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Sample records for allele frequency estimation

  1. The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of theta.

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2010-12-01

    Theoretical work focused on microsatellite variation has produced a number of important results, including the expected distribution of repeat sizes and the expected squared difference in repeat size between two randomly selected samples. However, closed-form expressions for the sampling distribution and frequency spectrum of microsatellite variation have not been identified. Here, we use coalescent simulations of the stepwise mutation model to develop gamma and exponential approximations of the microsatellite allele frequency spectrum, a distribution central to the description of microsatellite variation across the genome. For both approximations, the parameter of biological relevance is the number of alleles at a locus, which we express as a function of θ, the population-scaled mutation rate, based on simulated data. Discovered relationships between θ, the number of alleles, and the frequency spectrum support the development of three new estimators of microsatellite θ. The three estimators exhibit roughly similar mean squared errors (MSEs) and all are biased. However, across a broad range of sample sizes and θ values, the MSEs of these estimators are frequently lower than all other estimators tested. The new estimators are also reasonably robust to mutation that includes step sizes greater than one. Finally, our approximation to the microsatellite allele frequency spectrum provides a null distribution of microsatellite variation. In this context, a preliminary analysis of the effects of demographic change on the frequency spectrum is performed. We suggest that simulations of the microsatellite frequency spectrum under evolutionary scenarios of interest may guide investigators to the use of relevant and sometimes novel summary statistics.

  2. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids.

    PubMed

    Blischak, Paul D; Kubatko, Laura S; Wolfe, Andrea D

    2016-05-01

    Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high-throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty-ADU), which complicates the calculation of important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high-throughput sequencing data in the form of read counts. We bridge the gap from data collection (using restriction enzyme based techniques [e.g. GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's performance and to help guide the collection of empirical data. We also provide an implementation of our model in the R package polyfreqs and demonstrate its use with two example analyses that investigate (i) levels of expected and observed heterozygosity and (ii) model adequacy. Our simulations show that the number of individuals sampled from a population has a greater impact on estimation error than sequencing coverage. The example analyses also show that our model and software can be used to make inferences beyond the estimation of allele frequencies for autopolyploids by providing assessments of model adequacy and estimates of heterozygosity.

  3. Human acetylator polymorphism: estimate of allele frequency in Libya and details of global distribution.

    PubMed Central

    Karim, A K; Elfellah, M S; Evans, D A

    1981-01-01

    Acetylator phenotyping by means of a sulphadimidine tests revealed 65% of Libyan Arabs to be slow acetylators. Hence the frequency of the allele controlling slow acetylation (As) is estimated as q = 0.81 +/- 0.05. This estimate is similar to those previously recorded in European and adjacent Middle Eastern populations. PMID:7328611

  4. Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

    PubMed Central

    Jónás, Ágnes; Taus, Thomas; Kosiol, Carolin; Schlötterer, Christian; Futschik, Andreas

    2016-01-01

    The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest. PMID:27542959

  5. A method for estimating the intensity of overdominant selection from the distribution of allele frequencies.

    PubMed Central

    Slatkin, M; Muirhead, C A

    2000-01-01

    A method is proposed for estimating the intensity of overdominant selection scaled by the effective population size, S = 2Ns, from allele frequencies. The method is based on the assumption that, with strong overdominant selection, allele frequencies are nearly at their deterministic equilibrium values and that, to a first approximation, deviations depend only on S. Simulations verify that reasonably accurate estimates of S can be obtained for realistic sample sizes. The method is applied to data from several loci in the major histocompatibility complex (Mhc) in numerous human populations. For alleles distinguished by both serological typing and the sequence of the peptide-binding region, our estimates of S are comparable to those obtained by analysis of DNA sequences in showing that selection is strongest on HLA-B and weaker on HLA-A, HLA-DRB1, and HLA-DQA1. The intensity of selection on HLA-B varied considerably among populations. Two populations, Native American and Inuit, showed an excess rather than a deficiency in homozygosity. Comparable estimates of S were obtained for alleles at Mhc class II loci distinguished by serological reactions (serotyping) and by differences in the amino acid sequences of the peptide-binding region (molecular typing). A comparison of two types of data for DQA1 and DRB1 showed that serotyping led to generally lower estimates of S. PMID:11102400

  6. On the Bayesness, minimaxity and admissibility of point estimators of allelic frequencies.

    PubMed

    Martínez, Carlos Alberto; Khare, Kshitij; Elzo, Mauricio A

    2015-10-21

    In this paper, decision theory was used to derive Bayes and minimax decision rules to estimate allelic frequencies and to explore their admissibility. Decision rules with uniformly smallest risk usually do not exist and one approach to solve this problem is to use the Bayes principle and the minimax principle to find decision rules satisfying some general optimality criterion based on their risk functions. Two cases were considered, the simpler case of biallelic loci and the more complex case of multiallelic loci. For each locus, the sampling model was a multinomial distribution and the prior was a Beta (biallelic case) or a Dirichlet (multiallelic case) distribution. Three loss functions were considered: squared error loss (SEL), Kulback-Leibler loss (KLL) and quadratic error loss (QEL). Bayes estimators were derived under these three loss functions and were subsequently used to find minimax estimators using results from decision theory. The Bayes estimators obtained from SEL and KLL turned out to be the same. Under certain conditions, the Bayes estimator derived from QEL led to an admissible minimax estimator (which was also equal to the maximum likelihood estimator). The SEL also allowed finding admissible minimax estimators. Some estimators had uniformly smaller variance than the MLE and under suitable conditions the remaining estimators also satisfied this property. In addition to their statistical properties, the estimators derived here allow variation in allelic frequencies, which is closer to the reality of finite populations exposed to evolutionary forces. PMID:26271891

  7. The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data.

    PubMed

    Kofler, Robert; Nolte, Viola; Schlötterer, Christian

    2016-01-01

    Sequencing pools of individuals (Pool-Seq) is a cost-effective method to determine genome-wide allele frequency estimates. Given the importance of meta-analyses combining data sets, we determined the influence of different genomic library preparation protocols on the consistency of allele frequency estimates. We found that typically no more than 1% of the variation in allele frequency estimates could be attributed to differences in library preparation. Also read length had only a minor effect on the consistency of allele frequency estimates. By far, the most pronounced influence could be attributed to sequence coverage. Increasing the coverage from 30- to 50-fold improved the consistency of allele frequency estimates by at least 27%. We conclude that Pool-Seq data can be easily combined across different library preparation methods, but sufficient sequence coverage is key to reliable results.

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

    PubMed Central

    2013-01-01

    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

  9. PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

    PubMed Central

    De Maio, Nicola; Schrempf, Dominik; Kosiol, Carolin

    2015-01-01

    Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches. PMID:26209413

  10. Reducing bias of allele frequency estimates by modeling SNP genotype data with informative missingness.

    PubMed

    Lin, Wan-Yu; Liu, Nianjun

    2012-01-01

    The presence of missing single-nucleotide polymorphism (SNP) genotypes is common in genetic studies. For studies with low-density SNPs, the most commonly used approach to dealing with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is valid 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. Under the assumption of Hardy-Weinberg equilibrium and no genotyping error, we here 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. PMID:22719749

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

    PubMed Central

    2012-01-01

    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 < 0.01) mean allele frequency differentials between the low and high fertility groups were observed for 720 SNPs (58 NSS). Allele frequencies for 43 of the SNPs were also determined by genotyping the 150 individual animals (Sequenom® 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

  12. Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach.

    PubMed Central

    Berthier, Pierre; Beaumont, Mark A; Cornuet, Jean-Marie; Luikart, Gordon

    2002-01-01

    A new genetic estimator of the effective population size (N(e)) is introduced. This likelihood-based (LB) estimator uses two temporally spaced genetic samples of individuals from a population. We compared its performance to that of the classical F-statistic-based N(e) estimator (N(eFk)) by using data from simulated populations with known N(e) and real populations. The new likelihood-based estimator (N(eLB)) showed narrower credible intervals and greater accuracy than (N(eFk)) when genetic drift was strong, but performed only slightly better when genetic drift was relatively weak. When drift was strong (e.g., N(e) = 20 for five generations), as few as approximately 10 loci (heterozygosity of 0.6; samples of 30 individuals) are sufficient to consistently achieve credible intervals with an upper limit <50 using the LB method. In contrast, approximately 20 loci are required for the same precision when using the classical F-statistic approach. The N(eLB) estimator is much improved over the classical method when there are many rare alleles. It will be especially useful in conservation biology because it less often overestimates N(e) than does N(eLB) and thus is less likely to erroneously suggest that a population is large and has a low extinction risk. PMID:11861575

  13. Prevalence and allele frequency estimation of bovine leukocyte adhesion deficiency (BLAD) in Holstein-Friesian cattle in Japan.

    PubMed

    Nagahata, H; Miura, T; Tagaki, K; Ohtake, M; Noda, H; Yasuda, T; Nioka, K

    1997-04-01

    Blood samples from 796 Holstein dairy cows in 20 herds from 6 districts in Japan from June 1994 to August 1995 were examined to determine whether they were BLAD-free, BLAD carriers, or BLAD-affected by use of DNA-polymerase chain reaction (PCR) analysis. The usage of semen of confirmed BLAD-carriers for artificial insemination in the Hokkaido district and two selected dairy farms was examined to estimate the gene frequency of BLAD carriers of sires. BLAD-carrier prevalence in 20 herds (796 cows, over 2.5 years old) ranged from 0 to 23.5%, and the mean BLAD-carrier prevalence was 8.1%. The BLAD-carrier prevalence in 10 herds (363 cows) in which the occurrence of BLAD was not detected by the DNA-PCR test ranged from 0 to 12.5% with a mean of 5.4%. The BLAD-carrier prevalence in 10 herds (433 cows) in which the occurrence of BLAD was confirmed by DNA-PCR analysis ranged from 2.6 to 23.5% with a mean of 10.8%, and these values were significantly (P < 0.05) higher than those of dairy herds in which the occurrence of BLAD was not detected. The age distribution in BLAD carriers in these cows ranged from 2.5 to 11 years. The mean gene frequencies of BLAD among 796 cows from 20 herds and 433 cows from 10 herds in which the occurrence of BLAD was detected were 0.041 and 0.054, respectively. The proportional usage of semen of BLAD carriers for artificial insemination in the Hokkaido district in 1992 was 12.6%, and its gene frequency was 0.058. On two selected farms in which higher BLAD-carrier rates were detected, the prevalences were 35.5% and 25.8%, and their gene frequencies were 0.177 and 0.129, respectively. The occurrence of BLAD-affected in Holstein dairy cattle was estimated to be 0.16-0.31% at birth in Japan without genetic control. PMID:9152929

  14. Estimating Relatedness in the Presence of Null Alleles.

    PubMed

    Huang, Kang; Ritland, Kermit; Dunn, Derek W; Qi, Xiaoguang; Guo, Songtao; Li, Baoguo

    2016-01-01

    Studies of genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. However, with the presence of null alleles, an observed genotype can represent one of several possible true genotypes. This results in biased estimates of relatedness. As the numbers of marker loci are often limited, loci with null alleles cannot be abandoned without substantial loss of statistical power. Here, we show how loci with null alleles can be incorporated into six estimators of relatedness (two novel). We evaluate the performance of various estimators before and after correction for null alleles. If the frequency of a null allele is <0.1, some estimators can be used directly without adjustment; if it is >0.5, the potency of estimation is too low and such a locus should be excluded. We make available a software package entitled PolyRelatedness v1.6, which enables researchers to optimize these estimators to best fit a particular data set.

  15. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of "standardized allele frequencies" that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools-a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

  16. Allele frequencies at microsatellite loci: The stepwise mutation model revisited

    SciTech Connect

    Valdes, A.M.; Slatkin, M. ); Freimer, N.B. )

    1993-03-01

    The authors summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. They show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. It is also shown that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size. 39 refs., 6 figs., 4 tabs.

  17. Robust Identification of Local Adaptation from Allele Frequencies

    PubMed Central

    Günther, Torsten; Coop, Graham

    2013-01-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

  18. Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-01

    Gene conversion results in the nonreciprocal transfer of genetic information between two recombining sequences, and there is evidence that this process is biased toward G and C alleles. However, the strength of GC-biased gene conversion (gBGC) in human populations and its effects on hereditary disease have yet to be assessed on a genomic scale. Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data sets. We find that genetic distances (FST and population branch statistics) are modified by gBGC. In addition, the site frequency spectrum is left-shifted when ancestral alleles are favored by gBGC and right-shifted when derived alleles are favored by gBGC. Allele frequency shifts due to gBGC mimic the effects of natural selection. As expected, these effects are strongest in high-recombination regions of the human genome. By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb ≈ 0.05 to 0.09. We also find that derived alleles favored by gBGC are much more likely to be homozygous than derived alleles at unbiased SNPs (+42.2% to 62.8%). This results in a curse of the converted, whereby gBGC causes substantial increases in hereditary disease risks. Taken together, our findings reveal that GC-biased gene conversion has important population genetic and public health implications.

  19. ALFRED: an allele frequency resource for research and teaching

    PubMed Central

    Rajeevan, Haseena; Soundararajan, Usha; Kidd, Judith R.; Pakstis, Andrew J.; Kidd, Kenneth K.

    2012-01-01

    ALFRED (http://alfred.med.yale.edu) is a free, web accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. Currently, ALFRED has allele frequency tables on over 663 400 polymorphic sites; 170 of them have frequency tables for more than 100 different population samples. In ALFRED, a population may have multiple samples with each ‘sample’ consisting of many individuals on which an allele frequency is based. There are 3566 population samples from 710 different populations with allele frequency tables on at least one polymorphism. Fifty of those population samples have allele frequency data for over 650 000 polymorphisms. Records also have active links to relevant resources (dbSNP, PharmGKB, OMIM, Ethnologue, etc.). The flexible search options and data display and download capabilities available through the web interface allow easy access to the large quantity of high-quality data in ALFRED. PMID:22039151

  20. Estimating the age of alleles by use of intraallelic variability

    SciTech Connect

    Slatkin, M.; Rannala, B.

    1997-02-01

    A method is presented for estimating the age of an allele by use of its frequency and the extent of variation among different copies. The method uses the joint distribution of the number of copies in a population sample and the coalescence times of the intraallelic gene genealogy conditioned on the number of copies. The linear birth-death process is used to approximate the dynamics of a rare allele in a finite population. A maximum-likelihood estimate of the age of the allele is obtained by Monte Carlo integration over the coalescence times. The method is applied to two alleles at the cystic fibrosis (CFTR) locus, {Delta}F508 and G542X, for which intraallelic variability at three intronic microsatellite loci has been examined. Our results indicate that G542X is somewhat older than {Delta}F508. Although absolute estimates depend on the mutation rates at the microsatellite loci, our results support the hypothesis that {Delta}F508 arose <500 generations ({approx}10,000 years) ago. 32 refs., 4 figs.

  1. Mutated tumor alleles are expressed according to their DNA frequency.

    PubMed

    Castle, John C; Loewer, Martin; Boegel, Sebastian; Tadmor, Arbel D; Boisguerin, Valesca; de Graaf, Jos; Paret, Claudia; Diken, Mustafa; Kreiter, Sebastian; Türeci, Özlem; Sahin, Ugur

    2014-04-22

    The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency.

  2. The frequency of HLA alleles in the Romanian population.

    PubMed

    Constantinescu, Ileana; Boșcaiu, Voicu; Cianga, Petru; Dinu, Andrei-Antoniu; Gai, Elena; Melinte, Mihaela; Moise, Ana

    2016-03-01

    Knowledge of human leukocyte antigen (HLA) allele frequencies is essential for bone marrow and kidney donor searches. The Romanian Caucasian population is heterogeneous and information on HLA polymorphism has not been well studied. We characterized the HLA genetic profile and allele frequencies of regional populations in Romania. HLA-A, B and DRB1 alleles were examined in 8252 individuals, belonging to the four main regions of Romania. The most common alleles found in the Romanian population are the following: HLA-A*01, A*02, A*03, A*11, A*24; HLA-B*18, B*35, B*44, B*51 and HLA-DRB1*01, DRB1*03, DRB1*07, DRB1*11, DRB1*13, DRB1*15, DRB1*16. More than half of the alleles are non-homogeneously spread in Romania. These results provide a starting point for future analyses of genetic heterogeneity in Romania.

  3. The frequency of HLA alleles in the Romanian population.

    PubMed

    Constantinescu, Ileana; Boșcaiu, Voicu; Cianga, Petru; Dinu, Andrei-Antoniu; Gai, Elena; Melinte, Mihaela; Moise, Ana

    2016-03-01

    Knowledge of human leukocyte antigen (HLA) allele frequencies is essential for bone marrow and kidney donor searches. The Romanian Caucasian population is heterogeneous and information on HLA polymorphism has not been well studied. We characterized the HLA genetic profile and allele frequencies of regional populations in Romania. HLA-A, B and DRB1 alleles were examined in 8252 individuals, belonging to the four main regions of Romania. The most common alleles found in the Romanian population are the following: HLA-A*01, A*02, A*03, A*11, A*24; HLA-B*18, B*35, B*44, B*51 and HLA-DRB1*01, DRB1*03, DRB1*07, DRB1*11, DRB1*13, DRB1*15, DRB1*16. More than half of the alleles are non-homogeneously spread in Romania. These results provide a starting point for future analyses of genetic heterogeneity in Romania. PMID:26711124

  4. Supernova frequency estimates

    SciTech Connect

    Tsvetkov, D.Y.

    1983-01-01

    Estimates of the frequency of type I and II supernovae occurring in galaxies of different types are derived from observational material acquired by the supernova patrol of the Shternberg Astronomical Institute.

  5. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.

    PubMed

    Kiezun, Adam; Pulit, Sara L; Francioli, Laurent C; van Dijk, Freerk; Swertz, Morris; Boomsma, Dorret I; van Duijn, Cornelia M; Slagboom, P Eline; van Ommen, G J B; Wijmenga, Cisca; de Bakker, Paul I W; Sunyaev, Shamil R

    2013-01-01

    Large-scale population sequencing studies provide a complete picture of human genetic variation within the studied populations. A key challenge is to identify, among the myriad alleles, those variants that have an effect on molecular function, phenotypes, and reproductive fitness. Most non-neutral variation consists of deleterious alleles segregating at low population frequency due to incessant mutation. To date, studies characterizing selection against deleterious alleles have been based on allele frequency (testing for a relative excess of rare alleles) or ratio of polymorphism to divergence (testing for a relative increase in the number of polymorphic alleles). Here, starting from Maruyama's theoretical prediction (Maruyama T (1974), Am J Hum Genet USA 6:669-673) that a (slightly) deleterious allele is, on average, younger than a neutral allele segregating at the same frequency, we devised an approach to characterize selection based on allelic age. Unlike existing methods, it compares sets of neutral and deleterious sequence variants at the same allele frequency. When applied to human sequence data from the Genome of the Netherlands Project, our approach distinguishes low-frequency coding non-synonymous variants from synonymous and non-coding variants at the same allele frequency and discriminates between sets of variants independently predicted to be benign or damaging for protein structure and function. The results confirm the abundance of slightly deleterious coding variation in humans.

  6. Worldwide allele frequencies of the human apolipoprotein E gene: climate, local adaptations, and evolutionary history.

