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Sample records for allelic frequency distribution

  1. Comparative frequency and allelic distribution of ABO and Rh (D ...

    African Journals Online (AJOL)

    Background: Allelic distribution of major blood groups (ABO and rhesus) has not been defined in Bangladeshi population. Determinants of blood group frequency in this region have not been studied properly. Aim: To determine ABO and rhesus blood group frequency and allelic distribution in a multiethnic area of ...

  2. Comparative frequency and allelic distribution of ABO and Rh (D ...

    African Journals Online (AJOL)

    Gourab Dewan

    2015-02-18

    Feb 18, 2015 ... Abstract Background: Allelic distribution of major blood groups (ABO and rhesus) has not been defined in Bangladeshi population. Determinants of blood group frequency in this region have not been studied properly. Aim: To determine ABO and rhesus blood group frequency and allelic distribution in a.

  3. Distribution of forensic marker allelic frequencies in Pernambuco, Northestern Brazil.

    Science.gov (United States)

    Santos, S M; Souza, C A; Rabelo, K C N; Souza, P R E; Moura, R R; Oliveira, T C; Crovella, S

    2015-04-30

    Pernambuco is one of the 27 federal units of Brazil, ranking seventh in the number of inhabitants. We examined the allele frequencies of 13 short tandem repeat loci (CFS1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, vWA, and TPOX), the minimum recommended by the Federal Bureau of Investigation and commonly used in forensic genetics laboratories in Brazil, in a sample of 609 unrelated individuals from all geographic regions of Pernambuco. The allele frequencies ranged from 5 to 47.2%. No significant differences for any loci analyzed were observed compared with other publications in other various regions of Brazil. Most of the markers observed were in Hardy-Weinberg equilibrium. The occurrence of the allele 47.2 (locus FGA) and alleles 35.1 and 39 (locus D21S11), also described in a single study of the Brazilian population, was observed. The other forensic parameters analyzed (matching probability, power of discrimination, polymorphic information content, paternity exclusion, complement factor I, observed heterozygosity, expected heterozygosity) indicated that the studied markers are very informative for human forensic identification purposes in the Pernambuco population.

  4. MHC allele frequency distributions under parasite-driven selection: A simulation model

    Directory of Open Access Journals (Sweden)

    Radwan Jacek

    2010-10-01

    Full Text Available Abstract Background The extreme polymorphism that is observed in major histocompatibility complex (MHC genes, which code for proteins involved in recognition of non-self oligopeptides, is thought to result from a pressure exerted by parasites because parasite antigens are more likely to be recognized by MHC heterozygotes (heterozygote advantage and/or by rare MHC alleles (negative frequency-dependent selection. The Ewens-Watterson test (EW is often used to detect selection acting on MHC genes over the recent history of a population. EW is based on the expectation that allele frequencies under balancing selection should be more even than under neutrality. We used computer simulations to investigate whether this expectation holds for selection exerted by parasites on host MHC genes under conditions of heterozygote advantage and negative frequency-dependent selection acting either simultaneously or separately. Results In agreement with simple models of symmetrical overdominance, we found that heterozygote advantage acting alone in populations does, indeed, result in more even allele frequency distributions than expected under neutrality, and this is easily detectable by EW. However, under negative frequency-dependent selection, or under the joint action of negative frequency-dependent selection and heterozygote advantage, distributions of allele frequencies were less predictable: the majority of distributions were indistinguishable from neutral expectations, while the remaining runs resulted in either more even or more skewed distributions than under neutrality. Conclusions Our results indicate that, as long as negative frequency-dependent selection is an important force maintaining MHC variation, the EW test has limited utility in detecting selection acting on these genes.

  5. Allele frequency distribution of 1691G >A F5 (which confers Factor V Leiden) across Europe, including Slavic populations.

    Science.gov (United States)

    Clark, Jeremy S C; Adler, Grażyna; Salkic, Nermin N; Ciechanowicz, Andrzej

    2013-11-01

    The allele 1691A F5, conferring Factor V Leiden, is a common risk factor in venous thromboembolism. The frequency distribution for this allele in Western Europe has been well documented; but here data from Central, Eastern and South-Eastern Europe has been included. In order to assess the significance of the collated data, a chi-squared test was applied, and Tukey tests and z-tests with Bonferroni correction were compared. A distribution with a North-Southeast band of high frequency of the 1691A F5 allele was discovered with a pocket including some Southern Slavic populations with low frequency. European countries/regions can be arbitrarily delimited into low (group 1, <2.8 %, mean 1.9 % 1691A F5 allele) or high (group 2, ≥2.8 %, mean 4.0 %) frequency groups, with many significant differences between groups, but only one intra-group difference (the Tukey test is suggested to be superior to the z-tests). In Europe a North-Southeast band of 1691A F5 high frequency has been found, clarified by inclusion of data from Central, Eastern and South-Eastern Europe, which surrounds a pocket of low frequency in the Balkans which could possibly be explained by Slavic migration. There seem to be no indications of variation in environmental selection due to geographical location.

  6. Allele frequency distribution for 15 autosomal STR loci in Afridi Pathan population of Uttar Pradesh, India.

    Science.gov (United States)

    Noor, Sabahat; Ali, Shahnaz; Eaaswarkhanth, Muthukrishnan; Haque, Ikramul

    2009-11-01

    Allele frequencies of the 15 autosomal short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818 and FGA were determined in Afridi Pathan population of Uttar Pradesh, India. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all the loci with an exception of TPOX and FGA. The allele 12 in CSF1PO was found to be most frequent. The power of discrimination was found to be high ranging from a minimum of 0.858 for the locus CSFIPO to maximum of 0.962 for the locus FGA, thereby facilitating the validation and efficiency of these STR markers in human identification. Population differentiation test between the studied and neighboring populations revealed significant differences at several loci suggesting the endogamous nature of the studied population. To the best of our knowledge, Afridi Pathan population has not been explored genetically for generating forensic data on STR markers. Therefore, STR allele frequency data of this unique population is a valuable contribution to the existing DNA database on Indian populations.

  7. Frequency distribution of ABO and Rh (D) blood group alleles in ...

    African Journals Online (AJOL)

    Background: Frequency distribution of blood groups is important as it is used in modern medicine, genetic research, anthropology, and tracing ancestral relations of humans. The ABO and Rh blood groups are the most important blood groups despite the long list of several other blood groups discovered so far. Aim of the ...

  8. Allele frequency distribution of D8S592 (STR) and PDGFA (VNTR) among five endogamous population groups of India.

    Science.gov (United States)

    Ahmad, Shazia; Seshadri, M

    2004-07-01

    Allele frequency distribution have been analyzed at D8S592 (short tandem repeat) and PDGFA (variable number of tandem repeat) among five distinct endogamous groups of India namely Ezhavas, Nayers, Arayas, Vishwakarma and Muslims. Muslims are religio-ethnic group while other populations mentioned above belong to distinct section of Hindu religion. All these populations are from Kollam district of Kerala in Southern India and speak Malayalam, an Indo-Dravidian language. A total of 228 for D8S592 and 212 for PDGFA loci, random, healthy individuals were analyzed.

  9. Comparative analysis of HLA II allele and genotype frequency distribution in patients with type 1 diabetes mellitus and autoimmune thyroiditis

    Directory of Open Access Journals (Sweden)

    Ekaterina Aleksandrovna Repina

    2013-12-01

    Full Text Available Aim. To compare HLA II allele and genotype frequency distribution in type 1 diabetes mellitus (T1DM and autoimmune thyroiditis (AIT with that in isolated T1DM.Materials and Methods. A total of 92 T1DM patients were subdivided into two groups. The first group comprised 54 patients with established AIT comorbidity or elevation of anti-thyroid autoantibodies (ATA. Patients with isolated T1DM (ATA-negative formed the second group. HLA-genotyping was performed by multiprimer PCR set for the three following genes: DRB1, DQA1 and DQВ1.Results. Prevalence of alleles DRB1*01, *03(017, *04, *07, *11 and genotypes 01/03, 01/04, 03/04 tends to be higher among patients with AIT comorbidity. The comorbidity group was also characterized by the trend towards higher prevalence of “marker/marker” and “marker/non-marker” combinations favouring the former variant. Conversely, ATA-negative patients exhibited trend for higher prevalence of “non-marker/non-marker” combination.Conclusion. Statistically insignificant difference between HLA II alleles and genotypes in the two studied groups suggests that primary genetic factors are common in these two diseases. Plausibly, genes other than DRB1, DQA1 and DQВ1 determine the localization of the autoimmune process.

  10. Allele frequency distribution of CYP2C9 2 and CYP2C9 3 polymorphisms in six Mexican populations.

    Science.gov (United States)

    Castelán-Martínez, Osvaldo D; Hoyo-Vadillo, Carlos; Sandoval-García, Emmanuel; Sandoval-Ramírez, Lucila; González-Ibarra, Miriam; Solano-Solano, Gloria; Gómez-Díaz, Rita A; Parra, Esteban J; Cruz, Miguel; Valladares-Salgado, Adán

    2013-07-10

    Allele frequency differences of functional CYP2C9 polymorphisms are responsible for some of the variation in drug response observed in human populations. The most relevant CYP2C9 functional variants are CYP2C9*2 (rs1799853) and CYP2C9 3 (rs1057910). These polymorphisms show variation in allele frequencies among different population groups. The present study aimed to analyze these polymorphisms in 947 Mexican-Mestizo from Mexico City and 483 individuals from five indigenous Mexican populations: Nahua, Teenek, Tarahumara, Purepecha and Huichol. The CYP2C9*2 allele frequencies in the Mestizo, Nahua and Teenek populations were 0.051, 0.007 and 0.005, respectively. As for CYP2C9 3, the allelic frequencies in the Mestizo, Nahua and Teenek populations were 0.04, 0.005 and 0.005, respectively. The CYP2C9 2 and CYP2C9 3 alleles were not observed in the Tarahumara, Purepecha and Huichol populations. These findings are in agreement with previous studies reporting very low allele frequencies for these polymorphisms in American Indigenous populations. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Plasminogen Activator Inhibitor-1 (PAI-1) gene 4G/5G alleles frequency distribution in the Lebanese population.

    Science.gov (United States)

    Shammaa, Dina M R; Sabbagh, Amira S; Taher, Ali T; Zaatari, Ghazi S; Mahfouz, Rami A R

    2008-09-01

    Plasminogen activator inhibitor-1 (PAI-1) is an inhibitor of fibrinolysis. Increased plasma PAI-1 levels play an essential role in the pathogenesis of cardiovascular risk and other diseases associated with thrombosis. The 4G/5G polymorphism of the PAI-1 promoter region has been extensively studied in different populations. We studied 160 healthy unrelated Lebanese individuals using a reverse hybridization PCR assay to detect the 5G/5G, 4G/5G and, 4G/4G genotypes of the PAI-1 gene and the frequencies of the 4G and 5G alleles. We found that 4G/5G genotype was the most prevalent (45.6%) followed by 5G/5G (36.9%) and 4G/4G (17.5%). The frequencies of the 4G and 5G alleles were calculated to be 0.403 and 0.597, respectively. Compared to other ethnic communities, the Lebanese population was found to harbour a relatively high prevalence of the rare 4G allele. This, in turn, may predispose this population to develop cardiovascular diseases and other thrombotic clinical conditions. This study aids to enhance our understanding of the genetic features of the Lebanese population.

  12. Distribution of allelic and genotypic frequencies of IL1A, IL4, NFKB1 and PAR1 variants in Native American, African, European and Brazilian populations.

    Science.gov (United States)

    Amador, Marcos A T; Cavalcante, Giovanna C; Santos, Ney P C; Gusmão, Leonor; Guerreiro, João F; Ribeiro-dos-Santos, Ândrea; Santos, Sidney

    2016-02-16

    The inflammatory response plays a key role at different stages of cancer development. Allelic variants of the interleukin 1A (IL1A), interleukin 4 (IL4), nuclear factor kappa B1 (NFKB1) and protease-activated receptor 1 (PAR1) genes may influence not only the inflammatory response but also susceptibility to cancer development. Among major ethnic or continental groups, these polymorphic variants present different allelic frequencies. In admixed populations, such as the Brazilian population, data on distribution of these polymorphisms are limited. Here, we collected samples of cancer-free individuals from the north, northeast, midwest, south and southeast regions of Brazil and from the three main groups that gave rise to the Brazilian population: Native Americans from the Brazilian Amazon, Africans and Europeans. We describe the allelic distributions of four IL1A (rs3783553), IL4 (rs79071878), NFKB1 (rs28362491) and PAR1 (rs11267092) gene polymorphisms, which the literature describes as polymorphisms with a risk of cancer or worse prognosis for cancer. The genotypic distribution of the four polymorphisms was statistically distinct between Native Americans, Africans and Europeans. For the allelic frequency of these polymorphisms, the Native American population was the most distinct among the three parental populations, and it included the greatest number of alleles with a risk of cancer or worse prognosis for cancer. The PAR1 gene polymorphism allelic distribution was similar among all Brazilian regions. For the other three markers, the northern region population was statistically distinct from other Brazilian region populations. The IL1A, IL4, NFKB1 and PAR1 gene polymorphism allelic distributions are homogeneous among the regional Brazilian populations, except for the northern region, which significantly differs from the other four Brazilian regions. Among the parental populations, the Native American population exhibited a higher incidence of alleles with risk of

  13. Frequency distribution of HLA alleles and haplotypes in Uyghur women with advanced squamous cell cervical cancer and relation to HPV status and clinical outcome.

    Science.gov (United States)

    Alifu, Mayinuer; Fan, Peiwen; Kuerban, Gulina; Yao, Xuan; Peng, Yanchun; Dong, Tao; Wang, Ruozheng

    2018-03-01

    This study aims to investigate the association of human leukocyte antigen (HLA) alleles and haplotypes in Uyghur women with advanced squamous cell cervical cancer (SCC). A total of 131 Uyghur patients with advanced SCC (IIb-IVa) and 91 healthy subjects from Xinjiang province were genotyped for HLA-I and II genes using Polymerase Chain Reaction Sequence Based Typing. The different frequencies of HLA alleles and haplotypes between patients and controls were compared and the correlations were analyzed between HLA distribution and HPV status and prognosis. (1) The frequencies of B*51:01, DRB1*07:01, DQB1*02:01, A*01:01-C*06:02, A*01:01-DRB1*07:01, C*06:02-DQB1*02:01, DRB1*07:01-DQB1*02:01 and C*06:02-DRB1*07:01-DQB1*02:01 in cancer group were higher than control group whereas the frequencies of B*44:02, B*58:01, C*05:01, DRB1*04:01, DRB1*12:01, DRB1*13:01, DQB1*02:02, DQB1*05:02, DRB1*03:01-DQB1*02:02 and DRB1*04:01-DQB1*03:02 in cancer group were lower than control group (P HLA alleles and its haplotypes play an important role. B*58:01 allele may act as an independent predictor for DSS.

  14. Haplotypic Background of a Private Allele at High Frequency in the Americas

    OpenAIRE

    Schroeder, Kari B.; Jakobsson, Mattias; Crawford, Michael H.; Schurr, Theodore G.; Boca, Simina M.; Conrad, Donald F.; Tito, Raul Y.; Osipova, Ludmilla P.; Tarskaia, Larissa A.; Zhadanov, Sergey I.; Wall, Jeffrey D.; Pritchard, Jonathan K.; Malhi, Ripan S.; Smith, David G.; Rosenberg, Noah A.

    2009-01-01

    Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To invest...

  15. Estimation of allelic frequencies for ABO and Rh blood groups

    African Journals Online (AJOL)

    Mostafa Saadat

    2015-02-18

    Feb 18, 2015 ... Estimation of allelic frequencies for ABO and Rh blood groups. Dear Editor. Estimation of the allelic frequencies for genetic markers is very important in genetic studies. Also investigation of the concordance between observed and expected value based on the Hardy–Weinberg equilibrium (HWE) is strongly ...

  16. Frequencies distribution of dihydrofolate reductase and dihydropteroate synthetase mutant alleles associated with sulfadoxine-pyrimethamine resistance in Plasmodium falciparum population from Hadhramout Governorate, Yemen.

    Science.gov (United States)

    Bamaga, Omar A A; Mahdy, Mohammed A K; Lim, Yvonne A L

    2015-12-22

    Malaria in Yemen is mainly caused by Plasmodium falciparum and 25% of the population is at high risk. Sulfadoxine-pyrimethamine (SP) had been used as monotherapy against P. falciparum. Emergence of chloroquine resistance led to the shift in anti-malarial treatment policy in Yemen to artemisinin-based combination therapy, that is artesunate (AS) plus SP as first-line therapy for uncomplicated malaria and artemether-lumefantrine as second-line treatment. This study aimed to screen mutations in the dihydrofolate reductase (dhfr) and dihydropteroate synthetase (dhps) genes associated with SP resistance among P. falciparum population in Hadhramout governorate, Yemen. Genomic DNA was extracted from dried blood spots of 137 P. falciparum isolates collected from a community-based study. DNA was amplified using nested polymerase chain reaction (PCR) and subsequently sequenced for Pfdhfr and Pfdhps genes. Sequences were analysed for mutations in Pfdhfr gene codons 51, 59, 108, and 164 and in Pfdhps gene codons 436, 437, and 540. A total of 128 and 114 P. falciparum isolates were successfully sequenced for Pfdhfr and Pfdhps genes, respectively. Each Pfdhfr mutant allele (I51 and N108) in P. falciparum population had a frequency of 84%. Pfdhfr R59 mutant allele was detected in one isolate. Mutation at codon 437 (G437) in the Pfdhps gene was detected in 44.7% of falciparum malaria isolates. Frequencies of Pfdhfr double mutant genotype (I51C59N108I164) and Pfdhfr/Pfdhps triple mutant genotype (I51C59N108I164-S436G437K540) were 82.8 and 39.3%, respectively. One isolate harboured Pfdhfr triple mutant genotype (I51, R59, N108, I164) and Pfdhfr/Pfdhps quadruple mutant genotype (I51R59N108I164-S436G437K540). High frequencies of Pfdhfr and Pfdhps mutant alleles and genotypes in P. falciparum population in Hadhramout, Yemen, highlight the risk of developing resistance for SP, the partner drug of AS, which subsequently will expose the parasite to AS monotherapy increasing then the

  17. Inbreeding and PKU allele frequency: Estimating by microsatellite approaches.

    Science.gov (United States)

    Santos, Luciana L; da Fonseca, Cleusa G; Vaintraub, Marco T; Vaintraub, Patricia; Januário, José N; de Aguiar, Marcos J B; Raquel Santos Carvalho, Maria

    2010-01-01

    Estimates of allele frequencies for recessive diseases are generally based on the frequency of affected individuals (q(2)). However, these estimates can be strongly biased due to inbreeding in the population. The purpose of this study was to gain a better understanding of how inbreeding in the Minas Gerais State population affects phenylketonuria (PKU) incidence in the state and to determine the inbreeding coefficient based on microsatellites. Inbreeding coefficients of samples of 104 controls and 76 patients with PKU were estimated through a microsatellite approach. Besides, the amount and distribution of genetic variation within and among patients with PKU and control samples were characterized. No genetic differentiation was observed between the samples. However, the Fis value found for samples of patients with PKU (0.042) was almost 15 times higher than that found among controls (0.003). When corrected by the inbreeding coefficient found among the controls, the PKU allele frequency decreased to 0.0057. The results enables us to infer that at least 35% of the PKU recessive homozygotes from the Minas Gerais population could be due to consanguineous marriages and suggest that microsatellites can be an useful approach to estimate inbreeding coefficients. (c) 2010 Wiley-Liss, Inc.

  18. Experiments to Demonstrate Change in Allelic Frequency by ...

    Indian Academy of Sciences (India)

    /fulltext/reso/014/11/1110-1118. Keywords. Population genetics; genetic drift; allele frequency. Author Affiliations. N B Ramachandra1 M S Ranjini1. Unit on Evolution and Genetics DOS in Zoology Manasagangotri University of Mysore, India.

  19. Models of frequency-dependent selection with mutation from parental alleles.

    Science.gov (United States)

    Trotter, Meredith V; Spencer, Hamish G

    2013-09-01

    Frequency-dependent selection (FDS) remains a common heuristic explanation for the maintenance of genetic variation in natural populations. The pairwise-interaction model (PIM) is a well-studied general model of frequency-dependent selection, which assumes that a genotype's fitness is a function of within-population intergenotypic interactions. Previous theoretical work indicated that this type of model is able to sustain large numbers of alleles at a single locus when it incorporates recurrent mutation. These studies, however, have ignored the impact of the distribution of fitness effects of new mutations on the dynamics and end results of polymorphism construction. We suggest that a natural way to model mutation would be to assume mutant fitness is related to the fitness of the parental allele, i.e., the existing allele from which the mutant arose. Here we examine the numbers and distributions of fitnesses and alleles produced by construction under the PIM with mutation from parental alleles and the impacts on such measures due to different methods of generating mutant fitnesses. We find that, in comparison with previous results, generating mutants from existing alleles lowers the average number of alleles likely to be observed in a system subject to FDS, but produces polymorphisms that are highly stable and have realistic allele-frequency distributions.

  20. Allele frequencies of 15 autosomal STR loci in the Caymanian population.

    Science.gov (United States)

    Faris, Jonathan S; Tanzillo-Swarts, Angela

    2015-05-01

    Allele frequency distributions in the Caymanian population were determined using the AmpFlSTR® Identifiler® PCR amplification kit. Little evidence of departure from Hardy-Weinberg equilibrium or the association of alleles of different loci was detected. Comparison with relevant population groups supports the Caymanian population having a distinct allelic distribution. The 15 Identifiler® loci provide combined power of discrimination and exclusion values of 0.999999999999999995 and 0.9999992, respectively, proving suitable for the forensic and paternity testing requirements of the Cayman Islands.

  1. Allele frequency analysis of Chinese chestnut ( Castanea mollissima ...

    African Journals Online (AJOL)

    The aim of this study was to establish a method for allele frequency detection in bulk samples. The abundance of polymerase chain reaction (PCR) products in bulk leaf samples was detected using fluorescent labeled Simple sequence repeat (SSR) primers and an Applied biosystems (AB) automatic DNA analyzer.

  2. Allelic Frequency Analysis of Chinese Chestnut (Castanea mollissima)

    African Journals Online (AJOL)

    Chengxiang Ai

    The aim of this study was to establish a method for allele frequency detection in bulk samples. The abundance of polymerase chain reaction (PCR) products in bulk leaf samples was detected using fluorescent labeled Simple sequence repeat (SSR) primers and an Applied biosystems (AB) automatic. DNA analyzer.

  3. Determination of allele frequencies in nine short tandem repeat loci ...

    African Journals Online (AJOL)

    Determination of allele frequencies in nine short tandem repeat loci of five human sub-populations in Botswana. ... use in individual identification. ... Targeted regions of DNA (vWA, FGA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D18S51, D21S11 and the sex determining locus Amelogenin) were amplified using ...

  4. The Rh allele frequencies in Gaza city in Palestine

    Directory of Open Access Journals (Sweden)

    Skaik Younis

    2011-01-01

    Full Text Available Background: The Rh blood group system is the second most clinically significant blood group system. It includes 49 antigens, but only five (D, C, E, c and e are the most routinely identified due to their unique relation to hemolytic disease of the newborn (HDN and transfusion reactions. Frequency of the Rh alleles showed variation, with regard to race and ethnic. Objectives: The purpose of the study was to document the Rh alleles′ frequencies amongst males (M and females (F in Gaza city in Palestine. Materials and Methods: Two hundred and thirty-two blood samples (110 M and 122 F were tested against monoclonal IgM anti-C,anti-c, anti-E, anti-e and a blend of monoclonal/polyclonal IgM/IgG anti-D. The expected Rh phenotypes were calculated using gene counting method. Results: The most frequent Rh antigen in the total sample was e, while the least frequent was E.The order of the combined Rh allele frequencies in both M and F was CDe > cDe > cde > CdE > cDE > Cde > CDE. A significant difference was reported between M and F regarding the phenotypic frequencies (P < 0.05. However, no significance (P > 0.05 was reported with reference to the observed and expected Rh phenotypic frequencies in either M or F students. Conclusion: It was concluded that the Rh antigens, alleles and phenotypes in Gaza city have unique frequencies, which may be of importance to the Blood Transfusion Center in Gaza city and anthropology.

  5. Estimation of allele frequency and association mapping using next-generation sequencing data

    Directory of Open Access Journals (Sweden)

    Andersen Gitte

    2011-06-01

    Full Text Available Abstract Background Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., X. However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates. Results We evaluate a new maximum likelihood method for estimating allele frequencies in low and medium coverage next-generation sequencing data. The method is based on integrating over uncertainty in the data for each individual rather than first calling genotypes. This method can be applied to directly test for associations in case/control studies. We use simulations to compare the likelihood method to methods based on genotype calling, and show that the likelihood method outperforms the genotype calling methods in terms of: (1 accuracy of allele frequency estimation, (2 accuracy of the estimation of the distribution of allele frequencies across neutrally evolving sites, and (3 statistical power in association mapping studies. Using real re-sequencing data from 200 individuals obtained from an exon-capture experiment, we show that the patterns observed in the simulations are also found in real data. Conclusions Overall, our results suggest that association mapping and estimation of allele frequencies should not be based on genotype calling in low to medium coverage data. Furthermore, if genotype calling methods are used, it is usually better not to filter genotypes based on the call confidence score.

  6. How allele frequency and study design affect association test statistics with misrepresentation errors.

    Science.gov (United States)

    Escott-Price, Valentina; Ghodsi, Mansoureh; Schmidt, Karl Michael

    2014-04-01

    We evaluate the effect of genotyping errors on the type-I error of a general association test based on genotypes, showing that, in the presence of errors in the case and control samples, the test statistic asymptotically follows a scaled non-central $\\chi ^2$ distribution. We give explicit formulae for the scaling factor and non-centrality parameter for the symmetric allele-based genotyping error model and for additive and recessive disease models. They show how genotyping errors can lead to a significantly higher false-positive rate, growing with sample size, compared with the nominal significance levels. The strength of this effect depends very strongly on the population distribution of the genotype, with a pronounced effect in the case of rare alleles, and a great robustness against error in the case of large minor allele frequency. We also show how these results can be used to correct $p$-values.

  7. Haptoglobin genotyping of Vietnamese: global distribution of HP del, complete deletion allele of the HP gene.

    Science.gov (United States)

    Soejima, Mikiko; Agusa, Tetsuro; Iwata, Hisato; Fujihara, Junko; Kunito, Takashi; Takeshita, Haruo; Lan, Vi Thi Mai; Minh, Tu Binh; Takahashi, Shin; Trang, Pham Thi Kim; Viet, Pham Hung; Tanabe, Shinsuke; Koda, Yoshiro

    2015-01-01

    The haptoglobin (HP) gene deletion allele (HP(del)) is responsible for anhaptoglobinemia and a genetic risk factor for anaphylaxis reaction after transfusion due to production of the anti-HP antibody. The distribution of this allele has been explored by several groups including ours. Here, we studied the frequency of HP(del) in addition to the distribution of common HP genotypes in 293 Vietnamese. The HP(del) was encountered with the frequency of 0.020. The present result suggested that this deletion allele is restricted to East and Southeast Asians. Thus, this allele seems to be a potential ancestry informative marker for these populations. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  8. FINDbase: a worldwide database for genetic variation allele frequencies updated.

    Science.gov (United States)

    Georgitsi, Marianthi; Viennas, Emmanouil; Antoniou, Dimitris I; Gkantouna, Vassiliki; van Baal, Sjozef; Petricoin, Emanuel F; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P

    2011-01-01

    Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft's PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding.

  9. Determining the frequencies of B1, B2, B3 and E alleles of the ...

    African Journals Online (AJOL)

    The allelic frequencies of the B1, B2, B3 and E alleles were 0.927, 0.073, 0.390, and 0.272, respectively. B1 and B2 alleles did not affect milk yield and composition. B3 allele had significant effects on protein, fat, total solid (TS), solid not fat (SNF), casein and lactose percentages, but not on lactose yield. E allele significantly ...

  10. Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.

    Directory of Open Access Journals (Sweden)

    Ozerov Mikhail

    2013-01-01

    Full Text Available Abstract Background New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS. However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L. populations using an Illumina SNP-chip. Results In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99 between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals can provide accurate allele frequency estimates for a given sample. Conclusions Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost

  11. A new analysis tool for individual-level allele frequency for genomic studies.

    Science.gov (United States)

    Yang, Hsin-Chou; Lin, Hsin-Chi; Huang, Mei-Chu; Li, Ling-Hui; Pan, Wen-Harn; Wu, Jer-Yuarn; Chen, Yuan-Tsong

    2010-07-05

    Allele frequency is one of the most important population indices and has been broadly applied to genetic/genomic studies. Estimation of allele frequency using genotypes is convenient but may lose data information and be sensitive to genotyping errors. This study utilizes a unified intensity-measuring approach to estimating individual-level allele frequencies for 1,104 and 1,270 samples genotyped with the single-nucleotide-polymorphism arrays of the Affymetrix Human Mapping 100K and 500K Sets, respectively. Allele frequencies of all samples are estimated and adjusted by coefficients of preferential amplification/hybridization (CPA), and large ethnicity-specific and cross-ethnicity databases of CPA and allele frequency are established. The results show that using the CPA significantly improves the accuracy of allele frequency estimates; moreover, this paramount factor is insensitive to the time of data acquisition, effect of laboratory site, type of gene chip, and phenotypic status. Based on accurate allele frequency estimates, analytic methods based on individual-level allele frequencies are developed and successfully applied to discover genomic patterns of allele frequencies, detect chromosomal abnormalities, classify sample groups, identify outlier samples, and estimate the purity of tumor samples. The methods are packaged into a new analysis tool, ALOHA (Allele-frequency/Loss-of-heterozygosity/Allele-imbalance). This is the first time that these important genetic/genomic applications have been simultaneously conducted by the analyses of individual-level allele frequencies estimated by a unified intensity-measuring approach. We expect that additional practical applications for allele frequency analysis will be found. The developed databases and tools provide useful resources for human genome analysis via high-throughput single-nucleotide-polymorphism arrays. The ALOHA software was written in R and R GUI and can be downloaded at http://www.stat.sinica.edu.tw/hsinchou/genetics/aloha/ALOHA.htm.

  12. A new analysis tool for individual-level allele frequency for genomic studies

    Directory of Open Access Journals (Sweden)

    Pan Wen-Harn

    2010-07-01

    Full Text Available Abstract Background Allele frequency is one of the most important population indices and has been broadly applied to genetic/genomic studies. Estimation of allele frequency using genotypes is convenient but may lose data information and be sensitive to genotyping errors. Results This study utilizes a unified intensity-measuring approach to estimating individual-level allele frequencies for 1,104 and 1,270 samples genotyped with the single-nucleotide-polymorphism arrays of the Affymetrix Human Mapping 100K and 500K Sets, respectively. Allele frequencies of all samples are estimated and adjusted by coefficients of preferential amplification/hybridization (CPA, and large ethnicity-specific and cross-ethnicity databases of CPA and allele frequency are established. The results show that using the CPA significantly improves the accuracy of allele frequency estimates; moreover, this paramount factor is insensitive to the time of data acquisition, effect of laboratory site, type of gene chip, and phenotypic status. Based on accurate allele frequency estimates, analytic methods based on individual-level allele frequencies are developed and successfully applied to discover genomic patterns of allele frequencies, detect chromosomal abnormalities, classify sample groups, identify outlier samples, and estimate the purity of tumor samples. The methods are packaged into a new analysis tool, ALOHA (Allele-frequency/Loss-of-heterozygosity/Allele-imbalance. Conclusions This is the first time that these important genetic/genomic applications have been simultaneously conducted by the analyses of individual-level allele frequencies estimated by a unified intensity-measuring approach. We expect that additional practical applications for allele frequency analysis will be found. The developed databases and tools provide useful resources for human genome analysis via high-throughput single-nucleotide-polymorphism arrays. The ALOHA software was written in R and R GUI and

  13. GST M1-T1 null allele frequency patterns in geographically assorted human populations: a phylogenetic approach.

    Directory of Open Access Journals (Sweden)

    Senthilkumar Pitchalu Kasthurinaidu

    Full Text Available Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME. Among the XMEs, glutathione-S-transferases (GST gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs. Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs. The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs.

  14. GST M1-T1 null allele frequency patterns in geographically assorted human populations: a phylogenetic approach.

    Science.gov (United States)

    Kasthurinaidu, Senthilkumar Pitchalu; Ramasamy, Thirumurugan; Ayyavoo, Jayachitra; Dave, Dhvani Kirtikumar; Adroja, Divya Anantray

    2015-01-01

    Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs.

  15. GST M1-T1 null Allele Frequency Patterns in Geographically Assorted Human Populations: A Phylogenetic Approach

    Science.gov (United States)

    Ramasamy, Thirumurugan; Ayyavoo, Jayachitra

    2015-01-01

    Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs. PMID:25867025

  16. The role of climate and out-of-Africa migration in the frequencies of risk alleles for 21 human diseases.

    Science.gov (United States)

    Blair, Lily M; Feldman, Marcus W

    2015-07-14

    Demography and environmental adaptation can affect the global distribution of genetic variants and possibly the distribution of disease. Population heterozygosity of single nucleotide polymorphisms has been shown to decrease strongly with distance from Africa and this has been attributed to the effect of serial founding events during the migration of humans out of Africa. Additionally, population allele frequencies have been shown to change due to environmental adaptation. Here, we investigate the relationship of Out-of-Africa migration and climatic variables to the distribution of risk alleles for 21 diseases. For each disease, we computed the regression of average heterozygosity and average allele frequency of the risk alleles with distance from Africa and 9 environmental variables. We compared these regressions to a null distribution created by regressing statistics for SNPs not associated with disease on distance from Africa and these environmental variables. Additionally, we used Bayenv 2.0 to assess the signal of environmental adaptation associated with individual risk SNPs. For those SNPs in HGDP and HapMap that are risk alleles for type 2 diabetes, we cannot reject that their distribution is as expected from Out-of-Africa migration. However, the allelic statistics for many other diseases correlate more closely with environmental variables than would be expected from the serial founder effect and show signals of environmental adaptation. We report strong environmental interactions with several autoimmune diseases, and note a particularly strong interaction between asthma and summer humidity. Additionally, we identified several risk genes with strong environmental associations. For most diseases, migration does not explain the distribution of risk alleles and the worldwide pattern of allele frequencies for some diseases may be better explained by environmental associations, which suggests that some selection has acted on these diseases.

  17. Allele Frequency - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nd 39 SNPs are assayed in three (POP_*) and two (RIKEN_japanese_*) panels, respectively. Derived from Flat f... assay (JBIC-allele and RIKEN_japanese_*), TaqMan assay (RIKEN-allele) or direct sequencing / allelic discri...unteers under informed consent RIKEN_japanese_normal_weight - 711 unrelated japanese normal weight volunteer...s ( body mass index RIKEN_japanese_obese - 796 unrelated japanese obese patients

  18. A new analysis tool for individual-level allele frequency for genomic studies

    OpenAIRE

    Pan Wen-Harn; Li Ling-Hui; Huang Mei-Chu; Lin Hsin-Chi; Yang Hsin-Chou; Wu Jer-Yuarn; Chen Yuan-Tsong

    2010-01-01

    Abstract Background Allele frequency is one of the most important population indices and has been broadly applied to genetic/genomic studies. Estimation of allele frequency using genotypes is convenient but may lose data information and be sensitive to genotyping errors. Results This study utilizes a unified intensity-measuring approach to estimating individual-level allele frequencies for 1,104 and 1,270 samples genotyped with the single-nucleotide-polymorphism arrays of the Affymetrix Human...

  19. Parkinson’s disease and low frequency alleles found together throughout LRRK2

    Science.gov (United States)

    Paisán-Ruiz, Coro; Washecka, Nicole; Nath, Priti; Singleton, Andrew B.; Corder, Elizabeth H.

    2016-01-01

    Mutations within LRRK2, most notably p.G2019S, cause Parkinson’s disease (PD) in rare monogenic families, and sporadic occurrences in diverse populations. We investigated variation throughout LRRK2 (84 SNPs; genotype or diplotype found for 49 LD blocks) for 275 cases (European ancestry, onset at age 60 or older) and 275 neurologically healthy control subjects (NINDS Neurogenetics Repository). Three grade-of-membership groups, i.e. genetic risk sets, were identified that exactly matched many subjects (cases: 46, 4, 137; controls: 0, 178, 0), and distinguished 94% of the subjects (i.e. > 50% likeness to one set). Set I, affected, carried certain low frequency alleles located in multiple functional domains. Set II was unaffected. Set III, also affected, resembled II except for slightly elevated frequencies of minor alleles not defining set I. We conclude that certain low frequency alleles distributed throughout LRRK2 are a genetic background to a third of cases, defining a distinct subset. PMID:19489756

  20. Association of ABO Blood Group Phenotype and Allele Frequency with Chikungunya Fever

    Directory of Open Access Journals (Sweden)

    Pairaya Rujirojindakul

    2015-01-01

    Full Text Available Background. The objective of this study was to investigate the association of the ABO blood group phenotype and allele frequency with CHIK fever. Methods. A rural community survey in Southern Thailand was conducted in August and September 2010. A total of 506 villagers were enrolled. Cases were defined as individuals having anti-CHIK IgG by hemagglutination ≥1 : 10. Results. There were 314 cases (62.1% with CHIK seropositivity. Females were less likely to have positive anti-CHIK IgG with odds ratio (OR (95% CI of 0.63 (0.43, 0.93. All samples tested were Rh positive. Distribution of CHIK seropositivity versus seronegativity (P value in A, B, AB, and O blood groups was 80 versus 46 (0.003, 80 versus 48 (0.005, 24 versus 20 (0.55, and 130 versus 78 (<0.001, respectively. However, chi-square test between ABO and CHIK infection showed no statistical significance P=0.76. Comparison of the ABO blood group allele frequency between CHIK seropositivity and seronegativity was not statistically significant. Conclusion. This finding demonstrated no association of the ABO blood group phenotypes and allele frequencies with CHIK infection.

  1. Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project.

    Science.gov (United States)

    Cross, Deanna S; Ivacic, Lynn C; Stefanski, Elisha L; McCarty, Catherine A

    2010-06-17

    There is a lack of knowledge regarding the frequency of disease associated polymorphisms in populations and population attributable risk for many populations remains unknown. Factors that could affect the association of the allele with disease, either positively or negatively, such as race, ethnicity, and gender, may not be possible to determine without population based allele frequencies.Here we used a panel of 51 polymorphisms previously associated with at least one disease and determined the allele frequencies within the entire Personalized Medicine Research Project population based cohort. We compared these allele frequencies to those in dbSNP and other data sources stratified by race. Differences in allele frequencies between self reported race, region of origin, and sex were determined. There were 19544 individuals who self reported a single racial category, 19027 or (97.4%) self reported white Caucasian, and 11205 (57.3%) individuals were female. Of the 11,208 (57%) individuals with an identifiable region of origin 8337 or (74.4%) were German.41 polymorphisms were significantly different between self reported race at the 0.05 level. Stratification of our Caucasian population by self reported region of origin revealed 19 polymorphisms that were significantly different (p = 0.05) between individuals of different origins. Further stratification of the population by gender revealed few significant differences in allele frequencies between the genders. This represents one of the largest population based allele frequency studies to date. Stratification by self reported race and region of origin revealed wide differences in allele frequencies not only by race but also by region of origin within a single racial group. We report allele frequencies for our Asian/Hmong and American Indian populations; these two minority groups are not typically selected for population allele frequency detection. Population wide allele frequencies are important for the design and

  2. Allele frequency present within the DYS635, DYS437, DYS448 ...

    African Journals Online (AJOL)

    Ejiro

    2015-03-11

    Mar 11, 2015 ... science and criminology and to let evaluate and present the DNA weight evidences in Iraq medico-legal institute and courts of .... Standard error (SE). The standard error (SE) of allele frequencies was calculated as: Where, pi denotes the frequency of the ith allele at any given locus and N equals the total ...

  3. Experiments to Demonstrate Change in Allelic Frequency by ...

    Indian Academy of Sciences (India)

    Admin

    a number of factors such as migration from or to other populations, mutation, selection and random ... beneficial, neutral, or detrimental to reproductive success. The statistical effect of sampling error ... original population, and through the random sampling of alleles during reproduction of sub- sequent generations, continue ...

  4. AB0 blood subgroup allele frequencies in the Turkish population.

    Science.gov (United States)

    Akbas, Fahri; Aydin, Müge; Cenani, Asim

    2003-09-01

    We determined the AB0 blood group system with a PCR based technique termed APLP (Amplified Product Length Polymorphism) in the Turkish population. The method includes ten different allele specific primers and permits identification of the major AB0 genotypes and its suballeles (A1-A2-B-0A-02-0G-AG). The suballeles were amplified in a single tube reaction. We have determined AB0 phenotypes in 129 Turkish individuals. No significant deviation from the Hardy-Weinberg equilibrium was observed.

  5. Geographic distributions of Idh-1 alleles in a cricket are linked to differential enzyme kinetic performance across thermal environments

    Directory of Open Access Journals (Sweden)

    Huestis Diana L

    2009-05-01

    Full Text Available Abstract Background Geographic clines within species are often interpreted as evidence of adaptation to varying environmental conditions. However, clines can also result from genetic drift, and these competing hypotheses must therefore be tested empirically. The striped ground cricket, Allonemobius socius, is widely-distributed in the eastern United States, and clines have been documented in both life-history traits and genetic alleles. One clinally-distributed locus, isocitrate dehydrogenase (Idh-1, has been shown previously to exhibit significant correlations between allele frequencies and environmental conditions (temperature and rainfall. Further, an empirical study revealed a significant genotype-by-environmental interaction (GxE between Idh-1 genotype and temperature which affected fitness. Here, we use enzyme kinetics to further explore GxE between Idh-1 genotype and temperature, and test the predictions of kinetic activity expected under drift or selection. Results We found significant GxE between temperature and three enzyme kinetic parameters, providing further evidence that the natural distributions of Idh-1 allele frequencies in A. socius are maintained by natural selection. Differences in enzyme kinetic activity across temperatures also mirror many of the geographic patterns observed in allele frequencies. Conclusion This study further supports the hypothesis that the natural distribution of Idh-1 alleles in A. socius is driven by natural selection on differential enzymatic performance. This example is one of several which clearly document a functional basis for both the maintenance of common alleles and observed clines in allele frequencies, and provides further evidence for the non-neutrality of some allozyme alleles.

  6. Evolutionary control: Targeted change of allele frequencies in natural populations using externally directed evolution.

    Science.gov (United States)

    Shafiey, Hassan; Gossmann, Toni I; Waxman, David

    2017-04-21

    Random processes in biology, in particular random genetic drift, often make it difficult to predict the fate of a particular mutation in a population. Using principles of theoretical population genetics, we present a form of biological control that ensures a focal allele's frequency, at a given locus, achieves a prescribed probability distribution at a given time. This control is in the form of an additional evolutionary force that acts on a population. We provide the mathematical framework that determines the additional force. Our analysis indicates that generally the additional force depends on the frequency of the focal allele, and it may also depend on the time. We argue that translating this additional force into an externally controlled process, which has the possibility of being implemented in a number of different ways corresponding to selection, migration, mutation, or a combination of these, may provide a flexible instrument for targeted change of traits of interest in natural populations. This framework may be applied, or used as an informed form of guidance, in a variety of different biological scenarios including: yield and pesticide optimisation in crop production, biofermentation, the local regulation of human-associated natural populations, such as parasitic animals, or bacterial communities in hospitals. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Global Multihazard Frequency and Distribution

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Multihazard Frequency and Distribution is a 2.5 minute grid presenting a simple multihazard index based solely on summated single-hazard decile values. The...

  8. HLA Class I Allele Frequencies in Southern Iranian Women with Breast Cancer.

    Science.gov (United States)

    Razmkhah, Mahboobeh; Ghaderi, Abbas

    2013-02-01

    Breast cancer is the leading cause of cancer-related death in women worldwide. It has been revealed that elevated risk for malignancy may be associated with certain HLA alleles. This study was performed to assess the association of HLA class I alleles with breast cancer in women in Southern Iran. Eighty nine patients included for analyzing the HLA class I alleles frequency using complement dependent cytotoxicity microassay and results were compared to 86 gender-matched healthy volunteers. There were significantly more patients with A24(9) allele than those of healthy individuals (38.2% versus 16.3%) (P-value=0.002). In contrast, HLA-A1 had significantly much less expression in the patient group compared to the controls (P- value=0.04). A24(9) allele appears to be one of the factors increasing an individual's the susceptibility to breast cancer in our population but further investigation might be required.

  9. Experiments to Demonstrate Change in Allelic Frequency by ...

    Indian Academy of Sciences (India)

    Admin

    a number of factors such as migration from or to other populations, mutation, selection and random changes caused by small size of population. Genetic Drift is a random, non-adaptive change in gene frequencies in small populations. Sewall Wright, one of the giants in synthesizing the modern theory of evolution, was the.

  10. Allele and genotype frequencies of -β lactoglobulin gene in Iranian ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... marker systems. β-Lactoglobulin is the major milk whey protein in the ruminants. Studies have indicated that ... Najdi cattle and buffalo. The genotype frequencies of AA, AB, and BB in Najdi cattle and buffalo were 0, ... Agarose (2.5%) electrophoresis patterns of 247 bp PCR products of β- lactoglobulin gene ...

  11. Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

    NARCIS (Netherlands)

    Oddou-Muratorio, S.; Vendramin, G.G.; Buiteveld, J.; Fady, B.

    2009-01-01

    Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite

  12. Allelic structure and distribution of 103 STR loci in a Southern ...

    Indian Academy of Sciences (India)

    Unknown

    In particular, the use of DNA typing systems in forensic identification has been criticized, in part, on the grounds that the calculations used for asses- sing likelihood of matches were allele frequency depen- dent, which raised the question of what constituted a proper reference population for determining allele frequencies.

  13. Influence of admixture components on CYP2C9*2 allele frequency in eight indigenous populations from Northwest Mexico.

    Science.gov (United States)

    Sosa-Macías, M; Lazalde-Ramos, B P; Galaviz-Hernández, C; Rangel-Villalobos, H; Salazar-Flores, J; Martínez-Sevilla, V M; Martínez-Fierro, M L; Dorado, P; Wong, M L; Licinio, J; LLerena, A

    2013-12-01

    We previously documented the lowest frequency of CYP2C9*2 in Mexican indigenous Tepehuanos followed by Mestizos and Mexican-Americans populations, suggesting a negative correlation between the CYP2C9*2 frequency and the degree of Asian ancestry in indigenous Americans. We determined the influence of ethnic admixture components on the CYP2C9 allele distribution in 505 Amerindian from eight indigenous populations through genotyping CYP2C9*2, *3 and *6 alleles by real-time PCR and molecular evaluation of ancestry. The frequencies for CYP2C9*2 were 0.026 in Seris and 0.057 in Mayos, being higher than in Asians (PHuicholes (0.033) and Coras (0.037), with East Asians having lower frequencies than the former three groups (P<0.001). CYP2C9*6 was not found. The frequency of CYP2C9*2 was lower in Amerindians than in European populations, and higher than their Asian ancestors. The presence of this allele in ethnic groups in Mexico can be explained by European admixture.

  14. High frequency of intermediate alleles on Huntington disease-associated haplotypes in British Columbia's general population.

    Science.gov (United States)

    Semaka, Alicia; Kay, Chris; Doty, Crystal N; Collins, Jennifer A; Tam, Natalie; Hayden, Michael R

    2013-12-01

    Intermediate alleles (27-35 CAG, IAs) for Huntington disease (HD) usually do not confer the disease phenotype but are prone to CAG repeat instability. Consequently, offspring are at-risk of inheriting an expanded allele in the HD range (≥36 CAG). IAs that expand into a new mutation have been hypothesized to be more susceptible to instability compared to IAs identified on the non-HD side of a family from the general population. Frequency estimates for IAs are limited and have largely been determined using clinical samples of HD or related disorders, which may result in an ascertainment bias. This study aimed to establish the frequency of IAs in a sample of a British Columbia's (B.C.) general population with no known association to HD and examine the haplotype of new mutation and general population IAs. CAG sizing was performed on 1,600 DNA samples from B.C.'s general population. Haplotypes were determined using 22 tagging SNPs across the HTT gene. 5.8% of individuals were found to have an IA, of which 60% were on HD-associated haplotypes. There was no difference in the haplotype distribution of new mutation and general population IAs. These findings suggest that IAs are relatively frequent in the general population and are often found on haplotypes associated with expanded CAG lengths. There is likely no difference in the propensity of new mutation and general population IAs to expand into the disease range given that they are both found on disease-associated haplotypes. These findings have important implications for clinical practice. © 2013 Wiley Periodicals, Inc.

  15. Genetic Variability and Distribution of Mating Type Alleles in Field Populations of Leptosphaeria maculans from France

    Science.gov (United States)

    Gout, Lilian; Eckert, Maria; Rouxel, Thierry; Balesdent, Marie-Hélène

    2006-01-01

    Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used. PMID:16391041

  16. Low frequency of the scrapile resistance-associated allele and presence of lysine-171 allele of the prion protein gene in Italian Biellese ovine breed

    NARCIS (Netherlands)

    Acutis, P.L.; Sbaiz, L.; Verburg, F.J.; Riina, M.V.; Ru, G.; Moda, G.; Caramelli, M.; Bossers, A.

    2004-01-01

    Frequencies of polymorphisms at codons 136, 154 and 171 of the prion protein (PrP) gene were studied in 1207 pure-bred and cross-bred Italian Biellese rams, a small ovine breed of about 65 000 head in Italy. Aside from the five most common alleles (VRQ, ARQ, ARR, AHQ and ARH), the rare ARK allele

  17. Distribution and frequency of phenylthiocarbamide (PTC) taster and ...

    African Journals Online (AJOL)

    There is limited information on population genetics of the Nigerian population as regards taste perception. This study investigated the distribution and frequency of taster (T) and non-taster (t) alleles in the Nigerian population using phenylthiocarbamide [(PTC), % composition = 30 mcg/strip] taste strips. Overall, a total of ...

  18. Differences in genotype and allele frequency distributions of polymorphic drug metabolizing enzymes CYP2C19 and CYP2D6 in mainland Chinese Mongolian, Hui and Han populations.

    Science.gov (United States)

    Yin, S-J; Ni, Y-B; Wang, S-M; Wang, X; Lou, Y-Q; Zhang, G-L

    2012-06-01

    Cytochrome P450 2C19 (CYP2C19) and CYP2D6 are important xenobiotic metabolic enzymes and both show considerable genetic variability between Orientals and Caucasians. There are known marked heterogeneity in susceptibility to various cancers and hypertension among Chinese Mongolian, Hui and Han ethnic groups, but the molecular mechanisms are unknown. Our objective was to investigate the patterns of distribution of CYP2C19 and CYP2D6 polymorphisms among healthy Chinese subjects to determine whether any observed inter-ethnic variability might be worth further investigation as possible contributors to the known differences in disease prevalence. Blood samples were collected from 454 unrelated Chinese healthy subjects (214 Han, 111 Hui, 129 Mongolian) for genotyping analysis. The single nucleotide polymorphisms (SNPs) CYP2C19*2 (681G>A in exon 5), CYP2C19*3 (636G>A in exon 4) and CYP2D6*10 (188C>T in exon 1) were determined by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Significantly higher frequencies of the CYP2C19 poor metabolic genotypes were observed in Chinese Han (18·7%), Chinese Hui (25·0%) and Chinese Mongolian (10·9%) subjects than has been reported for Caucasians (1·7-3·0%, P Hui (32·4%) and Han (29·7%) than in Chinese Mongolian (18·2%, P Hui ethnic groups than have been reported for Caucasians (11·1-16·3% and 0-0·2%, P Hui (40·6% and 30·7%) and Mongolian subjects (31·3% and 9·6%, both P Hui and Han populations. These differences may be important in explaining reported inter-ethnic differences in disease prevalence and response to drugs. © 2011 Blackwell Publishing Ltd.

  19. Genotype and allelic frequencies of CYP2E1*5B polymorphism in the southwest population of Iran

    Directory of Open Access Journals (Sweden)

    Fatemeh Zanganeh

    2014-10-01

    Full Text Available Background: Cytochrome P450 2E1 (CYP2E1 is a main enzyme which plays a major role in activating and detoxifying many xenobiotics, carcinogens and drugs. Available studies suggest that CYP2E1 single nucleotide polymorphisms (SNPs are involved in the risk of developing certain cancers after exposure to carcinogens. The purpose of the present study was to assess genotype and allele frequencies of polymorphic CYP2E1*5B in the Iranian population. Material and Methods: This study was performed on 200 healthy individuals (female: 100, male: 100 in medical laboratories of Ahvaz during 2011. The CYP2E1 *5B (rs3813867 G-1293C assessment was carried out using PCR-RFLP method. The data were analyzed with ĸ2 and hardy-Weinberg Equation statistically methods. Results: The frequency of *1A/*1A (c1/c1, *1A/*5B (c1/c2 and *5B/*5B (c2/c2 genotypes was computed 97, 3 and 0 percent, respectively. The frequency of *1A (c1 and *5B (c2 alleles was computed 98.5 and 1.5 percent, respectively. No statistically significant difference was between two genders (p>0.05. Conclusion: The genotype distribution and allele frequencies of CYP2E1*5B polymorphism were similar to Turkish and some of the European populations. However, there are significant interethnic differences when the Iranian population is compared with the Eastern Asian, American and some of the European populations. The allelic distribution of this polymorphism did not vary with gender.

  20. Cytochrome P450 2D6 variants in a Caucasian population: Allele frequencies and phenotypic consequences

    Energy Technology Data Exchange (ETDEWEB)

    Sachse, C.; Brockmoeller, J.; Bauer, S.; Roots, I. [Humboldt Univ., Berlin (Germany)

    1997-02-01

    Cytochrome P450 2D6 (CYP2D6) metabolizes many important drugs. CYP2D6 activity ranges from complete deficiency to ultrafast metabolism, depending on at least 16 different known alleles. Their frequencies were determined in 589 unrelated German volunteers and correlated with enzyme activity measured by phenotyping with dextromethorphan or debrisoquine. For genotyping, nested PCR-RFLP tests from a PCR amplificate of the entire CYP2D6 gene were developed. The frequency of the CYP2D6*1 allele coding for extensive metabolizer (EM) phenotype was .364. The alleles coding for slightly (CYP2D6*2) or moderately (*9 and *10) reduced activity (intermediate metabolizer phenotype [IM]) showed frequencies of .324, .018, and .015, respectively. By use of novel PCR tests for discrimination, CYP2D6 gene duplication alleles were found with frequencies of.005 (*1 x 2), .013 (* 2 x 2), and .001 (*4 x 2). Frequencies of alleles with complete deficiency (poor metabolizer phenotype [PM]) were .207 (*4), .020 (*3 and *5), .009 (*6), and .001 (*7, *15, and *16). The defective CYP2D6 alleles *8, *11, *12, *13, and *14 were not found. All 41 PMs (7.0%) in this sample were explained by five mutations detected by four PCR-RFLP tests, which may suffice, together with the gene duplication test, for clinical prediction of CYP2D6 capacity. Three novel variants of known CYP2D6 alleles were discovered: *1C (T{sub 1957}C), *2B (additional C{sub 2558}T), and *4E (additional C{sub 2938}T). Analysis of variance showed significant differences in enzymatic activity measured by the dextromethorphan metabolic ratio (MR) between carriers of EN/PM (mean MR = .006) and IM/PM (mean MR = .014) alleles and between carriers of one (mean MR = .009) and two (mean MR = .003) functional alleles. The results of this study provide a solid basis for prediction of CYP2D6 capacity, as required in drug research and routine drug treatment. 35 refs., 4 figs., 5 tabs.

  1. Microsatellite D21D210 (GT-12) allele frequencies in sporadic Alzheimer's disease

    International Nuclear Information System (INIS)

    Lannfelt, L.; Lilius, L.; Viitanen, M.; Winblad, B.; Basun, H.; Houlden, H.; Rossor, M.; Hardy, J.

    1995-01-01

    Four disease-causing mutations have so far been described in the amyloid precursor protein gene on chromosome 21 in familial early-onset Alzheimer's disease. Linkage analysis with a fourteen-allele microsatellite at D21S210 named GT-12 has proven useful in the elucidation of amyloid presursor protein gene involvement in Alzheimer's disease families, as it is closely linked to the gene. Most cases of Alzheimer's disease are thought to be sporadic and not familial. However, evidence from earlier studies suggests an important genetic contribution also in sporadic cases, where gene-environment interaction may contribute to the disease. We have determined frequencies of the GT-12 alleles in 78 Swedish and 49 British sporadic Alzheimer's disease cases and 104 healthy elderly control subjects, to investigate if the disease associates with a particular genotype in GT-12. However, no differences in allele frequencies were observed between any of the groups. (au) (26 refs.)

  2. Allelic structure and distribution of 103 STR loci in a Southern ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 83; Issue 1. Allelic structure and distribution of 103 STR loci in a Southern Tunisian population. Abdellatif ... This demonstrated that in spite of a high inbreeding level in the population, few markers showed evidence for a different pattern of allelic distribution compared to CEPH.

  3. A Theoretical Framework for Association Studies in F2 Family Pools Using Allele Frequencies from Genotyping-By-Sequencing

    DEFF Research Database (Denmark)

    Janss, Luc L; Ashraf, Bilal H; Greve-Pedersen, Morten

    a sequencing approach to obtain Single Nucleotide Polymorphisms (SNPs) frequencies is considered here. In this work we develop the theoretical framework to perform association studies using allele frequencies from such F2 family pools. We show that expected allele frequencies in the F2 families will have...

  4. Huntington disease reduced penetrance alleles occur at high frequency in the general population

    Science.gov (United States)

    Kay, Chris; Collins, Jennifer A.; Miedzybrodzka, Zosia; Madore, Steven J.; Gordon, Erynn S.; Gerry, Norman; Davidson, Mark; Slama, Ramy A.

    2016-01-01

    Objective: To directly estimate the frequency and penetrance of CAG repeat alleles associated with Huntington disease (HD) in the general population. Methods: CAG repeat length was evaluated in 7,315 individuals from 3 population-based cohorts from British Columbia, the United States, and Scotland. The frequency of ≥36 CAG alleles was assessed out of a total of 14,630 alleles. The general population frequency of reduced penetrance alleles (36–39 CAG) was compared to the prevalence of patients with HD with genetically confirmed 36–39 CAG from a multisource clinical ascertainment in British Columbia, Canada. The penetrance of 36–38 CAG repeat alleles for HD was estimated for individuals ≥65 years of age and compared against previously reported clinical penetrance estimates. Results: A total of 18 of 7,315 individuals had ≥36 CAG, revealing that approximately 1 in 400 individuals from the general population have an expanded CAG repeat associated with HD (0.246%). Individuals with CAG 36–37 genotypes are the most common (36, 0.096%; 37, 0.082%; 38, 0.027%; 39, 0.000%; ≥40, 0.041%). General population CAG 36–38 penetrance rates are lower than penetrance rates extrapolated from clinical cohorts. Conclusion: HD alleles with a CAG repeat length of 36–38 occur at high frequency in the general population. The infrequent diagnosis of HD at this CAG length is likely due to low penetrance. Another important contributing factor may be reduced ascertainment of HD in those of older age. PMID:27335115

  5. Frequency of Cry1F resistance alleles in Spodoptera frugiperda (Lepidoptera: Noctuidae) in Brazil.

    Science.gov (United States)

    Farias, Juliano R; Andow, David A; Horikoshi, Renato J; Bernardi, Daniel; Ribeiro, Rebeca da S; Nascimento, Antonio Rb do; Santos, Antonio C Dos; Omoto, Celso

    2016-12-01

    The frequency of resistance alleles is a major factor influencing the rate of resistance evolution. Here, we adapted the F 2 screen procedure for Spodoptera frugiperda (J. E. Smith) with a discriminating concentration assay, and extended associated statistical methods to estimate the frequency of resistance to Cry1F protein in S. frugiperda in Brazil when resistance was not rare. We show that F 2 screen is efficient even when the resistance frequency is 0.250. It was possible to screen 517 isoparental lines from 12 populations sampled in five states of Brazil during the first half of 2012. Western Bahia had the highest allele frequency of Cry1F resistance, 0.192, with a 95% confidence interval (CI) between 0.163 and 0.220. All other states had a similar and lower frequency varying from 0.042 in Paraná to 0.080 in Mato Grosso do Sul. The high frequency in western Bahia may be related to year-round availability of maize, the high population density of S. frugiperda, the lack of refuges and the high adoption rate of Cry1F maize. Cry1F resistance alleles were not rare and occurred at frequencies that have already compromised the useful life of TC1507 maize in western Bahia. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  6. Frequency of CCR5Δ32 allele in healthy Bosniak population.

    Directory of Open Access Journals (Sweden)

    Grażyna Adler

    2014-08-01

    Full Text Available Recent evidence has demonstrated the role of CCR5Δ32 in a variety of human diseases: from infectious and inflammatory diseases to cancer. Several studies have confirmed that genetic variants in chemokine receptor CCR5 gene are correlated with susceptibility and resistance to HIV infection. A 32-nucleotide deletion within the CCR5 reading frame is associated with decreased susceptibility to HIV acquisition and a slower progression to AIDS. Mean frequency of CCR5Δ32 allele in Europe is approximately 10%. The highest allele frequency is observed among Nordic populations (about 12% and lower in the regions of Southeast Mediterranean (about 5%. Although the frequency of CCR5Δ32 was determined in numerous European populations, there is a lack of studies on this variant in the Bosnia and Hercegovina population. Therefore, the aim of our study was to assess the frequency of CCR5Δ32 allele in the cohort of Bosniaks and compare the results with European reports. CCR5Δ32 was detected by sequence-specific PCR in a sample of 100 healthy subjects from Bosnia and Herzegovina (DNA collected 2011-2013.  Mean age of the cohort being 58.8 (±10.7 years, with 82% of women. We identified 17 heterozygotes and one mutant homozygote in study group, with mean ∆32 allele frequency of 9.5%. CCR5∆32 allele frequency among Bosniaks is comparable to that found in Caucasian populations and follows the pattern of the north-southern gradient observed for Europe. Further studies on larger cohorts with adequate female-to-male ratio are necessary. 

  7. Allele frequencies of ten short tandem repeats loci in the central ...

    Indian Academy of Sciences (India)

    2009-04-03

    Apr 3, 2009 ... c Indian Academy of Sciences. RESEARCH NOTE. Allele frequencies of ten short tandem ... Statistical parameters of forensic importance, the power of discrimination (PD), observed and expected ... rameters indicated the usefulness of the loci in forensic per- sonal identification and paternity testing among ...

  8. Determining the frequencies of B1, B2, B3 and E alleles of the ...

    African Journals Online (AJOL)

    Ada

    2016-06-04

    Jun 4, 2016 ... AN, and AF) in Alpine, Saanen and Toggenburg goats (Vázquez-Flores et al., 2012). Despite the number of studies that determined the frequency of CSN1S1 alleles, investigations into the effects of the CSN1S1 gene on milk yield and composition are limited. Furthermore, there is no published information ...

  9. SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Korneliussen, Thorfinn Sand; Albrechtsen, Anders

    2012-01-01

    is calculated using a dynamic programming algorithm and numerically optimized using analytical derivatives. We then use a bayesian method for estimating the sample allele frequency in a single site, and show how the method can be used for genotype calling and SNP calling. We also show how the method can...

  10. Gene frequencies of ABO and Rh(D) blood group alleles in Lagos ...

    African Journals Online (AJOL)

    Subjects and methods: This study investigated the gene frequencies for the ABO and Rh(D) alleles in a population consisting of different ages in Lagos, Nigeria, over a period spanning 12 years (1998–2009). The 23,832 and 23,764 individuals were typed for ABO and Rh blood groups, respectively. We analyzed the ...

  11. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly.

    Science.gov (United States)

    Fountain, Toby; Nieminen, Marko; Sirén, Jukka; Wong, Swee Chong; Lehtonen, Rainer; Hanski, Ilkka

    2016-03-08

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.

  12. Phenotypic and allelic distribution of the ABO and Rhesus (D) blood groups in the Cameroonian population.

    Science.gov (United States)

    Ndoula, S T; Noubiap, J J N; Nansseu, J R N; Wonkam, A

    2014-06-01

    Data on blood group phenotypes are important for blood transfusion programs, for disease association and population genetics studies. This study aimed at reporting the phenotypic and allelic distribution of ABO and Rhesus (Rh) groups in various ethnolinguistic groups in the Cameroonians. We obtained ABO and Rhesus blood groups and self-identified ethnicity from 14,546 Cameroonian students. Ethnicity was classified in seven major ethnolinguistic groups: Afro-Asiatic, Nilo-Saharan, Niger-Kordofanian/West Atlantic, Niger-Kordofanian/Adamawa-Ubangui, Niger-Kordofanian/Benue-Congo/Bantu/Grassfield, Niger-Kordofanian/Benue-Congo/Bantu/Mbam and Niger-Kordofanian/Benue-Congo/Bantu/Equatorial. ABO allelic frequencies were determined using the Bernstein method. Differences in phenotypic distribution of blood groups were assessed using the chi-square test; a P value blood groups O, A, B and AB were 48.62%, 25.07%, 21.86% and 4.45%, respectively. Rhesus-positive was 96.32%. The allelic frequencies of O, A and B genes were 0.6978, 0.1605 and 0.1416, respectively. Phenotypic frequencies of the blood groups in the general study population and in the different ethnolinguistic groups were in agreement with Hardy-Weinberg equilibrium expectations (P > 0.05). The frequencies of O, A, and B blood phenotypes were significantly lower, respectively, in the Nilo-Saharan group (P = 0.009), the Niger-Kordofanian/Benue-Congo/Bantu groups (P = 0.021) and the Niger-Kordofanian/West-Atlantic group. AB blood group was most frequent in the Niger-Kordofanian/Adamawa-Ubangui group (P = 0.024). Our study provides the first data on ethnic distribution of ABO and Rhesus blood groups in the Cameroonian population and suggests that its general profile is similar to those of several sub-Saharan African populations. We found some significant differences in phenotypic distribution amongst major ethnolinguistic groups. These data may be important for blood donor recruitment policy and blood transfusion

  13. Distribution of a pseudodeficiency allele among Tay-Sachs carriers

    Energy Technology Data Exchange (ETDEWEB)

    Tomczak, J.; Grebner, E.E. (Thomas Jefferson Univ., Philadelphia, PA (United States)); Boogen, C. (Univ. of Essen Medical School (Germany))

    1993-08-01

    Recently Triggs-Raine et al. (1992) identified a new mutation in the gene coding for the [alpha]-subunit of [beta]-hexosaminidase A (hex A), the enzyme whose deficiency causes Tay-Sachs disease. This mutation, a C[sub 739]-to-T transition in exon 7, results in an altered enzyme that is active (albeit at reduced levels) in cells but that has essentially no activity in serum. This so-called pseudodeficient allele was first detected in compound heterozygotes who also carried a Tay-Sachs disease allele and therefore had no detectable hex A in their serum but who were in good health. Carriers of this apparently benign mutation are generally indistinguishable from carriers of a lethal mutation by means of routine enzyme-based screening tests, because the product of the pseudodeficient allele is not detectable in serum and has decreased activity in cells. This suggests that some individuals who have been classified as Tay-Sachs carriers are actually carriers of the pseudodeficient allele and are not at risk to have a child affected with Tay-Sachs disease. The pseudodeficient allele may also be responsible for some inconclusive diagnoses, where leukocyte values fall below the normal range but are still above the carrier range. The fact that there are now two mutant alleles (the psuedodeficient and the adult) that are indistinguishable from the lethal infantile mutations by means of enzyme assay yet that are phenotypically very different and that together may account for as much as 12% of enzyme-defined carriers on the basis of the data here suggests that DNA analysis should be part of a comprehensive screening program. It will be particularly useful to identify the mutations in couples at risk, before they undergo prenatal diagnosis. DNA analysis will also resolve some inconclusive diagnoses.

