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Sample records for frequency haplotype structure

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

    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.

  2. Detecting structure of haplotypes and local ancestry

    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...

  3. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR.

    Tyson, Jess; Armour, John A L

    2012-12-11

    Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

  4. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR

    Tyson Jess

    2012-12-01

    Full Text Available Abstract Background Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. Results In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. Conclusion This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

  5. Modeling coverage gaps in haplotype frequencies via Bayesian inference to improve stem cell donor selection.

    Louzoun, Yoram; Alter, Idan; Gragert, Loren; Albrecht, Mark; Maiers, Martin

    2018-05-01

    Regardless of sampling depth, accurate genotype imputation is limited in regions of high polymorphism which often have a heavy-tailed haplotype frequency distribution. Many rare haplotypes are thus unobserved. Statistical methods to improve imputation by extending reference haplotype distributions using linkage disequilibrium patterns that relate allele and haplotype frequencies have not yet been explored. In the field of unrelated stem cell transplantation, imputation of highly polymorphic human leukocyte antigen (HLA) genes has an important application in identifying the best-matched stem cell donor when searching large registries totaling over 28,000,000 donors worldwide. Despite these large registry sizes, a significant proportion of searched patients present novel HLA haplotypes. Supporting this observation, HLA population genetic models have indicated that many extant HLA haplotypes remain unobserved. The absent haplotypes are a significant cause of error in haplotype matching. We have applied a Bayesian inference methodology for extending haplotype frequency distributions, using a model where new haplotypes are created by recombination of observed alleles. Applications of this joint probability model offer significant improvement in frequency distribution estimates over the best existing alternative methods, as we illustrate using five-locus HLA frequency data from the National Marrow Donor Program registry. Transplant matching algorithms and disease association studies involving phasing and imputation of rare variants may benefit from this statistical inference framework.

  6. iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes

    Lim Yun Ping

    2006-12-01

    Full Text Available Abstract Background The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations. Results To facilitate analysis of HapMap data for characterizing the haplotype structure of genes or any chromosomal regions, we have developed an integrated web-based resource, iHAP. In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags. Based on the parameters defined at the input stage, iHAP performs on-the-fly analysis and displays the result graphically as a webpage. To facilitate analysis, intermediate and final result files can be downloaded. Conclusion The iHAP resource, available at http://ihap.bii.a-star.edu.sg, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies.

  7. Genetic relationships among native americans based on beta-globin gene cluster haplotype frequencies

    Rita de Cassia Mousinho-Ribeiro

    2003-01-01

    Full Text Available The distribution of b-globin gene haplotypes was studied in 209 Amerindians from eight tribes of the Brazilian Amazon: Asurini from Xingú, Awá-Guajá, Parakanã, Urubú-Kaapór, Zoé, Kayapó (Xikrin from the Bacajá village, Katuena, and Tiriyó. Nine different haplotypes were found, two of which (n. 11 and 13 had not been previously identified in Brazilian indigenous populations. Haplotype 2 (+ - - - - was the most common in all groups studied, with frequencies varying from 70% to 100%, followed by haplotype 6 (- + + - +, with frequencies between 7% and 18%. The frequency distribution of the b-globin gene haplotypes in the eighteen Brazilian Amerindian populations studied to date is characterized by a reduced number of haplotypes (average of 3.5 and low levels of heterozygosity and intrapopulational differentiation, with a single clearly predominant haplotype in most tribes (haplotype 2. The Parakanã, Urubú-Kaapór, Tiriyó and Xavante tribes constitute exceptions, presenting at least four haplotypes with relatively high frequencies. The closest genetic relationships were observed between the Brazilian and the Colombian Amerindians (Wayuu, Kamsa and Inga, and, to a lesser extent, with the Huichol of Mexico. North-American Amerindians are more differentiated and clearly separated from all other tribes, except the Xavante, from Brazil, and the Mapuche, from Argentina. A restricted pool of ancestral haplotypes may explain the low diversity observed among most present-day Brazilian and Colombian Amerindian groups, while interethnic admixture could be the most important factor to explain the high number of haplotypes and high levels of diversity observed in some South-American and most North-American tribes.

  8. Genetic relationships among native americans based on b-globin gene cluster haplotype frequencies

    Mousinho-Ribeiro Rita de Cassia; Pante-de-Sousa Gabriella; Santos Eduardo José Melo dos; Guerreiro João Farias

    2003-01-01

    The distribution of b-globin gene haplotypes was studied in 209 Amerindians from eight tribes of the Brazilian Amazon: Asurini from Xingú, Awá-Guajá, Parakanã, Urubú-Kaapór, Zoé, Kayapó (Xikrin from the Bacajá village), Katuena, and Tiriyó. Nine different haplotypes were found, two of which (n. 11 and 13) had not been previously identified in Brazilian indigenous populations. Haplotype 2 (+ - - - -) was the most common in all groups studied, with frequencies varying from 70% to 100%, followed...

  9. Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus.

    Black, Holly A; Khan, Fayeza F; Tyson, Jess; Al Armour, John

    2014-07-21

    The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3-16); hence, the mechanisms responsible for changes in copy number at this locus are unclear. In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

  10. Haplotype frequencies at the DRD2 locus in populations of the East European Plain

    Mikulich Alexey I

    2009-09-01

    Full Text Available Abstract Background It was demonstrated previously that the three-locus RFLP haplotype, TaqI B-TaqI D-TaqI A (B-D-A, at the DRD2 locus constitutes a powerful genetic marker and probably reflects the most ancient dispersal of anatomically modern humans. Results We investigated TaqI B, BclI, MboI, TaqI D, and TaqI A RFLPs in 17 contemporary populations of the East European Plain and Siberia. Most of these populations belong to the Indo-European or Uralic language families. We identified three common haplotypes, which occurred in more than 90% of chromosomes investigated. The frequencies of the haplotypes differed according to linguistic and geographical affiliation. Conclusion Populations in the northwestern (Byelorussians from Mjadel', northern (Russians from Mezen' and Oshevensk, and eastern (Russians from Puchezh parts of the East European Plain had relatively high frequencies of haplotype B2-D2-A2, which may reflect admixture with Uralic-speaking populations that inhabited all of these regions in the Early Middle Ages.

  11. Haplotypes frequencies of CYP2B6 in Malaysia

    N Musa

    2012-01-01

    Full Text Available Background: Drugs with complex pharmacology are used in the management of drug use disorder (DUD and HIV/AIDS in Malaysia and in parts of South-East Asia. Their multiethnic populations suggest complexity due to the genetic polymorphism, such as CYP2B6 that metabolizes methadone and anti-retroviral. Aims: Our aim was to explore the genetic polymorphism of CYP2B6 among Malays, Chinese, Indians, and opiate-dependent individuals in Malaysia. Settings and Design: The study utilized DNA from our previous studies on CYPs and new recruitments from opiate-dependent individuals. Materials and Methods: For the new recruitment, after obtaining consent and baseline demography, 5 ml blood was obtained from patients attending methadone maintenance therapy (MMT Clinics. Genomic DNA was extracted using standard methods. 10 nucleotide changes associated with CYP2B6FNx0110, CYP2B6FNx012, CYP2B6FNx0117, CYP2B6FNx0111, CYP2B6FNx018, CYP2B6FNx0114, CYP2B6FNx019, CYP2B6FNx014, CYP2B6FNx016, CYP2B6FNx0127, and CYP2B6FNx0120 were determined using multiplex nested allele-specific PCR. Statistical Analysis: Descriptive statistics were used to summarize demographic data. Differences in allele frequencies between populations were tested using Chi-squared test and were corrected using the Bonferroni test. Results: CYP2B6 polymorphism in Malaysia is variable with trends that suggest an ethnic difference. Reduced activity CYP2B6FNx016 occurred in 13% to 26% among Malays, Chinese, Indians and opiate-dependent individuals. Another ′reduced activity′, CYP2B6FNx012 allele, was found at much lower percentages in the groups. Conclusions: The relative commonness of reduced-activity CYP2B6 alleles in our study called for attention in terms of dosage requirements for MMT and ARV in Malaysia. It also implored follow-up association studies to determine its relevance and consequences in personalized medicine for drug use disorder and HIV/AIDS.

  12. MalHaploFreq: A computer programme for estimating malaria haplotype frequencies from blood samples

    Smith Thomas A

    2008-07-01

    Full Text Available Abstract Background Molecular markers, particularly those associated with drug resistance, are important surveillance tools that can inform policy choice. People infected with falciparum malaria often contain several genetically-distinct clones of the parasite; genotyping the patients' blood reveals whether or not the marker is present (i.e. its prevalence, but does not reveal its frequency. For example a person with four malaria clones may contain both mutant and wildtype forms of a marker but it is not possible to distinguish the relative frequencies of the mutant and wildtypes i.e. 1:3, 2:2 or 3:1. Methods An appropriate method for obtaining frequencies from prevalence data is by Maximum Likelihood analysis. A computer programme has been developed that allows the frequency of markers, and haplotypes defined by up to three codons, to be estimated from blood phenotype data. Results The programme has been fully documented [see Additional File 1] and provided with a user-friendly interface suitable for large scale analyses. It returns accurate frequencies and 95% confidence intervals from simulated dataset sets and has been extensively tested on field data sets. Additional File 1 User manual for MalHaploFreq. Click here for file Conclusion The programme is included [see Additional File 2] and/or may be freely downloaded from 1. It can then be used to extract molecular marker and haplotype frequencies from their prevalence in human blood samples. This should enhance the use of frequency data to inform antimalarial drug policy choice. Additional File 2 executable programme compiled for use on DOS or windows Click here for file

  13. On detecting incomplete soft or hard selective sweeps using haplotype structure

    Ferrer-Admetlla, Anna; Liang, Mason; Korneliussen, Thorfinn Sand

    2014-01-01

    We present a new haplotype-based statistic (nSL) for detecting both soft and hard sweeps in population genomic data from a single population. We compare our new method with classic single-population haplotype and site frequency spectrum (SFS)-based methods and show that it is more robust, particu......We present a new haplotype-based statistic (nSL) for detecting both soft and hard sweeps in population genomic data from a single population. We compare our new method with classic single-population haplotype and site frequency spectrum (SFS)-based methods and show that it is more robust......, particularly to recombination rate variation. However, all statistics show some sensitivity to the assumptions of the demographic model. Additionally, we show that nSL has at least as much power as other methods under a number of different selection scenarios, most notably in the cases of sweeps from standing...

  14. HLA-A, -B, -DRB1 allele and haplotype frequencies of 920 cord blood units from Central Chile.

    Schäfer, Christian; Sauter, Jürgen; Riethmüller, Tobias; Kashi, Zahra Mehdizadeh; Schmidt, Alexander H; Barriga, Francisco J

    2016-08-01

    We present human leukocyte antigen (HLA) haplotype and allele/antigenic group frequencies derived from a data set of 920 umbilical cord blood units collected in Central Chile. HLA-A and -B genotypes were typed using sequence specific oligonucleotide probe methods while HLA-DRB1 genotypes were obtained from sequencing-based typing. The most frequent haplotype is A*29~B*44~DRB1*07:01 with an estimated frequency of 2.1%. Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

  15. Frequency of alleles and haplotypes of the human leukocyte antigen system in Bauru, São Paulo, Brazil

    Luana de Cassia Salvadori

    2014-04-01

    Full Text Available Background: HLA allele identification is used in bone marrow transplant programs as HLA compatibility between the donor and recipient may prevent graft rejection. Objective: This study aimed to estimate the frequency of alleles and haplotypes of the HLA system in the region of Bauru and compare these with the frequencies found in other regions of the country. Methods: HLA-A*, HLA-B*, and HLA-DRB1* allele frequencies and haplotypes were analyzed in a sample of 3542 volunteer donors at the National Registry of Voluntary Bone Marrow Donors (REDOME in Bauru. HLA low resolution typing was performed using reverse line blot with the Dynal Reli(tm SSO-HLA Typing Kit and automated Dynal AutoReli(tm48 device (Invitrogen, USA. Results: Twenty, 36, and 13 HLA-A*, HLA-B*, and HLA-DRB1* allele groups, respectively, were identified. The most common alleles for each locus were HLA-A*02, HLA-B*35, and HLA-DRB1*07. The most frequent haplotype was A*01-B*08-DRB1*03. Allele and haplotype frequencies were compared to other regions in Brazil and the similarities and differences among populations are shown. Conclusion: The knowledge of the immunogenic profile of a population contributes to the comprehension of the historical and anthropological aspects of different regions. Moreover, this helps to find suitable donors quickly, thereby shortening waiting lists for transplants and thus increasing survival rates among recipients.

  16. The impact of sample size and marker selection on the study of haplotype structures

    Sun Xiao

    2004-03-01

    Full Text Available Abstract Several studies of haplotype structures in the human genome in various populations have found that the human chromosomes are structured such that each chromosome can be divided into many blocks, within which there is limited haplotype diversity. In addition, only a few genetic markers in a putative block are needed to capture most of the diversity within a block. There has been no systematic empirical study of the effects of sample size and marker set on the identified block structures and representative marker sets, however. The purpose of this study was to conduct a detailed empirical study to examine such impacts. Towards this goal, we have analysed three representative autosomal regions from a large genome-wide study of haplotypes with samples consisting of African-Americans and samples consisting of Japanese and Chinese individuals. For both populations, we have found that the sample size and marker set have significant impact on the number of blocks and the total number of representative markers identified. The marker set in particular has very strong impacts, and our results indicate that the marker density in the original datasets may not be adequate to allow a meaningful characterisation of haplotype structures. In general, we conclude that we need a relatively large sample size and a very dense marker panel in the study of haplotype structures in human populations.

  17. An unusual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism.

    Deng, Libin; Zhang, Yuezheng; Kang, Jian; Liu, Tao; Zhao, Hongbin; Gao, Yang; Li, Chaohua; Pan, Hao; Tang, Xiaoli; Wang, Dunmei; Niu, Tianhua; Yang, Huanming; Zeng, Changqing

    2008-10-01

    Chromosomal inversion is an important type of genomic variations involved in both evolution and disease pathogenesis. Here, we describe the refined genetic structure of a 3.8-Mb inversion polymorphism at chromosome 8p23. Using HapMap data of 1,073 SNPs generated from 209 unrelated samples from CEPH-Utah residents with ancestry from northern and western Europe (CEU); Yoruba in Ibadan, Nigeria (YRI); and Asian (ASN) samples, which were comprised of Han Chinese from Beijing, China (CHB) and Japanese from Tokyo, Japan (JPT)-we successfully deduced the inversion orientations of all their 418 haplotypes. In particular, distinct haplotype subgroups were identified based on principal component analysis (PCA). Such genetic substructures were consistent with clustering patterns based on neighbor-joining tree reconstruction, which revealed a total of four haplotype clades across all samples. Metaphase fluorescence in situ hybridization (FISH) in a subset of 10 HapMap samples verified their inversion orientations predicted by PCA or phylogenetic tree reconstruction. Positioning of the outgroup haplotype within one of YRI clades suggested that Human NCBI Build 36-inverted order is most likely the ancestral orientation. Furthermore, the population differentiation test and the relative extended haplotype homozygosity (REHH) analysis in this region discovered multiple selection signals, also in a population-specific manner. A positive selection signal was detected at XKR6 in the ASN population. These results revealed the correlation of inversion polymorphisms to population-specific genetic structures, and various selection patterns as possible mechanisms for the maintenance of a large chromosomal rearrangement at 8p23 region during evolution. In addition, our study also showed that haplotype-based clustering methods, such as PCA, can be applied in scanning for cryptic inversion polymorphisms at a genome-wide scale.

  18. A novel haplotype of low-frequency variants in the aldosterone synthase gene among northern Han Chinese with essential hypertension.

    Zhang, Hao; Li, Xueyan; Zhou, Li; Zhang, Keyong; Zhang, Qi; Li, Jingping; Wang, Ningning; Jin, Ming; Wu, Nan; Cong, Mingyu; Qiu, Changchun

    2017-09-01

    Low-frequency variants showed that there is more power to detect risk variants than to detect protective variants in complex diseases. Aldosterone plays an important role in the renin-angiotensin-aldosterone system, and aldosterone synthase catalyzes the speed-controlled steps of aldosterone biosynthesis. Polymorphisms of the aldosterone synthase gene (CYP11B2) have been reported to be associated with essential hypertension (EH). CYP11B2 polymorphisms such as -344T/C, have been extensively reported, but others are less well known. This study aimed to assess the association between human CYP11B2 and EH using a haplotype-based case-control study. A total of 1024 EH patients and 956 normotensive controls, which consist of north Han population peasants, were enrolled. Seven single nucleotide polymorphisms (SNPs) (rs28659182, rs10087214, rs73715282, rs542092383, rs4543, rs28491316, and rs7463212) covering the entire human CYP11B2 gene were genotyped as markers using the MassARRAY system. The major allele G frequency of rs542092383 was found to be risk against hypertension [odds ratio (OR) 3.478, 95% confidence interval (95% CI) 1.407-8.597, P = .004]. The AG genotype frequency of SNP rs542092383 was significantly associated with an increased risk of hypertension (OR 4.513, 95% CI 1.426-14.287, P = .010). In the haplotype-based case-control analysis, the frequency of the T-G-T haplotype was higher for EH patients than for controls (OR 5.729, 95% CI 1.889-17.371, P = .000495). All |D'| values of the seven SNPs were >0.9, and r values for rs28659182- rs10087214-rs28491316-rs7463212 SNPs were >0.8 and showed strong linkage intensity. Haplotype T-G-T may therefore be a useful genetic marker for EH.

  19. Analysis of HLA-A, HLA-B, HLA-DRB1 allelic, genotypic, and haplotypic frequencies in colombian population

    Yazmin Rocío Árias-Murillo; Miguel Ángel Castro-Jiménez; María Fernanda Ríos-Espinosa; Juan Javier López-Rivera; Sandra Johanna Echeverry-Coral; Oscar Martínez-Nieto

    2010-01-01

    Introduction: The high polymorphism of the HLA system allows its typification to be used as valuable tool in establishing association to various illnesses, immune and genetic profiles; it also provides a guide to identifying compatibility among donors and receptors of organs transplants. Objective: To establish HLA-A, HLA-B, and HLA.DRB1 allele, genotype and haplotype frequencies among patients treated at Clinica Colsanitas SA. Methods: 561 patients coming from different regions in Col...

  20. Congruence as a measurement of extended haplotype structure across the genome

    2012-01-01

    Background Historically, extended haplotypes have been defined using only a few data points, such as alleles for several HLA genes in the MHC. High-density SNP data, and the increasing affordability of whole genome SNP typing, creates the opportunity to define higher resolution extended haplotypes. This drives the need for new tools that support quantification and visualization of extended haplotypes as defined by as many as 2000 SNPs. Confronted with high-density SNP data across the major histocompatibility complex (MHC) for 2,300 complete families, compiled by the Type 1 Diabetes Genetics Consortium (T1DGC), we developed software for studying extended haplotypes. Methods The software, called ExHap (Extended Haplotype), uses a similarity measurement we term congruence to identify and quantify long-range allele identity. Using ExHap, we analyzed congruence in both the T1DGC data and family-phased data from the International HapMap Project. Results Congruent chromosomes from the T1DGC data have between 96.5% and 99.9% allele identity over 1,818 SNPs spanning 2.64 megabases of the MHC (HLA-DRB1 to HLA-A). Thirty-three of 132 DQ-DR-B-A defined haplotype groups have > 50% congruent chromosomes in this region. For example, 92% of chromosomes within the DR3-B8-A1 haplotype are congruent from HLA-DRB1 to HLA-A (99.8% allele identity). We also applied ExHap to all 22 autosomes for both CEU and YRI cohorts from the International HapMap Project, identifying multiple candidate extended haplotypes. Conclusions Long-range congruence is not unique to the MHC region. Patterns of allele identity on phased chromosomes provide a simple, straightforward approach to visually and quantitatively inspect complex long-range structural patterns in the genome. Such patterns aid the biologist in appreciating genetic similarities and differences across cohorts, and can lead to hypothesis generation for subsequent studies. PMID:22369243

  1. Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations.

    Saville, Amanda; Charles, Melodi; Chavan, Suchitra; Muñoz, Miguel; Gómez-Alpizar, Luis; Ristaino, Jean Beagle

    2017-12-01

    Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas.

  2. Haplotype frequency distribution for 7 microsatellites in chromosome 8 and 11 in relation to the metabolic syndrome in four ethnic groups: Tehran Lipid and Glucose Study.

    Daneshpour, Maryam Sadat; Hosseinzadeh, Nima; Zarkesh, Maryam; Azizi, Fereidoun

    2012-03-01

    Different variants of haplotype frequencies may lead to various frequencies of the same variants in individuals with drug resistance and disease susceptibility at the population level. In this study, the haplotype frequencies of 4 STR loci including the D8S1132, D8S1779, D8S514 and D8S1743, and 3 STR loci including D11S1304, D11S1998 and D11S934 were investigated in 563 individuals of four Iranian ethnic groups in the capital city of Iran, Tehran. One hundred thirty subjects had the metabolic syndrome. Haplotype frequencies of all markers were calculated. There were significant differences in the haplotype frequencies in short and long alleles between the metabolic affected subjects and controls. In addition, haplotype frequencies were significant in the four ethnic groups in both chromosomes 8 and 11. Our findings show a relation between the short allele of D8S1743 in all related haplotype frequencies of subjects with metabolic syndrome. These findings may require more studies of some candidate genes, including the lipoprotein lipase gene, in this chromosomal region. Copyright © 2011. Published by Elsevier B.V.

  3. Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers

    Im, Kate M; Kirchhoff, Tomas; Wang, Xianshu

    2011-01-01

    Three founder mutations in BRCA1 and BRCA2 contribute to the risk of hereditary breast and ovarian cancer in Ashkenazi Jews (AJ). They are observed at increased frequency in the AJ compared to other BRCA mutations in Caucasian non-Jews (CNJ). Several authors have proposed that elevated allele...... the tools of statistical genomics to examine the likelihood of long-range LD at a deleterious locus in a population that faced a genetic bottleneck. We studied the genotypes of hundreds of women from a large international consortium of BRCA1 and BRCA2 mutation carriers and found that AJ women exhibited long......-range haplotypes compared to CNJ women. More than 50% of the AJ chromosomes with the BRCA1 185delAG mutation share an identical 2.1 Mb haplotype and nearly 16% of AJ chromosomes carrying the BRCA2 6174delT mutation share a 1.4 Mb haplotype. Simulations based on the best inference of Ashkenazi population demography...

  4. Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: analysis of the haplotype structure and genealogy.

    Jaruzelska, J; Zietkiewicz, E; Batzer, M; Cole, D E; Moisan, J P; Scozzari, R; Tavaré, S; Labuda, D

    1999-07-01

    With 10 segregating sites (simple nucleotide polymorphisms) in the last intron (1089 bp) of the ZFX gene we have observed 11 haplotypes in 336 chromosomes representing a worldwide array of 15 human populations. Two haplotypes representing 77% of all chromosomes were distributed almost evenly among four continents. Five of the remaining haplotypes were detected in Africa and 4 others were restricted to Eurasia and the Americas. Using the information about the ancestral state of the segregating positions (inferred from human-great ape comparisons), we applied coalescent analysis to estimate the age of the polymorphisms and the resulting haplotypes. The oldest haplotype, with the ancestral alleles at all the sites, was observed at low frequency only in two groups of African origin. Its estimated age of 740 to 1100 kyr corresponded to the time to the most recent common ancestor. The two most frequent worldwide distributed haplotypes were estimated at 550 to 840 and 260 to 400 kyr, respectively, while the age of the continentally restricted polymorphisms was 120 to 180 kyr and smaller. Comparison of spatial and temporal distribution of the ZFX haplotypes suggests that modern humans diverged from the common ancestral stock in the Middle Paleolithic era. Subsequent range expansion prevented substantial gene flow among continents, separating African groups from populations that colonized Eurasia and the New World.

  5. Asian population frequencies and haplotype distribution of killer cell immunoglobulin-like receptor (KIR) genes among Chinese, Malay, and Indian in Singapore.

    Lee, Yi Chuan; Chan, Soh Ha; Ren, Ee Chee

    2008-11-01

    Killer cell immunoglobulin-like receptors (KIR) gene frequencies have been shown to be distinctly different between populations and contribute to functional variation in the immune response. We have investigated KIR gene frequencies in 370 individuals representing three Asian populations in Singapore and report here the distribution of 14 KIR genes (2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 3DL1, 3DL2, 3DL3, 3DS1) with two pseudogenes (2DP1, 3DP1) among Singapore Chinese (n = 210); Singapore Malay (n = 80), and Singapore Indian (n = 80). Four framework genes (KIR3DL3, 3DP1, 2DL4, 3DL2) and a nonframework pseudogene 2DP1 were detected in all samples while KIR2DS2, 2DL2, 2DL5, and 2DS5 had the greatest significant variation across the three populations. Fifteen significant linkage patterns, consistent with associations between genes of A and B haplotypes, were observed. Eighty-four distinct KIR profiles were determined in our populations, 38 of which had not been described in other populations. KIR haplotype studies were performed using nine Singapore Chinese families comprising 34 individuals. All genotypes could be resolved into corresponding pairs of existing haplotypes with eight distinct KIR genotypes and eight different haplotypes. The haplotype A2 with frequency of 63.9% was dominant in Singapore Chinese, comparable to that reported in Korean and Chinese Han. The A haplotypes predominate in Singapore Chinese, with ratio of A to B haplotypes of approximately 3:1. Comparison with KIR frequencies in other populations showed that Singapore Chinese shared similar distributions with Chinese Han, Japanese, and Korean; Singapore Indian was found to be comparable with North Indian Hindus while Singapore Malay resembled the Thai.

  6. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

    Moore Stephen

    2011-06-01

    Full Text Available Abstract Background 'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS| and population differentiation index (FST--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle. Results We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian FST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases the extreme FST values were found to be positioned in poor gene content regions which deviated significantly (p ST values were found in regions of some relevant genes such as SMCP and FGF1. Conclusions Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and FST suggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported to be a major QTL with strong effects on productive life

  7. Novel Nucleotide Variations, Haplotypes Structure and Associations with Growth Related Traits of Goat AT Motif-Binding Factor ( Gene

    Xiaoyan Zhang

    2015-10-01

    Full Text Available The AT motif-binding factor (ATBF1 not only interacts with protein inhibitor of activated signal transducer and activator of transcription 3 (STAT3 (PIAS3 to suppress STAT3 signaling regulating embryo early development and cell differentiation, but is required for early activation of the pituitary specific transcription factor 1 (Pit1 gene (also known as POU1F1 critically affecting mammalian growth and development. The goal of this study was to detect novel nucleotide variations and haplotypes structure of the ATBF1 gene, as well as to test their associations with growth-related traits in goats. Herein, a total of seven novel single nucleotide polymorphisms (SNPs (SNP 1-7 within this gene were found in two well-known Chinese native goat breeds. Haplotypes structure analysis demonstrated that there were four haplotypes in Hainan black goat while seventeen haplotypes in Xinong Saanen dairy goat, and both breeds only shared one haplotype (hap1. Association testing revealed that the SNP2, SNP5, SNP6, and SNP7 loci were also found to significantly associate with growth-related traits in goats, respectively. Moreover, one diplotype in Xinong Saanen dairy goats significantly linked to growth related traits. These preliminary findings not only would extend the spectrum of genetic variations of the goat ATBF1 gene, but also would contribute to implementing marker-assisted selection in genetics and breeding in goats.

  8. Frequency conversion of structured light.

    Steinlechner, Fabian; Hermosa, Nathaniel; Pruneri, Valerio; Torres, Juan P

    2016-02-15

    Coherent frequency conversion of structured light, i.e. the ability to manipulate the carrier frequency of a wave front without distorting its spatial phase and intensity profile, provides the opportunity for numerous novel applications in photonic technology and fundamental science. In particular, frequency conversion of spatial modes carrying orbital angular momentum can be exploited in sub-wavelength resolution nano-optics and coherent imaging at a wavelength different from that used to illuminate an object. Moreover, coherent frequency conversion will be crucial for interfacing information stored in the high-dimensional spatial structure of single and entangled photons with various constituents of quantum networks. In this work, we demonstrate frequency conversion of structured light from the near infrared (803 nm) to the visible (527 nm). The conversion scheme is based on sum-frequency generation in a periodically poled lithium niobate crystal pumped with a 1540-nm Gaussian beam. We observe frequency-converted fields that exhibit a high degree of similarity with the input field and verify the coherence of the frequency-conversion process via mode projection measurements with a phase mask and a single-mode fiber. Our results demonstrate the suitability of exploiting the technique for applications in quantum information processing and coherent imaging.

  9. Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus

    Black, Holly A; Khan, Fayeza F; Tyson, Jess; Armour, John AL

    2014-01-01

    Background The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a reg...

  10. Genetic diversity and haplotype structure of 21 Y-STRs, including nine noncore loci, in South Tunisian Population: Forensic relevance.

    Makki-Rmida, Faten; Kammoun, Arwa; Mahfoudh, Nadia; Ayadi, Adnene; Gibriel, Abdullah Ahmed; Mallek, Bakhta; Maalej, Leila; Hammami, Zouheir; Maatoug, Samir; Makni, Hafedh; Masmoudi, Saber

    2015-12-01

    Y chromosome STRs (Y-STRs) are being used frequently in forensic laboratories. Previous studies of Y-STR polymorphisms in different groups of the Tunisian population identified low levels of diversity and discrimination capacity (DC) using various commercial marker sets. This definitely limits the use of such systems for Y-STRs genotyping in Tunisia. In our investigation on South Tunisia, 200 unrelated males were typed for the 12 conventional Y-STRs included in the PowerPlex® Y System. Additional set of nine noncore Y-STRs including DYS446, DYS456, DYS458, DYS388, DYS444, DYS445, DYS449, DYS710, and DYS464 markers were genotyped and evaluated for their potential in improving DC. Allele frequency, gene diversity, haplotype diversity (HD), and DC calculation revealed that DYS464 was the most diverse marker followed by DYS710 and DYS449 markers. The standard panel of 12 Y-STRs (DC = 80.5%) and the nine markers were combined to obtain DC of 99%. Among the 198 different haplotypes observed, 196 haplotypes were unique (HD = 99.999). Out of the nine noncore set, six Y-STRs (DYS458, DYS456, DYS449, DYS710, DYS444, and DYS464) had the greatest impact on enhancing DC. Our data provided putative Y-STRs combination to be used for genetic and forensic applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Fitchi: haplotype genealogy graphs based on the Fitch algorithm.

    Matschiner, Michael

    2016-04-15

    : In population genetics and phylogeography, haplotype genealogy graphs are important tools for the visualization of population structure based on sequence data. In this type of graph, node sizes are often drawn in proportion to haplotype frequencies and edge lengths represent the minimum number of mutations separating adjacent nodes. I here present Fitchi, a new program that produces publication-ready haplotype genealogy graphs based on the Fitch algorithm. http://www.evoinformatics.eu/fitchi.htm : michaelmatschiner@mac.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. HLA class II variation in the Gila River Indian Community of Arizona: alleles, haplotypes, and a high frequency epitope at the HLA-DR locus.

    Williams, R C; McAuley, J E

    1992-01-01

    A genetic distribution for the HLA class II loci is described for 349 "full-blooded" Pima and Tohono O'odham Indians (Pimans) in the Gila River Indian Community. A high frequency epitope in the *DRw52 family was defined by reactions with 31 alloantisera, which we have designated *DR3X6. It segregates as a codominant allele at HLA-DR with alleles *DR2, *DR4, and *DRw8, and has the highest frequency yet reported for an HLA-DR specificity, 0.735. It forms a common haplotype with *DRw52 and *DQw3 that is a valuable marker for genetic admixture and anthropological studies. Phenotype and allele frequencies, and haplotype frequencies for two and three loci, are presented. Variation at these loci is highly restricted, the mean heterozygosity for HLA-DR and HLA-DQ being 0.361. The Pimans represent a contemporary model for the Paleo-Indians who first entered North America 20,000 to 40,000 years ago.

  13. Frequency and origin of haplotypes associated with the beta-globin gene cluster in individuals with trait and sickle cell anemia in the Atlantic and Pacific coastal regions of Colombia.

    Fong, Cristian; Lizarralde-Iragorri, María Alejandra; Rojas-Gallardo, Diana; Barreto, Guillermo

    2013-12-01

    Sickle cell anemia is a genetic disease with high prevalence in people of African descent. There are five typical haplotypes associated with this disease and the haplotypes associated with the beta-globin gene cluster have been used to establish the origin of African-descendant people in America. In this work, we determined the frequency and the origin of haplotypes associated with hemoglobin S in a sample of individuals with sickle cell anemia (HbSS) and sickle cell hemoglobin trait (HbAS) in coastal regions of Colombia. Blood samples from 71 HbAS and 79 HbSS individuals were obtained. Haplotypes were determined based on the presence of variable restriction sites within the β-globin gene cluster. On the Pacific coast of Colombia the most frequent haplotype was Benin, while on the Atlantic coast Bantu was marginally higher than Benin. Eight atypical haplotypes were observed on both coasts, being more diverse in the Atlantic than in the Pacific region. These results suggest a differential settlement of the coasts, dependent on where slaves were brought from, either from the Gulf of Guinea or from Angola, where the haplotype distributions are similar. Atypical haplotypes probably originated from point mutations that lost or gained a restriction site and/or by recombination events.

  14. HLA-A, HLA-B, and HLA-DRB1 Allele and Haplotype Frequencies in Renal Transplant Candidates in a Population in Southern Brazil.

    Saito, Patrícia Keiko; Yamakawa, Roger Haruki; Noguti, Erika Noda; Bedendo, Gustavo Borelli; Júnior, Waldir Veríssimo da Silva; Yamada, Sérgio Seiji; Borelli, Sueli Donizete

    2016-05-01

    Very few studies have examined the diversity of human leukocyte antigens (HLA) in the Brazilian renal transplant candidates. The frequencies of the HLA-A, HLA-B, and HLA-DRB1 alleles, haplotypes and phenotypes were studied in 522 patients with chronic renal failure, renal transplant candidates, registered at the Transplant Centers in north/northwestern Paraná State, southern Brazil. Patients were classified according to the ethnic group (319 whites [Caucasians], 134 mestizos [mixed race descendants of Europeans, Africans, and Amerindians; browns or "pardos"] and 69 blacks). The HLA typing was performed by the polymerase chain reaction sequence-specific oligonucleotide method (PCR-SSO), combined with Luminex technology. In the analysis of the total samples, 20 HLA-A, 32 HLA-B, and 13 HLA-DRB1 allele groups were identified. The most frequent allele groups for each HLA locus were HLA-A*02 (25.4%), HLA-B*44 (10.9%), and HLA-DRB1*13 (13.9%). The most frequent haplotypes were HLA-A*01-B*08-DRB1*03 (2.3%), A*02-B*44-DRB1*07 (1.2%), and A*03-B*07-DRB1*11 (1.0%). Significant differences (P < 0.05) were observed in the HLA-A*68, B*08, and B*58 allele frequencies among ethnic groups. This study provides the first data on the HLA-A, HLA-B, and HLA-DRB1 allele, phenotype and haplotype frequencies of renal transplant candidates in a population in southern Brazil. © 2015 Wiley Periodicals, Inc.

  15. Fine haplotype structure of a chromosome 17 region in the laboratory and wild mouse

    Trachtulec, Zdeněk; Vlček, Čestmír; Mihola, Ondřej; Gregorová, Soňa; Fotopulosová, Vladana; Forejt, Jiří

    2008-01-01

    Roč. 178, č. 3 (2008), s. 1777-1784 ISSN 0016-6731 R&D Projects: GA AV ČR IAA5052406; GA ČR GA301/05/0738; GA MŠk(CZ) 1M0520 Institutional research plan: CEZ:AV0Z50520514 Keywords : haplotype * hybrid sterility Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.002, year: 2008

  16. Diversity and population structure of Plasmodium falciparum in Thailand based on the spatial and temporal haplotype patterns of the C-terminal 19-kDa domain of merozoite surface protein-1.

    Simpalipan, Phumin; Pattaradilokrat, Sittiporn; Siripoon, Napaporn; Seugorn, Aree; Kaewthamasorn, Morakot; Butcher, Robert D J; Harnyuttanakorn, Pongchai

    2014-02-12

    The 19-kDa C-terminal region of the merozoite surface protein-1 of the human malaria parasite Plasmodium falciparum (PfMSP-119) constitutes the major component on the surface of merozoites and is considered as one of the leading candidates for asexual blood stage vaccines. Because the protein exhibits a level of sequence variation that may compromise the effectiveness of a vaccine, the global sequence diversity of PfMSP-119 has been subjected to extensive research, especially in malaria endemic areas. In Thailand, PfMSP-119 sequences have been derived from a single parasite population in Tak province, located along the Thailand-Myanmar border, since 1995. However, the extent of sequence variation and the spatiotemporal patterns of the MSP-119 haplotypes along the Thai borders with Laos and Cambodia are unknown. Sixty-three isolates of P. falciparum from five geographically isolated populations along the Thai borders with Myanmar, Laos and Cambodia in three transmission seasons between 2002 and 2008 were collected and culture-adapted. The msp-1 gene block 17 was sequenced and analysed for the allelic diversity, frequency and distribution patterns of PfMSP-119 haplotypes in individual populations. The PfMSP-119 haplotype patterns were then compared between parasite populations to infer the population structure and genetic differentiation of the malaria parasite. Five conserved polymorphic positions, which accounted for five distinct haplotypes, of PfMSP-119 were identified. Differences in the prevalence of PfMSP-119 haplotypes were detected in different geographical regions, with the highest levels of genetic diversity being found in the Kanchanaburi and Ranong provinces along the Thailand-Myanmar border and Trat province located at the Thailand-Cambodia border. Despite this variability, the distribution patterns of individual PfMSP-119 haplotypes seemed to be very similar across the country and over the three malarial transmission seasons, suggesting that gene flow

  17. Infection Frequency of Hepatitis C Virus and IL28B Haplotypes in Papua New Guinea, Fiji, and Kiribati

    Harrison, G. L. Abby; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Allain, Jean-Pierre; Barnes, Eleanor; Pybus, Oliver G.; Klenerman, Paul

    2013-01-01

    It has been estimated that there are more than 60 million Hepatitis C virus (HCV) carriers in the World Health Organisation's Western Pacific region (WHO-WPR), where liver cancer is among the top three causes of cancer death. WHO and the US Centres for Disease Control and Prevention report the prevalence of HCV in the South Pacific islands (countries within the WHO-WPR) to be high (5–10% and >2% respectively). However, since HCV is not tested for in many of these countries, there is sparse data available to support this assertion. We screened ∼2000 apparently healthy individuals from Papua New Guinea, Fiji and Kiribati and found a sero-prevalence of 2.0%, 0.1% and 0%, respectively. All sero-positive samples tested negative for HCV RNA. Curious as to why all the sero-positive individuals were negative for HCV-RNA, we also screened them for the HCV protective IL28B SNP markers rs12979860 and rs8099917. All antibody-positive participants bar one had HCV protective haplotypes. Our results suggest that HCV is present in these Pacific island countries, albeit at a prevalence lower than previous estimates. As none of our participants had undergone antiviral treatment, and therefore must have cleared infection naturally, we hypothesise that genotypes 1 and/or 4 are circulating in South Pacific Island people and that these peoples are genetically predisposed to be more likely to spontaneous resolve HCV infection than to become chronic carriers. PMID:23976941

  18. Influence of promoter/enhancer region haplotypes on MGMT transcriptional regulation: a potential biomarker for human sensitivity to alkylating agents.

    Xu, Meixiang; Nekhayeva, Ilona; Cross, Courtney E; Rondelli, Catherine M; Wickliffe, Jeffrey K; Abdel-Rahman, Sherif Z

    2014-03-01

    The O6-methylguanine-DNA methyltransferase gene (MGMT) encodes the direct reversal DNA repair protein that removes alkyl adducts from the O6 position of guanine. Several single-nucleotide polymorphisms (SNPs) exist in the MGMT promoter/enhancer (P/E) region. However, the haplotype structure encompassing these SNPs and their functional/biological significance are currently unknown. We hypothesized that MGMT P/E haplotypes, rather than individual SNPs, alter MGMT transcription and can thus alter human sensitivity to alkylating agents. To identify the haplotype structure encompassing the MGMT P/E region SNPs, we sequenced 104 DNA samples from healthy individuals and inferred the haplotypes using the data generated. We identified eight SNPs in this region, namely T7C (rs180989103), T135G (rs1711646), G290A (rs61859810), C485A (rs1625649), C575A (rs113813075), G666A (rs34180180), C777A (rs34138162) and C1099T (rs16906252). Phylogenetics and Sequence Evolution analysis predicted 21 potential haplotypes that encompass these SNPs ranging in frequencies from 0.000048 to 0.39. Of these, 10 were identified in our study population as 20 paired haplotype combinations. To determine the functional significance of these haplotypes, luciferase reporter constructs representing these haplotypes were transfected into glioblastoma cells and their effect on MGMT promoter activity was determined. Compared with the most common (reference) haplotype 1, seven haplotypes significantly upregulated MGMT promoter activity (18-119% increase; P alkylating agents.

  19. Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers

    Im, Kate M.; Kirchhoff, Tomas; Wang, Xianshu; Green, Todd; Chow, Clement Y.; Vijai, Joseph; Korn, Joshua; Gaudet, Mia M.; Fredericksen, Zachary; Shane Pankratz, V.; Guiducci, Candace; Crenshaw, Andrew; McGuffog, Lesley; Kartsonaki, Christiana; Morrison, Jonathan; Healey, Sue; Sinilnikova, Olga M.; Mai, Phuong L.; Greene, Mark H.; Piedmonte, Marion; Rubinstein, Wendy S.; Hogervorst, Frans B.; Rookus, Matti A.; Collée, J. Margriet; Hoogerbrugge, Nicoline; van Asperen, Christi J.; Meijers-Heijboer, Hanne E. J.; van Roozendaal, Cees E.; Caldes, Trinidad; Perez-Segura, Pedro; Jakubowska, Anna; Lubinski, Jan; Huzarski, Tomasz; Blecharz, Paweł; Nevanlinna, Heli; Aittomäki, Kristiina; Lazaro, Conxi; Blanco, Ignacio; Barkardottir, Rosa B.; Montagna, Marco; D'Andrea, Emma; Devilee, Peter; Olopade, Olufunmilayo I.; Neuhausen, Susan L.; Peissel, Bernard; Bonanni, Bernardo; Peterlongo, Paolo; Singer, Christian F.; Rennert, Gad; Lejbkowicz, Flavio; Andrulis, Irene L.; Glendon, Gord; Ozcelik, Hilmi; Toland, Amanda Ewart; Caligo, Maria Adelaide; Beattie, Mary S.; Chan, Salina; Domchek, Susan M.; Nathanson, Katherine L.; Rebbeck, Timothy R.; Phelan, Catherine; Narod, Steven; John, Esther M.; Hopper, John L.; Buys, Saundra S.; Daly, Mary B.; Southey, Melissa C.; Terry, Mary-Beth; Tung, Nadine; Hansen, Thomas V. O.; Osorio, Ana; Benitez, Javier; Durán, Mercedes; Weitzel, Jeffrey N.; Garber, Judy; Hamann, Ute; Peock, Susan; Cook, Margaret; Oliver, Clare T.; Frost, Debra; Platte, Radka; Evans, D. Gareth; Eeles, Ros; Izatt, Louise; Paterson, Joan; Brewer, Carole; Hodgson, Shirley; Morrison, Patrick J.; Porteous, Mary; Walker, Lisa; Rogers, Mark T.; Side, Lucy E.; Godwin, Andrew K.; Schmutzler, Rita K.; Wappenschmidt, Barbara; Laitman, Yael; Meindl, Alfons; Deissler, Helmut; Varon-Mateeva, Raymonda; Preisler-Adams, Sabine; Kast, Karin; Venat-Bouvet, Laurence; Stoppa-Lyonnet, Dominique; Chenevix-Trench, Georgia; Easton, Douglas F.; Klein, Robert J.; Daly, Mark J.; Friedman, Eitan; Dean, Michael; Clark, Andrew G.; Altshuler, David M.; Antoniou, Antonis C.; Couch, Fergus J.; Offit, Kenneth; Gold, Bert; Gauthier-Villars, Marion; Houdayer, Claude; Moncoutier, Virginie; Belotti, Muriel; de Pauw, Antoine; Bressac-de-Paillerets, Brigitte; Remenieras, Audrey; Byrde, Véronique; Caron, Olivier; Lenoir, Gilbert; Bignon, Yves-Jean; Uhrhammer, Nancy; Lasset, Christine; Bonadona, Valérie; Hardouin, Agnès; Berthet, Pascaline; Sobol, Hagay; Bourdon, Violaine; Noguchi, Tetsuro; Eisinger, François; Coulet, Florence; Colas, Chrystelle; Soubrier, Florent; Coupier, Isabelle; Peyrat, Jean-Philippe; Fournier, Joëlle; Révillion, Françoise; Vennin, Philippe; Adenis, Claude; Rouleau, Etienne; Lidereau, Rosette; Demange, Liliane; Nogues, Catherine; Muller, Danièle; Fricker, Jean-Pierre; Longy, Michel; Sevenet, Nicolas; Toulas, Christine; Guimbaud, Rosine; Gladieff, Laurence; Feillel, Viviane; Leroux, Dominique; Dreyfus, Hélène; Rebischung, Christine; Cassini, Cécile; Faivre, Laurence; Prieur, Fabienne; Ferrer, Sandra Fert; Frénay, Marc; Vénat-Bouvet, Laurence; Lynch, Henry T.; Thorne, Heather; Niedermayr, Eveline; Pierotti, Marco; Manoukian, Siranoush; Zaffaroni, Daniela; Ripamonti, Carla B.; Radice, Paolo; Barile, Monica; Bernard, Loris; Karlsson, Per; Nordling, Margareta; Bergman, Annika; Einbeigi, Zakaria; Stenmark-Askmalm, Marie; Liedgren, Sigrun; Borg, Åke; Loman, Niklas; Olsson, Håkan; Kristoffersson, Ulf; Jernström, Helena; Harbst, Katja; Henriksson, Karin; Lindblom, Annika; Arver, Brita; von Wachenfeldt, Anna; Liljegren, Annelie; Barbany-Bustinza, Gisela; Rantala, Johanna; Melin, Beatrice; Grönberg, Henrik; Stattin, Eva-Lena; Emanuelsson, Monica; Ehrencrona, Hans; Brandell, Richard Rosenquist; Dahl, Niklas; Hogervorst, F. B. L.; Verhoef, S.; Verheus, M.; van 't Veer, L. J.; van Leeuwen, F. E.; Rookus, M. A.; Collée, M.; van den Ouweland, A. M. W.; Jager, A.; Hooning, M. J.; Tilanus-Linthorst, M. M. A.; Seynaeve, C.; van Asperen, C. J.; Wijnen, J. T.; Vreeswijk, M. P.; Tollenaar, R. A.; Devilee, P.; Ligtenberg, M. J.; Hoogerbrugge, N.; Ausems, M. G.; van der Luijt, R. B.; Aalfs, C. M.; van Os, T. A.; Gille, J. J. P.; Waisfisz, Q.; Gomez-Garcia, E. B.; van Roozendaal, C. E.; Blok, Marinus J.; Caanen, B.; Oosterwijk, J. C.; van der Hout, A. H.; Mourits, M. J.; Vasen, H. F.; Miedzybrodzka, Zosia; Gregory, Helen; Morrison, Patrick; Jeffers, Lisa; Cole, Trevor; Ong, Kai-Ren; Hoffman, Jonathan; Donaldson, Alan; James, Margaret; Downing, Sarah; Taylor, Amy; Murray, Alexandra; McCann, Emma; Kennedy, M. John; Barton, David; Drummond, Sarah; Kivuva, Emma; Searle, Anne; Goodman, Selina; Hill, Kathryn; Davidson, Rosemarie; Murday, Victoria; Bradshaw, Nicola; Snadden, Lesley; Longmuir, Mark; Watt, Catherine; Gibson, Sarah; Haque, Eshika; Tobias, Ed; Duncan, Alexis; Jacobs, Chris; Langman, Caroline; Whaite, Anna; Dorkins, Huw; Randhawa, Kashmir; Barwell, Julian; Patel, Nafisa; Adlard, Julian; Chu, Carol; Miller, Julie; Ellis, Ian; Houghton, Catherine; Lalloo, Fiona; Taylor, Jane; Side, Lucy; Male, Alison; Berlin, Cheryl; Eason, Jacqueline; Collier, Rebecca; Douglas, Fiona; Claber, Oonagh; Jobson, Irene; McLeod, Diane; Halliday, Dorothy; Durell, Sarah; Stayner, Barbara; Shanley, Susan; Rahman, Nazneen; Houlston, Richard; Bancroft, Elizabeth; D'Mello, Lucia; Page, Elizabeth; Ardern-Jones, Audrey; Kohut, Kelly; Wiggins, Jennifer; Castro, Elena; Mitra, Anita; Robertson, Lisa; Cook, Jackie; Quarrell, Oliver; Bardsley, Cathryn; Brice, Glen; Winchester, Lizzie; Eddy, Charlotte; Tripathi, Vishakha; Attard, Virginia; Eccles, Diana; Lucassen, Anneke; Crawford, Gillian; McBride, Donna; Smalley, Sarah

    2011-01-01

    Three founder mutations in BRCA1 and BRCA2 contribute to the risk of hereditary breast and ovarian cancer in Ashkenazi Jews (AJ). They are observed at increased frequency in the AJ compared to other BRCA mutations in Caucasian non-Jews (CNJ). Several authors have proposed that elevated allele

  20. Fabrication of superconducting niobium radio frequency structures

    Kirchgessner, J.; Amato, J.; Brawley, J.

    1983-01-01

    During the last several years a variety of superconducting radio frequency structures have been designed, fabricated and tested. The diverse structures and fabrication techniques are described. This paper is a description of the authors' experiences in this field

  1. Contact resistance measurement structures for high frequencies

    Roy, Deepu; Pijper, Ralf M.T.; Tiemeijer, Luuk F.; Wolters, Robertus A.M.

    2011-01-01

    Knowledge of the interfacial contact impedance offered by the device at its operating frequency range is crucial for accurate modelling and understanding of the device. In this article, a novel modified TLM test-structure has been devised to extract interfacial contact parameters at frequencies upto

  2. Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a Subset of 237 Donors in the South African Bone Marrow Registry

    Mqondisi Tshabalala

    2018-01-01

    Full Text Available Human leukocyte antigen- (HLA- A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR. Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A∗02:02g (0.096, B∗07:02g (0.082, C∗07:02g (0.180, DQB1∗06:02 (0.157, and DRB1∗15:01 (0.072. The most common haplotype was A∗03:01g~B∗07:02g~C∗07:02g~DQB1∗06:02~DRB1∗15:01 (0.067, which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies.

  3. High Frequency of Haplotype HLA-DQ7 in Celiac Disease Patients from South Italy: Retrospective Evaluation of 5,535 Subjects at Risk of Celiac Disease.

    Nadia Tinto

    Full Text Available Celiac disease (CD has a strong genetic component mainly due to HLA DQ2/DQ8 encoding genes. However, a minority of CD patients are DQ2/DQ8-negative. To address this issue, we retrospectively characterized HLA haplotypes in 5,535 subjects at risk of CD (either relatives of CD patients or subjects with CD-like symptoms referred to our center during a 10-year period.We identified loci DQA1/DQB1/DRB1 by sequence-specific oligonucleotide-PCR and sequence-specific primer-PCR; anti-transglutaminase IgA/IgG and anti-endomysium IgA by ELISA and indirect immunofluorescence, respectively.We diagnosed CD in 666/5,535 individuals, 4.2% of whom were DQ2/DQ8-negative. Interestingly, DQ7 was one of the most abundant haplotypes in all CD patients and significantly more frequent in DQ2/DQ8-negative (38% than in DQ2/DQ8-positive CD patients (24% (p<0.05.Our data lend support to the concept that DQ7 represents an additive or independent CD risk haplotype with respect to DQ2/DQ8 haplotypes but this finding should be verified in other large CD populations.

  4. Analysis of polymorphisms and haplotype structure of the human thymidylate synthase genetic region: a tool for pharmacogenetic studies.

    Soma Ghosh

    Full Text Available 5-Fluorouracil (5FU, a widely used chemotherapeutic drug, inhibits the DNA replicative enzyme, thymidylate synthase (Tyms. Prior studies implicated a VNTR (variable numbers of tandem repeats polymorphism in the 5'-untranslated region (5'-UTR of the TYMS gene as a determinant of Tyms expression in tumors and normal tissues and proposed that these VNTR genotypes could help decide fluoropyrimidine dosing. Clinical associations between 5FU-related toxicity and the TYMS VNTR were reported, however, results were inconsistent, suggesting that additional genetic variation in the TYMS gene might influence Tyms expression. We thus conducted a detailed genetic analysis of this region, defining new polymorphisms in this gene including mononucleotide (poly A:T repeats and novel single nucleotide polymorphisms (SNPs flanking the VNTR in the TYMS genetic region. Our haplotype analysis of this region used data from both established and novel genetic variants and found nine SNP haplotypes accounting for more than 90% of the studied population. We observed non-exclusive relationships between the VNTR and adjacent SNP haplotypes, such that each type of VNTR commonly occurred on several haplotype backgrounds. Our results confirmed the expectation that the VNTR alleles exhibit homoplasy and lack the common ancestry required for a reliable marker of a linked adjacent locus that might govern toxicity. We propose that it may be necessary in a clinical trial to assay multiple types of genetic polymorphisms in the TYMS region to meaningfully model linkage of genetic markers to 5FU-related toxicity. The presence of multiple long (up to 26 nt, polymorphic monothymidine repeats in the promoter region of the sole human thymidylate synthetic enzyme is intriguing.

  5. Factor IX gene haplotypes in Amerindians.

    Franco, R F; Araújo, A G; Zago, M A; Guerreiro, J F; Figueiredo, M S

    1997-02-01

    We have determined the haplotypes of the factor IX gene for 95 Indians from 5 Brazilian Amazon tribes: Wayampí, Wayana-Apalaí, Kayapó, Arára, and Yanomámi. Eight polymorphisms linked to the factor IX gene were investigated: MseI (at 5', nt -698), BamHI (at 5', nt -561), DdeI (intron 1), BamHI (intron 2), XmnI (intron 3), TaqI (intron 4), MspI (intron 4), and HhaI (at 3', approximately 8 kb). The results of the haplotype distribution and the allele frequencies for each of the factor IX gene polymorphisms in Amerindians were similar to the results reported for Asian populations but differed from results for other ethnic groups. Only five haplotypes were identified within the entire Amerindian study population, and the haplotype distribution was significantly different among the five tribes, with one (Arára) to four (Wayampí) haplotypes being found per tribe. These findings indicate a significant heterogeneity among the Indian tribes and contrast with the homogeneous distribution of the beta-globin gene cluster haplotypes but agree with our recent findings on the distribution of alpha-globin gene cluster haplotypes and the allele frequencies for six VNTRs in the same Amerindian tribes. Our data represent the first study of factor IX-associated polymorphisms in Amerindian populations and emphasizes the applicability of these genetic markers for population and human evolution studies.

  6. [Genetic Variability and Structure of SNP Haplotypes in the DMPK Gene in Yakuts and Other Ethnic Groups of Northern Eurasia in Relation to Myotonic Dystrophy].

    Swarovskaya, M G; Stepanova, S K; Marussin, A V; Sukhomyasova, A L; Maximova, N R; Stepanov, V A

    2015-06-01

    The genetic variability of the DMPK locus has been studied in relation to six SNP markers (rs2070736, rs572634, rs1799894, rs527221, rs915915, and rs10415988) in Yakuts with myotonic dystrophy (MD) in the Yakut population and in populations of northern Eurasia. Significant differences were observed in the allele frequencies between patients and a population sample of Yakuts for three SNP loci (rs915915, rs1799894, and rs10415988) associated with a high chance of disease manifestation. The odds ratios (OR) of MD development in representatives of the Yakut population for these three loci were 2.59 (95% CI, p = 0,004), 4.99 (95% CI, p = 0.000), and 3.15 (95% CI, p = 0.01), respectively. Haplotype TTTCTC, which is associated with MD, and haplotype GTCCTT, which was observed only in Yakut MD patients (never in MD patients of non-Yakut origin), were revealed. A low level of variability in the locus of DMRK gene in Yakuts (H(e) = 0.283) compared with other examined populations was noted. An analysis of pairwise genetic relationships between populations revealed their significant differentiation for all the examined loci. In addition, a low level of differentiation in territorial groups of Yakut populations (F(ST) = 0.79%), which was related to the high subdivision of the northern Eurasian population (F(ST) = 11.83%), was observed.

  7. Haplotype block structure study of the CFTR gene. Most variants are associated with the M470 allele in several European populations.

    Pompei, Fiorenza; Ciminelli, Bianca Maria; Bombieri, Cristina; Ciccacci, Cinzia; Koudova, Monika; Giorgi, Silvia; Belpinati, Francesca; Begnini, Angela; Cerny, Milos; Des Georges, Marie; Claustres, Mireille; Ferec, Claude; Macek, Milan; Modiano, Guido; Pignatti, Pier Franco

    2006-01-01

    An average of about 1700 CFTR (cystic fibrosis transmembrane conductance regulator) alleles from normal individuals from different European populations were extensively screened for DNA sequence variation. A total of 80 variants were observed: 61 coding SNSs (results already published), 13 noncoding SNSs, three STRs, two short deletions, and one nucleotide insertion. Eight DNA variants were classified as non-CF causing due to their high frequency of occurrence. Through this survey the CFTR has become the most exhaustively studied gene for its coding sequence variability and, though to a lesser extent, for its noncoding sequence variability as well. Interestingly, most variation was associated with the M470 allele, while the V470 allele showed an 'extended haplotype homozygosity' (EHH). These findings make us suggest a role for selection acting either on the M470V itself or through an hitchhiking mechanism involving a second site. The possible ancient origin of the V allele in an 'out of Africa' time frame is discussed.

  8. Carrier frequency of a nonsense mutation in the adenosine deaminase (ADA) gene implies a high incidence of ADA-deficient severe combined immunodeficiency (SCID) in Somalia and a single, common haplotype indicates common ancestry

    Sanchez Sanchez, Juan Jose; Monaghan, Gemma; Børsting, Claus

    2007-01-01

    Inherited adenosine deaminase (ADA) deficiency is a rare metabolic disorder that causes immunodeficiency, varying from severe combined immunodeficiency (SCID) in the majority of cases to a less severe form in a small minority of patients. Five patients of Somali origin from four unrelated families......, with severe ADA-SCID, were registered in the Greater London area. Patients and their parents were investigated for the nonsense mutation Q3X (ADA c7C>T), two missense mutations K80R (ADA c239A>G) and R142Q (ADA c425G>A), and a TAAA repeat located at the 3' end of an Alu element (AluVpA) positioned 1.1 kb...... upstream of the ADA transcription start site. All patients were homozygous for the haplotype ADA-7T/ADA-239G/ADA-425G/AluVpA7. Among 207 Somali immigrants to Denmark, the frequency of ADA c7C>T and the maximum likelihood estimate of the frequency of the haplotype ADA-7T/ADA-239G/ADA-425G/AluVpA7 were both...

  9. Frequency Selective Surface for Structural Health Monitoring

    Norlyana Azemi, Saidatul; Mustaffa, Farzana Hazira Wan; Faizal Jamlos, Mohd; Abdullah Al-Hadi, Azremi; Soh, Ping Jack

    2018-03-01

    Structural health monitoring (SHM) technologies have attained attention to monitor civil structures. SHM sensor systems have been used in various civil structures such as bridges, buildings, tunnels and so on. However the previous sensor for SHM is wired and encounter with problem to cover large areas. Therefore, wireless sensor was introduced for SHM to reduce network connecting problem. Wireless sensors for Structural Health monitoring are new technology and have many advantages to overcome the drawback of conventional and wired sensor. This project proposed passive wireless SHM sensor using frequency selective surface (FSS) as an alternative to conventional sensors. The electromagnetic wave characteristic of FSS will change by geometrical changes of FSS due to mechanical strain or structural failure. The changes feature is used as a sensing function without any connecting wires. Two type of design which are circular ring and square loop along with the transmission and reflection characteristics of SHM using FSS were discussed in this project. A simulation process has shown that incident angle characteristics can be use as a data for SHM application.

  10. [Construction of haplotype and haplotype block based on tag single nucleotide polymorphisms and their applications in association studies].

    Gu, Ming-liang; Chu, Jia-you

    2007-12-01

    Human genome has structures of haplotype and haplotype block which provide valuable information on human evolutionary history and may lead to the development of more efficient strategies to identify genetic variants that increase susceptibility to complex diseases. Haplotype block can be divided into discrete blocks of limited haplotype diversity. In each block, a small fraction of ptag SNPsq can be used to distinguish a large fraction of the haplotypes. These tag SNPs can be potentially useful for construction of haplotype and haplotype block, and association studies in complex diseases. There are two general classes of methods to construct haplotype and haplotype blocks based on genotypes on large pedigrees and statistical algorithms respectively. The author evaluate several construction methods to assess the power of different association tests with a variety of disease models and block-partitioning criteria. The advantages, limitations and applications of each method and the application in the association studies are discussed equitably. With the completion of the HapMap and development of statistical algorithms for addressing haplotype reconstruction, ideas of construction of haplotype based on combination of mathematics, physics, and computer science etc will have profound impacts on population genetics, location and cloning for susceptible genes in complex diseases, and related domain with life science etc.

  11. Haplotype-based stratification of Huntington's disease.

    Chao, Michael J; Gillis, Tammy; Atwal, Ranjit S; Mysore, Jayalakshmi Srinidhi; Arjomand, Jamshid; Harold, Denise; Holmans, Peter; Jones, Lesley; Orth, Michael; Myers, Richard H; Kwak, Seung; Wheeler, Vanessa C; MacDonald, Marcy E; Gusella, James F; Lee, Jong-Min

    2017-11-01

    Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by expansion of a CAG trinucleotide repeat in HTT, resulting in an extended polyglutamine tract in huntingtin. We and others have previously determined that the HD-causing expansion occurs on multiple different haplotype backbones, reflecting more than one ancestral origin of the same type of mutation. In view of the therapeutic potential of mutant allele-specific gene silencing, we have compared and integrated two major systems of HTT haplotype definition, combining data from 74 sequence variants to identify the most frequent disease-associated and control chromosome backbones and revealing that there is potential for additional resolution of HD haplotypes. We have used the large collection of 4078 heterozygous HD subjects analyzed in our recent genome-wide association study of HD age at onset to estimate the frequency of these haplotypes in European subjects, finding that common genetic variation at HTT can distinguish the normal and CAG-expanded chromosomes for more than 95% of European HD individuals. As a resource for the HD research community, we have also determined the haplotypes present in a series of publicly available HD subject-derived fibroblasts, induced pluripotent cells, and embryonic stem cells in order to facilitate efforts to develop inclusive methods of allele-specific HTT silencing applicable to most HD patients. Our data providing genetic guidance for therapeutic gene-based targeting will significantly contribute to the developments of rational treatments and implementation of precision medicine in HD.

  12. Differentiation analysis for estimating individual ancestry from the Tibetan Plateau by an archaic altitude adaptation EPAS1 haplotype among East Asian populations.

    Jiang, Li; Peng, Jianxiong; Huang, Meisha; Liu, Jing; Wang, Ling; Ma, Quan; Zhao, Hui; Yang, Xin; Ji, Anquan; Li, Caixia

    2018-02-10

    Tibetans have adapted to the extreme environment of high altitude for hundreds of generations. A highly differentiated 5-SNP (Single Nucleotide Polymorphism) haplotype motif (AGGAA) on a hypoxic pathway gene, EPAS1, is observed in Tibetans and lowlanders. To evaluate the potential usage of the 5-SNP haplotype in ancestry inference for Tibetan or Tibetan-related populations, we analyzed this haplotype in 1053 individuals of 12 Chinese populations residing on the Tibetan Plateau, peripheral regions of Tibet, and plain regions. These data were integrated with the genotypes from the 1000 Genome populations and populations in a previously reported paper for population structure analyses. We found that populations representing highland and lowland groups have different dominant ancestry components. The core Denisovan haplotype (AGGAA) was observed at a frequency of 72.32% in the Tibetan Plateau, with a frequency range from 9.48 to 21.05% in the peripheral regions and Tibetan Plateau carried the archaic haplotype, while < 5% of the Chinese Han people carried the haplotype. Our findings indicate that the 5-SNP haplotype has a special distribution pattern in populations of Tibet and peripheral regions and could be integrated into AISNP (Ancestry Informative Single Nucleotide Polymorphism) panels to enhance ancestry resolution.

  13. MOLECULAR STRUCTURE AND VIBRATIONAL FREQUENCIES OF

    Fatih UCUN

    2009-02-01

    Full Text Available Abstract: The molecular structure, vibrational frequencies and the corresponding assignments of N-aminophthalimide (NAPH in the ground state have been calculated using the Hartree-Fock (HF and density functional methods (B3LYP with 6-31G (d, p basis set. The calculations were utilized in the CS symmetry of NAPH. The obtained vibrational frequencies and optimized geometric parameters (bond lengths and bond angles were seen to be in good agreement with the experimental data. The comparison of the observed and calculated results showed that B3LYP is superior to the scaled HF method. Theoretical infrared intensities and Raman activities were also reported. Key words: N-aminophthalimide; vibrations; IR spectra; Raman spectra; HF; DFT N-AMİNOFİTALOMİD'İN MOLEKÜLER YAPISI VE TİTREŞİM FREKANSLARI Özet: Temel haldeki N-aminofitalamidin (NAPH moleküler yapısı, titreşim frekansları ve uygun mod tanımlamaları, 6-31 G (d, p temel setli Hartree-Fock (HF ve yoğunluk fonksiyonu metodları (B3LYP kullanılarak hesaplandı. Hesaplamalar, NAPH'ın CS simetrisine uyarlandı. Elde edilen titreşim frekansları ve optimize geometrik parametreleri (bağ uzunlukları ve bağ açıları, deneysel değerlerle iyi bir uyum içinde olduğu görüldü. Deneysel ve teorik sonuçların karşılaştırılması, B3LYP'nin HF metodundan daha üstün olduğunu gösterdi. Ayrıca teorik infrared şiddetleri ve Raman aktiviteleri verildi. Anahtar Kelimeler: N-aminofitalamidin; titreşimler; IR spektrumu; Raman Spektrumu; HF; DFT

  14. Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity.