    PubMed

    Eisenberg, Dan T A; Kuzawa, Christopher W; Hayes, M Geoffrey

    2010-09-01

    The epsilon4 allele of the apolipoprotein E (APOE) gene is associated with increased cholesterol levels and heart disease. Population allele frequencies of APOE have previously been shown to vary, with epsilon4 frequencies generally increasing with latitude. We hypothesize that this trend resulted from natural selection protecting against low-cholesterol levels. In high-latitude cold environments and low-latitude hot environments, metabolic rate is elevated, which could require higher cholesterol levels. To explore this hypothesis, we compiled APOE allele frequencies, latitude, temperature, and elevation from populations around the world. epsilon4 allele frequencies show a curvilinear relationship with absolute latitude, with lowest frequencies found in the mid-latitudes where temperatures generally require less expenditure on cooling/thermogenesis. Controlling for population structure in a subset of populations did not appreciably change this pattern of association, consistent with selection pressures that vary by latitude shaping epsilon4 allele frequencies. Temperature records also predict APOE frequency in a curvilinear fashion, with lowest epsilon4 frequencies at moderate temperatures. The model fit between historical temperatures and epsilon4 is less than between latitude and epsilon4, but strengthened after correcting for estimated temperature differences during the Paleolithic. Contrary to our hypothesis, we find that elevation did not improve predictive power, and an integrated measure of the cholesterol effect of multiple APOE alleles was less related to latitude than was epsilon4 alone. Our results lend mixed support for a link between past temperature and human APOE allele distribution and point to the need to develop better models of past climate in future analyses.

  7. Allelic disequilibrium and allele frequency distribution as a function of social and demographic history.

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

    Allelic disequilibrium between closely linked genes is a common observation in human populations and often gives rise to speculation concerning the role of selective forces. In a previous treatment, we have developed a population model of the expected distribution of rare variants (including private polymorphisms) in Amerindians and have argued that, because of the great expansion of Amerindian numbers with the advent of agriculture, most of these rare variants are of relatively recent origin. Many other populations have similar histories of striking recent expansions. In this treatment, we demonstrate that, in consequence of this fact, a high degree of linkage disequilibrium between two nonhomologous alleles <0.5 cM apart is the "normal" expectation, even in the absence of selection. This expectation is enhanced by the previous subdivision of human populations into relatively isolated tribes characterized by a high level of endogamy and inbreeding. We also demonstrate that the alleles associated with a recessive disease phenotype are expected to exist in a population in very variable frequencies: there is no need to postulate positive selection with respect to the more common disease-associated alleles for such entities as phenylketonuria or cystic fibrosis. PMID:8981963

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

    PubMed

    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.

  9. The Joint Allele-Frequency Spectrum in Closely Related Species

    PubMed Central

    Chen, Hua; Green, Richard E.; Pääbo, Svante; Slatkin, Montgomery

    2007-01-01

    We develop the theory for computing the joint frequency spectra of alleles in two closely related species. We allow for arbitrary population growth in both species after they had a common ancestor. We focus on the case in which a single chromosome is sequenced from one of the species. We use classical diffusion theory to show that, if the ancestral species was at equilibrium under mutation and drift and a chromosome from one of the descendant species carries the derived allele, the frequency spectrum in the other species is uniform, independently of the demographic history of both species. We also predict the expected densities of segregating and fixed sites when the chromosome from the other species carries the ancestral allele. We compare the predictions of our model with the site-frequency spectra of SNPs in the four HapMap populations of humans when the nucleotide present in the Neanderthal DNA sequence is ancestral or derived, using the chimp genome as the outgroup. PMID:17603120

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

    PubMed Central

    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 investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across ∼500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the “American Modal Haplotype” (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all

  11. Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus

    PubMed Central

    Chakraborty, Ranajit; Fuerst, Paul A.; Nei, Masatoshi

    1980-01-01

    With the aim of understanding the mechanism of maintenance of protein polymorphism, we have studied the properties of allele frequency distribution and the number of alleles per locus, using gene-frequency data from a wide range of organisms (mammals, birds, reptiles, amphibians, Drosophila and non-Drosophila invertebrates) in which 20 or more loci with at least 100 genes were sampled. The observed distribution of allele frequencies was U-shaped in all of the 138 populations (mostly species or subspecies) examined and generally agreed with the theoretical distribution expected under the mutation-drift hypothesis, though there was a significant excess of rare alleles (gene frequency, 0 ∼ 0.05) in about a quarter of the populations. The agreement between the mutation-drift theory and observed data was quite satisfactory for the numbers of polymorphic (gene frequency, 0.05 ∼ 0.95) and monomorphic (0.95 ∼ 1.0) alleles.—The observed pattern of allele-frequency distribution was incompatible with the prediction from the overdominance hypothesis. The observed correlations of the numbers of rare alleles, polymorphic alleles and monomorphic alleles with heterozygosity were of the order of magnitude that was expected under the mutation-drift hypothesis. Our results did not support the view that intracistronic recombination is an important source of genetic variation. The total number of alleles per locus was positively correlated with molecular weight in most of the species examined, and the magnitude of the correlation was consistent with the theoretical prediction from mutation-drift hypothesis. The correlation between molecular weight and the number of alleles was generally higher than the correlation between molecular weight and heterozygosity, as expected. PMID:17249018

  12. VNTR allele frequency distributions under the stepwise mutation model: A computer simulation approach

    SciTech Connect

    Shriver, M.D.; Jin, L.; Chakraborty, R.; Boerwinkle, E. )

    1993-07-01

    Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size, and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). The authors estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. The authors then compared simulation expectations with actual data reported in the literature. They used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, it is hypothesized that these three classes of loci are subject to different mutational forces.

  13. Initial frequency of alleles conferring resistance to Bacillus thuringiensis poplar in a field population of Chrysomela tremulae.

    PubMed Central

    Génissel, Anne; Augustin, Sylvie; Courtin, Claudine; Pilate, Gilles; Lorme, Philippe; Bourguet, Denis

    2003-01-01

    Globally, the estimated total area planted with transgenic plants producing Bacillus thuringiensis (Bt) toxins was 12 million hectares in 2001. The risk of target pests becoming resistant to these toxins has led to the implementation of resistance-management strategies. The efficiency and sustainability of these strategies, including the high-dose plus refuge strategy currently recommended for North American maize, depend on the initial frequency of resistance alleles. In this study, we estimated the initial frequencies of alleles conferring resistance to transgenic Bt poplars producing Cry3A in a natural population of the poplar pest Chrysomela tremulae (Coleoptera: Chrysomelidae). We used the F(2) screen method developed for detecting resistance alleles in natural pest populations. At least three parents of the 270 lines tested were heterozygous for a major Bt resistance allele. We estimated mean resistance-allele frequency for the period 1999-2001 at 0.0037 (95% confidence interval = 0.00045-0.0080) with a detection probability of 90%. These results demonstrate that (i) the F(2) screen method can be used to detect major alleles conferring resistance to Bt-producing plants in insects and (ii) the initial frequency of alleles conferring resistance to Bt toxin can be close to the highest theoretical values that are expected prior to the use of Bt plants if considering fitness costs and typical mutation rates. PMID:12737656

  14. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

    Untoro, Evi; Atmadja, Djaja Surya; Pu, Chang-En; Wu, Fang-Chi

    2009-04-01

    Since the first application of DNA technology in 1985 in forensic cases, and the acceptance of this technology in 1988 at court, the DNA typing is widely used in personal identification, parentage cases and tracing the source of biological samples found in the crime scene. The FBI on 1990 had recommended the forensic labs to used 13 loci of Short Tandem Repeats (STR), known as CODIS 13, as the loci of choice for forensic use. The research on the population DNA database on these loci is extremely important for calculating the Paternity Index as well as Matching Probability for forensic application of DNA technology. As many as 402 unrelated persons, consisted of 322 from western part of Indonesia and 80 from eastern part of Indonesia, were chosen as the respondents of this research, after signing the informed consent. The peripheral blood sample was taken using sterile lancets and dropped onto FTA classic cards. The DNA was extracted by FTA purification solution (3x) and TE(-1) (2x), and amplified by PCR mix, either Cofiler or Profiler Plus (Perkin Elmers), followed by sequencing using ABI Prism type 3100 Avant Genetic Analyzer. The analysis showed that the alleles frequencies of Indonesian is specific, different with the other Asian populations with some specific alleles and microvariant were found.

  15. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

    Untoro, Evi; Atmadja, Djaja Surya; Pu, Chang-En; Wu, Fang-Chi

    2009-04-01

    Since the first application of DNA technology in 1985 in forensic cases, and the acceptance of this technology in 1988 at court, the DNA typing is widely used in personal identification, parentage cases and tracing the source of biological samples found in the crime scene. The FBI on 1990 had recommended the forensic labs to used 13 loci of Short Tandem Repeats (STR), known as CODIS 13, as the loci of choice for forensic use. The research on the population DNA database on these loci is extremely important for calculating the Paternity Index as well as Matching Probability for forensic application of DNA technology. As many as 402 unrelated persons, consisted of 322 from western part of Indonesia and 80 from eastern part of Indonesia, were chosen as the respondents of this research, after signing the informed consent. The peripheral blood sample was taken using sterile lancets and dropped onto FTA classic cards. The DNA was extracted by FTA purification solution (3x) and TE(-1) (2x), and amplified by PCR mix, either Cofiler or Profiler Plus (Perkin Elmers), followed by sequencing using ABI Prism type 3100 Avant Genetic Analyzer. The analysis showed that the alleles frequencies of Indonesian is specific, different with the other Asian populations with some specific alleles and microvariant were found. PMID:19261522

  16. Non-Equilibrium Allele Frequency Spectra Via Spectral Methods

    PubMed Central

    Hey, Jody; Chen, Kevin

    2011-01-01

    A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see [15]. In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright-Fisher process with migration of K populations, influx of mutations, and multiple population splitting events. PMID:21376069

  17. Initial frequency of alleles for resistance to Bacillus thuringiensis toxins in field populations of Heliothis virescens

    PubMed Central

    Gould, F.; Anderson, A.; Jones, A.; Sumerford, D.; Heckel, D. G.; Lopez, J.; Micinski, S.; Leonard, R.; Laster, M.

    1997-01-01

    The risk of rapid pest adaptation to an insecticide is highly dependent on the initial frequency of resistance alleles in field populations. Because we have lacked empirical estimates of these frequencies, population–genetic models of resistance evolution have relied on a wide range of theoretical estimates. The recent commercialization of genetically engineered cotton that constitutively produces an insecticidal protein derived from the biocontrol agent, Bacillus thuringiensis (Bt) has raised concern that we lack data needed to quantify the risk of insect pests such as Heliothis virescens rapidly adapting to this ecologically valuable class of toxins. By individually mating over 2,000 male H. virescens moths collected in four states to females of a Bt toxin-resistant laboratory strain, and screening F1 and F2 offspring for tolerance of the toxic protein, we were able to directly estimate the field frequency of alleles for resistance as 1.5 × 10−3. This high initial frequency underscores the need for caution in deploying transgenic cotton to control insect pests. Our single-pair mating technique greatly increases the efficiency of detecting recessive resistance alleles. Because alleles that decrease target site sensitivity to Bt toxins and other insecticides are often recessive, this technique could be useful in estimating resistance allele frequencies in other insects exposed to transgenic insecticidal crops or conventional insecticides. PMID:11038613

  18. New CODIS core loci allele frequencies for 96,400 Brazilian individuals.

    PubMed

    Aguiar, Vitor R C; de Castro, Amanda M; Almeida, Vanessa C O; Malta, Frederico S V; Ferreira, Alessandro C S; Louro, Iúri D

    2014-11-01

    We have reported the allele frequencies of 15 STR loci, including the original 13 CODIS core loci, in over 100,000 Brazilian individuals. A new CODIS core loci has been proposed, but the recently established Brazilian Integrated Network of DNA Databases made a decision in 2010 to postpone the implementation of this new set of loci due to the lack of allele frequency data for the Brazilian population. We aimed to report allele frequencies of 20 loci, estimated from 96,400 Brazilian individuals undergoing paternity testing during 2011-2013. The percentage of missing data was less than 0.6% for all loci, except for CSF1PO (3.15%) and D7S820 (2.5%). The dropout rates estimated by the MicroDrop software were 0.013 for CSF1PO, 0.000037 for D7S820 and less than 0.000001 for other loci. Small missing data percentages and dropout rates reflect the high quality of the data.

  19. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations.

    PubMed

    Gonzalez-Galarza, Faviel F; Christmas, Stephen; Middleton, Derek; Jones, Andrew R

    2011-01-01

    The allele frequency net database (http://www.allelefrequencies.net) is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. The extensive variability observed in genes and alleles related to the immune system response and its significance in transplantation, disease association studies and diversity in populations led to the development of this electronic resource. At present, the system contains data from 1133 populations in 608,813 individuals on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms. The project was designed to create a central source for the storage of frequency data and provide individuals with a set of bioinformatics tools to analyze the occurrence of these variants in worldwide populations. The resource has been used in a wide variety of contexts, including clinical applications (histocompatibility, immunology, epidemiology and pharmacogenetics) and population genetics. Demographic information, frequency data and searching tools can be freely accessed through the website.

  20. How-To-Do-It: Multiple Allelic Frequencies in Populations at Equilibrium: Algorithms and Applications.

    ERIC Educational Resources Information Center

    Nussbaum, Francis, Jr.

    1988-01-01

    Presents an algorithm for solving problems related to multiple allelic frequencies in populations at equilibrium. Considers sample problems and provides their solution using this tabular algorithm. (CW)

  1. Phylogenetic relationship analysis of Iranians and other world populations using allele frequencies at 12 polymorphic markers.

    PubMed

    Fazeli, Zahra; Vallian, Sadeq

    2012-12-01

    The estimation of genetic distance between populations could improve our viewpoint about human migration and its genetic origin. In this study, we used allele frequency data of 12 polymorphic markers on 250 individuals (500 alleles) from the Iranian population to estimate genetic distance between the Iranians and other world populations. The phylogenetic trees for three different sets of allele frequency data were constructed. Our results revealed the genetic similarity between the Iranians and European populations. The lowest genetic distance was observed between the Iranians and some populations reside in Russia. Furthermore, the high genetic distance was observed between the Iranians and East Asian populations. The data suggested that the Iranians might have relatively close evolutionary history with Europeans, but historically independent from East Asian populations. The evaluation of genetic distance between Indians populations and Iranians was also performed. The Indian groups showed low genetic distance with others, but high genetic distance with the Iranians. This study could provide a new insight into the evolutionary history of the Iranian population.

  2. Combining allele frequency uncertainty and population substructure corrections in forensic DNA calculations.

    PubMed

    Cowell, Robert

    2016-07-01

    In forensic DNA calculations of relatedness of individuals and in DNA mixture analyses, at least two sources of uncertainty are present concerning the allele frequencies used for evaluating genotype probabilities when evaluating likelihoods. They are: (i) imprecision in the estimates of the allele frequencies in the population by using an inevitably finite database of DNA profiles to estimate them; and (ii) the existence of population substructure. Green and Mortera [6] showed that these effects may be taken into account individually using a common Dirichlet model within a Bayesian network formulation, but that when taken in combination this is not the case; however they suggested an approximation that could be used. Here we develop a slightly different approximation that is shown to be exact in the case of a single individual. We demonstrate the numerical closeness of the approximation using a published database of allele counts, and illustrate the effect of incorporating the approximation into calculations of a recently published statistical model of DNA mixtures. PMID:27231804

  3. Estimating Allele Age and Selection Coefficient from Time-Serial Data

    PubMed Central

    Malaspinas, Anna-Sapfo; Malaspinas, Orestis; Evans, Steven N.; Slatkin, Montgomery

    2012-01-01

    Recent advances in sequencing technologies have made available an ever-increasing amount of ancient genomic data. In particular, it is now possible to target specific single nucleotide polymorphisms in several samples at different time points. Such time-series data are also available in the context of experimental or viral evolution. Time-series data should allow for a more precise inference of population genetic parameters and to test hypotheses about the recent action of natural selection. In this manuscript, we develop a likelihood method to jointly estimate the selection coefficient and the age of an allele from time-serial data. Our method can be used for allele frequencies sampled from a single diallelic locus. The transition probabilities are calculated by approximating the standard diffusion equation of the Wright–Fisher model with a one-step process. We show that our method produces unbiased estimates. The accuracy of the method is tested via simulations. Finally, the utility of the method is illustrated with an application to several loci encoding coat color in horses, a pattern that has previously been linked with domestication. Importantly, given our ability to estimate the age of the allele, it is possible to gain traction on the important problem of distinguishing selection on new mutations from selection on standing variation. In this coat color example for instance, we estimate the age of this allele, which is found to predate domestication. PMID:22851647

  4. HLA-A, -B and -DR allele and haplotype frequencies in Malays.

    PubMed

    Dhaliwal, J S; Shahnaz, M; Too, C L; Azrena, A; Maiselamah, L; Lee, Y Y; Irda, Y A; Salawati, M

    2007-03-01

    One thousand four hundreds and forty-five Malays registered with the Malaysian Marrow Donor Registry were typed for HLA-A, HLA-B and HLA-DR. Fifteen HLA-A, twenty nine HLA-B and fourteen HLA-DR alleles were detected. The most common HLA-A alleles and their frequencies were HLA-A24 (0.35), HLA-A11 (0.21) and HLA-A2 (0.15). The most common HLA-B alleles were HLA-B15 (0.26), HLA-B35 (0.11) and HLA-B18 (0.10) while the most common HLA-DR alleles were HLA-DR15 (0.28), HLA-DR12 (0.27) and HLA-DR7 (0.10). A24-B15-DR12 (0.047), A24-B15-DR15 (0.03) and the A24-B35-DR12 (0.03) were the most frequent haplotypes. This data may be useful in determining the probability of finding a matched donor and for estimating the incidence of HLA associated diseases.

  5. Confidence intervals for population allele frequencies: the general case of sampling from a finite diploid population of any size.

    PubMed

    Fung, Tak; Keenan, Kevin

    2014-01-01

    The estimation of population allele frequencies using sample data forms a central component of studies in population genetics. These estimates can be used to test hypotheses on the evolutionary processes governing changes in genetic variation among populations. However, existing studies frequently do not account for sampling uncertainty in these estimates, thus compromising their utility. Incorporation of this uncertainty has been hindered by the lack of a method for constructing confidence intervals containing the population allele frequencies, for the general case of sampling from a finite diploid population of any size. In this study, we address this important knowledge gap by presenting a rigorous mathematical method to construct such confidence intervals. For a range of scenarios, the method is used to demonstrate that for a particular allele, in order to obtain accurate estimates within 0.05 of the population allele frequency with high probability (> or = 95%), a sample size of > 30 is often required. This analysis is augmented by an application of the method to empirical sample allele frequency data for two populations of the checkerspot butterfly (Melitaea cinxia L.), occupying meadows in Finland. For each population, the method is used to derive > or = 98.3% confidence intervals for the population frequencies of three alleles. These intervals are then used to construct two joint > or = 95% confidence regions, one for the set of three frequencies for each population. These regions are then used to derive a > or = 95%% confidence interval for Jost's D, a measure of genetic differentiation between the two populations. Overall, the results demonstrate the practical utility of the method with respect to informing sampling design and accounting for sampling uncertainty in studies of population genetics, important for scientific hypothesis-testing and also for risk-based natural resource management. PMID:24465792

  6. Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon.

    PubMed

    da Costa Francez, Pablo Abdon; Rodrigues, Elzemar Martins Ribeiro; Frazão, Gleycianne Furtado; Dos Reis Borges, Nathalia Danielly; Dos Santos, Sidney Emanuel Batista

    2011-01-01

    The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (F(ST) coefficients) to the present database ranged from F(ST) = 0.0016 between Macapá and Belém to F(ST) = 0.0036 between Macapá and the Iberian Peninsula.

  7. Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon

    PubMed Central

    da Costa Francez, Pablo Abdon; Rodrigues, Elzemar Martins Ribeiro; Frazão, Gleycianne Furtado; dos Reis Borges, Nathalia Danielly; dos Santos, Sidney Emanuel Batista

    2011-01-01

    The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (FST coefficients) to the present database ranged from FST = 0.0016 between Macapá and Belém to FST = 0.0036 between Macapá and the Iberian Peninsula. PMID:21637540

  8. Frequencies of Null Alleles at Enzyme Loci in Natural Populations of Ponderosa and Red Pine

    PubMed Central

    Allendorf, Fred W.; Knudsen, Kathy L.; Blake, George M.