  14. Frequency of the CCR5-delta32 allele in Brazilian populations: A systematic literature review and meta-analysis.

    Science.gov (United States)

    Silva-Carvalho, Wlisses Henrique Veloso; de Moura, Ronald Rodrigues; Coelho, Antonio Victor Campos; Crovella, Sergio; Guimarães, Rafael Lima

    2016-09-01

    The CCR5 is a chemokine receptor widely expressed by several immune cells that are engaged in inflammatory responses. Some populations have individuals exhibiting a 32bp deletion in the CCR5 gene (CCR5-delta32) that produces a truncated non-functional protein not expressed on the cell surface. This polymorphism, known to be associated with susceptibility to infectious and inflammatory diseases, such as osteomyelitis, pre-eclampsia, systemic lupus erythematous, juvenile idiopathic arthritis, rheumatoid arthritis and HIV/AIDS, is more commonly found in European populations with average frequency of 10%. However, it is also possible to observe a significant frequency in other world populations, such as the Brazilian one. We performed a systematic review and meta-analysis of CCR5-delta32 genetic association studies in Brazilian populations throughout the country to estimate the frequency of this polymorphism. We also compared CCR5-delta32 frequencies across Brazilian regions. The systematic literature reviewed studies involving delta32 allele in Brazilian populations published from 1995 to 2015. Among the reviewed literature, 25 studies including 30 Brazilian populations distributed between the North, Northeast, South and Southeast regions were included in our meta-analysis. We observed an overall allelic frequency of 4% (95%-CI, 0.03-0.05), that was considered moderate and, notably, higher than some European populations, such as Cyprus (2.8%), Italy (3%) and Greece (2.4%). Regarding the regional frequency comparisons between North-Northeast (N-NE) and South-Southeast (S-SE) regions, we observed an allelic frequency of 3% (95%-CI, 0.02-0.04) and 4% (95%-CI, 0.03-0.05), respectively. The populations from S-SE regions had a slightly higher CCR5-delta32 frequency than N-NE regions (OR=1.41, p=0.002). Although there are several studies about the CCR5-delta32 polymorphism and its effect on the immune response of some infectious diseases, this report is the first meta

  15. Distribution of HIV-1 resistance-conferring polymorphic alleles SDF ...

    Indian Academy of Sciences (India)

    ... number of mutant alleles (for the three loci together) carried by each individual varies from 0.475 (in Vizag Brahmins) to 0.959 (in Bohra Muslims). The estimated relative hazard values for the populations, computed from the three-locus genotype data, are comparable to those from Africa and Southeast Asia, where AIDS is ...

  16. Association between population structure and allele frequencies of the glycogen synthase 1 mutation in the Austrian Noriker draft horse.

    Science.gov (United States)

    Druml, T; Grilz-Seger, G; Neuditschko, M; Brem, G

    2017-02-01

    The aim of this study was to determine the allele frequency of the glycogen synthase 1 (GYS1) mutation associated with polysaccharide storage myopathy type 1 in the Austrian Noriker horse. Furthermore, we examined the influence of population substructures on the allele distribution. The study was based upon a comprehensive population sample (208 breeding stallions and 309 mares) and a complete cohort of unselected offspring from the year 2014 (1553 foals). The mean proportion of GYS1 carrier animals in the foal cohort was 33%, ranging from 15% to 50% according to population substructures based on coat colours. In 517 mature breeding horses the mutation carrier frequency reached 34%, ranging on a wider scale from 4% to 62% within genetic substructures. We could show that the occurrence of the mutated GYS1 allele is influenced by coat colour; genetic bottlenecks; and assortative, rotating and random mating strategies. Highest GYS1 carrier frequencies were observed in the chestnut sample comprising 50% in foals, 54% in mares and 62% in breeding stallions. The mean inbreeding of homozygous carrier animals reached 4.10%, whereas non-carrier horses were characterized by an inbreeding coefficient of 3.48%. Lowest GYS1 carrier frequencies were observed in the leopard spotted Noriker subpopulation. Here the mean carrier frequency reached 15% in foals, 17% in mares and 4% in stallions and inbreeding decreased from 3.28% in homozygous non-carrier horses to 2.70% in heterozygous horses and 0.94% in homozygous carriers. This study illustrates that lineage breeding and specified mating strategies result in genetic substructures, which affect the frequencies of the GYS1 gene mutation. © 2016 Stichting International Foundation for Animal Genetics.

  17. Allele frequencies of AVPR1A and MAOA in the Afrikaner population

    Directory of Open Access Journals (Sweden)

    J. Christoff Erasmus

    2015-07-01

    Full Text Available The Afrikaner population was founded mainly by European immigrants that arrived in South Africa from 1652. However, female slaves from Asia and Africa and local KhoeSan women may have contributed as much as 7% to this population’s genes. We quantified variation at two tandem repeats to see if this historical founder effect and/or admixture could be detected. The two loci were chosen because they are in the promoters of genes of neurotransmitters that are known to be correlated with social behaviour. Specifically, arginine vasopressin receptor 1A’s (AVPR1A RS3 locus has been shown to correlate with age of sexual onset and happiness in monogamous relationships while the tandem repeat in the promoter of the monoamine oxidase A (MAOA gene correlates with reactive aggression. The Afrikaner population contained more AVPR1A RS3 alleles than other Caucasoid populations, potentially reflecting a history of admixture. Even though Afrikaners have one of the lowest recorded non-paternity rates in the world, the population did not differ at AVPR1A RS3 locus form other European populations, suggesting a non-genetic explanation, presumably religion, for the low non-paternity rate. By comparing population allele-frequency spectra it was found that different studies have confused AVPR1A RS3 alleles and we make some suggestions to rectify these mistakes in future studies. While MAOA allele frequencies differed between racial groups, the Afrikaner population showed no evidence of admixture. In fact, Afrikaners had more 4-repeat alleles than other populations of European origin, not fewer. The 4-repeat allele may have been selected for during colonisation.

  18. Association studies using family pools of outcrossing crops based on allele-frequency estimates from DNA sequencing

    DEFF Research Database (Denmark)

    Ashraf, Bilal; Jensen, Just; Asp, Torben

    2014-01-01

    from sequence read-counts for mapping. We show that, under additivity assumptions, there is a linear relationship between the family phenotype and family allele frequency, and that a regression of family phenotype on family allele frequency will estimate twice the allele substitution effect at a locus....... However, medium-to-low sequencing depth causes underestimation of the true allele substitution effect. An expression for this underestimation is derived for the case that parents are diploid, such that F2 families have up to four dosages of every allele. Using simulation studies, estimation of the allele...... effect from F2-family pools was verified and it was shown that the underestimation of the allele effect is correctly described. The optimal design for an association study when sequencing budget would be fixed is obtained using large sample size and lower sequence depth, and using higher SNP density...

  19. The frequency of allelic lethals and complementation maps in natural populations of drosophila melanogaster from Mexico

    Directory of Open Access Journals (Sweden)

    Salceda Victor M.

    2004-01-01

    Full Text Available Departing from a previous study on the genetic loads affecting the second chromosome of Drosophila melanogaster in four natural populations, 171 lethal chromosomes were recovered and maintained as a balanced stocks in the condition Cy L / 1 (l=lethal; of those lethais 24 correspond to population A, 50 to populations B and C and 47 to population D. later on an intra-population allelism test for the four populations was performed for each one. A total of 3807 inter lethal crosses were done yielding a total of i 10 allelic combinations, from them the respective percentage of allelism for each population was calculated and they are as follow: 3.98 % for population A, 1.80 % for population B, 3.67 % for population C and 2.96 % for population D. the observed values for the frequency of allelism in these populations are not significantly different from those reported by other authors in similar studies in natural and/or experimental populations. Beside these values the frequency for singles, doubles, triplets and even quadruplets present in each population were determined, they shown the presence of various complementation maps due to the clustering of few different lethals: also a large complementation map formed by a large cluster involving the presence of 26 different lethals found in population D all of them combined constituting a single unit was found.

  20. Allele Frequency Data for 17 Short Tandem Repeats in a Czech Population Sample

    Czech Academy of Sciences Publication Activity Database

    Šimková, H.; Faltus, Václav; Marván, Richard; Pexa, T.; Stenzl, V.; Brouček, J.; Hořínek, A.; Mazura, Ivan; Zvárová, Jana

    2009-01-01

    Roč. 4, č. 1 (2009), e15-e17 ISSN 1872-4973 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : short tandem repeat (STR) * allelic frequency * PowerPlex 16 System * AmpflSTR Identifiler * population genetics * Czech Republic Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.421, year: 2009

  1. Ethnic differences in allelic distribution of IFN-g in South African women but no link with cervical cancer

    Directory of Open Access Journals (Sweden)

    Govan Vandana A

    2003-05-01

    Full Text Available Abstract Background The failure of specific types of human papillomaviruses (HPV to raise effective immune responses may be important in the pathogenesis of cervical cancer, the second most common cancer in South African women. Polymorphisms of a number of cytokine genes have been implicated in inducing susceptibility or resistance to cancers caused by infectious agents owing to their role in determining host immune response. Polymorphisms of IL-10 and IFN-γ genes are believed to influence the expression and/or secretion levels of their respective cytokines. Methods and Results In this study, women with histologically proven cancer of the cervix (n = 458 and hospital-based controls (n = 587 were investigated for bi-allelic -1082 (A/G polymorphisms of IL-10 and the bi-allelic +874(A/T polymorphisms of IFN-γ. In addition, the distributions of the allelic frequencies were stratified in both the African and mixed race population groups of South Africa. We found striking differences in the allele distribution of IFN-γ (X2 = 0.02 among the two ethnic groups. A significant increase in the allele distribution of the IFN-γ AA genotype was found in the African group compared to the mixed population group (OR, 0.5; 95% CI, 0.2–1.0. For IL-10 there were no significant allelic differences between the two South African ethnic groups. Furthermore, when the ethnic groups were combined the IL-10 allelic frequencies in the combined South African data were similar to those observed in an Oriental population from Southern China and in an Italian population. However, the allele frequencies of the IFN-γ genotype among the two South African ethnic groups were different when compared to an Italian Caucasoid group. While crude analysis of these data showed both statistically significantly increased and diminished risks of cervical cancer among high producers of INF-γ and low producers of IL-10 respectively, these associations were no longer significant when the

  2. Distribution of apolipoprotein E alleles in coras and huicholes from Nayarit and Nahuas and Mestizos from Veracruz, Mexico.

    Science.gov (United States)

    Cruz-Fuentes, Carlos S; González-Sobrino, Blanca Zoila; Gómez-Sanchez, Ariadna; Martínez Rueda, Hortencia; Chávez-Eakle, Rosa Aurora; Serrano Sánchez, Carlos

    2005-12-01

    We report allele frequencies for the most common polymorphism of the APOE gene in Mexican individuals from two regions not previously described: Coras and Huicholes from Nayarit, and Nahuas and mestizos from Veracruz. We also report APOE allele frequencies for inhabitants of Mexico City. These descriptive data underscore the allelic heterogeneity for this particular locus in Mexico.

  3. Prevalence of alpha-1 antitrypsin deficiency and allele frequency in patients with COPD in Brazil

    Science.gov (United States)

    Russo, Rodrigo; Zillmer, Laura Russo; Nascimento, Oliver Augusto; Manzano, Beatriz; Ivanaga, Ivan Teruaki; Fritscher, Leandro; Lundgren, Fernando; Miravitlles, Marc; Gondim, Heicilainy Del Carlos; Santos, Gildo; Alves, Marcela Amorim; Oliveira, Maria Vera; de Souza, Altay Alves Lino; Sales, Maria Penha Uchoa; Jardim, José Roberto

    2016-01-01

    ABSTRACT Objective: To determine the prevalence of alpha 1-antitrypsin (AAT) deficiency (AATD), as well as allele frequency, in COPD patients in Brazil. Methods: This was a cross-sectional study involving 926 COPD patients 40 years of age or older, from five Brazilian states. All patients underwent determination of AAT levels in dried blood spot (DBS) samples by nephelometry. Those with DBS AAT levels ≤ 2.64 mg/dL underwent determination of serum AAT levels. Those with serum AAT levels of < 113 mg/dL underwent genotyping. In case of conflicting results, SERPINA1 gene sequencing was performed. Results: Of the 926 COPD patients studied, 85 had DBS AAT levels ≤ 2.64 mg/dL, and 24 (2.6% of the study sample) had serum AAT levels of < 113 mg/dL. Genotype distribution in this subset of 24 patients was as follows: PI*MS, in 3 (12.5%); PI*MZ, in 13 (54.2%); PI*SZ, in 1 (4.2%); PI*SS, in 1 (4.2%); and PI*ZZ, in 6 (25.0%). In the sample as a whole, the overall prevalence of AATD was 2.8% and the prevalence of the PI*ZZ genotype (severe AATD) was 0.8% Conclusions: The prevalence of AATD in COPD patients in Brazil is similar to that found in most countries and reinforces the recommendation that AAT levels be measured in all COPD patients. PMID:27812629

  4. Allele frequency changes due to hitch-hiking in genomic selection programs

    DEFF Research Database (Denmark)

    Liu, Huiming; Sørensen, Anders Christian; Meuwissen, Theo H E

    2014-01-01

    animals for 25 consecutive generations. Six genetic models were considered with different heritabilities and numbers of QTL (quantitative trait loci) affecting the trait. Four selection criteria were used, including selection on own phenotype and on estimated breeding values (EBV) derived using phenotype......-BLUP, Genomic BLUP and Bayesian Lasso. Changes in allele frequencies at QTL, markers and linked neutral loci were investigated for the different selection criteria and different scenarios, along with the loss of favourable alleles and the rate of inbreeding measured by pedigree and runs of homozygosity. Results......Background Genomic selection makes it possible to reduce pedigree-based inbreeding over best linear unbiased prediction (BLUP) by increasing emphasis on own rather than family information. However, pedigree inbreeding might not accurately reflect the loss of genetic variation and the true level...

  5. Allozyme frequency distribution patterns at two gene loci of the ...

    African Journals Online (AJOL)

    Allele frequencies for PGM1*-1, PGM2*-1 and FH1*-1 were highest in the deciduous forest zone. The alleles PGM1*-2, PGM2*-2 and FH1*-2 were highest in the Guinea savanna zone, while the highest frequencies for alleles PGM1*-3, PGM2*-3, PGM2*-4 and FH1*-3 occurred in the Sudan savanna zone. Alleles PGM2*-3 ...

  6. Could FIV zoonosis responsible of the breakdown of the pathocenosis which has reduced the European CCR5-Delta32 allele frequencies?

    Directory of Open Access Journals (Sweden)

    Faure Eric

    2008-10-01

    Full Text Available Abstract Background In Europe, the north-south downhill cline frequency of the chemokine receptor CCR5 allele with a 32-bp deletion (CCR5-Δ32 raises interesting questions for evolutionary biologists. We had suggested first that, in the past, the European colonizers, principally Romans, might have been instrumental of a progressively decrease of the frequencies southwards. Indeed, statistical analyses suggested strong negative correlations between the allele frequency and historical parameters including the colonization dates by Mediterranean civilisations. The gene flows from colonizers to native populations were extremely low but colonizers are responsible of the spread of several diseases suggesting that the dissemination of parasites in naive populations could have induced a breakdown rupture of the fragile pathocenosis changing the balance among diseases. The new equilibrium state has been reached through a negative selection of the null allele. Results Most of the human diseases are zoonoses and cat might have been instrumental in the decrease of the allele frequency, because its diffusion through Europe was a gradual process, due principally to Romans; and that several cat zoonoses could be transmitted to man. The possible implication of a feline lentivirus (FIV which does not use CCR5 as co-receptor is discussed. This virus can infect primate cells in vitro and induces clinical signs in macaque. Moreover, most of the historical regions with null or low frequency of CCR5-Δ32 allele coincide with historical range of the wild felid species which harbor species-specific FIVs. Conclusion We proposed the hypothesis that the actual European CCR5 allelic frequencies are the result of a negative selection due to a disease spreading. A cat zoonosis, could be the most plausible hypothesis. Future studies could provide if CCR5 can play an antimicrobial role in FIV pathogenesis. Moreover, studies of ancient DNA could provide more evidences regarding

  7. Could FIV zoonosis responsible of the breakdown of the pathocenosis which has reduced the European CCR5-Delta32 allele frequencies?

    Science.gov (United States)

    Faure, Eric

    2008-01-01

    Background In Europe, the north-south downhill cline frequency of the chemokine receptor CCR5 allele with a 32-bp deletion (CCR5-Δ32) raises interesting questions for evolutionary biologists. We had suggested first that, in the past, the European colonizers, principally Romans, might have been instrumental of a progressively decrease of the frequencies southwards. Indeed, statistical analyses suggested strong negative correlations between the allele frequency and historical parameters including the colonization dates by Mediterranean civilisations. The gene flows from colonizers to native populations were extremely low but colonizers are responsible of the spread of several diseases suggesting that the dissemination of parasites in naive populations could have induced a breakdown rupture of the fragile pathocenosis changing the balance among diseases. The new equilibrium state has been reached through a negative selection of the null allele. Results Most of the human diseases are zoonoses and cat might have been instrumental in the decrease of the allele frequency, because its diffusion through Europe was a gradual process, due principally to Romans; and that several cat zoonoses could be transmitted to man. The possible implication of a feline lentivirus (FIV) which does not use CCR5 as co-receptor is discussed. This virus can infect primate cells in vitro and induces clinical signs in macaque. Moreover, most of the historical regions with null or low frequency of CCR5-Δ32 allele coincide with historical range of the wild felid species which harbor species-specific FIVs. Conclusion We proposed the hypothesis that the actual European CCR5 allelic frequencies are the result of a negative selection due to a disease spreading. A cat zoonosis, could be the most plausible hypothesis. Future studies could provide if CCR5 can play an antimicrobial role in FIV pathogenesis. Moreover, studies of ancient DNA could provide more evidences regarding the implications of

  8. Genome Wide Allele Frequency Fingerprints (GWAFFs) of populations via genotyping by sequencing

    DEFF Research Database (Denmark)

    Byrne, Stephen; Czaban, Adrian; Studer, Bruno

    2013-01-01

    is an outbreeding species, and breeding programs are based upon selection on populations. We tested two restriction enzymes for their efficiency in complexity reduction of the perennial ryegrass genome. The resulting profiles have been termed Genome Wide Allele Frequency Fingerprints (GWAFFs), and we have shown how...... these fingerprints can be used to distinguish between plant populations. Even at current costs and throughput, using sequencing to directly evaluate populations on a genome-wide scale is viable. GWAFFs should find many applications, from varietal development in outbreeding species right through to playing a role...

  9. Determination of frequencies of alleles, associated with the pseudodeficiency of lysosomal hydrolases, in population of Ukraine.

    Science.gov (United States)

    Olkhovych, N V; Gorovenko, N G

    2016-01-01

    The pseudodeficiency of lysosomal hydrolases described as a significant reduction in enzyme activi­ty in vitro in clinically healthy individuals, can lead to diagnostic errors in the process of biochemical analysis of lysosomal storage disease in case of its combination with pathology of another origin. Pseudodeficiency is mostly caused by some non-pathogenic changes in the corresponding gene. These changes lead to the in vitro lability of the enzyme molecule, whereas in vivo the enzyme retains its functional activity. To assess the prevalence of the most common lysosomal hydrolases pseudodeficiency alleles in Ukraine, we have determined the frequency of alleles c.1055A>G and c.* 96A>G in the ARSA gene, substitutions c.739C>T (R247W) and c.745C>T (R249W) in the HEXA gene, c.1726G>A (G576S) and c.2065G>A (E689K) in the GAA gene, c.937G>T (D313Y) in the GLA1 gene and c.898G>A (A300T) in the IDUA gene in a group of 117 healthy individuals from different regions of the country and 14 heterozygous carriers of pathogenic mutations in the HEXA gene (parents of children with confirmed diagnosis of Tay-Sachs disease). The total frequency of haplotypes, associated with arylsulfatase A pseudodeficiency, in healthy people in Ukraine (c.1055G/c.*96G and c.1055G/c.*96A haplotypes) was 10.3%. The frequency of c.739C>T (R247W) allele, associated with hexo­saminidase A pseudodeficiency, among Tay-Sachs carriers from Ukraine was 7.1%. The total frequency of α-glucosidase pseudodeficiency haplotypes in healthy individuals in Ukraine (c.1726A/c.2065A and c.1726G/c.2065A haplotypes) was 2.6%. No person among examined individuals with the substitution c.937G>T (D313Y) in the GLA1 gene and c.898G>A (A300T) in the IDUA gene was found. The differential diagnostics of lysosomal storage diseases requires obligatory determination of the presence of the pseudodeficiency alleles, particularly the ones with high incidence in the total population. Ignoring phenomenon of pseudodeficiency may

  10. Prevalence of alpha-1 antitrypsin deficiency and allele frequency in patients with COPD in Brazil

    OpenAIRE

    Russo, Rodrigo; Zillmer, Laura Russo; Nascimento, Oliver Augusto; Manzano, Beatriz; Ivanaga, Ivan Teruaki; Fritscher, Leandro; Lundgren, Fernando; Miravitlles, Marc; Gondim, Heicilainy Del Carlos; Santos Junior, Gildo; Alves, Marcela Amorim; Oliveira, Maria Vera; Souza, Altay Alves Lino de; Sales, Maria Penha Uchoa; Jardim, José Roberto

    2016-01-01

    ABSTRACT Objective: To determine the prevalence of alpha 1-antitrypsin (AAT) deficiency (AATD), as well as allele frequency, in COPD patients in Brazil. Methods: This was a cross-sectional study involving 926 COPD patients 40 years of age or older, from five Brazilian states. All patients underwent determination of AAT levels in dried blood spot (DBS) samples by nephelometry. Those with DBS AAT levels ≤ 2.64 mg/dL underwent determination of serum AAT levels. Those with serum AAT levels of <...

  11. Determination of frequencies of alleles, associated with the pseudodeficiency of lysosomal hydrolases, in population of Ukraine

    Directory of Open Access Journals (Sweden)

    N. V. Olkhovych

    2016-10-01

    Full Text Available The pseudodeficiency of lysosomal hydrolases described as a significant reduction in enzyme activi­ty in vitro in clinically healthy individuals, can lead to diagnostic errors in the process of biochemical analysis of lysosomal storage disease in case of its combination with pathology of another origin. Pseudodeficiency is mostly caused by some non-pathogenic changes in the corresponding gene. These changes lead to the in vitro lability of the enzyme molecule, whereas in vivo the enzyme retains its functional activity. To assess the prevalence of the most common lysosomal hydrolases pseudodeficiency alleles in Ukraine, we have determined the frequency of alleles c.1055A>G and c.* 96A>G in the ARSA gene, substitutions c.739C>T (R247W and c.745C>T (R249W in the HEXA gene, c.1726G>A (G576S and c.2065G>A (E689K in the GAA gene, c.937G>T (D313Y in the GLA1 gene and c.898G>A (A300T in the IDUA gene in a group of 117 healthy individuals from different regions of the country and 14 heterozygous carriers of pathogenic mutations in the HEXA gene (parents of children with confirmed diagnosis of Tay-Sachs disease. The total frequency of haplotypes, associated with arylsulfatase A pseudodeficiency, in healthy people in Ukraine (c.1055G/c.*96G and c.1055G/c.*96A haplotypes was 10.3%. The frequency of c.739C>T (R247W allele, associated with hexo­saminidase A pseudodeficiency, among Tay-Sachs carriers from Ukraine was 7.1%. The total frequency of α-glucosidase pseudodeficiency haplotypes in healthy individuals in Ukraine (c.1726A/c.2065A and c.1726G/c.2065A haplotypes was 2.6%. No person among examined individuals with the substitution c.937G>T (D313Y in the GLA1 gene and c.898G>A (A300T in the IDUA gene was found. The differential diagnostics of lysosomal storage diseases requires obligatory determination of the presence of the pseudodeficiency alleles, particularly the ones with high incidence in the total population. Ignoring phenomenon of

  12. Distribution of HIV-1 resistance-conferring polymorphic alleles SDF ...

    Indian Academy of Sciences (India)

    Unknown

    The estimated relative hazard values for the populations, computed from the three-locus genotype data, are comparable to those from Africa and Southeast Asia, where AIDS is known to be widespread. [Ramana G. V., Vasanthi A., Khaja M., Su B., Govindaiah V., Jin L., Singh L. and Chakraborty R. 2001 Distribution of HIV-1.

  13. Frequency of the CCRdelta32 allele in Brazilians: a study in colorectal cancer and in HTLV-I infection

    OpenAIRE

    Pereira, Rinaldo W.; Pires, Edina R.; Duarte, Ana P.M.; Moura, Ricardo P. de; Monteiro, Elisangela; Torloni, Humberto; Proietti, Anna B.; Simpson, Andrew J.G.; Pena, Sérgio D.J.

    2000-01-01

    The identification of a 32-bp deletion in the cc-chemokine receptor-5 gene (CCR5delta32 allele) that renders homozygous individuals highly resistant to HIV infection has prompted worldwide investigations of the frequency of the CCR5delta32 allele in regional populations. It is important to ascertain if CCR5delta32 is a factor to be considered in the overall epidemiology of HIV in individual populations. With this in mind we determined the CCR5delta32 allele frequency in a large sample (907 in...

  14. Distribution of DRB1 and DQB1 HLA class II alleles in occupational asthma due to western red cedar.

    Science.gov (United States)

    Horne, C; Quintana, P J; Keown, P A; Dimich-Ward, H; Chan-Yeung, M

    2000-05-01

    Occupational asthma caused by western red cedar is a common problem in sawmill industries. The objective of this study was to examine a possible association of human leukocyte antigen (HLA) class II genetic markers with susceptibility or resistance to western red cedar induced asthma. The distribution of DRB1 and DQB1 HLA class II alleles and DRB1-DQB1 haplotypes was studied in 56 Caucasian patients with proven red cedar asthma and 63 healthy Caucasian control subjects exposed to red cedar dust. DRB1 and DQB1 high resolution typing was performed by the polymerase chain reaction-based method. Patients with red cedar asthma had a higher frequency of HLA DQB1*0603 and DQB1*0302 alleles compared to a group of healthy exposed control subjects and a reduced frequency of DQB1*0501 allele. The frequency of the DRB1*0401-DQB1* 0302 haplotype was increased and the DRB1*0101-DQB1*0501 haplotype was reduced. These findings suggest that genetic factors such as human leukocyte antigen class II antigens may be associated with susceptibility or resistance to development of red cedar asthma.

  15. Frequency of the GPR7 Tyr135Phe allelic variant in lean and obese subjects.

    Science.gov (United States)

    Pelosini, C; Maffei, M; Ceccarini, G; Marchi, M; Marsili, A; Galli, G; Scartabelli, G; Tamberi, A; Latrofa, F; Fierabracci, P; Vitti, P; Pinchera, A; Santini, F

    2013-10-01

    GPR7, the endogenous coupled receptor for neuropeptide B and neuropeptide W, is expressed in several regions of the central nervous system, which are involved in the regulation of feeding behavior. GPR7 affects the regulation of energy balance through a mechanism independent of leptin and melanocortin pathways. Aim of this study was to investigate whether GPR7 gene mutations can be detected in human subjects and, in that event, if they are differently distributed among lean and obese subjects. The coding region of GPR7 were sequenced in 150 obese patients and 100 normal-weight unrelated controls. Functional studies of the allelic variants were performed. One genetic GPR7 variant was found (Tyr135Phe - rs33977775) in obese subjects (13.3%) and lean control (25%). Functional studies did not reveal significant differences between the wild type and the Tyr135Phe allelic variants in their NPW-mediated capacity to inhibit forskolin-induced cAMP production. Screening of GPR7 gene mutations among lean and obese subjects revealed a Tyr135Phe allelic variant that was fairly common in the study population. As indicated by in vitro and in silico studies, this variant is unlikely to cause a functional derangement of the receptor.

  16. A genomic study on distribution of human leukocyte antigen (HLA-A and HLA-B alleles in Lak population of Iran

    Directory of Open Access Journals (Sweden)

    Farhad Shahsavar

    2017-03-01

    Full Text Available Anthropological studies based on the highly polymorphic gene, human leukocyte antigen (HLA, provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as infertility treatment, designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine HLA-A and HLA-B allele frequencies in 100 unrelated Lak/lᴂk/individuals from Lorestan province of Iran. Finally, we compared the results with that previously described in Iranian population. Commercial HLA-Type kits from BAG (Lich, Germany company were used for determination of the HLA-A and HLA-B allele frequencies in genomic DNA, based on polymerase chain reaction with sequence specific primer (PCR-SSP assay. The differences between the populations in distribution of HLA-A and HLA-B alleles were estimated by chi-squared test with Yate's correction. The most frequent HLA-A alleles were *24 (20%, *02 (18%, *03 (12% and *11 (10%, and the most frequent HLA-B alleles were *35 (24%, *51 (16%, *18 (6% and *38 (6% in Lak population. HLA-A*66 (1%, *74(1% and HLA-B*48 (1%, *55(1% were the least observed frequencies in Lak population. Our results based on HLA-A and HLA-B allele frequencies showed that Lak population possesses the previously reported general features of Iranians but still with unique.

  17. Apolipoprotein E epsilon 4 allele distribution in Wernicke-Korsakoff syndrome with or without global intellectual deficits.

    Science.gov (United States)

    Muramatsu, T; Kato, M; Matsui, T; Yoshimasu, H; Yoshino, A; Matsushita, S; Higuchi, S; Kashima, H

    1997-01-01

    Recent genetic studies show that the apolipoprotein E (ApoE) epsilon 4 allele is a risk factor for Alzheimer's disease (AD). Whether this allele is associated with other dementing diseases is the next important question. The information could provide a clue to the pathogenetic role of ApoE. In the present study, patients with Wernicke-Korsakoff syndrome (WKS) of alcoholic etiology were divided into two groups according to the severity of intellectual deficits, i.e., those of "classical" Korsakoff patients with preserved intellectual function other than amnesia and those with global intellectual deficits. Genotyping showed that the frequency of ApoE epsilon 4 allele was significantly higher in the patients with global deficits, suggesting the involvement of this allele in the intellectual decline of WKS. In contrast, distributions of other two markers, alpha 1-antichymotrypsin and presenilin-1, did not differ between the two groups. These results added further support to the notion that the consequence of acute insult to the brain is influenced by the ApoE genotype, and suggested ApoE's role in the development of a certain group of "alcoholic dementia."

  18. Distribution of Human Leukocyte Antigen alleles in Systemic Lupus Erythematosus patients with Angiotensin Converting Enzyme Insertion/Deletion Polymorphism

    Directory of Open Access Journals (Sweden)

    Nageen Hussain

    2013-02-01

    Full Text Available Systemic Lupus Erythematosus is one of the classic examples of autoimmune diseases among human beings and is a rare disease in Pakistani population. Clinically it is a quite diverse and complicated autoimmune disease in a sense that it involves multiple organs of the body and mimics with other diseases as well. This study focused on the distribution of HLA alleles in SLE patients with ACE I/D Polymorphism. A total of 122 individuals were enrolled in this study, 61 were the SLE patients who fulfilled revised ACR criteria and 61 were the healthy controls. Mean age of SLE patients at diagnosis was 30.35 ± 1.687 years (12-68 years. ACE gene I/D polymorphism was performed by nested PCR and DNA based HLA typing technique was used. ACE gene I/D polymorphism of Intron16 was studied and found to be involved in the activity of SLE. There is high frequency of HLA-A*01, HLA-B*40, HLA-DRB1*01 alleles in SLE patients with ACE DD genotype. The distribution of HLA-A, -B, -DRB1 alleles was analyzed in SLE patients with various disease phenotypes. HLA-A*01 and HLA-B*40 was the most common allele found in SLE patients with the involvement of skin. HLA-A*01, -A*03, HLA-B*13 and -B*46 were common in SLE patients with arthritis while HLA-A*26 and -A*69 were commonly found in Lupus nephritis cases. SLE patients involving both skin and kidney had an allele HLA-DRB1*01 common in them.

  19. Population Difference Analysis of Allele Frequencies of 24 Y-STR Loci.

    Science.gov (United States)

    Zhu, R X; Liu, J H; Zhao, Q; Lin, Y; Li, L

    2016-06-01

    To investigate the population genetic polymorphisms of 24 Y-STR loci in unrelated individuals in Eastern Chinese Han population, and to compare the difference of Han group between Eastern China and Guangdong. The population genetics of 24 Y-STR loci in 268 unrelated Han individuals from Eastern China were analyzed by GFS 24 Y-STR amplification kit. The allele frequencies in Eastern Chinese Han population were compared with the data in Guangdong Han population, and the difference analysis between two groups was performed. Among the 24 Y-STR loci of 268 unrelated Han individuals from Eastern China, 235 alleles and 267 haplotypes were observed. GD value ranged from 0.564 9 to 0.966 8. The difference between 12 loci ( DYS622 , DYS552 , DYS443 , et al. ) of Han population in Eastern China and in Guangdong was statistically significance. GFS 24Y STR amplification system shows favorable polymorphisms, which can be used in patrilineal genetic relationship identification. Copyright© by the Editorial Department of Journal of Forensic Medicine

  20. Further data on the microsatellite locus D12S67 in worldwide populations: an unusual distribution of D12S67 alleles in Native Americans.

    Science.gov (United States)

    Mitchell, R J; Federle, L; Sofro, A S; Papiha, S S; Briceno, I; Bernal, J E

    2000-08-01

    We report the frequencies of alleles at the microsatellite locus D12S67 in 2 widely separated ethnic groups of the world: 2 populations from Sulawesi, an island in the Indonesian archipelago, and 5 Native American tribes of Colombia, South America. The allele frequencies in the Minihasans and Torajans of Sulawesi are similar to each other (but the modal class allele is different) and in general agreement with those reported in mainland Asian groups, but different from both Europeans and Chinese Han of Taiwan. The 5 Native American tribes (Arsario, Kogui, Ijka, Wayuu, and Coreguaje) display different allele frequencies from those seen in Sulawesi populations, in other groups from Europe and mainland Asia, and in Chinese Han of Taiwan. Native Americans exhibit a bimodal distribution of alleles, unlike other groups, with significant differences among the tribes. The Arsario and Kogui have no admixture with Europeans or Africans and are the most distinctive, while the Wayuu have the most admixture and show most similarity to other groups. The data suggest that nonadmixed Native Americans may be quite distinctive with respect to this marker. The most common allele varies across the 5 tribes, from 249 base pairs to 261 base pairs. All samples exhibit Hardy-Weinberg genotype proportions; heterozygosities are lowest in the 2 nonadmixed Native American tribes. Examination of all the available data indicates that some east Asian and southeast Asian groups are characterized by a high frequency of smaller sized D12S67 alleles, while other populations have a greater proportion of the larger sized alleles. The cumulative, though still highly restricted, population data on locus D12S67 demonstrate that it may be of considerable value in anthropological genetic studies of ethnic groups. Data are required on Native Americans outside Colombia before this marker can be used in admixture studies of this group.

  1. Geographic differences in allele frequencies of susceptibility SNPs for cardiovascular disease

    Directory of Open Access Journals (Sweden)

    Kullo Iftikhar J

    2011-04-01

    Full Text Available Abstract Background We hypothesized that the frequencies of risk alleles of SNPs mediating susceptibility to cardiovascular diseases differ among populations of varying geographic origin and that population-specific selection has operated on some of these variants. Methods From the database of genome-wide association studies (GWAS, we selected 36 cardiovascular phenotypes including coronary heart disease, hypertension, and stroke, as well as related quantitative traits (eg, body mass index and plasma lipid levels. We identified 292 SNPs in 270 genes associated with a disease or trait at P -8. As part of the Human Genome-Diversity Project (HGDP, 158 (54.1% of these SNPs have been genotyped in 938 individuals belonging to 52 populations from seven geographic areas. A measure of population differentiation, FST, was calculated to quantify differences in risk allele frequencies (RAFs among populations and geographic areas. Results Large differences in RAFs were noted in populations of Africa, East Asia, America and Oceania, when compared with other geographic regions. The mean global FST (0.1042 for 158 SNPs among the populations was not significantly higher than the mean global FST of 158 autosomal SNPs randomly sampled from the HGDP database. Significantly higher global FST (P FST of 2036 putatively neutral SNPs. For four of these SNPs, additional evidence of selection was noted based on the integrated Haplotype Score. Conclusion Large differences in RAFs for a set of common SNPs that influence risk of cardiovascular disease were noted between the major world populations. Pairwise comparisons revealed RAF differences for at least eight SNPs that might be due to population-specific selection or demographic factors. These findings are relevant to a better understanding of geographic variation in the prevalence of cardiovascular disease.

  2. High frequency power distribution system

    Science.gov (United States)

    Patel, Mikund R.

    1986-01-01

    The objective of this project was to provide the technology of high frequency, high power transmission lines to the 100 kW power range at 20 kHz frequency. In addition to the necessary design studies, a 150 m long, 600 V, 60 A transmission line was built, tested and delivered for full vacuum tests. The configuration analysis on five alternative configurations resulted in the final selection of the three parallel Litz straps configuration, which gave a virtually concentric design in the electromagnetic sense. Low inductance, low EMI and flexibility in handling are the key features of this configuration. The final design was made after a parametric study to minimize the losses, weight and inductance. The construction of the cable was completed with no major difficulties. The R,L,C parameters measured on the cable agreed well with the calculated values. The corona tests on insulation samples showed a safety factor of 3.

  3. Allele and haplotype frequencies for HLA-DQ in Iranian celiac disease patients

    Science.gov (United States)

    Rostami-Nejad, Mohammad; Romanos, Jihane; Rostami, Kamran; Ganji, Azita; Ehsani-Ardakani, Mohammad Javad; Bakhshipour, Ali-Reza; Zojaji, Homayoun; Mohebbi, Seyed Reza; Zali, Mohammad-Reza; Wijmenga, Cisca

    2014-01-01

    AIM: To assess the distribution of human leukocyte antigen (HLA)-DQ2 and -DQ8 in Iranian celiac disease (CD) patients and compare them to healthy Iranian controls. METHODS: To predict the HLA-DQA1 and -DQB1 genes, we used six previously reported HLA-tagging single nucleotide polymorphism to determine HLA genotypes in 59 Iranian patients with ‘biopsy-confirmed’ CD and in 151 healthy Iranian individuals. To test the transferability of the method, 50 cases and controls were also typed using a commercial kit that identifies individual carriers of DQ2, DQ7 and DQ8 alleles. RESULTS: In this pilot study 97% of CD cases (n = 57) and 58% of controls (n = 87) were carriers of HLA-DQ2 and/or HLA-DQ8 heterodimers, either in the homozygous or heterozygous state. The HLA-DQ pattern of these 57 CD patients: heterozygous DQ2.2 (n = 14) and homozygous DQ2.2 (n = 1), heterozygous DQ2.5 (n = 33) and homozygous DQ2.5 (n = 8), heterozygous DQ8 (n = 13) and homozygous DQ8 (n = 2). Two CD patients were negative for both DQ2 and DQ8 (3%). CONCLUSION: The prevalence of DQ8 in our CD population was higher than that reported in other populations (25.4%). As reported in other populations, our results underline the primary importance of HLA-DQ alleles in the Iranian population’s susceptibility to CD. PMID:24876751

  4. Frequency distributions in population genetics parallel those in statistical physics

    Science.gov (United States)

    Higgs, Paul G.

    1995-01-01

    A class of problems from statistical physics is discussed that is shown to be identical to a class of problems in population genetics. The mathematical treatment of these problems has arisen independently in the two subjects. The important results of both literatures are presented here, together with cross references. In each case there is a stochastic process generating a set of variables xi that satisfy tsumixi=1. For example, the xi may represent the weights of valleys in a spin glass, the sizes of attractors in dynamical systems, the frequency of different alleles in a population, or the sizes of different families in a genealogical tree. The frequency distributions f(x) of the valleys or alleles are calculated, together with the distribution Π(Y) of the quantity Y=tsumix2i. The distribution Π(Y) can be written as a sum of universal functions Πk(Y) that are independent of the parameters of the problem. It is shown that the rather abstract concepts in the physical models are directly related to observables that are experimentally measurable in biology.

  5. Frequency of the CCRD32 allele in Brazilians: a study in colorectal cancer and in HTLV-I infection

    Directory of Open Access Journals (Sweden)

    Pereira Rinaldo W.

    2000-01-01

    Full Text Available The identification of a 32-bp deletion in the cc-chemokine receptor-5 gene (CCR5delta32 allele that renders homozygous individuals highly resistant to HIV infection has prompted worldwide investigations of the frequency of the CCR5delta32 allele in regional populations. It is important to ascertain if CCR5delta32 is a factor to be considered in the overall epidemiology of HIV in individual populations. With this in mind we determined the CCR5delta32 allele frequency in a large sample (907 individuals of the southeastern Brazilian urban population, stratified as follows: 322 healthy unrelated individuals, 354 unselected colorectal cancer patients, and 229 blood donors. The three groups displayed essentially identical allelic frequencies of CCR5delta32 and pairwise comparisons did not show significant differences. Thus, our results can be pooled to provide a reliable estimate of the CCR5delta32 allele frequency in the southeastern Brazil of 0.053 ± 0.005. The blood donors comprised 50 HTLV-I serologically negative individuals, 115 non-symptomatic individuals HTLV-I positive by ELISA but with indeterminate Western blot results, 49 healthy blood donors HTLV-I positive both at ELISA and Western blot and 15 patients with clinical spinal cord disease (HAM. A suggestive trend was observed, with the CCR5delta32 frequencies decreasing progressively in these four categories. However, when we applied Fischer's exact test no significant differences emerged. We believe that further studies in larger cohorts should be performed to ascertain whether the CCR5delta32 allele influences the chance of becoming infected or developing clinical symptoms of HTLV-I infection.

  6. Global Volcano Hazard Frequency and Distribution

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Volcano Hazard Frequency and Distribution is a 2.5 minute gridded data set based upon the National Geophysical Data Center (NGDC) Volcano Database spanning...

  7. Global Earthquake Hazard Frequency and Distribution

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Earthquake Hazard Frequency and Distribution is a 2.5 by 2.5 minute global utilizing Advanced National Seismic System (ANSS) Earthquake Catalog data of actual...

  8. Global Drought Hazard Frequency and Distribution

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Drought Hazard Frequency and Distribution is a 2.5 minute grid based upon the International Research Institute for Climate Prediction's (IRI) Weighted Anomaly...

  9. Global Earthquake Hazard Frequency and Distribution

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Earthquake Hazard Frequency and Distribution is a 2.5 minute grid utilizing Advanced National Seismic System (ANSS) Earthquake Catalog data of actual...

  10. Global Flood Hazard Frequency and Distribution

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Flood Hazard Frequency and Distribution is a 2.5 minute grid derived from a global listing of extreme flood events between 1985 and 2003 (poor or missing data...

  11. Global Cyclone Hazard Frequency and Distribution

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Cyclone Hazard Frequency and Distribution is a 2.5 minute grid based on more than 1,600 storm tracks for the period 1 January 1980 through 31 December 2000...

  12. Higher frequency of septic shock in septic patients with the 47C allele (rs4880) of the SOD2 gene.

    Science.gov (United States)

    Paludo, Francis Jackson de Oliveira; Picanço, Juliane Bentes; Fallavena, Paulo Roberto Vargas; Fraga, Lucas da Rosa; Graebin, Pietra; Nóbrega, Otávio de Toledo; Dias, Fernando Suparregui; Alho, Clarice Sampaio

    2013-03-15

    To analyze the effect of the two different versions of the manganese superoxide dismutase gene (SOD2) on sepsis. The SOD2 gene presents the 47C>T single nucleotide polymorphism (SNP; ID: rs4880) which produces MnSOD with different activities. The -9Val MnSOD (47T allele) is less efficient than the -9Ala version (47C allele). During sepsis there are abundance of ROS, high SOD2 expression and excess of H(2)O(2) synthesis. High concentrations of H(2)O(2) could affect the sepsis scenario and/or the sepsis outcome. We determined the 47C>T single nucleotide polymorphism (SNP) frequencies in 529 critically ill patients with or without sepsis, facing outcome. To collect information on population frequencies, we obtained a pilot 47C>T genotypic and allelic frequencies in a random group of 139 healthy subjects. We compared the 47C allele carriers (47CC+47CT genotypes) with 47TT homozygotes and noticed a significant association between 47C allele carriers and septic shock in septic patients (P=0.025). With an adjusted binary multivariate logistic regression, incorporating 47C>T SNP and the main clinical predictors, we showed high SOFA scores [P<0.001, OR=9.107 (95% CI=5.319-15.592)] and 47C allele [P=0.011, OR=2.125 (95% CI=1.190-3.794)] were significantly associated with septic shock outcome. With this information we presented a hypothesis suggesting that this negative outcome from sepsis is possibly explained by effects on cellular stress caused by 47C allele. In our population there was a significant higher frequency of septic shock in septic patients with the 47C allele of the SOD2 gene. This higher 47C allele frequency in septic patients with negative outcome could be explained by effects of higher activity MnSOD on cellular stress during the sepsis. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Alarmingly High Segregation Frequencies of Quinolone Resistance Alleles within Human and Animal Microbiomes Are Not Explained by Direct Clinical Antibiotic Exposure

    Science.gov (United States)

    Field, Wesley; Hershberg, Ruth

    2015-01-01

    Antibiotic resistance poses a major threat to human health. It is therefore important to characterize the frequency of resistance within natural bacterial environments. Many studies have focused on characterizing the frequencies with which horizontally acquired resistance genes segregate within natural bacterial populations. Yet, very little is currently understood regarding the frequency of segregation of resistance alleles occurring within the housekeeping targets of antibiotics. We surveyed a large number of metagenomic datasets extracted from a large variety of host-associated and non host-associated environments for such alleles conferring resistance to three groups of broad spectrum antibiotics: streptomycin, rifamycins, and quinolones. We find notable segregation frequencies of resistance alleles occurring within the target genes of each of the three antibiotics, with quinolone resistance alleles being the most frequent and rifamycin resistance alleles being the least frequent. Resistance allele frequencies varied greatly between different phyla and as a function of environment. The frequency of quinolone resistance alleles was especially high within host-associated environments, where it averaged an alarming ∼40%. Within host-associated environments, resistance to quinolones was most often conferred by a specific resistance allele. High frequencies of quinolone resistance alleles were also found within hosts that were not directly treated with antibiotics. Therefore, the high segregation frequency of quinolone resistance alleles occurring within the housekeeping targets of antibiotics in host-associated environments does not seem to be the sole result of clinical antibiotic usage. PMID:26019163

  14. Frequency of the MDR1 mutant allele associated with multidrug sensitivity in dogs from Brazil

    Directory of Open Access Journals (Sweden)

    Monobe MM

    2015-04-01

    Full Text Available Marina M Monobe,1 João P Araujo Junior,2 Kari V Lunsford,3 Rodrigo C Silva,4 Camilo Bulla41Department of Veterinary Clinics, School of Veterinary Medicine and Animal Science, 2Department of Microbiology and Immunology, Biosciences Institute, Sao Paulo State University (UNESP, Botucatu, Brazil; 3Department of Clinical Sciences and Animal Health Center, 4Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi, MS, USAAbstract: To date, a 4-bp deletion in the MDR1 gene has been detected in more than ten dog breeds, as well as in mixed breed dogs, in several countries, however information regarding this mutation in dogs from Brazil is lacking. For this reason, 103 Collies, 77 Border Collies, 76 Shetland Sheepdogs, 20 Old English Sheepdogs, 55 German Shepherds, 16 Australian Shepherds, and 53 Whippets from Brazil were screened for the presence of the mutation. The heterozygous mutated genotype, MDR1 (+/−, frequency found for Collies, Australian Shepherd, and Shetland Sheepdog was 50.5% (95% CI =41.1%–59.9%, 31.3% (95% CI =8.6%–53.2%, and 15.8% (95% CI =7.7%–23.9%, respectively. Homozygous mutated genotype, MDR1 (−/−, was detected only in Collies 35.9%. The MDR1 allele mutant frequency found for Collies, Australian Shepherd, and Shetland Sheepdog was 61.2% (95% CI =54.8%–67.5%, 15.6% (95% CI =3.1%–28.2%, and 7.9% (95% CI =3.7%–12.1%, respectively. Additionally, even free of the mutant allele, the maximum mutant prevalence (MMP in that population, with 95% CI, was 3.8%, 5.2%, 5.4%, and 13.8% for Border Collies, German Shepherds, Whippets, and Old English Sheepdogs, respectively. In this way, this information is important, not only for MDR1 genotype-based breeding programs and international exchange of breeding animals of predisposed breeds, but also for modification of drug therapy for breeds at risk.Keywords: P-glycoprotein, MDR1 mutation, ivermectin, dog, drug

  15. Allele and genotype frequencies of CYP3A4, CYP2C19, and CYP2D6 in Han, Uighur, Hui, and Mongolian Chinese populations.

    Science.gov (United States)

    Zuo, Liang Jin; Guo, Tao; Xia, Dong Ya; Jia, Li Hui

    2012-02-01

    This study was carried out to estimate the allele and genotype frequencies of common variants in the CYP3A4, CYP2C19, and CYP2D6 in the Han, Uighur, Hui, and Mongolian Chinese populations and compare genetic polymorphisms difference between the Han and minority Chinese ethnicities. We evaluated 672 unrelated, healthy Chinese volunteers (Han: 136; Uighur: 214; Hui: 164; Mongolian: 158). Genomic DNA was extracted from peripheral leukocytes and genotyped for CYP3A4*18, CYP2C19*2, *3, and CYP2D6*10 by polymerase chain reaction-restriction fragment length polymorphism analysis. The allele frequencies of CYP3A4*18 in the Han, Uighur, Hui, and Mongolian Chinese population were 18.4%, 14.0%, 19.2%, and 20.3%, respectively; the allele frequencies of CYP2C19*2 were 38.6%, 32.5%, 49.4%, and 41.5%, respectively; the allele frequencies of CYP2C19*3 were 5.2%, 2.1%, 5.2%, and 4.4%, respectively; and the allele frequencies of CYP2D6*10 were 57.4%, 22.4%, 39.7%, and 46.5%, respectively. The results showed that there was no significant ethnic difference in the distribution of CYP3A4*18 and CYP2C19*3 genotypes in the Han, Uighur, Hui, and Mongolian Chinese populations. For CYP2C19*2, the Han were not significantly different from the Uighur, Hui, or Mongolian; however, the Uighur were significantly lower than the Hui and the Mongolian, and the Mongolian were significantly lower than the Hui. For CYP2D6*10, the Mongolian were not significantly different from the Han and the Hui. However, the Uighur were significantly lower than the other three. Our findings confirm the existence of interethnic differences in the CYP2C9, CYP2C19, and CYP2D6 alleles and genotype frequencies in the Han, Uighur, Hui, and Mongolian Chinese populations.

  16. Frequencies of two CYP2C19 defective alleles (CYP2C19*2, and *3 among Iranian population in Mazandaran Province

    Directory of Open Access Journals (Sweden)

    Naghi Shahabi-Majd

    2013-02-01

    Conclusion: The result of the present study showed that the two inactive alleles of CYP2C19 accounted for 9.0% of CYP2C19 alleles in our sample versus 8.8 - 40.1% reported in other populations. The frequencies of the studied alleles resulted significant differences between our sample and African and Eastern Asian populations.

  17. Reducing Bias of Allele Frequency Estimates by Modeling SNP Genotype Data with Informative Missingness

    Directory of Open Access Journals (Sweden)

    Wan-Yu eLin

    2012-06-01

    Full Text Available The presence of missing single-nucleotide polymorphism (SNP genotypes is common in genetic data. For studies with low-density SNPs, the most commonly used approach to deal with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is appropriate only when the missingness is random. However, a given assay often has a different capability in genotyping heterozygotes and homozygotes, causing the phenomenon of ‘differential dropout’ in the sense that the missing rates of heterozygotes and homozygotes are different. In practice, differential dropout among genotypes exists in even carefully designed studies, such as the data from the HapMap project and the Wellcome Trust Case Control Consortium. In this study, we propose a statistical method to model the differential dropout among different genotypes. Compared with the naïve method, our method provides more accurate allele frequency estimates when the differential dropout is present. To demonstrate its practical use, we further apply our method to the HapMap data and a scleroderma data set.

  18. Inference of population splits and mixtures from genome-wide allele frequency data.

    Directory of Open Access Journals (Sweden)

    Joseph K Pickrell

    Full Text Available Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com.

  19. High frequency of NAT2 slow acetylator alleles in the Malay population of Indonesia: an awareness to the anti-tuberculosis drug induced liver injury and cancer

    Directory of Open Access Journals (Sweden)

    Retno W. Susilowati

    2017-05-01

    Full Text Available Background: Arylamine N-acetyltransferase 2 (NAT2 polymorphism was previously reported to have association with the risk of drug toxicities and the development of various diseases. Previous research on the Indonesian population, especially Javanese and Sundanese, showed that there were 33% NAT2 slow acetylator phenotype. The aim of this study was to map the NAT2 variation in the Malay ethnic to gain a deeper insight into NAT2 haplotypic composition in this ethnic.Methods: 50 healthy samples from the Indonesian Malay ethnic were obtained. They were interviewed about their ethnic backgrounds for the last three generations. DNA was extracted from peripheral blood and NAT2 genotyping was done using the PCR direct Sequencing. Data were compiled according to the genotype and allele frequencies estimated from the observed numbers of each specific allele. Haplotype reconstruction was performed using PHASE v2.1.1 software.Results: We found 7 haplotypes consisting of 6 SNPs and 14 NAT2 genotype variations in Indonesian Malay population. The most frequent allele was NAT2*6A (38% which was classified as a slow acetylator allele. According to bimodal distribution, the predicted phenotype of the Malay population was composed of 62% rapid acetylator and 38% slow acetylator. According to trimodal distribution, the predicted phenotypes for rapid, intermediate and slow acetylators were 10%, 52% and 38% respectively.Conclusion: Our result indicates the presence of the allelic distribution and revealed the most frequent acetylator status and phenotype for the Indonesian Malay population. The result of this study will be helpful for future epidemiological or clinical studies and for understanding the genetic basis of acetylation polymorphism in Indonesia.

  20. Allele distribution and genetic diversity of VNTR loci in Salmonella enterica serotype Enteritidis isolates from different sources

    Directory of Open Access Journals (Sweden)

    Bartkus Joanne M

    2008-09-01

    Full Text Available Abstract Background Salmonella enterica serotype Enteritidis (S. Enteritidis is a zoonotic pathogen, which can be found in many sources including animals and the environment. However, little is known about the molecular relatedness among S. Enteritidis isolates from different sources. We have applied multiple-locus variable number tandem repeat analysis (MLVA to study the genetic diversity of S. Enteritidis isolates from human and non-human sources. Results We identified 38 unique MLVA types using nine VNTR loci markers for discrimination between 145 S. Enteritidis isolates from different sources including humans (n = 41, chickens (n = 45, and eggs (n = 40. There were 20 distinct MLVA types identified from human isolates, 17 distinct MLVA types from chicken isolates, and 5 from egg isolates. We compared allele distribution and frequency for each VNTR marker and measured allelic polymorphism within each VNTR locus of S. Enteritidis isolates from the sources using Nei's diversity index (D. Differences in allele distribution and frequency were detected in most loci of study isolates. Different genetic diversity for certain loci was identified in isolates from different sources. The average of genetic diversity (D was lower in egg isolates (0.16 compared to human (0.41 and chicken (0.30. However, for loci SE3, SE7, and SE9, human isolates showed significantly higher diversity than both chicken and egg isolates. Whereas for loci SE5 and SE10, chicken isolates had significantly higher diversity than both human and egg isolates. Minimum-spanning tree (MST comprised one major cluster, a minor cluster, and four clonal expansions. MLVA application enabled a cluster analysis by the MST of the S. Enteritidis isolates by sources, which allows a great insight into the genetic relatedness and the possible flow of these organisms between different reservoirs and humans. Conclusion Differences in allele distribution and genetic diversity of VNTR loci in S

  1. Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection.

    Science.gov (United States)

    Hofer, T; Ray, N; Wegmann, D; Excoffier, L

    2009-01-01

    Several studies have found strikingly different allele frequencies between continents. This has been mainly interpreted as being due to local adaptation. However, demographic factors can generate similar patterns. Namely, allelic surfing during a population range expansion may increase the frequency of alleles in newly colonised areas. In this study, we examined 772 STRs, 210 diallelic indels, and 2834 SNPs typed in 53 human populations worldwide under the HGDP-CEPH Diversity Panel to determine to which extent allele frequency differs among four regions (Africa, Eurasia, East Asia, and America). We find that large allele frequency differences between continents are surprisingly common, and that Africa and America show the largest number of loci with extreme frequency differences. Moreover, more STR alleles have increased rather than decreased in frequency outside Africa, as expected under allelic surfing. Finally, there is no relationship between the extent of allele frequency differences and proximity to genes, as would be expected under selection. We therefore conclude that most of the observed large allele frequency differences between continents result from demography rather than from positive selection.

  2. HLA-DRB, DQA and DQB allele frequencies in Iranian patients with chronic hepatitis B by PCR-SSP

    Directory of Open Access Journals (Sweden)

    Baniaghil S

    2007-05-01

    Full Text Available Background: The outcome of acute hepatitis B infection may be influenced by host genetic factors like human leukocyte antigen (HLA. To investigate the association between the HLA-DRB, DQA1 and DQB1 alleles and chronic hepatitis B infection, 50 patients with chronic hepatitis B (based on 6 months positive of HBsAg and HBc antibody and HBeAg and antibody by serological test, were selected from Turkman population in north east of Iran .Allele frequency in patients were compared with a 65 aged and sex match control group from healthy blood donor of that ethnic population. Methods: HLA DRB, DQA1 and DQB1 alleles were determined using polymerase chain reaction based on sequence specific primer (PCR-SSP method. Allele frequencies in patients and control subjects were compared by Epi-info statistical soft-wear. Results: There was a significant increase and positive association in HLA-DRB1*0301, DQA1*0501 and DQB1*0604 allele frequency in patients group while the frequency of HLA-DRB1*1301, 1501 and DQB1*0401 and DQA1*0401, 0102 were lower in patients than control group and shows negative association. Conclusion: In Iranian Torkman population, HLA DRB1*0301, DQA1*0501 and DQB1*0604 have an important role in susceptibility to chronic hepatitis B infection and HLA DRB1*1301, 1501, DQB1*0401 are associated with protection to chronic hepatitis B infection. Larger case control studies may be helpful to confirm our investigation.

  3. Changes in allelic frequency over time in European bread wheat (Triticum aestivum L.) varieties revealed using DArT and SSR markers

    DEFF Research Database (Denmark)

    Orabi, Jihad; Jahoor, Ahmed; Backes, Gunter Martin

    2014-01-01

    and release date. Interestingly, we detected a decrease in genetic diversity in wheat accessions released over the period from 1960 to 1980. However, our results also showed that modern plant breeding have succeeded in maintaining genetic diversity in modern wheat cultivars. Studying allelic frequencies using...... insight into alleles linked to important traits that have been the subject of positive or negative selection in the past and that may be useful for marker-assisted breeding programs in the future.......A collection of 189 bread wheat landraces and cultivars, primarily of European origin, released between 1886 and 2009, was analyzed using two DNA marker systems. A set of 76 SSR markers and ~7,000 DArT markers distributed across the wheat genome were employed in these analyses. All of the SSR...

  4. Uneven distribution of mating type alleles in Iranian populations of Cercospora beticola, the causal agent of Cercospora leaf spot disease of sugar beet

    Directory of Open Access Journals (Sweden)

    Mounes BAKHSHI

    2011-05-01

    Full Text Available Normal 0 14 false false false IT ZH-TW X-NONE MicrosoftInternetExplorer4 Cercospora beticola, the causal agent of Cercospora leaf spot disease on sugar beet, is thought to be exclusively asexual because no teleomorph has yet been found. The possibility of a clandestine sexual cycle in the Iranian population of Cercospora beticola was evaluated by analyzing the distribution and frequency of the mating type alleles on a microspatial and a macrogeographical scale. A total of 89 single-conidial Cercospora beticola isolates were obtained from sugar beet fields in the Moghan, the Talesh and the Khoy regions. The isolates were identifed using a Cercospora beticola-specifc primer set in a PCR assay. A multiplex PCR method using previously designed mating type primers was used to study the distribution and the frequency of the mating type alleles. All isolates showed either the 805-bp fragment or the 442-bp fragment of the MAT1-1 and MAT1-2 genes, but no isolate had both fragments. The distribution of the mating type genes in the sampled areas was uneven. From three sugar beet fields sampled in the Moghan region, two fields had only MAT1-1 isolates; while in the third field all isolates had only the MAT1-2 allele. In the Talesh region only MAT1-1 isolates occurred, and in the Khoy region the mating type alleles were uniformly distributed amongst the isolates. The skewed distribution of mating type alleles in Northwestern Iran was in line with the lack of a sexual cycle for this species and may also indicate that sugar fields in the Moghan region were infected by C. beticola populations of different origins. Normal 0 false false false EN-US X-NONE FA

  5. Prevalence of alpha-1 antitrypsin deficiency and allele frequency in patients with COPD in Brazil.

    Science.gov (United States)

    Russo, Rodrigo; Zillmer, Laura Russo; Nascimento, Oliver Augusto; Manzano, Beatriz; Ivanaga, Ivan Teruaki; Fritscher, Leandro; Lundgren, Fernando; Miravitlles, Marc; Gondim, Heicilainy Del Carlos; Santos, Gildo; Alves, Marcela Amorim; Oliveira, Maria Vera; Souza, Altay Alves Lino de; Sales, Maria Penha Uchoa; Jardim, José Roberto

    2016-01-01

    To determine the prevalence of alpha 1-antitrypsin (AAT) deficiency (AATD), as well as allele frequency, in COPD patients in Brazil. This was a cross-sectional study involving 926 COPD patients 40 years of age or older, from five Brazilian states. All patients underwent determination of AAT levels in dried blood spot (DBS) samples by nephelometry. Those with DBS AAT levels ≤ 2.64 mg/dL underwent determination of serum AAT levels. Those with serum AAT levels of sangue seco por meio de nefelometria. Aqueles em que a concentração de AAT no sangue seco foi ≤ 2,64 mg/dl foram submetidos a dosagem sérica de AAT. Aqueles em que a concentração sérica de AAT foi sangue seco ≤ 2,64 mg/dl, e 24 (2,6% da amostra) apresentaram concentração sérica de AAT < 113 mg/dl. A distribuição genotípica nesse subgrupo de 24 pacientes foi a seguinte: PI*MS, em 3 (12,5%); PI*MZ, em 13 (54,2%); PI*SZ, em 1 (4,2%); PI*SS, em 1 (4,2%); e PI*ZZ, em 6 (25,0%). Na amostra estudada, a prevalência global da deficiência de AAT foi de 2,8% e a prevalência do genótipo PI*ZZ (deficiência grave de AAT) foi de 0,8%. A prevalência da deficiência de AAT em pacientes com DPOC no Brasil é semelhante àquela encontrada na maioria dos países e reforça a recomendação de que se deve medir a concentração de AAT em todos pacientes com DPOC.

  6. Identification of internal variation in the pseudoautosomal VNTR DXYS17, with nonrandom distribution of the alleles on the X and the Y chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Decorte, R.; Wu, R.; Marynen, P.; Cassiman, J.J.

    1994-03-01

    The PCR technique was used to analyze the DXYS17 locus in the pseudoautosomal region of the X and the Y chromosomes. Analysis on an automated DNA sequencer allowed for sensitive and highly accurate typing of 16 different alleles with a size between 480 and 1,100 bp. Two DXYS17 alleles migrated with the same size on agarose or denaturing polyacrylamide gels but with different mobilities on nondenaturing polyacrylamide gels. Sequence analysis showed that, while an identical number of repeats were present in both alleles, differences in the composition of the units were observed. The origin of these differences was found in the 28- and 33-bp units, which only had a specific repeat pattern at the 5' and 3' ends of the region. The genotype distribution for DXYS17 in a Caucasian population did not deviate from the values expected under Hardy-Weinberg equilibrium. However, the frequency of one allele and one genotype was significantly different between males and females. Segregation analysis showed that this difference was the result of a nonrandom distribution of certain alleles on the sex chromosomes in males. 31 refs., 4 figs., 2 tabs.

  7. Population distribution of methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C risk alleles for methotrexate toxicity in Israel.

    Science.gov (United States)

    Efrati, Edna; Elkin, Hela; Nahum, Sagi; Krivoy, Norberto

    2013-04-01

    Methylenetetrahydrofolate reductase (MTHFR) is a central regulatory enzyme in the folate pathway. Two non-synonymous single nucleotide polymorphisms in MTHFR, C677T (rs1801133) and A1298C (rs1801131) have been associated with reduced MTHFR enzyme activity. These polymorphisms, especially C677T, appear to be linked with methotrexate-related toxicity, particularly hepatotoxicity; thus, pretreatment identification of individuals carrying these polymorphisms may be of clinical relevance. The purpose of this study was to determine the frequency and distribution of MTHFR polymorphic variants, known to functionally impair MTHFR activity, in the highly heterogeneous Israeli population. MTHFR genotyping was carried out in the representatives of three major demographic groups in Israel by PCR-restriction fragment length polymorphism and high-resolution melting. The relative distribution of variant alleles 677T and 1298C was found to be similar in individuals of Jewish, Druze and Arab Moslem descent (p = 0.09). However, Ashkenazi Jews displayed a 1.9-fold higher frequency of variant 677T and a 1.8-fold lower frequency of variant 1298C compared to non-Ashkenazi Jews (p A1298C) or Ashkenazi Jews and Arab Moslem (p A1298C). These data underscore the importance of geographic genetic analysis for a better understanding of human pharmacotherapy and personalized medicine.

  8. Inbreeding of bottlenecked butterfly populations. Estimation using the likelihood of changes in marker allele frequencies.

    Science.gov (United States)

    Saccheri, I J; Wilson, I J; Nichols, R A; Bruford, M W; Brakefield, P M

    1999-03-01

    Polymorphic enzyme and minisatellite loci were used to estimate the degree of inbreeding in experimentally bottlenecked populations of the butterfly, Bicyclus anynana (Satyridae), three generations after founding events of 2, 6, 20, or 300 individuals, each bottleneck size being replicated at least four times. Heterozygosity fell more than expected, though not significantly so, but this traditional measure of the degree of inbreeding did not make full use of the information from genetic markers. It proved more informative to estimate directly the probability distribution of a measure of inbreeding, sigma2, the variance in the number of descendants left per gene. In all bottlenecked lines, sigma2 was significantly larger than in control lines (300 founders). We demonstrate that this excess inbreeding was brought about both by an increase in the variance of reproductive success of individuals, but also by another process. We argue that in bottlenecked lines linkage disequilibrium generated by the small number of haplotypes passing through the bottleneck resulted in hitchhiking of particular marker alleles with those haplotypes favored by selection. In control lines, linkage disequilibrium was minimal. Our result, indicating more inbreeding than expected from demographic parameters, contrasts with the findings of previous (Drosophila) experiments in which the decline in observed heterozygosity was slower than expected and attributed to associative overdominance. The different outcomes may both be explained as a consequence of linkage disequilibrium under different regimes of inbreeding. The likelihood-based method to estimate inbreeding should be of wide applicability. It was, for example, able to resolve small differences in sigma2 among replicate lines within bottleneck-size treatments, which could be related to the observed variation in reproductive viability.

  9. CYP2D6 and CYP2C19 in Papua New Guinea: High frequency of previously uncharacterized CYP2D6 alleles and heterozygote excess.