    Zietkiewicz, Ewa; Yotova, Vania; Gehl, Dominik; Wambach, Tina; Arrieta, Isabel; Batzer, Mark; Cole, David E C; Hechtman, Peter; Kaplan, Feige; Modiano, David; Moisan, Jean-Paul; Michalski, Roman; Labuda, Damian

    2003-11-01

    Although Africa has played a central role in human evolutionary history, certain studies have suggested that not all contemporary human genetic diversity is of recent African origin. We investigated 35 simple polymorphic sites and one T(n) microsatellite in an 8-kb segment of the dystrophin gene. We found 86 haplotypes in 1,343 chromosomes from around the world. Although a classical out-of-Africa topology was observed in trees based on the variant frequencies, the tree of haplotype sequences reveals three lineages accounting for present-day diversity. The proportion of new recombinants and the diversity of the T(n) microsatellite were used to estimate the age of haplotype lineages and the time of colonization events. The lineage that underwent the great expansion originated in Africa prior to the Upper Paleolithic (27,000-56,000 years ago). A second group, of structurally distinct haplotypes that occupy a central position on the tree, has never left Africa. The third lineage is represented by the haplotype that lies closest to the root, is virtually absent in Africa, and appears older than the recent out-of-Africa expansion. We propose that this lineage could have left Africa before the expansion (as early as 160,000 years ago) and admixed, outside of Africa, with the expanding lineage. Contemporary human diversity, although dominated by the recently expanded African lineage, thus represents a mosaic of different contributions.

  15. High-Frequency Antenna Arrays and Coupling Structures

    National Aeronautics and Space Administration — We are fabricating antenna arrays and coupling structure for frequencies in the 200-300 GHz frequency bands. The primary motivation of this work is to develop...

  16. Judging Criterion of Controlled Structures with Closely Spaced Natural Frequencies

    Xie Faxiang; Sun Limin

    2010-01-01

    The structures with closely spaced natural frequencies widely exist in civil engineering; however, the judging criterion of the density of closely spaced frequencies is in dispute. This paper suggests a judging criterion for structures with closely spaced natural frequencies based on the analysis on a controlled 2-DOF structure. The analysis results indicate that the optimal control gain of the structure with velocity feedback is dependent on the frequency density parameter of structure and the maximum attainable additional modal damping ratio is 1.72 times of the frequency density parameter when state feedback is applied. Based on a brief review on the previous researches, a judging criterion related the minimum frequency density parameter and the required mode damping ratio was proposed.

  17. High Frequency Traders and Market Structure

    Menkveld, A.J.

    2014-01-01

    The arrival of high-frequency traders (HFTs) coincided with the entry of new markets and, subsequently, strong fragmentation of the order flow. These trends might be related as new markets serve HFTs who seek low fees and high speed. New markets only thrive on competitive price quotes that

  18. Beta-globin gene cluster haplotypes of Amerindian populations from the Brazilian Amazon region.

    Guerreiro, J F; Figueiredo, M S; Zago, M A

    1994-01-01

    We have determined the beta-globin cluster haplotypes for 80 Indians from four Brazilian Amazon tribes: Kayapó, Wayampí, Wayana-Apalaí, and Arára. The results are analyzed together with 20 Yanomámi previously studied. From 2 to 4 different haplotypes were identified for each tribe, and 7 of the possible 32 haplotypes were found in a sample of 172 chromosomes for which the beta haplotypes were directly determined or derived from family studies. The haplotype distribution does not differ significantly among the five populations. The two most common haplotypes in all tribes were haplotypes 2 and 6, with average frequencies of 0.843 and 0.122, respectively. The genetic affinities between Brazilian Indians and other human populations were evaluated by estimates of genetic distance based on haplotype data. The lowest values were observed in relation to Asians, especially Chinese, Polynesians, and Micronesians.

  19. High frequency single mode traveling wave structure for particle acceleration

    Ivanyan, M.I.; Danielyan, V.A.; Grigoryan, B.A.; Grigoryan, A.H. [CANDLE Synchrotron Research Institute, 0040 Yerevan (Armenia); Tsakanian, A.V. [CANDLE Synchrotron Research Institute, 0040 Yerevan (Armenia); Technische Universität Darmstadt, Institut TEMF, 64289 Darmstadt (Germany); Tsakanov, V.M., E-mail: tsakanov@asls.candle.am [CANDLE Synchrotron Research Institute, 0040 Yerevan (Armenia); Vardanyan, A.S.; Zakaryan, S.V. [CANDLE Synchrotron Research Institute, 0040 Yerevan (Armenia)

    2016-09-01

    The development of the new high frequency slow traveling wave structures is one of the promising directions in accomplishment of charged particles high acceleration gradient. The disc and dielectric loaded structures are the most known structures with slowly propagating modes. In this paper a large aperture high frequency metallic two-layer accelerating structure is studied. The electrodynamical properties of the slowly propagating TM{sub 01} mode in a metallic tube with internally coated low conductive thin layer are examined.

  20. Casein haplotypes and their association with milk production traits in Norwegian Red cattle

    Nome Torfinn

    2009-02-01

    Full Text Available Abstract A high resolution SNP map was constructed for the bovine casein region to identify haplotype structures and study associations with milk traits in Norwegian Red cattle. Our analyses suggest separation of the casein cluster into two haplotype blocks, one consisting of the CSN1S1, CSN2 and CSN1S2 genes and another one consisting of the CSN3 gene. Highly significant associations with both protein and milk yield were found for both single SNPs and haplotypes within the CSN1S1-CSN2-CSN1S2 haplotype block. In contrast, no significant association was found for single SNPs or haplotypes within the CSN3 block. Our results point towards CSN2 and CSN1S2 as the most likely loci harbouring the underlying causative DNA variation. In our study, the most significant results were found for the SNP CSN2_67 with the C allele consistently associated with both higher protein and milk yields. CSN2_67 calls a C to an A substitution at codon 67 in β-casein gene resulting in histidine replacing proline in the amino acid sequence. This polymorphism determines the protein variants A1/B (CSN2_67 A allele versus A2/A3 (CSN2_67 C allele. Other studies have suggested that a high consumption of A1/B milk may affect human health by increasing the risk of diabetes and heart diseases. Altogether these results argue for an increase in the frequency of the CSN2_67 C allele or haplotypes containing this allele in the Norwegian Red cattle population by selective breeding.

  1. Novel structural flexibility identification in narrow frequency bands

    Zhang, J; Moon, F L

    2012-01-01

    A ‘Sub-PolyMAX’ method is proposed in this paper not only for estimating modal parameters, but also for identifying structural flexibility by processing the impact test data in narrow frequency bands. The traditional PolyMAX method obtains denominator polynomial coefficients by minimizing the least square (LS) errors of frequency response function (FRF) estimates over the whole frequency range, but FRF peaks in different structural modes may have different levels of magnitude, which leads to the modal parameters identified for the modes with small FRF peaks being inaccurate. In contrast, the proposed Sub-PolyMAX method implements the LS solver in each subspace of the whole frequency range separately; thus the results identified from a narrow frequency band are not affected by FRF data in other frequency bands. In performing structural identification in narrow frequency bands, not in the whole frequency space, the proposed method has the following merits: (1) it produces accurate modal parameters, even for the modes with very small FRF peaks; (2) it significantly reduces computation cost by reducing the number of frequency lines and the model order in each LS implementation; (3) it accurately identifies structural flexibility from impact test data, from which structural deflection under any static load can be predicted. Numerical and laboratory examples are investigated to verify the effectiveness of the proposed method. (paper)

  2. HERC1 polymorphisms: population-specific variations in haplotype composition.

    Yuasa, Isao; Umetsu, Kazuo; Nishimukai, Hiroaki; Fukumori, Yasuo; Harihara, Shinji; Saitou, Naruya; Jin, Feng; Chattopadhyay, Prasanta K; Henke, Lotte; Henke, Jürgen

    2009-08-01

    Human HERC1 is one of six HERC proteins and may play an important role in intracellular membrane trafficking. The human HERC1 gene is suggested to have been affected by local positive selection. To assess the global frequency distributions of coding and non-coding single nucleotide polymorphisms (SNPs) in the HERC1 gene, we developed a new simultaneous genotyping method for four SNPs, and applied this method to investigate 1213 individuals from 12 global populations. The results confirmed remarked differences in the allele and haplotype frequencies between East Asian and non-East Asian populations. One of the three common haplotypes observed was found to be characteristic of East Asians, who showed a relatively uniform distribution of haplotypes. Information on haplotypes would be useful for testing the function of polymorphisms in the HERC1 gene. This is the first study to investigate the distribution of HERC1 polymorphisms in various populations. (c) 2009 John Wiley & Sons, Ltd.

  3. Are molecular haplotypes worth the time and expense? A cost-effective method for applying molecular haplotypes.

    Mark A Levenstien

    2006-08-01

    Full Text Available Because current molecular haplotyping methods are expensive and not amenable to automation, many researchers rely on statistical methods to infer haplotype pairs from multilocus genotypes, and subsequently treat these inferred haplotype pairs as observations. These procedures are prone to haplotype misclassification. We examine the effect of these misclassification errors on the false-positive rate and power for two association tests. These tests include the standard likelihood ratio test (LRTstd and a likelihood ratio test that employs a double-sampling approach to allow for the misclassification inherent in the haplotype inference procedure (LRTae. We aim to determine the cost-benefit relationship of increasing the proportion of individuals with molecular haplotype measurements in addition to genotypes to raise the power gain of the LRTae over the LRTstd. This analysis should provide a guideline for determining the minimum number of molecular haplotypes required for desired power. Our simulations under the null hypothesis of equal haplotype frequencies in cases and controls indicate that (1 for each statistic, permutation methods maintain the correct type I error; (2 specific multilocus genotypes that are misclassified as the incorrect haplotype pair are consistently misclassified throughout each entire dataset; and (3 our simulations under the alternative hypothesis showed a significant power gain for the LRTae over the LRTstd for a subset of the parameter settings. Permutation methods should be used exclusively to determine significance for each statistic. For fixed cost, the power gain of the LRTae over the LRTstd varied depending on the relative costs of genotyping, molecular haplotyping, and phenotyping. The LRTae showed the greatest benefit over the LRTstd when the cost of phenotyping was very high relative to the cost of genotyping. This situation is likely to occur in a replication study as opposed to a whole-genome association study.

  4. MHC Class II haplotypes of Colombian Amerindian tribes

    Yunis, Juan J.; Yunis, Edmond J.; Yunis, Emilio

    2013-01-01

    We analyzed 1041 individuals belonging to 17 Amerindian tribes of Colombia, Chimila, Bari and Tunebo (Chibcha linguistic family), Embera, Waunana (Choco linguistic family), Puinave and Nukak (Maku-Puinave linguistic families), Cubeo, Guanano, Tucano, Desano and Piratapuyo (Tukano linguistic family), Guahibo and Guayabero (Guayabero Linguistic Family), Curripaco and Piapoco (Arawak linguistic family) and Yucpa (Karib linguistic family). for MHC class II haplotypes (HLA-DRB1, DQA1, DQB1). Approximately 90% of the MHC class II haplotypes found among these tribes are haplotypes frequently encountered in other Amerindian tribes. Nonetheless, striking differences were observed among Chibcha and non-Chibcha speaking tribes. The DRB1*04:04, DRB1*04:11, DRB1*09:01 carrying haplotypes were frequently found among non-Chibcha speaking tribes, while the DRB1*04:07 haplotype showed significant frequencies among Chibcha speaking tribes, and only marginal frequencies among non-Chibcha speaking tribes. Our results suggest that the differences in MHC class II haplotype frequency found among Chibcha and non-Chibcha speaking tribes could be due to genetic differentiation in Mesoamerica of the ancestral Amerindian population into Chibcha and non-Chibcha speaking populations before they entered into South America. PMID:23885196

  5. Influence of radio frequency power on structure and ionic

    Lithium phosphorus oxynitride (LiPON) thin films as solid electrolytes were prepared by radio frequency magnetron sputtering of a Li3PO4 target in ambient nitrogen atmosphere. The influence of radio frequency (rf) power on the structure and the ionic conductivity of LiPON thin films has been investigated. The morphology ...

  6. Frequency effects and structural change – the Afrikaans preterite ...

    According to emergent grammar and exemplar theory in cognitive linguistics, the frequency of an item affects its behaviour in terms of structural change. In this article, I illustrate how high frequency items, such as preterital modal auxiliaries and copulas in Afrikaans, resist regularising with the rest of the Afrikaans verbal ...

  7. Shell structure in superdeformed nuclei at high rotational frequencies

    Ploszajczak, M.

    1980-01-01

    Properties of the shell structure in superdeformed nuclei at high rotational frequencies are discussed. Moreover, stability of the high spin compound nucleus with respect to the fission and the emission of light particles is investigated. (author)

  8. Probabilistic frequency variations of structure-soil systems

    Hamilton, C.W.; Hadjian, A.H.

    1976-01-01

    During earthquakes, structure-soil systems act as filters greatly amplifying the response of equipment whose frequencies are at or near their natural frequencies. Thus, the estimation of these structure-soil system frequencies assumes significant importance both for safety and cost. Actual in-situ frequencies of structures differ from calculated frequencies due both to variations in mathematical modelling techniques and to variations of material properties. This paper studies the second source only. This variability is usually gauged by the 'worst case' analyses technique in which extreme high- and low- parameter values are assumed and the associated frequencies are used as upper and lower bounds. This approach is not entirely satisfactory because it does not provide any indication of the probability of these limits being exceeded, of the distribution between these limits, or of the level of conservation introduced into the design process. The present approach provides this additional information. The emphasis in this part is both on developing the methodology and on the results obtained. It covers both the fixed-base structure and the effects of soil-structure interaction. Empirical data on concrete proerties were obtained from previously published results. Much less is known about variability of soil properties, so the soil structure interaction coefficients are assumed to be normally distributed. As data on the variation of soil properties become available, they can be readily incorporated via the methodology developed here. (Auth.)

  9. Dimensional Anxiety Mediates Linkage of GABRA2 Haplotypes With Alcoholism

    Enoch, Mary-Anne; Schwartz, Lori; Albaugh, Bernard; Virkkunen, Matti; Goldman, David

    2015-01-01

    The GABAAα2 receptor gene (GABRA2) modulates anxiety and stress response. Three recent association studies implicate GABRA2 in alcoholism, however in these papers both common, opposite-configuration haplotypes in the region distal to intron3 predict risk. We have now replicated the GABRA2 association with alcoholism in 331 Plains Indian men and women and 461 Finnish Caucasian men. Using a dimensional measure of anxiety, harm avoidance (HA), we also found that the association with alcoholism is mediated, or moderated, by anxiety. Nine SNPs were genotyped revealing two haplotype blocks. Within the previously implicated block 2 region, we identified the two common, opposite-configuration risk haplotypes, A and B. Their frequencies differed markedly in Finns and Plains Indians. In both populations, most block 2 SNPs were significantly associated with alcoholism. The associations were due to increased frequencies of both homozygotes in alcoholics, indicating the possibility of alcoholic subtypes with opposite genotypes. Congruently, there was no significant haplotype association. Using HA as an indicator variable for anxiety, we found haplotype linkage to alcoholism with high and low dimensional anxiety, and to HA itself, in both populations. High HA alcoholics had the highest frequency of the more abundant haplotype (A in Finns, B in Plains Indians); low HA alcoholics had the highest frequency of the less abundant haplotype (B in Finns, A in Plains Indians) (Finns: P α0.007, OR α2.1, Plains Indians: P α0.040, OR α1.9). Non-alcoholics had intermediate frequencies. Our results suggest that within the distal GABRA2 region is a functional locus or loci that may differ between populations but that alters risk for alcoholism via the mediating action of anxiety. PMID:16874763

  10. Structural insertion/deletion variation in IRF5 is associated with a risk haplotype and defines the precise IRF5 isoforms expressed in systemic lupus erythematosus

    Kozyrev, Sergey V; Lewén, Susanna; Reddy, Prasad M V Linga

    2007-01-01

    -alpha. The SNP most strongly associated with SLE was SNP no. rs2070197 (P=5.2x10(-11)), which is a proxy of the risk haplotype, but does not appear to be functional. CONCLUSION: None of the functional variants investigated in this study is strongly associated with SLE, with the exception of the exon 1B donor......OBJECTIVE: To determine whether specific isoforms of IRF5 are transcribed in patients with systemic lupus erythematosus (SLE) who have risk genotypes in the exon 1B donor splice site at single-nucleotide polymorphism (SNP) no. rs2004640. METHODS: Peripheral blood mononuclear cells were obtained...... interaction domain. The insertion segregates in the risk haplotype with the high expression allele of a poly(A) site SNP no. rs10954213 and the exon 1B donor splice allele of the 5'-UTR SNP no. rs2004640. The poly(A) polymorphism correlated with levels of IRF5 in cells stimulated with interferon...

  11. Structural Health Monitoring Based on Combined Structural Global and Local Frequencies

    Jilin Hou

    2014-01-01

    Full Text Available This paper presents a parameter estimation method for Structural Health Monitoring based on the combined measured structural global frequencies and structural local frequencies. First, the global test is experimented to obtain the low order modes which can reflect the global information of the structure. Secondly, the mass is added on the member of structure to increase the local dynamic characteristic and to make the member have local primary frequency, which belongs to structural local frequency and is sensitive to local parameters. Then the parameters of the structure can be optimized accurately using the combined structural global frequencies and structural local frequencies. The effectiveness and accuracy of the proposed method are verified by the experiment of a space truss.

  12. Haplotyping Problem, A Clustering Approach

    Eslahchi, Changiz; Sadeghi, Mehdi; Pezeshk, Hamid; Kargar, Mehdi; Poormohammadi, Hadi

    2007-01-01

    Construction of two haplotypes from a set of Single Nucleotide Polymorphism (SNP) fragments is called haplotype reconstruction problem. One of the most popular computational model for this problem is Minimum Error Correction (MEC). Since MEC is an NP-hard problem, here we propose a novel heuristic algorithm based on clustering analysis in data mining for haplotype reconstruction problem. Based on hamming distance and similarity between two fragments, our iterative algorithm produces two clusters of fragments; then, in each iteration, the algorithm assigns a fragment to one of the clusters. Our results suggest that the algorithm has less reconstruction error rate in comparison with other algorithms

  13. Mapping Haplotype-haplotype Interactions with Adaptive LASSO

    Li Ming

    2010-08-01

    Full Text Available Abstract Background The genetic etiology of complex diseases in human has been commonly viewed as a complex process involving both genetic and environmental factors functioning in a complicated manner. Quite often the interactions among genetic variants play major roles in determining the susceptibility of an individual to a particular disease. Statistical methods for modeling interactions underlying complex diseases between single genetic variants (e.g. single nucleotide polymorphisms or SNPs have been extensively studied. Recently, haplotype-based analysis has gained its popularity among genetic association studies. When multiple sequence or haplotype interactions are involved in determining an individual's susceptibility to a disease, it presents daunting challenges in statistical modeling and testing of the interaction effects, largely due to the complicated higher order epistatic complexity. Results In this article, we propose a new strategy in modeling haplotype-haplotype interactions under the penalized logistic regression framework with adaptive L1-penalty. We consider interactions of sequence variants between haplotype blocks. The adaptive L1-penalty allows simultaneous effect estimation and variable selection in a single model. We propose a new parameter estimation method which estimates and selects parameters by the modified Gauss-Seidel method nested within the EM algorithm. Simulation studies show that it has low false positive rate and reasonable power in detecting haplotype interactions. The method is applied to test haplotype interactions involved in mother and offspring genome in a small for gestational age (SGA neonates data set, and significant interactions between different genomes are detected. Conclusions As demonstrated by the simulation studies and real data analysis, the approach developed provides an efficient tool for the modeling and testing of haplotype interactions. The implementation of the method in R codes can be

  14. Haplotype reconstruction error as a classical misclassification problem: introducing sensitivity and specificity as error measures.

    Claudia Lamina

    Full Text Available BACKGROUND: Statistically reconstructing haplotypes from single nucleotide polymorphism (SNP genotypes, can lead to falsely classified haplotypes. This can be an issue when interpreting haplotype association results or when selecting subjects with certain haplotypes for subsequent functional studies. It was our aim to quantify haplotype reconstruction error and to provide tools for it. METHODS AND RESULTS: By numerous simulation scenarios, we systematically investigated several error measures, including discrepancy, error rate, and R(2, and introduced the sensitivity and specificity to this context. We exemplified several measures in the KORA study, a large population-based study from Southern Germany. We find that the specificity is slightly reduced only for common haplotypes, while the sensitivity was decreased for some, but not all rare haplotypes. The overall error rate was generally increasing with increasing number of loci, increasing minor allele frequency of SNPs, decreasing correlation between the alleles and increasing ambiguity. CONCLUSIONS: We conclude that, with the analytical approach presented here, haplotype-specific error measures can be computed to gain insight into the haplotype uncertainty. This method provides the information, if a specific risk haplotype can be expected to be reconstructed with rather no or high misclassification and thus on the magnitude of expected bias in association estimates. We also illustrate that sensitivity and specificity separate two dimensions of the haplotype reconstruction error, which completely describe the misclassification matrix and thus provide the prerequisite for methods accounting for misclassification.

  15. Mid-frequency Band Dynamics of Large Space Structures

    Coppolino, Robert N.; Adams, Douglas S.

    2004-01-01

    High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

  16. Kinetic Scale Structure of Low-frequency Waves and Fluctuations

    López, Rodrigo A.; Yoon, Peter H. [Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 (United States); Viñas, Adolfo F. [NASA Goddard Space Flight Center, Heliophysics Science Division, Geospace Physics Laboratory, Mail Code 673, Greenbelt, MD 20771 (United States); Araneda, Jaime A., E-mail: rlopezh@umd.edu, E-mail: yoonp@umd.edu [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Concepción (Chile)

    2017-08-10

    The dissipation of solar wind turbulence at kinetic scales is believed to be important for the heating of the corona and for accelerating the wind. The linear Vlasov kinetic theory is a useful tool for identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, and ion-acoustic (or kinetic slow), and their possible roles in the dissipation. However, the kinetic mode structure in the vicinity of ion-cyclotron modes is not clearly understood. The present paper aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. The theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion-Bernstein modes versus quasi-modes. The spontaneous emission theory and simulation also confirm the findings of the Vlasov theory in that the kinetic Alfvén waves can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high-beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave–particle interactions.

  17. Influence of radio frequency power on structure and ionic ...

    Wintec

    frequency (rf) power on the structure and the ionic conductivity of LiPON thin films has been investigated. The morphology ... be used as a fine alternative to traditional sulfides and ... able lithium batteries (Kennedy and Zhang 1988; Ménétrier.

  18. Modal density of rectangular structures in a wide frequency range

    Parrinello, A.; Ghiringhelli, G. L.

    2018-04-01

    A novel approach to investigate the modal density of a rectangular structure in a wide frequency range is presented. First, the modal density is derived, in the whole frequency range of interest, on the basis of sound transmission through the infinite counterpart of the structure; then, it is corrected by means of the low-frequency modal behavior of the structure, taking into account actual size and boundary conditions. A statistical analysis reveals the connection between the modal density of the structure and the transmission of sound through its thickness. A transfer matrix approach is used to compute the required acoustic parameters, making it possible to deal with structures having arbitrary stratifications of different layers. A finite element method is applied on coarse grids to derive the first few eigenfrequencies required to correct the modal density. Both the transfer matrix approach and the coarse grids involved in the finite element analysis grant high efficiency. Comparison with alternative formulations demonstrates the effectiveness of the proposed methodology.

  19. Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency.

    Cho, Hyunjun; Kim, Mincheol; Tripathi, Binu; Adams, Jonathan

    2017-07-01

    Although disturbance is thought to be important in many ecological processes, responses of fungal communities to soil disturbance have been little studied experimentally. We subjected a soil microcosm to physical disturbance, at a range of frequencies designed to simulate ecological disturbance events. We analyzed the fungal community structure using Illumina HiSeq sequencing of the ITS1 region. Fungal diversity was found to decline with the increasing disturbance frequencies, with no sign of the "humpback" pattern found in many studies of larger sedentary organisms. There is thus no evidence of an effect of release from competition resulting from moderate disturbance-which suggests that competition and niche overlap may not be important in limiting soil fungal diversity. Changing disturbance frequency also led to consistent differences in community composition. There were clear differences in OTU-level composition, with different disturbance treatments each having distinct fungal communities. The functional profile of fungal groups (guilds) was changed by the level of disturbance frequency. These predictable differences in community composition suggest that soil fungi can possess different niches in relation to disturbance frequency, or time since last disturbance. Fungi appear to be most abundant relative to bacteria at intermediate disturbance frequencies, on the time scale we studied here.

  20. Time-variant random interval natural frequency analysis of structures

    Wu, Binhua; Wu, Di; Gao, Wei; Song, Chongmin

    2018-02-01

    This paper presents a new robust method namely, unified interval Chebyshev-based random perturbation method, to tackle hybrid random interval structural natural frequency problem. In the proposed approach, random perturbation method is implemented to furnish the statistical features (i.e., mean and standard deviation) and Chebyshev surrogate model strategy is incorporated to formulate the statistical information of natural frequency with regards to the interval inputs. The comprehensive analysis framework combines the superiority of both methods in a way that computational cost is dramatically reduced. This presented method is thus capable of investigating the day-to-day based time-variant natural frequency of structures accurately and efficiently under concrete intrinsic creep effect with probabilistic and interval uncertain variables. The extreme bounds of the mean and standard deviation of natural frequency are captured through the embedded optimization strategy within the analysis procedure. Three particularly motivated numerical examples with progressive relationship in perspective of both structure type and uncertainty variables are demonstrated to justify the computational applicability, accuracy and efficiency of the proposed method.

  1. Structural health monitoring in composite materials using frequency response methods

    Kessler, Seth S.; Spearing, S. Mark; Atalla, Mauro J.; Cesnik, Carlos E. S.; Soutis, Constantinos

    2001-08-01

    Cost effective and reliable damage detection is critical for the utilization of composite materials in structural applications. Non-destructive evaluation techniques (e.g. ultrasound, radiography, infra-red imaging) are available for use during standard repair and maintenance cycles, however by comparison to the techniques used for metals these are relatively expensive and time consuming. This paper presents part of an experimental and analytical survey of candidate methods for the detection of damage in composite materials. The experimental results are presented for the application of modal analysis techniques applied to rectangular laminated graphite/epoxy specimens containing representative damage modes, including delamination, transverse ply cracks and through-holes. Changes in natural frequencies and modes were then found using a scanning laser vibrometer, and 2-D finite element models were created for comparison with the experimental results. The models accurately predicted the response of the specimems at low frequencies, but the local excitation and coalescence of higher frequency modes make mode-dependent damage detection difficult and most likely impractical for structural applications. The frequency response method was found to be reliable for detecting even small amounts of damage in a simple composite structure, however the potentially important information about damage type, size, location and orientation were lost using this method since several combinations of these variables can yield identical response signatures.

  2. Vacuum arc localization in CLIC prototype radio frequency accelerating structures

    AUTHOR|(CDS)2091976; Koivunen, Visa

    2016-04-04

    A future linear collider capable of reaching TeV collision energies should support accelerating gradients beyond 100 MV/m. At such high fields, the occurrence of vacuum arcs have to be mitigated through conditioning, during which an accelerating structure’s resilience against breakdowns is slowly increased through repeated radio frequency pulsing. Conditioning is very time and resource consuming, which is why developing more efficient procedures is desirable. At CERN, conditioning related research is conducted at the CLIC high-power X-band test stands. Breakdown localization is an important diagnostic tool of accelerating structure tests. Abnormal position distributions highlight issues in structure design, manufacturing or operation and may consequently help improve these processes. Additionally, positioning can provide insight into the physics of vacuum arcs. In this work, two established positioning methods based on the time-difference-ofarrival of radio frequency waves are extended. The first method i...

  3. Insights into HLA-G genetics provided by worldwide haplotype diversity

    Erick C Castelli

    2014-10-01

    Full Text Available Human Leucocyte Antigen G (HLA-G belongs to the family of nonclassical HLA class I genes, located within the major histocompatibility complex (MHC. HLA-G has been the target of most recent research regarding the function of class I nonclassical genes. The main features that distinguish HLA-G from classical class I genes are: a limited protein variability; b alternative splicing generating several membrane bound and soluble isoforms; c short cytoplasmic tail; d modulation of immune response (immune tolerance; e restricted expression to certain tissues. In the present work, we describe the HLA-G gene structure and address the HLA-G variability and haplotype diversity among several populations around the world, considering each of its major segments (promoter, coding and 3’untranslated regions. For this purpose, we developed a pipeline to reevaluate the 1000Genomes data and recover miscalled or missing genotypes and haplotypes. It became clear that the overall structure of the HLA-G molecule has been maintained during the evolutionary process and that most of the variation sites found in the HLA-G coding region are either coding synonymous or intronic mutations. In addition, only a few frequent and divergent extended haplotypes are found when the promoter, coding and 3’ untranslated regions are evaluated together. The divergence is particularly evident for the regulatory regions. The population comparisons confirmed that most of the HLA-G variability has originated before human dispersion from Africa and that the allele and haplotype frequencies have probably been shaped by strong selective pressures.

  4. Longitudinal capture in the radio-frequency-quadrupole structure

    Inagaki, S.

    1980-03-01

    The radio-frequency-quadrupole (RFQ) linac structure not only can attain easily transverse focusing in the low-beta region, but also can obtain very high capture efficiency because of its low beta-lambda and low-particle rigidity. An optimization study of the zero space-charge longitudinal capture in an RFQ linac that yields configurations with large capture efficiency is described

  5. Approximation properties of haplotype tagging

    Dreiseitl Stephan

    2006-01-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are locations at which the genomic sequences of population members differ. Since these differences are known to follow patterns, disease association studies are facilitated by identifying SNPs that allow the unique identification of such patterns. This process, known as haplotype tagging, is formulated as a combinatorial optimization problem and analyzed in terms of complexity and approximation properties. Results It is shown that the tagging problem is NP-hard but approximable within 1 + ln((n2 - n/2 for n haplotypes but not approximable within (1 - ε ln(n/2 for any ε > 0 unless NP ⊂ DTIME(nlog log n. A simple, very easily implementable algorithm that exhibits the above upper bound on solution quality is presented. This algorithm has running time O((2m - p + 1 ≤ O(m(n2 - n/2 where p ≤ min(n, m for n haplotypes of size m. As we show that the approximation bound is asymptotically tight, the algorithm presented is optimal with respect to this asymptotic bound. Conclusion The haplotype tagging problem is hard, but approachable with a fast, practical, and surprisingly simple algorithm that cannot be significantly improved upon on a single processor machine. Hence, significant improvement in computatational efforts expended can only be expected if the computational effort is distributed and done in parallel.

  6. Negative Refraction Using Frequency-Tuned Oxide Multilayer Structure

    Yalin Lu

    2008-01-01

    Full Text Available An oxide-based multilayer structure was proposed to realize negative refraction. The multilayer composes of alternative layers having negative permittivity and negative permeability, respectively. In order to realize negative refraction, their dielectric and magnetic resonances of layers will be tuned to the frequency as close as possibly via changing their temperature, composition, structure, and so forth. Such oxide-based NIMs are attractive for their potential applications as optical super lenses, imagers, optical cloaking, sensors, and so forth, those are required with low-loss, low-cost, and good fabrication flexibility.

  7. Occurrence of the Southeast Asian/South American SVMNT haplotype of the chloroquine-resistance transporter gene in Plasmodium falciparum in Tanzania

    Alifrangis, Michael; Dalgaard, Michael B; Lusingu, John P

    2006-01-01

    Two main haplotypes, CVIET and SVMNT, of the Plasmodium falciparum chloroquine-resistance transporter gene (Pfcrt) are linked to 4-aminoquinoline resistance. The CVIET haplotype has been reported in most malaria-endemic regions, whereas the SVMNT haplotype has only been found outside Africa. We...... investigated Pfcrt haplotype frequencies in Korogwe District, Tanzania, in 2003 and 2004. The SVMNT haplotype was not detected in 2003 but was found in 19% of infected individuals in 2004. Amodiaquine use has increased in the region. The introduction and high prevalence of the SVMNT haplotype may reflect...... this and may raise concern regarding the use of amodiaquine in artemisinin-based combination therapies in Africa....

  8. Impact of soil-structure interaction on the probabilistic frequency variation of concrete structures

    Hadjian, A.H.; Hamilton, C.W.

    1975-01-01

    Earthquake response of equipment in nuclear power plants is characterized by floor response spectra. Since these spectra peak at the natural frequencies of the structure, it is important, both from safety and cost standpoints, to determine the degree of the expected variability of the calculated structural frequencies. A previous work is extended on the variability of the natural frequencies of structures due to the variations of concrete properties and a rigorous approach is presented to evaluate frequency variations based on the probability distributions of both the structural and soil parameters and jointly determine the distributions of the natural frequencies. It is assumed that the soil-structure interaction coefficients are normally distributed. With the proper choice of coordinates, the simultaneous random variations of both the structural properties and the interaction coefficients can be incorporated in the eigenvalue problem. The key methodology problem is to obtain the probability distribution of eigenvalues of matrices with random variable elements. Since no analytic relation exists between the eigenvalues and the elements, a numerical procedure had to be designed. It was found that the desired accuracy can be best achieved by splitting the joint variation into two parts: the marginal distribution of soil variations and the conditional distribution of structural variations at specific soil fractiles. Then after calculating the actual eigenvalues at judiciously selected paired values of soil and structure parameters, this information is recombined to obtain the desired cumulative distribution of natural frequencies

  9. Geographical distribution of a specific mitochondrial haplotype of Zymoseptoria tritici

    Sameh BOUKEF

    2014-01-01

    Full Text Available Severity of disease caused by the fungus Zymoseptoria tritici throughout world cereal growing regions has elicited much debate on the potential evolutionary mechanism conferring high adaptability of the pathogen to diverse climate conditions and different wheat hosts (Triticum durum and T. aestivum. Specific mitochondrial DNA sequence was used to investigate geographic distribution of the type 4 haplotype (mtRFLP4 within 1363 isolates of Z. tritici originating from 21 countries. The mtRFLP4 haplotype was detected from both durum and bread wheat hosts with greater frequency on durum wheat. The distribution of mtRFLP4 was limited to populations sampled from the Mediterranean and the Red Sea region. Greater frequencies of mtRFLP4 were found in Tunisia (87% and Algeria (60%. The haplotype was absent within European, Australian, North and South American populations except Argentina. While alternative hypotheses such as climatic adaptation could not be ruled out, it is postulated that mtRFLP4 originated in North Africa (e.g. Tunisia or Algeria as an adaptation to durum wheat as the prevailing cereal crop. The specialized haplotype has subsequently spread as indicated by lower frequency of occurrence in the surrounding Mediterranean countries and on bread wheat hosts.

  10. Low energy booster radio frequency cavity structural analysis

    Jones, K.

    1994-01-01

    The structural design of the Superconducting Super Collider Low Energy Booster (LEB) Radio Frequency (RF) Cavity is very unique. The cavity is made of three different materials which all contribute to its structural strength while at the same time providing a good medium for magnetic properties. Its outer conductor is made of thin walled stainless steel which is later copper plated to reduce the electrical losses. Its tuner housing is made of a fiber reinforced composite laminate, similar to G10, glued to stainless steel plating. The stainless steel of the tuner is slotted to significantly diminish the magnetically-induced eddy currents. The composite laminate is bonded to the stainless steel to restore the structural strength that was lost in slotting. The composite laminate is also a barrier against leakage of the pressurized internal ferrite coolant fluid. The cavity's inner conductor, made of copper and stainless steel, is subjected to high heat loads and must be liquid cooled. The requirements of the Cavity are very stringent and driven primarily by deflection, natural frequency and temperature. Therefore, very intricate finite element analysis was used to complement conventional hand analysis in the design of the cavity. Structural testing of the assembled prototype cavity is planned to demonstrate the compliance of the cavity design to all of its requirements

  11. Low energy booster radio frequency cavity structural analysis

    Jones, K.

    1993-04-01

    The structural design of the Superconducting Super Collider Low Energy Booster (LEB) Radio Frequency (RF) Cavity is very unique. The cavity is made of three different materials which all contribute to its structural strength while at the same time providing a good medium for magnetic properties. Its outer conductor is made of thin walled stainless steel which is later copper plated to reduce the electrical losses. Its tuner housing is made of a fiber reinforced composite laminate, similar to G10, glued to stainless steel plating. The stainless steel of the tuner is slotted to significantly diminish the magnetically-induced eddy currents. The composite laminate is bonded to the stainless steel to restore the structural strength that was lost in slotting. The composite laminate is also a barrier against leakage of the pressurized internal ferrite coolant fluid. The cavity's inner conductor, made of copper and stainless steel, is subjected to high heat loads and must be liquid cooled. The requirements of the Cavity are very stringent and driven primarily by deflection, natural frequency and temperature. Therefore, very intricate finite element analysis was used to complement conventional hand analysis in the design of the cavity. Structural testing of the assembled prototype cavity is planned to demonstrate the compliance of the cavity design to all of its requirements

  12. Common ataxia telangiectasia mutated haplotypes and risk of breast cancer: a nested case–control study

    Tamimi, Rulla M; Hankinson, Susan E; Spiegelman, Donna; Kraft, Peter; Colditz, Graham A; Hunter, David J

    2004-01-01

    The ataxia telangiectasia mutated (ATM) gene is a tumor suppressor gene with functions in cell cycle arrest, apoptosis, and repair of DNA double-strand breaks. Based on family studies, women heterozygous for mutations in the ATM gene are reported to have a fourfold to fivefold increased risk of breast cancer compared with noncarriers of the mutations, although not all studies have confirmed this association. Haplotype analysis has been suggested as an efficient method for investigating the role of common variation in the ATM gene and breast cancer. Five biallelic haplotype tagging single nucleotide polymorphisms are estimated to capture 99% of the haplotype diversity in Caucasian populations. We conducted a nested case–control study of breast cancer within the Nurses' Health Study cohort to address the role of common ATM haplotypes and breast cancer. Cases and controls were genotyped for five haplotype tagging single nucleotide polymorphisms. Haplotypes were predicted for 1309 cases and 1761 controls for which genotype information was available. Six unique haplotypes were predicted in this study, five of which occur at a frequency of 5% or greater. The overall distribution of haplotypes was not significantly different between cases and controls (χ 2 = 3.43, five degrees of freedom, P = 0.63). There was no evidence that common haplotypes of ATM are associated with breast cancer risk. Extensive single nucleotide polymorphism detection using the entire genomic sequence of ATM will be necessary to rule out less common variation in ATM and sporadic breast cancer risk

  13. HLA-E regulatory and coding region variability and haplotypes in a Brazilian population sample.

    Ramalho, Jaqueline; Veiga-Castelli, Luciana C; Donadi, Eduardo A; Mendes-Junior, Celso T; Castelli, Erick C

    2017-11-01

    The HLA-E gene is characterized by low but wide expression on different tissues. HLA-E is considered a conserved gene, being one of the least polymorphic class I HLA genes. The HLA-E molecule interacts with Natural Killer cell receptors and T lymphocytes receptors, and might activate or inhibit immune responses depending on the peptide associated with HLA-E and with which receptors HLA-E interacts to. Variable sites within the HLA-E regulatory and coding segments may influence the gene function by modifying its expression pattern or encoded molecule, thus, influencing its interaction with receptors and the peptide. Here we propose an approach to evaluate the gene structure, haplotype pattern and the complete HLA-E variability, including regulatory (promoter and 3'UTR) and coding segments (with introns), by using massively parallel sequencing. We investigated the variability of 420 samples from a very admixed population such as Brazilians by using this approach. Considering a segment of about 7kb, 63 variable sites were detected, arranged into 75 extended haplotypes. We detected 37 different promoter sequences (but few frequent ones), 27 different coding sequences (15 representing new HLA-E alleles) and 12 haplotypes at the 3'UTR segment, two of them presenting a summed frequency of 90%. Despite the number of coding alleles, they encode mainly two different full-length molecules, known as E*01:01 and E*01:03, which corresponds to about 90% of all. In addition, differently from what has been previously observed for other non classical HLA genes, the relationship among the HLA-E promoter, coding and 3'UTR haplotypes is not straightforward because the same promoter and 3'UTR haplotypes were many times associated with different HLA-E coding haplotypes. This data reinforces the presence of only two main full-length HLA-E molecules encoded by the many HLA-E alleles detected in our population sample. In addition, this data does indicate that the distal HLA-E promoter is by

  14. β-globin haplotypes in normal and hemoglobinopathic individuals from Reconcavo Baiano, State of Bahia, Brazil

    Wellington dos Santos Silva

    2010-01-01

    Full Text Available Five restriction site polymorphisms in the β-globin gene cluster (HincII-5'ε, HindIII-Gγ, HindIII-ªγ, HincII-'ψβ1 and HincII-3''ψβ1 were analyzed in three populations (n = 114 from Reconcavo Baiano, State of Bahia, Brazil. The groups included two urban populations from the towns of Cachoeira and Maragojipe and one rural Afro-descendant population, known as the "quilombo community", from Cachoeira municipality. The number of haplotypes found in the populations ranged from 10 to 13, which indicated higher diversity than in the parental populations. The haplotypes 2 (+----,3(----+,4(-+--+and6(-++-+onthe βA chromosomes were the most common, and two haplotypes, 9 (-++++and 14 (++--+, were found exclusively in the Maragojipe population. The other haplotypes (1, 5, 9, 11, 12, 13, 14 and 16 had lower frequencies. Restriction site analysis and the derived haplotypes indicated homogeneity among the populations. Thirty-two individuals with hemoglobinopathies (17 sickle cell disease, 12 HbSC disease and 3 HbCC disease were also analyzed. The haplotype frequencies of these patients differed significantly from those of the general population. In the sickle cell disease subgroup, the predominant haplotypes were BEN (Benin and CAR (Central African Republic, with frequencies of 52.9% and 32.4%, respectively. The high frequency of the BEN haplotype agreed with the historical origin of the afro-descendant population in the state of Bahia. However, this frequency differed from that of Salvador, the state capital, where the CAR and BEN haplotypes have similar frequencies, probably as a consequence of domestic slave trade and subsequent internal migrations to other regions of Brazil.

  15. Frequency-restrained structure-factor refinement. Pt. 1

    Lunin, V.Yu.; Skovoroda, T.P.

    1991-01-01

    An analysis of the frequencies of different values encountered in protein electron-density syntheses reveals characteristic shapes for their distributions (histograms). This property can be used to refine ill-defined phases (and, perhaps, some of the moduli) of structure factors, and thus to obtain more-interpretable electron-density maps. A simple empirical model is designed which can predict the histogram for a protein with an undetermined structure provided its unit-cell volume and charge are known. The parameters of the histogram model are derived from a set of proteins with known spatial structures. The application of the simulated histogram is illustrated by an improved electron-density map for the 'dry' form of the protein γ-crystallin IIIb. (orig.)

  16. Frequency-dependent springs in the seismic analysis of structures

    Tyapin, A.G.

    2005-01-01

    This paper presents a two-step algorithm for the seismic analysis of structure resting on the rigid embedded basement. Frequency-domain analysis of SSI is carried out on the second step for a platform model with special 'soil spring' which is complex, frequency-dependent, wave-dependent and non-balanced. Theory is presented to obtain the parameters of the soil spring on the first step of the analysis, performed without structure (only geometry of the basement is used) using well-known SASSI code (Lysmer et al, 1981) or in some other ways. On the second step in the SASSI analysis the soil spring is included in the model as a special finite element. Thus, the first step enables to save the computer resources on structure, the second step-to save resources on soil. Soil spring is the most general form for a SSI linear analysis: conventional springs and dashpots can be easily represented in such a format. Thus, the presented approach enables to study the impact of various factors (such as the embedment depth and soil-structure separation, the off-diagonal stiffness, various formulas for stiffness and damping, etc.) on the soil spring parameters. These parameters can be studied separately from the structure itself. As an example, the study of the horizontal soil mesh size is presented. Lumped soil spring may be used on the second step to obtain structural response spectra. To get stresses complex stiffness may be distributed over the basement slab and embedded walls. The proposed approach may be considered to be the alternative to the impedance method (see ASCE4-98). (authors)

  17. Antiproton-decelerating Radio-Frequency Quadrupole (RFQD), inner structure.

    Laurent Guiraud

    1999-01-01

    The inner structure of the RFQD, withdrawn from its tank. In picture _06, the upstream end is in the back and the view is on the downstream exit. The RFQD has a length of 3.5 m and operates at a frequency of 202.4 MHz. It further decelerates antiprotons from the Antiproton Decelerator (3.5 MeV/c to 100 MeV/c, or 5.3 MeV) to very low energies around 50 keV.

  18. High frequency flow-structural interaction in dense subsonic fluids

    Liu, Baw-Lin; Ofarrell, J. M.

    1995-01-01

    Prediction of the detailed dynamic behavior in rocket propellant feed systems and engines and other such high-energy fluid systems requires precise analysis to assure structural performance. Designs sometimes require placement of bluff bodies in a flow passage. Additionally, there are flexibilities in ducts, liners, and piping systems. A design handbook and interactive data base have been developed for assessing flow/structural interactions to be used as a tool in design and development, to evaluate applicable geometries before problems develop, or to eliminate or minimize problems with existing hardware. This is a compilation of analytical/empirical data and techniques to evaluate detailed dynamic characteristics of both the fluid and structures. These techniques have direct applicability to rocket engine internal flow passages, hot gas drive systems, and vehicle propellant feed systems. Organization of the handbook is by basic geometries for estimating Strouhal numbers, added mass effects, mode shapes for various end constraints, critical onset flow conditions, and possible structural response amplitudes. Emphasis is on dense fluids and high structural loading potential for fatigue at low subsonic flow speeds where high-frequency excitations are possible. Avoidance and corrective measure illustrations are presented together with analytical curve fits for predictions compiled from a comprehensive data base.

  19. Magnetic activity at infrared frequencies in structured metallic photonic crystals

    O'Brien, S.; Pendry, J.P.

    2002-01-01

    We derive the effective permeability and permittivity of a nanostructured metallic photonic crystal by analysing the complex reflection and transmission coefficients for slabs of various thicknesses. These quantities were calculated using the transfer matrix method. Our results indicate that these structures could be used to realize a negative effective permeability, at least up to infrared frequencies. The origin of the negative permeability is a resonance due to the internal inductance and capacitance of the structure. We also present an analytic model for the effective permeability of the crystal. The model reveals the importance of the inertial inductance due to the finite mass of the electrons in the metal. We find that this contribution to the inductance has implications for the design of metallic magnetic structures in the optical region of the spectrum. We show that the magnetic activity in the structure is accompanied by the concentration of the incident field energy into very small volumes within the structure. This property will allow us to considerably enhance non-linear effects with minute quantities of material. (author)

  20. Time-Frequency Methods for Structural Health Monitoring

    Alexander L. Pyayt

    2014-03-01

    Full Text Available Detection of early warning signals for the imminent failure of large and complex engineered structures is a daunting challenge with many open research questions. In this paper we report on novel ways to perform Structural Health Monitoring (SHM of flood protection systems (levees, earthen dikes and concrete dams using sensor data. We present a robust data-driven anomaly detection method that combines time-frequency feature extraction, using wavelet analysis and phase shift, with one-sided classification techniques to identify the onset of failure anomalies in real-time sensor measurements. The methodology has been successfully tested at three operational levees. We detected a dam leakage in the retaining dam (Germany and “strange” behaviour of sensors installed in a Boston levee (UK and a Rhine levee (Germany.

  1. A haplotype regression approach for genetic evaluation using sequences from the 1000 bull genomes Project

    Lakhssassi, K.; González-Recio, O.

    2017-01-01

    Haplotypes from sequencing data may improve the prediction accuracy in genomic evaluations as haplotypes are in stronger linkage disequilibrium with quantitative trait loci than markers from SNP chips. This study focuses first, on the creation of haplotypes in a population sample of 450 Holstein animals, with full-sequence data from the 1000 bull genomes project; and second, on incorporating them into the whole genome prediction model. In total, 38,319,258 SNPs (and indels) from Next Generation Sequencing were included in the analysis. After filtering variants with minor allele frequency (MAF< 0.025) 13,912,326 SNPs were available for the haplotypes extraction with findhap.f90. The number of SNPs in the haploblocks was on average 924 SNP (166,552 bp). Unique haplotypes were around 97% in all chromosomes and were ignored leaving 153,428 haplotypes. Estimated haplotypes had a large contribution to the total variance of genomic estimated breeding values for kilogram of protein, Global Type Index, Somatic Cell Score and Days Open (between 32 and 99.9%). Haploblocks containing haplotypes with large effects were selected by filtering for each trait, haplotypes whose effect was larger/lower than the mean plus/minus 3 times the standard deviation (SD) and 1 SD above the mean of the haplotypes effect distribution. Results showed that filtering by 3 SD would not be enough to capture a large proportion of genetic variance, whereas filtering by 1 SD could be useful but model convergence should be considered. Additionally, sequence haplotypes were able to capture additional genetic variance to the polygenic effect for traits undergoing lower selection intensity like fertility and health traits.

  2. A haplotype regression approach for genetic evaluation using sequences from the 1000 bull genomes Project

    Lakhssassi, K.; González-Recio, O.

    2017-07-01

    Haplotypes from sequencing data may improve the prediction accuracy in genomic evaluations as haplotypes are in stronger linkage disequilibrium with quantitative trait loci than markers from SNP chips. This study focuses first, on the creation of haplotypes in a population sample of 450 Holstein animals, with full-sequence data from the 1000 bull genomes project; and second, on incorporating them into the whole genome prediction model. In total, 38,319,258 SNPs (and indels) from Next Generation Sequencing were included in the analysis. After filtering variants with minor allele frequency (MAF< 0.025) 13,912,326 SNPs were available for the haplotypes extraction with findhap.f90. The number of SNPs in the haploblocks was on average 924 SNP (166,552 bp). Unique haplotypes were around 97% in all chromosomes and were ignored leaving 153,428 haplotypes. Estimated haplotypes had a large contribution to the total variance of genomic estimated breeding values for kilogram of protein, Global Type Index, Somatic Cell Score and Days Open (between 32 and 99.9%). Haploblocks containing haplotypes with large effects were selected by filtering for each trait, haplotypes whose effect was larger/lower than the mean plus/minus 3 times the standard deviation (SD) and 1 SD above the mean of the haplotypes effect distribution. Results showed that filtering by 3 SD would not be enough to capture a large proportion of genetic variance, whereas filtering by 1 SD could be useful but model convergence should be considered. Additionally, sequence haplotypes were able to capture additional genetic variance to the polygenic effect for traits undergoing lower selection intensity like fertility and health traits.

  3. Structure-borne sound structural vibrations and sound radiation at audio frequencies

    Cremer, L; Petersson, Björn AT

    2005-01-01

    Structure-Borne Sound"" is a thorough introduction to structural vibrations with emphasis on audio frequencies and the associated radiation of sound. The book presents in-depth discussions of fundamental principles and basic problems, in order to enable the reader to understand and solve his own problems. It includes chapters dealing with measurement and generation of vibrations and sound, various types of structural wave motion, structural damping and its effects, impedances and vibration responses of the important types of structures, as well as with attenuation of vibrations, and sound radi

  4. Discovery, evaluation and distribution of haplotypes of the wheat Ppd-D1 gene.

    Guo, Zhiai; Song, Yanxia; Zhou, Ronghua; Ren, Zhenglong; Jia, Jizeng

    2010-02-01

    Ppd-D1 is one of the most potent genes affecting the photoperiod response of wheat (Triticum aestivum). Only two alleles, insensitive Ppd-D1a and sensitive Ppd-D1b, were known previously, and these did not adequately explain the broad adaptation of wheat to photoperiod variation. In this study, five diagnostic molecular markers were employed to identify Ppd-D1 haplotypes in 492 wheat varieties from diverse geographic locations and 55 accessions of Aegilops tauschii, the D genome donor species of wheat. Six Ppd-D1 haplotypes, designated I-VI, were identified. Types II, V and VI were considered to be more ancient and types I, III and IV were considered to be derived from type II. The transcript abundances of the Ppd-D1 haplotypes showed continuous variation, being highest for haplotype I, lowest for haplotype III, and correlating negatively with varietal differences in heading time. These haplotypes also significantly affected other agronomic traits. The distribution frequency of Ppd-D1 haplotypes showed partial correlations with both latitudes and altitudes of wheat cultivation regions. The evolution, expression and distribution of Ppd-D1 haplotypes were consistent evidentially with each other. What was regarded as a pair of alleles in the past can now be considered a series of alleles leading to continuous variation.

  5. Frequency Response Function Based Damage Identification for Aerospace Structures

    Oliver, Joseph Acton

    Structural health monitoring technologies continue to be pursued for aerospace structures in the interests of increased safety and, when combined with health prognosis, efficiency in life-cycle management. The current dissertation develops and validates damage identification technology as a critical component for structural health monitoring of aerospace structures and, in particular, composite unmanned aerial vehicles. The primary innovation is a statistical least-squares damage identification algorithm based in concepts of parameter estimation and model update. The algorithm uses frequency response function based residual force vectors derived from distributed vibration measurements to update a structural finite element model through statistically weighted least-squares minimization producing location and quantification of the damage, estimation uncertainty, and an updated model. Advantages compared to other approaches include robust applicability to systems which are heavily damped, large, and noisy, with a relatively low number of distributed measurement points compared to the number of analytical degrees-of-freedom of an associated analytical structural model (e.g., modal finite element model). Motivation, research objectives, and a dissertation summary are discussed in Chapter 1 followed by a literature review in Chapter 2. Chapter 3 gives background theory and the damage identification algorithm derivation followed by a study of fundamental algorithm behavior on a two degree-of-freedom mass-spring system with generalized damping. Chapter 4 investigates the impact of noise then successfully proves the algorithm against competing methods using an analytical eight degree-of-freedom mass-spring system with non-proportional structural damping. Chapter 5 extends use of the algorithm to finite element models, including solutions for numerical issues, approaches for modeling damping approximately in reduced coordinates, and analytical validation using a composite

  6. Structure and vibrational frequencies of gaseous europium dibromide

    Giricheva, N.I.; Girichev, S.A.; Shlykov, S.A.; Pelipets, O.V.

    2000-01-01

    Structure of EuBr 2 molecule is studied in the framework of synchronous electron diffraction and mass-spectrometric experiment at the temperature of 1373(20) K. It is found that the molecule has a nonlinear equilibrium configuration, being characterized by the following effective parameters: r g (Eu - Br) = 2.767 A, r g (Br - Br) = 5.11(5) A, l g (Eu - Br) = 0.109(2) A, l g (Br - Br) = 0.388(5) A, valence angle (Br - Eu - Br) = 135.0(3.5) deg. The electron diffraction data permit ascertaining vibration frequencies ν 1 225(10) cm -1 and ν 2 = 40(4) cm -1 [ru

  7. Analysis and modelling of engineering structures in frequency domain

    Ishtev, K.; Bonev, Z.; Petrov, P.; Philipov, P.

    1987-01-01

    This paper deals with some possible applications for modelling and analysis of engineering structures, basing on technique, mentioned above. The governing system of equations is written by using frequency domain approach since elemination technique has computational significance in this field. Modelling is made basing on the well known relationship Y(jw) = W(jw) * X(jw). Here X(jw) is a complex Fourier spectra associated with the imput signals being defined as earthquake, wind, hydrodynamic, control or other type of action. W(jw) is a matrix complex transfer function which reveals the correlation between input X und output Y spectra. Y (ja) represents a complex Fourier spectra of output signals. Input and output signals are both associated with master degrees of freedom, thus matrix transfer function is composed of elements in such a manner that solve unknown parameters are implemented implicitly. It is available an integration algorithm of 'condensed' system of equations. (orig./GL)

  8. HLA-G regulatory haplotypes and implantation outcome in couples who underwent assisted reproduction treatment.

    Costa, Cynthia Hernandes; Gelmini, Georgia Fernanda; Wowk, Pryscilla Fanini; Mattar, Sibelle Botogosque; Vargas, Rafael Gustavo; Roxo, Valéria Maria Munhoz Sperandio; Schuffner, Alessandro; Bicalho, Maria da Graça

    2012-09-01

    The role of HLA-G in several clinical conditions related to reproduction has been investigated. Important polymorphisms have been found within the 5'URR and 3'UTR regions of the HLA-G promoter. The aim of the present study was to investigate 16 SNPs in the 5'URR and 14-bp insertion/deletion (ins/del) polymorphism located in the 3'UTR region of the HLA-G gene and its possible association with the implantation outcome in couples who underwent assisted reproduction treatments (ART). The case group was composed of 25 ART couples. Ninety-four couples with two or more term pregnancies composed the control group. Polymorphism haplotype frequencies of the HLA-G were determined for both groups. The Haplotype 5, Haplotype 8 and Haplotype 11 were absolute absence in ART couples. The HLA-G*01:01:02a, HLA-G*01:01:02b alleles and the 14-bp ins polymorphism, Haplotype 2, showed an increased frequency in case women and similar distribution between case and control men. However, this susceptibility haplotype is significantly presented in case women and in couple with failure implantation after treatment, which led us to suggest a maternal effect, associated with this haplotype, once their presence in women is related to a higher number of couples who underwent ART. Copyright © 2012. Published by Elsevier Inc.

  9. Haplotypes in the Dystrophin DNA Segment Point to a Mosaic Origin of Modern Human Diversity

    Ziętkiewicz, Ewa; Yotova, Vania; Gehl, Dominik; Wambach, Tina; Arrieta, Isabel; Batzer, Mark; Cole, David E.C.; Hechtman, Peter; Kaplan, Feige; Modiano, David; Moisan, Jean-Paul; Michalski, Roman; Labuda, Damian

    2003-01-01

    Although Africa has played a central role in human evolutionary history, certain studies have suggested that not all contemporary human genetic diversity is of recent African origin. We investigated 35 simple polymorphic sites and one Tn microsatellite in an 8-kb segment of the dystrophin gene. We found 86 haplotypes in 1,343 chromosomes from around the world. Although a classical out-of-Africa topology was observed in trees based on the variant frequencies, the tree of haplotype sequences re...

  10. Estimating haplotype effects for survival data

    Scheike, Thomas; Martinussen, Torben; Silver, J

    2010-01-01

    Genetic association studies often investigate the effect of haplotypes on an outcome of interest. Haplotypes are not observed directly, and this complicates the inclusion of such effects in survival models. We describe a new estimating equations approach for Cox's regression model to assess haplo...

  11. Haplotype-Based Genotyping in Polyploids

    Josh P. Clevenger

    2018-04-01

    Full Text Available Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2 was developed for Arachis hypogaea (peanut, an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

  12. Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes.

    Yamaguchi-Kabata, Yumi; Tsunoda, Tatsuhiko; Kumasaka, Natsuhiko; Takahashi, Atsushi; Hosono, Naoya; Kubo, Michiaki; Nakamura, Yusuke; Kamatani, Naoyuki

    2012-05-01

    Although the Japanese population has a rather low genetic diversity, we recently confirmed the presence of two main clusters (the Hondo and Ryukyu clusters) through principal component analysis of genome-wide single-nucleotide polymorphism (SNP) genotypes. Understanding the genetic differences between the two main clusters requires further genome-wide analyses based on a dense SNP set and comparison of haplotype frequencies. In the present study, we determined haplotypes for the Hondo cluster of the Japanese population by detecting SNP homozygotes with 388,591 autosomal SNPs from 18,379 individuals and estimated the haplotype frequencies. Haplotypes for the Ryukyu cluster were inferred by a statistical approach using the genotype data from 504 individuals. We then compared the haplotype frequencies between the Hondo and Ryukyu clusters. In most genomic regions, the haplotype frequencies in the Hondo and Ryukyu clusters were very similar. However, in addition to the human leukocyte antigen region on chromosome 6, other genomic regions (chromosomes 3, 4, 5, 7, 10 and 12) showed dissimilarities in haplotype frequency. These regions were enriched for genes involved in the immune system, cell-cell adhesion and the intracellular signaling cascade. These differentiated genomic regions between the Hondo and Ryukyu clusters are of interest because they (1) should be examined carefully in association studies and (2) likely contain genes responsible for morphological or physiological differences between the two groups.

  13. MGMT DNA repair gene promoter/enhancer haplotypes alter transcription factor binding and gene expression.

    Xu, Meixiang; Cross, Courtney E; Speidel, Jordan T; Abdel-Rahman, Sherif Z

    2016-10-01

    The O 6 -methylguanine-DNA methyltransferase (MGMT) protein removes O 6 -alkyl-guanine adducts from DNA. MGMT expression can thus alter the sensitivity of cells and tissues to environmental and chemotherapeutic alkylating agents. Previously, we defined the haplotype structure encompassing single nucleotide polymorphisms (SNPs) in the MGMT promoter/enhancer (P/E) region and found that haplotypes, rather than individual SNPs, alter MGMT promoter activity. The exact mechanism(s) by which these haplotypes exert their effect on MGMT promoter activity is currently unknown, but we noted that many of the SNPs comprising the MGMT P/E haplotypes are located within or in close proximity to putative transcription factor binding sites. Thus, these haplotypes could potentially affect transcription factor binding and, subsequently, alter MGMT promoter activity. In this study, we test the hypothesis that MGMT P/E haplotypes affect MGMT promoter activity by altering transcription factor (TF) binding to the P/E region. We used a promoter binding TF profiling array and a reporter assay to evaluate the effect of different P/E haplotypes on TF binding and MGMT expression, respectively. Our data revealed a significant difference in TF binding profiles between the different haplotypes evaluated. We identified TFs that consistently showed significant haplotype-dependent binding alterations (p ≤ 0.01) and revealed their role in regulating MGMT expression using siRNAs and a dual-luciferase reporter assay system. The data generated support our hypothesis that promoter haplotypes alter the binding of TFs to the MGMT P/E and, subsequently, affect their regulatory function on MGMT promoter activity and expression level.

  14. Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops

    Lunwen Qian

    2017-09-01

    Full Text Available In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP–trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately

  15. Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops.

    Qian, Lunwen; Hickey, Lee T; Stahl, Andreas; Werner, Christian R; Hayes, Ben; Snowdon, Rod J; Voss-Fels, Kai P

    2017-01-01

    In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool

  16. Structural and frequency dependencies of a.c. and dielectric ...

    6Thin Film Laboratory, Department of Physics, Faculty of Education, Ain Shams ... conductivity and its frequency exponents were interpreted in terms of correlated barrier hopping ... cations in high-electron-mobility and heterostructure bipolar.

  17. Vitamin D Receptor Gene Polymorphisms and Haplotypes in Hungarian Patients with Idiopathic Inflammatory Myopathy

    Levente Bodoki

    2015-01-01

    Full Text Available Idiopathic inflammatory myopathies are autoimmune diseases characterized by symmetrical proximal muscle weakness. Our aim was to identify a correlation between VDR polymorphisms or haplotypes and myositis. We studied VDR-BsmI, VDR-ApaI, VDR-TaqI, and VDR-FokI polymorphisms and haplotypes in 89 Hungarian poly-/dermatomyositis patients (69 females and 93 controls (52 females. We did not obtain any significant differences for VDR-FokI, BsmI, ApaI, and TaqI genotypes and allele frequencies between patients with myositis and healthy individuals. There was no association of VDR polymorphisms with clinical manifestations and laboratory profiles in myositis patients. Men with myositis had a significantly different distribution of BB, Bb, and bb genotypes than female patients, control male individuals, and the entire control group. Distribution of TT, Tt, and tt genotypes was significantly different in males than in females in patient group. According to four-marker haplotype prevalence, frequencies of sixteen possible haplotypes showed significant differences between patient and control groups. The three most frequent haplotypes in patients were the fbAt, FBaT, and fbAT. Our findings may reveal that there is a significant association: Bb and Tt genotypes can be associated with myositis in the Hungarian population we studied. We underline the importance of our result in the estimated prevalence of four-marker haplotypes.

  18. Y-STR haplotypes of Native American populations from the Brazilian Amazon region.

    Palha, Teresinha Jesus Brabo Ferreira; Rodrigues, Elzemar Martins Ribeiro; dos Santos, Sidney Emanuel Batista

    2010-10-01

    The allele and haplotype frequencies of nine Y-STRs (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385 I/II) were determined in a sample of six native tribes from the Brazilian Amazon (Tiriyó, Awa-Guajá, Waiãpi, Urubu-Kaapor, Zoé and Parakanã). Forty-eight different haplotypes were identified, 28 of which unique. Five haplotypes are very frequent and were shared by over 10 individuals. The estimated haplotype diversity (0.9114) was very low compared to other geographic groups, including Africans, Europeans and Asians. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  19. Control of high frequency microactuators using active structures

    Kreth, P A; Alvi, F S; Reese, B M; Oates, W S

    2015-01-01

    A fluidically driven microactuator that generates supersonic, pulsed microjets has been implemented with smart materials to actively and precisely control the frequency of the microjets in a closed-loop manner. Since this actuator relies on a number of microscale flow and acoustic phenomena to produce the pulsed microjets, its resonant frequency is determined by its geometry and other flow parameters. The design discussed in this paper integrates piezoelectric stacks by connecting them to movable sidewalls within the actuator such that the microactuator's internal geometry can be controlled by varying the voltage across the piezo-stacks. An open-loop control scheme demonstrates the frequency modulation capabilities that are enabled with this design: very large frequency deviations (up to ±500 Hz) around the actuator design frequency are attained at very high rates (up to 1 kHz). Closed-loop control of the microactuator's frequency was also demonstrated, and the results indicate that (combined with appropriate sensors) this actuator could be used effectively for active, feedback control in high-speed, resonance-dominated flowfields. This proof of concept study clearly illustrates the ability of this robust and compact actuator to produce perturbations that can be modulated and controlled based on the desired control objective. (paper)

  20. Sensitivity analysis of the stiffness between the frame structure and the frequency and vibration mode

    Chen, Wenyuan

    2018-03-01

    The modal parameters such as natural frequency and vibration mode of the frame structure of the layer stiffness sensitivity is inconsistent. This article focuses on the theoretical derivation of the frequency and mode of the frame structure layer stiffness of the first-order sensitivity. The numerical examples show that the frame structure of layer stiffness higher than with the first order sensitivity vibration frequency.