    1982-01-01

    Pinus ponderosa and P. resinosa population samples have mean frequencies of enzymatically inactive alleles of 0.0031 and 0.0028 at 29 and 27 enzyme loci, respectively. Such alleles are rare and are apparently maintained by selection-mutation balance. Ponderosa pine have much higher amounts of allozymic and polygenic phenotypic variation than red pine, yet both species have similar frequencies of null alleles. Thus, null alleles apparently do not contribute to polygenic variation, as has been suggested. The concordance between allozymic and polygenic variation adds support to the view that allozyme studies may be valuable in predicting the relative amount of polygenic variation in populations. PMID:17246067

  9. D9S1120, a simple STR with a common Native American-specific allele: forensic optimization, locus characterization and allele frequency studies.

    PubMed

    Phillips, C; Rodriguez, A; Mosquera-Miguel, A; Fondevila, M; Porras-Hurtado, L; Rondon, F; Salas, A; Carracedo, A; Lareu, M V

    2008-12-01

    The simple tetrameric STR D9S1120 exhibits a common population-specific allele of 9 repeats (9RA) reported to have an average frequency of 0.36 in Native Americans from both North and South of the continent. Apart from the presence of 9RA in two northeast Siberian populations, D9S1120 shows variability exclusive to, and universal in all American populations studied to date. This STR therefore provides an informative forensic marker applicable in countries with significant proportions of Native American populations or ancestry. We have re-designed PCR primers that reduce the amplified product sizes reported in NCBI UniSTS by more than a third and have characterized the repeat structure of D9S1120. The 9RA allele shares the same repeat structure as the majority of other D9S1120 alleles and so originates from a slippage-diminution mutation rather than an independent deletion. We confirm the previously reported allele frequencies from a range of populations indicating a global heterozygosity range for D9S1120 of 66-75% and estimate the proportion of Native American-diagnostic genotypes to average 53%, underlining the potential usefulness of this STR in both forensic identification and in population genetics studies of the Americas.

  10. Global distribution of allele frequencies at the human dopamine D4 receptor locus

    SciTech Connect

    Chang, F.M.; Kidd, J.R.; Livak, K.J.

    1994-09-01

    The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopaminergic system has been implicated in this neuropsychiatric disorder. Several research groups have reported an association between allelic variants at DRD4 and schizophrenia, while others have been unable to replicate that finding. Knowledge of the appropriate gene frequencies in the underlying populations may resolve these inconsistencies. We have determined the frequencies of 8 different alleles of the 48 bp imperfect tandem repeat of exon 3 at the DRD4 locus in samples from 33 populations around the world. The frequencies vary considerably in the different populations with the most common allele ranging from 16% to 95%. Frequencies and Fst values will be presented for the 3 most common alleles (4-, 7-, and 2- repeat) by continental groupings, but the individual populations vary significantly around the averages. The populations averaged 4.3 alleles (range 2 to 7).

  11. Minor Allele Frequency Changes the Nature of Genotype by Environment Interactions.

    PubMed

    Verhulst, Brad; Neale, Michael C

    2016-09-01

    In the classical twin study, phenotypic variation is often partitioned into additive genetic (A), common (C) and specific environment (E) components. From genetical theory, the outcome of genotype by environment interaction is expected to inflate A when the interacting factor is shared (i.e., C) between the members of a twin pair. We show that estimates of both A and C can be inflated. When the shared interacting factor changes the size of the difference between homozygotes' means, the expected sibling or DZ twin correlation is .5 if and only if the minor allele frequency (MAF) is .5; otherwise the expected DZ correlation is greater than this value, consistent (and confounded) with some additional effect of C. This result is considered in the light of the distribution of minor allele frequencies for polygenic traits. Also discussed is whether such interactions take place at the locus level or affect an aggregated biological structure or system. Interactions with structures or endophenotypes that result from the aggregated effects of many loci will generally emerge as part of the A estimate. PMID:27105628

  12. Estimations of uncertainties of frequencies

    NASA Astrophysics Data System (ADS)

    Eyer, Laurent; Nicoletti, Jean-Marc; Morgenthaler, Stephan

    2015-08-01

    Diverse variable phenomena in the Universe are periodic. Astonishingly many of the periodic signals present in stars have timescales coinciding with human ones (from minutes to years). The periods of signals often have to be deduced from time series which are irregularly sampled and sparse, furthermore correlations between the brightness measurements and their estimated uncertainties are common.The uncertainty on the frequency estimation is reviewed. We explore the astronomical and statistical literature, in both cases of regular and irregular samplings. The frequency uncertainty is depending on signal to noise ratio, the frequency, the observational timespan. The shape of the light curve should also intervene, since sharp features such as exoplanet transits, stellar eclipses, raising branches of pulsation stars give stringent constraints.We propose several procedures (parametric and nonparametric) to estimate the uncertainty on the frequency which are subsequently tested against simulated data to assess their performances.

  13. Dombrock genotyping in Brazilian blood donors reveals different regional frequencies of the HY allele

    PubMed Central

    Piassi, Fabiana Chagas Camargos; Santos, Silvana Maria Eloi; de Castilho, Lilian Maria; Baleotti Júnior, Wilson; Suzuki, Rodrigo Buzinaro; da Cunha, Débora Moura

    2013-01-01

    Background Dombrock blood group system genotyping has revealed various rearrangements of the Dombrock gene and identified new variant alleles in Brazil (i.e., DO*A-SH, DO*A-WL and DO*B-WL). Because of the high heterogeneity of the Brazilian population, interregional differences are expected during the investigation of Dombrock genotypes. Objective The present study aims to determine the frequencies of Dombrock genotypes in blood donors from Minas Gerais and compare the frequencies of the HY and JO alleles to those of another population in Brazil. Methods The frequencies of the DO alleles in Minas Gerais, a southeastern state of Brazil, were determined from the genotyping of 270 blood donors. Genotyping involved polymerase chain reaction and restriction fragment length polymorphism analysis to identify the 323G>T, 350C>T, 793A>G, and 898C>G mutations, which are related to the HY, JO, DO*A/DO*B, and DO*A-WL/DO*B-WL alleles, respectively. Moreover, the frequencies of rare HY and JO alleles were statistically compared using the chi-square test with data from another Brazilian region. Results The HY allele frequency in Minas Gerais (2.4%) was almost twice that of the JO allele (1.5%). The frequency of the HY allele was significantly higher (p-value = 0.001) than that in another Brazilian population and includes a rare homozygous donor with the Hy- phenotype. In addition, the DO*A-WL and DO*B-WL alleles, which were first identified in Brazil, were found in the state of Minas Gerais. Conclusions The data confirm that the frequencies of DO alleles differ between regions in Brazil. The population of Minas Gerais could be targeted in a screening strategy to identify the Hy- phenotype in order to develop a rare blood bank. PMID:24478605

  14. Frequency of HLA-A alleles in the Syrian population genotyped by sequence-based typing.

    PubMed

    Madania, A; Ghoury, I; Al-Ashkar, W; Nweder, S; Zarzour, H

    2014-10-01

    HLA-A molecules are highly polymorphic. Their accurate typing at a high-resolution level is crucial for successful organ, bone marrow and cord blood transplantation. Furthermore, several HLA alleles have been involved in susceptibility to autoimmune diseases, allergies, cancers and inflammations. In order to determine common HLA-A alleles in Syria and their frequencies, sequence-based typing (SBT) was used to genotype HLA-A alleles at high resolution (four digit level) among one hundred and thirty randomly selected Syrian individuals. Exons 2, 3 and 4 of the HLA-A gene were amplified by PCR and sequenced. The sbt-engine software was used for allele assignment. Ambiguities were solved using group-specific sequencing primers (GSSPs). We could identify 32 different HLA-A alleles which were divided into 3 groups: high frequency (approximately 10%, A*01:01; A*24:02; A*03:01; A*02:01), moderate frequency (approximately 3%, such as A*02:05, A*31:01 and A*33:01), and low frequency (approximately 1%, such as A*02:11, A*29:01, A*02:02 and A*36:01). Homozygosity rate was higher than expected (11.5% vs. 7.15%). For high frequency alleles, our results show similarity to neighbouring countries. However, 15 alleles (such as A*02:04, A*02:06, A*02:11 and A*02:17) found in our cohort in low frequencies were never reported in some or all neighbouring countries. This is the first report on HLA-A allele frequencies in Syria. In spite of the relatively low number of tested subjects, our results revealed a high degree of diversity, with 32 different alleles, reflecting the high ethnic heterogeneity of the Syrian population. The identification of alleles rarely or never reported in neighbouring countries indicates a higher genetic diversity in Syria.

  15. Inference in two dimensions: allele frequencies versus lengths of shared sequence blocks.

    PubMed

    Barton, N H; Etheridge, A M; Kelleher, J; Véber, A

    2013-08-01

    We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ(2), based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FST) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a 'local scale', κ; the rate of gene flow, σ(2), cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ(2). With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ(2).

  16. Allele frequency distributions of D1S80 in the Polish population.

    PubMed

    Ciesielka, M; Kozioł, P; Krajka, A

    1996-08-15

    The polymorphism of the D1S80 locus has been analyzed in a population sample of 208 unrelated individuals in the Southeast Poland and 103 mother/child pairs. PCR amplified alleles were separated by a vertical discontinuous polyacrylamide gel electrophoresis system. Nineteen different alleles and 52 phenotypes could be distinguished. The alleles 18 (f = 0.267) and 24 (f = 0.300) were most common in Poland. D1S80 genotype frequencies of Poland population do not deviate from Hardy-Weinberg equilibrium. All mother/child pairs shared at least one D1S80 allele.

  17. ApoE allele frequencies in Italian sporadic and familial Alzheimer's disease.

    PubMed

    Sorbi, S; Nacmias, B; Forleo, P; Latorraca, S; Gobbini, I; Bracco, L; Piacentini, S; Amaducci, L

    1994-08-15

    Recent studies have provided evidence of association of apolipoprotein E (ApoE) epsilon 4 allele and late onset familial and sporadic Alzheimer's disease (AD). Epidemiological studies have established allelic variation at the ApoE locus. We have analyzed the ApoE gene polymorphism in a sample of 446 Italian subjects. Our data confirm a significant association between epsilon 4 allele and sporadic AD. The frequency of epsilon 4 allele in early onset familial AD patients was comparable to control values suggesting that epsilon 4 allele does not represent a risk factor for early onset familial AD (EOFAD). Moreover, we found a not previously reported association between ApoE epsilon 2 allele and sporadic AD and EOFAD. PMID:7824157

  18. Models of Frequency-Dependent Selection with Mutation from Parental Alleles

    PubMed Central

    Trotter, Meredith V.; Spencer, Hamish G.

    2013-01-01

    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. PMID:23852384

  19. Power of IRT in GWAS: successful QTL mapping of sum score phenotypes depends on interplay between risk allele frequency, variance explained by the risk allele, and test characteristics.

    PubMed

    van den Berg, Stéphanie M; Service, Susan K

    2012-12-01

    As data from sequencing studies in humans accumulate, rare genetic variants influencing liability to disease and disorders are expected to be identified. Three simulation studies show that characteristics and properties of diagnostic instruments interact with risk allele frequency to affect the power to detect a quantitative trait locus (QTL) based on a test score derived from symptom counts or questionnaire items. Clinical tests, that is, tests that show a positively skewed phenotypic sum score distribution in the general population, are optimal to find rare risk alleles of large effect. Tests that show a negatively skewed sum score distribution are optimal to find rare protective alleles of large effect. For alleles of small effect, tests with normally distributed item parameters give best power for a wide range of allele frequencies. The item-response theory framework can help understand why an existing measurement instrument has more power to detect risk alleles with either low or high frequency, or both kinds.

  20. Geographical distribution of pyrethroid resistance allele frequency in head lice (Phthiraptera: Pediculidae) from Argentina.

    PubMed

    Toloza, Ariel Ceferino; Ascunce, Marina S; Reed, David; Picollo, María Inés

    2014-01-01

    The human head louse, Pediculus humanus capitis De Geer (Phthiraptera: Pediculidae), is an obligate ectoparasite that causes pediculosis capitis and has parasitized humans since the beginning of humankind. Head louse infestations are widespread throughout the world and have been increasing since the early 1990s partially because of ineffective pediculicides. In Argentina, the overuse of products containing pyrethroids has led to the development of resistant louse populations. Pyrethroid insecticides act on the nervous system affecting voltage-sensitive sodium channels. Three point mutations at the corresponding amino acid sequence positions M815I, T917I, and L920F in the voltage-gated sodium channel gene are responsible for contributing to knockdown resistance (kdr). The management of pyrethroid resistance requires either early detection or the characterization of the mechanisms involved in head louse populations. In the current study, we estimated the distribution of kdr alleles in 154 head lice from six geographical regions of Argentina. Pyrethroid resistance kdr alleles were found in high frequencies ranging from 67 to 100%. Of these, 131 (85.1%) were homozygous resistant, 13 (8.4%) were homozygous susceptible, and 10 (6.5%) were heterozygous. Exact tests for the Hardy-Weinberg equilibrium for each location showed that genotype frequencies differed significantly from expectation in four of the six sites studied. These results show that pyrethroid resistance is well established reaching an overall frequency of 88%, thus close to fixation. With 30 yr of pyrethroid-based pediculicides use in Argentina, kdr resistance has evolved rapidly among these head louse populations. PMID:24605463

  1. Geographical distribution of pyrethroid resistance allele frequency in head lice (Phthiraptera: Pediculidae) from Argentina.

    PubMed

    Toloza, Ariel Ceferino; Ascunce, Marina S; Reed, David; Picollo, María Inés

    2014-01-01

    The human head louse, Pediculus humanus capitis De Geer (Phthiraptera: Pediculidae), is an obligate ectoparasite that causes pediculosis capitis and has parasitized humans since the beginning of humankind. Head louse infestations are widespread throughout the world and have been increasing since the early 1990s partially because of ineffective pediculicides. In Argentina, the overuse of products containing pyrethroids has led to the development of resistant louse populations. Pyrethroid insecticides act on the nervous system affecting voltage-sensitive sodium channels. Three point mutations at the corresponding amino acid sequence positions M815I, T917I, and L920F in the voltage-gated sodium channel gene are responsible for contributing to knockdown resistance (kdr). The management of pyrethroid resistance requires either early detection or the characterization of the mechanisms involved in head louse populations. In the current study, we estimated the distribution of kdr alleles in 154 head lice from six geographical regions of Argentina. Pyrethroid resistance kdr alleles were found in high frequencies ranging from 67 to 100%. Of these, 131 (85.1%) were homozygous resistant, 13 (8.4%) were homozygous susceptible, and 10 (6.5%) were heterozygous. Exact tests for the Hardy-Weinberg equilibrium for each location showed that genotype frequencies differed significantly from expectation in four of the six sites studied. These results show that pyrethroid resistance is well established reaching an overall frequency of 88%, thus close to fixation. With 30 yr of pyrethroid-based pediculicides use in Argentina, kdr resistance has evolved rapidly among these head louse populations.

  2. Perceptual frames in frequency estimation.

    PubMed

    Zyłowska, Aleksandra; Kossek, Marcin; Wawrzyniak, Małgorzata

    2014-02-01

    This study is an introductory investigation of cognitive frames, focused on perceptual frames divided into information and formal perceptual frames, which were studied based on sub-additivity of frequency estimations. It was postulated that different presentations of a response scale would result in different percentage estimates of time spent watching TV or using the Internet. The results supported the existence of perceptual frames that influence the perception process and indicated that information perceptual frames had a stronger effect than formal frames. The measures made possible the exploration of the operation of perceptual frames and also outlined the relations between heuristics and cognitive frames. PMID:24765715

  3. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection

    PubMed Central

    Sams, Aaron J.; Hawks, John; Keinan, Alon

    2015-01-01

    The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles. PMID:25467111

  4. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection.

    PubMed

    Sams, Aaron J; Hawks, John; Keinan, Alon

    2015-02-01

    The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles.

  5. Analysis and frequency of bovine lymphocyte antigen DRB3.2 alleles in Jersey cows.

    PubMed

    Gilliespie, B E; Jayarao, B M; Dowlen, H H; Oliver, S P

    1999-09-01

    Jersey cows (n = 172) were genotyped for the bovine lymphocyte antigen (BoLA)-DRB3.2 allele by polymerase chain reaction and restriction fragment length polymorphism analysis. Bovine DNA was isolated from aliquots of whole blood. A two-step polymerase chain reaction followed by digestion with restriction endonucleases RsaI, BstyI, and HaeIII was conducted on the DNA from Jersey cattle. Twenty-four BoLA-DRB3.2 alleles were identified with frequencies ranging from 0.3 to 22.9%. Thirteen allele types were similar to those reported previously; and 11 were new allele types that have not been reported previously. Allele types reported previously include: BoLA-DRB3.2*2, *8, *10, *15, *17, *20, *21, *22, *23, *25, *28, *36, and *37. Their frequencies were 0.3, 11.3, 22.9, 13.6, 5.5, 3.7, 10.7, 3.5, 0.9, 0.3, 4.7, 9.3, and 0.9%, respectively. Of the new allele types detected, *ibe occurred at the highest frequency (6.1%) in Jersey cows from this herd. The six most frequently isolated alleles (BoLA-DRB3.2*8, *10, *15, *21, *36, and *ibe) accounted for 73.9% of the alleles in the population of this herd. Results of this study demonstrate that the BoLA-DRB3.2 locus is highly polymorphic in Jersey cattle.

  6. HLA Allele Frequencies in 5802 Koreans: Varied Allele Types Associated with SJS/TEN According to Culprit Drugs

    PubMed Central

    Park, Hye Jung; Kim, Young Joo; Kim, Dong Hyun; Kim, Junho; Park, Kyung Hee; Park, Jung-Won

    2016-01-01

    Purpose Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are very serious forms of drug-induced cutaneous adverse reaction. SJS/TEN induced by certain drug is well known to be associated with some human leukocyte antigen (HLA) gene type. We aimed to explore HLA allele frequencies and their association with SJS/TEN according to culprit drugs in Korea. Materials and Methods We enrolled 5802 subjects who had results of HLA typing test from August 2005 to July 2014. Total 28 SJS/TEN patients were categorized based on culprit drugs (allopurinol, lamotrigine, carbamazepine) and identified the presence of HLA-B*58:01, HLA-B*44:03, HLA-B*15:02, and HLA-A*31:01. Results HLA-A*24:02 (20.5%), HLA-B*44:03 (10.0%), and HLA-Cw*01:02 (17.1%) were the most frequent type in HLA-A, -B, and -C genes, respectively. Allele frequencies of HLA-B*58:01, HLA-B*44:03, HLA-A*31:01, and HLA-B*15:02 were 7.0%, 10.0%, 5.0%, and 0.3%, respectively. In 958 allopurinol users, 9 subjects (0.9%) were diagnosed with SJS/TEN. Among them, 8 subjects possessed HLA-B*58:01 allele. SJS/TEN induced by allopurinol was more frequently developed in subjects with HLA-B*58:01 than in subjects without it [odds ratio: 57.4; confidence interval (CI) 7.12-463.50; p<0.001]. Allopurinol treatment, based on screening by HLA-B*58:01 genotyping, could be more cost-effective than that not based on screening. HLA-B*44:03 may be associated with lamotrigine-induced SJS/TEN (odds ratio: 12.75; CI 1.03-157.14; p=0.053). Among carbamazepine users, only two patients experienced SJS/TEN and possessed neither HLA-B*15:02 nor HLA-A*31:03. Conclusion HLA gene frequencies varied in Korea. Screening of HLA-B*58:01 before the use of allopurinol might be needed to anticipate probability of SJS/TEN. PMID:26632391

  7. Estimating diversity via frequency ratios.

    PubMed

    Willis, Amy; Bunge, John

    2015-12-01

    We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of consecutive probabilities, we construct a nonlinear regression model for the ratios of consecutive frequency counts. This allows us to predict the unobserved count and hence estimate the total diversity. We believe that this is the first approach to depart from the classical mixed Poisson model in this problem. Our method is geometrically intuitive and yields good fits to data with reasonable standard errors. It is especially well-suited to analyzing high diversity datasets derived from next-generation sequencing in microbial ecology. We demonstrate the method's performance in this context and via simulation, and we present a dataset for which our method outperforms all competitors. PMID:26038228

  8. [RHD 1227A allele frequency among Rh negative population and random population].

