission disequilibrium test (TDT) for two-marker loci is explored from first principles. In this case, parents doubly heterozygous for a given haplotype at the pair of marker loci that are each in linkage disequilibrium with the disease gene with the further possibility of a second-order linkage ...

  17. Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studies

    Directory of Open Access Journals (Sweden)

    Gonzalez-Neira Anna

    2007-08-01

    Full Text Available Abstract Background The recent development of new high-throughput technologies for SNP genotyping has opened the possibility of taking a genome-wide linkage approach to the search for new candidate genes involved in heredity diseases. The two major breast cancer susceptibility genes BRCA1 and BRCA2 are involved in 30% of hereditary breast cancer cases, but the discovery of additional breast cancer predisposition genes for the non-BRCA1/2 breast cancer families has so far been unsuccessful. Results In order to evaluate the power improvement provided by using SNP markers in a real situation, we have performed a whole genome screen of 19 non-BRCA1/2 breast cancer families using 4720 genomewide SNPs with Illumina technology (Illumina's Linkage III Panel, with an average distance of 615 Kb/SNP. We identified six regions on chromosomes 2, 3, 4, 7, 11 and 14 as candidates to contain genes involved in breast cancer susceptibility, and additional fine mapping genotyping using microsatellite markers around linkage peaks confirmed five of them, excluding the region on chromosome 3. These results were consistent in analyses that excluded SNPs in high linkage disequilibrium. The results were compared with those obtained previously using a 10 cM microsatellite scan (STR-GWS and we found lower or not significant linkage signals with STR-GWS data compared to SNP data in all cases. Conclusion Our results show the power increase that SNPs can supply in linkage studies.

  18. ADSORPTION OF CHROMIUM (VI FROM AQUEOUS SOLUTIONS BY DIFFERENT ADMIXTURES – A BATCH EQUILIBRIUM TEST STUDY

    Directory of Open Access Journals (Sweden)

    K. SHIVA PRASHANTH KUMAR

    2014-08-01

    Full Text Available Wide variety of inorganic compounds such as nutrients and trace metals, organic chemicals, radioactive contaminants and pathogens are commonly present as contaminants in the groundwater. Migration of contaminants in soil involves important mechanisms such as molecular diffusion, dispersion under physical processes, adsorption, precipitation and oxidation - reduction under chemical processes and biodegradation under biological process. Cr (VI is a major and dangerous contaminant as per the ground water is concerned. There are numerous research work carried out with concentrated efforts by the researchers towards removal of Cr (VI contaminant from aqueous solutions. There are few studies relevant to Cr (VI removal with respect to utilization of low cost admixtures and also soil type. In the present study, different low cost admixtures like rice husk (RH, shredded tyre (ST and fly ash (FA are used to understand the performance in removal of Cr (VI from aqueous solution and also two different soil types are used along with the admixture. The results are discussed in terms of sorption capacity and performance of individual admixture and combination of admixture with soil in removal of contaminant. The fly ash, rice husk and shredded tyre admixtures are used and the results revealed that the shredded tyre showed higher performance in removal of contaminant concentration. Also, the soil which has more fine particle content (size<0.075 mm IS sieve showed reasonable reduction in concentration of contaminant at the lower levels of contaminant initial concentration. The sorption capacity results of Cr (VI contaminant, treated with various admixtures are further validated with the published work of other investigators. The shredded tyre (ST showed more adsorption capacity, i.e., 3.283 mg/g at pH of 4.8. For other admixtures, adsorption capacity value is varying in the range of 0.07 mg/g to 1.7 mg/g. Only in case of activated alumina and modified saw dust

  19. Analisis Kuat Tekan Beton Dengan Bahan Tambah Reduced Water Dan Accelerated Admixture

    OpenAIRE

    Rahmat, Rahmat; Hendriyani, Irna; Anwar, Moh. Syaiful

    2016-01-01

    Concrete consist of: cement mortar, coarse aggregate, fine aggregate, water, and addictive materials. The main ingredient in manufacturing of concrete: rock material that called as aggregates. Aggregate has an important role on the quality of the concrete. Various types and trademarks for admixture of concrete that can be used as addictive of the concrete mix with specific purpose. The study aims to determine the effect of the added material of Reduced Water and Accelerated Admixture (Bestmit...

  20. Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.

    Science.gov (United States)

    Onzima, R B; Upadhyay, M R; Mukiibi, R; Kanis, E; Groenen, M A M; Crooijmans, R P M A

    2018-02-01

    Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H O ) and expected (H E ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f 4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes. © 2018 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

  1. Admixture analysis and stocking impact assessment in brown trout ( Salmo trutta ), estimated with incomplete baseline data

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Eg Nielsen, Einar; Bekkevold, Dorte

    2001-01-01

    the populations contributing to admixture. We applied the method to analyse the genetic contribution of domesticated brown trout (Salmo trutta) in samples of anadromous trout from two stocked populations with no genetic data available before stocking. Further, we estimated population level admixture proportions...... by the mean of individual admixture coefficients. This method proved more informative than a multidimensional scaling analysis of individual-based genetic distances and assignment tests. The results showed almost complete absence of stocked, domesticated trout in samples of trout from the rivers. Consequently......, stocking had little effect on improving fisheries. In one population, the genetic contribution by domesticated trout was small, whereas in the other population, some genetic impact was suggested. Admixture in this sample of anadromous trout despite absence of stocked domesticated trout could be because...

  2. Concentration of carbonate admixture from opalized tuff into one separate fraction

    International Nuclear Information System (INIS)

    Bogoevski, Slobodan; Boshkovski, Boshko

    2016-01-01

    White opalized tuff (from the Strmosh locality, Probishtip), as a raw silicate amorphous material, contains some quantity of admixtures. The total quantity of admixtures amounts is about 8% mass. Mine powdery ingredients are homogeneously distributed into the basic silicate mass.Carbonate material is a significant part of present admixtures, and it is possible to be separated with controlled milling. Milling parameters (type and time of milling) enables to concentrate the present CaCO 3 in granulometric fraction<0.032 μm, after 30 min. milling. Reliable evidence about afore mentioned separation is shown with simultaneous view of the results of silicate chemical analysis, DT/TG analysis (750 - 850 °C), and sieve-analysis.From the X-ray analysis it is evident that the present carbonate material exists in crypto crystal to amorphous state. The space where CaCO 3 is hidden, presents the place between basic silicate particles inside the groups, generally with dimensions about 40 to 60 μm. The concentration of CaCO 3 appears when this particle group goes to the process of disintegration. (author)

  3. Probabilistic record linkage.

    Science.gov (United States)

    Sayers, Adrian; Ben-Shlomo, Yoav; Blom, Ashley W; Steele, Fiona

    2016-06-01

    Studies involving the use of probabilistic record linkage are becoming increasingly common. However, the methods underpinning probabilistic record linkage are not widely taught or understood, and therefore these studies can appear to be a 'black box' research tool. In this article, we aim to describe the process of probabilistic record linkage through a simple exemplar. We first introduce the concept of deterministic linkage and contrast this with probabilistic linkage. We illustrate each step of the process using a simple exemplar and describe the data structure required to perform a probabilistic linkage. We describe the process of calculating and interpreting matched weights and how to convert matched weights into posterior probabilities of a match using Bayes theorem. We conclude this article with a brief discussion of some of the computational demands of record linkage, how you might assess the quality of your linkage algorithm, and how epidemiologists can maximize the value of their record-linked research using robust record linkage methods. © The Author 2015; Published by Oxford University Press on behalf of the International Epidemiological Association.

  4. ANALYSIS OF PROPERTIES OF CONCRETE USING DRIED BANANA PEEL POWDER AS ADMIXTURE

    OpenAIRE

    Vishal Gadgihalli; MeenaY.R; Sindhu Shankar; Raghavendra Prasad Havanje Dinakar

    2017-01-01

    Ingredients other than cement, water& aggregates that import a specific quality to either plastic(fresh)mix or the hardened concrete (ASTMC 496) is called concrete admixture. In this paper analysis of properties of concrete using banana peel as admixture is studied and verified the strength of concrete and temperature emitted due to chemical reaction to the normal Portland cement. As banana’s peel is rich in natural fiber and it is well known source of potassium. The flexural strength of conc...

  5. Demographic Disequilibrium in Early Twentieth Century Thailand: Falling Mortality, Rising Fertility, or Both?

    OpenAIRE

    Carmichael, Gordon A.

    2008-01-01

    Estimates of Thai crude birth and death rates date from 1920 when the former was around 20 per thousand higher than the latter, implying natural increase of 2 percent per annum. Such disequilibrium cannot have been the norm over the long term historical past, when population growth must have been comparatively slow. This paper explores the bases for likely past relative equilibrium between Siamese birth and death rates, then seeks to explain the disequilibrium apparent by 1920. Classic demogr...

  6. The influence of oxygen admixture concentration on microdeformation behavior of niobium

    International Nuclear Information System (INIS)

    Ivantsov, V.I.

    2004-01-01

    The microplasticity behavior of solid solutions Nb-O (relative residual deformations ε = 2 centre dot 10 -7 ...10 -4 ) in dependence on oxygen admixture concentration (C = 0,06...1,4 at.% O) was studied. The values of microplastic deformation parameters (precision elastic limit σ E , micro yield stress σ A and elastic module E) of pure niobium and solid solutions Nb-O were determinated. The empiric correlation of dependence σ E and σ A versus oxygen concentration were got. It was discussed the mechanism of oxygen admixture influence on stage nature of microflow and deformation hardening of niobium

  7. Effects of drying conditions, admixtures and specimen size on shrinkage strains

    International Nuclear Information System (INIS)

    Al-Saleh, Saleh A.; Al-Zaid, Rajeh Z.

    2006-01-01

    The paper presents the results of an experimental investigation on the effects of drying conditions, specimen size and presence of plasticizing admixture on the development of shrinkage strains. The measurements are taken in a harsh (50 deg. C and 5% R.H.) and a moderate environment (28 deg. C and 50% R.H.). The results include strain development at various levels of cross sections of concrete prisms. The drying conditions are found to be the dominant parameter affecting the shrinkage strain development particularly in specimens of smaller sizes. The effect of plasticizing admixture on shrinkage strains is negligible

  8. The influence of compound admixtures on the properties of high-content slag cement

    Energy Technology Data Exchange (ETDEWEB)

    Dongxu, L.; Xuequan, W.; Jinlin, S.; Yujiang, W.

    2000-01-01

    Based on the activation theory of alkali and sulfate, the influence of compound admixtures on the properties of high-content slag cement was studied by testing the strength, pore structure, hydrates, and microstructure, Test results show that compound admixtures can obviously improve the properties of high-content slag cement. The emphasis of the present research is two-fold: substituting gypsum with anhydrite and calcining gypsum. These both can improve early and later performance.

  9. Admixture patterns and genetic differentiation in negrito groups from West Malaysia estimated from genome-wide SNP data.

    Science.gov (United States)

    Jinam, Timothy A; Phipps, Maude E; Saitou, Naruya

    2013-01-01

    Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the "negritos" who are believed to be descendants of the earliest settlers of Southeast Asia. Here we report patterns of genetic substructure and admixture in two Malaysian negrito populations (Jehai and Kensiu), using ~50,000 genome-wide single-nucleotide polymorphism (SNP) data. We found traces of recent admixture in both the negrito populations, particularly in the Jehai, with the Malay through principal component analysis and STRUCTURE analysis software, which suggested that the admixture was as recent as one generation ago. We also identified significantly differentiated nonsynonymous SNPs and haplotype blocks related to intracellular transport, metabolic processes, and detection of stimulus. These results highlight the different levels of admixture experienced by the two Malaysian negritos. Delineating admixture and differentiated genomic regions should be of importance in designing and interpretation of molecular anthropology and disease association studies. Copyright © 2013 Wayne State University Press, Detroit, Michigan 48201-1309.

  10. Thermal properties of alkali-activated aluminosilicates with CNT admixture

    Science.gov (United States)

    Zmeskal, Oldrich; Trhlikova, Lucie; Fiala, Lukas; Florian, Pavel; Cerny, Robert

    2017-07-01

    Material properties of electrically conductive cement-based materials with increased attention paid on electric and thermal properties were often studied in the last years. Both electric and thermal properties play an important role thanks to their possible utilization in various practical applications (e.g. snow-melting systems or building structures monitoring systems without the need of an external monitoring system). The DC/AC characteristics depend significantly on the electrical resistivity and the electrical capacity of bulk materials. With respect to the DC/AC characteristics of cement-based materials, such materials can be basically classified as electric insulators. In order to enhance them, various conductive admixtures such as those based on different forms of carbon, can be used. Typical representatives of carbon-based admixtures are carbon nanotubes (CNT), carbon fibers (CF), graphite powder (GP) and carbon black (CB). With an adequate amount of such admixtures, electric properties significantly change and new materials with higher added value can be prepared. However, other types of materials can be enhanced in the same way. Alkali-activated aluminosilicates (AAA) based on blast furnace slag are materials with high compressive strength comparable with cement-based materials. Moreover, the price of slag is lower than of Portland cement. Therefore, this paper deals with the study of thermal properties of this promising material with different concentrations of CNT. Within the paper a simple method of basic thermal parameters determination based on the thermal transient response to a heat power step is presented.

  11. Prestressed concrete bridge beams with microsilica admixture : final report.

    Science.gov (United States)

    1998-01-01

    Microsilica fume admixture in concrete beams was used in two coastal bridges to reduce chloride permeability. Cylinders were cast from the beam mixture for strength and permeability tests. : The fabricator found no problems with making these beams, e...

  12. Dialysis Disequilibrium Syndrome-Induced Cerebral Edema in a Patient with Uremia Following Hemodialysis: A Case Report

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jung Min; Kim, Heung Cheol [Dept. of Radiology, Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon (Korea, Republic of)

    2012-03-15

    Dialysis disequilibrium syndrome is a metabolic complication that can be caused by rapid removal of plasma urea during hemodialysis. Dialysis disequilibrium syndrome can lead to osmotic demyelinating syndrome. This case report describes one case of encephalopathy accompanied by dialysis disequilibrium syndrome with imaging findings acquired immediately after hemodialysis in a 55-year-old woman with chronic renal failure. The patient was observed to present repetitive seizures and sudden deterioration of consciousness immediately after hemodialysis. Shortly after the onset of symptoms, the patient underwent a CT scan. The imaging findings of the CT scan reveal symmetrical diffuse white matter edema of bilateral cerebral hemispheres that extends to the pons along the internal capsule. A follow-up MRI taken two years later shows that reversible changes without damage have occurred in the lesions. The patient can thus be seen to present symptoms characteristically associated with dialysis disequilibrium syndrome, while brain imaging reveals dif-fuse reversible brain edema.

  13. Research on curing behavior of concrete with anti-frost admixtures at subzero temperature

    Science.gov (United States)

    Ionov, Yulian; Kramar, Ludmila; Kirsanova, Alena; Kolegova, Irina

    2017-01-01

    The purpose of this paper is research on curing behavior of cold-weather concrete with anti-frost admixtures. During the study derivative thermal and X-ray phase analyses were performed and tests were carried out according to the standard GOST technique. The research results obtained reveal the peculiarities of cement hydration and concrete curing at subzero temperatures. The influence of subzero temperatures and anti-frost admixtures on hydrated phases of hardened cement paste and concrete strength formation was studied. It is found that cold-weather concrete does not cure at subzero temperatures, but when defrosting it attains 80 to 85% of its grade strength by the 28th day. Concrete achieves its grade strength when curing in normal conditions in 60 days only. Freezing concrete with anti-frost admixtures results in increase of calcium hydroxide content in hardened cement paste immediately when produced and has increased tendency of concrete to carbonation.

  14. Development of admixture mapping panels for African Americans from commercial high-density SNP arrays

    Directory of Open Access Journals (Sweden)

    Dunston Georgia M

    2010-07-01

    Full Text Available Abstract Background Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels of ancestry-informative markers (AIMs for admixture mapping, markers have to be genotyped de novo for each admixed study sample and samples representing the ancestral parental populations. The increased availability of dense marker data on commercial chips has made it feasible to develop panels wherein the markers need not be predetermined. Results We developed two panels of AIMs (~2,000 markers each based on the Affymetrix Genome-Wide Human SNP Array 6.0 for admixture mapping with African American samples. These two AIM panels had good map power that was higher than that of a denser panel of ~20,000 random markers as well as other published panels of AIMs. As a test case, we applied the panels in an admixture mapping study of hypertension in African Americans in the Washington, D.C. metropolitan area. Conclusions Developing marker panels for admixture mapping from existing genome-wide genotype data offers two major advantages: (1 no de novo genotyping needs to be done, thereby saving costs, and (2 markers can be filtered for various quality measures and replacement markers (to minimize gaps can be selected at no additional cost. Panels of carefully selected AIMs have two major advantages over panels of random markers: (1 the map power from sparser panels of AIMs is higher than that of ~10-fold denser panels of random markers, and (2 clusters can be labeled based on information from the parental populations. With current technology, chip-based genome-wide genotyping is less expensive than genotyping ~20,000 random markers. The major advantage of using random markers is the absence of ascertainment effects resulting from the process of selecting markers. The ability to develop marker panels informative for ancestry from

  15. Direct power comparisons between simple LOD scores and NPL scores for linkage analysis in complex diseases.

    Science.gov (United States)

    Abreu, P C; Greenberg, D A; Hodge, S E

    1999-09-01

    Several methods have been proposed for linkage analysis of complex traits with unknown mode of inheritance. These methods include the LOD score maximized over disease models (MMLS) and the "nonparametric" linkage (NPL) statistic. In previous work, we evaluated the increase of type I error when maximizing over two or more genetic models, and we compared the power of MMLS to detect linkage, in a number of complex modes of inheritance, with analysis assuming the true model. In the present study, we compare MMLS and NPL directly. We simulated 100 data sets with 20 families each, using 26 generating models: (1) 4 intermediate models (penetrance of heterozygote between that of the two homozygotes); (2) 6 two-locus additive models; and (3) 16 two-locus heterogeneity models (admixture alpha = 1.0,.7,.5, and.3; alpha = 1.0 replicates simple Mendelian models). For LOD scores, we assumed dominant and recessive inheritance with 50% penetrance. We took the higher of the two maximum LOD scores and subtracted 0.3 to correct for multiple tests (MMLS-C). We compared expected maximum LOD scores and power, using MMLS-C and NPL as well as the true model. Since NPL uses only the affected family members, we also performed an affecteds-only analysis using MMLS-C. The MMLS-C was both uniformly more powerful than NPL for most cases we examined, except when linkage information was low, and close to the results for the true model under locus heterogeneity. We still found better power for the MMLS-C compared with NPL in affecteds-only analysis. The results show that use of two simple modes of inheritance at a fixed penetrance can have more power than NPL when the trait mode of inheritance is complex and when there is heterogeneity in the data set.

  16. Elements-admixtures of fluorite. Research technique

    International Nuclear Information System (INIS)

    Fayziev, A.R.

    2002-01-01

    Present article is devoted to elements-admixtures of fluorite and research techniques used. As a material for researches the mono mineral samples of fluorite of various geologic deposits and ores were used. The determination of sodium and potassium was conducted by means of flame photometry. Strontium, uranium, thorium, lead and rubidium were determined by means of quantitative X-ray spectroscopic analysis. The barium analysis was conducted by means of quantitative method. The manganese analysis was conducted by means of electron paramagnetic resonance.

  17. Radiological impact of cement, concrete and admixtures in Spain

    International Nuclear Information System (INIS)

    Chinchon-Paya, S.; Piedecausa, B.; Hurtado, S.; Sanjuan, M.A.; Chinchon, S.

    2011-01-01

    It has been analyzed samples of portland cement (PC) with and without admixtures, samples of calcium aluminate cement (CAC) with different content of Al 2 O 3 and specimens of concrete made with PC and CAC using High Resolution Gamma Spectrometry. The activity concentration index (I) is much less than 0.5 mSv y -1 for all the concrete specimens according to the Radiation protection document 112 of the European Commission. The PC without admixtures (CEM I 52,5 R) and the PC with addition of limestone (CEM II/BL 32,5 N) also have an I value much lower than 0.5 and the PC with the addition of fly ash and blast furnace slag (CEM IV/B (V) 32,5 N and III/A 42.5 N/SR) have an I value close to 0.6. The I value of the CAC used in the manufacture of structural precast concrete is of the order of 1 mSv y -1 . Some of the CAC used in refractory concrete reaches a value close to 2 mSv y -1 . - Highlights: → The activity values (I) of spanish portland cement and admixtures studied are similar to those described by other authors. → For the first time in scientific publications we have shown results of several calcium aluminate cements (CAC). → CAC used in structural concrete has an approximate I value = 1 (similar to blast furnace slag and fly ash). → One type of CAC with Al 2 O 3 content of 51% used in refractory concretes has a value of I = 2.

  18. Subsidiary Linkage Patterns

    DEFF Research Database (Denmark)

    Andersson, Ulf; Perri, Alessandra; Nell, Phillip C.

    2012-01-01

    channels for spillovers to competitors. We find a curvilinear relationship between the extent of competitive pressure and the quality of a subsidiary's set of local linkages. Furthermore, the extent to which a subsidiary possesses capabilities moderates this relationship: Very capable subsidiaries...... in strongly competitive environments tend to shy away from high quality linkages. We discuss our findings in light of the literature on spillovers and inter-organizational linkages.......This paper investigates the pattern of subsidiaries' local vertical linkages under varying levels of competition and subsidiary capabilities. Contrary to most previous literature, we explicitly account for the double role of such linkages as conduits of learning prospects as well as potential...

  19. Effectiveness of shrinkage-reducing admixtures on Portland pozzolan cement concrete

    Directory of Open Access Journals (Sweden)

    Videla, C.

    2005-06-01

    Full Text Available Drying shrinkage causes tensile stress in restrained concrete members. Since all structural elements are subject to some degree of restraint, drying shrinkage is regarded to be one of the main causes of concrete cracking. The purpose of the present study was to evaluate the effectiveness of SRA in reducing drying shrinkage strain in Portland pozzolan cement concrete. The major variables examined included slump, admixture type and dose, and specimen size. The measured results indicate that any of the admixtures used in the study significantly reduced shrinkage. Concrete manufactured with shrinkage reducing admixtures shrank an average of 43% less than concrete without admixtures. As a rule, the higher the dose of admixture, the higher was its shrinkage reduction performance. The experimental results were compared to the shrinkage strain estimated with the ACI 209, CEB MC 90, B3, GL 2000, Sakata 1993 and Sakata 2001 models. Although none of these models was observed to accurately describe the behaviour of Portland pozzolan cement concrete with shrinkage reducing admixtures, the Sakata 2001 model, with a weighted coefficient of variation of under 30%, may be regarded to be roughly adequate.

    La retracción por secado es un fenómeno intrínseco del hormigón que produce tensiones de tracción en elementos restringidos de hormigón. Puesto que todos los elementos presentan algún grado de retracción, se considera a la retracción por secado como una de las principales causas de agrietamiento en proyectos de construcción en hormigón. Por lo tanto, el objetivo de esta investigación fue evaluar la efectividad de los aditivos reductores de retracción (SRA en hormigones fabricados con cemento Portland puzolánico. Las variables principales estudiadas incluyen el asentamiento de cono de Abrams, marca y dosis de aditivo reductor de retracción, y tamaño de espécimen de hormigón. Los resultados obtenidos permiten concluir que el uso de

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

    Science.gov (United States)

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

    2014-10-02

    The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  1. Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age.

    Science.gov (United States)

    Cahill, James A; Heintzman, Peter D; Harris, Kelley; Teasdale, Matthew D; Kapp, Joshua; Soares, Andre E R; Stirling, Ian; Bradley, Daniel; Edwards, Ceiridwen J; Graim, Kiley; Kisleika, Aliaksandr A; Malev, Alexander V; Monaghan, Nigel; Green, Richard E; Shapiro, Beth

    2018-05-01

    Recent genomic analyses have provided substantial evidence for past periods of gene flow from polar bears (Ursus maritimus) into Alaskan brown bears (Ursus arctos), with some analyses suggesting a link between climate change and genomic introgression. However, because it has mainly been possible to sample bears from the present day, the timing, frequency, and evolutionary significance of this admixture remains unknown. Here, we analyze genomic DNA from three additional and geographically distinct brown bear populations, including two that lived temporally close to the peak of the last ice age. We find evidence of admixture in all three populations, suggesting that admixture between these species has been common in their recent evolutionary history. In addition, analyses of ten fossil bears from the now-extinct Irish population indicate that admixture peaked during the last ice age, whereas brown bear and polar bear ranges overlapped. Following this peak, the proportion of polar bear ancestry in Irish brown bears declined rapidly until their extinction. Our results support a model in which ice age climate change created geographically widespread conditions conducive to admixture between polar bears and brown bears, as is again occurring today. We postulate that this model will be informative for many admixing species pairs impacted by climate change. Our results highlight the power of paleogenomics to reveal patterns of evolutionary change that are otherwise masked in contemporary data.

  2. Performance of alusilica as mineral admixture in cementitious systems

    DEFF Research Database (Denmark)

    Chi, Lin; Jensen, Ole Mejlhede

    2016-01-01

    This paper presents a preliminary study of the effect of alusilica (ALS) as a mineral admixture on the fresh properties and development of mechanical properties of cementitious systems. Cement was substituted with ALS with the ratio of 10% during grinding or blended during mixing. The produced ALS...

  3. Chemical, Mechanical, and Durability Properties of Concrete with Local Mineral Admixtures under Sulfate Environment in Northwest China.

    Science.gov (United States)

    Nie, Qingke; Zhou, Changjun; Shu, Xiang; He, Qiang; Huang, Baoshan

    2014-05-13

    Over the vast Northwest China, arid desert contains high concentrations of sulfate, chloride, and other chemicals in the ground water, which poses serious challenges to infrastructure construction that routinely utilizes portland cement concrete. Rapid industrialization in the region has been generating huge amounts of mineral admixtures, such as fly ash and slags from energy and metallurgical industries. These industrial by-products would turn into waste materials if not utilized in time. The present study evaluated the suitability of utilizing local mineral admixtures in significant quantities for producing quality concrete mixtures that can withstand the harsh chemical environment without compromising the essential mechanical properties. Comprehensive chemical, mechanical, and durability tests were conducted in the laboratory to characterize the properties of the local cementitious mineral admixtures, cement mortar and portland cement concrete mixtures containing these admixtures. The results from this study indicated that the sulfate resistance of concrete was effectively improved by adding local class F fly ash and slag, or by applying sulfate resistance cement to the mixtures. It is noteworthy that concrete containing local mineral admixtures exhibited much lower permeability (in terms of chloride ion penetration) than ordinary portland cement concrete while retaining the same mechanical properties; whereas concrete mixtures made with sulfate resistance cement had significantly reduced strength and much increased chloride penetration comparing to the other mixtures. Hence, the use of local mineral admixtures in Northwest China in concrete mixtures would be beneficial to the performance of concrete, as well as to the protection of environment.

  4. Gametic phase disequilibrium between the syntenic multiallelic HTG4 and HMS3 markers widely used for parentage testing in Thoroughbred horses.

    Science.gov (United States)

    Machado, Filipe Brum; de Vasconcellos Machado, Luana; Bydlowski, Cynthia Rachid; Bydlowski, Sergio Paulo; Medina-Acosta, Enrique

    2012-02-01

    Validation of parentage and horse breed registries through DNA typing relies on estimates of random match probabilities with DNA profiles generated from multiple polymorphic loci. Of the twenty-seven microsatellite loci recommended by the International Society for Animal Genetics for parentage testing in Thoroughbred horses, eleven are located on five chromosomes. An important aspect in determining combined exclusion probabilities is the ascertainment of the genetic linkage status of syntenic markers, which may affect reliable use of the product rule in estimating random match probabilities. In principle, linked markers can be in gametic phase disequilibrium (GD). We aimed at determining the extent, by frequency and strength, of GD between the HTG4 and HMS3 multiallelic loci, syntenic on chromosome 9. We typed the qualified offspring (n (1) = 27; n (2) = 14) of two Quarter Bred stallions (registered by the Brazilian Association of Quarter Horse Breeders) and 121 unrelated horses from the same breed. In the 41 informative meioses analyzed, the frequency of recombination between the HTG4 and HMS3 loci was 0.27. Consistent with genetic map distances, this recombination rate does not fit to the theoretical distribution for independently segregated markers. We estimated sign-based D' coefficients as a measure of GD, and showed that the HTG4 and HMS3 loci are in significant, yet partial and weak, disequilibrium, with two allele pairs involved (HTG4 M/HMS3 P, D'(+) = 0.6274; and HTG4 K/HMS3 P, D'(-) = -0.6096). These results warn against the inadequate inclusion of genetically linked markers in the calculation of combined power of discrimination for Thoroughbred parentage validation.

  5. Performance of alusilica as mineral admixture in cementitious systems

    DEFF Research Database (Denmark)

    Chi, Lin; Jensen, Ole Mejlhede

    admixture in concrete. The project has been carried out in cooperation with the company alufluor (Helsingborg, Sweden), and MSc Ebbe Skyum Jøns. The application of ALS was investigated as partial cement substitution in mortar. A total of three mortar mixtures were produced: 1) reference, i...... procedure. On the fresh mortar air content was measured by the pressure method, ASTM C231/C231M-14 and the flow was measured by ASTM C1437-13. Casting was done in standard mortar molds 4×4×16 cm3. After demolding, each mortar specimen was weighed over and under water to evaluate their homogeneity and air....... On hardened samples air content was additionally measured by point counting. The inclusion of ALS in the mortar as a mineral admixture with the cement substitution ratio of 10% resulted in a higher air content and lower flowability in comparison with the reference mortar. Compared with blending ALS during...

  6. Behavior of passive admixture in a vortical hydrodynamic field

    NARCIS (Netherlands)

    Bobrov, R.O.; Kyrylyuk, A.V; Zatovsky, A.V.

    2006-01-01

    The motion of passive admixture of spherical particles in the stationary hydrodynamic field of a swirling flow is studied. A spherical particle of a given mass in the hydrodynamic field of a swirling flow is located on a certain circular orbit, where the centrifugal force is compensated by the

  7. Novel use of disequilibrium ages in geothermal energy exploration

    International Nuclear Information System (INIS)

    Goles, G.G.; Seymour, R.S.

    1984-01-01

    Geothermal exploration commonly involves estimation of ages of young volcanic rocks. Few reliable techniques are available for this purpose, uranium-series disequilibrium being one. Several activity ratios may be used to estimate disequilibrium ages. Th-230/U-238 were used because of the convenient half-life of Th-230 and because excess Th-230 in volcanic rocks has been found and used to obtain reasonable ages. By analyzing mafic and felsic fractions of each rock studied, data were obtained to construct quasi-isochrons, assuming that minerals in each fraction had the same initial Th-230/Th-232 activity ratio. Analyses were done via epithermal instrumental activation analysis (Th-232, and U-238) and alpha spectrometry (Th-230 and Th-232), an approach that is simple, rapid and allows explicit estimation of chemical yields. Four rocks from the Oregon High Cascades yielded ages or a limit on age consistent with known geological relations. Several improvements in the method could be implemented without serious impact on its simplicity. 15 references, 1 figure, 1 table

  8. Learning with Admixture: Modeling, Optimization, and Applications in Population Genetics

    DEFF Research Database (Denmark)

    Cheng, Jade Yu

    2016-01-01

    the foundation for both CoalHMM and Ohana. Optimization modeling has been the main theme throughout my PhD, and it will continue to shape my work for the years to come. The algorithms and software I developed to study historical admixture and population evolution fall into a larger family of machine learning...... geneticists strive to establish working solutions to extract information from massive volumes of biological data. The steep increase in the quantity and quality of genomic data during the past decades provides a unique opportunity but also calls for new and improved algorithms and software to cope...... including population splits, effective population sizes, gene flow, etc. Since joining the CoalHMM development team in 2014, I have mainly contributed in two directions: 1) improving optimizations through heuristic-based evolutionary algorithms and 2) modeling of historical admixture events. Ohana, meaning...

  9. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2016-09-01

    Full Text Available Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs, and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS of A. flavus resistance and a characterisation of the causal gene.

  10. Shrinkage-reducing admixtures and early-age desiccation in cement pastes and mortars

    DEFF Research Database (Denmark)

    Bentz, D. P.; Geiker, Mette Rica; Hansen, Kurt Kielsgaard

    2001-01-01

    Fundamental studies of the early-age desiccation of cement-based materials with and without a shrinkage-reducing admixture (SRA) have been performed. Studies have been conducted under both sealed and drying conditions. Physical measurements include mass loss, surface tension, X-ray absorption to ...... to low w/c ratio concretes undergoing self-desiccation, in addition to their normal usage to reduce drying shrinkage.......Fundamental studies of the early-age desiccation of cement-based materials with and without a shrinkage-reducing admixture (SRA) have been performed. Studies have been conducted under both sealed and drying conditions. Physical measurements include mass loss, surface tension, X-ray absorption...

  11. Linkage disequilibrium and association mapping of drought ...

    African Journals Online (AJOL)

    sunny t

    2016-11-16

    Nov 16, 2016 ... related to drought tolerance (YongSheng et al., 2009). Among the variety of ... (Li et al., 2013), yield (LiFang et al., 2010) and fibre traits. (Islam et al., 2014). ..... such molecular markers as SSRs (Bertini et al., 2006;. Zhang et al.

  12. Utilizing linkage disequilibrium information from Indian Genome ...

    Indian Academy of Sciences (India)

    Using LD information derived from Indian Genome Variation database (IGVdb) on populations .... Line diagram represents the SNPs selected in Indian (upper panel) and CEPH .... out procedure for extracting DNA from human nucleated cells.

  13. Disequilibrium macro model and catastrophe theory: the case of an oil shock

    Energy Technology Data Exchange (ETDEWEB)

    German, I.

    1983-01-01

    This study builds a simple disequilibrium macromodel of a small open economy that imports oil from an exogenous unit. The model is motivated by very slow adjustment of prices and wages to disequilibrium. Output on the other hand adjusts to its final level instantaneously. A rationing scheme is specified that explicitly takes into account the spillover effects and differentiates between notional, effective, and actual quantities. In a Solow-Stiglitz (1968) setting, a dynamic model is developed in which the dynamic forces depend on the economic environment specified by the Malinvandian regimes: Classical Unemployment, Keynesian Unemployment, Repressed Inflation, and the Walrasian Equilibrium. Given that dynamic system, the author seeks to identify the stationary points of the system (quasi-equilibria) and to find their stability properties. To the disequilibrium model an oil shock is introduced and its effects on employment, real output, real wage, and the stationary points of the system are investigated. A one-time increase (decrease) in the real price of oil and a continuous increase (decrease) in the real price of oil are considered. The path the economy takes and, in particular, the continuous and discontinuous behavior of the quasi-equilibria are investigated. Finally, the model government policy is incorporated and different policy alternatives are studied.