    Science.gov (United States)

    von Ahsen, Nicolas; Tzvetkov, Mladen; Karunajeewa, Harin A; Gomorrai, Servina; Ura, Alice; Brockmöller, Jürgen; Davis, Timothy M E; Mueller, Ivo; Ilett, Kenneth F; Oellerich, Michael

    2010-08-18

    A high frequency of previously unknown CYP2D6 alleles have been reported in Oceania populations. Genetic and functional properties of these alleles remain unknown. We performed analyses of the genetic variability of CYP2D6 and CYP2C19 genes using AmpliChip genotyping in cohorts from two distinct Papua New Guinea (PNG) populations (Kunjingini, n=88; Alexishafen, n=84) focussing on the genetic characterisation of PNG-specific alleles by re-sequencing. Previously unknown CYP2D6 alleles have population frequencies of 24% (Kunjingini) and 12% (Alexishafen). An allele similar to CYP2D6*1, but carrying the 1661G>C substitution, was the second most frequent CYP2D6 allele (20% Kunjingini and 10% Alexishafen population frequency). Sequencing suggests the CYP2D6* 1661G>C allele originated from a cross-over between CYP2D6*1 and *2 and thus is predicted to confer fully active CYP2D6 enzyme. Two additional predicted full activity alleles [1661G>C;4180G>C] and 31G>A were found in the Kunjingini cohort (frequencies 3 c/c and 1%, respectively) and a novel predicted reduced activity allele [100C>T;1039C>T] was found in the Alexishafen cohort (frequency 2%). A high frequency of ultra-rapid (15%) and notably low frequencies of intermediate and poor CYP2D6 metabolizers (exogamy and recent introduction of alleles by migration that are yet to reach HWE in relatively isolated populations. The CYP2D6*1661 allele common in Oceania may be regarded as functionally equivalent to the full activity CYP2D6*1 allele.

  10. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes.

    Science.gov (United States)

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-11-11

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome.Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs.Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular

  11. Global Cyclone Hazard Frequency and Distribution

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Cyclone Hazard Frequency and Distribution is a 2.5 by 2.5 minute grid based on more than 1,600 storm tracks for the period 1 January 1980 through 31 December...

  12. High resolution human leukocyte antigen class I allele frequencies and HIV-1 infection associations in Chinese Han and Uyghur cohorts.

    Directory of Open Access Journals (Sweden)

    Yanhou Liu

    Full Text Available Host immunogenetic factors such as HLA class I polymorphism are important to HIV-1 infection risk and AIDS progression. Previous studies using high-resolution HLA class I profile data of Chinese populations appeared insufficient to provide information for HIV-1 vaccine development and clinical trial design. Here we reported HLA class I association with HIV-1 susceptibility in a Chinese Han and a Chinese Uyghur cohort.Our cohort included 327 Han and 161 Uyghur ethnic individuals. Each cohort included HIV-1 seropositive and HIV-1 seronegative subjects. Four-digit HLA class I typing was performed by sequencing-based typing and high-resolution PCR-sequence specific primer. We compared the HLA class I allele and inferred haplotype frequencies between HIV-1 seropositive and seronegative groups. A neighbor-joining tree between our cohorts and other populations was constructed based on allele frequencies of HLA-A and HLA-B loci. We identified 58 HLA-A, 75 HLA-B, and 32 HLA-Cw distinct alleles from our cohort and no novel alleles. The frequency of HLA-B*5201 and A*0301 was significantly higher in the Han HIV-1 negative group. The frequency of HLA-B*5101 was significantly higher in the Uyghur HIV-1 negative group. We observed statistically significant increases in expectation-maximization (EM algorithm predicted haplotype frequencies of HLA-A*0201-B*5101 in the Uyghur HIV-1 negative group, and of Cw*0304-B*4001 in the Han HIV-1 negative group. The B62s supertype frequency was found to be significantly higher in the Han HIV-1 negative group than in the Han HIV-1 positive group.At the four-digit level, several HLA class I alleles and haplotypes were associated with lower HIV-1 susceptibility. Homogeneity of HLA class I and Bw4/Bw6 heterozygosity were not associated with HIV-1 susceptibility in our cohort. These observations contribute to the Chinese HLA database and could prove useful in the development of HIV-1 vaccine candidates.

  13. Allele frequency present within the DYS635, DYS437, DYS448 ...

    African Journals Online (AJOL)

    Ejiro

    2015-03-11

    Mar 11, 2015 ... institute and courts of law. Key words: Allele ... individual identification and relatedness testing polymor- phic (Yamamoto et al. ... haplogroup an individual matches, STR analysis typically provides a person haplotype. Most tests on the Y chromosome examine between 12 and 67 STR markers. (Jobling et al.

  14. HLA-DRB and HLA-DQA/HLA-DQB allele and haplotype frequencies in Iranian patients with aggressive periodontitis.

    Science.gov (United States)

    Jazi, M Mousavi; Solgi, G; Roosta, H Asl; Noshad, S; Moslemi, N; Sadrimanesh, R; Moradi, B; Amirzargar, A A

    2013-08-01

    Genetic backgrounds play a key role in susceptibility to and protection against a spectrum of periodontal diseases. Like other infectious diseases, the human leukocyte antigen (HLA) have been found to be associated with periodontitis. This study aimed to investigate differences in allele and haplotype frequencies of HLA class II antigens in a sample of Iranian patients with aggressive periodontitis compared with a healthy control group. Fifty unrelated patients with aggressive periodontitis and 130 healthy volunteers were enrolled in this study. HLA genotyping for HLA-DRB, HLA-DQA1 and HLA-DQB1 was performed using the PCR with sequence-specific primers. Allele and haplotype frequencies were compared across groups. The frequencies of HLA-DQA1*03:01, HLA-DQB1*03:02 and HLA-DQB1*03:05 alleles, as well as that of the HLA-DRB1*04:01 allele, were significantly higher in patients with aggressive periodontitis compared with control subjects (p = 0.01, p = 0.04, p = 0.05 and p = 0.04, respectively). In contrast, the frequency of the HLA-DQB1*0603 allele was significantly lower in patients with aggressive periodontitis compared with control subjects (p = 0.006; odds ratio = 0.20). With regard to haplotype association, a significantly higher frequency of two haplotypes - HLA-DRB1*04:01/HLA-DQA1*03:01/HLA-DQB1*03:02 and HLA-DRB1*16:01/HLA-DQA1*01:03/HLA-DQB1*05:01 - was observed in patients with aggressive periodontitis compared with healthy controls (p = 0.01, odds ratio = 2.56 and p = 0.05, odds ratio = 5.38, respectively). These results provide additional evidence that class II HLA polymorphisms, particularly in the DQ locus, are associated with protection against and susceptibility to aggressive periodontitis. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  15. The distribution of the DRB4*01:03:01:02N null allele in HLA-DRB1~DQB1 haplotypes in the Croatian population.

    Science.gov (United States)

    Grubic, Z; Maskalan, M; Radmanic, L; Stingl Jankovic, K; Burek Kamenaric, M; Zunec, R

    2018-01-01

    The aim of the present study was to investigate frequency and haplotype distribution of DRB4 alleles in the Croatian population. The investigated sample consisted of 288 cadaveric donor samples positive for one of the DR53 alleles. HLA-A, -B, -C, -DRB1, and -DQB1 typing was performed using the polymerase chain reaction-sequence specific primers (PCR-SSP) low resolution method, while HLA-DRB4 and selected HLA class II specificities typing was performed using PCR-SSP at the allelic level. Three different DRB4 alleles were observed among DRB1*04 samples; DRB4*01:02 (2.38%), DRB4*01:03 (91.27%), and DRB4*01:03:01:02N (6.35%). The DRB4*01:03:01:02N allele was predominantly observed among DRB1*04:02-positive samples, while DRB4*01:02 and DRB4*01:03 alleles did not associate preferably with any of the DRB1*04 subtypes. Among DRB1*04~DRB4~DQB1 haplotypes, the predominant DQB1 allele was DQB1*03:02 (69.94%). Seven different DRB4 alleles were found among DRB1*07:01-positive samples. The analysis of DRB1*07~DRB4~DQB1 haplotypes showed that DRB4*01:03 was found in the majority of HLA-DRB1*07:01~DQB1*02:02 (49.09%) haplotypes while DRB1*07:01~DQB1*03:03 haplotypes carried the DRB4*01:03:01:02N allele almost exclusively (98.21%). Among six DRB1*09:01-positive samples, HLA-DRB1*09:01~DRB4*01:03~DQB1*03:03 was the only detected haplotype. The extended haplotype analysis showed a high frequency of HLA-B*15(B62)~C*03(Cw9)~DRB1*04:02~DRB4*01:03:01:02N~DQB1*03:02 and HLA-B*57~C*06~DRB1*07:01~DRB4*01:03:01:02N~DQB1*03:03 haplotypes. In conclusion, the data presented in this study should prompt other population studies focused on DRB3/4/5 genes and be used as a basis for future investigations of the clinical relevance of these genes in transplantation setting. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Development of a high resolution melting method for genotyping of risk HLA-DQA1 and PLA2R1 alleles and ethnic distribution of these risk alleles.

    Science.gov (United States)

    Cui, Guanglin; Zhang, Lina; Xu, Yujun; Cianflone, Katherine; Ding, Hu; Wang, Dao Wen

    2013-02-10

    Recent studies have demonstrated that alleles at single nucleotide polymorphisms (SNPs) rs2187668 and rs4664308 within genes HLA-DQA1 and PLA2R1, respectively, had a significant impact on the susceptibility to idiopathic membranous nephropathy (IMN). Analysis of the two genomic loci could identify alleles for individuals at risk for IMN. Conventional methods for genotyping are labor intensive, expensive or time consuming. High resolution melting (HRM) is a new technique for genotyping and has the advantages of simplicity, speed, high sensitivity and low cost. Here, we describe genotyping of SNPs rs2187668 and rs4664308 using HRM. In this study, we identified polymorphisms of rs2187668 and rs4664308 in 480 healthy unrelated Chinese volunteers of two ethnic groups from three different geographical areas in China. The two genomic loci were genotyped by HRM using a saturating fluorescent dye SYTO® 9 on 7900 HT and RG 6000 instruments, and were further confirmed by direct DNA sequencing. Three different SNP genotypes were sufficiently distinguished by HRM with mean sensitivity of 98.8% and mean error rate of 1.9%. In addition, the allele frequencies varied greatly based on ethnic or geographic origins. In conclusion, HRM is a rapid, cost efficient, sensitive, suitable technique for genotyping, and simple enough to be readily implemented in a diagnostic laboratory. We believe this will be a valuable technique for determining the genotype of rs2187668 and rs4664308 and for assessing individual susceptibility to IMN. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. ACTN3 allele frequency in humans covaries with global latitudinal gradient.

    Directory of Open Access Journals (Sweden)

    Scott M Friedlander

    Full Text Available A premature stop codon in ACTN3 resulting in α-actinin-3 deficiency (the ACTN3 577XX genotype is common in humans and reduces strength, muscle mass, and fast-twitch fiber diameter, but increases the metabolic efficiency of skeletal muscle. Linkage disequilibrium data suggest that the ACTN3 R577X allele has undergone positive selection during human evolution. The allele has been hypothesized to be adaptive in environments with scarce resources where efficient muscle metabolism would be selected. Here we test this hypothesis by using recently developed comparative methods that account for evolutionary relatedness and gene flow among populations. We find evidence that the ACTN3 577XX genotype evolved in association with the global latitudinal gradient. Our results suggest that environmental variables related to latitudinal variation, such as species richness and mean annual temperature, may have influenced the adaptive evolution of ACTN3 577XX during recent human history.

  18. Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations.

    Science.gov (United States)

    González-Galarza, Faviel F; Takeshita, Louise Y C; Santos, Eduardo J M; Kempson, Felicity; Maia, Maria Helena Thomaz; da Silva, Andrea Luciana Soares; Teles e Silva, André Luiz; Ghattaoraya, Gurpreet S; Alfirevic, Ana; Jones, Andrew R; Middleton, Derek

    2015-01-01

    It has been 12 years since the Allele Frequency Net Database (AFND; http://www.allelefrequencies.net) was first launched, providing the scientific community with an online repository for the storage of immune gene frequencies in different populations across the world. There have been a significant number of improvements from the first version, making AFND a primary resource for many clinical and scientific areas including histocompatibility, immunogenetics, pharmacogenetics and anthropology studies, among many others. The most widely used part of AFND stores population frequency data (alleles, genes or haplotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex class I chain-related genes (MIC) and a number of cytokine gene polymorphisms. AFND now contains >1400 populations from more than 10 million healthy individuals. Here, we report how the main features of AFND have been updated to include a new section on 'HLA epitope' frequencies in populations, a new section capturing the results of studies identifying HLA associations with adverse drug reactions (ADRs) and one for the examination of infectious and autoimmune diseases associated with KIR polymorphisms-thus extending AFND to serve a new user base in these growing areas of research. New criteria on data quality have also been included. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Type I plasminogen activator inhibitor 4G allele frequency is associated with chronic venous insufficiency.

    Science.gov (United States)

    Katrancioglu, N; Manduz, S; Ozen, F; Yilmaz, M Birhan; Karahan, O; Ozdemir, O; Berkan, O

    2010-01-01

    Chronic venous insufficiency (CVI) is a common disease associated with poor quality of life. Genetic polymorphisms causing coagulation abnormalities may account for some of the CVI pathogenesis. Type I plasminogen activator inhibitor (PAI-1) is responsible for fibrinolytic system regulation, and plasma levels of PAI-1 are strongly correlated with PAI-1 4G/5G gene polymorphism. The association between PAI-1 4G/5G gene polymorphism and CVI was investigated. In 34 consecutive patients with clinically overt CVI, the PAI-1 4G/4G polymorphism was detected in three cases (8.8%); the 4G/5G polymorphism was detected in 28 (82.4%). In 34 age- and sex-matched controls, the PAI-1 4G/4G polymorphism was detected in one case (2.9%) and the 4G/5G polymorphism was detected in 14 cases (41.2%). The PAI-1 4G allele was found significantly more frequently in CVI patients than in controls. The 4G allele was associated with a 3.25-fold increase in CVI risk. Thus, a relationship between CVI and the PAI-1 4G allele is apparent.

  20. Inverter design for high frequency power distribution

    Science.gov (United States)

    King, R. J.

    1985-01-01

    A class of simple resonantly commutated inverters are investigated for use in a high power (100 KW - 1000 KW) high frequency (10 KHz - 20 KHz) AC power distribution system. The Mapham inverter is found to provide a unique combination of large thyristor turn-off angle and good utilization factor, much better than an alternate 'current-fed' inverter. The effects of loading the Mapham inverter entirely with rectifier loads are investigated by simulation and with an experimental 3 KW 20 KHz inverter. This inverter is found to be well suited to a power system with heavy rectifier loading.

  1. The allele frequency of two single nucleotide polymorphisms in the von Hippel-Lindau (VHL tumor suppressor gene in the Taiwanese population

    Directory of Open Access Journals (Sweden)

    Wen-Chung Wang

    2011-10-01

    Conclusion: We found that the G allele frequency at these two loci in the Taiwanese population is much lower than that in people from Western countries. This phenomenon may be attributed to ethnic effects.

  2. The SCA1 (Spinocerebellar ataxia type 1 and MJD (Machado-Joseph disease CAG repeats in normal individuals: segregation analysis and allele frequencies

    Directory of Open Access Journals (Sweden)

    Wiezel Cláudia Emília Vieira

    2003-01-01

    Full Text Available Spinocerebellar ataxia type 1 (SCA1 and Machado-Joseph disease (MJD/SCA3 are autosomal dominant neurodegenerative diseases caused by expansions of a CAG trinucleotide repeat in the SCA1 and MJD genes. These expanded sequences are unstable upon transmission, leading to an intergeneration increase in the number of repeats (dynamic mutation. The transmission of the CAG repeat was studied in normal mother-father-child trios, referred for paternity testing (SCA1, n = 367; MJD, n = 879. No segregation distortion was detected. The CAG allele frequencies were determined in 330 unrelated individuals (fathers from couples tested for paternity. The allele frequency distributions did not differ from those previously reported for European populations. The estimated values for the statistic parameters indicating diversity at the SCA1 locus did not differ much from those reported previously for other STRs in the Brazilian population, while those for the MJD locus were close to or higher than the maximum values of previous reports. This shows that SCA1 and MJD are highly informative loci for applications in genetic and population studies and for forensic analysis.

  3. Is the European spatial distribution of the HIV-1-resistant CCR5-Delta32 allele formed by a breakdown of the pathocenosis due to the historical Roman expansion?

    Science.gov (United States)

    Faure, Eric; Royer-Carenzi, Manuela

    2008-12-01

    We studied the possible effects of the expansion of ancient Mediterranean civilizations during the five centuries before and after Christ on the European distribution of the mutant allele for the chemokine receptor gene CCR5 which has a 32-bp deletion (CCR5-Delta32). There is a strong evidence for the unitary origin of the CCR5-Delta32 mutation, this it is found principally in Europe and Western Asia, with generally a north-south downhill cline frequency. Homozygous carriers of this mutation show a resistance to HIV-1 infection and a slower progression towards AIDS. However, HIV has clearly emerged too recently to have been the selective force on CCR5. Our analyses showed strong negative correlations in Europe between the allele frequency and two historical parameters, i.e. the first colonization dates by the great ancient Mediterranean civilizations, and the distances from the Northern frontiers of the Roman Empire in its greatest expansion. Moreover, other studies have shown that the deletion frequencies in both German Bronze Age and Swedish Neolithic populations were similar to those found in the corresponding modern populations, and this deletion has been found in ancient DNA of around 7000 years ago, suggesting that in the past, the deletion frequency could have been relatively high in European populations. In addition, in West Nile virus pathogenesis, CCR5 plays an antimicrobial role showing that host genetic factors are highly pathogen-specific. Our results added to all these previous data suggest that the actual European allele frequency distribution might not be due to genes spreading, but to a negative selection resulting in the spread of pathogens principally during Roman expansion. Indeed, as gene flows from colonizers to European native populations were extremely low, the mutational changes might be associated with vulnerability to imported infections. To date, the nature of the parasites remains unknown; however, zoonoses could be incriminated.

  4. Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar).

    Science.gov (United States)

    Johnston, Susan E; Lindqvist, Meri; Niemelä, Eero; Orell, Panu; Erkinaro, Jaakko; Kent, Matthew P; Lien, Sigbjørn; Vähä, Juha-Pekka; Vasemägi, Anti; Primmer, Craig R

    2013-07-03

    DNA extracted from historical samples is an important resource for understanding genetic consequences of anthropogenic influences and long-term environmental change. However, such samples generally yield DNA of a lower amount and quality, and the extent to which DNA degradation affects SNP genotyping success and allele frequency estimation is not well understood. We conducted high density SNP genotyping and allele frequency estimation in both individual DNA samples and pooled DNA samples extracted from dried Atlantic salmon (Salmo salar) scales stored at room temperature for up to 35 years, and assessed genotyping success, repeatability and accuracy of allele frequency estimation using a high density SNP genotyping array. In individual DNA samples, genotyping success and repeatability was very high (> 0.973 and > 0.998, respectively) in samples stored for up to 35 years; both increased with the proportion of DNA of fragment size > 1000 bp. In pooled DNA samples, allele frequency estimation was highly repeatable (Repeatability = 0.986) and highly correlated with empirical allele frequency measures (Mean Adjusted R2 = 0.991); allele frequency could be accurately estimated in > 95% of pooled DNA samples with a reference group of at least 30 individuals. SNPs located in polyploid regions of the genome were more sensitive to DNA degradation: older samples had lower genotyping success at these loci, and a larger reference panel of individuals was required to accurately estimate allele frequencies. SNP genotyping was highly successful in degraded DNA samples, paving the way for the use of degraded samples in SNP genotyping projects. DNA pooling provides the potential for large scale population genetic studies with fewer assays, provided enough reference individuals are also genotyped and DNA quality is properly assessed beforehand. We provide recommendations for future studies intending to conduct high-throughput SNP genotyping and allele frequency estimation in

  5. Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies.

    Directory of Open Access Journals (Sweden)

    Marie L Hale

    Full Text Available One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is "how many individuals do I need to sample from each population?" This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses. However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5-100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect, population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise F(ST values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.

  6. Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies

    Science.gov (United States)

    Hale, Marie L.; Burg, Theresa M.; Steeves, Tammy E.

    2012-01-01

    One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is “how many individuals do I need to sample from each population?” This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5–100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise FST values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies. PMID:22984627

  7. The immunogenetics of multiple sclerosis. The frequency of HLA-alleles class 1 and 2 is lower in Southern Brazil than in the European population

    Directory of Open Access Journals (Sweden)

    Lineu Cesar Werneck

    2016-08-01

    Full Text Available ABSTRACT Objective To study the HLA of class 1and 2 in a multiple sclerosis (MS population to verify the susceptibility for the disease in the Southern Brazil. Methods We analyzed patients with MS and controls, by direct sequencing of the genes related to HLA DRB1, DQB1, DPB1, A, B and C alleles with high resolution techniques. Results We found a lower frequency of all HLA alleles class 1 and 2 in MS and controls comparing to the European population. Several alleles had statistical correlation, but after Bonferroni correction, the only allele with significance was the HLA-DQB1*02:03, which has a positive association with MS. Conclusions Our data have different frequency of HLA-alleles than the previous published papers in the Southeast Brazil and European population, possible due to several ethnic backgrounds.

  8. Asymptotic Time Averages and Frequency Distributions

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    Muhammad El-Taha

    2016-01-01

    Full Text Available Consider an arbitrary nonnegative deterministic process (in a stochastic setting {X(t,  t≥0} is a fixed realization, i.e., sample-path of the underlying stochastic process with state space S=(-∞,∞. Using a sample-path approach, we give necessary and sufficient conditions for the long-run time average of a measurable function of process to be equal to the expectation taken with respect to the same measurable function of its long-run frequency distribution. The results are further extended to allow unrestricted parameter (time space. Examples are provided to show that our condition is not superfluous and that it is weaker than uniform integrability. The case of discrete-time processes is also considered. The relationship to previously known sufficient conditions, usually given in stochastic settings, will also be discussed. Our approach is applied to regenerative processes and an extension of a well-known result is given. For researchers interested in sample-path analysis, our results will give them the choice to work with the time average of a process or its frequency distribution function and go back and forth between the two under a mild condition.

  9. Different HLA-DRB1 allele distributions in distinct clinical subgroups of sarcoidosis patients

    Directory of Open Access Journals (Sweden)

    Nisell Magnus

    2010-02-01

    Full Text Available Abstract Background A strong genetic influence by the MHC class II region has been reported in sarcoidosis, however in many studies with different results. This may possibly be caused by actual differences between distinct ethnic groups, too small sample sizes, or because of lack of accurate clinical subgrouping. Subjects and methods In this study we HLA typed a large patient population (n = 754 recruited from one single centre. Patients were sub-grouped into those with Löfgren's syndrome (LS (n = 302 and those without (non-Löfgren's (n = 452, and the majority of them were clinically classified into those with recovery within two years (resolving and those with signs of disease for more than two years (non-resolving. PCR was used for determination of HLA-DRB1 alleles. Swedish healthy blood donors (n = 1366 served as controls. Results There was a dramatic difference in the distribution of HLA alleles in LS compared to non-LS patients (p = 4 × 10-36. Most notably, DRB1*01, DRB1*03 and DRB1*14, clearly differed in LS and non-LS patients. In relation to disease course, DRB1*07, DRB1*14 and DRB1*15 generally associated with, while DRB1*01 and DRB1*03 protected against, a non-resolving disease. Interestingly, the clinical influence of DRB1*03 (good prognosis dominated over that of DRB1*15 (bad prognosis. Conclusions We found several significant differences between LS and non-LS patients and we therefore suggest that genetic association studies in sarcoidosis should include a careful clinical characterisation and sub-grouping of patients, in order to reveal true genetic associations. This may be particularly accurate to do in the heterogeneous non-LS group of patients.

  10. Allelic Diversity and Geographical Distribution of the Gene Encoding Plasmodium falciparum Merozoite Surface Protein-3 in Thailand.

    Science.gov (United States)

    Sawaswong, Vorthon; Simpalipan, Phumin; Siripoon, Napaporn; Harnyuttanakorn, Pongchai; Pattaradilokrat, Sittiporn

    2015-04-01

    Merozoite surface proteins (MSPs) of malaria parasites play critical roles during the erythrocyte invasion and so are potential candidates for malaria vaccine development. However, because MSPs are often under strong immune selection, they can exhibit extensive genetic diversity. The gene encoding the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum displays 2 allelic types, K1 and 3D7. In Thailand, the allelic frequency of the P. falciparum msp-3 gene was evaluated in a single P. falciparum population in Tak at the Thailand and Myanmar border. However, no study has yet looked at the extent of genetic diversity of the msp-3 gene in P. falciparum populations in other localities. Here, we genotyped the msp-3 alleles of 63 P. falciparum samples collected from 5 geographical populations along the borders of Thailand with 3 neighboring countries (Myanmar, Laos, and Cambodia). Our study indicated that the K1 and 3D7 alleles coexisted, but at different proportions in different Thai P. falciparum populations. K1 was more prevalent in populations at the Thailand-Myanmar and Thailand-Cambodia borders, whilst 3D7 was more prevalent at the Thailand-Laos border. Global analysis of the msp-3 allele frequencies revealed that proportions of K1 and 3D7 alleles of msp-3 also varied in different continents, suggesting the divergence of malaria parasite populations. In conclusion, the variation in the msp-3 allelic patterns of P. falciparum in Thailand provides fundamental knowledge for inferring the P. falciparum population structure and for the best design of msp-3 based malaria vaccines.

  11. Allele frequencies of human platelet antigens in Banjar, Bugis, Champa, Jawa and Kelantan Malays in Peninsular Malaysia.

    Science.gov (United States)

    Wan Syafawati, W U; Norhalifah, H K; Zefarina, Z; Zafarina, Z; Panneerchelvam, S; Norazmi, M N; Chambers, G K; Edinur, H A

    2015-10-01

    The major aims of this study are to characterise and compile allelic data of human platelet antigen (HPA)-1 to -6 and -15 systems in five Malay sub-ethnic groups in Peninsular Malaysia. HPAs are polymorphic glycoproteins expressed on the surface of platelet membranes and are genetically differentiated across ethnogeographically unrelated populations. Blood samples were obtained with informed consent from 192 volunteers: Banjar (n = 30), Bugis (n = 37), Champa (n = 51), Jawa (n = 39) and Kelantan (n = 35). Genotyping was done using polymerase chain reaction-sequence specific primer method. In general, frequencies of HPAs in the Malay sub-ethnic groups are more similar to those in Asian populations compared with other more distinct populations such as Indians, Australian Aborigines and Europeans. This study provides the first HPA datasets for the selected Malay sub-ethnic groups. Subsequent analyses including previously reported HPA data of Malays, Chinese and Indians revealed details of the genetic relationships and ancestry of various sub-populations in Peninsular Malaysia. Furthermore, the comprehensive HPA allele frequency information from Peninsular Malaysia provided in this report has potential applications for future study of diseases, estimating risks associated with HPA alloimmunization and for developing an efficient HPA-typed donor recruitment strategy. © 2015 British Blood Transfusion Society.

  12. The allelic distribution of -308 Tumor Necrosis Factor-alpha gene polymorphism in South African women with cervical cancer and control women

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    Williamson Anna-Lise

    2006-01-01

    Full Text Available Abstract Background Cervical cancer is due to infection with specific high-risk types of human papillomavirus (HPV. Although the incidence of genital HPV infection in various population groups is high, most of these regress without intervention. Investigating genetic host factors and cellular immune responses, particularly cytokines, could help to understand the association between genital HPV infection and carcinogenesis. The tumor necrosis factor alpha (TNF-α cytokine plays an important role in all stages of cervical cancer and has the ability to induce the regression of human tumors. Therefore the aim of the study was to investigate the allelic distribution of -308 TNF-α gene polymorphism in South African women with cervical cancer compared to control women. Methods Included in our study were women with histologically proven cancer of the cervix (n = 244 and hospital-based controls (n = 228. All patients and controls were from mixed race and black population groups in South Africa. The detection of a bi-allelic -308 (A/G polymorphism in the promoter region of TNF-α was investigated using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR technique. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups. Results In this study we observed no association between the distribution of -308 TNF-α polymorphism and the risk of developing cervical cancer even after combining the data from the two ethnic populations (X2 = 2.26. In addition, using the chi-squared test we found no significant association between the known risk factors for cervical cancer and the allele distribution of -308 TNF-α. However, the frequency of the rare high-producing allele -308A of TNF-α was significantly lower in the South African population when compared to Caucasians and Chinese population groups. Conclusion We demonstrated no association between -308 TNF

  13. The allelic distribution of -308 Tumor Necrosis Factor-alpha gene polymorphism in South African women with cervical cancer and control women

    International Nuclear Information System (INIS)

    Govan, Vandana A; Constant, Debbie; Hoffman, Margaret; Williamson, Anna-Lise

    2006-01-01

    Cervical cancer is due to infection with specific high-risk types of human papillomavirus (HPV). Although the incidence of genital HPV infection in various population groups is high, most of these regress without intervention. Investigating genetic host factors and cellular immune responses, particularly cytokines, could help to understand the association between genital HPV infection and carcinogenesis. The tumor necrosis factor alpha (TNF-α) cytokine plays an important role in all stages of cervical cancer and has the ability to induce the regression of human tumors. Therefore the aim of the study was to investigate the allelic distribution of -308 TNF-α gene polymorphism in South African women with cervical cancer compared to control women. Included in our study were women with histologically proven cancer of the cervix (n = 244) and hospital-based controls (n = 228). All patients and controls were from mixed race and black population groups in South Africa. The detection of a bi-allelic -308 (A/G) polymorphism in the promoter region of TNF-α was investigated using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) technique. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups. In this study we observed no association between the distribution of -308 TNF-α polymorphism and the risk of developing cervical cancer even after combining the data from the two ethnic populations (X 2 = 2.26). In addition, using the chi-squared test we found no significant association between the known risk factors for cervical cancer and the allele distribution of -308 TNF-α. However, the frequency of the rare high-producing allele -308A of TNF-α was significantly lower in the South African population when compared to Caucasians and Chinese population groups. We demonstrated no association between -308 TNF-α polymorphism and the risk of cervical cancer among two

  14. Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly.

    Science.gov (United States)

    van Hooft, Pim; Greyling, Ben J; Getz, Wayne M; van Helden, Paul D; Zwaan, Bas J; Bastos, Armanda D S

    2014-01-01

    Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations), we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has important

  15. Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly.

    Directory of Open Access Journals (Sweden)

    Pim van Hooft

    Full Text Available Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations, we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has

  16. High frequency of the DRD2/ANKK1 A1 allele in Mexican Native Amerindians and Mestizos and its association with alcohol consumption.

    Science.gov (United States)

    Panduro, Arturo; Ramos-Lopez, Omar; Campollo, Octavio; Zepeda-Carrillo, Eloy Alfonso; Gonzalez-Aldaco, Karina; Torres-Valadez, Rafael; Roman, Sonia

    2017-03-01

    Mexico has an ancient tradition of alcohol drinking influenced by genetic and sociocultural factors. This study aimed to determine the distribution of the DRD2/ANKK1 TaqIA polymorphism in Mexican populations and to analyze its association with heavy drinking. In a cross-sectional and analytical study, 680 unrelated subjects including two Native Amerindians groups (87 Nahuas and 139 Huicholes), and two Mestizos groups (158 subjects from Tepic, Nayarit and 296 subjects from Guadalajara, Jalisco) were enrolled. DRD2/ANKK1 genotyping was performed by PCR-RFLP and allelic discrimination assays. Genetic analyses were conducted by Arlequin and Structure software. Heavy drinking was defined as ≥300g alcohol/week. The association of the DRD2/ANKK1 TaqIA polymorphism with heavy drinking was estimated. Heavy drinking was prevalent in 64.7% of the study population. The DRD2/ANKK1 A1 allele prevailed in 67% and 65% of Nahuas and Huicholes, respectively and 51% and 47.3% in Mestizos from Tepic and Guadalajara, respectively. Heavy drinking was associated with the A1A1 genotype in the Mestizos of Guadalajara (A1A1 vs. A1A2 OR=4.79, 95%CI 1.81-12.68, p=0.0006; A1A1 vs. A1A2+A2A2, OR=4.09, 95%CI 1.56-10.68, p=0.0021) and in the Mestizos from Tepic (A1A1 vs. A1A2, OR=5.92, 95%CI 2.12-16.49, p=0.0002); A2A2, OR=14.56, 95%CI 3.57-59.24, p=0.00004); A1A2+A2A2, OR=6.68, 95%CI 2.42-18.42, p=0.00005). In Native Amerindians, a lack of association was found. High frequencies of the DRD2/ANKK1 A1 allele were present in Mexican populations. Native Amerindians exhibited the highest frequencies of the A1 allele documented worldwide to date. The A1A1 genotype was associated with heavy drinking in Mestizos. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers.

    Science.gov (United States)

    Hippolyte, I; Jenny, C; Gardes, L; Bakry, F; Rivallan, R; Pomies, V; Cubry, P; Tomekpe, K; Risterucci, A M; Roux, N; Rouard, M; Arnaud, E; Kolesnikova-Allen, M; Perrier, X

    2012-04-01

    The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships. Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed. We determine the closest diploid progenitors of the triploid 'Cavendish' and 'Gros Michel' subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. 'Cavendish', 'Plantain' and 'Mutika-Lujugira'), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference.

  18. Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: Potential breast cancer risk alleles and their distribution across human populations

    Directory of Open Access Journals (Sweden)

    Savas Sevtap

    2006-03-01

    Full Text Available Abstract Although highly penetrant alleles of BRCA1 and BRCA2 have been shown to predispose to breast cancer, the majority of breast cancer cases are assumed to result from the presence of low-moderate penetrant alleles and environmental carcinogens. Non-synonymous single nucleotide polymorphisms (nsSNPs are hypothesised to contribute to disease susceptibility and approximately 30 per cent of them are predicted to have a biological significance. In this study, we have applied a bioinformatics-based strategy to identify breast cancer-related nsSNPs from 981 carcinogenesis-related genes expressed in breast tissue. Our results revealed a total of 367 validated nsSNPs, 109 (29.7 per cent of which are predicted to affect the protein function (functional nsSNPs, suggesting that these nsSNPs are likely to influence the development and homeostasis of breast tissue and hence contribute to breast cancer susceptibility. Sixty-seven of the functional nsSNPs presented as commonly occurring nsSNPs (minor allele frequencies ≥ 5 per cent, representing excellent candidates for breast cancer susceptibility. Additionally, a non-uniform distribution of the common functional nsSNPs among different human populations was observed: 15 nsSNPs were reported to be present in all populations analysed, whereas another set of 15 nsSNPs was specific to particular population(s. We propose that the nsSNPs analysed in this study constitute a unique resource of potential genetic factors for breast cancer susceptibility. Furthermore, the variations in functional nsSNP allele frequencies across major population backgrounds may point to the potential variability of the molecular basis of breast cancer predisposition and treatment response among different human populations.

  19. Frequency of alleles conferring resistance to the Bacillus thuringiensis toxins Cry1Ac and Cry2Ab in Australian populations of Helicoverpa punctigera (Lepidoptera: Noctuidae) from 2002 to 2006.

    Science.gov (United States)

    Downes, S; Parker, T L; Mahon, R J

    2009-04-01

    Helicoverpa punctigera and Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) are important pests of field and horticultural crops in Australia. The former is endemic to the continent, whereas the latter is also distributed in Africa and Asia. Although H. armigera rapidly developed resistance to virtually every group of insecticide used against it, there is only one report of resistance to an insecticide in H. punctigera. In 1996 the Australian cotton industry adopted Ingard, which expresses the Bacillus thuringiensis (Bt) toxin gene cry1Ac. In 2004/2005, Bollgard II (which expresses Cry1Ac and Cry2Ab) replaced Ingard and has subsequently been grown on 80% of the area planted to cotton, Gossypium hirsutum L. From 2002/2003 to 2006/2007, F2 screens were used to detect resistance to Cry1Ac or Cry2Ab. We detected no alleles conferring resistance to Cry1Ac; the frequency was < 0.0005 (n = 2,180 alleles), with a 95% credibility interval between 0 and 0.0014. However, during the same period, we detected alleles that confer resistance to Cry2Ab at a frequency of 0.0018 (n = 2,192 alleles), with a 95% credibility interval between 0.0005 and 0.0040. For both toxins, the experiment-wise detection probability was 94%, i.e., if there actually was a resistance allele in any tested lines, we would have detected it 94% of the time. The first isolation of Cry2Ab resistance in H. punctigera was before the widespread deployment of Bollgard II. This finding supports our published notion for H. armigera that alleles conferring resistance to Cry2Ab may be present at detectable frequencies in populations before selection by transgenic crops.

  20. Analysis of the CCR5 gene coding region diversity in five South American populations reveals two new non-synonymous alleles in Amerindians and high CCR5*D32 frequency in Euro-Brazilians

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    Angelica B.W. Boldt

    2009-01-01

    Full Text Available The CC chemokine receptor 5 (CCR5 molecule is an important co-receptor for HIV. The effect of the CCR5*D32 allele in susceptibility to HIV infection and AIDS disease is well known. Other alleles than CCR5*D32 have not been analysed before, neither in Amerindians nor in the majority of the populations all over the world. We investigated the distribution of the CCR5 coding region alleles in South Brazil and noticed a high CCR5*D32 frequency in the Euro-Brazilian population of the Paraná State (9.3%, which is the highest thus far reported for Latin America. The D32 frequency is even higher among the Euro-Brazilian Mennonites (14.2%. This allele is uncommon in Afro-Brazilians (2.0%, rare in the Guarani Amerindians (0.4% and absent in the Kaingang Amerindians and the Oriental-Brazilians. R223Q is common in the Oriental-Brazilians (7.7% and R60S in the Afro-Brazilians (5.0%. A29S and L55Q present an impaired response to b-chemokines and occurred in Afro- and Euro-Brazilians with cumulative frequencies of 4.4% and 2.7%, respectively. Two new non-synonymous alleles were found in Amerindians: C323F (g.3729G > T in Guarani (1.4% and Y68C (g.2964A > G in Kaingang (10.3%. The functional characteristics of these alleles should be defined and considered in epidemiological investigations about HIV-1 infection and AIDS incidence in Amerindian populations.

  1. Allele frequencies of 18 autosomal STR loci in the Uyghur population living in Kashgar Prefecture, Northwest China.

    Science.gov (United States)

    Zhang, Jian; Li, Zhenghui; Mo, Xiaoting; Ma, Wenhua; Zhang, Hantao; Lin, Ziqing; Ye, Jian

    2018-03-10

    There is currently no large population data-based data set in Kashgar Prefecture Uyghur. The allele frequencies of 18 autosomal short tandem repeat (STR) loci included in the DNATyper™ 19 kit were evaluated in 2600 Uyghur individuals living in Kashgar Prefecture, Northwest China. The values of combined power of discrimination (CPD) and combined probability of exclusion (CPE) of all 18 autosomal STR loci were 0.99999999999999999998235 and 0.99999998670, respectively. Phylogenetic analyses revealed that the Uyghur population has a closer relationship with the Xinjiang-Kazakh, Inner Mongolia-Mongolian, and other three Uyghur populations. In addition, our results are consistent with the hypothesis that Uyghur population is an admixture of Eastern Asian and European populations.

  2. High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program.

    Science.gov (United States)

    Zhou, Xiao-Yang; Zhu, Fa-Ming; Li, Jian-Ping; Mao, Wei; Zhang, De-Mei; Liu, Meng-Li; Hei, Ai-Lian; Dai, Da-Peng; Jiang, Ping; Shan, Xiao-Yan; Zhang, Bo-Wei; Zhu, Chuan-Fu; Shen, Jie; Deng, Zhi-Hui; Wang, Zheng-Lei; Yu, Wei-Jian; Chen, Qiang; Qiao, Yan-Hui; Zhu, Xiang-Ming; Lv, Rong; Li, Guo-Ying; Li, Guo-Liang; Li, Heng-Cong; Zhang, Xu; Pei, Bin; Jiao, Li-Xin; Shen, Gang; Liu, Ying; Feng, Zhi-Hui; Su, Yu-Ping; Xu, Zhao-Xia; Di, Wen-Ying; Jiang, Yao-Qin; Fu, Hong-Lei; Liu, Xiang-Jun; Liu, Xiang; Zhou, Mei-Zhen; Du, Dan; Liu, Qi; Han, Ying; Zhang, Zhi-Xin; Cai, Jian-Ping

    2015-01-01

    Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis

  3. Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies.

    Science.gov (United States)

    Papadopoulos, Petros; Viennas, Emmanouil; Gkantouna, Vassiliki; Pavlidis, Cristiana; Bartsakoulia, Marina; Ioannou, Zafeiria-Marina; Ratbi, Ilham; Sefiani, Abdelaziz; Tsaknakis, John; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P

    2014-01-01

    FINDbase (http://www.findbase.org) aims to document frequencies of clinically relevant genomic variations, namely causative mutations and pharmacogenomic markers, worldwide. Each database record includes the population, ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related databases and the genetic variation together with its frequency in that population. Here, we report, in addition to the regular data content updates, significant developments in FINDbase, related to data visualization and querying, data submission, interrelation with other resources and a new module for genetic disease summaries. In particular, (i) we have developed new data visualization tools that facilitate data querying and comparison among different populations, (ii) we have generated a new FINDbase module, built around Microsoft's PivotViewer (http://www.getpivot.com) software, based on Microsoft Silverlight technology (http://www.silverlight.net), that includes 259 genetic disease summaries from five populations, systematically collected from the literature representing the documented genetic makeup of these populations and (iii) the implementation of a generic data submission tool for every module currently available in FINDbase.

  4. ABCC8 mutation allele frequency in the Ashkenazi Jewish population and risk of focal hyperinsulinemic hypoglycemia.

    Science.gov (United States)

    Glaser, Benjamin; Blech, Ilana; Krakinovsky, Yocheved; Ekstein, Josef; Gillis, David; Mazor-Aronovitch, Kineret; Landau, Heddy; Abeliovich, Dvorah

    2011-10-01

    Congenital hyperinsulinism of infancy (OMIM# 256450) is a devastating disease most commonly caused by dominant or recessive mutations in either ABCC8 or KCNJ11, the genes that encode for the β-cell adenosine triphosphate-regulated potassium channel. A unique combination of a paternally inherited germline mutation and somatic loss-of-heterozygosity causes the focal form of the disease (Focal-congenital hyperinsulinism of infancy [Focal-CHI]), the incidence of which in genetically susceptible individuals is not known. We genotyped 21,122 Ashkenazi Jewish individuals for two previously identified ABCC8 founder mutations and utilized a clinical database of 61 unrelated Ashkenazi patients with congenital hyperinsulinism of infancy to obtain an estimate of the risk of Focal-CHI in a genetically susceptible fetus. The combined mutation carrier rate in Ashkenazi Jews was 1:52, giving an estimated frequency of homozygosity or compound heterozygosity of 1:10,816 in this population. The risk of Focal-CHI is 1:540 per pregnancy in offspring of carrier fathers. We recommend that these mutations be included in the genetic screening program for the Ashkenazi Jewish population. As the risk of Focal-CHI is not expected to be mutation specific, the data reported in this study are useful for counseling all families in which the father was found to carry a recessive ABCC8 or KCNJ11 mutation.

  5. Zipfian Frequency Distributions Facilitate Word Segmentation in Context

    Science.gov (United States)

    Kurumada, Chigusa; Meylan, Stephan C.; Frank, Michael C.

    2013-01-01

    Word frequencies in natural language follow a highly skewed Zipfian distribution, but the consequences of this distribution for language acquisition are only beginning to be understood. Typically, learning experiments that are meant to simulate language acquisition use uniform word frequency distributions. We examine the effects of Zipfian…

  6. Further testing ofMelatonin Receptor 1afor out-of-season reproduction in the Cornell flock and allelic frequencies compared with Romney sheep.

    Science.gov (United States)

    Posbergh, C J; Murphy, R J; Thonney, M L

    2017-05-01

    Sheep are seasonally polyestrous breeders, meaning they breed when day length shortens in the autumn. Ewes respond to changing day length through chemical pathways involving melatonin receptors. Some breeds, such as Dorset, are known to be less seasonal with many ewes able to breed and lamb year-round. The Melatonin Receptor 1a () gene was identified as a candidate gene controlling out-of-season lambing. The first studies in the Cornell STAR accelerated lambing flock found that a allele was associated with a shorter time to first lambing and a shorter period between lambings. The favorable allele was denoted the allele and the unfavorable allele, the allele. This study evaluated additional data for the effect of the polymorphism on sheep reproduction. Genotypic frequencies among the 320 sheep in this study differed between Romney and breeds selected for accelerated lambing ( 0.05) between the allele and success for out-of-season lambing and no significant differences were observed in several production measures, such as number of lambs delivered per yr or number of lambs weaned ( > 0.05). With few ewes in the flock, these results may be due to the high level of selection for accelerated lambing. This study shows that the allele may not be a beneficial marker for use within flocks seeking to improve production and the ability to lamb out-of-season. These findings warrant additional research on the genetics of aseasonality in sheep.

  7. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

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    Mullen Michael P

    2012-01-01

    Full Text Available Abstract Background The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. Results In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952 of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612 were intronic and 9% (n = 464 were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS. Significant (P ® MassARRAY. No significant differences (P > 0.1 were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total. Conclusions The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving

  8. APOE allele frequencies in suspected non-amyloid pathophysiology (SNAP and the prodromal stages of Alzheimer's Disease.

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    Timothy J Hohman

    Full Text Available Biomarker definitions for preclinical Alzheimer's disease (AD have identified individuals with neurodegeneration (ND+ without β-amyloidosis (Aβ- and labeled them with suspected non-AD pathophysiology (SNAP. We evaluated Apolipoprotein E (APOE ε2 and ε4 allele frequencies across biomarker definitions-Aβ-/ND- (n = 268, Aβ+/ND- (n = 236, Aβ-/ND+ or SNAP (n = 78, Aβ+/ND+ (n = 204-hypothesizing that SNAP would have an APOE profile comparable to Aβ-/ND-. Using AD Neuroimaging Initiative data (n = 786, 72±7 years, 48% female, amyloid status (Aβ+ or Aβ- was defined by cerebrospinal fluid (CSF Aβ-42 levels, and neurodegeneration status (ND+ or ND- was defined by hippocampal volume from MRI. Binary logistic regression related biomarker status to APOE ε2 and ε4 allele carrier status, adjusting for age, sex, education, and cognitive diagnosis. Compared to the biomarker negative (Aβ-/ND- participants, higher proportions of ε4 and lower proportions of ε2 carriers were observed among Aβ+/ND- (ε4: OR = 6.23, p0.30. In supplemental analyses, comparable results were observed when coding SNAP using amyloid imaging and when using CSF tau levels. In contrast to APOE, a polygenic risk score for AD that excluded APOE did not show an association with amyloidosis or neurodegeneration (p-values>0.15, but did show an association with SNAP defined using CSF tau (β = 0.004, p = 0.02. Thus, in a population with low levels of cerebrovascular disease and a lower prevalence of SNAP than the general population, APOE and known genetic drivers of AD do not appear to contribute to the neurodegeneration observed in SNAP. Additional work in population based samples is needed to better elucidate the genetic contributors to various etiological drivers of SNAP.

  9. MGMT-Methylated Alleles Are Distributed Heterogeneously Within Glioma Samples Irrespective of IDH Status and Chromosome 10q Deletion.

    Science.gov (United States)

    Fontana, Laura; Tabano, Silvia; Bonaparte, Eleonora; Marfia, Giovanni; Pesenti, Chiara; Falcone, Rossella; Augello, Claudia; Carlessi, Nicole; Silipigni, Rosamaria; Guerneri, Silvana; Campanella, Rolando; Caroli, Manuela; Sirchia, Silvia; Bosari, Silvano; Miozzo, Monica

    2016-06-26

    Several molecular markers drive diagnostic classification, prognostic stratification, and/or prediction of response to therapy in patients with gliomas. Among them, IDH gene mutations are valuable markers for defining subtypes and are strongly associated with epigenetic silencing of the methylguanine DNA methyltransferase (MGMT) gene. However, little is known about the percentage of MGMT-methylated alleles in IDH-mutated cells or the potential association between MGMT methylation and deletion of chromosome 10q, which encompasses the MGMT locus. Here, we quantitatively assessed MGMT methylation and IDH1 mutation in 208 primary glioma samples to explore possible differences associated with the IDH genotype. We also explored a potential association between MGMT methylation and loss of chromosome 10q. We observed that MGMT methylation was heterogeneously distributed within glioma samples irrespective of IDH status suggesting an incomplete overlap between IDH1-mutated and MGMT-methylated alleles and indicating a partial association between these two events. Moreover, loss of one MGMT allele did not affect the methylation level of the remaining allele. MGMT was methylated in about half of gliomas harboring a 10q deletion; in those cases, loss of heterozygosity might be considered a second hit leading to complete inactivation of MGMT and further contributing to tumor progression. © 2016 American Association of Neuropathologists, Inc. All rights reserved.

  10. MGMT-Methylated Alleles Are Distributed Heterogeneously Within Glioma Samples Irrespective of IDH Status and Chromosome 10q Deletion

    Science.gov (United States)

    Fontana, Laura; Tabano, Silvia; Bonaparte, Eleonora; Marfia, Giovanni; Pesenti, Chiara; Falcone, Rossella; Augello, Claudia; Carlessi, Nicole; Silipigni, Rosamaria; Guerneri, Silvana; Campanella, Rolando; Caroli, Manuela; Maria Sirchia, Silvia; Bosari, Silvano

    2016-01-01

    Abstract Several molecular markers drive diagnostic classification, prognostic stratification, and/or prediction of response to therapy in patients with gliomas. Among them, IDH gene mutations are valuable markers for defining subtypes and are strongly associated with epigenetic silencing of the methylguanine DNA methyltransferase (MGMT) gene. However, little is known about the percentage of MGMT-methylated alleles in IDH-mutated cells or the potential association between MGMT methylation and deletion of chromosome 10q, which encompasses the MGMT locus. Here, we quantitatively assessed MGMT methylation and IDH1 mutation in 208 primary glioma samples to explore possible differences associated with the IDH genotype. We also explored a potential association between MGMT methylation and loss of chromosome 10q. We observed that MGMT methylation was heterogeneously distributed within glioma samples irrespective of IDH status suggesting an incomplete overlap between IDH1-mutated and MGMT-methylated alleles and indicating a partial association between these 2 events. Moreover, loss of one MGMT allele did not affect the methylation level of the remaining allele. MGMT was methylated in about half of gliomas harboring a 10q deletion; in those cases, loss of heterozygosity might be considered a second hit leading to complete inactivation of MGMT and further contributing to tumor progression. PMID:27346749

  11. Frequency of HLA-DQA1*0501 and DQB1*0201 alleles in patients with coeliac disease, their first-degree relatives and controls in Jordan.

    Science.gov (United States)

    El-Akawi, Z J; Al-Hattab, D M; Migdady, M A

    2010-01-01

    The primary genetic marker associated with coeliac disease (CD) is the HLA-DQ2 molecule, encoded by the DQA1*0501 and DQB1*0201 genes. To investigate the frequency of HLA-DQA1*0501 and DQB1*0201 alleles in Jordanian patients with CD and their first-degree relatives. An allele-specific DNA-based PCR-sequence-specific primer was used to investigate DQA1*0501 and DQB1*0201 alleles in 44 CD patients, 47 first-degree relatives and 53 healthy controls. The mean age of the patients at the time of diagnosis was 13.5 years (range 1-39) and at the time of the study was 19.3 years (range 5-42). The DQA1/B1 (0501; 0201) haplotype was present in 80% of patients and 66% of first-degree relatives compared with 32% of controls (p<0.0001 and <0.01, respectively). The remaining 20% of CD patients who were negative for the DQ2 molecule carried the DQB1*0201 allele only. A statistically significant difference was detected in the DQ2 hetero-dimer frequency between CD patients, their first-degree relatives and controls with a higher frequency in the patients group (p<0.001). The significant differences in the frequency of DQA1*0501, DQB1*0201 alleles in CD patients and their first-degree relatives compared with the control group demonstrated the important role of these alleles in the development of CD in the Jordanian population.

  12. Frequencies of 32 base pair deletion of the (Delta 32) allele of the CCR5 HIV-1 co-receptor gene in Caucasians: a comparative analysis.

    Science.gov (United States)

    Lucotte, Gérard

    2002-05-01

    The CCR5 gene encodes for the co-receptor for the major macrophage-tropics strains of human immunodeficiency virus (HIV-1), and a mutant allele of this gene (Delta 32) provide to homozygotes a strong resistance against infection by HIV. The frequency of the Delta 32 allele was investigated in 40 populations of 8842 non-infected subjects coming from Europe, the Middle-East and North Africa. A clear north-south decreasing gradient was evident for Delta 32 frequencies, with a significant correlation coefficient (r=0.83). The main frequency value of Delta 32 for Sweden, Norway, Denmark, Finland and Iceland (0.134) is significantly (chi(2)=63.818, PVikings might have been instrumental in disseminating the Delta 32 allele during the eighth to the tenth centuries during historical times. Possibly variola virus has discriminated the Delta 32 carriers in Europe since the eighth century AD, explaining the high frequency of the Delta 32 allele in Europe today.

  13. Maximum likelihood model based on minor allele frequencies and weighted Max-SAT formulation for haplotype assembly.

    Science.gov (United States)

    Mousavi, Sayyed R; Khodadadi, Ilnaz; Falsafain, Hossein; Nadimi, Reza; Ghadiri, Nasser

    2014-06-07

    Human haplotypes include essential information about SNPs, which in turn provide valuable information for such studies as finding relationships between some diseases and their potential genetic causes, e.g., for Genome Wide Association Studies. Due to expensiveness of directly determining haplotypes and recent progress in high throughput sequencing, there has been an increasing motivation for haplotype assembly, which is the problem of finding a pair of haplotypes from a set of aligned fragments. Although the problem has been extensively studied and a number of algorithms have already been proposed for the problem, more accurate methods are still beneficial because of high importance of the haplotypes information. In this paper, first, we develop a probabilistic model, that incorporates the Minor Allele Frequency (MAF) of SNP sites, which is missed in the existing maximum likelihood models. Then, we show that the probabilistic model will reduce to the Minimum Error Correction (MEC) model when the information of MAF is omitted and some approximations are made. This result provides a novel theoretical support for the MEC, despite some criticisms against it in the recent literature. Next, under the same approximations, we simplify the model to an extension of the MEC in which the information of MAF is used. Finally, we extend the haplotype assembly algorithm HapSAT by developing a weighted Max-SAT formulation for the simplified model, which is evaluated empirically with positive results. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations

    Directory of Open Access Journals (Sweden)

    De Kovel Carolien

    2005-12-01

    Full Text Available Abstract Recently, inter-population comparisons of allele frequencies to detect past selection haven gained popularity. Data from genome-wide scans are used to detect the number and position of genes that have responded to unknown selection pressures in natural populations, or known selection pressures in experimental lines. Yet, the limitations and possibilities of these methods have not been well studied. In this paper, the objectives were (1 to investigate the distance over which a signal of directional selection is detectable under various scenarios, and (2 to study the power of the method depending on the properties of the used markers, for both natural populations and experimental set-ups. A combination of recurrence equations and simulations was used. The results show that intermediate strength selection on new mutations can be detected with a marker spacing of about 0.5 cM in large natural populations, 200 to 400 generations after the divergence of subpopulations. In experimental situations, only strong selection will be detectable, while markers can be spaced a few cM apart. Adaptation from standing variation in the base population will be hard to detect, though some solutions are presented for experimental designs.

  15. Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation.

    Science.gov (United States)

    Stephan, Wolfgang

    2016-01-01

    In the past 15 years, numerous methods have been developed to detect selective sweeps underlying adaptations. These methods are based on relatively simple population genetic models, including one or two loci at which positive directional selection occurs, and one or two marker loci at which the impact of selection on linked neutral variation is quantified. Information about the phenotype under selection is not included in these models (except for fitness). In contrast, in the quantitative genetic models of adaptation, selection acts on one or more phenotypic traits, such that a genotype-phenotype map is required to bridge the gap to population genetics theory. Here I describe the range of population genetic models from selective sweeps in a panmictic population of constant size to evolutionary traffic when simultaneous sweeps at multiple loci interfere, and I also consider the case of polygenic selection characterized by subtle allele frequency shifts at many loci. Furthermore, I present an overview of the statistical tests that have been proposed based on these population genetics models to detect evidence for positive selection in the genome. © 2015 John Wiley & Sons Ltd.

  16. HLA alleles and haplotypes distribution in Dai population in Yunnan province, Southwest China.

    Science.gov (United States)

    Shi, L; Yao, Y F; Shi, L; Matsushita, M; Yu, L; Lin, Q K; Tao, Y F; Oka, T; Chu, J Y; Tokunaga, K

    2010-02-01

    Human leukocyte antigen (HLA) analysis would be a useful tool to trace the origin of modern humans. In this study, we provided the first four digital HLA-A, -B, -C and -DRB1 allele and haplotype data in the Dai ethnic population, which is a unique and representative Kam-Tai-speaking ethnic minority living in the Yunnan province of Southwestern China. Our results showed that the Dai population has unique HLA characteristic that are most closely related to the Southeastern Asia group and similar to the Kam-Tai speaking populations in China and Thailand.

  17. Allele distributions at hybrid incompatibility loci facilitate the potential for gene flow between cultivated and weedy rice in the US.

    Directory of Open Access Journals (Sweden)

    Stephanie M Craig

    Full Text Available The accumulation of independent mutations over time in two populations often leads to reproductive isolation. Reproductive isolation between diverging populations may be reinforced by barriers that occur either pre- or postzygotically. Hybrid sterility is the most common form of postzygotic isolation in plants. Four postzygotic sterility loci, comprising three hybrid sterility systems (Sa, s5, DPL, have been recently identified in Oryza sativa. These loci explain, in part, the limited hybridization that occurs between the domesticated cultivated rice varieties, O. sativa spp. japonica and O. sativa spp. indica. In the United States, cultivated fields of japonica rice are often invaded by conspecific weeds that have been shown to be of indica origin. Crop-weed hybrids have been identified in crop fields, but at low frequencies. Here we examined the possible role of these hybrid incompatibility loci in the interaction between cultivated and weedy rice. We identified a novel allele at Sa that seemingly prevents loss of fertility in hybrids. Additionally, we found wide-compatibility type alleles at strikingly high frequencies at the Sa and s5 loci in weed groups, and a general lack of incompatible alleles between crops and weeds at the DPL loci. Our results suggest that weedy individuals, particularly those of the SH and BRH groups, should be able to freely hybridize with the local japonica crop, and that prezygotic factors, such as differences in flowering time, have been more important in limiting weed-crop gene flow in the past. As the selective landscape for weedy rice changes due to increased use of herbicide resistant strains of cultivated rice, the genetic barriers that hinder indica-japonica hybridization cannot be counted on to limit the flow of favorable crop genes into weeds.

  18. Power laws for heavy-tailed distributions: modeling allele and haplotype diversity for the national marrow donor program.

    Directory of Open Access Journals (Sweden)

    Noa Slater

    2015-04-01

    Full Text Available Measures of allele and haplotype diversity, which are fundamental properties in population genetics, often follow heavy tailed distributions. These measures are of particular interest in the field of hematopoietic stem cell transplant (HSCT. Donor/Recipient suitability for HSCT is determined by Human Leukocyte Antigen (HLA similarity. Match predictions rely upon a precise description of HLA diversity, yet classical estimates are inaccurate given the heavy-tailed nature of the distribution. This directly affects HSCT matching and diversity measures in broader fields such as species richness. We, therefore, have developed a power-law based estimator to measure allele and haplotype diversity that accommodates heavy tails using the concepts of regular variation and occupancy distributions. Application of our estimator to 6.59 million donors in the Be The Match Registry revealed that haplotypes follow a heavy tail distribution across all ethnicities: for example, 44.65% of the European American haplotypes are represented by only 1 individual. Indeed, our discovery rate of all U.S. European American haplotypes is estimated at 23.45% based upon sampling 3.97% of the population, leaving a large number of unobserved haplotypes. Population coverage, however, is much higher at 99.4% given that 90% of European Americans carry one of the 4.5% most frequent haplotypes. Alleles were found to be less diverse suggesting the current registry represents most alleles in the population. Thus, for HSCT registries, haplotype discovery will remain high with continued recruitment to a very deep level of sampling, but population coverage will not. Finally, we compared the convergence of our power-law versus classical diversity estimators such as Capture recapture, Chao, ACE and Jackknife methods. When fit to the haplotype data, our estimator displayed favorable properties in terms of convergence (with respect to sampling depth and accuracy (with respect to diversity

  19. Hygroscopicity frequency distributions of secondary organic aerosols

    Science.gov (United States)

    Suda, S. R.; Petters, M. D.; Matsunaga, A.; Sullivan, R. C.; Ziemann, P. J.; Kreidenweis, S. M.

    2012-02-01

    Secondary organic compounds are an important component of ambient aerosol and potentially lower the supersaturation that is required for individual particles to serve as cloud condensation nuclei (CCN). Secondary organic aerosol (SOA) formed from the oxidation of a single precursor can be composed of many different compounds and their overall CCN efficiency has been reported for many different SOA systems. An aerosol's CCN efficiency can be described by a single hygroscopicity parameter, κ. However, this κ comprises an unknown distribution of underlying κ-values resulting from each individual compound in the SOA mixture. Here we report on a new technique for characterizing this distribution ofκ. Precursor hydrocarbons were oxidized in an environmental chamber to form SOA, which was collected on filters and extracted using ethyl acetate. Extracts were then fractionated by reversed-phase high-performance liquid chromatography using gradient elution with acetonitrile and water. The eluate was atomized, the solvent was removed by evaporation, and the residual aerosol particles were analyzed as a function of retention time using scanning flow CCN analysis. Kappa-values generally decreased with component retention time, consistent with expected decreasing polarity. Averaged SOAκ-values reconstructed by integrating over the chromatogram agreed well with values measured for SOA sampled directly from the environmental chamber, suggesting thatκfor SOA represents the volume-weighted average of the constituent compounds'κ-values. We anticipate that our measured hygroscopicity distributions will serve as validation points for mechanistic models that seek to predict the generation and evolution of organic aerosol composition and properties in the atmosphere.

  20. The frequency characteristics of medium voltage distribution system impedances

    Directory of Open Access Journals (Sweden)

    Liviu Emil Petrean

    2009-10-01

    Full Text Available In this paper we present the frequency characteristics of impedances involved in the electrical equivalent circuit of a large medium voltage distribution system. These impedances influence harmonics distortions propagation occurring due to the nonsinusoidal loads. We analyse the case of a 10 kV large urban distribution system which supplies industrial, commercial and residential customers. The influence of various parameters of the distribution network on the frequency characteristics are presented, in order to assess the interaction of harmonic distortion and distribution system network.

  1. Human leukocyte antigen class II (DRB1 and DQB1) alleles and haplotypes frequencies in patients with pemphigus vulgaris among the Serbian population.

    Science.gov (United States)

    Zivanovic, D; Bojic, S; Medenica, L; Andric, Z; Popadic, D

    2016-05-01

    The etiology of pemphigus vulgaris (PV) is multifactorial and includes genetic, environmental, hormonal, and immunological factors. Inheritance of certain Human class II leukocyte antigen (HLA) alleles is by far the best-established predisposing factor for the development of PV. Class II HLA alleles vary among racial/ethnic backgrounds. We have determined an association between HLA class II alleles and PV among the Serbian population. A total of 72 patients with confirmed diagnosis of PV were genotyped for HLA class II alleles. HLA frequencies were compared with unrelated healthy bone marrow donors. The statistical significance of differences between patients and controls was evaluated using Fisher's exact test. The DRB1*04 and DRB1*14 allelic groups were associated with PV (P adj = 4.45 × 10(-13) and 4.06 × 10(-19) respectively), while HLA-DRB1*11 was negatively associated with PV (P adj = 0.0067) suggesting a protective role. DRB1*04:02, DRB1*14:04, DQB1*03:02 and DQB1*05:03 alleles were shown to be strongly associated with PV (P adj = 1.63 × 10(-12), 5.20 × 10(-7), 1.28 × 10(-6), and 4.44 × 10(-5), respectively). The frequency of HLA DRB1*04-DQB1*03 and HLA DRB1*14-DQB1*05 haplotypes in PV patients was significantly higher than in controls (31.3% vs 8.8%, P adj =7.66 × 10(-8) and 30.6% vs 6.3%, P adj = 3.22 × 10(-10), respectively). At high-resolution level, statistical significance was observed in HLA-DRB1*04:02-DQB1*03:02 and HLA-DRB1*14:04-DQB1*05:03 haplotypes (P adj = 5.55 × 10(-12), and P adj = 3.91 × 10(-6), respectively). Our findings suggest that HLA-DRB1*04:02, DRB1*14:04, HLA-DQB1* 03:02 and DQB1*05:03 alleles and HLA-DRB1*04:02-DQB1*03:02 and HLA-DRB1*14:04-DQB1*05:03 haplotypes are genetic markers for susceptibility for PV, while DRB1*11 allelic group appears protective in Serbian population. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. ABO and Rh (D group distribution and gene frequency; the first multicentric study in India

    Directory of Open Access Journals (Sweden)

    Amit Agrawal

    2014-01-01

    Full Text Available Background and Objectives: The study was undertaken with the objective to provide data on the ABO and Rh(D blood group distribution and gene frequency across India. Materials and Methods: A total of 10,000 healthy blood donors donating in blood banks situated in five different geographical regions of the country (North, South, East and Center were included in the study. ABO and Rh (D grouping was performed on all these samples. Data on the frequency of ABO and Rh(D blood groups was reported in simple numbers and percentages. Results: The study showed that O was the most common blood group (37.12% in the country closely followed by B at 32.26%, followed by A at 22.88% while AB was the least prevalent group at 7.74%. 94.61% of the donor population was Rh positive and the rest were Rh negative. Regional variations were observed in the distribution. Using the maximum likelihood method, the frequencies of the I A , I B and I O alleles were calculated and tested according to the Hardy Weinberg law of Equilibrium. The calculated gene frequencies are 0.1653 for I A (p, 0.2254 for I B (q and 0.6093 for I O (r. In Indian Population, O (r records the highest value followed by B (q and A (p; O > B > A. Conclusion: The study provides information about the relative distribution of various alleles in the Indian population both on a pan-India basis as well as region-wise. This vital information may be helpful in planning for future health challenges, particularly planning with regards to blood transfusion services.

  3. Recurrent frequency-size distribution of characteristic events

    Directory of Open Access Journals (Sweden)

    S. G. Abaimov

    2009-04-01

    Full Text Available Statistical frequency-size (frequency-magnitude properties of earthquake occurrence play an important role in seismic hazard assessments. The behavior of earthquakes is represented by two different statistics: interoccurrent behavior in a region and recurrent behavior at a given point on a fault (or at a given fault. The interoccurrent frequency-size behavior has been investigated by many authors and generally obeys the power-law Gutenberg-Richter distribution to a good approximation. It is expected that the recurrent frequency-size behavior should obey different statistics. However, this problem has received little attention because historic earthquake sequences do not contain enough events to reconstruct the necessary statistics. To overcome this lack of data, this paper investigates the recurrent frequency-size behavior for several problems. First, the sequences of creep events on a creeping section of the San Andreas fault are investigated. The applicability of the Brownian passage-time, lognormal, and Weibull distributions to the recurrent frequency-size statistics of slip events is tested and the Weibull distribution is found to be the best-fit distribution. To verify this result the behaviors of numerical slider-block and sand-pile models are investigated and the Weibull distribution is confirmed as the applicable distribution for these models as well. Exponents β of the best-fit Weibull distributions for the observed creep event sequences and for the slider-block model are found to have similar values ranging from 1.6 to 2.2 with the corresponding aperiodicities CV of the applied distribution ranging from 0.47 to 0.64. We also note similarities between recurrent time-interval statistics and recurrent frequency-size statistics.