    PubMed

    Wu, Jun-Jie; Hong, Xiao-Zhen; Xu, Xian-Guo; Ma, Kai-Rong; Zhu, Fa-Ming; Yan, Li-Xing

    2006-12-01

    To investigate the frequency of RHD 1227A allele in Rh negative population and random population, an AS-PCR (allele specific-polymerase chain reaction) method was employed to detect RHD 1227A allele. RHD gene copy was determined by D zygosity test and RHD exon 9 nucleotide sequence analysis. The results showed that among 143 Rh negative donors, forty-one RHD 1227A allele carriers were detected, and 8 (19.51%) out of which were RhCCdee, 32 (78.05%) were RhCcdee, and 1 (2.44%) was RhCcdEe. Thirty-five Rh negative RHD 1227A carriers had RHD gene deletion, and the remaining carriers were RHD 1227A homozygous. Seven (1.43%) individuals were detected with RHD 1227A allele among 489 random donors. They were all G/A heterozygous at RHD 1227 site. Serological test indicated that they were normal Rh positive phenotype. It is concluded that the frequency of RHD 1227A allele is 16.43% among Rh negative population and 0.72% among the random population.

  9. A novel fluorescent quadruplex STR typing system and the allele frequency distributions in a Thai population.

    PubMed

    Yoshimoto, Takashi; Yamamoto, Toshimichi; Mizutani, Masaki; Uchihi, Rieko; Ohtaki, Hiroyuki; Katsumata, Yoshinao; Waiyawuth, Worawee; Songsivilai, Sirirurg

    2003-01-01

    We have previously reported a new triplex amplification and typing system by silver staining for three short tandem repeat (STR) loci, 9q2h2 (D2S3020), D15S233, and D14S299 without "microvariant" alleles such as .1, .2, and, .3 alleles in the Japanese population. In the present study, we established a new quadruplex system with an additional locus D7S809 using primer sets labeled with fluorescent multi-color dyes. Using this system, we genotyped 183 Thai people, found only one "microvariant" allele (allele 20.2) at D7S809, and calculated allele frequencies and some statistical properties at these four STR loci. From these allele frequencies at four STR loci, we performed three statistical analyses including a homozygosity test, a likelihood ratio test, and an exact test for Hardy-Weinberg equilibrium (HWE). Deviations from HWE (p < 0.05) were observed only in the two tests at the locus D7S809. In the present study, we compared the allele frequencies at these four loci in the Thai population to those in the Japanese population described previously. Consequently, all observed heterozygosities and power of discrimination (PD) at those loci in the Thai population were higher than 0.8 and 0.9, respectively, and all statistical values for discriminating power in the Thai population were slightly higher than those in the Japanese population. The combined paternity exclusion rate (combined PE) in the Thai population (0.978) was almost the same as that in the Japanese population (0.971). Therefore, this novel PCR amplification and typing system for four STR loci would be a convenient and informative DNA profiling system in the forensic field. PMID:12570210

  10. Frequency of CCR5Δ32 allele in healthy Bosniak population.

    PubMed

    Adler, Grażyna; Valjevac, Amina; Skonieczna-Żydecka, Karolina; Mackic-Djurovic, Mirela; Parczewski, Miłosz; Urbańska, Anna; Salkic, Nermin Nusret

    2014-08-28

    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.

  11. Frequency of CCR5Δ32 allele in healthy Bosniak population

    PubMed Central

    Adler, Grażyna; Valjevac, Amina; Skonieczna-Żydecka, Karolina; Mackic-Djurovic, Mirela; Parczewski, Miłosz; Urbańska, Anna; Salkic, Nermin N

    2014-01-01

    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 the lowest 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 Herzegovina 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 Bosniaks (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. PMID:25172974

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

    PubMed

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

    2016-03-01

    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.

  13. Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile.

    PubMed

    Vergara, Ismael A; Villouta, Pamela; Herrera, Sandra; Melo, Francisco

    2012-05-01

    The thirteen autosomal STR loci of the CODIS system were typed from DNA of 732 unrelated male individuals sampled from different locations in Chile. This is the first report of allele frequencies for the thirteen STRs loci defined in the CODIS system from the Chilean population.

  14. Allele frequency data of 15 autosomal STR loci in four major population groups of South Africa.

    PubMed

    Lucassen, Anton; Ehlers, Karen; Grobler, Paul J; Shezi, Adeline L

    2014-03-01

    Allele frequency distributions for 15 tetrameric short tandem repeat (STR) loci were determined using the AmpFlSTR® Identifiler Plus™ PCR amplification kit. There was little evidence of departures from Hardy-Weinberg equilibrium or association of alleles of different loci in the population samples. The probability of identity values for the different populations range from 1/3.3 × 10(17) (White) to 1/1.88 × 10(18) (Coloured). The combined probability of paternal exclusion for the different population groups ranges from 0.9995858 (Coloured) to 0.9997874 (Indian).

  15. DNA-PKcs mutations in dogs and horses: allele frequency and association with neoplasia.

    PubMed

    Ding, Qi; Bramble, Lori; Yuzbasiyan-Gurkan, Vilma; Bell, Thomas; Meek, Katheryn

    2002-01-23

    Previously, spontaneous genetic immunodeficiencies in mice, Arabian foals, and recently in Jack Russell terriers have been ascribed to defects in DNA-PKcs (catalytic subunit of the DNA dependent protein kinase) expression. In severe combined immunodeficiency (SCID) foals, a 5 bp deletion at codon 9480 results in a frameshift and a 967 amino acid deletion from the C terminus (including the entire PI3 kinase domain) and an unstable mutant protein. In SCID mice, a single base pair mutation results in a premature stop codon and deletion of 83 amino acids; as in SCID foals, the mutant protein is unstable. Here, we define the mutation within the canine DNA-PKcs gene that results in SCID. In this case, a point mutation results in a stop codon at nucleotide 10,828 and premature termination at a position 517 amino acids before the normal C terminus resulting in a functionally null allele. Thus, this is the third documentation of a spontaneous germline mutation in the C terminus of DNA-PKcs. Emerging data implicate DNA repair factors as potential tumor suppressors. Here, we have ascertained the carrier frequency of the defective DNA-PKcs genes in Arabian horses and in Jack Russell terriers. Our data indicate (in good agreement with a previous report) that the carrier frequency of the equine SCID allele is approximately 8%; in contrast, the carrier frequency of the canine SCID allele is less than 1.1%. We also assessed the frequency of the equine SCID allele in a series of 295 tumors from Arabian horses. We find a statistically significant correlation between the development of a virally induced tumor (sarcoid) and heterozygosity for the equine SCID allele. These data provide further support for an emerging consensus: that DNA-PK may normally act as a tumor suppressor through its caretaker role in maintaining chromosomal stability. PMID:11867233

  16. Increased TNFA*2, but not TNFB*1, allele frequency in Spanish atopic patients.

    PubMed

    Castro, J; Tellería, J J; Linares, P; Blanco-Quirós, A

    2000-01-01

    Tumor necrosis factor (TNF) is a potent proinflammatory cytokine involved in asthma and atopy. Increased TNF-alpha levels have been found in airway biopsies and bronchoalveolar lavage fluids from asthmatic patients. Constitutional variations in the TNF-alpha secretion levels in vitro are associated with molecular polymorphisms located within and around the TNF loci. Our study objective was to investigate the association between atopy and two described di-allelic polymorphisms in the TNF locus: a G to A transition at position -308 in the 5'-promoter region of the TNFA gene (TNFA*1 and TNFA*2 alleles) and an Ncol restriction fragment length polymorphism (RFLP) in the first intron of the TNFB gene (TNFB*1 and TNFB*2 alleles). The genetic study was performed in 65 unrelated atopic patients and 60 healthy controls. The regions of interest were amplified from genomic DNA using specific primers and polymerase chain reaction. SSP-PCR analysis for TNFA -308 polymorphism genotyping and endonuclease digestion analysis for the TNFB Ncol RFLP were used. The frequency of the TNFA*2 allele was significantly higher in atopic subjects compared to the control group (38.5% vs. 10.5%; chi2 = 32.06; p <0.0001). The TNFA*2 allele is associated with a higher risk for the development of atopy (risk ratio = 9.44; EF = 0.65; chi2 = 30.06 p <0.0005). On the other hand, no significant association between the TNFB alleles and atopy was found. In conclusion, the TNFA*2 allele could be also a genetic risk marker for the predisposition to atopy in our population, as has been reported in other studies. Either the TNFA gene itself or a linked gene on chromosome region 6p21, which has yet to be identified, is a candidate gene for susceptibility to atopy. PMID:10923589

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

    PubMed

    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

  18. Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars.

    PubMed

    Shahin, Arwa; Smulders, Marinus J M; van Tuyl, Jaap M; Arens, Paul; Bakker, Freek T

    2014-01-01

    Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

  19. HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies of 10 918 Koreans from bone marrow donor registry in Korea.

    PubMed

    Park, H; Lee, Y-J; Song, E Y; Park, M H

    2016-10-01

    The human leucocyte antigen (HLA) system is the most polymorphic genetic system in humans, and HLA matching is crucial in organ transplantation, especially in hematopoietic stem cell transplantation. We investigated HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies at allelic level in 10 918 Koreans from bone marrow donor registry in Korea. Intermediate resolution HLA typing was performed using Luminex technology (Wakunaga, Japan), and additional allelic level typing was performed using PCR-single-strand conformation polymorphism method and/or sequence-based typing (Abbott Molecular, USA). Allele and haplotype frequencies were calculated by direct counting and maximum likelihood methods, respectively. A total of 39 HLA-A, 66 HLA-B and 47 HLA-DRB1 alleles were identified. High-frequency alleles found at a frequency of ≥5% were 6 HLA-A (A*02:01, *02:06, *11:01, *24:02, *31:01 and *33:03), 6 HLA-B (B*15:01, *35:01, *44:03, *51:01, 54:01 and *58:01) and 8 HLA-DRB1 (DRB1*01:01, *04:05, *04:06, *07:01, *08:03, *09:01, *13:02 and *15:01) alleles. At each locus, A*02, B*15 and DRB1*14 generic groups were most diverse at allelic level, consisting of 9, 12 and 11 different alleles, respectively. A total of 366, 197 and 21 different HLA-A-B-DRB1 haplotypes were estimated with frequencies of ≥0.05%, ≥0.1% and ≥0.5%, respectively. The five most common haplotypes with frequencies of ≥2.0% were A*33:03-B*44:03-DRB1*13:02 (4.97%), A*33:03-B*58:01-DRB1*13:02, A*33:03-B*44:03-DRB1*07:01, A*24:02-B*07:02-DRB1*01:01 and A*24:02-B*52:01-DRB1*15:02. Among 34 serologic HLA-A-B-DR haplotypes with frequencies of ≥0.5%, 17 haplotypes revealed allele-level diversity and majority of the allelic variation was arising from A2, A26, B61, B62, DR4 and DR14 specificities. Haplotype diversity obtained in this study is the most comprehensive data thus far reported in Koreans, and the information will be useful for unrelated stem cell transplantation as well as for disease

  20. Genotype and allele frequency of CYP2C19*17 in a healthy Iranian population

    PubMed Central

    Payan, Maryam; Tajik, Nader; Rouini, Mohammad Reza; Ghahremani, Mohammad Hossein

    2015-01-01

    Background: Cytochrome P450 2C19 (CYP2C19) is important in metabolism of wide range of drugs. CYP2C19*17 is a novel variant allele which increases gene transcription and therefore results in ultra-rapid metabolizer phenotype (URM). Distribution of this variant allele has not been well studied worldwide. The aim of present study was to investigate allele and genotype frequencies of CYP2C19*17 in a healthy Iranian population and compare them with other ethnic groups. Methods: One hundred eighty healthy unrelated Iranian volunteer took part in this study and were genotyped for CYP2C19 *2, *3, *17 (-3402) by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and CYP2C19*17 (-806) by a nested-PCR assays. The distribution of CYP2C19*17 polymorphism in Iranian population was then compared with other ethnic groups. Results: The CYP2C19*17 allele frequency was 21.6% in Iranian population. Among studied subjects 5.5% were homozygous for CYP2C19*17 and phenotyped as ultra-rapid metabolizers; 28.8% were genotyped as CYP2C19*1*17 (extensive metabolizers) and 3.3% as CYP2C19*2*17 (intermediate metabolizers). Conclusion: The CYP2C19*17 genetic distribution in Iranian population is similar to Middle East or European countries. The high frequency of CYP2C19*17 in Iranian population highlights the importance of this new variant allele in metabolism of CYP2C19 substrates. Thus, future association studies are required to reveal clinical consequence of this genetic polymorphism in carrier individuals. PMID:26793660

  1. Allele frequency data for 15 autosomal STR loci in eight Indonesian subpopulations.

    PubMed

    Venables, Samantha J; Daniel, Runa; Sarre, Stephen D; Soedarsono, Nurtami; Sudoyo, Herawati; Suryadi, Helena; van Oorschot, Roland A H; Walsh, Simon J; Widodo, Putut T; McNevin, Dennis

    2016-01-01

    Evolutionary and cultural history can affect the genetic characteristics of a population and influences the frequency of different variants at a particular genetic marker (allele frequency). These characteristics directly influence the strength of forensic DNA evidence and make the availability of suitable allele frequency information for every discrete country or jurisdiction highly relevant. Population sub-structure within Indonesia has not been well characterised but should be expected given the complex geographical, linguistic and cultural architecture of the Indonesian population. Here we use forensic short tandem repeat (STR) markers to identify a number of distinct genetic subpopulations within Indonesia and calculate appropriate population sub-structure correction factors. This data represents the most comprehensive investigation of population sub-structure within Indonesia to date using these markers. The results demonstrate that significant sub-structure is present within the Indonesian population and must be accounted for using island specific allele frequencies and corresponding sub-structure correction factors in the calculation of forensic DNA match statistics.

  2. Allele frequencies of 14 STR loci in the population of Malta.

    PubMed

    Cassar, M; Farrugia, C; Vidal, C

    2008-05-01

    Allele frequencies of 14 STR loci (D13S317, D16S539, D2S1338, vWA, TPOX, D18S51, D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, TH01 and D3S1358) observed in the population of Malta are being reported. Polymerase chain reaction (PCR) amplification using the AmpFl STR Identifiler kit was performed in a random sample of 157 subjects (314 chromosomes). Markers D2S1338, D18S51 and FGA had the highest power of discrimination (PD) values while TPOX was the least informative marker. Allele frequencies observed in the Maltese population were also compared with those of other populations from the Mediterranean region, Europe and Africa. Our data is useful for anthropological and other comparative studies of populations and is powerful for forensic and paternity testing in the Maltese islands.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26903642

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

    PubMed

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

    2016-03-01

    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. PMID:26903642

  5. HLA class II allele and haplotype frequencies in Ethiopian Amhara and Oromo populations.

    PubMed

    Fort, M; de Stefano, G F; Cambon-Thomsen, A; Giraldo-Alvarez, P; Dugoujon, J M; Ohayon, E; Scano, G; Abbal, M

    1998-04-01

    HLA class II alleles were identified in 181 healthy unrelated Ethiopian children of both sexes and in 350 European controls from the South of France. The Ethiopian individuals belonged to the two major ethnic groups of the country: Oromo (N=83) and Amhara (N=98). In both panels, genetic polymorphism of HLA class II alleles was analysed for the first time by molecular typing of DRB1, DQA1 and DQB1 loci. Allelic and phenotypic frequencies were compared with those of European controls and other African populations. Construction of HLA class II three-locus haplotypes was also performed. The study revealed some differences between the two groups. Characteristic features of Central and North African populations appeared on the Ethiopian HLA genotypes. Surprisingly, DRB1*11 presented one of the lowest gene frequencies in both Ethiopian ethnic groups in contrast to Europeans and West Africans. Furthermore, this decrease was more marked than those observed using serological techniques in other geographically close East African countries. Oromo and Amhara only showed minor differences in spite of their different origins and histories. One significant difference consisted of a lower DRB1*01 gene frequency in Oromo as reported in most West African people. Some new or rare haplotypes were also observed in the Oromo group. Our results underline the distinctive features of the Ethiopian populations among the few HLA genotyping data available for East African groups and emphasise the major interest of such investigations in this region of Africa.

  6. Detection of Allelic Frequency Differences between the Sexes in Humans: A Signature of Sexually Antagonistic Selection

    PubMed Central

    Lucotte, Elise A.; Laurent, Romain; Heyer, Evelyne; Ségurel, Laure; Toupance, Bruno

    2016-01-01

    Sexually antagonistic (SA) selection, a form of selection that can occur when both sexes have different fitness optima for a trait, is a major force shaping the evolution of organisms. A seminal model developed by Rice (Rice WR. 1984. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38:735–742.) predicts that the X chromosome should be a hotspot for the accumulation of loci under SA selection as compared with the autosomes. Here, we propose a methodological framework designed to detect a specific signature of SA selection on viability, differences in allelic frequencies between the sexes. Applying this method on genome-wide single nucleotide polymorphism (SNP) data in human populations where no sex-specific population stratification could be detected, we show that there are overall significantly more SNPs exhibiting differences in allelic frequencies between the sexes on the X chromosome as compared with autosomes, supporting the predictions of Rice’s model. This pattern is consistent across populations and is robust to correction for potential biases such as differences in linkage disequilibrium, sample size, and genotyping errors between chromosomes. Although SA selection is not the only factor resulting in allelic frequency differences between the sexes, we further show that at least part of the identified X-linked loci is caused by such a sex-specific processes. PMID:27189992

  7. ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays

    PubMed Central

    Ortiz-Estevez, Maria; Bengtsson, Henrik; Rubio, Angel

    2010-01-01

    Motivation: Current algorithms for estimating DNA copy numbers (CNs) borrow concepts from gene expression analysis methods. However, single nucleotide polymorphism (SNP) arrays have special characteristics that, if taken into account, can improve the overall performance. For example, cross hybridization between alleles occurs in SNP probe pairs. In addition, most of the current CN methods are focused on total CNs, while it has been shown that allele-specific CNs are of paramount importance for some studies. Therefore, we have developed a summarization method that estimates high-quality allele-specific CNs. Results: The proposed method estimates the allele-specific DNA CNs for all Affymetrix SNP arrays dealing directly with the cross hybridization between probes within SNP probesets. This algorithm outperforms (or at least it performs as well as) other state-of-the-art algorithms for computing DNA CNs. It better discerns an aberration from a normal state and it also gives more precise allele-specific CNs. Availability: The method is available in the open-source R package ACNE, which also includes an add on to the aroma.affymetrix framework (http://www.aroma-project.org/). Contact: arubio@ceit.es Supplementaruy information: Supplementary data are available at Bioinformatics online. PMID:20529889

  8. An historical perspective on "The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus".

    PubMed

    Kidd, Kenneth K; Pakstis, Andrew J; Yun, Libing

    2014-04-01

    Human population genetics is a completely different science today compared to two decades ago, at least at the empiric level. Our paper [Chang (Hum Genet 98:91-101, 1996a)] demonstrated that three different alleles were common when one considered many populations although other low frequency alleles occurred. Because previous work had been largely done on European subjects, our findings involved 36 distinct populations and showed that East Asian populations had nearly lost the 7-repeat allele, and that Native American populations had the highest frequencies of that allele globally, was a significant early empiric demonstration of the potential magnitude of population variation at important genes. There are thousands of loci tested on many of the same populations and the gene frequency pattern seen for the DRD4 7-repeat allele is seen at other loci, arguing that this pattern commonly reflects the pattern of divergence of populations and accumulated random genetic drift.