  14. An inbreeding model of associative overdominance during a population bottleneck.

    Science.gov (United States)

    Bierne, N; Tsitrone, A; David, P

    2000-08-01

    Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situations have been considered. In the present study, associative overdominance is related to the distribution of individual inbreeding levels (i.e., genomic autozygosity). Our model integrates the effects of physical linkage and variation in inbreeding history among individual pedigrees. Hence, linkage and identity disequilibrium, traditionally presented as alternatives, are summarized within a single framework. This allows studying nonequilibrium situations in which both occur simultaneously. The model is applied to the case of an infinite population undergoing a sustained population bottleneck. The effects of bottleneck size, mating system, marker gene diversity, deleterious genomic mutation parameters, and physical linkage are evaluated. Bottlenecks transiently generate much larger associative overdominance than observed in equilibrium finite populations and represent a plausible explanation of empirical results obtained, for instance, in marine species. Moreover, the main origin of associative overdominance is random variation in individual inbreeding whereas physical linkage has little effect.

  15. HLA polymorphism in Sudanese renal donors

    Directory of Open Access Journals (Sweden)

    Ameer M Dafalla

    2011-01-01

    Full Text Available The main objective of this study is to provide a database for renal transplantation in Sudan and to determine the HLA antigens and haplotype frequencies (HFs in the study subjects. HLA typing was performed using the complement-dependant lymphocytotoxicity test in 250 unrelated healthy individuals selected as donors in the Sudanese Renal Transplantation Program. Considerable polymorphism was observed at each locus; A2 (0.28, A30 (0.12, A3 (0.09, A24 (0.09, A1 (0.09, and A68 (0.06 were the most frequent antigens in the A locus, while B51 (0.092, B41 (0.081, B39 (0.078, B57 (0.060, B35 (0.068, B 50 (0.053 and B 52 (0.051 were the most common B locus antigens. DR13 (0.444 and DR15 (0.160 showed the highest antigen frequencies (AFs in the DR locus. In the DQ locus, DQ1 showed the highest gene frequency (0.498, while DQ2 and DQ3 AFs were (0.185 and (0.238, respectively. The most common HLA-A and -B haplotypes in positive linkage disequilibrium were A24, B38; A1, B7; and A3, B52. The common HLA-A and -B HFs in positive linkage disequilibrium in the main three tribe-stocks of the study subjects (Gaalia, Nile Nubian and Johyna were A24, B38 for Gaalia; A24, B38 and A2, B7 for Johyna; and A2, B64 and A3, B53 for Nile Nubian. These results suggest that both class I and class II polymorphisms of the study subjects depict considerable heterogeneity, which reflects recent admixture of this group with neighboring Arabs and African populations.

  16. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

  17. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.

    Science.gov (United States)

    Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

    2017-01-01

    Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with

  18. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

    Science.gov (United States)

    de Oliveira, Thais C; Rodrigues, Priscila T; Menezes, Maria José; Gonçalves-Lopes, Raquel M; Bastos, Melissa S; Lima, Nathália F; Barbosa, Susana; Gerber, Alexandra L; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R; Alves, João Marcelo P; Ferreira, Marcelo U

    2017-07-01

    The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10-4 and 6.2 × 10-4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites

  19. Influence of Curing Conditions on Long-Term Compressive Strength of Mortars with Accelerating Admixtures

    Science.gov (United States)

    Pizoń, Jan; Łaźniewska-Piekarczyk, Beata

    2017-10-01

    One of disadvantages of accelerating admixtures usage is possibility of significant decline of long-term compressive strength of concrete in comparison to non-modified one. Described tests were intended to define scale of lowered long-term compressive strength of mortars caused by accelerating admixtures in different curing conditions. Portland cement and blended cement with ground granulated blast furnace slag (GGBFS) addition and four types of non-chloride accelerating agents were used. Compressive strength was tested after 7 up to 360 days. Curing conditions were designed to simulate probable conditions close to reality. Such conditions are simulation of internal concrete elements, external elements cast on start of summer and external elements cast on start of winter. Results had shown that it is invalid to state that every accelerating admixture will cause drop of long-term compressive strength in every conditions and for every cement type. Change of curing conditions even after a long time (in this case half of the year) leads to significant differences in compression strength.

  20. Portland cement hydration in the presence of admixtures: black gram pulse and superplasticizer

    Directory of Open Access Journals (Sweden)

    Viveka Nand Dwivedi

    2008-12-01

    Full Text Available Effect of admixtures such as black gram pulse (BGP and sulfonated naphthalene based superplasticizer (SP on the hydration of Portland cement has been studied. The hydration characteristics of OPC in the presence of BGP and SP were studied with the help of non evaporable water content determinations, calorimetric method, Mössbauer spectroscopic and atomic force microscopic techniques. Results have shown that both BGP and SP get adsorbed at the surface of cement and its hydration products. The hydration of Portland cement is retarded in the presence of both the admixtures and nanosize hydration products are formed.

  1. A Generic Procedure for the Assessment of the Effect of Concrete Admixtures on the Sorption of Radionuclides on Cement: Concept and Selected Results

    International Nuclear Information System (INIS)

    Glaus, M.A.; Laube, A.; Van Loon, L.R.

    2004-01-01

    A screening procedure is proposed for the assessment of the effect of concrete admixtures on the sorption of radionuclides by cement. The procedure is both broad and generic, and can thus be used as input for the assessment of concrete admixtures which might be used in the future. The experimental feasibility and significance of the screening procedure are tested using selected concrete admixtures: i.e. sulfonated naphthalene-formaldehyde condensates, lignosulfonates, and a plasticiser used at PSI for waste conditioning. The effect of these on the sorption properties of Ni(II), Eu(III) and Th(IV) in cement is investigated using crushed Hardened Cement Paste (HCP), as well as cement pastes prepared in the presence of these admixtures. Strongly adverse effects on the sorption of the radionuclides tested are observed only in single cases, and under extreme conditions: i.e. at high ratios of concrete admixtures to HCP, and at low ratios of HCP to cement pore water. Under realistic conditions, both radionuclide sorption and the sorption of isosaccharinic acid (a strong complexant produced in cement-conditioned wastes containing cellulose) remain unaffected by the presence of concrete admixtures, which can be explained by the sorption of them onto the HCP. The pore-water concentrations of the concrete admixtures tested are thereby reduced to levels at which the formation of radionuclide complexes is no longer of importance. Further, the Langmuir sorption model, proposed for the sorption of concrete admixtures on HCP, suggests that the HCP surface does not become saturated, at least for those concrete admixtures tested. (author)

  2. A Generic Procedure for the Assessment of the Effect of Concrete Admixtures on the Sorption of Radionuclides on Cement: Concept and Selected Results

    Energy Technology Data Exchange (ETDEWEB)

    Glaus, M.A.; Laube, A.; Van Loon, L.R

    2004-03-01

    A screening procedure is proposed for the assessment of the effect of concrete admixtures on the sorption of radionuclides by cement. The procedure is both broad and generic, and can thus be used as input for the assessment of concrete admixtures which might be used in the future. The experimental feasibility and significance of the screening procedure are tested using selected concrete admixtures: i.e. sulfonated naphthalene-formaldehyde condensates, lignosulfonates, and a plasticiser used at PSI for waste conditioning. The effect of these on the sorption properties of Ni(II), Eu(III) and Th(IV) in cement is investigated using crushed Hardened Cement Paste (HCP), as well as cement pastes prepared in the presence of these admixtures. Strongly adverse effects on the sorption of the radionuclides tested are observed only in single cases, and under extreme conditions: i.e. at high ratios of concrete admixtures to HCP, and at low ratios of HCP to cement pore water. Under realistic conditions, both radionuclide sorption and the sorption of isosaccharinic acid (a strong complexant produced in cement-conditioned wastes containing cellulose) remain unaffected by the presence of concrete admixtures, which can be explained by the sorption of them onto the HCP. The pore-water concentrations of the concrete admixtures tested are thereby reduced to levels at which the formation of radionuclide complexes is no longer of importance. Further, the Langmuir sorption model, proposed for the sorption of concrete admixtures on HCP, suggests that the HCP surface does not become saturated, at least for those concrete admixtures tested. (author)

  3. Linking environmental filtering and disequilibrium to biogeography with a community climate framework.

    Science.gov (United States)

    Blonder, Benjamin; Nogués-Bravo, David; Borregaard, Michael K; Donoghue, John C; Jørgensen, Peter M; Kraft, Nathan J B; Lessard, Jean-Philippe; Morueta-Holme, Naia; Sandel, Brody; Svenning, Jens-Christian; Violle, Cyrille; Rahbek, Carsten; Enquist, Brian J

    2015-04-01

    We present a framework to measure the strength of environmental filtering and disequilibrium of the species composition of a local community across time, relative to past, current, and future climates. We demonstrate the framework by measuring the impact of climate change on New World forests, integrating data for climate niches of more than 14000 species, community composition of 471 New World forest plots, and observed climate across the most recent glacial-interglacial interval. We show that a majority of communities have species compositions that are strongly filtered and are more in equilibrium with current climate than random samples from the regional pool. Variation in the level of current community disequilibrium can be predicted from Last Glacial Maximum climate and will increase with near-future climate change.

  4. Part 1: determination of radioactive disequilibrium in uranium ores by alpha-spectrometry

    International Nuclear Information System (INIS)

    Killeen, P.G.; Carmichael, C.M.

    1976-01-01

    An α-spectrometric method of detecting the presence of disequilibrium in the 238 U decay series has been developed. A silicon semi-conductor detector and a 1024 channel pulse height analyzer were used to obtain alpha particle energy spectra of uraniferous rocks and minerals. 'Infinitely thick' sources were used to avoid the problems involved in preparation of 'infinitely thin' sources. The method involves the generation of theoretical energy distributions for infinitely thick sources. Complete theoretical spectra were computed for comparison with experimentally obtained alpha particle energy spectra of rocks and minerals. The presence and extent of disequilibrium in the 238 U decay series in a rock is determined from the residual spectrum obtained by subtracting a fitted theoretical spectrum from the measured spectrum of a rock. (author)

  5. Role of syn-eruptive plagioclase disequilibrium crystallization in basaltic magma ascent dynamics.

    Science.gov (United States)

    La Spina, G; Burton, M; De' Michieli Vitturi, M; Arzilli, F

    2016-12-12

    Timescales of magma ascent in conduit models are typically assumed to be much longer than crystallization and gas exsolution for basaltic eruptions. However, it is now recognized that basaltic magmas may rise fast enough for disequilibrium processes to play a key role on the ascent dynamics. The quantification of the characteristic times for crystallization and exsolution processes are fundamental to our understanding of such disequilibria and ascent dynamics. Here we use observations from Mount Etna's 2001 eruption and a magma ascent model to constrain timescales for crystallization and exsolution processes. Our results show that plagioclase reaches equilibrium in 1-2 h, whereas ascent times were magma ascent rate and disequilibrium crystallization and exsolution plays a key role in controlling eruption dynamics in basaltic volcanism.

  6. Genetic admixture of eight Mexican indigenous populations: based on five polymarker, HLA-DQA1, ABO, and RH loci.

    Science.gov (United States)

    Buentello-Malo, Leonora; Peñaloza-Espinosa, Rosenda I; Salamanca-Gómez, Fabio; Cerda-Flores, Ricardo M

    2008-01-01

    This study explores the genetic admixture of eight Mexican indigenous populations (Otomi-Ixmiquilpan, Otomi-Actopan, Tzeltales, Nahua-Milpa-Alta, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Ixhuatlancillo, and Nahua-Coyolillo) on the basis of five PCR-based polymorphic DNA loci (LDLR, GYPA, HBGG, D7S8, GC), HLA_DQA1, and the blood groups ABO and Rh (CcDEe). Among the indigenous populations, the highest gene frequencies for O and D were 0.9703 and 1.000 for Zitlala (State of Guerrero) and 0.9955 and 0.9414 for Tzeltales (State of Chiapas), respectively. Maximum likelihood estimates of admixture components yield a trihybrid model with Amerindian (assuming that Nahua-Zitlala is the most representative indigenous population), Spanish, and African ancestry with the admixture proportions: 93.03, 6.03, and 0.94 for Tzeltales, and 28.99, 44.03, and 26.98 for Coyolillo. A contribution of the ancestral populations of Ixhuatlancillo, Actopan, Ixmiquilpan, Milpa-Alta, and Xochimilco were found with the following average of admixture proportions: 75.84, 22.50, and 1.66. The findings herein demonstrate that the genetic admixture of the Mexican indigenous populations who at present speak the same Amer-Indian language can be differentiated and that the majority of them have less ancestral indigenous contribution than those considered as Mestizo populations.

  7. The influence of shrinkage reducing admixtures on plastic shrinkage

    Directory of Open Access Journals (Sweden)

    Mora, J.

    2003-12-01

    Full Text Available Shrinkage reducing admixtures (SRAs are viable alternatives for reducing plastic shrinkage cracking in concrete. The objective of the present paper is to study early age plastic shrinkage in restrained concrete elements, where three different SRAs have been used. The influence of the admixture is analyzed through the following measurements: capillary pressure, evaporation, temperature evolution, crack evolution and settlement. The tests for studying the cracking and deformation were made on two different configurations (i.e., restrained prisms with reduced cross-section and restrained panel, in a wind tunnel, with controlled wind temperature and velocity. The conclusions obtained indicate the viability of the use of this type of admixture and the usefulness of the test methods.

    Los aditivos reductores de retracción (SRAs se plantean, hoy en día, como una alternativa viable para reducir la fisuración por retracción plástica. El objetivo del presente artículo es conocer mejor y predecir el comportamiento a primeras edades de la retracción plástica en elementos estructurales coaccionados, a los que se les ha añadido diversos aditivos reductores de retracción (tres tipos diferentes. Esta influencia se analiza a través de las siguientes propiedades: presión capilar, evaporación, evolución de temperaturas, evolución de fisuración, y deformaciones verticales de asentamiento. Los ensayos para estudiar la fisuración y las deformaciones se han realizado sobre diferentes configuraciones (prisma restringido con estrangulamiento y panel restringido, en un túnel de viento, con temperaturas y velocidades de viento controladas. Las conclusiones obtenidas señalan la viabilidad del empleo de este tipo de aditivos y la bondad de los métodos experimentales utilizados.

  8. Extensive Admixture and Selective Pressure Across the Sahel Belt

    Czech Academy of Sciences Publication Activity Database

    Triska, P.; Soares, P.; Patin, E.; Fernandes, V.; Černý, Viktor; Pereira, L.

    2015-01-01

    Roč. 7, č. 12 (2015), s. 3484-3495 ISSN 1759-6653 R&D Projects: GA ČR GA13-37998S Institutional support: RVO:67985912 Keywords : genome-wide diversity * admixture * selection * Sahel Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 4.098, year: 2015 http://gbe.oxfordjournals.org/content/7/12/3484.full.pdf+html

  9. Spanish genetic admixture is associated with larger V(O2) max decrement from sea level to 4338 m in Peruvian Quechua.

    Science.gov (United States)

    Brutsaert, Tom D; Parra, Esteban J; Shriver, Mark D; Gamboa, Alfredo; Palacios, Jose-Antonio; Rivera, Maria; Rodriguez, Ivette; León-Velarde, Fabiola

    2003-08-01

    Quechua in the Andes may be genetically adapted to altitude and able to resist decrements in maximal O2 consumption in hypoxia (DeltaVo2 max). This hypothesis was tested via repeated measures of Vo2 max (sea level vs. 4338 m) in 30 men of mixed Spanish and Quechua origins. Individual genetic admixture level (%Spanish ancestry) was estimated by using ancestry-informative DNA markers. Genetic admixture explained a significant proportion of the variability in DeltaVo2 max after control for covariate effects, including sea level Vo2 max and the decrement in arterial O2 saturation measured at Vo2 max (DeltaSpO2 max) (R2 for admixture and covariate effects approximately 0.80). The genetic effect reflected a main effect of admixture on DeltaVo2 max (P = 0.041) and an interaction between admixture and DeltaSpO2 max (P = 0.018). Admixture predicted DeltaVo2 max only in subjects with a large DeltaSpO2 max (P = 0.031). In such subjects, DeltaVo2 max was 12-18% larger in a subgroup of subjects with high vs. low Spanish ancestry, with least squares mean values (+/-SE) of 739 +/- 71 vs. 606 +/- 68 ml/min, respectively. A trend for interaction (P = 0.095) was also noted between admixture and the decrease in ventilatory threshold at 4338 m. As previously, admixture predicted DeltaVo2 max only in subjects with a large decrease in ventilatory threshold. These findings suggest that the genetic effect on DeltaVo2 max depends on a subject's aerobic fitness. Genetic effects may be more important (or easier to detect) in athletic subjects who are more likely to show gas-exchange impairment during exercise. The results of this study are consistent with the evolutionary hypothesis and point to a better gas-exchange system in Quechua.

  10. North African populations carry the signature of admixture with Neandertals

    DEFF Research Database (Denmark)

    Sánchez-Quinto, Federico; Botigué, Laura R.; Civit, Sergi

    2012-01-01

    One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient popu...

  11. Study on Strength and Microstructure of Cement-Based Materials Containing Combination Mineral Admixtures

    Directory of Open Access Journals (Sweden)

    Meijuan Rao

    2016-01-01

    Full Text Available The compressive strength of complex binders containing two or three blended mineral admixtures in terms of glass powder (GP, limestone powder (LP, and steel slag powder (SP was determined by a battery solution type compressive testing machine. The morphology and microstructure characteristics of complex binder hydration products were also studied by microscopic analysis methods, such as XRD, TG-DTA, and SEM. The mechanical properties of the cement-based materials were analyzed to reveal the most appropriate mineral admixture type and content. The early sample strength development with GP was very slow, but it rapidly grew at later stages. The micro aggregate effect and pozzolanic reaction mutually occurred in the mineral admixture. In the early stage, the micro aggregate effect reduced paste porosity and the small particles connected with the cement hydration products to enhance its strength. In the later stage, the pozzolanic reaction of some components in the complex powder occurred and consumed part of the calcium hydroxide to form C-S-H gel, thus improving the hydration environment. Also, the produced C-S-H gel made the structure more compact, which improved the structure’s strength.

  12. Genomic selection in maritime pine.

    Science.gov (United States)

    Isik, Fikret; Bartholomé, Jérôme; Farjat, Alfredo; Chancerel, Emilie; Raffin, Annie; Sanchez, Leopoldo; Plomion, Christophe; Bouffier, Laurent

    2016-01-01

    A two-generation maritime pine (Pinus pinaster Ait.) breeding population (n=661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r(2)=0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (rV(2)=0.006). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM). Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  13. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 94; Issue 4. Statistical ... Keywords. family-based genetic association; logistic regression; linkage disequilibrium. ... Unlike population-based tests for association, family-based tests for transmission disequilibrium are protected against population stratification. In this study, we ...

  14. What Causes Birth Order-Intelligence Patterns? The Admixture Hypothesis, Revived.

    Science.gov (United States)

    Rodgers, Joseph Lee

    2001-01-01

    Describes why birth order interests both parents and researchers, discussing what really causes apparent birth order effects on intelligence, examining problems with using cross-sectional intelligence data, and noting how to move beyond cross-sectional inferences. Explains the admixture hypothesis, which finds that family size is much more…

  15. Uranium disequilibrium dating of phosphate deposits from the Lau Group, Fiji

    International Nuclear Information System (INIS)

    Roe, K.K.; Burnett, W.C.

    1983-01-01

    A determination of the absolute age of two phosphate deposits in the Lau Group, Fiji by uranium-series disequilibrium techniques is reported. These measurements were undertaken in order to assist in the evaluation of their origin in terms of known palaeoclimatic information. (U.K.)

  16. Getting Started with GeneRecon — An Introduction to the Association Mapping Tool GeneRecon

    DEFF Research Database (Denmark)

    Mailund, T; Schauser, Leif

    2006-01-01

    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample...... of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position....

  17. Ancestry, admixture and fitness in Colombian genomes

    Science.gov (United States)

    Rishishwar, Lavanya; Conley, Andrew B.; Wigington, Charles H.; Wang, Lu; Valderrama-Aguirre, Augusto; King Jordan, I.

    2015-01-01

    The human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European (average = 74.6%, range = 45.0%–96.7%), followed by Native American (average = 18.1%, range = 2.1%–33.3%) and African (average = 7.3%, range = 0.2%–38.6%). Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes (HLA-B and MAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment. PMID:26197429

  18. THEORY OF ACTIVE HITTINGS IS IN PROCESSES OF ELECTRO-COAGULATION THE ADMIXTURES IN WATER TECHNOLOGICAL ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    В.В. Березуцький

    2012-10-01

    Full Text Available  In the article theoretical bases of electro-coagulation of admixtures are examined in a water technological environment with the use of theory of the active hittings, which are based on the results of the executed researches and analysis of scientific information. Application of theory of the active hittings is in coagulation, provides high efficiency of process of extraction of admixtures from water environments during minimization of energy consumption and expenses of materials.

  19. Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks.

    Science.gov (United States)

    Corrigan, Shannon; Maisano Delser, Pierpaolo; Eddy, Corey; Duffy, Clinton; Yang, Lei; Li, Chenhong; Bazinet, Adam L; Mona, Stefano; Naylor, Gavin J P

    2017-05-01

    We use a genomic sampling of both nuclear and mitochondrial DNA markers to examine a pattern of genetic admixture between Carcharhinus galapagensis (Galapagos sharks) and Carcharhinus obscurus (dusky sharks), two well-known and closely related sharks that have been recognized as valid species for more than 100years. We describe widespread mitochondrial-nuclear discordance in which these species are readily distinguishable based on 2152 nuclear single nucleotide polymorphisms from 910 independent autosomal regions, but show pervasive mitochondrial admixture. The species are superficially morphologically cryptic as adults but show marked differences in internal anatomy, as well as niche separation. There was no indication of ongoing hybridization between the species. We conclude that the observed mitochondrial-nuclear discordance is likely due to historical mitochondrial introgression following a range expansion. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Influence of radon daughter exposure rate, unattachment fraction, and disequilibrium on occurrence of lung tumours

    International Nuclear Information System (INIS)

    Cross, F.T.; Palmer, R.F.; Dagle, G.E.; Busch, R.H.; Buschbom, R.L.

    1984-01-01

    Groups of male, specific-pathogen-free (SPF), Wistar rats were exposed to several concentrations of radon daughters and uranium ore dust to clarify the roles of exposure rate, unattached RaA daughters, and the degree of radon daughter disequilibrium, in the development of respiratory system disease. Modelled, human dosimetric data indicate that the dose to sensitive tissues of the respiratory tract increases with increasing radon daughter unattachment fraction and degree of disequilibrium. Data bearing on these developments as well as updated results of experiments designed to test the role of radon daughter exposure rate on lung tumour incidence are reported. (author)

  1. Unravelling the genetic history of Negritos and indigenous populations of Southeast Asia.

    Science.gov (United States)

    Aghakhanian, Farhang; Yunus, Yushima; Naidu, Rakesh; Jinam, Timothy; Manica, Andrea; Hoh, Boon Peng; Phipps, Maude E

    2015-04-14

    Indigenous populations of Malaysia known as Orang Asli (OA) show huge morphological, anthropological, and linguistic diversity. However, the genetic history of these populations remained obscure. We performed a high-density array genotyping using over 2 million single nucleotide polymorphisms in three major groups of Negrito, Senoi, and Proto-Malay. Structural analyses indicated that although all OA groups are genetically closest to East Asian (EA) populations, they are substantially distinct. We identified a genetic affinity between Andamanese and Malaysian Negritos which may suggest an ancient link between these two groups. We also showed that Senoi and Proto-Malay may be admixtures between Negrito and EA populations. Formal admixture tests provided evidence of gene flow between Austro-Asiatic-speaking OAs and populations from Southeast Asia (SEA) and South China which suggest a widespread presence of these people in SEA before Austronesian expansion. Elevated linkage disequilibrium (LD) and enriched homozygosity found in OAs reflect isolation and bottlenecks experienced. Estimates based on Ne and LD indicated that these populations diverged from East Asians during the late Pleistocene (14.5 to 8 KYA). The continuum in divergence time from Negritos to Senoi and Proto-Malay in combination with ancestral markers provides evidences of multiple waves of migration into SEA starting with the first Out-of-Africa dispersals followed by Early Train and subsequent Austronesian expansions. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Estimation of kinship coefficient in structured and admixed populations using sparse sequencing data.

    Directory of Open Access Journals (Sweden)

    Jinzhuang Dou

    2017-09-01

    Full Text Available Knowledge of biological relatedness between samples is important for many genetic studies. In large-scale human genetic association studies, the estimated kinship is used to remove cryptic relatedness, control for family structure, and estimate trait heritability. However, estimation of kinship is challenging for sparse sequencing data, such as those from off-target regions in target sequencing studies, where genotypes are largely uncertain or missing. Existing methods often assume accurate genotypes at a large number of markers across the genome. We show that these methods, without accounting for the genotype uncertainty in sparse sequencing data, can yield a strong downward bias in kinship estimation. We develop a computationally efficient method called SEEKIN to estimate kinship for both homogeneous samples and heterogeneous samples with population structure and admixture. Our method models genotype uncertainty and leverages linkage disequilibrium through imputation. We test SEEKIN on a whole exome sequencing dataset (WES of Singapore Chinese and Malays, which involves substantial population structure and admixture. We show that SEEKIN can accurately estimate kinship coefficient and classify genetic relatedness using off-target sequencing data down sampled to ~0.15X depth. In application to the full WES dataset without down sampling, SEEKIN also outperforms existing methods by properly analyzing shallow off-target data (~0.75X. Using both simulated and real phenotypes, we further illustrate how our method improves estimation of trait heritability for WES studies.

  3. Palm Kernel Husk Ash (PKHA) as an Admixture (Accelerator) in ...

    African Journals Online (AJOL)

    This study was carried out to determine the suitability of PKHA as an admixture, while still retaining the compressive strength characteristics. Results revealed that the setting time of the mixture of the PKHA and cement cube decreases as the percentage of the PKHA increases as compared to the setting time of pure cement ...

  4. A pantograph linkage

    International Nuclear Information System (INIS)

    Cole, G.V.

    1982-01-01

    A pantograph linkage is actuated by two linear actuators, pivotally connected together at the linkage. The displacement of the actuators is monitored by rectilinear potentiometers to provide feedback signals to a microprocessor which also receives input signals related to a required movement of a slave end of the linkage. In response to these signals, the microprocessor provides signals to control the displacement of the linear actuators to effect the required movement of the slave end. The movement of the slave end might be straightline in a substantially horizontal or vertical direction. (author)

  5. Privacy preserving interactive record linkage (PPIRL).

    Science.gov (United States)

    Kum, Hye-Chung; Krishnamurthy, Ashok; Machanavajjhala, Ashwin; Reiter, Michael K; Ahalt, Stanley

    2014-01-01

    Record linkage to integrate uncoordinated databases is critical in biomedical research using Big Data. Balancing privacy protection against the need for high quality record linkage requires a human-machine hybrid system to safely manage uncertainty in the ever changing streams of chaotic Big Data. In the computer science literature, private record linkage is the most published area. It investigates how to apply a known linkage function safely when linking two tables. However, in practice, the linkage function is rarely known. Thus, there are many data linkage centers whose main role is to be the trusted third party to determine the linkage function manually and link data for research via a master population list for a designated region. Recently, a more flexible computerized third-party linkage platform, Secure Decoupled Linkage (SDLink), has been proposed based on: (1) decoupling data via encryption, (2) obfuscation via chaffing (adding fake data) and universe manipulation; and (3) minimum information disclosure via recoding. We synthesize this literature to formalize a new framework for privacy preserving interactive record linkage (PPIRL) with tractable privacy and utility properties and then analyze the literature using this framework. Human-based third-party linkage centers for privacy preserving record linkage are the accepted norm internationally. We find that a computer-based third-party platform that can precisely control the information disclosed at the micro level and allow frequent human interaction during the linkage process, is an effective human-machine hybrid system that significantly improves on the linkage center model both in terms of privacy and utility.

  6. Government deficits, private investment and the current account: an intertemporal disequilibrium analysis

    NARCIS (Netherlands)

    van Wijnbergen, S.J.G.

    1987-01-01

    An analysis of the fiscal policy in the account of a model with intertemporal optimisation underlying private behaviour. Besides is incorporated explicitly the possibility of (short-run) labour and goods market disequilibrium caused by Fischer (1977)--Gray (1978) type contract-based real-wage

  7. Association mapping for kernel phytosterol content in almond

    Directory of Open Access Journals (Sweden)

    Carolina eFont i Forcada

    2015-07-01

    Full Text Available Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping, also known as linkage disequilibrium, was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance, resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM approach using co-ancestry values from population structure and kinship estimates (K model as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

  8. Utilization of black liquor as concrete admixture and set retarder aid

    Directory of Open Access Journals (Sweden)

    Samar A. El-Mekkawi

    2011-04-01

    Full Text Available The utilization of black liquor, produced by the pulp and paper industry in Egypt, as a workability aid and set retarder admixture has been investigated. This approach may help eliminate the environmentally polluting black liquor waste. It also provides a low cost by-product, which can be widely used in the construction industry. The properties of black liquor and its performance on concrete at two different ratios of water to cement have been studied. The results revealed that black liquor from rice straw pulp increases concrete workability, improves compaction, and reduces honeycombing. Moreover, it retards the initial and final set time and enhances uniform compaction. The effect of incorporating small portions of silica fume has been investigated. The ageing effect of this material over a period of one year, to determine its safe storage period, has been studied. Finally, this admixture was found to comply with the relevant Egyptian standards.

  9. New biodegradable air-entraining admixture based on LAS for cement-based composites

    International Nuclear Information System (INIS)

    Mendes, J.C.; Moro, T.K.; Dias, L.S.; Campos, P.A.M.; Silva, G.J.B.; Peixoto, R.A.F.; Cury, A.A.

    2016-01-01

    The active principle of Air Entraining Admixtures (AEA) are surfactants, analogously to washing up liquids. Washing up (or dishwashing) liquids are widely available products, relatively inexpensive, non-toxic and biodegradable, thus presenting smaller environmental impact. Therefore, the present work proposes the use of a biodegradable surfactant comprised in washing up liquids, Linear Alkylbenzene Sulfonate (LAS), as sustainable air entraining agent for cement-based composites. In this sense, a performance evaluation of the proposed AEA is carried out, by comparing the properties of mortars with proposed AEA, commercial AEA and ones without any admixture. Through the physical, mechanical and microstructural analysis, it was possible to determine the efficiency of the proposed AEA, as well as its optimum range of dosage. As a result, we seek to contribute to the technical development of cement-based composites in Brazil and in the world. (author)

  10. Disequilibrium dynamics in a Keynesian model with time delays

    Science.gov (United States)

    Gori, Luca; Guerrini, Luca; Sodini, Mauro

    2018-05-01

    The aim of this research is to analyse a Keynesian goods market closed economy by considering a continuous-time setup with fixed delays. The work compares dynamic results based on linear and nonlinear adjustment mechanisms through which the aggregate supply (production) reacts to a disequilibrium in the goods market and consumption depends on income at a preceding date. Both analytical and geometrical (stability switching curves) techniques are used to characterise the stability properties of the stationary equilibrium.

  11. Phylogeography of haplotypes of five microsatellites located in a low-recombination region of the X chromosome: studies worldwide and in Brazilian populations.

    Science.gov (United States)

    Pereira, Rinaldo Wellerson; Pena, Sérgio D J

    2006-01-01

    We studied five microsatellites (DXS995, DXS8076, DXS8114, DXS1002 and DXS1050) located in a region of very low recombination rate in the long arm of the human X chromosome (Xq13.3-Xq21.3). No recombination was seen in 291 meioses in CEPH families. To test whether haplotypes composed of the five microsatellites could differentiate among distinct human continental populations, we studied an international panel containing 72 males from Africa, Europe, Asia and the America. Haplotypic diversity was very high within these groups and no haplotypes were shared among them. This led to the hope that we might be able to identify continent-specific lineages. However, in a median joining network there was no clear discrimination of the different continental groups. We then tested whether we could identify X chromosomal lineages from different continental origins in Brazilians. We typed 180 white Brazilians from four different geographical regions and examined their proportions of haplotype sharing with Africans, Asians, Europeans and Amerindians. No phylogeographical patterns emerged from the data. Moreover, there were several instances of the same haplotype being shared by many (and in one instance all) groups, suggesting that recombination might be occurring. We thus studied pairwise the level of linkage disequilibrium (LD) between the microsatellites. No detectable linkage disequilibrium between the most external loci DXS995 and DXS1050 was observed. Thus, even though recombination may be absent on short time spans, as seen in the CEPH pedigrees, on a long term basis it occurs often enough to dissipate all linkage disequilibrium. On the other hand, we observed very strong linkage disequilibrium between the pairs DXS995/DXS8076 and DXS1002/DXS8114, raising the possibility of resequencing the segment between them to identify single nucleotide polymorphisms (SNPs) in their intervals. The combination of X-linked microsatellites and SNPs in strong linkage disequilibrium might

  12. Effect of Dolomite as Expansive Agent and Shrinkage Reducing Admixture in Self-Compacting Shrinkage – Compensating Concrete

    OpenAIRE

    Qosai Sahib Radi Marshdi; Ahlam Hamid Jasim; Haider Abass Obeed

    2018-01-01

    The principle of using expansive agents has been recommended to manufacture shrinkage compensating concrete provided that an adequate wet curing is carried out. On the other hand, shrinkage-reducing admixture (SRA) in the concrete mixes, has been more recently suggested to reduce the risk of cracking in concrete structures caused by drying shrinkage. This paper is devoted to the study of the influence of complex modifier in the form of superplasticizer, shrinkage reducing admixture and e...

  13. Managerial responses to transaction cost disequilibrium in food supply chains and networks

    NARCIS (Netherlands)

    Bremmers, H.J.; Meulen, van der B.M.J.; Poppe, K.J.; Wijnands, J.H.M.

    2010-01-01

    Differences in transaction costs (i.e. costs of information processing, monitoring and control) between firms in local supply chains as well as in an international setting may have a negative impact on competitiveness and on creation of value added. Transaction cost disequilibrium is defined as a

  14. Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L..

    Directory of Open Access Journals (Sweden)

    Brad L Smith

    Full Text Available Previous genetic studies of Atlantic swordfish (Xiphias gladius L. revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.

  15. Standard test method for initial screening of corrosion inhibiting admixtures for steel in concrete

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2007-01-01

    1.1 This test method covers a procedure for determining the effects of chemical admixtures on the corrosion of metals in concrete. This test method can be used to evaluate materials intended to inhibit chloride-induced corrosion of steel in concrete. It can also be used to evaluate the corrosivity of admixtures by themselves or in a chloride environment. This test is not applicable for emulsions. 1.2 &solely-SI-units; 1.3 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use.