  4. Microarray-based detection of CYP1A1, CYP2C9, CYP2C19, CYP2D6, GSTT1, GSTM1, MTHFR, MTRR, NQO1, NAT2, HLA-DQA1, and AB0 allele frequencies in native Russians.

    Science.gov (United States)

    Gra, Olga; Mityaeva, Olga; Berdichevets, Iryna; Kozhekbaeva, Zhanna; Fesenko, Denis; Kurbatova, Olga; Goldenkova-Pavlova, Irina; Nasedkina, Tatyana

    2010-06-01

    Xenobiotic-metabolizing genes (e.g., Cytochromes P450, GST, NAT2, and NQO1), folate metabolism genes (e.g., MTHFR and MTRR), and major histocompatibility complex genes (e.g., HLA-DQA1) play multiple roles in the organism functioning. In addition, AB0 is the most clinically significant high-polymorphic gene in transfusion and transplantation medicine. Epidemiological data show that allele frequencies of these genes exhibit ethnic and geographic diversity. Besides, little is known about frequency distribution of the major polymorphic variants in native Russians. We developed biological microchips that allow us to analyze a spectrum of allelic variants in 12 different genes: CYP1A1, CYP2D6, CYP2C9, CYP2C19, GSTT1, GSTM1, MTHFR, MTRR, NQO1, NAT2, HLA-DQA1, and AB0. Using this composite methodological platform we have studied 352 DNA samples from healthy native Russian volunteers. The allelic frequencies of gene polymorphisms obtained are close to allelic frequencies observed in some European populations, as published earlier. These data were used in comparative studies to determine predisposition to tuberculosis, lymphoma, and leukemia in adults and to childhood acute leukemia. The HLA-DQA1 and AB0 allele frequencies were used to estimate forensic population parameters for these loci.

  5. Rapid genotyping assays for the 4-base pair deletion of canine MDR1/ABCB1 gene and low frequency of the mutant allele in Border Collie dogs.

    Science.gov (United States)

    Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

    2012-01-01

    P-glycoprotein, encoded by the MDR1 or ABCB1 gene, is an integral component of the blood-brain barrier as an efflux pump for xenobiotics crucial in limiting drug uptake into the central nervous system. Dogs homozygous for a 4-base pair deletion of the canine MDR1 gene show altered expression or function of P-glycoprotein, resulting in neurotoxicosis after administration of the substrate drugs. In the present study, the usefulness of microchip electrophoresis for genotyping assays detecting this deletion mutation was evaluated. Mutagenically separated polymerase chain reaction (MS-PCR) and real-time PCR assays were newly developed and evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies dogs in Japan to determine the allele frequency in this breed. Microchip electrophoresis showed advantages in detection sensitivity and time saving over other modes of electrophoresis. The MS-PCR assay clearly discriminated all genotypes. Real-time PCR assay was most suitable for a large-scale survey due to its high throughput and rapidity. The genotyping survey demonstrated that the carrier and mutant allele frequencies were 0.49% and 0.25%, respectively, suggesting that the mutant allele frequency in Border Collies is markedly low compared to that in the susceptible dog breeds such as rough and smooth Collies.

  6. Word frequencies: A comparison of Pareto type distributions

    Science.gov (United States)

    Wiegand, Martin; Nadarajah, Saralees; Si, Yuancheng

    2018-03-01

    Mehri and Jamaati (2017) [18] used Zipf's law to model word frequencies in Holy Bible translations for one hundred live languages. We compare the fit of Zipf's law to a number of Pareto type distributions. The latter distributions are shown to provide the best fit, as judged by a number of comparative plots and error measures. The fit of Zipf's law appears generally poor.

  7. Highly flexible distributions to fit multiple frequency financial returns

    Science.gov (United States)

    BenSaïda, Ahmed; Slim, Skander

    2016-01-01

    Financial data are usually studied via low flexible distributions, independently of the frequency of the data, due to their simplicity and analytical tractability. In this paper we analyze two highly flexible five-parameter distributions into fitting financial returns, these are the skewed generalized t (SGT) and the generalized hyperbolic (GH). Applications carried on two exchange rates (Euro-Dollar and Dollar-Yen), and two indexes (S&P 500 and Nikkei 225) over four frequencies: weekly, daily, 30-min and 5-min, confirm the superiority of the SGT and GH in approximating the distribution of a given data at a remarkable precision. Moreover, as we move from higher to lower frequency, the distribution's overall shape does indeed change radically, and the estimated parameters refute the tendency to normality, which calls into question the aggregational Gaussianity's stylized fact.

  8. Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions

    Science.gov (United States)

    Hybridization is known to occur between cultivated and wild populations of numerous plant species. This represents a major mechanism by which a wild population’s genetic structure and evolutionary dynamics could be altered. Studying crop-derived alleles in wild populations is also relevant to assess...

  9. High allele frequency of CYP2C9*3 (rs1057910) in a Negrito's subtribe population in Malaysia; Aboriginal people of Jahai.

    Science.gov (United States)

    Rosdi, Rasmaizatul Akma; Mohd Yusoff, Narazah; Ismail, Rusli; Soo Choon, Tan; Saleem, Mohamed; Musa, Nurfadhlina; Yusoff, Surini

    2016-09-01

    CYP2C9 gene polymorphisms modulate inter-individual variations in the human body's responses to various endogenous and exogenous drug substrates. To date, little is known about the CYP2C9 gene polymorphisms among the aboriginal populations of the world, including those in Malaysia. To characterise and compare the CYP2C9 polymorphisms (CYP2C9*2, CYP2C9*3, CYP2C9*4 and CYP2C9*5) between one of Malaysia's aboriginal populations, Jahai, with the national major ethnic, Malay. To also compare the allele frequencies from these two populations with available data of other aboriginal populations around the world. The extracted DNA of 155 Jahais and 183 Malays was genotyped for CYP2C9 polymorphisms using a nested multiplex allele-specific polymerase chain reaction technique. The results were confirmed by DNA direct sequencing. Genotyping results revealed that CYP2C9*2, CYP2C9*4 and CYP2C9*5 were absent in Jahais, while only the latter two were absent in Malays. The CYP2C9*3 allelic frequency in Jahais was 36.2%, making them the most frequent carriers of the allele thus far reported in any ethnic group from Southeast Asia. The high frequency of CYP2C9*3 and the absence of CYP2C9*2 in Jahais suggest that genetic drift may be occurring in this ethnic group. This is the first study to determine the CYP2C9 polymorphisms in an aboriginal population in Malaysia.

  10. Inosine triphosphatase allele frequency and association with ribavirin-induced anaemia in Brazilian patients receiving antiviral therapy for chronic hepatitis C

    Directory of Open Access Journals (Sweden)

    Nathália Delvaux

    2015-08-01

    Full Text Available Inosine triphosphatase (ITPA single nucleotide polymorphisms (SNPs are strongly associated with protection against ribavirin (RBV-induced anaemia in European, American and Asian patients; however, there is a paucity of data for Brazilian patients. The aim of this study was to evaluate the ITPA SNP (rs7270101/rs1127354 frequency in healthy and hepatitis C virus (HCV-infected patients from Brazil and the association with the development of severe anaemia during antiviral therapy. ITPA SNPs were determined in 200 HCV infected patients and 100 healthy individuals by sequencing. Biochemical parameters and haemoglobin (Hb levels were analysed in 97 patients who underwent antiviral therapy. A combination of AArs7270101+CCrs1127354 (100% ITPase activity was observed in 236/300 individuals. Anaemia was observed in 87.5% and 86.2% of treated patients with AA (rs7270101 and CC genotypes (rs1127354, respectively. Men with AA (rs7270101 showed a considerable reduction in Hb at week 12 compared to those with AC/CC (p = 0.1475. In women, there was no influence of genotype (p = 0.5295. For rs1127354, men with the CC genotype also showed a sudden reduction in Hb compared to those with AC. Allelic distribution of rs7270101 and rs1127354 shows high rates of the genotypes AA and CC, respectively, suggesting that the study population had a great propensity for developing RBV-induced anaemia. A progressive Hb reduction during treatment was observed; however, this reduction was greater in men at week 12 than in women.

  11. Allelic structure and distribution of 103 STR loci in a Southern ...

    Indian Academy of Sciences (India)

    Unknown

    ,Tunisia. 3Dispensaire de Bir ElHfai, Sidi Bouzid, Tunisia. Abstract. Genotypes of 103 short tandem repeat (STR) markers distributed at an average of 40 cM intervals throughout the genome were determined for 40 individuals from the village ...

  12. Correcting length-frequency distributions for imperfect detection

    Science.gov (United States)

    Breton, André R.; Hawkins, John A.; Winkelman, Dana L.

    2013-01-01

    Sampling gear selects for specific sizes of fish, which may bias length-frequency distributions that are commonly used to assess population size structure, recruitment patterns, growth, and survival. To properly correct for sampling biases caused by gear and other sources, length-frequency distributions need to be corrected for imperfect detection. We describe a method for adjusting length-frequency distributions when capture and recapture probabilities are a function of fish length, temporal variation, and capture history. The method is applied to a study involving the removal of Smallmouth Bass Micropterus dolomieu by boat electrofishing from a 38.6-km reach on the Yampa River, Colorado. Smallmouth Bass longer than 100 mm were marked and released alive from 2005 to 2010 on one or more electrofishing passes and removed on all other passes from the population. Using the Huggins mark–recapture model, we detected a significant effect of fish total length, previous capture history (behavior), year, pass, year×behavior, and year×pass on capture and recapture probabilities. We demonstrate how to partition the Huggins estimate of abundance into length frequencies to correct for these effects. Uncorrected length frequencies of fish removed from Little Yampa Canyon were negatively biased in every year by as much as 88% relative to mark–recapture estimates for the smallest length-class in our analysis (100–110 mm). Bias declined but remained high even for adult length-classes (≥200 mm). The pattern of bias across length-classes was variable across years. The percentage of unadjusted counts that were below the lower 95% confidence interval from our adjusted length-frequency estimates were 95, 89, 84, 78, 81, and 92% from 2005 to 2010, respectively. Length-frequency distributions are widely used in fisheries science and management. Our simple method for correcting length-frequency estimates for imperfect detection could be widely applied when mark–recapture data

  13. The frequency of the H402 allele of CFH and its involvement with age-related maculopathy in an aged Black African Xhosa population.

    Science.gov (United States)

    Ziskind, Ari; Bardien, Soraya; van der Merwe, Lize; Webster, Andrew R

    2008-09-01

    The H402 allele of the CFH gene is an established risk factor for age-related maculopathy (ARMD) in Caucasians, accounting for approximately 60% of the genetic risk at the population level. In general, the advanced forms of ARMD are rare in Black populations in Africa, as well as Black populations who have lived for generations in the United States or the West Indies, although there are reports that the earlier forms such as drusen may not be all that uncommon. The aim of the present study was to estimate the frequency of the C allele of the CFH Y402H variant in an aged South African Black Xhosa population and to describe the evidence of ARMD found.

  14. Frequency of Cry1F Non-Recessive Resistance Alleles in North Carolina Field Populations of Spodoptera frugiperda (Lepidoptera: Noctuidae.

    Directory of Open Access Journals (Sweden)

    Guoping Li

    Full Text Available Fall armyworm, Spodoptera frugiperda (J.E. Smith (Lepidoptera: Noctuidae, is a target species of transgenic corn (Zea mays L. that expresses single and pyramided Bacillus thuringiensis (Bt toxin. In 2014, S. frugiperda were collected from a light trap in North Carolina, and a total of 212 F1/F2 isofemale lines of S. frugiperda were screened for resistance to Bt and non-Bt corn. All of the 212 isolines were susceptible to corn tissue expressing Cry1A.105 + Cry2Ab, Cry1F + Cry1A.105 + Cry2Ab, and Cry1F + Cry1Ab + Vip3Aa20. Growth rate bioassays were performed to isolate non-recessive Bt resistance alleles. Seven individuals out of the 212 isofemale lines carried major non-recessive alleles conferring resistance to Cry1F. A pooled colony was created from the seven individuals. This colony was 151.21 times more resistant to Cry1F than a known-susceptible population and was also resistant to Cry1A.105, but was not resistant to Cry2Ab and Vip3Aa20. The results demonstrate that field populations of S. frugiperda collected from North Carolina are generally susceptible to Cry1F, but that some individuals carry resistant alleles. The data generated in this study can be used as baseline data for resistance monitoring.

  15. Frequency of Cry1F Non-Recessive Resistance Alleles in North Carolina Field Populations of Spodoptera frugiperda (Lepidoptera: Noctuidae)

    Science.gov (United States)

    Li, Guoping; Reisig, Dominic; Miao, Jin; Gould, Fred; Huang, Fangneng; Feng, Hongqiang

    2016-01-01

    Fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a target species of transgenic corn (Zea mays L.) that expresses single and pyramided Bacillus thuringiensis (Bt) toxin. In 2014, S. frugiperda were collected from a light trap in North Carolina, and a total of 212 F1/F2 isofemale lines of S. frugiperda were screened for resistance to Bt and non-Bt corn. All of the 212 isolines were susceptible to corn tissue expressing Cry1A.105 + Cry2Ab, Cry1F + Cry1A.105 + Cry2Ab, and Cry1F + Cry1Ab + Vip3Aa20. Growth rate bioassays were performed to isolate non-recessive Bt resistance alleles. Seven individuals out of the 212 isofemale lines carried major non-recessive alleles conferring resistance to Cry1F. A pooled colony was created from the seven individuals. This colony was 151.21 times more resistant to Cry1F than a known-susceptible population and was also resistant to Cry1A.105, but was not resistant to Cry2Ab and Vip3Aa20. The results demonstrate that field populations of S. frugiperda collected from North Carolina are generally susceptible to Cry1F, but that some individuals carry resistant alleles. The data generated in this study can be used as baseline data for resistance monitoring. PMID:27119741

  16. A Novel Frequency Communication Technology in Power Distribution Communication Network

    Directory of Open Access Journals (Sweden)

    Li Ying-Jun

    2017-01-01

    Full Text Available With the expansion of the power terminal access network scale, the main road corridor resources, branch line cable Laying difficulties has become an important factor restricting the construction of the network. In this paper, we focus on the frequency communication technology in power distribution communication network, and design a novel technology in communication mode, error correcting coding and data transfer frame format. We also discuss the influence of voltage phase difference on power frequency communication. Meanwhile, we present the application scenario Electricity information collection, electricity remote control and other power business in smart grid with the novel frequency communication technology.

  17. Optimizing Power–Frequency Droop Characteristics of Distributed Energy Resources

    Energy Technology Data Exchange (ETDEWEB)

    Guggilam, Swaroop S.; Zhao, Changhong; Dall Anese, Emiliano; Chen, Yu Christine; Dhople, Sairaj V.

    2018-05-01

    This paper outlines a procedure to design power-frequency droop slopes for distributed energy resources (DERs) installed in distribution networks to optimally participate in primary frequency response. In particular, the droop slopes are engineered such that DERs respond in proportion to their power ratings and they are not unfairly penalized in power provisioning based on their location in the distribution network. The main contribution of our approach is that a guaranteed level of frequency regulation can be guaranteed at the feeder head, while ensuring that the outputs of individual DERs conform to some well-defined notion of fairness. The approach we adopt leverages an optimization-based perspective and suitable linearizations of the power-flow equations to embed notions of fairness and information regarding the physics of the power flows within the distribution network into the droop slopes. Time-domain simulations from a differential algebraic equation model of the 39-bus New England test-case system augmented with three instances of the IEEE 37-node distribution-network with frequency-sensitive DERs are provided to validate our approach.

  18. QTL analysis of the photoperiodic response and clinal distribution of period alleles in Nasonia vitripennis.

    Science.gov (United States)

    Paolucci, Silvia; Salis, Lucia; Vermeulen, Cornelis J; Beukeboom, Leo W; van de Zande, Louis

    2016-10-01

    In seasonal environments, organisms synchronize their life cycle with the annual cycle of environmental factors. In many insect species, this includes a diapause response: a timed dormant stage that allows to survive harsh winter conditions. Previously, we have shown that larval diapause in the parasitic wasp Nasonia vitripennis is induced by the mother upon exposure to a threshold number of short photoperiods (named switch point) and diapause response follows a latitudinal cline in natural populations. Here, we present a QTL analysis using two lines derived from the extremes of this clinal distribution: a northern line from Oulu, Finland and a southern line from Corsica, France. A genomic region on chromosome 1 and one on chromosome 5 were found to be associated with photoperiodic diapause induction. Interestingly, these regions contain the putative clock genes period, cycle (chromosome 1) and cryptochrome (chromosome 5). An analysis of period polymorphisms in seven European populations showed a clinal distribution of two main haplotypes that correlate with the latitudinal cline for diapause induction. © 2016 John Wiley & Sons Ltd.

  19. Distribution of HLA-A, -B, and -C Alleles and HLA/KIR Combinations in Han Population in China

    Directory of Open Access Journals (Sweden)

    Yunsong Shen

    2014-01-01

    Full Text Available We investigated polymorphisms of the human leukocyte antigen (HLA class I (A, B, and C loci of a Han population (n, 239 from the Yunnan province, Southwest China, using high-resolution polymerase chain reaction-Luminex (PCR-Luminex typing. We combined the HLA data from this study with the KIR genotypes from a previous study of this Han population to analyze the combination of KIR/HLA ligands. A total of 27 HLA-A, 54 HLA-B, and 31 HLA-C alleles were found in this population. The frequencies of A*11:01, A*24:02, B*40:01, B*46:01, C*01:02, C*03:04, and C*07:02 were all > 10%. The following haplotypes were common, with frequencies > 5%: 1 A-B (A*02:07-B*46:01, 2 A-C (A*02:07-C*01:02, and A*11:01-C*07:02, 4 C-B (B*13:01-C*03:04, B*40:01-C*07:02, B*46:01-C*01:02 and B*58:01-C*03:02, and 1 A-C-B (A*02:07-C*01:02-B*46:01. Analysis of KIR3D and their ligands HLA-A3/A11 and HLA-Bw4 showed that the frequencies of 3DL2+-A3/A11+ and 3DL2+-A3/A11− were 0.527 and 0.473, and the frequencies of 3DL1+-Bw4+, 3DL1+-Bw4−, 3DL1−-Bw4+, and 3DL1−-Bw4− were 0.552, 0.397, 0.038, and 0.013, respectively. The results of KIR/HLA-C combination analysis showed that all individuals had at least one inhibitory or activating KIR/HLA-C pair, and one KIR/HLA-C pair was the most frequent (157/239, followed by two pairs (46/239, three pairs (33/239, and no pairs (3/239. Comparison of KIR gene and HLA gene and their pair frequency between Yunnan Han and the isolated Han (FYDH who also lived in Yunnan province showed no significant difference (P>0.05 in KIR frequencies, but significant differences (P0.05 between the two populations for KIR/HLA pairs.

  20. Cystic fibrosis in Jews: frequency and mutation distribution.

    Science.gov (United States)

    Kerem, B; Chiba-Falek, O; Kerem, E

    1997-01-01

    The incidence of cystic fibrosis and the frequency of disease causing mutations varies among different ethnic groups and geographical regions around the world. The Jewish population is comprised of two major ethnic groups. Ashkenazi and Non-Ashkenazi. The latter is further classified according to country of origin. An extreme variability in the disease frequency (from 1:2400-1:39,000) was found among the different Jewish ethnic groups. In the entire Jewish CF population, only 12 mutations were identified that altogether enable the identification of 91% of the CF chromosomes. However, in each Jewish ethnic group, the disease is caused by a different repertoire of a small number of mutations. In several ethnic groups, there is a major CFTR mutation that accounts for at least 48% of the CF chromosomes. High proportion of the CF chromosomes can be identified in Ashkenazi Jews (95%), Jews originating from Tunisia (100%), Libya (91%), Turkey (90%), and Georgia (88%). High frequencies of CFTR mutations were found among infertile males with CBAVD who might not have additional CF clinical characteristics. Of the Jewish males with CBAVD, 77% carried at least one CFTR mutation. The 5T mutation is the major mutation in Jewish CBAVD affecteds accounting for 32% of the chromosomes among Ashkenazi Jews and 36% among the non-Ashkenazi Jews. Five additional CFTR mutations, W1282X (12%), delta F508 (9%), N1303K (3%), D1152H, (5%)), and R117H (1%) were identified among Ashkenazi Jews with CBAVD. Only two mutations, delta F508 and R117H, were found among non-Ashkenazi males with CBAVD. An increased frequency of the 5T allele was also found among Jewish patients with atypical CF presentation, 18% in Ashkenazi, and 10% in non-Ashkenazi Jews. In summary, we present the required information for genetic counseling of Jewish families with typical and atypical CF and for carrier screening of healthy Jewish individuals.

  1. Incoherent Optical Frequency Domain Reflectometry for Distributed Thermal Sensing

    DEFF Research Database (Denmark)

    Karamehmedovic, Emir

    2006-01-01

    This thesis reports the main results from an investigation of a fibre-optic distributed temperature sensor based on spontaneous Raman scattering. The technique used for spatial resolving is the incoherent optical frequency domain reflectometry, where a pump laser is sine modulated with a stepwise...

  2. The frequency-independent control method for distributed generation systems

    DEFF Research Database (Denmark)

    Naderi, Siamak; Pouresmaeil, Edris; Gao, Wenzhong David

    2012-01-01

    In this paper a novel frequency-independent control method suitable for distributed generation (DG) is presented. This strategy is derived based on the . abc/. αβ transformation and . abc/. dq transformation of the ac system variables. The active and reactive currents injected by the DG...

  3. Length Frequency Distribution And Sex Ratio Of Macrobrachium ...

    African Journals Online (AJOL)

    Length frequency distribution and sex ratio of Macrobrachium macrobrachion sampled by cane traps in the Lagos –Lekki lagoon system were estimated from May 2002 to April 2004. The total number of size classes for the first and second year for both male and female ranged from 10 – 12. The length range was 3 to 14cm ...

  4. HLA-Cw Allele Frequency in Definite Meniere’s Disease Compared to Probable Meniere’s Disease and Healthy Controls in an Iranian Sample

    Directory of Open Access Journals (Sweden)

    Sasan Dabiri

    2016-05-01

    Full Text Available Introduction Several lines of evidence support the contribution of autoimmune mechanisms in the pathogenesis of Meniere’s disease. The aim of this study was determining the association between HLA-Cw Alleles in patients with definite Meniere’s disease and patients with probable Meniere’s disease and a control group.  Materials and Methods: HLA-Cw genotyping was performed in 23 patients with definite Meniere’s disease, 24 with probable Meniere’s disease, and 91 healthy normal subjects, using sequence specific primers polymerase chain reaction technique. The statistical analysis was performed using stata 8 software.  Results: There was a significant association between HLA-Cw*04 and HLA-Cw*16 in both definite and probable Meniere’s disease compared to normal healthy controls. We observed a significant difference in HLA-Cw*12 frequencies between patients with definite Meniere’s disease compared to patients with probable Meniere’s disease (P=0.04. The frequency of HLA-Cw*18 is significantly higher in healthy controls (P=0.002.  Conclusion: Our findings support the rule of HLA-Cw Alleles in both definite and probable Meniere’s disease. In addition, differences in HLA-Cw*12 frequency in definite and probable Meniere’s disease in our study’s population might indicate distinct immune and inflammatory mechanisms involved in each condition.

  5. HLA-Cw Allele Frequency in Definite Meniere's Disease Compared to Probable Meniere's Disease and Healthy Controls in an Iranian Sample.

    Science.gov (United States)

    Dabiri, Sasan; Ghadimi, Fatemeh; Firouzifar, Mohammadreza; Yazdani, Nasrin; Mohammad-Amoli, Mahsa; Vakili, Varasteh; Mahvi, Zahra

    2016-07-01

    Several lines of evidence support the contribution of autoimmune mechanisms in the pathogenesis of Meniere's disease. The aim of this study was determining the association between HLA-Cw Alleles in patients with definite Meniere's disease and patients with probable Meniere's disease and a control group. HLA-Cw genotyping was performed in 23 patients with definite Meniere's disease, 24 with probable Meniere's disease, and 91 healthy normal subjects, using sequence specific primers polymerase chain reaction technique. The statistical analysis was performed using stata 8 software. There was a significant association between HLA-Cw*04 and HLA-Cw*16 in both definite and probable Meniere's disease compared to normal healthy controls. We observed a significant difference in HLA-Cw*12 frequencies between patients with definite Meniere's disease compared to patients with probable Meniere's disease (P=0.04). The frequency of HLA-Cw*18 is significantly higher in healthy controls (P=0.002). Our findings support the rule of HLA-Cw Alleles in both definite and probable Meniere's disease. In addition, differences in HLA-Cw*12 frequency in definite and probable Meniere's disease in our study's population might indicate distinct immune and inflammatory mechanisms involved in each condition.

  6. Prevalence and distribution of Listeria monocytogenes inlA alleles prone to phase variation and inlA alleles with premature stop codon mutations among human, food, animal, and environmental isolates.

    Science.gov (United States)

    Manuel, Clyde S; Van Stelten, Anna; Wiedmann, Martin; Nightingale, Kendra K; Orsi, Renato H

    2015-12-01

    In Listeria monocytogenes, 18 mutations leading to premature stop codons (PMSCs) in the virulence gene inlA have been identified to date. While most of these mutations represent nucleotide substitutions, a frameshift deletion in a 5' seven-adenine homopolymeric tract (HT) in inlA has also been reported. This HT may play a role in phase variation and was first identified among L. monocytogenes lineage II ribotype DUP-1039C isolates. In order to better understand the distribution of different inlA mutations in this ribotype, a newly developed multiplex real-time PCR assay was used to screen 368 DUP-1039C isolates from human, animal, and food-associated sources for three known 5' inlA HT alleles: (i) wild-type (WT) (A7), (ii) frameshift (FS) (A6), and (iii) guanine interruption (A2GA4) alleles. Additionally, 228 DUP-1039C isolates were screened for all inlA PMSCs; data on the presence of all inlA PMSCs for the other 140 isolates were obtained from previous studies. The statistical analysis based on 191 epidemiologically unrelated strains showed that strains with inlA PMSC mutations (n = 41) were overrepresented among food-associated isolates, while strains encoding full-length InlA (n = 150) were overrepresented among isolates from farm animals and their environments. Furthermore, the A6 allele was overrepresented and the A7 allele was underrepresented among food isolates, while the A6 allele was underrepresented among farm and animal isolates. Our results indicate that genetic variation in inlA contributes to niche adaptation within the lineage II subtype DUP-1039C. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  7. Influences on flood frequency distributions in Irish river catchments

    Directory of Open Access Journals (Sweden)

    S. Ahilan

    2012-04-01

    Full Text Available This study explores influences on flood frequency distributions in Irish rivers. A Generalised Extreme Value (GEV type I distribution is recommended in Ireland for estimating flood quantiles in a single site flood frequency analysis. This paper presents the findings of an investigation that identified the GEV statistical distributions that best fit the annual maximum (AM data series extracted from 172 gauging stations of 126 rivers in Ireland. Analysis of these data was undertaken to explore hydraulic and hydro-geological factors that influence flood frequency distributions. A hierarchical approach of increasing statistical power that used probability plots, moment and L-moment diagrams, the Hosking goodness of fit algorithm and a modified Anderson-Darling (A-D statistical test was followed to determine whether a type I, type II or type III distribution was valid. Results of the Hosking et al. method indicated that of the 143 stations with flow records exceeding 25 yr, data for 95 (67% was best represented by GEV type I distributions and a further 9 (6% and 39 (27% stations followed type II and type III distributions respectively. Type I, type II and type III distributions were determined for 83 (58%, 16 (11% and 34 (24% stations respectively using the modified A-D method (data from 10 stations was not represented by GEV family distributions. The influence of karst terrain on these flood frequency distributions was assessed by incorporating results on an Arc-GIS platform showing karst features and using Monte Carlo simulations to assess the significance of the number and clustering of the observed distributions. Floodplain effects were identified by using two-sample t-tests to identify statistical correlations between the distributions and catchment properties that are indicative of strong floodplain activity. The data reveals that type I distributions are spatially well represented throughout the country. While also well represented throughout

  8. Derived flood frequency distributions considering individual event hydrograph shapes

    Science.gov (United States)

    Hassini, Sonia; Guo, Yiping

    2017-04-01

    Derived in this paper is the frequency distribution of the peak discharge rate of a random runoff event from a small urban catchment. The derivation follows the derived probability distribution procedure and incorporates a catchment rainfall-runoff model with approximating shapes for individual runoff event hydrographs. In the past, only simple triangular runoff event hydrograph shapes were used, in this study approximating runoff event hydrograph shapes better representing all the possibilities are considered. The resulting closed-form mathematical equations are converted to the commonly required flood frequency distributions for use in urban stormwater management studies. The analytically determined peak discharge rates of different return periods for a wide range of hypothetical catchment conditions were compared to those determined from design storm modeling. The newly derived equations generated results that are closer to those from design storm modeling and provide a better alternative for use in urban stormwater management studies.

  9. Stochastic subspace system identification using multivariate time-frequency distributions

    Science.gov (United States)

    Chang, Chia-Ming; Huang, Shieh-Kung

    2017-04-01

    Structural health monitoring assesses structural integrity by processing the measured responses of structures. One particular group in the structural health monitoring research is to conduct the operational modal analysis and then to extract the dynamic characteristics of structures from vibrational responses. These characteristics include natural frequencies, damping ratios, and mode shapes. Deviations in these characteristics represent the changes in structural properties and also imply possible damage to structures. In this study, a new stochastic system identification is developed using multivariate time-frequency distributions. These time-frequency distributions are derived from the short-time Fourier transform and subsequently yield a time-frequency matrix by stacking them with respect to time. As the derivation in the data-driven stochastic subspace system identification, the future time-frequency matrix is projected onto the past time-frequency matrix. By exploiting the singular value decomposition, the system and measurement matrices of a stochastic state-space representation are derived. Consequently, the dynamic characteristics of a structure are obtained. As compared to the time-domain stochastic subspace system identification, the proposed method utilizes the past and future matrices with a lower dimension in projection. A spectral magnitude envelope can be applied to the time-frequency matrix to highlight the major frequency components as well as to eliminate the components with less influence. To validate the proposed method, a numerical example is developed. This method is also applied to experimental data in order to evaluate its effectiveness. As a result, performance of the proposed method is superior to the time-domain stochastic subspace system identification.

  10. k-Casein, b-lactoglobulin and growth hormone allele frequencies and genetic distances in Nelore, Gyr, Guzerá, Caracu, Charolais, Canchim and Santa Gertrudis cattle

    Directory of Open Access Journals (Sweden)

    Paola Augusta Kemenes

    1999-12-01

    Full Text Available The genotypes for k-casein (k-CN, b-lactoglobulin (b-LG and growth hormone (GH were determined by polymerase chain reaction (PCR and restriction enzyme digestion in seven breeds of cattle (Nelore, Gyr, Guzerá, Caracu, Charolais, Canchim and Santa Gertrudis. k-Casein had two alleles with the A allele occurring at a higher frequency in Bos indicus breeds (0.93, 0.92 and 0.91% for Gyr, Guzerá and Nelore, respectively. The b-lactoglobulin locus had two alleles in all of the breeds. European breeds had a higher frequency of the b-LG A allele than Zebu breeds. The GH locus had two alleles (L and V in Bos taurus and was monomorphic (L allele only in all of the Bos indicus breeds evaluated. The highest frequency for the V allele was observed in Charolais cattle. The markers used revealed a considerable similarity among breeds, with two main groups being discernible. One group consisted of Zebu and Santa Gertrudis breeds and the other consisted of European and Canchim breeds.Os genótipos de k-caseína (k-CN, b-lactoglobulina (b-LG e hormônio de crescimento foram determinados por reação em cadeia de polimerase (PCR e digestão com enzima de restrição em sete raças de bovinos (Nelore, Gir, Guzerá, Caracu, Charolesa, Canchim and Santa Gertrudis. A k-caseína apresentou dois alelos e as freqüências mais elevadas para o alelo A foram observadas em Bos indicus (0,93, 0,92 e 0,91% para as raças Gir, Guzerá e Nelore, respectivamente. A b-lactoglobulina apresentou dois alelos em todas as raças estudadas, sendo a freqüência do alelo A mais elevada nas raças européias. O loco de hormônio de crescimento apresentou dois alelos em Bos taurus e foi monomórfico (alelo L em todas as raças zebuínas. A maior freqüência para o alelo V foi observado na raça Charolesa. Os marcadores investigados revelaram alta similaridade entre as raças, com a formação de dois grupos principais: um composto de raças zebuínas e a raça Santa Gertrudis e outro

  11. Distribution of the CCR5delta32 allele (gene variant CCR5) in Rondônia, Western Amazonian region, Brazil

    Science.gov (United States)

    de Farias, Josileide Duarte; Santos, Marlene Guimarães; de França, Andonai Krauze; Delani, Daniel; Tada, Mauro Shugiro; Casseb, Almeida Andrade; Simões, Aguinaldo Luiz; Engracia, Vera

    2012-01-01

    Since around 1723, on the occasion of its initial colonization by Europeans, Rondonia has received successive waves of immigrants. This has been further swelled by individuals from northeastern Brazil, who began entering at the beginning of the twentieth century. The ethnic composition varies across the state according to the various sites of settlement of each wave of immigrants. We analyzed the frequency of the CCR5Δ32 allele of the CCR5 chemokine receptor, which is considered a Caucasian marker, in five sample sets from the population. Four were collected in Porto Velho, the state capital and the site of several waves of migration. Of these, two, from the Hospital de Base were comprised of HB Mothers and HB Newborns presenting allele frequencies of 3.5% and 3.1%, respectively, a third from the peri-urban neighborhoods of Candelária/Bate-Estaca (1.8%), whereas a fourth, from the Research Center on Tropical Medicine/CEPEM (0.6%), was composed of malaria patients under treament. The fifth sample (3.4%) came from the inland Quilombola village of Pedras Negras. Two homozygous individuals (CCR5Δ32/CCR5Δ32) were detected among the HB Mother samples. The frequency of this allele was heterogeneous and higher where the European inflow was more pronounced. The presence of the allele in Pedras Negras revealed European miscegenation in a community largely comprising Quilombolas. PMID:22481870

  12. Frequency and distribution of Notch mutations in tumor cell lines

    International Nuclear Information System (INIS)

    Mutvei, Anders Peter; Fredlund, Erik; Lendahl, Urban

    2015-01-01

    Deregulated Notch signaling is linked to a variety of tumors and it is therefore important to learn more about the frequency and distribution of Notch mutations in a tumor context. In this report, we use data from the recently developed Cancer Cell Line Encyclopedia to assess the frequency and distribution of Notch mutations in a large panel of cancer cell lines in silico. Our results show that the mutation frequency of Notch receptor and ligand genes is at par with that for established oncogenes and higher than for a set of house-keeping genes. Mutations were found across all four Notch receptor genes, but with notable differences between protein domains, mutations were for example more prevalent in the regions encoding the LNR and PEST domains in the Notch intracellular domain. Furthermore, an in silico estimation of functional impact showed that deleterious mutations cluster to the ligand-binding and the intracellular domains of NOTCH1. For most cell line groups, the mutation frequency of Notch genes is higher than in associated primary tumors. Our results shed new light on the spectrum of Notch mutations after in vitro culturing of tumor cells. The higher mutation frequency in tumor cell lines indicates that Notch mutations are associated with a growth advantage in vitro, and thus may be considered to be driver mutations in a tumor cell line context. The online version of this article (doi:10.1186/s12885-015-1278-x) contains supplementary material, which is available to authorized users

  13. Simple method of generating and distributing frequency-entangled qudits

    Science.gov (United States)

    Jin, Rui-Bo; Shimizu, Ryosuke; Fujiwara, Mikio; Takeoka, Masahiro; Wakabayashi, Ryota; Yamashita, Taro; Miki, Shigehito; Terai, Hirotaka; Gerrits, Thomas; Sasaki, Masahide

    2016-11-01

    High-dimensional, frequency-entangled photonic quantum bits (qudits for d-dimension) are promising resources for quantum information processing in an optical fiber network and can also be used to improve channel capacity and security for quantum communication. However, up to now, it is still challenging to prepare high-dimensional frequency-entangled qudits in experiments, due to technical limitations. Here we propose and experimentally implement a novel method for a simple generation of frequency-entangled qudts with d\\gt 10 without the use of any spectral filters or cavities. The generated state is distributed over 15 km in total length. This scheme combines the technique of spectral engineering of biphotons generated by spontaneous parametric down-conversion and the technique of spectrally resolved Hong-Ou-Mandel interference. Our frequency-entangled qudits will enable quantum cryptographic experiments with enhanced performances. This distribution of distinct entangled frequency modes may also be useful for improved metrology, quantum remote synchronization, as well as for fundamental test of stronger violation of local realism.

  14. Combination of restriction endonuclease digestion with the ΔΔCt method in real-time PCR to monitor etoxazole resistance allele frequency in the two-spotted spider mite.

    Science.gov (United States)

    Osakabe, Masahiro; Imamura, Tsuyoshi; Nakano, Ryohei; Kamikawa, Satoshi; Tadatsu, Misono; Kunimoto, Yoshinori; Doi, Makoto

    2017-06-01

    Monitoring resistance allele frequency at the early stage of resistance development is important for the successful acaricide resistance management. Etoxazole is a mite growth inhibitor to which resistance is conferred by an amino acid substitution in the chitin synthase 1 (CHS1; I1017F) in T. urticae. If the susceptible allele can be specifically digested by restriction endonuclease, the ΔΔCt method using real-time PCR for genomic DNA (RED-ΔΔCt method) may be available for monitoring the resistance allele frequency. We tested whether the etoxazole resistance allele frequency in a pooled sample was accurately measured by the RED-ΔΔCt method and validated whether the resistance variant frequency was correlated with etoxazole resistance phenotype in a bioassay. Finally, we performed a pilot test using field populations. Strong linearity of the measures by the RED-ΔΔCt method with practical resistance allele frequencies; resistance allele frequency in the range between 0.5% to at least 0.75% was strictly represented. The strong linear relationship between hatchability of haploid male eggs after the etoxazole treatments (phenotype) and resistance allele frequencies in their mothers provided direct evidence that I1017F is a primary resistance factor to etoxazole in the strains used for experiments. The pilot test revealed a significant correlation between egg hatchability (including both diploid female eggs and haploid male eggs) and estimators in field populations. Consequently, we concluded that the RED-ΔΔCt method is a powerful tool for monitoring a resistance allele in a pooled sample. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Genetic variation among the Mapuche Indians from the Patagonian region of Argentina: mitochondrial DNA sequence variation and allele frequencies of several nuclear genes.

    Science.gov (United States)

    Ginther, C; Corach, D; Penacino, G A; Rey, J A; Carnese, F R; Hutz, M H; Anderson, A; Just, J; Salzano, F M; King, M C

    1993-01-01

    DNA samples from 60 Mapuche Indians, representing 39 maternal lineages, were genetically characterized for (1) nucleotide sequences of the mtDNA control region; (2) presence or absence of a nine base duplication in mtDNA region V; (3) HLA loci DRB1 and DQA1; (4) variation at three nuclear genes with short tandem repeats; and (5) variation at the polymorphic marker D2S44. The genetic profile of the Mapuche population was compared to other Amerinds and to worldwide populations. Two highly polymorphic portions of the mtDNA control region, comprising 650 nucleotides, were amplified by the polymerase chain reaction (PCR) and directly sequenced. The 39 maternal lineages were defined by two or three generation families identified by the Mapuches. These 39 lineages included 19 different mtDNA sequences that could be grouped into four classes. The same classes of sequences appear in other Amerinds from North, Central, and South American populations separated by thousands of miles, suggesting that the origin of the mtDNA patterns predates the migration to the Americas. The mtDNA sequence similarity between Amerind populations suggests that the migration throughout the Americas occurred rapidly relative to the mtDNA mutation rate. HLA DRB1 alleles 1602 and 1402 were frequent among the Mapuches. These alleles also occur at high frequency among other Amerinds in North and South America, but not among Spanish, Chinese or African-American populations. The high frequency of these alleles throughout the Americas, and their specificity to the Americas, supports the hypothesis that Mapuches and other Amerind groups are closely related.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. Allele and haplotype distribution for 16 Y-STRs (AmpFlSTR Y-filer kit) in the state of Chihuahua at North Center of Mexico.

    Science.gov (United States)

    Gutiérrez-Alarcón, A B; Moguel-Torres, M; León-Jiménez, A K; Cuéllar-Nevárez, G E; Rangel-Villalobos, H

    2007-05-01

    The AmpFlSTR Y-filer kit, including 16 Y-STRs was analyzed in 326 males from Chihuahua, at North Central, Mexico. Allele frequencies and gene diversity for each locus were estimated. Four allele duplications, namely DYS389II, DYS390, DYS391 and DYS439; and one allele null at DYS448 were observed in the sample. The haplotype diversity was 99.97+/-0.3%. The AMOVA results, including a previous report from West of Mexico (Jalisco), showed that most of the genetic variability between these Mexican populations is attributable to intrapopulational differences (99.87%). This result supports a low-genetic differentiation between males from North and West regions of Mexico.

  17. Frequency of a natural truncated allele ofMdMLO19in the germplasm ofMalus domestica.

    Science.gov (United States)

    Pessina, Stefano; Palmieri, Luisa; Bianco, Luca; Gassmann, Jennifer; van de Weg, Eric; Visser, Richard G F; Magnago, Pierluigi; Schouten, Henk J; Bai, Yuling; Riccardo Velasco, R; Malnoy, Mickael

    2017-01-01

    Podosphaera leucotricha is the causal agent of powdery mildew (PM) in apple. To reduce the amount of fungicides required to control this pathogen, the development of resistant apple cultivars should become a priority. Resistance to PM was achieved in various crops by knocking out specific members of the MLO gene family that are responsible for PM susceptibility (S-genes). In apple, the knockdown of MdMLO19 resulted in PM resistance. However, since gene silencing technologies such as RNAi are perceived unfavorably in Europe, a different approach that exploits this type of resistance is needed. This work evaluates the presence of non-functional naturally occurring alleles of MdMLO19 in apple germplasm. The screening of the re-sequencing data of 63 apple individuals led to the identification of 627 single nucleotide polymorphisms (SNPs) in five MLO genes ( MdMLO5, MdMLO7, MdMLO11, MdMLO18 , and MdMLO19 ), 127 of which were located in exons. The T-1201 insertion of a single nucleotide in MdMLO19 caused the formation of an early stop codon, resulting in a truncated protein lacking 185 amino acids, including the calmodulin-binding domain. The presence of the insertion was evaluated in 115 individuals. It was heterozygous in 64 and homozygous in 25. Twelve of the 25 individuals carrying the insertion in homozygosity were susceptible to PM. After barley, pea, cucumber, and tomato, apple would be the fifth species for which a natural non-functional mlo allele has been found.

  18. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China.

    Directory of Open Access Journals (Sweden)

    Hao Sun

    Full Text Available Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency.

  19. Frequency distribution function of stellar flares in the Orion association

    International Nuclear Information System (INIS)

    Parsamian, E.S.

    1981-01-01

    The temporal distributions of flare stars in the Orion association and the numbers of stars with different flare frequencies are determined by means of Ambartsumian's (1978) method, which uses the chronology of discovery of 'first' flares and the chronology of confirmations, i.e., the temporal distributions of 'repeated' flares. It is shown that flare stars with high flare frequency (not greater than 1000 hours) in the Pleiades are basically stars of low luminosity with M(U) not less than 13m. Two independent methods of determining the number of flare stars in the aggregates confirm that there are about 1.5 times more flare stars in the Orion association than in the Pleiades

  20. Seasonally adjusted birth frequencies follow the Poisson distribution.

    Science.gov (United States)

    Barra, Mathias; Lindstrøm, Jonas C; Adams, Samantha S; Augestad, Liv A

    2015-12-15

    Variations in birth frequencies have an impact on activity planning in maternity wards. Previous studies of this phenomenon have commonly included elective births. A Danish study of spontaneous births found that birth frequencies were well modelled by a Poisson process. Somewhat unexpectedly, there were also weekly variations in the frequency of spontaneous births. Another study claimed that birth frequencies follow the Benford distribution. Our objective was to test these results. We analysed 50,017 spontaneous births at Akershus University Hospital in the period 1999-2014. To investigate the Poisson distribution of these births, we plotted their variance over a sliding average. We specified various Poisson regression models, with the number of births on a given day as the outcome variable. The explanatory variables included various combinations of years, months, days of the week and the digit sum of the date. The relationship between the variance and the average fits well with an underlying Poisson process. A Benford distribution was disproved by a goodness-of-fit test (p variables is significantly improved (p variable. Altogether 7.5% more children are born on Tuesdays than on Sundays. The digit sum of the date is non-significant as an explanatory variable (p = 0.23), nor does it increase the explained variance. INERPRETATION: Spontaneous births are well modelled by a time-dependent Poisson process when monthly and day-of-the-week variation is included. The frequency is highest in summer towards June and July, Friday and Tuesday stand out as particularly busy days, and the activity level is at its lowest during weekends.

  1. Patients with unstable angina pectoris show an increased frequency of the Fc gamma RIIa R131 allele.

    Science.gov (United States)

    Raaz-Schrauder, Dorette; Ekici, Arif B; Munoz, Luis E; Klinghammer, Lutz; Voll, Reinhard E; Leusen, Jeanette H W; van de Winkel, Jan G J; Reis, André; Schett, Georg; Garlichs, Christoph D; Herrmann, Martin

    2012-11-01

    Patients with Systemic Lupus Erythematosus (SLE) carry an increased risk for the development of coronary artery disease (CAD). The R131 allele of the Fc gamma receptor IIa (FcγRIIa) is associated with SLE incidence and disease severity but also with CAD. Compared to stable angina pectoris (SAP) the unstable angina (UAP), as a manifestation of destabilizing CAD, is associated with increased risk of persistent instability, myocardial infarction, and death. Identification of clinically relevant determinants for unstable angina promises reduction of UAP-associated mortality in patients with SLE. We conducted a clinical study among 553 consecutive patients with stable angina pectoris (n = 330) and unstable angina pectoris (n = 223). All patients were genotyped for a frequent functional variant at position 131 of the mature FcγRIIa. UAP, but not SAP was significantly associated with the R/R131 genotype (P angina carrying the R/R131 genotype the odds ratio for suffering from UAP was 4.02 (95% confidence interval, 2.52-6.41) compared to those with non-R/R131 genotypes. In a multivariable analysis, the R/R131 genotype independently predicted the risk for development of UAP in a model adjusted for classical atherogenic risk factors. Our data imply that risk stratification of SLE- and other high risk patients with troponin-negative angina could be significantly improved by FcγRIIa genotyping.

  2. Blockwise Frequency Domain Active Noise Controller Over Distributed Networks

    Directory of Open Access Journals (Sweden)

    Christian Antoñanzas

    2016-04-01

    Full Text Available This work presents a practical active noise control system composed of distributed and collaborative acoustic nodes. To this end, experimental tests have been carried out in a listening room with acoustic nodes equipped with loudspeakers and microphones. The communication among the nodes is simulated by software. We have considered a distributed algorithm based on the Filtered-x Least Mean Square (FxLMS method that introduces collaboration between nodes following an incremental strategy. For improving the processing efficiency in practical scenarios where data acquisition systems work by blocks of samples, the frequency-domain partitioned block technique has been used. Implementation aspects such as computational complexity, processing time of the network and convergence of the algorithm have been analyzed. Experimental results show that, without constraints in the network communications, the proposed distributed algorithm achieves the same performance as the centralized version. The performance of the proposed algorithm over a network with a given communication delay is also included.

  3. Novel rapid genotyping assays for neuronal ceroid lipofuscinosis in Border Collie dogs and high frequency of the mutant allele in Japan.

    Science.gov (United States)

    Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Kawahara, Natsuko; Hayashi, Daisuke; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

    2011-11-01

    Neuronal ceroid lipofuscinosis (NCL) constitutes a group of recessively inherited lysosomal storage diseases that primarily affect neuronal cells. Such diseases share certain clinical and pathologic features in human beings and animals. Neuronal ceroid lipofuscinosis in Border Collie dogs was first detected in Australia in the 1980s, and the pathogenic mutation was shown to be a nonsense mutation (c.619C>T) in exon 4 in canine CLN5 gene. In the present study, novel rapid genotyping assays including polymerase chain reaction (PCR)-restriction fragment length polymorphism, PCR primer-induced restriction analysis, mutagenically separated PCR, and real-time PCR with TaqMan minor groove binder probes, were developed. The utility of microchip electrophoresis was also evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies in Japan using these assays to determine the current allele frequency in Japan, providing information to control and prevent this disease in the next stage. All assays developed in the current study are available to discriminate these genotypes, and microchip electrophoresis showed a timesaving advantage over agarose gel electrophoresis. Of all assays, real-time PCR was the most suitable for large-scale examination because of its high throughput. The genotyping survey demonstrated that the carrier frequency was 8.1%. This finding suggested that the mutant allele frequency of NCL in Border Collies is high enough in Japan that measures to control and prevent the disease would be warranted. The genotyping assays developed in the present study could contribute to the prevention of NCL in Border Collies.

  4. Frequency of Class I and II HLA alleles in patients with lung cancer according to chemotherapy response and 5-year survival.

    Science.gov (United States)

    Araz, Omer; Ucar, Elif Yilmazel; Meral, Mehmet; Yalcin, Aslıhan; Acemoglu, Hamit; Dogan, Hasan; Karaman, Adem; Aydin, Yener; Gorguner, Metin; Akgun, Metin

    2015-07-01

    Lung cancer is the most common cause of cancer death in the world, and the most common type is non-small-cell lung cancer (NSCLC). At present, surgical resection, chemotherapy, and radiation therapy are the main treatments for patients with NSCLC, but unfortunately outcome remains unsatisfactory. This study aimed to determine whether Class I and II histocompatibility leukocyte antigen (HLA) alleles are related with response to chemotherapy and survival of lung cancer. A total of 65 NSCLC patients (56 men and 9 women, mean age 58.4 ± 11 years) were included in the study. Patient groups were compared with a control group of 88 unrelated healthy kidney or bone marrow donors in order to clearly identify susceptible and protective HLA alleles in lung cancer. Target lesions and tumor response were assessed using the Response Evaluation Criteria for Solid Tumors (RECIST) guidelines. Results were classified into two groups: complete-partial response and stable-progressive disease. We found that expression of HLA-A32, HLA-B41, HLA-B57, HLA-DRB1*13, and HLA-DQ5 were more frequent in the complete and partial response groups to chemotherapy than in the control group. The frequency of HLA-A11, HLA-A29, HLA-BW6, HLA-CW3, HLA-DR1*1, and HLA-DRB1*3 were determined to be higher in the stable and progressive disease groups taking chemotherapy than in the control group. Additionally, expressions of HLA-A2 and HLA-B49 were statistically related with 5-year survival. Our results suggested that expressions of HLA-BW6 and HLA-DRB1*13 alleles may be predictable markers for response to chemotherapy in lung cancer patients. © 2014 John Wiley & Sons Ltd.

  5. Frequency distributions: from the sun to the earth

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    N. B. Crosby

    2011-11-01

    Full Text Available The space environment is forever changing on all spatial and temporal scales. Energy releases are observed in numerous dynamic phenomena (e.g. solar flares, coronal mass ejections, solar energetic particle events where measurements provide signatures of the dynamics. Parameters (e.g. peak count rate, total energy released, etc. describing these phenomena are found to have frequency size distributions that follow power-law behavior. Natural phenomena on Earth, such as earthquakes and landslides, display similar power-law behavior. This suggests an underlying universality in nature and poses the question of whether the distribution of energy is the same for all these phenomena. Frequency distributions provide constraints for models that aim to simulate the physics and statistics observed in the individual phenomenon. The concept of self-organized criticality (SOC, also known as the "avalanche concept", was introduced by Bak et al. (1987, 1988, to characterize the behavior of dissipative systems that contain a large number of elements interacting over a short range. The systems evolve to a critical state in which a minor event starts a chain reaction that can affect any number of elements in the system. It is found that frequency distributions of the output parameters from the chain reaction taken over a period of time can be represented by power-laws. During the last decades SOC has been debated from all angles. New SOC models, as well as non-SOC models have been proposed to explain the power-law behavior that is observed. Furthermore, since Bak's pioneering work in 1987, people have searched for signatures of SOC everywhere. This paper will review how SOC behavior has become one way of interpreting the power-law behavior observed in natural occurring phenomenon in the Sun down to the Earth.

  6. Allele frequency and gene expression of a putative carboxylesterase-encoding gene in a pyrethroid resistant strain of the tick Boophilus microplus.

    Science.gov (United States)

    Hernandez, R; Guerrero, F D; George, J E; Wagner, G G

    2002-09-01

    We utilized RNA Northern blot analysis and ribonuclease protection assays (RPA) to study the mRNA expression level of a putative carboxylesterase-encoding gene from several strains of Boophilus microplus (Canestrini). Both the Northern analysis and RPAs indicated that an esterase transcript was more abundant in the pyrethroid resistant strain, Coatzacoalcos (Cz), compared to a susceptible control strain and a resistant strain whose pyrethroid resistance is mediated through a target site insensitivity mechanism. A PCR-based assay was designed to identify the presence of a previously reported point mutation in this B. microplus esterase gene. The reported G-->A substitution at nucleotide 1120 creates an EcoR I site in the mutant allele which can be detected by EcoR I digestion of the amplification products. The PCR assays showed that the frequency of the mutant allele was highest in the Cz-resistant strain, which has been shown to have an esterase-mediated resistance mechanism. The PCR assay can be performed either on individual tick larvae or hemolymph from adults.

  7. Distributive estimation of frequency selective channels for massive MIMO systems

    KAUST Repository

    Zaib, Alam

    2015-12-28

    We consider frequency selective channel estimation in the uplink of massive MIMO-OFDM systems, where our major concern is complexity. A low complexity distributed LMMSE algorithm is proposed that attains near optimal channel impulse response (CIR) estimates from noisy observations at receive antenna array. In proposed method, every antenna estimates the CIRs of its neighborhood followed by recursive sharing of estimates with immediate neighbors. At each step, every antenna calculates the weighted average of shared estimates which converges to near optimal LMMSE solution. The simulation results validate the near optimal performance of proposed algorithm in terms of mean square error (MSE). © 2015 EURASIP.

  8. Explaining Ethnic Variability of Transporter Substrate Pharmacokinetics in Healthy Asian and Caucasian Subjects with Allele Frequencies of OATP1B1 and BCRP: A Mechanistic Modeling Analysis.

    Science.gov (United States)

    Li, Rui; Barton, Hugh A

    2018-04-01

    Ethnic variability in the pharmacokinetics of organic anion transporting polypeptide (OATP) 1B1 substrates has been observed, but its basis is unclear. A previous study hypothesizes that, without applying an intrinsic ethnic variability in transporter activity, allele frequencies of transporters cannot explain observed ethnic variability in pharmacokinetics. However, this hypothesis contradicts the data collected from compounds that are OATP1B1 substrates but not breast cancer resistance protein (BCRP) substrates. The objective of this study is to evaluate a hypothesis that is physiologically reasonable and more consistent with clinical observations. We evaluated if allele frequencies of two transporters (OATP1B1 and BCRP) are key contributors to ethnic variability. In this hypothesis, the same genotype leads to the same activity independent of ethnicity, in contrast to the previous hypothesis of intrinsic ethnic variability in OATP1B1 activity. As a validation, we perform mechanistic pharmacokinetic modeling for SLCO1B1 (encoding OATP1B1) and ABCG2 (encoding BCRP) genotyped pharmacokinetic data from 18 clinical studies with healthy Caucasian and/or Asian subjects. Simulations based on the current hypothesis reasonably describe SLCO1B1 and ABCG2 genotyped pharmacokinetic time course data for five transporter substrates (atorvastatin, pitavastatin, pravastatin, repaglinide, and rosuvastatin) in Caucasian and Asian populations. This hypothesis covers the observations that can (e.g., ethnic differences in rosuvastatin pharmacokinetics) or cannot (e.g., lack of differences for pitavastatin pharmacokinetics) be explained by the previous hypothesis. It helps to characterize sources of ethnic variability and provides a foundation for predicting ethnic variability in transporter substrate pharmacokinetics.

  9. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.

    Science.gov (United States)

    Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  10. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910 in medieval central europe.

    Directory of Open Access Journals (Sweden)

    Annina Krüttli

    Full Text Available Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72% exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic

  11. Single Frequency Network Based Distributed Passive Radar Technology

    Directory of Open Access Journals (Sweden)

    Wan Xian-rong

    2015-01-01

    Full Text Available The research and application of passive radar are heading from single transmitter-receiver pair to multiple transmitter-receiver pairs. As an important class of the illuminators of opportunity, most of modern digital broadcasting and television systems work on Single Frequency Network (SFN, which intrinsically determines that the passive radar based on such illuminators must be distributed and networked. In consideration of the remarkable working and processing mode of passive radar under SFN configuration, this paper proposes the concept of SFN-based Distributed Passive Radar (SDPR. The main characteristics and key problems of SDPR are first described. Then several potential solutions are discussed for part of the key technologies. The feasibility of SDPR is demonstrated by preliminary experimental results. Finally, the concept of four network convergence that includes the broadcast based passive radar network is conceived, and its application prospects are discussed.

  12. Five-year tracking of Plasmodium falciparum allele frequencies in a holoendemic area with indistinct seasonal transitions

    Directory of Open Access Journals (Sweden)

    Akala HM

    2014-11-01

    Full Text Available Hoseah M Akala, Angela O Achieng, Fredrick L Eyase, Dennis W Juma, Luiser Ingasia, Agnes C Cheruiyot, Charles Okello, Duke Omariba, Eunice A Owiti, Catherine Muriuki, Redemptah Yeda, Ben Andagalu, Jacob D Johnson, Edwin Kamau Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya Background: The renewed malaria eradication efforts require an understanding of the seasonal patterns of frequency of polymorphic variants in order to focus limited funds productively. Although cross-sectional studies in holoendemic areas spanning a single year could be useful in describing parasite genotype status at a given point, such information is inadequate in describing temporal trends in genotype polymorphisms. For Plasmodium falciparum isolates from Kisumu District Hospital, Plasmodium falciparum chloroquine-resistance transporter gene (Pfcrt-K76T and P. falciparum multidrug resistance gene 1 (PfMDR1-N86Y, were analyzed for polymorphisms and parasitemia changes in the 53 months from March 2008 to August 2012. Observations were compared with prevailing climatic factors, including humidity, rainfall, and temperature. Methods: Parasitemia (the percentage of infected red blood cells per total red blood cells was established by microscopy for P. falciparum malaria-positive samples. P. falciparum DNA was extracted from whole blood using a Qiagen DNA Blood Mini Kit. Single nucleotide polymorphism identification at positions Pfcrt-K76T and PfMDR1-N86Y was performed using real-time polymerase chain reaction and/or sequencing. Data on climatic variables were obtained from http://www.tutiempo.net/en/. Results: A total of 895 field isolates from 2008 (n=169, 2009 (n=161, 2010 (n=216, 2011 (n=223, and 2012 (n=126 showed large variations in monthly frequency of PfMDR1-N86Y and Pfcrt-K76T as the mutant genotypes decreased from 68.4%±15% and 38.1%±13% to

  13. Using the distribution of the CCR5-Δ32 allele in third-generation Maltese citizens to disprove the Black Death hypothesis.

    Science.gov (United States)

    Baron, B; Schembri-Wismayer, P

    2011-04-01

    Malta was under Norman rule for over 400 years and has had three major documented plague outbreaks (and a number of minor ones) since the 14th century with death tolls of 5-15% of the population at the time. This makes the Maltese population ideal for testing the hypothesis that the Black Death (particularly that of 1346-52) was responsible for a genetic shift that spread the CCR5-Δ32 allele. By enrolling 300 blood donors to determine the percentage of the Maltese population resistant to HIV-1 (which uses the CCR5-receptor to infect cells), it was established that the CCR5-Δ32 allele frequency is almost zero in third-generation Maltese citizens and sequencing showed that the deletion observed in the region of interest is the 32-base deletion expected. Thus, despite the extensive Norman occupation and the repeated plague cullings, the CCR5-Δ32 allele frequency is extremely low. This provides a basis for the discussion of conflicting hypotheses regarding the possible origin, function and spread of the CCR5-Δ32 deletion. © 2010 Blackwell Publishing Ltd.

  14. [Discovery of a novel A2 allel in ABO blood group system and investigation of its distribution in Han population of Chinese Fujian province].

    Science.gov (United States)

    Zhang, Ai; Chi, Quan; Ren, Ben-Chun

    2012-10-01

    This study was aimed to investigate the distribution of A2 subgroup in Han Population of Chinese Fujian province and its molecular mechanisms. One individual with serologic ABO blood grouping discrepancy was identified with commercially available monoclonal and polyclonal antibodies and lectin: anti-A, anti-B, anti-AB, anti-A1, and anti-H reagents according to the routine laboratory methods. DNA sequences of exon 6, 7 and intron 6 of ABO gene were analyzed by polymerase chain reaction using genomic DNA and direct DNA sequencing or sequencing after gene cloning. Red cells of 3 176 A or AB unrelated individuals were tested with anti-A1. The results showed that this individual was identified as A2 subgroup by serological technology, sequencing analysis indicated the A2 subgroup with novel A variant allele, the novel A allele being different from the allele A101 by 467C > T and 607G > A missense mutation in exon 7, no A2 subgroup was identified from the 3 176 individuals by using standard serological technology. It is concluded that a novel A allele responsible for A2 subgroup composing of 467C > T and 607G > A has been firstly confirmed, and the A2 subgroup is very rare in Chinese Fujian Han population.

  15. Distribution of HLA-A, -B and -DRB1 alleles in the Kensiu and Semai Orang Asli sub-groups in Peninsular Malaysia.

    Science.gov (United States)

    Tasnim, Abd Razak; Allia, Shahril; Edinur, Hisham Atan; Panneerchelvam, Sundararajulu; Zafarina, Zainuddin; Norazmi, Mohd Nor

    2016-08-01

    The earliest settlers in Peninsular Malaysia are the Orang Asli population, namely Semang, Senoi and Proto Malays. In the present study, we typed the HLA-A, -B and -DRB1 loci of the Kensiu and Semai Orang Asli sub-groups. Sequence-based HLA typing was performed on 59 individuals from two Orang Asli sub-groups. A total of 11, 18 and 14 HLA-A, -B and -DRB1 alleles were identified, respectively. These data are available in the Allele Frequencies Net Database under the population name "Malaysia Kedah Kensiu" and "Malaysia Pahang Semai". Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

  16. Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases

    Science.gov (United States)

    Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T.; Morgan, Alex A.; Moreno-Estrada, Andres; Nilsen, Geoffrey B.; Ruau, David; Lincoln, Stephen E.; Bustamante, Carlos D.; Butte, Atul J.

    2012-01-01

    Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed

  17. Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.

    Directory of Open Access Journals (Sweden)

    Rong Chen

    Full Text Available Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may

  18. LPI Radar Waveform Recognition Based on Time-Frequency Distribution

    Directory of Open Access Journals (Sweden)

    Ming Zhang

    2016-10-01

    Full Text Available In this paper, an automatic radar waveform recognition system in a high noise environment is proposed. Signal waveform recognition techniques are widely applied in the field of cognitive radio, spectrum management and radar applications, etc. We devise a system to classify the modulating signals widely used in low probability of intercept (LPI radar detection systems. The radar signals are divided into eight types of classifications, including linear frequency modulation (LFM, BPSK (Barker code modulation, Costas codes and polyphase codes (comprising Frank, P1, P2, P3 and P4. The classifier is Elman neural network (ENN, and it is a supervised classification based on features extracted from the system. Through the techniques of image filtering, image opening operation, skeleton extraction, principal component analysis (PCA, image binarization algorithm and Pseudo–Zernike moments, etc., the features are extracted from the Choi–Williams time-frequency distribution (CWD image of the received data. In order to reduce the redundant features and simplify calculation, the features selection algorithm based on mutual information between classes and features vectors are applied. The superiority of the proposed classification system is demonstrated by the simulations and analysis. Simulation results show that the overall ratio of successful recognition (RSR is 94.7% at signal-to-noise ratio (SNR of −2 dB.

  19. Frequencies and ethnic distribution of ABO and Rh(D) blood groups in Mauritania: results of first nationwide study.

    Science.gov (United States)

    Hamed, C T; Bollahi, M A; Abdelhamid, I; Med Mahmoud, M A; Ba, B; Ghaber, S; Habti, N; Houmeida, A

    2012-04-01

    There is no data available on the ABO/Rh(D) frequencies in the Mauritanian population. We retrospectively analysed records of a 5-year database that contained ABO/Rh phenotype and ethnic origin of 10 116 volunteers giving blood at the national blood transfusion centre to derive the frequencies of ABO/Rh(D) groups in the Mauritanian population. The two race categories in the country and their sub-ethnic groups: the Moors (whites and black) and the black Africans (Pulhars, Soninkes and Wolof) were included in this study. Globally, group O had the highest frequency (49.10%) followed by A (28.28%), B (18.56%) and AB (4.05%). This order more common in North African populations was found in four of the five ethnic groups composing our population. Allele frequencies were, respectively, 70.20%, 17.74% and 12.04% giving the same order of O > A > B. We observed no significant variation in these frequencies between the different ethnic groups. Rhesus study showed that with a percentage of 94.23% Rh(D) positive is by far the most prevalent, while Rh(D) negative is present only in 5.77% of the total population. This frequency distribution supports the mixed-race composition of the Mauritanian population. © 2011 Blackwell Publishing Ltd.

  20. Allele-specific primer polymerase chain reaction for a single nucleotide polymorphism (C1205T) of swine Toll-like receptor 5 and comparison of the allelic frequency among several pig breeds in Japan and the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Muneta, Y.; Minagawa, Y.; Kusumoto, M.; Shinkai, H.; Uenishi, H.; Šplíchal, Igor

    2012-01-01

    Roč. 56, č. 6 (2012), s. 385-391 ISSN 0385-5600 R&D Projects: GA ČR GA524/09/0365 Institutional support: RVO:61388971 Keywords : allele-specific PCR * Salmonella enterica serovar Choleraesuis * single nucleotide polymorphism Subject RIV: EC - Immunology Impact factor: 1.545, year: 2012

  1. Landslide scaling and magnitude-frequency distribution (Invited)

    Science.gov (United States)

    Stark, C. P.; Guzzetti, F.

    2009-12-01

    Landslide-driven erosion is controlled by the scale and frequency of slope failures and by the consequent fluxes of debris off the hillslopes. Here I focus on the magnitude-frequency part of the process and develop a theory of initial slope failure and debris mobilization that reproduces the heavy-tailed distributions (PDFs) observed for landslide source areas and volumes. Landslide rupture propagation is treated as a quasi-static, non-inertial process of simplified elastoplastic deformation with strain weakening; debris runout is not considered. The model tracks the stochastically evolving imbalance of frictional, cohesive, and body forces across a failing slope, and uses safety-factor concepts to convert the evolving imbalance into a series of incremental rupture growth or arrest probabilities. A single rupture is simulated with a sequence of weighted ``coin tosses'' with weights set by the growth probabilities. Slope failure treated in this stochastic way is a survival process that generates asymptotically power-law-tail PDFs of area and volume for rock and debris slides; predicted scaling exponents are consistent with analyses of landslide inventories. The primary control on the shape of the model PDFs is the relative importance of cohesion over friction in setting slope stability: the scaling of smaller, shallower failures, and the size of the most common landslide volumes, are the result of the low cohesion of soil and regolith, whereas the negative power-law tail scaling for larger failures is tied to the greater cohesion of bedrock. The debris budget may be dominated by small or large landslides depending on the scaling of both the PDF and of the depth-length relation. I will present new model results that confirm the hypothesis that depth-length scaling is linear. Model PDF of landslide volumes.