  1. How to deal with Haplotype data: An Extension to the Conceptual Schema of the Human Genome

    José Fabián Reyes Román

    2016-12-01

    Full Text Available The goal of this work is to describe the advantages of the application of Conceptual Modeling (CM in complex domains, such as genomics. Nowadays, the study and comprehension of the human genome is a major challenge due to its high level of complexity. The constant evolution in the genomic domain contributes to the generation of ever larger amounts of new data, which means that if we do not manage it correctly data quality could be compromised (i.e., problems related with heterogeneity and inconsistent data. In this paper, we propose the use of a Conceptual Schema of the Human Genome (CSHG, designed to understand and improve our ontological commitment to the domain and also extend (enrich this schema with the integration of a novel concept: Haplotypes. Our focus is on improving the understanding of the relationship between genotype and phenotype, since new findings show that this question is more complex than was originally thought. Here we present the first steps in our data management approach with haplotypes (variations, frequencies and populations and discuss the database evolution to support this data. Each new version in our conceptual schema (CS introduces changes to the underlying database structure that has essential and practical implications for better understanding and managing the relevant information. A solution based on conceptual models gives a clear definition of the domain with direct implications in the medical field (Precision Medicine, in which Genomic Information Systems (GeIS play a very important role.

  2. Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition

    Sun Ah Kim

    2016-12-01

    Full Text Available Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine, MIG++ implemented in PLINK 1.9 and S-MIG++. We used several experimental datasets obtained by sampling subsets of single nucleotide polymorphism (SNP markers of chromosome 22 region in the 1000 Genomes Project data and also the HapMap phase 3 data to compare the results of haplotype block partitions by five methods. With decreasing sampling ratio down to 20% of the original SNP markers, the total number of haplotype blocks decreases and the length of haplotype blocks increases for all algorithms. When we examined the marker-independence of the haplotype block locations constructed from the datasets of different density, the results using below 50% of the entire SNP markers were very different from the results using the entire SNP markers. We conclude that the haplotype block construction results should be used and interpreted carefully depending on the selection of markers and the purpose of the study.

  3. Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control

    Bing Li

    2012-04-01

    Full Text Available In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results.

  4. Haplotypes of CYP3A4 and their close linkage with CYP3A5 haplotypes in a Japanese population.

    Fukushima-Uesaka, Hiromi; Saito, Yoshiro; Watanabe, Hidemi; Shiseki, Kisho; Saeki, Mayumi; Nakamura, Takahiro; Kurose, Kouichi; Sai, Kimie; Komamura, Kazuo; Ueno, Kazuyuki; Kamakura, Shiro; Kitakaze, Masafumi; Hanai, Sotaro; Nakajima, Toshiharu; Matsumoto, Kenji; Saito, Hirohisa; Goto, Yu-ichi; Kimura, Hideo; Katoh, Masaaki; Sugai, Kenji; Minami, Narihiro; Shirao, Kuniaki; Tamura, Tomohide; Yamamoto, Noboru; Minami, Hironobu; Ohtsu, Atsushi; Yoshida, Teruhiko; Saijo, Nagahiro; Kitamura, Yutaka; Kamatani, Naoyuki; Ozawa, Shogo; Sawada, Jun-ichi

    2004-01-01

    In order to identify single nucleotide polymorphisms (SNPs) and haplotype frequencies of CYP3A4 in a Japanese population, the distal enhancer and proximal promoter regions, all exons, and the surrounding introns were sequenced from genomic DNA of 416 Japanese subjects. We found 24 SNPs, including 17 novel ones: two in the distal enhancer, four in the proximal promoter, one in the 5'-untranslated region (UTR), seven in the introns, and three in the 3'-UTR. The most common SNP was c.1026+12G>A (IVS10+12G>A), with a 0.249 frequency. Four non-synonymous SNPs, c.554C>G (p.T185S, CYP3A4(*)16), c.830_831insA (p.E277fsX8, (*)6), c.878T>C (p.L293P, (*)18), and c.1088 C>T (p.T363M, (*)11) were found with frequencies of 0.014, 0.001, 0.028, and 0.002, respectively. No SNP was found in the known nuclear transcriptional factor-binding sites in the enhancer and promoter regions. Using these 24 SNPs, 16 haplotypes were unambiguously identified, and nine haplotypes were inferred by aid of an expectation-maximization-based program. In addition, using data from 186 subjects enabled a close linkage to be found between CYP3A4 and CYP3A5 SNPs, especially among the SNPs at c.1026+12 in CYP3A4 and c.219-237 (IVS3-237, a key SNP site for CYP3A5(*)3), c.865+77 (IVS9+77) and c.1523 in CYP3A5. This result suggested that CYP3A4 and CYP3A5 are within the same gene block. Haplotype analysis between CYP3A4 and CYP3A5 revealed several major haplotype combinations in the CYP3A4-CYP3A5 block. Our findings provide fundamental and useful information for genotyping CYP3A4 (and CYP3A5) in the Japanese, and probably Asian populations. Copyright 2003 Wiley-Liss, Inc.

  5. Y-chromosome STR haplotypes in Somalis

    Hallenberg, Charlotte; Simonsen, Bo; Sanchez Sanchez, Juan Jose

    2005-01-01

    A total of 201 males from Somalia were typed for the Y-chromosome STRs DYS19, DYS385a/b, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 with the PowerPlex Y kit (Promega). A total of 96 different haplotypes were observed and the haplotype diversity was 0.9715. The ......A total of 201 males from Somalia were typed for the Y-chromosome STRs DYS19, DYS385a/b, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 with the PowerPlex Y kit (Promega). A total of 96 different haplotypes were observed and the haplotype diversity was 0...

  6. Syllable Frequency and Syllable Structure in Apraxia of Speech

    Aichert, Ingrid; Ziegler, Wolfram

    2004-01-01

    Recent accounts of the pathomechanism underlying apraxia of speech (AOS) were based on the speech production model of Levelt, Roelofs, and Meyer, and Meyer (1999)1999. The apraxic impairment was localized to the phonetic encoding level where the model postulates a mental store of motor programs for high-frequency syllables. Varley and Whiteside…

  7. Frequency effects and structural change – the Afrikaans preterite

    According to emergent grammar and exemplar theory in cognitive linguistics, the frequency of an item affects its ... cognitive representation of language and language processing, and illustrates how the use of language .... large clouds of recalled tokens of specific categories, which is organised in a cognitive map where.

  8. Fundamental problem of forensic mathematics--the evidential value of a rare haplotype.

    Brenner, Charles H

    2010-10-01

    Y-chromosomal and mitochondrial haplotyping offer special advantages for criminal (and other) identification. For different reasons, each of them is sometimes detectable in a crime stain for which autosomal typing fails. But they also present special problems, including a fundamental mathematical one: When a rare haplotype is shared between suspect and crime scene, how strong is the evidence linking the two? Assume a reference population sample is available which contains n-1 haplotypes. The most interesting situation as well as the most common one is that the crime scene haplotype was never observed in the population sample. The traditional tools of product rule and sample frequency are not useful when there are no components to multiply and the sample frequency is zero. A useful statistic is the fraction κ of the population sample that consists of "singletons" - of once-observed types. A simple argument shows that the probability for a random innocent suspect to match a previously unobserved crime scene type is (1-κ)/n - distinctly less than 1/n, likely ten times less. The robust validity of this model is confirmed by testing it against a range of population models. This paper hinges above all on one key insight: probability is not frequency. The common but erroneous "frequency" approach adopts population frequency as a surrogate for matching probability and attempts the intractable problem of guessing how many instances exist of the specific haplotype at a certain crime. Probability, by contrast, depends by definition only on the available data. Hence if different haplotypes but with the same data occur in two different crimes, although the frequencies are different (and are hopelessly elusive), the matching probabilities are the same, and are not hard to find. Copyright © 2009 Elsevier Ireland Ltd. All rights reserved.

  9. Definition of novel GP6 polymorphisms and major difference in haplotype frequencies between populations by a combination of in-depth exon resequencing and genotyping with tag single nucleotide polymorphisms.

    Watkins, N A; O'Connor, M N; Rankin, A; Jennings, N; Wilson, E; Harmer, I J; Davies, L; Smethurst, P A; Dudbridge, F; Farndale, R W; Ouwehand, W H

    2006-06-01

    Common genetic variants of cell surface receptors contribute to differences in functional responses and disease susceptibility. We have previously shown that single nucleotide polymorphisms (SNPs) in platelet glycoprotein VI (GP6) determine the extent of response to agonist. In addition, SNPs in the GP6 gene have been proposed as risk factors for coronary artery disease. To completely characterize genetic variation in the GP6 gene we generated a high-resolution SNP map by sequencing the promoter, exons and consensus splice sequences in 94 non-related Caucasoids. In addition, we sequenced DNA encoding the ligand-binding domains of GP6 from non-human primates to determine the level of evolutionary conservation. Eighteen SNPs were identified, six of which encoded amino acid substitutions in the mature form of the protein. The single non-synonymous SNP identified in the exons encoding the ligand-binding domains, encoding for a 103Leu > Val substitution, resulted in reduced ligand binding. Two common protein isoforms were confirmed in Caucasoid with frequencies of 0.82 and 0.15. Variation at the GP6 locus was characterized further by determining SNP frequency in over 2000 individuals from different ethnic backgrounds. The SNPs were polymorphic in all populations studied although significant differences in allele frequencies were observed. Twelve additional GP6 protein isoforms were identified from the genotyping results and, despite extensive variation in GP6, the sequence of the ligand-binding domains is conserved. Sequences from non-human primates confirmed this observation. These data provide valuable information for the optimal selection of genetic variants for use in future association studies.

  10. Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2.

    Sébastien Fritz

    Full Text Available The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1% showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals. Thirty-four candidate haplotypes (p<10(-4 including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total. Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina, SLC35A3 (CVM, APAF1 (HH1 and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.

  11. Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2.

    Fritz, Sébastien; Capitan, Aurelien; Djari, Anis; Rodriguez, Sabrina C; Barbat, Anne; Baur, Aurélia; Grohs, Cécile; Weiss, Bernard; Boussaha, Mekki; Esquerré, Diane; Klopp, Christophe; Rocha, Dominique; Boichard, Didier

    2013-01-01

    The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (pHH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.

  12. Detection of Haplotypes Associated with Prenatal Death in Dairy Cattle and Identification of Deleterious Mutations in GART, SHBG and SLC37A2

    Fritz, Sébastien; Capitan, Aurelien; Djari, Anis; Rodriguez, Sabrina C.; Barbat, Anne; Baur, Aurélia; Grohs, Cécile; Weiss, Bernard; Boussaha, Mekki; Esquerré, Diane; Klopp, Christophe; Rocha, Dominique; Boichard, Didier

    2013-01-01

    The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10−4) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle. PMID:23762392

  13. Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants

    2014-01-01

    Background Following transmission, HIV-1 evolves into a diverse population, and next generation sequencing enables us to detect variants occurring at low frequencies. Studying viral evolution at the level of whole genomes was hitherto not possible because next generation sequencing delivers relatively short reads. Results We here provide a proof of principle that whole HIV-1 genomes can be reliably reconstructed from short reads, and use this to study the selection of immune escape mutations at the level of whole genome haplotypes. Using realistically simulated HIV-1 populations, we demonstrate that reconstruction of complete genome haplotypes is feasible with high fidelity. We do not reconstruct all genetically distinct genomes, but each reconstructed haplotype represents one or more of the quasispecies in the HIV-1 population. We then reconstruct 30 whole genome haplotypes from published short sequence reads sampled longitudinally from a single HIV-1 infected patient. We confirm the reliability of the reconstruction by validating our predicted haplotype genes with single genome amplification sequences, and by comparing haplotype frequencies with observed epitope escape frequencies. Conclusions Phylogenetic analysis shows that the HIV-1 population undergoes selection driven evolution, with successive replacement of the viral population by novel dominant strains. We demonstrate that immune escape mutants evolve in a dependent manner with various mutations hitchhiking along with others. As a consequence of this clonal interference, selection coefficients have to be estimated for complete haplotypes and not for individual immune escapes. PMID:24996694

  14. Explicit solution for the natural frequency of structures with partial viscoelastic treatment

    Høgsberg, Jan Becker

    2016-01-01

    The free vibration characteristics of structures with viscoelastic treatment are represented by the complex-valued natural frequencies. The assumed single mode representation associated with the low-frequency stiffness of the viscoelastic treatment is modified by a correction term representing the influence from residual vibration modes. The correction term is eliminated in terms of the corresponding natural frequency associated with the high-frequency stiffness of the viscoelastic treatment,...

  15. Distribution pattern of Plasmodium falciparum chloroquine transporter (pfcrt) gene haplotypes in Sri Lanka 1996-2006

    Zhang, Jenny J; Senaratne, Tharanga N; Daniels, Rachel

    2011-01-01

    Abstract. Widespread antimalarial resistance has been a barrier to malaria elimination efforts in Sri Lanka. Analysis of genetic markers in historic parasites may uncover trends in the spread of resistance. We examined the frequency of Plasmodium falciparum chloroquine transporter (pfcrt; codons 72......-76) haplotypes in Sri Lanka in 1996-1998 and 2004-2006 using a high-resolution melting assay. Among 59 samples from 1996 to 1998, we detected the SVMNT (86%), CVMNK (10%), and CVIET (2%) haplotypes, with a positive trend in SVMNT and a negative trend in CVMNK frequency (P = 0.004) over time. Among 24 samples...

  16. Time-frequency Methods for Structural Health Monitoring

    Pyayt, A.L.; Kozionov, A.P.; Mokhov, I.I.; Lang, B.; Meijer, R.J.; Krzhizhanovskaya, V.V.; Sloot, P.M.A.

    2014-01-01

    Detection of early warning signals for the imminent failure of large and complex engineered structures is a daunting challenge with many open research questions. In this paper we report on novel ways to perform Structural Health Monitoring (SHM) of flood protection systems (levees, earthen dikes and

  17. Time-frequency methods for structural health monitoring

    Pyayt, A.L.; Kozionov, A.P.; Mokhov, I.I.; Lang, B.; Meijer, R.J.; Krzhizhanovskaya, V.V.; Sloot, P.M.A.

    2014-01-01

    Detection of early warning signals for the imminent failure of large and complex engineered structures is a daunting challenge with many open research questions. In this paper we report on novel ways to perform Structural Health Monitoring (SHM) of flood protection systems (levees, earthen dikes and

  18. New fractal structures for frequencies close to the visible range

    Malureanu, Radu; Sandru, A.; Andryieuski, Andrei

    2011-01-01

    In this paper we present a new type of fractal resonator to be used in the red/NIR region of the spectra. The structure presents high-transmission band in 795-825nm range. The stop band is in the 683-731 nm range. Due to the huge difference in the spectra within such a short range, the structure...

  19. Unique haplotypes of cacao trees as revealed by trnH-psbA chloroplast DNA

    Nidia Gutiérrez-López

    2016-04-01

    Full Text Available Cacao trees have been cultivated in Mesoamerica for at least 4,000 years. In this study, we analyzed sequence variation in the chloroplast DNA trnH-psbA intergenic spacer from 28 cacao trees from different farms in the Soconusco region in southern Mexico. Genetic relationships were established by two analysis approaches based on geographic origin (five populations and genetic origin (based on a previous study. We identified six polymorphic sites, including five insertion/deletion (indels types and one transversion. The overall nucleotide diversity was low for both approaches (geographic = 0.0032 and genetic = 0.0038. Conversely, we obtained moderate to high haplotype diversity (0.66 and 0.80 with 10 and 12 haplotypes, respectively. The common haplotype (H1 for both networks included cacao trees from all geographic locations (geographic approach and four genetic groups (genetic approach. This common haplotype (ancient derived a set of intermediate haplotypes and singletons interconnected by one or two mutational steps, which suggested directional selection and event purification from the expansion of narrow populations. Cacao trees from Soconusco region were grouped into one cluster without any evidence of subclustering based on AMOVA (FST = 0 and SAMOVA (FST = 0.04393 results. One population (Mazatán showed a high haplotype frequency; thus, this population could be considered an important reservoir of genetic material. The indels located in the trnH-psbA intergenic spacer of cacao trees could be useful as markers for the development of DNA barcoding.

  20. Cluster analysis of European Y-chromosomal STR haplotypes using the discrete Laplace method

    Andersen, Mikkel Meyer; Eriksen, Poul Svante; Morling, Niels

    2014-01-01

    The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models the probabi......The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models...... the probability distribution of the Y-STR haplotypes. Creating a consistent statistical model of the haplotypes enables us to perform a wide range of analyses. Previously, haplotype frequency estimation using the discrete Laplace method has been validated. In this paper we investigate how the discrete Laplace...... method can be used for cluster analysis to further validate the discrete Laplace method. A very important practical fact is that the calculations can be performed on a normal computer. We identified two sub-clusters of the Eastern and Western European Y-STR haplotypes similar to results of previous...

  1. Endothelial Nitric Oxide Synthase Haplotypes Are Associated with Preeclampsia in Maya Mestizo Women

    Díaz-Olguín, Lizbeth; Coral-Vázquez, Ramón Mauricio; Canto-Cetina, Thelma; Canizales-Quinteros, Samuel; Ramírez Regalado, Belem; Fernández, Genny; Canto, Patricia

    2011-01-01

    Preeclampsia is a specific disease of pregnancy and believed to have a genetic component. The aim of this study was to investigate if three polymorphisms in eNOS or their haplotypes are associated with preeclampsia in Maya mestizo women. A case-control study was performed where 127 preeclamptic patients and 263 controls were included. Genotyped and haplotypes for the -768T→C, intron 4 variants, Glu298Asp of eNOS were determined by PCR and real-time PCR allelic discrimination. Logistic regression analysis with adjustment for age and body mass index (BMI) was used to test for associations between genotype and preeclampsia under recessive, codominant and dominant models. Pairwise linkage disequilibrium between single nucleotide polymorphisms was calculated by direct correlation r2, and haplotype analysis was conducted. Women homozygous for the Asp298 allele showed an association of preeclampsia. In addition, analysis of the haplotype frequencies revealed that the -786C-4b-Asp298 haplotype was significantly more frequent in preeclamptic patients than in controls (0.143 vs. 0.041, respectively; OR = 3.01; 95% CI = 1.74–5.23; P = 2.9 × 10−4). Despite the Asp298 genotype in a recessive model associated with the presence of preeclampsia in Maya mestizo women, we believe that in this population the -786C-4b-Asp298 haplotype is a better genetic marker. PMID:21897002

  2. The JAK2 GGCC (46/1 Haplotype in Myeloproliferative Neoplasms: Causal or Random?

    Luisa Anelli

    2018-04-01

    Full Text Available The germline JAK2 haplotype known as “GGCC or 46/1 haplotype” (haplotypeGGCC_46/1 consists of a combination of single nucleotide polymorphisms (SNPs mapping in a region of about 250 kb, extending from the JAK2 intron 10 to the Insulin-like 4 (INLS4 gene. Four main SNPs (rs3780367, rs10974944, rs12343867, and rs1159782 generating a “GGCC” combination are more frequently indicated to represent the JAK2 haplotype. These SNPs are inherited together and are frequently associated with the onset of myeloproliferative neoplasms (MPN positive for both JAK2 V617 and exon 12 mutations. The association between the JAK2 haplotypeGGCC_46/1 and mutations in other genes, such as thrombopoietin receptor (MPL and calreticulin (CALR, or the association with triple negative MPN, is still controversial. This review provides an overview of the frequency and the role of the JAK2 haplotypeGGCC_46/1 in the pathogenesis of different myeloid neoplasms and describes the hypothetical mechanisms at the basis of the association with JAK2 gene mutations. Moreover, possible clinical implications are discussed, as different papers reported contrasting data about the correlation between the JAK2 haplotypeGGCC_46/1 and blood cell count, survival, or disease progression.

  3. Interrelationships between Amerindian tribes of lower Amazonia as manifest by HLA haplotype disequilibria.

    Black, F L

    1984-11-01

    HLA B-C haplotypes exhibit common disequilibria in populations drawn from four continents, indicating that they are subject to broadly active selective forces. However, the A-B and A-C associations we have examined show no consistent disequilibrium pattern, leaving open the possibility that these disequilibria are due to descent from common progenitors. By examining HLA haplotype distributions, I have explored the implications that would follow from the hypothesis that biological selection played no role in determining A-C disequilibria in 10 diverse tribes of the lower Amazon Basin. Certain haplotypes are in strong positive disequilibria across a broad geographic area, suggesting that members of diverse tribes descend from common ancestors. On the basis of the extent of diffusion of the components of these haplotypes, one can estimate that the progenitors lived less than 6,000 years ago. One widely encountered lineage entered the area within the last 1,200 years. When haplotype frequencies are used in genetic distance measurements, they give a pattern of relationships very similar to that obtained by conventional chord measurements based on several genetic markers; but more than that, when individual haplotype disequilibria in the several tribes are compared, multiple origins of a single tribe are discernible and relationships are revealed that correlate more closely to geographic and linguistic patterns than do the genetic distance measurements.

  4. An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression.

    Tokiho Akiyama

    Full Text Available Humans show various responses to the environmental stimulus in individual levels as "physiological variations." However, it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological data from 43 subjects, including light-induced melatonin suppression, and performed haplotype analyses on the clock genes, PER2 and PER3, exhibiting geographical differentiation of allele frequencies. Among the haplotypes of PER3, no significant difference in light sensitivity was found. However, three common haplotypes of PER2 accounted for more than 96% of the chromosomes in subjects, and 1 of those 3 had a significantly low-sensitive response to light-stimulus (P < 0.05. The homozygote of the low-sensitive PER2 haplotype showed significantly lower percentages of melatonin suppression (P < 0.05, and the heterozygotes of the haplotypes varied their ratios, indicating that the physiological variation for light-sensitivity is evidently related to the PER2 polymorphism. Compared with global haplotype frequencies, the haplotype with a low-sensitive response was more frequent in Africans than in non-Africans, and came to the root in the phylogenetic tree, suggesting that the low light-sensitive haplotype is the ancestral type, whereas the other haplotypes with high sensitivity to light are the derived types. Hence, we speculate that the high light-sensitive haplotypes have spread throughout the world after the Out-of-Africa migration of modern humans.

  5. Language learners privilege structured meaning over surface frequency

    Culbertson, Jennifer; Adger, David

    2014-01-01

    Although it is widely agreed that learning the syntax of natural languages involves acquiring structure-dependent rules, recent work on acquisition has nevertheless attempted to characterize the outcome of learning primarily in terms of statistical generalizations about surface distributional information. In this paper we investigate whether surface statistical knowledge or structural knowledge of English is used to infer properties of a novel language under conditions of impoverished input. We expose learners to artificial-language patterns that are equally consistent with two possible underlying grammars—one more similar to English in terms of the linear ordering of words, the other more similar on abstract structural grounds. We show that learners’ grammatical inferences overwhelmingly favor structural similarity over preservation of superficial order. Importantly, the relevant shared structure can be characterized in terms of a universal preference for isomorphism in the mapping from meanings to utterances. Whereas previous empirical support for this universal has been based entirely on data from cross-linguistic language samples, our results suggest it may reflect a deep property of the human cognitive system—a property that, together with other structure-sensitive principles, constrains the acquisition of linguistic knowledge. PMID:24706789

  6. Low Frequency Vibration approach to asess the Performance of wood structural Systems

    Xiping Wang; Robert J. Ross; Michael O. Hunt

    2004-01-01

    The primary means of inspecting buildings and other structures is to evaluate each structure member individually. This is a time consuming process that is expensive, particularly if sheathing or other covering materials must be removed to access the structural members. This paper presents an effort to use a low frequency vibration method for assessing the structural...

  7. HLA alleles and haplotypes in Burmese (Myanmarese) and Karen in Thailand.

    Kongmaroeng, C; Romphruk, A; Puapairoj, C; Leelayuwat, C; Kulski, J K; Inoko, H; Dunn, D S; Romphruk, A V

    2015-09-01

    This is the first report on human leukocyte antigen (HLA) allele and haplotype frequencies at three class I loci and two class II loci in unrelated healthy individuals from two ethnic groups, 170 Burmese and 200 Karen, originally from Burma (Myanmar), but sampled while residing in Thailand. Overall, the HLA allele and haplotype frequencies detected by polymerase chain reaction sequence-specific primer (PCR-SSP) at five loci (A, B, C, DRB1 and DRQB1) at low resolution showed distinct differences between the Burmese and Karen. In Burmese, five HLA-B*15 haplotypes with different HLA-A and HLA-DR/DQ combinations were detected with three of these not previously reported in other Asian populations. The data are important in the fields of anthropology, transplantation and disease-association studies. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules.

    Sun, Weitao

    2018-01-01

    The global shape of a protein molecule is believed to be dominant in determining low-frequency deformational motions. However, how structure dynamics relies on residue interactions remains largely unknown. The global residue community structure and the local residue interactions are two important coexisting factors imposing significant effects on low-frequency normal modes. In this work, an algorithm for community structure partition is proposed by integrating Miyazawa-Jernigan empirical potential energy as edge weight. A sensitivity parameter is defined to measure the effect of local residue interaction on low-frequency movement. We show that community structure is a more fundamental feature of residue contact networks. Moreover, we surprisingly find that low-frequency normal mode eigenvectors are sensitive to some local critical residue interaction pairs (CRIPs). A fair amount of CRIPs act as bridges and hold distributed structure components into a unified tertiary structure by bonding nearby communities. Community structure analysis and CRIP detection of 116 catalytic proteins reveal that breaking up of a CRIP can cause low-frequency allosteric movement of a residue at the far side of protein structure. The results imply that community structure and CRIP may be the structural basis for low-frequency motions.

  9. EEMD-MUSIC-Based Analysis for Natural Frequencies Identification of Structures Using Artificial and Natural Excitations

    David Camarena-Martinez

    2014-01-01

    Full Text Available This paper presents a new EEMD-MUSIC- (ensemble empirical mode decomposition-multiple signal classification- based methodology to identify modal frequencies in structures ranging from free and ambient vibration signals produced by artificial and natural excitations and also considering several factors as nonstationary effects, close modal frequencies, and noisy environments, which are common situations where several techniques reported in literature fail. The EEMD and MUSIC methods are used to decompose the vibration signal into a set of IMFs (intrinsic mode functions and to identify the natural frequencies of a structure, respectively. The effectiveness of the proposed methodology has been validated and tested with synthetic signals and under real operating conditions. The experiments are focused on extracting the natural frequencies of a truss-type scaled structure and of a bridge used for both highway traffic and pedestrians. Results show the proposed methodology as a suitable solution for natural frequencies identification of structures from free and ambient vibration signals.

  10. EEMD-MUSIC-Based Analysis for Natural Frequencies Identification of Structures Using Artificial and Natural Excitations

    Amezquita-Sanchez, Juan P.; Romero-Troncoso, Rene J.; Osornio-Rios, Roque A.; Garcia-Perez, Arturo

    2014-01-01

    This paper presents a new EEMD-MUSIC- (ensemble empirical mode decomposition-multiple signal classification-) based methodology to identify modal frequencies in structures ranging from free and ambient vibration signals produced by artificial and natural excitations and also considering several factors as nonstationary effects, close modal frequencies, and noisy environments, which are common situations where several techniques reported in literature fail. The EEMD and MUSIC methods are used to decompose the vibration signal into a set of IMFs (intrinsic mode functions) and to identify the natural frequencies of a structure, respectively. The effectiveness of the proposed methodology has been validated and tested with synthetic signals and under real operating conditions. The experiments are focused on extracting the natural frequencies of a truss-type scaled structure and of a bridge used for both highway traffic and pedestrians. Results show the proposed methodology as a suitable solution for natural frequencies identification of structures from free and ambient vibration signals. PMID:24683346

  11. Low frequency torsional vibration gaps in the shaft with locally resonant structures

    Yu Dianlong; Liu Yaozong; Wang Gang; Cai Li; Qiu Jing

    2006-01-01

    The propagation of torsional wave in the shaft with periodically attached local resonators is studied with the transfer matrix theory and the finite element method. The analytical dispersion relation and the complex band structure of such a structure is presented for the first time, which indicates the existence of low frequency gaps. The effect of shaft material on the vibration attenuation in band gap is investigated. The frequency response function of the shaft with finite periodic locally resonant oscillators is simulated with finite element method, which shows large vibration attenuation in the frequency range of the gap as expected. The low frequency torsional gap in shafts provides a new idea for vibration control

  12. Estimating haplotype effects for survival data.

    Scheike, Thomas H; Martinussen, Torben; Silver, Jeremy D

    2010-09-01

    Genetic association studies often investigate the effect of haplotypes on an outcome of interest. Haplotypes are not observed directly, and this complicates the inclusion of such effects in survival models. We describe a new estimating equations approach for Cox's regression model to assess haplotype effects for survival data. These estimating equations are simple to implement and avoid the use of the EM algorithm, which may be slow in the context of the semiparametric Cox model with incomplete covariate information. These estimating equations also lead to easily computable, direct estimators of standard errors, and thus overcome some of the difficulty in obtaining variance estimators based on the EM algorithm in this setting. We also develop an easily implemented goodness-of-fit procedure for Cox's regression model including haplotype effects. Finally, we apply the procedures presented in this article to investigate possible haplotype effects of the PAF-receptor on cardiovascular events in patients with coronary artery disease, and compare our results to those based on the EM algorithm. © 2009, The International Biometric Society.

  13. Adjoint sensitivity analysis of high frequency structures with Matlab

    Bakr, Mohamed; Demir, Veysel

    2017-01-01

    This book covers the theory of adjoint sensitivity analysis and uses the popular FDTD (finite-difference time-domain) method to show how wideband sensitivities can be efficiently estimated for different types of materials and structures. It includes a variety of MATLAB® examples to help readers absorb the content more easily.

  14. A broadband frequency-tunable dynamic absorber for the vibration control of structures

    Komatsuzaki, T; Inoue, T; Terashima, O

    2016-01-01

    A passive-type dynamic vibration absorber (DVA) is basically a mass-spring system that suppresses the vibration of a structure at a particular frequency. Since the natural frequency of the DVA is usually tuned to a frequency of particular excitation, the DVA is especially effective when the excitation frequency is close to the natural frequency of the structure. Fixing the physical properties of the DVA limits the application to a narrowband, harmonically excited vibration problem. A frequency-tunable DVA that can modulate its stiffness provides adaptability to the vibration control device against non-stationary disturbances. In this paper, we suggest a broadband frequency-tunable DVA whose natural frequency can be extended by 300% to the nominal value using the magnetorheological elastomers (MREs). The frequency adjustability of the proposed absorber is first shown. The real-time vibration control performance of the frequency-tunable absorber for an acoustically excited plate having multiple resonant peaks is then evaluated. Investigations show that the vibration of the structure can be effectively reduced with an improved performance by the DVA in comparison to the conventional passive- type absorber. (paper)

  15. Eulerian frequency analysis of structural vibrations from high-speed video

    Venanzoni, Andrea; De Ryck, Laurent; Cuenca, Jacques

    2016-01-01

    An approach for the analysis of the frequency content of structural vibrations from high-speed video recordings is proposed. The techniques and tools proposed rely on an Eulerian approach, that is, using the time history of pixels independently to analyse structural motion, as opposed to Lagrangian approaches, where the motion of the structure is tracked in time. The starting point is an existing Eulerian motion magnification method, which consists in decomposing the video frames into a set of spatial scales through a so-called Laplacian pyramid [1]. Each scale — or level — can be amplified independently to reconstruct a magnified motion of the observed structure. The approach proposed here provides two analysis tools or pre-amplification steps. The first tool provides a representation of the global frequency content of a video per pyramid level. This may be further enhanced by applying an angular filter in the spatial frequency domain to each frame of the video before the Laplacian pyramid decomposition, which allows for the identification of the frequency content of the structural vibrations in a particular direction of space. This proposed tool complements the existing Eulerian magnification method by amplifying selectively the levels containing relevant motion information with respect to their frequency content. This magnifies the displacement while limiting the noise contribution. The second tool is a holographic representation of the frequency content of a vibrating structure, yielding a map of the predominant frequency components across the structure. In contrast to the global frequency content representation of the video, this tool provides a local analysis of the periodic gray scale intensity changes of the frame in order to identify the vibrating parts of the structure and their main frequencies. Validation cases are provided and the advantages and limits of the approaches are discussed. The first validation case consists of the frequency content

  16. Complex modes and frequencies in damped structural vibrations

    Krenk, Steen

    2004-01-01

    It is demonstrated that the state space formulation of the equation of motion of damped structural elements like cables and beams leads to a symmetric eigenvalue problem if the stiffness and damping operators are self-adjoint, and that this is typically the case in the absence of gyroscopic forces....... The corresponding theory of complex modal analysis of continuous systems is developed and illustrated in relation to optimal damping and impulse response of cables and beams with discrete dampers....

  17. Finite-element method modeling of hyper-frequency structures

    Zhang, Min

    1990-01-01

    The modelization of microwave propagation problems, including Eigen-value problem and scattering problem, is accomplished by the finite element method with vector functional and scalar functional. For Eigen-value problem, propagation modes in waveguides and resonant modes in cavities can be calculated in a arbitrarily-shaped structure with inhomogeneous material. Several microwave structures are resolved in order to verify the program. One drawback associated with the vector functional is the appearance of spurious or non-physical solutions. A penalty function method has been introduced to reduce spurious' solutions. The adaptive charge method is originally proposed in this thesis to resolve waveguide scattering problem. This method, similar to VSWR measuring technique, is more efficient to obtain the reflection coefficient than the matrix method. Two waveguide discontinuity structures are calculated by the two methods and their results are compared. The adaptive charge method is also applied to a microwave plasma excitor. It allows us to understand the role of different physical parameters of excitor in the coupling of microwave energy to plasma mode and the mode without plasma. (author) [fr

  18. Soil-structure interaction analysis of NPP containments: substructure and frequency domain methods

    Venancio-Filho, F.; Almeida, M.C.F.; Ferreira, W.G.; De Barros, F.C.P.

    1997-01-01

    Substructure and frequency domain methods for soil-structure interaction are addressed in this paper. After a brief description of mathematical models for the soil and of excitation, the equations for dynamic soil-structure interaction are developed for a rigid surface foundation and for an embedded foundation. The equations for the frequency domain analysis of MDOF systems are provided. An example of soil-structure interaction analysis with frequency-dependent soil properties is given and examples of identification of foundation impedance functions and soil properties are presented. (orig.)

  19. Low frequency phononic band structures in two-dimensional arc-shaped phononic crystals

    Xu, Zhenlong; Wu, Fugen; Guo, Zhongning

    2012-01-01

    The low frequency phononic band structures of two-dimensional arc-shaped phononic crystals (APCs) were studied by the transfer matrix method in cylindrical coordinates. The results showed the first phononic band gaps (PBGs) of APCs from zero Hz with low modes. Locally resonant (LR) gaps were obtained with higher-order rotation symmetry, due to LR frequencies corresponding to the speeds of acoustic waves in the materials. These properties can be efficiently used in a structure for low frequencies that are forbidden, or in a device that permits a narrow window of frequencies. -- Highlights: ► We report a new class of quasi-periodic hetero-structures, arc-shaped phononic crystals (APCs). ► The results show the first PBGs start with zero Hz with low modes. ► Locally resonant (LR) gaps were obtained with higher-order rotation symmetry, due to LR frequencies corresponding to the speeds of acoustic waves in the materials.

  20. Low-frequency features of the ultrasound echo from an adhesively bonded layer-substrate structure

    WANG Xiaomin; LI Mingxuan; MAO Jie; LIAN Guoxuan

    2005-01-01

    The low-frequency features of the ultrasound reflection spectra from the structure of a single layer on a substrate bonded by a thin adhesive layer are theoretically studied; the low-frequency here means the frequency of the interrogating ultrasonic wave is less than the quart-wavelength resonance frequency of the adhesive layer. The possibility of the inversion of the thickness and the evaluation of the cohesion strength of the adhesive layer from the resonance frequency shifts of the layered system is indicated. An analytic solution to the nonlinear equation satisfied by the resonance frequency is presented by Taylor expansion method showing satisfactory agreement with the numerical results by Newton iterative method. The results indicate larger range for application than the traditional spring model for the thin adhesive layer. In a much lower frequency range the thin adhesive layer may be regarded to be a spring.

  1. Divergence at the casein haplotypes in dairy and meat goat breeds.

    Küpper, Julia; Chessa, Stefania; Rignanese, Daniela; Caroli, Anna; Erhardt, Georg

    2010-02-01

    Casein genes have been proved to have an influence on milk properties, and are in addition appropriate for phylogeny studies. A large number of casein polymorphisms exist in goats, making their analysis quite complex. The four casein loci were analyzed by molecular techniques for genetic polymorphism detection in the two dairy goat breeds Bunte Deutsche Edelziege (BDE; n=96), Weisse Deutsche Edelziege (WDE; n=91), and the meat goat breed Buren (n=75). Of the 35 analyzed alleles, 18 were found in BDE, and 17 in Buren goats and WDE. In addition, a new allele was identified at the CSN1S1 locus in the BDE, showing a frequency of 0.05. This variant, named CSN1S1*A', is characterized by a t-->c transversion in intron 9. Linkage disequilibrium was found at the casein haplotype in all three breeds. A total of 30 haplotypes showed frequencies higher than 0.01. In the Buren breed only one haplotype showed a frequency higher than 0.1. The ancestral haplotype B-A-A-B (in the order: CSN1S1-CSN2-CSN1S2-CSN3) occurred in all three breeds, showing a very high frequency (>0.8) in the Buren.

  2. Explicit solution for the natural frequency of structures with partial viscoelastic treatment

    Høgsberg, Jan Becker

    2016-01-01

    The free vibration characteristics of structures with viscoelastic treatment are represented by the complex-valued natural frequencies. The assumed single mode representation associated with the low-frequency stiffness of the viscoelastic treatment is modified by a correction term representing...

  3. High-frequency permeability in double-layered structure of amorphous Co-Ta-Zr films

    Ochiai, Y.; Hayakawa, M.; Hayashi, K.; Aso, K.

    1988-01-01

    The high-frequency permeability of amorphous Co-Ta-Zr films was studied and the frequency dependence was described in terms of the eddy-current-loss formula. For the double-layered structure intervened with SiO 2 film, the degradation of the permeability became apparent with the decrease of SiO 2 thickness

  4. A Frequency-List of Sentence Structures: Distribution of Kernel Sentences

    Geens, Dirk

    1974-01-01

    A corpus of 10,000 sentences extracted from British theatrical texts was used to construct a frequency list of kernel sentence structures. Thirty-one charts illustrate the analyzed results. The procedures used and an interpretation of the frequencies are given. Such lists might aid foreign language teachers in course organization. Available from…

  5. Multi-cavity locally resonant structure with the low frequency and broad band-gaps

    Jiulong Jiang

    2016-11-01

    Full Text Available A multi-cavity periodic structure with the characteristic of local resonance was proposed in the paper. The low frequency band-gap structure was comparatively analyzed by the finite element method (FEM and electric circuit analogy (ECA. Low frequency band-gap can be opened through the dual influence of the coupling’s resonance in the cavity and the interaction among the couplings between structures. Finally, the influence of the structural factors on the band-gap was analyzed. The results show that the structure, which is divided into three parts equally, has a broader effective band-gap below the frequency of 200 Hz. It is also proved that reducing the interval between unit structures can increase the intensity of the couplings among the structures. And in this way, the width of band-gap would be expanded significantly. Through the parameters adjustment, the structure enjoys a satisfied sound insulation effect below the frequency of 500Hz. In the area of low frequency noise reduction, the structure has a lot of potential applications.

  6. Experimental modal analysis of fractal-inspired multi-frequency structures for piezoelectric energy converters

    Castagnetti, D

    2012-01-01

    An important issue in the field of energy harvesting through piezoelectric materials is the design of simple and efficient structures which are multi-frequency in the ambient vibration range. This paper deals with the experimental assessment of four fractal-inspired multi-frequency structures for piezoelectric energy harvesting. These structures, thin plates of square shape, were proposed in a previous work by the author and their modal response numerically analysed. The present work has two aims. First, to assess the modal response of these structures through an experimental investigation. Second, to evaluate, through computational simulation, the performance of a piezoelectric converter relying on one of these fractal-inspired structures. The four fractal-inspired structures are examined in the range between 0 and 100 Hz, with regard to both eigenfrequencies and eigenmodes. In the same frequency range, the modal response and power output of the piezoelectric converter are investigated. (paper)

  7. An open-structure sound insulator against low-frequency and wide-band acoustic waves

    Chen, Zhe; Fan, Li; Zhang, Shu-yi; Zhang, Hui; Li, Xiao-juan; Ding, Jin

    2015-10-01

    To block sound, i.e., the vibration of air, most insulators are based on sealed structures and prevent the flow of the air. In this research, an acoustic metamaterial adopting side structures, loops, and labyrinths, arranged along a main tube, is presented. By combining the accurately designed side structures, an extremely wide forbidden band with a low cut-off frequency of 80 Hz is produced, which demonstrates a powerful low-frequency and wide-band sound insulation ability. Moreover, by virtue of the bypass arrangement, the metamaterial is based on an open structure, and thus air flow is allowed while acoustic waves can be insulated.

  8. A comprehensive literature review of haplotyping software and methods for use with unrelated individuals

    Salem Rany M

    2005-03-01

    Full Text Available Abstract Interest in the assignment and frequency analysis of haplotypes in samples of unrelated individuals has increased immeasurably as a result of the emphasis placed on haplotype analyses by, for example, the International HapMap Project and related initiatives. Although there are many available computer programs for haplotype analysis applicable to samples of unrelated individuals, many of these programs have limitations and/or very specific uses. In this paper, the key features of available haplotype analysis software for use with unrelated individuals, as well as pooled DNA samples from unrelated individuals, are summarised. Programs for haplotype analysis were identified through keyword searches on PUBMED and various internet search engines, a review of citations from retrieved papers and personal communications, up to June 2004. Priority was given to functioning computer programs, rather than theoretical models and methods. The available software was considered in light of a number of factors: the algorithm(s used, algorithm accuracy, assumptions, the accommodation of genotyping error, implementation of hypothesis testing, handling of missing data, software characteristics and web-based implementations. Review papers comparing specific methods and programs are also summarised. Forty-six haplotyping programs were identified and reviewed. The programs were divided into two groups: those designed for individual genotype data (a total of 43 programs and those designed for use with pooled DNA samples (a total of three programs. The accuracy of programs using various criteria are assessed and the programs are categorised and discussed in light of: algorithm and method, accuracy, assumptions, genotyping error, hypothesis testing, missing data, software characteristics and web implementation. Many available programs have limitations (eg some cannot accommodate missing data and/or are designed with specific tasks in mind (eg estimating

  9. The Importance of Pressure Sampling Frequency in Models for Determination of Critical Wave Loadingson Monolithic Structures

    Burcharth, Hans F.; Andersen, Thomas Lykke; Meinert, Palle

    2008-01-01

    This paper discusses the influence of wave load sampling frequency on calculated sliding distance in an overall stability analysis of a monolithic caisson. It is demonstrated by a specific example of caisson design that for this kind of analyses the sampling frequency in a small scale model could...... be as low as 100 Hz in model scale. However, for design of structure elements like the wave wall on the top of a caisson the wave load sampling frequency must be much higher, in the order of 1000 Hz in the model. Elastic-plastic deformations of foundation and structure were not included in the analysis....

  10. Frequency splitter based on the directional emission from surface modes in dielectric photonic crystal structures.

    Tasolamprou, Anna C; Zhang, Lei; Kafesaki, Maria; Koschny, Thomas; Soukoulis, Costas M

    2015-06-01

    We demonstrate the numerical design and the experimental validation of frequency dependent directional emission from a dielectric photonic crystal structure. The wave propagates through a photonic crystal line-defect waveguide, while a surface layer at the termination of the photonic crystal enables the excitation of surface modes and a subsequent grating layer transforms the surface energy into outgoing propagating waves of the form of a directional beam. The angle of the beam is controlled by the frequency and the structure operates as a frequency splitter in the intermediate and far field region.

  11. Effect of High Frequency Pulsing on the Interfacial Structure of Anodised Aluminium-TiO2

    Gudla, Visweswara Chakravarthy; Jensen, Flemming; Bordo, Kirill

    2015-01-01

    High frequency anodizing of friction stir processed Al-TiO2 surface composites was investigated. The effect of anodizing parameters on the structure and morphology of the anodic layer including the incorporation of the TiO2 particles into the anodic layer is studied. Anodizing process was carried...... out using a high frequency pulse and pulse reverse pulse technique at a fixed frequency in a sulfuric acid bath. The structure of the composites and the anodized layer was studied using scanning and transmission electron microscopy. The pulse reverse pulse anodizing technique, using a negative...

  12. Distribution of QPY and RAH haplotypes of granzyme B gene in distinct Brazilian populations

    Fernanda Bernadelli Garcia

    2012-08-01

    Full Text Available INTRODUCTION: The cytolysis mediated by granules is one of the most important effector functions of cytotoxic T lymphocytes and natural killer cells. Recently, three single nucleotide polymorphisms (SNPs were identified at exons 2, 3, and 5 of the granzyme B gene, resulting in a haplotype in which three amino acids of mature protein Q48P88Y245 are changed to R48A88H245, which leads to loss of cytotoxic activity of the protein. In this study, we evaluated the frequency of these polymorphisms in Brazilian populations. METHODS: We evaluated the frequency of these polymorphisms in Brazilian ethnic groups (white, Afro-Brazilian, and Asian by sequencing these regions. RESULTS: The allelic and genotypic frequencies of SNP 2364A/G at exon 2 in Afro-Brazilian individuals (42.3% and 17.3% were significantly higher when compared with those in whites and Asians (p < 0.0001 and p = 0.0007, respectively. The polymorphisms 2933C/G and 4243C/T also were more frequent in Afro-Brazilians but without any significant difference regarding the other groups. The Afro-Brazilian group presented greater diversity of haplotypes, and the RAH haplotype seemed to be more frequent in this group (25%, followed by the whites (20.7% and by the Asians (11.9%, similar to the frequency presented in the literature. CONCLUSIONS: There is a higher frequency of polymorphisms in Afro-Brazilians, and the RAH haplotype was more frequent in these individuals. We believe that further studies should aim to investigate the correlation of this haplotype with diseases related to immunity mediated by cytotoxic lymphocytes, and if this correlation is confirmed, novel treatment strategies might be elaborated.

  13. Effects of weak nonlinearity on dispersion relations and frequency band-gaps of periodic structures

    Sorokin, Vladislav; Thomsen, Jon Juel

    2015-01-01

    of these for nonlinear problems is impossible or cumbersome, since Floquet theory is applicable for linear systems only. Thus the nonlinear effects for periodic structures are not yet fully uncovered, while at the same time applica-tions may demand effects of nonlinearity on structural response to be accounted for....... The present work deals with analytically predicting dynamic responses for nonlinear continuous elastic periodic structures. Specifically, the effects of weak nonlinearity on the dispersion re-lation and frequency band-gaps of a periodic Bernoulli-Euler beam performing bending os-cillations are analyzed......The analysis of the behaviour of linear periodic structures can be traced back over 300 years, to Sir Isaac Newton, and still attracts much attention. An essential feature of periodic struc-tures is the presence of frequency band-gaps, i.e. frequency ranges in which waves cannot propagate...

  14. The effect of genealogy-based haplotypes on genomic prediction

    Edriss, Vahid; Fernando, Rohan L.; Su, Guosheng

    2013-01-01

    on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information. Methods A total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using...... local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (pi) of the haplotype covariates had zero effect......, i.e. a Bayesian mixture method. Results About 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some...

  15. Multi-frequency complex network from time series for uncovering oil-water flow structure.

    Gao, Zhong-Ke; Yang, Yu-Xuan; Fang, Peng-Cheng; Jin, Ning-De; Xia, Cheng-Yi; Hu, Li-Dan

    2015-02-04

    Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncover the flow structures from experimental multivariate measurements. In particular, based on the Fast Fourier transform, we demonstrate how to derive multi-frequency complex network from multivariate time series. We construct complex networks at different frequencies and then detect community structures. Our results indicate that the community structures faithfully represent the structural features of oil-water flow patterns. Furthermore, we investigate the network statistic at different frequencies for each derived network and find that the frequency clustering coefficient enables to uncover the evolution of flow patterns and yield deep insights into the formation of flow structures. Current results present a first step towards a network visualization of complex flow patterns from a community structure perspective.

  16. PADI4 Haplotypes in Association with RA Mexican Patients, a New Prospect for Antigen Modulation

    Maria Guadalupe Zavala-Cerna

    2013-01-01

    Full Text Available Peptidyl arginine deiminase IV (PAD 4 is the responsible enzyme for a posttranslational modification called citrullination, originating the antigenic determinant recognized by anti-cyclic citrullinated peptide antibodies (ACPA. Four SNPs (single nucleotide polymorphisms have been described in PADI4 gene to form a susceptibility haplotype for rheumatoid arthritis (RA; nevertheless, results in association studies appear contradictory in different populations. The aim of the study was to analyze if the presence of three SNPs in PADI4 gene susceptibility haplotype (GTG is associated with ACPA positivity in patients with RA. This was a cross-sectional study that included 86 RA patients and 98 healthy controls. Polymorphisms PADI4_89, PADI4_90, and PADI4_92 in the PADI4 gene were genotyped. The susceptibility haplotype (GTG was more frequent in RA patients; interestingly, we found a new haplotype associated with RA with a higher frequency (GTC. There were no associations between polymorphisms and high scores in Spanish HAQ-DI and DAS-28, but we did find an association between RARBIS index and PADI4_89, PADI4_90 polymorphisms. We could not confirm an association between susceptibility haplotype presence and ACPA positivity. Further evidence about proteomic expression of this gene will determine its participation in antigenic generation and autoimmunity.

  17. The evolutionary history of the DMRT3 'Gait keeper' haplotype.

    Staiger, E A; Almén, M S; Promerová, M; Brooks, S; Cothran, E G; Imsland, F; Jäderkvist Fegraeus, K; Lindgren, G; Mehrabani Yeganeh, H; Mikko, S; Vega-Pla, J L; Tozaki, T; Rubin, C J; Andersson, L

    2017-10-01

    A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow-up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3:Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits. © 2017 Stichting International Foundation for Animal Genetics.

  18. Haplotypes and Sequence Variation in the Ovine Adiponectin Gene (ADIPOQ

    Qing-Ming An

    2015-11-01

    Full Text Available The adiponectin gene (ADIPOQ plays an important role in energy homeostasis. In this study five separate regions (regions 1 to 5 of ovine ADIPOQ were analysed using PCR-SSCP. Four different PCR-SSCP patterns (A1-D1, A2-D2 were detected in region-1 and region-2, respectively, with seven and six SNPs being revealed. In region-3, three different patterns (A3-C3 and three SNPs were observed. Two patterns (A4-B4, A5-B5 and two and one SNPs were observed in region-4 and region-5, respectively. In total, nineteen SNPs were detected, with five of them in the coding region and two (c.46T/C and c.515G/A putatively resulting in amino acid changes (p.Tyr16His and p.Lys172Arg. In region-1, -2 and -3 of 316 sheep from eight New Zealand breeds, variants A1, A2 and A3 were the most common, although variant frequencies differed in the eight breeds. Across region-1 and region-3, nine haplotypes were identified and haplotypes A1-A3, A1-C3, B1-A3 and B1-C3 were most common. These results indicate that the ADIPOQ gene is polymorphic and suggest that further analysis is required to see if the variation in the gene is associated with animal production traits.

  19. Dual resonant structure for energy harvesting from random vibration sources at low frequency

    Shanshan Li

    2016-01-01

    Full Text Available We introduce a design with dual resonant structure which can harvest energy from random vibration sources at low frequency range. The dual resonant structure consists of two spring-mass subsystems with different frequency responses, which exhibit strong coupling and broad bandwidth when the two masses collide with each other. Experiments with piezoelectric elements show that the energy harvesting device with dual resonant structure can generate higher power output than the sum of the two separate devices from random vibration sources.

  20. HLA-haplotypes, anti- beta-cell antibodies: their role in prognostication of type 1 diabetes mellitus (results of 11-year observation

    Elena Vital'evna Titovich

    2010-12-01

    Full Text Available The risk of type 1 diabetes mellitus (DM1 depends in the first place on the presence of predetermining HLA DR haplotypes, DQ genes, and specific autoantibodies.Aim. Prospective observation of DM1 risk groups (healthy sibs of DM patients for the elucidation of the role of genetic and autoimmune abnormalities in thedevelopment of DM1. Materials and methods. Predetermining and protective haplotypes (HLA-DRBI, DQ genes in combination with immunological markers (autoantibodiesto cytoplasmic structures of betbeta-cells (ICA, anti-insulin autoantibodies (IAA, anti-glutamate decarboxylase autoantibodies (GAD were studied in healthysibs of mean age 11.9?5.8 years selected from 143 discordant families of patients with DM1. In addition, a random sample of 599 DM1 patients (mean age7.5?6.2 years was enrolled for molecular genetic studies (HLA-DRBI-DG genes. The control group comprised 200 subjects. Results. DQAI*0501-DQB1+0201 (DQ2 and DQAI*0301-DQBI*0302 (DG8 haplotype heterozygosity creating the highest risk of DM1, the healthy sibswere divided into 3 risk groups. The high risk group 1 (DQ2/DQ8 included 23 (13.5% subjects, moderate risk group 2 (DQ2/X, DQ8/X 85 (59.7%, andlow risk group 3 (X/X; X - any haplotype besides DQ2, DQ8 63 (36.8%. The frequency of autoantibodies (AB of 2 or 3 species in group 1 was higher thanin groups 2 and 3 (26.1, 14.1, 11.1% respectively, p>0.05; 8.7, 2.4, 0%, p

  1. Seismic performance evaluation of high natural frequency mechanical structure from the viewpoint of energy balance

    Minagawa, Keisuke; Fujita, Satoshi; Endo, Rokuro; Amemiya, Mitsuhiko

    2009-01-01

    In this study, vibration characteristics of mechanical structure having high natural frequency are investigated from the viewpoint of energy balance. Mechanical structures having high natural frequency in a nuclear power plant are generally designed statically and elastically. However it has been reported that fracture of ordinary piping is produced not by momentary large load but by cumulative fatigue damage. Therefore it is very important to grasp seismic performance dynamically by considering cyclic load. This paper deals with an investigation regarding seismic performance evaluation of high natural frequency mechanical structure. The energy balance equation that is one of valid methods for structural calculation is applied through the investigation. The main feature of the energy balance equation is that it explains accumulated information of motion. Therefore the energy balance equation is adequate for the investigation of the influence of cumulative load such as seismic response. In this paper, vibration experiment and simulation using sinusoidal waves and artificial seismic waves were examined in order to investigate relationship between natural frequency of structure and energy. As a result, we found that input energy decreases with an increase in the natural frequency. (author)

  2. A Haplotype Information Theory Method Reveals Genes of Evolutionary Interest in European vs. Asian Pigs.

    Hudson, Nicholas J; Naval-Sánchez, Marina; Porto-Neto, Laercio; Pérez-Enciso, Miguel; Reverter, Antonio

    2018-06-05

    Asian and European wild boars were independently domesticated ca. 10,000 years ago. Since the 17th century, Chinese breeds have been imported to Europe to improve the genetics of European animals by introgression of favourable alleles, resulting in a complex mosaic of haplotypes. To interrogate the structure of these haplotypes further, we have run a new haplotype segregation analysis based on information theory, namely compression efficiency (CE). We applied the approach to sequence data from individuals from each phylogeographic region (n = 23 from Asia and Europe) including a number of major pig breeds. Our genome-wide CE is able to discriminate the breeds in a manner reflecting phylogeography. Furthermore, 24,956 non-overlapping sliding windows (each comprising 1,000 consecutive SNP) were quantified for extent of haplotype sharing within and between Asia and Europe. The genome-wide distribution of extent of haplotype sharing was quite different between groups. Unlike European pigs, Asian pigs haplotype sharing approximates a normal distribution. In line with this, we found the European breeds possessed a number of genomic windows of dramatically higher haplotype sharing than the Asian breeds. Our CE analysis of sliding windows capture some of the genomic regions reported to contain signatures of selection in domestic pigs. Prominent among these regions, we highlight the role of a gene encoding the mitochondrial enzyme LACTB which has been associated with obesity, and the gene encoding MYOG a fundamental transcriptional regulator of myogenesis. The origin of these regions likely reflects either a population bottleneck in European animals, or selective targets on commercial phenotypes reducing allelic diversity in particular genes and/or regulatory regions.

  3. Frequency Dispersion of the Impedance of Capacitor Structures with Asymmetrically Connected Electrodes

    Emel'yanov, O. A.; Ivanov, I. O.

    2018-01-01

    A method to estimate the frequency dispersion of the impedance of capacitance structures with asymmetric opposite connection of electrodes is considered. The proposed equations are used to derive exact solutions for spatially nonuniform distributions of potential and current. The solutions are in agreement with the results of the 3D simulation using the COMSOL Multiphysics software. The frequency dispersion of the impedance must be taken into account in the development of modern capacitors needed for construction of efficient energy storages.

  4. Sub-Frequency Interval Approach in Electromechanical Impedance Technique for Concrete Structure Health Monitoring

    Bahador Sabet Divsholi

    2010-12-01

    Full Text Available The electromechanical (EM impedance technique using piezoelectric lead zirconate titanate (PZT transducers for structural health monitoring (SHM has attracted considerable attention in various engineering fields. In the conventional EM impedance technique, the EM admittance of a PZT transducer is used as a damage indicator. Statistical analysis methods such as root mean square deviation (RMSD have been employed to associate the damage level with the changes in the EM admittance signatures, but it is difficult to determine the location of damage using such methods. This paper proposes a new approach by dividing the large frequency (30–400 kHz range into sub-frequency intervals and calculating their respective RMSD values. The RMSD of the sub-frequency intervals (RMSD-S will be used to study the severity and location of damage. An experiment is carried out on a real size concrete structure subjected to artificial damage. It is observed that damage close to the PZT changes the high frequency range RMSD-S significantly, while the damage far away from the PZT changes the RMSD-S in the low frequency range significantly. The relationship between the frequency range and the PZT sensing region is also presented. Finally, a damage identification scheme is proposed to estimate the location and severity of damage in concrete structures.

  5. Electrostatic energy harvesting device with dual resonant structure for wideband random vibration sources at low frequency.

    Zhang, Yulong; Wang, Tianyang; Zhang, Ai; Peng, Zhuoteng; Luo, Dan; Chen, Rui; Wang, Fei

    2016-12-01

    In this paper, we present design and test of a broadband electrostatic energy harvester with a dual resonant structure, which consists of two cantilever-mass subsystems each with a mass attached at the free edge of a cantilever. Comparing to traditional devices with single resonant frequency, the proposed device with dual resonant structure can resonate at two frequencies. Furthermore, when one of the cantilever-masses is oscillating at resonance, the vibration amplitude is large enough to make it collide with the other mass, which provides strong mechanical coupling between the two subsystems. Therefore, this device can harvest a decent power output from vibration sources at a broad frequency range. During the measurement, continuous power output up to 6.2-9.8 μW can be achieved under external vibration amplitude of 9.3 m/s 2 at a frequency range from 36.3 Hz to 48.3 Hz, which means the bandwidth of the device is about 30% of the central frequency. The broad bandwidth of the device provides a promising application for energy harvesting from the scenarios with random vibration sources. The experimental results indicate that with the dual resonant structure, the vibration-to-electricity energy conversion efficiency can be improved by 97% when an external random vibration with a low frequency filter is applied.

  6. Gear fault diagnosis based on the structured sparsity time-frequency analysis

    Sun, Ruobin; Yang, Zhibo; Chen, Xuefeng; Tian, Shaohua; Xie, Yong

    2018-03-01

    Over the last decade, sparse representation has become a powerful paradigm in mechanical fault diagnosis due to its excellent capability and the high flexibility for complex signal description. The structured sparsity time-frequency analysis (SSTFA) is a novel signal processing method, which utilizes mixed-norm priors on time-frequency coefficients to obtain a fine match for the structure of signals. In order to extract the transient feature from gear vibration signals, a gear fault diagnosis method based on SSTFA is proposed in this work. The steady modulation components and impulsive components of the defective gear vibration signals can be extracted simultaneously by choosing different time-frequency neighborhood and generalized thresholding operators. Besides, the time-frequency distribution with high resolution is obtained by piling different components in the same diagram. The diagnostic conclusion can be made according to the envelope spectrum of the impulsive components or by the periodicity of impulses. The effectiveness of the method is verified by numerical simulations, and the vibration signals registered from a gearbox fault simulator and a wind turbine. To validate the efficiency of the presented methodology, comparisons are made among some state-of-the-art vibration separation methods and the traditional time-frequency analysis methods. The comparisons show that the proposed method possesses advantages in separating feature signals under strong noise and accounting for the inner time-frequency structure of the gear vibration signals.

  7. Frequency response function (FRF) based updating of a laser spot welded structure

    Zin, M. S. Mohd; Rani, M. N. Abdul; Yunus, M. A.; Sani, M. S. M.; Wan Iskandar Mirza, W. I. I.; Mat Isa, A. A.

    2018-04-01

    The objective of this paper is to present frequency response function (FRF) based updating as a method for matching the finite element (FE) model of a laser spot welded structure with a physical test structure. The FE model of the welded structure was developed using CQUAD4 and CWELD element connectors, and NASTRAN was used to calculate the natural frequencies, mode shapes and FRF. Minimization of the discrepancies between the finite element and experimental FRFs was carried out using the exceptional numerical capability of NASTRAN Sol 200. The experimental work was performed under free-free boundary conditions using LMS SCADAS. Avast improvement in the finite element FRF was achieved using the frequency response function (FRF) based updating with two different objective functions proposed.

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

    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.

  9. Resonant frequency of the silicon micro-structure of MEMS vector hydrophone in fluid-structure interaction

    Guojun Zhang

    2015-04-01

    Full Text Available The MEMS vector hydrophone developed by the North University of China has advantages of high Signal to Noise Ratio, ease of array integration, etc. However, the resonance frequency of the MEMS device in the liquid is different from that in the air due to the fluid-structure interaction (FSI. Based on the theory of Fluid-Solid Coupling, a generalized distributed mass attached on the micro-structure has been found, which results in the resonance frequency of the microstructure in the liquid being lower than that in the air. Then, an FSI simulation was conducted by ANSYS software. Finally, the hydrophone was measured by using a shaking table and a vector hydrophone calibration system respectively. Results show that, due to the FSI, the resonance frequency of the MEMS devices of the bionic vector hydrophone in the liquid declines approximately 30% compared to the case in the air.

  10. The vibrational behaviour of the generator support structure for Koeberg nuclear power station at high frequencies

    Lee, D.E.

    1988-06-01

    The vibrational behaviour of the generator support structure at Koeberg nuclear power station at frequencies primarily in the region of 80 Hz to 110 Hz was examined. The effect of soil-structure interaction and the change in stiffness of the foundation soil was investigated. Vibration tests were performed on the generator support structure and the results were compared with a theoretical finite element analysis of the structure. By varying the soil-cement foundation stiffness it was possible to demonstrate the change in dynamic behaviour of the structure in the higher frequency band 80 Hz to 110 Hz. Comment has been made on the design code DIN 4024 in view of the findings of this thesis. It was concluded that the empirical rules regarding the inclusion of the foundation in an analysis specified by the code do not cover all cases and greater cognisance of the effect of the foundation stiffness on the vibration behaviour of such machine foundations is necessary. Obvious machine frequencies higher than the operational frequencies should be analysed where it is considered necessary. 24 refs., 25 tabs., 83 figs

  11. Estimation of age structure of fish populations from length-frequency data

    Kumar, K.D.; Adams, S.M.

    1977-01-01

    A probability model is presented to determine the age structure of a fish population from length-frequency data. It is shown that when the age-length key is available, maximum-likelihood estimates of the age structure can be obtained. When the key is not available, approximate estimates of the age structure can be obtained. The model is used for determination of the age structure of populations of channel catfish and white crappie. Practical applications of the model to impact assessment are discussed

  12. Low band gap frequencies and multiplexing properties in 1D and 2D mass spring structures

    Aly, Arafa H; Mehaney, Ahmed

    2016-01-01

    This study reports on the propagation of elastic waves in 1D and 2D mass spring structures. An analytical and computation model is presented for the 1D and 2D mass spring systems with different examples. An enhancement in the band gap values was obtained by modeling the structures to obtain low frequency band gaps at small dimensions. Additionally, the evolution of the band gap as a function of mass value is discussed. Special attention is devoted to the local resonance property in frequency ranges within the gaps in the band structure for the corresponding infinite periodic lattice in the 1D and 2D mass spring system. A linear defect formed of a row of specific masses produces an elastic waveguide that transmits at the narrow pass band frequency. The frequency of the waveguides can be selected by adjusting the mass and stiffness coefficients of the materials constituting the waveguide. Moreover, we pay more attention to analyze the wave multiplexer and DE-multiplexer in the 2D mass spring system. We show that two of these tunable waveguides with alternating materials can be employed to filter and separate specific frequencies from a broad band input signal. The presented simulation data is validated through comparison with the published research, and can be extended in the development of resonators and MEMS verification. (paper)

  13. Evidence that the ancestral haplotype in Australian hemochromatosis patients may be associated with a common mutation in the gene

    Crawford, D.H.G.; Powell, L.W.; Leggett, B.A. [Univ. of Queensland (Australia)] [and others

    1995-08-01

    Hemochromatosis (HC) is a common inherited disorder of iron metabolism for which neither the gene nor biochemical defect have yet been identified. The aim of this study was to look for clinical evidence that the predominant ancestral haplotype in Australian patients is associated with a common mutation in the gene. We compared indices of iron metabolism and storage in three groups of HC patients categorized according to the presence of the ancestral haplotype (i.e., patients with two copies, one copy, and no copies of the ancestral haplotype). We also examined iron indices in two groups of HC heterozygotes (those with the ancestral haplotype and those without) and in age-matched controls. These analyses indicate that (i) HC patients with two copies of the ancestral haplotype show significantly more severe expression of the disorder than those with one copy or those without, (ii) HC heterozygotes have partial clinical expression, which may be influenced by the presence of the ancestral haplotype in females but not in males, and (iii) the high population frequency of the HC gene may be the result of the selective advantage conferred by protecting heterozygotes against iron deficiency. 18 refs., 3 tabs.

  14. Posttraumatic Stress Disorder's Frequency and Intensity Ratings Are Associated with Factor Structure Differences in Military Veterans

    Elhai, Jon D.; Palmieri, Patrick A.; Biehn, Tracey L.; Frueh, B. Christopher; Magruder, Kathryn M.