  16. Toxicity of coal fly ash (CFA) and toxicological response of switchgrass in mycorrhiza-mediated CFA-soil admixtures.

    Science.gov (United States)

    Awoyemi, Olushola M; Dzantor, E Kudjo

    2017-10-01

    Increasing support for the use of Coal fly ash (CFA) in agriculture has necessitated a better understanding of the effects of the CFA in various cropping schemes. Experiments were conducted to assess mutagenic response of a mutant strain of Salmonella enterica serovar Typhimurium (TA100) to varying concentrations of CFA-water extracts, determine oxidative stress in switchgrass (Panicum virgatum L.) at varying levels of CFA-soil admixtures, and evaluate mycorrhiza-mediated modulation of oxidative stress responses of CFA-grown switchgrass. The TA100 exposed to 0%, 5%, 10%, 15%, 20% and 25% (w/v) CFA-water extracts elicited significant (p CFA-soil admixtures at 7.5% and 15% (w/w) significantly (p CFA/soil). Under the same conditions, activities of glutathione peroxidase (GPx) decreased by 75.9% and 66.9%. In contrast to the antioxidant enzyme activities, levels of malondialdehyde (MDA) an indicator of lipid peroxidation increased significantly (p CFA-soil admixtures with arbuscular mycorrhizal fungi (AMF), Rhizophaga clarus enhanced the activities of both SOD and GPx in the switchgrass, while it significantly (p CFA (at concentrations considered to be non-mutagenic against TA100) as soil amendment produced concentration-dependent oxidative stress responses in switchgrass; however, inoculation of the CFA-soil admixtures with AMF significantly modulated the oxidative stress responses. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Localizing genes using linkage disequilibrium in plants: integrating ...

    African Journals Online (AJOL)

    A large proportion of these false associations (or lack of it) result from population stratification, while the rest may be caused by other demographic and evolutionary processes that create a statistical association between a marker allele and the trait, such as bottlenecks, natural selection, hybridization and genetic drift.

  18. Distribution and linkage disequilibrium analysis of polymorphisms of ...

    Indian Academy of Sciences (India)

    2Five-Star Animal Health Pharmaceutical Factory of Jilian Province, 5333 Xi'an Road, Changchun, Jilin 130062,. People's .... showed that GH peptide sequence of mature protein in. Rongjiang pig ..... 1, white. (PIC value <0.25, low polymorphism; 0.25

  19. VT Wildlife Linkage Habitat

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) The Wildlife Linkage Habitat Analysis uses landscape scale data to identify or predict the location of potentially significant wildlife linkage...

  20. Secondary Contact and Admixture between Independently Invading Populations of the Western Corn Rootworm, Diabrotica virgifera virgifera in Europe

    Science.gov (United States)

    Bermond, Gérald; Ciosi, Marc; Lombaert, Eric; Blin, Aurélie; Boriani, Marco; Furlan, Lorenzo; Toepfer, Stefan; Guillemaud, Thomas

    2012-01-01

    The western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is one of the most destructive pests of corn in North America and is currently invading Europe. The two major invasive outbreaks of rootworm in Europe have occurred, in North-West Italy and in Central and South-Eastern Europe. These two outbreaks originated from independent introductions from North America. Secondary contact probably occurred in North Italy between these two outbreaks, in 2008. We used 13 microsatellite markers to conduct a population genetics study, to demonstrate that this geographic contact resulted in a zone of admixture in the Italian region of Veneto. We show that i) genetic variation is greater in the contact zone than in the parental outbreaks; ii) several signs of admixture were detected in some Venetian samples, in a Bayesian analysis of the population structure and in an approximate Bayesian computation analysis of historical scenarios and, finally, iii) allelic frequency clines were observed at microsatellite loci. The contact between the invasive outbreaks in North-West Italy and Central and South-Eastern Europe resulted in a zone of admixture, with particular characteristics. The evolutionary implications of the existence of a zone of admixture in Northern Italy and their possible impact on the invasion success of the western corn rootworm are discussed. PMID:23189184

  1. Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models.

    Science.gov (United States)

    He, Zhangyi; Beaumont, Mark; Yu, Feng

    2017-07-05

    We explore the effect of different mechanisms of natural selection on the evolution of populations for one- and two-locus systems. We compare the effect of viability and fecundity selection in the context of the Wright-Fisher model with selection under the assumption of multiplicative fitness. We show that these two modes of natural selection correspond to different orderings of the processes of population regulation and natural selection in the Wright-Fisher model. We find that under the Wright-Fisher model these two different orderings can affect the distribution of trajectories of haplotype frequencies evolving with genetic recombination. However, the difference in the distribution of trajectories is only appreciable when the population is in significant linkage disequilibrium. We find that as linkage disequilibrium decays the trajectories for the two different models rapidly become indistinguishable. We discuss the significance of these findings in terms of biological examples of viability and fecundity selection, and speculate that the effect may be significant when factors such as gene migration maintain a degree of linkage disequilibrium. Copyright © 2017 He et al.

  2. Influence of the calcium concentration in the presence of organic phosphorus on the physicochemical compatibility and stability of all-in-one admixtures for neonatal use

    Directory of Open Access Journals (Sweden)

    de Sousa Valeria

    2009-10-01

    Full Text Available Abstract Background Preterm infants need high amounts of calcium and phosphorus for bone mineralization, which is difficult to obtain with parenteral feeding due to the low solubility of these salts. The objective of this study was to evaluate the physicochemical compatibility of high concentrations of calcium associated with organic phosphate and its influence on the stability of AIO admixtures for neonatal use. Methods Three TPN admixture formulas were prepared in multilayered bags. The calcium content of the admixtures was adjusted to 0, 46.5 or 93 mg/100 ml in the presence of a fixed organic phosphate concentration as well as lipids, amino acids, inorganic salts, glucose, vitamins and oligoelements at pH 5.5. Each admixture was stored at 4°C, 25°C or 37°C and evaluated over a period of 7 days. The physicochemical stability parameters evaluated were visual aspect, pH, sterility, osmolality, peroxide formation, precipitation, and the size of lipid globules. Results Color alterations occurred from the first day on, and reversible lipid film formation from the third day of study for the admixtures stored at 25°C and 37°C. According to the parameters evaluated, the admixtures were stable at 4°C; and none of them presented precipitated particles due to calcium/phosphate incompatibility or lipid globules larger than 5 μm, which is the main parameter currently used to evaluate lipid emulsion stability. The admixtures maintained low peroxide levels and osmolarity was appropriate for parenteral administration. Conclusion The total calcium and calcium/phosphorus ratios studied appeared not to influence the physicochemical compatibility and stability of AIO admixtures.

  3. Effect of additives with common cation on the radiolysis of ammonium, sodium and potassium nitrates in admixtures

    International Nuclear Information System (INIS)

    Kulkarni, S.P.; Garg, A.N.

    1988-01-01

    Gamma radiolysis of admixtures of NH 4 NO 3 , NaNO 3 and KNO 3 with additive salts having common cation has been studied over a wide range of nitrate salt concentration and absorbed dose. Radiolytic decomposition of nitrate salt depends on the concentration of nitrate in the admixture as well as the total absorbed dose. G(NO 2 - ) values calculated on the basis of electron fraction of the nitrate salt decrease with the increase in mol% of the nitrate salt in somewhat exponential manner. In (NaNO 3 + Na 2 SO 4 ) and (KNO 3 + KX, where X = Cl, Br, I) systems decomposition was found to increase linearly with the absorbed dose in the composition range of 20-100 mol%. The additives seem to exhibit sensitization effect causing extra decomposition by the energy transfer process in solid state. The efficiency of energy transfer depends on the nature of added salt, concentration of the nitrate in admixture and absorbed dose. (author)

  4. Investigation of Mechanism of Action of Modifying Admixtures Based on Products of Petrochemical Synthesis on Concrete Structure

    Science.gov (United States)

    Tukhareli, V. D.; Tukhareli, A. V.; Cherednichenko, T. F.

    2017-11-01

    The creation of composite materials for generating structural elements with the desired properties has always been and still remains relevant. The basis of a modern concrete technology is the creation of a high-quality artificial stone characterized by low defectiveness and structure stability. Improving the quality of concrete compositions can be achieved by using chemical admixtures from local raw materials which is a very promising task of modern materials’ science for creation of a new generation of concretes. The new generation concretes are high-tech, high-quality, multicomponent concrete mixes and compositions with admixtures that preserve the required properties in service under all operating conditions. The growing complexity of concrete caused by systemic effects that allow you to control the structure formation at all stages of the technology ensures the obtaining of composites with "directional" quality, compositions, structure and properties. The possibility to use the organic fraction of oil refining as a multifunctional hydrophobic-plasticizing admixture in the effective cement concrete is examined.

  5. Design of special planar linkages

    CERN Document Server

    Zhao, Jing-Shan; Ma, Ning; Chu, Fulei

    2013-01-01

    Planar linkages play a very important role in mechanical engineering. As the simplest closed chain mechanisms, planar four-bar linkages are widely used in mechanical engineering, civil engineering and aerospace engineering.Design of Special Planar Linkages proposes a uniform design theory for planar four-bar linkages. The merit of the method proposed in this book is that it allows engineers to directly obtain accurate results when there are such solutions for the specified n precise positions; otherwise, the best approximate solutions will be found. This book discusses the kinematics and reach

  6. Aerosol Characteristics of Admixture of Budesonide Inhalation Suspension with a Beta2-Agonist, Procaterol

    Directory of Open Access Journals (Sweden)

    Toshiko Itazawa

    2013-01-01

    Conclusions: There is a possibility that admixture might influence of aerodynamic characteristics of procaterol, but not budesonide. In vivo data will be needed for the clinical implications of our findings.

  7. Techniques and methods of characterization of admixtures for the concrete

    Directory of Open Access Journals (Sweden)

    Palacios, M.

    2003-03-01

    Full Text Available Admixtures are defined as those products that are incorporated in the moment of the process of mixture of the concrete in a quantity not bigger than 5 by mass of the cement %, with relationship to the cement content in the concrete, with object of modifying the properties of the mixture in .state fresh and/or hardened. The behaviour of the admixtures depends on its chemical and ionic composition, the organic functional groups present, and the structure of the polymer and the distribution of molecular weight of the different polymers. In the present work the techniques and methods of characterization physical-chemistry, chemistry and ionic, structural, as well as of the polymers that constitute this admixtures, are described. A lot of techniques have been employed like: ionic chromatography, ultraviolet-visible spectroscopy (UV-VIS, Fourier transform infrared spectroscopy (FTIR, Fourier transform Raman spectroscopy (FT-Raman, nuclear magnetic resonance spectroscopy (1H-RMN and 13C-RMN, gel permeation chromatography (GPC. Two commercial admixtures have been selected to carry out this characterization, a superplastificant based on policarboxilates, and a reducer of the shrinkage based on polipropilenglycol.

    RESUMEN Se definen los aditivos como aquellos productos que son incorporados en el momento del amasado del hormigón en una cantidad no mayor del 5% en masa, con relación al contenido de cemento en el hormigón, con objeto de modificar las propiedades de la mezcla en estado fresco y/o endurecido. El comportamiento de los aditivos depende de su composición química e iónica, de los grupos funcionales orgánicos presentes, de la estructura del polímero y de la distribución de pesos moleculares de los diferentes polímeros que lo constituyen. En el presente trabajo se describen diferentes técnicas y métodos de caracterización físico-química, química e iónica, estructural, así como de los polímeros que

  8. Phenomenological model of sintering of oxide nuclear fuel with doping admixtures

    Science.gov (United States)

    Baranov, V. G.; Devyatko, Yu. N.; Tenishev, A. V.; Khomyakov, O. V.

    2015-12-01

    It is shown that a change in the linear dimension of compacted UO2 in the sintering process is associated with its plastic yielding under the action of the forces of residual stress and capillary forces. From the curves of sintering of a fuel with doping admixtures in various gaseous media, its rate of creep is reduced.

  9. Tracing the origin of the east-west population admixture in the Altai region (Central Asia.

    Directory of Open Access Journals (Sweden)

    Mercedes González-Ruiz

    Full Text Available A recent discovery of Iron Age burials (Pazyryk culture in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1 whether it was a result of migratory events (eastward firstly, westward secondly, or 2 whether it was a result of a local demographic expansion in a 'contact zone' between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan. Thus, this people not only shared the same culture (Pazyryk, but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.

  10. Tracing the origin of the east-west population admixture in the Altai region (Central Asia).

    Science.gov (United States)

    González-Ruiz, Mercedes; Santos, Cristina; Jordana, Xavier; Simón, Marc; Lalueza-Fox, Carles; Gigli, Elena; Aluja, Maria Pilar; Malgosa, Assumpció

    2012-01-01

    A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a 'contact zone' between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.

  11. Efficient Record Linkage Algorithms Using Complete Linkage Clustering.

    Science.gov (United States)

    Mamun, Abdullah-Al; Aseltine, Robert; Rajasekaran, Sanguthevar

    2016-01-01

    Data from different agencies share data of the same individuals. Linking these datasets to identify all the records belonging to the same individuals is a crucial and challenging problem, especially given the large volumes of data. A large number of available algorithms for record linkage are prone to either time inefficiency or low-accuracy in finding matches and non-matches among the records. In this paper we propose efficient as well as reliable sequential and parallel algorithms for the record linkage problem employing hierarchical clustering methods. We employ complete linkage hierarchical clustering algorithms to address this problem. In addition to hierarchical clustering, we also use two other techniques: elimination of duplicate records and blocking. Our algorithms use sorting as a sub-routine to identify identical copies of records. We have tested our algorithms on datasets with millions of synthetic records. Experimental results show that our algorithms achieve nearly 100% accuracy. Parallel implementations achieve almost linear speedups. Time complexities of these algorithms do not exceed those of previous best-known algorithms. Our proposed algorithms outperform previous best-known algorithms in terms of accuracy consuming reasonable run times.

  12. North-South Business Linkages

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull; Kuada, John

    2006-01-01

    Based on empirical studies of linkages between TNCs and local firms in India, Malaysia, Vietnam, Ghana and South Africa, five themes are discussed and related to present theoretical perspectives. The themes are (1) Linakge Governance; (2) Globalisation and the dynamics in developing countries (the...... TNC-driven markets in developing countries); (3) The upgrading impact of FDI; (4) Non-equity linkages as a platform for business development, and (5) The learning perspective on international business linakges. The chapter offers at the end a three-dimanional model for impacts of business linkages....

  13. Population admixture, biological invasions and the balance between local adaptation and inbreeding depression

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Macel, M.; Wolfe, L.M.; Biere, A.

    2011-01-01

    When previously isolated populations meet and mix, the resulting admixed population can benefit from several genetic advantages, including increased genetic variation, the creation of novel genotypes and the masking of deleterious mutations. These admixture benefits are thought to play an important

  14. Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees.

    Science.gov (United States)

    Crous, Casparus J; Burgess, Treena I; Le Roux, Johannes J; Richardson, David M; Slippers, Bernard; Wingfield, Michael J

    2016-12-23

    Non-native trees have become dominant components of many landscapes, including urban ecosystems, commercial forestry plantations, fruit orchards, and as invasives in natural ecosystems. Often, these trees have been separated from their natural enemies (i.e. insects and pathogens) leading to ecological disequilibrium, that is, the immediate breakdown of historically co-evolved interactions once introduced into novel environments. Long-established, non-native tree plantations provide useful experiments to explore the dimensions of such ecological disequilibria. We quantify the status quo of non-native insect pests and pathogens catching up with their tree hosts (planted Acacia, Eucalyptus and Pinus species) in South Africa, and examine which native South African enemy species utilise these trees as hosts. Interestingly, pines, with no confamilial relatives in South Africa and the longest residence time (almost two centuries), have acquired only one highly polyphagous native pathogen. This is in contrast to acacias and eucalypts, both with many native and confamilial relatives in South Africa that have acquired more native pathogens. These patterns support the known role of phylogenetic relatedness of non-native and native floras in influencing the likelihood of pathogen shifts between them. This relationship, however, does not seem to hold for native insects. Native insects appear far more likely to expand their feeding habits onto non-native tree hosts than are native pathogens, although they are generally less damaging. The ecological disequilibrium conditions of non-native trees are deeply rooted in the eco-evolutionary experience of the host plant, co-evolved natural enemies, and native organisms from the introduced range. We should expect considerable spatial and temporal variation in ecological disequilibrium conditions among non-native taxa, which can be significantly influenced by biosecurity and management practices. Published by Oxford University Press on

  15. Linkage and association of haplotypes at the APOA1/C3/A4/A5 genecluster to familial combined hyperlipidemia

    Energy Technology Data Exchange (ETDEWEB)

    Eichenbaum-Voline, Sophie; Olivier, Michael; Jones, Emma L.; Naoumova, Rossitza P.; Jones, Bethan; Gau, Brian; Seed, Mary; Betteridge,D. John; Galton, David J.; Rubin, Edward M.; Scott, James; Shoulders,Carol C.; Pennacchio, Len A.

    2002-09-15

    Combined hyperlipidemia (CHL) is a common disorder of lipidmetabolism that leads to an increased risk of cardiovascular disease. Thelipid profile of CHL is characterised by high levels of atherogeniclipoproteins and low levels of high-density-lipoprotein-cholesterol.Apolipoprotein (APO) A5 is a newly discovered gene involved in lipidmetabolism located within 30kbp of the APOA1/C3/A4 gene cluster. Previousstudies have indicated that sequence variants in this cluster areassociated with increased plasma lipid levels. To establish whethervariation at the APOA5 gene contributes to the transmission of CHL, weperformed linkage and linkage disequilibrium (LD) tests on a large cohortof families (n=128) with familial CHL (FCHL). The linkage data producedevidence for linkage of the APOA1/C3/A4/A5 genomic interval to FCHL (NPL= 1.7, P = 0.042). The LD studies substantiated these data. Twoindependent rare alleles, APOA5c.56G and APOC3c.386G of this gene clusterwere over-transmitted in FCHL (P = 0.004 and 0.007, respectively), andthis was associated with a reduced transmission of the most commonAPOA1/C3/A4/A5 haplotype (frequency 0.4425) to affected subjects (P =0.013). The APOA5c.56G allele was associated with increased plasmatriglyceride levels in FCHL probands, whereas the second, andindependent, APOC3c.386G allele was associated with increased plasmatriglyceride levels in FCHL pedigree founders. Thus, this allele (or anallele in LD) may mark a quantitative trait associated with FCHL, as wellas representing a disease susceptibility locus for the condition. Thisstudy establishes that sequence variation in the APOA1/C3/A4/A5 genecluster contributes to the transmission of FCHL in a substantialproportion of affected families, and that these sequence variants mayalso contribute to the lipid abnormalities of the metabolic syndrome,which is present in up to 40 percent of persons with cardiovasculardisease.

  16. Population haplotype analysis and evolutionary relations of the COL2A1 gene

    NARCIS (Netherlands)

    Meulenbelt, I.; Williams, G.J.; Koppele, J.M.T.E.; Giessen, G.C.D.E. van; Slagboom, P.E.

    1996-01-01

    We have determined the allele frequencies mad pairwise linkage disequilibria of restriction fragment length polymorphisms (RFLPs) distributed over the entire COL2A1 gene (spanning 23 · 6 kb) in a population of unrelated Dutch Caucasians. Pairwise linkage disequilibrium analysis of RFLP sites between

  17. Disequilibrium implications on dose assessment in the use of NORM as building material

    International Nuclear Information System (INIS)

    Rosa, R.; Amaral, E.C.S.

    2002-01-01

    The need of reusing industrial wastes to avoid environmental impact resulting from their deposition and to reduce the management costs, indicates the building industry as an important user of large quantities of industrial wastes, mainly those generated in the ore milling. The industry of phosphate fertilizers is a typical example of this situation. The phosphate rock contains radionuclides of the U and Th decay series. During the chemical attack these radionuclides are distributed in different proportions between the phosphoric acid and the phosphogypsum, depending on the process. Several countries adopt a methodology based on the Ra-226, Th-232 and K-40 content in order to allow the use of materials with natural radionuclides. Dose assessment for the use of phosphogypsum as building material have shown that methodology is not adequate when disequilibrium exists. This paper will present some implications on dose assessment and on the use of that methodology when disequilibrium exists, using two phosphogypsum radionuclides distribution patterns obtained through different milling processes in Brazil. (author)

  18. INFLUENCE OF BACKGROUND AIR ON MICROBIAL-CONTAMINATION DURING SIMULATED IV-ADMIXTURE PREPARATION

    NARCIS (Netherlands)

    VANDOORNE, H; BAKKER, JH; MEEVIS, RF; MARSKAMP, A

    The effect of the cleanliness of environmental air on the microbial contamination of a simulated i.v.-admixture during its preparation by aseptic transfer was studied under three conditions: (i) in a laminar air flow (LAF) bench situated in a class 1000 clean room, (ii) in an LAF bench in a

  19. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

    Directory of Open Access Journals (Sweden)

    Thais C de Oliveira

    2017-07-01

    Full Text Available The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax.We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences, Peru (PER, n = 23, Colombia (COL, n = 31, and Mexico (MEX, n = 19.We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10-4 and 6.2 × 10-4 as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092. Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically

  20. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax

    Science.gov (United States)

    de Oliveira, Thais C.; Rodrigues, Priscila T.; Menezes, Maria José; Gonçalves-Lopes, Raquel M.; Bastos, Melissa S.; Lima, Nathália F.; Barbosa, Susana; Gerber, Alexandra L.; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R.

    2017-01-01

    Background The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. Methods We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). Principal findings/Conclusions We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between

  1. Unconsciously Indigenous Leadership: The Role of Cognitive Disequilibrium in Preparing Democratic Educational Leaders

    Science.gov (United States)

    Farmer, Tod Allen

    2008-01-01

    This paper focuses on the role of cognitive disequilibrium in preparing democratic educational leaders. Followers emerge into leaders with what are many times unconsciously socialized norms and values indigenous to their local culture. One of the roles of a democratic leadership preparation program is to challenge these unconsciously accepted…

  2. Application of a polycarboxylate ether admixture in RCC dam construction[ACI SP-239

    Energy Technology Data Exchange (ETDEWEB)

    Asmus, S.M.F.; Christensen, B.J.; Varley, N.J. [BASF Construction Chemicals Asia Pacific, Shanghai (China)

    2006-07-01

    Chemical admixtures are used in dam construction to improve plasticity of the dry materials mixture over time. Roller compacted concrete (RCC) has been used on many dam projects in China. However, the use of RCC has frequently resulted in water reduction problems. This paper provided details of an admixture based on polycarboxylate ether (PCE) which was developed to improve the quality of RCC constructions at the JinHong dam in China. Use of the polymer at the JinHong dam resulted in a vibration sensitive concrete that was sustained over time. Under identical mix-design and compaction conditions in the laboratory, specific gravity of the RCC was increased from 2417 kg/m{sup 3} to 2463 kg/m{sup 3}. The high specific gravity of the material resulted in satisfactory strength data from the dam project. The key-ratio of the splitting tensile strength versus compressive strength was higher than 8 per cent in all cases. A key advantage of the tailored PCE-RCC was the short Vebe times sustained over elapsed time in the RCC. Without additional compaction or vibration efforts, the specific density of RCC was better than conventional admixture technologies. The reduced viscosity provided cement paste films which formed on the surface of each layer of the RCC, which resulted in better bonding between the layers. It was concluded that the new PCE polymer is compatible with alternative retarder systems, which contributes to more extensive setting times under strict hydration regimes. 7 refs., 4 tabs., 4 figs.

  3. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

    Directory of Open Access Journals (Sweden)

    Omberg Larsson

    2012-06-01

    Full Text Available Abstract Background Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Results Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. Conclusions By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

  4. Population Genetic Structure of the People of Qatar

    Science.gov (United States)

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A.; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W.; Fuller, Jennifer; Hackett, Neil R.; Crystal, Ronald G.; Clark, Andrew G.

    2010-01-01

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. PMID:20579625

  5. Population genetic structure of the people of Qatar.

    Science.gov (United States)

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W; Fuller, Jennifer; Hackett, Neil R; Crystal, Ronald G; Clark, Andrew G

    2010-07-09

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  6. Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations.

    Science.gov (United States)

    Haber, Marc; Mezzavilla, Massimo; Bergström, Anders; Prado-Martinez, Javier; Hallast, Pille; Saif-Ali, Riyadh; Al-Habori, Molham; Dedoussis, George; Zeggini, Eleftheria; Blue-Smith, Jason; Wells, R Spencer; Xue, Yali; Zalloua, Pierre A; Tyler-Smith, Chris

    2016-12-01

    Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750-7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700-7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%-30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  7. Studies on the Effect of Rice Husk Ash as Cement Admixture * M.U ...

    African Journals Online (AJOL)

    acer

    Studies on the Effect of Rice Husk Ash as Cement Admixture. *. 1. M.U Dabai,. 1 ... production of durable concrete and at the same time it is a ... indigenous and waste, materials in concrete. One .... (4.08%). The Iron oxide may be from laterite.

  8. Influence of random daughter exposure rate, unattachment fraction, and disequilibrium on occurrence of lung tumors

    International Nuclear Information System (INIS)

    Cross, F.T.; Palmer, R.F.; Dagle, G.E.; Busch, R.H.; Buschbom, R.L.

    1983-10-01

    Groups of male, specific-pathogen-free (SPF), Wistar rats were exposed to several concentrations of radon daughters and uranium ore dust to clarify the roles of exposure rate, unattached RaA daughters, and the degree of radon daughter disequilibrium, in the development of respiratory system disease. Modeled, human-dosimetric data indicate that the dose to sensitive tissues of the respiratory tract increases with increasing radon-daughter unattachment fraction and degree of disequilibrium. Experimental verification of these dose-effect relationships is needed to protect the health of workers and of the public exposed to radon-daughter environments. Data bearing on these relationships as well as updated results of experiments designed to test the role of radon-daughter exposure rate on lung-tumor incidence are reported. 13 references, 3 tables

  9. Statistical and Detailed Analysis on Fiber Reinforced Self-Compacting Concrete Containing Admixtures- A State of Art of Review

    Science.gov (United States)

    Athiyamaan, V.; Mohan Ganesh, G.

    2017-11-01

    Self-Compacting Concrete is one of the special concretes that have ability to flow and consolidate on its own weight, completely fill the formwork even in the presence of dense reinforcement; whilst maintaining its homogeneity throughout the formwork without any requirement for vibration. Researchers all over the world are developing high performance concrete by adding various Fibers, admixtures in different proportions. Various different kinds Fibers like glass, steel, carbon, Poly propylene and aramid Fibers provide improvement in concrete properties like tensile strength, fatigue characteristic, durability, shrinkage, impact, erosion resistance and serviceability of concrete[6]. It includes fundamental study on fiber reinforced self-compacting concrete with admixtures; its rheological properties, mechanical properties and overview study on design methodology statistical approaches regarding optimizing the concrete performances. The study has been classified into seven basic chapters: introduction, phenomenal study on material properties review on self-compacting concrete, overview on fiber reinforced self-compacting concrete containing admixtures, review on design and analysis of experiment; a statistical approach, summary of existing works on FRSCC and statistical modeling, literature review and, conclusion. It is so eminent to know the resent studies that had been done on polymer based binder materials (fly ash, metakaolin, GGBS, etc.), fiber reinforced concrete and SCC; to do an effective research on fiber reinforced self-compacting concrete containing admixtures. The key aim of the study is to sort-out the research gap and to gain a complete knowledge on polymer based Self compacting fiber reinforced concrete.

  10. Admixture mapping of African-American women in the AMBER Consortium identifies new loci for breast cancer and estrogen-receptor subtypes

    Directory of Open Access Journals (Sweden)

    Edward Antonio Ruiz-Narvaez

    2016-09-01

    Full Text Available Recent genetic admixture coupled with striking differences in incidence of estrogen receptor (ER breast cancer subtypes, as well as severity, between women of African and European ancestry, provides an excellent rationale for performing admixture mapping in African American women with breast cancer risk. We performed the largest breast cancer admixture mapping study with in African American women to identify novel genomic regions associated with the disease. We conducted a genome-wide admixture scan using 2,624 autosomal ancestry informative markers (AIMs in 3,629 breast cancer cases (including 1,968 ER-positive, 1093 ER-negative and 601 triple-negative and 4,658 controls from the African American Breast Cancer Epidemiology and Risk (AMBER Consortium, a collaborative study of four large geographically different epidemiological studies of breast cancer in African American women. We used an independent case-control study to test for SNP association in regions with genome-wide significant admixture signals. We found two novel genome-wide significant regions of excess African ancestry, 4p16.1 and 17q25.1, associated with ER-positive breast cancer. Two regions known to harbor breast cancer variants, 10q26 and 11q13, were also identified with excess of African ancestry. Fine-mapping of the identified genome-wide significant regions suggests the presence of significant genetic associations with ER-positive breast cancer in 4p16.1 and 11q13. In summary, we identified three novel genomic regions associated with breast cancer risk by ER status, suggesting that additional previously unidentified variants may contribute to the racial differences in breast cancer risk in the African American population.

  11. The effect of structured triglycerides on the kinetic stability of total nutrient admixtures.

    Science.gov (United States)

    Balogh, Judit; Bubenik, Júlia; Dredán, Judit; Csempesz, Ferenc; Kiss, Dorottya; Zelkó, Romána

    2005-10-05

    The physical stability of two types of total parenteral nutrient (TPN) admixtures was studied as a function of storage time and temperature. One of them contained only structured triglycerides and the other exclusively long-chain triglycerides as lipid components. Droplet size of the mixtures was followed by photon correlation spectroscopy for 10 days. Zeta potential and dynamic surface tension measurements were carried out to evaluate the possible changes in the charge and interfacial surface tension of the emulsion droplets during the storage. pH values were monitored in order to follow the possible decomposition processes in the course of storage. Droplet size of emulsions prepared with lipids containing exclusively long-chain triglycerides showed remarkable increase after 4 days of storage in contrast with that of the mixtures containing structured lipids. The obtained results indicate that besides the advantageous metabolic effects of structured triglycerides, their application is recommended to improve the physical stability of TPN admixtures.

  12. Influence of chloride admixtures on cement matrix durability

    International Nuclear Information System (INIS)

    Sheikh, I.A.; Zamorani, E.; Serrini, G.

    1989-01-01

    The influence of various inorganic salts, as chloride admixtures to Portland cement, on the mechanical properties and the durability of the matrix has been studied. The salts used in this study are chromium, nickel and cadmium chlorides. Improved compressive strength values are obtained which have been correlated to the stable metal hydroxide formation in high pH environment. Under static water conditions at 50 0 C, hydrolyzed chloride ions exhibit adverse effects on the matrix durability through rapid release of calcium as calcium chloride in the initial period of leaching. On the contrary, enhanced matrix durability is obtained on long term leaching in the case of cement containing chromium chloride

  13. Assessment of anti-factor Xa activity of heparin in binary parenteral nutrition admixtures for premature neonates.

    Science.gov (United States)

    Foinard, A; Perez, M; Barthélémy, C; Lannoy, D; Flamein, F; Storme, L; Tournoys, A; Décaudin, B; Odou, P

    2015-07-01

    An in vitro study was carried out to determine the anti-Xa activity of heparin in binary parenteral nutrition (BPN) admixtures for premature neonates in our neonatal intensive care unit (NICU) after a 24-hour infusion, as well as to assess drug interaction with a 50% glucose solution. Two types of bags were prepared: (1) BPN admixtures (composition defined in the NICU) including sodium heparin at 77 UI/mL and (2) bags containing only G50% with sodium heparin at 193 UI/mL. The anti-Xa activity of heparin was measured in bags at T0, after the 24-hour infusion and in eluates at the outlet of the infusion line after 24hours, using a validated chromogenic anti-Xa method. Comparisons of the mean concentration observed with the theoretical value for anti-Xa activity were performed with the Student t-test. Mean values of anti-Xa activity do not differ significantly from the values expected for all conditions. We found a slight variation in anti-Xa activity when infused over 24hours for both types of bags, with and without in-line filtration, showing that heparin remains stable during this infusion period in both BPN admixtures and G50%. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  14. Performance Using Bamboo Fiber Ash Concrete as Admixture Adding Superplasticizer

    Science.gov (United States)

    Vasudevan, Gunalaan

    2017-06-01

    The increasing demand on natural resources for housing provisions in developing countries have called for sourcing and use of sustainable local materials for building and housing delivery. Natural materials to be considered sustainable for building construction should be ‘green’ and obtained from local sources, including rapidly renewable plant materials like palm fronds and bamboo, recycled materials and other products that are reusable and renewable. Each year, tens of millions of tons of bamboo are utilized commercially, generating a vast amount of waste. Besides that, bamboo fiber is easy availability, low density, low production cost and satisfactory mechanical properties. One solution is to activate this waste by using it as an additive admixture in concrete to keep it out of landfills and save money on waste disposal. The research investigates the mechanical and physical properties of bamboo fiber powder in a blended Portland cement. The structural value of the bamboo fiber powder in a blended Portland cement was evaluated with consideration for its suitability in concrete. Varied percentage of bamboo fiber powder (BFP) at 0%, 5%, 10%, 15%, and 20% as an admixture in 1:2:4 concrete mixes. The workability of the mix was determined through slump; standard consistency test was carried on the cement. Compressive strength of hardened cured (150 x 150 x 150) mm concrete cubes at 7days, 14days and 28days were tested.

  15. [MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data].

    Science.gov (United States)

    Liu, Ren-Hu; Meng, Jin-Ling

    2003-05-01

    MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However, the PC version, MAPMAKER 3.0 for PC, could not draw the genetic linkage maps that its Macintosh version, MAPMAKER 3.0 for Macintosh,was able to do. Especially in recent years, Macintosh computer is much less popular than PC. Most of the geneticists use PC to analyze their genetic linkage data. So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for. Microsoft Excel,one component of Microsoft Office package, is one of the most popular software in laboratory data processing. Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel. Using this program language, we can take creative control of Excel, including genetic linkage map construction, automatic data processing and more. In this paper, a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data. Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application. This software is just an Excel format file. You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel's Visual Basic Editor.

  16. From Enclave to Linkage Economies?

    DEFF Research Database (Denmark)

    Hansen, Michael W.

    as the enclave economy par excellence, moving in with fully integrated value chains, extracting resources and exporting them as commodities having virtually no linkages to the local economy. However, new opportunities for promoting linkages are offered by changing business strategies of local African enterprises...... as well as foreign multinational corporations (MNCs). MNCs in extractives are increasingly seeking local linkages as part of their efficiency, risk, and asset-seeking strategies, and linkage programmes are becoming integral elements in many MNCs’ corporate social responsibility (CSR) activities....... At the same time, local African enterprises are eager to, and increasingly capable of, linking up to the foreign investors in order to expand their activities and acquire technology, skills and market access. The changing strategies of MNCs and the improving capabilities of African enterprises offer new...

  17. Demographic Disequilibrium in Early Twentieth Century Thailand: Falling Mortality, Rising Fertility, or Both?

    Science.gov (United States)

    Carmichael, Gordon A

    2008-07-17

    Estimates of Thai crude birth and death rates date from 1920 when the former was around 20 per thousand higher than the latter, implying natural increase of 2 percent per annum. Such disequilibrium cannot have been the norm over the long term historical past, when population growth must have been comparatively slow. This paper explores the bases for likely past relative equilibrium between Siamese birth and death rates, then seeks to explain the disequilibrium apparent by 1920. Classic demographic transition theory postulates initially high birth and death rates, this equilibrium eventually being broken by falling mortality. In Thailand, however, there is likely to have been both significant mortality decline and appreciable fertility increase after 1850, as the virtual elimination of indigenous warfare, rapid growth of the export rice economy and the demise of slavery and corvée labour created a new domestic environment. Characterized by more dispersed, often frontier, settlement, this environment was unprecedentedly sedate and settled, afforded ordinary households a previously unknown level of control over their resources of labour, and generated optimism about prospects for the next generation.