  9. Intracellular Population Genetics: Evidence for Random Drift of Mitochondrial Allele Frequencies in SACCHAROMYCES CEREVISIAE and SCHIZOSACCHAROMYCES POMBE

    PubMed Central

    Thrailkill, Kathryn M.; Birky, C. William; Lückemann, Gudrun; Wolf, Klaus

    1980-01-01

    We report evidence for random drift of mitochondrial allele frequencies in zygote clones of Saccharomyces cerevisiae and Schizosaccharomyces pombe. Monofactorial and bifactorial crosses were done, using strains resistant or sensitive to erythromycin (alleles ER, ES), oligomycin (OR, OS), or diuron (DR, DS). The frequencies of resistant and sensitive cells (and thus the frequencies of the resistant and sensitive alleles) were determined for each of a number of clones of diploid cells arising from individual zygotes. Allele frequencies were extremely variable among these zygote clones; some clones were "uniparental," with mitochondrial alleles from only one parent present. These observations suggest random drift of the allele frequencies in the population of mitochondrial genes within an individual zygote and its diploid progeny. Drift would cease when all the cells in a clone become homoplasmic, due to segregation of the mitochondrial genomes during vegetative cell divisions. To test this, we delayed cell division (and hence segregation) for varying times by starving zygotes in order to give drift more time to operate. As predicted, delaying cell division resulted in an increase in the variance of allele frequencies among the zygote clones and an increase in the proportion of uniparental zygote clones. The changes in form of the allele frequency distributions resembled those seen during random drift in finite Mendelian populations. In bifactorial crosses, genotypes as well as individual alleles were fixed or lost in some zygote clones. However, the mean recombination frequency for a large number of clones did not increase when cell division was delayed. Several possible molecular mechanisms for intracellular random drift are discussed. PMID:7009322

  10. The non-equilibrium allele frequency spectrum in a Poisson random field framework.

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

    In population genetic studies, the allele frequency spectrum (AFS) efficiently summarizes genome-wide polymorphism data and shapes a variety of allele frequency-based summary statistics. While existing theory typically features equilibrium conditions, emerging methodology requires an analytical understanding of the build-up of the allele frequencies over time. In this work, we use the framework of Poisson random fields to derive new representations of the non-equilibrium AFS for the case of a Wright-Fisher population model with selection. In our approach, the AFS is a scaling-limit of the expectation of a Poisson stochastic integral and the representation of the non-equilibrium AFS arises in terms of a fixation time probability distribution. The known duality between the Wright-Fisher diffusion process and a birth and death process generalizing Kingman's coalescent yields an additional representation. The results carry over to the setting of a random sample drawn from the population and provide the non-equilibrium behavior of sample statistics. Our findings are consistent with and extend a previous approach where the non-equilibrium AFS solves a partial differential forward equation with a non-traditional boundary condition. Moreover, we provide a bridge to previous coalescent-based work, and hence tie several frameworks together. Since frequency-based summary statistics are widely used in population genetics, for example, to identify candidate loci of adaptive evolution, to infer the demographic history of a population, or to improve our understanding of the underlying mechanics of speciation events, the presented results are potentially useful for a broad range of topics.

  11. The non-equilibrium allele frequency spectrum in a Poisson random field framework.

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

    In population genetic studies, the allele frequency spectrum (AFS) efficiently summarizes genome-wide polymorphism data and shapes a variety of allele frequency-based summary statistics. While existing theory typically features equilibrium conditions, emerging methodology requires an analytical understanding of the build-up of the allele frequencies over time. In this work, we use the framework of Poisson random fields to derive new representations of the non-equilibrium AFS for the case of a Wright-Fisher population model with selection. In our approach, the AFS is a scaling-limit of the expectation of a Poisson stochastic integral and the representation of the non-equilibrium AFS arises in terms of a fixation time probability distribution. The known duality between the Wright-Fisher diffusion process and a birth and death process generalizing Kingman's coalescent yields an additional representation. The results carry over to the setting of a random sample drawn from the population and provide the non-equilibrium behavior of sample statistics. Our findings are consistent with and extend a previous approach where the non-equilibrium AFS solves a partial differential forward equation with a non-traditional boundary condition. Moreover, we provide a bridge to previous coalescent-based work, and hence tie several frameworks together. Since frequency-based summary statistics are widely used in population genetics, for example, to identify candidate loci of adaptive evolution, to infer the demographic history of a population, or to improve our understanding of the underlying mechanics of speciation events, the presented results are potentially useful for a broad range of topics. PMID:27378747

  12. Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection...

  13. Linear Frequency Estimation Technique for Reducing Frequency Based Signals

    PubMed Central

    Woodbridge, Jonathan; Bui, Alex; Sarrafzadeh, Majid

    2016-01-01

    This paper presents a linear frequency estimation (LFE) technique for data reduction of frequency-based signals. LFE converts a signal to the frequency domain by utilizing the Fourier transform and estimates both the real and imaginary parts with a series of vectors much smaller than the original signal size. The estimation is accomplished by selecting optimal points from the frequency domain and interpolating data between these points with a first order approximation. The difficulty of such a problem lies in determining which points are most significant. LFE is unique in the fact that it is generic to a wide variety of frequency-based signals such as electromyography (EMG), voice, and electrocardiography (ECG). The only requirement is that spectral coefficients are spatially correlated. This paper presents the algorithm and results from both EMG and voice data. We complete the paper with a description of how this method can be applied to pattern types of recognition, signal indexing, and compression.

  14. Determination of the Allelic Frequency in Smith-Lemli-Opitz Syndrome by Analysis of Massively Parallel Sequencing Data Sets

    PubMed Central

    Cross, Joanna L.; Iben, James; Simpson, Claire; Thurm, Audrey; Swedo, Susan; Tierney, Elaine; Bailey-Wilson, Joan; Biesecker, Leslie G.; Porter, Forbes D.; Wassif, Christopher A.

    2014-01-01

    Data from massively parallel sequencing or “Next Generation Sequencing” of the human exome has reached a critical mass in both public and private databases, in that these collections now allow researchers to critically evaluate population genetics in a manner that was not feasible a decade ago. The ability to determine pathogenic allele frequencies by evaluation of the full coding sequences and not merely a single SNP or series of SNPs will lead to more accurate estimations of incidence. For demonstrative purposes we analyzed the causative gene for the disorder Smith-Lemli-Opitz Syndrome (SLOS), the 7-dehydrocholesterol reductase (DHCR7) gene and determined both the carrier frequency for DHCR7 mutations, and predicted an expected incidence of the disorder. Estimations of the incidence of SLOS have ranged widely from 1:10,000 to 1:70,000 while the carrier frequency has been reported as high as 1 in 30. Using four exome data sets with a total of 17,836 chromosomes, we ascertained a carrier frequency of pathogenic DHRC7 mutations of 1.01%, and predict a SLOS disease incidence of 1/39,215 conceptions. This approach highlights yet another valuable aspect of the exome sequencing databases, to inform clinical and health policy decisions related to genetic counseling, prenatal testing and newborn screening. PMID:24813812

  15. Semantic Web-based integration of cancer pathways and allele frequency data.

    PubMed

    Holford, Matthew E; Rajeevan, Haseena; Zhao, Hongyu; Kidd, Kenneth K; Cheung, Kei-Hoi

    2009-01-01

    We demonstrate the use of Semantic Web technology to integrate the ALFRED allele frequency database and the Starpath pathway resource. The linking of population-specific genotype data with cancer-related pathway data is potentially useful given the growing interest in personalized medicine and the exploitation of pathway knowledge for cancer drug discovery. We model our data using the Web Ontology Language (OWL), drawing upon ideas from existing standard formats BioPAX for pathway data and PML for allele frequency data. We store our data within an Oracle database, using Oracle Semantic Technologies. We then query the data using Oracle's rule-based inference engine and SPARQL-like RDF query language. The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions. Among the possibilities is the ability to identify genetic variants which are associated with cancer pathways and whose frequency varies significantly between ethnic groups. This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine. It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies.

  16. Frequency and characterization of known and novel RHD variant alleles in 37 782 Dutch D-negative pregnant women.

    PubMed

    Stegmann, Tamara C; Veldhuisen, Barbera; Bijman, Renate; Thurik, Florentine F; Bossers, Bernadette; Cheroutre, Goedele; Jonkers, Remco; Ligthart, Peter; de Haas, Masja; Haer-Wigman, Lonneke; van der Schoot, C Ellen

    2016-05-01

    To guide anti-D prophylaxis, Dutch D- pregnant women are offered a quantitative fetal-RHD-genotyping assay to determine the RHD status of their fetus. This allowed us to determine the frequency of different maternal RHD variants in 37 782 serologically D- pregnant women. A variant allele is present in at least 0·96% of Dutch D- pregnant women The D- serology could be confirmed after further serological testing in only 54% of these women, which emphasizes the potential relevance of genotyping of blood donors. 43 different RHD variant alleles were detected, including 15 novel alleles (11 null-, 2 partial D- and 2 DEL-alleles). Of those novel null alleles, one allele contained a single missense mutation (RHD*443C>G) and one allele had a single amino acid deletion (RHD*424_426del). The D- phenotype was confirmed by transduction of human D- erythroblasts, consolidating that, for the first time, a single amino acid change or deletion causes the D- phenotype. Transduction also confirmed the phenotypes for the two new variant DEL-alleles (RHD*721A>C and RHD*884T>C) and the novel partial RHD*492C>A allele. Notably, in three additional cases the DEL phenotype was observed but sequencing of the coding sequence, flanking introns and promoter region revealed an apparently wild-type RHD allele without mutations. PMID:27018217

  17. Comparison of allele frequencies of eight STR loci from Argentinian Amerindian and European populations.

    PubMed

    Sala, A; Penacino, G; Corach, D

    1998-10-01

    Eight STR systems (THO1, FABP, VWA, FES/FPS, HPRTB, F13A1, CSF1PO, and D6S366) were investigated in different ethnic groups of Argentina. Allele and genotype frequencies, power of exclusion, and discriminative power were investigated. Hardy-Weinberg expectations were calculated from heterozygosity levels. FST and G tests demonstrated that significant differences exist among the investigated populations for some of the eight STRs markers. The Wichi Indians are clearly separated from the Mapuche and Tehuelche, who in turn are closer to the European population, suggesting non-Amerindian admixture.

  18. Frequency of CYP2C9 alleles in Koreans and their effects on losartan pharmacokinetics

    PubMed Central

    Bae, Jung-woo; Choi, Chang-ik; Kim, Mi-jeong; Oh, Da-hee; Keum, Seul-ki; Park, Jung-in; Kim, Bo-hye; Bang, Hye-kyoung; Oh, Sung-gon; Kang, Byung-sung; Park, Hyun-joo; Kim, Hae-deun; Ha, Ji-hey; Shin, Hee-jung; Kim, Young-hoon; Na, Han-sung; Chung, Myeon-woo; Jang, Choon-gon; Lee, Seok-yong

    2011-01-01

    Aim: CYP2C9 enzyme metabolizes numerous clinically important drugs. The aim of this study is to investigate the frequencies of CYP2C9 genotypes and the effects of selected alleles on losartan pharmacokinetics in a large sample of the Korean population. Methods: The CYP2C9 gene was genotyped in 1796 healthy Korean subjects. CYP2C9 alleles (CYP2C9*1, *2, *3 and *13 alleles) were measured using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay and direct sequencing assay. The enzymatic activity of each CYP2C9 genotype was evaluated using losartan as the substrate. Results: The frequencies of CYP2C9*1, *3 and *13 allele were 0.952 (95% confidence interval 0.945–0.959), 0.044 (95% CI 0.037–0.051) and 0.005 (95% CI 0.003–0.007), respectively. The frequencies of the CYP2C9*1/*1, *1/*3, *1/*13 and *3/*3 genotypes were 0.904 (95% CI 0.890–0.918), 0.085 (95% CI 0.072–0.098), 0.009 (95% CI 0.005–0.013) and 0.001 (95% CI 0.000–0.002), respectively. In the pharmacokinetics studies, the AUC0–∞ of losartan in CYP2C9*3/*3 subjects was 1.42-fold larger than that in CYP2C9*1/*1 subjects, and the AUC0–∞ of E-3174, a more active metabolite of losartan, in CYP2C9*3/*3 subjects was only 12% of that in CYP2C9*1/*1 subjects. Conclusion: The results confirmed the frequencies of CYP2C9 genotypes in a large cohort of Koreans, and detected the CYP2C9*3/*3 genotype. CYP2C9*3/*3 subjects metabolized much less losartan into E-3174 than CYP2C9*1/*1 subjects. PMID:21841812

  19. Allele and genotype frequencies of metabolic genes in Native Americans from Argentina and Paraguay.

    PubMed

    Bailliet, G; Santos, M R; Alfaro, E L; Dipierri, J E; Demarchi, D A; Carnese, F R; Bianchi, N O

    2007-03-01

    Interethnic differences in the allele frequencies of CYP2D6, NAT2, GSTM1 and GSTT1 deletions have been documented for Caucasians, Asians, and Africans population. On the other hand, data on Amerindians are scanty and limited to a few populations from southern areas of South America. In this report we analyze the frequencies of 11 allele variants of CYP2D6 and 4 allele variants of NAT2 genes, and the frequency of GSTM1 and GSTT1 homozygous deleted genotypes in a sample of 90 donors representing 8 Native American populations from Argentina and Paraguay, identified as Amerindians on the basis of their geographic location, genealogical data, mitochondrial- and Y-chromosome DNA markers. For CYP2D6, 88.6% of the total allele frequency corresponded to *1, *2, *4 and *10 variants. Average frequencies for NAT2 *4, *5, *6 and *7 alleles were 51.2%, 25%, 6.1%, and 20.1%, respectively. GSTM1 deletion ranged from 20% to 66%, while GSTT1 deletion was present in four populations in less than 50%. We assume that CYP2D6 *2, *4, *10, *14; NAT2 *5, *7 alleles and GSTM1 and GSTT1 *0/*0 genotypes are founder variants brought to America by the first Asian settlers. PMID:17194620

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

    PubMed

    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.

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

    PubMed

    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.

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

    PubMed Central

    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

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

    PubMed

    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. PMID:25867025

  4. Differences in allele frequencies of autosomal dominant hypercholesterolemia SNPs in the Malaysian population.

    PubMed

    Alex, Livy; Chahil, Jagdish Kaur; Lye, Say Hean; Bagali, Pramod; Ler, Lian Wee

    2012-06-01

    Hypercholesterolemia is caused by different interactions of lifestyle and genetic determinants. At the genetic level, it can be attributed to the interactions of multiple polymorphisms, or as in the example of familial hypercholesterolemia (FH), it can be the result of a single mutation. A large number of genetic markers, mostly single nucleotide polymorphisms (SNP) or mutations in three genes, implicated in autosomal dominant hypercholesterolemia (ADH), viz APOB (apolipoprotein B), LDLR (low density lipoprotein receptor) and PCSK9 (proprotein convertase subtilisin/kexin type-9), have been identified and characterized. However, such studies have been insufficiently undertaken specifically in Malaysia and Southeast Asia in general. The main objective of this study was to identify ADH variants, specifically ADH-causing mutations and hypercholesterolemia-associated polymorphisms in multiethnic Malaysian population. We aimed to evaluate published SNPs in ADH causing genes, in this population and to report any unusual trends. We examined a large number of selected SNPs from previous studies of APOB, LDLR, PCSK9 and other genes, in clinically diagnosed ADH patients (n=141) and healthy control subjects (n=111). Selection of SNPs was initiated by searching within genes reported to be associated with ADH from known databases. The important finding was 137 mono-allelic markers (44.1%) and 173 polymorphic markers (55.8%) in both subject groups. By comparing to publicly available data, out of the 137 mono-allelic markers, 23 markers showed significant differences in allele frequency among Malaysians, European Whites, Han Chinese, Yoruba and Gujarati Indians. Our data can serve as reference for others in related fields of study during the planning of their experiments.

  5. Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation.

    PubMed

    Racimo, Fernando

    2016-02-01

    A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called "3-population composite likelihood ratio" (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events. PMID:26596347

  6. Allele frequency distribution of 10 MiniSTRs in the Pashtun population of Pakistan.

    PubMed

    Shafique, Muhammad; Shahzad, Muhammad Saqib; Perveen, Uzma; Parveen, Rukhsana; Ali, Azam; Hussain, Manzoor; Rehman, Ziaur; Shahid, Ahmad Ali; Husnain, Tayyab

    2015-05-01

    Two hundred individual samples of Pashtun population from Khyber Pakhtunkhwa province of Pakistan were randomly evaluated through 10 MiniSTR loci (CSF1PO, D7S820, TPOX, D18S51, D2S1338, D13S317, FGA, D5S818, D21S11, and D16S539). The PCR product size was reduced in the range of 65 to 280 bp. A total of 112 alleles were observed containing allelic frequency ranging from 0.0025 to 0.4325. Statistical values for forensic and parentage analysis were calculated including combined power of discrimination (PD), combined power of exclusion (PE), and cumulative probability of matching (PM) and equaled to 0.99999999999768, 0.99984944, and 2.33 × 10(-12), respectively. These MiniSTRs show a high degree of polymorphism information content and discriminatory power which would be helpful to resolve forensic cases and establish DNA database for major population groups of Pakistan. In contrast to different populations, significant differences were also observed on these loci. PMID:25821203

  7. Frequency of null allele of Human Leukocyte Antigen-G (HLA-G) locus in subjects to recurrent miscarriage

    PubMed Central

    Alizadeh, Nazila; Mosaferi, Elnaz; Farzadi, Laya; Majidi, Jafar; Monfaredan, Amir; Yousefi, Bahman; Baradaran, Behzad

    2016-01-01

    Background: Human leukocyte antigen-G (HLA-G) is a non-classical class I molecule highly expressed by extravillous cytotrophoblast cells. Due to a single base pair deletion, its function can be compensated by other isoforms. Investigating the frequency of null allele in Recurrent Miscarriage (RM) subjects could be useful in understanding the relationship between frequency of this allele and RM in a given population. Objective: This study aimed to determine the frequency of HLA-G*0105N null allele and its potential association with down-regulation of HLA-G in subjects with RM. Materials and Methods: Western blotting was used to assess the level of HLA-G protein expression. For investigating the frequency of HLA-G*0105N null allele in RM subjects, PCR-RFLP method was used. Exon 3 of HLA-G gene was amplified by polymerase chain reaction (PCR). Subsequently, PpuM-1 enzyme was employed to digest the PCR products and fragments were analyzed using gel electrophoresis. Results: Digestion using restriction enzyme showed the presence of heterozygous HLA-G*0105N null allele in 10% of the test population. Western blotting results confirmed the decrease in expression of HLA-G in the placental tissue of subjects with RM compared to subjects who could give normal birth. Conclusion: The frequency of heterozygous HLA-G*0105N null allele was high to some extent in subjects with RM. The mutation rate in subjects suggested that there is a significant association between RM and frequency of mutations in this allele. PMID:27525330

  8. Estimations of object frequency are frequently overestimated.

    PubMed

    Greene, Michelle R

    2016-04-01

    Real-world scenes are complex but lawful: blenders are more likely to be found in kitchens than beaches, and elephants are not generally found inside homes. Research over the past 40years has demonstrated that contextual associations influence object recognition, change eye movement distributions, and modulate brain activity. However, the majority of these studies choose object-scene pairs from experimenters' intuitions because the statistical relationships between objects and scenes had yet to be systematically quantified. How do intuitive estimations compare to actual object frequencies? Across six experiments, observers estimated the frequency with which an object is found in a particular environment, such as the frequency of "mug" in an office. Estimated frequencies were compared to observed frequencies in two fully labeled scene databases (Greene, 2013). Although inter-observer similarity was high, observers systematically overestimated object frequency by an average of 32% across experiments. Altogether, these results speak to the richness of scene schemata and to the necessity of measuring object frequencies. PMID:26774103

  9. Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants.