    2010-01-01

    We examined possible differences in the factor structure of posttraumatic stress disorder (PTSD) on the basis of whether frequency or intensity symptom response formats were used to assess PTSD. Participants included 669 veterans recruited from an epidemiological study of four Veterans Affairs Medical Centers' primary care clinics in the…

  15. The use of displacement threshold for switching frequency strategy for structural vibration mitigation

    Widjaja, Joko; Samali, Bijan; Li, Jianchun

    2007-01-01

    This paper presents a study of controllable real-time frequency shift using a fluid pin damper, so called 'smart pin', mounted at a beam-column connection. Unlike the stationary frequency shifter, the pin can increase or decrease the rotational stiffness of the connection, leading to an actively adjustable structural frequency due to real-time responses of polarised magneto-rheological (MR) fluid, whose rheological properties can change in milliseconds. The feedback to the pin damper governs the structural frequency changes. To demonstrate this concept, a single storey plane steel frame model with one hinge and one 'smart pin' damper, mounted at each beam-column connection and subjected to two scaled earthquake excitations, namely El-Centro 1940 and Northridge 1994, which respectively represent near- and farfield excitations, was tested using the shake table at the University of Technology, Sydney (UTS) structures laboratory, for 'proof-of-concept' investigation. Further, the dynamic performance of the model using a proposed switching strategy with a displacement threshold as an indicator for alternately supplied current level (flip-flop) was examined, assuming the earthquake records were known. The results showed some potential use of this control technique for structural vibration mitigation, however, further study to optimize the performance of the switching strategy is still required

  16. Preconditioned finite-difference frequency-domain for modelling periodic dielectric structures - comparisons with FDTD

    Chabory, A.; Hon, de B.P.; Schilders, W.H.A.; Tijhuis, A.G.

    2008-01-01

    Finite-difference techniques are very popular and versatile numerical tools in computational electromagnetics. In this paper, we propose a preconditioned finite-difference frequency-domain method (FDFD) to model periodic structures in 2D and 3D. The preconditioner follows from a modal decoupling

  17. Preconditioned finite-difference frequency-domain for modelling periodic dielectric structures : comparisons with FDTD

    Chabory, A.; Hon, de B.P.; Schilders, W.H.A.; Tijhuis, A.G.

    2008-01-01

    Finite-difference techniques are very popular and versatile numerical tools in computational electromagnetics. In this paper, we propose a preconditioned finite-difference frequency-domain method (FDFD) to model periodic structures in 2D and 3D. The preconditioner follows from a modal decoupling

  18. The analysis of APOL1 genetic variation and haplotype diversity provided by 1000 Genomes project.

    Peng, Ting; Wang, Li; Li, Guisen

    2017-08-11

    The APOL1 gene variants has been shown to be associated with an increased risk of multiple kinds of diseases, particularly in African Americans, but not in Caucasians and Asians. In this study, we explored the single nucleotide polymorphism (SNP) and haplotype diversity of APOL1 gene in different races provided by 1000 Genomes project. Variants of APOL1 gene in 1000 Genome Project were obtained and SNPs located in the regulatory region or coding region were selected for genetic variation analysis. Total 2504 individuals from 26 populations were classified as four groups that included Africa, Europe, Asia and Admixed populations. Tag SNPs were selected to evaluate the haplotype diversities in the four populations by HaploStats software. APOL1 gene was surrounded by some of the most polymorphic genes in the human genome, variation of APOL1 gene was common, with up to 613 SNP (1000 Genome Project reported) and 99 of them (16.2%) with MAF ≥ 1%. There were 79 SNPs in the URR and 92 SNPs in 3'UTR. Total 12 SNPs in URR and 24 SNPs in 3'UTR were considered as common variants with MAF ≥ 1%. It is worth noting that URR-1 was presents lower frequencies in European populations, while other three haplotypes taken an opposite pattern; 3'UTR presents several high-frequency variation sites in a short segment, and the differences of its haplotypes among different population were significant (P < 0.01), UTR-1 and UTR-5 presented much higher frequency in African population, while UTR-2, UTR-3 and UTR-4 were much lower. APOL1 coding region showed that two SNP of G1 with higher frequency are actually pull down the haplotype H-1 frequency when considering all populations pooled together, and the diversity among the four populations be widen by the G1 two mutation (P 1  = 3.33E-4 vs P 2  = 3.61E-30). The distributions of APOL1 gene variants and haplotypes were significantly different among the different populations, in either regulatory or coding regions. It could provide

  19. Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps.

    Garud, Nandita R; Rosenberg, Noah A

    2015-06-01

    Soft selective sweeps represent an important form of adaptation in which multiple haplotypes bearing adaptive alleles rise to high frequency. Most statistical methods for detecting selective sweeps from genetic polymorphism data, however, have focused on identifying hard selective sweeps in which a favored allele appears on a single haplotypic background; these methods might be underpowered to detect soft sweeps. Among exceptions is the set of haplotype homozygosity statistics introduced for the detection of soft sweeps by Garud et al. (2015). These statistics, examining frequencies of multiple haplotypes in relation to each other, include H12, a statistic designed to identify both hard and soft selective sweeps, and H2/H1, a statistic that conditional on high H12 values seeks to distinguish between hard and soft sweeps. A challenge in the use of H2/H1 is that its range depends on the associated value of H12, so that equal H2/H1 values might provide different levels of support for a soft sweep model at different values of H12. Here, we enhance the H12 and H2/H1 haplotype homozygosity statistics for selective sweep detection by deriving the upper bound on H2/H1 as a function of H12, thereby generating a statistic that normalizes H2/H1 to lie between 0 and 1. Through a reanalysis of resequencing data from inbred lines of Drosophila, we show that the enhanced statistic both strengthens interpretations obtained with the unnormalized statistic and leads to empirical insights that are less readily apparent without the normalization. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes.

    Jinhui Wang

    Full Text Available Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp and FIN111 (1.20 Mbp, were obtained from carrot psyllids (Trioza apicalis harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species.

  1. Pressure effect on the amide I frequency of the solvated α-helical structure in water

    Takekiyo, T; Yoshimura, Y; Shimizu, A; Koizumi, T; Kato, M; Taniguchi, Y

    2007-01-01

    As a model system of the pressure dependence of the amide I mode of the solvated α-helical structure in a helical peptide, we have calculated the frequency shifts of the amide I modes as a function of the distance between trans-N-methylacetamide (t-NMA) dimer and a water molecule (d C=O···H-O ) by the density-functional theory (DFT) method at the B3LYP/6-31G++(d,p) level. Two amide I frequencies at 1652 and 1700 cm -1 were observed under this calculation. The former is ascribed to the amide I mode forming the intermolecular hydrogen bond (H-bond) between t-NMA and H 2 O in addition to the intermolecular H-bond in the t-NMA dimer. The latter is due to the amide I mode forming only the intermolecular H-bond in the t-NMA dimer. We have found that the amide I frequency at 1652 cm -1 shifts to a lower frequency with decreasing d C=O···H-O ) (i.e., increasing pressure), whereas that at 1700 cm -1 shifts to a higher frequency. The amide I frequency shift of 1652 cm -1 is larger than that of 1700 cm -1 by the intermolecular H-bond. Thus, our results clearly indicate that the pressure-induced amide I frequency shift of the solvated α-helical structure correlates with the change in d C=O···H-O )

  2. Structured waves near the plasma frequency observed in three auroral rocket flights

    M. Samara

    2006-11-01

    Full Text Available We present observations of waves at and just above the plasma frequency (fpe from three high frequency electric field experiments on three recent rockets launched to altitudes of 300–900 km in active aurora. The predominant observed HF waves just above fpe are narrowband, short-lived emissions with amplitudes ranging from <1 mV/m to 20 mV/m, often associated with structured electron density. The nature of these HF waves, as determined from frequency-time spectrograms, is highly variable: in some cases, the frequency decreases monotonically with time as in the "HF-chirps" previously reported (McAdams and LaBelle, 1999, but in other cases rising frequencies are observed, or features which alternately rise and fall in frequency. They exhibit two timescales of amplitude variation: a short timescale, typically 50–100 ms, associated with individual discrete features, and a longer timescale associated with the general decrease in the amplitudes of the emissions as the rocket moves away from where the condition f~fpe holds. The latter timescale ranges from 0.6 to 6.0 s, corresponding to distances of 2–7 km, assuming the phenomenon to be stationary and using the rocket velocity to convert time to distance.

  3. Structured waves near the plasma frequency observed in three auroral rocket flights

    M. Samara

    2006-11-01

    Full Text Available We present observations of waves at and just above the plasma frequency (fpe from three high frequency electric field experiments on three recent rockets launched to altitudes of 300–900 km in active aurora. The predominant observed HF waves just above fpe are narrowband, short-lived emissions with amplitudes ranging from <1 mV/m to 20 mV/m, often associated with structured electron density. The nature of these HF waves, as determined from frequency-time spectrograms, is highly variable: in some cases, the frequency decreases monotonically with time as in the "HF-chirps" previously reported (McAdams and LaBelle, 1999, but in other cases rising frequencies are observed, or features which alternately rise and fall in frequency. They exhibit two timescales of amplitude variation: a short timescale, typically 50–100 ms, associated with individual discrete features, and a longer timescale associated with the general decrease in the amplitudes of the emissions as the rocket moves away from where the condition f~fpe holds. The latter timescale ranges from 0.6 to 6.0 s, corresponding to distances of 2–7 km, assuming the phenomenon to be stationary and using the rocket velocity to convert time to distance.

  4. Structure of bending resonances frequencies in supercritical rotors of gaseous centrifuges

    Andronov, I.N.; Grigor'ev, G.Yu.; Vyazovetskij, Yu.V.; Senchenkov, A.P.; Senchenkov, S.A.

    2000-01-01

    The position and the structure bending resonances for the model supercritical rotors with different construction of the tube are measured. Considerable complication of the resonance system for the tubes with nonuniform properties was established. The effect of the structure of the resonance on the complication of its realization and the ways of optimization of the rotor resonance system is discussed. Made measuring point to possibility for creation highly productive centrifuges relating to supercritical rotors with uniform concrete size carbon composite tube and structure of winding, working after the third bending resonance. The frequency of the fifth resonance falls in the zone of the performance frequency on the rotors with bellows crimps. Carbon composite tubes with the areas of raised flexibility is provided with greater in several times decrement [ru

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

    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.

  6. Effects of mistuning and matrix structure on the topology of frequency response curves

    Afolabi, Dare

    1989-01-01

    The stability of a frequency response curve under mild perturbations of the system's matrix is investigated. Using recent developments in the theory of singularities of differentiable maps, it is shown that the stability of a response curve depends on the structure of the system's matrix. In particular, the frequency response curves of a cylic system are shown to be unstable. Consequently, slight parameter variations engendered by mistuning will induce a significant difference in the topology of the forced response curves, if the mistuning transformation crosses the bifurcation set.

  7. Low-Frequency Acoustic Noise Mitigation Characteristics of Metamaterials-Inspired Vibro-Impact Structures

    Rekhy, Anuj

    Acoustic absorbers like foams, fiberglass or liners have been used commonly in structures for infrastructural, industrial, automotive and aerospace applications to mitigate noise. However, these conventional materials have limited effectiveness to mitigate low-frequency (LF) acoustic waves with frequency less than 400 Hz owing to the need for impractically large mass or volume. LF acoustic waves contribute significantly towards environmental noise pollution as well as unwanted structural responses. Therefore, there is a need to develop lightweight, compact, structurally-integrated solutions to mitigate LF noise in several applications. Inspired by metamaterials, which are man-made structural materials that derive their unique dynamic behavior not just from material constituents but more so from engineered configurations, tuned mass-loaded membranes as vibro-impact attachments on a baseline structure are investigated to determine their performance as a LF acoustic barrier. The hypothesis is that the LF incident waves are up-converted via impact to higher modes in the baseline structure which are far more evanescent and may then be effectively mitigated using conventional means. Such Metamaterials-Inspired Vibro-Impact Structures (MIVIS) could be tuned to match the dominant frequency content of LF acoustic sources in specific applications. Prototype MIVIS unit cells were designed and tested to study the energy transfer mechanism via impact-induced frequency up-conversion, and the consequent sound transmission loss. Structural acoustic simulations were done to predict responses using models based on normal incidence transmission loss tests. Experimental proof-of-concept was achieved and further correlations to simulations were utilized to optimize the energy up-conversion mechanism using parametric studies. Up to 36 dB of sound transmission loss increase is obtained at the anti-resonance frequency (326 Hz) within a tunable LF bandwidth of about 200 Hz while impact

  8. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation.

    Potter, Kevin M; Hipkins, Valerie D; Mahalovich, Mary F; Means, Robert E

    2013-08-01

    Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.

  9. A refined Frequency Domain Decomposition tool for structural modal monitoring in earthquake engineering

    Pioldi, Fabio; Rizzi, Egidio

    2017-07-01

    Output-only structural identification is developed by a refined Frequency Domain Decomposition ( rFDD) approach, towards assessing current modal properties of heavy-damped buildings (in terms of identification challenge), under strong ground motions. Structural responses from earthquake excitations are taken as input signals for the identification algorithm. A new dedicated computational procedure, based on coupled Chebyshev Type II bandpass filters, is outlined for the effective estimation of natural frequencies, mode shapes and modal damping ratios. The identification technique is also coupled with a Gabor Wavelet Transform, resulting in an effective and self-contained time-frequency analysis framework. Simulated response signals generated by shear-type frames (with variable structural features) are used as a necessary validation condition. In this context use is made of a complete set of seismic records taken from the FEMA P695 database, i.e. all 44 "Far-Field" (22 NS, 22 WE) earthquake signals. The modal estimates are statistically compared to their target values, proving the accuracy of the developed algorithm in providing prompt and accurate estimates of all current strong ground motion modal parameters. At this stage, such analysis tool may be employed for convenient application in the realm of Earthquake Engineering, towards potential Structural Health Monitoring and damage detection purposes.

  10. Rotational structure of the five lowest frequency fundamental vibrational states of dimethylsulfoxide

    Cuisset, Arnaud; Drumel, Marie-Aline Martin; Hindle, Francis; Mouret, Gaël; Sadovskií, Dmitrií A.

    2013-10-01

    We report on the successful extended analysis of the high-frequency (200-700 GHz) part of the gas phase (sub)mm-wave spectra of dimethylsulfoxide (DMSO). The spectrum was recorded at 100 kHz resolution using a solid state subTHz spectrometer. The five lowest energy fundamental vibrational states of DMSO with frequencies below 400 cm-1 were observed as sidebands along with the main 0←0 band. Neglecting the internal rotation of methyls, our rotational Hamiltonian reproduced the spectrum to the subMHz accuracy. We have found that the asymmetric bending state ν23 is the only low frequency fundamental vibrational state with the "anomalous" rotational structure uncovered in Cuisset et al. [1]. dmsomw 2013-09-04 15:03

  11. Study of the round edge disk hole's effects on the frequency and wakefield in disc structure

    Wang Lanfa; Hou Mi; Zhang Chuang

    2001-01-01

    The effects of the round edge beam hole on the frequency and wake field are studied using variational method, which allows for rounded iris disk hole without any approximation in shape treatment. The frequencies and wake fields of accelerating mode and dipole mode are studied for different edge radius cases, including the flat edge shape that is often used to approximately represent the actual structure geometry. The edge hole shape has weak effect on the frequency, but strong effect on the wakefield. The study shows that the amounts of wake fields are not precise enough with the assumption of the flat edge beam hole as of round edge. The shape assumption brings loss factor 15% err for the most dangerous EH 16 mode

  12. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    Rapacz, J.; Hasler-Rapacz, J.O. (Univ. of Wisconsin, Madison (United States)); Chen, L.; Wu, Mingjiuan; Schumaker, V.N. (Univ. of California, Los Angeles (United States)); Butler-Brunner, E.; Butler, R. (Swiss Red Cross Blood Transfusion Service, Bern (Switzerland))

    1991-02-15

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes.

  13. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    Rapacz, J.; Hasler-Rapacz, J.O.; Chen, L.; Wu, Mingjiuan; Schumaker, V.N.; Butler-Brunner, E.; Butler, R.

    1991-01-01

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes

  14. On the profile of frequency and voltage dependent interface states and series resistance in MIS structures

    Doekme, Ilbilge [Science Education Department, Faculty of Kirsehir Education, Gazi University, Kirsehir (Turkey)]. E-mail: ilbilgedokme@gazi.edu.tr; Altindal, Semsettin [Physics Department, Faculty of Arts and Sciences, Gazi University, 06500, Teknikokullar, Ankara (Turkey)

    2007-04-30

    The variation in the capacitance-voltage (C-V) and conductance-voltage (G/{omega}-V) characteristics of Au/SiO{sub 2}/n-Si metal-insulator-semiconductor (MIS) structure have been systematically investigated as a function of frequencies in the frequency range 0.5 kHz-10 MHz at room temperature. In addition, the forward and reverse bias current-voltage (I-V) characteristics of this structure were measured at room temperature. The high value of ideality factor was attributed to the high density of interface states localized at Si/SiO{sub 2} interface and interfacial oxide layer. The density of interface states (N{sub ss}) and the series resistance (R{sub ss}) were calculated from I-V and C-V measurements using different methods and the effect of them on C-V and G/{omega}-V characteristics were deeply researched. At the same energy position near the top of valance band, the calculated N{sub ss} values, obtained without taking into account the series resistance of the devices almost one order of magnitude larger than N{sub ss} values obtained by taking into account R{sub ss} values. It is found that the C-V and G/{omega}-V curves exhibit a peak at low frequencies and the peak values of C and G/{omega} decrease with increasing frequency. Also, the plots of R {sub s} as a function of bias give two peaks in the certain voltage range at low frequencies. These observations indicate that at low frequencies, the charges at interface states can easily follow an AC signal and the number of them increases with decreasing frequency. The I-V, C-V and G/{omega}-V characteristics of the MIS structure are affected not only with R {sub s} but also N {sub ss}. Experimental results show that both the R{sub s} and C{sub o} values should be taken into account in determining frequency-dependent electrical characteristics.

  15. Structural partitioning of complex structures in the medium-frequency range. An application to an automotive vehicle

    Kassem, M.; Soize, C.; Gagliardini, L.

    2011-02-01

    In a recent work [ Journal of Sound and Vibration 323 (2009) 849-863] the authors presented an energy-density field approach for the vibroacoustic analysis of complex structures in the low and medium frequency ranges. In this approach, a local vibroacoustic energy model as well as a simplification of this model were constructed. In this paper, firstly an extension of the previous theory is performed in order to include the case of general input forces and secondly, a structural partitioning methodology is presented along with a set of tools used for the construction of a partitioning. Finally, an application is presented for an automotive vehicle.

  16. Frequency response function-based explicit framework for dynamic identification in human-structure systems

    Wei, Xiaojun; Živanović, Stana

    2018-05-01

    The aim of this paper is to propose a novel theoretical framework for dynamic identification in a structure occupied by a single human. The framework enables the prediction of the dynamics of the human-structure system from the known properties of the individual system components, the identification of human body dynamics from the known dynamics of the empty structure and the human-structure system and the identification of the properties of the structure from the known dynamics of the human and the human-structure system. The novelty of the proposed framework is the provision of closed-form solutions in terms of frequency response functions obtained by curve fitting measured data. The advantages of the framework over existing methods are that there is neither need for nonlinear optimisation nor need for spatial/modal models of the empty structure and the human-structure system. In addition, the second-order perturbation method is employed to quantify the effect of uncertainties in human body dynamics on the dynamic identification of the empty structure and the human-structure system. The explicit formulation makes the method computationally efficient and straightforward to use. A series of numerical examples and experiments are provided to illustrate the working of the method.

  17. Molecular variation at the HLA-A, B, C, DRB1, DQA1, and DQB1 loci in full heritage American Indians in Arizona: private haplotypes and their evolution.

    Williams, R; Chen, Y-F; Endres, R; Middleton, D; Trucco, M; Williams, J Dunn; Knowler, W

    2009-12-01

    A sample of 492 full heritage, unrelated residents of the Gila River Indian Community (GRIC) of Arizona were characterized for their high-resolution DNA alleles at the HLA-A, B, C, DRB1, DQA1, and DQB1 loci. Only five allelic categories are found at HLA-A, 10 at HLA-B, 8 at HLA-C and HLA-DR, and 4 at DQA1 and DQB1. There is little evidence for population structure at the 6 loci. Two 'private' alleles, B*5102 and B*4005, which are found nearly exclusively in American Indian populations in the desert southwest and northern Mexico, are likely new mutations after the first inhabitation of the area, the evolution of which are reflected in the contemporary distribution of their respective haplotypes. DRB1*1402 has the highest reported frequency of any specificity at the DRB1 locus, 0.7461, and serves as a sensitive probe for locating related east Asian populations. The haplotypes in this population also exhibit a highly restricted distribution and strong genetic disequilibria, which has important implications for matching solid organ and bone marrow allografts. It is shown that, when one considers HLA-A-B-DRB1 homozygotes as allograft donors for all full heritage members of the GRIC, 50% of the community would find a non-mismatched organ within the homozygotes for the six most common haplotypes. This raises questions about transplantation policy and whether, in the presence of high-frequency private alleles and a restricted number of haplotypes, the full heritage American Indian community of the desert southwest should act as its own pool of donors for its affected members.

  18. Reducing Undue Conservatism in "Higher Frequency" Structural Design Loads in Aerospace Components

    Knight, J. Brent

    2012-01-01

    This study is intended to investigate the frequency dependency of significant strain due to vibratory loads in aerospace vehicle components. The notion that "higher frequency" dynamic loads applied as static loads is inherently conservative is perceived as widely accepted. This effort is focused on demonstrating that principle and attempting to evolve methods to capitalize on it to mitigate undue conservatism. It has been suggested that observations of higher frequency modes that resulted in very low corresponding strain did so due to those modes not being significant. Two avionics boxes, one with its first significant mode at 341 Hz and the other at 857 Hz, were attached to a flat panel installed on a curved orthogrid panel which was driven acoustically in tests performed at NASA/MSFC. Strain and acceleration were measured at select locations on each of the boxes. When possible, strain gage rosettes and accelerometers were installed on either side of a given structural member so that measured strain and acceleration data would directly correspond to one another. Ultimately, a frequency above which vibratory loads can be disregarded for purposes of static structural analyses and sizing of typical robust aerospace components is sought.

  19. HIGHER MODE FREQUENCY EFFECTS ON RESONANCE IN MACHINERY, STRUCTURES, AND PIPE SYSTEMS

    Leishear, R.

    2010-05-02

    The complexities of resonance in multi-degree of freedom systems (multi-DOF) may be clarified using graphic presentations. Multi-DOF systems represent actual systems, such as beams or springs, where multiple, higher order, natural frequencies occur. Resonance occurs when a cyclic load is applied to a structure, and the frequency of the applied load equals one of the natural frequencies. Both equations and graphic presentations are available in the literature for single degree of freedom (SDOF) systems, which describe the response of spring-mass-damper systems to harmonically applied, or cyclic, loads. Loads may be forces, moments, or forced displacements applied to one end of a structure. Multi-DOF systems are typically described only by equations in the literature, and while equations certainly permit a case by case analysis for specific conditions, graphs provide an overall comprehension not gleaned from single equations. In fact, this collection of graphed equations provides novel results, which describe the interactions between multiple natural frequencies, as well as a comprehensive description of increased vibrations near resonance.

  20. Applications of hybrid time-frequency methods in nonlinear structural dynamics

    Politopoulos, I.; Piteau, Ph.; Borsoi, L.; Antunes, J.

    2014-01-01

    This paper presents a study on methods which may be used to compute the nonlinear response of systems whose linear properties are determined in the frequency or Laplace domain. Typically, this kind of situation may arise in soil-structure and fluid-structure interaction problems. In particular three methods are investigated: (a) the hybrid time-frequency method, (b) the computation of the convolution integral which requires an inverse Fourier or Laplace transform of the system's transfer function, and (c) the identification of an equivalent system defined in the time domain which may be solved with classical time integration methods. These methods are illustrated by their application to some simple, one degree of freedom, non-linear systems and their advantages and drawbacks are highlighted. (authors)

  1. Use of Time- and Frequency-Domain Approaches for Damage Detection in Civil Engineering Structures

    V. H. Nguyen

    2014-01-01

    Full Text Available The aim of this paper is to apply both time- and frequency-domain-based approaches on real-life civil engineering structures and to assess their capability for damage detection. The methodology is based on Principal Component Analysis of the Hankel matrix built from output-only measurements and of Frequency Response Functions. Damage detection is performed using the concept of subspace angles between a current (possibly damaged state and a reference (undamaged state. The first structure is the Champangshiehl Bridge located in Luxembourg. Several damage levels were intentionally created by cutting a growing number of prestressed tendons and vibration data were acquired by the University of Luxembourg for each damaged state. The second example consists in reinforced and prestressed concrete panels. Successive damages were introduced in the panels by loading heavy weights and by cutting steel wires. The illustrations show different consequences in damage identification by the considered techniques.

  2. Low-frequency and wideband vibration energy harvester with flexible frame and interdigital structure

    Pengwei Li

    2015-04-01

    Full Text Available As an alternative to traditional cantilever beam structures and their evolutions, a flexible beam based, interdigital structure, vibration energy harvester has been presented and investigated. The proposed interdigital-shaped oscillator consists of a rectangular flexible frame and series of cantilever beams interdigitally bonded to it. In order to achieve low frequency and wide-bandwidth harvesting, Young’s modulus of materials, frame size and the amount of the cantilevers have been studied systematically. The measured frequency responses of the designed device (PDMS frame, quintuple piezoelectric cantilever beams show a 460% increase in bandwidth below 80Hz. When excited at an acceleration of 1.0 g, the energy harvester achieves to a maximum open-circuit voltage of 65V, and the maximum output power 4.5 mW.

  3. Low-frequency and wideband vibration energy harvester with flexible frame and interdigital structure

    Li, Pengwei, E-mail: lipengwei@tyut.edu.cn; Wang, Yanfen; Luo, Cuixian; Li, Gang; Hu, Jie; Zhang, Wendong [MicroNano System Research Center of College of Information Engineering and Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Liu, Ying [MicroNano System Research Center of College of Information Engineering and Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Baicheng Ordnance Test Center of China, Baicheng 137000, Jilin (China); Liu, Wei [Baicheng Ordnance Test Center of China, Baicheng 137000, Jilin (China)

    2015-04-15

    As an alternative to traditional cantilever beam structures and their evolutions, a flexible beam based, interdigital structure, vibration energy harvester has been presented and investigated. The proposed interdigital-shaped oscillator consists of a rectangular flexible frame and series of cantilever beams interdigitally bonded to it. In order to achieve low frequency and wide-bandwidth harvesting, Young’s modulus of materials, frame size and the amount of the cantilevers have been studied systematically. The measured frequency responses of the designed device (PDMS frame, quintuple piezoelectric cantilever beams) show a 460% increase in bandwidth below 80Hz. When excited at an acceleration of 1.0 g, the energy harvester achieves to a maximum open-circuit voltage of 65V, and the maximum output power 4.5 mW.

  4. High frequency characterization of conductive inks embedded within a structural composite

    Pa, Peter; McCauley, Raymond; Larimore, Zachary; Mills, Matthew; Yarlaggada, Shridhar; Mirotznik, Mark S.

    2015-06-01

    Woven fabric composites provide an attractive platform for integrating electromagnetic functionality—such as conformal load-bearing antennas and frequency selective surfaces—into a structural platform. One practical fabrication method for integrating conductive elements within a woven fabric composite system involves using additive manufacturing systems such as screen printing. While screen printing is an inherently scalable, flexible and cost effective method, little is known about the high frequency electrical properties of its conductive inks when they are embedded within the woven fabric composite. Thus, we have completed numerical and experimental studies to determine the electrical conductivity of screen printable conductive inks that are embedded within this composite. We have also performed mechanical studies to evaluate how printing affects the structural performance of the composite.

  5. Connecting structural relaxation with the low frequency modes in a hard-sphere colloidal glass.

    Ghosh, Antina; Chikkadi, Vijayakumar; Schall, Peter; Bonn, Daniel

    2011-10-28

    Structural relaxation in hard-sphere colloidal glasses has been studied using confocal microscopy. The motion of individual particles is followed over long time scales to detect the rearranging regions in the system. We have used normal mode analysis to understand the origin of the rearranging regions. The low-frequency modes, obtained over short time scales, show strong spatial correlation with the rearrangements that happen on long time scales.

  6. Development of Lightweight, Compact, Structurally-Integrated Acoustic Liners for Broadband Low-Frequency Noise Mitigation

    Chambers, Andrew T.

    Airborne noise with a low dominant frequency content (scope of conventional acoustic noise mitigation techniques using liners, foams or claddings owing to mass and volume considerations. Its low evanescence contributes significantly to environmental noise pollution, and unwanted structural vibrations causing diminished efficiency, comfort, payload integrity and mission capabilities. An alternative approach using liner configurations with realistic mass and volume constraints having innovative 'folded' core geometries is investigated to ascertain its low-frequency noise absorption characteristics. In contrast to mass-driven approaches, the folded core approach relies on tailoring interactions between acoustic resonances to tune the liner's impedance to suit the dominant low-frequency content of the source. This allows to keep non-structural mass-addition to a minimum, while retaining an overall thickness comparable to conventional liners for these low-frequency liner designs. The relative acoustic performance of various candidate folded core designs is evaluated by means of a new composite metric termed the Low-Frequency Performance (LFP) factor, which is educed from the absorption coefficient spectrum obtained using Zwikker-Kosten Transmission Line (ZKTL) theory-based numerical studies. An LFP-based software tool is developed to determine optimal 3D cavity packing for a prescribed liner volume and target frequency range. ZKTL-based parametric studies on core dimensions and face sheet porosity are utilized for detailed design of test articles. Experimental verification of absorption coefficient spectra conducted using 3D printed test articles in a normal incidence acoustic impedance tube yield good correlation with simulations. More than 100 Hz of continuous bandwidth with an absorption coefficient greater than 0.6 is shown to be possible in the 300 to 400 Hz range with a 38.1-mm (1.5-inch) thick liner. Further, the influence of face sheet type, Mach number, and

  7. Hyper capacity of MCM-41 supramoleculer structure in the radio- frequency range

    I.I. Grygorchak; S.A. Vojtovych; Z.A. Stotsko; B.A. Seredyuk; N.K. Tovstyuk

    2011-01-01

    Purpose: of this paper was: 1) to synthesize supramolecular МСМ-41 structure (p-cyanogen phenyl ether of n-heptyl benzoic acid - 40%)>> with inserted guested nematic and 2) to study its dielectric properties.Design/methodology/approach: Supramolecular МСМ-41 structure has been synthesized by vacuum encapsulated method at room temperature. Dielectric properties have been studied by impedance spectroscopy method in the frequency range 10-3-106 Hz by “AUTOLAB” complex of “ECO CHEMIE” (Holland),...

  8. Novel radio-frequency gun structures for ultrafast relativistic electron diffraction.

    Musumeci, P; Faillace, L; Fukasawa, A; Moody, J T; O'Shea, B; Rosenzweig, J B; Scoby, C M

    2009-08-01

    Radio-frequency (RF) photoinjector-based relativistic ultrafast electron diffraction (UED) is a promising new technique that has the potential to probe structural changes at the atomic scale with sub-100 fs temporal resolution in a single shot. We analyze the limitations on the temporal and spatial resolution of this technique considering the operating parameters of a standard 1.6 cell RF gun (which is the RF photoinjector used for the first experimental tests of relativistic UED at Stanford Linear Accelerator Center; University of California, Los Angeles; Brookhaven National Laboratory), and study the possibility of employing novel RF structures to circumvent some of these limits.

  9. Musical aptitude is associated with AVPR1A-haplotypes.

    Liisa T Ukkola

    Full Text Available Artistic creativity forms the basis of music culture and music industry. Composing, improvising and arranging music are complex creative functions of the human brain, which biological value remains unknown. We hypothesized that practicing music is social communication that needs musical aptitude and even creativity in music. In order to understand the neurobiological basis of music in human evolution and communication we analyzed polymorphisms of the arginine vasopressin receptor 1A (AVPR1A, serotonin transporter (SLC6A4, catecol-O-methyltranferase (COMT, dopamin receptor D2 (DRD2 and tyrosine hydroxylase 1 (TPH1, genes associated with social bonding and cognitive functions in 19 Finnish families (n = 343 members with professional musicians and/or active amateurs. All family members were tested for musical aptitude using the auditory structuring ability test (Karma Music test; KMT and Carl Seashores tests for pitch (SP and for time (ST. Data on creativity in music (composing, improvising and/or arranging music was surveyed using a web-based questionnaire. Here we show for the first time that creative functions in music have a strong genetic component (h(2 = .84; composing h(2 = .40; arranging h(2 = .46; improvising h(2 = .62 in Finnish multigenerational families. We also show that high music test scores are significantly associated with creative functions in music (p<.0001. We discovered an overall haplotype association with AVPR1A gene (markers RS1 and RS3 and KMT (p = 0.0008; corrected p = 0.00002, SP (p = 0.0261; corrected p = 0.0072 and combined music test scores (COMB (p = 0.0056; corrected p = 0.0006. AVPR1A haplotype AVR+RS1 further suggested a positive association with ST (p = 0.0038; corrected p = 0.00184 and COMB (p = 0.0083; corrected p = 0.0040 using haplotype-based association test HBAT. The results suggest that the neurobiology of music perception and production is likely to be related to the pathways affecting intrinsic attachment

  10. Mechanical low-frequency filter via modes separation in 3D periodic structures

    D'Alessandro, L.; Belloni, E.; Ardito, R.; Braghin, F.; Corigliano, A.

    2017-12-01

    This work presents a strategy to design three-dimensional elastic periodic structures endowed with complete bandgaps, the first of which is ultra-wide, where the top limits of the first two bandgaps are overstepped in terms of wave transmission in the finite structure. Thus, subsequent bandgaps are merged, approaching the behaviour of a three-dimensional low-pass mechanical filter. This result relies on a proper organization of the modal characteristics, and it is validated by performing numerical and analytical calculations over the unit cell. A prototype of the analysed layout, made of Nylon by means of additive manufacturing, is experimentally tested to assess the transmission spectrum of the finite structure, obtaining good agreement with numerical predictions. The presented strategy paves the way for the development of a class of periodic structures to be used in robust and reliable wave attenuation over a wide frequency band.

  11. Fine structure in plasma waves and radiation near the plasma frequency in Earth's foreshock

    Cairns, Iver H.

    1994-01-01

    Novel observations are presented of intrunsic fine structure in the frequency spectrum of electomagnetic (EM) radiation and plasma waves near the electron plasma frequency f(sub p) during a period of unusually high interplanetary magnetic field strength. Measured using the wideband receiver on the International Sun-Earth Explorer (ISEE) 1 spacecraft, fine-structured emissions are observed both in the solar wind and the foreshock, The fine structure is shown to correspond to emissions spaced above f(sub p) near half harmonies of the electon cyclotron frequency f(sub ce), i.e., near f(sub p) + nf(sub ce)/2. These appear to be the first space physics observations of emissions spaced by f(sub ce)/2. Indirect but strong arguments are used to discriminate between EM and electrostatic (ES) signals, to identify whether ISEE 1 is in the solar wind or the foreshock, and to determine the relative frequencies of the emissions and the local f(sub p). The data are consistent with generation of the ES and EM emissions in the foreshock, with subsequent propagation of the EM emissions into the solar wind. It remains possible that some emissions currently identified as ES have significant EM character. The ES and EM emisions often merge into one another with minimal changes in frequency, arguing that their source regions and generation mechanisms are related and imposing significant constraints on theories. The f(sub ce)/2 ES and EM fine structures observed may be intrinsic to the emission mechanisms or to superposition of two series of signals with f(sub ce) spacing that differ in starting frequency by f(sub ce)/2. Present theories for nonlinear wave coupling processes, cyclotron maser emission, and other linear instability processes are all unable to explain multiple EM and/or ES components spaced by approximately f(sub ce)/2 above f(sub p) for f(sub p)/f(sub ce) much greater than 1 and typical for shock beams parameters. Suitable avenues for further theoretical research are

  12. Origami-based mechanical metamaterials with tunable frequency band structures (Conference Presentation)

    Yasuda, Hiromi; Pratt, Riley; Yang, Jinkyu

    2017-04-01

    We investigate wave dynamics in origami-based mechanical metamaterials composed of bellows-like origami structures, specifically the Tachi-Miura Polyhedron (TMP). One of the unique features of the TMP is that its structural deformations take place only along the crease lines, therefore the structure can be made of rigid plates and hinges. By utilizing this feature, we introduce linear torsional springs to model the crease lines and derive the force and displacement relationship of the TMP structure along the longitudinal direction. Our analysis shows strain softening/hardening behaviors in compression/tensile regions respectively, and the force-displacement curve can be manipulated by altering the initial configuration of the TMP (e.g., the initial folding angle). We also fabricate physical prototypes and measure the force-displacement behavior to verify our analytical model. Based on this static analysis on the TMP, we simplify the TMP structure into a linkage model, preserving the tunable strain softening/hardening behaviors. Dynamic analysis is also conducted numerically to analyze the frequency response of the simplified TMP unit cell under harmonic excitations. The simplified TMP exhibits a transition between linear and nonlinear behaviors, which depends on the amplitude of the excitation and the initial configuration. In addition, we design a 1D system composed of simplified TMP unit cells and analyze the relationship between frequency and wave number. If two different configurations of the unit cell (e.g., different initial folding angles) are connected in an alternating arrangement, the system develops frequency bandgaps. These unique static/dynamic behaviors can be exploited to design engineering devices which can handle vibrations and impact in an efficient manner.

  13. Musical Aptitude Is Associated with AVPR1A-Haplotypes

    Ukkola, Liisa T.; Onkamo, Päivi; Raijas, Pirre; Karma, Kai; Järvelä, Irma

    2009-01-01

    Artistic creativity forms the basis of music culture and music industry. Composing, improvising and arranging music are complex creative functions of the human brain, which biological value remains unknown. We hypothesized that practicing music is social communication that needs musical aptitude and even creativity in music. In order to understand the neurobiological basis of music in human evolution and communication we analyzed polymorphisms of the arginine vasopressin receptor 1A (AVPR1A), serotonin transporter (SLC6A4), catecol-O-methyltranferase (COMT), dopamin receptor D2 (DRD2) and tyrosine hydroxylase 1 (TPH1), genes associated with social bonding and cognitive functions in 19 Finnish families (n = 343 members) with professional musicians and/or active amateurs. All family members were tested for musical aptitude using the auditory structuring ability test (Karma Music test; KMT) and Carl Seashores tests for pitch (SP) and for time (ST). Data on creativity in music (composing, improvising and/or arranging music) was surveyed using a web-based questionnaire. Here we show for the first time that creative functions in music have a strong genetic component (h2 = .84; composing h2 = .40; arranging h2 = .46; improvising h2 = .62) in Finnish multigenerational families. We also show that high music test scores are significantly associated with creative functions in music (pmusic test scores (COMB) (p = 0.0056; corrected p = 0.0006). AVPR1A haplotype AVR+RS1 further suggested a positive association with ST (p = 0.0038; corrected p = 0.00184) and COMB (p = 0.0083; corrected p = 0.0040) using haplotype-based association test HBAT. The results suggest that the neurobiology of music perception and production is likely to be related to the pathways affecting intrinsic attachment behavior. PMID:19461995

  14. Musical aptitude is associated with AVPR1A-haplotypes.

    Ukkola, Liisa T; Onkamo, Päivi; Raijas, Pirre; Karma, Kai; Järvelä, Irma

    2009-05-20

    Artistic creativity forms the basis of music culture and music industry. Composing, improvising and arranging music are complex creative functions of the human brain, which biological value remains unknown. We hypothesized that practicing music is social communication that needs musical aptitude and even creativity in music. In order to understand the neurobiological basis of music in human evolution and communication we analyzed polymorphisms of the arginine vasopressin receptor 1A (AVPR1A), serotonin transporter (SLC6A4), catecol-O-methyltranferase (COMT), dopamin receptor D2 (DRD2) and tyrosine hydroxylase 1 (TPH1), genes associated with social bonding and cognitive functions in 19 Finnish families (n = 343 members) with professional musicians and/or active amateurs. All family members were tested for musical aptitude using the auditory structuring ability test (Karma Music test; KMT) and Carl Seashores tests for pitch (SP) and for time (ST). Data on creativity in music (composing, improvising and/or arranging music) was surveyed using a web-based questionnaire. Here we show for the first time that creative functions in music have a strong genetic component (h(2) = .84; composing h(2) = .40; arranging h(2) = .46; improvising h(2) = .62) in Finnish multigenerational families. We also show that high music test scores are significantly associated with creative functions in music (pmusic test scores (COMB) (p = 0.0056; corrected p = 0.0006). AVPR1A haplotype AVR+RS1 further suggested a positive association with ST (p = 0.0038; corrected p = 0.00184) and COMB (p = 0.0083; corrected p = 0.0040) using haplotype-based association test HBAT. The results suggest that the neurobiology of music perception and production is likely to be related to the pathways affecting intrinsic attachment behavior.

  15. Structure and dielectric properties in the radio frequency range of polymer composites based on vanadium dioxide

    Kolbunov V.R.

    2015-06-01

    Full Text Available Polymer composites with active fillers are recently considered to be promising materials for the design of new functional devices with controllable properties and are intensively investigated. Dielectric studies are one of the most effective methods for studying structural features and mechanisms of conductivity formation for this type of two-component systems. The paper presents research results of the dielectric characteristics in the range of radio frequency of 50 kHz — 10 MHz and temperature range of 30—60°C of polyethylene composites of vanadium dioxide with different volume fractions of filler. Two dispersion areas were found: a high-frequency area caused by the Maxwell charge separation on the boundaries of the polyethylene matrix — conductive filler of VI2 crystallites, and a low frequency area associated with the presence of the transition layer at this boundary. The relative permittivity of the composite has a tendency to a decrease in absolute value with increasing temperature. The analysis of the low-frequency dependence of the dielectric constant of the value of the filler’s volume fraction revealed that the investigated composite belongs to two-component statistical mixtures with a transition layer between the components.

  16. The Low Pitch of High-Frequency Complex Tones Relies on Temporal Fine Structure Information

    Santurette, Sébastien; Dau, Torsten

    2010-01-01

    High-frequency complex tones containing only unresolved harmonic components with a frequency spacing Δf usually evoke a low pitch equal to Δf. However, for inharmonic components, the low pitch is often found to deviate slightly from Δf. Whether this pitch shift relies exclusively on temporal fine...... structure (TFS) cues has been a matter of debate. It is also controversial up to which frequency TFS information remains available, and to what extent envelope cues become dominant as frequency increases. Using a pitch-matching paradigm, this study investigated whether the pitch of transposed tones.......5]. All stimuli were presented at 50 dB SPL in broadband pink-noise (13.5 dB/Hz at 1 kHz), and 40 matches per condition were obtained. For fenv = fc/11.5, the results favored hypothesis A for all values of fc, indicating that TFS cues are available and used for pitch extraction, up to at least 7 k...

  17. SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle.

    Huang, Yong-Zhen; Zhan, Zhao-Yang; Li, Xin-Yi; Wu, Sheng-Ru; Sun, Yu-Jia; Xue, Jing; Lan, Xian-Yong; Lei, Chu-Zhao; Zhang, Chun-Lei; Jia, Yu-Tang; Chen, Hong

    2014-02-01

    Insulin-like growth factor 2 (IGF2) is a potent cell growth and differentiation factor and is implicated in mammals' growth and development. The objective of this study was to evaluate the effects of the mutations in the bovine IGF2 with growth traits in Chinese Qinchuan cattle. Four single nucleotide polymorphisms (SNPs) were detected of the bovine IGF2 by DNA pool sequencing and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. We also investigated haplotype structure and linkage disequilibrium (LD) coefficients for four SNPs in 817 individuals representing two main cattle breeds from China. The result of haplotype analysis showed eight different haplotypes and 27 combined genotypes within the study population. The statistical analyses indicated that the four SNPs, combined genotypes and haplotypes are associated with the withers height, body length, chest breadth, chest depth and body weight in Qinchuan cattle population (P growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.

  18. Modeling High Frequency Data with Long Memory and Structural Change: A-HYEGARCH Model

    Yanlin Shi

    2018-03-01

    Full Text Available In this paper, we propose an Adaptive Hyperbolic EGARCH (A-HYEGARCH model to estimate the long memory of high frequency time series with potential structural breaks. Based on the original HYGARCH model, we use the logarithm transformation to ensure the positivity of conditional variance. The structural change is further allowed via a flexible time-dependent intercept in the conditional variance equation. To demonstrate its effectiveness, we perform a range of Monte Carlo studies considering various data generating processes with and without structural changes. Empirical testing of the A-HYEGARCH model is also conducted using high frequency returns of S&P 500, FTSE 100, ASX 200 and Nikkei 225. Our simulation and empirical evidence demonstrate that the proposed A-HYEGARCH model outperforms various competing specifications and can effectively control for structural breaks. Therefore, our model may provide more reliable estimates of long memory and could be a widely useful tool for modelling financial volatility in other contexts.

  19. Effects of past burning frequency on plant species structure and composition in dry dipterocarp forest

    Wanthongchai, Dr.; Bauhus, Prof.; Goldammer, Prof.

    2009-04-01

    Anthropogenic burning in dry dipterocarp forests (DDF) has become a common phenomenon throughout Thailand. It is feared that too frequent fires may affect vegetation structure and composition and thus impact on ecosystem productivity. The aim of this study was to quantify the effects of prescribed fires on sites with different past burning regimes on vegetation structure and composition in the Huay Kha Khaeng Wildlife Sanctuary (HKK), Thailand. Fire frequency was determined from satellite images and ranged from frequent, infrequent, rare and unburned with fire occurrences of 7, 2, 1 and 0 out of the past 10 years, respectively. The pre-burn fuel loads, the overstorey and understorey vegetation structure and composition were determined to investigate the effects of the contrasting past burning regimes. The burning experiment was carried out, applying a three-strip head-fire burning technique. The vegetation structure and composition were sampled again one year after the fire to assess the fire impacts. Aboveground fine fuel loads increased with the length of fire-free interval. The woody plant structures of the frequently burned stand differed from those of the other less frequently burned stands. The species composition of the overstorey on the frequently burned site, in particular that of small sized trees (4.5-10 cm dbh), also differed significantly from that of the other sites. Whilst the ground vegetation including shrubs and herbs did not differ between the past burning regimes, frequent burning obviously promoted the proliferation of graminoid vegetation. There was no clear evidence showing that the prescribed fires affected the mortality of trees (dbh> 4.5 cm) on the sites of the different past burning regimes. The effects of prescribed burning on the understorey vegetation structures varied between the past burning regimes and the understorey vegetation type. Therefore, it is recommended that the DDF at HKK should be subjected to a prescribed fire frequency

  20. HapCol : Accurate and memory-efficient haplotype assembly from long reads

    Pirola, Yuri; Zaccaria, Simone; Dondi, Riccardo; Klau, Gunnar W.; Pisanti, Nadia; Bonizzoni, Paola

    2016-01-01

    Motivation: Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from the advent

  1. HapCol: Accurate and Memory-efficient Haplotype Assembly from Long Reads

    Y. Pirola (Yuri); S. Zaccaria (Simone); R. Dondi (Riccardo); G.W. Klau (Gunnar); N. Pisanti (Nadia); P. Bonizzoni (Paola)

    2015-01-01

    htmlabstractMotivation: Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from

  2. A common haplotype in the G-protein-coupled receptor gene GPR74 is associated with leanness and increased lipolysis

    Dahlman, Ingrid; Dicker, Andrea; Jiao, Hong

    2007-01-01

    0.36; P=.036) among those selected for obese or lean phenotypes. The ATAG haplotype was associated with increased adipocyte lipid mobilization (lipolysis) in vivo and in vitro. In human fat cells, GPR74 receptor stimulation and inhibition caused a significant and marked decrease and increase......, respectively, of lipolysis, which could be linked to catecholamine stimulation of adipocytes through beta -adrenergic receptors. These findings suggest that a common haplotype in the GPR74 gene protects against obesity, which, at least in part, is caused by a relief of inhibition of lipid mobilization from......The G-protein-coupled receptor GPR74 is a novel candidate gene for body weight regulation. In humans, it is predominantly expressed in brain, heart, and adipose tissue. We report a haplotype in the GPR74 gene, ATAG, with allele frequency ~4% in Scandinavian cohorts, which was associated...

  3. Prediction of pressure induced structural phase transitions and internal mode frequency changes in solid N2+

    Etters, R.D.; Kobashi, K.; Chandrasekharan, V.

    1983-01-01

    A rhombohedral distortion of the Pm3n structure is introduced which shows that a low temperature phase transition occurs from P4 2 /mnm into the R3c calcite structure at P approx. = 19.2 kbar with a volume change of 0.125 cm 3 /mole. This transition agrees with recent Raman scattering measurements. Another transition from R3c into R3m is predicted at P approx. = 67.5 kbar, with a volume change of 0.1 cm 3 /mole. The pressure dependence of the intramolecular mode frequencies for the R3c structure is in reasonably good agreement with the two main branches observed experimentally

  4. Yield Frequency Spectra and seismic design of code-compatible RC structures: an illustrative example

    Katsanos, Evangelos; Vamvatsikos, Dimitrios

    2017-01-01

    with given yield displacement and capacity curve shape. For the 8-story case study building, deformation checking is the governing limit state. A conventional code-based design was performed using seismic intensities tied to the desired MAF for safety checking. Then, the YFS-based approach was employed......The seismic design of an 8-story reinforced concrete space frame building is undertaken using a Yield Frequency Spectra (YFS) performance-based approach. YFS offer a visual representation of the entire range of a system’s performance in terms of the mean annual frequency (MAF) of exceeding...... to redesign the resulting structure working backwards from the desired MAF of response (rather than intensity) to estimate an appropriate value of seismic intensity for use within a typical engineering design process. For this high-seismicity and high-importance midrise building, a stiffer system with higher...

  5. The influence of sense-contingent argument structure frequencies on ambiguity resolution in aphasia.

    Huck, Anneline; Thompson, Robin L; Cruice, Madeline; Marshall, Jane

    2017-06-01

    Verbs with multiple senses can show varying argument structure frequencies, depending on the underlying sense. When acknowledge is used to mean 'recognise', it takes a direct object (DO), but when it is used to mean 'admit' it prefers a sentence complement (SC). The purpose of this study was to investigate whether people with aphasia (PWA) can exploit such meaning-structure probabilities during the reading of temporarily ambiguous sentences, as demonstrated for neurologically healthy individuals (NHI) in a self-paced reading study (Hare et al., 2003). Eleven people with mild or moderate aphasia and eleven neurologically healthy control participants read sentences while their eyes were tracked. Using adapted materials from the study by Hare et al. target sentences containing an SC structure (e.g. He acknowledged (that) his friends would probably help him a lot) were presented following a context prime that biased either a direct object (DO-bias) or sentence complement (SC-bias) reading of the verbs. Half of the stimuli sentences did not contain that so made the post verbal noun phrase (his friends) structurally ambiguous. Both groups of participants were influenced by structural ambiguity as well as by the context bias, indicating that PWA can, like NHI, use their knowledge of a verb's sense-based argument structure frequency during online sentence reading. However, the individuals with aphasia showed delayed reading patterns and some individual differences in their sensitivity to context and ambiguity cues. These differences compared to the NHI may contribute to difficulties in sentence comprehension in aphasia. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. A reduced number of mtSNPs saturates mitochondrial DNA haplotype diversity of worldwide population groups.

    Salas, Antonio; Amigo, Jorge

    2010-05-03

    The high levels of variation characterising the mitochondrial DNA (mtDNA) molecule are due ultimately to its high average mutation rate; moreover, mtDNA variation is deeply structured in different populations and ethnic groups. There is growing interest in selecting a reduced number of mtDNA single nucleotide polymorphisms (mtSNPs) that account for the maximum level of discrimination power in a given population. Applications of the selected mtSNP panel range from anthropologic and medical studies to forensic genetic casework. This study proposes a new simulation-based method that explores the ability of different mtSNP panels to yield the maximum levels of discrimination power. The method explores subsets of mtSNPs of different sizes randomly chosen from a preselected panel of mtSNPs based on frequency. More than 2,000 complete genomes representing three main continental human population groups (Africa, Europe, and Asia) and two admixed populations ("African-Americans" and "Hispanics") were collected from GenBank and the literature, and were used as training sets. Haplotype diversity was measured for each combination of mtSNP and compared with existing mtSNP panels available in the literature. The data indicates that only a reduced number of mtSNPs ranging from six to 22 are needed to account for 95% of the maximum haplotype diversity of a given population sample. However, only a small proportion of the best mtSNPs are shared between populations, indicating that there is not a perfect set of "universal" mtSNPs suitable for all population contexts. The discrimination power provided by these mtSNPs is much higher than the power of the mtSNP panels proposed in the literature to date. Some mtSNP combinations also yield high diversity values in admixed populations. The proposed computational approach for exploring combinations of mtSNPs that optimise the discrimination power of a given set of mtSNPs is more efficient than previous empirical approaches. In contrast to

  7. Y chromosome haplotype diversity of domestic sheep (Ovis aries) in northern Eurasia.

    Zhang, Min; Peng, Wei-Feng; Yang, Guang-Li; Lv, Feng-Hua; Liu, Ming-Jun; Li, Wen-Rong; Liu, Yong-Gang; Li, Jin-Quan; Wang, Feng; Shen, Zhi-Qiang; Zhao, Sheng-Guo; Hehua, Eer; Marzanov, Nurbiy; Murawski, Maziek; Kantanen, Juha; Li, Meng-Hua

    2014-12-01

    Variation in two SNPs and one microsatellite on the Y chromosome was analyzed in a total of 663 rams representing 59 breeds from a large geographic range in northern Eurasia. SNPA-oY1 showed the highest allele frequency (91.55%) across the breeds, whereas SNPG-oY1 was present in only 56 samples. Combined genotypes established seven haplotypes (H4, H5, H6, H7, H8, H12 and H19). H6 dominated in northern Eurasia, and H8 showed the second-highest frequency. H4, which had been earlier reported to be absent in European breeds, was detected in one European breed (Swiniarka), whereas H7, which had been previously identified to be unique to European breeds, was present in two Chinese breeds (Ninglang Black and Large-tailed Han), one Buryatian (Transbaikal Finewool) and two Russian breeds (North Caucasus Mutton-Wool and Kuibyshev). H12, which had been detected only in Turkish breeds, was also found in Chinese breeds in this work. An overall low level of haplotype diversity (median h = 0.1288) was observed across the breeds with relatively higher median values in breeds from the regions neighboring the Near Eastern domestication center of sheep. H6 is the dominant haplotype in northwestern and eastern China, in which the haplotype distribution could be explained by the historical translocations of the H4 and H8 Y chromosomes to China via the Mongol invasions followed by expansions to northwestern and eastern China. Our findings extend previous results of sheep Y chromosomal genetic variability and indicate probably recent paternal gene flows between sheep breeds from distinct major geographic regions. © 2014 Stichting International Foundation for Animal Genetics.

  8. Worldwide distribution of the MYH9 kidney disease susceptibility alleles and haplotypes: evidence of historical selection in Africa.

    Taras K Oleksyk

    2010-07-01

    Full Text Available MYH9 was recently identified as renal susceptibility gene (OR 3-8, p or = 60% than in European Americans (< 4%, revealing a genetic basis for a major health disparity. The population distributions of MYH9 risk alleles and the E-1 risk haplotype and the demographic and selective forces acting on the MYH9 region are not well explored. We reconstructed MYH9 haplotypes from 4 tagging single nucleotide polymorphisms (SNPs spanning introns 12-23 using available data from HapMap Phase II, and by genotyping 938 DNAs from the Human Genome Diversity Panel (HGDP. The E-1 risk haplotype followed a cline, being most frequent within sub-Saharan African populations (range 50-80%, less frequent in populations from the Middle East (9-27% and Europe (0-9%, and rare or absent in Asia, the Americas, and Oceania. The fixation indexes (F(ST for pairwise comparisons between the risk haplotypes for continental populations were calculated for MYH9 haplotypes; F(ST ranged from 0.27-0.40 for Africa compared to other continental populations, possibly due to selection. Uniquely in Africa, the Yoruba population showed high frequency extended haplotype length around the core risk allele (C compared to the alternative allele (T at the same locus (rs4821481, iHs = 2.67, as well as high population differentiation (F(ST(CEU vs. YRI = 0.51 in HapMap Phase II data, also observable only in the Yoruba population from HGDP (F(ST = 0.49, pointing to an instance of recent selection in the genomic region. The population-specific divergence in MYH9 risk allele frequencies among the world's populations may prove important in risk assessment and public health policies to mitigate the burden of kidney disease in vulnerable populations.

  9. Structure and orientation of interfacial proteins determined by sum frequency generation vibrational spectroscopy: method and application.

    Ye, Shuji; Wei, Feng; Li, Hongchun; Tian, Kangzhen; Luo, Yi

    2013-01-01

    In situ and real-time characterization of molecular structures and orientation of proteins at interfaces is essential to understand the nature of interfacial protein interaction. Such work will undoubtedly provide important clues to control biointerface in a desired manner. Sum frequency generation vibrational spectroscopy (SFG-VS) has been demonstrated to be a powerful technique to study the interfacial structures and interactions at the molecular level. This paper first systematically introduced the methods for the calculation of the Raman polarizability tensor, infrared transition dipole moment, and SFG molecular hyperpolarizability tensor elements of proteins/peptides with the secondary structures of α-helix, 310-helix, antiparallel β-sheet, and parallel β-sheet, as well as the methodology to determine the orientation of interfacial protein secondary structures using SFG amide I spectra. After that, recent progresses on the determination of protein structure and orientation at different interfaces by SFG-VS were then reviewed, which provides a molecular-level understanding of the structures and interactions of interfacial proteins, specially understanding the nature of driving force behind such interactions. Although this review has focused on analysis of amide I spectra, it will be expected to offer a basic idea for the spectral analysis of amide III SFG signals and other complicated molecular systems such as RNA and DNA. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. Frequency selective surface based passive wireless sensor for structural health monitoring

    Jang, Sang-Dong; Kang, Byung-Woo; Kim, Jaehwan

    2013-01-01

    Wireless sensor networks or ubiquitous sensor networks are a promising technology giving useful information to people. In particular, the chipless passive wireless sensor is one of the most important developments in wireless sensor technology because it is compact and does not need a battery or chip for the sensor operation. So it has many possibilities for use in various types of sensor system with economical efficiency and robustness in harsh environmental conditions. This sensor uses an electromagnetic resonance frequency or phase angle shift associated with a geometrical change of the sensor tag or an impedance change of the sensor. In this paper, a chipless passive wireless structural health monitoring (SHM) sensor is made using a frequency selective surface (FSS). The cross type FSS is introduced, and its SHM principle is explained. The electromagnetic characteristics of the FSS are simulated in terms of transmission and reflection coefficients using simulation software, and an experimental verification is conducted. The electromagnetic characteristic change of the FSS in the presence of mechanical strain or a structural crack is investigated by means of simulation and experiment. Since large-area structures can be covered by deploying FSS, it is possible to detect the location of any cracks. (paper)

  11. A variable-frequency structural health monitoring system based on omnidirectional shear horizontal wave piezoelectric transducers

    Huan, Qiang; Miao, Hongchen; Li, Faxin

    2018-02-01

    Structural health monitoring (SHM) is of great importance for engineering structures as it may detect the early degradation and thus avoid life and financial loss. Guided wave based inspection is very useful in SHM due to its capability for long distance and wide range monitoring. The fundamental shear horizontal (SH0) wave based method should be most promising since SH0 is the unique non-dispersive wave mode in plate-like structures. In this work, a sparse array SHM system based on omnidirectional SH wave piezoelectric transducers (OSH-PT) was proposed and the multi data fusion method was used for defect inspection in a 2 mm thick aluminum plate. Firstly, the performances of three types OSH-PTs was comprehensively compared and the thickness-poled d15 mode OSH-PT used in this work was demonstrated obviously superior to the other two. Then, the signal processing method and imaging algorithm for this SHM system was presented. Finally, experiments were carried out to examine the performance of the proposed SHM system in defect localization and imaging. Results indicated that this SHM system can locate a through hole as small as 0.12λ (4 mm) in diameter (where λ is the wavelength corresponding to the central operation frequency) under frequencies from 90 to 150 kHz. It can also locate multiple defects accurately based on the baseline subtraction method. Obviously, this SHM system can detect larger areas with sparse sensors because of the adopted single mode, non-dispersive and low frequency SH0 wave which can propagate long distance with small attenuation. Considering its good performances, simple data processing and sparse array, this SH0 wave-based SHM system is expected to greatly promote the applications of guided wave inspection.

  12. Theoretical and experimental investigation into structural and fluid motions at low frequencies in water distribution pipes

    Gao, Yan; Liu, Yuyou

    2017-06-01

    Vibrational energy is transmitted in buried fluid-filled pipes in a variety of wave types. Axisymmetric (n = 0) waves are of practical interest in the application of acoustic techniques for the detection of leaks in underground pipelines. At low frequencies n = 0 waves propagate longitudinally as fluid-dominated (s = 1) and shell-dominated (s = 2) waves. Whilst sensors such as hydrophones and accelerometers are commonly used to detect leaks in water distribution pipes, the mechanism governing the structural and fluid motions is not well documented. In this paper, the low-frequency behaviour of the pipe wall and the contained fluid is investigated. For most practical pipework systems, these two waves are strongly coupled; in this circumstance the ratios of the radial pipe wall displacements along with the internal pressures associated with these two wave types are obtained. Numerical examples show the relative insensitivity of the structural and fluid motions to the s = 2 wave for both metallic and plastic pipes buried in two typical soils. It is also demonstrated that although both acoustic and vibration sensors at the same location provide the identical phase information of the transmitted signals, pressure responses have significantly higher levels than acceleration responses, and thus hydrophones are better suited in a low signal-to-noise ratio (SNR) environment. This is supported by experimental work carried out at a leak detection facility. Additional pressure measurements involved excitation of the fluid and the pipe fitting (hydrant) on a dedicated water pipe. This work demonstrates that the s = 1 wave is mainly responsible for the structural and fluid motions at low frequencies in water distribution pipes as a result of water leakage and direct pipe excitation.

  13. Non destructive testing of heterogeneous structures with a step frequency radar

    Cattin, V.; Chaillout, J.J.

    1998-01-01

    Ground penetrating radar have shown increasing potential in diagnostic of soils or concrete, but the realisation of such a system and the interpretation of data produced by this technique require a clear understanding of the physical electromagnetic processes that appear between media and waves. In this paper are studied the performances of a step frequency radar as a nondestructive technique to evaluate different heterogeneous laboratory size structures. Some critical points are studied like material properties, antenna effect and image reconstruction algorithm, to determine its viability to distinguish smallest region of interest

  14. Structural control of metamaterial oscillator strength and electric field enhancement at terahertz frequencies

    Keiser, G. R.; Seren, H. R.; Strikwerda, Andrew C.

    2014-01-01

    The design of artificial nonlinear materials requires control over internal resonant charge densities and local electric field distributions. We present a MM design with a structurally controllable oscillator strength and local electric field enhancement at terahertz frequencies. The MM consists...... of a split ring resonator (SRR) array stacked above an array of closed conducting rings. An in-plane, lateral shift of a half unit cell between the SRR and closed ring arrays results in an increase of the MM oscillator strength by a factor of 4 and a 40% change in the amplitude of the resonant electric field...

  15. Analysis of Higher Order Modes in Large Superconducting Radio Frequency Accelerating Structures

    Galek, Tomasz; Brackebusch, Korinna; Van Rienen, Ursula

    2015-01-01

    Superconducting radio frequency cavities used for accelerating charged particle beams are commonly used in accelerator facilities around the world. The design and optimization of modern superconducting RF cavities requires intensive numerical simulations. Vast number of operational parameters must be calculated to ensure appropriate functioning of the accelerating structures. In this study, we primarily focus on estimation and behavior of higher order modes in superconducting RF cavities connected in chains. To calculate large RF models the state-space concatenation scheme, an efficient hybrid method, is employed.

  16. A spatial haplotype copying model with applications to genotype imputation.

    Yang, Wen-Yun; Hormozdiari, Farhad; Eskin, Eleazar; Pasaniuc, Bogdan

    2015-05-01

    Ever since its introduction, the haplotype copy model has proven to be one of the most successful approaches for modeling genetic variation in human populations, with applications ranging from ancestry inference to genotype phasing and imputation. Motivated by coalescent theory, this approach assumes that any chromosome (haplotype) can be modeled as a mosaic of segments copied from a set of chromosomes sampled from the same population. At the core of the model is the assumption that any chromosome from the sample is equally likely to contribute a priori to the copying process. Motivated by recent works that model genetic variation in a geographic continuum, we propose a new spatial-aware haplotype copy model that jointly models geography and the haplotype copying process. We extend hidden Markov models of haplotype diversity such that at any given location, haplotypes that are closest in the genetic-geographic continuum map are a priori more likely to contribute to the copying process than distant ones. Through simulations starting from the 1000 Genomes data, we show that our model achieves superior accuracy in genotype imputation over the standard spatial-unaware haplotype copy model. In addition, we show the utility of our model in selecting a small personalized reference panel for imputation that leads to both improved accuracy as well as to a lower computational runtime than the standard approach. Finally, we show our proposed model can be used to localize individuals on the genetic-geographical map on the basis of their genotype data.

  17. A DRD1 haplotype is associated with risk for autism spectrum disorders in male-only affected sib-pair families.

    Hettinger, Joe A; Liu, Xudong; Schwartz, Charles E; Michaelis, Ron C; Holden, Jeanette J A

    2008-07-05

    Individuals with autism spectrum disorders (ASDs) have impairments in executive function and social cognition, with males generally being more severely affected in these areas than females. Because the dopamine D1 receptor (encoded by DRD1) is integral to the neural circuitry mediating these processes, we examined the DRD1 gene for its role in susceptibility to ASDs by performing single marker and haplotype case-control comparisons, family-based association tests, and genotype-phenotype assessments (quantitative transmission disequilibrium tests: QTDT) using three DRD1 polymorphisms, rs265981C/T, rs4532A/G, and rs686T/C. Our previous findings suggested that the dopaminergic system may be more integrally involved in families with affected males only than in other families. We therefore restricted our study to families with two or more affected males (N = 112). There was over-transmission of rs265981-C and rs4532-A in these families (P = 0.040, P = 0.038), with haplotype TDT analysis showing over-transmission of the C-A-T haplotype (P = 0.022) from mothers to affected sons (P = 0.013). In addition, haplotype case-control comparisons revealed an increase of this putative risk haplotype in affected individuals relative to a comparison group (P = 0.004). QTDT analyses showed associations of the rs265981-C, rs4532-A, rs686-T alleles, and the C-A-T haplotype with more severe problems in social interaction, greater difficulties with nonverbal communication and increased stereotypies compared to individuals with other haplotypes. Preferential haplotype transmission of markers at the DRD1 locus and an increased frequency of a specific haplotype support the DRD1 gene as a risk gene for core symptoms of ASD in families having only affected males. Copyright 2008 Wiley-Liss, Inc.