  18. The evolutionary history of Drosophila buzzatii. XXXII. Linkage disequilibrium between allozymes and chromosome inversions in two colonizing populations.

    Science.gov (United States)

    Betrán, E; Quezada-Díaz, J E; Ruiz, A; Santos, M; Fontdevila, A

    1995-02-01

    Chromosome polymorphism in Drosophila buzzatii is under selection but the genes responsible for the effect of the inversions of fitness are unknown. On the other hand, there is evidence for selection on several allozyme loci but the presence of paracentric inversions on the second chromosome, where most of the polymorphic loci are located, complicates the interpretation. Studies of the associations between allozymes and inversions are thus necessary to help understand the effect of selection at both the chromosomal and allozymic level. Until now this kind of information has only been available in D. buzzatii for two loci, Est-1 and Est-2, in Australian populations. Here we describe the genetic constitution of two Old World populations, Carboneras and Colera. Emphasis has been placed on the analysis of the linkage disequilibria between the second chromosome arrangements and three allozyme loci, Est-2, Pept-2 and Aldox, located on this chromosome. In addition, the recombination frequencies between the loci, and between the loci and the inversion breakpoints, have been estimated and a genetic map of the three loci has been produced. The two populations differ in allele and arrangement frequencies, as well as in the pattern of one-locus disequilibria. Est-2 and Aldox are associated with the second chromosome arrangements in both populations. On the other hand, Pept-2 is associated with the inversions in Colera but not in Carboneras. The gametic associations among the three loci are discussed taking into account the position of these loci on the chromosome map and the lack of recombination in the heterokaryotypes.

  19. Quantitative trait loci mapping of calving and conformation traits on Bos taurus autosome 18 in the German Holstein population.

    Science.gov (United States)

    Brand, B; Baes, C; Mayer, M; Reinsch, N; Seidenspinner, T; Thaller, G; Kühn, Ch

    2010-03-01

    Linkage, linkage disequilibrium, and combined linkage and linkage disequilibrium analyses were performed to map quantitative trait loci (QTL) affecting calving and conformation traits on Bos taurus autosome 18 (BTA18) in the German Holstein population. Six paternal half-sib families consisting of a total of 1,054 animals were genotyped on 28 genetic markers in the telomeric region on BTA18 spanning approximately 30 Mb. Calving traits, body type traits, and udder type traits were investigated. Using univariately estimated breeding values, maternal and direct effects on calving ease and stillbirth were analyzed separately for first- and further-parity calvings. The QTL initially identified by separate linkage and linkage disequilibrium analyses could be confirmed by a combined linkage and linkage disequilibrium analysis for udder composite index, udder depth, fore udder attachment, front teat placement, body depth, rump angle, and direct effects on calving ease and stillbirth. Concurrence of QTL peaks and a similar shape of restricted log-likelihood ratio profiles were observed between udder type traits and for body depth and calving traits, respectively. Association analyses were performed for markers flanking the most likely QTL positions by applying a mixed model including a fixed allele effect of the maternally inherited allele and a random polygenic effect. Results indicated that microsatellite marker DIK4234 (located at 53.3 Mb) is associated with maternal effects on stillbirth, direct effects on calving ease, and body depth. A comparison of effects for maternally inherited DIK4234 alleles indicated a favorable, positive correlation of maternal and direct effects on calving. Additionally, the association of maternally inherited DIK4234 marker alleles with body depth implied that conformation traits might provide the functional background of the QTL for calving traits. For udder type traits, the strong coincidence of QTL peaks and the position of the QTL in a

  20. Challenges in administrative data linkage for research

    Directory of Open Access Journals (Sweden)

    Katie Harron

    2017-12-01

    Full Text Available Linkage of population-based administrative data is a valuable tool for combining detailed individual-level information from different sources for research. While not a substitute for classical studies based on primary data collection, analyses of linked administrative data can answer questions that require large sample sizes or detailed data on hard-to-reach populations, and generate evidence with a high level of external validity and applicability for policy making. There are unique challenges in the appropriate research use of linked administrative data, for example with respect to bias from linkage errors where records cannot be linked or are linked together incorrectly. For confidentiality and other reasons, the separation of data linkage processes and analysis of linked data is generally regarded as best practice. However, the ‘black box’ of data linkage can make it difficult for researchers to judge the reliability of the resulting linked data for their required purposes. This article aims to provide an overview of challenges in linking administrative data for research. We aim to increase understanding of the implications of (i the data linkage environment and privacy preservation; (ii the linkage process itself (including data preparation, and deterministic and probabilistic linkage methods and (iii linkage quality and potential bias in linked data. We draw on examples from a number of countries to illustrate a range of approaches for data linkage in different contexts.

  1. Equilibrium and disequilibrium chemistry of adiabatic, solar-composition planetary atmospheres

    Science.gov (United States)

    Lewis, J. S.

    1976-01-01

    The impact of atmospheric and cloud-structure models on the nonequilibrium chemical behavior of the atmospheres of the Jovian planets is discussed. Quantitative constraints on photochemical, lightning, and charged-particle production of organic matter and chromophores are emphasized whenever available. These considerations imply that inorganic chromophore production is far more important than that of organic chromophores, and that lightning is probably a negligibly significant process relative to photochemistry on Jupiter. Production of complex molecules by gas-phase disequilibrium processes on Saturn, Uranus, and Neptune is severely limited by condensation of even simple intermediates.

  2. The origin of early age expansions induced in cementitious materials containing shrinkage reducing admixtures

    International Nuclear Information System (INIS)

    Sant, Gaurav; Lothenbach, Barbara; Juilland, Patrick; Le Saout, Gwenn; Weiss, Jason; Scrivener, Karen

    2011-01-01

    Studies on the early-age shrinkage behavior of cement pastes, mortars, and concretes containing shrinkage reducing admixtures (SRAs) have indicated these mixtures frequently exhibit an expansion shortly after setting. While the magnitude of the expansion has been noted to be a function of the chemistry of the cement and the admixture dosage; the cause of the expansion is not clearly understood. This investigation uses measurements of autogenous deformation, X-ray diffraction, pore solution analysis, thermogravimetry, and scanning electron microscopy to study the early-age properties and describe the mechanism of the expansion in OPC pastes made with and without SRA. The composition of the pore solution indicates that the presence of the SRA increases the portlandite oversaturation level in solution which can result in higher crystallization stresses which could lead to an expansion. This observation is supported by deformation calculations for the systems examined.

  3. On polluted by admixtures plasma cloud state diagnostics

    International Nuclear Information System (INIS)

    Temko, S.W.; Temko, K.W.; Kuz'min, S.K.

    1993-01-01

    The state of bounded plasma is dependent on perturbations which are caused from changing of inner and outer thermodynamical parameters. The authors describe interactions in a plasma cloud by potential functions. Potential functions are mathematical models of real interactions of particles with each others and with ionized cloud surface. Potential functions define potential energy of corresponding interactions at ionized cloud. Potential functions are sums of far-action and near-action potentials. An ionized cloud is formed under action of inner, outer and surface forces nearly connected with each others. The result of the indicated forces joint action is geometrical form and dimensions of the weakly ionized plasma cloud. Geometrical form of the cloud and its dimensions are able to be changed. They consider only the small changing of small perturbations type. Surface geometrical form and dimensions of the cloud are not given a priori. They are to be obtained by self-consistent problem solving. The self-consistent problem is solved by space non-linear statistical thermodynamics proposed before by the authors. They use abstract potential theory, distribution theory, results by N.M. Krylov and N.N. Bogoljubov and known N.N. Bogoljubov methods of statistical physics. To choose potential functions, their numerical parameters, surface form and dimensions of the cloud, they use optimal experiment planning, likelihood method, Monte-Carlo, directed random search and computer experiment methods. To be likelihood function they used free energy of ionized cloud with admixtures. They refuse describing single particle behavior at small volume. They consider particles to be washed spots and describe particles by distributions. According to R. Feinman it is lawful. Bounded plasma state is described by vector-density of particles distribution. Term distribution is used in Sobolev-Schwartc sence. To precipitate admixtures is effective ultrasound coagulation

  4. Uranium series disequilibrium in the coastal surface sediments and sea water of the Arabian sea

    Digital Repository Service at National Institute of Oceanography (India)

    Joshi, L.U.; Zingde, M.D.

    activity ratios in leachates, and residues after removal of surface organic matter from the sediment particles by treatment with hydrogen peroxide and 0.05M HCl, revealed disequilibrium between sup(238) U and sup(234) U only in the surface organic matter...

  5. Analysis of admixture and genetic structure of two Native American groups of Southern Argentinean Patagonia.

    Science.gov (United States)

    Sala, Andrea; Corach, Daniel

    2014-03-01

    Argentinean Patagonia is inhabited by people that live principally in urban areas and by small isolated groups of individuals that belong to indigenous aboriginal groups; this territory exhibits the lowest population density of the country. Mapuche and Tehuelche (Mapudungun linguistic branch), are the only extant Native American groups that inhabit the Argentinean Patagonian provinces of Río Negro and Chubut. Fifteen autosomal STRs, 17 Y-STRs, mtDNA full length control region sequence and two sets of Y and mtDNA-coding region SNPs were analyzed in a set of 434 unrelated individuals. The sample set included two aboriginal groups, a group of individuals whose family name included Native American linguistic root and urban samples from Chubut, Río Negro and Buenos Aires provinces of Argentina. Specific Y Amerindian haplogroup Q1 was found in 87.5% in Mapuche and 58.82% in Tehuelche, while the Amerindian mtDNA haplogroups were present in all the aboriginal sample contributors investigated. Admixture analysis performed by means of autosomal and Y-STRs showed the highest degree of admixture in individuals carrying Mapuche surnames, followed by urban populations, and finally by isolated Native American populations as less degree of admixture. The study provided novel genetic information about the Mapuche and Tehuelche people and allowed us to establish a genetic correlation among individuals with Mapudungun surnames that demonstrates not only a linguistic but also a genetic relationship to the isolated aboriginal communities, representing a suitable proxy indicator for assessing genealogical background.

  6. Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers.

    Science.gov (United States)

    Marcheco-Teruel, Beatriz; Parra, Esteban J; Fuentes-Smith, Evelyn; Salas, Antonio; Buttenschøn, Henriette N; Demontis, Ditte; Torres-Español, María; Marín-Padrón, Lilia C; Gómez-Cabezas, Enrique J; Alvarez-Iglesias, Vanesa; Mosquera-Miguel, Ana; Martínez-Fuentes, Antonio; Carracedo, Angel; Børglum, Anders D; Mors, Ole

    2014-07-01

    We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

  7. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

    DEFF Research Database (Denmark)

    Vilhjálmsson, Bjarni J; Yang, Jian; Finucane, Hilary K

    2015-01-01

    to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred...

  8. The Lu-Hf isotope composition of cratonic lithosphere: disequilibrium between garnet and clinopyroxene in kimberlite xenoliths

    NARCIS (Netherlands)

    Simon, N.S.C.; Carlson, R.W.; Pearson, D.G.; Davies, G.R.

    2002-01-01

    12th Annual V.M. Goldschmidt Conference Davos Switzerland, The Lu-Hf isotope composition of cratonic lithosphere: disequilibrium between garnet and clinopyroxene in kimberlite xenoliths (DTM, Carnegie Institution of Washington), Pearson, D.G. (University of Durham)

  9. Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping.

    Directory of Open Access Journals (Sweden)

    Carolina Font i Forcada

    Full Text Available To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain, and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM approach using co-ancestry values from population structure and kinship estimates (K model as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.

  10. [Accuracy, precision and speed of parenteral nutrition admixture bags manufacturing: comparison between automated and manual methods].

    Science.gov (United States)

    Zegbeh, H; Pirot, F; Quessada, T; Durand, T; Vételé, F; Rose, A; Bréant, V; Aulagner, G

    2011-01-01

    The parenteral nutrition admixture (PNA) manufacturing in hospital pharmacy is realized by aseptic transfer (AT) or sterilizing filtration (SF). The development of filling systems for PNA manufacturing requires, without standard, an evaluation comparing to traditional methods of SF. The filling accuracy of automated AT and SF was evaluated by mass and physical-chemistry tests in repeatability conditions (identical composition of PNA; n=five bags) and reproducibility conditions (different composition of PNA; n=57 bags). For each manufacturing method, the filling precision and the average time for PNA bags manufacturing were evaluated starting from an identical composition and volume PNA (n=five trials). Both manufacturing methods did not show significant difference of accuracy. Precision of both methods was lower than limits generally admitted for acceptability of mass and physical-chemistry tests. However, the manufacturing time for SF was superior (five different binary admixtures in five bags) or inferior (one identical binary admixture in five bags) to time recorded for automated AT. We show that serial manufacturing of PNA bags by SF with identical composition is faster than automated AT. Nevertheless, automated AT is faster than SF in variable composition of PNA. The manufacturing method choice will be motivate by the nature (i. e., variable composition or not) of the manufactured bags. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  11. Physicochemical stability of ternary admixtures of butorphanol, ketamine, and droperidol in polyolefin bags for patient-controlled analgesia use

    Directory of Open Access Journals (Sweden)

    Fang BX

    2016-11-01

    Full Text Available Baoxia Fang,1 Linhai Wang,2 Junfeng Gu,3 Fuchao Chen,1 Xiao-ya Shi1 1Department of Pharmacy, Dongfeng Hospital, 2Department of Pharmacy, 3Department of Anesthesiology, Renmin Hospital, Hubei University of Medicine, Hubei, People’s Republic of China Background: Delivery of drug admixtures by intravenous patient-controlled analgesia is a common practice for the management of postoperative pain; however, analytical confirmation of the compatibility and stability of butorphanol tartrate, ketamine hydrochloride, and droperidol combined in ternary admixtures is not available.Methods: Butorphanol tartrate, ketamine hydrochloride, and droperidol have been examined for compatibility and stability when combined with 0.9% sodium chloride injection stored at 4°C and 25°C with light protection for a total of 14 days. Concentrations were 0.067 mg/mL, 1.33 mg/mL, and 0.033 mg/mL for butorphanol tartrate, ketamine hydrochloride, and droperidol, respectively. Drug concentrations were determined using high-performance liquid chromatographic analysis.Results: All three drugs were very stable (>97% at 4°C and 25°C for 14 days. The ternary admixtures were initially clear and colorless throughout the observation period, and the pH value did not change significantly.Conclusion: The results confirm that the ternary admixture of butorphanol tartrate 0.067 mg/mL, ketamine hydrochloride 1.33 mg/mL, and droperidol 0.033 mg/mL in 0.9% sodium chloride injection were stable for 14 days when stored in polyolefin bags at 4°C and 25°C and protected from light. Keywords: analgesia, patient-controlled analgesia, drug stability, butorphanol, ketamine, droperidol, HPLC

  12. Probabilistic linkage to enhance deterministic algorithms and reduce data linkage errors in hospital administrative data.

    Science.gov (United States)

    Hagger-Johnson, Gareth; Harron, Katie; Goldstein, Harvey; Aldridge, Robert; Gilbert, Ruth

    2017-06-30

     BACKGROUND: The pseudonymisation algorithm used to link together episodes of care belonging to the same patients in England (HESID) has never undergone any formal evaluation, to determine the extent of data linkage error. To quantify improvements in linkage accuracy from adding probabilistic linkage to existing deterministic HESID algorithms. Inpatient admissions to NHS hospitals in England (Hospital Episode Statistics, HES) over 17 years (1998 to 2015) for a sample of patients (born 13/28th of months in 1992/1998/2005/2012). We compared the existing deterministic algorithm with one that included an additional probabilistic step, in relation to a reference standard created using enhanced probabilistic matching with additional clinical and demographic information. Missed and false matches were quantified and the impact on estimates of hospital readmission within one year were determined. HESID produced a high missed match rate, improving over time (8.6% in 1998 to 0.4% in 2015). Missed matches were more common for ethnic minorities, those living in areas of high socio-economic deprivation, foreign patients and those with 'no fixed abode'. Estimates of the readmission rate were biased for several patient groups owing to missed matches, which was reduced for nearly all groups. CONCLUSION: Probabilistic linkage of HES reduced missed matches and bias in estimated readmission rates, with clear implications for commissioning, service evaluation and performance monitoring of hospitals. The existing algorithm should be modified to address data linkage error, and a retrospective update of the existing data would address existing linkage errors and their implications.

  13. A Formalization of Linkage Analysis

    DEFF Research Database (Denmark)

    Ingolfsdottir, Anna; Christensen, A.I.; Hansen, Jens A.

    In this report a formalization of genetic linkage analysis is introduced. Linkage analysis is a computationally hard biomathematical method, which purpose is to locate genes on the human genome. It is rooted in the new area of bioinformatics and no formalization of the method has previously been ...

  14. On the use of crystalline admixtures in cement based construction materials: from porosity reducers to promoters of self healing

    Science.gov (United States)

    Ferrara, Liberato; Krelani, Visar; Moretti, Fabio

    2016-08-01

    The project detailed in this paper aims at a thorough characterization of the effects of crystalline admixtures, currently employed as porosity reducing admixtures, on the self-healing capacity of the cementitious composites, i.e. their capacity to completely or partially re-seal cracks and, in case, also exhibit recovery of mechanical properties. The problem has been investigated with reference to both a normal strength concrete (NSC) and a high performance fibre reinforced cementitious composite (HPFRCC). In the latter case, the influence of flow-induced fibre alignment has also been considered in the experimental investigation. With reference to either 3-point (for NSC) or 4-point (for HPFRCC) bending tests performed up to controlled crack opening and up to failure, respectively before and after exposure/conditioning recovery of stiffness and stress bearing capacity has been evaluated to assess the self-healing capacity. In a durability-based design framework, self-healing indices to quantify the recovery of mechanical properties will also be defined. In NSC, crystalline admixtures are able to promote up to 60% of crack sealing even under exposure to open air. In the case of HPFRCCs, which would already feature autogenous healing capacity because of their peculiar mix compositions, the synergy between the dispersed fibre reinforcement and the action of the crystalline admixture has resulted in a likely ‘chemical pre-stressing’ of the same reinforcement, from which the recovery of mechanical performance of the material has greatly benefited, up to levels even higher than the performance of the virgin un-cracked material.

  15. Rectification cleaning AsCl3 from the admixture of oxygen

    Directory of Open Access Journals (Sweden)

    Maznitska O. V.

    2008-06-01

    Full Text Available The process of the rectification cleaning of three-chlorous arsenic from the admixtures of products of his hydrolysis in the atmosphere of chlorous hydrogen has been considered in the article. Dependence of coefficient of relative volatility a three-chlorous arsenic from his concentration in muriatic solution is explored. The conduct of coefficient of relative volatility with concentrations of HCl and AsCl3 is compared. Saving of equalization of balance and equalization of working curve of column at such conduct of process of rectification is shown.

  16. Employment in Disequilibrium: a Disaggregated Approach on a Panel of French Firms

    OpenAIRE

    Brigitte Dormont

    1989-01-01

    The purpose of this paper is to understand disequilibrium phenomena at a disaggregated level. By using data on French firms, we carry out the estimation of labor demand model with two regimes, which correspond to the Keynesian and classical hypotheses. The results enable us to characterize classical firms as being particularly good performers: they have more rapid growth, younger productive plant and higher productivity gains and profitability. Classical firms stand out, with respect to their...

  17. Fine Mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds

    DEFF Research Database (Denmark)

    Sahana, G; Lund, M S; Andersson-Eklund, L

    2008-01-01

    A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over...... the whole chromosome in the 16 original families and 18 additional half-sib families. This enabled linkage disequilibrium information to be used in the analysis. Data were analysed by an approach that combines information from linkage and linkage disequilibrium, which allowed the QTL affecting clinical...... mastitis to be mapped to a small interval (BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker...

  18. Thermally actuated linkage arrangement

    International Nuclear Information System (INIS)

    Anderson, P.M.

    1981-01-01

    A reusable thermally actuated linkage arrangement includes a first link member having a longitudinal bore therein adapted to receive at least a portion of a second link member therein, the first and second members being sized to effect an interference fit preventing relative movement there-between at a temperature below a predetermined temperature. The link members have different coefficients of thermal expansion so that when the linkage is selectively heated by heating element to a temperature above the predetermined temperature, relative longitudinal and/or rotational movement between the first and second link members is enabled. Two embodiments of a thermally activated linkage are disclosed which find particular application in actuators for a grapple head positioning arm in a nuclear reactor fuel handling mechanism to facilitate back-up safety retraction of the grapple head independently from the primary fuel handling mechanism drive system. (author)

  19. The impact of accelerating faster than exponential population growth on genetic variation.

    Science.gov (United States)

    Reppell, Mark; Boehnke, Michael; Zöllner, Sebastian

    2014-03-01

    Current human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models' effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times.

  20. Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts.

    Directory of Open Access Journals (Sweden)

    Jean-Tristan Brandenburg

    2017-03-01

    Full Text Available Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans.

  1. Utilization of black liquor as concrete admixture and set retarder aid

    OpenAIRE

    El-Mekkawi, Samar A.; Ismail, Ibrahim M.; El-Attar, Mohammed M.; Fahmy, Alaa A.; Mohammed, Samia S.

    2011-01-01

    The utilization of black liquor, produced by the pulp and paper industry in Egypt, as a workability aid and set retarder admixture has been investigated. This approach may help eliminate the environmentally polluting black liquor waste. It also provides a low cost by-product, which can be widely used in the construction industry. The properties of black liquor and its performance on concrete at two different ratios of water to cement have been studied. The results revealed that black liquor f...

  2. Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

    Science.gov (United States)

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  3. A comprehensive overview about the influence of different admixtures and additives on the properties of alkali-activated fly ash

    International Nuclear Information System (INIS)

    Rashad, Alaa M.

    2014-01-01

    Highlights: • PVA fiber changed the impact failure mode from brittle pattern to ductile pattern. • Superplasticizer of lignosulphonates-based improved the workability. • Slag in AAFA decreased workability and increased shrinkage and compressive strength. • MK in AAFA improved workability and compressive strength and prolonged setting time. • 5% Gypsum in AAFA increased compressive strength, but FGDG decreased it. - Abstract: The development of new binders, as an alternative to Portland cement (PC), by alkaline activation, is a current researchers interest. Alkali-activated fly ash (AAFA) binder is obtained by a manufacturing process less energy-intensive than PC and involves lower greenhouse gasses emission. Utilizing AAFA system as binder material can limit the consumption of virgin materials (limestone and sand) required in PC manufacture. AAFA belongs to be prospective material in the field of Civil Engineering where it can resist aggressive acids, resist sulfate attacks, resist aggregate alkali reaction, and resist elevated temperatures. Researchers have employed different fibers, chemical admixtures, mineral admixtures, additives and other materials in AAFA system aiming to modify special properties of this system. This paper presents a comprehensive overview of the previous works carried out on using different admixtures and additives in AAFA system

  4. Combined Use of Shrinkage Reducing Admixture and CaO in Cement Based Materials

    Science.gov (United States)

    Tittarelli, Francesca; Giosuè, Chiara; Monosi, Saveria

    2017-10-01

    The combined addition of a Shrinkage-Reducing Admixture (SRA) with a CaO-based expansive agent (CaO) has been found to have a synergistic effect to improve the dimensional stability of cement based materials. In this work, aimed to further investigate the effect, mortar and self-compacting concrete specimens were prepared either without admixtures, as reference, or with SRA alone and/or CaO. Their performance was compared in terms of compressive strength and free shrinkage measurements. Results showed that the synergistic effect in reducing shrinkage is confirmed in the specimens manufactured with SRA and CaO. In order to clarify this phenomenon, the effect of SRA on the hydration of CaO as well as cement was evaluated through different techniques. The obtained results show that SRA induces a finer microstructure of the CaO hydration products and a retarding effect on the microstructure development of cement based materials. A more deformable mortar or concrete, due to the delay in microstructure development by SRA, coupled with a finer microstructure of CaO hydration products could allow higher early expansion, which might contribute in contrasting better the successive drying shrinkage.

  5. Variants for HDL-C, LDL-C, and triglycerides identified from admixture mapping and fine-mapping analysis in African American families.

    Science.gov (United States)

    Shetty, Priya B; Tang, Hua; Feng, Tao; Tayo, Bamidele; Morrison, Alanna C; Kardia, Sharon L R; Hanis, Craig L; Arnett, Donna K; Hunt, Steven C; Boerwinkle, Eric; Rao, Dabeeru C; Cooper, Richard S; Risch, Neil; Zhu, Xiaofeng

    2015-02-01

    Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African Americans. The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. The analysis was performed in 1905 unrelated African American subjects from the National Heart, Lung and Blood Institute's Family Blood Pressure Program (FBPP). Regions showing admixture evidence were followed-up with family-based association analysis in 3556 African American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age(2), sex, body mass index, and genome-wide mean ancestry to minimize the confounding caused by population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (low-density lipoprotein cholesterol), 8 (high-density lipoprotein cholesterol), 14 (triglycerides), and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52 939 single-nucleotide polymorphisms (SNPs) were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with high-density lipoprotein cholesterol (2 SNPs), low-density lipoprotein cholesterol (4 SNPs), and triglycerides (5 SNPs). The family data were used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions, including genes with known associations for cardiovascular disease. This study identified regions on chromosomes 7, 8, 14, and 19 and 11 SNPs from the fine-mapping analysis that were associated with high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides for further studies of cardiovascular disease in African Americans. © 2014 American Heart Association, Inc.

  6. Variants for HDL-C, LDL-C and Triglycerides Identified from Admixture Mapping and Fine-Mapping Analysis in African-American Families

    Science.gov (United States)

    Shetty, Priya B.; Tang, Hua; Feng, Tao; Tayo, Bamidele; Morrison, Alanna C.; Kardia, Sharon L.R.; Hanis, Craig L.; Arnett, Donna K.; Hunt, Steven C.; Boerwinkle, Eric; Rao, D.C.; Cooper, R.S.; Risch, Neil; Zhu, Xiaofeng

    2015-01-01

    Background Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African-Americans. Methods and Results The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglycerides. The analysis was performed in 1,905 unrelated African-American subjects from the National Heart, Lung and Blood Institute’s Family Blood Pressure Program. Regions showing admixture evidence were followed-up with family-based association analysis in 3,556 African-American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age2, sex, body-mass-index, and genome-wide mean ancestry to minimize the confounding due to population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (LDL-C), 8 (HDL-C), 14 (triglycerides) and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52,939 SNPs were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with HDL-C (2 SNPs), LDL-C (4 SNPs) and triglycerides (5 SNPs). The family data was used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions including genes with known associations for cardiovascular disease. Conclusions This study identified regions on chromosomes 7, 8, 14 and 19 and 11 SNPs from the fine-mapping analysis that were associated with HDL-C, LDL-C and triglycerides for further studies of cardiovascular disease in African-Americans. PMID:25552592

  7. Heterogeneity in genetic admixture across different regions of Argentina.

    Directory of Open Access Journals (Sweden)

    Sergio Avena

    Full Text Available The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63-68%, 31% Indigenous American (28-33% and 4% African (3-4%. We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA 76%, 95%CI: 73-79%; Northeast (NEA 54%, 95%CI: 49-58%; Northwest (NWA 33%, 95%CI: 21-41%; South 54%, 95%CI: 49-59%; p<0.0001] as well as between the capital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75-86% versus 68% (95%CI: 58-77%, p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88-94% compared to 54% (95%CI: 51-57% among those with no European grandparents (p<0.001. Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population.

  8. Heterogeneity in Genetic Admixture across Different Regions of Argentina

    Science.gov (United States)

    Avena, Sergio; Via, Marc; Ziv, Elad; Pérez-Stable, Eliseo J.; Gignoux, Christopher R.; Dejean, Cristina; Huntsman, Scott; Torres-Mejía, Gabriela; Dutil, Julie; Matta, Jaime L.; Beckman, Kenneth; Burchard, Esteban González; Parolin, María Laura; Goicoechea, Alicia; Acreche, Noemí; Boquet, Mariel; Ríos Part, María Del Carmen; Fernández, Vanesa; Rey, Jorge; Stern, Mariana C.; Carnese, Raúl F.; Fejerman, Laura

    2012-01-01

    The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs) was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63–68%), 31% Indigenous American (28–33%) and 4% African (3–4%). We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA) 76%, 95%CI: 73–79%; Northeast (NEA) 54%, 95%CI: 49–58%; Northwest (NWA) 33%, 95%CI: 21–41%; South 54%, 95%CI: 49–59%; pcapital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75–86%) versus 68% (95%CI: 58–77%), p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88–94%) compared to 54% (95%CI: 51–57%) among those with no European grandparents (p<0.001). Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population. PMID:22506044

  9. Multiobjective optimization of a steering linkage

    Energy Technology Data Exchange (ETDEWEB)

    Sleesonsom, S.; Bureerat, S. [Sustainable and Infrastructure Research and Development Center, Dept. of Mechanical Engineering, Faculty of Engineering, Khon Kaen University, Khon Kaen (Thailand)

    2016-08-15

    In this paper, multi-objective optimization of a rack-and-pinion steering linkage is proposed. This steering linkage is a common mechanism used in small cars with three advantages as it is simple to construct, economical to manufacture, and compact and easy to operate. In the previous works, many researchers tried to minimize a steering error but minimization of a turning radius is somewhat ignored. As a result, a multi-objective optimization problem is assigned to simultaneously minimize a steering error and a turning radius. The design variables are linkage dimensions. The design problem is solved by the hybrid of multi-objective population-based incremental learning and differential evolution with various constraint handling schemes. The new design strategy leads to effective design of rack-and-pinion steering linkages satisfying both steering error and turning radius criteria.

  10. Multiobjective optimization of a steering linkage

    International Nuclear Information System (INIS)

    Sleesonsom, S.; Bureerat, S.

    2016-01-01

    In this paper, multi-objective optimization of a rack-and-pinion steering linkage is proposed. This steering linkage is a common mechanism used in small cars with three advantages as it is simple to construct, economical to manufacture, and compact and easy to operate. In the previous works, many researchers tried to minimize a steering error but minimization of a turning radius is somewhat ignored. As a result, a multi-objective optimization problem is assigned to simultaneously minimize a steering error and a turning radius. The design variables are linkage dimensions. The design problem is solved by the hybrid of multi-objective population-based incremental learning and differential evolution with various constraint handling schemes. The new design strategy leads to effective design of rack-and-pinion steering linkages satisfying both steering error and turning radius criteria

  11. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

    Science.gov (United States)

    Miller, Webb; Schuster, Stephan C.; Welch, Andreanna J.; Ratan, Aakrosh; Bedoya-Reina, Oscar C.; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C.; Drautz, Daniela I.; Wittekindt, Nicola E.; Tomsho, Lynn P.; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K.; Rode, Karyn D.; Obbard, Martyn E.; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Ólafur; Aars, Jon; Mailund, Thomas; Wiig, Øystein; Talbot, Sandra L.; Lindqvist, Charlotte

    2012-01-01

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

  12. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.

    Science.gov (United States)

    Miller, Webb; Schuster, Stephan C; Welch, Andreanna J; Ratan, Aakrosh; Bedoya-Reina, Oscar C; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C; Drautz, Daniela I; Wittekindt, Nicola E; Tomsho, Lynn P; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K; Rode, Karyn; Obbard, Martyn; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Olafur; Aars, Jon; Mailund, Thomas; Wiig, Oystein; Talbot, Sandra L; Lindqvist, Charlotte

    2012-09-04

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

  13. Some methods for blindfolded record linkage

    Directory of Open Access Journals (Sweden)

    Christen Peter

    2004-06-01

    Full Text Available Abstract Background The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects – a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. Methods A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. Results The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. Conclusion Although the protocols described in

  14. An investigation of the effect of some gaseous admixtures on the ionization currents in the air in the discharge chambers of the proportional counter type

    International Nuclear Information System (INIS)

    Berdowska, E.; Zastawny, A.

    1981-01-01

    Voltage-current characteristics of the ionization discharge in chambers of the proportional counter filled with air with admixtures of CO, CO 2 , CH 4 and H 2 O have been investigated. It was found that in the transition region between dependent and self-maintained discharge the characteristics change sufficiently for detection of the presence of those admixtures in the air. (author)

  15. QTL-Kartierung und funktionelle Kandidatengenanalyse für das Merkmal Totgeburt in einer fortgeschrittenen Fleckvieh- x Red-Holstein-Rückkreuzungspopulation

    OpenAIRE

    Gomeringer, Verena

    2007-01-01

    Das Ziel dieser Arbeit war die Kartierung eines QTL mit Effekt auf paternalen Kalbeverlauf und paternale Totgeburt auf Bos Taurus Autosom 9 (BTA09) in einer fortgeschrittenen Fleckvieh x Red-Holstein Rückkreuzungspopulation mit positioneller und funktioneller Kandidatengenanalyse. Dazu wurden Untersuchungen mit verschiedenen Kartierungsdesigns in Granddaughter und Daughter Designs durchgeführt. Intervallkartierung und Linkage / Linkage-Disequilibrium-Kartierung wurden verwendet um den QTL ...

  16. Admixture mapping in the Hispanic Community Health Study/Study of Latinos reveals regions of genetic associations with blood pressure traits.

    Directory of Open Access Journals (Sweden)

    Tamar Sofer

    Full Text Available Admixture mapping can be used to detect genetic association regions in admixed populations, such as Hispanics/Latinos, by estimating associations between local ancestry allele counts and the trait of interest. We performed admixture mapping of the blood pressure traits systolic and diastolic blood pressure (SBP, DBP, mean arterial pressure (MAP, and pulse pressure (PP, in a dataset of 12,116 participants from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL. Hispanics/Latinos have three predominant ancestral populations (European, African, and Amerindian, for each of which we separately tested local ancestry intervals across the genome. We identified four regions that were significantly associated with a blood pressure trait at the genome-wide admixture mapping level. A 6p21.31 Amerindian ancestry association region has multiple known associations, but none explained the admixture mapping signal. We identified variants that completely explained this signal. One of these variants had p-values of 0.02 (MAP and 0.04 (SBP in replication testing in Pima Indians. A 11q13.4 Amerindian ancestry association region spans a variant that was previously reported (p-value = 0.001 in a targeted association study of Blood Pressure (BP traits and variants in the vitamin D pathway. There was no replication evidence supporting an association in the identified 17q25.3 Amerindian ancestry association region. For a region on 6p12.3, associated with African ancestry, we did not identify any candidate variants driving the association. It may be driven by rare variants. Whole genome sequence data may be necessary to fine map these association signals, which may contribute to disparities in BP traits between diverse populations.