    PubMed

    Shearer, A Eliot; Eppsteiner, Robert W; Booth, Kevin T; Ephraim, Sean S; Gurrola, José; Simpson, Allen; Black-Ziegelbein, E Ann; Joshi, Swati; Ravi, Harini; Giuffre, Angelica C; Happe, Scott; Hildebrand, Michael S; Azaiez, Hela; Bayazit, Yildirim A; Erdal, Mehmet Emin; Lopez-Escamez, Jose A; Gazquez, Irene; Tamayo, Marta L; Gelvez, Nancy Y; Leal, Greizy Lopez; Jalas, Chaim; Ekstein, Josef; Yang, Tao; Usami, Shin-ichi; Kahrizi, Kimia; Bazazzadegan, Niloofar; Najmabadi, Hossein; Scheetz, Todd E; Braun, Terry A; Casavant, Thomas L; LeProust, Emily M; Smith, Richard J H

    2014-10-01

    Ethnic-specific differences in minor allele frequency impact variant categorization for genetic screening of nonsyndromic hearing loss (NSHL) and other genetic disorders. We sought to evaluate all previously reported pathogenic NSHL variants in the context of a large number of controls from ethnically distinct populations sequenced with orthogonal massively parallel sequencing methods. We used HGMD, ClinVar, and dbSNP to generate a comprehensive list of reported pathogenic NSHL variants and re-evaluated these variants in the context of 8,595 individuals from 12 populations and 6 ethnically distinct major human evolutionary phylogenetic groups from three sources (Exome Variant Server, 1000 Genomes project, and a control set of individuals created for this study, the OtoDB). Of the 2,197 reported pathogenic deafness variants, 325 (14.8%) were present in at least one of the 8,595 controls, indicating a minor allele frequency (MAF) > 0.00006. MAFs ranged as high as 0.72, a level incompatible with pathogenicity for a fully penetrant disease like NSHL. Based on these data, we established MAF thresholds of 0.005 for autosomal-recessive variants (excluding specific variants in GJB2) and 0.0005 for autosomal-dominant variants. Using these thresholds, we recategorized 93 (4.2%) of reported pathogenic variants as benign. Our data show that evaluation of reported pathogenic deafness variants using variant MAFs from multiple distinct ethnicities and sequenced by orthogonal methods provides a powerful filter for determining pathogenicity. The proposed MAF thresholds will facilitate clinical interpretation of variants identified in genetic testing for NSHL. All data are publicly available to facilitate interpretation of genetic variants causing deafness. PMID:25262649

  10. Frequency tracking and parameter estimation for robust quantum state estimation

    SciTech Connect

    Ralph, Jason F.; Jacobs, Kurt; Hill, Charles D.

    2011-11-15

    In this paper we consider the problem of tracking the state of a quantum system via a continuous weak measurement. If the system Hamiltonian is known precisely, this merely requires integrating the appropriate stochastic master equation. However, even a small error in the assumed Hamiltonian can render this approach useless. The natural answer to this problem is to include the parameters of the Hamiltonian as part of the estimation problem, and the full Bayesian solution to this task provides a state estimate that is robust against uncertainties. However, this approach requires considerable computational overhead. Here we consider a single qubit in which the Hamiltonian contains a single unknown parameter. We show that classical frequency estimation techniques greatly reduce the computational overhead associated with Bayesian estimation and provide accurate estimates for the qubit frequency.

  11. Knockdown Resistance Allele Frequencies in North American Head Louse (Anoplura: Pediculidae) Populations

    PubMed Central

    Yoon, Kyong Sup; Previte, Domenic J.; Hodgdon, Hilliary E.; Poole, Bryan C.; Kwon, Deok Ho; El-Ghar, Gamal E. Abo; Lee, Si Hyeock; Clark, J. Marshall

    2014-01-01

    The study examines the extent and frequency of a knockdown-type resistance allele (kdr type) in North American populations of human head lice. Lice were collected from 32 locations in Canada and the United States. DNA was extracted from individual lice and used to determine their zygosity using the serial invasive signal amplification technique to detect the kdr-type T917I (TI) mutation, which is most responsible for nerve insensitivity that results in the kdr phenotype and permethrin resistance. Previously sampled sites were resampled to determine if the frequency of the TI mutation was changing. The TI frequency was also reevaluated using a quantitative sequencing method on pooled DNA samples from selected sites to validate this population genotyping method. Genotyping substantiated that TI occurs at high levels in North American lice (88.4%). Overall, the TI frequency in U.S. lice was 84.4% from 1999 to 2009, increased to 99.6% from 2007 to 2009, and was 97.1% in Canadian lice in 2008. Genotyping results using the serial invasive signal amplification reaction (99.54%) and quantitative sequencing (99.45%) techniques were highly correlated. Thus, the frequencies of TI in North American head louse populations were found to be uniformly high, which may be due to the high selection pressure from the intensive and widespread use of the pyrethrins- or pyrethroid-based pediculicides over many years, and is likely a main cause of increased pediculosis and failure of pyrethrins- or permethrin-based products in Canada and the United States. Alternative approaches to treatment of head lice infestations are critically needed. PMID:24724296

  12. Haemoglobin polymorphism in atlantic cod (Gadus morhua): Allele frequency variation between yearclasses in a Norwegian fjord stock

    NASA Astrophysics Data System (ADS)

    Mork, J.; Sundnes, G.

    1985-03-01

    A total of 262 specimens (0-, and 1-group) of Atlantic cod (Gadus morhua) representing 4 different yearclasses were caught in Trondheimsfjorden, Norway, during 1977 1984. They were genotyped by agar gel electrophoresis for the polymorphic haemoglobin locus HbI (Sick, 1961). The analyses revealed a highly significant (P=0.0003) heterogeneity of HbI allele frequencies between yearclasses. The difference in the frequency of the HbI-1 allele between the first (1977) and the last (1983) yearclass amounted to 0.18 (±0.07). The results appear to support recent reports on considerable selection effects at HbI, and stress the unreliability of allele frequencies at this locus for use in studies of the genetic population structure of cod.

  13. Distribution of DI*A and DI*B Allele Frequencies and Comparisons among Central Thai and Other Populations

    PubMed Central

    Nathalang, Oytip; Panichrum, Puangpaka; Intharanut, Kamphon; Thattanon, Phatchira; Nathalang, Siriporn

    2016-01-01

    Alloantibodies to the Diego (DI) blood group system, anti-Dia and anti-Dib are clinically significant in causing hemolytic transfusion reactions (HTRs) and hemolytic disease of the fetus and newborn (HDFN), especially in Asian populations with Mongolian ancestry. This study aimed to report the frequency of the DI*A and DI*B alleles in a Central Thai population and to compare them with those of other populations previously published. Altogether, 1,011 blood samples from unrelated healthy blood donors at the National Blood Centre, Thai Red Cross Society, Bangkok were included. Only 391 samples were tested with anti-Dia by conventional tube technique. All samples were genotyped for DI*A and DI*B alleles using an in-house polymerase chain reaction with sequence-specific primer (PCR-SSP) technique. The DI phenotyping and genotyping results were in 100% concordance. The DI*A and DI*B allele frequencies among 1,011 Central Thais were 0.0183 (37/2,022) and 0.9817 (1,985/2,022), respectively. Allele frequencies were compared between Central Thai and other populations. Our data shows that DI*A and DI*B allele frequencies are similar to Southeast Asian, Brazilian, Southern Brazilian and American Native populations; whereas, these frequencies significantly differ from those reported in East Asian, Italian, Alaska Native/Aleut, Hawaiian/Pacific Islander and Filipino populations (P<0.05), corresponding to the results of a matrix of geometric genetic distances. This study confirms that the prevalence of DI*A and DI*B alleles among Central Thais is similar to Southeast Asians and different to others populations of the world. A PCR-based identification of DI genotyping should overcome some of the serological limitations in transfusion medicine and provides a complementary tool for further population-genetic studies. PMID:27764238

  14. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).

    PubMed

    Bodner, Martin; Bastisch, Ingo; Butler, John M; Fimmers, Rolf; Gill, Peter; Gusmão, Leonor; Morling, Niels; Phillips, Christopher; Prinz, Mechthild; Schneider, Peter M; Parson, Walther

    2016-09-01

    The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups. It has been demonstrated with databases of haploid markers (EMPOP for mitochondrial mtDNA, and YHRD for Y-chromosomal loci) that centralized quality control and data curation is essential to minimize error. The concepts employed for quality control involve software-aided likelihood-of-genotype, phylogenetic, and population genetic checks that allow the researchers to compare novel data to established datasets and, thus, maintain the high quality required in forensic genetics. Here, we present STRidER (http://strider.online), a publicly available, centrally curated online allele frequency database and quality control platform for autosomal STRs. STRidER expands on the previously established ENFSI DNA WG STRbASE and applies standard concepts established for haploid and autosomal markers as well as novel tools to reduce error and increase the quality of autosomal STR data. The platform constitutes a significant improvement and innovation for the scientific community, offering autosomal STR data quality control and reliable STR genotype estimates. PMID:27352221

  15. A note on the change in gene frequency of a selected allele in partial full-sib mating populations

    SciTech Connect

    Caballero, A.

    1996-02-01

    The change in gene frequency of a selected allele in partial full-sib mating populations was analyzed. The implications of these papers is important in terms of the fixation probability of genes because, for the same equilibrium inbreeding coefficient, fixation rates of mutant genes would be larger for partial full-sib mating than for partial selfing. 4 refs.

  16. Determination of the allelic frequencies of an L-myc and a p53 polymorphism in human lung cancer.

    PubMed

    Weston, A; Ling-Cawley, H M; Caporaso, N E; Bowman, E D; Hoover, R N; Trump, B F; Harris, C C

    1994-04-01

    The L-myc and p53 genes have been implicated in lung cancer. Both of these genes have restriction fragment length polymorphisms (RFLPs) that could account for differential expression or activity of variant forms. An EcoRI restriction site in the L-myc gene was previously reported to be a predictor of poor prognosis in Japanese lung cancer patients. There are several RFLPs in the p53 gene. In exon 4 there is a polymorphism that codes for either an arginine or proline residue at codon 72. We previously reported the frequency of DNA-RFLPs at these gene loci revealed by EcoRI and AccII respectively. Here we report results from a study comparing lung cancer cases (n = 31) with chronic obstructive pulmonary disease controls (n = 49). No association was found between these RFLPs and disease status. Previous observations that the frequencies of these RFLPs varied by race were confirmed. The p53 arginine allele was found to be more common in Caucasians (0.71) than African-Americans (0.50). The EcoRI restriction site present allele in L-myc was more frequent in African-Americans (0.71) than Caucasians (0.49). Thus, the allelic frequency for L-myc was similar in African-Americans to that reported for Japanese, and the allelic frequency for p53 was similar in Caucasians to that reported for Japanese.

  17. Frequencies of HKαα and anti-HKαα Alleles in Chinese Carriers of Silent Deletional α-Thalassemia.

    PubMed

    Wu, Man-Yu; Li, Jian; Li, Shu-Chen; Li, Yan; Li, Dong-Zhi

    2015-01-01

    The HKαα (HongKongαα) allele is an unusual rearrangement of the α-globin gene cluster containing both the -α(3.7) (rightward) and ααα(anti 4.2) crossover deletion/duplication. The anti-HKαα (anti-HongKongαα) allele is the reciprocal product containing both the -α(4.2) (leftward) and ααα(anti 3.7) unequal crossover deletion/duplication. In clinical practice of thalassemia screening, gap-polymerase chain reaction (gap-PCR) approaches are used to detect the common -α(3.7) and -α(4.2) deletions of α-thalassemia (α-thal). Because the HKαα and anti-HKαα alleles also contain the single α-globin gene deletion, individuals with these alleles would be misdiagnosed as -α(3.7) or -α(4.2) carriers. This would likely produce misleading or incorrect information in genetic counseling. In this study, we investigated the HKαα and anti-HKαα alleles in Chinese carriers of silent deletional α-thal, and reported their frequencies to be 2.27 and 0.35% in -α(3.7) and -α(4.2) carriers, respectively. Given the rarity of the HKαα and anti-HKαα alleles, a routine screening for these two rearrangements are unlikely to be necessary on most occasions.

  18. Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies.

    PubMed

    Pagnamenta, Alistair T; Lise, Stefano; Harrison, Victoria; Stewart, Helen; Jayawant, Sandeep; Quaghebeur, Gerardine; Deng, Alexander T; Murphy, Valerie Elizabeth; Sadighi Akha, Elham; Rimmer, Andy; Mathieson, Iain; Knight, Samantha J L; Kini, Usha; Taylor, Jenny C; Keays, David A

    2012-01-01

    The development of next generation sequencing (NGS) has radically transformed the scientific landscape, making it possible to sequence the exome of any given individual in a cost-effective way. The power of this approach has been demonstrated by a number of groups who have identified pathogenic mutations in small pedigrees that have been resistant to traditional genetic mapping. Recently it has become clear that exome sequencing has great potential with respect to sporadic disease and the identification of de novo mutations. This is highlighted by studies reporting whole-exome sequencing of patient-parental trios affected by learning disability, autism and schizophrenia. It is widely anticipated that the introduction of this technique into a clinical setting will revolutionise genetic diagnosis. However, the sensitivity of NGS exome sequencing is currently unclear. Here, we describe the exome sequencing of DNA samples from a patient with double cortex syndrome and her parents, resulting in the detection of a mosaic splicing mutation in LIS1. This variant was found at an allele frequency of just 18%, demonstrating that NGS methods have the capacity to identify pathogenic mosaic mutations present at a low level. PMID:22129557

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

    PubMed

    Pickrell, Joseph K; Pritchard, Jonathan K

    2012-01-01

    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. PMID:23166502

  20. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

    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. PMID:23166502

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

    PubMed

    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 allele and haplotype frequencies in the Albanian population and their relationship with the other European populations.

    PubMed

    Sulcebe, G; Sanchez-Mazas, A; Tiercy, J-M; Shyti, E; Mone, I; Ylli, Z; Kardhashi, V

    2009-12-01

    Human leucocyte antigen (HLA) alleles are very interesting markers in identifying population relationships. Moreover, their frequency distribution data are important in the implementation of donor-recipient registry programs for transplantation purposes and also in determining the genetic predisposition for many diseases. For these reasons, we studied the HLA class I and II allele and haplotype frequencies in 160 healthy, unrelated Albanian individuals originating from all regions of the country. The HLA genotyping was performed through a 2-digit resolution SSOP method. The data were analysed with Arlequin and Phylip programs. No deviation was found from the Hardy-Weinberg equilibrium. A total of 17 A*, 30 B*, 12 Cw*, 13 DRB1* and 5 DQB1* alleles were identified. The six most frequent HLA-A-B-DRB1 haplotypes were A*02-B*18-DRB1*11 (5.60%), A*02-B*51-DRB1*16 (4.74%), A*01-B*08-DRB1*03 (3.48%), A*24-B*35-DRB1*11 (2.77%), A*02-B*51-DRB1*13 (2.21%), A*24-B*35-DRB1*14 (1.89%). Interestingly, 12 HLA-A-B-Cw-DRB1-DQB1 haplotypes occurred at a frequency >1%. When compared with the other populations, a close relationship was found with North Greek, Bulgarian, Macedonian, Romanian, Turkish, Cretan, Serbian, Croatian and Italian populations. A higher differentiation in allele frequency level was found with Western Europe populations. These data are the first report of HLA allele and haplotype distribution in an Albanian population inside this country. When compared with other populations, their distribution frequencies show close similarities with neighbouring populations of the entire Balkan area. PMID:19703234

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

    PubMed

    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 (P<0.001). CYP2C9*3 was found in Tarahumaras (0.104), Mayos (0.091), Tepehuanos (0.075), Guarijíos (0.067), Huicholes (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.

  4. Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry

    PubMed Central

    Kiesler, Kevin M.; Vallone, Peter M.

    2013-01-01

    Aim To type a set of 194 US African American, Caucasian, and Hispanic samples (self-declared ancestry) for 40 autosomal single nucleotide polymorphism (SNP) markers intended for human identification purposes. Methods Genotyping was performed on an automated commercial electrospray ionization time-of-flight mass spectrometer, the PLEX-ID. The 40 SNP markers were amplified in eight unique 5plex PCRs, desalted, and resolved based on amplicon mass. For each of the three US sample groups statistical analyses were performed on the resulting genotypes. Results The assay was found to be robust and capable of genotyping the 40 SNP markers consuming approximately 4 nanograms of template per sample. The combined random match probabilities for the 40 SNP assay ranged from 10−16 to 10−21. Conclusion The multiplex PLEX-ID SNP-40 assay is the first fully automated genotyping method capable of typing a panel of 40 forensically relevant autosomal SNP markers on a mass spectrometry platform. The data produced provided the first allele frequencies estimates for these 40 SNPs in a National Institute of Standards and Technology US population sample set. No population bias was detected although one locus deviated from its expected level of heterozygosity. PMID:23771752

  5. Fundamental frequency estimation of singing voice

    NASA Astrophysics Data System (ADS)

    de Cheveigné, Alain; Henrich, Nathalie

    2002-05-01

    A method of fundamental frequency (F0) estimation recently developped for speech [de Cheveigné and Kawahara, J. Acoust. Soc. Am. (to be published)] was applied to singing voice. An electroglottograph signal recorded together with the microphone provided a reference by which estimates could be validated. Using standard parameter settings as for speech, error rates were low despite the wide range of F0s (about 100 to 1600 Hz). Most ``errors'' were due to irregular vibration of the vocal folds, a sharp formant resonance that reduced the waveform to a single harmonic, or fast F0 changes such as in high-amplitude vibrato. Our database (18 singers from baritone to soprano) included examples of diphonic singing for which melody is carried by variations of the frequency of a narrow formant rather than F0. Varying a parameter (ratio of inharmonic to total power) the algorithm could be tuned to follow either frequency. Although the method has not been formally tested on a wide range of instruments, it seems appropriate for musical applications because it is accurate, accepts a wide range of F0s, and can be implemented with low latency for interactive applications. [Work supported by the Cognitique programme of the French Ministry of Research and Technology.