  18. Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea.

    Kim, Hye Ri; Park, Yung Chul

    2015-11-10

    The aim of this study was to investigate the genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae in Korea. The Korean A. a. coreae is characterized by high levels of haplotype diversity (Hd=0.967) and low levels of nucleotide diversity (π=0.00683). Haplogroup 1 is well separated from the haplotypes of the neighboring regions of the Korean Peninsula, while the other haplogroups are closely related to those from the Russian Far East. Thus, further investigations are required to confirm the validity of the subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations present in the Korean Peninsula and its neighboring countries. Haplogroup 1 includes most Korean haplotypes and forms a star-like haplotype network structure, which reveals relatively low levels of sequence divergence and high frequency of unique mutations (only few mutations are shared in most of the haplotype nodes). The results indicate that the haplotypes of Haplogroup 1 might have experienced population expansion since their migration into Korea, which was further corroborated with negative results of neutrality tests for Korean population of A. a. coreae. Copyright © 2015. Published by Elsevier B.V.

  19. A direct method for soil-structure interaction analysis based on frequency-dependent soil masses

    Danisch, R.; Delinic, K.; Marti, J.; Trbojevic, V.M.

    1993-01-01

    In a soil-structure interaction analysis, the soil, as a subsystem of the global vibrating system, exerts a strong influence on the response of the nuclear reactor building to the earthquake excitation. The volume of resources required for dealing with the soil have led to a number of different types of frequency-domain solutions, most of them based on the impedance function approach. These procedures require coupling the soil to the lumped-mass finite-element model of the reactor building. In most practical cases, the global vibrating system is analysed in the time domain (i.e. modal time history, linear or non-linear direct time-integration). Hence, it follows that the frequency domain solution for soil must be converted to an 'equivalent' soil model in the time domain. Over the past three decades, different approaches have been developed and used for earthquake analysis of nuclear power plants. In some cases, difficulties experienced in modelling the soil have affected the methods of global analysis, thus leading to approaches like the substructuring technique, e.g. 3-step method. In the practical applications, the limitations of each specific method must be taken into account in order to avoid unrealistic results. The aim of this paper is to present the recent development on an equivalent SDOF system for soil including frequency-dependent soil masses. The method will be compared with the classical 3-step method. (author)

  20. Global Discontinuity Structure of the Mantle Transition Zone from Finite-Frequency Tomography of SS Precursors

    Guo, Z.; Zhou, Y.

    2017-12-01

    We report global structure of the 410-km and 660-km discontinuities from finite-frequency tomography using frequency-dependent traveltime measurements of SS precursors recorded at the Global Seismological Network (GSN). Finite-frequency sensitivity kernels for discontinuity depth perturbations are calculated in the framework of traveling-wave mode coupling. We parametrize the global discontinuities using a set of spherical triangular grid points and solve the tomographic inverse problem based on singular value decomposition. Our global 410-km and 660-km discontinuity models reveal distinctly different characteristics beneath the oceans and subduction zones. In general, oceanic regions are associated with a thinner mantle transition zone and depth perturbations of the 410-km and 660-km discontinuities are anti-correlated, in agreement with a thermal origin and an overall warm and dry mantle beneath the oceans. The perturbations are not uniform throughout the oceans but show strong small-scale variations, indicating complex processes in the mantle transition zone. In major subduction zones (except for South America where data coverage is sparse), depth perturbations of the 410-km and 660-km discontinuities are correlated, with both the 410-km and the 660-km discontinuities occurring at greater depths. The distributions of the anomalies are consistent with cold stagnant slabs just above the 660-km discontinuity and ascending return flows in a superadiabatic upper mantle.

  1. The doubly conditioned frequency spectrum does not distinguish between ancient population structure and hybridization

    Eriksson, Anders

    2014-03-13

    Distinguishing between hybridization and population structure in the ancestral species is a key challenge in our understanding of how permeable species boundaries are to gene flow. The doubly conditioned frequency spectrum (dcfs) has been argued to be a powerful metric to discriminate between these two explanations, and it was used to argue for hybridization between Neandertal and anatomically modern humans. The shape of the observed dcfs for these two species cannot be reproduced by a model that represents ancient population structure in Africa with two populations, while adding hybridization produces realistic shapes. In this letter, we show that this result is a consequence of the spatial coarseness of the demographic model and that a spatially structured stepping stone model can generate realistic dcfs without hybridization. This result highlights how inferences on hybridization between recently diverged species can be strongly affected by the choice of how population structure is represented in the underlying demographic model. We also conclude that the dcfs has limited power in distinguishing between the signals left by hybridization and ancient structure. 2014 The Author.

  2. The doubly conditioned frequency spectrum does not distinguish between ancient population structure and hybridization

    Eriksson, Anders; Manica, Andrea

    2014-01-01

    Distinguishing between hybridization and population structure in the ancestral species is a key challenge in our understanding of how permeable species boundaries are to gene flow. The doubly conditioned frequency spectrum (dcfs) has been argued to be a powerful metric to discriminate between these two explanations, and it was used to argue for hybridization between Neandertal and anatomically modern humans. The shape of the observed dcfs for these two species cannot be reproduced by a model that represents ancient population structure in Africa with two populations, while adding hybridization produces realistic shapes. In this letter, we show that this result is a consequence of the spatial coarseness of the demographic model and that a spatially structured stepping stone model can generate realistic dcfs without hybridization. This result highlights how inferences on hybridization between recently diverged species can be strongly affected by the choice of how population structure is represented in the underlying demographic model. We also conclude that the dcfs has limited power in distinguishing between the signals left by hybridization and ancient structure. 2014 The Author.

  3. Solving Component Structural Dynamic Failures Due to Extremely High Frequency Structural Response on the Space Shuttle Program

    Frady, Greg; Nesman, Thomas; Zoladz, Thomas; Szabo, Roland

    2010-01-01

    For many years, the capabilities to determine the root-cause failure of component failures have been limited to the analytical tools and the state of the art data acquisition systems. With this limited capability, many anomalies have been resolved by adding material to the design to increase robustness without the ability to determine if the design solution was satisfactory until after a series of expensive test programs were complete. The risk of failure and multiple design, test, and redesign cycles were high. During the Space Shuttle Program, many crack investigations in high energy density turbomachines, like the SSME turbopumps and high energy flows in the main propulsion system, have led to the discovery of numerous root-cause failures and anomalies due to the coexistences of acoustic forcing functions, structural natural modes, and a high energy excitation, such as an edge tone or shedding flow, leading the technical community to understand many of the primary contributors to extremely high frequency high cycle fatique fluid-structure interaction anomalies. These contributors have been identified using advanced analysis tools and verified using component and system tests during component ground tests, systems tests, and flight. The structural dynamics and fluid dynamics communities have developed a special sensitivity to the fluid-structure interaction problems and have been able to adjust and solve these problems in a time effective manner to meet budget and schedule deadlines of operational vehicle programs, such as the Space Shuttle Program over the years.

  4. The Frequency and Damping of Soil-Structure Systems with Embedded Foundation

    Ghannad, M. Ali; Rahmani, Mohammad T.; Jahankhah, Hossein

    2008-01-01

    The effect of foundation embedment on fundamental period and damping of buildings has been the title of several researches in three past decades. A review of the literature reveals some discrepancies between proposed formulations for dynamic characteristics of soil-embedded foundation-structure systems that raise the necessity of more investigation on this issue. Here, first a set of approximate polynomial equations for soil impedances, based on numerical data calculated from well known cone models, are presented. Then a simplified approach is suggested to calculate period and damping of the whole system considering soil medium as a viscoelastic half space. The procedure includes both material and radiation damping while frequency dependency of soil impedance functions is not ignored. Results show that soil-structure interaction can highly affect dynamic properties of system. Finally the results are compared with one of the commonly referred researches

  5. Proposed use of the radio-frequency quadrupole structure to funnel high-current ion beams

    Stokes, R.H.; Minerbo, G.N.

    1985-01-01

    In this paper, we describe a new approach to funneling beams that are initially accelerated in two radio-frequency quadrupole (RFQ) accelerators. Instead of discrete optical elements, we propose to funnel within an RFQ structure, so that during the funneling process the beam is always confined by periodic transverse focusing. Beams with high space charge experience irreversible emittance growth when they emerge from a periodic focusing system. To alleviate this problem, in the proposed funneling system it should be possible to maintain the same focusing periodicity as that of the accelerators preceding the funnel. Also, instead of conventional deflection systems, we propose to use the properties of a modified RFQ structure to deflect two parallel beams toward each other and to merge them into a single final beam. 1 ref., 3 figs

  6. Time-domain representation of frequency dependent inertial forces on offshore structures

    Krenk, Steen

    2013-01-01

    dependence is then approximated by a rational function, corresponding to a set of ordinary differential equations in the time domain. The MacCamy-Fuchs solution leads to a representation of the inertial force coefficient as a complex function with argument mainly corresponding to a 'phase lead', in contrast...... history of the inertial force is determined by processing the stable part of the transformation by a forward time integration, followed by an integration in the negative time-direction to obtain the final inertial force time history. The differential equations of the local inertial force at a cross......The inertial wave force on a vertical cylinder decreases with decreasing wave length, when the wave length is less than about six times the diameter of the diameter of the cylinder. In structures with a largediameter component like mono-towers the resonance frequency of the structure is typically...

  7. Spider web-structured labyrinthine acoustic metamaterials for low-frequency sound control

    Krushynska, A. O.; Bosia, F.; Miniaci, M.; Pugno, N. M.

    2017-10-01

    Attenuating low-frequency sound remains a challenge, despite many advances in this field. Recently-developed acoustic metamaterials are characterized by unusual wave manipulation abilities that make them ideal candidates for efficient subwavelength sound control. In particular, labyrinthine acoustic metamaterials exhibit extremely high wave reflectivity, conical dispersion, and multiple artificial resonant modes originating from the specifically-designed topological architectures. These features enable broadband sound attenuation, negative refraction, acoustic cloaking and other peculiar effects. However, hybrid and/or tunable metamaterial performance implying enhanced wave reflection and simultaneous presence of conical dispersion at desired frequencies has not been reported so far. In this paper, we propose a new type of labyrinthine acoustic metamaterials (LAMMs) with hybrid dispersion characteristics by exploiting spider web-structured configurations. The developed design approach consists in adding a square surrounding frame to sectorial circular-shaped labyrinthine channels described in previous publications (e.g. (11)). Despite its simplicity, this approach provides tunability in the metamaterial functionality, such as the activation/elimination of subwavelength band gaps and negative group-velocity modes by increasing/decreasing the edge cavity dimensions. Since these cavities can be treated as extensions of variable-width internal channels, it becomes possible to exploit geometrical features, such as channel width, to shift the band gap position and size to desired frequencies. Time transient simulations demonstrate the effectiveness of the proposed metastructures for wave manipulation in terms of transmission or reflection coefficients, amplitude attenuation and time delay at subwavelength frequencies. The obtained results can be important for practical applications of LAMMs such as lightweight acoustic barriers with enhanced broadband wave

  8. Spider web-structured labyrinthine acoustic metamaterials for low-frequency sound control

    Krushynska, A O; Bosia, F; Miniaci, M; Pugno, N M

    2017-01-01

    Attenuating low-frequency sound remains a challenge, despite many advances in this field. Recently-developed acoustic metamaterials are characterized by unusual wave manipulation abilities that make them ideal candidates for efficient subwavelength sound control. In particular, labyrinthine acoustic metamaterials exhibit extremely high wave reflectivity, conical dispersion, and multiple artificial resonant modes originating from the specifically-designed topological architectures. These features enable broadband sound attenuation, negative refraction, acoustic cloaking and other peculiar effects. However, hybrid and/or tunable metamaterial performance implying enhanced wave reflection and simultaneous presence of conical dispersion at desired frequencies has not been reported so far. In this paper, we propose a new type of labyrinthine acoustic metamaterials (LAMMs) with hybrid dispersion characteristics by exploiting spider web-structured configurations. The developed design approach consists in adding a square surrounding frame to sectorial circular-shaped labyrinthine channels described in previous publications (e.g. (11)). Despite its simplicity, this approach provides tunability in the metamaterial functionality, such as the activation/elimination of subwavelength band gaps and negative group-velocity modes by increasing/decreasing the edge cavity dimensions. Since these cavities can be treated as extensions of variable-width internal channels, it becomes possible to exploit geometrical features, such as channel width, to shift the band gap position and size to desired frequencies. Time transient simulations demonstrate the effectiveness of the proposed metastructures for wave manipulation in terms of transmission or reflection coefficients, amplitude attenuation and time delay at subwavelength frequencies. The obtained results can be important for practical applications of LAMMs such as lightweight acoustic barriers with enhanced broadband wave

  9. alpha-thalassemia, HbS, and beta-globin gene cluster haplotypes in two Afro-Uruguayan sub-populations from northern and southern Uruguay

    Julio A. da Luz

    2006-01-01

    Full Text Available Hemoglobinopathies are the most common monogenic disorders worldwide; however, they have never been systematically studied from a genetic perspective in Uruguay. In this study, we determined the frequencies of hemoglobin variants in Afro-Uruguayans. A sample of 52 healthy unrelated Afro-Uruguayans from the northern (N = 28 and southern (N = 24 regions of the country was analyzed. Eight individuals (15.4% were heterozygous for -alpha3,7thalassemia; seven of them (29.2% were originally from the southern region, whereas one of them (3.6% was from the northern region; the differences between both regions were statistically significant (p = 0.016 +/-0.003. The only structural mutation detected was betaS, which is typical of African populations. Four individuals (10% were heterozygous for betaS, three of them (13.6% from the South, and one (5.6% from the North. The betaS haplotypes were analyzed in eight individuals: two were homozygous betaS/betaS, two were heterozygous betaS/betathal, and four were heterozygous betaS/betaª. This haplotype distribution (60% Bantu, 20% Benin, and 20% Bantu A2 is in agreement with historical records reporting a predominantly Bantu origin for the enslaved Africans brought to Uruguay. Even though this is a preliminary study, due to the small sample size, our results are suggestive of a relatively high incidence of hemoglobinopathies in the Afro-Uruguayan population.

  10. Analytical and numerical calculations of resistive wall impedances for thin beam pipe structures at low frequencies

    Niedermayer, U., E-mail: u.niedermayer@gsi.de [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstrasse 8, 64289 Darmstadt (Germany); Boine-Frankenheim, O. [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstrasse 8, 64289 Darmstadt (Germany)

    2012-09-21

    The resistive wall impedance is one of the main sources for beam instabilities in synchrotrons and storage rings. The fast ramped SIS18 synchrotron at GSI and the projected SIS100 synchrotron for FAIR both employ thin (0.3 mm) stainless steel beam pipes in order to reduce eddy current effects. The lowest betatron sidebands are at about 100 kHz, which demands accurate impedance predictions in the low frequency (LF) range where the beam pipe and possibly also the structures behind the pipe are the dominating impedance sources. The longitudinal and transverse resistive wall impedances of a circular multi-layer pipe are calculated analytically using the field matching technique. We compare the impedances obtained from a radial wave model, which corresponds to the setup used in bench measurements, with the axial wave model, which corresponds to an actual beam moving with relativistic velocity. For thin beam pipes the induced wall current and the corresponding shielding properties of the pipe are important. In both models the wall current is obtained analytically. The characteristic frequencies for the onset of the wall current are calculated from equivalent lumped element circuits corresponding to the radial model. For more complex structures, like the SIS100 beam pipe, we use a numerical method, in which the impedance is obtained from the total power loss. The method is validated by the analytic expressions for circular beam pipes.

  11. Frequency formats, probability formats, or problem structure? A test of the nested-sets hypothesis in an extensional reasoning task

    William P. Neace

    2008-02-01

    Full Text Available Five experiments addressed a controversy in the probability judgment literature that centers on the efficacy of framing probabilities as frequencies. The natural frequency view predicts that frequency formats attenuate errors, while the nested-sets view predicts that highlighting the set-subset structure of the problem reduces error, regardless of problem format. This study tested these predictions using a conjunction task. Previous studies reporting that frequency formats reduced conjunction errors confounded reference class with problem format. After controlling this confound, the present study's findings show that conjunction errors can be reduced using either a probability or a frequency format, that frequency effects depend upon the presence of a reference class, and that frequency formats do not promote better statistical reasoning than probability formats.

  12. Mitochondrial haplotype distribution and phylogenetic relationship of an endangered species Reeve's turtle (Mauremys reevesii in East Asia

    Hong-Shik Oh

    2017-03-01

    Full Text Available This study was examined to reveal haplotype distribution and phylogenetic relationship using mitochondrial DNA CYTB gene sequences of Reeve’s turtle (Mauremys reevesii of East Asia. CYTB sequences of Reeve’s turtles were divided into 6 haplotypes (Hap01–Hap06. Chinese turtles were found in Hap01, Hap02, Hap04, and Hap05, and Hap01 was the highest frequency of 85.0%. Korean Turtles were found in Hap01, Hap03, Hap04, and Hap05, and Hap03 was the highest frequency of 52.1%. Although there was no haplotype which includes only the CYTB sequence exclusive for Reeve’s turtles of Korea, since no CYTB sequence of China was found in Hap03, it would be possible that Hap03 turtles of Korea are separated from those of China. The haplotypes of Reeve’s turtles of East Asia were monophyletic, which indicated that they had been evolved from a single maternal lineage, but went through local evolution after geographical migration and isolation in East Asia.

  13. Structural Damage Detection Using Changes in Natural Frequencies: Theory and Applications

    He, K.; Zhu, W. D.

    2011-07-01

    A vibration-based method that uses changes in natural frequencies of a structure to detect damage has advantages over conventional nondestructive tests in detecting various types of damage, including loosening of bolted joints, using minimum measurement data. Two major challenges associated with applications of the vibration-based damage detection method to engineering structures are addressed: accurate modeling of structures and the development of a robust inverse algorithm to detect damage, which are defined as the forward and inverse problems, respectively. To resolve the forward problem, new physics-based finite element modeling techniques are developed for fillets in thin-walled beams and for bolted joints, so that complex structures can be accurately modeled with a reasonable model size. To resolve the inverse problem, a logistical function transformation is introduced to convert the constrained optimization problem to an unconstrained one, and a robust iterative algorithm using a trust-region method, called the Levenberg-Marquardt method, is developed to accurately detect the locations and extent of damage. The new methodology can ensure global convergence of the iterative algorithm in solving under-determined system equations and deal with damage detection problems with relatively large modeling error and measurement noise. The vibration-based damage detection method is applied to various structures including lightning masts, a space frame structure and one of its components, and a pipeline. The exact locations and extent of damage can be detected in the numerical simulation where there is no modeling error and measurement noise. The locations and extent of damage can be successfully detected in experimental damage detection.

  14. Structural Damage Detection Using Changes in Natural Frequencies: Theory and Applications

    He, K; Zhu, W D

    2011-01-01

    A vibration-based method that uses changes in natural frequencies of a structure to detect damage has advantages over conventional nondestructive tests in detecting various types of damage, including loosening of bolted joints, using minimum measurement data. Two major challenges associated with applications of the vibration-based damage detection method to engineering structures are addressed: accurate modeling of structures and the development of a robust inverse algorithm to detect damage, which are defined as the forward and inverse problems, respectively. To resolve the forward problem, new physics-based finite element modeling techniques are developed for fillets in thin-walled beams and for bolted joints, so that complex structures can be accurately modeled with a reasonable model size. To resolve the inverse problem, a logistical function transformation is introduced to convert the constrained optimization problem to an unconstrained one, and a robust iterative algorithm using a trust-region method, called the Levenberg-Marquardt method, is developed to accurately detect the locations and extent of damage. The new methodology can ensure global convergence of the iterative algorithm in solving under-determined system equations and deal with damage detection problems with relatively large modeling error and measurement noise. The vibration-based damage detection method is applied to various structures including lightning masts, a space frame structure and one of its components, and a pipeline. The exact locations and extent of damage can be detected in the numerical simulation where there is no modeling error and measurement noise. The locations and extent of damage can be successfully detected in experimental damage detection.

  15. Honey bee-inspired algorithms for SNP haplotype reconstruction problem

    PourkamaliAnaraki, Maryam; Sadeghi, Mehdi

    2016-03-01

    Reconstructing haplotypes from SNP fragments is an important problem in computational biology. There have been a lot of interests in this field because haplotypes have been shown to contain promising data for disease association research. It is proved that haplotype reconstruction in Minimum Error Correction model is an NP-hard problem. Therefore, several methods such as clustering techniques, evolutionary algorithms, neural networks and swarm intelligence approaches have been proposed in order to solve this problem in appropriate time. In this paper, we have focused on various evolutionary clustering techniques and try to find an efficient technique for solving haplotype reconstruction problem. It can be referred from our experiments that the clustering methods relying on the behaviour of honey bee colony in nature, specifically bees algorithm and artificial bee colony methods, are expected to result in more efficient solutions. An application program of the methods is available at the following link. http://www.bioinf.cs.ipm.ir/software/haprs/

  16. Haplotype inference in general pedigrees with two sites

    Doan Duong D

    2011-04-01

    Full Text Available Abstract Background Genetic disease studies investigate relationships between changes in chromosomes and genetic diseases. Single haplotypes provide useful information for these studies but extracting single haplotypes directly by biochemical methods is expensive. A computational method to infer haplotypes from genotype data is therefore important. We investigate the problem of computing the minimum number of recombination events for general pedigrees with two sites for all members. Results We show that this NP-hard problem can be parametrically reduced to the Bipartization by Edge Removal problem and therefore can be solved by an O(2k · n2 exact algorithm, where n is the number of members and k is the number of recombination events. Conclusions Our work can therefore be useful for genetic disease studies to track down how changes in haplotypes such as recombinations relate to genetic disease.

  17. De novo assembly of a haplotype-resolved human genome.

    Cao, Hongzhi; Wu, Honglong; Luo, Ruibang; Huang, Shujia; Sun, Yuhui; Tong, Xin; Xie, Yinlong; Liu, Binghang; Yang, Hailong; Zheng, Hancheng; Li, Jian; Li, Bo; Wang, Yu; Yang, Fang; Sun, Peng; Liu, Siyang; Gao, Peng; Huang, Haodong; Sun, Jing; Chen, Dan; He, Guangzhu; Huang, Weihua; Huang, Zheng; Li, Yue; Tellier, Laurent C A M; Liu, Xiao; Feng, Qiang; Xu, Xun; Zhang, Xiuqing; Bolund, Lars; Krogh, Anders; Kristiansen, Karsten; Drmanac, Radoje; Drmanac, Snezana; Nielsen, Rasmus; Li, Songgang; Wang, Jian; Yang, Huanming; Li, Yingrui; Wong, Gane Ka-Shu; Wang, Jun

    2015-06-01

    The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

  18. Identification of Tribolium castaneum (Herbst) haplotypes, the pest of ...

    SARAH

    2016-07-31

    Jul 31, 2016 ... haplotypes of T. castaneum and their distribution in Senegal. Methodology ... very strong marketing of cereals and vegetables in that area. The mutations ..... for each channel by sampling the various parameters every 1000 ...

  19. Frequency-Modulated Continuous-Wave Fm-Cw Radar for Evaluation of Refractory Structures Used in Glass Manufacturing Furnaces

    Carroll, B.; Kharkovsky, S.; Zoughi, R.; Limmer, R.

    2009-03-01

    A frequency-modulated continuous-wave (FM-CW) handheld radar operating in the frequency range of 8-18 GHz, resulting in a relatively fine range resolution was designed and constructed for on-site inspection of refractory structure thickness. This paper presents the design of the radar and the results of measurements conducted on typical refractory furnace structures assembled in the laboratory.

  20. Analysis of DR4 haplotypes in insulin dependent diabetes (IDD)

    Monos, D.S.; Radka, S.F.; Zmijewski, C.M.; Kamoun, M.

    1986-01-01

    Population studies indicate that HLA-DR4 is implicated in the susceptibility of IDD. However, biochemical characterization of the serologically defined DR4 haplotype from normal individuals revealed five DR4 and three DQW3 molecular forms. Hence, in this study, they investigated the heterogeneity of the DR4 haplotype, using B-lymphoblastoid cell lines (B-LCL) generated from patients with IDD and seropositive for DR4. Class II molecules, metabolically labeled with 35 S-methionine, were immunoprecipitated with monoclonal antibodies specific for DR(L243), DQ(N297), DQW3(IVD12) or DR and DQ(SG465) and analyzed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). The isoelectrofocusing (IEF) conditions employed in this study allow representation only of the DR4 haplotype from either DR3/4 or DR4/4 cell lines. The analysis of six different DR4 haplotypes from seven IDD patients, revealed the presence of two DR4 β and two DQW3 β chains. Three of the six DR4 β haplotypes analyzed shared the same DR4 β chain and three others shared a different one. Additionally five of the six haplotypes shared a different one. Additionally five of the six haplotypes shared the same DQW3 β chain and only one was carrying a different one. Different combinations of the two DR4 and two DQW3 β chains constitute three distinct patterns of DR4 haplotypes. These results suggest the prevalence of a DQW3 β chain in the small sample of IDD patients studied. Studies of a large number of patients should clarify whether IDD is associated with unique variants of DR4 or DQW3 β chains

  1. Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella.

    Yaniv Brandvain

    Full Text Available The shift from outcrossing to self-fertilization is among the most common evolutionary transitions in flowering plants. Until recently, however, a genome-wide view of this transition has been obscured by both a dearth of appropriate data and the lack of appropriate population genomic methods to interpret such data. Here, we present a novel population genomic analysis detailing the origin of the selfing species, Capsella rubella, which recently split from its outcrossing sister, Capsella grandiflora. Due to the recency of the split, much of the variation within C. rubella is also found within C. grandiflora. We can therefore identify genomic regions where two C. rubella individuals have inherited the same or different segments of ancestral diversity (i.e. founding haplotypes present in C. rubella's founder(s. Based on this analysis, we show that C. rubella was founded by multiple individuals drawn from a diverse ancestral population closely related to extant C. grandiflora, that drift and selection have rapidly homogenized most of this ancestral variation since C. rubella's founding, and that little novel variation has accumulated within this time. Despite the extensive loss of ancestral variation, the approximately 25% of the genome for which two C. rubella individuals have inherited different founding haplotypes makes up roughly 90% of the genetic variation between them. To extend these findings, we develop a coalescent model that utilizes the inferred frequency of founding haplotypes and variation within founding haplotypes to estimate that C. rubella was founded by a potentially large number of individuals between 50 and 100 kya, and has subsequently experienced a twenty-fold reduction in its effective population size. As population genomic data from an increasing number of outcrossing/selfing pairs are generated, analyses like the one developed here will facilitate a fine-scaled view of the evolutionary and demographic impact of the

  2. Frequency Response of Near-Wall Coherent Structures to Localized Periodic Blowing and Suction in Turbulent Boundary Layer

    Jian-Hua, Liu; Nan, Jiang

    2008-01-01

    We experimentally investigate the frequency response of near-wall coherent structures to localized periodic blowing and suction through a spanwise slot in a turbulent boundary layer by changing the frequency of periodic disturbance at similar velocities of free stream. The effects of blowing and suction disturbance on energy redistribution, turbulent intensity u' rms + , over y + and waveforms of phase-averaged velocity during sweeping process are respectively discussed under three frequencies of periodic blowing and suction in near-wall region of turbulent boundary layer, compared with those in a standard turbulent boundary layer. The most effective disturbance frequency is figured out in this system. (fundamental areas of phenomenology (including applications))

  3. Structure and Topology Dynamics of Hyper-Frequency Networks during Rest and Auditory Oddball Performance.

    Müller, Viktor; Perdikis, Dionysios; von Oertzen, Timo; Sleimen-Malkoun, Rita; Jirsa, Viktor; Lindenberger, Ulman

    2016-01-01

    Resting-state and task-related recordings are characterized by oscillatory brain activity and widely distributed networks of synchronized oscillatory circuits. Electroencephalographic recordings (EEG) were used to assess network structure and network dynamics during resting state with eyes open and closed, and auditory oddball performance through phase synchronization between EEG channels. For this assessment, we constructed a hyper-frequency network (HFN) based on within- and cross-frequency coupling (WFC and CFC, respectively) at 10 oscillation frequencies ranging between 2 and 20 Hz. We found that CFC generally differentiates between task conditions better than WFC. CFC was the highest during resting state with eyes open. Using a graph-theoretical approach (GTA), we found that HFNs possess small-world network (SWN) topology with a slight tendency to random network characteristics. Moreover, analysis of the temporal fluctuations of HFNs revealed specific network topology dynamics (NTD), i.e., temporal changes of different graph-theoretical measures such as strength, clustering coefficient, characteristic path length (CPL), local, and global efficiency determined for HFNs at different time windows. The different topology metrics showed significant differences between conditions in the mean and standard deviation of these metrics both across time and nodes. In addition, using an artificial neural network approach, we found stimulus-related dynamics that varied across the different network topology metrics. We conclude that functional connectivity dynamics (FCD), or NTD, which was found using the HFN approach during rest and stimulus processing, reflects temporal and topological changes in the functional organization and reorganization of neuronal cell assemblies.

  4. Strategies for haplotype-based association mapping in complex pedigreed populations

    Boleckova, J; Christensen, Ole Fredslund; Sørensen, Peter

    2012-01-01

    In association mapping, haplotype-based methods are generally regarded to provide higher power and increased precision than methods based on single markers. For haplotype-based association mapping most studies use a fixed haplotype effect in the model. However, an increase in haplotype length inc...

  5. Flexible structured high-frequency film bulk acoustic resonator for flexible wireless electronics

    Zhou, Changjian; Shu, Yi; Yang, Yi; Ren, Tian-Ling; Jin, Hao; Dong, Shu-Rong; Chan, Mansun

    2015-01-01

    Flexible electronics have inspired many novel and very important applications in recent years and various flexible electronic devices such as diodes, transistors, circuits, sensors, and radiofrequency (RF) passive devices including antennas and inductors have been reported. However, the lack of a high-performance RF resonator is one of the key bottlenecks to implement flexible wireless electronics. In this study, for the first time, a novel ultra-flexible structured film bulk acoustic resonator (FBAR) is proposed. The flexible FBAR is fabricated on a flexible polyimide substrate using piezoelectric thin film aluminum nitride (AlN) for acoustic wave excitation. Both the shear wave and longitudinal wave can be excited under the surface interdigital electrodes configuration we proposed. In the case of the thickness extension mode, a flexible resonator with a working frequency as high as of 5.2325 GHz has been realized. The resonators stay fully functional under bending status and after repeated bending and re-flattening operations. This flexible high-frequency resonator will serve as a key building block for the future flexible wireless electronics, greatly expanding the application scope of flexible electronics. (paper)

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

    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.

  7. Fine structure near the starting frequency of solar type III radio bursts

    Benz, A.O.; Zlobec, P.; Jaeggi, M.

    1982-06-01

    We have systematically analyzed the period in time and frequency adjacent to the beginning of type III bursts digitally recorded at Bleien during the second half of 1980. A surprisingly high percentage (10%, possibly more than 20%) of the type III bursts show fine structure in the form of narrow-banded spikes of 0.05 s and less duration, which form clusters of relatively large bandwidth. These spikes are not totally polarized (contrary to claims in the literature) and they are uniformly distributed over the disk. Individual spikes often show highly variable polarization, which may even change sense. The average degree of polarization of the clouds has a wider distribution than that of the associated type III bursts, but generally the same sign. Spikes are considerably different from type I bursts.

  8. Review of Radio Frequency Identification and Wireless Technology for Structural Health Monitoring

    Dhital, Dipesh; Chia, Chen Ciang; Lee, Jung Ryul; Park, Chan Yik

    2010-01-01

    Radio frequency identification(RFID) combined with wireless technology has good potential for structural health monitoring(SHM). We describe several advantages of RFID and wireless technologies for SHM, and review SHM examples with working principles, design and technical details for damage detection, heat exposure monitoring, force/strain sensing, and corrosion detection in concrete, steel, carbon fiber reinforced polymer(CFRP), and other materials. Various sensors combined with wireless communication are also discussed. These methodologies can be readily developed, implemented, and customized. There are some technical difficulties, but solutions are being addressed. Lastly, a surface acoustic wave-based RFID system is presented, and possible future trends of SHM based on RFID and wireless technology are presented

  9. Review of Radio Frequency Identification and Wireless Technology for Structural Health Monitoring

    Dhital, Dipesh; Chia, Chen Ciang; Lee, Jung Ryul [Chonbuk National University, Jeonju (Korea, Republic of); Park, Chan Yik [Aeronautical Technology Directorate, Agency for Defense Development, Daejeon (Korea, Republic of)

    2010-06-15

    Radio frequency identification(RFID) combined with wireless technology has good potential for structural health monitoring(SHM). We describe several advantages of RFID and wireless technologies for SHM, and review SHM examples with working principles, design and technical details for damage detection, heat exposure monitoring, force/strain sensing, and corrosion detection in concrete, steel, carbon fiber reinforced polymer(CFRP), and other materials. Various sensors combined with wireless communication are also discussed. These methodologies can be readily developed, implemented, and customized. There are some technical difficulties, but solutions are being addressed. Lastly, a surface acoustic wave-based RFID system is presented, and possible future trends of SHM based on RFID and wireless technology are presented

  10. A novel reduced-complexity group detection structure in MIMO frequency selective fading channels

    Qaraqe, Khalid A.; Ahimian, Nariman R.; Alouini, Mohamed-Slim

    2010-01-01

    In this paper a novel reduced complexity detection method named modified symbol flipping method is introduced and its advantages on reducing the burden of the calculations at the receiver compared to the optimum maximum likelihood detection method on multiple input- multiple output frequency selective fading channels are explained. The initial concept of the symbol flipping method is derived from a preliminary detection scheme named bit flipping which was introduced in [1]. The detection structure employed in this paper is ing, detection, and cancellation. On the detection stage, the proposed method is employed and the results are compared to the group maximum likelihood detection scheme proposed in [2]. Simulation results show that a 6 dB performance gain can be achieved at the expense of a slight increase in complexity in comparison with the conventional symbol flipping scheme. © 2010 Crown.

  11. A novel reduced-complexity group detection structure in MIMO frequency selective fading channels

    Qaraqe, Khalid A.

    2010-09-01

    In this paper a novel reduced complexity detection method named modified symbol flipping method is introduced and its advantages on reducing the burden of the calculations at the receiver compared to the optimum maximum likelihood detection method on multiple input- multiple output frequency selective fading channels are explained. The initial concept of the symbol flipping method is derived from a preliminary detection scheme named bit flipping which was introduced in [1]. The detection structure employed in this paper is ing, detection, and cancellation. On the detection stage, the proposed method is employed and the results are compared to the group maximum likelihood detection scheme proposed in [2]. Simulation results show that a 6 dB performance gain can be achieved at the expense of a slight increase in complexity in comparison with the conventional symbol flipping scheme. © 2010 Crown.

  12. An Efficient Framework for Analysis of Wire-Grid Shielding Structures over a Broad Frequency Range

    A. Karwowski

    2016-12-01

    Full Text Available A computationally efficient MoM-based framework for broadband electromagnetic simulation of wire-grid shielding structures is presented in the paper. Broadband capability of the approach is attained through supporting MoM by an adaptive frequency sweep combined with rational interpolation of the observable implemented via Stoer-Bulirsch algorithm. The performance increase is gained by employing CUDA-enabled CPU+GPU co-processing. For large-size problems exceeding the amount of memory available on the GPU device, a hybrid out-of-GPU memory LU decomposition algorithm is employed. The demonstration examples are provided to illustrate the the accuracy and high efficiency of the approach.

  13. Fine-structure processing, frequency selectivity and speech perception in hearing-impaired listeners

    Strelcyk, Olaf; Dau, Torsten

    2008-01-01

    Hearing-impaired people often experience great difficulty with speech communication when background noise is present, even if reduced audibility has been compensated for. Other impairment factors must be involved. In order to minimize confounding effects, the subjects participating in this study...... consisted of groups with homogeneous, symmetric audiograms. The perceptual listening experiments assessed the intelligibility of full-spectrum as well as low-pass filtered speech in the presence of stationary and fluctuating interferers, the individual's frequency selectivity and the integrity of temporal...... modulation were obtained. In addition, these binaural and monaural thresholds were measured in a stationary background noise in order to assess the persistence of the fine-structure processing to interfering noise. Apart from elevated speech reception thresholds, the hearing impaired listeners showed poorer...

  14. An estimation method of system failure frequency using both structure and component failure data

    Takaragi, Kazuo; Sasaki, Ryoichi; Shingai, Sadanori; Tominaga, Kenji

    1981-01-01

    In recent years, the importance of reliability analysis is appreciated for large systems such as nuclear power plants. A reliability analysis method is described for a whole system, using structure failure data for its main working subsystem and component failure data for its safety protection subsystem. The subsystem named main working system operates normally, and the subsystem named safety protection system acts as standby or protection. Thus the main and the protection systems are given mutually different failure data; then, between the subsystems, there exists common mode failure, i.e. the component failure affecting the reliability of both two. A calculation formula for sytem failure frequency is first derived. Then, a calculation method with digraphs is proposed for conditional system failure probability. Finally the results of numerical calculation are given for the purpose of explanation. (J.P.N.)

  15. Generation of crystal-structure transverse patterns via a self-frequency-doubling laser.

    Yu, Haohai; Zhang, Huaijin; Wang, Yicheng; Wang, Zhengping; Wang, Jiyang; Petrov, V

    2013-01-01

    Two-dimensional (2D) visible crystal-structure patterns analogous to the quantum harmonic oscillator (QHO) have been experimentally observed in the near- and far-fields of a self-frequency-doubling (SFD) microchip laser. Different with the fundamental modes, the localization of the SFD light is changed with the propagation. Calculation based on Hermite-Gaussian (HG) functions and second harmonic generation theory reproduces well the patterns both in the near- and far-field which correspond to the intensity distribution in coordinate and momentum spaces, respectively. Considering the analogy of wave functions of the transverse HG mode and 2D harmonic oscillator, we propose that the simple monolithic SFD lasers can be used for developing of new materials and devices and testing 2D quantum mechanical theories.

  16. Inlfuence of Different-Frequency Glucocorticoid Induction on Morphological Structures of Humeri, Soft Tissues and Immune System in Rats

    LI Jian-min; LI Heng

    2016-01-01

    Objective: To explore the influence of different-frequency glucocorticoid (GC) induction on morphological structures of humeri and soft tissues as well as immune system in rats. Methods: A total of 32 speciifc pathogen-free (SPF) SD rats at the age of 3 months were selected and randomly divided into 4 groups, 8 cases in each group. The rats in control group were not given any treatment, while those in low-, moderate- and high-frequency groups were treated with intramuscular injection of dexamethasone 1 mg/kg per time for twice, 4 times and 6 times per week, respectively. All the rats were sacriifced on d30 to measure their body mass and qualities of soft tissues and immune organs, and bone histomorphometry was applied to analyze humeral bone mass and bone structural changes. Results: Compared with control group, there was no change in cancellous bone mass and bone structures of upper humeri in low-frequency group, but serious loss of bone mass, signiifcantly degenerated bone structure, markedly reduced trabecular thickness and number as well as notably increased trabecular separation was all observed in moderate- and high-frequency groups. The size of cortical bones, total size of bone structure, thickness of cortical bones and size percentage of cortical bones in middle humeri reduced apparently, while the size percentage of medullary cavity increased dramatically in high-frequency group. Growth plate thickness of upper humeri decreased in low-, moderate- and high-frequency groups, and the diameters of mastocytes diminished in moderate- and high-frequency groups. Compared with control group, body mass decreased obviously, qualities and indexes of spleen and thymus showed decreasing tendency along with the increase of drug administration frequency in low-, moderate- and high-frequency groups. Conclusion: Low-frequency GC cannot change humeral morphology. The higher the frequency of drug administration is, the more the loss of cancellous bone mass is. When the

  17. Role of MAPT mutations and haplotype in frontotemporal lobar degeneration in Northern Finland

    Tuominen Hannu

    2008-12-01

    Full Text Available Abstract Background Frontotemporal lobar degeneration (FTLD consists of a clinically and neuropathologically heterogeneous group of syndromes affecting the frontal and temporal lobes of the brain. Mutations in microtubule-associated protein tau (MAPT, progranulin (PGRN and charged multi-vesicular body protein 2B (CHMP2B are associated with familial forms of the disease. The prevalence of these mutations varies between populations. The H1 haplotype of MAPT has been found to be closely associated with tauopathies and with sporadic FTLD. Our aim was to investigate MAPT mutations and haplotype frequencies in a clinical series of patients with FTLD in Northern Finland. Methods MAPT exons 1, 2 and 9–13 were sequenced in 59 patients with FTLD, and MAPT haplotypes were analysed in these patients, 122 patients with early onset Alzheimer's disease (eoAD and 198 healthy controls. Results No pathogenic mutations were found. The H2 allele frequency was 11.0% (P = 0.028 in the FTLD patients, 9.8% (P = 0.029 in the eoAD patients and 5.3% in the controls. The H2 allele was especially clustered in patients with a positive family history (P = 0.011 but did not lower the age at onset of the disease. The ApoE4 allele frequency was significantly increased in the patients with eoAD and in those with FTLD. Conclusion We conclude that although pathogenic MAPT mutations are rare in Northern Finland, the MAPT H2 allele may be associated with increased risks of FTLD and eoAD in the Finnish population.

  18. HLA-A and -B alleles and haplotypes in 240 index patients with common variable immunodeficiency and selective IgG subclass deficiency in central Alabama

    Barton James C

    2003-06-01

    Full Text Available Abstract Background We wanted to quantify HLA-A and -B phenotype and haplotype frequencies in Alabama index patients with common variable immunodeficiency (CVID and selective IgG subclass deficiency (IgGSD, and in control subjects. Methods Phenotypes were detected using DNA-based typing (index cases and microlymphocytotoxicity typing (controls. Results A and B phenotypes were determined in 240 index cases (114 CVID, 126 IgGSD and 1,321 controls and haplotypes in 195 index cases and 751 controls. Phenotyping revealed that the "uncorrected" frequencies of A*24, B*14, B*15, B*35, B*40, B*49, and B*50 were significantly greater in index cases, and frequencies of B*35, B*58, B*62 were significantly lower in index cases. After Bonferroni corrections, the frequencies of phenotypes A*24, B*14, and B*40 were significantly greater in index cases, and the frequency of B*62 was significantly lower in index cases. The most common haplotypes in index cases were A*02-B*44 (frequency 0.1385, A*01-B*08 (frequency 0.1308, and A*03-B*07 (frequency 0.1000, and the frequency of each was significantly greater in index cases than in control subjects ("uncorrected" values of p p p = 0.0166. Most phenotype and haplotype frequencies in CVID and IgGSD were similar. 26.7% of index patients were HLA-haploidentical with one or more other index patients. We diagnosed CVID or IgGSD in first-degree or other relatives of 26 of 195 index patients for whom HLA-A and -B haplotypes had been ascertained; A*01-B*08, A*02-B*44, and A*29-B*44 were most frequently associated with CVID or IgGSD in these families. We conservatively estimated the combined population frequency of CVID and IgGSD to be 0.0092 in adults, based on the occurrence of CVID and IgGSD in spouses of the index cases. Conclusions CVID and IgGSD in adults are significantly associated with several HLA haplotypes, many of which are also common in the Alabama Caucasian population. Immunoglobulin phenotype variability

  19. Genetic polymorphisms in MDR1 and CYP3A4 genes in Asians and the influence of MDR1 haplotypes on cyclosporin disposition in heart transplant recipients.

    Chowbay, Balram; Cumaraswamy, Sivathasan; Cheung, Yin Bun; Zhou, Qingyu; Lee, Edmund J D

    2003-02-01

    Intestinal cytochrome P450 3A4 (CYP3A4) and P-glycoprotein (P-gp) both play a vital role in the metabolism of oral cyclosporine (CsA). We investigated the genetic polymorphisms in CYP3A4(promoter region and exons 5, 7 and 9) and MDR1 (exons 12, 21 and 26) genes and the impact of these polymorphisms on the pharmacokinetics of oral CsA in stable heart transplant patients (n = 14). CYP3A4 polymorphisms were rare in the Asian population and transplant patients. Haplotype analysis revealed 12 haplotypes in the Chinese, eight in the Malays and 10 in the Indians. T-T-T was the most common haplotype in all ethnic groups. The frequency of the homozygous mutant genotype at all three loci (TT-TT-TT) was highest in the Indians (31%) compared to 19% and 15% in the Chinese and Malays, respectively. In heart transplant patients, CsA exposure (AUC(0-4 h), AUC(0-12 h) and C(max)) was high in patients with the T-T-T haplotypes compared to those with C-G-C haplotypes. These findings suggest that haplotypes rather than genotypes influence CsA disposition in transplant patients.

  20. Associations of Haplotypes Upstream of IRS1 with Insulin Resistance, Type 2 Diabetes, Dyslipidemia, Preclinical Atherosclerosis, and Skeletal Muscle LOC646736 mRNA Levels

    Selma M. Soyal

    2015-01-01

    Full Text Available The genomic region ~500 kb upstream of IRS1 has been implicated in insulin resistance, type 2 diabetes, adverse lipid profile, and cardiovascular risk. To gain further insight into this chromosomal region, we typed four SNPs in a cross-sectional cohort and subjects with type 2 diabetes recruited from the same geographic region. From 16 possible haplotypes, 6 haplotypes with frequencies >0.01 were observed. We identified one haplotype that was protective against insulin resistance (determined by HOMA-IR and fasting plasma insulin levels, type 2 diabetes, an adverse lipid profile, increased C-reactive protein, and asymptomatic atherosclerotic disease (assessed by intima media thickness of the common carotid arteries. BMI and total adipose tissue mass as well as visceral and subcutaneous adipose tissue mass did not differ between the reference and protective haplotypes. In 92 subjects, we observed an association of the protective haplotype with higher skeletal muscle mRNA levels of LOC646736, which is located in the same haplotype block as the informative SNPs and is mainly expressed in skeletal muscle, but only at very low levels in liver or adipose tissues. These data suggest a role for LOC646736 in human insulin resistance and warrant further studies on the functional effects of this locus.

  1. Haplotype analysis of the genes encoding glutamine synthetase plastic isoforms and their association with nitrogen-use- and yield-related traits in bread wheat.

    Li, Xin-Peng; Zhao, Xue-Qiang; He, Xue; Zhao, Guang-Yao; Li, Bin; Liu, Dong-Cheng; Zhang, Ai-Min; Zhang, Xue-Yong; Tong, Yi-Ping; Li, Zhen-Sheng

    2011-01-01

    Glutamine synthetase (GS) plays a key role in the growth, nitrogen (N) use and yield potential of cereal crops. Investigating the haplotype variation of GS genes and its association with agronomic traits may provide useful information for improving wheat N-use efficiency and yield. We isolated the promoter and coding region sequences of the plastic glutamine synthetase isoform (GS2) genes located on chromosomes 2A, 2B and 2D in bread wheat. By analyzing nucleotide sequence variations of the coding region, two, six and two haplotypes were distinguished for TaGS2-A1 (a and b), TaGS2-B1 (a-f) and TaGS2-D1 (a and b), respectively. By analyzing the frequency data of different haplotypes and their association with N use and agronomic traits, four major and favorable TaGS2 haplotypes (A1b, B1a, B1b, D1a) were revealed. These favorable haplotypes may confer better seedling growth, better agronomic performance, and improved N uptake during vegetative growth or grain N concentration. Our data suggest that certain TaGS2 haplotypes may be valuable in breeding wheat varieties with improved agronomic performance and N-use efficiency. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

  2. Wide-ranging phylogeographic structure of invasive red lionfish in the Western Atlantic and Greater Caribbean

    Butterfield, John S.; Díaz-Ferguson, Edgardo; Silliman, Brian R.; Saunders, Jonathan W.; Buddo, Dayne; Mignucci-Giannoni, Antonio A.; Searle, Linda; Allen, Aarin Conrad; Hunter, Margaret E.

    2015-01-01

    The red lionfish (Pterois volitans) is an invasive predatory marine fish that has rapidly expanded its presence in the Western Hemisphere. We collected 214 invasive red lionfish samples from nine countries and territories, including seven unpublished locations. To more comprehensively evaluate connectivity, we compiled our d-loop sequence data with 846 published sequences, resulting in 1,060 samples from 14 locations. We found low nucleotide diversity (π = 0.003) and moderate haplotype diversity (h = 0.59). Using haplotype population pairwise ΦST tests, we analyzed possible phylogeographic breaks that were previously proposed based on other reef organisms. We found support for the Bahamas/Turks/Caicos versus Caribbean break (ΦST = 0.12) but not for the Northwestern Caribbean, Eastern Caribbean, or US East Coast versus Bahamas breaks. The Northern Region had higher variation and more haplotypes, supporting introductions of at least five haplotypes to the region. Our wide-ranging samples showed that a lower-frequency haplotype in the Northern Region dominated the Southern Region and suggested multiple introductions, possibly to the south. We tested multiple scenarios of phylogeographic structure with analyses of molecular variance and found support for a Northern and Southern Region split at the Bahamas/Turks/Caicos versus Caribbean break (percentage of variation among regions = 8.49 %). We found that Puerto Rico clustered with the Southern Region more strongly than with the Northern Region, as opposed to previous reports. We also found the rare haplotype H03 for the first time in the southern Caribbean (Panama), indicating that either secondary releases occurred or that the low-frequency haplotypes have had time to disperse to extreme southern Caribbean locations.

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

    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.

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

    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.

  5. Different DRB1*03:01-DQB1*02:01 haplotypes confer different risk for celiac disease.

    Alshiekh, S; Zhao, L P; Lernmark, Å; Geraghty, D E; Naluai, Å T; Agardh, D

    2017-08-01

    Celiac disease is associated with the HLA-DR3-DQA1*05:01-DQB1*02:01 and DR4-DQA1*03:01-DQB1*03:02 haplotypes. In addition, there are currently over 40 non-HLA loci associated with celiac disease. This study extends previous analyses on different HLA haplotypes in celiac disease using next generation targeted sequencing. Included were 143 patients with celiac disease and 135 non-celiac disease controls investigated at median 9.8 years (1.4-18.3 years). PCR-based amplification of HLA and sequencing with Illumina MiSeq technology were used for extended sequencing of the HLA class II haplotypes HLA-DRB1, DRB3, DRB4, DRB5, DQA1 and DQB1, respectively. Odds ratios were computed marginally for every allele and haplotype as the ratio of allelic frequency in patients and controls as ratio of exposure rates (RR), when comparing a null reference with equal exposure rates in cases and controls. Among the extended HLA haplotypes, the strongest risk haplotype for celiac disease was shown for DRB3*01:01:02 in linkage with DQA1*05:01-DQB1*02:01 (RR = 6.34; P-value celiac disease among non-Scandinavians (RR = 7.94; P = .011). The data also revealed 2 distinct celiac disease risk DR3-DQA1*05:01-DQB*02:01 haplotypes distinguished by either the DRB3*01:01:02 or DRB3*02:02:01 alleles, indicating that different DRB1*03:01-DQB1*02:01 haplotypes confer different risk for celiac disease. The associated risk of celiac disease for DR3-DRB3*01:01:02-DQA1*05:01-DQB1*02:01 is predominant among patients of Scandinavian ethnicity. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  6. Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle

    Hayes Ben J

    2011-08-01

    Full Text Available Abstract Background Previous fine mapping studies in Norwegian Red cattle (NRC in the region 86-90.4 Mb on Bos taurus chromosome 6 (BTA6 has revealed a quantitative trait locus (QTL for protein yield (PY around 88 Mb and a QTL for clinical mastitis (CM around 90 Mb. The close proximity of these QTLs may partly explain the unfavorable genetic correlation between these two traits in NRC. A long range haplotype covering this region was introduced into the NRC population through the importation of a Holstein-Friesian bull (1606 Frasse from Sweden in the 1970s. It has been suggested that this haplotype has a favorable effect on milk protein content but an unfavorable effect on mastitis susceptibility. Selective breeding for milk production traits is likely to have increased the frequency of this haplotype in the NRC population. Results Association mapping for PY and CM in NRC was performed using genotypes from 556 SNPs throughout the region 86-97 Mb on BTA6 and daughter-yield-deviations (DYDs from 2601 bulls made available from the Norwegian dairy herd recording system. Highest test scores for PY were found for single-nucleotide polymorphisms (SNPs within and surrounding the genes CSN2 and CSN1S2, coding for the β-casein and αS2-casein proteins. High coverage re-sequencing by high throughput sequencing technology enabled molecular characterization of a long range haplotype from 1606 Frasse encompassing these two genes. Haplotype analysis of a large number of descendants from this bull indicated that the haplotype was not markedly disrupted by recombination in this region. The haplotype was associated with both increased milk protein content and increased susceptibility to mastitis, which might explain parts of the observed genetic correlation between PY and CM in NRC. Plausible causal polymorphisms affecting PY were detected in the promoter region and in the 5'-flanking UTR of CSN1S2. These polymorphisms could affect transcription or translation of

  7. An improved partially interleaved transformer structure for high-voltage high-frequency multiple-output applications

    Zhao, Bin; Ouyang, Ziwei; Andersen, Michael A. E.

    2017-01-01

    . The proposed structure features lower leakage inductance, smaller AC capacitance and lower rate of AC-DC resistance, which is suitable for high-frequency high-efficiency applications. A planar transformer with the proposed structure was built and tested in an LCLC resonant converter, where the input voltage...

  8. Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus.

    Fabian Staubach

    Full Text Available General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1, homologues of human genes involved in adaptations (e.g. alpha-amylase genes or in genetic diseases (e.g. Huntingtin and Parkin. Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice

  9. Bi-resonant structure with piezoelectric PVDF films for energy harvesting from random vibration sources at low frequency

    Liang, Shanshan; Crovetto, Andrea; Peng, Zhuoteng

    2016-01-01

    and experiments with piezoelectric elements show that the energy harvesting device with the bi-resonant structure can generate higher power output than that of the sum of the two separate devices from random vibration sources at low frequency, and hence significantly improves the vibration-to- electricity......This paper reports on a bi-resonant structure of piezoelectric PVDF films energy harvester (PPEH), which consists of two cantilevers with resonant frequencies of 15 Hz and 22 Hz. With increased acceleration, the vibration amplitudes of the two cantilever-mass structures are increased and collision...

  10. Frequency Analysis of Acoustic Emission Signal to Monitor Damage Evolution in Masonry Structures

    Masera, D; Bocca, P; Grazzini, A

    2011-01-01

    A crucial aspect in damage evaluation of masonry structures is the analysis of long-term behaviour and for this reason fatigue analysis has a great influence on safety assessment of this structures. Acoustic Emission (AE) are very effective non-destructive techniques applied to identify micro and macro-defects and their temporal evolution in several materials. This technique permits to estimate the velocity of ultrasound waves propagation and the amount of energy released during fracture propagation to obtain information on the criticality of the ongoing process. By means of AE monitoring, an experimental analysis on a set of reinforced and unreinforced masonry walls under variable amplitude and static loading has been carried out. During these tests, the AE signals were recorded. The AE signals were analysed using Fast Fourier Transform (FFT) to examine the frequency distribution of the micro and macro cracking. It possible to evaluate the evolution of the wavelength of the AE signal through the two characteristic peak in the AE spectrum signals and the wave speed of the P or S waves. This wavelength evolution can be represent the microcrak and macrocrack evolution in masonry walls. This procedure permits to estimate the fracture dimension characteristic in several loading condition and for several masonry reinforced condition.

  11. Low-Frequency Internal Friction Study on the Structural Changes in Polymer Melts

    Xue-Bang, Wu; Qiao-Ling, Xu; Shu-Ying, Shang; Jia-Peng, Shui; Chang-Song, Liu; Zhen-Gang, Zhu

    2008-01-01

    With the help of the low-frequency internal friction method, we investigate the structural properties of polymer melts, such as amorphous polystyrene (PS), poly(methyl methacrylate) (PMMA), and semi-crystalline poly(ethylene oxide) (PEO). An obvious peak of relaxation type is found in each of the internal friction curves. The peak temperature T p follows the relation T p ≈ (1.15 – 1.18) T g for PS and PMMA melts, while it follows T p ≈ 1.22T m for PEO melt, with T g being the glass transition temperature and T m the melting temperature. Based on the analysis of the features of this peak, it is found that this peak is related to the liquid-liquid transition temperature T u of polymer melts. Mechanism of the liquid-liquid transition is suggested to be thermally-activated collective relaxation through cooperation. This finding may be helpful to understand the structural changes in polymer melts. In addition, the internal friction technique proves to be effective in studying dynamics in polymer melts

  12. Host population structure and treatment frequency maintain balancing selection on drug resistance

    Baskerville, Edward B.; Colijn, Caroline; Hanage, William; Fraser, Christophe; Lipsitch, Marc

    2017-01-01

    It is a truism that antimicrobial drugs select for resistance, but explaining pathogen- and population-specific variation in patterns of resistance remains an open problem. Like other common commensals, Streptococcus pneumoniae has demonstrated persistent coexistence of drug-sensitive and drug-resistant strains. Theoretically, this outcome is unlikely. We modelled the dynamics of competing strains of S. pneumoniae to investigate the impact of transmission dynamics and treatment-induced selective pressures on the probability of stable coexistence. We find that the outcome of competition is extremely sensitive to structure in the host population, although coexistence can arise from age-assortative transmission models with age-varying rates of antibiotic use. Moreover, we find that the selective pressure from antibiotics arises not so much from the rate of antibiotic use per se but from the frequency of treatment: frequent antibiotic therapy disproportionately impacts the fitness of sensitive strains. This same phenomenon explains why serotypes with longer durations of carriage tend to be more resistant. These dynamics may apply to other potentially pathogenic, microbial commensals and highlight how population structure, which is often omitted from models, can have a large impact. PMID:28835542

  13. Effect of a low-frequency magnetic field on the structure of globular blood proteins

    Zalesskaya, G. A.; Ulashchik, V. S.; Mit'kovskaya, N. P.; Laskina, O. V.; Kuchinskii, A. V.

    2007-09-01

    We used IR Fourier absorption spectra of blood to study changes in the structure of globular blood proteins with extracorporeal autohemomagnetotherapy, used to treat ischemic heart disease. We compare the spectra of blood before and after magnetotherapy in the regions: amide I (1655 cm-1), amide II (1545 cm-1), amide III (1230-1350 cm-1), amide IV and amide V (400-700 cm-1). We have shown that pronounced changes in the spectra in the indicated regions on direct exposure of blood in vivo to a low-frequency pulsed magnetic field are connected with conformational changes in the secondary structure of globular blood proteins, which are apparent in the increase in the contribution of the α-helix conformation. We discuss the magnetotherapy-initiated appearance of new IR absorption bands at 1018 and 1038 cm-1 and an increase in the intensity of a number of other bands located in the 1000-1200 cm-1 region, which suggests a change in the concentration of some blood components.

  14. Investigation of niobium surface structure and composition for improvement of superconducting radio-frequency cavities

    Trenikhina, Yulia

    Nano-scale investigation of intrinsic properties of niobium near-surface is a key to control performance of niobium superconducting radio-frequency cavities. Mechanisms responsible for the performance limitations and their empirical remedies needs to be justified in order to reproducibly control fabrication of SRF cavities with desired characteristics. The high field Q-slope and mechanism behind its cure (120°C mild bake) were investigated by comparison of the samples cut out of the cavities with high and low dissipation regions. Material evolution during mild field Q-slope nitrogen treatment was characterized using the coupon samples as well as samples cut out of nitrogen treated cavity. Evaluation of niobium near-surface state after some typical and novel cavity treatments was accomplished. Various TEM techniques, SEM, XPS, AES, XRD were used for the structural and chemical characterization of niobium near-surface. Combination of thermometry and structural temperature-dependent comparison of the cavity cutouts with different dissipation characteristics revealed precipitation of niobium hydrides to be the reason for medium and high field Q-slopes. Step-by-step effect of the nitrogen treatment processing on niobium surface was studied by analytical and structural characterization of the cavity cutout and niobium samples, which were subject to the treatment. Low concentration nitrogen doping is proposed to explain the benefit of nitrogen treatment. Chemical characterization of niobium samples before and after various surface processing (Electropolishing (EP), 800°C bake, hydrofluoric acid (HF) rinsing) showed the differences that can help to reveal the microscopic effects behind these treatments as well as possible sources of surface contamination.

  15. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

    Calus, M.P.L.; Meuwissen, T.H.E.; Windig, J.J.; Knol, E.F.; Schrooten, C.; Vereijken, A.L.J.; Veerkamp, R.F.

    2009-01-01

    The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e.

  16. Cross-frequency coupling in deep brain structures upon processing the painful sensory inputs.

    Liu, C C; Chien, J H; Kim, J H; Chuang, Y F; Cheng, D T; Anderson, W S; Lenz, F A

    2015-09-10

    Cross-frequency coupling has been shown to be functionally significant in cortical information processing, potentially serving as a mechanism for integrating functionally relevant regions in the brain. In this study, we evaluate the hypothesis that pain-related gamma oscillatory responses are coupled with low-frequency oscillations in the frontal lobe, amygdala and hippocampus, areas known to have roles in pain processing. We delivered painful laser pulses to random locations on the dorsal hand of five patients with uncontrolled epilepsy requiring depth electrode implantation for seizure monitoring. Two blocks of 40 laser stimulations were delivered to each subject and the pain-intensity was controlled at five in a 0-10 scale by adjusting the energy level of the laser pulses. Local-field-potentials (LFPs) were recorded through bilaterally implanted depth electrode contacts to study the oscillatory responses upon processing the painful laser stimulations. Our results show that painful laser stimulations enhanced low-gamma (LH, 40-70 Hz) and high-gamma (HG, 70-110 Hz) oscillatory responses in the amygdala and hippocampal regions on the right hemisphere and these gamma responses were significantly coupled with the phases of theta (4-7 Hz) and alpha (8-1 2 Hz) rhythms during pain processing. Given the roles of these deep brain structures in emotion, these findings suggest that the oscillatory responses in these regions may play a role in integrating the affective component of pain, which may contribute to our understanding of the mechanisms underlying the affective information processing in humans. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

  17. BMFO-PVDF electrospun fiber based tunable metamaterial structures for electromagnetic interference shielding in microwave frequency region

    Revathi, Venkatachalam; Dinesh Kumar, Sakthivel; Subramanian, Venkatachalam; Chellamuthu, Muthamizhchelvan

    2015-11-01

    Metamaterial structures are artificial structures that are useful in controlling the flow of electromagnetic radiation. In this paper, composite fibers of sub-micron thickness of barium substituted magnesium ferrite (Ba0.2Mg0.8Fe2O4) - polyvinylidene fluoride obtained by electrospinning is used as a substrate to design electromagnetic interference shielding structures. While electrospinning improves the ferroelectric properties of the polyvinylidene fluoride, the presence of barium magnesium ferrite modifies the magnetic property of the composite fiber. The dielectric and magnetic properties at microwave frequency measured using microwave cavity perturbation technique are used to design the reflection as well as absorption based tunable metamaterial structures for electromagnetic interference shielding in microwave frequency region. For one of the structures, the simulation indicates that single negative metamaterial structure becomes a double negative metamaterial under the external magnetic field.

  18. High-frequency and time resolution rocket observations of structured low- and medium-frequency whistler mode emissions in the auroral ionosphere

    LaBelle, J.; McAdams, K. L.; Trimpi, M. L.

    High bandwidth electric field waveform measurements on a recent auroral sounding rocket reveal structured whistler mode signals at 400-800 kHz. These are observed intermittently between 300 and 500 km with spectral densities 0-10 dB above the detection threshold of 1.5×10-11V2/m2Hz. The lack of correlation with local particle measurements suggests a remote source. The signals are composed of discrete structures, in one case having bandwidths of about 10 kHz and exhibiting rapid frequency variations of the order of 200 kHz per 100 ms. In one case, emissions near the harmonic of the whistler mode signals are detected simultaneously. Current theories of auroral zone whistler mode emissions have not been applied to explain quantitatively the fine structure of these signals, which resemble auroral kilometric radiation (AKR) rather than auroral hiss.

  19. Natural Frequency Testing and Model Correlation of Rocket Engine Structures in Liquid Hydrogen - Phase I, Cantilever Beam

    Brown, Andrew M.; DeLessio, Jennifer L.; Jacobs, Preston W.

    2018-01-01

    Many structures in the launch vehicle industry operate in liquid hydrogen (LH2), from the hydrogen fuel tanks through the ducts and valves and into the pump sides of the turbopumps. Calculating the structural dynamic response of these structures is critical for successful qualification of this hardware, but accurate knowledge of the natural frequencies is based entirely on numerical or analytical predictions of frequency reduction due to the added-fluid-mass effect because testing in LH2 has always been considered too difficult and dangerous. This fluid effect is predicted to be approximately 4-5% using analytical formulations for simple cantilever beams. As part of a comprehensive test/analysis program to more accurately assess pump inducers operating in LH2, a series of frequency tests in LH2 were performed at NASA/Marshall Space Flight Center's unique cryogenic test facility. These frequency tests are coupled with modal tests in air and water to provide critical information not only on the mass effect of LH2, but also the cryogenic temperature effect on Young's Modulus for which the data is not extensive. The authors are unaware of any other reported natural frequency testing in this media. In addition to the inducer, a simple cantilever beam was also tested in the tank to provide a more easily modeled geometry as well as one that has an analytical solution for the mass effect. This data will prove critical for accurate structural dynamic analysis of these structures, which operate in a highly-dynamic environment.

  20. A new mathematical modeling for pure parsimony haplotyping problem.

    Feizabadi, R; Bagherian, M; Vaziri, H R; Salahi, M

    2016-11-01

    Pure parsimony haplotyping (PPH) problem is important in bioinformatics because rational haplotyping inference plays important roles in analysis of genetic data, mapping complex genetic diseases such as Alzheimer's disease, heart disorders and etc. Haplotypes and genotypes are m-length sequences. Although several integer programing models have already been presented for PPH problem, its NP-hardness characteristic resulted in ineffectiveness of those models facing the real instances especially instances with many heterozygous sites. In this paper, we assign a corresponding number to each haplotype and genotype and based on those numbers, we set a mixed integer programing model. Using numbers, instead of sequences, would lead to less complexity of the new model in comparison with previous models in a way that there are neither constraints nor variables corresponding to heterozygous nucleotide sites in it. Experimental results approve the efficiency of the new model in producing better solution in comparison to two state-of-the art haplotyping approaches. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Mineralocorticoid receptor haplotype, oral contraceptives and emotional information processing.