  17. A genome-wide association study of serum uric acid in African Americans

    Directory of Open Access Journals (Sweden)

    Gerry Norman P

    2011-02-01

    Full Text Available Abstract Background Uric acid is the primary byproduct of purine metabolism. Hyperuricemia is associated with body mass index (BMI, sex, and multiple complex diseases including gout, hypertension (HTN, renal disease, and type 2 diabetes (T2D. Multiple genome-wide association studies (GWAS in individuals of European ancestry (EA have reported associations between serum uric acid levels (SUAL and specific genomic loci. The purposes of this study were: 1 to replicate major signals reported in EA populations; and 2 to use the weak LD pattern in African ancestry population to better localize (fine-map reported loci and 3 to explore the identification of novel findings cognizant of the moderate sample size. Methods African American (AA participants (n = 1,017 from the Howard University Family Study were included in this study. Genotyping was performed using the Affymetrix® Genome-wide Human SNP Array 6.0. Imputation was performed using MACH and the HapMap reference panels for CEU and YRI. A total of 2,400,542 single nucleotide polymorphisms (SNPs were assessed for association with serum uric acid under the additive genetic model with adjustment for age, sex, BMI, glomerular filtration rate, HTN, T2D, and the top two principal components identified in the assessment of admixture and population stratification. Results Four variants in the gene SLC2A9 achieved genome-wide significance for association with SUAL (p-values ranging from 8.88 × 10-9 to 1.38 × 10-9. Fine-mapping of the SLC2A9 signals identified a 263 kb interval of linkage disequilibrium in the HapMap CEU sample. This interval was reduced to 37 kb in our AA and the HapMap YRI samples. Conclusions The most strongly associated locus for SUAL in EA populations was also the most strongly associated locus in this AA sample. This finding provides evidence for the role of SLC2A9 in uric acid metabolism across human populations. Additionally, our findings demonstrate the utility of following-up EA

  18. Fulltext PDF

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    with the wild-type sequence at position 3435, and so linkage disequilibrium was not ... of microenvironmental control of translation elongation rate in eukaryotic cells ... Synonymous codon substitutions affect ribosome traffic and protein folding.

  19. SORBS1 gene, a new candidate for diabetic nephropathy

    DEFF Research Database (Denmark)

    Germain, Marine; Pezzolesi, Marcus G; Sandholm, Niina

    2015-01-01

    -wide statistical significance. The 46 top hits (p independent population of 820 cases and 885 controls. Two SNPs in strong linkage disequilibrium with each other and located in the SORBS1 gene were...

  20. Effects of admixture gas on the production of {sup 18}F radioisotope in plasma focus devices

    Energy Technology Data Exchange (ETDEWEB)

    Talaei, Ahmad [Nuclear Science and Technology Research Institute (NSTR), Nuclear Science Research School, A.E.O.I., 14155-1339 Tehran (Iran, Islamic Republic of); Sadat Kiai, S.M., E-mail: sadatkiai@yahoo.co [Nuclear Science and Technology Research Institute (NSTR), Nuclear Science Research School, A.E.O.I., 14155-1339 Tehran (Iran, Islamic Republic of); Zaeem, A.A. [Department of Physics, Khaje Nasir University of Technology (K.N. Toosi), 1541846911 Tehran (Iran, Islamic Republic of)

    2010-12-15

    In this article, the effect of admixture gas on the heating and cooling of pinched plasma directly related to the enhancement or reduction of {sup 18}F production through the {sup 16}O({sup 3}He, p){sup 18}F is considered in the plasma focus devices. It is shown that by controlling the velocity of added Oxygen particles mixed with the working helium gas into the plasma focus chamber, one can increase the current and decrease the confinement time (plasma heating) or vice verse (plasma cooling). The highest level of nuclear activities of {sup 18}F was found around 16% of the Oxygen admixture participation and was about 0.35 MBq in the conditions of 20 kJ, 0.1 Hz and after 2 min operating of Dena PF. However, in the same condition, but for the frequency of 1 Hz, the level of activity increased up to 3.4 MBq.

  1. Laboratory Evaluation of Expedient Low-Temperature Admixtures for Runway Craters in Cold Weather

    Science.gov (United States)

    2014-10-01

    it consists of a pre- blend of Type III Portland cement (calcium sulfoaluminate [CSA] cement with some small amount of admixtures for workability...more information on similar crater repair methods, equipment, and materials used by the U.S. Ar- my, see Center for Army Lessons Learned (2011). ERDC...all measurements with a TA Instrument TAM Air isothermal calorimeter operated at 23°C. To capture the initial wetting of the cement and early-age

  2. Linkage Behavior and Practices of Agencies in the Agricultural ...

    African Journals Online (AJOL)

    The study examined the linkage behaviour and practices of agencies in the ... institutes; while (61.5%,65.5%and 50.0%) indicated that linkages with universities of ... Existing institutional framework for linkages between research and extension ...

  3. Reconstructing Roma history from genome-wide data.

    Directory of Open Access Journals (Sweden)

    Priya Moorjani

    Full Text Available The Roma people, living throughout Europe and West Asia, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1,000-1,500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosome and mitochondrial DNA. To explore what additional information can be learned from genome-wide data, we analyzed data from six Roma groups that we genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs. We estimate that the Roma harbor about 80% West Eurasian ancestry-derived from a combination of European and South Asian sources-and that the date of admixture of South Asian and European ancestry was about 850 years before present. We provide evidence for Eastern Europe being a major source of European ancestry, and North-west India being a major source of the South Asian ancestry in the Roma. By computing allele sharing as a measure of linkage disequilibrium, we estimate that the migration of Roma out of the Indian subcontinent was accompanied by a severe founder event, which appears to have been followed by a major demographic expansion after the arrival in Europe.

  4. Exploitation of linkage learning in evolutionary algorithms

    CERN Document Server

    Chen, Ying-ping

    2010-01-01

    The exploitation of linkage learning is enhancing the performance of evolutionary algorithms. This monograph examines recent progress in linkage learning, with a series of focused technical chapters that cover developments and trends in the field.

  5. ANALYSIS OF INTER SECTORAL LINKAGES IN SEMARANG REGENCY

    Directory of Open Access Journals (Sweden)

    Fafurida

    2014-03-01

    Full Text Available This research aims to analyze inter economic sectoral linkages and to arrange the Klassen typology of economic sectors in Semarang Regency. The Klassen typology is composed from the result of the linkage analysis. To construct the analysis, this paper also utulizes the input-output analysis. It finds that service sector has the highest backward linkage while farming sector has the highest forward linkage. Based on the Klassen typology analysis, sectors with the highest backward and forward linkages and potential to be the leading sector are farming sector, dan trade, hotel and restaurant sector.Keywords: Backward linkage,forward linkage, Klassen typologyJEL classification number: R15, O21AbstrakPenelitian ini bertujuan untuk mengkaji seberapa besar keterkaitan antar sektor ekonomi di Kabupaten Semarang dan memetakan tipologi Klassennya. Tipologi Klasen disusun berdasarkan hasil perhitungan analisis keterkaitannya. Untuk menyusun analisis tersebut, paper ini juga menggunakan analisis input-output. Hasil penelitian menunjukkan bahwa sektor jasa memiliki keterkaitan ke belakang tertinggi dibandingkan dengan sektor lainnya. Sementara itu, sektor pertanian merupakan sektor yang memiliki keterkaitan ke depan tertinggi. Berdasarkan hasil analisis tipologi Klassen, sektor yang memiliki keterkaitan ke depan dan ke belakang yang tinggi dan dapat menjadi sektor unggulan adalah sektor perdagangan, hotel dan sektor restoran.Kata kunci: Keterkaitan ke belakang, keterkaitan ke depan, tipologi KlassenJEL classification numbers: R15, O21

  6. Posterior probability of linkage and maximal lod score.

    Science.gov (United States)

    Génin, E; Martinez, M; Clerget-Darpoux, F

    1995-01-01

    To detect linkage between a trait and a marker, Morton (1955) proposed to calculate the lod score z(theta 1) at a given value theta 1 of the recombination fraction. If z(theta 1) reaches +3 then linkage is concluded. However, in practice, lod scores are calculated for different values of the recombination fraction between 0 and 0.5 and the test is based on the maximum value of the lod score Zmax. The impact of this deviation of the test on the probability that in fact linkage does not exist, when linkage was concluded, is documented here. This posterior probability of no linkage can be derived by using Bayes' theorem. It is less than 5% when the lod score at a predetermined theta 1 is used for the test. But, for a Zmax of +3, we showed that it can reach 16.4%. Thus, considering a composite alternative hypothesis instead of a single one decreases the reliability of the test. The reliability decreases rapidly when Zmax is less than +3. Given a Zmax of +2.5, there is a 33% chance that linkage does not exist. Moreover, the posterior probability depends not only on the value of Zmax but also jointly on the family structures and on the genetic model. For a given Zmax, the chance that linkage exists may then vary.

  7. Quality assessment of total parenteral nutrition admixtures by the use of fractional factorial design

    Directory of Open Access Journals (Sweden)

    Mirković Dušica

    2013-01-01

    Full Text Available Background/Aim. Parenteral nutrition as a specific aspect of providing nutritients still remains a permanent topic of both theoretical and experimental research. Total parenteral nutrition (TPN admixtures have complex contents making difficult to maintain their stability. The most critical parameter is the diameter of a lipid droplet, i.e. droplet size distribution. It is recommended that droplet size should not be more than 5

  8. Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African Pygmies and non-Pygmies.

    Science.gov (United States)

    Verdu, Paul; Becker, Noémie S A; Froment, Alain; Georges, Myriam; Grugni, Viola; Quintana-Murci, Lluis; Hombert, Jean-Marie; Van der Veen, Lolke; Le Bomin, Sylvie; Bahuchet, Serge; Heyer, Evelyne; Austerlitz, Frédéric

    2013-04-01

    Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter-gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history.

  9. Development of an eco-friendly Ultra-High Performance Concrete (UHPC) with efficient cement and mineral admixtures uses

    NARCIS (Netherlands)

    Yu, R.; Spiesz, P.R.; Brouwers, H.J.H.

    2015-01-01

    This paper addresses the development of an eco-friendly Ultra-High Performance Concrete (UHPC) with efficient cement and mineral admixtures uses are investigated. The modified Andreasen & Andersen particle packing model is utilized to achieve a densely compacted cementitious matrix. Fly ash (FA),

  10. Linkage and related analyses of Barrett's esophagus and its associated adenocarcinomas.

    Science.gov (United States)

    Sun, Xiangqing; Elston, Robert; Falk, Gary W; Grady, William M; Faulx, Ashley; Mittal, Sumeet K; Canto, Marcia I; Shaheen, Nicholas J; Wang, Jean S; Iyer, Prasad G; Abrams, Julian A; Willis, Joseph E; Guda, Kishore; Markowitz, Sanford; Barnholtz-Sloan, Jill S; Chandar, Apoorva; Brock, Wendy; Chak, Amitabh

    2016-07-01

    Familial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC). We genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model-based and model-free linkage analyses, using S.A.G.E. and other software. Segregation models were fitted, from the data on both the 42 pedigrees and the 1000 pedigrees, to determine parameters for performing model-based linkage analysis. Model-based and model-free linkage analyses were conducted in two sets of pedigrees: the 42 pedigrees and a subset of 18 pedigrees with female affected members that are expected to be more genetically homogeneous. Genome-wide associations were also tested in these families. Linkage analyses on the 42 pedigrees identified several regions consistently suggestive of linkage by different linkage analysis methods on chromosomes 2q31, 12q23, and 4p14. A linkage on 15q26 is the only consistent linkage region identified in the 18 female-affected pedigrees, in which the linkage signal is higher than in the 42 pedigrees. Other tentative linkage signals are also reported. Our linkage study of BE/EAC pedigrees identified linkage regions on chromosomes 2, 4, 12, and 15, with some reported associations located within our linkage peaks. Our linkage results can help prioritize association tests to delineate the genetic determinants underlying susceptibility to BE and EAC.

  11. Uranium isotopic disequilibrium in ground water as an indicator of anomalies

    International Nuclear Information System (INIS)

    Osmond, J.K.; Cowart, J.B.; Ivanovich, M.

    1983-01-01

    Because of the unique elemental and isotopic properties of uranium, ground water surveys are a most appropriate approach to prospecting for surficial and secondary uranium deposits. Uranium4+ is generally immobile, but in oxidising and carbonate bearing waters U 6 + is mobile and conservative. Uranium 234 is the radiogenic daughter of 238 U. The intervening α-decay event causes recoil displacements and radioactive disequilibrium between the two isotopes in open systems such as surficial aquifers. Extreme variations in dissolved uranium composition of ground waters combined with significant variations in the ratio 234 U/ 238 U are indicative of the proximity and stage of evolution of secondary deposits. (author)

  12. Aspects of uranium/thorium series disequilibrium applications to radionuclide migration studies

    International Nuclear Information System (INIS)

    Ivanovich, M.

    1989-11-01

    The aim of this paper is to consider the contribution which the uranium/thorium series disequilibrium concept can make to understanding the retardation and transport of radionuclides in the far-field of a radioactive waste repository. In principle, naturally occurring isotopes of uranium, thorium and radium can be regarded as geochemical analogues of the divalent radionuclides and multivalent actinides expected to be present in the radioactive waste inventory. The study of their retardation and/or transport in real rock/water systems which have taken place over geological timescales, can make an important contribution to establishing a rational basis for long-term predictive modelling of radionuclide transport required for safety assessments. (author)

  13. Genome-wide admixture and association study of subclinical atherosclerosis in the Women's Interagency HIV Study (WIHS.

    Directory of Open Access Journals (Sweden)

    Aditi Shendre

    Full Text Available Cardiovascular disease (CVD is a major comorbidity among HIV-infected individuals. Common carotid artery intima-media thickness (cCIMT is a valid and reliable subclinical measure of atherosclerosis and is known to predict CVD. We performed genome-wide association (GWA and admixture analysis among 682 HIV-positive and 288 HIV-negative Black, non-Hispanic women from the Women's Interagency HIV study (WIHS cohort using a combined and stratified analysis approach. We found some suggestive associations but none of the SNPs reached genome-wide statistical significance in our GWAS analysis. The top GWAS SNPs were rs2280828 in the region intergenic to mediator complex subunit 30 and exostosin glycosyltransferase 1 (MED30 | EXT1 among all women, rs2907092 in the catenin delta 2 (CTNND2 gene among HIV-positive women, and rs7529733 in the region intergenic to family with sequence similarity 5, member C and regulator of G-protein signaling 18 (FAM5C | RGS18 genes among HIV-negative women. The most significant local European ancestry associations were in the region intergenic to the zinc finger and SCAN domain containing 5D gene and NADH: ubiquinone oxidoreductase complex assembly factor 1 (ZSCAN5D | NDUF1 pseudogene on chromosome 19 among all women, in the region intergenic to vomeronasal 1 receptor 6 pseudogene and zinc finger protein 845 (VN1R6P | ZNF845 gene on chromosome 19 among HIV-positive women, and in the region intergenic to the SEC23-interacting protein and phosphatidic acid phosphatase type 2 domain containing 1A (SEC23IP | PPAPDC1A genes located on chromosome 10 among HIV-negative women. A number of previously identified SNP associations with cCIMT were also observed and included rs2572204 in the ryanodine receptor 3 (RYR3 and an admixture region in the secretion-regulating guanine nucleotide exchange factor (SERGEF gene. We report several SNPs and gene regions in the GWAS and admixture analysis, some of which are common across HIV-positive and

  14. Dynamics of a durable commodity market involving trade at disequilibrium

    Science.gov (United States)

    Panchuk, A.; Puu, T.

    2018-05-01

    The present work considers a simple model of a durable commodity market involving two agents who trade stocks of two different types. Stock commodities, in contrast to flow commodities, remain on the market from period to period and, consequently, there is neither unique demand function nor unique supply function exists. We also set up exact conditions for trade at disequilibrium, the issue being usually neglected, though a fact of reality. The induced iterative system has infinite number of fixed points and path dependent dynamics. We show that a typical orbit is either attracted to one of the fixed points or eventually sticks at a no-trade point. For the latter the stock distribution always remains the same while the price displays periodic or chaotic oscillations.

  15. Privacy-preserving record linkage on large real world datasets.

    Science.gov (United States)

    Randall, Sean M; Ferrante, Anna M; Boyd, James H; Bauer, Jacqueline K; Semmens, James B

    2014-08-01

    Record linkage typically involves the use of dedicated linkage units who are supplied with personally identifying information to determine individuals from within and across datasets. The personally identifying information supplied to linkage units is separated from clinical information prior to release by data custodians. While this substantially reduces the risk of disclosure of sensitive information, some residual risks still exist and remain a concern for some custodians. In this paper we trial a method of record linkage which reduces privacy risk still further on large real world administrative data. The method uses encrypted personal identifying information (bloom filters) in a probability-based linkage framework. The privacy preserving linkage method was tested on ten years of New South Wales (NSW) and Western Australian (WA) hospital admissions data, comprising in total over 26 million records. No difference in linkage quality was found when the results were compared to traditional probabilistic methods using full unencrypted personal identifiers. This presents as a possible means of reducing privacy risks related to record linkage in population level research studies. It is hoped that through adaptations of this method or similar privacy preserving methods, risks related to information disclosure can be reduced so that the benefits of linked research taking place can be fully realised. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. DISEQUILIBRIUM CARBON, OXYGEN, AND NITROGEN CHEMISTRY IN THE ATMOSPHERES OF HD 189733b AND HD 209458b

    International Nuclear Information System (INIS)

    Moses, Julianne I.; Visscher, C.; Fortney, J. J.; Showman, A. P.; Lewis, N. K.; Griffith, C. A.; Klippenstein, S. J.; Shabram, M.; Friedson, A. J.; Marley, M. S.; Freedman, R. S.

    2011-01-01

    We have developed a one-dimensional photochemical and thermochemical kinetics and diffusion model to study the effects of disequilibrium chemistry on the atmospheric composition of 'hot-Jupiter' exoplanets. Here we investigate the coupled chemistry of neutral carbon, hydrogen, oxygen, and nitrogen species on HD 189733b and HD 209458b and we compare the model results with existing transit and eclipse observations. We find that the vertical profiles of molecular constituents are significantly affected by transport-induced quenching and photochemistry, particularly on the cooler HD 189733b; however, the warmer stratospheric temperatures on HD 209458b help maintain thermochemical equilibrium and reduce the effects of disequilibrium chemistry. For both planets, the methane and ammonia mole fractions are found to be enhanced over their equilibrium values at pressures of a few bar to less than an mbar due to transport-induced quenching, but CH 4 and NH 3 are photochemically removed at higher altitudes. Disequilibrium chemistry also enhances atomic species, unsaturated hydrocarbons (particularly C 2 H 2 ), some nitriles (particularly HCN), and radicals like OH, CH 3 , and NH 2 . In contrast, CO, H 2 O, N 2 , and CO 2 more closely follow their equilibrium profiles, except at pressures ∼ 2 O, and N 2 are photochemically destroyed and CO 2 is produced before its eventual high-altitude destruction. The enhanced abundances of CH 4 , NH 3 , and HCN are expected to affect the spectral signatures and thermal profiles of HD 189733b and other relatively cool, transiting exoplanets. We examine the sensitivity of our results to the assumed temperature structure and eddy diffusion coefficients and discuss further observational consequences of these models.

  17. Strength characteristics of light weight concrete blocks using mineral admixtures

    Science.gov (United States)

    Bhuvaneshwari, P.; Priyadharshini, U.; Gurucharan, S.; Mithunram, B.

    2017-07-01

    This paper presents an experimental study to investigate the characteristics of light weight concrete blocks. Cement was partially replaced with mineral admixtures like Fly ash (FA), limestone powder waste (LPW), Rice husk ash (RHA), sugarcane fiber waste (SCW) and Chrysopogonzizanioides (CZ). The maximum replacement level achieved was 25% by weight of cement and sand. Total of 56 cubes (150 mm x 150 mm x150 mm) and 18 cylinders (100mmφ and 50mm depth) were cast. The specimens being (FA, RHA, SCW, LPW, CZ, (FA-RHA), (FA-LPW), (FA-CZ), (LPW-CZ), (FA-SCW), (RHA-SCW)).Among the different combination, FA,FA-SCW,CZ,FA-CZ showed enhanced strength and durability, apart from achieving less density.

  18. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.

    Directory of Open Access Journals (Sweden)

    Omer Gokcumen

    2013-04-01

    Full Text Available Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10⁻¹⁵. Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003 and positive Tajima's D (p = 0.00285 statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European

  19. Admixture into and within sub-Saharan Africa

    Science.gov (United States)

    Busby, George BJ; Band, Gavin; Si Le, Quang; Jallow, Muminatou; Bougama, Edith; Mangano, Valentina D; Amenga-Etego, Lucas N; Enimil, Anthony; Apinjoh, Tobias; Ndila, Carolyne M; Manjurano, Alphaxard; Nyirongo, Vysaul; Doumba, Ogobara; Rockett, Kirk A; Kwiatkowski, Dominic P; Spencer, Chris CA

    2016-01-01

    Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI: http://dx.doi.org/10.7554/eLife.15266.001 PMID:27324836

  20. The effect of genotyping errors on the robustness of composite ...

    Indian Academy of Sciences (India)

    2011-12-20

    Dec 20, 2011 ... We conclude that composite linkage disequilibrium (LD) measures be adopted in population-based LD mapping or associa- ... this report, we derived deterministic formulas to evaluate the impact ... But, in the local region with.

  1. Genome-wide linkage analysis for human longevity

    DEFF Research Database (Denmark)

    Beekman, Marian; Blanché, Hélène; Perola, Markus

    2013-01-01

    Clear evidence exists for heritability of human longevity, and much interest is focused on identifying genes associated with longer lives. To identify such longevity alleles, we performed the largest genome-wide linkage scan thus far reported. Linkage analyses included 2118 nonagenarian Caucasian...

  2. Preparation of briquettes on the basis of desintegrated phyto-materials and the admixture of fine-grained coal and coke

    Directory of Open Access Journals (Sweden)

    Jakabský Štefan

    2002-03-01

    Full Text Available The contribution deals with the preparation of small-diameter briquettes on the basis of desintegrated phyto-materials and the admixture of coal and coke. The phyto-materials are classified as a dry biomass that can be, on the one hand, the wastes from wood-working industry,(sawdust, chips, bark, etc. or dried mass from the plant production and, on the other hand, the mass of quick-growing plants cultivated on special plantations. In present time this renewable energy resource attracts attention by its heating value ranging from 10 to 16 MJ.kg-1 (EkoWATT, 2001, a low ash content of 0.5 – 6.5 % and by a low sulphur content in a water free sample of 0.05 –0.12 %.As a phyto-material the spruce sawdusts having a grain size of –2 mm were used. The admixture of brown coal, hard coal and coke with a grain size of 0.040 mm was added to the sawdust and in such way prepared mixtures were subjected to briquetting with the aim to obtain small-diameter briquettes. The influence of admixtures amount on the density, and the suitable briquetting press have been studied. A saleability of briquettes on the basis of phyto-materials is conditioned by their density that must be higher than 1,000 kg.m-3. Thus, an adding of denser material with a relatively high calorific value would enable to attain the required density as well as to retain and/or to improve the main utility properties, i.e. calorific value and ash content.The adding evinces itself in an enhancement of briquetting press, but also density of obtained briquettes is often much higher that required by the market. It was showed that in the case of clear spruce sawdust the density of 1,059 kg.m-3 under the briquetting press of 250 MPa can be attained. According to other results, an admixture of brown coal is not very favourable because briquetting press exceeds the value of 300 MPa. As to hard coal adding, the presses under 250 MPa were achieved at the content of 25 – 30 %. The density of these

  3. Measurement of ozone production scaling in a helium plasma jet with oxygen admixture

    Science.gov (United States)

    Sands, Brian; Ganguly, Biswa

    2012-10-01

    Capillary dielectric barrier plasma jet devices that generate confined streamer-like discharges along a rare gas flow can produce significant quantities of reactive oxygen species with average input powers ranging from 100 mW to >1 W. We have measured spatially-resolved ozone production in a He plasma jet with O2 admixture concentrations up to 5% using absorption spectroscopy of the O3 Hartley band system. A 20-ns risetime, 10-13 kV positive unipolar voltage pulse train was used to power the discharge, with pulse repetition rates varied from 1-20 kHz. The discharge was operated in a transient glow mode to scale the input power by adjusting the gap width between the anode and downstream cathodic plane. Peak ozone number densities in the range of 10^16 - 10^17 cm-3 were measured. At a given voltage, the density of ozone increased monotonically up to 3% O2 admixture (6 mm gap) as the peak discharge current decreased by an order of magnitude. Ozone production increased with distance from the capillary, consistent with observations by other groups. Atomic oxygen production inferred from O-atom 777 nm emission intensity did not scale with ozone as the input power was increased. The spatial distribution of ozone and scaling with input power will be presented.

  4. Estimating parameters for probabilistic linkage of privacy-preserved datasets.

    Science.gov (United States)

    Brown, Adrian P; Randall, Sean M; Ferrante, Anna M; Semmens, James B; Boyd, James H

    2017-07-10

    Probabilistic record linkage is a process used to bring together person-based records from within the same dataset (de-duplication) or from disparate datasets using pairwise comparisons and matching probabilities. The linkage strategy and associated match probabilities are often estimated through investigations into data quality and manual inspection. However, as privacy-preserved datasets comprise encrypted data, such methods are not possible. In this paper, we present a method for estimating the probabilities and threshold values for probabilistic privacy-preserved record linkage using Bloom filters. Our method was tested through a simulation study using synthetic data, followed by an application using real-world administrative data. Synthetic datasets were generated with error rates from zero to 20% error. Our method was used to estimate parameters (probabilities and thresholds) for de-duplication linkages. Linkage quality was determined by F-measure. Each dataset was privacy-preserved using separate Bloom filters for each field. Match probabilities were estimated using the expectation-maximisation (EM) algorithm on the privacy-preserved data. Threshold cut-off values were determined by an extension to the EM algorithm allowing linkage quality to be estimated for each possible threshold. De-duplication linkages of each privacy-preserved dataset were performed using both estimated and calculated probabilities. Linkage quality using the F-measure at the estimated threshold values was also compared to the highest F-measure. Three large administrative datasets were used to demonstrate the applicability of the probability and threshold estimation technique on real-world data. Linkage of the synthetic datasets using the estimated probabilities produced an F-measure that was comparable to the F-measure using calculated probabilities, even with up to 20% error. Linkage of the administrative datasets using estimated probabilities produced an F-measure that was higher

  5. RLT-S: A Web System for Record Linkage.

    Directory of Open Access Journals (Sweden)

    Abdullah-Al Mamun

    Full Text Available Record linkage integrates records across multiple related data sources identifying duplicates and accounting for possible errors. Real life applications require efficient algorithms to merge these voluminous data sources to find out all records belonging to same individuals. Our recently devised highly efficient record linkage algorithms provide best-known solutions to this challenging problem.We have developed RLT-S, a freely available web tool, which implements our single linkage clustering algorithm for record linkage. This tool requires input data sets and a small set of configuration settings about these files to work efficiently. RLT-S employs exact match clustering, blocking on a specified attribute and single linkage based hierarchical clustering among these blocks.RLT-S is an implementation package of our sequential record linkage algorithm. It outperforms previous best-known implementations by a large margin. The tool is at least two times faster for any dataset than the previous best-known tools.RLT-S tool implements our record linkage algorithm that outperforms previous best-known algorithms in this area. This website also contains necessary information such as instructions, submission history, feedback, publications and some other sections to facilitate the usage of the tool.RLT-S is integrated into http://www.rlatools.com, which is currently serving this tool only. The tool is freely available and can be used without login. All data files used in this paper have been stored in https://github.com/abdullah009/DataRLATools. For copies of the relevant programs please see https://github.com/abdullah009/RLATools.

  6. High recombination rate in natural populations of Plasmodium falciparum

    NARCIS (Netherlands)

    Conway, D. J.; Roper, C.; Oduola, A. M.; Arnot, D. E.; Kremsner, P. G.; Grobusch, M. P.; Curtis, C. F.; Greenwood, B. M.

    1999-01-01

    Malaria parasites are sexually reproducing protozoa, although the extent of effective meiotic recombination in natural populations has been debated. If meiotic recombination occurs frequently, compared with point mutation and mitotic rearrangement, linkage disequilibrium between polymorphic sites is

  7. Genomic Characterization of Interspecific Hybrids and an Admixture Population Derived from Panicum amarum × P. virgatum

    Directory of Open Access Journals (Sweden)

    Christopher Heffelfinger

    2015-07-01

    Full Text Available Switchgrass ( L. and its relatives are regarded as top bioenergy crop candidates; however, one critical barrier is the introduction of useful genetic diversity and the development of new cultivars and hybrids. Combining genomes from related cultivars and species provides an opportunity to introduce new traits. In switchgrass, a breeding advantage would be achieved by combining the genomes of intervarietal ecotypes or interspecific hybrids. The recovery of wide crosses, however, is often tedious and may involve complicated embryo rescue and numerous backcrosses. Here, we demonstrate a straightforward approach to wide crosses involving the use of a selectable transgene for recovery of interspecific [ cv. Alamo × Ell var or Atlantic Coastal Panicgrass (ACP] F hybrids followed by backcrossing to generate a nontransgenic admixture population. A nontransgenic herbicide-sensitive (HbS admixture population of 83 FBC progeny was analyzed by genotyping-by-sequencing (GBS to characterize local ancestry, parental contribution, and patterns of recombination. These results demonstrate a widely applicable breeding strategy that makes use of transgenic selectable resistance to identify and recover true hybrids.

  8. Sex versus asex: An analysis of the role of variance conversion.

    Science.gov (United States)

    Lewis-Pye, Andrew E M; Montalbán, Antonio

    2017-04-01

    The question as to why most complex organisms reproduce sexually remains a very active research area in evolutionary biology. Theories dating back to Weismann have suggested that the key may lie in the creation of increased variability in offspring, causing enhanced response to selection. Under appropriate conditions, selection is known to result in the generation of negative linkage disequilibrium, with the effect of recombination then being to increase genetic variance by reducing these negative associations between alleles. It has therefore been a matter of significant interest to understand precisely those conditions resulting in negative linkage disequilibrium, and to recognise also the conditions in which the corresponding increase in genetic variation will be advantageous. Here, we prove rigorous results for the multi-locus case, detailing the build up of negative linkage disequilibrium, and describing the long term effect on population fitness for models with and without bounds on fitness contributions from individual alleles. Under the assumption of large but finite bounds on fitness contributions from alleles, the non-linear nature of the effect of recombination on a population presents serious obstacles in finding the genetic composition of populations at equilibrium, and in establishing convergence to those equilibria. We describe techniques for analysing the long term behaviour of sexual and asexual populations for such models, and use these techniques to establish conditions resulting in higher fitnesses for sexually reproducing populations. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. NFKBIZ polymorphisms and susceptibility to pneumococcal disease in European and African populations

    Science.gov (United States)

    Chapman, Stephen J; Khor, Chiea C; Vannberg, Fredrik O; Rautanen, Anna; Segal, Shelley; Moore, Catrin E; Davies, Robert J O; Day, Nicholas P; Peshu, Norbert; Crook, Derrick W; Berkley, James A; Williams, Thomas N; Scott, J Anthony; Hill, Adrian V S

    2011-01-01

    The proinflammatory transcription factor nuclear factor-kappaB (NF-κB) plays a central role in host defence against pneumococcal disease. Both rare mutations and common polymorphisms in the NFKBIA gene encoding the NF-κB inhibitor IκB-α associate with susceptibility to bacterial disease, but the possible role of polymorphisms within the related IκB-ζ gene NFKBIZ in the development of invasive pneumococcal disease has not previously been reported. To investigate this further, we examined the frequencies of 22 single-nucleotide polymorphisms spanning NFKBIZ in two case-control studies, comprising UK Caucasian (n=1008) and Kenyan (n=723) individuals. Nine polymorphisms within a single UK linkage disequilibrium block and all four polymorphisms within the equivalent, shorter Kenyan linkage disequilibrium block displayed either significant association with invasive pneumococcal disease or a trend towards association. For each polymorphism, heterozygosity was associated with protection from invasive pneumococcal disease when compared to the combined homozygous states (e.g. for rs600718, Mantel-Haenszel 2×2 χ2=7.576, P=0.006, OR=0.67, 95% CI for OR: 0.51-0.88; for rs616597, Mantel-Haenszel 2×2 χ2=8.715, P=0.003, OR=0.65, 95% CI: 0.49-0.86). We conclude that multiple NFKBIZ polymorphisms associate with susceptibility to invasive pneumococcal disease in humans. The study of multiple populations may aid fine-mapping of associations within extensive regions of strong linkage disequilibrium (‘transethnic mapping’). PMID:19798075

  10. Two-locus linkage analysis in multiple sclerosis (MS)

    Energy Technology Data Exchange (ETDEWEB)

    Tienari, P.J. (National Public Health Institute, Helsinki (Finland) Univ. of Helsinki (Finland)); Terwilliger, J.D.; Ott, J. (Columbia Univ., New York (United States)); Palo, J. (Univ. of Helsinki (Finland)); Peltonen, L. (National Public Health Institute, Helsinki (Finland))

    1994-01-15

    One of the major challenges in genetic linkage analyses is the study of complex diseases. The authors demonstrate here the use of two-locus linkage analysis in multiple sclerosis (MS), a multifactorial disease with a complex mode of inheritance. In a set of Finnish multiplex families, they have previously found evidence for linkage between MS susceptibility and two independent loci, the myelin basic protein gene (MBP) on chromosome 18 and the HLA complex on chromosome 6. This set of families provides a unique opportunity to perform linkage analysis conditional on two loci contributing to the disease. In the two-trait-locus/two-marker-locus analysis, the presence of another disease locus is parametrized and the analysis more appropriately treats information from the unaffected family member than single-disease-locus analysis. As exemplified here in MS, the two-locus analysis can be a powerful method for investigating susceptibility loci in complex traits, best suited for analysis of specific candidate genes, or for situations in which preliminary evidence for linkage already exists or is suggested. 41 refs., 6 tabs.

  11. Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS

    DEFF Research Database (Denmark)

    Wang, Yunpeng; Thompson, Wesley K; Schork, Andrew J

    2016-01-01

    Most of the genetic architecture of schizophrenia (SCZ) has not yet been identified. Here, we apply a novel statistical algorithm called Covariate-Modulated Mixture Modeling (CM3), which incorporates auxiliary information (heterozygosity, total linkage disequilibrium, genomic annotations, pleiotr...

  12. Effect of an admixture from Agave americana on the physical and mechanical properties of plaster

    Directory of Open Access Journals (Sweden)

    Ochoa, J. C.

    2013-03-01

    Full Text Available Physical and mechanical properties of a plaster paste added with an organic admixture, of the leaves of Agave americana, were studied. Plastic consistency behavior was evaluated and the water/gypsum(w/g ratio was determined for each dosage of the admixture. Admixtur eeffect on setting was evaluated too. The chemical transformation of the hemihydrated form to gypsum (dihydrated form was studied using a novel technique based on a moisture analyzer by halogen light. Flexural and compressive strengths were measured. The results show that ,for the same consistency, accordingly mechanical strengths were improved too. The setting times were increased which would enhance the application time of plaster and would reduce plastic shrinkage, common problems in this type of material. The changes in these physical properties not substantially affect the final mechanical strengths.

    Se estudiaron algunas propiedades físicas y mecánicas de pastas de yeso de construcción adicionadas con un aditivo de origen orgánico, producto de las hojas de la planta Agave americana. Se evaluó el comportamiento plástico de la pasta mediante ensayos de consistencia y se determinó, para cada dosificación, su relación agua/ yeso (a/y. Se evaluó la incidencia del aditivo en los tiempos de fraguado. La transformación química del hemihidrato a yeso dihidrato se estudió mediante una novedosa técnica basada en un analizador de humedad por luz halógena. Se midieron las resistencias mecánicas a flexo-tracción y a compresión. Los resultados del estudio muestran que, para una misma consistencia, se mejoran las resistencias mecánicas. Los tiempos de fraguado de la pasta se aumentaron lo que ayudaría mejorar los tiempos de aplicación del yeso y a disminuir las retracciones plásticas. Las modificaciones de estas propiedades físicas no afectan considerablemente las resistencias mecánicas finales.