  6. High Susceptibility to Cry1Ac and Low Resistance Allele Frequency Reduce the Risk of Resistance of Helicoverpa armigera to Bt Soybean in Brazil

    PubMed Central

    Bacalhau, Fabiana B.; Amado, Douglas; Carvalho, Renato A.; Martinelli, Samuel; Head, Graham P.; Omoto, Celso

    2016-01-01

    The Old World bollworm, Helicoverpa armigera (Hübner), was recently introduced into Brazil, where it has caused extensive damage to cotton and soybean crops. MON 87701 × MON 89788 soybean, which expresses the Bt protein Cry1Ac, was recently deployed in Brazil, providing high levels of control against H. armigera. To assess the risk of resistance to the Cry1Ac protein expressed by MON 87701 × MON 89788 soybean in Brazil, we conducted studies to evaluate the baseline susceptibility of H. armigera to Cry1Ac, in planta efficacy including the assessment of the high-dose criterion, and the initial resistance allele frequency based on an F2 screen. The mean Cry1Ac lethal concentration (LC50) ranged from 0.11 to 1.82 μg·mL−1 of diet among all H. armigera field populations collected from crop seasons 2013/14 to 2014/15, which indicated about 16.5-fold variation. MON 87701 × MON 89788 soybean exhibited a high level of efficacy against H. armigera and most likely met the high dose criterion against this target species in leaf tissue dilution bioassays up to 50 times. A total of 212 F2 family lines of H. armigera were established from field collections sampled from seven locations across Brazil and were screened for the presence of MON 87701 × MON 89788 soybean resistance alleles. None of the 212 families survived on MON 87701 × MON 89788 soybean leaf tissue (estimated allele frequency = 0.0011). The responses of H. armigera to Cry1Ac protein, high susceptibility to MON 87701 × MON 89788 soybean, and low frequency of resistance alleles across the main soybean-producing regions support the assumptions of a high-dose/refuge strategy. However, maintenance of reasonable compliance with the refuge recommendation will be essential to delay the evolution of resistance in H. armigera to MON 87701 × MON 89788 soybean in Brazil. PMID:27532632

  7. High Susceptibility to Cry1Ac and Low Resistance Allele Frequency Reduce the Risk of Resistance of Helicoverpa armigers to Bt Soybean in Brazil

    PubMed Central

    Bacalhau, Fabiana B.; Amado, Douglas; Carvalho, Renato A.; Martinelli, Samuel; Head, Graham P.; Omoto, Celso

    2016-01-01

    The Old World bollworm, Helicoverpa armigera (Hübner), was recently introduced into Brazil, where it has caused extensive damage to cotton and soybean crops. MON 87701 × MON 89788 soybean, which expresses the Bt protein Cry1Ac, was recently deployed in Brazil, providing high levels of control against H. armigera. To assess the risk of resistance to the Cry1Ac protein expressed by MON 87701 × MON 89788 soybean in Brazil, we conducted studies to evaluate the baseline susceptibility of H. armigera to Cry1Ac, in planta efficacy including the assessment of the high-dose criterion, and the initial resistance allele frequency based on an F2 screen. The mean Cry1Ac lethal concentration (LC50) ranged from 0.11 to 1.82 μg·mL−1 of diet among all H. armigera field populations collected from crop seasons 2013/14 to 2014/15, which indicated about 16.5-fold variation. MON 87701 × MON 89788 soybean exhibited a high level of efficacy against H. armigera and most likely met the high dose criterion against this target species in leaf tissue dilution bioassays up to 50 times. A total of 212 F2 family lines of H. armigera were established from field collections sampled from seven locations across Brazil and were screened for the presence of MON 87701 × MON 89788 soybean resistance alleles. None of the 212 families survived on MON 87701 × MON 89788 soybean leaf tissue (estimated allele frequency = 0.0011). The responses of H. armigera to Cry1Ac protein, high susceptibility to MON 87701 × MON 89788 soybean, and low frequency of resistance alleles across the main soybean-producing regions support the assumptions of a high-dose/refuge strategy. However, maintenance of reasonable compliance with the refuge recommendation will be essential to delay the evolution of resistance in H. armigera to MON 87701 × MON 89788 soybean in Brazil. PMID:27532632

  8. High Susceptibility to Cry1Ac and Low Resistance Allele Frequency Reduce the Risk of Resistance of Helicoverpa armigers to Bt Soybean in Brazil.

    PubMed

    Dourado, Patrick M; Bacalhau, Fabiana B; Amado, Douglas; Carvalho, Renato A; Martinelli, Samuel; Head, Graham P; Omoto, Celso

    2016-01-01

    The Old World bollworm, Helicoverpa armigera (Hübner), was recently introduced into Brazil, where it has caused extensive damage to cotton and soybean crops. MON 87701 × MON 89788 soybean, which expresses the Bt protein Cry1Ac, was recently deployed in Brazil, providing high levels of control against H. armigera. To assess the risk of resistance to the Cry1Ac protein expressed by MON 87701 × MON 89788 soybean in Brazil, we conducted studies to evaluate the baseline susceptibility of H. armigera to Cry1Ac, in planta efficacy including the assessment of the high-dose criterion, and the initial resistance allele frequency based on an F2 screen. The mean Cry1Ac lethal concentration (LC50) ranged from 0.11 to 1.82 μg·mL-1 of diet among all H. armigera field populations collected from crop seasons 2013/14 to 2014/15, which indicated about 16.5-fold variation. MON 87701 × MON 89788 soybean exhibited a high level of efficacy against H. armigera and most likely met the high dose criterion against this target species in leaf tissue dilution bioassays up to 50 times. A total of 212 F2 family lines of H. armigera were established from field collections sampled from seven locations across Brazil and were screened for the presence of MON 87701 × MON 89788 soybean resistance alleles. None of the 212 families survived on MON 87701 × MON 89788 soybean leaf tissue (estimated allele frequency = 0.0011). The responses of H. armigera to Cry1Ac protein, high susceptibility to MON 87701 × MON 89788 soybean, and low frequency of resistance alleles across the main soybean-producing regions support the assumptions of a high-dose/refuge strategy. However, maintenance of reasonable compliance with the refuge recommendation will be essential to delay the evolution of resistance in H. armigera to MON 87701 × MON 89788 soybean in Brazil. PMID:27532632

  9. Frequency of the apolipoprotein E epsilon 4 allele in a case-control study of early onset Parkinson's disease.

    PubMed Central

    Whitehead, A S; Bertrandy, S; Finnan, F; Butler, A; Smith, G D; Ben-Shlomo, Y

    1996-01-01

    OBJECTIVES: It has been suggested that Parkinson's disease and Alzheimer's disease may share a common or at least overlapping aetiology. The prevalence of dementia among cases of Parkinson's disease is known to be greater than expected in the general population. The frequency of the apolipoprotein epsilon 4 allele in a large case-control study of early onset Parkinson's disease has been examined. METHODS: 215 patients and 212 population based controls were recruited from the Republic of Ireland between 1992 and 1994. Cases had to have disease onset at 55 years or younger and be born after 1925. RESULTS: The frequency of the epsilon 4 allele was almost identical between cases of Parkinson's disease (14.6%) and healthy controls (13.3%). There was no relation between epsilon 4 status and disease onset, disease duration, Hoehn and Yahr score, and disease progression. The frequency of the epsilon 4 allele was not increased among 10 patients with Parkinson's disease with dementia (10.0%) compared with the other patients without dementia (14.8%). There was no association between epsilon 4 allele status and either a history of smoking, family history of dementia, or Parkinson's disease, or being born in a rural area. The odds ratio for the ApoE epsilon 4 allele associated with Parkinson's disease was 1.10 (95% confidence interval (95% CI) 0.68-1.79), adjusting for age group, sex, and residential status. The pooled odds ratio from a meta-analysis of six studies of ApoE epsilon 4 status and Parkinson's disease was 0.94 (95% CI 0.69-1.27). CONCLUSIONS: The results from our study as well as the pooled meta-analysis exclude any important role for ApoE epsilon 4 status in the development of Parkinson's disease. Our results similarly do not support its role either in dementia associated with Parkinson's disease or disease prognosis. PMID:8890771

  10. Prion protein genotype survey confirms low frequency of scrapie-resistant K222 allele in British goat herds.

    PubMed

    Goldmann, W; Marier, E; Stewart, P; Konold, T; Street, S; Langeveld, J; Windl, O; Ortiz-Pelaez, A

    2016-02-13

    Scrapie in goats is a transmissible, fatal prion disease, which is endemic in the British goat population. The recent success in defining caprine PRNP gene variants that provide resistance to experimental and natural classical scrapie has prompted the authors to conduct a survey of PRNP genotypes in 10 goat breeds and 52 herds to find goats with the resistant K222 allele. They report here the frequencies in 1236 tested animals of the resistance-associated K222 and several other alleles by breed and herd. Eight animals were found to be heterozygous QK222 goats (0.64 per cent genotype frequency, 95 per cent CI 0.28 to 1.27 per cent) but no homozygous KK222 goats were detected. The K222 allele was found in Saanen, Toggenburg and Anglo-Nubian goats. The fact that only a few goats with the K222 allele have been identified does not preclude the possibility to design and implement successful breeding programmes at national level.

  11. Prion protein genotype survey confirms low frequency of scrapie-resistant K222 allele in British goat herds

    PubMed Central

    Goldmann, W.; Stewart, P.; Konold, T.; Street, S.; Langeveld, J.; Windl, O.; Ortiz-Pelaez, A.

    2016-01-01

    Scrapie in goats is a transmissible, fatal prion disease, which is endemic in the British goat population. The recent success in defining caprine PRNP gene variants that provide resistance to experimental and natural classical scrapie has prompted the authors to conduct a survey of PRNP genotypes in 10 goat breeds and 52 herds to find goats with the resistant K222 allele. They report here the frequencies in 1236 tested animals of the resistance-associated K222 and several other alleles by breed and herd. Eight animals were found to be heterozygous QK222 goats (0.64 per cent genotype frequency, 95 per cent CI 0.28 to 1.27 per cent) but no homozygous KK222 goats were detected. The K222 allele was found in Saanen, Toggenburg and Anglo-Nubian goats. The fact that only a few goats with the K222 allele have been identified does not preclude the possibility to design and implement successful breeding programmes at national level. PMID:26755614

  12. Case-control study of allele frequencies of 15 short tandem repeat loci in males with impulsive violent behavior

    PubMed Central

    Yang, Chun; Ba, Huajie; Gao, Zhiqin; Zhao, Hanqing; Yu, Haiying; Guo, Wei

    2013-01-01

    Background Analysis of genetic polymorphisms in short tandem repeats (STRs) is an accepted method for detecting associations between genotype and phenotype but it has not previously been used in the study of the genetics of impulsive violent behavior. Objective Compare the prevalence of different polymorphisms in 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) between men with a history of impulsive violence and male control subjects without a history of impulsive violence. Methods The distributions of the alleles of the 15 STR loci were compared between 407 cases with impulsive violent behavior and 415 controls using AmpFlSTR® Identifiler™ kits. Results Compared to controls, the average frequencies of the following alleles were significantly lower in individuals with a history of violent behavior: allele 10 of TH01 (OR=0.29, 95%CI=0.16-0.52, p<0.0001,), allele 8 of TPOX (OR=0.71, 95%CI=0.58-0.86, p=0.0005), allele 9 of TPOX (OR=0.65, 95%CI=0.47-0.89, p=0.0072) and allele 14 of CSF1PO (OR=0.27, 95%CI=0.11-0.68, p=0.0035). One allele was significantly higher in cases than controls: allele 11 of TPOX (OR=1.79, 95%CI=1.45-2.22, p<0.0001). Conclusions To the best of our knowledge, this is the first behavioral genetic study that clearly demonstrates a close relationship between specific genetic markers and impulsive aggression in non-psychiatric offenders. Further prospective work will be needed to determine whether or not the alleles identified can be considered risk factors for impulsive aggression and, if so, the underlying mechanisms that result in this relationship. PMID:24991178

  13. Genetically Determined Amerindian Ancestry Correlates with Increased Frequency of Risk Alleles for Systemic Lupus Erythematosus

    PubMed Central

    Sanchez, E; Webb, R; Rasmussen, A.; Kelly, J.A; Riba, L.; Kaufman, K.M.; Garcia-de la Torre, I.; Moctezuma, J.F.; Maradiaga-Ceceña, M.A.; Cardiel, M.; Acevedo, E.; Cucho-Venegas, M.; Garcia, M.A.; Gamron, S.; Pons-Estel, B.A.; Vasconcelos, C.; Martin, J.; Tusié-Luna, T.; Harley, J.B.; Richardson, B.; Sawalha, A.H.; Alarcón-Riquelme, M.E.

    2011-01-01

    Objectives To analyze if genetically determined Amerindian ancestry predicts the increased presence of risk alleles of known susceptibility genes for systemic lupus erythematosus. Methods Single nucleotide polymorphisms within 16 confirmed genetic susceptibility loci for SLE were genotyped in a set of 804 Mestizo lupus patients and 667 Mestizo normal healthy controls. In addition, 347 admixture informative markers were genotyped. Individual ancestry proportions were determined using STRUCTURE. Association analysis was performed using PLINK, and correlation of the presence of risk alleles with ancestry was done using linear regression. Results A meta-analysis of the genetic association of the 16 SNPs across populations showed that TNFSF4, STAT4, PDCD1, ITGAM, and IRF5 were associated with lupus in a Hispanic-Mestizo cohort enriched for European and Amerindian ancestry. In addition, two SNPs within the MHC region, previously associated in a genome-wide association study in Europeans, were also associated in Mestizos. Using linear regression we predict an average increase of 2.34 risk alleles when comparing a lupus patient with 100% Amerindian ancestry to an SLE patient with 0% American Indian Ancestry (p<0.0001). SLE patients with 43% more Amerindian ancestry are predicted to carry one additional risk allele. Conclusion Amerindian ancestry increased the number of risk alleles for lupus. PMID:20848568

  14. Two-voice fundamental frequency estimation

    NASA Astrophysics Data System (ADS)

    de Cheveigné, Alain

    2002-05-01

    An algorithm is presented that estimates the fundamental frequencies of two concurrent voices or instruments. The algorithm models each voice as a periodic function of time, and jointly estimates both periods by cancellation according to a previously proposed method [de Cheveigné and Kawahara, Speech Commun. 27, 175-185 (1999)]. The new algorithm improves on the old in several respects; it allows an unrestricted search range, effectively avoids harmonic and subharmonic errors, is more accurate (it uses two-dimensional parabolic interpolation), and is computationally less costly. It remains subject to unavoidable errors when periods are in certain simple ratios and the task is inherently ambiguous. The algorithm is evaluated on a small database including speech, singing voice, and instrumental sounds. It can be extended in several ways; to decide the number of voices, to handle amplitude variations, and to estimate more than two voices (at the expense of increased processing cost and decreased reliability). It makes no use of instrument models, learned or otherwise, although it could usefully be combined with such models. [Work supported by the Cognitique programme of the French Ministry of Research and Technology.

  15. High Resolution Human Leukocyte Antigen Class I Allele Frequencies and HIV-1 Infection Associations in Chinese Han and Uyghur Cohorts

    PubMed Central

    Liu, Yanhou; Zhao, Zhongfang; Li, Tianyi; Liao, Qi; Kushner, Nicholas; Touzjian, Neal Y.; Shao, Yiming; Sun, Yongtao; Strong, Amie J.; Lu, Yichen

    2012-01-01

    Background 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. Methodology/Principal Findings 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. Conclusions 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

  16. Allelic frequencies and association with carcass traits of six genes in local subpopulations of Japanese Black cattle.

    PubMed

    Nishimaki, Takahiro; Ibi, Takayuki; Siqintuya; Kobayashi, Naohiko; Matsuhashi, Tamako; Akiyama, Takayuki; Yoshida, Emi; Imai, Kazumi; Matsui, Mayu; Uemura, Keiichi; Eto, Hisayoshi; Watanabe, Naoto; Fujita, Tatsuo; Saito, Yosuke; Komatsu, Tomohiko; Hoshiba, Hiroshi; Mannen, Hideyuki; Sasazaki, Shinji; Kunieda, Tetsuo

    2016-04-01

    Marker-assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits.

  17. Mytilus galloprovincialis-type foot-protein-1 alleles occur at low frequency among mussels in the Dutch Wadden Sea

    NASA Astrophysics Data System (ADS)

    Luttikhuizen, Pieternella C.; Koolhaas, Anita; Bol, Anneke; Piersma, Theunis

    2002-11-01

    The presence of M. galloprovincialis-type genes among the population of mussels in the Dutch Wadden Sea, historically described as M. edulis, was assessed. We applied the molecular technique in which a fragment of the gene coding for an adhesive protein of the byssus of mussels is amplified by PCR and assayed for length using electrophoresis. Among 321 individual mussels collected in August-October 2001 at 14 sites (5 intertidal, 9 subtidal) widely dispersed over the Dutch Wadden Sea, 6 specimens (collected at 5 sites) were found that showed a heterozygote genotype with both the M. edulis- and the M. galloprovincialis-type alleles being amplified; all others were identified as homozygotes for the M. edulis-type allele. Differentiation in frequencies of heterozygotes among sites was not detected. The fact that the M. galloprovincialis-type allele was present at low frequency (0.0093) may be attributed to one of three possible, and not mutually exclusive, causes: incomplete diagnosticity of this marker, an historically stable introgression zone in the Wadden Sea, or a recent invasion.

  18. Unequal allelic frequencies at the self-incompatibility locus within local populations of Prunus avium L.: an effect of population structure?

    PubMed

    Stoeckel, S; Castric, V; Mariette, S; Vekemans, X

    2008-05-01

    In this paper, we investigated the genetic structure and distribution of allelic frequencies at the gametophytic self-incompatibility locus in three populations of Prunus avium L. In line with theoretical predictions under balancing selection, genetic structure at the self-incompatibility locus was almost three times lower than at seven unlinked microsatellites. Furthermore, we found that S-allele frequencies in wild cherry populations departed significantly from the expected isoplethic distribution towards which balancing selection is expected to drive allelic frequencies (i.e. identical frequency equal to the inverse of the number of alleles in the population). To assess whether this departure could be caused either by drift alone or by population structure, we used numerical simulations to compare our observations with allelic frequency distributions expected : (1) within a single deme from a subdivided population with various levels of differentiation; and (2) within a finite panmictic population with identical allelic diversity. We also investigated the effects of sample size and degree of population structure on tests of departure from isoplethic equilibrium. Overall, our results showed that the observed allele frequency distributions were consistent with a model of subdivided population with demes linked by moderate migration rate.

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

    PubMed Central

    González-Galarza, Faviel F.; Takeshita, Louise Y.C.; Santos, Eduardo J.M.; Kempson, Felicity; Maia, Maria Helena Thomaz; Silva, Andrea Luciana Soares da; Silva, André Luiz Teles e; 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. PMID:25414323

  20. Mamu-DQA1 allele and genotype frequencies in a randomly sampled breeding colony of rhesus macaques (Macaca mulatta).

    PubMed

    Rolfs, B K; Lorenz, J G; Wu, C C; Lerche, N W; Smith, D G

    2001-04-01

    We studied the allelic and genotypic distribution of the major histocompatibility class-II locus DQA1 observed in a random sample of Indian rhesus macaques (Macaca mulatta) from a major breeding facility in the United States. The DNA was isolated from whole blood samples collected between 1991 and 1994 from 65 Indian rhesus monkeys. Polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP), which involves use of specific amplification of DQA1 exon 2 and subsequent restriction digestion of the 242-base pair fragment, was used to genotype the animals for the 20 known macaque (Mamu)-DQA1 alleles. Frequencies for four alleles (DQA1*240x, *2502, *2503 and *0102) differed significantly from those reported in a smaller sample of rhesus macaques from the German Primate Center. The modest genetic survey of Mamu-DQA1 genotypes presented here will be particularly useful in designing epidemiologic studies that investigate associations between immunogenetic background and disease susceptibility in macaque models of human disease.

  1. Genetic comparison of lake sturgeon populations: Differentiation based on allelic frequencies at seven microsatellite loci

    USGS Publications Warehouse

    McQuown, E.; Krueger, C.C.; Kincaid, H.L.; Gall, G.A.E.; May, B.

    2003-01-01

    The lake sturgeon (Acipenser fulvescens) has recently become a high priority for restoration management because of the near extinction of the species from many areas of North America. The identification of the level of population differentiation that naturally exists among lake sturgeon populations will be useful in the development of management plans to conserve and restore diversity, and in the choice of donor populations to use for re-introduction. Genetic variation among and within 210 lake sturgeon collected from seven locations (St. Lawrence River, Des Prairies River (tributary to the St. Lawrence River), Mattagami River (Hudson Bay drainage), Menominee River (Lake Michigan drainage), Wolf River (Lake Michigan drainage), Niagara River, and Lake Erie) was examined based on allelic variation at seven microsatellite loci (four disomic and three putative tetrasomic). High levels of variability were detected at these loci. Analyses revealed an average of 8.6 alleles per locus (range 5 to 12 alleles per locus) and heterozygosity values at the four disomic loci ranging from 0.46 to 0.66. Multivariate factor analysis of Nei's genetic distance values produced three distinct population groups that were organized by geography: 1) Mattagami (northern Quebec), 2) Menominee/ Wolf (Lake Michigan - Wisconsin), and 3) St. Lawrence/ Des Prairies/ Niagara/ Erie (lower Great Lakes). Differences based on G-tests summed over all loci occurred between all possible paired comparisons of the collections (P < 0.01). These analyses indicated that lake sturgeon populations are differentiated within the Great Lakes basin. Managers of this species will need to identify individual populations in their jurisdictions and provide separate consideration for their conservation and rehabilitation.

  2. Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans.

    PubMed

    Keinan, Alon; Mullikin, James C; Patterson, Nick; Reich, David

    2007-10-01

    Large data sets on human genetic variation have been collected recently, but their usefulness for learning about history and natural selection has been limited by biases in the ways polymorphisms were chosen. We report large subsets of SNPs from the International HapMap Project that allow us to overcome these biases and to provide accurate measurement of a quantity of crucial importance for understanding genetic variation: the allele frequency spectrum. Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians.