    Hamstra, D A; de Kloet, E R; van Hemert, A M; de Rijk, R H; Van der Does, A J W

    2015-02-12

    Oral contraceptives (OCs) affect mood in some women and may have more subtle effects on emotional information processing in many more users. Female carriers of mineralocorticoid receptor (MR) haplotype 2 have been shown to be more optimistic and less vulnerable to depression. To investigate the effects of oral contraceptives on emotional information processing and a possible moderating effect of MR haplotype. Cross-sectional study in 85 healthy premenopausal women of West-European descent. We found significant main effects of oral contraceptives on facial expression recognition, emotional memory and decision-making. Furthermore, carriers of MR haplotype 1 or 3 were sensitive to the impact of OCs on the recognition of sad and fearful faces and on emotional memory, whereas MR haplotype 2 carriers were not. Different compounds of OCs were included. No hormonal measures were taken. Most naturally cycling participants were assessed in the luteal phase of their menstrual cycle. Carriers of MR haplotype 2 may be less sensitive to depressogenic side-effects of OCs. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

  2. In Vivo Characterization of Human APOA5 Haplotypes

    Ahituv, Nadav; Akiyama, Jennifer; Chapman-Helleboid, Audrey; Fruchart, Jamila; Pennacchio, Len A.

    2006-10-01

    Increased plasma triglycerides concentrations are an independent risk factor for cardiovascular disease. Numerous studies support a reproducible genetic association between two minor haplotypes in the human apolipoprotein A5 gene (APOA5) and increased plasma triglyceride concentrations. We thus sought to investigate the effect of these minor haplotypes (APOA5*2 and APOA5*3) on ApoAV plasma levels through the precise insertion of single-copy intact APOA5 haplotypes at a targeted location in the mouse genome. While we found no difference in the amount of human plasma ApoAV in mice containing the common APOA5*1 and minor APOA5*2 haplotype, the introduction of the single APOA5*3 defining allele (19W) resulted in 3-fold lower ApoAV plasma levels consistent with existing genetic association studies. These results indicate that S19W polymorphism is likely to be functional and explain the strong association of this variant with plasma triglycerides supporting the value of sensitive in vivo assays to define the functional nature of human haplotypes.

  3. Founder haplotype analysis of Fanconi anemia in the Korean population finds common ancestral haplotypes for a FANCG variant.

    Park, Joonhong; Kim, Myungshin; Jang, Woori; Chae, Hyojin; Kim, Yonggoo; Chung, Nack-Gyun; Lee, Jae-Wook; Cho, Bin; Jeong, Dae-Chul; Park, In Yang; Park, Mi Sun

    2015-05-01

    A common ancestral haplotype is strongly suggested in the Korean and Japanese patients with Fanconi anemia (FA), because common mutations have been frequently found: c.2546delC and c.3720_3724delAAACA of FANCA; c.307+1G>C, c.1066C>T, and c.1589_1591delATA of FANCG. Our aim in this study was to investigate the origin of these common mutations of FANCA and FANCG. We genotyped 13 FA patients consisting of five FA-A patients and eight FA-G patients from the Korean FA population. Microsatellite markers used for haplotype analysis included four CA repeat markers which are closely linked with FANCA and eight CA repeat markers which are contiguous with FANCG. As a result, Korean FA-A patients carrying c.2546delC or c.3720_3724delAAACA did not share the same haplotypes. However, three unique haplotypes carrying c.307+1G>C, c.1066C > T, or c.1589_1591delATA, that consisted of eight polymorphic loci covering a flanking region were strongly associated with Korean FA-G, consistent with founder haplotypes reported previously in the Japanese FA-G population. Our finding confirmed the common ancestral haplotypes on the origins of the East Asian FA-G patients, which will improve our understanding of the molecular population genetics of FA-G. To the best of our knowledge, this is the first report on the association between disease-linked mutations and common ancestral haplotypes in the Korean FA population. © 2015 John Wiley & Sons Ltd/University College London.

  4. HLA-DQA1 and HLA-DQB1 allele diversity and its extended haplotypes in Madeira Island (Portugal).

    Spínola, H; Lemos, A; Couto, A R; Parreira, B; Soares, M; Dutra, I; Bruges-Armas, J; Brehm, A

    2017-02-01

    This study shows, for the first time, high-resolution allele frequencies of HLA-DQA1 loci in Madeira Island (Portugal) and allows us to better understand and refine present knowledge on DQB1 variation, with the identification of several alleles not previously reported in this population. Estimates on haplotype profile, involving HLA-A, HLA-B, HLA-DRB1, HLA-DQA1 and HLA-DQB1, are also reported. © 2016 John Wiley & Sons Ltd.

  5. Effective collision frequency method in the theory of the conductivity of Coulomb systems. II. Strong interion interaction and plasma structure

    Bobrov, V.B.; Triger, S.A.

    1994-01-01

    The effective collision frequency method developed earlier by the authors for Coulomb systems characterized by strong interion interaction is developed further. An explicit expression is obtained for the effective electron collision frequency on the basis of the exact diagram representation obtained in Part I and the use of the model of a one-component plasma as initial approximation. The description of plasma structure in the corresponding approximation is considered. 25 refs

  6. Molecular Structure And Vibrational Frequencies of Tetrafluoro isophthalonitrile By Hartree-Fock And Density Functional Theory Calculations

    Ayikoglu, A.

    2008-01-01

    The molecular structure, vibrational frequencies and corresponding vibrational assignments of tetrafluoro isophthalonitrile (TFPN) in the ground state have been calculated using the Hartree-Fock (HF) and density functional methods (B3LYP) with 6-311++G (d, p) basis set. The calculations were utilized in the CS symmetry of TFPN. The obtained vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) were seen to be in good agreement with the experimental data. The comparison of the observed and calculated results showed that the B3LYP method is superior to the HF method for both the vibrational frequencies and geometric parameters

  7. Structural Validation of a French Food Frequency Questionnaire of 94 Items.

    Gazan, Rozenn; Vieux, Florent; Darmon, Nicole; Maillot, Matthieu

    2017-01-01

    Food frequency questionnaires (FFQs) are used to estimate the usual food and nutrient intakes over a period of time. Such estimates can suffer from measurement errors, either due to bias induced by respondent's answers or to errors induced by the structure of the questionnaire (e.g., using a limited number of food items and an aggregated food database with average portion sizes). The "structural validation" presented in this study aims to isolate and quantify the impact of the inherent structure of a FFQ on the estimation of food and nutrient intakes, independently of respondent's perception of the questionnaire. A semi-quantitative FFQ ( n  = 94 items, including 50 items with questions on portion sizes) and an associated aggregated food composition database (named the item-composition database) were developed, based on the self-reported weekly dietary records of 1918 adults (18-79 years-old) in the French Individual and National Dietary Survey 2 (INCA2), and the French CIQUAL 2013 food-composition database of all the foods ( n  = 1342 foods) declared as consumed in the population. Reference intakes of foods ("REF_FOOD") and nutrients ("REF_NUT") were calculated for each adult using the food-composition database and the amounts of foods self-reported in his/her dietary record. Then, answers to the FFQ were simulated for each adult based on his/her self-reported dietary record. "FFQ_FOOD" and "FFQ_NUT" intakes were estimated using the simulated answers and the item-composition database. Measurement errors (in %), spearman correlations and cross-classification were used to compare "REF_FOOD" with "FFQ_FOOD" and "REF_NUT" with "FFQ_NUT". Compared to "REF_NUT," "FFQ_NUT" total quantity and total energy intake were underestimated on average by 198 g/day and 666 kJ/day, respectively. "FFQ_FOOD" intakes were well estimated for starches, underestimated for most of the subgroups, and overestimated for some subgroups, in particular vegetables. Underestimation were

  8. Structural Validation of a French Food Frequency Questionnaire of 94 Items

    Rozenn Gazan

    2017-12-01

    Full Text Available BackgroundFood frequency questionnaires (FFQs are used to estimate the usual food and nutrient intakes over a period of time. Such estimates can suffer from measurement errors, either due to bias induced by respondent’s answers or to errors induced by the structure of the questionnaire (e.g., using a limited number of food items and an aggregated food database with average portion sizes. The “structural validation” presented in this study aims to isolate and quantify the impact of the inherent structure of a FFQ on the estimation of food and nutrient intakes, independently of respondent’s perception of the questionnaire.MethodsA semi-quantitative FFQ (n = 94 items, including 50 items with questions on portion sizes and an associated aggregated food composition database (named the item-composition database were developed, based on the self-reported weekly dietary records of 1918 adults (18–79 years-old in the French Individual and National Dietary Survey 2 (INCA2, and the French CIQUAL 2013 food-composition database of all the foods (n = 1342 foods declared as consumed in the population. Reference intakes of foods (“REF_FOOD” and nutrients (“REF_NUT” were calculated for each adult using the food-composition database and the amounts of foods self-reported in his/her dietary record. Then, answers to the FFQ were simulated for each adult based on his/her self-reported dietary record. “FFQ_FOOD” and “FFQ_NUT” intakes were estimated using the simulated answers and the item-composition database. Measurement errors (in %, spearman correlations and cross-classification were used to compare “REF_FOOD” with “FFQ_FOOD” and “REF_NUT” with “FFQ_NUT”.ResultsCompared to “REF_NUT,” “FFQ_NUT” total quantity and total energy intake were underestimated on average by 198 g/day and 666 kJ/day, respectively. “FFQ_FOOD” intakes were well estimated for starches, underestimated for most of the subgroups, and

  9. Effect of surface structure on catalytic reactions: A sum frequency generation surface vibrational spectroscopy study

    McCrea, Keith R.

    2001-01-01

    In the results discussed above, it is clear that Sum Frequency Generation (SFG) is a unique tool that allows the detection of vibrational spectra of adsorbed molecules present on single crystal surfaces under catalytic reaction conditions. Not only is it possible to detect active surface intermediates, it is also possible to detect spectator species which are not responsible for the measured turnover rates. By correlating high-pressure SFG spectra under reaction conditions and gas chromatography (GC) kinetic data, it is possible to determine which species are important under reaction intermediates. Because of the flexibility of this technique for studying surface intermediates, it is possible to determine how the structures of single crystal surfaces affect the observed rates of catalytic reactions. As an example of a structure insensitive reaction, ethylene hydrogenation was explored on both Pt(111) and Pt(100). The rates were determined to be essentially the same. It was observed that both ethylidyne and di-(sigma) bonded ethylene were present on the surface under reaction conditions on both crystals, although in different concentrations. This result shows that these two species are not responsible for the measured turnover rate, as it would be expected that one of the two crystals would be more active than the other, since the concentration of the surface intermediate would be different on the two crystals. The most likely active intermediates are weakly adsorbed molecules such as(pi)-bonded ethylene and ethyl. These species are not easily detected because their concentration lies at the detection limit of SFG. The SFG spectra and GC data essentially show that ethylene hydrogenation is structure insensitive for Pt(111) and Pt(100). SFG has proven to be a unique and excellent technique for studying adsorbed species on single crystal surfaces under high-pressure catalytic reactions. Coupled with kinetic data obtained from gas chromatography measurements, it can

  10. Grouping preprocess for haplotype inference from SNP and CNV data

    Shindo, Hiroyuki; Chigira, Hiroshi; Nagaoka, Tomoyo; Inoue, Masato; Kamatani, Naoyuki

    2009-01-01

    The method of statistical haplotype inference is an indispensable technique in the field of medical science. The authors previously reported Hardy-Weinberg equilibrium-based haplotype inference that could manage single nucleotide polymorphism (SNP) data. We recently extended the method to cover copy number variation (CNV) data. Haplotype inference from mixed data is important because SNPs and CNVs are occasionally in linkage disequilibrium. The idea underlying the proposed method is simple, but the algorithm for it needs to be quite elaborate to reduce the calculation cost. Consequently, we have focused on the details on the algorithm in this study. Although the main advantage of the method is accuracy, in that it does not use any approximation, its main disadvantage is still the calculation cost, which is sometimes intractable for large data sets with missing values.

  11. Grouping preprocess for haplotype inference from SNP and CNV data

    Shindo, Hiroyuki; Chigira, Hiroshi; Nagaoka, Tomoyo; Inoue, Masato [Department of Electrical Engineering and Bioscience, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555 (Japan); Kamatani, Naoyuki, E-mail: masato.inoue@eb.waseda.ac.j [Institute of Rheumatology, Tokyo Women' s Medical University, 10-22, Kawada-cho, Shinjuku-ku, Tokyo 162-0054 (Japan)

    2009-12-01

    The method of statistical haplotype inference is an indispensable technique in the field of medical science. The authors previously reported Hardy-Weinberg equilibrium-based haplotype inference that could manage single nucleotide polymorphism (SNP) data. We recently extended the method to cover copy number variation (CNV) data. Haplotype inference from mixed data is important because SNPs and CNVs are occasionally in linkage disequilibrium. The idea underlying the proposed method is simple, but the algorithm for it needs to be quite elaborate to reduce the calculation cost. Consequently, we have focused on the details on the algorithm in this study. Although the main advantage of the method is accuracy, in that it does not use any approximation, its main disadvantage is still the calculation cost, which is sometimes intractable for large data sets with missing values.

  12. Structure, temperature and frequency dependent electrical conductivity of oxidized and reduced electrochemically exfoliated graphite

    Radoń, Adrian; Włodarczyk, Patryk; Łukowiec, Dariusz

    2018-05-01

    The article presents the influence of reduction by hydrogen in statu nascendi and modification by hydrogen peroxide on the structure and electrical conductivity of electrochemically exfoliated graphite. It was confirmed that the electrochemical exfoliation can be used to produce oxidized nanographite with an average number of 25 graphene layers. The modified electrochemical exfoliated graphite and reduced electrochemical exfoliated graphite were characterized by high thermal stability, what was associated with removing of labile oxygen-containing groups. The presence of oxygen-containing groups was confirmed using Fourier-transform infrared spectroscopy. Influence of chemical modification by hydrogen and hydrogen peroxide on the electrical conductivity was determined in wide frequency (0.1 Hz-10 kHz) and temperature range (-50 °C-100 °C). Material modified by hydrogen peroxide (0.29 mS/cm at 0 °C) had the lowest electrical conductivity. This can be associated with oxidation of unstable functional groups and was also confirmed by analysis of Raman spectra. The removal of oxygen-containing functional groups by hydrogen in statu nascendi resulted in a 1000-fold increase in the electrical conductivity compared to the electrochemical exfoliated graphite.

  13. Radio frequency-induced temperature elevations in the human head considering small anatomical structures

    Schmid, G.; Ueberbacher, R.; Samaras, T.

    2007-01-01

    In order to enable a detailed numerical radio frequency (RF) dosimetry and the computations of RF-induced temperature elevations, high-resolution (0.1 mm) numerical models of the human eye, the inner ear organs and the pineal gland were developed and inserted into a commercially available head model. As radiation sources, generic models of handsets at 400, 900 and 1850 MHz operating in close proximity to the head were considered. The results, obtained by finite-difference time domain-based computations, showed a highly heterogeneous specific absorption rate (SAR) distribution and SAR-peaks inside the inner ear structures; however, the corresponding RF-induced temperature elevations were well below 0.1 deg. C, when considering typical output power values of hand-held devices. In case of frontal exposure, with the radiation sources ∼2.5 cm in front of the closed eye, maximum temperature elevations in the eye in the range of ∼0.2-0.6 deg. C were found for typical device output powers. A reduction in tissue perfusion mainly affected the maximum RF-induced temperature elevation of tissues deep inside the head. Similarly, worst-case considerations regarding pulsed irradiation affected temperature elevations in deep tissue significantly more than in superficial tissues. (authors)

  14. Can temporal fine structure represent the fundamental frequency of unresolved harmonics?

    Oxenham, Andrew J; Micheyl, Christophe; Keebler, Michael V

    2009-04-01

    At least two modes of pitch perception exist: in one, the fundamental frequency (F0) of harmonic complex tones is estimated using the temporal fine structure (TFS) of individual low-order resolved harmonics; in the other, F0 is derived from the temporal envelope of high-order unresolved harmonics that interact in the auditory periphery. Pitch is typically more accurate in the former than in the latter mode. Another possibility is that pitch can sometimes be coded via the TFS from unresolved harmonics. A recent study supporting this third possibility [Moore et al. (2006a). J. Acoust. Soc. Am. 119, 480-490] based its conclusion on a condition where phase interaction effects (implying unresolved harmonics) accompanied accurate F0 discrimination (implying TFS processing). The present study tests whether these results were influenced by audible distortion products. Experiment 1 replicated the original results, obtained using a low-level background noise. However, experiments 2-4 found no evidence for the use of TFS cues with unresolved harmonics when the background noise level was raised, or the stimulus level was lowered, to render distortion inaudible. Experiment 5 measured the presence and phase dependence of audible distortion products. The results provide no evidence that TFS cues are used to code the F0 of unresolved harmonics.

  15. HLA-G Haplotypes Are Differentially Associated with Asthmatic Features

    Camille Ribeyre

    2018-02-01

    Full Text Available Human leukocyte antigen (HLA-G, a HLA class Ib molecule, interacts with receptors on lymphocytes such as T cells, B cells, and natural killer cells to influence immune responses. Unlike classical HLA molecules, HLA-G expression is not found on all somatic cells, but restricted to tissue sites, including human bronchial epithelium cells (HBEC. Individual variation in HLA-G expression is linked to its genetic polymorphism and has been associated with many pathological situations such as asthma, which is characterized by epithelium abnormalities and inflammatory cell activation. Studies reported both higher and equivalent soluble HLA-G (sHLA-G expression in different cohorts of asthmatic patients. In particular, we recently described impaired local expression of HLA-G and abnormal profiles for alternatively spliced isoforms in HBEC from asthmatic patients. sHLA-G dosage is challenging because of its many levels of polymorphism (dimerization, association with β2-microglobulin, and alternative splicing, thus many clinical studies focused on HLA-G single-nucleotide polymorphisms as predictive biomarkers, but few analyzed HLA-G haplotypes. Here, we aimed to characterize HLA-G haplotypes and describe their association with asthmatic clinical features and sHLA-G peripheral expression and to describe variations in transcription factor (TF binding sites and alternative splicing sites. HLA-G haplotypes were differentially distributed in 330 healthy and 580 asthmatic individuals. Furthermore, HLA-G haplotypes were associated with asthmatic clinical features showed. However, we did not confirm an association between sHLA-G and genetic, biological, or clinical parameters. HLA-G haplotypes were phylogenetically split into distinct groups, with each group displaying particular variations in TF binding or RNA splicing sites that could reflect differential HLA-G qualitative or quantitative expression, with tissue-dependent specificities. Our results, based on a

  16. Prion gene haplotypes of U.S. cattle

    Harhay Gregory P

    2006-11-01

    Full Text Available Abstract Background Bovine spongiform encephalopathy (BSE is a fatal neurological disorder characterized by abnormal deposits of a protease-resistant isoform of the prion protein. Characterizing linkage disequilibrium (LD and haplotype networks within the bovine prion gene (PRNP is important for 1 testing rare or common PRNP variation for an association with BSE and 2 interpreting any association of PRNP alleles with BSE susceptibility. The objective of this study was to identify polymorphisms and haplotypes within PRNP from the promoter region through the 3'UTR in a diverse sample of U.S. cattle genomes. Results A 25.2-kb genomic region containing PRNP was sequenced from 192 diverse U.S. beef and dairy cattle. Sequence analyses identified 388 total polymorphisms, of which 287 have not previously been reported. The polymorphism alleles define PRNP by regions of high and low LD. High LD is present between alleles in the promoter region through exon 2 (6.7 kb. PRNP alleles within the majority of intron 2, the entire coding sequence and the untranslated region of exon 3 are in low LD (18.0 kb. Two haplotype networks, one representing the region of high LD and the other the region of low LD yielded nineteen different combinations that represent haplotypes spanning PRNP. The haplotype combinations are tagged by 19 polymorphisms (htSNPS which characterize variation within and across PRNP. Conclusion The number of polymorphisms in the prion gene region of U.S. cattle is nearly four times greater than previously described. These polymorphisms define PRNP haplotypes that may influence BSE susceptibility in cattle.

  17. Haplotype analysis of the HFE gene among populations of Northern Eurasia, in patients with metabolic disorders or stomach cancer, and in long-lived people.

    Mikhailova, S V; Babenko, V N; Ivanoshchuk, D E; Gubina, M A; Maksimov, V N; Solovjova, I G; Voevoda, M I

    2016-06-17

    Previously, it was shown that the HFE gene (associated with human hereditary hemochromatosis) has several haplotypes of intronic polymorphisms. Some haplotype frequencies are race specific and hence can be used in phylogenetic analysis. We assumed that analysis of Caucasoid patients-living now in Western Siberia and having diseases associated with dietary habits and metabolic rate-will allow us to understand the processes of possible selection during settling of the northern part of Asia. Haplotype analysis of Northern Eurasian native and recently settled ethnic groups was performed on polymorphisms rs1799945, rs1800730, rs1800562, rs2071303, rs1800708, rs1572982, rs2794719, rs807209, and rs2032451 of this gene. The CCA haplotype of the rs2071303, rs1800708, and rs1572982 was found to be associated with HLA-A2 (39 %) in Asian populations. Haplotype analysis for the rs1799945, rs1800730, rs1800562, rs2071303, rs1800708, and rs1572982 was performed on Russian patients with some metabolic disorders or stomach cancer and among long-lived people. Decreased frequencies of the TTA haplotype (T in rs2071303, T in rs1800708, and A in rs1572982) were observed in the groups of patients with diseases associated with overweight (fatty liver disease, type 2 diabetes mellitus, or metabolic syndrome + arterial hypertension) as compared with the control sample. We detected significant differences in this haplotype's frequency between the patients with type 2 diabetes mellitus and Russian adolescents, elderly citizens, and long-lived people (χ(2) P value = 0.003, 0.010, and 0.015, respectively). No significant differences in frequencies of the alleles with mutations in coding regions of the HFE gene (C282Y, H63D, and S65C) were detected between the analyzed patients (with stomach cancer, metabolic syndrome, fatty liver disease, or type 2 diabetes mellitus) and the control Caucasoid sample. Monophyletic origin of H63D (rs1799945) was confirmed in Caucasoids and Northern

  18. Haplotype analysis and linkage disequilibrium for DGAT1

    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. Mineralocorticoid receptor haplotype, estradiol, progesterone and emotional information processing.

    Hamstra, Danielle A; de Kloet, E Ronald; Quataert, Ina; Jansen, Myrthe; Van der Does, Willem

    2017-02-01

    Carriers of MR-haplotype 1 and 3 (GA/CG; rs5522 and rs2070951) are more sensitive to the influence of oral contraceptives (OC) and menstrual cycle phase on emotional information processing than MR-haplotype 2 (CA) carriers. We investigated whether this effect is associated with estradiol (E2) and/or progesterone (P4) levels. Healthy MR-genotyped premenopausal women were tested twice in a counterbalanced design. Naturally cycling (NC) women were tested in the early-follicular and mid-luteal phase and OC-users during OC-intake and in the pill-free week. At both sessions E2 and P4 were assessed in saliva. Tests included implicit and explicit positive and negative affect, attentional blink accuracy, emotional memory, emotion recognition, and risky decision-making (gambling). MR-haplotype 2 homozygotes had higher implicit happiness scores than MR-haplotype 2 heterozygotes (p=0.031) and MR-haplotype 1/3 carriers (pemotion recognition test than MR-haplotype 1/3 (p=0.001). Practice effects were observed for most measures. The pattern of correlations between information processing and P4 or E2 differed between sessions, as well as the moderating effects of the MR genotype. In the first session the MR-genotype moderated the influence of P4 on implicit anxiety (sr=-0.30; p=0.005): higher P4 was associated with reduction in implicit anxiety, but only in MR-haplotype 2 homozygotes (sr=-0.61; p=0.012). In the second session the MR-genotype moderated the influence of E2 on the recognition of facial expressions of happiness (sr=-0.21; p=0.035): only in MR-haplotype 1/3 higher E2 was correlated with happiness recognition (sr=0.29; p=0.005). In the second session higher E2 and P4 were negatively correlated with accuracy in lag2 trials of the attentional blink task (pemotional information processing. This moderating effect may depend on the novelty of the situation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Haplotype and genetic relationship of 27 Y-STR loci in Han population of Chaoshan area of China

    Qing-hua TIAN

    2017-04-01

    Full Text Available Objective  To investigate the genetic polymorphisms of 27 Y-chromosomal short tandem repeats (Y-STR loci included in Yfiler® Plus kit in Han population of Chaoshan area, and explore the population genetic relationships and evaluate its application value on forensic medicine. Methods  By detecting 795 unrelated Chaoshan Han males with Yfiler® Plus kit, haplotype frequencies and population genetics parameters of the 27 Y-STR loci were statistically analyzed and compared with available data of other populations from different races and regions for analyzing the genetic distance and clustering relation of Chaoshan Han population. Results  Seven hundred and eighty-seven different haplotypes were observed in 795 unrelated male individuals, of which 779 haplotypes were unique, and 8 haplotypes occurred twice. The haplotype diversity (HD was 0.999975 with discriminative capacity (DC of 98.99%. The gene diversity (GD at the 27 Y-STR loci ranged from 0.3637(DYS391 to 0.9559(DYS385a/b. Comparing with Asian reference populations, the genetic distance (Rst between Chaoshan Han and Guangdong Han was the smallest (0.0036, while it was relatively larger between Chaoshan Han and Gansu Tibetan population (0.0935. The multi-dimensional scaling (MDS plot based on Rst values was similar to the results of clustering analysis. Conclusion  Multiplex detection of the 27 Y-STR loci reveals a highly polymorphic genetic distribution in Chaoshan Han population, which demonstrates the important significance of Yfiler® Plus kit for establishing a Y-STR database, studying population genetics, and for good practice in forensic medicine. DOI: 10.11855/j.issn.0577-7402.2017.03.08

  1. Genetic variability and haplotypes of Echinococcus isolates from Tunisia.

    Boufana, Belgees; Lahmar, Samia; Rebaï, Waël; Ben Safta, Zoubeir; Jebabli, Leïla; Ammar, Adel; Kachti, Mahmoud; Aouadi, Soufia; Craig, Philip S

    2014-11-01

    The species/genotypes of Echinococcus infecting a range of intermediate, canid and human hosts were examined as well as the intraspecific variation and population structure of Echinococcus granulosus sensu lato (s.l.) within these hosts. A total of 174 Echinococcus isolates from humans and ungulate intermediate hosts and adult tapeworms from dogs and jackals were used. Genomic DNA was used to amplify a fragment within a mitochondrial gene and a nuclear gene, coding for cytochrome c oxidase subunit 1 (cox1; 828 bp) and elongation factor 1-alpha (ef1a; 656 bp), respectively. E. granulosus sensu stricto was identified from all host species examined, E. canadensis (G6) in a camel and, for the first time, fertile cysts of E. granulosus (s.s.) and E. equinus in equids (donkeys) and E. granulosus (s.s.) from wild boars and goats. Considerable genetic variation was seen only for the cox1 sequences of E. granulosus (s.s.). The pairwise fixation index (Fst) for cox1 E. granulosus (s.s.) sequences from donkeys was high and was statistically significant compared with that of E. granulosus populations from other intermediate hosts. A single haplotype (EqTu01) was identified for the cox1 nucleotide sequences of E. equinus. The role of donkeys in the epidemiology of echinococcosis in Tunisia requires further investigation. © The Author 2014. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Crack identification method in beam-like structures using changes in experimentally measured frequencies and Particle Swarm Optimization

    Khatir, Samir; Dekemele, Kevin; Loccufier, Mia; Khatir, Tawfiq; Abdel Wahab, Magd

    2018-02-01

    In this paper, a technique is presented for the detection and localization of an open crack in beam-like structures using experimentally measured natural frequencies and the Particle Swarm Optimization (PSO) method. The technique considers the variation in local flexibility near the crack. The natural frequencies of a cracked beam are determined experimentally and numerically using the Finite Element Method (FEM). The optimization algorithm is programmed in MATLAB. The algorithm is used to estimate the location and severity of a crack by minimizing the differences between measured and calculated frequencies. The method is verified using experimentally measured data on a cantilever steel beam. The Fourier transform is adopted to improve the frequency resolution. The results demonstrate the good accuracy of the proposed technique.

  3. Fire frequency and tree canopy structure influence plant species diversity in a forest-grassland ecotone

    David W. Peterson; Peter B. Reich

    2008-01-01

    Disturbances and environmental heterogeneity are two factors thought to influence plant species diversity, but their effects are still poorly understood in many ecosystems. We surveyed understory vegetation and measured tree canopy cover on permanent plots spanning an experimental fire frequency gradient to test fire frequency and tree canopy effects on plant species...

  4. Preparation, crystal structure, and dielectric characterization of Li2W2O7 ceramic at RF and microwave frequency range

    Jinwu Chen

    2017-02-01

    Full Text Available Single phase Li2W2O7 with anorthic structure was prepared by the conventional solid-state reaction method at 550∘C and the anorthic structure was stable up to 660∘C. The dielectric properties at radio frequency (RF and microwave frequency range were characterized. The sample sintered at 640∘C exhibited the optimum microwave dielectric properties with a relative permittivity of 12.2, a quality factor value of 17,700GHz (at 9.8GHz, and a temperature coefficient of the resonant frequency of −232ppm/∘C as well as a high relative density ∼94.1%. Chemical compatibility measurement indicated Li2W2O7 did not react with aluminum electrodes when sintered at 640∘C for 4h.

  5. Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.

    Gillet-Markowska, Alexandre; Richard, Hugues; Fischer, Gilles; Lafontaine, Ingrid

    2015-03-15

    The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging. Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Detection of NAM-A1 Natural Variants in Bread Wheat Reveals Differences in Haplotype Distribution between a Worldwide Core Collection and European Elite Germplasm

    Fabien Cormier

    2015-04-01

    Full Text Available In wheat, remobilization of nitrogen absorbed before anthesis and regulation of monocarpic senescence is a major issue in breeding for nutrient use efficiency. We identified natural variants of NAM-A1, a gene having the same role as its well-characterized homoeolog NAM-B1, a NAC transcription factor associated with senescence kinetics and nutrient remobilization to the grain. Differences in haplotype frequencies between a worldwide core collection and a panel of European elite varieties were assessed and discussed. Moreover, hypotheses for the loss of function of the most common haplotype in elite European germplasm are discussed.

  7. Relevance feature selection of modal frequency-ambient condition pattern recognition in structural health assessment for reinforced concrete buildings

    He-Qing Mu

    2016-08-01

    Full Text Available Modal frequency is an important indicator for structural health assessment. Previous studies have shown that this indicator is substantially affected by the fluctuation of ambient conditions, such as temperature and humidity. Therefore, recognizing the pattern between modal frequency and ambient conditions is necessary for reliable long-term structural health assessment. In this article, a novel machine-learning algorithm is proposed to automatically select relevance features in modal frequency-ambient condition pattern recognition based on structural dynamic response and ambient condition measurement. In contrast to the traditional feature selection approaches by examining a large number of combinations of extracted features, the proposed algorithm conducts continuous relevance feature selection by introducing a sophisticated hyperparameterization on the weight parameter vector controlling the relevancy of different features in the prediction model. The proposed algorithm is then utilized for structural health assessment for a reinforced concrete building based on 1-year daily measurements. It turns out that the optimal model class including the relevance features for each vibrational mode is capable to capture the pattern between the corresponding modal frequency and the ambient conditions.

  8. Design and FPGA Implementation of Variable Cutoff Frequency Filter based on Continuously Variable Fractional Delay Structure and Interpolation Technique

    Sumedh Dhabu

    2015-09-01

    Full Text Available This paper presents the design and FPGA implementation of interpolated continuously variable fractional delay structure based filter (ICVFD filter with fine control over the cutoff frequency. In the ICVFD filter, each unit delay of the prototype lowpass filter is replaced by a continuously variable fractional delay (CVFD element proposed in this paper. The CVFD element requires the same number of multiplications as that of the second-order fractional delay structure used in the existing fractional delay structure based variable filter (FDS based filter, however it provides fractional delays corresponding to the higher-order fractional delay structures. Hence, the proposed ICVFD filter provides wider cutoff frequency range compared to the FDS based filter. The ICVFD filter is also capable of providing variable bandpass and highpass responses. We use two-stage approach for the FPGA implementation of the ICVFD filter. First, we use pipelining stages to shorten the critical path and improve the operating frequency. Then, we make use of specific hardware resource, i.e. RAM-based Shift Register (SRL to further improve the operating frequency and resource usage.

  9. Bayesian genomic selection: the effect of haplotype lenghts and priors

    Villumsen, Trine Michelle; Janss, Luc

    2009-01-01

    Breeding values for animals with marker data are estimated using a genomic selection approach where data is analyzed using Bayesian multi-marker association models. Fourteen model scenarios with varying haplotype lengths, hyper parameter and prior distributions were compared to find the scenario ...

  10. Direct chromosome-length haplotyping by single-cell sequencing

    Porubský, David; Sanders, Ashley D; van Wietmarschen, Niek; Falconer, Ester; Hills, Mark; Spierings, Diana C J; Bevova, Marianna R; Guryev, Victor; Lansdorp, Peter Michael

    Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single-cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid

  11. Dense and accurate whole-chromosome haplotyping of individual genomes

    Porubsky, David; Garg, Shilpa; Sanders, Ashley D.; Korbel, Jan O.; Guryev, Victor; Lansdorp, Peter M.; Marschall, Tobias

    2017-01-01

    The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate

  12. Association of specific haplotype of TNFα with Helicobacter pylori ...

    Home; Journals; Journal of Genetics; Volume 87; Issue 3. Association of specific haplotype of TNF with Helicobacter pylori-mediated duodenal ulcer in eastern Indian population. Meenakshi Chakravorty Dipanjana Datta De Abhijit Choudhury Amal Santra Susanta Roychoudhury. Research Note Volume 87 Issue 3 ...

  13. Genetics of chloroquine-resistant malaria: a haplotypic view

    Gauri Awasthi

    2013-12-01

    Full Text Available The development and rapid spread of chloroquine resistance (CQR in Plasmodium falciparum have triggered the identification of several genetic target(s in the P. falciparum genome. In particular, mutations in the Pfcrt gene, specifically, K76T and mutations in three other amino acids in the region adjoining K76 (residues 72, 74, 75 and 76, are considered to be highly related to CQR. These various mutations form several different haplotypes and Pfcrt gene polymorphisms and the global distribution of the different CQR- Pfcrt haplotypes in endemic and non-endemic regions of P. falciparum malaria have been the subject of extensive study. Despite the fact that the Pfcrt gene is considered to be the primary CQR gene in P. falciparum , several studies have suggested that this may not be the case. Furthermore, there is a poor correlation between the evolutionary implications of the Pfcrt haplotypes and the inferred migration of CQR P. falciparum based on CQR epidemiological surveillance data. The present paper aims to clarify the existing knowledge on the genetic basis of the different CQR- Pfcrt haplotypes that are prevalent in worldwide populations based on the published literature and to analyse the data to generate hypotheses on the genetics and evolution of CQR malaria.

  14. Eurasian otters, Lutra lutra, have a dominant mtDNA haplotype from the Iberian Peninsula to Scandinavia.

    Ferrando, Ainhoa; Ponsà, Montserrat; Marmi, Josep; Domingo-Roura, Xavier

    2004-01-01

    The Eurasian otter, Lutra lutra, has a Palaearctic distribution and has suffered a severe decline throughout Europe during the last century. Previous studies in this and other mustelids have shown reduced levels of variability in mitochondrial DNA, although otter phylogeographic studies were restricted to central-western Europe. In this work we have sequenced 361 bp of the mtDNA control region in 73 individuals from eight countries and added our results to eight sequences available from GenBank and the literature. The range of distribution has been expanded in relation to previous works north towards Scandinavia, east to Russia and Belarus, and south to the Iberian Peninsula. We found a single dominant haplotype in 91.78% of the samples, and six more haplotypes deviating a maximum of two mutations from the dominant haplotype restricted to a single country. Variability was extremely low in western Europe but higher in eastern countries. This, together with the lack of phylogeographical structuring, supports the postglacial recolonization of Europe from a single refugium. The Eurasian otter mtDNA control region has a 220-bp variable minisatellite in Domain III that we sequenced in 29 otters. We found a total of 19 minisatellite haplotypes, but they showed no phylogenetic information.

  15. Interpolation-Based Condensation Model Reduction Part 1: Frequency Window Reduction Method Application to Structural Acoustics

    Ingel, R

    1999-01-01

    .... Projection operators are employed for the model reduction or condensation process. Interpolation is then introduced over a user defined frequency window, which can have real and imaginary boundaries and be quite large. Hermitian...

  16. Haplotype-based case-control study between human apurinic/apyrimidinic endonuclease 1/redox effector factor-1 gene and cerebral infarction.

    Naganuma, Takahiro; Nakayama, Tomohiro; Sato, Naoyuki; Fu, Zhenyan; Yamaguchi, Mai; Soma, Masayoshi; Aoi, Noriko; Usami, Ron; Doba, Nobutaka; Hinohara, Shigeaki

    2009-10-01

    The aim of this study was to investigate the relationship between cerebral infarction (CI) and the human apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/REF-1) gene using single-nucleotide polymorphisms (SNPs) and a haplotype-based case-control study. We selected 5 SNPs in the human APE1/REF1 gene (rs1760944, rs3136814, rs17111967, rs3136817 and rs1130409), and performed case-control studies in 177 CI patients and 309 control subjects. rs17111967 was found to have no heterogeneity in Japanese. The overall distribution of the haplotype-based case-control study constructed by rs1760944, rs3136814 and rs1130409 showed a significant difference. The frequency of the G-C-T haplotype was significantly higher in the CI group than in the control group (2.5% vs. 0.0%, p>0.001). Based on the results of the haplotype-based case-control-study, the G-C-T haplotype may be a genetic marker of CI, and the APE1/REF-1 gene may be a CI susceptibility gene.

  17. Excitation of hypersonic acoustic waves in diamond-based piezoelectric layered structure on the microwave frequencies up to 20GHz.

    Sorokin, B P; Kvashnin, G M; Novoselov, A S; Bormashov, V S; Golovanov, A V; Burkov, S I; Blank, V D

    2017-07-01

    First ultrahigh frequency (UHF) investigation of quality factor Q for the piezoelectric layered structure «Al/(001)AlN/Mo/(100) diamond» has been executed in a broad frequency band from 1 up to 20GHz. The record-breaking Q·f quality parameter up to 2.7·10 14 Hz has been obtained close to 20GHz. Frequency dependence of the form factor m correlated with quality factor has been analyzed by means of computer simulation, and non-monotonic frequency dependence can be explained by proper features of thin-film piezoelectric transducer (TFPT). Excluding the minimal Q magnitudes measured at the frequency points associated with minimal TFPT effectiveness, one can prove a rule of Qf∼f observed for diamond on the frequencies above 1GHz and defined by Landau-Rumer's acoustic attenuation mechanism. Synthetic IIa-type diamond single crystal as a substrate material for High-overtone Bulk Acoustic Resonator (HBAR) possesses some excellent acoustic properties in a wide microwave band and can be successfully applied for design of acoustoelectronic devices, especially the ones operating at a far UHF band. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. The role of temporal fine structure information for the low pitch of high-frequency complex tones

    Santurette, Sébastien; Dau, Torsten

    2011-01-01

    The fused low pitch evoked by complex tones containing only unresolved high-frequency components demonstrates the ability of the human auditory system to extract pitch using a temporal mechanism in the absence of spectral cues. However, the temporal features used by such a mechanism have been...... amplitude fluctuations, or temporal fine structure (TFS), of the conveyed signal can be processed. Using a pitch-matching paradigm, the present study found that the low pitch of inharmonic transposed tones with unresolved components was consistent with the timing between the most prominent TFS maxima...... coding as such, and that TFS representation might persist at higher frequencies than previously thought....

  19. Investigating the performance of reconstruction methods used in structured illumination microscopy as a function of the illumination pattern's modulation frequency

    Shabani, H.; Sánchez-Ortiga, E.; Preza, C.

    2016-03-01

    Surpassing the resolution of optical microscopy defined by the Abbe diffraction limit, while simultaneously achieving optical sectioning, is a challenging problem particularly for live cell imaging of thick samples. Among a few developing techniques, structured illumination microscopy (SIM) addresses this challenge by imposing higher frequency information into the observable frequency band confined by the optical transfer function (OTF) of a conventional microscope either doubling the spatial resolution or filling the missing cone based on the spatial frequency of the pattern when the patterned illumination is two-dimensional. Standard reconstruction methods for SIM decompose the low and high frequency components from the recorded low-resolution images and then combine them to reach a high-resolution image. In contrast, model-based approaches rely on iterative optimization approaches to minimize the error between estimated and forward images. In this paper, we study the performance of both groups of methods by simulating fluorescence microscopy images from different type of objects (ranging from simulated two-point sources to extended objects). These simulations are used to investigate the methods' effectiveness on restoring objects with various types of power spectrum when modulation frequency of the patterned illumination is changing from zero to the incoherent cut-off frequency of the imaging system. Our results show that increasing the amount of imposed information by using a higher modulation frequency of the illumination pattern does not always yield a better restoration performance, which was found to be depended on the underlying object. Results from model-based restoration show performance improvement, quantified by an up to 62% drop in the mean square error compared to standard reconstruction, with increasing modulation frequency. However, we found cases for which results obtained with standard reconstruction methods do not always follow the same trend.

  20. Mice, humans and haplotypes--the hunt for disease genes in SLE.

    Rigby, R J; Fernando, M M A; Vyse, T J

    2006-09-01

    Defining the polymorphisms that contribute to the development of complex genetic disease traits is a challenging, although increasingly tractable problem. Historically, the technical difficulties in conducting association studies across the entire human genome are such that murine models have been used to generate candidate genes for analysis in human complex diseases, such as SLE. In this article we discuss the advantages and disadvantages of this approach and specifically address some assumptions made in the transition from studying one species to another, using lupus as an example. These issues include differences in genetic structure and genetic organisation which are a reflection on the population history. Clearly there are major differences in the histories of the human population and inbred laboratory strains of mice. Both human and murine genomes do exhibit structure at the genetic level. That is to say, they comprise haplotypes which are genomic regions that carry runs of polymorphisms that are not independently inherited. Haplotypes therefore reduce the number of combinations of the polymorphisms in the DNA in that region and facilitate the identification of disease susceptibility genes in both mice and humans. There are now novel means of generating candidate genes in SLE using mutagenesis (with ENU) in mice and identifying mice that generate antinuclear autoimmunity. In addition, murine models still provide a valuable means of exploring the functional consequences of genetic variation. However, advances in technology are such that human geneticists can now screen large fractions of the human genome for disease associations using microchip technologies that provide information on upwards of 100,000 different polymorphisms. These approaches are aimed at identifying haplotypes that carry disease susceptibility mutations and rely less on the generation of candidate genes.

  1. The Systemic Lupus Erythematosus IRF5 Risk Haplotype Is Associated with Systemic Sclerosis

    Beretta, Lorenzo; Simeón, Carmen P.; Carreira, Patricia E.; Callejas, José Luis; Fernández-Castro, Mónica; Sáez-Comet, Luis; Beltrán, Emma; Camps, María Teresa; Egurbide, María Victoria; Airó, Paolo; Scorza, Raffaella; Lunardi, Claudio; Hunzelmann, Nicolas; Riemekasten, Gabriela; Witte, Torsten; Kreuter, Alexander; Distler, Jörg H. W.; Madhok, Rajan; Shiels, Paul; van Laar, Jacob M.; Fonseca, Carmen; Denton, Christopher; Herrick, Ariane; Worthington, Jane; Schuerwegh, Annemie J.; Vonk, Madelon C.; Voskuyl, Alexandre E.; Radstake, Timothy R. D. J.; Martín, Javier

    2013-01-01

    Systemic sclerosis (SSc) is a fibrotic autoimmune disease in which the genetic component plays an important role. One of the strongest SSc association signals outside the human leukocyte antigen (HLA) region corresponds to interferon (IFN) regulatory factor 5 (IRF5), a major regulator of the type I IFN pathway. In this study we aimed to evaluate whether three different haplotypic blocks within this locus, which have been shown to alter the protein function influencing systemic lupus erythematosus (SLE) susceptibility, are involved in SSc susceptibility and clinical phenotypes. For that purpose, we genotyped one representative single-nucleotide polymorphism (SNP) of each block (rs10488631, rs2004640, and rs4728142) in a total of 3,361 SSc patients and 4,012 unaffected controls of Caucasian origin from Spain, Germany, The Netherlands, Italy and United Kingdom. A meta-analysis of the allele frequencies was performed to analyse the overall effect of these IRF5 genetic variants on SSc. Allelic combination and dependency tests were also carried out. The three SNPs showed strong associations with the global disease (rs4728142: P  = 1.34×10−8, OR  = 1.22, CI 95%  = 1.14–1.30; rs2004640: P  = 4.60×10−7, OR  = 0.84, CI 95%  = 0.78–0.90; rs10488631: P  = 7.53×10−20, OR  = 1.63, CI 95%  = 1.47–1.81). However, the association of rs2004640 with SSc was not independent of rs4728142 (conditioned P  = 0.598). The haplotype containing the risk alleles (rs4728142*A-rs2004640*T-rs10488631*C: P  = 9.04×10−22, OR  = 1.75, CI 95%  = 1.56–1.97) better explained the observed association (likelihood P-value  = 1.48×10−4), suggesting an additive effect of the three haplotypic blocks. No statistical significance was observed in the comparisons amongst SSc patients with and without the main clinical characteristics. Our data clearly indicate that the SLE risk haplotype also influences SSc predisposition, and that

  2. RTEL1 tagging SNPs and haplotypes were associated with glioma development.

    Li, Gang; Jin, Tianbo; Liang, Hongjuan; Zhang, Zhiguo; He, Shiming; Tu, Yanyang; Yang, Haixia; Geng, Tingting; Cui, Guangbin; Chen, Chao; Gao, Guodong

    2013-05-17

    As glioma ranks as the first most prevalent solid tumors in primary central nervous system, certain single-nucleotide polymorphisms (SNPs) may be related to increased glioma risk, and have implications in carcinogenesis. The present case-control study was carried out to elucidate how common variants contribute to glioma susceptibility. Ten candidate tagging SNPs (tSNPs) were selected from seven genes whose polymorphisms have been proven by classical literatures and reliable databases to be tended to relate with gliomas, and with the minor allele frequency (MAF)>5% in the HapMap Asian population. The selected tSNPs were genotyped in 629 glioma patients and 645 controls from a Han Chinese population using the multiplexed SNP MassEXTEND assay calibrated. Two significant tSNPs in RTEL1 gene were observed to be associated with glioma risk (rs6010620, P=0.0016, OR: 1.32, 95% CI: 1.11-1.56; rs2297440, P=0.001, OR: 1.33, 95% CI: 1.12-1.58) by χ2 test. It was identified the genotype "GG" of rs6010620 acted as the protective genotype for glioma (OR, 0.46; 95% CI, 0.31-0.7; P=0.0002), while the genotype "CC" of rs2297440 as the protective genotype in glioma (OR, 0.47; 95% CI, 0.31-0.71; P=0.0003). Furthermore, haplotype "GCT" in RTEL1 gene was found to be associated with risk of glioma (OR, 0.7; 95% CI, 0.57-0.86; Fisher's P=0.0005; Pearson's P=0.0005), and haplotype "ATT" was detected to be associated with risk of glioma (OR, 1.32; 95% CI, 1.12-1.57; Fisher's P=0.0013; Pearson's P=0.0013). Two single variants, the genotypes of "GG" of rs6010620 and "CC" of rs2297440 (rs6010620 and rs2297440) in the RTEL1 gene, together with two haplotypes of GCT and ATT, were identified to be associated with glioma development. And it might be used to evaluate the glioma development risks to screen the above RTEL1 tagging SNPs and haplotypes. The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1993021136961998.

  3. A single frequency component-based re-estimated MUSIC algorithm for impact localization on complex composite structures

    Yuan, Shenfang; Bao, Qiao; Qiu, Lei; Zhong, Yongteng

    2015-01-01

    The growing use of composite materials on aircraft structures has attracted much attention for impact monitoring as a kind of structural health monitoring (SHM) method. Multiple signal classification (MUSIC)-based monitoring technology is a promising method because of its directional scanning ability and easy arrangement of the sensor array. However, for applications on real complex structures, some challenges still exist. The impact-induced elastic waves usually exhibit a wide-band performance, giving rise to the difficulty in obtaining the phase velocity directly. In addition, composite structures usually have obvious anisotropy, and the complex structural style of real aircrafts further enhances this performance, which greatly reduces the localization precision of the MUSIC-based method. To improve the MUSIC-based impact monitoring method, this paper first analyzes and demonstrates the influence of measurement precision of the phase velocity on the localization results of the MUSIC impact localization method. In order to improve the accuracy of the phase velocity measurement, a single frequency component extraction method is presented. Additionally, a single frequency component-based re-estimated MUSIC (SFCBR-MUSIC) algorithm is proposed to reduce the localization error caused by the anisotropy of the complex composite structure. The proposed method is verified on a real composite aircraft wing box, which has T-stiffeners and screw holes. Three typical categories of 41 impacts are monitored. Experimental results show that the SFCBR-MUSIC algorithm can localize impact on complex composite structures with an obviously improved accuracy. (paper)

  4. Association analysis of calpain 10 gene variants/haplotypes with gestational diabetes mellitus among Mexican women.

    Castro-Martínez, Anna Gabriela; Sánchez-Corona, José; Vázquez-Vargas, Adriana Patricia; García-Zapién, Alejandra Guadalupe; López-Quintero, Andres; Villalpando-Velazco, Héctor Javier; Flores-Martínez, Silvia Esperanza

    2018-02-28

    Gestational diabetes mellitus (GDM) is a metabolically complex disease with major genetic determinants. GDM has been associated with insulin resistance and dysfunction of pancreatic beta cells, so the GDM candidate genes are those that encode proteins modulating the function and secretion of insulin, such as that for calpain 10 (CAPN10). This study aimed to assess whether single nucleotide polymorphism (SNP)-43, SNP-44, SNP-63, and the indel-19 variant, and specific haplotypes of the CAPN10 gene were associated with gestational diabetes mellitus. We studied 116 patients with gestational diabetes mellitus and 83 women with normal glucose tolerance. Measurements of anthropometric and biochemical parameters were performed. SNP-43, SNP-44, and SNP-63 were identified by polymerase chain reaction (PCR)-restriction fragment length polymorphisms, while the indel-19 variant was detected by TaqMan qPCR assays.  The allele, genotype, and haplotype frequencies of the four variants did not differ significantly between women with gestational diabetes mellitus and controls. However, in women with gestational diabetes mellitus, glucose levels were significantly higher bearing the 3R/3R genotype than in carriers of the 3R/2R genotype of the indel-19 variant (p = 0.006). In conclusion, the 3R/3R genotype of the indel-19 variant of the CAPN-10 gene influenced increased glucose levels in these Mexican women with gestational diabetes mellitus.

  5. Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs.

    Bosse, Mirte; Lopes, Marcos S; Madsen, Ole; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Frantz, Laurent A F; Harlizius, Barbara; Bastiaansen, John W M; Groenen, Martien A M

    2015-12-22

    Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs. © 2015 The Author(s).

  6. Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.

    Andreas Wallberg

    2017-05-01

    Full Text Available Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations. We find that in general, levels of genetic differentiation between highland and lowland populations are very low, consistent with them being a single panmictic population. However, we identify two loci on chromosomes 7 and 9, each several hundred kilobases in length, which exhibit near fixation for different haplotypes between highland and lowland populations. The highland haplotypes at these loci are extremely rare in samples from the rest of the world. Patterns of segregation of genetic variants suggest that recombination between haplotypes at each locus is suppressed, indicating that they comprise independent structural variants. The haplotype on chromosome 7 harbors nearly all octopamine receptor genes in the honey bee genome. These have a role in learning and foraging behavior in honey bees and are strong candidates for adaptation to highland habitats. Molecular analysis of a putative breakpoint indicates that it may disrupt the coding sequence of one of these genes. Divergence between the highland and lowland haplotypes at both loci is extremely high suggesting that they are ancient balanced polymorphisms that greatly predate divergence between the extant honey bee subspecies.

  7. Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees

    Schöning, Caspar

    2017-01-01

    Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations. We find that in general, levels of genetic differentiation between highland and lowland populations are very low, consistent with them being a single panmictic population. However, we identify two loci on chromosomes 7 and 9, each several hundred kilobases in length, which exhibit near fixation for different haplotypes between highland and lowland populations. The highland haplotypes at these loci are extremely rare in samples from the rest of the world. Patterns of segregation of genetic variants suggest that recombination between haplotypes at each locus is suppressed, indicating that they comprise independent structural variants. The haplotype on chromosome 7 harbors nearly all octopamine receptor genes in the honey bee genome. These have a role in learning and foraging behavior in honey bees and are strong candidates for adaptation to highland habitats. Molecular analysis of a putative breakpoint indicates that it may disrupt the coding sequence of one of these genes. Divergence between the highland and lowland haplotypes at both loci is extremely high suggesting that they are ancient balanced polymorphisms that greatly predate divergence between the extant honey bee subspecies. PMID:28542163

  8. Compact state-space models for complex superconducting radio-frequency structures based on model order reduction and concatenation methods

    Flisgen, Thomas

    2015-01-01

    The modeling of large chains of superconducting cavities with couplers is a challenging task in computational electrical engineering. The direct numerical treatment of these structures can easily lead to problems with more than ten million degrees of freedom. Problems of this complexity are typically solved with the help of parallel programs running on supercomputing infrastructures. However, these infrastructures are expensive to purchase, to operate, and to maintain. The aim of this thesis is to introduce and to validate an approach which allows for modeling large structures on a standard workstation. The novel technique is called State-Space Concatenations and is based on the decomposition of the complete structure into individual segments. The radio-frequency properties of the generated segments are described by a set of state-space equations which either emerge from analytical considerations or from numerical discretization schemes. The model order of these equations is reduced using dedicated model order reduction techniques. In a final step, the reduced-order state-space models of the segments are concatenated in accordance with the topology of the complete structure. The concatenation is based on algebraic continuity constraints of electric and magnetic fields on the decomposition planes and results in a compact state-space system of the complete radio-frequency structure. Compared to the original problem, the number of degrees of freedom is drastically reduced, i.e. a problem with more than ten million degrees of freedom can be reduced on a standard workstation to a problem with less than one thousand degrees of freedom. The final state-space system allows for determining frequency-domain transfer functions, field distributions, resonances, and quality factors of the complete structure in a convenient manner. This thesis presents the theory of the state-space concatenation approach and discusses several validation and application examples. The examples

  9. Genetic polymorphisms and haplotypes of the organic cation transporter 1 gene (SLC22A1 in the Xhosa population of South Africa

    Clifford Jacobs

    2014-06-01

    Full Text Available Human organic cation transporter 1 is primarily expressed in hepatocytes and mediates the electrogenic transport of various endogenous and exogenous compounds, including clinically important drugs. Genetic polymorphisms in the gene coding for human organic cation transporter 1, SLC22A1, are increasingly being recognized as a possible mechanism explaining the variable response to clinical drugs, which are substrates for this transporter. The genotypic and allelic distributions of 19 nonsynonymous and one intronic SLC22A1 single nucleotide polymorphisms were determined in 148 healthy Xhosa participants from South Africa, using a SNAPshot® multiplex assay. In addition, haplotype structure for SLC22A1 was inferred from the genotypic data. The minor allele frequencies for S14F (rs34447885, P341L (rs2282143, V519F (rs78899680, and the intronic variant rs622342 were 1.7%, 8.4%, 3.0%, and 21.6%, respectively. None of the participants carried the variant allele for R61C (rs12208357, C88R (rs55918055, S189L (rs34104736, G220V (rs36103319, P283L (rs4646277, R287G (rs4646278, G401S (rs34130495, M440I (rs35956182, or G465R (rs34059508. In addition, no variant alleles were observed for A306T (COSM164365, A413V (rs144322387, M420V (rs142448543, I421F (rs139512541, C436F (rs139512541, V501E (rs143175763, or I542V (rs137928512 in the population. Eight haplotypes were inferred from the genotypic data. This study reports important genetic data that could be useful for future pharmacogenetic studies of drug transporters in the indigenous Sub-Saharan African populations.

  10. Bar Frequency & Galaxy Host Properties using the Spitzer Survey of Stellar Structure in Galaxies (S4G)

    Sheth, Kartik; Mizusawa, T.; Kim, T.; Munoz-Mateos, J.; Regan, M. W.; de Swardt, B.; Gadotti, D.; S4G Team

    2011-01-01

    Using the volume limited sample of 2,331 nearby galaxies from the Spitzer Survey of Stellar Structure in Galaxies (S4G), we have classified the frequency of barred spiral galaxies. The literature abounds with frequency ranges from as low as 20% to as high as 80% but these variations are driven by the quality of the data, the sample size and the methodology of the studies. Using the 3.6 and 4.5 micron IRAC images from S4G, we are able to make a definitive measurement of the local bar fraction as a function of the galaxy host and environment. We present the results from this survey and discuss how the current bar fraction compares to the declining frequency of bars from the present day to z 1.

  11. A note on eigenfrequency sensitivities and structural eigenfrequency optimization based on local sub-domain frequencies

    Pedersen, Pauli; Pedersen, Niels Leergaard

    2014-01-01

    foundation. A numerical heuristic redesign procedure is proposed and illustrated with examples. For the ideal case, an optimality criterion is fulfilled if the design have the same sub-domain frequency (local Rayleigh quotient). Sensitivity analysis shows an important relation between squared system...... eigenfrequency and squared local sub-domain frequency for a given eigenmode. Higher order eigenfrequenciesmay also be controlled in this manner. The presented examples are based on 2D finite element models with the use of subspace iteration for analysis and a heuristic recursive design procedure based...... on the derived optimality condition. The design that maximize a frequency depend on the total amount of available material and on a necessary interpolation as illustrated by different design cases.In this note we have assumed a linear and conservative eigenvalue problem without multiple eigenvalues. The presence...

  12. Novel CYP2E1 haplotype identified in a South African cohort

    Laura J. Heathfield

    2014-09-01

    Full Text Available Alcohol abuse accounts for approximately 2.5 million deaths annually and is the third highest risk factor for disease and disability. Alcohol is metabolised by polymorphic enzymes and the status of an individual with respect to alcohol metabolising enzymes may have forensic relevance in post-mortems. Baseline frequencies of gene variants involved in alcohol metabolism need to be established to aid the identification of suitable population-specific polymorphisms to genotype during molecular autopsies. The principal alcohol metabolising enzymes include alcohol dehydrogenase (ADH, aldehyde dehydrogenase (ALDH and cytochrome P450 2E1 (CYP2E1. Six single nucleotide polymorphisms (SNPs – rs1229984G>A and rs2066702C>T in ADH1B, rs671G>A in ALDH2, and rs3813867G>C, rs2031920C>T and rs6413432T>A in CYP2E1 – were genotyped in 150 individuals from four South African populations: Xhosa, Zulu, South African white and South African coloured. Allele frequencies for each SNP in the four population groups were 0–10% for rs1229984A, 2–12% for rs2066702T, 0–2% for rs671A, 1–4% for rs3813867C, 0–1% for rs2031920T and 3–15% for rs6413432A. Haplotype analysis revealed a novel combination of three SNPs in CYP2E1 whose effects on alcohol metabolism need further investigation. Establishment of baseline frequencies adds to our knowledge of genetic variation in alcohol metabolising enzymes and additional research is required to determine the functional significance of this novel CYP2E1 haplotype.

  13. Spectrally Efficient OFDMA Lattice Structure via Toroidal Waveforms on the Time-Frequency Plane

    Sultan Aldirmaz

    2010-01-01

    Full Text Available We investigate the performance of frequency division multiplexed (FDM signals, where multiple orthogonal Hermite-Gaussian carriers are used to increase the bandwidth efficiency. Multiple Hermite-Gaussian functions are modulated by a data set as a multicarrier modulation scheme in a single time-frequency region constituting toroidal waveform in a rectangular OFDMA system. The proposed work outperforms in the sense of bandwidth efficiency compared to the transmission scheme where only single Gaussian pulses are used as the transmission base. We investigate theoretical and simulation results of the proposed methods.

  14. Theoretical and Experimental Studies of High-Frequency Plasma Structures; Etudes Theoriques et Experimentales sur les Structures HF a Plasma

    Consoli, T. [CEA, Centre d' Etudes Nucleaires de Saclay (France)

    1969-03-15

    The author has studied high-frequency structures at the resonance {omega}{sub ec} = {omega}{sub HF} in an inhomogeneous magnetic field. The following points have been developed theoretically: the complete (relativistic and non-linear) analytical description of individual movement, taking into account the fact that the number of revolutions of the particles in the resonance zone is high; study of the self-consistent space charge field, with a view to establishing the conditions necessary for the energy of the ions to be of the order of the energy gained by the electrons in the resonance zone; calculation of the self-consistent HF field in the accelerated plasma, with a view to establishing the conditions for optimum operation of the HF accelerator; the problem of the mirror losses. The experimental results were obtained with various devices constructed for the purpose of verifying the theoretical predictions. With the Circe-Pleiade, where the ionization and acceleration functions have been separated by means of ionization with a Circe device ({lambda} = 3 cm, 300 W), it has been verified the relativistic law of variation of the parallel ion energy as a function of the injected density (existence of a minimum density for the entrainment of ions) and of the applied HF power (TE{sub 111} cavity, 3 GHz, 700 W). With the Circe accelerator ({lambda} =3 cm, P = 2.5kW, CW) it has been verified that, for n{sub plasma} n{sub c} , because of the strong attenuation of the field due to the high index. With the Icare device ({lambda} = 25 cm, P{sub HF} = 1 MW for 100 {mu}s), operating with pre-ionization by laser focalization on a solid D{sub 2} target with an injection density always higher than the cut-off density, accelerated deuteron

  15. Fatigue characteristics of high strength fire resistance steel for frame structure and time-frequency analysis its acoustic emission signal

    Kim, Hyun Soo; Nam, Ki Woo; Kang, Chang Young

    2000-01-01

    Demand for now nondestructive evaluation are growing to detect fatigue crack growth behavior to predict long term performance of materials and structure in aggressive environments, especially when they are in non-visible area. Acoustic emission technique is well suited to these problems and has drawn a keen interests because of its dynamic detection ability, extreme sensitivity and location of growing defects. In this study, we analysed acoustic emission signals obtained in fatigue and tensile test of high strength fire resistance steel for frame structure with time-frequency analysis methods. The main frequency range is different in the noise and the fatigue crack propagation. It could be classified that it were also generated by composite fracture mechanics of cleavage, dimple, inclusion separation etc

  16. Epistatic interaction between haplotypes of the ghrelin ligand and receptor genes influence susceptibility to myocardial infarction and coronary artery disease.

    Baessler, Andrea; Fischer, Marcus; Mayer, Bjoern; Koehler, Martina; Wiedmann, Silke; Stark, Klaus; Doering, Angela; Erdmann, Jeanette; Riegger, Guenter; Schunkert, Heribert; Kwitek, Anne E; Hengstenberg, Christian

    2007-04-15

    Data from both experimental models and humans provide evidence that ghrelin and its receptor, the growth hormone secretagogue receptor (ghrelin receptor, GHSR), possess a variety of cardiovascular effects. Thus, we hypothesized that genetic variants within the ghrelin system (ligand ghrelin and its receptor GHSR) are associated with susceptibility to myocardial infarction (MI) and coronary artery disease (CAD). Seven single nucleotide polymorphisms (SNPs) covering the GHSR region as well as eight SNPs across the ghrelin gene (GHRL) region were genotyped in index MI patients (864 Caucasians, 'index MI cases') from the German MI family study and in matched controls without evidence of CAD (864 Caucasians, 'controls', MONICA Augsburg). In addition, siblings of these MI patients with documented severe CAD (826 'affected sibs') were matched likewise with controls (n = 826 Caucasian 'controls') and used for verification. The effect of interactions between genetic variants of both genes of the ghrelin system was explored by conditional classification tree models. We found association of several GHSR SNPs with MI [best SNP odds ratio (OR) 1.7 (1.2-2.5); P = 0.002] using a recessive model. Moreover, we identified a common GHSR haplotype which significantly increases the risk for MI [multivariate adjusted OR for homozygous carriers 1.6 (1.1-2.5) and CAD OR 1.6 (1.1-2.5)]. In contrast, no relationship between genetic variants and the disease could be revealed for GHRL. However, the increase in MI/CAD frequency related to the susceptible GHSR haplotype was abolished when it coincided with a common GHRL haplotype. Multivariate adjustments as well as permutation-based methods conveyed the same results. These data are the first to demonstrate an association of SNPs and haplotypes within important genes of the ghrelin system and the susceptibility to MI, whereas association with MI/CAD could be identified for genetic variants across GHSR, no relationship could be revealed for GHRL

  17. Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1 and association with bipolar affective disorder in Taiwan

    Lin Yi-Mei J

    2005-03-01

    Full Text Available Abstract Background Disturbances in serotonin neurotransmission are implicated in the etiology of many psychiatric disorders, including bipolar affective disorder (BPD. The tryptophan hydroxylase gene (TPH, which codes for the enzyme catalyzing the rate-limiting step in serotonin biosynthetic pathway, is one of the leading candidate genes for psychiatric and behavioral disorders. In a preliminary study, we found that TPH1 intron7 A218C polymorphism was associated with BPD. This study was designed to investigate sequence variants of the TPH1 gene in Taiwanese and to test whether the TPH1 gene is a susceptibility factor for the BPD. Methods Using a systematic approach, we have searched the exons and promoter region of the TPH1 gene for sequence variants in Taiwanese Han and have identified five variants, A-1067G, G-347T, T3804A, C27224T, and A27237G. These five variants plus another five taken from the literature and a public database were examined for an association in 108 BPD patients and 103 controls; no association was detected for any of the 10 variants. Results Haplotype constructions using these 10 SNPs showed that the 3 most common haplotypes in both patients and controls were identical. One of the fourth common haplotype in the patient group (i.e. GGGAGACCCA was unique and showed a trend of significance with the disease (P = 0.028. However, the significance was abolished after Bonferroni correction thus suggesting the association is weak. In addition, three haplotype-tagged SNPs (htSNPs were selected to represent all haplotypes with frequencies larger than 2% in the Taiwanese Han population. The defined TPH1 htSNPs significantly reduce the marker number for haplotype analysis thus provides useful information for future association studies in our population. Conclusion Results of this study did not support the role of TPH1 gene in BPD etiology. As the current studies found the TPH1 gene under investigation belongs to the peripheral

  18. Haplotype association analysis of human disease traits using genotype data of unrelated individuals

    Tan, Qihua; Christiansen, Lene; Christensen, Kaare

    2005-01-01

    unphased multi-locus genotype data, ranging from the early approach by the simple gene-counting method to the recent work using the generalized linear model. However, these methods are either confined to case – control design or unable to yield unbiased point and interval estimates of haplotype effects....... Based on the popular logistic regression model, we present a new approach for haplotype association analysis of human disease traits. Using haplotype-based parameterization, our model infers the effects of specific haplotypes (point estimation) and constructs confidence interval for the risks...... on the well-known logistic regression model is a useful tool for haplotype association analysis of human disease traits....