  13. Using Bureaucratic and Cultural Linkages to Improve Instruction: The Principal's Contribution.

    Science.gov (United States)

    Firestone, William A.; Wilson, Bruce L.

    1985-01-01

    Principals can influence teachers and instructional behavior by working through linkage mechanisms within the organizational structure of the school. Two types of linkages are identified: bureaucratic and cultural. Principals have access to linkages of both kinds; using linkages effectively, they can generate a common purpose in their schools. (MD)

  14. Genetic structure and admixture between Bayash Roma from northwestern Croatia and general Croatian population: evidence from Bayesian clustering analysis.

    Science.gov (United States)

    Novokmet, Natalija; Galov, Ana; Marjanović, Damir; Škaro, Vedrana; Projić, Petar; Lauc, Gordan; Primorac, Dragan; Rudan, Pavao

    2015-01-01

    The European Roma represent a transnational mosaic of minority population groups with different migration histories and contrasting experiences in their interactions with majority populations across the European continent. Although historical genetic contributions of European lineages to the Roma pool were investigated before, the extent of contemporary genetic admixture between Bayash Roma and non-Romani majority population remains elusive. The aim of this study was to assess the genetic structure of the Bayash Roma population from northwestern Croatia and the general Croatian population and to investigate the extent of admixture between them. A set of genetic data from two original studies (100 Bayash Roma from northwestern Croatia and 195 individuals from the general Croatian population) was analyzed by Bayesian clustering implemented in STRUCTURE software. By re-analyzing published data we intended to focus for the first time on genetic differentiation and structure and in doing so we clearly pointed to the importance of considering social phenomena in understanding genetic structuring. Our results demonstrated that two population clusters best explain the genetic structure, which is consistent with social exclusion of Roma and the demographic history of Bayash Roma who have settled in NW Croatia only about 150 years ago and mostly applied rules of endogamy. The presence of admixture was revealed, while the percentage of non-Croatian individuals in general Croatian population was approximately twofold higher than the percentage of non-Romani individuals in Roma population corroborating the presence of ethnomimicry in Roma.

  15. Childhood trauma is associated with a specific admixture of affective, anxiety, and psychosis symptoms cutting across traditional diagnostic boundaries

    NARCIS (Netherlands)

    van Nierop, M.; Viechtbauer, W.; Gunther, N.; van Zelst, C.; de Graaf, R.; ten Have, M.; van Dorsselaer, S.; Bak, M.; van Winkel, R.; Bruggeman, Richard; Wiersma, Durk; Cahn, Wiepke; Kahn, Rene S.; de Haan, Lieuwe; Meijer, Carin J.; Myin-Germeys, Inez; van Os, Jim

    2015-01-01

    Background. Meta-analyses link childhood trauma to depression, mania, anxiety disorders, and psychosis. It is unclear, however, whether these outcomes truly represent distinct disorders following childhood trauma, or that childhood trauma is associated with admixtures of affective, psychotic,

  16. Childhood trauma is associated with a specific admixture of affective, anxiety, and psychosis symptoms cutting across traditional diagnostic boundaries

    NARCIS (Netherlands)

    van Nierop, M; Viechtbauer, W; Gunther, N; van Zelst, C; de Graaf, R; Ten Have, M; van Dorsselaer, S; Bak, M; van Winkel, R; Cahn, W

    BACKGROUND: Meta-analyses link childhood trauma to depression, mania, anxiety disorders, and psychosis. It is unclear, however, whether these outcomes truly represent distinct disorders following childhood trauma, or that childhood trauma is associated with admixtures of affective, psychotic,

  17. Perisoreus infaustus

    Indian Academy of Sciences (India)

    avian genome evolution from cross-species amplification tests. MENG-HUA LI* ..... We tested for Hardy-. Weinberg equilibrium and linkage disequilibrium (LD) using ... 12 loci, two loci (Ase50 and Phtr3) were assigned to the Z- chromosome by ...

  18. Effect of polycarboxylate admixture structure on cement paste rheology

    Directory of Open Access Journals (Sweden)

    Aranda, M. A. G.

    2007-06-01

    Full Text Available The purpose of the present study was to analyze the effect of the structural differences in four polycarboxylate and polyether admixtures on the rheological properties of cement pastes with different chemical and mineralogical compositions and different active additions (CEM I 42.5 R, CEM I 52.5 R, CEM I 52.5 N/SR, CEM II/AV 42.5R, CEM II/B-L 32.5 R, CEM III/B 32.5R, BL I 52.5R and CAC – European standard EN 197-1:2000. The results of the minislump test concurred with the variations observed in the values of the rheological parameters (shear stress and plastic viscosity. The structural characteristic of the admixtures found to play the most prominent role in their fluidizing effect was the proportion of carboxylate (CG and polyether (EG group components. In cements characteristics such as fineness and the C3A/calcium sulphate and C3S/C3A ratios were also observed to be essential to admixture effectiveness. In this regard, the rheological parameters varied most widely in CEM I 52.5N/SR pastes and least in BL I 52.5R cement pastes. Of the additioned cements, the CEM III/B 32.5R pastes, which contained granulated blast furnace slag, showed the highest rises in flowability. Finally, the fluidizing effect of polycarboxylate superplasticizers was much more intense in calcium aluminate cements, although flowability declined rapidly in this material.El objetivo de este trabajo ha sido estudiar el efecto de las diferencias estructurales de cuatro aditivos basados en policarboxilatos y poliéteres sobre las propiedades reológicas de pastas de cemento con diferente composición química, mineralógica y con distintas adiciones activas (CEM I 42,5 R, CEM I 52,5 R, CEM I 52,5 N/SR, CEM II/AV 42,5R, CEM II/ B-L 32,5 R, CEM III/B 32,5R, BL I 52,5R y CAC - Norma EN 197-1:2000. Los resultados obtenidos sobre la fluidez de la pasta en el ensayo del “Minislump” coinciden con la evolución de los valores de los parámetros reológicos (esfuerzo de

  19. Distribution of lod scores in oligogenic linkage analysis.

    Science.gov (United States)

    Williams, J T; North, K E; Martin, L J; Comuzzie, A G; Göring, H H; Blangero, J

    2001-01-01

    In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the ith quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oligogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood-ratio statistic.

  20. Data Linkage: A powerful research tool with potential problems

    Directory of Open Access Journals (Sweden)

    Scott Ian

    2010-12-01

    Full Text Available Abstract Background Policy makers, clinicians and researchers are demonstrating increasing interest in using data linked from multiple sources to support measurement of clinical performance and patient health outcomes. However, the utility of data linkage may be compromised by sub-optimal or incomplete linkage, leading to systematic bias. In this study, we synthesize the evidence identifying participant or population characteristics that can influence the validity and completeness of data linkage and may be associated with systematic bias in reported outcomes. Methods A narrative review, using structured search methods was undertaken. Key words "data linkage" and Mesh term "medical record linkage" were applied to Medline, EMBASE and CINAHL databases between 1991 and 2007. Abstract inclusion criteria were; the article attempted an empirical evaluation of methodological issues relating to data linkage and reported on patient characteristics, the study design included analysis of matched versus unmatched records, and the report was in English. Included articles were grouped thematically according to patient characteristics that were compared between matched and unmatched records. Results The search identified 1810 articles of which 33 (1.8% met inclusion criteria. There was marked heterogeneity in study methods and factors investigated. Characteristics that were unevenly distributed among matched and unmatched records were; age (72% of studies, sex (50% of studies, race (64% of studies, geographical/hospital site (93% of studies, socio-economic status (82% of studies and health status (72% of studies. Conclusion A number of relevant patient or population factors may be associated with incomplete data linkage resulting in systematic bias in reported clinical outcomes. Readers should consider these factors in interpreting the reported results of data linkage studies.

  1. Quality assessment of total parenteral nutrition admixtures by the use of fractional factorial design

    OpenAIRE

    Mirković, Dušica; Ibrić, Svetlana; Antunović, Mirjana

    2013-01-01

    Background/Aim. Parenteral nutrition as a specific aspect of providing nutritients still remains a permanent topic of both theoretical and experimental research. Total parenteral nutrition (TPN) admixtures have complex contents making difficult to maintain their stability. The most critical parameter is the diameter of a lipid droplet, i.e. droplet size distribution. It is recommended that droplet size should not be more than 5 m and that the presence of greater droplets should not exceed th...

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

    Directory of Open Access Journals (Sweden)

    Velculescu Victor E

    2008-04-01

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

  3. Empirical and deterministic accuracies of across-population genomic prediction

    NARCIS (Netherlands)

    Wientjes, Y.C.J.; Veerkamp, R.F.; Bijma, P.; Bovenhuis, H.; Schrooten, C.; Calus, M.P.L.

    2015-01-01

    Background: Differences in linkage disequilibrium and in allele substitution effects of QTL (quantitative trait loci) may hinder genomic prediction across populations. Our objective was to develop a deterministic formula to estimate the accuracy of across-population genomic prediction, for which

  4. Thirty autosomal insertion-deletion polymorphisms analyzed using the Investigator(®) DIPplex Kit in populations from Iraq, Lithuania, Slovenia, and Turkey

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Poulsen, L; Drobnič, K

    2016-01-01

    located in the primer binding sites. Population and forensic parameters were calculated. No significant deviations from Hardy-Weinberg equilibrium or significant linkage disequilibrium were detected. The observed heterozygosities ranged from 33% to 61% depending on the marker and the population...

  5. The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.)

    DEFF Research Database (Denmark)

    Semon, Mande; Nielsen, Rasmus; Jones, Monty P.

    2005-01-01

    Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown...

  6. Parus humilis

    Indian Academy of Sciences (India)

    The 29 primer pairs were further tested in 30 individuals, of which, seven were ... turing polyacrylamide gels, bands with a size of 50–350 bp were analysed using ... wise linkage disequilibrium (LD) and Hardy–Weinberg equi- librium (HWE) ...

  7. Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

    Science.gov (United States)

    Ruiz-Linares, Andrés; Adhikari, Kaustubh; Acuña-Alonzo, Victor; Quinto-Sanchez, Mirsha; Jaramillo, Claudia; Arias, William; Fuentes, Macarena; Pizarro, María; Everardo, Paola; de Avila, Francisco; Gómez-Valdés, Jorge; León-Mimila, Paola; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C.; Burley, Mari-Wyn; Konca, Esra; de Oliveira, Marcelo Zagonel; Veronez, Mauricio Roberto; Rubio-Codina, Marta; Attanasio, Orazio; Gibbon, Sahra; Ray, Nicolas; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Schuler-Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Balding, David; Gonzalez-José, Rolando

    2014-01-01

    The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry. PMID:25254375

  8. Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals.

    Science.gov (United States)

    Ruiz-Linares, Andrés; Adhikari, Kaustubh; Acuña-Alonzo, Victor; Quinto-Sanchez, Mirsha; Jaramillo, Claudia; Arias, William; Fuentes, Macarena; Pizarro, María; Everardo, Paola; de Avila, Francisco; Gómez-Valdés, Jorge; León-Mimila, Paola; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C; Burley, Mari-Wyn; Konca, Esra; de Oliveira, Marcelo Zagonel; Veronez, Mauricio Roberto; Rubio-Codina, Marta; Attanasio, Orazio; Gibbon, Sahra; Ray, Nicolas; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Schuler-Faccini, Lavinia; Salzano, Francisco M; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Balding, David; Gonzalez-José, Rolando

    2014-09-01

    The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.

  9. Standard test method for determining effects of chemical admixtures on corrosion of embedded steel reinforcement in concrete exposed to chloride environments

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2007-01-01

    1.1 This test method covers a procedure for determining the effects of chemical admixtures on the corrosion of metals in concrete. This test method can be used to evaluate materials intended to inhibit chloride-induced corrosion of steel in concrete. It can also be used to evaluate the corrosivity of admixtures in a chloride environment. 1.2 The values stated in SI units are to be regarded as the standard. The values given in parentheses are for information only. 1.3 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use.

  10. An estimating function approach to linkage heterogeneity

    Indian Academy of Sciences (India)

    Testing linkage heterogeneity between two loci is an important issue in genetics. Currently, there are ... on linkage heterogeneity can help people to better understand complex .... χ2(F − 2) + cχ2 (1), where c is a constant (see Appendix). Here, it can be ..... gin, ancestry, gender, age, etc., for purpose of dividing sub- groups to ...

  11. Bayesian linkage and segregation analysis: factoring the problem.

    Science.gov (United States)

    Matthysse, S

    2000-01-01

    Complex segregation analysis and linkage methods are mathematical techniques for the genetic dissection of complex diseases. They are used to delineate complex modes of familial transmission and to localize putative disease susceptibility loci to specific chromosomal locations. The computational problem of Bayesian linkage and segregation analysis is one of integration in high-dimensional spaces. In this paper, three available techniques for Bayesian linkage and segregation analysis are discussed: Markov Chain Monte Carlo (MCMC), importance sampling, and exact calculation. The contribution of each to the overall integration will be explicitly discussed.

  12. Mobile assemblies of Bennett linkages from four-crease origami patterns

    Science.gov (United States)

    Zhang, Xiao; Chen, Yan

    2018-02-01

    This paper deals with constructing mobile assemblies of Bennett linkages inspired by four-crease origami patterns. A transition technique has been proposed by taking the thick-panel form of an origami pattern as an intermediate bridge. A zero-thickness rigid origami pattern and its thick-panel form share the same sector angles and folding behaviours, while the thick-panel origami and the mobile assembly of linkages are kinematically equivalent with differences only in link profiles. Applying this transition technique to typical four-crease origami patterns, we have found that the Miura-ori and graded Miura-ori patterns lead to assemblies of Bennett linkages with identical link lengths. The supplementary-type origami patterns with different mountain-valley crease assignments correspond to different types of Bennett linkage assemblies with negative link lengths. And the identical linkage-type origami pattern generates a new mobile assembly. Hence, the transition technique offers a novel approach to constructing mobile assemblies of spatial linkages from origami patterns.

  13. Dimensional threshold for fracture linkage and hooking

    Science.gov (United States)

    Lamarche, Juliette; Chabani, Arezki; Gauthier, Bertrand D. M.

    2018-03-01

    Fracture connectivity in rocks depends on spatial properties of the pattern including length, abundance and orientation. When fractures form a single-strike set, they hardly cross-cut each other and the connectivity is limited. Linkage probability increases with increasing fracture abundance and length as small fractures connect to each other to form longer ones. A process for parallel fracture linkage is the "hooking", where two converging fracture tips mutually deviate and then converge to connect due to the interaction of their crack-tip stresses. Quantifying the processes and conditions for fracture linkage in single-strike fracture sets is crucial to better predicting fluid flow in Naturally Fractured Reservoirs. For 1734 fractures in Permian shales of the Lodève Basin, SE France, we measured geometrical parameters in 2D, characterizing three stages of the hooking process: underlapping, overlapping and linkage. We deciphered the threshold values, shape ratios and limiting conditions to switch from one stage to another one. The hook set up depends on the spacing (S) and fracture length (Lh) with the relation S ≈ 0.15 Lh. Once the hooking is initiated, with the fracture deviation length (L) L ≈ 0.4 Lh, the fractures reaches the linkage stage only when the spacing is reduced to S ≈ 0.02 Lh and the convergence (C) is < 0.1 L. These conditions apply to multi-scale fractures with a shape ratio L/S = 10 and for fracture curvature of 10°-20°.

  14. Admixture analysis of age of onset in generalized anxiety disorder.

    Science.gov (United States)

    Rhebergen, Didi; Aderka, Idan M; van der Steenstraten, Ira M; van Balkom, Anton J L M; van Oppen, Patricia; Stek, Max L; Comijs, Hannie C; Batelaan, Neeltje M

    2017-08-01

    Age of onset is a marker of clinically relevant subtypes in various medical and psychiatric disorders. Past research has also reported that age of onset in generalized anxiety disorder (GAD) is clinically significant; but, in research to date, arbitrary cut-off ages have been used. In the present study, admixture analysis was used to determine the best fitting model for age of onset distribution in GAD. Data were derived from 459 adults with a diagnosis of GAD who took part in the Netherlands Study of Depression and Anxiety (NESDA). Associations between age of onset subtypes, identified by admixture analysis, and sociodemographic, clinical, and vulnerability factors were examined using univariate tests and multivariate logistic regression analyses. Two age of onset distributions were identified: an early-onset group (24 years of age and younger) and a late-onset group (greater than 24 years of age). Multivariate analysis revealed that early-onset GAD was associated with female gender (OR 2.1 (95%CI 1.4-3.2)), higher education (OR 1.1 (95%CI 1.0-1.2)), and higher neuroticism (OR 1.4 (95%CI 1.1-1.7)), while late-onset GAD was associated with physical illnesses (OR 1.3 (95%CI 1.1-1.7)). Study limitations include the possibility of recall bias given that age of onset was assessed retrospectively, and an inability to detect a possible very-late-onset GAD subtype. Collectively, the results of the study indicate that GAD is characterized by a bimodal age of onset distribution with an objectively determined early cut-off at 24 years of age. Early-onset GAD is associated with unique factors that may contribute to its aetiology; but, it does not constitute a more severe subtype compared to late-onset GAD. Future research should use 24 years of age as the cut-off for early-onset GAD to when examining the clinical relevance of age of onset for treatment efficacy and illness course. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Admixtures of shell and cluster states in 18F

    International Nuclear Information System (INIS)

    Sakuda, Toshimi; Nemoto, Fumiki; Nagata, Sinobu.

    1976-01-01

    The properties of the low-lying T=0 positive-parity levels in 18 F are shown to be well understood by considering admixtures of 2p shell-model states and ''4p-2h'' states with alpha-cluster structures. In order to represent the ''4p-2h'' states, α- 14 N cluster model is introduced. By this model, weak coupling features and coupling between shell and cluster states are well described. The binding energies of the ground 1 + and the lowest 3 + levels are reproduced by the couplings with the ''4p-2h'' cluster states. On the other hand, weak coupling features of ''4p-2h'' cluster states are disturbed to some extent. As a result, the energy spectrum, E2-transition rates and reduced α-widths of all T=0 positive-parity levels below 7 MeV excitation energy are systematically reproduced. (auth.)

  16. A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus populations

    Directory of Open Access Journals (Sweden)

    Li Meng-Hua

    2010-08-01

    Full Text Available Abstract Background Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci. Methods We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1 and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection. Results No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively were significantly (P FST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium. Conclusion Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations.

  17. Record linkage for pharmacoepidemiological studies in cancer patients.

    Science.gov (United States)

    Herk-Sukel, Myrthe P P van; Lemmens, Valery E P P; Poll-Franse, Lonneke V van de; Herings, Ron M C; Coebergh, Jan Willem W

    2012-01-01

    An increasing need has developed for the post-approval surveillance of (new) anti-cancer drugs by means of pharmacoepidemiology and outcomes research in the area of oncology. To create an overview that makes researchers aware of the available database linkages in Northern America and Europe which facilitate pharmacoepidemiology and outcomes research in cancer patients. In addition to our own database, i.e. the Eindhoven Cancer Registry (ECR) linked to the PHARMO Record Linkage System, we considered database linkages between a population-based cancer registry and an administrative healthcare database that at least contains information on drug use and offers a longitudinal perspective on healthcare utilization. Eligible database linkages were limited to those that had been used in multiple published articles in English language included in Pubmed. The HMO Cancer Research Network (CRN) in the US was excluded from this review, as an overview of the linked databases participating in the CRN is already provided elsewhere. Researchers who had worked with the data resources included in our review were contacted for additional information and verification of the data presented in the overview. The following database linkages were included: the Surveillance, Epidemiology, and End-Results-Medicare; cancer registry data linked to Medicaid; Canadian cancer registries linked to population-based drug databases; the Scottish cancer registry linked to the Tayside drug dispensing data; linked databases in the Nordic Countries of Europe: Norway, Sweden, Finland and Denmark; and the ECR-PHARMO linkage in the Netherlands. Descriptives of the included database linkages comprise population size, generalizability of the population, year of first data availability, contents of the cancer registry, contents of the administrative healthcare database, the possibility to select a cancer-free control cohort, and linkage to other healthcare databases. The linked databases offer a longitudinal

  18. The influence of the admixture of the fullerene C60 on the strength properties of aluminum and copper under shock-wave loading

    International Nuclear Information System (INIS)

    Bezruchko, G S; Razorenov, S V; Popov, M Y

    2014-01-01

    Hugoniot elastic limit (HEL) and dynamic (spall) strength measurements of pressed aluminum and copper samples with an admixture of the fullerene C60 with 2-5 wt% under shock-wave loading were carried out. The peak pressure in the shock-wave was equal to 6 GPa. The measurements of the elastic-plastic and strength properties were based on the recording and the subsequent analysis of the sample free surface velocity histories, recorded by Velocity Interferometric System for Any Reflection (VISAR). It was found that the admixture of 5 wt% fullerene in aluminum samples led to an increase of the Hugoniot elastic limit for aluminum samples by a factor of ten. The copper samples with the admixture of 2 wt% fullerene also demonstrated an increase of the Hugoniot elastic limit in comparison with commercial copper. The measured values of the Hugoniot elastic limit were equal to 0.82-1.56 GPa for aluminum samples and 1.35-3.46 GPa for copper samples, depending on their porosity. As expected, the spall strength of the samples with fullerene decreased by about three times in comparison with the undoped samples as a result of the influence of the solid fullerene particles which were concentrators of tension stresses in the material under dynamic fracture.

  19. A guide to evaluating linkage quality for the analysis of linked data.

    Science.gov (United States)

    Harron, Katie L; Doidge, James C; Knight, Hannah E; Gilbert, Ruth E; Goldstein, Harvey; Cromwell, David A; van der Meulen, Jan H

    2017-10-01

    Linked datasets are an important resource for epidemiological and clinical studies, but linkage error can lead to biased results. For data security reasons, linkage of personal identifiers is often performed by a third party, making it difficult for researchers to assess the quality of the linked dataset in the context of specific research questions. This is compounded by a lack of guidance on how to determine the potential impact of linkage error. We describe how linkage quality can be evaluated and provide widely applicable guidance for both data providers and researchers. Using an illustrative example of a linked dataset of maternal and baby hospital records, we demonstrate three approaches for evaluating linkage quality: applying the linkage algorithm to a subset of gold standard data to quantify linkage error; comparing characteristics of linked and unlinked data to identify potential sources of bias; and evaluating the sensitivity of results to changes in the linkage procedure. These approaches can inform our understanding of the potential impact of linkage error and provide an opportunity to select the most appropriate linkage procedure for a specific analysis. Evaluating linkage quality in this way will improve the quality and transparency of epidemiological and clinical research using linked data. © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

  20. Agriculture–Tourism Linkages in Botswana: Evidence from the ...

    African Journals Online (AJOL)

    Tourism researchers are increasingly recognising that strengthened linkages between the sectors of tourism and agriculture are significant for maximising local multipliers and especially for pro-poor impacts. This article examines the linkages between the tourism and agriculture sectors in Botswana using evidence ...

  1. Systemic lupus erythematosus in a multi-ethnic cohort (LUMINA) XXXII: [corrected] contributions of admixture and socioeconomic status to renal involvement.

    Science.gov (United States)

    Alarcón, G S; Bastian, H M; Beasley, T M; Roseman, J M; Tan, F K; Fessler, B J; Vilá, L M; McGwin, G

    2006-01-01

    Renal involvement in systemic lupus erythematosus (SLE) is more frequent in minorities. We examined whether genetic or socioeconomic status (SES) explain these disparities in a large multiethnic (Hispanics from Texas and Puerto Rico, African Americans and Caucasians) SLE cohort. Renal involvement was defined as WHO Class II-V and/or proteinuria (> 0.5 g/24 h or 3+) attributable to SLE and/or abnormal urinary sediment, proteinuria 2+, elevated serum creatinine/ decreased creatinine clearance twice, 6 months apart present any time over the course of the disease. Ancestry informative markers (AIMS) were used to define the admixture proportions in each patient and group. Logistic regression models were examined to determine the percentage variance (R2) in renal involvement related to ethnicity that is explained by socio-economic status (SES) and admixture (adjusting for age, gender and disease duration, basic model). Four-hundred and fifty-nine (out of 575) patients were included; renal involvement occurred in 44.6% Texas Hispanics, 11.3% Puerto Rico Hispanics, 45.8% African Americans, 18.3% Caucasians. SES accounted for 14.5% of the variance due to ethnicity (after adjusting for basic model variables), admixture 36.8% and both, 12.2%; 45.9% of the variance remained unexplained. Alternative models for decreased glomerula filtration rate and end-stage renal disease were comparable in the distribution of the explanatory variables. Our data indicate that genetic factors appear to be more important than SES in explaining the ethnic disparities in the occurrence of renal involvement.

  2. Availability of Insurance Linkage Programs in U.S. Emergency Departments

    Directory of Open Access Journals (Sweden)

    Mia Kanak

    2014-07-01

    Full Text Available Introduction: As millions of uninsured citizens who use emergency department (ED services are now eligible for health insurance under the Affordable Care Act, the ED is ideally situated to facilitate linkage to insurance. Forty percent of U.S. EDs report having an insurance linkage program. This is the first national study to examine the characteristics of EDs that offer or do not offer these programs. Methods: This was a secondary analysis of data from the National Survey for Preventive Health Services in U.S. EDs conducted in 2008-09. We compared EDs with and without insurance programs across demographic and operational factors using univariate analysis. We then tested our hypotheses using multivariable logistic regression. We also further examined program capacity and priority among the sub-group of EDs with no insurance linkage program. Results: After adjustment, ED-insurance linkage programs were more likely to be located in the West (RR= 2.06, 95% CI = 1.33 – 2.72. The proportion of uninsured patients in an ED, teaching hospital status, and public ownership status were not associated with insurance linkage availability. EDs with linkage programs also offer more preventive services (RR = 1.87, 95% CI = 1.37–2.35 and have greater social worker availability (RR = 1.71, 95% CI = 1.12–2.33 than those who do not. Four of five EDs with a patient mix of ≥25% uninsured and no insurance linkage program reported that they could not offer a program with existing staff and funding. Conclusion: Availability of insurance linkage programs in the ED is not associated with the proportion of uninsured patients served by an ED. Policy or hospital-based interventions to increase insurance linkage should first target the 27% of EDs with high rates of uninsured patients that lack adequate program capacity. Further research on barriers to implementation and cost effectiveness may help to facilitate increased adoption of insurance linkage programs. [West J

  3. U-series disequilibrium constraints on magma generation at the Jan Mayen hotspot

    Science.gov (United States)

    Rivers, E. R.; Chernow, R.; Elkins, L. J.; Sims, K. W.; Blichert-Toft, J.; Devey, C. W.

    2013-12-01

    The incompatible element-enriched magma source beneath the Jan Mayen Island hotspot influences melt generation on the adjacent northern Mid-Atlantic Ridge system and likely derives from either a small, local mantle plume, ancient Icelandic plume material emplaced in the mantle source, and/or sub-continental lithospheric mantle remnants emplaced locally by rifting of Greenland. The slow spreading Northern Kolbeinsey and Southern Mohns Ridges are immediately adjacent to Jan Mayen Island. Both have relatively shallow ridge axes, particularly the extremely shallow Eggvin Bank region of the Northern Kolbeinsey Ridge, which host anomalously large central volcanic edifices. We are currently collecting U-series disequilibrium and long-lived radiogenic isotope data for fresh, glassy mid-ocean ridge basalts from the Northern Kolbeinsey and Southern Mohns Ridge segments to better constrain source composition, depth of melting in the garnet peridotite stability field, solid mantle upwelling rates, and the nature of melt extraction beneath those segments. In particular, we are measuring isotopic data for geographically well-located samples collected from hummocky pillow basalt flows within the axial valley of the Northern Kolbeinsey Ridge segment as well as from the large volcanoes on both ridge segments, to further determine the role of the Jan Mayen hotspot in crustal construction on the Mid-Atlantic Ridge. Recently collected data show particularly high strontium isotope ratios consistent with trace element patterns that suggest a distinct local plume located beneath the Jan Mayen hotspot. A plume model for Jan Mayen is supported by new bathymetric imaging of adjacent ridge segments that reveals excess volcanism beneath the large axial volcanoes and a radial distribution of enrichment surrounding Jan Mayen Island. We predict that age-constrained U-series disequilibrium measurements will support active mantle upwelling focused beneath both Jan Mayen Island and the large axial

  4. Quantifying sources of bias in longitudinal data linkage studies of child abuse and neglect: measuring impact of outcome specification, linkage error, and partial cohort follow-up.

    Science.gov (United States)

    Parrish, Jared W; Shanahan, Meghan E; Schnitzer, Patricia G; Lanier, Paul; Daniels, Julie L; Marshall, Stephen W

    2017-12-01

    Health informatics projects combining statewide birth populations with child welfare records have emerged as a valuable approach to conducting longitudinal research of child maltreatment. The potential bias resulting from linkage misspecification, partial cohort follow-up, and outcome misclassification in these studies has been largely unexplored. This study integrated epidemiological survey and novel administrative data sources to establish the Alaska Longitudinal Child Abuse and Neglect Linkage (ALCANLink) project. Using these data we evaluated and quantified the impact of non-linkage misspecification and single source maltreatment ascertainment use on reported maltreatment risk and effect estimates. The ALCANLink project integrates the 2009-2011 Alaska Pregnancy Risk Assessment Monitoring System (PRAMS) sample with multiple administrative databases through 2014, including one novel administrative source to track out-of-state emigration. For this project we limited our analysis to the 2009 PRAMS sample. We report on the impact of linkage quality, cohort follow-up, and multisource outcome ascertainment on the incidence proportion of reported maltreatment before age 6 and hazard ratios of selected characteristics that are often available in birth cohort linkage studies of maltreatment. Failure to account for out-of-state emigration biased the incidence proportion by 12% (from 28.3% w to 25.2% w ), and the hazard ratio (HR) by as much as 33% for some risk factors. Overly restrictive linkage parameters biased the incidence proportion downwards by 43% and the HR by as much as 27% for some factors. Multi-source linkages, on the other hand, were of little benefit for improving reported maltreatment ascertainment. Using the ALCANLink data which included a novel administrative data source, we were able to observe and quantify bias to both the incidence proportion and HR in a birth cohort linkage study of reported child maltreatment. Failure to account for out

  5. Frequencies of HID-ion ampliseq ancestry panel markers among greenlanders

    DEFF Research Database (Denmark)

    Espregueira Themudo, Gonçalo; Smidt Mogensen, Helle; Børsting, Claus

    2016-01-01

    set of 89 individuals and a test set of 15 individuals. All loci showed genotype distributions consistent with Hardy-Weinberg expectations. Linkage disequilibrium tests indicated that 14 pairs of loci were in association in Greenlanders. Population assignment of the training set to populations...

  6. Isolation and characterization of twelve microsatellite loci for the Japanese Devilray (Mobula japanica)

    NARCIS (Netherlands)

    Poortvliet, Marloes; Galvan-Magana, Felipe; Bernardi, Giacomo; Croll, Donald A.; Olsen, Jeanine L.

    2011-01-01

    Twelve polymorphic microsatellites loci were characterized for Mobula japanica (Japanese Devilray) using an enrichment protocol. All but two loci were in Hardy-Weinberg equilibrium with no evidence of linkage disequilibrium or null-alleles for a sample of 40 individuals from two populations. The

  7. Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES

    Directory of Open Access Journals (Sweden)

    Le Marchand Loic

    2009-11-01

    Full Text Available Abstract Background Population structure and admixture have strong confounding effects on genetic association studies. Discordant frequencies for age-related macular degeneration (AMD risk alleles and for AMD incidence and prevalence rates are reported across different ethnic groups. We examined the genomic ancestry characterizing 538 Latinos drawn from the Los Angeles Latino Eye Study [LALES] as part of an ongoing AMD-association study. To help assess the degree of Native American ancestry inherited by Latino populations we sampled 25 Mayans and 5 Mexican Indians collected through Coriell's Institute. Levels of European, Asian, and African descent in Latinos were inferred through the USC Multiethnic Panel (USC MEP, formed from a sample from the Multiethnic Cohort (MEC study, the Yoruba African samples from HapMap II, the Singapore Chinese Health Study, and a prospective cohort from Shanghai, China. A total of 233 ancestry informative markers were genotyped for 538 LALES Latinos, 30 Native Americans, and 355 USC MEP individuals (African Americans, Japanese, Chinese, European Americans, Latinos, and Native Hawaiians. Sensitivity of ancestry estimates to relative sample size was considered. Results We detected strong evidence for recent population admixture in LALES Latinos. Gradients of increasing Native American background and of correspondingly decreasing European ancestry were observed as a function of birth origin from North to South. The strongest excess of homozygosity, a reflection of recent population admixture, was observed in non-US born Latinos that recently populated the US. A set of 42 SNPs especially informative for distinguishing between Native Americans and Europeans were identified. Conclusion These findings reflect the historic migration patterns of Native Americans and suggest that while the 'Latino' label is used to categorize the entire population, there exists a strong degree of heterogeneity within that population, and that

  8. Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES).

    Science.gov (United States)

    Shtir, Corina J; Marjoram, Paul; Azen, Stanley; Conti, David V; Le Marchand, Loic; Haiman, Christopher A; Varma, Rohit

    2009-11-10

    Population structure and admixture have strong confounding effects on genetic association studies. Discordant frequencies for age-related macular degeneration (AMD) risk alleles and for AMD incidence and prevalence rates are reported across different ethnic groups. We examined the genomic ancestry characterizing 538 Latinos drawn from the Los Angeles Latino Eye Study [LALES] as part of an ongoing AMD-association study. To help assess the degree of Native American ancestry inherited by Latino populations we sampled 25 Mayans and 5 Mexican Indians collected through Coriell's Institute. Levels of European, Asian, and African descent in Latinos were inferred through the USC Multiethnic Panel (USC MEP), formed from a sample from the Multiethnic Cohort (MEC) study, the Yoruba African samples from HapMap II, the Singapore Chinese Health Study, and a prospective cohort from Shanghai, China. A total of 233 ancestry informative markers were genotyped for 538 LALES Latinos, 30 Native Americans, and 355 USC MEP individuals (African Americans, Japanese, Chinese, European Americans, Latinos, and Native Hawaiians). Sensitivity of ancestry estimates to relative sample size was considered. We detected strong evidence for recent population admixture in LALES Latinos. Gradients of increasing Native American background and of correspondingly decreasing European ancestry were observed as a function of birth origin from North to South. The strongest excess of homozygosity, a reflection of recent population admixture, was observed in non-US born Latinos that recently populated the US. A set of 42 SNPs especially informative for distinguishing between Native Americans and Europeans were identified. These findings reflect the historic migration patterns of Native Americans and suggest that while the 'Latino' label is used to categorize the entire population, there exists a strong degree of heterogeneity within that population, and that it will be important to assess this heterogeneity

  9. [Linkage to care among new human immunodeficiency virus diagnoses in Spain].