  2. Association between the CCR5 32-bp deletion allele and late onset of schizophrenia

    DEFF Research Database (Denmark)

    Rasmussen, H.B.; Timm, S.; Wang, A.G.

    2006-01-01

    OBJECTIVE: The 32-bp deletion allele in chemokine receptor CCR5 has been associated with several immune-mediated diseases and might be implicated in schizophrenia as well. METHOD: The authors genotyped DNA samples from 268 schizophrenia patients and 323 healthy subjects. Age at first admission...... to a psychiatric hospital department served as a measure of disease onset. RESULTS: Patients and comparison subjects differed marginally in their genotype distribution, with a slightly higher frequency of the deletion allele seen in the patients. The authors found the deletion allele to be associated with higher......-onset schizophrenia) and healthy subjects differed significantly. This was reflected in an increased frequency of the deletion allele in the patient subgroup. Patients with ages at first admission below and above 40 years significantly differed in distribution of genotypes and alleles, with an overrepresentation...

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

    Directory of Open Access Journals (Sweden)

    Sonja Petrović

    2012-12-01

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

  4. A WIDE DISTRIBUTION OF A NEW VRN-B1c ALLELE OF WHEAT TRITICUM AESTIVUM L. IN RUSSIA, UKRAINE AND ADJACENT REGIONS: A LINK WITH THE HEADING TIME AND ADAPTIVE POTENTIAL

    Directory of Open Access Journals (Sweden)

    Shcherban A.

    2012-08-01

    Full Text Available The adaptation of common wheat (T. aestivum L. to diverse environmental conditions is greatly under the control of genes involved in determination of vernalization response (Vrn-1 genes. It was found that the variation in common wheat heading time is affected not only by combination of Vrn-1 homoeoalleles but also by multiple alleles at a separate Vrn-1 locus. Previously, we described the Vrn-B1c allele from T.aestivum cv. 'Saratovskaya 29' and found significant differences in the structure of the first (1st intron of this allele when compared to another highly abundant Vrn-B1a allele, specifically, the deletion of 0.8 kb coupled with the duplication of 0.4 kb. We suggested that the changes in the intron 1 of Vrn-B1c allele caused earlier ear emergence in the near-isogenic line and cultivars, carrying this allele. In this study we investigate the distribution of the Vrn-B1c allele in a wide set of spring wheat cultivars from Russia, Ukraine and adjacent regions. The analysis revealed that 40% of Russian and 53% of Ukranian spring wheat cultivars contain the Vrn-B1c allele. The high distribution of the Vrn-B1c allele can be explained by a frequent using of 'Saratovskaya 29' in the breeding process inside the studied area. From the other hand, the predominance of the Vrn-B1c allele among cultivars cultivated in West Siberia and Kazakhstan may be due to the selective advantage of this allele for the region where there is a high risk of early fall frosts.

  5. Associations of HLA-A, HLA-B and HLA-C Alleles Frequency with Prevalence of Herpes Simplex Virus Infections and Diseases Across Global Populations: Implication for the Development of an Universal CD8+ T-Cell Epitope-Based Vaccine

    Science.gov (United States)

    Samandary, Sarah; Kridane-Miledi, Hédia; Sandoval, Jacqueline S.; Choudhury, Zareen; Langa-Vives, Francina; Spencer, Doran; Chentoufi, Aziz A.; Lemonnier, François A.; BenMohamed, Lbachir

    2014-01-01

    A significant portion of the world’s population is infected with herpes simplex virus type 1 and/or type 2 (HSV-1 and/or HSV-2), that cause a wide range of diseases including genital herpes, oro-facial herpes, and the potentially blinding ocular herpes. While the global prevalence and distribution of HSV-1 and HSV-2 infections cannot be exactly established, the general trends indicate that: (i) HSV-1 infections are much more prevalent globally than HSV-2; (ii) Over half billion people worldwide are infected with HSV-2; (iii) the sub-Saharan African populations account for a disproportionate burden of genital herpes infections and diseases; (iv) the dramatic differences in the prevalence of herpes infections between regions of the world appear to be associated with differences in the frequencies of human leukocyte antigen (HLA) alleles. The present report: (i) analyzes the prevalence of HSV-1 and HSV-2 infections across various regions of the world; (ii) analyzes potential associations of common HLA-A, HLA-B and HLA-C alleles with the prevalence of HSV-1 and HSV-2 infections in the Caucasoid, Oriental, Hispanic and Black major populations; and (iii) discusses how our recently developed HLA-A, HLA-B, and HLA-C transgenic/H-2 class I null mice will help validate HLA/herpes prevalence associations. Overall, high prevalence of herpes infection and disease appears to be associated with high frequency of HLA-A*24, HLA-B*27, HLA-B*53 and HLA-B*58 alleles. In contrast, low prevalence of herpes infection and disease appears to be associated with high frequency of HLA-B*44 allele. The finding will aid in developing a T-cell epitope-based universal herpes vaccine and immunotherapy. PMID:24798939

  6. Dynamic Response to Pedestrian Loads with Statistical Frequency Distribution

    DEFF Research Database (Denmark)

    Krenk, Steen

    2012-01-01

    on the magnitude of the resulting response. A frequency representation of vertical pedestrian load is developed, and a compact explicit formula is developed for the magnitude of the resulting response, in terms of the damping ratio of the structure, the bandwidth of the pedestrian load, and the mean footfall...... frequency. The accuracy of the formula is verified by a statistical moment analysis using the Lyapunov equations....

  7. Dual matrilineal geographic distribution of Korean type 2 diabetes mellitus-associated -11,377 G adiponectin allele.

    Science.gov (United States)

    Choi, Jee-Hye; Min, Na Young; Park, Sang Kil; Gavaachimed, Lkhagvasuren; Ko, Young Jong; Han, Sung Hoon; Kim, Kyung Yong; Kim, Kijung; Lee, Kwang Ho; Park, Ae Ja

    2014-12-01

    The present study was performed to identify the susceptible single nucleotide polymorphisms (SNPs) for the prediction of Korean type 2 diabetes mellitus (T2DM) and to clarify the matrilineal origin of Korean T2DM‑specific SNPs. Fourteen SNPs from the adiponectin (ADIPOQ), hepatocyte nuclear factor 4α, phosphoenolpyruvate carboxykinase 1 and glucokinase genes in the Korean population were analyzed. Only one SNP, ‑11,377 C/G on the ADIPOQ gene, was finally determined to be responsible for the incidence of Korean T2DM (P=0.028). The G‑T‑T‑A haplotype at positions ‑11,377, +45, +276 and +349 on the ADIPOQ gene was also associated with a high incidence of Korean T2DM (P=0.023). In addition, the susceptibility of Korean individuals to T2DM appears to be affected by their matrilineal origin. Of note, the group of Southern origin, consisting of mitochondrial DNA macrohaplogroups F and R, was predisposed to T2DM, whereas the group of Northern origin, consisting of haplogroups A and Y, was resistant to T2DM. This implied that the differential genetics between the two groups, which were formed from the initial peopling of the proto‑Korean population via Southern and Northern routes to the present time, may explain their differing susceptibility to T2DM. In conclusion, from Southern Asia Northward, a matrilineal origin of Korean individuals appears to be responsible for the prevalence of Korean T2DM caused by the ‑11,377 G allele.

  8. Frequency of the allelic variant (Trp8Arg/Ile15Thr) of the luteinizing hormone gene in a Brazilian cohort of healthy subjects and in patients with hypogonadotropic hypogonadism

    OpenAIRE

    Berger, Karina; Billerbeck, Ana Elisa Correia; Costa, Elaine Maria Frade; Carvalho, Luciani Silveira; Arnhold, Ivo Jorge Prado; Mendonca, Berenice Bilharinho

    2005-01-01

    PURPOSE: To evaluate the frequency of allelic variant Trp8Arg/Ile15Thr in the luteinizing hormone beta-subunit gene in a Brazilian population of healthy subjects and in patients with hypogonadotropic hypogonadism. SUBJECTS AND METHODS: Two hundred and two adults (115 women) with normal sexual function and 48 patients (24 women) with hypogonadotropic hypogonadism underwent a molecular study of the the luteinizing hormone beta-subunit gene using a polymerase chain reaction technique followed by...

  9. Benefits of time-frequency coding for quantum key distribution

    Science.gov (United States)

    Rödiger, J.; Perlot, N.; Benson, O.; Freund, R.

    2017-09-01

    Quantum key distribution (QKD), the first applicable quantum technology, is able to distribute a secret key to two parties. This key can then be used as a one-time-pad for absolutely secure communication. The first QKD protocol was the polarization based BB84 protocol proposed in [1]. Since then many QKD protocols have been proposed and investigated [2, 3].

  10. Statistical Tests for Frequency Distribution of Mean Gravity Anomalies

    African Journals Online (AJOL)

    The hypothesis that a very large number of lOx 10mean gravity anomalies are normally distributed has been rejected at 5% Significance level based on the X2 and the unit normal deviate tests. However, the 50 equal area mean anomalies derived from the lOx 10data, have been found to be normally distributed at the same ...

  11. Entropy-based derivation of generalized distributions for hydrometeorological frequency analysis

    Science.gov (United States)

    Chen, Lu; Singh, Vijay P.

    2018-02-01

    Frequency analysis of hydrometeorological and hydrological extremes is needed for the design of hydraulic and civil infrastructure facilities as well as water resources management. A multitude of distributions have been employed for frequency analysis of these extremes. However, no single distribution has been accepted as a global standard. Employing the entropy theory, this study derived five generalized distributions for frequency analysis that used different kinds of information encoded as constraints. These distributions were the generalized gamma (GG), the generalized beta distribution of the second kind (GB2), and the Halphen type A distribution (Hal-A), Halphen type B distribution (Hal-B) and Halphen type inverse B distribution (Hal-IB), among which the GG and GB2 distribution were previously derived by Papalexiou and Koutsoyiannis (2012) and the Halphen family was first derived using entropy theory in this paper. The entropy theory allowed to estimate parameters of the distributions in terms of the constraints used for their derivation. The distributions were tested using extreme daily and hourly rainfall data. Results show that the root mean square error (RMSE) values were very small, which indicated that the five generalized distributions fitted the extreme rainfall data well. Among them, according to the Akaike information criterion (AIC) values, generally the GB2 and Halphen family gave a better fit. Therefore, those general distributions are one of the best choices for frequency analysis. The entropy-based derivation led to a new way for frequency analysis of hydrometeorological extremes.

  12. Frequency distribution 0f ABO, RH blood groups and blood ...

    African Journals Online (AJOL)

    One hundred and fifty students (150) were randomly selected from the Department of Cell Biology and Genetics of University of Lagos, Akoka, Nigeria for ABO, RH blood groups and 6 haemoglobin genotypes studies. Blood group O was the highest with the percentage frequency of 55.3%, followed by blood group A (25.3%) ...

  13. Tuningless Load Frequency Control Through Active Engagement of Distributed Resources

    DEFF Research Database (Denmark)

    Prostejovsky, Alexander; Marinelli, Mattia; Rezkalla, Michel M.N.

    2017-01-01

    The increasing share of volatile and inverter-based energy sources render electric power grids increasingly susceptible to disturbances. Established Load Frequency Control (LFC) schemes are rigid and require careful tuning, making them unsuitable for dynamically changing environments. In this paper...

  14. Development of Allele-Specific Primer PCR for a Swine TLR2 SNP and Comparison of the Frequency among Several Pig Breeds of Japan and the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Muneta, Y.; Minagawa, Y.; Kusumoto, M.; Shinkai, H.; Uenishi, H.; Šplíchal, Igor

    2012-01-01

    Roč. 74, č. 5 (2012), s. 553-559 ISSN 0916-7250 R&D Projects: GA ČR GA524/09/0365 Institutional support: RVO:61388971 Keywords : allele-specific PCR * Mycoplasma hyopneumoniae * single nucleotide polymorphism Subject RIV: EC - Immunology Impact factor: 0.876, year: 2012

  15. Frequency and distribution studies of asymmetrical versus symmetrical chromosome aberrations

    International Nuclear Information System (INIS)

    Savage, J.R.K.; Papworth, D.G.

    1982-01-01

    Two aspects of the relationship between Asymmetrical (A) and Symmetrical (S) radiation-induced chromosomal aberrations are considered in this paper. (1) Are A and S truly alternative modes of lesion interaction. Relative frequencies for chromatid-type and chromosome-type are examined, and new lymphocyte data using banding is used to look at this, and also for parallelism in chromosome participation of the two forms for various aberration categories. All the tests applied suggest that A and S are alternative interaction modes. (2) The long-term survival characteristics of A and S are discussed, and the differences in expected frequencies of derived S per surviving cell from chromosome-type and chromatid-types are stressed. Since many in vivo tissues have varying mixtures of potential chromatid and chromosome aberration-bearing target cells, ultimate cell survival and derived S frequencies may differ between tissues for the same absorbed dose. An Appendix gives Relative Corrected Lengths (RCL) for chromosomes of the human karyotype which should be used when testing the various exchange aberration categories for random chromosome participation. (orig.)

  16. Topology Optimization of Distributed Mass Dampers for Low-frequency Vibration Suppression

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard; Lazarov, Boyan Stefanov

    2007-01-01

    In this paper the method of topology optimization is used to find optimized parameter distributions for a multiple mass damper system with the purpose of minimizing the low-frequency steady-state response of a carrier structure. An effective density model that describes the steady-state effect...... of the dampers is derived based on a continuous approximation of the damper distribution. The dampers are optimized with respect to the point-wise distribution of mass ratio, natural frequency, and damping ratio....

  17. Randomized algorithms for tracking distributed count, frequencies, and ranks

    DEFF Research Database (Denmark)

    Zengfeng, Huang; Ke, Yi; Zhang, Qin

    2012-01-01

    We show that randomization can lead to significant improvements for a few fundamental problems in distributed tracking. Our basis is the count-tracking problem, where there are k players, each holding a counter ni that gets incremented over time, and the goal is to track an ∑-approximation of the...

  18. statistical tests for frequency distribution of mean gravity anomalies

    African Journals Online (AJOL)

    ES Obe

    1980-03-01

    Mar 1, 1980 ... ABSTRACT. The hypothesis that a very large number of lOx 10mean gravity anomalies are normally distributed has been rejected at 5%. Significance level based on the X2 and the unit normal deviate tests. However, the 50 equal area mean anomalies derived from the lOx 10data, have been found to be ...

  19. Performance Comparison of Time-Frequency Distributions for Estimation of Instantaneous Frequency of Heart Rate Variability Signals

    Directory of Open Access Journals (Sweden)

    Nabeel Ali Khan

    2017-02-01

    Full Text Available The instantaneous frequency (IF of a non-stationary signal is usually estimated from a time-frequency distribution (TFD. The IF of heart rate variability (HRV is an important parameter because the power in a frequency band around the IF can be used for the interpretation and analysis of the respiratory rate but also for a more accurate analysis of heart rate (HR signals. In this study, we compare the performance of five states of the art kernel-based time-frequency distributions (TFDs in terms of their ability to accurately estimate the IF of HR signals. The selected TFDs include three widely used fixed kernel methods: the modified B distribution, the S-method and the spectrogram; and two adaptive kernel methods: the adaptive optimal kernel TFD and the recently developed adaptive directional TFD. The IF of the respiratory signal, which is usually easier to estimate as the respiratory signal is a mono-component with small amplitude variations with time, is used as a reference to examine the accuracy of the HRV IF estimates. Experimental results indicate that the most reliable estimates are obtained using the adaptive directional TFD in comparison to other commonly used methods such as the adaptive optimal kernel TFD and the modified B distribution.

  20. High-Frequency ac Power-Distribution System

    Science.gov (United States)

    Hansen, Irving G.; Mildice, James

    1987-01-01

    Loads managed automatically under cycle-by-cycle control. 440-V rms, 20-kHz ac power system developed. System flexible, versatile, and "transparent" to user equipment, while maintaining high efficiency and low weight. Electrical source, from dc to 2,200-Hz ac converted to 440-V rms, 20-kHz, single-phase ac. Power distributed through low-inductance cables. Output power either dc or variable ac. Energy transferred per cycle reduced by factor of 50. Number of parts reduced by factor of about 5 and power loss reduced by two-thirds. Factors result in increased reliability and reduced costs. Used in any power-distribution system requiring high efficiency, high reliability, low weight, and flexibility to handle variety of sources and loads.

  1. HYPOCENTER DISTRIBUTION OF LOW FREQUENCY EVENT AT PAPANDAYAN VOLCANO

    Directory of Open Access Journals (Sweden)

    Muhammad Mifta Hasan

    2016-10-01

    Full Text Available Papandayan volcano is a stratovolcano with irregular cone-shaped has eight craters around the peak. The most active crater in Papandayan is a Mas crater. Distribution of relocated event calculated using Geiger Adaptive Damping Algorithm (GAD shows that the epicenter of the event centered below Mas crater with maximum rms 0.114. While depth of the hypocenter range between 0-2 km and 5-6 km due to activity of steam and gas.

  2. Frequency of the HLA-B*1502 allele contributing to carbamazepine-induced hypersensitivity reactions in a cohort of Malaysian epilepsy patients.

    Science.gov (United States)

    Then, Sue-Mian; Rani, Zam Zureena Mohd; Raymond, Azman Ali; Ratnaningrum, Safrina; Jamal, Rahman

    2011-09-01

    We describe the association of the HLA-B*1502 allele in 27 epilepsy patients (19 Malays, 8 Chinese) treated with carbamazepine (CBZ) at the UKM Medical Center (UKMMC), 6 with CBZ-Steven Johnson Syndrome (CBZ-SJS), 11 with CBZ-induced rash, 2 with suspected phenytoin-induced rash and 8 negative controls. Our study showed that 10 (6 Malay, 4 Chinese) patients were positive for HLA-B*1502. Out of the 10 patients, six were confirmed to have CBZ-SJS (p = 0.0006), while four patients developed a skin rash. However there were 6 Malay patients and 1 Chinese patient that developed a skin rash after CBZ administration who were not positive for the allele, indicating that there might be more that one allele associated with CBZ-induced hypersensitivity. Another 2 patients were suspected of having phenytoin-induced rash, instead of CBZ, and these patients did not have HLA-B*1502. In conclusion, this study confirmed the association of HLA-B*1502 with CBZ-SJS among Malaysian epilepsy patients, however there might be other genes that could be responsible for the CBZ-induced rash.

  3. Multiple phosphoglucomutase alleles in Toxorhynchites splendens (Diptera: Culcidae).

    Science.gov (United States)

    Yong, H S; Chan, K L; Dhaliwal, S S; Burton, J J; Cheong, W H; Mak, J W

    1980-09-15

    Multiple phosphoglucomutase (E.C. 2.7.5.1) alleles are found in the mosquito Toxorhynchites splendens. The sample studied reveals 3 Pgm alleles whose frequencies are in good accord with Hardy-Weinberg expectations. The most frequent allele is that controlling a phenotype with an intermediate electrophoretic mobility. Each Pgm allele determines a two-band electrophoretic pattern.

  4. Distribution of mating-type alleles and M13 PCR markers in the black leaf spot fungus Mycosphaerella fijiensis of bananas in Brazil.

    Science.gov (United States)

    Queiroz, C B; Miranda, E C; Hanada, R E; Sousa, N R; Gasparotto, L; Soares, M A; Silva, G F

    2013-02-08

    The fungus Mycosphaerella fijiensis is the causative agent of black sigatoka, which is one of the most destructive diseases of banana plants. Infection with this pathogen results in underdeveloped fruit, with no commercial value. We analyzed the distribution of the M. fijiensis mating-type system and its genetic variability using M13 phage DNA markers. We found a 1:1 distribution of mating-type alleles, indicating MAT1-1 and MAT1-2 idiomorphs. A polymorphism analysis using three different primers for M13 markers showed that only the M13 minisatellite primers generated polymorphic products. We then utilized this polymorphism to characterize 40 isolates from various Brazilian states. The largest genetic distances were found between isolates from the same location and between isolates from different parts of the country. Therefore, there was no correlation between the genetic similarity and the geographic origin of the isolates. The M13 marker was used to generate genetic fingerprints for five isolates; these fingerprints were compared with the band profiles obtained from inter-simple sequence repeat (UBC861) and inter-retrotransposon amplified polymorphism analyses. We found that the M13 marker was more effective than the other two markers for differentiating these isolates.

  5. Damage Detection Based on Cross-Term Extraction from Bilinear Time-Frequency Distributions

    Directory of Open Access Journals (Sweden)

    Ma Yuchao

    2014-01-01

    Full Text Available Abundant damage information is implicated in the bilinear time-frequency distribution of structural dynamic signals, which could provide effective support for structural damage identification. Signal time-frequency analysis methods are reviewed, and the characters of linear time-frequency distribution and bilinear time-frequency distribution typically represented by the Wigner-Ville distribution are compared. The existence of the cross-term and its application in structural damage detection are demonstrated. A method of extracting the dominant term is proposed, which combines the short-time Fourier spectrum and Wigner-Ville distribution; then two-dimensional time-frequency transformation matrix is constructed and the complete cross-term is extracted finally. The distribution character of which could be applied to the structural damage identification. Through theoretical analysis, model experiment and numerical simulation of the girder structure, the change rate of cross-term amplitude is validated to identify the damage location and degree. The effectiveness of the cross-term of bilinear time-frequency distribution for damage detection is confirmed and the analytical method of damage identification used in structural engineering is available.

  6. Frequency distributions of helminths of wolves in Kazakhstan.

    Science.gov (United States)

    Abdybekova, A M; Torgerson, P R

    2012-03-23

    Between 2001 and 2008 a total of 41 wolves (Canis lupus) were necropsied in southern Kazakhstan and their intestinal parasite fauna evaluated. Of these animals 8 (19.5%) were infected with Echinococcus granulosus, 15 (36%) with Taenia spp, 13 (31.7%) with Dypilidium caninum, 5 (12.2%) with Mesocestoides lineatus, 15 (36.6%) with Toxocara canis, 16 (39%) with Toxascaris leonina, 8 (19.5%) with Trichuris vulpis, 9 (22%) with Macracanthorhynchus catulinus and 1 (2.4%) with Moniliformis moniliformis. All parasites had an aggregated distribution which followed a zero inflated or hurdle model. Although a small convenience sample of wolves, the results indicate a high prevalence of infection with E. granulosus. The mean abundance (1275 E. granulosus per wolf) was high with individual infected wolves carrying intensities of several thousand parasites. As wolves are common in Kazakhstan they may act as an important host in the transmission of this zoonotic parasite. The wolves were sampled from an area of Kazakhstan where there is a high prevalence of hydatid cysts in livestock and where echinococcosis has been observed in wild ungulates. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Distribution and frequency of wildfire in California riparian ecosystems

    Science.gov (United States)

    Bendix, Jacob; Commons, Michael G.

    2017-07-01

    Although wildfire has been recognized as having important ecological impacts on California’s riparian environments, understanding of its occurrence is largely anecdotal, based on studies of fire impacts in scattered locations. In this paper we use data for 21 years of wildfires to examine the distribution, seasonality and climatic context of riparian wildfire across the state. We used the Monitoring Trends in Burn Severity and LANDFIRE databases to identify fires that had burned in areas classified as having riparian vegetation, and matched those fires with the Fire and Resource Assessment Program database to determine the date of occurrence of each. From 1990 through 2010, an average of 1197 ha of riparian vegetation burned per year, which extrapolates to a fire return interval of 843 years. The statewide totals are misleading, however, because there is substantial geographic variance in the occurrence of riparian fire. In southern California ecoregions, extrapolated return intervals are as low as 74 years, contrasting with the Basin and Range ecoregions, where return intervals exceed 1000 years. Moreover, there is substantial geographic variation in the season of riparian fire, and in the relationship between fire occurrence and climatic variables. Both the widespread occurrence of riparian fire and its spatial variability are potentially important for management of critical riparian habitat.

  8. Cross-Language Distributions of High Frequency and Phonetically Similar Cognates

    Science.gov (United States)

    Schepens, Job; Dijkstra, Ton; Grootjen, Franc; van Heuven, Walter J. B.

    2013-01-01

    The coinciding form and meaning similarity of cognates, e.g. ‘flamme’ (French), ‘Flamme’ (German), ‘vlam’ (Dutch), meaning ‘flame’ in English, facilitates learning of additional languages. The cross-language frequency and similarity distributions of cognates vary according to evolutionary change and language contact. We compare frequency and orthographic (O), phonetic (P), and semantic similarity of cognates, automatically identified in semi-complete lexicons of six widely spoken languages. Comparisons of P and O similarity reveal inconsistent mappings in language pairs with deep orthographies. The frequency distributions show that cognate frequency is reduced in less closely related language pairs as compared to more closely related languages (e.g., French-English vs. German-English). These frequency and similarity patterns may support a better understanding of cognate processing in natural and experimental settings. The automatically identified cognates are available in the supplementary materials, including the frequency and similarity measurements. PMID:23675449

  9. Distributed Optimization Design of Continuous-Time Multiagent Systems With Unknown-Frequency Disturbances.

    Science.gov (United States)

    Wang, Xinghu; Hong, Yiguang; Yi, Peng; Ji, Haibo; Kang, Yu

    2017-05-24

    In this paper, a distributed optimization problem is studied for continuous-time multiagent systems with unknown-frequency disturbances. A distributed gradient-based control is proposed for the agents to achieve the optimal consensus with estimating unknown frequencies and rejecting the bounded disturbance in the semi-global sense. Based on convex optimization analysis and adaptive internal model approach, the exact optimization solution can be obtained for the multiagent system disturbed by exogenous disturbances with uncertain parameters.

  10. Frequency of the allelic variant c.1150T > C in exon 10 of the fibroblast growth factor receptor 3 (FGFR3 gene is not increased in patients with pathogenic mutations and related chondrodysplasia phenotypes

    Directory of Open Access Journals (Sweden)

    Thatiane Yoshie Kanazawa

    2014-12-01

    Full Text Available Mutations in the FGFR3 gene cause the phenotypic spectrum of FGFR3 chondrodysplasias ranging from lethal forms to the milder phenotype seen in hypochondroplasia (Hch. The p.N540K mutation in the FGFR3 gene occurs in ~70% of individuals with Hch, and nearly 30% of individuals with the Hch phenotype have no mutations in the FGFR3, which suggests genetic heterogeneity. The identification of a severe case of Hch associated with the typical mutation c.1620C > A and the occurrence of a c.1150T > C change that resulted in a p.F384L in exon 10, together with the suspicion that this second change could be a modulator of the phenotype, prompted us to investigate this hypothesis in a cohort of patients. An analysis of 48 patients with FGFR3 chondrodysplasia phenotypes and 330 healthy (control individuals revealed no significant difference in the frequency of the C allele at the c.1150 position (p = 0.34. One patient carrying the combination `pathogenic mutation plus the allelic variant c.1150T > C' had a typical achondroplasia (Ach phenotype. In addition, three other patients with atypical phenotypes showed no association with the allelic variant. Together, these results do not support the hypothesis of a modulatory role for the c.1150T > C change in the FGFR3 gene.

  11. Secondary Frequency and Voltage Control of Islanded Microgrids via Distributed Averaging

    DEFF Research Database (Denmark)

    W. Simpson-Porco, John; Shafiee, Qobad; Dorfler, Florian

    2015-01-01

    actions. The frequency controller rapidly regulates the microgrid frequency to its nominal value while maintaining active power sharing among the distributed generators. Tuning of the voltage controller provides a simple and intuitive trade-off between the conflicting goals of voltage regulation...

  12. Highly stable microwave carrier generation using a dual-frequency distributed feedback laser

    NARCIS (Netherlands)

    Khan, M.R.H.; Bernhardi, Edward; Marpaung, D.A.I.; Burla, M.; de Ridder, R.M.; Worhoff, Kerstin; Pollnau, Markus; Roeloffzen, C.G.H.

    2012-01-01

    Photonic generation of microwave carriers by using a dual-frequency distributed feedback waveguide laser in ytterbium-doped aluminum oxide is demonstrated. A highperformance optical frequency locked loop is implemented to stabilize the microwave carrier. This approach results in a microwave

  13. Daris, a low-frequency distributed aperture array for radio astronomy in space

    NARCIS (Netherlands)

    Boonstra, A.J.; Saks, N.; Bentum, Marinus Jan; van 't Klooster, K.; Falcke, H.

    2010-01-01

    DARIS (Distributed Aperture Array for Radio Astronomy in Space) is a radio astronomy space mission concept aimed at observing the low-frequency radio sky in the range 1-10 MHz. Because of the Earth's ionospheric disturbances and opaqueness, this frequency range can only be observed from space. The

  14. Haplotype allelic classes for detecting ongoing positive selection

    Directory of Open Access Journals (Sweden)

    Lefebvre Jean-François

    2010-01-01

    Full Text Available Abstract Background Natural selection eliminates detrimental and favors advantageous phenotypes. This process leaves characteristic signatures in underlying genomic segments that can be recognized through deviations in allelic or haplotypic frequency spectra. To provide an identifiable signature of recent positive selection that can be detected by comparison with the background distribution, we introduced a new way of looking at genomic polymorphisms: haplotype allelic classes. Results The model combines segregating sites and haplotypic information in order to reveal useful data characteristics. We developed a summary statistic, Svd, to compare the distribution of the haplotypes carrying the selected allele with the distribution of the remaining ones. Coalescence simulations are used to study the distributions under standard population models assuming neutrality, demographic scenarios and selection models. To test, in practice, haplotype allelic class performance and the derived statistic in capturing deviation from neutrality due to positive selection, we analyzed haplotypic variation in detail in the locus of lactase persistence in the three HapMap Phase II populations. Conclusions We showed that the Svd statistic is less sensitive than other tests to confounding factors such as demography or recombination. Our approach succeeds in identifying candidate loci, such as the lactase-persistence locus, as targets of strong positive selection and provides a new tool complementary to other tests to study natural selection in genomic data.

  15. The Influence of Orthographic Neighborhood Density and Word Frequency on Visual Word Recognition: Insights from RT Distributional Analyses

    Directory of Open Access Journals (Sweden)

    Stephen Wee Hun eLim

    2016-03-01

    Full Text Available The effects of orthographic neighborhood density and word frequency in visual word recognition were investigated using distributional analyses of response latencies in visual lexical decision. Main effects of density and frequency were observed in mean latencies. Distributional analyses, in addition, revealed a density x frequency interaction: for low-frequency words, density effects were mediated predominantly by distributional shifting whereas for high-frequency words, density effects were absent except at the slower RTs, implicating distributional skewing. The present findings suggest that density effects in low-frequency words reflect processes involved in early lexical access, while the effects observed in high-frequency words reflect late postlexical checking processes.

  16. Distribution function of frequency of stellar flares in the Orion association

    International Nuclear Information System (INIS)

    Parsamyan, Eh.S.

    1980-01-01

    Using the chronology of discoveries of new flares and the chronology of confirmation i.e. the time distribution of second flares (Ambartsumian's method), the distribution function of frequency of flares on stars in the Orion association is obtained. A number of stars having different frequencies is also found. It is shown that flare stars with high flare frequency (ν -1 13sup(m). The quantities of flare stars in aggregates determined by two independent methods show that the number of flare stars in Orion association is about 1.5 times greater than in the Pleiades cluster [ru

  17. Frequency distribution of the reduced unit cells of centred lattices from the Protein Data Bank.

    Science.gov (United States)

    Swaminathan, Kunchithapadam

    2012-03-01

    In crystallography, a centred conventional lattice unit cell has its corresponding reduced primitive unit cell. This study presents the frequency distribution of the reduced unit cells of all centred lattice entries of the Protein Data Bank (as of 23 August 2011) in four unit-cell-dimension-based groups and seven interaxial-angle-based subgroups. This frequency distribution is an added layer of support during space-group assignment in new crystals. In addition, some interesting patterns of distribution are discussed as well as how some reduced unit cells could be wrongly accepted as primitive lattices in a different crystal system.

  18. Body Size Diversity and Frequency Distributions of Neotropical Cichlid Fishes (Cichliformes: Cichlidae: Cichlinae)

    OpenAIRE

    Steele, Sarah E.; López-Fernández, Hernán

    2014-01-01

    Body size is an important correlate of life history, ecology and distribution of species. Despite this, very little is known about body size evolution in fishes, particularly freshwater fishes of the Neotropics where species and body size diversity are relatively high. Phylogenetic history and body size data were used to explore body size frequency distributions in Neotropical cichlids, a broadly distributed and ecologically diverse group of fishes that is highly representative of body size d...

  19. [Association between genotype and allele frequencies of CYP2A6*12 and rs16969968 in CHRNA5 variants with smoking and body mass index in young subjects from Northeast Mexico].

    Science.gov (United States)

    Borrego-Soto, Gissela; Costilla-Esquivel, Antonio; Padilla-Rivas, Gerardo Raymundo; Cázares-Samaniego, Paulina Janeth; Posadas-Valay, Rodolfo; Velasco-Castañón, José Gerardo; Mercado-Longoria, Roberto; Ortiz-López, Rocío; Rojas-Martínez, Augusto

    2015-11-01

    Several studies have reported that variants rs16969968 G>A of the CHRNA5 gene and CYP2A6*12 of the CYP2A6 gene are associated with smoking and smoking refusal, respectively. In addition, some studies report that a higher cigarette consumption is associated with low body mass index (BMI). To analyze the allele and genotypic frequencies of these variants and their impact on smoking and BMI. A blood sample was obtained and a survey about smoking habits was answered by 319 university students aged 18 to 35 years (127 women, 171 smokers), living in Northeastern Mexico. Genetic variants were studied by polymerase chain reaction/restriction fragment length polymorphism and their frequencies were associated with smoking and BMI. No associations were found between the analyzed variants and smoking in the study groups. However, there was an association among non-smoking subjects between the A allele of rs16969968 and high a BMI (p < 0.01). This last variant may be involved in food-addiction disorders.

  20. Ultra-stable long distance optical frequency distribution using the Internet fiber network.

    Science.gov (United States)

    Lopez, Olivier; Haboucha, Adil; Chanteau, Bruno; Chardonnet, Christian; Amy-Klein, Anne; Santarelli, Giorgio

    2012-10-08

    We report an optical link of 540 km for ultrastable frequency distribution over the Internet fiber network. The stable frequency optical signal is processed enabling uninterrupted propagation on both directions. The robustness and the performance of the link are enhanced by a cost effective fully automated optoelectronic station. This device is able to coherently regenerate the return optical signal with a heterodyne optical phase locking of a low noise laser diode. Moreover the incoming signal polarization variation are tracked and processed in order to maintain beat note amplitudes within the operation range. Stable fibered optical interferometer enables optical detection of the link round trip phase signal. The phase-noise compensated link shows a fractional frequency instability in 10 Hz bandwidth of 5 × 10(-15) at one second measurement time and 2 × 10(-19) at 30,000 s. This work is a significant step towards a sustainable wide area ultrastable optical frequency distribution and comparison network.

  1. Evaluation of the correlation between KRAS mutated allele frequency and pathologist tumorous nuclei percentage assessment in colorectal cancer suggests a role for zygosity status.

    Science.gov (United States)

    Libbrecht, Louis; Baldin, Pamela; Dekairelle, Anne-France; Jouret-Mourin, Anne

    2018-04-27

    Evaluation of molecular tumour heterogeneity relies on the tumorous nuclei percentage (TNP) assessment by a pathologist, which has been criticised for being inaccurate and suffering from interobserver variability. Based on the 'Big Bang theory' which states that KRAS mutation in colorectal cancer is mostly homogeneous, we investigated this issue by performing a critical analysis of the correlation of the KRAS mutant allele fraction with the TNP in 99 colorectal tumour samples with a positive KRAS mutation status as determined by next-generation sequencing. Our results yield indirect evidence that the KRAS zygosity status influences the correlation between these parameters and we show that a well-trained pathologist is indeed capable of accurately assessing TNP. Our findings indicate that tumour zygosity, a feature which has largely been neglected until now, should be taken into account in future studies on (colorectal) molecular tumour heterogeneity. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  2. Application of Choi—Williams Reduced Interference Time Frequency Distribution to Machinery Diagnostics

    Directory of Open Access Journals (Sweden)

    Howard A. Gaberson

    1995-01-01

    Full Text Available This article discusses time frequency analysis of machinery diagnostic vibration signals. The short time Fourier transform, the Wigner, and the Choi–Williams distributions are explained and illustrated with test cases. Examples of Choi—Williams analyses of machinery vibration signals are presented. The analyses detect discontinuities in the signals and their timing, amplitude and frequency modulation, and the presence of different components in a vibration signal.

  3. Predominance of N-acetyl transferase 2 slow acetylator alleles in ...

    African Journals Online (AJOL)

    Student

    The human N-acetyltransferase II (NAT2) gene may vary between individuals resulting in variability in the incidence of adverse drug reactions. We set out in this adhoc analysis to determine the distribution of allele frequencies of NAT2 gene variants among children less than ten years treated with artemisinin-based.

  4. Nonstationary Frequency Analysis of Extreme Floods Using the Time-varying Two-component Mixture Distributions

    Science.gov (United States)

    Yan, L.; Xiong, L.; Liu, D.; Hu, T.; Xu, C. Y.

    2016-12-01

    The basic IID assumption of the traditional flood frequency analysis has been challenged by nonstationarity. The most popular practice for analyzing nonstationarity of flood series is to use a fixed single-type probability distribution incorporated with the time-varying moments. However, the type of probability distribution could be both complex because of distinct flood populations and time-varying under changing environments. To allow the investigation of this complex nature, the time-varying two-component mixture distributions (TTMD) method is proposed in this study by considering the time variations of not only the moments of its component distributions but also the weighting coefficients. Having identified the existence of mixed flood populations based on circular statistics, the proposed TTMD was applied to model the annual maximum flood series (AMFS) of two stations in the Weihe River basin (WRB), with the model parameters calibrated by the meta-heuristic maximum likelihood (MHML) method. The performance of TTMD was evaluated by different diagnostic plots and indexes and compared with stationary single-type distributions, stationary mixture distributions and time-varying single-type distributions. The results highlighted the advantages of using TTMD models and physically-based covariates in nonstationary flood frequency analysis. Besides, the optimal TTMD models were considered to be capable of settling the issue of nonstationarity and capturing the mixed flood populations satisfactorily. It is concluded that the TTMD model is a good alternative in the nonstationary frequency analysis and can be applied to other regions with mixed flood populations.

  5. Finite Time Control for Fractional Order Nonlinear Hydroturbine Governing System via Frequency Distributed Model

    Directory of Open Access Journals (Sweden)

    Bin Wang

    2016-01-01

    Full Text Available This paper studies the application of frequency distributed model for finite time control of a fractional order nonlinear hydroturbine governing system (HGS. Firstly, the mathematical model of HGS with external random disturbances is introduced. Secondly, a novel terminal sliding surface is proposed and its stability to origin is proved based on the frequency distributed model and Lyapunov stability theory. Furthermore, based on finite time stability and sliding mode control theory, a robust control law to ensure the occurrence of the sliding motion in a finite time is designed for stabilization of the fractional order HGS. Finally, simulation results show the effectiveness and robustness of the proposed scheme.

  6. Dependence of exponents on text length versus finite-size scaling for word-frequency distributions

    Science.gov (United States)

    Corral, Álvaro; Font-Clos, Francesc

    2017-08-01

    Some authors have recently argued that a finite-size scaling law for the text-length dependence of word-frequency distributions cannot be conceptually valid. Here we give solid quantitative evidence for the validity of this scaling law, using both careful statistical tests and analytical arguments based on the generalized central-limit theorem applied to the moments of the distribution (and obtaining a novel derivation of Heaps' law as a by-product). We also find that the picture of word-frequency distributions with power-law exponents that decrease with text length [X. Yan and P. Minnhagen, Physica A 444, 828 (2016), 10.1016/j.physa.2015.10.082] does not stand with rigorous statistical analysis. Instead, we show that the distributions are perfectly described by power-law tails with stable exponents, whose values are close to 2, in agreement with the classical Zipf's law. Some misconceptions about scaling are also clarified.

  7. On the Frequency Distribution of Neutral Particles from Low-Energy Strong Interactions

    Directory of Open Access Journals (Sweden)

    Federico Colecchia

    2017-01-01

    Full Text Available The rejection of the contamination, or background, from low-energy strong interactions at hadron collider experiments is a topic that has received significant attention in the field of particle physics. This article builds on a particle-level view of collision events, in line with recently proposed subtraction methods. While conventional techniques in the field usually concentrate on probability distributions, our study is, to our knowledge, the first attempt at estimating the frequency distribution of background particles across the kinematic space inside individual collision events. In fact, while the probability distribution can generally be estimated given a model of low-energy strong interactions, the corresponding frequency distribution inside a single event typically deviates from the average and cannot be predicted a priori. We present preliminary results in this direction and establish a connection between our technique and the particle weighting methods that have been the subject of recent investigation at the Large Hadron Collider.

  8. GMLC Hawaii Regional Partnership: Distributed Inverter-Based Grid Frequency Support

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Austin; Hoke, Andy

    2017-05-04

    This presentation is part of a panel session at the IEEE ISGT conference on Grid Modernization Initiative projects. This segment of the panel session provides a brief overview of a Hawaii Regional Partnership project focusing grid frequency support from distributed resources on the fastest time scales.

  9. Single-frequency thulium-doped distributed-feedback fibre laser

    DEFF Research Database (Denmark)

    Agger, Søren; Povlsen, Jørn Hedegaard; Varming, Poul

    2004-01-01

    We have successfully demonstrated a single-frequency distributed-feedback (DFB) thulium-doped silica fiber laser emitting at a wavelength of 1735 nm. The laser cavity is less than 5 cm long and is formed by intracore UV-written Bragg gratings with a phase shift. The laser is pumped at 790 nm from...

  10. Study of the performance of collision short time approximation for neutron scattering using discrete frequency distribution

    International Nuclear Information System (INIS)

    D'Oliveira, A.B.; Amorim, E.S. do; Galvao, O.B.

    1981-03-01

    Double differential cross sections for thermal neutrons, based on incoherent approximation, using continum distribution as discrete frequency set are theoretically estimated, regarding two models previously done. The FASTT computer program is used in order to obtain a numerical estimation. (L.C.) [pt

  11. Time-Frequency Distribution of Music based on Sparse Wavelet Packet Representations

    DEFF Research Database (Denmark)

    Endelt, Line Ørtoft

    We introduce a new method for generating time-frequency distributions, which is particularly useful for the analysis of music signals. The method presented here is based on $\\ell1$ sparse representations of music signals in a redundant wavelet packet dictionary. The representations are found using...

  12. Real-Time Analysis of an Active Distribution Network - Coordinated Frequency Control for Islanding Operation

    DEFF Research Database (Denmark)

    Cha, Seung-Tae

    distribution networks makes it possible to operate the distribution networks independently which is called islanding operation. However, it is a challenge to ensure secure and reliable operation of the islanded system due to a num-ber of reasons, e.g. low inertia in the islanded system, intermittency of some...... be used as a benchmark model for smart grid testing purposes. In both cases, the simulation results are compared and pro-vided a desirable performance with very high degree of accuracy. Secondly, the simplified battery model is adopted and has been modeled in the RTDS in order to investigate the role...... of the BESS as a primary frequency regulator during island-ing transition. The effectiveness of proposed primary frequency control strategy is illus-trated by using two test cases (i.e. IEEE 9-bus and Bornholm). In both cases, the fre-quency regulation performance is highly improved without degrading...

  13. Real-Time Analysis of an Active Distribution Network - Coordinated Frequency Control for Islanding Operation

    DEFF Research Database (Denmark)

    Cha, Seung-Tae

    distribution networks makes it possible to operate the distribution networks independently which is called islanding operation. However, it is a challenge to ensure secure and reliable operation of the islanded system due to a num-ber of reasons, e.g. low inertia in the islanded system, intermittency of some...... of the DERs, etc. Particularly during islanding operation, with relatively few DG units, the frequency and voltage control of the islanded system is not straightforward. DG units, specially based on renewable energy sources (RESs), i.e. wind and solar, have an inter-mittent nature and intrinsic...... system (BESS) and two secondary frequency control scenarios with BESS and DG units. During the island-ing transition, the frequency is regulated by the fast-acting primary control of the BESS. The secondary control of the main management system (MMS) detects the status of the BESS and tries to return...

  14. Under-Frequency Load Shedding Technique Considering Event-Based for an Islanded Distribution Network

    Directory of Open Access Journals (Sweden)

    Hasmaini Mohamad

    2016-06-01

    Full Text Available One of the biggest challenge for an islanding operation is to sustain the frequency stability. A large power imbalance following islanding would cause under-frequency, hence an appropriate control is required to shed certain amount of load. The main objective of this research is to develop an adaptive under-frequency load shedding (UFLS technique for an islanding system. The technique is designed considering an event-based which includes the moment system is islanded and a tripping of any DG unit during islanding operation. A disturbance magnitude is calculated to determine the amount of load to be shed. The technique is modeled by using PSCAD simulation tool. A simulation studies on a distribution network with mini hydro generation is carried out to evaluate the UFLS model. It is performed under different load condition: peak and base load. Results show that the load shedding technique have successfully shed certain amount of load and stabilized the system frequency.

  15. Association of HLA-DQA1 and DQB1 alleles with keloids in Chinese Hans.

    Science.gov (United States)

    Lu, Wen-Sheng; Wang, Jian-Feng; Yang, Sen; Xiao, Feng-Li; Quan, Cheng; Cheng, Hui; Wang, Pei-Guang; Zhang, An-Ping; Cai, Li-Qiong; Zhang, Xue-Jun

    2008-11-01

    Some studies have suggested that human HLA status might potentiate development of keloids phenotype, and exists ethnic differences. No report has been published about HLA-DQA1 and DQB1 alleles associated with keloids in Chinese Hans. To investigate whether HLA-DQA1 and DQB1 alleles are associated with genetic susceptibility to keloids in Chinese Hans. Polymerase chain reaction-sequence-specific primer (PCR-SSP) method was used to analyze the distribution of HLA-DQA1 and DQB1 alleles among 192 patients with keloids and 273 healthy controls in Chinese Hans. (1) The frequencies of HLA-DQA1*0104, DQB1*0501 and DQB1*0503 (OR = 2.13, P(c) = 0.0063; OR = 14.42, P(c) HLA-DQA1 and DQB1 alleles and haplotypes with keloids.

  16. Comprehensive identification of MHC class II alleles in a cohort of Chinese rhesus macaques.

    Science.gov (United States)

    Zhang, Huiling; Deng, Qing; Jin, Yabin; Liu, Beilei; Zhuo, Min; Ling, Fei

    2014-10-01

    Rhesus macaque is a very important animal model for various human diseases, especially for AIDS and vaccine research. The susceptibility and/or resistance to some of these diseases are related to the major histocompatibility complex (MHC). To gain insight into the MHC background and to facilitate the experimental use of Chinese rhesus macaques, Mamu-DPB1, Mamu-DQB1, and Mamu-DRB alleles were investigated in 30 Chinese rhesus macaques through gene cloning and sequencing. A total of 66 alleles were identified in this study, including 14 Mamu-DPB1, 20 Mamu-DQB1, and 30 Mamu-DRB alleles as well as 2 high-frequency Mamu-DPB1 alleles. Interestingly, one of the high-frequency Mamu-DPB1 alleles had been undocumented in earlier studies. Eleven of the other alleles, including four Mamu-DPB1, three Mamu-DQB1, and four Mamu-DRB alleles were also novel. Importantly, like MHC-DRB, more than two Mamu-DPB1 sequences per animal were detected in 13 monkeys, which suggested that they might represent gene duplication. Our data also indicated quite a few differences in the distribution of MHC class II alleles between the Chinese rhesus macaques and the previously reported Indian rhesus macaques. To our knowledge, our results revealed comprehensively the combination of MHC II alleles. This information will not only promote the understanding of Chinese rhesus macaque MHC polymorphism but will also facilitate the use of Chinese rhesus macaques in studies of human disease.

  17. Maximum natural frequencies of polymer composite micro-beams by optimum distribution of carbon nanotubes

    International Nuclear Information System (INIS)

    Rokni, Hossein; Milani, Abbas S.; Seethaler, Rudolf J.

    2011-01-01

    Highlights: → Optimum distributions of MWCNTs within the polymer micro-beams are obtained. → Natural frequencies of nanocomposite beam enhance if its root portion is reinforced with CNTs. → Adding MWCNTs to pure polymer micro-beams has an insignificant effect on mode shapes. → Fundamental frequency value is improved by 12.6-15.9% for various boundary conditions. → New CNT dispersion equations are suggested based on the optimum CNT loading pattern. -- Abstract: Optimum distribution of multi-walled carbon nanotubes (MWCNTs) within a polymer composite micro-beam is sought to achieve its highest natural frequencies given a weight percent (wt.%) of MWCNTs. To this end, the micro-beam is divided into ten segments which are perfectly bonded to their neighbors. Each segment is made of low-viscosity, thermosetting polyester epoxy/amine resin LY-5052 and is reinforced by MWCNTs. A computer program, written in the Python programming language, is compiled with ABAQUS to generate a three-dimensional (3D) finite element (FE) model of the micro-beam and subsequently to evaluate an optimum CNT distribution under various vibration modes and boundary conditions. The influence of uniform and optimum MWCNT distributions on the natural frequencies, mode shapes and equivalent stiffness of the micro-beams is investigated and the results are compared with those of the pure polymer micro-beam. Subsequently, after acquiring the optimum distribution of the MWCNTs, two new CNT dispersion functions are proposed for maximizing fundamental frequencies of the clamped-free and clamped-clamped micro-beams. The results of the FE analysis reveal that the optimal reinforcement distribution pattern significantly depends on vibration mode shapes, particularly the micro-beam curvature under each mode. It is observed that fundamental frequencies of clamped-free, clamped-guided and clamped-clamped micro-beams are enhanced up to 15.9%, 13.1% and 12.6%, respectively, by choosing optimum MWCNT

  18. Acquisition of 3D temperature distributions in fluid flow using proton resonance frequency thermometry.

    Science.gov (United States)

    Buchenberg, Waltraud B; Wassermann, Florian; Grundmann, Sven; Jung, Bernd; Simpson, Robin

    2016-07-01

    Proton resonance frequency thermometry is well established for monitoring small temperature changes in tissue. Application of the technique to the measurement of complex temperature distributions within fluid flow is of great interest to the engineering community and could also have medical applications. This work presents an experimental approach to reliably measure three-dimensional (3D) temperature fields in fluid flow using proton resonance frequency thermometry. A velocity-compensated three-dimensional gradient echo sequence was used. A flexible pumping system was attached to an MR compatible double pipe heat exchanger. The temperature of two separate flow circuits could be adjusted to produce various three-dimensional spatial temperature distributions within the fluid flow. Validation was performed using MR compatible temperature probes in a uniformly heated flow. A comparative study was conducted with thermocouples in the presence of a spatially varying temperature distribution. In uniformly heated flow, temperature changes were accurately measured to within 0.5 K using proton resonance frequency thermometry, while spatially varying temperature changes measured with MR showed good qualitative agreement with pointwise measurements using thermocouples. Proton resonance frequency thermometry can be used in a variety of complex flow situations to address medical as well as engineering questions. This work makes it possible to gain new insights into fundamental heat transfer phenomena. Magn Reson Med 76:145-155, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  19. Spindle frequency activity in the sleep EEG: individual differences and topographic distribution.

    Science.gov (United States)

    Werth, E; Achermann, P; Dijk, D J; Borbély, A A

    1997-11-01

    The brain topography of EEG power spectra in the frequency range of sleep spindles was investigated in 34 sleep recordings from 20 healthy young men. Referential (F3-A2, C3-A2, P3-A2 and O1-A2) and bipolar derivations (F3-C3, C3-P3 and P3-O1) along the anteroposterior axis were used. Sleep spindles gave rise to a distinct peak in the EEG power spectrum. The distribution of the peak frequencies pooled over subjects and derivations showed a bimodal pattern with modes at 11.5 and 13.0 Hz, and a trough at 12.25 Hz. The large inter-subject variation in peak frequency (range: 1.25 Hz) contrasted with the small intra-subject variation between derivations, non-REM sleep episodes and different nights. In some individuals and/or some derivations, only a single spindle peak was present. The topographic distributions from referential and bipolar recordings showed differences. The power showed a declining trend over consecutive non-REM sleep episodes in the low range of spindle frequency activity and a rising trend in the high range. The functional and topographic heterogeneity of sleep spindles in conjunction with the intra-subject stability of their frequency are important characteristics for the analysis of sleep regulation on the basis of the EEG.

  20. Frequency distribution of Radium-226, Thorium-228 and Potassium-40 concentration in ploughed soils

    International Nuclear Information System (INIS)

    Drichko, V.F.; Krisyuk, B.E.; Travnikova, I.G.; Lisachenko, E.P.; Dubenskaya, M.A.

    1977-01-01

    The results of studying Ra-226, Th-228 and K-40 concentration distribution laws in podsol, chernozem and saline soils are considered. Radionuclide concentrations were determined by gamma-spectrometric method in the samples chosen from arable soil layer according to the generally accepted agrotechnical procedure. Measuring procedure is described. The results show that frequency distributions of radionuclide concentrations transform from asymmetric form in normal coordinates into symmetric form in logarithmic coordinates. The usage of the lognormal law to describe frequency concentration distributions is substantiated. The values of concentration distribution parameters are given. The analysis of the data obtained permits to establish that Ra-226 and Th-228 concentrations in soils distribute lognormally and K-40 concentrations - normally and lognormally. According to the degree of decreasing mean concentrations of Ra-226 and Th-228, soils lie in line: chernozems=chernozem salterns > podsols; and according to the degree of decreasing mean quadratic deviation - in line: podsols>chernozems=salterns. It is necessary to determine the value of mean quadratic deviation and distribution type for full characteristics of the studied soil radioactivity

  1. Regional parent flood frequency distributions in Europe – Part 2: Climate and scale controls

    Directory of Open Access Journals (Sweden)

    J. L. Salinas

    2014-11-01

    Full Text Available This study aims to better understand the effect of catchment scale and climate on the statistical properties of regional flood frequency distributions. A database of L-moment ratios of annual maximum series (AMS of peak discharges from Austria, Italy and Slovakia, involving a total of 813 catchments with more than 25 yr of record length is presented, together with mean annual precipitation (MAP and basin area as catchment descriptors surrogates of climate and scale controls. A purely data-based investigation performed on the database shows that the generalized extreme value (GEV distribution provides a better representation of the averaged sample L-moment ratios compared to the other distributions considered, for catchments with medium to higher values of MAP independently of catchment area, while the three-parameter lognormal distribution is probably a more appropriate choice for drier (lower MAP intermediate-sized catchments, which presented higher skewness values. Sample L-moment ratios do not follow systematically any of the theoretical two-parameter distributions. In particular, the averaged values of L-coefficient of skewness (L-Cs are always larger than Gumbel's fixed L-Cs. The results presented in this paper contribute to the progress in defining a set of "process-driven" pan-European flood frequency distributions and to assess possible effects of environmental change on its properties.

  2. Use of commercial vessels in survey augmentation: the size-frequency distribution

    Directory of Open Access Journals (Sweden)

    Eric N. Powell

    2006-09-01

    Full Text Available The trend towards use of commercial vessels to enhance survey data requires assessment of the advantages and limitations of various options for their use. One application is to augment information on size-frequency distributions obtained in multispecies trawl surveys where stratum boundaries and sampling density are not optimal for all species. Analysis focused on ten recreationally and commercially important species: bluefish, butterfish, Loligo squid, weakfish, summer flounder, winter flounder, silver hake (whiting, black sea bass, striped bass, and scup (porgy. The commercial vessel took 59 tows in the sampled domain south of Long Island, New York and the survey vessel 18. Black sea bass, Loligo squid, and summer flounder demonstrated an onshore-offshore gradient such that smaller fish were caught disproportionately inshore and larger fish offshore. Butterfish, silver hake, and weakfish were characterized by a southwest-northeast gradient such that larger fish were caught disproportionately northeast of the southwestern-most sector. All sizes of scup, striped bass, and bluefish were caught predominately inshore. Winter flounder were caught predominately offshore. The commercial vessel was characterized by an increased frequency of large catches for most species. Consequently, patchiness was assayed to be higher by the commercial vessel in nearly all cases. The size-frequency distribution obtained by the survey vessel for six of the ten species, bluefish, butterfish, Loligo squid, summer flounder, weakfish, and silver hake, could not be obtained by chance from the size-frequency distribution obtained by the commercial vessel. The difference in sample density did not significantly influence the size-frequency distribution. Of the six species characterized by significant differences in size-frequency distribution between boats, all but one was patchy at the population level and all had one or more size classes so characterized. Although the

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-09-01

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

  4. Maximum-likelihood methods for array processing based on time-frequency distributions

    Science.gov (United States)

    Zhang, Yimin; Mu, Weifeng; Amin, Moeness G.

    1999-11-01

    This paper proposes a novel time-frequency maximum likelihood (t-f ML) method for direction-of-arrival (DOA) estimation for non- stationary signals, and compares this method with conventional maximum likelihood DOA estimation techniques. Time-frequency distributions localize the signal power in the time-frequency domain, and as such enhance the effective SNR, leading to improved DOA estimation. The localization of signals with different t-f signatures permits the division of the time-frequency domain into smaller regions, each contains fewer signals than those incident on the array. The reduction of the number of signals within different time-frequency regions not only reduces the required number of sensors, but also decreases the computational load in multi- dimensional optimizations. Compared to the recently proposed time- frequency MUSIC (t-f MUSIC), the proposed t-f ML method can be applied in coherent environments, without the need to perform any type of preprocessing that is subject to both array geometry and array aperture.

  5. Haplotype Diversity at Sub1 Locus and Allelic Distribution Among Rice Varieties of Tide and Flood Prone Areas of South-East Asia

    Directory of Open Access Journals (Sweden)

    A.S.M. Masuduzzaman

    2017-07-01

    Full Text Available Single nucleotide polymorphisms and restriction digestion-based haplotype variations among 160 flood prone rice varieties were analyzed with enzymes Alu I and Cac8 I to generate polymorphisms at Sub1A and Sub1C loci (conferring submergence tolerance, respectively. Haplotype associated with phenotype was used to study the haplotype variations at Sub1A and Sub1C loci and to determine their functional influence on submergence tolerance and stem elongation. Three patterns at Sub1A locus, Sub1A0 (null allele, Sub1A1 (does not cut and Sub1A2 (one SNP, and four patterns at Sub1C locus, Sub1C1, Sub1C2, Sub1C3 and Sub1C4, were generated. Both tolerant Sub1A1 and intolerant Sub1A2 had the same length, but the difference was presence of a restriction site in the Sub1A2, but absent at the Sub1A1. Further, two types of polymorphism were detected at the Sub1C, one included major length polymorphisms (165, 170 and 175 bp and the other was a single restriction site at different position. Eight haplotypes (different combinations of the two loci, A1C1, A1C2, A1C4, A2C2, A2C4, A0C2, A0C3 and A0C4, were detected among 160 varieties. Haplotype A1C1 was comparatively more related to haplotypes A1C2 and A1C4, having the same Sub1A allele, and these haplotypes were found only in Bangladeshi, Sri Lankan and Indian varieties. Most tolerant varieties in A1C1 haplotype showed slow elongation, having tolerant specific Sub1A1 and Sub1C1 alleles. Further, the varieties Madabaru and Kottamali (A2C2 also showed moderate level of tolerance without Sub1A1 allele. These varieties were different with FR13A and also suspected to carry different novel tolerant genes at other loci. These materials could be used for hybridization with Sub1 varieties for pyramiding additional tolerant specific alleles into a single genotype for improving submergence tolerance in rice.

  6. Short alleles revealed by PCR demonstrate no heterozygote deficiency at minisatellite loci D1S7, D7S21, and D12S11

    Energy Technology Data Exchange (ETDEWEB)

    Alonso, S.; Castro, A.; Fernandez-Fernandez, I.; Pancorbo, M.M. de [Universidad del Pais Vasco, Vizcaya (Spain)

    1997-02-01

    Short VNTR alleles that go undetected after conventional Southern blot hybridization may constitute an alternative explanation for the heterozygosity deficiency observed at some minisatellite loci. To examine this hypothesis, we have employed a screening procedure based on PCR amplification of those individuals classified as homozygotes in our databases for the loci D1S7, D7S21, and D12S11. The results obtained indicate that the frequency of these short alleles is related to the heterozygosity deficiency observed. For the most polymorphic locus, D1S7, {approximately}60% of those individuals previously classified as homozygotes were in fact heterozygotes for a short allele. After the inclusion of these new alleles, the agreement between observed and expected heterozygosity, along with other statistical tests employed, provide additional evidence for lack of population substructuring. Comparisons of allele frequency distributions reveal greater differences between racial groups than between closely related populations. 45 refs., 3 figs., 6 tabs.

  7. Development of a distributed polarization-OTDR to measure two vibrations with the same frequency

    Science.gov (United States)

    Pan, Yun; Wang, Feng; Wang, Xiangchuan; Zhang, Mingjiang; Zhou, Ling; Sun, Zhenqing; Zhang, Xuping

    2015-08-01

    A polarization optical time-domain reflectometer (POTDR) can distributedly measure the vibration of fiber by detecting the vibration induced polarization variation only with a polarization analyzer. It has great potential in the monitoring of the border intrusion, structural healthy, anti-stealing of pipeline and so on, because of its simple configuration, fast response speed and distributed measuring ability. However, it is difficult to distinguish two vibrations with the same frequency for POTDR because the signal induced by the first vibration would bury the other vibration induced signal. This paper proposes a simple method to resolve this problem in POTDR by analyzing the phase of the vibration induced signal. The effectiveness of this method in distinguishing two vibrations with the same frequency for POTDR is proved by simulation.

  8. The Distribution and Frequency of the Terms "Pride" and "Prejudice" in Jane Austen's Pride and Prejudice

    Directory of Open Access Journals (Sweden)

    Tanja Dromnes

    2009-03-01

    Full Text Available In this article we examine the title terms of Jane Austen's Pride and Prejudice (1813 with particular attention to their distribution and frequency in the text. Our method is to connect the statistical material gathered on frequency and distribution to a narratological analysis of the terms, with special emphasis on whether they occur within the focalization of the external narrator, or that of character-focalizers. In order to approach this task, we have availed ourselves of the narratological theories of Mieke Bal. We conclude that there is a differentiation among types of focalization in the novel that enhances the thematic structure of match-making. Although Jane Austen wrote and published her major works two centuries ago, they continue to fascinate literary scholars and general readers alike.

  9. Engineering Inertial and Primary-Frequency Response for Distributed Energy Resources: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Dall-Anese, Emiliano [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Zhao, Changhong [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Guggilam, Swaroop [University of Minnesota; Dhople, Sairaj V [University of Minnesota; Chen, Yu C [University of British Columbia; Zhao, Changhong [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-12-19

    We propose a framework to engineer synthetic-inertia and droop-control parameters for distributed energy resources (DERs) so that the system frequency in a network composed of DERs and synchronous generators conforms to prescribed transient and steady-state performance specifications. Our approach is grounded in a second-order lumped-parameter model that captures the dynamics of synchronous generators and frequency-responsive DERs endowed with inertial and droop control. A key feature of this reduced-order model is that its parameters can be related to those of the originating higher-order dynamical model. This allows one to systematically design the DER inertial and droop-control coefficients leveraging classical frequency-domain response characteristics of second-order systems. Time-domain simulations validate the accuracy of the model-reduction method and demonstrate how DER controllers can be designed to meet steady-state-regulation and transient-performance specifications.

  10. Power conversion distribution system using a resonant high-frequency AC link

    Science.gov (United States)

    Sood, P. K.; Lipo, T. A.

    1986-01-01

    Static power conversion systems based on a resonant high frequency (HF) link offers a significant reduction in the size and weight of the equipment over that achieved with conventional approaches, especially when multiple sources and loads are to be integrated. A faster system response and absence of audible noise are the other principal characteristics of such systems. A conversion configuration based on a HF link which is suitable for applications requiring distributed power is proposed.

  11. Differences in Crossover Frequency and Distribution among Three Sibling Species of Drosophila

    OpenAIRE

    True, J. R.; Mercer, J. M.; Laurie, C. C.

    1996-01-01

    Comparisons of the genetic and cytogenetic maps of three sibling species of Drosophila reveal marked differences in the frequency and cumulative distribution of crossovers during meiosis. The maps for two of these species, Drosophila melanogaster and D. simulans, have previously been described, while this report presents new map data for D. mauritiana, obtained using a set of P element markers. A genetic map covering nearly the entire genome was constructed by estimating the recombination fra...

  12. A two-component generalized extreme value distribution for precipitation frequency analysis

    Czech Academy of Sciences Publication Activity Database

    Rulfová, Zuzana; Buishand, A.; Roth, M.; Kyselý, Jan

    2016-01-01

    Roč. 534, March (2016), s. 659-668 ISSN 0022-1694 R&D Projects: GA ČR(CZ) GA14-18675S Institutional support: RVO:68378289 Keywords : precipitation extremes * two-component extreme value distribution * regional frequency analysis * convective precipitation * stratiform precipitation * Central Europe Subject RIV: DG - Athmosphere Sciences, Meteorology Impact factor: 3.483, year: 2016 http://www.sciencedirect.com/science/article/pii/S0022169416000500

  13. Spectral Energy Distribution and Radio Halo of NGC 253 at Low Radio Frequencies

    Energy Technology Data Exchange (ETDEWEB)

    Kapińska, A. D.; Staveley-Smith, L.; Meurer, G. R.; For, B.-Q. [International Centre for Radio Astronomy Research (ICRAR), University of Western Australia, 35 Stirling Hwy, WA 6009 (Australia); Crocker, R. [Research School of Astronomy and Astrophysics, Australian National University, Canberra, ACT 2611 (Australia); Bhandari, S.; Callingham, J. R.; Gaensler, B. M.; Hancock, P. J.; Lenc, E. [ARC Centre of Excellence for All-Sky Astrophysics (CAASTRO), Sydney NSW (Australia); Hurley-Walker, N.; Seymour, N. [International Centre for Radio Astronomy Research (ICRAR), Curtin University, Bentley, WA 6102 (Australia); Offringa, A. R. [Netherlands Institute for Radio Astronomy (ASTRON), P.O. Box 2, 7990 AA Dwingeloo (Netherlands); Hanish, D. J. [Spitzer Science Center, California Institute of Technology, MC 220-6, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Ekers, R. D.; Bell, M. E. [CSIRO Astronomy and Space Science (CASS), P.O. Box 76, Epping, NSW 1710 (Australia); Dwarakanath, K. S. [Raman Research Institute, Bangalore 560080 (India); Hindson, L. [Centre of Astrophysics Research, University of Hertfordshire, College Lane, Hatfield AL10 9AB (United Kingdom); Johnston-Hollitt, M. [School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140 (New Zealand); McKinley, B., E-mail: anna.kapinska@uwa.edu.au [School of Physics, The University of Melbourne, Parkville, VIC 3010 (Australia); and others

    2017-03-20

    We present new radio continuum observations of NGC 253 from the Murchison Widefield Array at frequencies between 76 and 227 MHz. We model the broadband radio spectral energy distribution for the total flux density of NGC 253 between 76 MHz and 11 GHz. The spectrum is best described as a sum of a central starburst and extended emission. The central component, corresponding to the inner 500 pc of the starburst region of the galaxy, is best modeled as an internally free–free absorbed synchrotron plasma, with a turnover frequency around 230 MHz. The extended emission component of the spectrum of NGC 253 is best described as a synchrotron emission flattening at low radio frequencies. We find that 34% of the extended emission (outside the central starburst region) at 1 GHz becomes partially absorbed at low radio frequencies. Most of this flattening occurs in the western region of the southeast halo, and may be indicative of synchrotron self-absorption of shock-reaccelerated electrons or an intrinsic low-energy cutoff of the electron distribution. Furthermore, we detect the large-scale synchrotron radio halo of NGC 253 in our radio images. At 154–231 MHz the halo displays the well known X-shaped/horn-like structure, and extends out to ∼8 kpc in the z -direction (from the major axis).