  19. Serpin peptidase inhibitor (SERPINB5) haplotypes are associated with susceptibility to hepatocellular carcinoma

    Yang, Shun-Fa; Yeh, Chao-Bin; Chou, Ying-Erh; Lee, Hsiang-Lin; Liu, Yu-Fan

    2016-05-01

    Hepatocellular carcinoma (HCC) represents the second leading cause of cancer-related death worldwide. The serpin peptidase inhibitor SERPINB5 is a tumour-suppressor gene that promotes the development of various cancers in humans. However, whether SERPINB5 gene variants play a role in HCC susceptibility remains unknown. In this study, we genotyped 6 SNPs of the SERPINB5 gene in an independent cohort from a replicate population comprising 302 cases and 590 controls. Additionally, patients who had at least one rs2289520 C allele in SERPINB5 tended to exhibit better liver function than patients with genotype GG (Child-Pugh grade A vs. B or C; P = 0.047). Next, haplotype blocks were reconstructed according to the linkage disequilibrium structure of the SERPINB5 gene. A haplotype “C-C-C” (rs17071138 + rs3744941 + rs8089204) in SERPINB5-correlated promoter showed a significant association with an increased HCC risk (AOR = 1.450 P = 0.031). Haplotypes “T-C-A” and “C-C-C” (rs2289519 + rs2289520 + rs1455555) located in the SERPINB5 coding region had a decreased (AOR = 0.744 P = 0.031) and increased (AOR = 1.981 P = 0.001) HCC risk, respectively. Finally, an additional integrated in silico analysis confirmed that these SNPs affected SERPINB5 expression and protein stability, which significantly correlated with tumour expression and subsequently with tumour development and aggressiveness. Taken together, our findings regarding these biomarkers provide a prediction model for risk assessment.

  20. Worldwide genealogy of Entamoeba histolytica: an overview to understand haplotype distribution and infection outcome.

    Zermeño, Valeria; Ximénez, Cecilia; Morán, Patricia; Valadez, Alicia; Valenzuela, Olivia; Rascón, Edgar; Diaz, Daniel; Cerritos, René

    2013-07-01

    Although Entamoeba histolytica is one of the most prevalent intestinal parasites, how the different strains of this species are distributed all over the world and how different genotypes are associated with the infection outcome are yet to be fully understood. Recently, the use of a number of molecular markers has made the characterization of several genotypes in those regions with high incidence of amoebiasis possible. This work proposes the first genealogy of E. histolytica, with an haplotype network based on two tRNA gene-linked array of Short Tandem Repeats (STRs) reported until today, and 47 sequences from 39 new isolates of Mexican Amoebic Liver Abscesses (ALA) samples. One hundred and three sequences were obtained from D-A locus, their information about the geographic region of isolation as well as clinical diagnosis were also collected. One hundred and five sequences from N-K2 locus were also obtained as well as the region of isolation, but the information about clinical diagnosis was not available in all cases. The most abundant and widely distributed haplotype in the world is the one of E. histolytica HM1:IMSS strain. This was found in Mexico, Bangladesh, Japan, China and USA and is associated to symptomatic patients as well as asymptomatic cyst passers. Many other haplotypes were found only in a single country. Both genealogies suggest that there are no lineages within the networks that may be related to a particular geographic region or infection outcome. A concatenated analysis of the two molecular markers revealed 12 different combinations, which suggests the possibility of genetic recombination events. The present study is the first to propose a global genealogy of this species and suggests that there are still many genotypes to be discovered. The genotyping of new isolates will help to understand the great diversity and genetic structure of this parasite. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Structural, magnetic characterization (dependencies of coercivity and loss with the frequency) of magnetic cores based in Finemet

    Osinalde, M.; Infante, P.; Domínguez, L.; Blanco, J. M.; del Val, J. J.; Chizhik, A.; González, J.

    2017-12-01

    We report changes of coercivity, induced magnetic anisotropy, magneto-optical domain structure and frequency dependencies of coercivity and energy loss (up to 10 MHz) associated with the structural modifications produced by thermal treatments under applied magnetic field (field annealing) in toroidal wound cores of Fe73.5Cu1Nb3Si15.5B7 amorphous alloy. The thermal treatment (535 °C, 1 h) leads to the typical nanocrystalline structure of α-Fe(Si) nanograins (60-65% relative volume, 10-20 nm average grain size embedded in a residual amorphous matrix, while the magnetic field with the possibility to be applied in two directions to the toroidal core axis, that is in transverse (which is equivalent to the transverse direction of the ribbon) or longitudinal (equivalent to the longitudinal direction of the ribbon), develops a macroscopic uniaxial magnetic anisotropy in the transverse (around 245 J/m3) or longitudinal (around 85 J/m3) direction of the ribbon, respectively. It is remarkable the quasi-unhysteretic character of the cores with these two kinds of field annealing as comparing with that of the as-quenched one. Magneto-optical study by Kerr-effect of the ribbons provides useful information on the domain structure of the surface in agreement with the direction and intensity of the induced magnetic anisotropy. This induced uniaxial magnetic anisotropy plays a very important role on the Hc(f) and EL(f) curves, (f: frequency), being drastic the presence and direction of the induced magnetic anisotropy. In addition, these frequency dependencies show a significant change at the frequency around 100 Hz.

  2. Characterization of N-acetyltransferase 1 and 2 polymorphisms and haplotype analysis for inflammatory bowel disease and sporadic colorectal carcinoma

    Cobbs Gary A

    2007-05-01

    Full Text Available Abstract Background N-acetyltransferase 1 (NAT1 and 2 (NAT2 are polymorphic isoenzymes responsible for the metabolism of numerous drugs and carcinogens. Acetylation catalyzed by NAT1 and NAT2 are important in metabolic activation of arylamines to electrophilic intermediates that initiate carcinogenesis. Inflammatory bowel diseases (IBD consist of Crohn's disease (CD and ulcerative colitis (UC, both are associated with increased colorectal cancer (CRC risk. We hypothesized that NAT1 and/or NAT2 polymorphisms contribute to the increased cancer evident in IBD. Methods A case control study was performed with 729 Caucasian participants, 123 CRC, 201 CD, 167 UC, 15 IBD dysplasia/cancer and 223 controls. NAT1 and NAT2 genotyping were performed using Taqman based techniques. Eight single nucleotide polymorphisms (SNPs were characterized for NAT1 and 7 SNPs for NAT2. Haplotype frequencies were estimated using an Expectation-Maximization (EM method. Disease groups were compared to a control group for the frequencies at each individual SNP separately. The same groups were compared for the frequencies of NAT1 and NAT2 haplotypes and deduced NAT2 phenotypes. Results No statistically significant differences were found for any comparison. Strong linkage disequilibrium was present among both the NAT1 SNPs and the NAT2 SNPs. Conclusion This study did not demonstrate an association between NAT1 and NAT2 polymorphisms and IBD or sporadic CRC, although power calculations indicate this study had sufficient sample size to detect differences in frequency as small as 0.05 to 0.15 depending on SNP or haplotype.

  3. A Dynamic Programming Algorithm for the k-Haplotyping Problem

    Zhen-ping Li; Ling-yun Wu; Yu-ying Zhao; Xiang-sun Zhang

    2006-01-01

    The Minimum Fragments Removal (MFR) problem is one of the haplotyping problems: given a set of fragments, remove the minimum number of fragments so that the resulting fragments can be partitioned into k classes of non-conflicting subsets. In this paper, we formulate the k-MFR problem as an integer linear programming problem, and develop a dynamic programming approach to solve the k-MFR problem for both the gapless and gap cases.

  4. RFLP's for the human pepsinogen A haplotypes (PGA)

    Taggart, R T; Boudi, F B; Bell, G I

    1988-10-11

    PGA 101 is a 1340 bp cDNA clone containing exons 1-9 of the predicted human pepsinogen A coding sequence. Two distinct polymorphisms are detected with EcoRI and Bg1 II. Analysis with these enzymes provides for discrimination of the PGA haplotypes A, B, and C containing three, two and one PGA genes respectively. The PGA complex is located at 11q13. Mendelian inheritance was demonstrated in 20 families.

  5. Extended HLA-D region haplotype associated with celiac disease

    Howell, M.D.; Smith, J.R.; Austin, R.K.; Kelleher, D.; Nepom, G.T.; Volk, B.; Kagnoff, M.F.

    1988-01-01

    Celiac disease has one of the strongest associations with HLA (human leukocyte antigen) class II markers of the known HLA-linked diseases. This association is primarily with the class II serologic specificities HLA-DR3 and -DQw2. The authors previously described a restriction fragment length polymorphism (RFLP) characterized by the presence of a 4.0-kilobase Rsa I fragment derived from an HLA class II β-chain gene, which distinguishes the class II HLA haplotype of celiac disease patients from those of many serologically matched controls. They now report the isolation of this β-chain gene from a bacteriophage genomic library constructed from the DNA of a celiac disease patient. Based on restriction mapping and differential hybridization with class II cDNA and oligonucleotide probes, this gene was identified as one encoding an HLA-DP β-chain. This celiac disease-associated HLA-DP β-chain gene was flanked by HLA-DP α-chain genes and, therefore, was probably in its normal chromosomal location. The HLA-DPα-chain genes of celiac disease patients also were studied by RFLP analysis. Celiac disease is associated with a subset of HLA-DR3, -DQw2 haplotypes characterized by HLA-DP α- and β-chain gene RFLPs. Within the celiac-disease patient population, the joint segregation of these HLA-DP genes with those encoding the serologic specificities HLA-DR3 and -DQw2 indicates: (i) that the class II HLA haplotype associated with celiac disease is extended throughout the entire HLA-D region, and (ii) that celiac-disease susceptibility genes may reside as far centromeric on this haplotype as the HLA-DP subregion

  6. Extended HLA-D region haplotype associated with celiac disease

    Howell, M.D.; Smith, J.R.; Austin, R.K.; Kelleher, D.; Nepom, G.T.; Volk, B.; Kagnoff, M.F.

    1988-01-01

    Celiac disease has one of the strongest associations with HLA (human leukocyte antigen) class II markers of the known HLA-linked diseases. This association is primarily with the class II serologic specificities HLA-DR3 and -DQw2. The authors previously described a restriction fragment length polymorphism (RFLP) characterized by the presence of a 4.0-kilobase Rsa I fragment derived from an HLA class II ..beta..-chain gene, which distinguishes the class II HLA haplotype of celiac disease patients from those of many serologically matched controls. They now report the isolation of this ..beta..-chain gene from a bacteriophage genomic library constructed from the DNA of a celiac disease patient. Based on restriction mapping and differential hybridization with class II cDNA and oligonucleotide probes, this gene was identified as one encoding an HLA-DP ..beta..-chain. This celiac disease-associated HLA-DP ..beta..-chain gene was flanked by HLA-DP ..cap alpha..-chain genes and, therefore, was probably in its normal chromosomal location. The HLA-DP..cap alpha..-chain genes of celiac disease patients also were studied by RFLP analysis. Celiac disease is associated with a subset of HLA-DR3, -DQw2 haplotypes characterized by HLA-DP ..cap alpha..- and ..beta..-chain gene RFLPs. Within the celiac-disease patient population, the joint segregation of these HLA-DP genes with those encoding the serologic specificities HLA-DR3 and -DQw2 indicates: (i) that the class II HLA haplotype associated with celiac disease is extended throughout the entire HLA-D region, and (ii) that celiac-disease susceptibility genes may reside as far centromeric on this haplotype as the HLA-DP subregion.

  7. Combinatorial aspects of genome rearrangements and haplotype networks

    Labarre , Anthony

    2008-01-01

    The dissertation covers two problems motivated by computational biology: genome rearrangements, and haplotype networks. Genome rearrangement problems are a particular case of edit distance problems, where one seeks to transform two given objects into one another using as few operations as possible, with the additional constraint that the set of allowed operations is fixed beforehand; we are also interested in computing the corresponding distances between those objects, i.e. merely computing t...

  8. Two-dimensional sum-frequency generation (2D SFG) reveals structure and dynamics of a surface-bound peptide

    Laaser, Jennifer E.; Skoff, David R.; Ho, Jia-Jung; Joo, Yongho; Serrano, Arnaldo L.; Steinkruger, Jay D.; Gopalan, Padma; Gellman, Samuel H.; Zanni, Martin T.

    2014-01-01

    Surface-bound polypeptides and proteins are increasingly used to functionalize inorganic interfaces such as electrodes, but their structural characterization is exceedingly difficult with standard technologies. In this paper, we report the first two-dimensional sum-frequency generation (2D SFG) spectra of a peptide monolayer, which is collected by adding a mid-IR pulse shaper to a standard femtosecond SFG spectrometer. On a gold surface, standard FTIR spectroscopy is inconclusive about the peptide structure because of solvation-induced frequency shifts, but the 2D lineshapes, anharmonic shifts, and lifetimes obtained from 2D SFG reveal that the peptide is largely α-helical and upright. Random coil residues are also observed, which do not themselves appear in SFG spectra due to their isotropic structural distribution, but which still absorb infrared light and so can be detected by cross-peaks in 2D SFG spectra. We discuss these results in the context of peptide design. Because of the similar way in which the spectra are collected, these 2D SFG spectra can be directly compared to 2D IR spectra, thereby enabling structural interpretations of surface-bound peptides and biomolecules based on the well-studied structure/2D IR spectra relationships established from soluble proteins. PMID:24372101

  9. The effect of using genealogy-based haplotypes for genomic prediction.

    Edriss, Vahid; Fernando, Rohan L; Su, Guosheng; Lund, Mogens S; Guldbrandtsen, Bernt

    2013-03-06

    Genomic prediction uses two sources of information: linkage disequilibrium between markers and quantitative trait loci, and additive genetic relationships between individuals. One way to increase the accuracy of genomic prediction is to capture more linkage disequilibrium by regression on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information. A total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (π) of the haplotype covariates had zero effect, i.e. a Bayesian mixture method. About 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some cases, decreased the bias of prediction. With the Bayesian method, accuracy of prediction was less sensitive to parameter π when fitting haplotypes compared to fitting markers. Use of haplotypes based on genealogy can slightly increase the accuracy of genomic prediction. Improved methods to cluster the haplotypes constructed from local genealogy could lead to additional gains in accuracy.

  10. A unified framework for haplotype inference in nuclear families.

    Iliadis, Alexandros; Anastassiou, Dimitris; Wang, Xiaodong

    2012-07-01

    Many large genome-wide association studies include nuclear families with more than one child (trio families), allowing for analysis of differences between siblings (sib pair analysis). Statistical power can be increased when haplotypes are used instead of genotypes. Currently, haplotype inference in families with more than one child can be performed either using the familial information or statistical information derived from the population samples but not both. Building on our recently proposed tree-based deterministic framework (TDS) for trio families, we augment its applicability to general nuclear families. We impose a minimum recombinant approach locally and independently on each multiple children family, while resorting to the population-derived information to solve the remaining ambiguities. Thus our framework incorporates all available information (familial and population) in a given study. We demonstrate that using all the constraints in our approach we can have gains in the accuracy as opposed to breaking the multiple children families to separate trios and resorting to a trio inference algorithm or phasing each family in isolation. We believe that our proposed framework could be the method of choice for haplotype inference in studies that include nuclear families with multiple children. Our software (tds2.0) is downloadable from www.ee.columbia.edu/∼anastas/tds. © 2012 The Authors Annals of Human Genetics © 2012 Blackwell Publishing Ltd/University College London.

  11. Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana).

    Baurens, Franc-Christophe; Bocs, Stéphanie; Rouard, Mathieu; Matsumoto, Takashi; Miller, Robert N G; Rodier-Goud, Marguerite; MBéguié-A-MBéguié, Didier; Yahiaoui, Nabila

    2010-07-16

    Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. A

  12. Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia.

    Chang, Yuet Meng; Perumal, Revathi; Keat, Phoon Yoong; Kuehn, Daniel L C

    2007-03-22

    We have analyzed 16 Y-STR loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) from the non-recombining region of the human Y-chromosome in 980 male individuals from three main ethnic populations in Malaysia (Malay, Chinese, Indian) using the AmpFlSTR((R)) Y-filertrade mark (Applied Biosystems, Foster City, CA). The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three ethnic populations. Analysis of molecular variance indicated that 88.7% of the haplotypic variation is found within population and 11.3% is between populations (fixation index F(ST)=0.113, p=0.000). This study has revealed Y-chromosomes with null alleles at several Y-loci, namely DYS458, DYS392, DYS389I, DYS389II, DYS439, DYS448 and Y-GATA H4; and several occurrences of duplications at the highly polymorphic DYS385 loci. Some of these deleted loci were in regions of the Y(q) arm that have been implicated in the occurrence of male infertility.

  13. Power secant method applied to natural frequency extraction of Timoshenko beam structures

    C.A.N. Dias

    Full Text Available This work deals with an improved plane frame formulation whose exact dynamic stiffness matrix (DSM presents, uniquely, null determinant for the natural frequencies. In comparison with the classical DSM, the formulation herein presented has some major advantages: local mode shapes are preserved in the formulation so that, for any positive frequency, the DSM will never be ill-conditioned; in the absence of poles, it is possible to employ the secant method in order to have a more computationally efficient eigenvalue extraction procedure. Applying the procedure to the more general case of Timoshenko beams, we introduce a new technique, named "power deflation", that makes the secant method suitable for the transcendental nonlinear eigenvalue problems based on the improved DSM. In order to avoid overflow occurrences that can hinder the secant method iterations, limiting frequencies are formulated, with scaling also applied to the eigenvalue problem. Comparisons with results available in the literature demonstrate the strength of the proposed method. Computational efficiency is compared with solutions obtained both by FEM and by the Wittrick-Williams algorithm.

  14. Haplotype diversity of 17 Y-chromosomal STRs in three native Sarawak populations (Iban, Bidayuh and Melanau) in East Malaysia.

    Chang, Yuet Meng; Swaran, Yuvaneswari; Phoon, Yoong Keat; Sothirasan, Kavin; Sim, Hang Thiew; Lim, Kong Boon; Kuehn, Daniel

    2009-06-01

    17 Y-STRs (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) have been analyzed in 320 male individuals from Sarawak, an eastern state of Malaysia on the Borneo island using the AmpFlSTR Y-filer (Applied Biosystems, Foster City, CA). These individuals were from three indigenous ethnic groups in Sarawak comprising of 103 Ibans, 113 Bidayuhs and 104 Melanaus. The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three groups. Analysis of molecular variance (AMOVA) indicated that 87.6% of the haplotypic variation was found within population and 12.4% between populations (fixation index F(ST)=0.124, p=0.000). This study has revealed that the indigenous populations in Sarawak are distinctly different to each other, and to the three major ethnic groups in Malaysia (Malays, Chinese and Indians), with the Melanaus having a strikingly high degree of shared haplotypes within. There are rare unusual variants and microvariants that were not present in Malaysian Malay, Chinese or Indian groups. In addition, occurrences of DYS385 duplications which were only noticeably present in Chinese group previously was also observed in the Iban group whilst null alleles were detected at several Y-loci (namely DYS19, DYS392, DYS389II and DYS448) in the Iban and Melanau groups.

  15. MCP1 haplotypes associated with protection from pulmonary tuberculosis

    Owusu-Dabo Ellis

    2011-04-01

    Full Text Available Abstract Background The monocyte chemoattractant protein 1 (MCP-1 is involved in the recruitment of lymphocytes and monocytes and their migration to sites of injury and cellular immune reactions. In a Ghanaian tuberculosis (TB case-control study group, associations of the MCP1 -362C and the MCP1 -2581G alleles with resistance to TB were recently described. The latter association was in contrast to genetic effects previously described in study groups originating from Mexico, Korea, Peru and Zambia. This inconsistency prompted us to further investigate the MCP1 gene in order to determine causal variants or haplotypes genetically and functionally. Results A 14 base-pair deletion in the first MCP1 intron, int1del554-567, was strongly associated with protection against pulmonary TB (OR = 0.84, CI 0.77-0.92, Pcorrected = 0.00098. Compared to the wildtype combination, a haplotype comprising the -2581G and -362C promoter variants and the intronic deletion conferred an even stronger protection than did the -362C variant alone (OR = 0.78, CI 0.69-0.87, Pnominal = 0.00002; adjusted Pglobal = 0.0028. In a luciferase reporter gene assay, a significant reduction of luciferase gene expression was observed in the two constructs carrying the MCP1 mutations -2581 A or G plus the combination -362C and int1del554-567 compared to the wildtype haplotype (P = 0.02 and P = 0.006. The associated variants, in particular the haplotypes composed of these latter variants, result in decreased MCP-1 expression and a decreased risk of pulmonary TB. Conclusions In addition to the results of the previous study of the Ghanaian TB case-control sample, we have now identified the haplotype combination -2581G/-362C/int1del554-567 that mediates considerably stronger protection than does the MCP1 -362C allele alone (OR = 0.78, CI 0.69-0.87 vs OR = 0.83, CI 0.76-0.91. Our findings in both the genetic analysis and the reporter gene study further indicate a largely negligible role of the

  16. An equivalent frequency approach for determining non-linear effects on pre-tensioned-cable cross-braced structures

    Giaccu, Gian Felice

    2018-05-01

    Pre-tensioned cable braces are widely used as bracing systems in various structural typologies. This technology is fundamentally utilized for stiffening purposes in the case of steel and timber structures. The pre-stressing force imparted to the braces provides to the system a remarkable increment of stiffness. On the other hand, the pre-tensioning force in the braces must be properly calibrated in order to satisfactorily meet both serviceability and ultimate limit states. Dynamic properties of these systems are however affected by non-linear behavior due to potential slackening of the pre-tensioned brace. In the recent years the author has been working on a similar problem regarding the non-linear response of cables in cable-stayed bridges and braced structures. In the present paper a displacement-based approach is used to examine the non-linear behavior of a building system. The methodology operates through linearization and allows obtaining an equivalent linearized frequency to approximately characterize, mode by mode, the dynamic behavior of the system. The equivalent frequency depends on both the mechanical characteristics of the system, the pre-tensioning level assigned to the braces and a characteristic vibration amplitude. The proposed approach can be used as a simplified technique, capable of linearizing the response of structural systems, characterized by non-linearity induced by the slackening of pre-tensioned braces.

  17. Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches†

    Alexandre Presas

    2017-03-01

    Full Text Available To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs, which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the

  18. Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches†.

    Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

    2017-03-22

    To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

  19. Recurrence and frequency of disturbance have cumulative effect on methanotrophic activity, abundance, and community structure.

    Adrian eHo

    2016-01-01

    Full Text Available Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by two-fold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency.

  20. Effect of ripple taper on band-gap overlap in a coaxial Bragg structure operating at terahertz frequency

    Ding Xueyong; Li Hongfan; Lv Zhensu

    2012-01-01

    Based on the mode-coupling method, numerical analysis is presented to demonstrate the influence of ripple taper on band-gap overlap in a coaxial Bragg structure operating at terahertz frequency. Results show that the interval between the band-gaps of the competing mode and the desired working mode is narrowed by use of positive-taper ripples, but is expanded if negative-taper ripples are employed, and the influence of the negative-taper ripples is obviously more advantageous than the positive-taper ripples; the band-gap overlap of modes can be efficiently separated by use of negative-taper ripples. The residual side-lobes of the frequency response in a coaxial Bragg structure with ripple taper also can be effectively suppressed by employing the windowing-function technique. These peculiarities provide potential advantage in constructing a coaxial Bragg cavity with high quality factor for single higher-order-mode operation of a high-power free-electron maser in the terahertz frequency range.

  1. Time-frequency analysis to a particular type of scattering problems involving metallic-polymer tubing structures.

    Elhanaoui, Abdelkader; Aassif, Elhoucein; Maze, Gérard; Décultot, Dominique

    2018-01-01

    In this paper, recent studies of backscattered acoustic signals in thinner steel-polymer tubing structures have been presented. Reassigned smoothed pseudo Wigner-Ville (rspWV) analysis has been adopted in order to diminish the cross-term effect, and achieve high resolution spectral. Vibration modes, which are associated to the resonances of circumferential waves, have been determined by using the modal isolation plan representation. At normalized frequencies below 140, an appreciable influence from the polymer coating thickness on the A 0 + and S 0 modes has been noticed. Furthermore, the trajectory of the A 0 - wave has been modified in the normalized frequency band 40-42. Group velocity curves of the A 0 - wave have, then, been graphically illustrated. The findings have shown a particular curvature change at reduced frequency 41 in the case of an immersed two-layer tube in water. Studies of acoustic backscattering involving steel-polymer tubing structures have confirmed the significant coupling of A 0 + and S 0 waves. Besides, the disappearance of the A 0 + resonance trajectory has been observed; which is a very important phenomenon to understand. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Frequency-comb based collinear laser spectroscopy of Be for nuclear structure investigations and many-body QED tests

    Krieger, A

    2017-01-01

    Absolute transition frequencies of the $2s\\,^2{\\rm{S}}_{1/2}$ $\\rightarrow$ $2p\\,^2{\\rm{P}}_{1/2,3/2}$ transitions in Be$^+$ were measured with a frequency comb in stable and short-lived isotopes at ISOLDE (CERN) using collinear laser spectroscopy. Quasi-simultaneous measurements in copropagating and counterpropagating geometry were performed to become independent from acceleration voltage determinations for Doppler-shift corrections of the fast ion beam. Isotope shifts and fine structure splittings were obtained from the absolute transition frequencies with accuracies better than 1\\,MHz and led to a precise determination of the nuclear charge radii of $^{7,10-12}$Be relative to the stable isotope $^9$Be. Moreover, an accurate determination of the $2p$ fine structure splitting allowed a test of high-precision bound-state QED calculations in the three-electron system. Here, we describe the laser spectroscopic method in detail, including several tests that were carried out to determine or estimate systematic un...

  3. Frequency Modulation and Absorption Improvement of THz Micro-bolometer with Micro-bridge Structure by Spiral-Type Antennas.

    Gou, Jun; Niu, Qingchen; Liang, Kai; Wang, Jun; Jiang, Yadong

    2018-03-05

    Antenna-coupled micro-bridge structure is proven to be a good solution to extend infrared micro-bolometer technology for THz application. Spiral-type antennas are proposed in 25 μm × 25 μm micro-bridge structure with a single separate linear antenna, two separate linear antennas, or two connected linear antennas on the bridge legs, in addition to traditional spiral-type antenna on the support layer. The effects of structural parameters of each antenna on THz absorption of micro-bridge structure are discussed for optimized absorption of 2.52 THz wave radiated by far infrared CO 2 lasers. The design of spiral-type antenna with two separate linear antennas for wide absorption peak and spiral-type antenna with two connected linear antennas for relatively stable absorption are good candidates for high absorption at low absorption frequency with a rotation angle of 360*n (n = 1.6). Spiral-type antenna with extended legs also provides a highly integrated micro-bridge structure with fast response and a highly compatible, process-simplified way to realize the structure. This research demonstrates the design of several spiral-type antenna-coupled micro-bridge structures and provides preferred schemes for potential device applications in room temperature sensing and real-time imaging.

  4. Distinct genotype distribution and haplotype profiles in MDR1 gene among Chinese Han, Bai, Wa and Tibetan ethnic groups.

    Lai, Yong; Huang, Min; Li, Hui; Wang, Xue-Ding; Li, Jia-Li

    2012-11-01

    P-Glycoprotein (P-gp, encoded by MDR1 gene) plays an important role in determining bioavailability and pharmacologic effects of many drugs. There is increasing evidence that P-gp activity may be genetically determined. In this study, we investigated the genotype distribution and the haplotype profiles of MDR1 gene in Chinese Han, Bai, Wa and Tibetan subjects. Much lower frequencies of the 1236T allele and the 2677T allele were found in Wa subjects than those in other three ethnic groups, while the 2677A allele was found about 6-fold more frequently in Han subjects than in subjects of other three ethnic groups. The Han, Bai and Tibetan subjects share the same three predominant haplotypes (T-T-T, T-G-C and C-G-C), and T-T-T is the highest and accounts for more than one third of the number of haplotypes in the subjects from each ethnic group. However, T-T-T was less common than T-G-C, T-G-T and C-G-C and occurring at only 13.8% in Wa subjects, furthermore, higher frequencies of T-G-T, C-T-C, C-G-T and C-T-T were observed in Wa subjects compared to those in other three ethnic groups. Frequencies of C-A-C and T-A-C in Han subjects were higher than those in other three ethnic groups. The findings of this study will be of some relevance in predicting MDR1 phenotype and pharmacokinetics as well as pharmacodynamic effects of many commonly used drugs that are P-gp substrates in these four Chinese ethnic groups.

  5. Salt Effects on Surface Structures of Polyelectrolyte Multilayers (PEMs) Investigated by Vibrational Sum Frequency Generation (SFG) Spectroscopy.

    Ge, Aimin; Matsusaki, Michiya; Qiao, Lin; Akashi, Mitsuru; Ye, Shen

    2016-04-26

    Sum frequency generation (SFG) vibrational spectroscopy was employed to investigate the surface structures of polyelectrolyte multilayers (PEMs) constructed by sequentially alternating adsorption of poly(diallyldimethylammonium chloride) (PDDA) and poly(styrenesulfonate) (PSS). It was found that the surface structures and surface charge density of the as-deposited PEMs of PDDA/PSS significantly depend on the concentration of sodium chloride (NaCl) present in the polyelectrolyte solutions. Furthermore, it was found that the surface structure of the as-deposited PEMs is in a metastable state and will reach the equilibrium state by diffusion of the polyelectrolyte chain after an aging process, resulting in a polyelectrolyte mixture on the PEM surfaces.

  6. Nonlinear low frequency electrostatic structures in a magnetized two-component auroral plasma

    Rufai, O. R., E-mail: rajirufai@gmail.com [University of the Western Cape, Bellville 7535, Cape-Town (South Africa); Scientific Computing, Memorial University of Newfoundland, St John' s, Newfoundland and Labrador A1C 5S7 (Canada); Bharuthram, R., E-mail: rbharuthram@uwc.ac.za [University of the Western Cape, Bellville 7535, Cape-Town (South Africa); Singh, S. V., E-mail: satyavir@iigs.iigm.res.in; Lakhina, G. S., E-mail: lakhina@iigs.iigm.res.in [University of the Western Cape, Bellville 7535, Cape-Town (South Africa); Indian Institute of Geomagnetism, New Panvel (W), Navi Mumbai 410218 (India)

    2016-03-15

    Finite amplitude nonlinear ion-acoustic solitons, double layers, and supersolitons in a magnetized two-component plasma composed of adiabatic warm ions fluid and energetic nonthermal electrons are studied by employing the Sagdeev pseudopotential technique and assuming the charge neutrality condition at equilibrium. The model generates supersoliton structures at supersonic Mach numbers regime in addition to solitons and double layers, whereas in the unmagnetized two-component plasma case only, soliton and double layer solutions can be obtained. Further investigation revealed that wave obliqueness plays a critical role for the evolution of supersoliton structures in magnetized two-component plasmas. In addition, the effect of ion temperature and nonthermal energetic electron tends to decrease the speed of oscillation of the nonlinear electrostatic structures. The present theoretical results are compared with Viking satellite observations.

  7. Low-frequency nondestructive analysis of cracks in multilayer structures using a scanning magnetic microscope

    Adamo, M; Nappi, C; Sarnelli, E, E-mail: m.adamo@cib.na.cnr.i [Istituto di Cibernetica ' E Caianiello' , Via Campi Flegrei 34, I-80078 Pozzuoli (Italy)

    2010-09-15

    The use of a scanning magnetic microscope (SMM) with a high temperature superconducting quantum interference device (SQUID) for quantitative measurements in eddy current nondestructive analysis (NDA) is presented. The SQUID has been used to detect the weak magnetic field variations around a small defect, close to a structural part generating an intensive magnetic field. The experimental data for a deep crack close to a rivet in a multilayer conducting plate have been taken in a RF-shielded environment and discussed in the light of the theoretical predictions. The results show that eddy current NDA can distinguish subsurface crack signals from wider structural signals, with defects located 10 mm below the surface. Moreover, in order to visualize the structure of the probing current when a circular induction coil is used, the simulation of eddy currents in a thick unflawed conducting plate has been carried out.

  8. Low-frequency nondestructive analysis of cracks in multilayer structures using a scanning magnetic microscope

    Adamo, M; Nappi, C; Sarnelli, E

    2010-01-01

    The use of a scanning magnetic microscope (SMM) with a high temperature superconducting quantum interference device (SQUID) for quantitative measurements in eddy current nondestructive analysis (NDA) is presented. The SQUID has been used to detect the weak magnetic field variations around a small defect, close to a structural part generating an intensive magnetic field. The experimental data for a deep crack close to a rivet in a multilayer conducting plate have been taken in a RF-shielded environment and discussed in the light of the theoretical predictions. The results show that eddy current NDA can distinguish subsurface crack signals from wider structural signals, with defects located 10 mm below the surface. Moreover, in order to visualize the structure of the probing current when a circular induction coil is used, the simulation of eddy currents in a thick unflawed conducting plate has been carried out.

  9. Three dimensional complex plasma structures in a combined radio frequency and direct current discharge

    Mitic, S.; Morfill, G. E.; Klumov, B. A.; Khrapak, S. A.

    2013-01-01

    We report on the first detailed analysis of large three dimensional (3D) complex plasma structures in experiments performed in pure rf and combined rf+dc discharge modes. Inductively coupled plasma is generated by an rf coil wrapped around the vertically positioned cylindrical glass tube at a pressure of 0.3 mbar. In addition, dc plasma can be generated by applying voltage to the electrodes at the ends of the tube far from the rf coil. The injected monodisperse particles are levitated in the plasma below the coil. A scanning laser sheet and a high resolution camera are used to determine the 3D positions of about 10 5 particles. The observed bowl-shaped particle clouds reveal coexistence of various structures, including well-distinguished solid-like, less ordered liquid-like, and pronounced string-like phases. New criteria to identify string-like structures are proposed.

  10. Damped fiber optic low-frequency tiltmeter for real-time monitoring of structural displacements

    Meng, Dewei; Ansari, Farhad

    2013-01-01

    This study reports on the design, development and testing of a fiber optic Bragg grating (FBG)-based tiltmeter. The tiltmeter design is based on the correlation between the bending strains and rotations of a lumped mass ended cantilever beam. The design of the system includes incorporation of a damping fluid to control the dynamic response. Temperature compensation for the sensor was achieved by using two symmetrically placed FBGs for cancellation of thermal effects. The tiltmeter is designed to exhibit linearity over the range of measurements common in low-frequency vibrations in bridges and exhibits measurement resolution of 0.005°. The study reports on the static calibration tests, correlations with the theoretical relationships, and dynamic characterization and response. (paper)

  11. Frequency and prioritization of patient health risks from a structured health risk assessment.

    Phillips, Siobhan M; Glasgow, Russell E; Bello, Ghalib; Ory, Marcia G; Glenn, Beth A; Sheinfeld-Gorin, Sherri N; Sabo, Roy T; Heurtin-Roberts, Suzanne; Johnson, Sallie Beth; Krist, Alex H

    2014-01-01

    To describe the frequency and patient-reported readiness to change, desire to discuss, and perceived importance of 13 health risk factors in a diverse range of primary care practices. Patients (n = 1,707) in 9 primary care practices in the My Own Health Report (MOHR) trial reported general, behavioral, and psychosocial risk factors (body mass index [BMI], health status, diet, physical activity, sleep, drug use, stress, anxiety or worry, and depression). We classified responses as "at risk" or "healthy" for each factor, and patients indicated their readiness to change and/or desire to discuss identified risk factors with providers. Patients also selected 1 of the factors they were ready to change as most important. We then calculated frequencies within and across these factors and examined variation by patient characteristics and across practices. On average, patients had 5.8 (SD = 2.12; range, 0-13) unhealthy behaviors and mental health risk factors. About 55% of patients had more than 6 risk factors. On average, patients wanted to change 1.2 and discuss 0.7 risks. The most common risks were inadequate fruit/vegetable consumption (84.5%) and overweight/obesity (79.6%). Patients were most ready to change BMI (33.3%) and depression (30.7%), and most wanted to discuss depression (41.9%) and anxiety or worry (35.2%). Overall, patients rated health status as most important. Implementing routine comprehensive health risk assessments in primary care will likely identify a high number of behavioral and psychosocial health risks. By soliciting patient priorities, providers and patients can better manage counseling and behavior change. © 2014 Annals of Family Medicine, Inc.

  12. Natural Frequency and Damping Estimation of an Offshore Wind Turbine Structure

    Damgaard, Mads; Andersen, Jacob K. F.; Ibsen, Lars Bo

    2012-01-01

    During the last years, offshore wind turbines have increased significantly in size with larger rotors and more powerful generators. The costs are kept as low as possible by reducing the overall weight, which leads to very slender and flexible structures. An improper design may cause resonance due...... of an offshore wind turbine located in the North Sea. Simple Fourier Transformation and least square fitting to the vibration decay of ten “rotor stop” tests make it possible to evaluate the dynamic properties of the wind turbine structure. Based on the traditionally p-y curve method (Winkler type approach...

  13. Connecting structural relaxation with the low frequency modes in a hard-sphere colloidal glass

    Ghosh, A.; Chikkadi, V.; Schall, P.; Bonn, D.

    2011-01-01

    Structural relaxation in hard-sphere colloidal glasses has been studied using confocal microscopy. The motion of individual particles is followed over long time scales to detect the rearranging regions in the system. We have used normal mode analysis to understand the origin of the rearranging

  14. A Flexible 5G Frame Structure Design for Frequency-Division Duplex Cases

    Pedersen, Klaus I.; Berardinelli, Gilberto; Frederiksen, Frank

    2016-01-01

    A 5G frame structure designed for efficient support of users with highly diverse service requirements is proposed. It includes support for mobile broadband data, mission-critical communication, and massive machine communication. The solution encompasses flexible multiplexing of users on a shared...

  15. Source Identification in Structural Acoustics with an Inverse Frequency Response Function Technique

    Visser, Rene

    2002-01-01

    Inverse source identification based on acoustic measurements is essential for the investigation and understanding of sound fields generated by structural vibrations of various devices and machinery. Acoustic pressure measurements performed on a grid in the nearfield of a surface can be used to

  16. Strong association between a splice mutation (IVS12+5G{r_arrow}A) and haplotype 6 in hereditary tyrosinemia type I

    Tanguay, R.M.; St-Louis, M.; Gibson, K. [Universite Laval, Ste-Foy (Canada)] [and others

    1994-09-01

    Hereditary tyrosinemia type I (HT I; McKusick 276700) is a severe inborn error of tyrosine catabolism pathway caused by a deficiency of fumarylacetoacetate hydrolase (FAH). The highest frequency reported is the one in Saguenay-Lac St-Jean (Quebec, Canada) where 1:1,846 births are affected. The FAH gene has been cloned and several mutations have been described. Allele specific oligonucleotide (ASO) hybridization was used to examine the frequency of a splice (IVS12-5G{r_arrow}A) mutation recently reported and RFLP analysis was done to identify haplotypes related to HT I. The splice mutation was found on 45/50 alleles (90%) in patients from SLSJ and 12/66 (18%) alleles from patients world-wide. All 25 patients from the SLSJ region were positive with 20 being homozygous, indicating that this mutation is the major cause of HT I in French Canada. Of these 25 patients, 96% were positive for one haplotype called no 6 which is these 25 patients, 96% were positive for one haplotype called no 6 which is identified by TaqI, RsaI, BglII, MspI and KpnI digestions. These data show a really strong association between the mutation (IVS12+5G{r_arrow}A) and haplotype 6. Among our patients from around the world, {approximately}52% were positive for haplotype 6 indicating its strong relation with HT I. These results provide the rationale for DNA-based carrier testing for HT I in the F-C population at risk as well as in HT I patients in general.

  17. Structures of Xishan village landslide in Li County, Sichuan, China, inferred from high-frequency receiver functions of local earthquakes

    Wei, Z.; Chu, R.

    2017-12-01

    Teleseismic receiver function methods are widely used to study the deep structural information beneath the seismic station. However, teleseismic waveforms are difficult to extract the high-frequency receiver function, which are insufficient to constrain the shallow structure because of the inelastic attenuation effect of the earth. In this study, using the local earthquake waveforms collected from 3 broadband stations deployed on the Xishan village landslide in Li County in Sichuan Province, we used the high-frequency receiver function method to study the shallow structure beneath the landslide. We developed the Vp-k (Vp/Vs) staking method of receiver functions, and combined with the H-k stacking and waveform inversion methods of receiver functions to invert the landslide's thickness, S-wave velocity and average Vp/Vs ratio beneath these stations, and compared the thickness with the borehole results. Our results show small-scale lateral variety of velocity structure, a 78-143m/s lower S-wave velocity in the bottom layer and 2.4-3.1 Vp/Vs ratio in the landslide. The observed high Vp/Vs ratio and low S-wave velocity in the bottom layer of the landslide are consistent with low electrical resistivity and water-rich in the bottom layer, suggesting a weak shear strength and potential danger zone in landslide h1. Our study suggest that the local earthquake receiver function can obtain the shallow velocity structural information and supply some seismic constrains for the landslide catastrophe mitigation.

  18. Nitrogen and argon doping of niobium for superconducting radio frequency cavities: a pathway to highly efficient accelerating structures

    Grassellino, A.; Romanenko, A.; Sergatskov, D.; Melnychuk, O.; Trenikhina, Y.; Crawford, A.; Rowe, A.; Wong, M.; Khabiboulline, T.; Barkov, F.

    2013-10-01

    We report a surface treatment that systematically improves the quality factor of niobium radio frequency cavities beyond the expected limit for niobium. A combination of annealing in a partial pressure of nitrogen or argon gas and subsequent electropolishing of the niobium cavity surface leads to unprecedented low values of the microwave surface resistance, and an improvement in the efficiency of the accelerating structures up to a factor of 3, reducing the cryogenic load of superconducting cavities for both pulsed and continuous duty cycles. The field dependence of the surface resistance is reversed compared to standardly treated niobium.

  19. Devil’s Vortex Phase Structure as Frequency Plane Mask for Image Encryption Using the Fractional Mellin Transform

    Sunanda Vashisth

    2014-01-01

    Full Text Available A frequency plane phase mask based on Devil’s vortex structure has been used for image encryption using the fractional Mellin transform. The phase key for decryption is obtained by an iterative phase retrieval algorithm. The proposed scheme has been validated for grayscale secret target images, by numerical simulation. The efficacy of the scheme has been evaluated by computing mean-squared-error between the secret target image and the decrypted image. Sensitivity analysis of the decryption process to variations in various encryption parameters has been carried out. The proposed encryption scheme has been seen to exhibit reasonable robustness against occlusion attack.

  20. Stress and subsidy effects of seagrass wrack duration, frequency, and magnitude on salt marsh community structure.

    Hanley, Torrance C; Kimbro, David L; Hughes, Anne Randall

    2017-07-01

    Environmental perturbations can strongly affect community processes and ecosystem functions by acting primarily as a subsidy that increases productivity, a stress that decreases productivity, or both, with the predominant effect potentially shifting from subsidy to stress as the overall intensity of the perturbation increases. While perturbations are often considered along a single axis of intensity, they consist of multiple components (e.g., magnitude, frequency, and duration) that may not have equivalent stress and/or subsidy effects. Thus, different combinations of perturbation components may elicit community and ecosystem responses that differ in strength and/or direction (i.e., stress or subsidy) even if they reflect a similar overall perturbation intensity. To assess the independent and interactive effects of perturbation components, we experimentally manipulated the magnitude, frequency, and duration of wrack deposition, a common stress-subsidy in a variety of coastal systems. The effects of wrack perturbation on salt marsh community and ecosystem properties were assessed both in the short-term (at the end of a 12-week experimental manipulation) and long-term (6 months after the end of the experiment). In the short-term, plants and associated benthic invertebrates exhibited primarily stress-based responses to wrack perturbation. The extent of these stress effects on density of the dominant plant Spartina alterniflora, total plant percent cover, invertebrate abundance, and sediment oxygen availability were largely determined by perturbation duration. Yet, higher nitrogen content of Spartina, which indicates a subsidy effect of wrack, was influenced primarily by perturbation magnitude in the short-term. In the longer term, perturbation magnitude determined the extent of both stress and subsidy effects of wrack perturbation, with lower subordinate plant percent cover and snail density, and higher Spartina nitrogen content in high wrack biomass treatments

  1. Quantitative trait loci and the relevance of phased haplotypes

    Gregersen, Vivi Raundahl

    Genetic control of different production traits and diseases within livestock has been of great interest since domenstication. SNPs have greatly facilitated the use of QTL studies in the search of genomic regions affecting different phenotypes. The studies have been conducted to identify regions...... underlying gentic control both as traditional linkage studies relying on genetic maps and as GWAS where an approach of phasing haplotypes within the QTL have been conducted to validate the regions. Overall, regions of interest have been identified for chronic pleuritis and osteochondrosis in addition to meat...... quality and boar taint in pigs, and for improved chees production within cows...

  2. A haplotype specific to North European wheat (Triticum aestivum L.)

    Tsombalova, J.; Karafiátová, Miroslava; Vrána, Jan; Kubaláková, Marie; Peusa, H.; Jakobson, I.; Jarve, M.; Valárik, Miroslav; Doležel, Jaroslav; Jarve, K.

    2017-01-01

    Roč. 64, č. 4 (2017), s. 653-664 ISSN 0925-9864 R&D Projects: GA MŠk(CZ) LO1204; GA ČR(CZ) GA14-07164S Institutional support: RVO:61389030 Keywords : bread wheat * genetic diversity * polyploid wheat * introgression lines * molecular analysis * tetraploid wheat * hexaploid wheat * powdery mildew * spelta l. * map * Common wheat * Triticum aestivum L * Spelt * Triticum spelta L * Chromosome 4A * Zero alleles * Haplotype * Linkage disequilibrium Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 1.294, year: 2016

  3. High resolution, high sensitivity, dynamic distributed structural monitoring using optical frequency domain reflectometry

    Kreger, Stephen T.; Sang, Alex K.; Garg, Naman; Michel, Julia

    2013-05-01

    Fiber-optic ultrasonic transducers are an important component of an active ultrasonic testing system for structural health monitoring. Fiber-optic transducers have several advantages such as small size, light weight, and immunity to electromagnetic interference that make them much more attractive than the current available piezoelectric transducers, especially as embedded and permanent transducers in active ultrasonic testing for structural health monitoring. In this paper, a distributed fiber-optic laser-ultrasound generation based on the ghost-mode of tilted fiber Bragg gratings is studied. The influences of the laser power and laser pulse duration on the laser-ultrasound generation are investigated. The results of this paper are helpful to understand the working principle of this laser-ultrasound method and improve the ultrasonic generation efficiency.

  4. Surface and buried interfacial structures of epoxy resins used as underfills studied by sum frequency generation vibrational spectroscopy.

    Vázquez, Anne V; Holden, Brad; Kristalyn, Cornelius; Fuller, Mike; Wilkerson, Brett; Chen, Zhan

    2011-05-01

    Flip chip technology has greatly improved the performance of semiconductor devices, but relies heavily on the performance of epoxy underfill adhesives. Because epoxy underfills are cured in situ in flip chip semiconductor devices, understanding their surface and interfacial structures is critical for understanding their adhesion to various substrates. Here, sum frequency generation (SFG) vibrational spectroscopy was used to study surface and buried interfacial structures of two model epoxy resins used as underfills in flip chip devices, bisphenol A digylcidyl ether (BADGE) and 1,4-butanediol diglycidyl ether (BDDGE). The surface structures of these epoxies were compared before and after cure, and the orientations of their surface functional groups were deduced to understand how surface structural changes during cure may affect adhesion properties. Further, the effect of moisture exposure, a known cause of adhesion failure, on surface structures was studied. It was found that the BADGE surface significantly restructured upon moisture exposure while the BDDGE surface did not, showing that BADGE adhesives may be more prone to moisture-induced delamination. Lastly, although surface structure can give some insight into adhesion, buried interfacial structures more directly correspond to adhesion properties of polymers. SFG was used to study buried interfaces between deuterated polystyrene (d-PS) and the epoxies before and after moisture exposure. It was shown that moisture exposure acted to disorder the buried interfaces, most likely due to swelling. These results correlated with lap shear adhesion testing showing a decrease in adhesion strength after moisture exposure. The presented work showed that surface and interfacial structures can be correlated to adhesive strength and may be helpful in understanding and designing optimized epoxy underfill adhesives.

  5. A robust multi-frequency mixing algorithm for suppression of rivet signal in GMR inspection of riveted structures

    Safdernejad, Morteza S.; Karpenko, Oleksii; Ye, Chaofeng; Udpa, Lalita; Udpa, Satish

    2016-02-01

    The advent of Giant Magneto-Resistive (GMR) technology permits development of novel highly sensitive array probes for Eddy Current (EC) inspection of multi-layer riveted structures. Multi-frequency GMR measurements with different EC pene-tration depths show promise for detection of bottom layer notches at fastener sites. However, the distortion of the induced magnetic field due to flaws is dominated by the strong fastener signal, which makes defect detection and classification a challenging prob-lem. This issue is more pronounced for ferromagnetic fasteners that concentrate most of the magnetic flux. In the present work, a novel multi-frequency mixing algorithm is proposed to suppress rivet signal response and enhance defect detection capability of the GMR array probe. The algorithm is baseline-free and does not require any assumptions about the sample geometry being inspected. Fastener signal suppression is based upon the random sample consensus (RANSAC) method, which iteratively estimates parameters of a mathematical model from a set of observed data with outliers. Bottom layer defects at fastener site are simulated as EDM notches of different length. Performance of the proposed multi-frequency mixing approach is evaluated on finite element data and experimental GMR measurements obtained with unidirectional planar current excitation. Initial results are promising demonstrating the feasibility of the approach.

  6. Surface chemical structure of poly(ethylene naphthalate) films during degradation in low-pressure high-frequency plasma treatments

    Kamata, Noritsugu; Yuji, Toshifumi; Thungsuk, Nuttee; Arunrungrusmi, Somchai; Chansri, Pakpoom; Kinoshita, Hiroyuki; Mungkung, Narong

    2018-06-01

    The surface chemical structure of poly(ethylene naphthalate) (PEN) films treated with a low-pressure, high-frequency plasma was investigated by storing in a box at room temperature to protect the PEN film surface from dust. The functional groups on the PEN film surface changed over time. The functional groups of –C=O, –COH, and –COOH were abundant in the Ar + O2 mixture gas plasma-treated PEN samples as compared with those in untreated PEN samples. The changes occurred rapidly after 2 d following the plasma treatment, reaching steady states 8 d after the treatment. Hydrophobicity had an inverse relationship with the concentration of these functional groups on the surface. Thus, the effect of the low-pressure high-frequency plasma treatment on PEN varies as a function of storage time. This means that radical oxygen and oxygen molecules are clearly generated in the plasma, and this is one index to confirm that radical reaction has definitely occurred between the gas and the PEN film surface with a low-pressure high-frequency plasma.

  7. Using low-frequency pulsar observations to study the 3-D structure of the Galactic magnetic field

    Sobey, C.; LOFAR Collaboration; MWA Collaboration

    2018-05-01

    The Galactic magnetic field (GMF) plays a role in many astrophysical processes and is a significant foreground to cosmological signals, such as the Epoch of Reionization (EoR), but is not yet well understood. Dispersion and Faraday rotation measurements (DMs and RMs, respectively) towards a large number of pulsars provide an efficient method to probe the three-dimensional structure of the GMF. Low-frequency polarisation observations with large fractional bandwidth can be used to measure precise DMs and RMs. This is demonstrated by a catalogue of RMs (corrected for ionospheric Faraday rotation) from the Low Frequency Array (LOFAR), with a growing complementary catalogue in the southern hemisphere from the Murchison Widefield Array (MWA). These data further our knowledge of the three-dimensional GMF, particularly towards the Galactic halo. Recently constructed or upgraded pathfinder and precursor telescopes, such as LOFAR and the MWA, have reinvigorated low-frequency science and represent progress towards the construction of the Square Kilometre Array (SKA), which will make significant advancements in studies of astrophysical magnetic fields in the future. A key science driver for the SKA-Low is to study the EoR, for which pulsar and polarisation data can provide valuable insights in terms of Galactic foreground conditions.

  8. Time and frequency structure of causal correlation networks in the China bond market

    Wang, Zhongxing; Yan, Yan; Chen, Xiaosong

    2017-07-01

    There are more than eight hundred interest rates published in the China bond market every day. Identifying the benchmark interest rates that have broad influences on most other interest rates is a major concern for economists. In this paper, a multi-variable Granger causality test is developed and applied to construct a directed network of interest rates, whose important nodes, regarded as key interest rates, are evaluated with CheiRank scores. The results indicate that repo rates are the benchmark of short-term rates, the central bank bill rates are in the core position of mid-term interest rates network, and treasury bond rates lead the long-term bond rates. The evolution of benchmark interest rates from 2008 to 2014 is also studied, and it is found that SHIBOR has generally become the benchmark interest rate in China. In the frequency domain we identify the properties of information flows between interest rates, and the result confirms the existence of market segmentation in the China bond market.

  9. Structural Damage Detection using Frequency Response Function Index and Surrogate Model Based on Optimized Extreme Learning Machine Algorithm

    R. Ghiasi

    2017-09-01

    Full Text Available Utilizing surrogate models based on artificial intelligence methods for detecting structural damages has attracted the attention of many researchers in recent decades. In this study, a new kernel based on Littlewood-Paley Wavelet (LPW is proposed for Extreme Learning Machine (ELM algorithm to improve the accuracy of detecting multiple damages in structural systems.  ELM is used as metamodel (surrogate model of exact finite element analysis of structures in order to efficiently reduce the computational cost through updating process. In the proposed two-step method, first a damage index, based on Frequency Response Function (FRF of the structure, is used to identify the location of damages. In the second step, the severity of damages in identified elements is detected using ELM. In order to evaluate the efficacy of ELM, the results obtained from the proposed kernel were compared with other kernels proposed for ELM as well as Least Square Support Vector Machine algorithm. The solved numerical problems indicated that ELM algorithm accuracy in detecting structural damages is increased drastically in case of using LPW kernel.

  10. Static and high-frequency magnetic properties of stripe domain structure in a plate of finite sizes

    Mal'ginova, S.D.; Doroshenko, R.A.; Shul'ga, N.V.

    2006-01-01

    A model that enables to carry out self-consistent calculations of the main parameters of stripe domain structure (DS) and at the same time those of properties of domain walls (DW) of a multiple-axis finite (in all directions) ferromagnet depending on the sizes of a sample, material parameters and intensity of a magnetic field is offered. The calculations of the properties of DS (direction of magnetization in domains, widths, ferromagnetic resonance, etc.) are carried out on a computer for plates (1 1 0), rectangular shapes of a cubic ferromagnet with axes of light magnetization along trigonal directions in a magnetic field [-1 1 0]. It is shown, that in plates of different shapes there can be a structure with Neel DW alongside with DS with Bloch DW. Their features are noticeably exhibited, in particular, in different dependence of the number of domains, and also frequencies of a ferromagnetic resonance from a magnetic field

  11. Human cytochrome P450 2B6 genetic variability in Botswana: a case of haplotype diversity and convergent phenotypes

    Tawe, Leabaneng

    2018-03-14

    Identification of inter-individual variability for drug metabolism through cytochrome P450 2B6 (CYP2B6) enzyme is important for understanding the differences in clinical responses to malaria and HIV. This study evaluates the distribution of CYP2B6 alleles, haplotypes and inferred metabolic phenotypes among subjects with different ethnicity in Botswana. A total of 570 subjects were analyzed for CYP2B6 polymorphisms at position 516 G > T (rs3745274), 785 A > G (rs2279343) and 983 T > C (rs28399499). Samples were collected in three districts of Botswana where the population belongs to Bantu (Serowe/Palapye and Chobe) and San-related (Ghanzi) ethnicity. The three districts showed different haplotype composition according to the ethnic background but similar metabolic inferred phenotypes, with 59.12%, 34.56%, 2.10% and 4.21% of the subjects having, respectively, an extensive, intermediate, slow and rapid metabolic profile. The results hint at the possibility of a convergent adaptation of detoxifying metabolic phenotypes despite a different haplotype structure due to the different genetic background. The main implication is that, while there is substantial homogeneity of metabolic inferred phenotypes among the country, the response to drugs metabolized via CYP2B6 could be individually associated to an increased risk of treatment failure and toxicity. These are important facts since Botswana is facing malaria elimination and a very high HIV prevalence.

  12. Human cytochrome P450 2B6 genetic variability in Botswana: a case of haplotype diversity and convergent phenotypes

    Tawe, Leabaneng; Motshoge, Thato; Ramatlho, Pleasure; Mutukwa, Naledi; Muthoga, Charles Waithaka; Dongho, Ghyslaine Bruna Djeunang; Martinelli, Axel; Peloewetse, Elias; Russo, Gianluca; Quaye, Isaac Kweku; Paganotti, Giacomo Maria

    2018-01-01

    Identification of inter-individual variability for drug metabolism through cytochrome P450 2B6 (CYP2B6) enzyme is important for understanding the differences in clinical responses to malaria and HIV. This study evaluates the distribution of CYP2B6 alleles, haplotypes and inferred metabolic phenotypes among subjects with different ethnicity in Botswana. A total of 570 subjects were analyzed for CYP2B6 polymorphisms at position 516 G > T (rs3745274), 785 A > G (rs2279343) and 983 T > C (rs28399499). Samples were collected in three districts of Botswana where the population belongs to Bantu (Serowe/Palapye and Chobe) and San-related (Ghanzi) ethnicity. The three districts showed different haplotype composition according to the ethnic background but similar metabolic inferred phenotypes, with 59.12%, 34.56%, 2.10% and 4.21% of the subjects having, respectively, an extensive, intermediate, slow and rapid metabolic profile. The results hint at the possibility of a convergent adaptation of detoxifying metabolic phenotypes despite a different haplotype structure due to the different genetic background. The main implication is that, while there is substantial homogeneity of metabolic inferred phenotypes among the country, the response to drugs metabolized via CYP2B6 could be individually associated to an increased risk of treatment failure and toxicity. These are important facts since Botswana is facing malaria elimination and a very high HIV prevalence.

  13. Haplotype analysis of TP53 polymorphisms, Arg72Pro and Ins16, in BRCA1 and BRCA2 mutation carriers of French Canadian descent

    Cavallone, Luca; Arcand, Suzanna L; Maugard, Christine; Ghadirian, Parviz; Mes-Masson, Anne-Marie; Provencher, Diane; Tonin, Patricia N

    2008-01-01

    The TP53 polymorphisms Arg72Pro (Ex4+199 G>C) and Ins16 (IVS3+24 ins16) have been proposed to modify risk of breast cancer associated with germline BRCA1 and BRCA2 mutations. Allele frequencies of these polymorphisms were investigated to determine if they modify risk in BRCA mutation carriers in breast cancer cases drawn from French Canadian cancer families, a population shown to exhibit strong founder effects. The frequencies of the TP53 alleles, genotypes and haplotypes of 157 index breast cancer cases comprised of 42 BRCA1 mutation carriers, 57 BRCA2 mutation carriers, and 58 BRCA mutation-negative cases, where each case was drawn from independently ascertained families were compared. The effect of TP53 variants on the age of diagnosis was also investigated for these groups. The TP53 polymorphisms were also investigated in 112 women of French Canadian descent with no personal history of cancer. The BRCA mutation-positive groups had the highest frequency of homozygous carriers of the 72Pro allele compared with mutation-negative group. The TP53 polymorphisms exhibited linkage disequilibrium (p < 0.001), where the 72Arg and Ins16minus alleles occurred in strong disequilibrium. The highest frequency of carriers of Ins16minus-72Arg haplotype occurred in the BRCA mutation-negative groups. The BRCA1 mutation carriers homozygous for the 72Pro allele had the youngest ages of diagnosis of breast cancer. However none of these observations were statistically significant. In contrast, the BRCA2 mutation carriers homozygous for the 72Pro allele had a significantly older age of diagnosis of breast cancer (p = 0.018). Moreover, in this group, the mean age of diagnosis of breast cancer in carriers of the Ins16minus-72Arg haplotype was significantly younger than that of the individuals who did not this carry this haplotype (p = 0.009). We observed no significant association of breast cancer risk with TP53 genetic variants based on BRCA1/2 mutation carrier status. Although the

  14. Effects of TMEM154 haplotypes 1 and 3 on susceptibility to ovine progressive pneumonia virus following natural exposure in sheep.

    Leymaster, K A; Chitko-McKown, C G; Clawson, M L; Harhay, G P; Heaton, M P

    2013-11-01

    "1 1." These results are consistent with complete dominance of haplotype 3 relative to haplotype 1. The probability of infection at 9 mo of age for lambs with either diplotype "1 3" or "3 3" averaged 3.56 times that of lambs with diplotype "1 1." Genetic susceptibility to OPPV infection can be reduced by selection to increase the frequency of haplotype 1, resulting in a greater proportion of lambs with diplotype "1 1."

  15. Influence of substrate temperature on structural, morphological and electrical properties of PbSe film deposited by radio frequency sputtering

    Feng, Wenran, E-mail: fengwenran@bipt.edu.cn [College of Materials Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617 (China); Beijing Key Lab of Special Elastomer Composite Materials, Beijing 102617 (China); Wang, Xiaoyang [College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029 (China); Chen, Fei [College of Materials Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617 (China); Beijing Key Lab of Special Elastomer Composite Materials, Beijing 102617 (China); Liu, Wan [College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029 (China); Zhou, Hai; Wang, Shuo; Li, Haoran [College of Materials Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617 (China); Beijing Key Lab of Special Elastomer Composite Materials, Beijing 102617 (China)

    2015-03-02

    PbSe films were prepared by radio frequency magnetron sputtering from PbSe slices target under different substrate temperatures (from room temperature to 300 °C). The effect of substrate temperature on structural properties of PbSe thin film was investigated. The surface morphology and the crystal structure of film were determined using field emission scanning electron microscopy and X-ray diffractometry, respectively. It was found that the grain shape changed with substrate temperature. When the substrate temperature was below 250 °C, most of the crystal grains were spherical in shape. For temperatures above 250 °C, the grains transformed to triangle or prismatic ones. Meanwhile, with increasing substrate temperature, the preferential orientation of the film changed from (200) to (220). To figure out the intrinsic mechanisms for this behavior, the texture coefficient, as well as the comparison between surface energy and elastic strain energy was performed. At lower temperature, the film growth was determined by surface energy, which was replaced by strain energy at higher temperature. Therefore, the diversity of crystal structure and morphology of the films at different substrate temperatures occurred. Moreover, the electrical properties of the p-type PbSe films are also quite dependent on substrate temperature. With substrate temperature increased, the electrical resistivity decreased from 1.88 to 0.14 Ω cm, while the carrier concentration increased from 1.74 × 10{sup 18} to 4.08 × 10{sup 19} cm{sup −3} as the mobility was enhanced from 0.54 to 2.21 cm{sup 2}/Vs. - Highlights: • PbSe thin films were deposited by radio frequency magnetron sputtering. • Substrate temperature determines crystal structure of PbSe films. • Transformation behaviors of PbSe films were explained by energy calculations.

  16. Association of CAPN10 SNPs and haplotypes with polycystic ovary syndrome among South Indian Women.

    Shilpi Dasgupta

    Full Text Available Polycystic Ovary Syndrome (PCOS is known to be characterized by metabolic disorder in which hyperinsulinemia and peripheral insulin resistance are central features. Given the physiological overlap between PCOS and type-2 diabetes (T2DM, and calpain 10 gene (CAPN10 being a strong candidate for T2DM, a number of studies have analyzed CAPN10 SNPs among PCOS women yielding contradictory results. Our study is first of its kind to investigate the association pattern of CAPN10 polymorphisms (UCSNP-44, 43, 56, 19 and 63 with PCOS among Indian women. 250 PCOS cases and 299 controls from Southern India were recruited for this study. Allele and genotype frequencies of the SNPs were determined and compared between the cases and controls. Results show significant association of UCSNP-44 genotype CC with PCOS (p = 0.007 with highly significant odds ratio when compared to TC (OR = 2.51, p = 0.003, 95% CI = 1.37-4.61 as well as TT (OR = 1.94, p = 0.016, 95% CI = 1.13-3.34. While the haplotype carrying the SNP-44 and SNP-19 variants (21121 exhibited a 2 fold increase in the risk for PCOS (OR = 2.37, p = 0.03, the haplotype containing SNP-56 and SNP-19 variants (11221 seems to have a protective role against PCOS (OR = 0.20, p = 0.004. Our results support the earlier evidence for a possible role of UCSNP-44 of the CAPN10 gene in the manifestation of PCOS.

  17. High-frequency characteristics of glass/ceramic composite and alumina multilayer structures

    Niwa, K.; Suzuki, H.; Yokoyama, H.; Kamechara, N.; Tsubone, K.; Tanisawa, H.; Sugiki, H.

    1990-01-01

    This paper reports the transmission characteristics of glass/ceramic composite (borosilicate glass/alumina) and alumina multilayer structures examined. The triplate stripline formed in the glass/ceramic multilayer shows low conductor and dielectric loss. Alumina multilayer, however, has twice the transmission loss at 10 GHz, because the resistivity of W in the alumina multilayer is higher than the Cu in the glass/ceramic multilayer. Crosstalk between striplines in the glass/ceramics is less than -80 dB up to 11 GHz and 9 GHz for alumina

  18. Structure of proton centers and associated nonthermal bursts at microwave frequencies

    Enome, S.; Tanaka, H.

    1972-01-01

    In the flaring region of the sun, a large variety of plasmas with various densities and a wide range of temperatures or energies is implied. These plasmas are heated and accelerated to subrelativistic and relativistic energies. Observational evidence is given on the characteristics of active regions which produced proton flares and on the structure of the associated nonthermal microwave bursts of the sun. The behavior of subrelativistic electrons on the sun is also described. Data are based on observations made with the Toyota interferometers at 3 and 8 cm, which have the same spatial resolution. (U.S.)

  19. Increased low-frequency oscillation amplitude of sensorimotor cortex associated with the severity of structural impairment in cervical myelopathy.