    Science.gov (United States)

    Oliva, Jesús; Malo, Carmen; Fernández, Ana; Izquierdo, Ana; Marcos, Henar; Cevallos, Carlos; Castilla, Jesús; García, Rocio; Díez, Mercedes

    2014-03-01

    To describe linkage to care among new HIV diagnoses in Spain; and to estimate factors associated to linkage to care within three months after diagnosis. The distribution of the time elapsing between the date of HIV diagnosis and the date of first determination of CD4 (considered to be the date of linkage to care) was calculated among new HIV diagnoses in 2010 in the seven Autonomous Regions participating, where data on date of CD4 count was available. Linkage to care was considered «correct» if done within three months after diagnosis. Factors associated to correct linkage to care were estimated using logistic regression. A total of 1769 new HIV diagnoses were included. Of them, 83.1% had evidence of linkage to care within a year, and 75.7% were linked within three months after diagnosis. Being an injectable drug user (IDU) was the only factor inversely associated with linkage to care within 3 months (OR = 0.3; 95% CI: 0.2-0.6). In Spain linkage to care after HIV diagnosis is good, but there is still room for improvement, especially among IDUs. Copyright © 2013 Elsevier España, S.L. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  10. Phase-Division-Based Dynamic Optimization of Linkages for Drawing Servo Presses

    Science.gov (United States)

    Zhang, Zhi-Gang; Wang, Li-Ping; Cao, Yan-Ke

    2017-11-01

    Existing linkage-optimization methods are designed for mechanical presses; few can be directly used for servo presses, so development of the servo press is limited. Based on the complementarity of linkage optimization and motion planning, a phase-division-based linkage-optimization model for a drawing servo press is established. Considering the motion-planning principles of a drawing servo press, and taking account of work rating and efficiency, the constraints of the optimization model are constructed. Linkage is optimized in two modes: use of either constant eccentric speed or constant slide speed in the work segments. The performances of optimized linkages are compared with those of a mature linkage SL4-2000A, which is optimized by a traditional method. The results show that the work rating of a drawing servo press equipped with linkages optimized by this new method improved and the root-mean-square torque of the servo motors is reduced by more than 10%. This research provides a promising method for designing energy-saving drawing servo presses with high work ratings.

  11. A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy.

    Science.gov (United States)

    Corbett-Detig, Russell; Nielsen, Rasmus

    2017-01-01

    Admixture-the mixing of genomes from divergent populations-is increasingly appreciated as a central process in evolution. To characterize and quantify patterns of admixture across the genome, a number of methods have been developed for local ancestry inference. However, existing approaches have a number of shortcomings. First, all local ancestry inference methods require some prior assumption about the expected ancestry tract lengths. Second, existing methods generally require genotypes, which is not feasible to obtain for many next-generation sequencing projects. Third, many methods assume samples are diploid, however a wide variety of sequencing applications will fail to meet this assumption. To address these issues, we introduce a novel hidden Markov model for estimating local ancestry that models the read pileup data, rather than genotypes, is generalized to arbitrary ploidy, and can estimate the time since admixture during local ancestry inference. We demonstrate that our method can simultaneously estimate the time since admixture and local ancestry with good accuracy, and that it performs well on samples of high ploidy-i.e. 100 or more chromosomes. As this method is very general, we expect it will be useful for local ancestry inference in a wider variety of populations than what previously has been possible. We then applied our method to pooled sequencing data derived from populations of Drosophila melanogaster on an ancestry cline on the east coast of North America. We find that regions of local recombination rates are negatively correlated with the proportion of African ancestry, suggesting that selection against foreign ancestry is the least efficient in low recombination regions. Finally we show that clinal outlier loci are enriched for genes associated with gene regulatory functions, consistent with a role of regulatory evolution in ecological adaptation of admixed D. melanogaster populations. Our results illustrate the potential of local ancestry

  12. Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption.

    Science.gov (United States)

    Lu, Wen-Jie; Yamada, Yoshiji; Sakuma, Jun

    2015-01-01

    Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Our solution supports evaluation of the D' measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical.

  13. Identification of a shared genetic susceptibility locus for coronary heart disease and periodontitis.

    Directory of Open Access Journals (Sweden)

    Arne S Schaefer

    2009-02-01

    Full Text Available Recent studies indicate a mutual epidemiological relationship between coronary heart disease (CHD and periodontitis. Both diseases are associated with similar risk factors and are characterized by a chronic inflammatory process. In a candidate-gene association study, we identify an association of a genetic susceptibility locus shared by both diseases. We confirm the known association of two neighboring linkage disequilibrium regions on human chromosome 9p21.3 with CHD and show the additional strong association of these loci with the risk of aggressive periodontitis. For the lead SNP of the main associated linkage disequilibrium region, rs1333048, the odds ratio of the autosomal-recessive mode of inheritance is 1.99 (95% confidence interval 1.33-2.94; P = 6.9 x 10(-4 for generalized aggressive periodontitis, and 1.72 (1.06-2.76; P = 2.6 x 10(-2 for localized aggressive periodontitis. The two associated linkage disequilibrium regions map to the sequence of the large antisense noncoding RNA ANRIL, which partly overlaps regulatory and coding sequences of CDKN2A/CDKN2B. A closely located diabetes-associated variant was independent of the CHD and periodontitis risk haplotypes. Our study demonstrates that CHD and periodontitis are genetically related by at least one susceptibility locus, which is possibly involved in ANRIL activity and independent of diabetes associated risk variants within this region. Elucidation of the interplay of ANRIL transcript variants and their involvement in increased susceptibility to the interactive diseases CHD and periodontitis promises new insight into the underlying shared pathogenic mechanisms of these complex common diseases.

  14. Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba

    Directory of Open Access Journals (Sweden)

    Martínez-Fuentes Antonio

    2008-07-01

    Full Text Available Abstract Background Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I and five single nucleotide polymorphisms (SNPs in the mitochondrial DNA (mtDNA coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. Results The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. Conclusion While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.

  15. A Study on the Reuse of Plastic Concrete Using Extended Set-Retarding Admixtures

    Science.gov (United States)

    Lobo, Colin; Guthrie, William F.; Kacker, Raghu

    1995-01-01

    The disposal of ready mixed concrete truck wash water and returned plastic concrete is a growing concern for the ready mixed concrete industry. Recently, extended set-retarding admixtures, or stabilizers, which slow or stop the hydration of portland cement have been introduced to the market. Treating truck wash-water or returned plastic concrete with stabilizing admixtures delays its setting and hardening, thereby facilitating the incorporation of these typically wasted materials in subsequent concrete batches. In a statistically designed experiment, the properties of blended concrete containing stabilized plastic concrete were evaluated. The variables in the study included (1) concrete age when stabilized, (2) stabilizer dosage, (3) holding period of the treated (stabilized) concrete prior to blending with fresh ingredients, and (4) amount of treated concrete in the blended batch. The setting time, strength, and drying shrinkage of the blended concretes were evaluated. For the conditions tested, batching 5 % treated concrete with fresh material did not have a significant effect on the setting time, strength, or drying shrinkage of the resulting blended concrete. Batching 50 % treated concrete with fresh materials had a significant effect on the setting characteristics of the blended cocnrete, which in turn affected the water demand to maintain slump. The data suggests that for a known set of conditions, the stabilizer dosage can be optimized within a relatively narrow range to produce desired setting characteristics. The strength and drying shrinkage of the blended concretes were essentially a function of the water content at different sampling ages and the relationship followed the general trend of control concrete. PMID:29151762

  16. A Study on the Reuse of Plastic Concrete Using Extended Set-Retarding Admixtures.

    Science.gov (United States)

    Lobo, Colin; Guthrie, William F; Kacker, Raghu

    1995-01-01

    The disposal of ready mixed concrete truck wash water and returned plastic concrete is a growing concern for the ready mixed concrete industry. Recently, extended set-retarding admixtures, or stabilizers, which slow or stop the hydration of portland cement have been introduced to the market. Treating truck wash-water or returned plastic concrete with stabilizing admixtures delays its setting and hardening, thereby facilitating the incorporation of these typically wasted materials in subsequent concrete batches. In a statistically designed experiment, the properties of blended concrete containing stabilized plastic concrete were evaluated. The variables in the study included (1) concrete age when stabilized, (2) stabilizer dosage, (3) holding period of the treated (stabilized) concrete prior to blending with fresh ingredients, and (4) amount of treated concrete in the blended batch. The setting time, strength, and drying shrinkage of the blended concretes were evaluated. For the conditions tested, batching 5 % treated concrete with fresh material did not have a significant effect on the setting time, strength, or drying shrinkage of the resulting blended concrete. Batching 50 % treated concrete with fresh materials had a significant effect on the setting characteristics of the blended cocnrete, which in turn affected the water demand to maintain slump. The data suggests that for a known set of conditions, the stabilizer dosage can be optimized within a relatively narrow range to produce desired setting characteristics. The strength and drying shrinkage of the blended concretes were essentially a function of the water content at different sampling ages and the relationship followed the general trend of control concrete.

  17. Effects of aquaculture researchers' job characteristics on linkage ...

    African Journals Online (AJOL)

    The study examined the effects of researchers' job characteristics on linkage activities in Nigeria due to the fact that many fish farmers have not been properly reached with technologies and the problem of poor fish production has been attributed to the weak linkages existing between research, extension and fish farmers.

  18. Nature–society linkages in the Aral Sea region

    Directory of Open Access Journals (Sweden)

    Kristopher D. White

    2013-01-01

    Full Text Available Central Asia's Aral Sea crisis represents a disaster of monumental proportions, a tragedy for both the region's ecology and its human inhabitants. While the human and natural environments had operated in a sustainable co-joined system for millennia, Tsarist Russian expansion into Central Asia, followed by Soviet expansion of both the cotton industry and unsustainable irrigation practices to anchor it spelled doom for the Aral Sea. Today, many of the political and economic stimuli for such misguided practices continue, as do the continued retreat of the Sea and the proliferation of poor human health. The Aral Sea crisis has received ample scholarly attention, though somewhat surprising is a relative dearth of research explicitly investigating the nature, variety, and directionality of nature–society linkages today within the region. The purpose of this paper is to elucidate the contemporary nature–society linkages operating within the Aral Sea region of Central Asia. Historical nexuses will provide necessary background, and the linkages operating currently within the spheres of regional economy, human health, and political considerations will be detailed. Couching the current crisis within the framework of coupled human–environment system contexts reveals a region in which these linkages are largely inextricable. This paper concludes with a call for a reconsideration of the nature-society linkages and a greater emphasis placed on the local region's ecological and social sustainability.

  19. Isolation and characterization of 29 microsatellite markers for the bumphead parrotfish, Bolbometopon muricatum, and cross amplification in 12 related species

    KAUST Repository

    Priest, Mark; Almany, Glenn R.; Braun, Camrin D.; Hamilton, Richard J.; Lozano-Corté s, Diego; Saenz Agudelo, Pablo; Berumen, Michael L.

    2014-01-01

    individuals sampled from the Solomon Islands. The number of alleles ranged from two to ten. Evidence of linkage disequilibrium was found for only one pair of loci (Bm54 and Bm112). Two loci (Bm20 and Bm119) showed significant departure from Hardy

  20. Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars

    NARCIS (Netherlands)

    Matthies, I.E.; Hintum, van T.J.L.; Weise, S.; Röder, M.S.

    2012-01-01

    Diversity arrays technology (DArT) and simple sequence repeat (SSR) markers were applied to investigate population structure, extent of linkage disequilibrium and genetic diversity (kinship) on a genome-wide level in European barley (Hordeum vulgare L.) cultivars. A set of 183 varieties could be

  1. Genome-wide association study of rust traits in orchardgrass using SLAF-seq technology.

    Science.gov (United States)

    Zeng, Bing; Yan, Haidong; Liu, Xinchun; Zang, Wenjing; Zhang, Ailing; Zhou, Sifan; Huang, Linkai; Liu, Jinping

    2017-01-01

    While orchardgrass ( Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass. In this study, a genome-wide association study (GWAS) was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in orchardgrass. A total of 2,334,889 SLAF tags were generated to produce 2,309,777 SNPs. ADMIXTURE analysis revealed unstructured subpopulations for 33 accessions, indicating that this orchardgrass population could be used for association analysis. Linkage disequilibrium (LD) analysis revealed an average r 2 of 0.4 across all SNP pairs, indicating a high extent of LD in these samples. Through GWAS, a total of 4,604 SNPs were found to be significantly ( P  rust trait. The bulk analysis discovered a number of 5,211 SNPs related to rust trait. Two candidate genes, including cytochrome P450, and prolamin were implicated in disease resistance through prediction of functional genes surrounding each high-quality SNP ( P  rust traits based on GWAS analysis and bulk analysis. The large number of SNPs associated with rust traits and these two candidate genes may provide the basis for further research on rust resistance mechanisms and marker-assisted selection (MAS) for rust-resistant lineages.

  2. High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.

    Science.gov (United States)

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

    2014-09-15

    We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima's D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication. Copyright © 2014 Reddy et al.

  3. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.

    Directory of Open Access Journals (Sweden)

    Guillaume Lettre

    2011-02-01

    Full Text Available Coronary heart disease (CHD is the leading cause of mortality in African Americans. To identify common genetic polymorphisms associated with CHD and its risk factors (LDL- and HDL-cholesterol (LDL-C and HDL-C, hypertension, smoking, and type-2 diabetes in individuals of African ancestry, we performed a genome-wide association study (GWAS in 8,090 African Americans from five population-based cohorts. We replicated 17 loci previously associated with CHD or its risk factors in Caucasians. For five of these regions (CHD: CDKN2A/CDKN2B; HDL-C: FADS1-3, PLTP, LPL, and ABCA1, we could leverage the distinct linkage disequilibrium (LD patterns in African Americans to identify DNA polymorphisms more strongly associated with the phenotypes than the previously reported index SNPs found in Caucasian populations. We also developed a new approach for association testing in admixed populations that uses allelic and local ancestry variation. Using this method, we discovered several loci that would have been missed using the basic allelic and global ancestry information only. Our conclusions suggest that no major loci uniquely explain the high prevalence of CHD in African Americans. Our project has developed resources and methods that address both admixture- and SNP-association to maximize power for genetic discovery in even larger African-American consortia.

  4. Effects of Leaching Behavior of Calcium Ions on Compression and Durability of Cement-Based Materials with Mineral Admixtures

    Science.gov (United States)

    Cheng, An; Chao, Sao-Jeng; Lin, Wei-Ting

    2013-01-01

    Leaching of calcium ions increases the porosity of cement-based materials, consequently resulting in a negative effect on durability since it provides an entry for aggressive harmful ions, causing reinforcing steel corrosion. This study investigates the effects of leaching behavior of calcium ions on the compression and durability of cement-based materials. Since the parameters influencing the leaching behavior of cement-based materials are unclear and diverse, this paper focuses on the influence of added mineral admixtures (fly ash, slag and silica fume) on the leaching behavior of calcium ions regarding compression and durability of cemented-based materials. Ammonium nitrate solution was used to accelerate the leaching process in this study. Scanning electron microscopy, X-ray diffraction analysis, and thermogravimetric analysis were employed to analyze and compare the cement-based material compositions prior to and after calcium ion leaching. The experimental results show that the mineral admixtures reduce calcium hydroxide quantity and refine pore structure through pozzolanic reaction, thus enhancing the compressive strength and durability of cement-based materials. PMID:28809247

  5. Stability of total nutrient admixtures with lipid injectable emulsions in glass versus plastic packaging.

    Science.gov (United States)

    Driscoll, David F; Silvestri, Anthony P; Bistrian, Bruce R; Mikrut, Bernard A

    2007-02-15

    The physical stability of two emulsions compounded as part of a total nutrient admixture (TNA) was studied in lipids packaged in either glass or plastic containers. Five weight-based adult TNA formulations that were designed to meet the full nutritional needs of adults with body weights between 40 and 80 kg were studied. Triplicate preparations of each TNA were assessed over 30 hours at room temperature by applying currently proposed United States Pharmacopeia (USP) criteria for mean droplet diameter, large-diameter tail, and globule-size distribution (GSD) for lipid injectable emulsions. In accordance with conditions set forth in USP chapter 729, the higher levels of volume-weighted percent of fat exceeding 5 microm (PFAT(5)) should not exceed 0.05% of the total lipid concentration. Significant differences were noted among TNA admixtures based on whether the lipid emulsion product was manufactured in glass or plastic. The plastic-contained TNAs failed the proposed USP methods for large-diameter fat globules in all formulations from the outset, and 60% had significant growth in large-diameter fat globules over time. In contrast, glass-contained TNAs were stable throughout and in all cases would have passed proposed USP limits. Certain lipid injectable emulsions packaged in plastic containers have baseline abnormal GSD profiles compared with those packaged in glass containers. When used to compound TNAs, the abnormal profile worsens and produces less stable TNAs than those compounded with lipid injectable emulsions packaged in glass containers.

  6. HLA class I variation controlled for genetic admixture in the Gila River Indian Community of Arizona: a model for the Paleo-Indians.

    Science.gov (United States)

    Williams, R C; McAuley, J E

    1992-01-01

    The genetic distribution of the HLA class I loci is presented for 619 "full blooded" Pima and Tohono O'odham Native Americans (Pimans) in the Gila River Indian Community. Variation in the Pimans is highly restricted. There are only three polymorphic alleles at the HLA-A locus, *A2, *A24, and *A31, and only 10 alleles with a frequency greater than 0.01 at HLA-B where *Bw48 (0.187), *B35 (0.173), and the new epitope *BN21 (0.143) have the highest frequencies. Two and three locus disequilibria values and haplotype frequencies are presented. Ten three-locus haplotypes account for more than 50% of the class I variation, with *A24 *BN21 *Cw3 (0.085) having the highest frequency. Gm allotypes demonstrate that little admixture from non-Indian populations has entered the Community since the 17th century when Europeans first came to this area. As a consequence many alleles commonly found in Europeans and European Americans are efficient markers for Caucasian admixture, while the "private" Indian alleles, *BN21 and *Bw48, can be used to measure Native American admixture in Caucasian populations. It is suggested that this distribution in "full blooded" Pimans approximates that of the Paleo-Indian migrants who first entered the Americas between 20,000 and 40,000 years ago.

  7. Intragroup Emotions: Physiological Linkage and Social Presence.

    Science.gov (United States)

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion-communicative expression and physiological state-to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence.

  8. A high-density SNP linkage scan with 142 combined subtype ADHD sib pairs identifies linkage regions on chromosomes 9 and 16.

    Science.gov (United States)

    Asherson, P; Zhou, K; Anney, R J L; Franke, B; Buitelaar, J; Ebstein, R; Gill, M; Altink, M; Arnold, R; Boer, F; Brookes, K; Buschgens, C; Butler, L; Cambell, D; Chen, W; Christiansen, H; Feldman, L; Fleischman, K; Fliers, E; Howe-Forbes, R; Goldfarb, A; Heise, A; Gabriëls, I; Johansson, L; Lubetzki, I; Marco, R; Medad, S; Minderaa, R; Mulas, F; Müller, U; Mulligan, A; Neale, B; Rijsdijk, F; Rabin, K; Rommelse, N; Sethna, V; Sorohan, J; Uebel, H; Psychogiou, L; Weeks, A; Barrett, R; Xu, X; Banaschewski, T; Sonuga-Barke, E; Eisenberg, J; Manor, I; Miranda, A; Oades, R D; Roeyers, H; Rothenberger, A; Sergeant, J; Steinhausen, H-C; Taylor, E; Thompson, M; Faraone, S V

    2008-05-01

    As part of the International Multi-centre ADHD Genetics project we completed an affected sibling pair study of 142 narrowly defined Diagnostic and Statistical Manual of Mental Disorders, fourth edition combined type attention deficit hyperactivity disorder (ADHD) proband-sibling pairs. No linkage was observed on the most established ADHD-linked genomic regions of 5p and 17p. We found suggestive linkage signals on chromosomes 9 and 16, respectively, with the highest multipoint nonparametric linkage signal on chromosome 16q23 at 99 cM (log of the odds, LOD=3.1) overlapping data published from the previous UCLA (University of California, Los Angeles) (LOD>1, approximately 95 cM) and Dutch (LOD>1, approximately 100 cM) studies. The second highest peak in this study was on chromosome 9q22 at 90 cM (LOD=2.13); both the previous UCLA and German studies also found some evidence of linkage at almost the same location (UCLA LOD=1.45 at 93 cM; German LOD=0.68 at 100 cM). The overlap of these two main peaks with previous findings suggests that loci linked to ADHD may lie within these regions. Meta-analysis or reanalysis of the raw data of all the available ADHD linkage scan data may help to clarify whether these represent true linked loci.

  9. Asian Financial Linkages: The Case of Japan

    OpenAIRE

    Fialová, Anežka

    2014-01-01

    This work reviews the topic of international financial linkages, including theoretical definitions and the main methodological approaches of the empirical measurement based on vector autoregressive models. One of the approaches, the Spillover Index methodology based on Diebold & Yilmaz (2009), is then used to analyze the developments of financial linkages of the Japanese stock market in the period from 1995 to 2012. The attention is paid both to the relations with western developed economies ...

  10. Nance-Horan syndrome: linkage analysis in a family from The Netherlands

    NARCIS (Netherlands)

    Bergen, A. A.; ten Brink, J.; Schuurman, E. J.; Bleeker-Wagemakers, E. M.

    1994-01-01

    Linkage analysis was carried out in a Dutch family with Nance-Horan (NH) syndrome. Close linkage without recombination between NH and the Xp loci DXS207, DXS43, and DXS365 (zmax = 3.23) was observed. Multipoint linkage analysis and the analysis of recombinations in multiple informative meioses

  11. African ancestry and its correlation to type 2 diabetes in African Americans: a genetic admixture analysis in three U.S. population cohorts.

    Directory of Open Access Journals (Sweden)

    Ching-Yu Cheng

    Full Text Available The risk of type 2 diabetes is approximately 2-fold higher in African Americans than in European Americans even after adjusting for known environmental risk factors, including socioeconomic status (SES, suggesting that genetic factors may explain some of this population difference in disease risk. However, relatively few genetic studies have examined this hypothesis in a large sample of African Americans with and without diabetes. Therefore, we performed an admixture analysis using 2,189 ancestry-informative markers in 7,021 African Americans (2,373 with type 2 diabetes and 4,648 without from the Atherosclerosis Risk in Communities Study, the Jackson Heart Study, and the Multiethnic Cohort to 1 determine the association of type 2 diabetes and its related quantitative traits with African ancestry controlling for measures of SES and 2 identify genetic loci for type 2 diabetes through a genome-wide admixture mapping scan. The median percentage of African ancestry of diabetic participants was slightly greater than that of non-diabetic participants (study-adjusted difference = 1.6%, P<0.001. The odds ratio for diabetes comparing participants in the highest vs. lowest tertile of African ancestry was 1.33 (95% confidence interval 1.13-1.55, after adjustment for age, sex, study, body mass index (BMI, and SES. Admixture scans identified two potential loci for diabetes at 12p13.31 (LOD = 4.0 and 13q14.3 (Z score = 4.5, P = 6.6 × 10(-6. In conclusion, genetic ancestry has a significant association with type 2 diabetes above and beyond its association with non-genetic risk factors for type 2 diabetes in African Americans, but no single gene with a major effect is sufficient to explain a large portion of the observed population difference in risk of diabetes. There undoubtedly is a complex interplay among specific genetic loci and non-genetic factors, which may both be associated with overall admixture, leading to the observed ethnic differences in diabetes

  12. Equilibrium and Disequilibrium of River Basins: Effects on Stream Captures in Serra do Mar and Serra da Mantiqueira, Brazil

    Science.gov (United States)

    DA Silva, L. M.

    2015-12-01

    Landscapes are mainly driven by river processes that control the dynamic reorganization of networks. Discovering and identifying whether river basins are in geometric equilibrium or disequilibrium requires an analysis of water divides, channels that shift laterally or expand upstream and river captures. Issues specifically discussed include the variation of drainage area change and erosion rates of the basins. In southeastern Brazil there are two main escarpments with extensive geomorphic surfaces: Serra do Mar and Serra da Mantiqueira Mountains. These landscapes are constituted of Neoproterozoic and early Paleozoic rocks, presenting steep escarpments with low-elevation coastal plains and higher elevation interior plateaus. To identify whether river basins and river profiles are in equilibrium or disequilibrium in Serra do Mar and Serra da Mantiqueira Mountains, we used the proxy (χ), evaluating the effect of drainage area change and erosion rates. We selected basins that drain both sides of these two main escarpments (oceanic and continental sides) and have denudation rates derived from pre-existing cosmogenic isotopes data (Rio de Janeiro, Paraná and Minas Gerais). Despite being an ancient and tectonically stable landscape, part of the coastal plain of Serra do Mar Mountain in Rio de Janeiro and Paraná is in geometric disequilibrium, with water divides moving in the direction of higher χ values. To achieve equilibrium, some basins located in the continental side are retracting and disappearing, losing area to the coastal basins. On the contrary, there are some adjacent sub-basins that are close to equilibrium, without strong contrasts in χ values. The same pattern was observed in Serra da Mantiqueira (Minas Gerais state), with stream captures and river network reorganization in its main rivers. The initial results suggest a strong contrast between erosion rates in the continental and the oceanic portions of the escarpments.

  13. Northern range expansion of European populations of the wasp spider Argiope bruennichi is associated with global warming-correlated genetic admixture and population-specific temperature adaptations.

    Science.gov (United States)

    Krehenwinkel, Henrik; Tautz, Diethard

    2013-04-01

    Poleward range expansions are observed for an increasing number of species, which may be an effect of global warming during the past decades. However, it is still not clear in how far these expansions reflect simple geographical shifts of species ranges, or whether new genetic adaptations play a role as well. Here, we analyse the expansion of the wasp spider Argiope bruennichi into Northern Europe during the last century. We have used a range-wide sampling of contemporary populations and historical specimens from museums to trace the phylogeography and genetic changes associated with the range shift. Based on the analysis of mitochondrial, microsatellite and SNP markers, we observe a higher level of genetic diversity in the expanding populations, apparently due to admixture of formerly isolated lineages. Using reciprocal transplant experiments for testing overwintering tolerance, as well as temperature preference and tolerance tests in the laboratory, we find that the invading spiders have possibly shifted their temperature niche. This may be a key adaptation for survival in Northern latitudes. The museum samples allow a reconstruction of the invasion's genetic history. A first, small-scale range shift started around 1930, in parallel with the onset of global warming. A more massive invasion of Northern Europe associated with genetic admixture and morphological changes occurred in later decades. We suggest that the latter range expansion into far Northern latitudes may be a consequence of the admixture that provided the genetic material for adaptations to new environmental regimes. Hence, global warming could have facilitated the initial admixture of populations and this resulted in genetic lineages with new habitat preferences. © 2013 Blackwell Publishing Ltd.

  14. Validation of an instrument to measure inter-organisational linkages in general practice.

    Science.gov (United States)

    Amoroso, Cheryl; Proudfoot, Judith; Bubner, Tanya; Jayasinghe, Upali W; Holton, Christine; Winstanley, Julie; Beilby, Justin; Harris, Mark F

    2007-12-03

    Linkages between general medical practices and external services are important for high quality chronic disease care. The purpose of this research is to describe the development, evaluation and use of a brief tool that measures the comprehensiveness and quality of a general practice's linkages with external providers for the management of patients with chronic disease. In this study, clinical linkages are defined as the communication, support, and referral arrangements between services for the care and assistance of patients with chronic disease. An interview to measure surgery-level (rather than individual clinician-level) clinical linkages was developed, piloted, reviewed, and evaluated with 97 Australian general practices. Two validated survey instruments were posted to patients, and a survey of locally available services was developed and posted to participating Divisions of General Practice (support organisations). Hypotheses regarding internal validity, association with local services, and patient satisfaction were tested using factor analysis, logistic regression and multilevel regression models. The resulting General Practice Clinical Linkages Interview (GP-CLI) is a nine-item tool with three underlying factors: referral and advice linkages, shared care and care planning linkages, and community access and awareness linkages. Local availability of chronic disease services has no affect on the comprehensiveness of services with which practices link, however, comprehensiveness of clinical linkages has an association with patient assessment of access, receptionist services, and of continuity of care in their general practice. The GP-CLI may be useful to researchers examining comparable health care systems for measuring the comprehensiveness and quality of linkages at a general practice-level with related services, possessing both internal and external validity. The tool can be used with large samples exploring the impact, outcomes, and facilitators of high

  15. Validation of an instrument to measure inter-organisational linkages in general practice

    Directory of Open Access Journals (Sweden)

    Cheryl Amoroso

    2007-11-01

    Full Text Available Purpose: Linkages between general medical practices and external services are important for high quality chronic disease care. The purpose of this research is to describe the development, evaluation and use of a brief tool that measures the comprehensiveness and quality of a general practice’s linkages with external providers for the management of patients with chronic disease. In this study, clinical linkages are defined as the communication, support, and referral arrangements between services for the care and assistance of patients with chronic disease. Methods: An interview to measure surgery-level (rather than individual clinician-level clinical linkages was developed, piloted, reviewed, and evaluated with 97 Australian general practices. Two validated survey instruments were posted to patients, and a survey of locally available services was developed and posted to participating Divisions of General Practice (support organisations. Hypotheses regarding internal validity, association with local services, and patient satisfaction were tested using factor analysis, logistic regression and multilevel regression models. Results: The resulting General Practice Clinical Linkages Interview (GP-CLI is a nine-item tool with three underlying factors: referral and advice linkages, shared care and care planning linkages, and community access and awareness linkages. Local availability of chronic disease services has no affect on the comprehensiveness of services with which practices link, however comprehensiveness of clinical linkages has an association with patient assessment of access, receptionist services, and of continuity of care in their general practice. Conclusions: The GP-CLI may be useful to researchers examining comparable health care systems for measuring the comprehensiveness and quality of linkages at a general practice-level with related services, possessing both internal and external validity. The tool can be used with large samples

  16. The Barley Chromosome 5 Linkage Map

    DEFF Research Database (Denmark)

    Jensen, J.; Jørgensen, Jørgen Helms

    1975-01-01

    The distances between nine loci on barley chromosome 5 have been studied in five two-point tests, three three-point tests, and one four-point test. Our previous chromosome 5 linkage map, which contained eleven loci mapped from literature data (Jensen and Jørgensen 1975), is extended with four loci......-position is fixed on the map by a locus (necl), which has a good marker gene located centrally in the linkage group. The positions of the other loci are their distances in centimorgans from the 0-position; loci in the direction of the short chromosome arm are assigned positive values and those...

  17. Clause linkage in Ket

    NARCIS (Netherlands)

    Nefedov, Andrey

    2015-01-01

    This work provides a typologically oriented description of clause linkage strategies in Ket, a highly endangered language spoken in Central Siberia. It is now the only surviving member of the Yeniseian language family with the last remaining speakers residing in the north of Russia’s Krasnoyarsk

  18. Fine-scale mapping of a locus for severe bipolar mood disorder on chromosome 18p11.3 in the Costa Rican population

    OpenAIRE

    McInnes, L. Alison; Service, Susan K.; Reus, Victor I.; Barnes, Glenn; Charlat, Olga; Jawahar, Satya; Lewitzky, Steve; Yang, Qing; Duong, Quyen; Spesny, Mitzi; Araya, Carmen; Araya, Xinia; Gallegos, Alvaro; Meza, Luis; Molina, Julio

    2001-01-01

    We have searched for genes predisposing to bipolar disorder (BP) by studying individuals with the most extreme form of the affected phenotype, BP-I, ascertained from the genetically isolated population of the Central Valley of Costa Rica (CVCR). The results of a previous linkage analysis on two extended CVCR BP-I pedigrees, CR001 and CR004, and of linkage disequilibrium (LD) analyses of a CVCR population sample of BP-I patients implicated a candidate region on 18p11.3....

  19. SCA12 case study

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 88; Issue 1. Utilizing linkage disequilibrium information from Indian Genome Variation Database for mapping mutations: SCA12 case study. Samira Bahl Ikhlak Ahmed The Indian Genome Variation Consortium Mitali Mukerji. Research Article Volume 88 Issue 1 April 2009 pp 55- ...

  20. Development and validation of the Axiom

    NARCIS (Netherlands)

    Bianco, Luca; Cestaro, Alessandro; Linsmith, Gareth; Muranty, Hélène; Denancé, Caroline; Théron, Anthony; Poncet, Charles; Micheletti, Diego; Kerschbamer, Emanuela; Pierro, Di Erica A.; Larger, Simone; Pindo, Massimo; De Weg, Van Eric; Davassi, Alessandro; Laurens, François; Velasco, Riccardo; Durel, Charles Eric; Troggio, Michela

    2016-01-01

    Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it

  1. Intragroup emotions: physiological linkage and social presence

    Directory of Open Access Journals (Sweden)

    Simo eJärvelä

    2016-02-01

    Full Text Available We investigated how technologically mediating two different components of emotion – communicative expression and physiological state – to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression and visualization of group level physiological heart rates and their dyadic linkage (physiology was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member’s physiological components of emotion by technological means to enhance mediated communication and strengthen social presence.

  2. Intragroup Emotions: Physiological Linkage and Social Presence

    Science.gov (United States)

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion—communicative expression and physiological state—to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence. PMID:26903913

  3. Identifying and Mapping Linkages between Actors in the Climate ...

    African Journals Online (AJOL)

    Promoting innovations in climate change requires innovation partnerships and linkages and also creating an enabling environment for actors. The paper reviewed available information on the identification and mapping of linkages between actors in the climate change innovation system. The findings showed different ...

  4. Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages.

    Science.gov (United States)

    Yang, Xianbin

    2017-09-18

    The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  5. Haplotyping the human T-cell receptor β-chain gene complex by use of restriction fragment length polymorphisms

    International Nuclear Information System (INIS)

    Charmley, P.; Chao, A.; Gatti, R.A.; Concannon, P.; Hood, L.

    1990-01-01

    The authors have studied the genetic segregation of human T-cell receptor β-chain (TCRβ) genes on chromosome 7q in 40 CEPH (Centre d'Etude du Polymorphisme Humain) families by using restriction fragment length polymorphisms (RFLPs). They constructed haplotypes from eight RFLPs by using variable- and constant-region cDNA probes, which detect polymorphisms that span more than 600 kilobases of the TCRβ gene complex. Analysis of allele distributions between TCRβ genes revealed significant linkage disequilibrium between only 6 of the 28 different pairs of RFLPs. This linkage disequilibrium strongly influences the most efficient order to proceed for typing of these RFLPs in order to achieve maximum genetic informativeness, which in this study revealed a 97.3% level of heterozygosity within the TCRβ gene complex. The results should provide new insight into recent reports of disease associations with the TCRβ gene complex and should assist in designing future experiments to detect or confirm the existence of disease-susceptibility loci in this region of the human genome

  6. A reliability design method for a lithium-ion battery pack considering the thermal disequilibrium in electric vehicles

    Science.gov (United States)

    Xia, Quan; Wang, Zili; Ren, Yi; Sun, Bo; Yang, Dezhen; Feng, Qiang

    2018-05-01

    With the rapid development of lithium-ion battery technology in the electric vehicle (EV) industry, the lifetime of the battery cell increases substantially; however, the reliability of the battery pack is still inadequate. Because of the complexity of the battery pack, a reliability design method for a lithium-ion battery pack considering the thermal disequilibrium is proposed in this paper based on cell redundancy. Based on this method, a three-dimensional electric-thermal-flow-coupled model, a stochastic degradation model of cells under field dynamic conditions and a multi-state system reliability model of a battery pack are established. The relationships between the multi-physics coupling model, the degradation model and the system reliability model are first constructed to analyze the reliability of the battery pack and followed by analysis examples with different redundancy strategies. By comparing the reliability of battery packs of different redundant cell numbers and configurations, several conclusions for the redundancy strategy are obtained. More notably, the reliability does not monotonically increase with the number of redundant cells for the thermal disequilibrium effects. In this work, the reliability of a 6 × 5 parallel-series configuration is the optimal system structure. In addition, the effect of the cell arrangement and cooling conditions are investigated.