  14. Frequency distribution of Echinococcus multilocularis and other helminths of foxes in Kyrgyzstan.

    Science.gov (United States)

    Ziadinov, I; Deplazes, P; Mathis, A; Mutunova, B; Abdykerimov, K; Nurgaziev, R; Torgerson, P R

    2010-08-04

    Echinococcosis is a major emerging zoonosis in central Asia. A study of the helminth fauna of foxes from Naryn Oblast in central Kyrgyzstan was undertaken to investigate the abundance of Echinococcus multilocularis in a district where a high prevalence of this parasite had previously been detected in dogs. A total of 151 foxes (Vulpes vulpes) were investigated in a necropsy study. Of these 96 (64%) were infected with E. multilocularis with a mean abundance of 8669 parasites per fox. This indicates that red foxes are a major definitive host of E. multilocularis in this country. This also demonstrates that the abundance and prevalence of E. multilocularis in the natural definitive host are likely to be high in geographical regions where there is a concomitant high prevalence in alternative definitive hosts such as dogs. In addition Mesocestoides spp., Dipylidium caninum, Taenia spp., Toxocara canis, Toxascaris leonina, Capillaria and Acanthocephala spp. were found in 99 (66%), 50 (33%), 48 (32%), 46 (30%), 9 (6%), 34 (23%) and 2 (1%) of foxes, respectively. The prevalence but not the abundance of E. multilocularis decreased with age. The abundance of D. caninum also decreased with age. The frequency distribution of E. multilocularis and Mesocestoides spp. followed a zero-inflated negative binomial distribution, whilst all other helminths had a negative binomial distribution. This demonstrates that the frequency distribution of positive counts and not just the frequency of zeros in the data set can determine if a zero-inflated or non-zero-inflated model is more appropriate. This is because the prevalences of E. multolocularis and Mesocestoides spp. were the highest (and hence had fewest zero counts) yet the parasite distribution nevertheless gave a better fit to the zero-inflated models. Copyright 2010 Elsevier B.V. All rights reserved.

  15. Body size diversity and frequency distributions of Neotropical cichlid fishes (Cichliformes: Cichlidae: Cichlinae.

    Directory of Open Access Journals (Sweden)

    Sarah E Steele

    Full Text Available Body size is an important correlate of life history, ecology and distribution of species. Despite this, very little is known about body size evolution in fishes, particularly freshwater fishes of the Neotropics where species and body size diversity are relatively high. Phylogenetic history and body size data were used to explore body size frequency distributions in Neotropical cichlids, a broadly distributed and ecologically diverse group of fishes that is highly representative of body size diversity in Neotropical freshwater fishes. We test for divergence, phylogenetic autocorrelation and among-clade partitioning of body size space. Neotropical cichlids show low phylogenetic autocorrelation and divergence within and among taxonomic levels. Three distinct regions of body size space were identified from body size frequency distributions at various taxonomic levels corresponding to subclades of the most diverse tribe, Geophagini. These regions suggest that lineages may be evolving towards particular size optima that may be tied to specific ecological roles. The diversification of Geophagini appears to constrain the evolution of body size among other Neotropical cichlid lineages; non-Geophagini clades show lower species-richness in body size regions shared with Geophagini. Neotropical cichlid genera show less divergence and extreme body size than expected within and among tribes. Body size divergence among species may instead be present or linked to ecology at the community assembly scale.

  16. Oxide vapor distribution from a high-frequency sweep e-beam system

    Energy Technology Data Exchange (ETDEWEB)

    Chow, R.; Tassano, P.L.; Tsujimoto, N.

    1995-03-01

    Oxide vapor distributions have been determined as a function of operating parameters of a high frequency sweep e-beam source combined with a programmable sweep controller. We will show which parameters are significant, the parameters that yield the broadest oxide deposition distribution, and the procedure used to arrive at these conclusions. A design-of-experimental strategy was used with five operating parameters: evaporation rate, sweep speed, sweep pattern (pre-programmed), phase speed (azimuthal rotation of the pattern), profile (dwell time as a function of radial position). A design was chosen that would show which of the parameters and parameter pairs have a statistically significant effect on the vapor distribution. Witness flats were placed symmetrically across a 25 inches diameter platen. The stationary platen was centered 24 inches above the e-gun crucible. An oxide material was evaporated under 27 different conditions. Thickness measurements were made with a stylus profilometer. The information will enable users of the high frequency e-gun systems to optimally locate the source in a vacuum system and understand which parameters have a major effect on the vapor distribution.

  17. Coastal waters monitoring data: frequency distributions of the principal water quality variables

    Directory of Open Access Journals (Sweden)

    Bianca DI LORENZO

    2006-08-01

    Full Text Available Examining the results of the Italian national programme of marine coastal monitoring, the old problem has arisen about the choice of the most appropriate procedures and methods to validate data and screen preliminary data. Therefore, statistical distributions of water quality parameters have been taken into consideration, in order to assign appropriate frequency distributions to all the routinely measured variables. Each sample distribution has been analysed and defined by a probability density function (p.d.f., by means of a powerful method of data analysis (Johnson 1949 that allows for the computation of statistical parameters of a wide variety of non-normal distributions. The resulting Johnson distributions are then classified depending on four fundamental categories of frequency distributions: normal, log-normal, bounded and unbounded. Theoretical aspects of the method are explained and discussed in an adequate way, so as to allow for practical applications. The shape and nature of these curves require further consideration, in order to understand the behaviour of water quality variables and to make comparison among different coastal zones. To this end, two coastal systems were considered in this work: the Emilia-Romagna coastal area of the NW Adriatic Sea and the Tuscany littoral of the Northern Tyrrhenian Sea. There are notable advantages to the adopted approach. First it offers the possibility to overcome severe constraints requested by the normality assumption, and avoids the troublesome search for the most appropriate transformation function (i.e. for ensuring normality. Second, it avoids searching for other kinds of theoretical distributions that are appropriate for the data. In our approach, the density functions are opportunely integrated, in such a way that, for whatever value assumed by a given variable, the corresponding expected percentage point value under the respective frequency curve, can be calculated, and vice versa. We

  18. Distributed Secondary Voltage and Frequency Control for Islanded Microgrids with Uncertain Communication Links

    DEFF Research Database (Denmark)

    Lu, Xiaoqing; Yu, Xinghuo; Lai, Jingang

    2017-01-01

    intermittently in a low-bandwidth communication manner. This way, the communication costs are greatly reduced, and some sufficient conditions on the system stability and robustness to the uncertainties are also derived by using the tools of Lyapunov stability theory, algebraic graph theory, and matrix inequality......This paper presents a robust distributed secondary control (DSC) scheme for inverter-based microgrids (MGs) in a distribution sparse network with uncertain communication links. By using the iterative learning mechanics, two discrete-time DSC controllers are designed, which enable all distributed...... theory. The proposed controllers are implemented on local DERs, and thus no central controller is required. Moreover, the desired control objective can also be guaranteed even if all DERs are subject to internal uncertainties and external noises including initial voltage and/or frequency resetting errors...

  19. An analysis of the temperature distribution in the pipe bending using high frequency induction heating

    International Nuclear Information System (INIS)

    Fukue, Hisayoshi; Mochizuki, Yoji; Nakamura, Harushige; Kobo, Hiroshi; Nitta, Tetsuo; Kawakami, Kiyoshi

    1986-01-01

    A pipe bending apparatus has recently been developed by applying high frequency induction heating. However, the smaller the radius of pipe bending, the greater becomes the reduction in wall thickness and the ovality of the pipe form. This makes it impossible to manufacture pipe bending which will meet the nuclear pipe design code. In order to solve this problem it is crucial to obtain a temperature distributions in a pipe which is moving. It is calculated by giving the following boundary conditions : distribution of the heat generation rate, and that of heat transfer of cooling water. In the process of analyzing these distributions, the following results were obtained. (1) The distribution of the heat generation rate is determined by the sink of energy flux of Poynting vectors. The coil efficiency thus calculated was sixty percent. This figure accords with the test data. (2) The distribution of heat transfer coefficient of cooling water is mainly determined by the rate of liquid film heat transfer, but departure from nucleate boiling and dryout has to be taken into consideration. (3) TRUMP CODE is modified so that the temperature distribution in moving pipes can be calculated by taking the boundary conditions into account. The calculated results were in accordance with the test data. (author)

  20. Lack of polymorphism at MC1R wild-type allele and evidence of domestic allele introgression across European wild boar populations

    DEFF Research Database (Denmark)

    Canu, Antonio; Vilaça, Sibelle T.; Iacolina, Laura

    2016-01-01

    Domestication promotes the emergence of novel phenotypic and behavioural traits in domesticated animals compared to their wild ancestors. We analysed variation at the melanocortin receptor I (MC1R) and nuclear receptor subfamily 6, group A, member 1 (NR6A1) genes in European wild boar populations......, two loci which have been under strong artificial selection during domestication. These loci influence coat colour and number of vertebrae, respectively. A total of 145 wild boars were sampled throughout Europe, to evaluate frequency and spatial distribution of domestic alleles and patterns...... of hybridization between wild and domestic forms. Most of the wild boars (94%) were homozygous for the European wild-type (E+) MC1R allele. We did not observe any synonymous substitution in the European E+ allele, confirming its monomorphism even in areas known to be hotspots of wild boar genetic diversity...

  1. Frequency distribution of gastro esophageal reflux disease in inhalation injury: A historical cohort study

    Directory of Open Access Journals (Sweden)

    Ashraf Karbasi

    2015-01-01

    Full Text Available Background: There is no data on the prevalence and the association of gastro esophageal reflux disease (GERD with toxic fume inhalation. Therefore, we aimed to evaluate the frequency distribution of GERD symptoms among the individuals with mild respiratory disorder due to the past history of toxic fume exposure to sulfur mustard (SM. Materials and Methods: In a historical cohort study, subjects were randomly selected from 7000 patients in a database of all those who had a history of previous exposure to a single high dose of SM gas during war. The control group was randomly selected from adjacent neighbors of the patients, and two healthy male subjects were chosen per patient. In this study, we used the validated Persian translation of Mayo Gastroesophageal Reflux Questionnaire to assess the frequency distribution of reflux disease. Results: Relative frequency of GERD symptoms, was found to be significantly higher in the inhalation injury patients with an odds ratio of 8.30 (95% confidence interval [CI]: 4.73-14.55, and after adjustment for cigarette smoking, tea consumption, age, and body mass index, aspirin and chronic cough the odds ratio was found to be 4.41 (95% CI: 1.61-12.07. Conclusion: The most important finding of our study was the major GERD symptoms (heartburn and/or acid regurgitation once or more per week among the individuals with the past history of exposure to SM toxic gas is substantially higher (4.4-fold than normal populations.

  2. Research on Distributed PV Storage Virtual Synchronous Generator System and Its Static Frequency Characteristic Analysis

    Directory of Open Access Journals (Sweden)

    Xiangwu Yan

    2018-03-01

    Full Text Available The increasing penetration rate of grid connected renewable energy power generation reduces the primary frequency regulation capability of the system and poses a challenge to the security and stability of the power grid. In this paper, a distributed photovoltaic (PV storage virtual synchronous generator system is constructed, which realizes the external characteristics of synchronous generator/motor. For this kind of input/output bidirectional devices (e.g., renewable power generation/storage combined systems, pumped storage power stations, battery energy storage systems, and vehicle-to-grid electric vehicles, a synthesis analysis method for system power-frequency considering source-load static frequency characteristics (S-L analysis method is proposed in order to depict the system’s power balance dynamic adjustment process visually. Simultaneously, an inertia matching method is proposed to solve the problem of inertia matching in the power grid. Through the simulation experiment in MATLAB, the feasibility of the distributed PV storage synchronous virtual machine system is verified as well as the effectiveness of S-L analysis method and inertia matching method.

  3. Cired 2015 full paper: DISTRIBUTED AND COORDINATED DEMAND RESPONSE FOR THE SUPPLY OF FREQUENCY CONTAINMENT RESERVE (FCR)

    OpenAIRE

    LEBEL, Gaspard; KUYPERS, Karel; CAIRE, Raphaël; HADJSAID, Nouredine; BEDIOU, Stéphane; GLATIGNY, Alain

    2015-01-01

    The availability of frequency-controlled reserves is essential for any Utility to secure the power system in both interconnected and microgrid contexts. This paper presents a concept of coordinated Distributed Energy Resources (DER), load modulation willing to supply frequency-controlled reserves. These reserves, compliant with both Frequency Containment Reserves (FCR) and Under Frequency Load Shedding (UFLS) requirements, are provided through a structure of Virtual Power Plant (VPP). Physica...

  4. Using frequency maps to explore the distribution function of the Milky Way stellar halo

    Directory of Open Access Journals (Sweden)

    Valluri M.

    2012-02-01

    Full Text Available Resolved surveys of the Milky Way's stellar halo can obtain all 6 phase space coordinates of tens of thousands of individual stars, making it possible to compute their 3-dimensional orbits. When frequency mapping is applied to such orbits they also represent the underlying phase space distribution function since the orbits that the are drawn from 3. A frequency maps clearly separates out the major types of orbits that constitute the DF and their relative abundances. The structure of the frequency maps, especially the locations of resonant orbits, reflects the formation history and shape of the dark matter potential and its orientation relative to the disk. The application of frequency analysis to cosmological hydrodynamic simulations of disk galaxies shows that the orbital families occupied by halo stars and dark matter particles are very similar, implying that stellar halo orbits can be used to constrain the DF of the dark matter halo, possibly impacting the interpretation of results from direct dark matter detection experiments. An application of these methods to a sample of ~ 16,000 Milky Way halo and thick disk stars from the SDSS-SEGUE survey yields a frequency map with strong evidence for resonant trapping of halo stars by the Milky Way disk, in a manner predicted by controlled simulations in which the disk grows adiabatically. The application of frequency analysis methods to current and future phase space data for Milky Way halo stars will provide new insights into the formation history of the different components of the Galaxy and the DF of the halo.

  5. Estimation of target vibration spectra from laser radar backscatter using time-frequency distributions

    Science.gov (United States)

    Cole, Timothy D.; El-Dinary, Ashruf S.

    1993-10-01

    A time-frequency distribution (TFD) signal processor, developed at the Applied Physics Laboratory, is currently under evaluation using simulated signals and actual laser vibration sensor (LVS) data that we collected on various ship targets. Preliminary results for one instantaneous frequency (IF) estimator implementation, the smoothed cross Wigner-Ville Distribution (XWVD), indicate 8 to 10 dB demodulation (CNR) advantage compared to a digital FM limiter-discriminator. A second approach, using the unsmoothed XWVD TFD, demonstrated a 3-5 dB advantage. Regarding spectral estimation, we are investigating performance of our reduced interference distribution (RID) implementation through comparison with the short-time Fourier transform (STFT). From the LVS data processed, indications are that a significant increase in spectral and temporal resolution exists using our RID approach. Our processor also provided improved detectability over the STFT for transient signals and short-lived sinusoids. Significant correlation between accepted acoustic lines and LVS-derived vibration lines are indicated. Details are presented that describe our signal simulation, the LVS measurements, and signal processing implementations along with assumptions based on measured speckle-induced amplitude modulation.

  6. Vehicle-to-Grid Systems for Frequency Regulation in an Islanded Danish Distribution Network

    DEFF Research Database (Denmark)

    Pillai, Jayakrishnan Radhakrishna; Bak-Jensen, Birgitte

    2010-01-01

    vehicles could provide power system ancillary services in the form of power balancing reserves to support the large-scale integration of variable renewable energy sources like wind power. This paper investigates the dynamic frequency response of an islanded Danish distribution system operation with large...... amount of wind power supported by the Vehicle-to-grid systems. The power system simulations are analysed for scenarios with 48% and 65% of wind power penetration. The simulation results show that the V2G systems provide a faster and stable frequency control than the conventional generation units. V2G......Electric vehicles (EVs) have gained significant attention in the recent years due to their prospects in reducing greenhouse gas emissions benefitting the transportation sector directly and the electricity sector indirectly. Vehicle-to-grid (V2G) systems using the battery storages of electric...

  7. Short collision time approximation for neutron scattering using discrete frequency distributions

    International Nuclear Information System (INIS)

    Ryskamp, J.M.

    1980-01-01

    A completely general form for computing any scattering cross section based on the incoherent approximation without extending f(ω) to negative frequencies and without integrating over the complex plane is presented. A simple derivation of the short collision time approximation for discrete frequency distributions is also given. The approximation works well for large incident neutron energies when the duration of a collision is short compared with the natural periods of atomic motion. Single-differential scattering cross sections for light water as computed with the free proton and Nelkin scattering models at 561 0 K, and the short collision time approximation with T/sub eff/ = 1468 0 K, are shown for an incident neutron energy of 1.0 eV. 1 figure

  8. Frequency of HLA alleles class I and II in a cohort of northwestern Colombian patients with spondyloarthritis Frecuencia de alelos HLA de clase I y II en una cohorte de pacientes del noroccidente colombiano con espondiloartritis

    OpenAIRE

    Luis F ernando Pinto; Javier Darío Márquez; Carlos Jaime Velásquez; Julio Cesar Quintero; Beatriz Helena Aristizábal; Olga Lucía Rincón; Eliana Patricia Velásquez

    2011-01-01

    Introduction. Spondyloarthritis are chronic rheumatic diseases that affect the axial skeleton and peripheral joints, with several extra-articular manifestations. The association with HLA-B27 remains one of the strongest links known between these entities and the major histocompatibility complex, but the global distribution of HLA-B27 varies considerably and associations with non-HLA-B27 genes have been described.
    Objective. To determine the frequency of HLA class I and II in north...

  9. Novel microsatellite markers for the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) and effects of null alleles on population genetics analyses.

    Science.gov (United States)

    Song, W; Cao, L-J; Wang, Y-Z; Li, B-Y; Wei, S-J

    2017-06-01

    The oriental fruit moth (OFM) Grapholita molesta (Lepidoptera: Tortricidae) is an important economic pest of stone and pome fruits worldwide. We sequenced the OFM genome using next-generation sequencing and characterized the microsatellite distribution. In total, 56,674 microsatellites were identified, with 11,584 loci suitable for primer design. Twenty-seven polymorphic microsatellites, including 24 loci with trinucleotide repeat and three with pentanucleotide repeat, were validated in 95 individuals from four natural populations. The allele numbers ranged from 4 to 40, with an average value of 13.7 per locus. A high frequency of null alleles was observed in most loci developed for the OFM. Three marker panels, all of the loci, nine loci with the lowest null allele frequencies, and nine loci with the highest null allele frequencies, were established for population genetics analyses. The null allele influenced estimations of genetic diversity parameters but not the OFM's genetic structure. Both a STRUCTURE analysis and a discriminant analysis of principal components, using the three marker panels, divided the four natural populations into three groups. However, more individuals were incorrectly assigned by the STRUCTURE analysis when the marker panel with the highest null allele frequency was used compared with the other two panels. Our study provides empirical research on the effects of null alleles on population genetics analyses. The microsatellites developed will be valuable markers for genetic studies of the OFM.

  10. Ultrasound pressure distributions generated by high frequency transducers in large reactors.

    Science.gov (United States)

    Leong, Thomas; Coventry, Michael; Swiergon, Piotr; Knoerzer, Kai; Juliano, Pablo

    2015-11-01

    The performance of an ultrasound reactor chamber relies on the sound pressure level achieved throughout the system. The active volume of a high frequency ultrasound chamber can be determined by the sound pressure penetration and distribution provided by the transducers. This work evaluated the sound pressure levels and uniformity achieved in water by selected commercial scale high frequency plate transducers without and with reflector plates. Sound pressure produced by ultrasonic plate transducers vertically operating at frequencies of 400 kHz (120 W) and 2 MHz (128 W) was characterized with hydrophones in a 2 m long chamber and their effective operating distance across the chamber's vertical cross section was determined. The 2 MHz transducer produced the highest pressure amplitude near the transducer surface, with a sharp decline of approximately 40% of the sound pressure occurring in the range between 55 and 155 mm from the transducer. The placement of a reflector plate 500 mm from the surface of the transducer was shown to improve the sound pressure uniformity of 2 MHz ultrasound. Ultrasound at 400 kHz was found to penetrate the fluid up to 2 m without significant losses. Furthermore, 400 kHz ultrasound generated a more uniform sound pressure distribution regardless of the presence or absence of a reflector plate. The choice of the transducer distance to the opposite reactor wall therefore depends on the transducer plate frequency selected. Based on pressure measurements in water, large scale 400 kHz reactor designs can consider larger transducer distance to opposite wall and larger active cross-section, and therefore can reach higher volumes than when using 2 MHz transducer plates. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

  11. Wind and wave frequency distributions for sites around the British Isles

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    This report presents wind and wave frequency distributions and roses for forty sites around the British Isles. These have been produced using hindcast wind and wave time series data from the NEXT model, for the combined periods January 1977 to December 1979 and January 1989 to December 1994. The database has been subdivided into eight areas: Hebrides Shelf, seven grid points; West Shetland Shelf, four grid points; Northern North Sea, eight grid points; Central North Sea, eight grid points; Southern North Sea, six grid points; English Channel, two grid points; Celtic Sea, three grid points; Irish Sea, two grid points. (author)

  12. Colony size-frequency distribution of pocilloporid juvenile corals along a natural environmental gradient in the Red Sea

    KAUST Repository

    Lozano-Cortes, Diego

    2015-10-29

    Coral colony size-frequency distributions can be used to assess population responses to local environmental conditions and disturbances. In this study, we surveyed juvenile pocilloporids, herbivorous fish densities, and algal cover in the central and southern Saudi Arabian Red Sea. We sampled nine reefs with different disturbance histories along a north–south natural gradient of physicochemical conditions (higher salinity and wider temperature fluctuations in the north, and higher turbidity and productivity in the south). Since coral populations with negatively skewed size-frequency distributions have been associated with unfavorable environmental conditions, we expected to find more negative distributions in the southern Red Sea, where corals are potentially experiencing suboptimal conditions. Although juvenile coral and parrotfish densities differed significantly between the two regions, mean colony size and size-frequency distributions did not. Results suggest that pocilloporid colony size-frequency distribution may not be an accurate indicator of differences in biological or oceanographic conditions in the Red Sea.

  13. Higher moments method for generalized Pareto distribution in flood frequency analysis

    Science.gov (United States)

    Zhou, C. R.; Chen, Y. F.; Huang, Q.; Gu, S. H.

    2017-08-01

    The generalized Pareto distribution (GPD) has proven to be the ideal distribution in fitting with the peak over threshold series in flood frequency analysis. Several moments-based estimators are applied to estimating the parameters of GPD. Higher linear moments (LH moments) and higher probability weighted moments (HPWM) are the linear combinations of Probability Weighted Moments (PWM). In this study, the relationship between them will be explored. A series of statistical experiments and a case study are used to compare their performances. The results show that if the same PWM are used in LH moments and HPWM methods, the parameter estimated by these two methods is unbiased. Particularly, when the same PWM are used, the PWM method (or the HPWM method when the order equals 0) shows identical results in parameter estimation with the linear Moments (L-Moments) method. Additionally, this phenomenon is significant when r ≥ 1 that the same order PWM are used in HPWM and LH moments method.

  14. Distributed strain measurement in perfluorinated polymer optical fibres using optical frequency domain reflectometry

    International Nuclear Information System (INIS)

    Liehr, Sascha; Wendt, Mario; Krebber, Katerina

    2010-01-01

    We present the latest advances in distributed strain measurement in perfluorinated polymer optical fibres (POFs) using backscatter techniques. Compared to previously introduced poly(methyl methacrylate) POFs, the measurement length can be extended to more than 500 m at improved spatial resolution of a few centimetres. It is shown that strain in a perfluorinated POF can be measured up to 100%. In parallel to these investigations, the incoherent optical frequency domain reflectometry (OFDR) technique is introduced to detect strained fibre sections and to measure distributed length change along the fibre with sub-millimetre resolution by applying a cross-correlation algorithm to the backscatter signal. The overall superior performance of the OFDR technique compared to the optical time domain reflectometry in terms of accuracy, dynamic range, spatial resolution and measurement speed is presented. The proposed sensor system is a promising technique for use in structural health monitoring applications where the precise detection of high strain is required

  15. Distributed Optical Fiber Sensors Based on Optical Frequency Domain Reflectometry: A review.

    Science.gov (United States)

    Ding, Zhenyang; Wang, Chenhuan; Liu, Kun; Jiang, Junfeng; Yang, Di; Pan, Guanyi; Pu, Zelin; Liu, Tiegen

    2018-04-03

    Distributed optical fiber sensors (DOFS) offer unprecedented features, the most unique one of which is the ability of monitoring variations of the physical and chemical parameters with spatial continuity along the fiber. Among all these distributed sensing techniques, optical frequency domain reflectometry (OFDR) has been given tremendous attention because of its high spatial resolution and large dynamic range. In addition, DOFS based on OFDR have been used to sense many parameters. In this review, we will survey the key technologies for improving sensing range, spatial resolution and sensing performance in DOFS based on OFDR. We also introduce the sensing mechanisms and the applications of DOFS based on OFDR including strain, stress, vibration, temperature, 3D shape, flow, refractive index, magnetic field, radiation, gas and so on.

  16. Improving Frequency Stability Based on Distributed Control of Multiple Load Aggregators

    DEFF Research Database (Denmark)

    Hu, Jianqiang; Cao, Jinde; Guerrero, Josep M.

    2017-01-01

    In the power demand side, responsive loads can provide fast regulation and ancillary services as reserve capacities in interconnected power systems. This paper presents a distributed pinning demand side control (DSC) strategy for coordinating multiple load aggregators, i.e., aggregated responsive...... with a small fraction of load aggregators. Moreover, a multi-step algorithm is proposed to determine the control gains in the DSC, which not only guarantees the stability of the close-loop system, but also restrains the plant disturbance. Furthermore, the distributed pinning DSC algorithm is integrated...... into the traditional centralized proportional-integral-based automatic generation control (AGC) framework, which has formed the coupled secondary frequency control structure. It has been shown that the total power mismatch in each control area is shared with both AGC units and load aggregators, and the system...

  17. Exact results for the Kuramoto model with a bimodal frequency distribution

    DEFF Research Database (Denmark)

    Martens, Erik Andreas; Barreto, E.; Strogatz, S. H.

    2009-01-01

    We analyze a large system of globally coupled phase oscillators whose natural frequencies are bimodally distributed. The dynamics of this system has been the subject of long-standing interest. In 1984 Kuramoto proposed several conjectures about its behavior; ten years later, Crawford obtained...... the first analytical results by means of a local center manifold calculation. Nevertheless, many questions have remained open, especially about the possibility of global bifurcations. Here we derive the system’s stability diagram for the special case where the bimodal distribution consists of two equally......, where all the oscillators are desynchronized; partial synchrony, where a macro- scopic group of phase-locked oscillators coexists with a sea of desynchronized ones; and a standing wave state, where two counter-rotating groups of phase-locked oscillators emerge. Analytical results are presented...

  18. Coordinated control of distributed energy resources to support load frequency control

    International Nuclear Information System (INIS)

    Ravikumar Pandi, V.; Al-Hinai, A.; Feliachi, Ali

    2015-01-01

    Highlights: • We aims to maintain feeder power flow by the coordination of DER units. • The error in feeder flow with respect to scheduled value is used by the controller. • The particle swarm optimization is employed to minimize the error in feeder flow. • Implemented on a transmission system along with 37 bus distribution feeder. • The results of proposed feeder control is analyzed with no feeder control scheme. - Abstract: The control of generating resources to follow the unscheduled load changes is considered to be an essential process in the power system in order to maintain the frequency of power supply. This load frequency control (LFC) problem has been given more importance in the recent smart grid environment because of the impact from high penetration of distributed energy resources (DER) installed at the distribution level. The renewable sources are highly intermittent in nature, so it is required to coordinate and control the DER units to maintain the feeder power flow at substation bus bar which is seen by transmission system operator during the LFC process. This paper aims to identify the impact of distributed generation and its control method to reduce the deviation of feeder power flow from the scheduled value in real time operation. The error in feeder power flow with respect to scheduled value is utilized by the PI controller to estimate the change in power reference of all DER units. The power output of DER units are maintained to reference values by the individual PI controllers. The particle swarm optimization algorithm is employed to minimize the error in feeder power flow by optimally tuning the gain values of all PI controllers. The proposed method is examined on a small transmission system along with the feeder of IEEE 37 bus distribution system with balanced loading condition. The complete system along with DER units is implemented in the MATLAB based stability package named Power Analysis Toolbox (PAT) for performing time domain

  19. Comparison of HLA allelic imputation programs.

    Directory of Open Access Journals (Sweden)

    Jason H Karnes

    Full Text Available Imputation of human leukocyte antigen (HLA alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]. SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs. These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations.

  20. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

    Directory of Open Access Journals (Sweden)

    Carol A Soderlund

    Full Text Available Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor, where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense, and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available

  1. Allelic variation in a willow warbler genomic region is associated with climate clines.

    Directory of Open Access Journals (Sweden)

    Keith W Larson

    Full Text Available Local adaptation is an important process contributing to population differentiation which can occur in continuous or isolated populations connected by various amounts of gene flow. The willow warbler (Phylloscopus trochilus is one of the most common songbirds in Fennoscandia. It has a continuous breeding distribution where it is found in all forested habitats from sea level to the tree line and therefore constitutes an ideal species for the study of locally adapted genes associated with environmental gradients. Previous studies in this species identified a genetic marker (AFLP-WW1 that showed a steep north-south cline in central Sweden with one allele associated with coastal lowland habitats and the other with mountainous habitats. It was further demonstrated that this marker is embedded in a highly differentiated chromosome region that spans several megabases. In the present study, we sampled 2,355 individuals at 128 sites across all of Fennoscandia to study the geographic and climatic variables associated with the allele frequency distributions of WW1. Our results demonstrate that 1 allele frequency patterns significantly differ between mountain and lowland populations, 2 these allele differences coincide with extreme temperature conditions and the short growing season in the mountains, and milder conditions in coastal areas, and 3 the northern-allele or "altitude variant" of WW1 occurs in willow warblers that occupy mountainous habitat regardless of subspecies. Finally these results suggest that climate may exert selection on the genomic region associated with these alleles and would allow us to develop testable predictions for the distribution of the genetic marker based on climate change scenarios.

  2. Hurricane frequency and landfall distribution for coastal wetlands of the Gulf coast, USA

    Science.gov (United States)

    Doyle, T.W.

    2009-01-01

    The regularity and severity of tropical storms are major determinants controlling ecosystem structure and succession for coastal ecosystems. Hurricane landfall rates vary greatly with high and low frequency for given coastal stretches of the southeastern United States. Site-specific meteorological data of hurricane wind speeds and direction, however, are only available for select populated cities of relatively sparse distribution and inland from the coast. A spatial simulation model of hurricane circulation, HURASIM, was applied to reconstruct chronologies of hurricane wind speeds and vectors for northern Gulf coast locations derived from historical tracking data of North Atlantic tropical storms dating back to 1851. Contrasts of storm frequencies showed that tropical storm incidence is nearly double for Florida coastal ecosystems than the westernmost stretches of Texas coastline. Finer-scale spatial simulations for the north-central Gulf coast exhibited sub-regional differences in storm strength and frequency with coastal position and latitude. The overall pattern of storm incidence in the Gulf basin indicates that the disturbance regime of coastal areas varies greatly along the coast, inland from the coast, and temporally over the period of record. Field and modeling studies of coastal ecosystems will benefit from this retrospective analysis of hurricane incidence and intensity both on a local or regional basis. ?? 2009 The Society of Wetland Scientists.

  3. Impact of protection settings of the distributed generation frequency under 1MW in the national electric system

    International Nuclear Information System (INIS)

    Alpizar Chavarria, Oscar

    2013-01-01

    A literature review is conducted to understand the distributed generation, the reason for the introduction into modern power systems and other distributed generation technologies based on renewable energies that have been installed around the country. The frequency protections of distributed generation equipment under 1MW are studied according to international standards like IEEE-1547 and specifications of equipment manufacturers. The influence of the recommended international standards settings are investigated for systems of distributed generation, the performance in frequency that have presented under some frequency perturbation, as well as the influence that can have on the national and regional electrical system, with different amounts of technologies included in the national system. The recommended settings are evaluated through simulations in PSSE program in the context of the behavior of the frequency in the national electric system [es

  4. NODC Standard Product: International ocean atlas Volume 4 - Atlas of temperature / salinity frequency distributions (2 disc set) (NCEI Accession 0101473)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This Atlas presents more than 80,000 plots of the empirical frequency distributions of temperature and salinity for each 5-degree square area of the North Atlantic...

  5. Spectral distribution of the efficiency of terahertz difference frequency generation upon collinear propagation of interacting waves in semiconductor crystals

    International Nuclear Information System (INIS)

    Orlov, Sergei N; Polivanov, Yurii N

    2007-01-01

    Dispersion phase matching curves and spectral distributions of the efficiency of difference frequency generation in the terahertz range are calculated for collinear propagation of interacting waves in zinc blende semiconductor crystals (ZnTe, CdTe, GaP, GaAs). The effect of the pump wavelength, the nonlinear crystal length and absorption in the terahertz range on the spectral distribution of the efficiency of difference frequency generation is analysed. (nonlinear optical phenomena)

  6. Local Adaptation by Alleles of Small Effect.

    Science.gov (United States)

    Yeaman, Sam

    2015-10-01

    Population genetic models predict that alleles with small selection coefficients may be swamped by migration and will not contribute to local adaptation. But if most alleles contributing to standing variation are of small effect, how does local adaptation proceed? Here I review predictions of population and quantitative genetic models and use individual-based simulations to illustrate how the architecture of local adaptation depends on the genetic redundancy of the trait, the maintenance of standing genetic variation (V(G)), and the susceptibility of alleles to swamping. Even when population genetic models predict swamping for individual alleles, considerable local adaptation can evolve at the phenotypic level if there is sufficient V(G). However, in such cases the underlying architecture of divergence is transient: F(ST) is low across all loci, and no locus makes an important contribution for very long. Because this kind of local adaptation is mainly due to transient frequency changes and allelic covariances, these architectures will be difficult--if not impossible--to detect using current approaches to studying the genomic basis of adaptation. Even when alleles are large and resistant to swamping, architectures can be highly transient if genetic redundancy and mutation rates are high. These results suggest that drift can play a critical role in shaping the architecture of local adaptation, both through eroding V(G) and affecting the rate of turnover of polymorphisms with redundant phenotypic effects.

  7. Identification of the Rare, Four Repeat Allele of IL-4 Intron-3 VNTR Polymorphism in Indian Populations.

    Science.gov (United States)

    Verma, Henu Kumar; Jha, Aditya Nath; Khodiar, Prafulla Kumar; Patra, Pradeep Kumar; Bhaskar, Lakkakula Venkata Kameswara Subrahmanya

    2016-06-01

    Cytokines are cell signaling molecules which upon release by cells facilitate the recruitment of immune-modulatory cells towards the sites of inflammation. Genetic variations in cytokine genes are shown to regulate their production and affect the risk of infectious as well as autoimmune diseases. Intron-3 of interleukin-4 gene (IL-4) harbors 70-bp variable number of tandem repeats (VNTR) that may alter the expression level of IL-4 gene. To determine the distribution of IL-4 70-bp VNTR polymorphism in seven genetically heterogeneous populations of Chhattisgarh, India and their comparison with the finding of other Indian and world populations. A total of 371 healthy unrelated individuals from 5 caste and 2 tribal populations were included in the present study. The IL-4 70-bp VNTR genotyping was carried out using PCR and electrophoresis. Overall, 3 alleles of IL-4 70-bp VNTR (a2, a3 and a4) were detected. The results demonstrated the variability of the IL-4 70-bp VNTR polymorphism in Chhattisgarh populations. Allele a3 was the most common allele at the 70-bp VNTR locus in all populations followed by a2 allele. This study reports the presence four repeat allele a4 at a low frequency in the majority of the Chhattisgarh populations studied. Further, the frequency of the minor allele (a2) in Chhattisgarh populations showed similarity with the frequencies of European populations but not with the East Asian populations where the a2 allele is a major allele. Our study provides a baseline for future research into the role of the IL-4 locus in diseases linked to inflammation in Indian populations.

  8. Development of a novel multiplex PCR assay to detect functional subtypes of KIR3DL1 alleles.

    Directory of Open Access Journals (Sweden)

    Jeanette E Boudreau

    Full Text Available Among NK cell receptor-ligand partnerships, KIR3DL1 and HLA-Bw4 demonstrate the greatest diversity; permutations of their allelic combinations titrate NK reactivity. Balancing selection has maintained distinct subtypes of KIR3DL1 alleles in global populations, implying that each may provide unique fitness advantages and variably influence disease processes. Though approaches exist for determining HLA-B allotypes, practical methods for identifying KIR3DL1 alleles are lacking. We have developed a PCR-based approach that identifies functional subtypes of KIR3DL1 alleles; it is suitable for research and may have clinical application. Six allele subsets were identified based on expression characteristics of the eleven most common KIR3DL1 alleles represented in reported populations. The remaining 62 low-frequency alleles were distributed into these groups based on sequence homology to coding regions. Subtype-specific SNPs were found in exons 3, 4, and 7, and used as priming sites for five multiplex PCR reactions. Genomic DNA derived from 175 unrelated donors and 52 related individuals from 6 families demonstrated >99.5% concordance between sequence-based typing and our novel approach. Finally, PCR-based typing accurately predicted NK phenotypes obtained by flow cytometry after staining with DX9 and Z27 monoclonal antibodies. This novel approach facilitates high-throughput analysis of KIR3DL1 allotypes to enable a broader understanding of KIR3DL1 and HLA-Bw4 interaction in health and disease.

  9. Development of a novel multiplex PCR assay to detect functional subtypes of KIR3DL1 alleles.

    Science.gov (United States)

    Boudreau, Jeanette E; Le Luduec, Jean-Benoît; Hsu, Katharine C

    2014-01-01

    Among NK cell receptor-ligand partnerships, KIR3DL1 and HLA-Bw4 demonstrate the greatest diversity; permutations of their allelic combinations titrate NK reactivity. Balancing selection has maintained distinct subtypes of KIR3DL1 alleles in global populations, implying that each may provide unique fitness advantages and variably influence disease processes. Though approaches exist for determining HLA-B allotypes, practical methods for identifying KIR3DL1 alleles are lacking. We have developed a PCR-based approach that identifies functional subtypes of KIR3DL1 alleles; it is suitable for research and may have clinical application. Six allele subsets were identified based on expression characteristics of the eleven most common KIR3DL1 alleles represented in reported populations. The remaining 62 low-frequency alleles were distributed into these groups based on sequence homology to coding regions. Subtype-specific SNPs were found in exons 3, 4, and 7, and used as priming sites for five multiplex PCR reactions. Genomic DNA derived from 175 unrelated donors and 52 related individuals from 6 families demonstrated >99.5% concordance between sequence-based typing and our novel approach. Finally, PCR-based typing accurately predicted NK phenotypes obtained by flow cytometry after staining with DX9 and Z27 monoclonal antibodies. This novel approach facilitates high-throughput analysis of KIR3DL1 allotypes to enable a broader understanding of KIR3DL1 and HLA-Bw4 interaction in health and disease.

  10. Surface-distributed low-frequency asynchronous stimulation delays fatigue of stimulated muscles.

    Science.gov (United States)

    Maneski, Lana Z Popović; Malešević, Nebojša M; Savić, Andrej M; Keller, Thierry; Popović, Dejan B

    2013-12-01

    One important reason why functional electrical stimulation (FES) has not gained widespread clinical use is the limitation imposed by rapid muscle fatigue due to non-physiological activation of the stimulated muscles. We aimed to show that asynchronous low-pulse-rate (LPR) electrical stimulation applied by multipad surface electrodes greatly postpones the occurrence of muscle fatigue compared with conventional stimulation (high pulse rate, HPR). We compared the produced force vs. time of the forearm muscles responsible for finger flexion in 2 stimulation protocols, LPR (fL = 10 Hz) and HPR (fH = 40 Hz). Surface-distributed low-frequency asynchronous stimulation (sDLFAS) doubles the time interval before the onset of fatigue (104 ± 80%) compared with conventional synchronous stimulation. Combining the performance of multipad electrodes (increased selectivity and facilitated positioning) with sDLFAS (decreased fatigue) can improve many FES applications in both the lower and upper extremities. Copyright © 2013 Wiley Periodicals, Inc.

  11. The frequency and distribution of high-velocity gas in the Galaxy

    Science.gov (United States)

    Nichols, Joy S.

    1995-01-01

    The purpose of this study was to estimate the frequency and distribution of high-velocity gas in the Galaxy using UV absorption line measurements from archival high-dispersion IUE spectra and to identify particularly interesting regions for future study. Approximately 500 spectra have been examined. The study began with the creation of a database of all 0 and B stars with b less than or = to 30 deg observed with IUE at high dispersion over its 18-year lifetime. The original database of 2500 unique objects was reduced to 1200 objects which had optimal exposures available. The next task was to determine the distances of these stars so the high-velocity structures could be mapped in the Galaxy. Spectroscopic distances were calculated for each star for which photometry was available. The photometry was acquired for each star using the SIMBAD database. Preference was given to the ubvy system where available; otherwise the UBV system was used.

  12. Discrete- and finite-bandwidth-frequency distributions in nonlinear stability applications

    Science.gov (United States)

    Kuehl, Joseph J.

    2017-02-01

    A new "wave packet" formulation of the parabolized stability equations method is presented. This method accounts for the influence of finite-bandwidth-frequency distributions on nonlinear stability calculations. The methodology is motivated by convolution integrals and is found to appropriately represent nonlinear energy transfer between primary modes and harmonics, in particular nonlinear feedback, via a "nonlinear coupling coefficient." It is found that traditional discrete mode formulations overestimate nonlinear feedback by approximately 70%. This results in smaller maximum disturbance amplitudes than those observed experimentally. The new formulation corrects this overestimation, accounts for the generation of side lobes responsible for spectral broadening, and results in disturbance representation more consistent with the experiment than traditional formulations. A Mach 6 flared-cone example is presented.

  13. LARGE SCALE DISTRIBUTED PARAMETER MODEL OF MAIN MAGNET SYSTEM AND FREQUENCY DECOMPOSITION ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    ZHANG,W.; MARNERIS, I.; SANDBERG, J.

    2007-06-25

    Large accelerator main magnet system consists of hundreds, even thousands, of dipole magnets. They are linked together under selected configurations to provide highly uniform dipole fields when powered. Distributed capacitance, insulation resistance, coil resistance, magnet inductance, and coupling inductance of upper and lower pancakes make each magnet a complex network. When all dipole magnets are chained together in a circle, they become a coupled pair of very high order complex ladder networks. In this study, a network of more than thousand inductive, capacitive or resistive elements are used to model an actual system. The circuit is a large-scale network. Its equivalent polynomial form has several hundred degrees. Analysis of this high order circuit and simulation of the response of any or all components is often computationally infeasible. We present methods to use frequency decomposition approach to effectively simulate and analyze magnet configuration and power supply topologies.

  14. Comparative Study on the Selection Criteria for Fitting Flood Frequency Distribution Models with Emphasis on Upper-Tail Behavior

    Directory of Open Access Journals (Sweden)

    Xiaohong Chen

    2017-05-01

    Full Text Available The upper tail of a flood frequency distribution is always specifically concerned with flood control. However, different model selection criteria often give different optimal distributions when the focus is on the upper tail of distribution. With emphasis on the upper-tail behavior, five distribution selection criteria including two hypothesis tests and three information-based criteria are evaluated in selecting the best fitted distribution from eight widely used distributions by using datasets from Thames River, Wabash River, Beijiang River and Huai River. The performance of the five selection criteria is verified by using a composite criterion with focus on upper tail events. This paper demonstrated an approach for optimally selecting suitable flood frequency distributions. Results illustrate that (1 there are different selections of frequency distributions in the four rivers by using hypothesis tests and information-based criteria approaches. Hypothesis tests are more likely to choose complex, parametric models, and information-based criteria prefer to choose simple, effective models. Different selection criteria have no particular tendency toward the tail of the distribution; (2 The information-based criteria perform better than hypothesis tests in most cases when the focus is on the goodness of predictions of the extreme upper tail events. The distributions selected by information-based criteria are more likely to be close to true values than the distributions selected by hypothesis test methods in the upper tail of the frequency curve; (3 The proposed composite criterion not only can select the optimal distribution, but also can evaluate the error of estimated value, which often plays an important role in the risk assessment and engineering design. In order to decide on a particular distribution to fit the high flow, it would be better to use the composite criterion.

  15. How Old are Lunar Lobate Scarps? 1. Seismic Resetting of Crater Size-Frequency Distributions

    Science.gov (United States)

    Van Der Bogert, Carolyn H.; Clark, Jaclyn D.; Hiesinger, Harald; Banks, Maria E.; Watters, Thomas R.; Robinson, Mark S.

    2018-01-01

    Previous studies have estimated the ages of lunar lobate scarps, some of the youngest tectonic landforms on the Moon, based on the estimated life-times of their fresh morphologies and associated small graben, using crater degradation ages, or via buffered and traditional crater size-frequency distribution (CSFD) measurements. Here, we reexamine five scarps previously dated by Binder and Gunga (1985) with crater degradation ages to benchmark the evaluation of both the buffered and traditional CSFD approaches for determination of absolute model ages (AMAs) at scarps. Both CSFD methods yield similar ages for each individual scarp, indicating that fault activity not only can be measured on the scarp itself, but also in the surrounding terrain - an indication that tectonic activity causes surface renewal both adjacent to and even kilometers distant from scarps. Size-frequency variations in the regions surrounding the scarps are thus useful for studying the extent and severity of the ground motion caused by coseismic slip events during scarp formation. All age determination approaches continue to indicate that lunar lobate scarps were active in the late Copernican, with some scarps possibly experiencing activity within the last 100 Ma.

  16. Analysis and applications of a frequency selective surface via a random distribution method

    International Nuclear Information System (INIS)

    Xie Shao-Yi; Huang Jing-Jian; Yuan Nai-Chang; Liu Li-Guo

    2014-01-01

    A novel frequency selective surface (FSS) for reducing radar cross section (RCS) is proposed in this paper. This FSS is based on the random distribution method, so it can be called random surface. In this paper, the stacked patches serving as periodic elements are employed for RCS reduction. Previous work has demonstrated the efficiency by utilizing the microstrip patches, especially for the reflectarray. First, the relevant theory of the method is described. Then a sample of a three-layer variable-sized stacked patch random surface with a dimension of 260 mm×260 mm is simulated, fabricated, and measured in order to demonstrate the validity of the proposed design. For the normal incidence, the 8-dB RCS reduction can be achieved both by the simulation and the measurement in 8 GHz–13 GHz. The oblique incidence of 30° is also investigated, in which the 7-dB RCS reduction can be obtained in a frequency range of 8 GHz–14 GHz. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  17. MT1A (A>G, MT1A (C>G, MT1M (A>C and MT4 (G>A single nucleotide polymorphism allele frequencies in Iranian populations

    Directory of Open Access Journals (Sweden)

    Javad Babaei

    2016-09-01

    Full Text Available It has been widely reported that metallothioneins (MTs play pivotal roles in the metabolism of the relatively nontoxic essential metals, as well as of toxic heavy metals. MT gene polymorphisms in an individual may increase or decrease the expression efficiency of the gene. The present study was aimed to investigate the frequency of genetic variation of four MTs in the Iranian population. Whole blood samples were collected from 300 Iranian healthy individuals. Polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP and automated Sanger sequencing were used for DNA genotype determination. The frequencies of major homozygous, heterozygous and minor homozygous genotypes in MT1 (A>G were, respectively, 76.0%, 24.0% and 0.0%; in MT1A (C>G, 88.0%, 12.0% and 0.0%; in MT1M (A>C, 86.0%, 14.0% and 0.0%; in MT4 (G>A, 80.0%, 18.7% and 1.3%. The present study showed for the first time that the polymorphism frequency distribution of these four MTs significantly differed between the studied Iranian population and other populations around the world, except for the MT4 polymorphism in the Iranian population and populations from the USA and New Zealand, which were similar. In conclusion, it could be suggested that regional and ethnic differences are the main reasons for this varied prevalence.

  18. Silvicultural management and the manipulation of rare alleles

    Science.gov (United States)

    Paul G. Schaberg; Gary J. Hawley; Donald H. DeHayes; Samuel E. Nijensohn

    2004-01-01

    Because rare alleles provide a means for adaptation to environmental change they are often considered important to long-term forest health. Through the selective removal of trees (and genes), silvicultural management may alter the genetic structure of forests, with rare alleles perhaps being uniquely vulnerable to manipulation due to their low frequencies or...

  19. Dew Frequency, Duration, Amount, and Distribution in Corn and Soybean During SMEX05

    Science.gov (United States)

    Kabela, E. D.; Hornbuckle, B. K.; Cosh, M. H.; Anderson, M. C.; Gleason, M. L.

    2008-12-01

    Dew affects the brightness temperature of vegetation and backscatter from vegetation at microwave wavelengths. Must this effect must be taken into account in order to avoid corrupting remotely-sensed observations of important ecosystem variables such as soil moisture? As a first step towards answering this question, we report the frequency and duration of dew events, the total amount of dew in the canopy, and the distribution of dew within the canopy for two different types of crop canopy, corn and soybean, during SMEX05, a twenty-one day field experiment conducted during June and July, 2005, in Iowa, USA. We observed dew to be present more than 50% of the time in both corn and soybean at common satellite overpass times of 1:30 and 6:00 CST. Dew was most likely to be present between 12:00 and 6:30 CST, and as late as 9:00 CST. Two different methods to scale the liquid water measured on single leaves to the entire vegetation canopy produced similar results, and we observed dew amounts that were comparable, and in some cases higher, than those that have been shown to affect the microwave brightness temperature and backscatter. The distribution of dew within the canopy among the top and bottom of a leaf and (for corn) the leaf collar may influence its effect on remotely-sensed measurements. We found that this distribution is different for light, moderate, and heavy dew events. A modeling approach will be necessary to estimate dew at larger spatial scales associated with satellite remote sensing. The Atmosphere-Land Exchange (ALEX) model, a land surface process model that accounts for both dewfall and distillation, produced estimates of dew amount and duration that were in agreement with manual observations and observations made with leaf wetness sensors.

  20. Tuning and optimization of the field distribution for 4-rod Radio Frequency Quadrupole linacs

    International Nuclear Information System (INIS)

    Schmidt, Janet Susan

    2014-01-01

    In this thesis, the tuning process of the 4-rod Radio Frequency Quadrupole has been analyzed and a theory for the prediction of the tuning plate's influence on the longitudinal voltage distribution was developed together with RF design options for the optimization of the fringe fields. The basic principles of the RFQ's particle dynamics and resonant behavior are introduced in the theory part of this thesis. All studies that are presented are based on the work on four RFQs of recent linac projects. These RFQs are described in one chapter. Here, the projects are introduced together with details about the RFQ parameters and performance. In the meantime two of these RFQs are in full operation at NSCL at MSU and FNAL. One is operating in the test phase of the MedAustron Cancer Therapy Center and the fourth one for LANL is about to be built. The longitudinal voltage distribution has been studied in detail with a focus on the influence of the RF design with tuning elements and parameters like the electrodes overlap or the distance between stems. The theory for simulation methods for the field flatness that were developed as part of this thesis, as well as its simulation with CST MWS have been analyzed and compared to measurements. The lumped circuit model has proven to predict results with an accuracy that can be used in the tuning process of 4-rod RFQs. Together with results from the tuning studies, the studies on the fringe fields of the 4-rod structure lead to a proposal for a 4-rod RFQ model with an improved field distribution in the transverse and longitudinal electric field.

  1. An informational view of accession rarity and allele specificity in germplasm banks for management and conservation.

    Science.gov (United States)

    Reyes-Valdés, M Humberto; Burgueño, Juan; Singh, Sukhwinder; Martínez, Octavio; Sansaloni, Carolina Paola

    2018-01-01

    Germplasm banks are growing in their importance, number of accessions and amount of characterization data, with a large emphasis on molecular genetic markers. In this work, we offer an integrated view of accessions and marker data in an information theory framework. The basis of this development is the mutual information between accessions and allele frequencies for molecular marker loci, which can be decomposed in allele specificities, as well as in rarity and divergence of accessions. In this way, formulas are provided to calculate the specificity of the different marker alleles with reference to their distribution across accessions, accession rarity, defined as the weighted average of the specificity of its alleles, and divergence, defined by the Kullback-Leibler formula. Albeit being different measures, it is demonstrated that average rarity and divergence are equal for any collection. These parameters can contribute to the knowledge of the structure of a germplasm collection and to make decisions about the preservation of rare variants. The concepts herein developed served as the basis for a strategy for core subset selection called HCore, implemented in a publicly available R script. As a proof of concept, the mathematical view and tools developed in this research were applied to a large collection of Mexican wheat accessions, widely characterized by SNP markers. The most specific alleles were found to be private of a single accession, and the distribution of this parameter had its highest frequencies at low levels of specificity. Accession rarity and divergence had largely symmetrical distributions, and had a positive, albeit non-strictly linear relationship. Comparison of the HCore approach for core subset selection, with three state-of-the-art methods, showed it to be superior for average divergence and rarity, mean genetic distance and diversity. The proposed approach can be used for knowledge extraction and decision making in germplasm collections of

  2. Extended-bandwidth frequency sweeps of a distributed feedback laser using combined injection current and temperature modulation

    Science.gov (United States)

    Hefferman, Gerald; Chen, Zhen; Wei, Tao

    2017-07-01

    This article details the generation of an extended-bandwidth frequency sweep using a single, communication grade distributed feedback (DFB) laser. The frequency sweep is generated using a two-step technique. In the first step, injection current modulation is employed as a means of varying the output frequency of a DFB laser over a bandwidth of 99.26 GHz. A digital optical phase lock loop is used to lock the frequency sweep speed during current modulation, resulting in a linear frequency chirp. In the second step, the temperature of the DFB laser is modulated, resulting in a shifted starting laser output frequency. A laser frequency chirp is again generated beginning at this shifted starting frequency, resulting in a frequency-shifted spectrum relative to the first recorded data. This process is then repeated across a range of starting temperatures, resulting in a series of partially overlapping, frequency-shifted spectra. These spectra are then aligned using cross-correlation and combined using averaging to form a single, broadband spectrum with a total bandwidth of 510.9 GHz. In order to investigate the utility of this technique, experimental testing was performed in which the approach was used as the swept-frequency source of a coherent optical frequency domain reflectometry system. This system was used to interrogate an optical fiber containing a 20 point, 1-mm pitch length fiber Bragg grating, corresponding to a period of 100 GHz. Using this technique, both the periodicity of the grating in the frequency domain and the individual reflector elements of the structure in the time domain were resolved, demonstrating the technique's potential as a method of extending the sweeping bandwidth of semiconductor lasers for frequency-based sensing applications.

  3. [Frequency, nature and distribution of school sport injuries at different types of schools].

    Science.gov (United States)

    Greier, K; Riechelmann, H

    2012-12-01

    A high percentage of all sports injuries occur during school sports. It was analysed whether there are differences in frequency, nature and distribution of school sport injuries at two different types of schools. School sport injuries of all secondary modern schools (n = 106) and in lower classes of grammar Schools (n = 17) in the federal state of Tyrol, Austria, from the ten school years 2001/02 to 2010/11 were analysed. All physical injuries occurring during school sports and resulting in the consultation of a medical doctor and therefore being reported to the general accident department (Allgemeine Unfallversicherungsanstalt [AUVA]) were assessed. During the evaluation period an average number of 32,935 (±1584) school children attended the two types of schools in Tyrol per year. The average incidence of school sports injuries in this ten-year period in both types of schools was 36.4/1,000 (mean) with a standard deviation of 4.4/1,000 per school child per year. The incidence increased from 30.3 in the school year 2001/02 to 40.4 in the school year 2010/11 (r = 0.91; b = 1.34; p sport injuries at secondary modern schools (37.4 ± 4.9 per 1,000 school children per year) was higher than at the lower classes of grammar schools (32.9 ± 4.0 per 1,000 school children per year; relative risk 1.138; 95% CI = 1.09-1.19; p = 1.8 × 10-8). In addition, the sports injuries of the school year 2010/11 were analysed in detail and a comparison was made between the two types of schools. The distribution pattern of school sports injuries did not show any significant differences between both school types. At the secondary modern schools, as well as in the lower classes of grammar schools, injuries to the upper extremities prevailed (>50%). Ball sports were responsible for every second injury. Secondary modern school pupils had a significantly higher risk of suffering a school sports injury than pupils in the lower classes of grammar schools. The injury pattern did not show

  4. Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape.

    Science.gov (United States)

    Georghiou, S B; Seifert, M; Catanzaro, D; Garfein, R S; Valafar, F; Crudu, V; Rodrigues, C; Victor, T C; Catanzaro, A; Rodwell, T C

    2016-07-01

    Molecular diagnostic assays, with their ability to rapidly detect resistance-associated mutations in bacterial genes, are promising technologies to control the spread of drug-resistant tuberculosis (DR-TB). Sequencing assays provide detailed information for specific gene regions and can help diagnostic assay developers prioritize mutations for inclusion in their assays. We performed pyrosequencing of seven Mycobacterium tuberculosis gene regions (katG, inhA, ahpC, rpoB, gyrA, rrs, and eis) for 1,128 clinical specimens from India, Moldova, and South Africa. We determined the frequencies of each mutation among drug-resistant and -susceptible specimens based on phenotypic drug susceptibility testing results and examined mutation distributions by country. The most common mutation among isoniazid-resistant (INH(r)) specimens was the katG 315ACC mutation (87%). However, in the Eastern Cape, INH(r) specimens had a lower frequency of katG mutations (44%) and higher frequencies of inhA (47%) and ahpC (10%) promoter mutations. The most common mutation among rifampin-resistant (RIF(r)) specimens was the rpoB 531TTG mutation (80%). The mutation was common in RIF(r) specimens in Mumbai (83%) and Moldova (84%) but not the Eastern Cape (17%), where the 516GTC mutation appeared more frequently (57%). The most common mutation among fluoroquinolone-resistant specimens was the gyrA 94GGC mutation (44%). The rrs 1401G mutation was found in 84%, 84%, and 50% of amikacin-resistant, capreomycin-resistant, and kanamycin (KAN)-resistant (KAN(r)) specimens, respectively. The eis promoter mutation -12T was found in 26% of KAN(r) and 4% of KAN-susceptible (KAN(s)) specimens. Inclusion of the ahpC and eis promoter gene regions was critical for optimal test sensitivity for the detection of INH resistance in the Eastern Cape and KAN resistance in Moldova. (This study has been registered at ClinicalTrials.gov under registration number NCT02170441.). Copyright © 2016, American Society for

  5. Multimilling-Insert Wear Assessment Using Non-Linear Virtual Sensor, Time-Frequency Distribution and Neural Networks

    Science.gov (United States)

    James Li, C.; Tzeng, Tzong-Chyi

    2000-11-01

    The objective of this study is to establish a signal processing methodology that can infer the state of milling insert wear from translational vibration measured on the spindle housing of a milling machine. First, the tool wear signature in a translational vibration is accentuated by mapping the translational vibration into a torsional vibration using a previously identified non-linear relationship between the two, i.e. a virtual sensor. Second, a time-frequency distribution, i.e. a Choi-Williams distribution, is calculated from the torsional vibration. Third, scattering matrices and orthogonalisation are employed to identify the time-frequency components that are best correlated to the state of wear. Fourth, a neural network is trained to estimate the extent of wear from these critical time frequency components. The combination of the virtual sensor, time-frequency analysis and neural network is then validated with data obtained from real cutting tests.

  6. Frequency stabilization of distributed-feedback laser diodes at 1572 nm for lidar measurements of atmospheric carbon dioxide.

    Science.gov (United States)

    Numata, Kenji; Chen, Jeffrey R; Wu, Stewart T; Abshire, James B; Krainak, Michael A

    2011-03-01

    We demonstrate a wavelength-locked laser source that rapidly steps through six wavelengths distributed across a 1572.335 nm carbon dioxide (CO(2)) absorption line to allow precise measurements of atmospheric CO(2) absorption. A distributed-feedback laser diode (DFB-LD) was frequency-locked to the CO(2) line center by using a frequency modulation technique, limiting its peak-to-peak frequency drift to 0.3 MHz at 0.8 s averaging time over 72 hours. Four online DFB-LDs were then offset locked to this laser using phase-locked loops, retaining virtually the same absolute frequency stability. These online and two offline DFB-LDs were subsequently amplitude switched and combined. This produced a precise wavelength-stepped laser pulse train, to be amplified for CO(2) measurements. © 2011 Optical Society of America

  7. Diversification Rates and the Evolution of Species Range Size Frequency Distribution

    Directory of Open Access Journals (Sweden)

    Silvia Castiglione

    2017-11-01

    Full Text Available The geographic range sizes frequency distribution (RFD within clades is typically right-skewed with untransformed data, and bell-shaped or slightly left-skewed under the log-transformation. This means that most species within clades occupy diminutive ranges, whereas just a few species are truly widespread. A number of ecological and evolutionary explanations have been proposed to account for this pattern. Among the latter, much attention has been given to the issue of how extinction and speciation probabilities influence RFD. Numerous accounts now convincingly demonstrate that extinction rate decreases with range size, both in living and extinct taxa. The relationship between range size and speciation rate, though, is much less obvious, with either small or large ranged species being proposed to originate more daughter taxa. Herein, we used a large fossil database including 21 animal clades and more than 80,000 fossil occurrences distributed over more than 400 million years of marine metazoans (exclusive of vertebrates evolution, to test the relationship between extinction rate, speciation rate, and range size. As expected, we found that extinction rate almost linearly decreases with range size. In contrast, speciation rate peaks at the large (but not the largest end of the range size spectrum. This is consistent with the peripheral isolation mode of allopatric speciation being the main mechanism of species origination. The huge variation in phylogeny, fossilization potential, time of fossilization, and the overarching effect of mass extinctions suggest caution must be posed at generalizing our results, as individual clades may deviate significantly from the general pattern.

  8. Spatiotemporal variations in the b-value of earthquake magnitude-frequency distributions: Classification and causes

    Science.gov (United States)

    El-Isa, Z. H.; Eaton, David W.

    2014-03-01

    Interpretation of the b-value of earthquake frequency-magnitude distributions has received considerable attention in recent decades. This paper provides a comprehensive review of previous investigations of spatial and temporal variations in b-value, including their classification and possible causes. Based on least-squares regression of seismicity data compiled from the NEIC, IRIS and ISC catalogs, we find an average value of 1.02 ± 0.03 for the whole Earth and its two hemispheres, consistent with the general view that in seismically active regions the long-term average value is close to unity. Nevertheless, wide-ranging b-variations (0.3 ≤ b ≤ 2.5) have been reported in the literature. This variability has been interpreted to arise from one or more of the following factors: prevailing stress state, crustal heterogeneity, focal depth, pore pressure, geothermal gradient, tectonic setting, petrological/environmental/geophysical characteristics, clustering of events, incomplete catalog data, and/or method of calculation. Excluding the latter, all of these factors appear to be linked, directly or indirectly, with the effective state of stress. Although time-dependent changes in b-value are well documented, conflicting observations reveal either a precursory increase or decrease in b value before major earthquakes. Our compilation of published analyses suggests that statistically significant b-variations occur globally on various timescales, including annual, monthly and perhaps diurnal. Taken together, our review suggests that b-variations are most plausibly linked with changes in effective stress.

  9. Seasonal Variation and Frequency Distribution of Ectoparasites in Crossbreed Cattle in Southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Maria do Socorro Ferraz da Costa

    2014-01-01

    Full Text Available The aims of this study were to evaluate the seasonal variation and frequency distribution of Rhipicephalus (Boophilus microplus, Haematobia irritans, and Dermatobia hominis on crossbred heifers under field conditions in the northeast of Minas Gerais state, southeastern Brazil. From November 2007 to September 2009 (23 months, 40 heifers aged 16.6±2.4 months were divided into groups A (1/4 Holstein × 3/4 Gir and B (1/2 Holstein × 1/2 Gir and had the monthly infestation estimated along with the climatic conditions. The mean maximum and minimum temperatures were 28.5 and 19°C, respectively. The ectoparasites were present on animals in all months of the year. The levels of ticks on the animals were low (3.0±0.2 ticks/animal, with the highest density in midwinter. The temperature was the climatic factor that most influenced the tick levels. The population of H. irritans (13.9±0.3 flies/animal and D. hominis (1.5±0.2 larvae/animal on heifers was more influenced by rainfall and exhibited two population peaks during the year. 1/2 Holstein heifers harbored significantly more H. irritans and D. hominis than 1/4 Holstein heifers. The results are discussed considering the most appropriate periods to apply ectoparasiticides and the genetic make-up of the animals.

  10. Seasonal Variation and Frequency Distribution of Ectoparasites in Crossbreed Cattle in Southeastern Brazil

    Science.gov (United States)

    Ferraz da Costa, Maria do Socorro; Guimarães, Marcos Pezzi; Lima, Walter dos Santos; Ferraz da Costa, Ana Julia; Facury Filho, Elias Jorge; Araujo, Ricardo Nascimento

    2014-01-01

    The aims of this study were to evaluate the seasonal variation and frequency distribution of Rhipicephalus (Boophilus) microplus, Haematobia irritans, and Dermatobia hominis on crossbred heifers under field conditions in the northeast of Minas Gerais state, southeastern Brazil. From November 2007 to September 2009 (23 months), 40 heifers aged 16.6 ± 2.4 months were divided into groups A (1/4 Holstein × 3/4 Gir) and B (1/2 Holstein × 1/2 Gir) and had the monthly infestation estimated along with the climatic conditions. The mean maximum and minimum temperatures were 28.5 and 19°C, respectively. The ectoparasites were present on animals in all months of the year. The levels of ticks on the animals were low (3.0 ± 0.2 ticks/animal), with the highest density in midwinter. The temperature was the climatic factor that most influenced the tick levels. The population of H. irritans (13.9 ± 0.3 flies/animal) and D. hominis (1.5 ± 0.2 larvae/animal) on heifers was more influenced by rainfall and exhibited two population peaks during the year. 1/2 Holstein heifers harbored significantly more H. irritans and D. hominis than 1/4 Holstein heifers. The results are discussed considering the most appropriate periods to apply ectoparasiticides and the genetic make-up of the animals. PMID:26464941

  11. High-frequency oscillations in distributed neural networks reveal the dynamics of human decision making

    Directory of Open Access Journals (Sweden)

    Adrian G Guggisberg

    2008-03-01

    Full Text Available We examine the relative timing of numerous brain regions involved in human decisions that are based on external criteria, learned information, personal preferences, or unconstrained internal considerations. Using magnetoencephalography (MEG and advanced signal analysis techniques, we were able to non-invasively reconstruct oscillations of distributed neural networks in the high-gamma frequency band (60–150 Hz. The time course of the observed neural activity suggested that two-alternative forced choice tasks are processed in four overlapping stages: processing of sensory input, option evaluation, intention formation, and action execution. Visual areas are activated fi rst, and show recurring activations throughout the entire decision process. The temporo-occipital junction and the intraparietal sulcus are active during evaluation of external values of the options, 250–500 ms after stimulus presentation. Simultaneously, personal preference is mediated by cortical midline structures. Subsequently, the posterior parietal and superior occipital cortices appear to encode intention, with different subregions being responsible for different types of choice. The cerebellum and inferior parietal cortex are recruited for internal generation of decisions and actions, when all options have the same value. Action execution was accompanied by activation peaks in the contralateral motor cortex. These results suggest that high-gamma oscillations as recorded by MEG allow a reliable reconstruction of decision processes with excellent spatiotemporal resolution.