    Fuqing Zhou

    Full Text Available Decreases in metabolites and increased motor-related, but decreased sensory-related activation of the sensorimotor cortex (SMC have been observed in patients with cervical myelopathy (CM using advanced MRI techniques. However, the nature of intrinsic neuronal activity in the SMC, and the relationship between cerebral function and structural damage of the spinal cord in patients with CM are not fully understood. The purpose of this study was to assess intrinsic neuronal activity by calculating the regional amplitude of low frequency fluctuations (ALFF using resting-state functional MRI (rs-fMRI, and correlations with clinical and imaging indices. Nineteen patients and 19 age- and sex-matched healthy subjects underwent rs-fMRI scans. ALFF measurements were performed in the SMC, a key brain network likely to impaired or reorganized patients with CM. Compared with healthy subjects, increased amplitude of cortical low-frequency oscillations (LFO was observed in the right precentral gyrus, right postcentral gyrus, and left supplementary motor area. Furthermore, increased z-ALFF values in the right precentral gyrus and right postcentral gyrus correlated with decreased fractional anisotropy values at the C2 level, which indicated increased intrinsic neuronal activity in the SMC corresponding to the structural impairment in the spinal cord of patients with CM. These findings suggest a complex and diverging relationship of cortical functional reorganization and distal spinal anatomical compression in patients with CM and, thus, add important information in understanding how spinal cord integrity may be a factor in the intrinsic covariance of spontaneous low-frequency fluctuations of BOLD signals involved in cortical plasticity.

  20. DETECTING FLARING STRUCTURES IN SAGITTARIUS A* WITH HIGH-FREQUENCY VLBI

    Doeleman, Sheperd S.; Fish, Vincent L.; Rogers, Alan E. E.; Broderick, Avery E.; Loeb, Abraham

    2009-01-01

    The super-massive black hole candidate, Sagittarius A*, exhibits variability from radio to X-ray wavelengths on timescales that correspond to <10 Schwarzschild radii. We survey the potential of millimeter wavelength very long baseline interferometry (VLBI) to detect and constrain time-variable structures that could give rise to such variations, focusing on a model in which an orbiting hot spot is embedded in an accretion disk. Nonimaging algorithms are developed that use interferometric closure quantities to test for periodicity, and applied to an ensemble of hot spot models that sample a range of parameter space. We find that structural periodicity in a wide range of cases can be detected on most potential VLBI arrays using modern VLBI instrumentation. Future enhancements of millimeter/submillimeter VLBI arrays including phased-array processors to aggregate VLBI station collecting area, increased bandwidth recording, and addition of new VLBI sites all significantly aid periodicity detection. The methods described herein can be applied to other models of Sagittarius A*, including jet outflows and magnetohydrodynamic accretion simulations.

  1. Updated listing of haplotypes at the human phenylalanine hydroxylase (PAH) locus

    Eisensmith, R.C.; Woo, S.L.C. (Baylor College of Medicine, Houston, TX (United States))

    1992-12-01

    Analysis of mutant PAH chromosomes has identified approximately 60 different single-base substitutions and deletions within the PAH locus. Nearly all of these molecular lesions are in strong linkage disequilibrium with specific RFLP haplotypes in different ethnic populations. Thus, haplotype analysis is not only useful for diagnostic purposes but is proving to be a valuable tool in population genetic studies of the origin and spread of phenylketonuria alleles in human populations. PCR-based methods have been developed to detect six of the eight polymorphic restriction sites used for determination of RFLP haplotypes at the PAH locus. A table of the proposed expanded haplotypes is given.

  2. Determinants of environmental audit frequency: the role of firm organizational structure.

    Earnhart, Dietrich; Leonard, J Mark

    2013-10-15

    This study empirically examines the extent of environmental management practiced by US chemical manufacturing facilities, as reflected in the number of environmental internal audits conducted annually. As its focus, this study analyzes the effects of firm-level organizational structure on facility-level environmental management practices. For this empirical analysis, the study exploits unique data from a survey distributed to all U.S. chemical manufacturing permitted to discharge wastewater in 2001; the data reflect internal audits conducted during the years 1999-2001. Empirical results reveal differences in auditing behavior based on whether facilities are owned by publicly held or non-publicly held firms, owned by U.S.-based or non-U.S.-based firms, and owned by larger or smaller firms. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. DETECTING CHANGING POLARIZATION STRUCTURES IN SAGITTARIUS A* WITH HIGH FREQUENCY VLBI

    Fish, Vincent L; Doeleman, Sheperd S; Rogers, Alan E. E. [Massachusetts Institute of Technology, Haystack Observatory, Route 40, Westford, MA 01886 (United States); Broderick, Avery E [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Loeb, Abraham [Institute for Theory and Computation, Harvard University, Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

    2009-12-01

    Sagittarius A* is the source of near infrared, X-ray, radio, and (sub)millimeter emission associated with the supermassive black hole at the Galactic Center. In the submillimeter regime, Sgr A* exhibits time-variable linear polarization on timescales corresponding to <10 Schwarzschild radii of the presumed 4 x 10{sup 6} M {sub sun} black hole. In previous work, we demonstrated the potential for total-intensity (sub)millimeter-wavelength very long baseline interferometry (VLBI) to detect time-variable-and periodic-source structure changes in the Sgr A* black hole system using nonimaging analyses. Here, we extend this work to include full polarimetric VLBI observations. We simulate full-polarization (sub)millimeter VLBI data of Sgr A* using a hot spot model that is embedded within an accretion disk, with emphasis on nonimaging polarimetric data products that are robust against calibration errors. Although the source-integrated linear polarization fraction in the models is typically only a few percent, the linear polarization fraction on small angular scales can be much higher, enabling the detection of changes in the polarimetric structure of Sgr A* on a wide variety of baselines. The shortest baselines track the source-integrated linear polarization fraction, while longer baselines are sensitive to polarization substructures that are beam-diluted by connected-element interferometry. The detection of periodic variability in source polarization should not be significantly affected even if instrumental polarization terms cannot be calibrated out. As more antennas are included in the (sub)millimeter-VLBI array, observations with full polarization will provide important new diagnostics to help disentangle intrinsic source polarization from Faraday rotation effects in the accretion and outflow region close to the black hole event horizon.

  4. DETECTING CHANGING POLARIZATION STRUCTURES IN SAGITTARIUS A* WITH HIGH FREQUENCY VLBI

    Fish, Vincent L.; Doeleman, Sheperd S.; Rogers, Alan E. E.; Broderick, Avery E.; Loeb, Abraham

    2009-01-01

    Sagittarius A* is the source of near infrared, X-ray, radio, and (sub)millimeter emission associated with the supermassive black hole at the Galactic Center. In the submillimeter regime, Sgr A* exhibits time-variable linear polarization on timescales corresponding to 6 M sun black hole. In previous work, we demonstrated the potential for total-intensity (sub)millimeter-wavelength very long baseline interferometry (VLBI) to detect time-variable-and periodic-source structure changes in the Sgr A* black hole system using nonimaging analyses. Here, we extend this work to include full polarimetric VLBI observations. We simulate full-polarization (sub)millimeter VLBI data of Sgr A* using a hot spot model that is embedded within an accretion disk, with emphasis on nonimaging polarimetric data products that are robust against calibration errors. Although the source-integrated linear polarization fraction in the models is typically only a few percent, the linear polarization fraction on small angular scales can be much higher, enabling the detection of changes in the polarimetric structure of Sgr A* on a wide variety of baselines. The shortest baselines track the source-integrated linear polarization fraction, while longer baselines are sensitive to polarization substructures that are beam-diluted by connected-element interferometry. The detection of periodic variability in source polarization should not be significantly affected even if instrumental polarization terms cannot be calibrated out. As more antennas are included in the (sub)millimeter-VLBI array, observations with full polarization will provide important new diagnostics to help disentangle intrinsic source polarization from Faraday rotation effects in the accretion and outflow region close to the black hole event horizon.

  5. The direct field boundary impedance of two-dimensional periodic structures with application to high frequency vibration prediction.

    Langley, Robin S; Cotoni, Vincent

    2010-04-01

    Large sections of many types of engineering construction can be considered to constitute a two-dimensional periodic structure, with examples ranging from an orthogonally stiffened shell to a honeycomb sandwich panel. In this paper, a method is presented for computing the boundary (or edge) impedance of a semi-infinite two-dimensional periodic structure, a quantity which is referred to as the direct field boundary impedance matrix. This terminology arises from the fact that none of the waves generated at the boundary (the direct field) are reflected back to the boundary in a semi-infinite system. The direct field impedance matrix can be used to calculate elastic wave transmission coefficients, and also to calculate the coupling loss factors (CLFs), which are required by the statistical energy analysis (SEA) approach to predicting high frequency vibration levels in built-up systems. The calculation of the relevant CLFs enables a two-dimensional periodic region of a structure to be modeled very efficiently as a single subsystem within SEA, and also within related methods, such as a recently developed hybrid approach, which couples the finite element method with SEA. The analysis is illustrated by various numerical examples involving stiffened plate structures.

  6. Finite-Frequency Seismic Tomography of Body Waves and Surface Waves from Ambient Seismic Noise: Crustal and Mantle Structure Beneath Eastern Eurasia

    Ren, Yong; Zhang, Wei; Yang, Ting; Shen, Yang; Yang, Xiaoping

    2008-01-01

    To improve seismic calibration for nuclear explosion monitoring, we use 3D sensitivity kernels of finite-frequency body and surface waves to develop models of the crustal and mantle structures beneath eastern Eurasia...

  7. Two haplotype clusters of Echinococcus granulosus sensu stricto in northern Iraq (Kurdistan region) support the hypothesis of a parasite cradle in the Middle East.

    Hassan, Zuber Ismael; Meerkhan, Azad Abdullah; Boufana, Belgees; Hama, Abdullah A; Ahmed, Bayram Dawod; Mero, Wijdan Mohammed Salih; Orsten, Serra; Interisano, Maria; Pozio, Edoardo; Casulli, Adriano

    2017-08-01

    Human cystic echinococcosis (CE) caused by Echinococcus granulosus s.s. is a major public health problem in Iraqi Kurdistan with a reported surgical incidence of 6.3 per 100,000 Arbil inhabitants. A total of 125 Echinococcus isolates retrieved from sheep, goats and cattle were used in this study. Our aim was to determine species/genotypes infecting livestock in Iraqi Kurdistan and examine intraspecific variation and population structure of Echinococcus granulosus s.s. in this region and relate it to that of other regions worldwide. Using nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (cox 1) we identified E. granulosus s.s. as the cause of hydatidosis in all examined animals. The haplotype network displayed a double-clustered topology with two main E. granulosus s.s. haplotypes, (KU05) and (KU33). The 'founder' haplotype (KU05) confirmed the presence of a common lineage of non-genetically differentiated populations as inferred by the low non-significant fixation index values. Overall diversity and neutrality indices indicated demographic expansion. We used E. granulosus s.s. nucleotide sequences from GenBank to draw haplotype networks for the Middle East (Iran, Jordan and Turkey), Europe (Albania, Greece, Italy, Romania and Spain), China, Mongolia, Russia, South America (Argentina, Brazil, Chile and Mexico) and Tunisia. Networks with two haplotype clusters like that reported here for Iraqi Kurdistan were seen for the Middle East, Europe, Mongolia, Russia and Tunisia using both 827bp and 1609bp cox1 nucleotide sequences, whereas a star-like network was observed for China and South America. We hypothesize that the double clustering seen at what is generally assumed to be the cradle of domestication may have emerged independently and dispersed from the Middle East to other regions and that haplotype (KU33) may be the main haplotype within a second cluster in the Middle East from where it has spread into Europe, Mongolia, Russia and North

  8. Detecting Changing Polarization Structures in Sagittarius A* with High Frequency VLBI

    Fish, Vincent L.; Doeleman, Sheperd S.; Broderick, Avery E.; Loeb, Abraham; Rogers, Alan E. E.

    2009-12-01

    Sagittarius A* is the source of near infrared, X-ray, radio, and (sub)millimeter emission associated with the supermassive black hole at the Galactic Center. In the submillimeter regime, Sgr A* exhibits time-variable linear polarization on timescales corresponding to errors. Although the source-integrated linear polarization fraction in the models is typically only a few percent, the linear polarization fraction on small angular scales can be much higher, enabling the detection of changes in the polarimetric structure of Sgr A* on a wide variety of baselines. The shortest baselines track the source-integrated linear polarization fraction, while longer baselines are sensitive to polarization substructures that are beam-diluted by connected-element interferometry. The detection of periodic variability in source polarization should not be significantly affected even if instrumental polarization terms cannot be calibrated out. As more antennas are included in the (sub)millimeter-VLBI array, observations with full polarization will provide important new diagnostics to help disentangle intrinsic source polarization from Faraday rotation effects in the accretion and outflow region close to the black hole event horizon.

  9. Hierarchical structure of genetic distances: Effects of matrix size, spatial distribution and correlation structure among gene frequencies

    Flávia Melo Rodrigues

    1998-06-01

    Full Text Available Geographic structure of genetic distances among local populations within species, based on allozyme data, has usually been evaluated by estimating genetic distances clustered with hierarchical algorithms, such as the unweighted pair-group method by arithmetic averages (UPGMA. The distortion produced in the clustering process is estimated by the cophenetic correlation coefficient. This hierarchical approach, however, can fail to produce an accurate representation of genetic distances among populations in a low dimensional space, especially when continuous (clinal or reticulate patterns of variation exist. In the present study, we analyzed 50 genetic distance matrices from the literature, for animal taxa ranging from Platyhelminthes to Mammalia, in order to determine in which situations the UPGMA is useful to understand patterns of genetic variation among populations. The cophenetic correlation coefficients, derived from UPGMA based on three types of genetic distance coefficients, were correlated with other parameters of each matrix, including number of populations, loci, alleles, maximum geographic distance among populations, relative magnitude of the first eigenvalue of covariance matrix among alleles and logarithm of body size. Most cophenetic correlations were higher than 0.80, and the highest values appeared for Nei's and Rogers' genetic distances. The relationship between cophenetic correlation coefficients and the other parameters analyzed was defined by an "envelope space", forming triangles in which higher values of cophenetic correlations are found for higher values in the parameters, though low values do not necessarily correspond to high cophenetic correlations. We concluded that UPGMA is useful to describe genetic distances based on large distance matrices (both in terms of elevated number of populations or alleles, when dimensionality of the system is low (matrices with large first eigenvalues or when local populations are separated

  10. Chronic inflammatory state in sickle cell anemia patients is associated with HBB(*)S haplotype.

    Bandeira, Izabel C J; Rocha, Lillianne B S; Barbosa, Maritza C; Elias, Darcielle B D; Querioz, José A N; Freitas, Max Vitor Carioca; Gonçalves, Romélia P

    2014-02-01

    The chronic inflammatory state in sickle cell anemia (SCA) is associated with several factors such as the following: endothelial damage; increased production of reactive oxygen species; hemolysis; increased expression of adhesion molecules by leukocytes, erythrocytes, and platelets; and increased production of proinflammatory cytokines. Genetic characteristics affecting the clinical severity of SCA include variations in the hemoglobin F (HbF) level, coexistence of alpha-thalassemia, and the haplotype associated with the HbS gene. The different haplotypes of SCA are Bantu, Benin, Senegal, Cameroon, and Arab-Indian. These haplotypes are associated with ethnic groups and also based on the geographical origin. Studies have shown that the Bantu haplotype is associated with higher incidence of clinical complications than the other haplotypes and is therefore considered to have the worst prognosis. This study aimed to evaluate the profile of the proinflammatory cytokines interleukin-6, tumor necrosis factor-α, and interleukin-17 in patients with SCA and also to assess the haplotypes associated with beta globin cluster S (HBB(*)S). We analyzed a total of 62 patients who had SCA and had been treated with hydroxyurea; they had received a dose ranging between 15 and 25 (20.0±0.6)mg/kg/day for 6-60 (18±3.4)months; their data were compared with those for 30 normal individuals. The presence of HbS was detected and the haplotypes of the beta S gene cluster were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Our study demonstrated that SCA patients have increased inflammatory profile when compared to the healthy individuals. Further, analysis of the association between the haplotypes and inflammatory profile showed that the levels of IL-6 and TNF-α were greater in subjects with the Bantu/Bantu haplotype than in subjects with the Benin/Benin haplotype. The Bantu/Benin haplotype individuals had lower levels of cytokines than those with

  11. Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill.

    Budde, Katharina B; González-Martínez, Santiago C; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G; Verdú, Miguel; Pausas, Juli G; Heuertz, Myriam

    2017-04-01

    The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits

  12. Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes.

    Sophie Garnier

    Full Text Available In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. 19,805 RNA probes were assessed for cis haplotypic regulation through investigation of ~2,1 × 10(9 haplotypic combinations. 2,650 probes demonstrated haplotypic p-values >10(4-fold smaller than the best single SNP p-value. Replication of significant haplotype effects were tested for 412 probes for which SNPs (or proxies that defined the detected haplotypes were available in the Gutenberg Health Study composed of 1,374 individuals. At the Bonferroni correction level of 1.2 × 10(-4 (~0.05/412, 193 haplotypic signals replicated. 1000 G imputation was then conducted, and 105 haplotypic signals still remained more informative than imputed SNPs. In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. As 24 of the 105 cis eQTL have previously been reported to be disease-associated loci, this work highlights the need for conducting haplotype-based and 1000 G imputed cis eQTL analysis before commencing functional studies at disease-associated loci.

  13. Energy-density field approach for low- and medium-frequency vibroacoustic analysis of complex structures using a statistical computational model

    Kassem, M.; Soize, C.; Gagliardini, L.

    2009-06-01

    In this paper, an energy-density field approach applied to the vibroacoustic analysis of complex industrial structures in the low- and medium-frequency ranges is presented. This approach uses a statistical computational model. The analyzed system consists of an automotive vehicle structure coupled with its internal acoustic cavity. The objective of this paper is to make use of the statistical properties of the frequency response functions of the vibroacoustic system observed from previous experimental and numerical work. The frequency response functions are expressed in terms of a dimensionless matrix which is estimated using the proposed energy approach. Using this dimensionless matrix, a simplified vibroacoustic model is proposed.

  14. Haplotype-based association analysis of general cognitive ability in Generation Scotland, the English Longitudinal Study of Ageing, and UK Biobank [version 1; referees: 2 approved

    David M. Howard

    2017-08-01

    Full Text Available Background: Cognitive ability is a heritable trait with a polygenic architecture, for which several associated variants have been identified using genotype-based and candidate gene approaches. Haplotype-based analyses are a complementary technique that take phased genotype data into account, and potentially provide greater statistical power to detect lower frequency variants. Methods: In the present analysis, three cohort studies (ntotal = 48,002 were utilised: Generation Scotland: Scottish Family Health Study (GS:SFHS, the English Longitudinal Study of Ageing (ELSA, and the UK Biobank. A genome-wide haplotype-based meta-analysis of cognitive ability was performed, as well as a targeted meta-analysis of several gene coding regions. Results: None of the assessed haplotypes provided evidence of a statistically significant association with cognitive ability in either the individual cohorts or the meta-analysis. Within the meta-analysis, the haplotype with the lowest observed P-value overlapped with the D-amino acid oxidase activator (DAOA gene coding region. This coding region has previously been associated with bipolar disorder, schizophrenia and Alzheimer’s disease, which have all been shown to impact upon cognitive ability. Another potentially interesting region highlighted within the current genome-wide association analysis (GS:SFHS: P = 4.09 x 10-7, was the butyrylcholinesterase (BCHE gene coding region. The protein encoded by BCHE has been shown to influence the progression of Alzheimer’s disease and its role in cognitive ability merits further investigation. Conclusions: Although no evidence was found for any haplotypes with a statistically significant association with cognitive ability, our results did provide further evidence that the genetic variants contributing to the variance of cognitive ability are likely to be of small effect.

  15. Haplotype-based case-control study on human apurinic/apyrimidinic endonuclease 1/redox effector factor-1 gene and essential hypertension.

    Naganuma, Takahiro; Nakayama, Tomohiro; Sato, Naoyuki; Fu, Zhenyan; Soma, Masayoshi; Yamaguchi, Mai; Shimodaira, Masanori; Aoi, Noriko; Usami, Ron

    2010-02-01

    Oxidative DNA damage is involved in the pathophysiology of essential hypertension (EH), which is a multifactorial disorder. Apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/REF-1) is an essential endonuclease in the base excision repair pathway of oxidatively damaged DNA, in addition to having reducing properties that promote the binding of redox-sensitive transcription factors. Blood pressure in APE1/REF-1-knockout mice is reported to be significantly higher than in wild-type mice. The aim of this study was to investigate the relationship between EH and the human APE1/REF-1 gene through a haplotype-based case-control study using single-nucleotide polymorphisms (SNPs). We selected five SNPs in the human APE1/REF-1 gene (rs1760944, rs3136814, rs17111967, rs3136817, and rs1130409), and performed case-control studies in 265 EH patients and 266 age-matched normotensive (NT) subjects. rs17111967 was found to show nonheterogeneity among Japanese subjects. There were no significant differences in the overall distribution of genotypes or alleles for each SNP between EH and NT groups. In the overall distribution of the haplotype-based case-control study constructed based on rs1760944, rs3136817, and rs1130409, the frequency of the G-T-T haplotype was significantly higher in the EH group than in the NT group (2.1% vs. 0.0%, P = 0.001). Multiple logistic regression analysis also revealed significant differences for the G-T-T haplotype, even after adjustment for confounding factors (OR = 8.600, 95% CI: 1.073-68.951, P = 0.043). Based on the present results, the G-T-T haplotype appears to be a genetic marker of EH, and the APE1/REF-1 gene appears to be a susceptibility gene for EH.

  16. Reduced-order computational model in nonlinear structural dynamics for structures having numerous local elastic modes in the low-frequency range. Application to fuel assemblies

    Batou, A.; Soize, C.; Brie, N.

    2013-01-01

    Highlights: • A ROM of a nonlinear dynamical structure is built with a global displacements basis. • The reduced order model of fuel assemblies is accurate and of very small size. • The shocks between grids of a row of seven fuel assemblies are computed. -- Abstract: We are interested in the construction of a reduced-order computational model for nonlinear complex dynamical structures which are characterized by the presence of numerous local elastic modes in the low-frequency band. This high modal density makes the use of the classical modal analysis method not suitable. Therefore the reduced-order computational model is constructed using a basis of a space of global displacements, which is constructed a priori and which allows the nonlinear dynamical response of the structure observed on the stiff part to be predicted with a good accuracy. The methodology is applied to a complex industrial structure which is made up of a row of seven fuel assemblies with possibility of collisions between grids and which is submitted to a seismic loading

  17. Reduced-order computational model in nonlinear structural dynamics for structures having numerous local elastic modes in the low-frequency range. Application to fuel assemblies

    Batou, A., E-mail: anas.batou@univ-paris-est.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee (France); Soize, C., E-mail: christian.soize@univ-paris-est.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee (France); Brie, N., E-mail: nicolas.brie@edf.fr [EDF R and D, Département AMA, 1 avenue du général De Gaulle, 92140 Clamart (France)

    2013-09-15

    Highlights: • A ROM of a nonlinear dynamical structure is built with a global displacements basis. • The reduced order model of fuel assemblies is accurate and of very small size. • The shocks between grids of a row of seven fuel assemblies are computed. -- Abstract: We are interested in the construction of a reduced-order computational model for nonlinear complex dynamical structures which are characterized by the presence of numerous local elastic modes in the low-frequency band. This high modal density makes the use of the classical modal analysis method not suitable. Therefore the reduced-order computational model is constructed using a basis of a space of global displacements, which is constructed a priori and which allows the nonlinear dynamical response of the structure observed on the stiff part to be predicted with a good accuracy. The methodology is applied to a complex industrial structure which is made up of a row of seven fuel assemblies with possibility of collisions between grids and which is submitted to a seismic loading.

  18. VNTR internal structure mapping at the {alpha}-globin 3{prime}HVR locus reveals a hierachy of related lineages in oceania

    Martinson, J.J.; Clegg, J.B.; Boyce, A.J. [Univ. of Oxford (United Kingdom)

    1994-09-01

    Analysis of the {alpha}-globin gene complex in Oceania has revealed many different rearrangements which remove one of the adult globin genes. Frequencies of these deletion chromosomes are elevated by malarial resistance conferred by the resulting {alpha}-thalassaemia. One particular deletion chromosome, designated -{alpha}{sup 3.7}III, is found at high levels in Melanesia and Polynesia: RFLP haplotype analysis shows that this deletion is always found on chromosomes bearing the IIIa haplotype and is likely to be the product of one single rearrangement event. A subset of the -{alpha}{sup 3.7}III chromosomes carries a more recent mutation which generates the haemoglobin variant HbJ{sup Tongariki}. We have characterized the allelic variation at the 3{prime}HVR VNTR locus located 6 kb from the globin genes in each of these groups of chromosomes. We have determined the internal structure of these alleles by RFLP mapping of PCR-amplified DNA: within each group, the allelic diversity results from the insertion and/or deletion of small {open_quotes}motifs{close_quotes} of up to 6 adjacent repeats. Mapping of 3{prime}HVR alleles associated with other haplotypes reveals that these are composed of repeat arrays that are substantially different to those derived from IIIa chromosomes, indicating that interchromosomal recombination between heterologous haplotypes does not account for any of the diversity seen to date. We have recently shown that allelic size variation at the two VNTR loci flanking the {alpha}-globin complex is very closely linked to the haplotypes known to be present at this locus. Here we show that, within a haplotype, VNTR alleles are very closely related to each other on the basis of internal structure and demonstrate that intrachromosomal mutation processes involving small numbers of tandem repeats are the main cause of variation at this locus.

  19. Tunes stuck in your brain: The frequency and affective evaluation of involuntary musical imagery correlate with cortical structure.

    Farrugia, Nicolas; Jakubowski, Kelly; Cusack, Rhodri; Stewart, Lauren

    2015-09-01

    Recent years have seen a growing interest in the neuroscience of spontaneous cognition. One form of such cognition is involuntary musical imagery (INMI), the non-pathological and everyday experience of having music in one's head, in the absence of an external stimulus. In this study, aspects of INMI, including frequency and affective evaluation, were measured by self-report in 44 subjects and related to variation in brain structure in these individuals. Frequency of INMI was related to cortical thickness in regions of right frontal and temporal cortices as well as the anterior cingulate and left angular gyrus. Affective aspects of INMI, namely the extent to which subjects wished to suppress INMI or considered them helpful, were related to gray matter volume in right temporopolar and parahippocampal cortices respectively. These results provide the first evidence that INMI is a common internal experience recruiting brain networks involved in perception, emotions, memory and spontaneous thoughts. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Modeling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals.

    Stram, Daniel O; Leigh Pearce, Celeste; Bretsky, Phillip; Freedman, Matthew; Hirschhorn, Joel N; Altshuler, David; Kolonel, Laurence N; Henderson, Brian E; Thomas, Duncan C

    2003-01-01

    The US National Cancer Institute has recently sponsored the formation of a Cohort Consortium (http://2002.cancer.gov/scpgenes.htm) to facilitate the pooling of data on very large numbers of people, concerning the effects of genes and environment on cancer incidence. One likely goal of these efforts will be generate a large population-based case-control series for which a number of candidate genes will be investigated using SNP haplotype as well as genotype analysis. The goal of this paper is to outline the issues involved in choosing a method of estimating haplotype-specific risk estimates for such data that is technically appropriate and yet attractive to epidemiologists who are already comfortable with odds ratios and logistic regression. Our interest is to develop and evaluate extensions of methods, based on haplotype imputation, that have been recently described (Schaid et al., Am J Hum Genet, 2002, and Zaykin et al., Hum Hered, 2002) as providing score tests of the null hypothesis of no effect of SNP haplotypes upon risk, which may be used for more complex tasks, such as providing confidence intervals, and tests of equivalence of haplotype-specific risks in two or more separate populations. In order to do so we (1) develop a cohort approach towards odds ratio analysis by expanding the E-M algorithm to provide maximum likelihood estimates of haplotype-specific odds ratios as well as genotype frequencies; (2) show how to correct the cohort approach, to give essentially unbiased estimates for population-based or nested case-control studies by incorporating the probability of selection as a case or control into the likelihood, based on a simplified model of case and control selection, and (3) finally, in an example data set (CYP17 and breast cancer, from the Multiethnic Cohort Study) we compare likelihood-based confidence interval estimates from the two methods with each other, and with the use of the single-imputation approach of Zaykin et al. applied under both

  1. Allelic and haplotype frequencies of the p53 polymorphisms in brain tumor patients

    Biroš, Erik; Kalina, I.; Kohút, A.; Bogyiová, E.; Šalagovič, J.; Šulla, I.

    2002-01-01

    Roč. 51, č. 1 (2002), s. 59-64 ISSN 0862-8408 R&D Projects: GA MŽP SI/340/1/97 Institutional research plan: CEZ:AV0Z5039906 Keywords : Brain tumor * Susceptibility * p53 Subject RIV: FD - Oncology ; Hematology Impact factor: 0.984, year: 2002

  2. Characterization of polymer surface structure and surface mechanical behaviour by sum frequency generation surface vibrational spectroscopy and atomic force microscopy

    Opdahl, Aric; Koffas, Telly S; Amitay-Sadovsky, Ella; Kim, Joonyeong; Somorjai, Gabor A

    2004-01-01

    Sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM) have been used to study polymer surface structure and surface mechanical behaviour, specifically to study the relationships between the surface properties of polymers and their bulk compositions and the environment to which the polymer is exposed. The combination of SFG surface vibrational spectroscopy and AFM has been used to study surface segregation behaviour of polyolefin blends at the polymer/air and polymer/solid interfaces. SFG surface vibrational spectroscopy and AFM experiments have also been performed to characterize the properties of polymer/liquid and polymer/polymer interfaces, focusing on hydrogel materials. A method was developed to study the surface properties of hydrogel contact lens materials at various hydration conditions. Finally, the effect of mechanical stretching on the surface composition and surface mechanical behaviour of phase-separated polyurethanes, used in biomedical implant devices, has been studied by both SFG surface vibrational spectroscopy and AFM. (topical review)

  3. Slowdown of group velocity of light in dual-frequency laser-pumped cascade structure of Er3+-doped optical fiber at room temperature

    Qiu, Wei; Yang, Yujing; Gao, Yuan; Liu, Jianjun; Lv, Pin; Jiang, Qiuli

    2018-04-01

    Slow light is demonstrated in the cascade structure of an erbium-doped fiber with two forward propagation pumps. The results of the numerical simulation of the time delay and the optimum modulation frequency complement each other. The time delay and the optimum modulation frequency depend on the pump ratio G (G  =  {{P}1480}:{{P}980} ). The discussion results of this paper show that a larger time delay of slow light propagation can be obtained in the cascade structure of Er3+-doped optical fibers with dual-frequency laser pumping. Compared to previous research methods, the dual-frequency laser-pumped cascade structure of an Er3+-doped optical fiber is more controllable. Based on our discussion the pump ratio G should be selected in order to obtain a more appropriate time delay and the slowdown of group velocity.

  4. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

    Schrooten Chris

    2009-01-01

    Full Text Available Abstract The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.

  5. The putative oncogene Pim-1 in the mouse: its linkage and variation among t haplotypes.

    Nadeau, J H; Phillips, S J

    1987-11-01

    Pim-1, a putative oncogene involved in T-cell lymphomagenesis, was mapped between the pseudo-alpha globin gene Hba-4ps and the alpha-crystallin gene Crya-1 on mouse chromosome 17 and therefore within the t complex. Pim-1 restriction fragment variants were identified among t haplotypes. Analysis of restriction fragment sizes obtained with 12 endonucleases demonstrated that the Pim-1 genes in some t haplotypes were indistinguishable from the sizes for the Pim-1b allele in BALB/c inbred mice. There are now three genes, Pim-1, Crya-1 and H-2 I-E, that vary among independently derived t haplotypes and that have indistinguishable alleles in t haplotypes and inbred strains. These genes are closely linked within the distal inversion of the t complex. Because it is unlikely that these variants arose independently in t haplotypes and their wild-type homologues, we propose that an exchange of chromosomal segments, probably through double crossingover, was responsible for indistinguishable Pim-1 genes shared by certain t haplotypes and their wild-type homologues. There was, however, no apparent association between variant alleles of these three genes among t haplotypes as would be expected if a single exchange introduced these alleles into t haplotypes. If these variant alleles can be shown to be identical to the wild-type allele, then lack of association suggests that multiple exchanges have occurred during the evolution of the t complex.

  6. Analysis of Multiallelic CNVs by Emulsion Haplotype Fusion PCR.

    Tyson, Jess; Armour, John A L

    2017-01-01

    Emulsion-fusion PCR recovers long-range sequence information by combining products in cis from individual genomic DNA molecules. Emulsion droplets act as very numerous small reaction chambers in which different PCR products from a single genomic DNA molecule are condensed into short joint products, to unite sequences in cis from widely separated genomic sites. These products can therefore provide information about the arrangement of sequences and variants at a larger scale than established long-read sequencing methods. The method has been useful in defining the phase of variants in haplotypes, the typing of inversions, and determining the configuration of sequence variants in multiallelic CNVs. In this description we outline the rationale for the application of emulsion-fusion PCR methods to the analysis of multiallelic CNVs, and give practical details for our own implementation of the method in that context.

  7. Distribution of HLA-A, -B and -DRB1 genes and haplotypes in the Tujia population living in the Wufeng Region of Hubei Province, China.

    Li Zhang

    Full Text Available BACKGROUND: The distribution of HLA alleles and haplotypes varies widely between different ethnic populations and geographic areas. Before any genetic marker can be used in a disease-associated study it is therefore essential to investigate allelic frequencies and establish a genetic database. METHODOLOGY/PRINCIPAL FINDINGS: This is the first report of HLA typing in the Tujia group using the Luminex HLA-SSO method HLA-A, -B and -DRB1 allelic distributions were determined in 124 unrelated healthy Tujia individuals, and haplotypic frequencies and linkage disequilibrium parameters were estimated using the maximum-likelihood method. In total 10 alleles were detected at the HLA-A locus, 21 alleles at the HLA-B locus and 14 alleles at the HLA-DRB1 locus. The most frequently observed alleles in the HLA-I group were HLA-A*02 (35.48%, A*11 (28.23%, A*24 (15.73%; HLA-B*40 (25.00%, B*46 (16.13%, and B*15 (15.73%. Among HLA-DRB1 alleles, high frequencies of HLA-DRB1*09 (25.81% were observed, followed by HLA-DRB1*15 (12.9%, and DRB1*12 (10.89%. The two-locus haplotypes at the highest frequency were A*02-B*46A (8.47%, followed by A*11-B*40 (7.66%, A*02-B*40 (8.87%, A*11-B*15 (6.45%, A*02-B*15 (6.05%, B*40-DRB1*09 (9.27% and B*46-DRB1*09 (6.45%. The most common three-locus haplotypes found in the Tujia population were A*02-B*46-DRB1*09 (4.84% and A*02-B*40-DRB1*09 (4.03%. Fourteen two-loci haplotypes had significant linkage disequilibrium. Construction of a neighbor-joining phylogenetic tree and principal component analysis using the allelic frequencies at HLA-A was performed to compare the Tujia group and twelve other previously reported populations. The Tujia population in the Wufeng of Hubei Province had the closest genetic relationship with the central Han population, and then to the Shui, the Miao, the southern Han and the northern Han ethnic groups. CONCLUSIONS/SIGNIFICANCE: These results will become a valuable source of data for tracing population

  8. Laser Doppler vibrometry on rotating structures in coast-down: resonance frequencies and operational deflection shape characterization

    Martarelli, M; Castellini, P; Santolini, C; Tomasini, E P

    2011-01-01

    In rotating machinery, variations of modal parameters with rotation speed may be extremely important in particular for very light and undamped structures, such as helicopter rotors or wind turbines. The natural frequency dependence on rotation speed is conventionally measured by varying the rotor velocity and plotting natural frequencies versus speed in the so-called Campbell diagram. However, this kind of analysis does not give any information about the vibration spatial distribution i.e. the mode shape variation with the rotation speed must be investigated with dedicated procedures. In several cases it is not possible to fully control the rotating speed of the machine and only coast-down tests can be performed. Due to the reduced inertia of rotors, the coast-down process is usually an abrupt transient and therefore an experimental technique, able to determine operational deflection shapes (ODSs) in short time, with high spatial density and accuracy, appears very promising. Moreover coast-down processes are very difficult to control, causing unsteady vibrations. Hence, a very efficient approach for the rotation control and synchronous acquisition must be developed. In this paper a continuous scanning system able to measure ODSs and natural frequencies excited during rotor coast-down is shown. The method is based on a laser Doppler vibrometer (LDV) whose laser beam is driven to scan continuously over the rotor surface, in order to measure the ODS, and to follow the rotation of the rotor itself even in coast-down. With a single measurement the ODSs can be recovered from the LDV output time history in short time and with huge data saving. This technique has been tested on a laboratory test bench, i.e. a rotating two-blade fan, and compared with a series of non-contact approaches based on LDV: - traditional experimental modal analysis (EMA) results obtained under non-rotating conditions by measuring on a sequence of points on the blade surface excited by an impact

  9. Frequency and Nature of Infectious Risk Moments During Acute Care Based on the INFORM Structured Classification Taxonomy.

    Clack, Lauren; Passerini, Simone; Wolfensberger, Aline; Sax, Hugo; Manser, Tanja

    2018-03-01

    OBJECTIVE In this study, we sought to establish a comprehensive inventory of infectious risk moments (IRMs), defined as seemingly innocuous yet frequently occurring care manipulations potentially resulting in transfer of pathogens to patients. We also aimed to develop and employ an observational taxonomy to quantify the frequency and nature of IRMs in acute-care settings. DESIGN Prospective observational study and establishment of observational taxonomy. SETTING Intensive care unit, general medical ward, and emergency ward of a university-affiliated hospital. PARTICIPANTS Healthcare workers (HCWs) METHODS Exploratory observations were conducted to identify IRMs, which were coded based on the surfaces involved in the transmission pathway to establish a structured taxonomy. Structured observations were performed using this taxonomy to quantify IRMs in all 3 settings. RESULTS Following 129.17 hours of exploratory observations, identified IRMs involved HCW hands, gloves, care devices, mobile objects, and HCW clothing and accessories. A structured taxonomy called INFORM (INFectiOus Risk Moment) was established to classify each IRM according to the source, vector, and endpoint of potential pathogen transfer. We observed 1,138 IRMs during 53.77 hours of structured observations (31.25 active care hours) for an average foundation of 42.8 IRMs per active care hour overall, and average densities of 34.9, 36.8, and 56.3 IRMs in the intensive care, medical, and emergency wards, respectively. CONCLUSIONS Hands and gloves remain among the most important contributors to the transfer of pathogens within the healthcare setting, but medical devices, mobile objects, invasive devices, and HCW clothing and accessories may also contribute to patient colonization and/or infection. The INFORM observational taxonomy and IRM inventory presented may benefit clinical risk assessment, training and education, and future research. Infect Control Hosp Epidemiol 2018;39:272-279.

  10. Organelle DNA haplotypes reflect crop-use characteristics and geographic origins of Cannabis sativa.

    Gilmore, Simon; Peakall, Rod; Robertson, James

    2007-10-25

    Comparative sequencing of cannabis individuals across 12 chloroplast and mitochondrial DNA loci revealed 7 polymorphic sites, including 5 length variable regions and 2 single nucleotide polymorphisms. Simple PCR assays were developed to assay these polymorphisms, and organelle DNA haplotypes were obtained for 188 cannabis individuals from 76 separate populations, including drug-type, fibre-type and wild populations. The haplotype data were analysed using parsimony, UPGMA and neighbour joining methods. Three haplotype groups were recovered by each analysis method, and these groups are suggestive of the crop-use characteristics and geographical origin of the populations, although not strictly diagnostic. We discuss the relationship between our haplotype data and taxonomic opinions of cannabis, and the implications of organelle DNA haplotyping to forensic investigations of cannabis.

  11. A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes

    Cruciani, Fulvio; Santolamazza, Piero; Shen, Peidong; Macaulay, Vincent; Moral, Pedro; Olckers, Antonel; Modiano, David; Holmes, Susan; Destro-Bisol, Giovanni; Coia, Valentina; Wallace, Douglas C.; Oefner, Peter J.; Torroni, Antonio; Cavalli-Sforza, L. Luca; Scozzari, Rosaria; Underhill, Peter A.

    2002-01-01

    The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a nonuniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity (ΦST=0.342), which appears to be partially related to the geography (ΦCT=0.230). In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population (ΦST=0.332) and geographic (ΦCT=0.179) structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and sub-Saharan Africans. Among the latter, the Khoisan, the Pygmies, and the northern Cameroonians are clearly distinct from a tight cluster formed by the Niger-Congo–speaking populations from western, central western, and southern Africa. Phylogeographic analyses suggest that a large component of the present Khoisan gene pool is eastern African in origin and that Asia was the source of a back migration to sub-Saharan Africa. Haplogroup IX Y chromosomes appear to have been involved in such a migration, the traces of which can now be observed mostly in northern Cameroon. PMID:11910562

  12. Haplotype assembly in polyploid genomes and identical by descent shared tracts.

    Aguiar, Derek; Istrail, Sorin

    2013-07-01

    Genome-wide haplotype reconstruction from sequence data, or haplotype assembly, is at the center of major challenges in molecular biology and life sciences. For complex eukaryotic organisms like humans, the genome is vast and the population samples are growing so rapidly that algorithms processing high-throughput sequencing data must scale favorably in terms of both accuracy and computational efficiency. Furthermore, current models and methodologies for haplotype assembly (i) do not consider individuals sharing haplotypes jointly, which reduces the size and accuracy of assembled haplotypes, and (ii) are unable to model genomes having more than two sets of homologous chromosomes (polyploidy). Polyploid organisms are increasingly becoming the target of many research groups interested in the genomics of disease, phylogenetics, botany and evolution but there is an absence of theory and methods for polyploid haplotype reconstruction. In this work, we present a number of results, extensions and generalizations of compass graphs and our HapCompass framework. We prove the theoretical complexity of two haplotype assembly optimizations, thereby motivating the use of heuristics. Furthermore, we present graph theory-based algorithms for the problem of haplotype assembly using our previously developed HapCompass framework for (i) novel implementations of haplotype assembly optimizations (minimum error correction), (ii) assembly of a pair of individuals sharing a haplotype tract identical by descent and (iii) assembly of polyploid genomes. We evaluate our methods on 1000 Genomes Project, Pacific Biosciences and simulated sequence data. HapCompass is available for download at http://www.brown.edu/Research/Istrail_Lab/. Supplementary data are available at Bioinformatics online.

  13. Polymorphism at Expressed DQ and DR Loci in Five Common Equine MHC Haplotypes

    Miller, Donald; Tallmadge, Rebecca L.; Binns, Matthew; Zhu, Baoli; Mohamoud, Yasmin Ali; Ahmed, Ayeda; Brooks, Samantha A.; Antczak, Douglas F.

    2016-01-01

    The polymorphism of Major Histocompatibility Complex (MHC) class II DQ and DR genes in five common Equine Leukocyte Antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine Bacterial Artificial Chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next Generation Sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse. PMID:27889800

  14. Haplotype phasing and inheritance of copy number variants in nuclear families.

    Palta, Priit; Kaplinski, Lauris; Nagirnaja, Liina; Veidenberg, Andres; Möls, Märt; Nelis, Mari; Esko, Tõnu; Metspalu, Andres; Laan, Maris; Remm, Maido

    2015-01-01

    DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.

  15. Haplotype phasing and inheritance of copy number variants in nuclear families.

    Priit Palta

    Full Text Available DNA copy number variants (CNVs that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i phase normal and CNV-carrying haplotypes in the copy number variable regions, ii resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.

  16. Plasmodium falciparum isolates from Angola show the StctVMNT haplotype in the pfcrt gene

    2010-01-01

    Background Effective treatment remains a mainstay of malaria control, but it is unfortunately strongly compromised by drug resistance, particularly in Plasmodium falciparum, the most important human malaria parasite. Although P. falciparum chemoresistance is well recognized all over the world, limited data are available on the distribution and prevalence of pfcrt and pfmdr1 haplotypes that mediate resistance to commonly used drugs and that show distinct geographic differences. Methods Plasmodium falciparum-infected blood samples collected in 2007 at four municipalities of Luanda, Angola, were genotyped using PCR and direct DNA sequencing. Single nucleotide polymorphisms in the P. falciparum pfcrt and pfmdr1 genes were assessed and haplotype prevalences were determined. Results and Discussion The most prevalent pfcrt haplotype was StctVMNT (representing amino acids at codons 72-76). This result was unexpected, since the StctVMNT haplotype has previously been seen mainly in parasites from South America and India. The CVIET, CVMNT and CVINT drug-resistance haplotypes were also found, and one previously undescribed haplotype (CVMDT) was detected. Regarding pfmdr1, the most prevalent haplotype was YEYSNVD (representing amino acids at codons 86, 130, 184, 1034, 1042, 1109 and 1246). Wild haplotypes for pfcrt and pfmdr1 were uncommon; 3% of field isolates harbored wild type pfcrt (CVMNK), whereas 21% had wild type pfmdr1 (NEYSNVD). The observed predominance of the StctVMNT haplotype in Angola could be a result of frequent travel between Brazil and Angola citizens in the context of selective pressure of heavy CQ use. Conclusions The high prevalence of the pfcrt SVMNT haplotype and the pfmdr1 86Y mutation confirm high-level chloroquine resistance and might suggest reduced efficacy of amodiaquine in Angola. Further studies must be encouraged to examine the in vitro sensitivity of pfcrt SVMNT parasites to artesunate and amodiaquine for better conclusive data. PMID:20565881

  17. Difference-frequency generation in the field of a few-cycle laser pulse propagating in a GaAs crystal with a domain structure

    Oganesyan, David L; Vardanyan, Aleksandr O; Oganesyan, G D

    2013-01-01

    Difference-frequency generation in a GaAs crystal with a periodic domain structure in the field of a few-cycle laser pulse is considered for the case of weakly pronounced material dispersion. The straight-line method is used to solve numerically the system of coupled nonlinear partial differential equations describing the evolution of the electric field of this laser pulse in GaAs crystals with periodic and chirped domain structures. It is shown that application of a GaAs crystal with a chirped domain structure makes it possible to control the frequency-modulation law for a broadband differencefrequency pulse. (nonlinear optical phenomena)

  18. Coupling Analysis of Low-Speed Multiphase Flow and High-Frequency Electromagnetic Field in a Complex Pipeline Structure

    Xiaokai Huo

    2014-01-01

    Full Text Available Accurate estimation of water content in an oil-water mixture is a key technology in oil exploration and production. Based on the principles of the microwave transmission line (MTL, the logging probe is an important water content measuring apparatus. However, the effects of mixed fluid flow on the measurement of electromagnetic field parameters are rarely considered. This study presents the coupling model for low-speed multiphase flow and high-frequency electromagnetic field in a complex pipeline structure. We derived the S-parameter equations for the stratified oil/water flow model. The corresponding relationship between the S-parameters and water holdup is established. Evident coupling effects of the fluid flow and the electromagnetic field are confirmed by comparing the calculated S-parameters for both stratified and homogeneous flow patterns. In addition, a multiple-solution problem is analyzed for the inversion of dielectric constant from the S-parameters. The most sensitive phase angle range is determined to improve the detection of variation in the dielectric constant. Suggestions are proposed based on the influence of the oil/water layer on measurement sensitivity to optimize the geometric parameters of a device structure. The method proposed elucidates how accuracy and sensitivity can be improved in water holdup measurements under high water content conditions.

  19. Genetic structure of Quechua-speakers of the Central Andes and geographic patterns of gene frequencies in South Amerindian populations.

    Luiselli, D; Simoni, L; Tarazona-Santos, E; Pastor, S; Pettener, D

    2000-09-01

    A sample of 141 Quechua-speaking individuals of the population of Tayacaja, in the Peruvian Central Andes, was typed for the following 16 genetic systems: ABO, Rh, MNSs, P, Duffy, AcP1, EsD, GLOI, PGM1, AK, 6-PGD, Hp, Gc, Pi, C3, and Bf. The genetic structure of the population was analyzed in relation to the allele frequencies available for other South Amerindian populations, using a combination of multivariate and multivariable techniques. Spatial autocorrelation analysis was performed independently for 13 alleles to identify patterns of gene flow in South America as a whole and in more specific geographic regions. We found a longitudinal cline for the AcP1*a and EsD*1 alleles which we interpreted as the result of an ancient longitudinal expansion of a putative ancestral population of modern Amerindians. Monmonnier's algorithm, used to identify areas of sharp genetic discontinuity, suggested a clear east-west differentiation of native South American populations, which was confirmed by analysis of the distribution of genetic distances. We suggest that this pattern of genetic structures is the consequence of the independent peopling of western and eastern South America or to low levels of gene flow between these regions, related to different environmental and demographic histories. Copyright 2000 Wiley-Liss, Inc.

  20. Revealing molecular-level surface structure of amyloid fibrils in liquid by means of frequency modulation atomic force microscopy

    Fukuma, Takeshi [Frontier Science Organization, Kanazawa University, Kakuma-machi, Kanazawa 920-1192 (Japan); Mostaert, Anika S; Jarvis, Suzanne P [Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Republic of Ireland (Ireland); Serpell, Louise C [Department of Biochemistry, University of Sussex, John Maynard Building, Falmer BN1 9QG (United Kingdom)], E-mail: fukuma@staff.kanazawa-u.ac.jp, E-mail: Anika.Mostaert@ucd.ie, E-mail: L.C.Serpell@sussex.ac.uk, E-mail: Suzi.Jarvis@ucd.ie

    2008-09-24

    We have investigated the surface structure of islet amyloid polypeptide (IAPP) fibrils and {alpha}-synuclein protofibrils in liquid by means of frequency modulation atomic force microscopy (FM-AFM). Angstroem-resolution FM-AFM imaging of isolated macromolecules in liquid is demonstrated for the first time. Individual {beta}-strands aligned perpendicular to the fibril axis with a spacing of 0.5 nm are resolved in FM-AFM images, which confirms cross-{beta} structure of IAPP fibrils in real space. FM-AFM images also reveal the existence of 4 nm periodic domains along the axis of IAPP fibrils. Stripe features with 0.5 nm spacing are also found in images of {alpha}-synuclein protofibrils. However, in contrast to the case for IAPP fibrils, the stripes are oriented 30 deg. from the axis, suggesting the possibility of {beta}-strand alignment in protofibrils different from that in mature fibrils or the regular arrangement of thioflavin T molecules present during the fibril preparation aligned at the surface of the protofibrils.

  1. Revealing molecular-level surface structure of amyloid fibrils in liquid by means of frequency modulation atomic force microscopy

    Fukuma, Takeshi; Mostaert, Anika S; Jarvis, Suzanne P; Serpell, Louise C

    2008-01-01

    We have investigated the surface structure of islet amyloid polypeptide (IAPP) fibrils and α-synuclein protofibrils in liquid by means of frequency modulation atomic force microscopy (FM-AFM). Angstroem-resolution FM-AFM imaging of isolated macromolecules in liquid is demonstrated for the first time. Individual β-strands aligned perpendicular to the fibril axis with a spacing of 0.5 nm are resolved in FM-AFM images, which confirms cross-β structure of IAPP fibrils in real space. FM-AFM images also reveal the existence of 4 nm periodic domains along the axis of IAPP fibrils. Stripe features with 0.5 nm spacing are also found in images of α-synuclein protofibrils. However, in contrast to the case for IAPP fibrils, the stripes are oriented 30 deg. from the axis, suggesting the possibility of β-strand alignment in protofibrils different from that in mature fibrils or the regular arrangement of thioflavin T molecules present during the fibril preparation aligned at the surface of the protofibrils

  2. LOW-FREQUENCY OBSERVATIONS OF LINEARLY POLARIZED STRUCTURES IN THE INTERSTELLAR MEDIUM NEAR THE SOUTH GALACTIC POLE

    Lenc, E.; Gaensler, B. M.; Sun, X. H.; Sadler, E. M.; Callingham, J. R. [Sydney Institute for Astronomy, School of Physics, The University of Sydney, NSW 2006 (Australia); Willis, A. G. [National Research Council of Canada, Herzberg Astronomy and Astrophysics, P.O. Box 248, Penticton, BC (Canada); Barry, N.; Beardsley, A. P.; Carroll, P. [Department of Physics, University of Washington, Seattle, WA 98195 (United States); Bell, M. E.; Briggs, F. [ARC Centre of Excellence for All-sky Astrophysics (CAASTRO) (Australia); Bernardi, G. [Department of Physics and Electronics, Rhodes University, P.O. Box 94, Grahamstown 6140 (South Africa); Bowman, J. D. [School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287 (United States); Cappallo, R. J.; Corey, B. E. [MIT Haystack Observatory, Westford, MA 01886 (United States); Oliveira-Costa, A. de; Dillon, J. S. [MIT Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Deshpande, A. A.; Dwarkanath, K. S. [Raman Research Institute, Bangalore 560080 (India); Emrich, D. [International Centre for Radio Astronomy Research, Curtin University, Bentley, WA 6102 (Australia); and others

    2016-10-10

    We present deep polarimetric observations at 154 MHz with the Murchison Widefield Array (MWA), covering 625 deg{sup 2} centered on α = 0{sup h}and δ = −27°. The sensitivity available in our deep observations allows an in-band, frequency-dependent analysis of polarized structure for the first time at long wavelengths. Our analysis suggests that the polarized structures are dominated by intrinsic emission but may also have a foreground Faraday screen component. At these wavelengths, the compactness of the MWA baseline distribution provides excellent snapshot sensitivity to large-scale structure. The observations are sensitive to diffuse polarized emission at ∼54′ resolution with a sensitivity of 5.9 mJy beam{sup −1} and compact polarized sources at ∼2.′4 resolution with a sensitivity of 2.3 mJy beam{sup −1} for a subset (400 deg{sup 2}) of this field. The sensitivity allows the effect of ionospheric Faraday rotation to be spatially and temporally measured directly from the diffuse polarized background. Our observations reveal large-scale structures (∼1°–8° in extent) in linear polarization clearly detectable in ∼2 minute snapshots, which would remain undetectable by interferometers with minimum baseline lengths of >110 m at 154 MHz. The brightness temperature of these structures is on average 4 K in polarized intensity, peaking at 11 K. Rotation measure synthesis reveals that the structures have Faraday depths ranging from −2 to 10 rad m{sup −2} with a large fraction peaking at approximately +1 rad m{sup −2}. We estimate a distance of 51 ± 20 pc to the polarized emission based on measurements of the in-field pulsar J2330–2005. We detect four extragalactic linearly polarized point sources within the field in our compact source survey. Based on the known polarized source population at 1.4 GHz and non-detections at 154 MHz, we estimate an upper limit on the depolarization ratio of 0.08 from 1.4 GHz to 154 MHz.

  3. Determination of βS haplotypes in patients with sickle-cell anemia in the state of Rio Grande do Norte, Brazil

    Cynthia Hatsue Kitayama Cabral

    2011-01-01

    Full Text Available βS haplotypes were studied in 47 non-related patients with sickle-cell anemia from the state of Rio Grande do Norte, Brazil. Molecular analysis was conducted by PCR/RFLP using restriction endonucleases XmnI, HindIII, HincII and HinfI to analyze six polymorphic sites from the beta cluster. Twenty-seven patients (57.5% were identified with genotype CAR/CAR, 9 (19.1% CAR/BEN, 6 (12.8% CAR/CAM, 1 (2.1% BEN/BEN, 2 (4.3% CAR/Atp, 1 (2.1% BEN/Atp and 1 (2.1% with genotype Atp/Atp. The greater frequency of Cameroon haplotypes compared to other Brazilian states suggests the existence of a peculiarity of African origin in the state of Rio Grande do Norte.

  4. Broadband photosensor with a tunable frequency range, built on the basis of nanoscale carbon structure with field localization

    Yakunin, Alexander N.; Akchurin, Garif G.; Aban'shin, Nikolay P.; Gorfinkel, Boris I.

    2014-03-01

    The work is devoted to the development of a new direction in creating of broadband photo sensors which distinctive feature is the possibility of dynamic adjustment of operating frequency range. The author's results of study of red threshold control of classic photoelectric effect were the basis for the work implementation. This effect was predicted theoretically and observed experimentally during irradiation of nanoscale carbon structure of planar-edge type by stream of low-energy photons. The variation of the accelerating voltage within a small range allows you to change photoelectric threshold for carbon in a wide range - from UV to IR. This is the consequence of the localization of electrostatic field at tip of the blade planar structure and of changes in the conditions of non-equilibrium electrons tunneling from the boundary surface of the cathode into the vacuum. The generation of nonequilibrium electrons in the carbon film thickness of 20 nm has a high speed which provides high performance of photodetector. The features of the use of nanoscale carbon structure photocurrent registration as in the prethreshold regime, and in the mode of field emission existence are discussed. The results of simulation and experimental examination of photosensor samples are given. It is shown that the observed effect is a single-photon tunneling. This in combination with the possibility of highspeed dynamic tuning determines the good perspectives for creation of new devices working in the mode of select multiple operating spectral bands for the signal recording. The architecture of such devices is expected to be significantly simpler than the conventional ones, based on the use of tunable filters.

  5. Structure-borne low-frequency noise from multi-span bridges: A prediction method and spatial distribution

    Song, X. D.; Wu, D. J.; Li, Q.; Botteldooren, D.

    2016-04-01

    Structure-borne noise from railway bridges at far-field points is an important indicator in environmental noise assessment. However, studies that predict structure-borne noise tend to model only single-span bridges, thus ignoring the sound pressure radiating from adjacent spans. To simulate the noise radiating from multi-span bridges induced by moving vehicles, the vibrations of a multi-span bridge are first obtained from a three-dimensional (3D) vehicle-track-bridge dynamic interaction simulation using the mode superposition method. A procedure based on the 2.5-dimensional (2.5D) boundary element method (BEM) is then presented to promote the efficiency of acoustical computation compared with the 3D BEM. The simulated results obtained from both the single-span and multi-span bridge models are compared with the measured results. The sound predictions calculated from the single-span model are accurate only for a minority of near-field points. In contrast, the sound pressures calculated from the multi-span bridge model match the measured results in both the time and frequency domains for all of the near-field and far-field points. The number of bridge spans required in the noise simulation is then recommended related to the distance between the track center and the field points of interest. The spatial distribution of multi-span structure-borne noise is also studied. The variation in sound pressure levels is insignificant along the length of the bridge, which validates the finding that the sound test section can be selected at an arbitrary plane perpendicular to the multi-span bridge.

  6. Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides.

    Shiau, Yo-Jin; Cai, Yuanfeng; Lin, Yu-Te; Jia, Zhongjun; Chiu, Chih-Yu

    2018-04-01

    Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH 4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of 13 CH 4 DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.

  7. Haplotype Study in SCA10 Families Provides Further Evidence for a Common Ancestral Origin of the Mutation.

    Bampi, Giovana B; Bisso-Machado, Rafael; Hünemeier, Tábita; Gheno, Tailise C; Furtado, Gabriel V; Veliz-Otani, Diego; Cornejo-Olivas, Mario; Mazzeti, Pillar; Bortolini, Maria Cátira; Jardim, Laura B; Saraiva-Pereira, Maria Luiza

    2017-12-01

    Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disorder characterized by progressive cerebellar ataxia and epilepsy. The disease is caused by a pentanucleotide ATTCT expansion in intron 9 of the ATXN10 gene on chromosome 22q13.3. SCA10 has shown a geographical distribution throughout America with a likely degree of Amerindian ancestry from different countries so far. Currently available data suggest that SCA10 mutation might have spread out early during the peopling of the Americas. However, the ancestral origin of SCA10 mutation remains under speculation. Samples of SCA10 patients from two Latin American countries were analysed, being 16 families from Brazil (29 patients) and 21 families from Peru (27 patients) as well as 49 healthy individuals from Indigenous Quechua population and 51 healthy Brazilian individuals. Four polymorphic markers spanning a region of 5.2 cM harbouring the ATTCT expansion were used to define the haplotypes, which were genotyped by different approaches. Our data have shown that 19-CGGC-14 shared haplotype was found in 47% of Brazilian and in 63% of Peruvian families. Frequencies from both groups are not statistically different from Quechua controls (57%), but they are statistically different from Brazilian controls (12%) (p Quechuas, 19-15-CGGC-14-10, is found in 50% of Brazilian and in 65% of Peruvian patients with SCA10. These findings bring valuable evidence that ATTCT expansion may have arisen in a Native American chromosome.

  8. Molecular Structure And Vibrational Frequencies of 2,3,4 Nitro anilines By Hartree-Fock And Density Functional Theory Calculations

    Sert, Y.

    2008-01-01

    The optimised molecular structure, vibrational frequencies and corresponding vibrational assignments of 2-, 3- and 4- nitro anilines have been calculated using the Hartree-Fock (HF) and density functional methods (B3LYP) with 6-311++G (d, p) basis set. The calculations were adapted to the C S symmetries of all the molecules. The calculated vibrational frequencies and geometric parameters (bond lengths and bond angles) were seen to be in good agreement with the experimental data. The comparison of the experimental and theoretical results showed that the HF method is superior to the B3LYP method for both the vibrational frequencies and geometric parameters

  9. STUDY OF ARC IMPULSE FREQUENCY EFFECT ON THE STRUCTURE AND PROPERTIES OF WELDED CONNECTION ELEMENTS IN ALUMINIUM PIPELINE SYSTEMS, MADE WITH MASTERTIG 3500

    Mr. Pavel V. Bakhmatov

    2016-06-01

    Full Text Available Summary . The article focuses on the arc impulse frequency effect on the structure and properties of welded connections in aluminum pipeline systems hand-operated with argon-arc welding nonconsumable rod on MasterTig3500. It was revealed that the frequency of the welding current impulses plays an important role in the forming of the welded connection. The authors determined the optimal value of the welding current frequency significantly accelerating the welding process to ensure consistent quality of the weld. The authors detailed some features of cleaning assembly parts with a wire brush prior to welding process.

  10. Mutation Analysis in Classical Phenylketonuria Patients Followed by Detecting Haplotypes Linked to Some PAH Mutations.

    Dehghanian, Fatemeh; Silawi, Mohammad; Tabei, Seyed M B

    2017-02-01

    Deficiency of phenylalanine hydroxylase (PAH) enzyme and elevation of phenylalanine in body fluids cause phenylketonuria (PKU). The gold standard for confirming PKU and PAH deficiency is detecting causal mutations by direct sequencing of the coding exons and splicing involved sequences of the PAH gene. Furthermore, haplotype analysis could be considered as an auxiliary approach for detecting PKU causative mutations before direct sequencing of the PAH gene by making comparisons between prior detected mutation linked-haplotypes and new PKU case haplotypes with undetermined mutations. In this study, 13 unrelated classical PKU patients took part in the study detecting causative mutations. Mutations were identified by polymerase chain reaction (PCR) and direct sequencing in all patients. After that, haplotype analysis was performed by studying VNTR and PAHSTR markers (linked genetic markers of the PAH gene) through application of PCR and capillary electrophoresis (CE). Mutation analysis was performed successfully and the detected mutations were as follows: c.782G>A, c.754C>T, c.842C>G, c.113-115delTCT, c.688G>A, and c.696A>G. Additionally, PAHSTR/VNTR haplotypes were detected to discover haplotypes linked to each mutation. Mutation detection is the best approach for confirming PAH enzyme deficiency in PKU patients. Due to the relatively large size of the PAH gene and high cost of the direct sequencing in developing countries, haplotype analysis could be used before DNA sequencing and mutation detection for a faster and cheaper way via identifying probable mutated exons.

  11. Two families from New England with usher syndrome type IC with distinct haplotypes.

    DeAngelis, M M; McGee, T L; Keats, B J; Slim, R; Berson, E L; Dryja, T P

    2001-03-01

    To search for patients with Usher syndrome type IC among those with Usher syndrome type I who reside in New England. Genotype analysis of microsatellite markers closely linked to the USH1C locus was done using the polymerase chain reaction. We compared the haplotype of our patients who were homozygous in the USH1C region with the haplotypes found in previously reported USH1C Acadian families who reside in southwestern Louisiana and from a single family residing in Lebanon. Of 46 unrelated cases of Usher syndrome type I residing in New England, two were homozygous at genetic markers in the USH1C region. Of these, one carried the Acadian USH1C haplotype and had Acadian ancestors (that is, from Nova Scotia) who did not participate in the 1755 migration of Acadians to Louisiana. The second family had a haplotype that proved to be the same as that of a family with USH1C residing in Lebanon. Each of the two families had haplotypes distinct from the other. This is the first report that some patients residing in New England have Usher syndrome type IC. Patients with Usher syndrome type IC can have the Acadian haplotype or the Lebanese haplotype compatible with the idea that at least two independently arising pathogenic mutations have occurred in the yet-to-be identified USH1C gene.

  12. Mineralocorticoid receptor haplotype moderates the effects of oral contraceptives and menstrual cycle on emotional information processing.

    Hamstra, Danielle A; de Kloet, E Ronald; Tollenaar, Marieke; Verkuil, Bart; Manai, Meriem; Putman, Peter; Van der Does, Willem

    2016-10-01

    The processing of emotional information is affected by menstrual cycle phase and by the use of oral contraceptives (OCs). The stress hormone cortisol is known to affect emotional information processing via the limbic mineralocorticoid receptor (MR). We investigated in an exploratory study whether the MR-genotype moderates the effect of both OC-use and menstrual cycle phase on emotional cognition. Healthy premenopausal volunteers (n=93) of West-European descent completed a battery of emotional cognition tests. Forty-nine participants were OC users and 44 naturally cycling, 21 of whom were tested in the early follicular (EF) and 23 in the mid-luteal (ML) phase of the menstrual cycle. In MR-haplotype 1/3 carriers, ML women gambled more than EF women when their risk to lose was relatively small. In MR-haplotype 2, ML women gambled more than EF women, regardless of their odds of winning. OC-users with MR-haplotype 1/3 recognised fewer facial expressions than ML women with MR-haplotype 1/3. MR-haplotype 1/3 carriers may be more sensitive to the influence of their female hormonal status. MR-haplotype 2 carriers showed more risky decision-making. As this may reflect optimistic expectations, this finding may support previous observations in female carriers of MR-haplotype 2 in a naturalistic cohort study. © The Author(s) 2016.

  13. Fetal hemoglobin in sickle cell anemia: The Arab-Indian haplotype and new therapeutic agents.

    Habara, Alawi H; Shaikho, Elmutaz M; Steinberg, Martin H

    2017-11-01

    Fetal hemoglobin (HbF) has well-known tempering effects on the symptoms of sickle cell disease and its levels vary among patients with different