  7. Data Linkage in VET Research: Opportunities, Challenges and Principles. Discussion Paper

    Science.gov (United States)

    Osborne, Kristen; Fowler, Craig; Circelli, Michelle

    2018-01-01

    This discussion paper explores the possibilities and risks that data linkage presents for the vocational education and training (VET) sector. Along with a broad overview of the nature of data linkage, it highlights possible applications for data linkage in the VET sector and examines the key challenges associated with its use. A number of case…

  8. Arctic-midlatitude weather linkages in North America

    Science.gov (United States)

    Overland, James E.; Wang, Muyin

    2018-06-01

    There is intense public interest in whether major Arctic changes can and will impact midlatitude weather such as cold air outbreaks on the central and east side of continents. Although there is progress in linkage research for eastern Asia, a clear gap is conformation for North America. We show two stationary temperature/geopotential height patterns where warmer Arctic temperatures have reinforced existing tropospheric jet stream wave amplitudes over North America: a Greenland/Baffin Block pattern during December 2010 and an Alaska Ridge pattern during December 2017. Even with continuing Arctic warming over the past decade, other recent eastern US winter months were less susceptible for an Arctic linkage: the jet stream was represented by either zonal flow, progressive weather systems, or unfavorable phasing of the long wave pattern. The present analysis lays the scientific controversy over the validity of linkages to the inherent intermittency of jet stream dynamics, which provides only an occasional bridge between Arctic thermodynamic forcing and extended midlatitude weather events.

  9. A microsatellite linkage map of Drosophila mojavensis

    Directory of Open Access Journals (Sweden)

    Schully Sheri

    2004-05-01

    Full Text Available Abstract Background Drosophila mojavensis has been a model system for genetic studies of ecological adaptation and speciation. However, despite its use for over half a century, no linkage map has been produced for this species or its close relatives. Results We have developed and mapped 90 microsatellites in D. mojavensis, and we present a detailed recombinational linkage map of 34 of these microsatellites. A slight excess of repetitive sequence was observed on the X-chromosome relative to the autosomes, and the linkage groups have a greater recombinational length than the homologous D. melanogaster chromosome arms. We also confirmed the conservation of Muller's elements in 23 sequences between D. melanogaster and D. mojavensis. Conclusions The microsatellite primer sequences and localizations are presented here and made available to the public. This map will facilitate future quantitative trait locus mapping studies of phenotypes involved in adaptation or reproductive isolation using this species.

  10. High-frequency stock linkage and multi-dimensional stationary processes

    Science.gov (United States)

    Wang, Xi; Bao, Si; Chen, Jingchao

    2017-02-01

    In recent years, China's stock market has experienced dramatic fluctuations; in particular, in the second half of 2014 and 2015, the market rose sharply and fell quickly. Many classical financial phenomena, such as stock plate linkage, appeared repeatedly during this period. In general, these phenomena have usually been studied using daily-level data or minute-level data. Our paper focuses on the linkage phenomenon in Chinese stock 5-second-level data during this extremely volatile period. The method used to select the linkage points and the arbitrage strategy are both based on multi-dimensional stationary processes. A new program method for testing the multi-dimensional stationary process is proposed in our paper, and the detailed program is presented in the paper's appendix. Because of the existence of the stationary process, the strategy's logarithmic cumulative average return will converge under the condition of the strong ergodic theorem, and this ensures the effectiveness of the stocks' linkage points and the more stable statistical arbitrage strategy.

  11. Stability of i.v. admixture containing metoclopramide, diphenhydramine hydrochloride, and dexamethasone sodium phosphate in 0.9% sodium chloride injection.

    Science.gov (United States)

    Kintzel, Polly E; Zhao, Ting; Wen, Bo; Sun, Duxin

    2014-12-01

    The chemical stability of a sterile admixture containing metoclopramide 1.6 mg/mL, diphenhydramine hydrochloride 2 mg/mL, and dexamethasone sodium phosphate 0.16 mg/mL in 0.9% sodium chloride injection was evaluated. Triplicate samples were prepared and stored at room temperature without light protection for a total of 48 hours. Aliquots from each sample were tested for chemical stability immediately after preparation and at 1, 4, 8, 24, and 48 hours using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Metoclopramide, diphenhydramine hydrochloride, and dexamethasone sodium phosphate were selectively monitored using multiple-reaction monitoring. Samples were diluted differently for quantitation using three individual LC-MS/MS methods. To determine the drug concentration of the three compounds in the samples, three calibration curves were constructed by plotting the peak area or the peak area ratio versus the concentration of the calibration standards of each tested compound. Apixaban was used as an internal standard. Linearity of the calibration curve was evaluated by the correlation coefficient r(2). Constituents of the admixture of metoclopramide 1.6 mg/mL, diphenhydramine hydrochloride 2 mg/mL, and dexamethasone sodium phosphate 0.16 mg/mL in 0.9% sodium chloride injection retained more than 90% of their initial concentrations over 48 hours of storage at room temperature without protection from light. The observed variability in concentrations of these three compounds was within the limits of assay variability. An i.v. admixture containing metoclopramide 1.6 mg/mL, diphenhydramine hydrochloride 2 mg/mL, and dexamethasone sodium phosphate 0.16 mg/mL in 0.9% sodium chloride injection was chemically stable for 48 hours when stored at room temperature without light protection. Copyright © 2014 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

  12. Autosomal dominant distal myopathy: Linkage to chromosome 14

    Energy Technology Data Exchange (ETDEWEB)

    Laing, N.G.; Laing, B.A.; Wilton, S.D.; Dorosz, S.; Mastaglia, F.L.; Kakulas, B.A. [Australian Neuromuscular Research Institute, Perth (Australia); Robbins, P.; Meredith, C.; Honeyman, K.; Kozman, H.

    1995-02-01

    We have studied a family segregating a form of autosomal dominant distal myopathy (MIM 160500) and containing nine living affected individuals. The myopathy in this family is closest in clinical phenotype to that first described by Gowers in 1902. A search for linkage was conducted using microsatellite, VNTR, and RFLP markers. In total, 92 markers on all 22 autosomes were run. Positive linkage was obtained with 14 of 15 markers tested on chromosome 14, with little indication of linkage elsewhere in the genome. Maximum two-point LOD scores of 2.60 at recombination fraction .00 were obtained for the markers MYH7 and D14S64 - the family structure precludes a two-point LOD score {ge} 3. Recombinations with D14S72 and D14S49 indicate that this distal myopathy locus, MPD1, should lie between these markers. A multipoint analysis assuming 100% penetrance and using the markers D14S72, D14S50, MYH7, D14S64, D14S54, and D14S49 gave a LOD score of exactly 3 at MYH7. Analysis at a penetrance of 80% gave a LOD score of 2.8 at this marker. This probable localization of a gene for distal myopathy, MPD1, on chromosome 14 should allow other investigators studying distal myopathy families to test this region for linkage in other types of the disease, to confirm linkage or to demonstrate the likely genetic heterogeneity. 24 refs., 3 figs., 1 tab.

  13. History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico

    Science.gov (United States)

    Via, Marc; Gignoux, Christopher R.; Roth, Lindsey A.; Fejerman, Laura; Galanter, Joshua; Choudhry, Shweta; Toro-Labrador, Gladys; Viera-Vera, Jorge; Oleksyk, Taras K.; Beckman, Kenneth; Ziv, Elad; Risch, Neil

    2011-01-01

    Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations. PMID:21304981

  14. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics. Mitali Mukerji. Articles written in Journal of Genetics. Volume 88 Issue 1 April 2009 pp 55-60 Research Article. Utilizing linkage disequilibrium information from Indian Genome Variation Database for mapping mutations: SCA12 case study · Samira Bahl Ikhlak Ahmed The Indian Genome ...

  15. 1000 Bull Genomes - Toward genomic Selectionf from whole genome sequence Data in Dairy and Beef Cattle

    NARCIS (Netherlands)

    Hayes, B.; Daetwyler, H.D.; Fries, R.; Guldbrandtsen, B.; Mogens Sando Lund, M.; Didier A. Boichard, D.A.; Stothard, P.; Veerkamp, R.F.; Hulsegge, B.; Rocha, D.; Tassell, C.; Mullaart, E.; Gredler, B.; Druet, T.; Bagnato, A.; Goddard, M.E.; Chamberlain, H.L.

    2013-01-01

    Genomic prediction of breeding values is now used as the basis for selection of dairy cattle, and in some cases beef cattle, in a number of countries. When genomic prediction was introduced most of the information was to thought to be derived from linkage disequilibrium between markers and causative

  16. Detecting structure of haplotypes and local ancestry

    Science.gov (United States)

    We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local an...

  17. Novel association in chromosome 4q27 region with rheumatoid arthritis and confirmation of type 1 diabetes point to a general risk locus for autoimmune diseases

    NARCIS (Netherlands)

    Zhernakova, Alexandra; Alizadeh, Behrooz Z.; Bevova, Marianna; van Leeuwen, Miek A.; Coenen, Marieke J. H.; Franke, Barbara; Franke, Lude; Posthumus, Marcel D.; van Heel, David A.; van der Steege, Gerrit; Radstake, Timothy R. D. J.; Barrera, Pilar; Roep, Bart O.; Koeleman, Bobby P. C.; Wijmenga, Cisca

    2007-01-01

    Recently, association of celiac disease with common single-nucleotide polymorphism (SNP) variants in an extensive linkage-disequilibrium block of 480 kb containing the KIAA1109, Tenr, IL2, and IL21 genes has been demonstrated in three independent populations (rs6822844P(combined) = 1.3 x 10(-14)).

  18. Novel association in chromosome 4q27 region with rheumatoid arthritis and confirmation of type 1 diabetes point to a general risk locus for autoimmune diseases.

    NARCIS (Netherlands)

    Zhernakova, A.; Alizadeh, B.Z.; Bevova, M.; Leeuwen, M.A. van; Coenen, M.J.H.; Franke, B.; Franke, L.; Posthumus, M.D.; Heel, D.A. van; Steege, G. van der; Radstake, T.R.D.J.; Barrera, P.; Roep, B.O.; Koeleman, B.P.; Wijmenga, C.

    2007-01-01

    Recently, association of celiac disease with common single-nucleotide polymorphism (SNP) variants in an extensive linkage-disequilibrium block of 480 kb containing the KIAA1109, Tenr, IL2, and IL21 genes has been demonstrated in three independent populations (rs6822844P combined=1.3 x 10(-14)). The

  19. Improving the geotechnical behavior of sand through cohesive admixtures

    Directory of Open Access Journals (Sweden)

    Mohie eldin Mohamed Afify Elmashad

    2018-04-01

    Full Text Available Irrigation projects in Egypt have been facing tremendous challenges, mostly is the scarcity of irrigation water. The current research presents the effect of different cohesive admixture on the conductivity of siliceous sand in general and its other geotechnical properties. Two different types of conventional swelling clay from (Toshka, 6th of October as well as bentonite were used to construct the irrigation canals and embankment. The results indicated that increase in the plasticity properties of the treated soil also decrease the permeability and infiltration. Moreover, the dry density of 2.08 t/m3 was obtained from sand and 20% 6th of October mixture, also the CBR of 31.20% were obtained from sand and 8% 6th of October mixture. Increasing the bentonite ratio increases the cohesion and decreasing the permeability. The swelling ratios of sand 6th of October Clay mixture is equal to 0.28%, and the fictitious stress at which the swelling ratio is nil, is equal to 16 kPa. Keywords: Sand, Swelling clay, Bentonite, Compaction test, Consolidation test, Triaxial test

  20. A dynamic general disequilibrium model of a sequential monetary production economy

    International Nuclear Information System (INIS)

    Raberto, Marco; Teglio, Andrea; Cincotti, Silvano

    2006-01-01

    A discrete, deterministic, economic model, based on the framework of non-Walrasian or disequilibrium economics, is presented. The main feature of this approach is the presence of non-clearing markets, where not all demands and supplies are satisfied and some agents may be rationed. The model is characterized by three agents (i.e., a representative firm, a representative consumer, and a central bank), three commodities (i.e., goods, labour and money, each homogeneous) and three markets for their exchange. The imbalance between demand and supply in each market determines the dynamics of price, nominal wage and nominal interest rate. The central bank provides the money supply according to an operating target interest rate that is fixed accordingly to Taylor's rule. The model has been studied by means of computer simulations. Results pointed out the presence of business cycles that can be controlled by proper policies of the central bank

  1. Numerical study on characteristics of radio-frequency discharge at atmospheric pressure in argon with small admixtures of oxygen

    Science.gov (United States)

    Wang, Yinan; Liu, Yue

    2017-07-01

    In this paper, a 1D fluid model is developed to study the characteristics of a discharge in argon with small admixtures of oxygen at atmospheric pressure. This model consists of a series of equations, including continuity equations for electrons, positive ions, negative ions and neutral particles, the energy equation, and the Poisson equation for electric potential. Special attention has been paid to the electron energy dissipation and the mechanisms of electron heating, while the admixture of oxygen is in the range of 0.1%-0.6%. It is found that when the oxygen-to-argon ratio grows, the discharge is obviously divided into three stages: electron growth, electron reduction and the electron remaining unchanged. Furthermore, the cycle-averaged electric field, electron temperature, electron Ohmic heating, electron collisionless heating, electron energy dissipation and the net electron production are also studied in detail, and when the oxygen-to-argon ratio is relatively larger (R = 0.6%), double value peaks of electron Ohmic heating appear in the sheath. According to the results of the numerical simulation, various oxygen-to-argon ratios result in different amounts of electron energy dissipation and electron heating.

  2. Genetic admixture estimates by Alu elements in Afro-Colombian and Mestizo populations from Antioquia, Colombia.

    Science.gov (United States)

    Gómez-Pérez, Luis; Alfonso-Sánchez, Miguel A; Pérez-Miranda, Ana M; García-Obregón, Susana; Builes, Juan J; Bravo, Maria L; De Pancorbo, Marian M; Peña, José A

    2010-08-01

    This work was intended to gain insights into the admixture processes occurring in Latin American populations by examining the genetic profiles of two ethnic groups from Antioquia (Colombia). To analyse the genetic variability, eight Alu insertions were typed in 64 Afro-Colombians and a reference group of 34 Hispanics (Mestizos). Admixture proportions were estimated using the Weighted Least Squares and the Gene Identity methods. The usefulness of the Alu elements as Ancestry Informative Markers (AIMs) was evaluated through differences in weighted allelic frequencies (delta values) and by hierarchical analysis of the molecular variance (AMOVA). The Afro-Colombian gene pool was largely determined by the African component (88.5-88.8%), but the most prominent feature was the null contribution of European genes. Mestizos were characterized by a major European component (60.0-63.8%) and a comparatively low proportion of Amerindian (19.2-20.7%) and African (17.0-19.3%) genes. Five of the Alu loci examined (ACE, APO, FXIIIB, PV92 and TPA25) showed an adequate resolving power to differentiate between continental groups, as indicated by delta values and AMOVA results. The peculiarity of the Afro-Colombian gene pool seems to be associated with intense genetic drift episodes that occurred in isolated communities founded by small groups of runaway slaves. ACE, APO, FXIIIB, PV92 and TPA25 could be efficiently utilized in studies dealing with demographic history and biogeographical ancestry in human populations.

  3. The effect of chemical admixtures and mineral additives on the properties of self-compacting mortars

    Energy Technology Data Exchange (ETDEWEB)

    Mustafa Sahmaran; Heru Ari Christianto; Ismail Ozgur Yaman [Middle East Technical University, Ankara (Turkey). Department of Civil Engineering

    2006-05-15

    Mortar serves as the basis for the workability properties of self-compacting concrete (SCC) and these properties could be assessed by self-compacting mortars (SCM). In fact, assessing the properties of SCM is an integral part of SCC design. The objective of this study was to evaluate the effectiveness of various mineral additives and chemical admixtures in producing SCMs. For this purpose, four mineral additives (fly ash, brick powder, limestone powder, and kaolinite), three superplasticizers (SP), and two viscosity modifying admixtures (VMA) were used. Within the scope of the experimental program, 43 mixtures of SCM were prepared keeping the amount of mixing water and total powder content (Portland cement and mineral additives) constant. Workability of the fresh mortar was determined using mini V-funnel and mini slump flow tests. The setting time of the mortars, were also determined. The hardened properties that were determined included ultrasonic pulse velocity and strength determined at 28 and 56 days. It was concluded that among the mineral additives used, fly ash and limestone powder significantly increased the workability of SCMs. On the other hand, especially fly ash significantly increased the setting time of the mortars, which can, however, be eliminated through the use of ternary mixtures, such as mixing fly ash with limestone powder. The two polycarboxyl based SPs yield approximately the same workability and the melamine formaldehyde based SP was not as effective as the other two.

  4. Admixture analysis of the diagnostic subtypes of social anxiety disorder: implications for the DSM-V.

    Science.gov (United States)

    Aderka, Idan M; Nickerson, Angela; Hofmann, Stefan G

    2012-06-01

    Much controversy exists regarding diagnostic subtypes of social anxiety disorder (SAD). The present study used admixture analysis to examine whether individuals with generalized and nongeneralized SAD belong to the same or different populations of origin. This can inform diagnostic subtyping of SAD in the forthcoming DSM-V. Treatment-seeking individuals with generalized SAD (n = 154) and nongeneralized SAD (n = 48) completed a battery of questionnaires. Based on participants' responses to the Liebowitz Social Anxiety Scale (LSAS), we estimated log likelihood and chi-square goodness-of-fit for models with 1, 2, 3, or 4 populations of origin, and compared models using forward stepwise estimation and maximum likelihood ratio tests. Admixture analyses suggested that the two diagnostic subtypes of SAD belong to the same underlying population of origin. In addition, observable differences in depression, general anxiety, and comorbidity were no longer significant when controlling for social anxiety severity. Our sample was recruited in the U.S. and was a treatment-seeking sample. Future studies should examine whether our results generalize to different cultures, and community samples. Support for qualitative differences between SAD subtypes was not found. Rather, our findings support the notion that the diagnostic subtypes of SAD differ quantitatively, and that SAD exists on a continuum of severity. This finding informs diagnostic subtyping of SAD in the forthcoming DSM-V. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. Fast admixture analysis and population tree estimation for SNP and NGS data

    DEFF Research Database (Denmark)

    Cheng, Jade Yu; Mailund, Thomas; Nielsen, Rasmus

    2017-01-01

    assumption for identifying ancestry components correctly and for inferring the correct tree. In most cases, ancestry components are inferred correctly, although sample sizes and times since admixture can influence the results. We show that the popular Gaussian approximation tends to perform poorly under......-calling associated with Next Generation Sequencing (NGS) data. We also present a new method for estimating population trees from ancestry components using a Gaussian approximation. Using coalescence simulations of diverging populations, we explore the adequacy of the STRUCTURE-style models and the Gaussian...... extreme divergence scenarios e.g. with very long branch lengths, but the topologies of the population trees are accurately inferred in all scenarios explored. The new methods are implemented together with appropriate visualization tools in the software package Ohana....

  6. Used cooking oil as a green chemical admixture in concrete

    International Nuclear Information System (INIS)

    Salmia, B; Sidek, L M; Hidayah, B; Muda, Zakaria Che; Alam, Md Ashraful

    2013-01-01

    According to National Statistics Approximately 1.35 billion gallons of used oil are generated yearly. With the increasing of the concrete usage, a more cost effective and economic new type of admixtures may give positive impacts on the Malaysian construction building as well as worldwide concrete usage. To objective of this is study is to investigate the effect of used cooking oil in terms of slump test, compressive strength test and rebound hammer. By adding the used cooking oil to the concrete, it increases the slump value from 4% to 72%. And the compressive strength have an increment from 1% to 16.8%. The used cooking oil obtains the optimum contribution to the concrete mix proportion of containing used cooking oil of 1.50% from the cement content. The result of used cooking oil from experimental program of slump value and compressive strength proved that used cooking oil have positive effects on replacement of commercially available superplasticizer.

  7. Optimal Cement Mixtures Containing Mineral Admixtures under Multiple and Conflicting Criteria

    Directory of Open Access Journals (Sweden)

    Nitza M. García

    2018-01-01

    Full Text Available In modern construction industry, fabrication of sustainable concrete has turned the decision-making process into a challenging endeavor. One alternative is using fly ash and nanostructured silica as cement replacements. In these modern mixtures, proper concrete bulk density, percentage of voids, and compressive strength normally cannot be optimized individually. Hereby, a decision-making strategy on the replacement of those components is presented while taking into account those three performance measurements. The relationships among those components upon concrete fabrication required a design of experiments of mixtures to characterize those mineral admixtures. This approach integrates different objective functions that are in conflict and obtains the best compromise mixtures for the performance measures being considered. This optimization strategy permitted to recommend the combined use of fly ash and nanosilica to improve the concrete properties at its early age.

  8. Identification of Major Quantitative Trait Loci for Seed Oil Content in Soybeans by Combining Linkage and Genome-Wide Association Mapping.

    Science.gov (United States)

    Cao, Yongce; Li, Shuguang; Wang, Zili; Chang, Fangguo; Kong, Jiejie; Gai, Junyi; Zhao, Tuanjie

    2017-01-01

    Soybean oil is the most widely produced vegetable oil in the world and its content in soybean seed is an important quality trait in breeding programs. More than 100 quantitative trait loci (QTLs) for soybean oil content have been identified. However, most of them are genotype specific and/or environment sensitive. Here, we used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley. One recombinant inbred line (RIL) population (NJMN-RIL), with 104 lines developed from a cross between M8108 and NN1138-2 , was planted in five environments to investigate phenotypic data, and a new genetic map with 2,062 specific-locus amplified fragment markers was constructed to map oil content QTLs. A derived F 2 population between MN-5 (a line of NJMN-RIL) and NN1138-2 was also developed to confirm one major QTL. A soybean breeding germplasm population (279 lines) was established to perform a genome-wide association study (GWAS) using 59,845 high-quality single nucleotide polymorphism markers. In the NJMN-RIL population, 8 QTLs were found that explained a range of phenotypic variance from 6.3 to 26.3% in certain planting environments. Among them, qOil-5-1, qOil-10-1 , and qOil-14-1 were detected in different environments, and qOil-5-1 was further confirmed using the secondary F 2 population. Three loci located on chromosomes 5 and 20 were detected in a 2-year long GWAS, and one locus that overlapped with qOil-5-1 was found repeatedly and treated as the same locus. qOil-5-1 was further localized to a linkage disequilibrium block region of approximately 440 kb. These results will not only increase our understanding of the genetic control of seed oil content in soybean, but will also be helpful in marker-assisted selection for breeding high seed oil content soybean and gene cloning to elucidate the mechanisms of seed oil content.

  9. Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.).

    Science.gov (United States)

    Yagi, Masafumi; Yamamoto, Toshiya; Isobe, Sachiko; Hirakawa, Hideki; Tabata, Satoshi; Tanase, Koji; Yamaguchi, Hiroyasu; Onozaki, Takashi

    2013-10-26

    Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. The improved genetic linkage maps and SSR markers developed

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

    DEFF Research Database (Denmark)

    Shi, Jiajun; Zhang, Yanfeng; Zheng, Wei

    2016-01-01

    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...

  11. Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk

    NARCIS (Netherlands)

    Hu, Xinli; Deutsch, Aaron J; Lenz, Tobias L; Onengut-Gumuscu, Suna; Han, Buhm; Chen, Wei-Min; Howson, Joanna M M; Todd, John A; de Bakker, Paul I W; Rich, Stephen S; Raychaudhuri, Soumya

    Variation in the human leukocyte antigen (HLA) genes accounts for one-half of the genetic risk in type 1 diabetes (T1D). Amino acid changes in the HLA-DR and HLA-DQ molecules mediate most of the risk, but extensive linkage disequilibrium complicates the localization of independent effects. Using

  12. Quantification of type I error probabilities for heterogeneity LOD scores.

    Science.gov (United States)

    Abreu, Paula C; Hodge, Susan E; Greenberg, David A

    2002-02-01

    Locus heterogeneity is a major confounding factor in linkage analysis. When no prior knowledge of linkage exists, and one aims to detect linkage and heterogeneity simultaneously, classical distribution theory of log-likelihood ratios does not hold. Despite some theoretical work on this problem, no generally accepted practical guidelines exist. Nor has anyone rigorously examined the combined effect of testing for linkage and heterogeneity and simultaneously maximizing over two genetic models (dominant, recessive). The effect of linkage phase represents another uninvestigated issue. Using computer simulation, we investigated type I error (P value) of the "admixture" heterogeneity LOD (HLOD) score, i.e., the LOD score maximized over both recombination fraction theta and admixture parameter alpha and we compared this with the P values when one maximizes only with respect to theta (i.e., the standard LOD score). We generated datasets of phase-known and -unknown nuclear families, sizes k = 2, 4, and 6 children, under fully penetrant autosomal dominant inheritance. We analyzed these datasets (1) assuming a single genetic model, and maximizing the HLOD over theta and alpha; and (2) maximizing the HLOD additionally over two dominance models (dominant vs. recessive), then subtracting a 0.3 correction. For both (1) and (2), P values increased with family size k; rose less for phase-unknown families than for phase-known ones, with the former approaching the latter as k increased; and did not exceed the one-sided mixture distribution xi = (1/2) chi1(2) + (1/2) chi2(2). Thus, maximizing the HLOD over theta and alpha appears to add considerably less than an additional degree of freedom to the associated chi1(2) distribution. We conclude with practical guidelines for linkage investigators. Copyright 2002 Wiley-Liss, Inc.

  13. The importance of identity-by-state information for the accuracy of genomic selection

    Directory of Open Access Journals (Sweden)

    Luan Tu

    2012-08-01

    Full Text Available Abstract Background It is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and QTL but also on genetic relationships. Here, we investigated the reliability of predicting genome-wide breeding values based on population-wide linkage disequilibrium information, based on identity-by-descent relationships within the known pedigree, and to what extent linkage disequilibrium information improves predictions based on identity-by-descent genomic relationship information. Methods The study was performed on milk, fat, and protein yield, using genotype data on 35 706 SNP and deregressed proofs of 1086 Italian Brown Swiss bulls. Genome-wide breeding values were predicted using a genomic identity-by-state relationship matrix and a genomic identity-by-descent relationship matrix (averaged over all marker loci. The identity-by-descent matrix was calculated by linkage analysis using one to five generations of pedigree data. Results We showed that genome-wide breeding values prediction based only on identity-by-descent genomic relationships within the known pedigree was as or more reliable than that based on identity-by-state, which implicitly also accounts for genomic relationships that occurred before the known pedigree. Furthermore, combining the two matrices did not improve the prediction compared to using identity-by-descent alone. Including different numbers of generations in the pedigree showed that most of the information in genome-wide breeding values prediction comes from animals with known common ancestors less than four generations back in the pedigree. Conclusions Our results show that, in pedigreed breeding populations, the accuracy of genome-wide breeding values obtained by identity-by-descent relationships was not improved by identity-by-state information. Although, in principle, genomic selection based on identity-by-state does not require

  14. Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data

    DEFF Research Database (Denmark)

    2017-01-01

    The classic epileptic encephalopathies, including infantile spasms (IS) and Lennox-Gastaut syndrome (LGS), are severe seizure disorders that usually arise sporadically. De novo variants in genes mainly encoding ion channel and synaptic proteins have been found to account for over 15% of patients...... with IS or LGS. The contribution of autosomal recessive genetic variation, however, is less well understood. We implemented a rare variant transmission disequilibrium test (TDT) to search for autosomal recessive epileptic encephalopathy genes in a cohort of 320 outbred patient-parent trios that were generally...... not find evidence of a role for individual autosomal recessive genes, our current sample is insufficiently powered to assess the overall role of autosomal recessive genotypes in an outbred epileptic encephalopathy population....

  15. Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

    Science.gov (United States)

    Olsen, Aaron M; Westneat, Mark W

    2016-12-01

    Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing

  16. Targeted scan of fifteen regions for nonsyndromic cleft lip and palate in Filipino families.

    Science.gov (United States)

    Schultz, R E; Cooper, M E; Daack-Hirsch, S; Shi, M; Nepomucena, B; Graf, K A; O'Brien, E K; O'Brien, S E; Marazita, M L; Murray, J C

    2004-02-15

    Cleft lip with or without cleft palate (CL/P) is a congenital anomaly with variable birth prevalence based on geographic origins, with the highest rates commonly found in Asian populations. About 70% of cases are nonsyndromic (NS), in which the affected individual has no other abnormalities. NS CL/P is a complex disorder with genetic and environmental effects and no specific genetic loci yet confirmed. Fifteen candidate regions were examined for linkage to NS CL/P. Regions were chosen based on previous suggestive linkage and/or association in human families, or suggestive animal model data. Polymorphic markers in these regions were genotyped for analysis on 36 Filipino families comprised of 126 affected and 218 unaffected individuals. An additional 70 families with 149 affecteds were used for replication of suggestive results. Parametric (LOD score) and nonparametric (SIMIBD) linkage analyses were performed as well as transmission disequilibrium test (TDT) analysis. Five markers yielded suggestive results from the 36 families. The parametric LOD scores for the MSX1-CA and D4S1629 were >1.0 and the SIMIBD P values for D6S1029 and RFC1 are suggestive (value of 0.01 for TGFA was significant. Since the Msx1 mouse knockout has cleft palate and MSX1 mutations have been found in rare cases of syndromic CL/P, this locus is especially plausible for linkage. Previous studies have also found linkage of NS CL/P to 4q31 and 6p23. These regions contain several candidate genes, including AP2 at 6p23 and FGF2, BMPR1B, and MADH1 at 4q31. TGFA has both linkage and linkage disequilibrium data supporting it as a candidate gene for NS CL/P. While no region was definitively confirmed for linkage to NS CL/P, the data do support further investigation using larger sample sizes and candidate gene studies at 2p13.2, 4p16.2, 4q31, 6p23, and 16q22-24. Copyright 2003 Wiley-Liss, Inc.

  17. 238 series isotopes at different soil depths and disequilibrium over various geology and soil classifications along transects in selected parts of Ireland

    International Nuclear Information System (INIS)

    McAulay, I.R.; Hayes, A.

    1996-01-01

    Sampling of soils was carried out along linear transects in selected regions of the country, a technique known as Transect Sampling. This was a controlled rather than a random sampling technique. The transects were located in regions which were previously known to contain high levels of the 226 Ra isotope, from the 238 U series. The soil sampling was carried out at selected sites along these transects. At each transect site, two different soil depths were examined and the soil samples collected were identified as the top and bottom soil samples. This transect data set, consisting of the isotope activity levels and the influencing variables transect geology and soil types, provided a data base for investigation. Comparisons were made between the soil isotope activity levels measured at different soil depths. An examination of the 238 U decay series showed the existence of disequilibrium. Relationships between the disequilibrium data and the associated geology and soil types were investigated. (author)

  18. STAKEHOLDER LINKAGES FOR SUSTAINABLE LAND ...

    African Journals Online (AJOL)

    Osondu

    Key words: Stakeholders; farmer-expert linkages; resource management; Ethiopia. Introduction ... decentralized democratic decision making processes and thus ..... district offices within the given time limits. They were often .... -less willing and less ready to hearing weaker performance reports (expect more success with ...

  19. ANALISIS KEBIJAKAN LINKAGE PROGRAM LEMBAGA KEUANGAN SYARIAH DALAM RANGKA PEMBERDAYAAN UKM DI INDONESIA

    Directory of Open Access Journals (Sweden)

    Siti Hamidah

    2016-03-01

    Linkage program adalah program yang menghubungkan bank dengan pelaku usaha mikro kecil melalui lembaga keuangan mikro. Kelemahan dalam Linkage program adalah pada aspek peraturan yang tersebar dalam berbagai aturan, dan khusus bagi lembaga keuangan syariah terdapat pula kendala berkaitan dengan kesesuaian dengan ketentuan syariah. Dari penelitian dengan pendekatan perundang-undangan dan pendekatan konseptual ini diperoleh inventarisasi serta analisis kebijakan Linkage Program bagi Lembaga Keuangan Syariah dalam hukum positif Indonesia. Kebijakan terkait Linkage program, diklasifikasi dalam 2 kelompok, yaitu kebijakan substansi dan prosedural. Aturan inilah yang menjadi rujukan bagi lembaga keuangan syariah rangka pemberdayaan usaha kecil mikro di Indonesia. Kata kunci: Linkage program, lembaga keuangan syariah, usaha mikro kecil

  20. Genetic differentiation of Mexican Holstein cattle and its relationship with Canadian and U.S. Holsteins

    Directory of Open Access Journals (Sweden)

    Felipe De Jesus Ruiz-Lopez

    2015-02-01

    Full Text Available The Mexican Holstein industry has imported Canadian and US (CAN+USA Holstein germplasm for use in two different production systems, the conventional (Conv and the low income system (Lowi. The objective of this work was to study the genetic composition and differentiation of the Mexican Holstein cattle, considering the production system in which they perform and their relationship with the Canadian and US Holstein populations. The analysis included information from 149, 303 and 173 unrelated or with unknown pedigree Holstein (HO animals from the Conv, Lowi and CAN+USA populations, respectively. Canadian and US Jersey (JE and Brown Swiss (BS genotypes (162 and 86, respectively were used to determine if Mexican Holsteins were hybridized with either of these breeds. After quality control filtering, a total of 6,617 out of 6,836 SNP markers were used. To describe the genetic diversity across the populations, principal component (PC, admixture composition, and linkage disequilibrium (r2 analyses were performed. Through the PC analysis, HOxJE and HOxBS crossbreeding was detected in the Lowi system. The Conv system appeared to be in between Lowi and CAN+USA populations. Admixture analysis differentiated between the genetic composition of the Conv and Lowi systems, and five ancestry groups associated to sire’s country of origin were identified. The minimum distance between markers to estimate a useful LD was found to be 54.5 kb for the Mexican HO populations. At this average distance, the persistence of phase across autosomes of Conv and Lowi systems was 0.94, for Conv and CAN+USA was 0.92 and for the Lowi and CAN+USA was 0.91. Results supported the flow of germplasm among populations being Conv a source for Lowi, and dependent on migration from CAN+USA. Mexican Holstein cattle in Conv and Lowi populations share common ancestry with CAN+USA but have different genetic signatures.