  12. Frequency Distribution of Hearing Disorders Among the Student of Public Elementary School in Neishaboor

    Directory of Open Access Journals (Sweden)

    Dr. Mohammad Kamali

    2000-05-01

    Full Text Available Objectives: determining the frequency distribution of hearing disorders among the student of public elementary school by Otoscopy, Puretone Audiometry, Impedance Audiometiy and questionnaires. Methods and Materials: This study was carried out in a cross - sectional descriptive survey - on 1200 students (600 girls and 600 boys among the student of primary school of Neishabbor, academic year 1376-77 Results: 1- Otoscopy examination; abnormal conditions of external ear canal was found in 14.1% of cases; mostly impacted ceruman (13.6%; Abnormal conditions of tympanic membrane (0.4% and foreign body 0.16%. Abnormal conditions of external ear canal was statistically unmeaningful. (P V=0 .8 2- Impedance Audiometiy: 5. 75% Abnormal tympanograms were observed, mostly type C (3.15% 3- Pure Tone Audiometry: An overall 5.5% hearing loss was found in this population including 3% bilateral and 1.25% unilateral hearing loss. Only conductive hearing loss was found in this population (2.7% in right ear and 3.5% in left ear, PV=0.9. Hearing loss observed mostly in girls but the difference was slight. Family background showed no effects on the hearing disorders.9.8% of cases were in need of medical care and 0.3% were in need of rehabilitation services. Only 28.8% of parents, 36.3% of teachers and 40.9% of afflicted students were aware of the problem.

  13. Structure and stability upon maternal transmission of common and intermediate FMR1 (Fragile X Mental Retardation 1 alleles in a sample of the Brazilian population

    Directory of Open Access Journals (Sweden)

    Leonardo P. Capelli

    2005-03-01

    Full Text Available In order to investigate the stability of the FMR1 (Fragile X Mental Retardation 1 alleles from the normal population, when maternally inherited, we analyzed 75 mother-to-son transmissions. Sixty-eight alleles fell within the common range with 20-40 CGG repeats, and seven alleles were intermediate, with 41-48 repeats. No change was observed either in the length or in the structure of these repeats upon transmission. Fifty-three alleles were ascertained in different families, and their size distribution was similar to those described for European and European-derived populations, with three peaks of frequency: 66% of the alleles with (CGG29, (CGG30 or (CGG31, 7.5% with (CGG20, and 5.7% with (CGG23. Regarding the AGG interspersion pattern, 69.8% had two AGG repeats, 20.8% had one, 5.7% had three and 3.8% had none. The most common patterns were 10+9+9 (30.2%, 9+9+9 (18.9%, 10+9 (7.5%, and 10+9+10 (7.5%. About 70% of the alleles with up to 40 repeats were linked to the DXS548/FRAXAC1 haplotype 7-3, the most commonly reported in normal populations. Four out of five intermediate alleles were in linkage with the two haplotypes most frequently associated to the FMR1 full mutation, 2-1 and 6-4. These four alleles showed long uninterrupted CGG repeats at the 3' end. The 9+9+22, 9+9+23 and 9+9+28 alleles were linked to the haplotype 2-1, and the 9+37 allele, to the haplotype 6-4. The pattern of AGG interspersion of these alleles and the associated haplotypes were in accordance with the two main pathways toward mutation previously proposed.

  14. Empirical Distributions of FST from Large-Scale Human Polymorphism Data

    Science.gov (United States)

    Elhaik, Eran

    2012-01-01

    Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright’s FST that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-FST may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically FST analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global FST distribution closely follows an exponential distribution. Third, although the overall FST distribution is similarly shaped (inverse J), FST distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-FST of these groups is linear in allele frequency. These results suggest that investigating the extremes of the FST distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection. PMID

  15. Heterogenous Distribution of MTHFR Gene Variants among Mestizos and Diverse Amerindian Groups from Mexico

    Science.gov (United States)

    Contreras-Cubas, Cecilia; Sánchez-Hernández, Beatríz E.; García-Ortiz, Humberto; Martínez-Hernández, Angélica; Barajas-Olmos, Francisco; Cid, Miguel; Mendoza-Caamal, Elvia C.; Centeno-Cruz, Federico; Ortiz-Cruz, Gabriela; Jiménez-López, José Concepción; Córdova, Emilio J.; Salas-Bautista, Eva Gabriela; Saldaña-Alvarez, Yolanda; Fernández-López, Juan Carlos; Mutchinick, Osvaldo M.

    2016-01-01

    Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in folate metabolism. Folate deficiency has been related to several conditions, including neural tube defects (NTDs) and cardiovascular diseases. Hence, MTHFR genetic variants have been studied worldwide, particularly the C677T and A1298C. We genotyped the C677T and A1298C MTHFR polymorphisms in Mexican Amerindians (MAs), from the largest sample included in a genetic study (n = 2026, from 62 ethnic groups), and in a geographically-matched Mexican Mestizo population (MEZ, n = 638). The 677T allele was most frequent in Mexican individuals, particularly in MAs. The frequency of this allele in both MAs and MEZs was clearly enriched in the South region of the country, followed by the Central East and South East regions. In contrast, the frequency of the 1298C risk allele in Mexicans was one of the lowest in the world. Both in MAs and MEZs the variants 677T and 1298C displayed opposite allele frequency gradients from southern to northern Mexico. Our findings suggest that in Mestizos the 677T allele was derived from Amerindians while the 1298C allele was a European contribution. Some subgroups showed an allele frequency distribution that highlighted their genetic diversity. Notably, the distribution of the frequency of the 677T allele was consistent with that of the high incidence of NTDs reported in MEZ. PMID:27649570

  16. Heterogenous Distribution of MTHFR Gene Variants among Mestizos and Diverse Amerindian Groups from Mexico.

    Directory of Open Access Journals (Sweden)

    Cecilia Contreras-Cubas

    Full Text Available Methylenetetrahydrofolate reductase (MTHFR is a key enzyme in folate metabolism. Folate deficiency has been related to several conditions, including neural tube defects (NTDs and cardiovascular diseases. Hence, MTHFR genetic variants have been studied worldwide, particularly the C677T and A1298C. We genotyped the C677T and A1298C MTHFR polymorphisms in Mexican Amerindians (MAs, from the largest sample included in a genetic study (n = 2026, from 62 ethnic groups, and in a geographically-matched Mexican Mestizo population (MEZ, n = 638. The 677T allele was most frequent in Mexican individuals, particularly in MAs. The frequency of this allele in both MAs and MEZs was clearly enriched in the South region of the country, followed by the Central East and South East regions. In contrast, the frequency of the 1298C risk allele in Mexicans was one of the lowest in the world. Both in MAs and MEZs the variants 677T and 1298C displayed opposite allele frequency gradients from southern to northern Mexico. Our findings suggest that in Mestizos the 677T allele was derived from Amerindians while the 1298C allele was a European contribution. Some subgroups showed an allele frequency distribution that highlighted their genetic diversity. Notably, the distribution of the frequency of the 677T allele was consistent with that of the high incidence of NTDs reported in MEZ.

  17. A statistical approach to quantification of genetically modified organisms (GMO) using frequency distributions.

    Science.gov (United States)

    Gerdes, Lars; Busch, Ulrich; Pecoraro, Sven

    2014-12-14

    According to Regulation (EU) No 619/2011, trace amounts of non-authorised genetically modified organisms (GMO) in feed are tolerated within the EU if certain prerequisites are met. Tolerable traces must not exceed the so-called 'minimum required performance limit' (MRPL), which was defined according to the mentioned regulation to correspond to 0.1% mass fraction per ingredient. Therefore, not yet authorised GMO (and some GMO whose approvals have expired) have to be quantified at very low level following the qualitative detection in genomic DNA extracted from feed samples. As the results of quantitative analysis can imply severe legal and financial consequences for producers or distributors of feed, the quantification results need to be utterly reliable. We developed a statistical approach to investigate the experimental measurement variability within one 96-well PCR plate. This approach visualises the frequency distribution as zygosity-corrected relative content of genetically modified material resulting from different combinations of transgene and reference gene Cq values. One application of it is the simulation of the consequences of varying parameters on measurement results. Parameters could be for example replicate numbers or baseline and threshold settings, measurement results could be for example median (class) and relative standard deviation (RSD). All calculations can be done using the built-in functions of Excel without any need for programming. The developed Excel spreadsheets are available (see section 'Availability of supporting data' for details). In most cases, the combination of four PCR replicates for each of the two DNA isolations already resulted in a relative standard deviation of 15% or less. The aims of the study are scientifically based suggestions for minimisation of uncertainty of measurement especially in -but not limited to- the field of GMO quantification at low concentration levels. Four PCR replicates for each of the two DNA isolations

  18. Frequency distributions of Escherichia coli in the confectionery products offered in retail market in Isfahan

    Directory of Open Access Journals (Sweden)

    Rasoul Rezaei

    2016-06-01

    Full Text Available Introduction: Raw ingredients used in confectionary carry high risk of infection with Escherichia coli. Since confectionaries are offered in the market in quite varied forms and types and there is a great difference in the sanitary status of the confectionaries, this study aimed at evaluation of E.coli   frequency distribution in different types of confectionery products in Isfahan market. In addition, the effect of moisture content, products category and the sanitary level of the confectionaries as well as product types (Industrially or traditionally produced on the contamination level were studied. Materials and methods: A total of 200 samples were randomly collected from confectioneries in Isfahan city through simple random sampling method. Preparation and dilution procedures were conducted under sterile conditions. Samples were cultured on EMB agar medium. Later, some of the positive isolates were randomly selected and confirmed by TSI and IMVIC test. Data analysis was performed using descriptive indices. Also, one way ANOVA and LSD test or independent t test were applied to determine the statistically significant difference between the mean E.coli cell numbers in the categorized groups of sweets. Results: It was found that 19% of the total tested samples were contaminated with E.coli strains. The mean, median and maximum of contamination were (35±.5, (0 and (3.4 CFU/gr, respectively. Moisture content, products category and being traditionally or industrially produced have significant effects on the level of contamination; while, the sanitary status of the traditional confectionaries as graded in this study has no impact on the average E.coli cell count. Discussion and conclusion: Regarding the microbial quality, at least about 25% of the sweets in the market do not meet the national standards of confectionary products. Implementation of strict hygiene regulation in the traditional confectionaries is in need to provide the public with

  19. Human minisatellite alleles detectable only after PCR amplification.

    Science.gov (United States)

    Armour, J A; Crosier, M; Jeffreys, A J

    1992-01-01

    We present evidence that a proportion of alleles at two human minisatellite loci is undetected by standard Southern blot hybridization. In each case the missing allele(s) can be identified after PCR amplification and correspond to tandem arrays too short to detect by hybridization. At one locus, there is only one undetected allele (population frequency 0.3), which contains just three repeat units. At the second locus, there are at least five undetected alleles (total population frequency 0.9) containing 60-120 repeats; they are not detected because these tandem repeats give very poor signals when used as a probe in standard Southern blot hybridization, and also cross-hybridize with other sequences in the genome. Under these circumstances only signals from the longest tandemly repeated alleles are detectable above the nonspecific background. The structures of these loci have been compared in human and primate DNA, and at one locus the short human allele containing three repeat units is shown to be an intermediate state in the expansion of a monomeric precursor allele in primates to high copy number in the longer human arrays. We discuss the implications of such loci for studies of human populations, minisatellite isolation by cloning, and the evolution of highly variable tandem arrays.

  20. Determination of High-Frequency Current Distribution Using EMTP-Based Transmission Line Models with Resulting Radiated Electromagnetic Fields

    Energy Technology Data Exchange (ETDEWEB)

    Mork, B; Nelson, R; Kirkendall, B; Stenvig, N

    2009-11-30

    Application of BPL technologies to existing overhead high-voltage power lines would benefit greatly from improved simulation tools capable of predicting performance - such as the electromagnetic fields radiated from such lines. Existing EMTP-based frequency-dependent line models are attractive since their parameters are derived from physical design dimensions which are easily obtained. However, to calculate the radiated electromagnetic fields, detailed current distributions need to be determined. This paper presents a method of using EMTP line models to determine the current distribution on the lines, as well as a technique for using these current distributions to determine the radiated electromagnetic fields.

  1. Meal Frequency and Nutrient Distribution: What is Ideal for Body Composition?

    OpenAIRE

    Ryan P Lowery

    2014-01-01

    This article explores the effects of meal frequency on protein synthesis, muscle mass and fat mass. Current research appears to indicate that manipulating meal frequency increases net protein balance and body composition when each meal provides an adequate supply of the amino acid leucine to optimize skeletal muscle anabolism. In contrast, research demonstrating no benefits to increased meal frequency generally employed small, inadequate boluses of protein per meal. The purpose of this paper ...

  2. Identification of the third/extra allele for forensic application in cases with TPOX tri-allelic pattern.

    Science.gov (United States)

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; Motta, Carlos Henrique Ares Silveira da; Rodenbusch, Rodrigo; Gusmão, Leonor; Alho, Clarice Sampaio

    2015-05-01

    Genotyping of polymorphic short tandem repeats (STRs) loci is widely used in forensic DNA analysis. STR loci eventually present tri-allelic pattern as a genotyping irregularity and, in that situation, the doubt about the tri-allele locus frequency calculation can reduce the analysis strength. In the TPOX human STR locus, tri-allelic genotypes have been reported with a widely varied frequency among human populations. We investigate whether there is a single extra allele (the third allele) in the TPOX tri-allelic pattern, what it is, and where it is, aiming to understand its genomic anatomy and to propose the knowledge of this TPOX extra allele from genetic profile, thus preserving the two standard TPOX alleles in forensic analyses. We looked for TPOX tri-allelic subjects in 75,113 Brazilian families. Considering only the parental generation (mother+father) we had 150,226 unrelated subjects evaluated. From this total, we found 88 unrelated subjects with tri-allelic pattern in the TPOX locus (0.06%; 88/150,226). Seventy three of these 88 subjects (73/88; 83%) had the Clayton's original Type 2 tri-allelic pattern (three peaks of even intensity). The remaining 17% (15/88) show a new Type 2 derived category with heterozygote peak imbalance (one double dose peak plus one regular sized peak). In this paper we present detailed data from 66 trios (mother+father+child) with true biological relationships. In 39 of these families (39/66; 59%) the extra TPOX allele was transmitted either from the mother or from the father to the child. Evidences indicated the allele 10 as the extra TPOX allele, and it is on the X chromosome. The present data, which support the previous Lane hypothesis, improve the knowledge about tri-allelic pattern of TPOX CODIS' locus allowing the use of TPOX profile in forensic analyses even when with tri-allelic pattern. This evaluation is now available for different forensic applications. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  3. Influence of a distribution of deflecting-mode frequencies on the transient dynamics of cumulative beam breakup

    International Nuclear Information System (INIS)

    Bohn, C.L.; Delayen, J.R.

    1992-01-01

    A distribution of deflecting-mode frequencies in the constituent cavities of a linear accelerator can lead to Q-independent damping of cumulative beam breakup. A probability density for the deflecting-mode frequencies generates an effective transverse wake function. The effective wake function can be used to calculate the transient dynamics of cumulative beam breakup within the framework of a continuum approximation provided the transverse beam displacement changes little over the correlation length of the deflecting-mode frequencies as the beam moves down the linac. We adopt this approach to show that the damping induced by the effective wake function causes the rate of approach to the steady state to depend strongly on the operative probability density for the deflecting-mode frequencies

  4. Frequency Distribution in Domestic Microwave Ovens and Its Influence on Heating Pattern.

    Science.gov (United States)

    Luan, Donglei; Wang, Yifen; Tang, Juming; Jain, Deepali

    2017-02-01

    In this study, snapshots of operating frequency profiles of domestic microwave ovens were collected to reveal the extent of microwave frequency variations under different operation conditions. A computer simulation model was developed based on the finite difference time domain method to analyze the influence of the shifting frequency on heating patterns of foods in a microwave oven. The results showed that the operating frequencies of empty and loaded domestic microwave ovens varied widely even among ovens of the same model purchased on the same date. Each microwave oven had its unique characteristic operating frequencies, which were also affected by the location and shape of the load. The simulated heating patterns of a gellan gel model food when heated on a rotary plate agreed well with the experimental results, which supported the reliability of the developed simulation model. Simulation indicated that the heating patterns of a stationary model food load changed with the varying operating frequency. However, the heating pattern of a rotary model food load was not sensitive to microwave frequencies due to the severe edge heating overshadowing the effects of the frequency variations. © 2016 Institute of Food Technologists®.

  5. Investigation of the type, frequency, and sex distribution of fistulas in Crohn's disease

    International Nuclear Information System (INIS)

    Kulke, H.; Kasper, H.; Auer, I.

    1987-01-01

    Various types of fistula development are described in a population of 206 patients with a pravious diagnosis of Crohn's disease. In addition, the frequency of occurence of Crohn's disease in a population and the frequency of Crohn's reoccurrence for a given patient is reported. Furthermore a subdivision of patients with respect to sex is possible. (orig.) [de

  6. M-protein gene-type distribution and hyaluronic acid capsule in group A Streptococcus clinical isolates in Chile: association of emm gene markers with csrR alleles.

    Science.gov (United States)

    Wozniak, A; Rojas, P; Rodríguez, C; Undabarrena, A; Garate, C; Riedel, I; Román, J C; Kalergis, A M; García, P

    2012-07-01

    Streptococcus pyogenes causes a variety of infections because of virulence factors such as capsular hyaluronic acid and M protein. The aim of this study was to determine emm types and capsule phenotype in 110 isolates of S. pyogenes from patients with invasive (sterile sites) and non-invasive (mainly pharyngitis) infections in Chile, and the relationship between both virulence factors. The most abundant types found were emm12, emm1, emm4 and emm28 and their distribution was similar to that seen in Latin America and developed countries, but very different from that in Asia and Pacific Island countries. Ten of 16 emm types identified in pharyngeal isolates were found in sterile-site isolates, and three of nine emm types of sterile-site isolates occurred in pharyngeal isolates; three emm subtypes were novel. The amount of hyaluronic acid was significantly higher in sterile-site isolates but did not differ substantially among emm types. Only three isolates were markedly capsulate and two of them had mutations in the csrR gene that codes for a repressor of capsule synthesis genes. We found a non-random association between emm types and csrR gene alleles suggesting that horizontal gene transfer is not freely occurring in the population.

  7. Combined effects of food deprivation and food frequency on the amount and temporal distribution of schedule-induced drinking.

    Science.gov (United States)

    Castilla, José Luis; Pellón, Ricardo

    2013-11-01

    Under intermittent food schedules animals develop temporally organized behaviors throughout interfood intervals, with behaviors early in the intervals (interim) normally occurring in excess. Schedule-induced drinking (a prototype of interim, adjunctive behavior) is related to food deprivation and food frequency. This study investigated the interactions that resulted from combining different food-deprivation levels (70%, 80% or 90% free-feeding weights) with different food-occurrence frequencies (15-, 30- or 60-s interfood intervals) in a within-subjects design. Increases in food deprivation and food frequency generally led to increased licking, with greater differences due to food deprivation as interfood intervals became shorter. Distributions of licking were modestly shifted to later in the interfood interval as interfood intervals lengthened, a result that was most marked under 90% food deprivation, which also resulted in flatter distributions. It would therefore appear that food deprivation modulates the licking rate and the distribution of licking in different ways. Effects of food deprivation and food frequency are adequately explained by a theory of adjunctive behavior based on delayed food reinforcement, in contrast to alternative hypotheses. © Society for the Experimental Analysis of Behavior.

  8. Spatial distribution of cold-season lightning frequency in the coastal areas of the Sea of Japan

    Science.gov (United States)

    Tsurushima, Daiki; Sakaida, Kiyotaka; Honma, Noriyasu

    2017-12-01

    The coastal areas of the Sea of Japan are a well-known hotspot of winter lightning activity. This study distinguishes between three common types of winter lightning in that region (types A-C), based on their frequency distributions and the meteorological conditions under which they occur. Type A lightning occurs with high frequency in the Tohoku district. It is mainly caused by cold fronts that accompany cyclones passing north of the Japanese islands. Type B, which occurs most frequently in the coastal areas of the Hokuriku district, is mainly caused by topographically induced wind convergence and convective instability, both of which are associated with cyclones having multiple centers. Type C's lightning frequency distribution pattern is similar to that of type B, but its principal cause is a topographically induced wind convergence generated by cold air advection from the Siberian continent. Type A is most frequently observed from October to November, while types B and C tend to appear from November to January, consistent with seasonal changes in lightning frequency distribution in Japan's Tohoku and Hokuriku districts.

  9. Distributed Generation Integration in the Electric Grid: Energy Storage System for Frequency Control

    Directory of Open Access Journals (Sweden)

    Maurizio Delfanti

    2014-01-01

    Full Text Available During the last few years generation from renewable energy sources (RESs has grown considerably in European electrical networks. Transmission system operators are greatly concerned about the impact of RESs on the operational security and efficiency of their networks and more in general of the ENTSO-E interconnected system. Grid codes are to be revised in order to harmonise the rules regarding the connection of RES power plants. A main issue concerns frequency control: frequency is greatly affected by RESs intermittency and its deviations must be limited as much as possible in order to guarantee a suitable level of power quality. To improve frequency stability, in the future, Grid codes could extend frequency control requirements also to RES units, whereas today they are applied only to conventional power plants. Energy storage systems can be a possible solution to increase the flexibility and performance of RES power plants: they allow generators to modulate their power injections without wasting renewable energy. In this paper, the authors studied the suitability of extending frequency control to RES units integrating them with energy storage systems. In particular, the paper focuses on the impact of frequency control on the storage lifetime by analysing the power charge/discharge in response to real frequency oscillations.

  10. HLA Dr beta 1 alleles in Pakistani patients with rheumatoid arthritis

    International Nuclear Information System (INIS)

    Naqi, N.; Ahmed, T.A.; Bashir, M.M.

    2011-01-01

    Objective: To determine frequencies of HLA DR beta 1 alleles in rheumatoid arthritis in Pakistani patients. Study Design: Cross sectional / analytical study. Place and Duration of Study: Department of Immunology, Armed Forces Institute of Pathology, Rawalpindi in collaboration with Rheumatology departments of Military Hospital, Rawalpindi and Fauji Foundation Hospital, Rawalpindi, from January 2009 to January 2010. Methodology: HLA DR beta 1 genotyping of one hundred Pakistani patients, diagnosed as having RA as per American College of Rheumatology revised criteria 1987, was done. HLA DR beta 1 genotyping was carried out at allele group level (DR beta 1*01-DR beta 1*16) by sequence specific primers in RA patients. Comparison of HLA DR beta 1 allele frequencies between patients and control groups was made using Pearson's chi-square test to find possible association of HLA DR?1 alleles with RA in Pakistani rheumatoid patients. Results: HLA DR beta 1*04 was expressed with significantly increased frequency in patients with rheumatoid arthritis (p <0.05). HLA DR?1*11 was expressed statistically significantly more in control group as compared to rheumatoid patients indicating a possible protective effect. There was no statistically significant difference observed in frequencies of HLA DR beta 1 allele *01, DR beta 1 allele *03, DR beta 1 allele *07, DR beta 1 allele *08, DR beta 1 allele *09, DR beta 1 allele *10, DR beta 1 allele *12, DR beta 1 allele *13, DR beta 1 allele *14, DR?1 allele *15 and DR beta 1 allele *16 between patients and control groups. Conclusion: The identification of susceptible HLA DR beta 1 alleles in Pakistani RA patients may help physicians to make early decisions regarding initiation of early intensive therapy with disease modifying anti rheumatic medicines and biological agents decreasing disability in RA patients. (author)

  11. ABO locus O1 allele and risk of myocardial infarction.

    Science.gov (United States)

    von Beckerath, Nicolas; Koch, Werner; Mehilli, Julinda; Gorchakova, Olga; Braun, Siegmund; Schömig, Albert; Kastrati, Adnan

    2004-01-01

    An association between ABO blood group and myocardial infarction (MI) has been described. One probable mechanism underlying this association is the influence of ABO blood group on plasma von Willebrand factor (vWF) levels. We conducted this genetic study to test whether the ABO O1 allele is associated with low vWF plasma levels and with a reduced risk of MI. Cases consisted of 793 consecutive, angiographically examined patients with either acute or prior MI. As controls served 340 angiographically examined patients with neither coronary artery disease nor signs of MI. ABO1 locus alleles (A1, A2, B, O1, O2) were identified with polymerase chain reaction and fluorogenic probes. The distribution of O1 alleles in the MI group versus the control group was: no O1 allele (15.4%/10.0%), one O1 allele (49.7%/50.0%) and two O1 alleles (34.9%/40.0%) (P = 0.035). O1 allele carriage was associated with a 39% reduction in the risk of MI unadjusted odds ratio, 0.61; 95% confidence interval, 0.41-0.91). The significant association was maintained after adjustment for other cardiovascular risk factors. vWF antigen levels correlated with the number of O1 alleles (P = 0.00003) in a separate control group (n = 164). Carriage of the O1 allele is associated with a decreased risk of myocardial infarction, with homozygosity providing the greatest protection. Copyright 2004 Lippincott Williams and Wilkins

  12. Correlation between carboxylesterase alleles and insecticide resistance in Culex pipiens complex from China

    Directory of Open Access Journals (Sweden)

    Liu Yangyang

    2011-12-01

    Full Text Available Abstract Background In China, large amounts of chemical insecticides are applied in fields or indoors every year, directly or indirectly bringing selection pressure on vector mosquitoes. Culex pipiens complex has evolved to be resistant to all types of chemical insecticides, especially organophosphates, through carboxylesterases. Six resistant carboxylesterase alleles (Ester were recorded previously and sometimes co-existed in one field population, representing a complex situation for the evolution of Ester genes. Results In order to explore the evolutionary scenario, we analyzed the data from an historical record in 2003 and a recent investigation on five Culex pipiens pallens populations sampled from north China in 2010. Insecticide bioassays showed that these five populations had high resistance to pyrethroids, medium resistance to organophosphates, and low resistance to carbamates. Six types of Ester alleles, EsterB1, Ester2, Ester8, Ester9, EsterB10, and Ester11 were identified, and the overall pattern of their frequencies in geographic distribution was consistent with the report seven years prior to this study. Statistical correlation analysis indicated that Ester8 and Ester9 positively correlated with resistance to four insecticides, and EsterB10 to one insecticide. The occurrences of these three alleles were positively correlated, while the occurrence of EsterB1 was negatively correlated with Ester8, indicating an allelic competition. Conclusion Our analysis suggests that one insecticide can select multiple Ester alleles and one Ester allele can work on multiple insecticides. The evolutionary scenario of carboxylesterases under insecticide selection is possibly "one to many".

  13. Generation of low-frequency drift pulse trains by direct modulation of a distributed-feedback laser array

    Science.gov (United States)

    Kuroda, Keiji; Yoshikuni, Yuzo

    2016-01-01

    We propose a simple method to generate low-frequency drift pulse trains by direct modulation of a laser diode system consisting of a distributed-feedback laser array and a semiconductor optical amplifier. We measure the temporal profiles, beat signals and spectra of pulses generated under three different sets of conditions. We found that low-frequency drift pulse trains are generated by application of a DC voltage to one of the laser diodes and a pulse voltage to the semiconductor optical amplifier.

  14. Coordinated Primary and Secondary Control with Frequency-Bus-Signaling for Distributed Generation and Storage in Islanded Microgrids

    DEFF Research Database (Denmark)

    Wu, Dan; Tang, Fen; Dragicevic, Tomislav

    2013-01-01

    In this paper, a distributed coordinated control scheme based on frequency-bus-signaling (FBS) method for a low-voltage AC three phase microgrid is proposed. The control scheme is composed by two levels. Firstly a primary local control which is different for the DGs and the ESS is proposed. The ESS...... control is implemented to restore the frequency deviation produced by the primary ESS controller while preserving the coordinated control performance. Real-time simulation results show the feasibility of the proposed approach by showing the operation of the microgrid in different scenarios....

  15. Tailoring electron energy distribution functions through energy confinement in dual radio-frequency driven atmospheric pressure plasmas

    Energy Technology Data Exchange (ETDEWEB)

    O' Neill, C.; Waskoenig, J. [Centre for Plasma Physics, School of Maths and Physics, Queen' s University Belfast, Belfast BT7 1NN (United Kingdom); Gans, T. [Centre for Plasma Physics, School of Maths and Physics, Queen' s University Belfast, Belfast BT7 1NN (United Kingdom); York Plasma Institute, Department of Physics, University of York, York YO10 5DD (United Kingdom)

    2012-10-08

    A multi-scale numerical model based on hydrodynamic equations with semi-kinetic treatment of electrons is used to investigate the influence of dual frequency excitation on the effective electron energy distribution function (EEDF) in a radio-frequency driven atmospheric pressure plasma. It is found that variations of power density, voltage ratio, and phase relationship provide separate control over the electron density and the mean electron energy. This is exploited to directly influence both the phase dependent and time averaged effective EEDF. This enables tailoring the EEDF for enhanced control of non-equilibrium plasma chemical kinetics at ambient pressure and temperature.

  16. Controller design for flexible, distributed parameter mechanical arms via combined state space and frequency domain techniques

    Science.gov (United States)

    Book, W. J.; Majett, M.

    1982-01-01

    The potential benefits of the ability to control more flexible mechanical arms are discussed. A justification is made in terms of speed of movement. A new controller design procedure is then developed to provide this capability. It uses both a frequency domain representation and a state variable representation of the arm model. The frequency domain model is used to update the modal state variable model to insure decoupled states. The technique is applied to a simple example with encouraging results.

  17. Allelic frequency of G380A polymorphism of tumor necrosis factor alpha gene and relation with cardiovascular risk factors and adipocytokines in obese patients Frecuencia alélica del polimorfismo G380A del factor de necrosis tumoral alpha y relación con factores de riesgo cardiovascular y adipocitoquinas en pacientes obesos

    OpenAIRE

    D. A. De Luis; R. Aller; O. Izaola; M. González Sagrado; R. Conde; B. de la Fuente; H. F. Ovalle

    2011-01-01

    Background: The aim of our study was to investigate the allelic frequency of the G308A polymorphism in the TNF alpha gene and the influence of G308A this polymorphism on cardiovascular risk factors and adipokine levels in obese patients. Design: A population of 834 obesity patients was analyzed. A nutritional evaluation and a blood analysis were performed. The statistical analysis was performed for the combined G308A and A308A as mutant group and type G308G as wild group. Results: A total of ...

  18. Innovation in globally distributed teams: the role of LMX, communication frequency, and member influence on team decisions.

    Science.gov (United States)

    Gajendran, Ravi S; Joshi, Aparna

    2012-11-01

    For globally distributed teams charged with innovation, member contributions to the team are crucial for effective performance. Prior research, however, suggests that members of globally distributed teams often feel isolated and excluded from their team's activities and decisions. How can leaders of such teams foster member inclusion in team decisions? Drawing on leader-member exchange (LMX) theory, we propose that for distributed teams, LMX and communication frequency jointly shape member influence on team decisions. Findings from a test of our hypotheses using data from 40 globally distributed teams suggest that LMX can enhance member influence on team decisions when it is sustained through frequent leader-member communication. This joint effect is strengthened as team dispersion increases. At the team level, member influence on team decisions has a positive effect on team innovation. (c) 2012 APA, all rights reserved.

  19. Analytical investigation of response of birefringent fiber Bragg grating sensors in distributed monitoring system based on optical frequency domain reflectometry

    Science.gov (United States)

    Wada, D.; Murayama, H.

    2014-01-01

    When Fiber Bragg gratings (FBGs) are used as strain sensors, both longitudinal and lateral strain can be applied uniformly or non-uniformly over the length of the FBGs. In order for the demodulation of such FBG signal, this paper investigates the response of birefringent FBGs which are monitored by distributed measurement system based on optical frequency domain reflectometry. A numerical model of the distributed measurement system is built based on piece-wise uniform approach, which considers polarization states of propagating lights. The numerical model simulates analytical response of birefringent FBGs especially when birefringence induces power fluctuations in the distributed spectra, which can be noise or new opportunity for sensitive monitoring of birefringence. Simulation results show the relationships between the power fluctuations and the polarization states of the propagating lights. Consequently, appropriate methods of polarization control for sensitive distributed birefringent FBG monitoring are discussed.

  20. Low Frequency Electrostatic Waves in Weakly Inhomogeneous Magnetoplasma Modeled by Lorentzian (kappa) Distributions

    National Research Council Canada - National Science Library

    Basu, Bamandas

    2008-01-01

    Linear dispersion relations for electrostatic waves in spatially inhomogeneous, current-carrying anisotropic plasma, where the equilibrium particle velocity distributions are modeled by various Lorentzian (kappa...

  1. Allele coding in genomic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F

    2011-06-01

    Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

  2. The role of human demographic history in determining the distribution and frequency of transferase-deficient galactosaemia mutations.

    LENUS (Irish Health Repository)

    Flanagan, J M

    2010-02-01

    Classical or transferase-deficient galactosaemia is an inherited metabolic disorder caused by mutation in the human Galactose-1-phosphate uridyl transferase (GALT) gene. Of some 170 causative mutations reported, fewer than 10% are observed in more than one geographic region or ethnic group. To better understand the population history of the common GALT mutations, we have established a haplotyping system for the GALT locus incorporating eight single nucleotide polymorphisms and three short tandem repeat markers. We analysed haplotypes associated with the three most frequent GALT gene mutations, Q188R, K285N and Duarte-2 (D2), and estimated their age. Haplotype diversity, in conjunction with measures of genetic diversity and of linkage disequilibrium, indicated that Q188R and K285N are European mutations. The Q188R mutation arose in central Europe within the last 20 000 years, with its observed east-west cline of increasing relative allele frequency possibly being due to population expansion during the re-colonization of Europe by Homo sapiens in the Mesolithic age. K285N was found to be a younger mutation that originated in Eastern Europe and is probably more geographically restricted as it arose after all major European population expansions. The D2 variant was found to be an ancient mutation that originated before the expansion of Homo sapiens out of Africa.

  3. Selection on alleles affecting human longevity and late-life disease: the example of apolipoprotein E.

    Directory of Open Access Journals (Sweden)

    Fotios Drenos

    2010-04-01

    Full Text Available It is often claimed that genes affecting health in old age, such as cardiovascular and Alzheimer diseases, are beyond the reach of natural selection. We show in a simulation study based on known genetic (apolipoprotein E and non-genetic risk factors (gender, diet, smoking, alcohol, exercise that, because there is a statistical distribution of ages at which these genes exert their influence on morbidity and mortality, the effects of selection are in fact non-negligible. A gradual increase with each generation of the epsilon2 and epsilon3 alleles of the gene at the expense of the epsilon4 allele was predicted from the model. The epsilon2 allele frequency was found to increase slightly more rapidly than that for epsilon3, although there was no statistically significant difference between the two. Our result may explain the recent evolutionary history of the epsilon 2, 3 and 4 alleles of the apolipoprotein E gene and has wider relevance for genes affecting human longevity.

  4. Comparison of minute distribution frequency for anesthesia start and end times from an anesthesia information management system and paper records.

    Science.gov (United States)

    Phelps, Michael; Latif, Asad; Thomsen, Robert; Slodzinski, Martin; Raghavan, Rahul; Paul, Sharon Leigh; Stonemetz, Jerry

    2017-08-01

    Use of an anesthesia information management system (AIMS) has been reported to improve accuracy of recorded information. We tested the hypothesis that analyzing the distribution of times charted on paper and computerized records could reveal possible rounding errors, and that this effect could be modulated by differences in the user interface for documenting certain event times with an AIMS. We compared the frequency distribution of start and end times for anesthesia cases completed with paper records and an AIMS. Paper anesthesia records had significantly more times ending with "0" and "5" compared to those from the AIMS (p < 0.001). For case start times, AIMS still exhibited end-digit preference, with times whose last digits had significantly higher frequencies of "0" and "5" than other integers. This effect, however, was attenuated compared to that for paper anesthesia records. For case end times, the distribution of minutes recorded with AIMS was almost evenly distributed, unlike those from paper records that still showed significant end-digit preference. The accuracy of anesthesia case start times and case end times, as inferred by statistical analysis of the distribution of the times, is enhanced with the use of an AIMS. Furthermore, the differences in AIMS user interface for documenting case start and case end times likely affects the degree of end-digit preference, and likely accuracy, of those times.

  5. Plasma Temperature Determination of Hydrogen Containing High-Frequency Electrodeless Lamps by Intensity Distribution Measurements of Hydrogen Molecular Band

    OpenAIRE

    Gavare, Zanda; Revalde, Gita; Skudra, Atis

    2010-01-01

    The goal of the present work was the investigation of the possibility to use intensity distribution of the Q-branch lines of the hydrogen Fulcher-α diagonal band (d3Πu−→a3∑g+ electronic transition; Q-branch with v=v′=2) to determine the temperature of hydrogen containing high-frequency electrodeless lamps (HFEDLs). The values of the rotational temperatures have been obtained from the relative intensity distributions for hydrogen-helium and hydrogen-argon HFEDLs depending on the applied curren...

  6. The 'rare allele phenomenon' in a ribosomal spacer

    NARCIS (Netherlands)

    Schilthuizen, M.; Hoekstra, R.F.; Gittenberger, E.

    2001-01-01

    We describe the increased frequency of a particular length variant of the internal transcribed spacer 1 (ITS-1) of the ribosomal DNA in a hybrid zone of the land snail Albinaria hippolyti. The phenomenon that normally rare alleles or other markers can increase in frequency in the centre of hybrid

  7. Frequency analysis for planned islanding operation in the Danish distribution system - Bornholm

    DEFF Research Database (Denmark)

    Chen, Yu; Xu, Zhao; Østergaard, Jacob

    2008-01-01

    The power system in the Danish island Bornholm is a distribution system with a high penetration of wind generation, which is representative for expected future power systems. During the period from 11th to 14th September 2007, the Distribution System Operator (DSO) Ostkraft in Bornholm conducted ...

  8. A Low-Order System Frequency Response Model for DFIG Distributed Wind Power Generation Systems Based on Small Signal Analysis

    Directory of Open Access Journals (Sweden)

    Rui Quan

    2017-05-01

    Full Text Available Integrating large amounts of wind power into power systems brings a large influence on the dynamic frequency response characteristic (DFRC. The traditional low-order system frequency response (SFR model is no longer applicable at the current time. Based on the small signal analysis theory, a set of novel low-order SFR models for doubly-fed induction generator (DFIG distributed wind power generation systems (DWPGS are derived under low, medium, and high wind speed conditions, respectively. Time-domain simulations have been conducted on PSCAD/EMTDC, and the novel SFR model is tested and evaluated on a real system. The simulation results from the novel model agree with those from the detailed model. The novel SFR model can also directly show the impact of the initial wind speed and auxiliary frequency controller (AFC parameters on DFRC, but not on the detailed model.

  9. Tri-allelic pattern at the TPOX locus: a familial study.

    Science.gov (United States)

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; Paskulin, Giorgio Adriano; Alvarez, Luís; Amorim, António; Batista Dos Santos, Sidney Emanuel; Alho, Clarice Sampaio

    2014-02-10

    Alleles at the TPOX STR locus have 6-14 different numbers of a four-nucleotide (AATG) repeat motif arranged in tandem. Although tri-allelic genotypes are generally rare, the TPOX tri-allelic pattern has a higher frequency, varying widely among populations. Despite this, there are few accurate reports to disclose the nature of the TPOX third allele. In this work we present data obtained from 45 individuals belonging to the same pedigree, in which there are cases of tri-allelic TPOX genotypes. The subjects were apparently healthy with a normal biological development. We noticed six tri-allelic cases in this family, and all of them were women. Karyotype analysis showed no occurrence of partial 2p trisomy. All the tri-allelic cases had the genotype 8-10-11, probably due to three copies of the TPOX STR sequence in all cells (Type 2 tri-allelic pattern). Based on previous data we assumed the allele 10 as the TPOX third allele. The pedigree analyses show evidences that the TPOX extra-allele was the allele10, it is placed far from the main TPOX locus, and that there is a potential linkage of the TPOX extra-allele-10 with Xq. This was the first study that included a large pedigree analysis in order to understand the nature TPOX tri-allelic pattern. © 2013.

  10. Radio-frequency properties of stacked long Josephson junctions with nonuniform bias current distribution

    DEFF Research Database (Denmark)

    Filatrella, G; Pedersen, Niels Falsig

    1999-01-01

    We have numerically investigated the behavior of stacks of long Josephson junctions considering a nonuniform bias profile. In the presence of a microwave field the nonuniform bias, which favors the formation of fluxons, can give rise to a change of the sequence of radio-frequency induced steps...

  11. All-Optical Frequency Modulated High Pressure MEMS Sensor for Remote and Distributed Sensing

    DEFF Research Database (Denmark)

    Reck, Kasper; Thomsen, Erik Vilain; Hansen, Ole

    2011-01-01

    We present the design, fabrication and characterization of a new all-optical frequency modulated pressure sensor. Using the tangential strain in a circular membrane, a waveguide with an integrated nanoscale Bragg grating is strained longitudinally proportional to the applied pressure causing a sh...

  12. The frequency and distribution of recent landslides in three montane tropical regions of Puerto Rico

    Science.gov (United States)

    Matthew C. Larsen; Angel J. Torres-Sanchez

    1998-01-01

    Landslides are common in steep mountainous areas of Puerto Rico where mean annual rainfall and the frequency of intense storms are high. Each year, landslides cause extensive damage to property and occasionally result in loss of life. Average population density is high, 422 peoplerkm2, and is increasing. This increase in population density is accompanied by growing...

  13. A low-frequency distributed aperture array for radio astronomy in space

    NARCIS (Netherlands)

    Boonstra, A.J.; Saks, N.; Falcke, H.; Klein-Wolt, M.; Bentum, Marinus Jan; Rajan, R.T.; Rajan, Raj; Wijnholds, S.J.; Arts, M.; van 't Klooster, K.; Beliën, F.

    2010-01-01

    The frequency band below 30 MHz is one of the last unexplored bands in radio astronomy. This band is well suited for studying the early cosmos at high hydrogen redshifts, the so-called dark ages, extragalactic surveys, (extra) solar planetary bursts, and high energy particle physics. In addition,

  14. DARIS : a low-frequency distributed aperture array for radio astronomy in space

    NARCIS (Netherlands)

    Boonstra, A.J.; Saks, N.; Falcke, H.; Klein-Wolt, M.; Bentum, Marinus Jan; Rajan, R.T.; Rajan, Raj; Wijnholds, M.; Arts, M.; van 't Klooster, K.; Beliën, F.

    2010-01-01

    The frequency band below 30 MHz is one of the last unexplored bands in radio astronomy. This band is well suited for studying the early cosmos at high hydrogen redshifts, the so-called dark ages, extragalactic surveys, (extra) solar planetary bursts, and high energy particle physics. In addition,

  15. Root system topology and diameter distribution of species from habitats differing in inundation frequency

    NARCIS (Netherlands)

    Bouma, T.J.; Nielsen, K.F.; Van Hal, J.; Koutstaal, B.P.

    2001-01-01

    1. We compared the root systems of seven halophytic species that occur at different elevations on a salt marsh, in order to (i) test the hypothesis that variations in root system architecture reflect adaptation to inundation frequency or nitrogen limitation, and (ii) verify the theoretically

  16. Orbiting low frequency antennas for radio astronomy(OLFAR): Distributing signal processing

    NARCIS (Netherlands)

    Rajan, Raj; Rajan, R.T.; Budianu, A.; Engelen, Steven; van der Veen, Alle-Jan; Bentum, Marinus Jan; Boonstra, Albert Jan; Verhoeven, Chris

    2011-01-01

    Recently, new and interesting science drivers have emerged in the ultra low frequency range of 0.3-30 MHz ranging from the epoch of re-ionization, exo-planets, ultra-high energy cosmic rays and studies of the astronomical dark ages. However at these wavelengths, ground based observations are

  17. Neutral and Stable Equilibria of Genetic Systems and The Hardy-Weinberg Principle: Limitations of the Chi-Square Test and Advantages of Auto-Correlation Functions of Allele Frequencies

    Directory of Open Access Journals (Sweden)

    Francisco A Bosco

    2012-12-01

    Full Text Available Since the foundations of Population Genetics the notion of genetic equilibrium (in close analogy to Classical Mechanics has been associated with the Hardy-Weinberg (HW Principle and the identification of equilibrium is currently assumed by stating that the HW axioms are valid if appropriate values of Chi-Square (p<0.05 are observed in experiments. Here we show by numerical experiments with the genetic system of one locus/two alleles that considering large ensembles of populations the Chi-Square test is not decisive and may lead to false negatives in random mating populations and false positives in nonrandom mating populations. This result confirms the logical statement that statistical tests cannot be used to deduce if the genetic population is under the HW conditions. Furthermore, we show that under the HW conditions populations of any size evolve in time according to what can be identified as neutral dynamics to which the very notion of equilibrium is unattainable for any practical purpose. Therefore, under the HW conditions the identification of equilibrium properties needs a different approach and the use of more appropriate concepts. We also show that by relaxing the condition of random mating the dynamics acquires all the characteristics of asymptotic stable equilibrium. As a consequence our results show that the question of equilibrium in genetic systems should be approached in close analogy to non-equilibrium statistical physics and its observability should be focused on dynamical quantities like the typical decay properties of the allelic auto correlation function in time. In this perspective one should abandon the classical notion of genetic equilibrium and its relation to the HW proportions and open investigations in the direction of searching for unifying general principles of population genetic transformations capable to take in consideration these systems in their full complexity.

  18. The contribution of local distribution substations and associated area distribution system to personal exposure to power frequency magnetic fields.

    Science.gov (United States)

    Grainger, P; Preece, A W

    2000-12-01

    A number of epidemiological studies has shown a significant correlation between wire coding, magnetic fields and childhood cancer, although a more recent study has not [McBride et al. (1999) Am. J. Epidemiol. 149 (9), 831-842]. In the UK there is currently no equivalent to wire-codes and there is some uncertainty about the extent to which the UK medium-voltage electricity distribution systems contribute to personal exposure and how this compares with US overhead supply systems. Studies on four different area types were carried out to measure magnetic field intensities from typical electricity supply utility substations and cabling in the vicinity of domestic housing. Typically at distances of two metres from the substations mean magnetic field intensities were 20 nano teslas (nT) or less, increasing to 0.98 microT or less at the closest public access point. The mean magnetic field exposure level sampled around the four main test areas varied between 0.012 and 0.27 microT increasing to 0.30-0.80 microT at road junctions.

  19. HLA-A and HLA-B alleles associated in psoriasis patients from Mumbai, Western India

    Directory of Open Access Journals (Sweden)

    Shankarkumar Umapathy

    2011-01-01

    Full Text Available Background: Psoriasis, a common autoimmune disorder characterized by T cell-mediated keratinocyte hyperproliferation, is known to be associated with the presence of certain specific Human Leukocyte Antigen (HLA alleles. Aim: To evaluate distribution of HLA-A and HLA-B alleles and hence identify the susceptible allele of psoriasis from patients in Western India. Materials and Methods: The study design included 84 psoriasis patients and 291 normal individuals as controls from same geographical region. HLA-A and HLA-B typing was done using Serology typing. Standard statistical analysis was followed to identify the odds ratio (OR, allele frequencies, and significant P value using Graphpad software. Results: The study revealed significant increase in frequencies of HLA-A2 (OR-3.976, P<0.0001, B8 (OR-5.647, P<0.0001, B17 (OR-5.452, P<0.0001, and B44 (OR-50.460, P<0.0001, when compared with controls. Furthermore, the frequencies of HLA-A28 (OR-0.074, P=0.0024, B5 (OR-0.059, P<0.0001, B12 (OR-0.051, P=0.0002, and B15 (OR-0.237, P=0.0230 were significantly decreased in psoriasis patients. Conclusion: This study shows the strong association of HLA-A2, B8, and B17 antigens with psoriasis conferring susceptibility to psoriasis patients from Western India, while the antigens HLA-A28, B5, and B12 show strong negative association with the disease.

  20. HLA-A AND HLA-B ALLELES ASSOCIATED IN PSORIASIS PATIENTS FROM MUMBAI, WESTERN INDIA

    Science.gov (United States)

    Umapathy, Shankarkumar; Pawar, Aruna; Mitra, R; Khuperkar, D; Devaraj, J P; Ghosh, K; Khopkar, U

    2011-01-01

    Background: Psoriasis, a common autoimmune disorder characterized by T cell-mediated keratinocyte hyperproliferation, is known to be associated with the presence of certain specific Human Leukocyte Antigen (HLA) alleles. Aim: To evaluate distribution of HLA-A and HLA-B alleles and hence identify the susceptible allele of psoriasis from patients in Western India. Materials and Methods: The study design included 84 psoriasis patients and 291 normal individuals as controls from same geographical region. HLA-A and HLA-B typing was done using Serology typing. Standard statistical analysis was followed to identify the odds ratio (OR), allele frequencies, and significant P value using Graphpad software. Results: The study revealed significant increase in frequencies of HLA-A2 (OR-3.976, P<0.0001), B8 (OR-5.647, P<0.0001), B17 (OR-5.452, P<0.0001), and B44 (OR-50.460, P<0.0001), when compared with controls. Furthermore, the frequencies of HLA-A28 (OR-0.074, P=0.0024), B5 (OR-0.059, P<0.0001), B12 (OR-0.051, P=0.0002), and B15 (OR-0.237, P=0.0230) were significantly decreased in psoriasis patients. Conclusion: This study shows the strong association of HLA-A2, B8, and B17 antigens with psoriasis conferring susceptibility to psoriasis patients from Western India, while the antigens HLA-A28, B5, and B12 show strong negative association with the disease. PMID:22121262

  1. Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts.

    Science.gov (United States)

    Bouwman, Aniek C; Hayes, Ben J; Calus, Mario P L

    2017-10-30

    Genomic evaluation is used to predict direct genomic values (DGV) for selection candidates in breeding programs, but also to estimate allele substitution effects (ASE) of single nucleotide polymorphisms (SNPs). Scaling of allele counts influences the estimated ASE, because scaling of allele counts results in less shrinkage towards the mean for low minor allele frequency (MAF) variants. Scaling may become relevant for estimating ASE as more low MAF variants will be used in genomic evaluations. We show the impact of scaling on estimates of ASE using real data and a theoretical framework, and in terms of power, model fit and predictive performance. In a dairy cattle dataset with 630 K SNP genotypes, the correlation between DGV for stature from a random regression model using centered allele counts (RRc) and centered and scaled allele counts (RRcs) was 0.9988, whereas the overall correlation between ASE using RRc and RRcs was 0.27. The main difference in ASE between both methods was found for SNPs with a MAF lower than 0.01. Both the ratio (ASE from RRcs/ASE from RRc) and the regression coefficient (regression of ASE from RRcs on ASE from RRc) were much higher than 1 for low MAF SNPs. Derived equations showed that scenarios with a high heritability, a large number of individuals and a small number of variants have lower ratios between ASE from RRc and RRcs. We also investigated the optimal scaling parameter [from - 1 (RRcs) to 0 (RRc) in steps of 0.1] in the bovine stature dataset. We found that the log-likelihood was maximized with a scaling parameter of - 0.8, while the mean squared error of prediction was minimized with a scaling parameter of - 1, i.e., RRcs. Large differences in estimated ASE were observed for low MAF SNPs when allele counts were scaled or not scaled because there is less shrinkage towards the mean for scaled allele counts. We derived a theoretical framework that shows that the difference in ASE due to shrinkage is heavily influenced by the

  2. Low-frequency analog signal distribution on digital photonic networks by optical delta-sigma modulation

    Science.gov (United States)

    Kanno, Atsushi; Kawanishi, Tetsuya

    2013-12-01

    We propose a delta-sigma modulation scheme for low- and medium-frequency signal transmission in a digital photonic network system. A 10-Gb/s-class optical transceiver with a delta-sigma modulator utilized as a high-speed analog-to-digital converter (ADC) provides a binary optical signal. On the signal reception side, a low-cost and slow-speed photonic receiver directly converts the binary signal into an analog signal at frequencies from several hundreds of kilohertz several tens of megahertz. Further, by using a clock and data recovery circuit at the receiver to reduce jitters, the single-sideband phase noise of the generated signals can be significantly reduced.

  3. Joint accurate time and stable frequency distribution infrastructure sharing fiber footprint with research network

    Czech Academy of Sciences Publication Activity Database

    Vojtěch, J.; Šlapák, M.; Škoda, P.; Radil, J.; Havliš, O.; Altmann, M.; Münster, P.; Velč, R.; Kundrát, J.; Altmannová, L.; Vohnout, R.; Horváth, T.; Hůla, M.; Smotlacha, V.; Čížek, Martin; Pravdová, Lenka; Řeřucha, Šimon; Hrabina, Jan; Číp, Ondřej

    2017-01-01

    Roč. 56, č. 2 (2017), s. 1-7, č. článku 027101. ISSN 0091-3286 R&D Projects: GA ČR GB14-36681G Institutional support: RVO:68081731 Keywords : accurate time * stable frequency * wavelength division multiplexing * bidirectional reciprocal path * Sagnac effect Subject RIV: BH - Optics, Masers, Lasers OBOR OECD: Optics (including laser optics and quantum optics) Impact factor: 1.082, year: 2016

  4. Parallelizing Serial Code for a Distributed Processing Environment with an Application to High Frequency Electromagnetic Scattering

    Science.gov (United States)

    1991-12-01

    build and are not always an accurate reproduction of the final design. Field measurements, on the other hand , can be expensive or extremely difficult to...on the other hand , can be quite pronounced at frequencies typically used by radars (2 - 16 GJlz). The only contribution from diffraction in a...corresponding element in the controlling variable as each) {contribution to the partial strenght is calculated) 6(Vi : 0 < i < vol-points :: D(V j : 0 < j

  5. Altered Frequency Distribution in the Electroencephalogram is Correlated to the Analgesic Effect of Remifentanil

    DEFF Research Database (Denmark)

    Graversen, Carina; Malver, Lasse P; Kurita, Geana P

    2015-01-01

    Opioids alter resting state brain oscillations by multiple and complex factors, which are still to be elucidated. To increase our knowledge, multi-channel electroencephalography (EEG) was subjected to multivariate pattern analysis (MVPA), to identify the most descriptive frequency bands and scalp...... remifentanil treatment. As the EEG alterations were correlated to the analgesic effect, the approach may prove to be a novel methodology for monitoring individual efficacy to opioids....

  6. Experimental and numerical assessment of low-frequency current distributions from UMTS and GSM mobile phones.

    Science.gov (United States)

    Gosselin, Marie-Christine; Kühn, Sven; Kuster, Niels

    2013-12-07

    The evaluation of the exposure from mobile communication devices requires consideration of electromagnetic fields (EMFs) over a broad frequency range from dc to GHz. Mobile phones in operation have prominent spectral components in the low-frequency (LF) and radio-frequency (RF) ranges. While the exposure to RF fields from mobile phones has been comprehensively assessed in the past, the LF fields have received much less attention. In this study, LF fields from mobile phones are assessed experimentally and numerically for the global system for mobile (GSM) and universal mobile telecommunications system (UMTS) communication systems and conclusions about the global (LF and RF) EMF exposure from both systems are drawn. From the measurements of the time-domain magnetic fields, it was found that the contribution from the audio signal at a normal speech level, i.e., -16 dBm0, is the same order of magnitude as the fields induced by the current bursts generated from the implementation of the GSM communication system at maximum RF output level. The B-field induced by currents in phones using the UMTS is two orders of magnitude lower than that induced by GSM. Knowing that the RF exposure from the UMTS is also two orders of magnitude lower than from GSM, it is now possible to state that there is an overall reduction of the exposure from this communication system.

  7. Experimental and numerical assessment of low-frequency current distributions from UMTS and GSM mobile phones

    International Nuclear Information System (INIS)

    Gosselin, Marie-Christine; Kühn, Sven; Kuster, Niels

    2013-01-01

    The evaluation of the exposure from mobile communication devices requires consideration of electromagnetic fields (EMFs) over a broad frequency range from dc to GHz. Mobile phones in operation have prominent spectral components in the low-frequency (LF) and radio-frequency (RF) ranges. While the exposure to RF fields from mobile phones has been comprehensively assessed in the past, the LF fields have received much less attention. In this study, LF fields from mobile phones are assessed experimentally and numerically for the global system for mobile (GSM) and universal mobile telecommunications system (UMTS) communication systems and conclusions about the global (LF and RF) EMF exposure from both systems are drawn. From the measurements of the time-domain magnetic fields, it was found that the contribution from the audio signal at a normal speech level, i.e., −16 dBm0, is the same order of magnitude as the fields induced by the current bursts generated from the implementation of the GSM communication system at maximum RF output level. The B-field induced by currents in phones using the UMTS is two orders of magnitude lower than that induced by GSM. Knowing that the RF exposure from the UMTS is also two orders of magnitude lower than from GSM, it is now possible to state that there is an overall reduction of the exposure from this communication system. (paper)

  8. Experimental and numerical assessment of low-frequency current distributions from UMTS and GSM mobile phones

    Science.gov (United States)

    Gosselin, Marie-Christine; Kühn, Sven; Kuster, Niels

    2013-12-01

    The evaluation of the exposure from mobile communication devices requires consideration of electromagnetic fields (EMFs) over a broad frequency range from dc to GHz. Mobile phones in operation have prominent spectral components in the low-frequency (LF) and radio-frequency (RF) ranges. While the exposure to RF fields from mobile phones has been comprehensively assessed in the past, the LF fields have received much less attention. In this study, LF fields from mobile phones are assessed experimentally and numerically for the global system for mobile (GSM) and universal mobile telecommunications system (UMTS) communication systems and conclusions about the global (LF and RF) EMF exposure from both systems are drawn. From the measurements of the time-domain magnetic fields, it was found that the contribution from the audio signal at a normal speech level, i.e., -16 dBm0, is the same order of magnitude as the fields induced by the current bursts generated from the implementation of the GSM communication system at maximum RF output level. The B-field induced by currents in phones using the UMTS is two orders of magnitude lower than that induced by GSM. Knowing that the RF exposure from the UMTS is also two orders of magnitude lower than from GSM, it is now possible to state that there is an overall reduction of the exposure from this communication system.

  9. The Impact Crater Size-Frequency Distribution on Pluto Follows a Truncated Pareto Distribution: Results from a First Data Set Based on the Recent New Horizons' Flyby

    Directory of Open Access Journals (Sweden)

    Zaninetti L.

    2016-01-01

    Full Text Available Recently it could be shown (Scholkmann, Prog. in Phys. , 2016, v. 12(1, 26-29 that the impact crater size-frequency distribution of Pluto (based on an analysis of first images obtained by the recent New Horizons’ flyby follows a power law (α =2.4926±0.3309 in the interval of diameter ( D values ranging from 3.75±1.14 km to the largest deter- mined value of 37.77 km. A reanalysis of this data set revealed that the whole crater SFD (i.e., with values in the interval of 1.2–37.7 km can be described by a truncated Pareto distribution.

  10. Voltage and frequency control in the Islanded portion of the CIGRE Low Voltage distribution network

    DEFF Research Database (Denmark)

    Mustafa, Ghullam; Bak, Claus Leth; Buriro, Ehsan Ali

    2017-01-01

    Islanding is a condition where a portion of the power network comprising of the loads and Distributed Generation units is isolated from the rest of the power grid and forms a Micro Grid. In this condition, it becomes essential for the islanded MG to operate in a stable and controlled manner by pr...

  11. 17 CFR 270.19b-1 - Frequency of distribution of capital gains.

    Science.gov (United States)

    2010-04-01

    ... trust may distribute capital gain dividends received from a “regulated investment company” within a reasonable time after receipt. (c) The provisions of this rule shall not apply to a unit investment trust (hereinafter referred to as the “Trust”) engaged exclusively in the business of investing in eligible trust...

  12. Frequency distribution of virulence factors in uropathogenic Escherichia coli isolated from Kermanshah in 2011-2012.

    Science.gov (United States)

    Mohajeri, Parviz; Khademi, Hosna; Ebrahimi, Roya; Farahani, Abbas; Rezaei, Mansour

    2014-07-01

    Uropathogenic Escherichia coli (UPEC) can cause urinary tract infection (UTI). To prevent urine flow lavage, UPEC has acquired several virulence factors called adhesins. These adhesins are expressed and controlled by different genes. This study was aimed to determine some of the most important genes that control virulence factors of UPEC (pyelonephritis associated pili [pap], S fimbrial adhesion [sfa] and A fimbrial adhesion [afa] genes), which code for adhesins and phenotypic factors. In total, 205 UPEC isolates from in- and out-patients with UTI were obtained. Polymerase chain reaction was used for gene amplification. One drop of bacterial suspension, one of red blood cells and one of peripheral blood smear were mixed for hemagglutination (HA). Formation of a clump was considered to be positive. Bacteria were grown on blood agar to determine hemolysis. Surface hydrophobicity was determined using the SAT test. Frequencies of pap, afa and sfa were 42 (20.5%), 17 (8.3%) and 44 (21.5%), respectively. Frequencies of HA, hemolysis and hydrophobicity were 138 (67.3%), 56 (27.3%) and 39 (19%), respectively. Among HA-positive bacteria, 103 (74.6%) were mannose resistant. Our results highlight higher frequency of HA than that of other virulence factors, indicating a crucial role of this virulence factor in UPEC. We concluded that major differences exist in the prevalence of virulence factors among different UPEC isolated from different countries. The association observed between pathogenicity and virulence factors may promote UPEC survival and growth within the urinary tract. Detecting these genes as the primary controllers of UPEC virulence factors may aid in better management of related infections.

  13. Association of HLA-DQA1 and DQB1 alleles with alolpecia areata in Chinese Hans.

    Science.gov (United States)

    Xiao, Feng-Li; Zhou, Fu-Sheng; Liu, Jiang-Bo; Yan, Kai-Lin; Cui, Yong; Gao, Min; Liang, Yan-Hua; Sun, Liang-Dan; Zhou, Shun-Ming; Zhu, Ya-Gang; Zhang, Xue-Jun; Yang, Sen

    2005-11-01

    Accumulative evidences have shown that certain HLA loci are associated with alopecia areata (AA), but with existing differences in ethnic distribution. No report has ever been published about this in Chinese Hans. To investigate whether HLA-DQA1 and DQB1 alleles are associated with AA, and the correlation of the HLA profile with age of onset, severity, duration of current attack, recurrence and family history of AA in Chinese Hans. The polymerase chain reaction-sequence-specific primer (PCR-SSP) method was used to analyze the distribution of HLA-DQA1 and DQB1 alleles in 192 patients with AA and 273 healthy controls in Chinese Hans. The significant increased frequencies of HLA-DQA1*0104 (OR=3.38, P(c)HLA-DQA1*0606 (OR=3.73, P(c)HLA-DQA1*0104 (OR=5.31, P(c)HLA-DQA1 and DQB1 alleles and haplotypes with AA. There may be differences in genetic background in patients with different duration.

  14. HLA-DRB1 alleles in four Amerindian populations from Argentina and Paraguay

    Science.gov (United States)

    2009-01-01

    The major histocompatibility complex (MHC) is one of the biological systems of major polymorphisms. The study of HLA class II variability has allowed the identification of several alleles that are characteristic to Amerindian populations, and it is an excellent tool to define the relations and biological affinities among them. In this work, we analyzed the allelic distribution of the HLA-DRB1 class II locus in four Amerindian populations: Mapuche (n = 34) and Tehuelche (n = 23) from the Patagonian region of Argentina, and Wichi SV (n = 24) and Lengua (n = 17) from the Argentinean and Paraguayan Chaco regions, respectively. In all of these groups, relatively high frequencies of Amerindian HLA-DRB1 alleles were observed (DRB1*0403, DRB1*0407, DRB1*0411, DRB1*0417, DRB1*0802, DRB1*0901, DRB1*1402, DRB1*1406 and DRB1*1602). However, we also detected the presence of non-Amerindian variants in Mapuche (35%) and Tehuelche (22%). We compared our data with those obtained in six indigenous groups of the Argentinean Chaco region and in a sample from Buenos Aires City. The genetic distance dendrogram showed a clear-cut division between the Patagonian and Chaco populations, which formed two different clusters. In spite of their linguistic differences, it can be inferred that the biological affinities observed are in concordance with the geographic distributions and interethnic relations established among the groups studied. PMID:21637670

  15. The neurotopography of written word production: an fMRI investigation of the distribution of sensitivity to length and frequency.

    Science.gov (United States)

    Rapp, Brenda; Dufor, Olivier

    2011-12-01

    This research is directed at charting the neurotopography of the component processes of the spelling system by using fMRI to identify the neural substrates that are sensitive to the factors of lexical frequency and word length. In spelling, word frequency effects index orthographic long-term memory whereas length effects, as measured by the number of letters, index orthographic working memory (grapheme buffering). Using the task of spelling to dictation in the scanner, we found a highly differentiated neural distribution of sensitivity to the factors of length and lexical frequency, with areas exhibiting sensitivity to length but not frequency and vice versa. In addition, a direct comparison with the results of a previous study [Rapp, B., & Lipka, K. The literate brain: The relationship between spelling and reading. Journal of Cognitive Neuroscience, 23, 1180-1197, 2011] that used a very different spelling task yielded a converging pattern of findings regarding the neural substrates of the central components of spelling. Also, with regard to relationship between reading and spelling, we replicated previous functional neuroimaging studies that have shown overlapping regions of activation in the left posterior inferior frontal gyrus and midfusiform gyrus for word reading and spelling.

  16. Allele coding in genomic evaluation

    DEFF Research Database (Denmark)

    Standen, Ismo; Christensen, Ole Fredslund

    2011-01-01

    Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker...... effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous...... this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. \\paragraph*{Results:} Theoretical derivations showed that parameter...

  17. Experimental measurement of the electron energy distribution function in the radio frequency electron cyclotron resonance inductive discharge

    International Nuclear Information System (INIS)

    Chung, ChinWook; Kim, S.S.; Chang, H.Y.

    2004-01-01

    Recently, the existence of electron cyclotron resonance (ECR) in a weakly magnetized inductively coupled plasma (MICP) has been evidenced [ChinWook Chung et al., Phys. Rev. Lett. 80, 095002 (2002)]. The distinctive feature of the ECR effect in the MICP is efficacious heating of low-energy electrons. In the present paper, electron heating characteristics in the MICP have been investigated by observing electron energy distribution function dependencies on various external parameters such as gas pressure, driving frequency, and rf power (electron density). It is found that the ECR effect on electron heating becomes enhanced with decreasing pressure or increasing driving frequency. The ECR heating becomes weak at high rf power due to the electron-electron collisions

  18. Investigation of the interpolation method to improve the distributed strain measurement accuracy in optical frequency domain reflectometry systems.

    Science.gov (United States)

    Cui, Jiwen; Zhao, Shiyuan; Yang, Di; Ding, Zhenyang

    2018-02-20

    We use a spectrum interpolation technique to improve the distributed strain measurement accuracy in a Rayleigh-scatter-based optical frequency domain reflectometry sensing system. We demonstrate that strain accuracy is not limited by the "uncertainty principle" that exists in the time-frequency analysis. Different interpolation methods are investigated and used to improve the accuracy of peak position of the cross-correlation and, therefore, improve the accuracy of the strain. Interpolation implemented by padding zeros on one side of the windowed data in the spatial domain, before the inverse fast Fourier transform, is found to have the best accuracy. Using this method, the strain accuracy and resolution are both improved without decreasing the spatial resolution. The strain of 3 μϵ within the spatial resolution of 1 cm at the position of 21.4 m is distinguished, and the measurement uncertainty is 3.3 μϵ.

  19. Self-induced frequency scanning and distributed Bragg reflection in semiconductor lasers with phase-conjugate feedback

    Energy Technology Data Exchange (ETDEWEB)

    Cronin-Golomb; Yariv

    1986-07-01

    A GaA1As semiconductor laser with feedback from a barium titanate photorefractive ring passive phase-conjugate mirror can be made to perform repeating or nonrepeating frequency scans over a 10-nm range toward either the blue or the red. The direction of scanning and whether the scans repeat may be controlled by adjusting the overlap of the interaction beams in the crystal. This overlap region may be adjusted so that the diode frequency spectrum, originally occupying about 10 longitudinal modes, scans and narrows as the conjugate signal builds up, coming to rest often in one, but sometimes two or three, longitudinal modes as a result of self-generated distributed-feedback effects. Also reported similar effects caused by feedback from the total-internal-reflection passive phase-conjugate mirror. The alignment-control mechanism of the ring mirror is, however, not available in this case.

  20. Self-induced frequency scanning and distributed Bragg reflection in semiconductor lasers with phase-conjugate feedback

    Energy Technology Data Exchange (ETDEWEB)

    Cronin-Golomb, M.; Yariv, A.

    1986-07-01

    A GaAlAs semiconductor laser with feedback from a barium titanate photorefractive ring passive phase-conjugate mirror can be made to perform repeating or nonrepeating frequency scans over a 10-nm range toward either the blue or the red. The direction of scanning and whether the scans repeat may be controlled by adjusting the overlap of the interaction beams in the crystal. This overlap region may be adjusted so that the diode frequency spectrum, originally occupying about 10 longitudinal modes, scans and narrows as the conjugate signal builds up, coming to rest often in one, but sometimes two or three, longitudinal modes as a result of self-generated distributed-feedback effects. We also report similar effects caused by feedback from the total-internal-reflection passive phase-conjugate mirror. The alignment-control mechanism of the ring mirror is, however, not available in this case.

  1. Self-induced frequency scanning and distributed bragg reflection in semiconductor lasers with phase-conjugate feedback

    Science.gov (United States)

    Cronin-Golomb, Mark; Yariv, Amnon

    1986-07-01

    A GaAlAs semiconductor laser with feedback from a barium titanate photorefractive ring passive phase-conjugate mirror can be made to perform repeating or nonrepeating frequency scans over a 10-nm range toward either the blue or the red. The direction of scanning and whether the scans repeat may be controlled by adjusting the overlap of the interaction beams in the crystal. This overlap region may be adjusted so that the diode frequency spectrum, originally occupying about 10 longitudinal modes, scans and narrows as the conjugate signal builds up, coming to rest often in one, but sometimes two or three, longitudinal modes as a result of self-generated distributed-feedback effects. We also report similar effects caused by feedback from the total-internal-reflection passive phase-conjugate mirror. The alignment-control mechanism of the ring mirror is, however, not available in this case.

  2. I-BIEM calculations of the frequency dispersion and AC current distribution at disk and ring-disk electrodes

    Science.gov (United States)

    Cahan, Boris D.

    1991-01-01

    The Iterative Boundary Integral Equation Method (I-BIEM) has been applied to the problem of frequency dispersion at a disk electrode in a finite geometry. The I-BIEM permits the direct evaluation of the AC potential (a complex variable) using complex boundary conditions. The point spacing was made highly nonuniform, to give extremely high resolution in those regions where the variables change most rapidly, i.e., in the vicinity of the edge of the disk. Results are analyzed with respect to IR correction, equipotential surfaces, and reference electrode placement. The current distribution is also examined for a ring-disk configuration, with the ring and the disk at the same AC potential. It is shown that the apparent impedance of the disk is inductive at higher frequencies. The results are compared to analytic calculations from the literature, and usually agree to better than 0.001 percent.

  3. Rabi-Bloch oscillations in spatially distributed systems: Temporal dynamics and frequency spectra

    Science.gov (United States)

    Levie, Ilay; Kastner, Raphael; Slepyan, Gregory

    2017-10-01

    We consider one-dimensional chains of two-level quantum systems coupled via tunneling. The chain is driven by the superposition of dc and ac fields in the strong coupling regime. Based on the fundamental principles of electrodynamics and quantum theory, we have developed a generalized model of quantum dynamics for such interactions, free of rotating-wave approximation. The system of equations of motion was studied numerically. We analyzed the dynamics and spectra of the inversion density, dipole current density, and tunneling current density. In the case of resonant interaction with the ac component, the particle dynamics exhibits itself in the oscillatory regime, which may be interpreted as a combination of Rabi and Bloch oscillations with their strong mutual influence. Such scenario for an obliquely incident ac field dramatically differs from the individual picture of both types of oscillations due to the interactions. This effect is counterintuitive because of the existence of markedly different frequency ranges for such two types of oscillations. These dynamics manifest themselves in multiline spectra in different combinations of Rabi and Bloch frequencies. The effect is promising as a framework of a new type of spectroscopy in nanoelectronics and electrical control of nanodevices.

  4. Winds from Luminous Late-Type Stars: II. Broadband Frequency Distribution of Alfven Waves

    Science.gov (United States)

    Airapetian, V.; Carpenter, K. G.; Ofman, L.

    2010-01-01

    We present the numerical simulations of winds from evolved giant stars using a fully non-linear, time dependent 2.5-dimensional magnetohydrodynamic (MHD) code. This study extends our previous fully non-linear MHD wind simulations to include a broadband frequency spectrum of Alfven waves that drive winds from red giant stars. We calculated four Alfven wind models that cover the whole range of Alfven wave frequency spectrum to characterize the role of freely propagated and reflected Alfven waves in the gravitationally stratified atmosphere of a late-type giant star. Our simulations demonstrate that, unlike linear Alfven wave-driven wind models, a stellar wind model based on plasma acceleration due to broadband non-linear Alfven waves, can consistently reproduce the wide range of observed radial velocity profiles of the winds, their terminal velocities and the observed mass loss rates. Comparison of the calculated mass loss rates with the empirically determined mass loss rate for alpha Tau suggests an anisotropic and time-dependent nature of stellar winds from evolved giants.

  5. Reconsidering the smart metering data collection frequency for distribution state estimation

    OpenAIRE

    Chen, Qipeng; Kaleshi, Dritan; Armour, Simon; Fan, Zhong

    2015-01-01

    The current UK Smart Metering Technical Specification requires smart meter readings to be collected once a day, primarily to support accurate billing without violating users' privacy. In this paper we consider the use of Smart Metering data for Distribution State Estimation (DSE), and compare the effectiveness of daily data collection strategy with a more frequent, half-hourly SM data collection strategy. We first assess the suitability of using the data for load forecasting at Low Voltage (L...

  6. Category effects on stimulus estimation: Shifting and skewed frequency distributions-A reexamination.

    Science.gov (United States)

    Duffy, Sean; Smith, John

    2017-10-18

    Duffy, Huttenlocher, Hedges, and Crawford (Psychonomic Bulletin & Review, 17(2), 224-230, 2010) report on experiments where participants estimate the lengths of lines. These studies were designed to test the category adjustment model (CAM), a Bayesian model of judgments. The authors report that their analysis provides evidence consistent with CAM: that there is a bias toward the running mean and not recent stimuli. We reexamine their data. First, we attempt to replicate their analysis, and we obtain different results. Second, we conduct a different statistical analysis. We find significant recency effects, and we identify several specifications where the running mean is not significantly related to judgment. Third, we conduct tests of auxiliary predictions of CAM. We do not find evidence that the bias toward the mean increases with exposure to the distribution. We also do not find that responses longer than the maximum of the distribution or shorter than the minimum become less likely with greater exposure to the distribution. Fourth, we produce a simulated dataset that is consistent with key features of CAM, and our methods correctly identify it as consistent with CAM. We conclude that the Duffy et al. (2010) dataset is not consistent with CAM. We also discuss how conventions in psychology do not sufficiently reduce the likelihood of these mistakes in future research. We hope that the methods that we employ will be used to evaluate other datasets.

  7. Frequency of legionella contamination in conditional & water distribution systems of Tehran hospitals

    Directory of Open Access Journals (Sweden)

    Davod Esmaieli

    2008-09-01

    Full Text Available Background: Legionella species are ubiquitous in natural aquatic environments, capable of existing in waters with varied temperatures, PH levels, and nutrient and oxygen contents. Of 49 known legionella species, 20 species have been linked to pneumonia in humans. Contamination by legionella has occurred in the distribution systems of many hospitals. Aerosol-generating systems such as faucets, showerheads, cooling towers, and nebulizers are responsible for their transmission from water to air. Methods: A total of 113 water samples were gathered from different wards of 32 hospitals in different geographical regions of Tehran city. These samples were concentrated by filtration, treated with the acid and temperature buffers, and isolated on a BCYE agar culture medium. Results: A total of 22 hospitals out of 33 (26.5% were contaminated by legionella species, and 30 samples (26.5% out of 113 were positive. Chlorine concentration and pH level of the water samples were 0.18-2.2 mg/l and 6.6-7.6, respectively. Conclusion: The high rate of waste water contamination in Tehran hospitals with Legionella indicates the resistance of this microorganism to chlorine and other disinfectants, or inadequate disinfection process, representing the insufficiency of the current decontamination of hospital water distribution system. Thus identifying legionella species and their controlling in water distribution system of hospitals is of great importance.

  8. Magnitude-frequency characteristics and preparatory factors for spatial debris-slide distribution in the northern Faroe Islands

    Science.gov (United States)

    Dahl, Mads-Peter J.; Mortensen, Lis E.; Jensen, Niels H.; Veihe, Anita

    2013-04-01

    The Faroe Islands in the North Atlantic Ocean are highly susceptible to debris-avalanches and debris-flows originating from debris-slide activity in shallow colluvial soils. To provide data for hazard and risk assessment of debris-avalanches and debris-flows, this study aims at quantifying the magnitude and frequency of their debris-slide origins as well as identifying which preparatory factors are responsible for the spatial debris-slide distribution in the landscape. For that purpose a debris-slide inventory was generated from aerial photo interpretation (API), fieldwork and anecdotal sources, covering a 159 km2 study area in the northern Faroe Islands. A magnitude-cumulative frequency (MCF) curve was derived to predict magnitude dependant debris-slide frequencies, while preparatory factors responsible for spatial debris-slide distribution were quantified through GIS-supported discriminant function analysis (DFA). Nine factors containing geological (lithology, dip), geomorphological (slope angle, altitude, aspect, plan and profile curvature) and land use (infield/outfield, sheep density) information were included in the multivariate analysis. Debris-slides larger than 100 m2 with magnitude expressed as topographic scar area can be predicted from the power-law function: Y = 936.26X- 1.277, r2 = 0.98 while a physical explanation is preferred for the roll-over pattern of smaller slope failures. The DFA is able to correctly classify app. 70% of the modeled terrain units into their pre-determined stable/unstable groups. Preparatory factors responsible for the spatial debris-slide distribution are aspect, slope angle, sheep density, plan curvature and altitude, while influence of the remaining factors is negligible.

  9. Observation and simulation of space-charge effects in a radio-frequency photoinjector using a transverse multibeamlet distribution

    Directory of Open Access Journals (Sweden)

    M. Rihaoui

    2009-12-01

    Full Text Available We report on an experimental study of space-charge effects in a radio-frequency (rf photoinjector. A 5 MeV electron bunch, consisting of a number of beamlets separated transversely, was generated in an rf photocathode gun and propagated in the succeeding drift space. The collective interaction of these beamlets was studied for different experimental conditions. The experiment allowed the exploration of space-charge effects and its comparison with 3D particle-in-cell simulations. Our observations also suggest the possible use of a multibeam configuration to tailor the transverse distribution of an electron beam.

  10. Magnitude-frequency characteristics and preparatory factors for spatial debris-slide distribution in the northern Faroe Islands

    DEFF Research Database (Denmark)

    Dahl, Mads-Peter Jakob; Jensen, Niels H.; Veihe, Anita

    2013-01-01

    the magnitude and frequency of their debris-slide origins as well as identifying which preparatory factors are responsible for the spatial debris-slide distribution in the landscape. For that purpose a debris-slide inventory was generated from aerial photo interpretation (API), fieldwork and anecdotal sources...... function analysis (DFA). Nine factors containing geological (lithology, dip), geomorphological (slope angle, altitude, aspect; plan and profile curvature) and land use (infield/outfield, sheep density) information were included in the multivariate analysis. Debris-slides larger than 100 m(2) with magnitude...

  11. Performance testing of a high frequency link converter for Space Station power distribution system

    Science.gov (United States)

    Sul, S. K.; Alan, I.; Lipo, T. A.

    1989-01-01

    The testing of a brassboard version of a 20-kHz high-frequency ac voltage link prototype converter dynamics for Space Station application is presented. The converter is based on a three-phase six-pulse bridge concept. The testing includes details of the operation of the converter when it is driving an induction machine source/load. By adapting a field orientation controller (FOC) to the converter, four-quadrant operation of the induction machine from the converter has been achieved. Circuit modifications carried out to improve the performance of the converter are described. The performance of two 400-Hz induction machines powered by the converter with simple V/f regulation mode is reported. The testing and performance results for the converter utilizing the FOC, which provides the capability for rapid torque changes, speed reversal, and four-quadrant operation, are reported.

  12. An explicit transition density expansion for a multi-allelic Wright-Fisher diffusion with general diploid selection.

    Science.gov (United States)

    Steinrücken, Matthias; Wang, Y X Rachel; Song, Yun S

    2013-02-01

    Characterizing time-evolution of allele frequencies in a population is a fundamental problem in population genetics. In the Wright-Fisher diffusion, such dynamics is captured by the transition density function, which satisfies well-known partial differential equations. For a multi-allelic model with general diploid selection, various theoretical results exist on representations of the transition density, but finding an explicit formula has remained a difficult problem. In this paper, a technique recently developed for a diallelic model is extended to find an explicit transition density for an arbitrary number of alleles, under a general diploid selection model with recurrent parent-independent mutation. Specifically, the method finds the eigenvalues and eigenfunctions of the generator associated with the multi-allelic diffusion, thus yielding an accurate spectral representation of the transition density. Furthermore, this approach allows for efficient, accurate computation of various other quantities of interest, including the normalizing constant of the stationary distribution and the rate of convergence to this distribution. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Using radio frequency and ultrasonic antennas for inspecting pin-type insulators on medium-voltage overhead distribution lines

    Directory of Open Access Journals (Sweden)

    Cícero Lefort Borges

    2013-05-01

    Full Text Available This paper summarises the activities undertaken when using antennas (ultrasound and radiofrequency for identifying insulators in pre-failure state by detecting the noise emitted by the distribution line and correlating this with these insulators (porcelain pin type dielectric breakdown. This has led to developing low-cost maintenance procedures and providing support and criteria for engineer-ing decisions regarding replacing these insulators. The technique used two detectors; a radio frequency detector was used in a first investigation of a particular distribution line, set to 40 MHz and installed on the roof of a moving vehicle. The ultrasound detector was used for inspecting (phases A, B, C each structure (pole selected. Atmospheric conditions had no influence on defining pre-failure insulators (pin type based on the noise detection technique. Pin type insulators emitting noise should be replaced since measurement was made from the ground and near the base of the post.

  14. Frequency distribution of zinc in leaves with and without zinc-deficiency symptoms, all collected from a single orange tree

    Energy Technology Data Exchange (ETDEWEB)

    Wallace, A. (Univ. of Caifornia, Los Angeles); Alexander, G.V.; Kinnear, J.; Procopiou, J.; Haritou-Andriotaki, A.; Papanicolaou, X.

    1982-07-01

    Leaves with zinc-deficiency symptoms had a lower Zn concentration than corresponding leaves without symptoms and of the same age from the same orange (Citrus senensis L.) tree on sour orange (C. aurantium L.) rootstock grown in Rhodes, Greece. There was considerable overlap, however, with the frequency distribution of each group approximating a normal curve. But both kinds of leaves combined showed a more normal distribution. Some leaves with symptoms had higher zinc concentrations than some without symptoms. There was a threefold range in Zn concentration for each group of leaves. Zinc-deficient leaves had less phosphorus, calcium, and manganese and more iron, aluminum, silicon, and titanium (the so-called dust elements) than did leaves with no deficiency symptoms. Some of these elements gave normal curves for both Zn-deficient and non-Zn-deficient leaves.

  15. Use of critical pathway models and log-normal frequency distributions for siting nuclear facilities

    International Nuclear Information System (INIS)

    Waite, D.A.; Denham, D.H.

    1975-01-01

    The advantages and disadvantages of potential sites for nuclear facilities are evaluated through the use of environmental pathway and log-normal distribution analysis. Environmental considerations of nuclear facility siting are necessarily geared to the identification of media believed to be sifnificant in terms of dose to man or to be potential centres for long-term accumulation of contaminants. To aid in meeting the scope and purpose of this identification, an exposure pathway diagram must be developed. This type of diagram helps to locate pertinent environmental media, points of expected long-term contaminant accumulation, and points of population/contaminant interface for both radioactive and non-radioactive contaminants. Confirmation of facility siting conclusions drawn from pathway considerations must usually be derived from an investigatory environmental surveillance programme. Battelle's experience with environmental surveillance data interpretation using log-normal techniques indicates that this distribution has much to offer in the planning, execution and analysis phases of such a programme. How these basic principles apply to the actual siting of a nuclear facility is demonstrated for a centrifuge-type uranium enrichment facility as an example. A model facility is examined to the extent of available data in terms of potential contaminants and facility general environmental needs. A critical exposure pathway diagram is developed to the point of prescribing the characteristics of an optimum site for such a facility. Possible necessary deviations from climatic constraints are reviewed and reconciled with conclusions drawn from the exposure pathway analysis. Details of log-normal distribution analysis techniques are presented, with examples of environmental surveillance data to illustrate data manipulation techniques and interpretation procedures as they affect the investigatory environmental surveillance programme. Appropriate consideration is given these

  16. Palomar-Leiden minor planets - Proper elements, frequency distributions, belt boundaries, and family memberships

    Science.gov (United States)

    Williams, J. G.; Hierath, J. E.

    1987-01-01

    Tabulations are presented for the proper elements of 1227 higher accuracy orbits of faint minor planets encompassing earth and deep Mars crossers, Trojans, and Hildas. The distribution of the closest approach distance to Mars drops off sharply near zero, while that for Jupiter vanishes near 1.1 AU; it is suggested that Mars and Jupiter have caused these boundaries, so that the asteroid belt must have been larger early in the solar system's history. Some 3.5 percent of the sample, primarily shallow crossers, can impact Mars; the fortuitous alignments required for impact occur with near-simultaneity for these objects, so that they will episodically bombard Mars.

  17. No effects of power line frequency extremely low frequency electromagnetic field exposure on selected neurobehavior tests of workers inspecting transformers and distribution line stations versus controls.

    Science.gov (United States)

    Li, Li; Xiong, De-fu; Liu, Jia-wen; Li, Zi-xin; Zeng, Guang-cheng; Li, Hua-liang

    2014-03-01

    We aimed to evaluate the interference of 50 Hz extremely low frequency electromagnetic field (ELF-EMF) occupational exposure on the neurobehavior tests of workers performing tour-inspection close to transformers and distribution power lines. Occupational short-term "spot" measurements were carried out. 310 inspection workers and 300 logistics staff were selected as exposure and control. The neurobehavior tests were performed through computer-based neurobehavior evaluation system, including mental arithmetic, curve coincide, simple visual reaction time, visual retention, auditory digit span and pursuit aiming. In 500 kV areas electric field intensity at 71.98% of total measured 590 spots were above 5 kV/m (national occupational standard), while in 220 kV areas electric field intensity at 15.69% of total 701 spots were above 5 kV/m. Magnetic field flux density at all the spots was below 1,000 μT (ICNIRP occupational standard). The neurobehavior score changes showed no statistical significance. Results of neurobehavior tests among different age, seniority groups showed no significant changes. Neurobehavior changes caused by daily repeated ELF-EMF exposure were not observed in the current study.

  18. In-plane modal frequencies and mode shapes of two stay cables interconnected by uniformly distributed cross-ties

    Science.gov (United States)

    Jing, Haiquan; He, Xuhui; Zou, Yunfeng; Wang, Hanfeng

    2018-03-01

    Stay cables are important load-bearing structural elements of cable-stayed bridges. Suppressing the large vibrations of the stay cables under the external excitations is of worldwide concern for the bridge engineers and researchers. Over the past decade, the use of crosstie has become one of the most practical and effective methods. Extensive research has led to a better understanding of the mechanics of cable networks, and the effects of different parameters, such as length ratio, mass-tension ratio, and segment ratio on the effectiveness of the crosstie have been investigated. In this study, uniformly distributed elastic crossties serve to replace the traditional single, or several cross-ties, aiming to delay "mode localization." A numerical method is developed by replacing the uniformly distributed, discrete elastic cross-tie model with an equivalent, continuously distributed, elastic cross-tie model in order to calculate the modal frequencies and mode shapes of the cable-crosstie system. The effectiveness of the proposed method is verified by comparing the elicited results with those obtained using the previous method. The uniformly distributed elastic cross-ties are shown to significantly delay "mode localization."

  19. High rhesus (Rh(D)) negative frequency and ethnic-group based ABO blood group distribution in Ethiopia.

    Science.gov (United States)

    Golassa, Lemu; Tsegaye, Arega; Erko, Berhanu; Mamo, Hassen

    2017-07-26

    Knowledge of the distribution of ABO-Rh(D) blood groups in a locality is vital for safe blood services. However, the distribution of these blood systems among Ethiopians in general is little explored. This study was, therefore, designed to determine the ABO-Rh(D) blood group distribution among patients attending Gambella hospital, southwestern Ethiopia. A cross-sectional study was conducted between November and December 2013 (N = 449). The patients were grouped into two broad categories. Those who originally moved from different parts of Ethiopia and currently residing in Gambella are named 'highlanders' (n = 211). The other group consisted of natives (Nilotics) to the locality (n = 238). ABO-Rh(D) blood groups were typed by agglutination, open-slide test method, using commercial antisera (Biotech laboratories Ltd, Ipswich, Suffolk, UK). Overall, majority of the participants (41.20%) had blood type 'O' followed by types 'A' (34.96%), 'B' (20.48%) and 'AB' (3.34%). However, blood type 'A' was the most frequent (44.07%) blood group among the 'highlanders' and 50.42% of Nilotic natives had type 'O'. The proportion of participants devoid of the Rh factor was 19.37%. While the ABO blood group distribution is similar to previous reports, the Rh(D) frequency is much higher than what was reported so far for Ethiopia and continental Africa.

  20. Assessment of landslide distribution map reliability in Niigata prefecture - Japan using frequency ratio approach

    Science.gov (United States)

    Rahardianto, Trias; Saputra, Aditya; Gomez, Christopher

    2017-07-01

    Research on landslide susceptibility has evolved rapidly over the few last decades thanks to the availability of large databases. Landslide research used to be focused on discreet events but the usage of large inventory dataset has become a central pillar of landslide susceptibility, hazard, and risk assessment. Indeed, extracting meaningful information from the large database is now at the forth of geoscientific research, following the big-data research trend. Indeed, the more comprehensive information of the past landslide available in a particular area is, the better the produced map will be, in order to support the effective decision making, planning, and engineering practice. The landslide inventory data which is freely accessible online gives an opportunity for many researchers and decision makers to prevent casualties and economic loss caused by future landslides. This data is advantageous especially for areas with poor landslide historical data. Since the construction criteria of landslide inventory map and its quality evaluation remain poorly defined, the assessment of open source landslide inventory map reliability is required. The present contribution aims to assess the reliability of open-source landslide inventory data based on the particular topographical setting of the observed area in Niigata prefecture, Japan. Geographic Information System (GIS) platform and statistical approach are applied to analyze the data. Frequency ratio method is utilized to model and assess the landslide map. The outcomes of the generated model showed unsatisfactory results with AUC value of 0.603 indicate the low prediction accuracy and unreliability of the model.

  1. Low Frequency Vibration Energy Harvester Using Spherical Permanent Magnet with Non-uniform Mass Distribution

    International Nuclear Information System (INIS)

    Choi, Y; Ju, S; Chae, S H; Jun, S; Park, S M; Lee, S; Ji, C-H; Lee, H W

    2013-01-01

    We present a non-resonant vibration energy harvesting device using springless spherical permanent magnet with non-uniform mass distribution as a proof mass. The magnet has its center-of-mass below the geometrical center, which generates a roly-poly-like motion in response to external vibrations. Two different types of magnet assemblies with different center-of-mass position have been fabricated and tested. Using the roly-poly-like magnets, proof-of-concept electromagnetic energy harvesters have been fabricated and tested. Moreover, effect of ferrofluid as a lubricant has been tested with the fabricated energy harvester. Maximum open-circuit voltage of 154.4mV and output power of 4.53μW have been obtained at 3g vibration at 12Hz with the fabricated device

  2. Global Frequency and Distribution of Lightning as Observed from Space by the Optical Transient Detector

    Science.gov (United States)

    Christian, Hugh J.; Blakeslee, Richard J.; Boccippio, Dennis J.; Boeck, William L.; Bucchler, Dennis E.; Driscoll, Kevin T.; Goodman, Steven J.; Hall, John M.; Koshak, William J.; Mach, Douglas M.; hide

    2002-01-01

    The Optical Transient Detector (OTD) is a space-based instrument specifically designed to detect and locate lightning discharges as it orbits the Earth. This instrument is a scientific payload on the MicroLab-1 satellite that was launched into a low-earth, 70 deg. inclination orbit in April 1995. Given the orbital trajectory of the satellite, most regions of the earth are observed by the OTD instrument more than 400 times during a one year period, and the average duration of each observation is 2 minutes. The OTD instrument optically detects lightning flashes that occur within its 1300x1300 sq km field-of-view during both day and night conditions. A statistical examination of OTD lightning data reveals that nearly 1.4 billion flashes occur annually over the entire earth. This annual flash count translates to an average of 44 +/- 5 lightning flashes (intracloud and cloud-to-ground combined) occurring around the globe every second, which is well below the traditional estimate of 100 flashes per second that was derived in 1925 from world thunder-day records. The range of uncertainty for the OTD global totals represents primarily the uncertainty (and variability) in the flash detection efficiency of the instrument. The OTD measurements have been used to construct lightning climatology maps that demonstrate the geographical and seasonal distribution of lightning activity for the globe. An analysis of this annual lightning distribution confirms that lightning occurs mainly over land areas, with an average land:ocean ratio of 10:1. A dominant Northern Hemisphere summer peak occurs in the annual cycle, and evidence is found for a tropically-driven semiannual cycle.

  3. Detecting low frequent loss-of-function alleles in genome wide association studies with red hair color as example

    NARCIS (Netherlands)

    F. Liu (Fan); M.V. Struchalin (Maksim); K. van Duijn (Kate); A. Hofman (Albert); A.G. Uitterlinden (André); Y.S. Aulchenko (Yurii); M.H. Kayser (Manfred)

    2011-01-01

    textabstractMultiple loss-of-function (LOF) alleles at the same gene may influence a phenotype not only in the homozygote state when alleles are considered individually, but also in the compound heterozygote (CH) state. Such LOF alleles typically have low frequencies and moderate to large effects.

  4. Frequency of the allelic variant (Trp8Arg/Ile15Thr) of the luteinizing hormone gene in a Brazilian cohort of healthy subjects and in patients with hypogonadotropic hypogonadism Freqüência da variante alélica (Trp8Arg/Ile15Thr) do gene do hormônio luteinizante em um grupo de brasileiros saudáveis e pacientes portadores de hipogonadismo hipogonadotrófico

    OpenAIRE

    Karina Berger; Ana Elisa Correia Billerbeck; Elaine Maria Frade Costa; Luciani Silveira Carvalho; Ivo Jorge Prado Arnhold; Berenice Bilharinho Mendonca

    2005-01-01

    PURPOSE: To evaluate the frequency of allelic variant Trp8Arg/Ile15Thr in the luteinizing hormone beta-subunit gene in a Brazilian population of healthy subjects and in patients with hypogonadotropic hypogonadism. SUBJECTS AND METHODS: Two hundred and two adults (115 women) with normal sexual function and 48 patients (24 women) with hypogonadotropic hypogonadism underwent a molecular study of the the luteinizing hormone beta-subunit gene using a polymerase chain reaction technique followed by...

  5. Age frequency distribution and revised stable isotope curves for New Zealand speleothems: palaeoclimatic implications

    Directory of Open Access Journals (Sweden)

    Williams Paul W.

    2010-07-01

    Full Text Available The occurrence of speleothems in New Zealand with reversed magnetism indicates that secondary calcite deposition in caves has occurred for more than 780 thousand years (ka. 394 uranium-series dates on 148 speleothems show that such deposition has taken place somewhere in the country with little interruption for more than 500 ka. A relative probability distribution of speleothem ages indicates that most growth occurred in mild, moist interglacial and interstadial intervals, a conclusion reinforced by comparing peaks and troughs in the distribution with time series curves of speleothem δ18O and δ13C values. The stable isotope time series were constructed using data from 15 speleothems from two different regions of the country. The greater the number of overlapping speleothem series (i.e. the greater the sample depth for any one region, the more confidence is justified in considering the stacked record to be representative of the region. Revising and extending earlier work, composite records are produced for central-west North Island (CWNI and north-west South Island (NWSI. Both demonstrate that over the last 15 ka the regions responded similarly to global climatic events, but that the North Island site was also influenced by the waxing and waning of regional subtropical marine influences that penetrated from the north but did not reach the higher latitudes of the South Island. Cooling marking the commencement of the last glacial maximum (LGM was evident from about 28 ka. There was a mid-LGM interstadial at 23-21.7 ka and Termination 1 occurred around 18.1 ka. The glacial-interglacial transition was marked by a series of negative excursions in δ18O that coincide with dated recessional moraines in South Island glaciers. A late glacial cooling event, the NZ Late Glacial Reversal, occurred from 13.4-11.2 ka and this was followed by an early Holocene optimum at 10.8 ka. Comparison of δ18O records from NWSI and EPICA DML ice-core shows climatic

  6. Frequency Distribution of Edentulous Posterior Mandibular Ridge Types using Cone Beam Computed Tomography in an Iranian Population

    Directory of Open Access Journals (Sweden)

    2016-07-01

    Full Text Available Introduction: The existing bone is regarded as an important criteria in dental implants. In this regard, the radiographic modality is of great significance in quantifying the remaining bone, and CBCT accurately represents height and width of the existing bone. Therefore, this study aimed to evaluate the frequency distribution of the edentulous posterior mandibular ridge types using cone beam computed tomography in an Iranian population. Methods: In this cross-sectional descriptive study, CBCT scans of 127 patients with full edentulous mandible with an average age of 61.15 were evaluated who referred to a radiology clinic in Tehran. The images were analyzed applying OnDemand3D application and bone height and width of each area were determined. To analyze the collected data, SPSS software (ver,17 was employed applying Fisher's exact test. Results: The ridges were classified in 4 different groups (A,B+,B-w,C-w. The frequency of ridge types A and B + in male and ridge types B-w and C-w in females were demonstrated to be higher. An increase in age led to a reduction in the frequency of type A and a rise in the frequency of type C-w. The mean bone height was higher in males in all areas. In addition, the mean bone width was higher in males in all areas except for the first molar area. Conclusions:  The study results indicated that as the age increases, the height of edentulous mandible reduces, while no significant relationship was detected between the bone width and aging. As a result, with aging the evolution of bone was held to be from type A to type C-W.

  7. Transient hepatic attenuation difference (THAD) in patients without neoplasm. Frequency, shape, distribution, and causes

    Energy Technology Data Exchange (ETDEWEB)

    Yamasaki, Michio; Furukawa, Akira; Murata, Kiyoshi; Morita, Rikushi [Shiga Univ. of Medical Science, Otsu (Japan)

    1999-03-01

    Transient hepatic attenuation difference (THAD) is a valuable finding in detecting hypervascular lesions. However, similar findings are also observed in patients even without known hepatic diseases. We elucidate the characteristic findings and the causes of THAD in patients without hepatic neoplasm in this article. Dual-phased contrast-enhanced CT studies performed in 450 patients were reviewed, and THAD was observed in 42 (9.3%). THAD was linear or wedge-shaped and was seen contiguous to the liver surface with a relatively obscure margin in 40 of the 42 cases. The most common cause of THAD was chronic cholecystitis followed by previous biliary surgery. THAD was also seen in 30 patients with no hepatic diseases in whom it had a tendency to locate around the gallbladder fossa or in the periphery of the liver particularly in the left lobe. The knowledge of the prevalence, shape, distribution and causes of THAD is essential for the evaluation of contrast-enhanced CT images obtained during the arterial phase. (author)

  8. Southern San Andreas Fault seismicity is consistent with the Gutenberg-Richter magnitude-frequency distribution

    Science.gov (United States)

    Page, Morgan T.; Felzer, Karen

    2015-01-01

    The magnitudes of any collection of earthquakes nucleating in a region are generally observed to follow the Gutenberg-Richter (G-R) distribution. On some major faults, however, paleoseismic rates are higher than a G-R extrapolation from the modern rate of small earthquakes would predict. This, along with other observations, led to formulation of the characteristic earthquake hypothesis, which holds that the rate of small to moderate earthquakes is permanently low on large faults relative to the large-earthquake rate (Wesnousky et al., 1983; Schwartz and Coppersmith, 1984). We examine the rate difference between recent small to moderate earthquakes on the southern San Andreas fault (SSAF) and the paleoseismic record, hypothesizing that the discrepancy can be explained as a rate change in time rather than a deviation from G-R statistics. We find that with reasonable assumptions, the rate changes necessary to bring the small and large earthquake rates into alignment agree with the size of rate changes seen in epidemic-type aftershock sequence (ETAS) modeling, where aftershock triggering of large earthquakes drives strong fluctuations in the seismicity rates for earthquakes of all magnitudes. The necessary rate changes are also comparable to rate changes observed for other faults worldwide. These results are consistent with paleoseismic observations of temporally clustered bursts of large earthquakes on the SSAF and the absence of M greater than or equal to 7 earthquakes on the SSAF since 1857.

  9. Inferring Protective CD8+ T-Cell Epitopes for NS5 Protein of Four Serotypes of Dengue Virus Chinese Isolates Based on HLA-A, -B and -C Allelic Distribution: Implications for Epitope-Based Universal Vaccine Design.

    Directory of Open Access Journals (Sweden)

    Jiandong Shi

    Full Text Available Dengue is one of the most globally serious vector-borne infectious diseases in tropical and subtropical areas for which there are currently no effective vaccines. The most highly conserved flavivirus protein, NS5, is an indispensable target of CD8+ T-cells, making it an ideal vaccine design target. Using the Immune Epitope Database (IEDB, CD8+ T-cell epitopes of the dengue virus (DENV NS5 protein were predicted by genotypic frequency of the HLA-A,-B, and-C alleles in Chinese population. Antigenicity scores of all predicted epitopes were analyzed using VaxiJen v2.0. The IEDB analysis revealed that 116 antigenic epitopes for HLA-A (21,-B (53, and-C (42 had high affinity for HLA molecules. Of them, 14 had 90.97-99.35% conversancy among the four serotypes. Moreover, five candidate epitopes, including 200NS5210 (94.84%, A*11:01, 515NS5525 (98.71%, A*24:02, 225NS5232 (99.35%, A*33:03, 516NS5523 (98.71%, A*33:03, and 284NS5291 (98.06%, A*33:03, were presented by HLA-A. Four candidate epitopes, including 234NS5241 (96.77%, B*13:01, 92NS599 (98.06%, B*15:01, B*15:02, and B*46:01, 262NS5269 (92.90%, B*38:02, and 538NS5547 (90.97%, B*51:01, were presented by HLA-B. Another 9 candidate epitopes, including 514NS5522 (98.71%, C*01:02, 514NS5524 (98.71%, C*01:02 and C*14:02, 92NS599 (98.06%, C*03:02 and C*15:02, 362NS5369 (44.84%, C*03:04 and C*08:01, 225NS5232 (99.35%, C*04:01, 234NS5241(96.77%, C*04:01, 361NS5369 (94.84%, C*04:01, 515NS5522 (98.71%, C*14:02, 515NS5524 (98.71%, C*14:02, were presented by HLA-C. Further data showed that the four-epitope combination of 92NS599 (B*15:01, B*15:02, B*46:01, C*03:02 and C*15:02, 200NS5210 (A*11:01, 362NS5369 (C*03:04, C*08:01, and 514NS5524 (C*01:02, C*14:02 could vaccinate >90% of individuals in China. Further in vivo study of our inferred novel epitopes will be needed for a T-cell epitope-based universal vaccine development that may prevent all four China-endemic DENV serotypes.

  10. Diversity, frequency, and geographic distribution of facultative bacterial endosymbionts in introduced aphid pests.

    Science.gov (United States)

    Sepúlveda, Daniela A; Zepeda-Paulo, Francisca; Ramírez, Claudio C; Lavandero, Blas; Figueroa, Christian C

    2017-06-01

    Facultative bacterial endosymbionts in insects have been under intense study during the last years. Endosymbionts can modify the insect's phenotype, conferring adaptive advantages under environmental stress. This seems particularly relevant for a group of worldwide agricultural aphid pests, because endosymbionts modify key fitness-related traits, including host plant use, protection against natural enemies and heat tolerance. Aimed to understand the role of facultative endosymbionts on the success of introduced aphid pests, the distribution and abundance of 5 facultative endosymbionts (Hamiltonella defensa, Regiella insecticola, Serratia symbiotica, Rickettsia and Spiroplasma) were studied and compared in 4 cereal aphids (Sitobion avenae, Diuraphis noxia, Metopolophium dirhodum and Schizaphis graminium) and in the pea aphid Acyrthosiphon pisum complex from 2 agroclimatic zones in Chile. Overall, infections with facultative endosymbionts exhibited a highly variable and characteristic pattern depending on the aphid species/host race and geographic zone, which could explain the success of aphid pest populations after their introduction. While S. symbiotica and H. defensa were the most frequent endosymbionts carried by the A. pisum pea-race and A. pisum alfalfa-race aphids, respectively, the most frequent facultative endosymbiont carried by all cereal aphids was R. insecticola. Interestingly, a highly variable composition of endosymbionts carried by S. avenae was also observed between agroclimatic zones, suggesting that endosymbionts are responding differentially to abiotic variables (temperature and precipitations). In addition, our findings constitute the first report of bacterial endosymbionts in cereal aphid species not screened before, and also the first report of aphid endosymbionts in Chile. © 2016 Institute of Zoology, Chinese Academy of Sciences.

  11. The microcephalin ancestral allele in a Neanderthal individual.

    Directory of Open Access Journals (Sweden)

    Martina Lari

    Full Text Available BACKGROUND: The high frequency (around 0.70 worldwide and the relatively young age (between 14,000 and 62,000 years of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1 locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the first PCR amplification and high-throughput sequencing of nuclear DNA at the microcephalin (MCPH1 locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy. We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. CONCLUSIONS/SIGNIFICANCE: The MCPH1 genotype of the Monti Lessini (MLS Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA.

  12. Use of Frequency Distribution Functions to Establish Safe Conditions in Relation to the Foodborne Pathogen Bacillus cereus

    Directory of Open Access Journals (Sweden)

    Begoña Delgado

    2005-01-01

    Full Text Available Minimal processing implementation greatly depends on a detailed knowledge of the effects of preservation factors and their combinations on the spoilage and foodborne pathogenic microorganisms. The effectiveness of mild preservation conditions will become increasingly dependent on a more stochastic approach linking microbial physiological factors with product preservation factors. In this study, the validity of frequency distributions to efficiently describe the inactivation and growth of Bacillus cereus in the presence of natural antimicrobials (essential oils has been studied. For this purpose, vegetative cells were exposed to 0.6 mM of thymol or cymene, obtaining survival curves that were best described by the distribution of Weibull, since a tailing effect was observed. B. cereus was also exposed in a growth medium to a low concentration (0.1 mM of both antimicrobials, separately or combined, and the lag times obtained were fitted to a normal distribution, which allowed a description of dispersion of the start of growth. This allowed a more efficient evaluation of the experimental data to establish safe processing conditions according to accurate parameters and their implementation in risk assessment.

  13. Modeling and distributed gain scheduling strategy for load frequency control in smart grids with communication topology changes.

    Science.gov (United States)

    Liu, Shichao; Liu, Xiaoping P; El Saddik, Abdulmotaleb

    2014-03-01

    In this paper, we investigate the modeling and distributed control problems for the load frequency control (LFC) in a smart grid. In contrast with existing works, we consider more practical and real scenarios, where the communication topology of the smart grid changes because of either link failures or packet losses. These topology changes are modeled as a time-varying communication topology matrix. By using this matrix, a new closed-loop power system model is proposed to integrate the communication topology changes into the dynamics of a physical power system. The globally asymptotical stability of this closed-loop power system is analyzed. A distributed gain scheduling LFC strategy is proposed to compensate for the potential degradation of dynamic performance (mean square errors of state vectors) of the power system under communication topology changes. In comparison to conventional centralized control approaches, the proposed method can improve the robustness of the smart grid to the variation of the communication network as well as to reduce computation load. Simulation results show that the proposed distributed gain scheduling approach is capable to improve the robustness of the smart grid to communication topology changes. © 2013 ISA. Published by ISA. All rights reserved.

  14. Plasma Temperature Determination of Hydrogen Containing High-Frequency Electrode less Lamps by Intensity Distribution Measurements of Hydrogen Molecular Band

    International Nuclear Information System (INIS)

    Gavare, Z.; Revalde, G.; Skudra, A.

    2011-01-01

    The goal of the present work was the investigation of the possibility to use intensity distribution of the Q-branch lines of the hydrogen Fulcher-a diagonal band (d3η u- a3Σg + electronic transition; Q-branch with ν=ν=2) to determine the temperature of hydrogen containing high-frequency electrode less lamps (HFEDLs). The values of the rotational temperatures have been obtained from the relative intensity distributions for hydrogen-helium and hydrogen-argon HFEDLs depending on the applied current. The results have been compared with the method of temperature derivation from Doppler profiles of He 667.8 nm and Ar 772.4 nm lines. The results of both methods are in good agreement, showing that the method of gas temperature determination from the intensity distribution in the hydrogen Fulcher-a (2-2)Q band can be used for the hydrogen containing HFEDLs. It was observed that the admixture of 10% hydrogen in the argon HFEDLs significantly reduces the gas temperature

  15. Molecular monitoring of resistant dhfr and dhps allelic haplotypes in ...

    African Journals Online (AJOL)

    Objective: The present study assesses the frequency of resistant dhfr and dhps alleles in Morogoro-Mvomero district in south eastern Tanzania and contrast their rate of change during 17 years of SP second line use against five years of SP first line use. Methodology: Cross sectional surveys of asymptomatic infections were ...

  16. Comparison of bovine lymphocyte antigen DRB3.2 allele ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-08-04

    Aug 4, 2008 ... polymorphic bovine MHC class II gene which encodes the peptide-binding groove. Since different ... patibility Complex (MHC) of cattle is known as Bovine .... Table 1. Frequencies of BoLA-DRB3.2 alleles detected by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP).

  17. Allelic variation of HMW glutenin subunits of Ethiopian bread wheat ...

    African Journals Online (AJOL)

    There were highly significant differences between genotypes and banding patterns for the SDS-sedimentation test, mixograph development time, alveograph strength and loaf volume; but not for protein content. The frequency of subunits 5+10 among genotypes was 73%. The accumulation of high scoring alleles in our ...

  18. Association of apolipoprotein E allele {epsilon}4 with late-onset sporadic Alzheimer`s disease

    Energy Technology Data Exchange (ETDEWEB)

    Lucotte, G.; David, F.; Berriche, S. [Regional Center of Neurogenetics, Reims (France)] [and others

    1994-09-15

    Apolipoprotein E, type {epsilon}4 allele (ApoE {epsilon}4), is associated with late-onset sporadic Alzheimer`s disease (AD) in French patients. The association is highly significant (0.45 AD versus 0.12 controls for {epsilon}4 allele frequencies). These data support the involvement of ApoE {epsilon}4 allele as a very important risk factor for the clinical expression of AD. 22 refs., 1 fig., 3 tabs.

  19. Simultaneous purifying selection on the ancestral MC1R allele and positive selection on the melanoma-risk allele V60L in south Europeans.

    Science.gov (United States)

    Martínez-Cadenas, Conrado; López, Saioa; Ribas, Gloria; Flores, Carlos; García, Oscar; Sevilla, Arrate; Smith-Zubiaga, Isabel; Ibarrola-Villaba, Maider; Pino-Yanes, Maria del Mar; Gardeazabal, Jesús; Boyano, Dolores; García de Galdeano, Alicia; Izagirre, Neskuts; de la Rúa, Concepción; Alonso, Santos

    2013-12-01

    In humans, the geographical apportionment of the coding diversity of the pigmentary locus melanocortin-1 receptor (MC1R) is, unusually, higher in Eurasians than in Africans. This atypical observation has been interpreted as the result of purifying selection due to functional constraint on MC1R in high UV-B radiation environments. By analyzing 3,142 human MC1R alleles from different regions of Spain in the context of additional haplotypic information from the 1000 Genomes (1000G) Project data, we show that purifying selection is also strong in southern Europe, but not so in northern Europe. Furthermore, we show that purifying and positive selection act simultaneously on MC1R. Thus, at least in Spain, regions at opposite ends of the incident UV-B radiation distribution show significantly different frequencies for the melanoma-risk allele V60L (a mutation also associated to red hair and fair skin and even blonde hair), with higher frequency of V60L at those regions of lower incident UV-B radiation. Besides, using the 1000G south European data, we show that the V60L haplogroup is also characterized by an extended haplotype homozygosity (EHH) pattern indicative of positive selection. We, thus, provide evidence for an adaptive value of human skin depigmentation in Europe and illustrate how an adaptive process can simultaneously help to maintain a disease-risk allele. In addition, our data support the hypothesis proposed by Jablonski and Chaplin (Human skin pigmentation as an adaptation to UVB radiation. Proc Natl Acad Sci U S A. 2010;107:8962-8968), which posits that habitation of middle latitudes involved the evolution of partially depigmented phenotypes that are still capable of suitable tanning.

  20. Association between HLA Class I and Class II Alleles and the Outcome of West Nile Virus Infection: An Exploratory Study

    Science.gov (United States)

    Lanteri, Marion C.; Kaidarova, Zhanna; Peterson, Trevor; Cate, Steven; Custer, Brian; Wu, Shiquan; Agapova, Maria; Law, Jacqueline P.; Bielawny, Thomas; Plummer, Frank; Tobler, Leslie H.; Loeb, Mark; Busch, Michael P.; Bramson, Jonathan; Luo, Ma; Norris, Philip J.

    2011-01-01

    Background West Nile virus (WNV) infection is asymptomatic in most individuals, with a minority developing symptoms ranging from WNV fever to serious neuroinvasive disease. This study investigated the impact of host HLA on the outcome of WNV disease. Methods A cohort of 210 non-Hispanic mostly white WNV+ subjects from Canada and the U.S. were typed for HLA-A, B, C, DP, DQ, and DR. The study subjects were divided into three WNV infection outcome groups: asymptomatic (AS), symptomatic (S), and neuroinvasive disease (ND). Allele frequency distribution was compared pair-wise between the AS, S, and ND groups using χ2 and Fisher's exact tests and P values were corrected for multiple comparisons (Pc). Allele frequencies were compared between the groups and the North American population (NA) used as a control group. Logistic regression analysis was used to evaluate the potential synergistic effect of age and HLA allele phenotype on disease outcome. Results The alleles HLA-A*68, C*08 and DQB*05 were more frequently associated with severe outcomes (ND vs. AS, P A*68 = 0.013/Pc = 0.26, P C*08 = 0.0075/Pc = 0.064, and P DQB1*05 = 0.029/Pc = 0.68), However the apparent DQB1*05 association was driven by age. The alleles HLA-B*40 and C*03 were more frequently associated with asymptomatic outcome (AS vs. S, P B*40 = 0.021/Pc = 0.58 and AS vs. ND P C*03 = 0.039/Pc = 0.64) and their frequencies were lower within WNV+ subjects with neuroinvasive disease than within the North American population (NA vs. S, P B*40 = 0.029 and NA vs. ND, P C*03 = 0.032). Conclusions Host HLA may be associated with the outcome of WNV disease; HLA-A*68 and C*08 might function as “susceptible” alleles, whereas HLA-B*40 and C*03 might function as “protective” alleles. PMID:21829673

  1. Study on the performance of quantum key distribution scheme with the single photon frequency up-conversion detector

    Science.gov (United States)

    Shi, Lei; Luo, Jun Wen; Xue, Yang; Wei, Jiahua

    2017-10-01

    In order to improve the detection efficiency in QKD system, this paper has put forward a new quantum key distribution scheme based on the single photon frequency up-conversion detection technology and decoy-state BB84 protocol. A long wavelength pump light is adopted in single photon detector (SPD) to avoid the noise caused by spontaneous parametric down conversion (SPDC), thus an overall 28% detection efficiency is achieved which is five times of 4.5% in conventional InGaAs-based detectors. Moreover, the propagating distances has reached 90km and 150km with weak coherent pulse (WCP) and decoy weak coherent pulse (DWCP) respectively, which is 1.3 times and 1.05 times of the conventional InGaAs-based detectors of 70km and 140km.

  2. Semicircular canal dehiscence: Frequency and distribution on temporal bone CT and its relationship with the clinical outcomes

    International Nuclear Information System (INIS)

    Elmali, Muzaffer; Polat, Ahmet Veysel; Kucuk, Harun; Atmaca, Sinan; Aksoy, Ahmet

    2013-01-01

    Purpose: In this study, we aimed to investigate the frequency of SCD and its distribution and relationship with clinical outcomes on thin-section CT of the temporal bone. Materials and methods: Digital temporal bone CT images of 850 consecutive patients (1700 temporal bone CTs, 5100 SCs) who presented with a range of complaints such as vertigo, deafness, ear pain, fullness, and discharge between January 2008 and December 2011 were re-evaluated. Axial and oblique coronal reconstruction images of the temporal bone were made with a reconstruction thickness of 0.5 mm. Additionally, superior SC was evaluated in two perpendicular planes. Results: Out of 850 patients, 70 had completely normal temporal bone CT. Ninety-three patients had at least one SCD. In the temporal bone-based evaluation, 119 (26 bilateral, 67 unilateral) of 1700 temporal bones (7%) showed dehiscence. The SC-based evaluation revealed 125 SCD (2.5%) in 5100 SCs. The total number and rates of SCD were as follows: superior 103 (82.4%), posterior 13 (10.4%), and lateral nine (7.2%). Twenty of the 93 patients with SCD (21.5%) revealed no other findings on their temporal bone CTs. We determined a significant correlation between vestibular complaints, conductive hearing loss and SCD but there was no correlation between mixed, sensorineural hearing loss and SCD. Conclusion: We determined the frequency of SCD in 11% of patients and 7% of temporal bones. With regards to the distribution, the superior SC showed the highest dehiscence rate (82.4%). We found a significant correlation between vestibular symptoms, conductive hearing loss and SCD

  3. Semicircular canal dehiscence: Frequency and distribution on temporal bone CT and its relationship with the clinical outcomes

    Energy Technology Data Exchange (ETDEWEB)

    Elmali, Muzaffer, E-mail: muzafel@yahoo.com.tr [Department of Radiology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Polat, Ahmet Veysel, E-mail: veyselp@hotmail.com [Department of Radiology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Kucuk, Harun, E-mail: hardrmd@yahoo.com [Department of Otorhinolaryngology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Atmaca, Sinan, E-mail: sinanatmaca@yahoo.com [Department of Otorhinolaryngology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Aksoy, Ahmet, E-mail: toxocara47@hotmail.com [Department of Otorhinolaryngology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey)

    2013-10-01

    Purpose: In this study, we aimed to investigate the frequency of SCD and its distribution and relationship with clinical outcomes on thin-section CT of the temporal bone. Materials and methods: Digital temporal bone CT images of 850 consecutive patients (1700 temporal bone CTs, 5100 SCs) who presented with a range of complaints such as vertigo, deafness, ear pain, fullness, and discharge between January 2008 and December 2011 were re-evaluated. Axial and oblique coronal reconstruction images of the temporal bone were made with a reconstruction thickness of 0.5 mm. Additionally, superior SC was evaluated in two perpendicular planes. Results: Out of 850 patients, 70 had completely normal temporal bone CT. Ninety-three patients had at least one SCD. In the temporal bone-based evaluation, 119 (26 bilateral, 67 unilateral) of 1700 temporal bones (7%) showed dehiscence. The SC-based evaluation revealed 125 SCD (2.5%) in 5100 SCs. The total number and rates of SCD were as follows: superior 103 (82.4%), posterior 13 (10.4%), and lateral nine (7.2%). Twenty of the 93 patients with SCD (21.5%) revealed no other findings on their temporal bone CTs. We determined a significant correlation between vestibular complaints, conductive hearing loss and SCD but there was no correlation between mixed, sensorineural hearing loss and SCD. Conclusion: We determined the frequency of SCD in 11% of patients and 7% of temporal bones. With regards to the distribution, the superior SC showed the highest dehiscence rate (82.4%). We found a significant correlation between vestibular symptoms, conductive hearing loss and SCD.

  4. Characterization of Quercus species distributed in Jordan using ...

    African Journals Online (AJOL)

    User

    2013-03-20

    Mar 20, 2013 ... randomly distributed in the genome. Moreover, as com- pared to SSRs, these marker systems allow a more precise estimate of marker allele frequencies at single loci and faster estimate of population polymorphisms over several loci. From the similarity matrix, the highest values of simila- rity between ...

  5. Combined Deterministic and Stochastic Approach to Determine Spatial Distribution of Drought Frequency and Duration in the Great Hungarian Plain

    Science.gov (United States)

    Szabó, J. A.; Kuti, L.; Bakacsi, Zs.; Pásztor, L.; Tahy, Á.

    2009-04-01

    Drought is one of the major weather driven natural hazards, which has most harm impacts on environment, agricultural and hydrological factors than the other hazards. In spite of the fact that Hungary - that country is situated in Central Europe - belongs to the continental climate zone (influenced by Atlantic and Mediterranean streams) and this weather conditions should be favourable for agricultural production, the drought is a serious risk factor in Hungary, especially on the so called "Great Hungarian Plain", which area has been hit by severe drought events. These drought events encouraged the Ministry of Environment and Water of Hungary to embark on a countrywide drought planning programme to coordinate drought planning efforts throughout the country, to ensure that available water is used efficiently and to provide guidance on how drought planning can be accomplished. With regard to this plan, it is indispensable to analyze the regional drought frequency and duration in the target region of the programme as fundamental information for the further works. According to these aims, first we initiated a methodological development for simulating drought in a non-contributing area. As a result of this work, it has been agreed that the most appropriate model structure for our purposes using a spatially distributed physically based Soil-Vegetation-Atmosphere Transfer (SVAT) model embedded into a Markov Chain-Monte Carlo (MCMC) algorithm for estimate multi-year drought frequency and duration. In this framework: - the spatially distributed SVAT component simulates all the fundamental SVAT processes (such as: interception, snow-accumulation and melting, infiltration, water uptake by vegetation and evapotranspiration, vertical and horizontal distribution of soil moisture, etc.) taking the groundwater table as lower, and the hydrometeorological fields as upper boundary conditions into account; - and the MCMC based stochastic component generates time series of daily weather

  6. Measuring the length distribution of self-assembled lipid nanotubes by orientation control with a high-frequency alternating current electric field in aqueous solutions.

    Science.gov (United States)

    Hirano, Ken; Aoyagi, Masaru; Ishido, Tomomi; Ooie, Toshihiko; Frusawa, Hiroshi; Asakawa, Masumi; Shimizu, Toshimi; Ishikawa, Mitsuru

    2009-02-15

    The present work addresses the length distribution of self-assembled lipid nanotubes (LNTs) by controlling the orientation of the LNTs using an alternating current (ac) electric field in aqueous solutions. The effect of the ac field on the orientation and rotation of individual LNTs was examined to evaluate the optimum orientation frequency by visualizing the individual LNTs in real time. By using the high-frequency ac field, we have successfully measured the length distribution for two different types of LNTs and have quantitatively analyzed the maximum occurrences of the length distribution as well as the extension of the longer length region.

  7. Frequency and spatial distribution of animal and object hoarder behavior in Curitiba, Paraná State, Brazil

    Directory of Open Access Journals (Sweden)

    Graziela Ribeiro da Cunha

    Full Text Available Abstract: This study aimed to establish the frequency and spatial distribution of animal and object hoarding in Curitiba (Paraná State, the eighth most populous city in Brazil. All hoarding complaints received by the City Secretaries of Health, Environment and Social Assistance between September 2013 and April 2015 were collected (n = 226 and suspicious cases were individually investigated. A total of 113/226 (50% of complaints were confirmed as hoarding cases, representing an overall ratio of 6.45 cases per 100,000 inhabitants in Curitiba, of which 48/113 (42.5% involved object hoarders, 41/113 (36.3% animal hoarders and 24/113 (21.2% both animal and object hoarders. A correlation of total identified cases with neighborhood population density and all population stratums analyzed (total, gender, age was significantly positive (p < 0.01, and with neighborhood mean monthly income (r = -0.2; p = 0.03 significantly negative. A spatial cluster of cases was found in the north of the city (OR = 8.57; p < 0.01. Hoarding cases were relatively frequent in Curitiba and were associated with population distribution patterns and inversely related to neighborhood income.

  8. Rock size-frequency distributions analysis at lunar landing sites based on remote sensing and in-situ imagery

    Science.gov (United States)

    Li, Bo; Ling, Zongcheng; Zhang, Jiang; Chen, Jian

    2017-10-01

    Rock populations can supply fundamental geological information about origin and evolution of a planet. In this paper, we used Lunar Reconnaissance Orbiter (LRO) narrow-angle camera (NAC) images to identify rocks at the lunar landing sites (including Chang'e 3 (CE-3), Apollo and Surveyor series). The diameter and area of each identified rock were measured to generate distributions of rock cumulative fractional area and size-frequency on a log-log plot. The two distributions both represented the same shallow slopes at smaller diameters followed by steeper slopes at larger diameters. A reasonable explanation for the lower slopes may be the resolution and space weathering effects. By excluding the smaller diameters, rock populations derived from NAC images showed approximately linear relationships and could be fitted well by power laws. In the last, the entire rock populations derived from both NAC and in-situ imagery could be described by one power function at the lunar landing sites except the CE-3 and Apollo 11 landing sites. This may be because that the process of a large rock breaking down to small rocks even fine particles can be modeled by fractal theories. Thus, rock populations on lunar surfaces can be extrapolated along the curves of rock populations derived from NAC images to smaller diameters. In the future, we can apply rock populations from remote sensing images to estimate the number of rocks with smaller diameters to select the appropriate landing sites for the CE-4 and CE-5 missions.

  9. Updating the geographical distribution and frequency of Aedes albopictus in Brazil with remarks regarding its range in the Americas

    Directory of Open Access Journals (Sweden)

    Roberta Gomes Carvalho/

    2014-09-01

    Full Text Available The geographical distribution of Aedes albopictus in Brazil was updated according to the data recorded across the country over the last eight years. Countrywide house indexes (HI for Ae. albopictus in urban and suburban areas were described for the first time using a sample of Brazilian municipalities. This mosquito is currently present in at least 59% of the Brazilian municipalities and in 24 of the 27 federal units (i.e., 26 states and the Federal District. In 34 Brazilian municipalities, the HI values for Ae. albopictus were higher than those recorded for Ae. aegypti, reaching figures as high as HI = 7.72 in the Southeast Region. Remarks regarding the current range of this mosquito species in the Americas are also presented. Nineteen American countries are currently infested and few mainland American countries have not confirmed the occurrence of Ae. albopictus. The large distribution and high frequency of Ae. albopictus in the Americas may become a critical factor in the spread of arboviruses like chikungunya in the new world.

  10. Effect of trophic level on the radiocesium frequency distribution in aquatic and terrestrial ecosystems at Chornobyl and nuclear sites in the United States

    International Nuclear Information System (INIS)

    Smith, Michael H.; Tsyusko-Omeltchenko, Olga; Oleksyk, Taras K.

    2003-01-01

    There are significant linear relationship between the standard deviation and the mean of radiocesium concentration for samples of soils, sediments, plants, and animals from Chornobyl and nuclear sites in the United States. The universal occurrence of this relationship in all types of samples suggests that a non-normal frequency distribution should be expected. The slopes of these relationships are similar for fish and mammals from the two regions of the world but those for plants are not. The slopes for plants are similar for aquatic and terrestrial ecosystems within each region. We hypothesize that there are relationships between the four moments of the frequency distribution of radiocesium (mean, variance, skewness, and kurtosis), and that these relationships are caused by the functional properties of the organisms and other characteristics of the ecosystem. The way in which radiocesium was distributed across the landscape does not seem to be a factor in determining the form of the frequency distribution. (author)

  11. Distribution of very low frequency earthquakes in the Nankai accretionary prism influenced by a subducting-ridge

    Science.gov (United States)

    Toh, Akiko; Obana, Koichiro; Araki, Eiichiro

    2018-01-01

    We investigated the distribution of very low frequency earthquakes (VLFEs) that occurred in the shallow accretionary prism of the eastern Nankai trough during one week of VLFE activity in October 2015. They were recorded very close from the sources by an array of broadband ocean bottom seismometers (BBOBSs) equipped in Dense Oceanfloor Network system for Earthquakes and Tsunamis 1 (DONET1). The locations of VLFEs estimated using a conventional envelope correlation method appeared to have a large scatter, likely due to effects of 3D structures near the seafloor and/or sources that the method could not handle properly. Therefore, we assessed their relative locations by introducing a hierarchal clustering analysis based on patterns of relative peak times of envelopes within the array measured for each VLFE. The results suggest that, in the northeastern side of the network, all the detected VLFEs occur 30-40 km landward of the trench axis, near the intersection of a splay fault with the seafloor. Some likely occurred along the splay fault. On the other hand, many VLFEs occur closer to the trench axis in the southwestern side, likely along the plate boundary, and the VLFE activity in the shallow splay fault appears less intense, compared to the northeastern side. Although this could be a snap-shot of activity that becomes more uniform over longer-term, the obtained distribution can be reasonably explained by the change in shear stresses and pore pressures caused by a subducting-ridge below the northeastern side of DONET1. The change in stress state along the strike of the plate boundary, inferred from the obtained VLFE distribution, should be an important indicator of the strain release pattern and localised variations in the tsunamigenic potential of this region.

  12. Allelic variance among ABO blood group genotypes in a population from the western region of Saudi Arabia.

    Science.gov (United States)

    Mohamed, Abdularahman B O; Hindawi, Salwa Ibrahim; Al-Harthi, Sameer; Alam, Qamre; Alam, Mohammad Zubair; Haque, Absarul; Ahmad, Waseem; Damanhouri, Ghazi A

    2016-12-01

    Characterization of the ABO blood group at the phenotype and genotype levels is clinically essential for transfusion, forensics, and population studies. This study elucidated ABO phenotypes and genotypes, and performed an evaluation of their distribution in individuals from the western region of Saudi Arabia. One-hundred and seven samples underwent standard serological techniques for ABO blood group phenotype analysis. ABO alleles and genotypes were identified using multiplex polymerase chain reaction, and electrophoretic analysis was performed to evaluate the highly polymorphic ABO locus. A phenotype distribution of 37.4%, 30.8%, 24.3%, and 7.5% was found for blood groups O, A, B, and AB respectively in our study cohort. Genotype analysis identified 10 genotype combinations with the O01/O02 and A102/O02 genotypes being the most frequent with frequencies of 33.6% and 14.95%, respectively. Common genotypes such as A101/A101 , A101/A102 , A101/B101 , B101/B101 , and O01/O01 were not detected. Similarly, the rare genotypes, cis-AB01/O02 , cis-AB01/O01 , and cis-AB01/A102 were not found in our cohort. The most frequently observed allele was O02 (35.98%) followed by the A102 allele (17.76%). Furthermore, our findings are discussed in reference to ABO allele and genotype frequencies found in other ethnic groups. The study has a significant implication on the management of blood bank and transfusion services in Saudi Arabian patients.

  13. End plate marrow changes in the asymptomatic lumbosacral spine: frequency, distribution and correlation with age and degenerative changes

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Christine B. [Department of Radiology, VA Healthcare System, 3350 La Jolla Village Drive, CA 92161, La Jolla (United States); Vande Berg, Bruno C.; Malghem, Jacques [Department of Radiology, Cliniques Universitaires St Luc Universite Catholique de Louvain, 10 av Hippocrate, 1200, Brussels (Belgium); Tavernier, Thierry [Service de Radiologie, Clinique de la Sauvegarde, Av David Ben Gourion, 69009, Lyon (France); Cotten, Anne [Service de Radiologie Osteoarticulaire, Hopital R Salengro, 59037, Lille Cedex (France); Laredo, Jean-Denis [Service de Radiologie Osteo-articulaire, Hopital Lariboisiere, 2 rue Ambroise Pare, 75475, Paris Cedex 10 (France); Vallee, Christian [Service d' imagerie medicale, Hopital Raymond Poincare, 104 Boulevard R.Poincare, 92380, Garches (France)

    2004-07-01

    To investigate the frequency and distribution of end plate marrow signal intensity changes in an asymptomatic population and to correlate these findings with patient age and degenerative findings in the spine. MR imaging studies of the lumbosacral (LS) spine in 59 asymptomatic subjects were retrospectively reviewed by 2 musculoskeletal radiologists to determine the presence and location of fat-like and edema-like marrow signal changes about the end plates of the L1-2 through L5-S1 levels. The presence of degenerative changes in the spine was recorded as was patient age. Descriptive statistics were utilized to determine the frequency and associations of end plate findings and degenerative changes in the spine. Interobserver variability was determined by a kappa score. Binomial probability was used to predict the prevalence of the end plate changes in a similar subject population. The Fisher exact test was performed to determine statistical significance of the relationship of end plate changes with degenerative changes in the spine, superior versus inferior location about the disc and age of the patient population. Focal fat-like signal intensity adjacent to the vertebral end-plate was noted in 15 out of 59 subjects by both readers, and involved 38 and 36 out of 590 end plates by readers 1 and 2, respectively. Focal edema-like signal intensity adjacent to the vertebral end plate was noted in 8 out of 59 subjects by both readers and involved 11 and 10 out of 590 end plates by readers 1 and 2, respectively. Either fat or edema signal intensity occurred most often at the anterior (p<.05) aspects of the mid-lumbar spine and was seen in an older sub-population of the study (p<.05). End plate marrow signal intensity changes are present in the lumbar spine of some asymptomatic subjects with a characteristic location along the spine and in vertebral end plates. (orig.)

  14. Constancy, Distribution, and Frequency of Lepidoptera Defoliators of Eucalyptus grandis and Eucalyptus urophylla (Myrtaceae) in Four Brazilian Regions.

    Science.gov (United States)

    Ribeiro, G T; Zanuncio, J C; de S Tavares, W; de S Ramalho, F; Serrão, J E

    2016-12-01

    The growth of the Brazilian forest sector with monocultures favors the adaptation of Arthropoda pests. The Lepidoptera order includes major pests of Eucalyptus spp. (Myrtaceae). The aim of this work is to study the population constancy, distribution, and frequency of Lepidoptera primary pests of Eucalyptus spp. Lepidoptera pests in Eucalyptus spp. plantations were collected in Três Marias and Guanhães (state of Minas Gerais), Niquelândia (state of Goiás), and Monte Dourado (state o