  3. Allele frequencies of BRAFV600 mutations in primary melanomas and matched metastases and their relevance for BRAF inhibitor therapy in metastatic melanoma

    PubMed Central

    Satzger, Imke; Marks, Lena; Kerick, Martin; Klages, Sven; Berking, Carola; Herbst, Rudolf; Völker, Bernward; Schacht, Vivien; Timmermann, Bernd; Gutzmer, Ralf

    2015-01-01

    Background The detection of BRAFV600 mutations in patients with metastatic melanoma is important because of the availability of BRAF inhibitor therapy. However, the clinical relevance of the frequency of BRAFV600 mutant alleles is unclear. Patients and Methods Allele frequencies of BRAFV600 mutations were analyzed by ultra-deep next-generation sequencing in formalin-fixed, paraffin-embedded melanoma tissue (75 primary melanomas and 88 matched metastases). In a second study, pretreatment specimens from 76 patients who received BRAF inhibitors were retrospectively analyzed, and BRAFV600 allele frequencies were correlated with therapeutic results. Results Thirty-five patients had concordantly BRAF-positive and 36 (48%) patients had concordantly BRAF-negative primary melanomas and matched metastases, and four patients had discordant samples with low allele frequencies (3.4–5.2%). Twenty-six of 35 patients with concordant samples had BRAFV600E mutations, three of whom had additional mutations (V600K in two patients and V600R in one) and nine patients had exclusively non-V600E mutations (V600K in eight patients and V600E -c.1799_1800TG > AA- in one patient). The frequency of mutated BRAFV600 alleles was similar in the primary melanoma and matched metastasis in 27/35 patients, but differed by >3-fold in 8/35 of samples. BRAFV600E allele frequencies in pretreatment tumor specimens were not significantly correlated with treatment outcomes in 76 patients with metastatic melanoma who were treated with BRAF inhibitors. Conclusions BRAFV600 mutation status and allele frequency is consistent in the majority of primary melanomas and matched metastases. A small subgroup of patients has double mutations. BRAFV600 allele frequencies are not correlated with the response to BRAF inhibitors. PMID:26498143

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

    PubMed Central

    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

  5. Robust Blind Frequency and Transition Time Estimation for Frequency Hopping Systems

    NASA Astrophysics Data System (ADS)

    Fu, Kuo-Ching; Chen, Yung-Fang

    2010-12-01

    In frequency hopping spread spectrum (FHSS) systems, two major problems are timing synchronization and frequency estimation. A blind estimation scheme is presented for estimating frequency and transition time without using reference signals. The scheme is robust in the sense that it can avoid the unbalanced sampling block problem that occurs in existing maximum likelihood-based schemes, which causes large errors in one of the estimates of frequency. The proposed scheme has a lower computational cost than the maximum likelihood-based greedy search method. The estimated parameters are also used for the subsequent time and frequency tracking. The simulation results demonstrate the efficacy of the proposed approach.

  6. 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.

    PubMed

    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

  7. HLA-DRB1 and HLA-DQB1 allele associations in an Albanian patient population with rheumatoid arthritis: correlations with the specific autoantibody markers and inter-population DRB1 allele frequency variability.

    PubMed

    Prifti-Kurti, Margarita; Nunes, José Manuel; Shyti, Erkena; Ylli, Zamira; Sanchez-Mazas, Alicia; Sulcebe, Genc

    2014-08-01

    The prevalence of rheumatoid arthritis and its specific autoantibodies varies in different populations. This variability depends on the genetic polymorphism of the immune response genes among which the HLA system plays a major role. In this context, we studied the HLA-DRB1 and HLA-DQB1 first-level allele frequencies in 100 Albanian patients with rheumatoid arthritis (RA), and taking into account their rheumatoid factor (RF) and anticitrullinated peptide antibodies (ACPA) serologic subgroups, we compared them with the respective frequencies in a population of 191 Albanian individuals without known pathology. No differences were found between the controls and the RA patient group as a whole, but three statistically significant differences were found: an increase in DRB1*04 among ACPA+, RF+ and ACPA+/RF+ patients, a significant decrease in DRB1*11 among ACPA+/RF+ and also a decrease in DRB1*13 among RF+ patient subgroups. Comparing allele frequencies of putatively associated RA alleles in different European populations revealed a significant negative correlation between the RA predisposing DRB1*04 and protective DRB1*11 allele frequencies. A statistically significant correlation was also found between RA prevalence rates and DRB1*04 as well as DRB1*11 frequencies. The relatively low frequencies of DRB1*04 and high DRB1*11 in the Albanian population might explain the rather low positivity rate of ACPA and RF antibodies among the Albanian RA patients. These specific association patterns suggest that this first study of RA in an Albanian population should be followed up to include second level or higher definition of HLA alleles and to compare RA patterns among European populations.

  8. Estimating rapidly varying frequencies in the presence of noise

    SciTech Connect

    Machorro, E

    2010-10-01

    A variable window length least-squares fitting and the interpolated fast Fourier transform methods are used to estimate the rapidly changing frequency of a signal with measurement noise. The least-squares method is computationally more expensive, but provides more accurate frequency estimates

  9. Allele frequency for Cystic fibrosis in Indians vis-a/-vis global populations.

    PubMed

    Bepari, Karnajit Kumar; Malakar, Arup Kumar; Paul, Prosenjit; Halder, Binata; Chakraborty, Supriyo

    2015-01-01

    Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene. This gene encodes a protein involved in epithelial anion channel. Cystic fibrosis is the most common life-limiting genetic disorder in Caucasians; it also affects other ethnic groups like the Blacks and the Native Americans. Cystic fibrosis is considered to be rare among individuals from the Indian subcontinent. We analyzed a total of 29 world׳s populations for cystic fibrosis on the basis of gene frequency and heterozygosity. Among 29 countries Switzerland revealed the highest gene frequency and heterozygosity for CF (0.022, 0.043) whereas Japan recorded the lowest values (0.002, 0.004) followed by India (0.004, 0.008). Our analysis suggests that the prevalence of cystic fibrosis is very low in India. PMID:26339151

  10. An Analysis of HLA-A, -B, and -DRB1 Allele and Haplotype Frequencies of 21,918 Residents Living in Liaoning, China

    PubMed Central

    Li, Xiao-Feng; Zhang, Xu; Chen, Yang; Zhang, Kun-Lian; Liu, Xiang-Jun; Li, Jian-Ping

    2014-01-01

    HLA-A, -B and -DRB1 allele frequencies and their haplotype frequencies in 21,918 Chinese residents living in Liaoning Province, who were registered as volunteer donors of China Marrow Donor Registry, were investigated. They are composed of 93.37% Han Chinese, 5.1% Manchus, 0.57% Mongols, 0.46% Hui persons, 0.29% Koreans and 0.14% Xibe ethnic group. In total eighteen different HLA-A alleles, forty-eight different HLA-B alleles and fourteen different HLA-DRB1 alleles have been identified. Their frequencies are in agreement with the Hardy-Weinberg equilibrium. For Han Chinese in Liaoning, 1,534 different HLA-A-B-DRB1 haplotypes were identified, with a frequency of higher than 0.01%. A*30-B*13-DRB1*07, A*02-B*46-DRB1*09 and A*02-B*13-DRB1*12 are the most frequent haplotypes among Liaoning Han. While Liaoning Han, Liaoning Manchu, Liaoning Mongol, Liaoning Hui and Liaoning Korean share the northern Han characteristic haplotypes, all minority ethnic groups with the exception of Liaoning Manchu have developed their own unique HLA profiles. This dataset characterizes the HLA allele and haplotype frequencies in the Liaoning area and suggests that it is different from those in other parts of China and ethnic groups, which implicates transplant donor searching strategies and studies on population genetics. PMID:24691290

  11. Frequency Estimator Performance for a Software-Based Beacon Receiver

    NASA Technical Reports Server (NTRS)

    Zemba, Michael J.; Morse, Jacquelynne Rose; Nessel, James A.; Miranda, Felix

    2014-01-01

    As propagation terminals have evolved, their design has trended more toward a software-based approach that facilitates convenient adjustment and customization of the receiver algorithms. One potential improvement is the implementation of a frequency estimation algorithm, through which the primary frequency component of the received signal can be estimated with a much greater resolution than with a simple peak search of the FFT spectrum. To select an estimator for usage in a QV-band beacon receiver, analysis of six frequency estimators was conducted to characterize their effectiveness as they relate to beacon receiver design.

  12. Frequency Estimator Performance for a Software-Based Beacon Receiver

    NASA Technical Reports Server (NTRS)

    Zemba, Michael J.; Morse, Jacquelynne R.; Nessel, James A.

    2014-01-01

    As propagation terminals have evolved, their design has trended more toward a software-based approach that facilitates convenient adjustment and customization of the receiver algorithms. One potential improvement is the implementation of a frequency estimation algorithm, through which the primary frequency component of the received signal can be estimated with a much greater resolution than with a simple peak search of the FFT spectrum. To select an estimator for usage in a Q/V-band beacon receiver, analysis of six frequency estimators was conducted to characterize their effectiveness as they relate to beacon receiver design.

  13. Estimation of frequency offset in mobile satellite modems

    NASA Technical Reports Server (NTRS)

    Cowley, W. G.; Rice, M.; Mclean, A. N.

    1993-01-01

    In mobilesat applications, frequency offset on the received signal must be estimated and removed prior to further modem processing. A straightforward method of estimating the carrier frequency offset is to raise the received MPSK signal to the M-th power, and then estimate the location of the peak spectral component. An analysis of the lower signal to noise threshold of this method is carried out for BPSK signals. Predicted thresholds are compared to simulation results. It is shown how the method can be extended to pi/M MPSK signals. A real-time implementation of frequency offset estimation for the Australian mobile satellite system is described.

  14. POPTREEW: web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities.

    PubMed

    Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro

    2014-06-01

    POPTREE software, including the command line (POPTREE) and the Windows (POPTREE2) versions, is available to perform evolutionary analyses of allele frequency data, computing distance measures for constructing population trees and average heterozygosity (H) (measure of genetic diversity within populations) and G(ST) (measure of genetic differentiation among subdivided populations). We have now developed a web version POPTREEW (http://www.med.kagawa-u.ac.jp/∼genomelb/takezaki/poptreew/) to provide cross-platform access to all POPTREE functions including interactive tree editing. Furthermore, new POPTREE software (POPTREE, POPTREE2, and POPTREEW) computes standardized G(ST) and Jost's D, which may be appropriate for data with high variability, and accepts genotype data in GENEPOP format as an input.

  15. Allele frequencies data and statistic parameters for 13 STR loci in a population of the Brazilian Amazon Region.

    PubMed

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

    2007-05-24

    Allele frequencies for 13 short tandem repeat (D3S1358, vWA, D21S11, D18S51, D5S818, D13S317, D7S820, TH01, TPOX, D16S539, CSF1PO, D8S1179 and FGA) loci were determined in a sample of 325 unrelated individuals from the population of the Amazon of Belém, Brazil. These loci are the most commonly used in forensic and paternity testing. The forensic parameters investigated presented high values. The power of discrimination and the probability of exclusion for these 13 STRs are 99.999999999992% and 99.9998%, respectively. In conclusion, these 13 markers are suitable for forensic analysis and paternity tests of the Amazonian population.

  16. Robust time and frequency domain estimation methods in adaptive control

    NASA Technical Reports Server (NTRS)

    Lamaire, Richard Orville

    1987-01-01

    A robust identification method was developed for use in an adaptive control system. The type of estimator is called the robust estimator, since it is robust to the effects of both unmodeled dynamics and an unmeasurable disturbance. The development of the robust estimator was motivated by a need to provide guarantees in the identification part of an adaptive controller. To enable the design of a robust control system, a nominal model as well as a frequency-domain bounding function on the modeling uncertainty associated with this nominal model must be provided. Two estimation methods are presented for finding parameter estimates, and, hence, a nominal model. One of these methods is based on the well developed field of time-domain parameter estimation. In a second method of finding parameter estimates, a type of weighted least-squares fitting to a frequency-domain estimated model is used. The frequency-domain estimator is shown to perform better, in general, than the time-domain parameter estimator. In addition, a methodology for finding a frequency-domain bounding function on the disturbance is used to compute a frequency-domain bounding function on the additive modeling error due to the effects of the disturbance and the use of finite-length data. The performance of the robust estimator in both open-loop and closed-loop situations is examined through the use of simulations.

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

    PubMed

    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.

  18. Confidence of the three-point estimator of frequency drift

    NASA Technical Reports Server (NTRS)

    Weiss, Marc A.; Hackman, Christine

    1993-01-01

    It was shown that a three-point second difference estimator is nearly optimal for estimating frequency drift in many common atomic oscillators. A formula for the uncertainty of this estimate as a function of the integration time and of the Allan variance associated with this integration time is derived.

  19. A phase match based frequency estimation method for sinusoidal signals

    NASA Astrophysics Data System (ADS)

    Shen, Yan-Lin; Tu, Ya-Qing; Chen, Lin-Jun; Shen, Ting-Ao

    2015-04-01

    Accurate frequency estimation affects the ranging precision of linear frequency modulated continuous wave (LFMCW) radars significantly. To improve the ranging precision of LFMCW radars, a phase match based frequency estimation method is proposed. To obtain frequency estimation, linear prediction property, autocorrelation, and cross correlation of sinusoidal signals are utilized. The analysis of computational complex shows that the computational load of the proposed method is smaller than those of two-stage autocorrelation (TSA) and maximum likelihood. Simulations and field experiments are performed to validate the proposed method, and the results demonstrate the proposed method has better performance in terms of frequency estimation precision than methods of Pisarenko harmonic decomposition, modified covariance, and TSA, which contribute to improving the precision of LFMCW radars effectively.

  20. Temporal changes in allele frequencies in a small marble trout Salmo marmoratus population threatened by extreme flood events.

    PubMed

    Pujolar, J M; Vincenzi, S; Zane, L; Crivelli, A J

    2016-03-01

    The effect of extreme floods on the genetic composition of marble trout Salmo marmoratus living in Lipovscek, a tributary of the Soca River in Slovenia, which has been affected by multiple destructive flood events for centuries was investigated. By monitoring genetic variability during the period 2004-2011, apparent signatures of genetic erosion including a decline in observed and expected heterozygosities and allelic richness were observed. Contemporary effective population size was estimated between 11 and 55 individuals, which is congruent with census data. The data suggest asymmetric gene flow between the two sections of the river. The existence of substantial downstream migration (15-19%) was confirmed by paternity analysis. A small (1-3%) upstream migration was also suggested, which was confirmed by tagging data. Overall, low genetic diversity has not prevented the survival of the Lipovscek population, which might be a common feature of salmonid freshwater populations. PMID:26832308

  1. Frequency of BLAD and CVM alleles in sires and elite heifers of Czech Holstein cattle.

    PubMed

    Cítek, J; Rehout, V; Schröffelová, D; Hradecká, E

    2008-12-01

    In this paper, we analyse the occurrence of BLAD and CVM heterozygous animals in Holstein cattle in the Czech Republic in 1993-2005. The occurrence of BLAD heterozygous sires and heifers (BL) during the period 1993-1998 in Czech Holsteins was 13.9% and 10.7%. Radical measures have been taken to restore the population. Evidently, the measures have been efficient, in 2005 one BLAD heterozygous sire of 101 was found. Continuous testing is necessary, because in commercial herds, the eradication process is not short-term. The found occurrence ofCVM heterozygous sires (CV) decreased from 20% in 2001 to 8% (7 positive of 85) in 2005.This is still quite a high frequency. The occurrence in CV females of 20% remains higher. Therefore, the use of CV sires should be restricted thoroughly. Identification of the molecular basis for inherited diseases, should lead to control measures which would enable the quick recovery of the population. PMID:19113030

  2. Lower frequency of sister chromatid exchanges and altered frequency of HLA B-region alleles among individuals with sporadic dysplastic nevi.

    PubMed

    Illeni, M T; Rovini, D; Di Lernia, M; Cascinelli, N; Ghidoni, A

    1997-01-01

    Sister chromatid exchanges (SCE) were analyzed in peripheral blood lymphocytes of 24 individuals, following diagnosis, and prior to surgical removal, of a sporadic dysplastic nevus (DN). Lower SCE values and variability were found in 23 sporadic DN individuals compared with controls (2.52 +/- 0.12 and 3.76 +/- 0.22 SCE/cell, respectively). These DN individuals, contrarily to healthy controls and some types of tumor patients whose cells are hypersensitive to mutagenic agents, did not show increased SCE rates as a consequence of cigarette smoking, alcohol consumption and diagnostic radiation treatments. These observations are in contrast with clinical evidence that similar lesions are both markers or risk and precursors of malignancy in individuals with multiple nevi, affected by the dysplastic nevus syndrome (DNS) or belonging to FMM (familial malignant melanoma) families. Three HLA class I alleles out of 72 tested were found more frequently in sporadic DN individuals compared with controls: B37 (p < 0.05), B52 (p < 0.01) and B70 (p < 0.01). Whether the greater chromosomal stability (as shown by the SCE analysis), and/or the altered frequency of some HLA alleles could influence the chance of developing cutaneous malignancy in DN individuals is yet to be evaluated.

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

    PubMed Central

    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

  4. Gene frequencies of ABO and Rh (D) blood group alleles in a healthy infant population in Ibadan, Nigeria.

    PubMed

    Omotade, O O; Adeyemo, A A; Kayode, C M; Falade, S L; Ikpeme, S

    1999-01-01

    The ABO and Rhesus blood group systems remain the most important blood group systems clinically. In order to provide gene frequency values for the ABO and Rh (D) alleles in a healthy infant population in south west Nigeria, 4748 healthy infants were typed for ABO and Rh (D) blood groups over a five year period (1988-1992). Overall, 2575 (54.2%) were blood group O, 1023 (21.6%) were blood group A, 1017 (21.4%) were blood group B and 133 (2.8%) were blood group AB. The distribution of the ABO blood groups did not differ significantly from those expected under the Hardy Weinberg equilibrium (Goodness-of-fit X2 = 6.09, df = 3, p = 0.1075). The proportions of the infants belonging to the various ABO blood groups did not vary significantly over the period of the study (X2 = 14.53, df = 12, p = 0.268). Overall gene frequencies for the O, A and B genes were 0.7398, 0.1305 and 0.1298 respectively. For the Rh (D) gene, 4520 (95.2%) were Rh-positive while 228 (4.8%) were Rh-negative. However, the proportions of Rh (D) negative infants varied significantly over the period of the study, with a particular year (1991) having nearly twice the usual frequency of Rh-negative individuals (X2 = 31.17, df =, p < 0.001). The frequency of the Rh (D) gene was 0.7809. These figures are reported in the hope that they may find some use as reference for studies of ABO blood groups in health and disease, especially since they were obtained in an infant population in which it is expected that selection pressures should not have started to act to any significant extent.

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

    PubMed

    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

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

    PubMed Central

    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

  7. Apolipoprotein E Allelic Frequency Altered in Women with Early-onset Breast Cancer.

    PubMed

    Porrata-Doria, Tirtsa; Matta, Jaime L; Acevedo, Summer F

    2010-05-24

    Among women, the most prevalent type of cancer is breast cancer, affecting 1 out of every 8 women in the United States; in Puerto Rico, 70 out of every 100,000 will develop some type of breast cancer. Therefore, a better understand of the potential risk factors for breast cancer could lead to the development of early detection tools. A gene that has been proposed as a risk factor in several populations around the world is Apolipoprotein E (apoE). ApoE functions as a mechanism of transport for lipoproteins and cholesterol throughout the body, with 3 main isoforms present in humans (apoE2, apoE3, and apoE4). Whether or not apoE4 is a risk factor for breast cancer remains controversial. Previous studies have either included test subjects of all ages (20-80) or have focused on late-onset (after age 50) breast cancer; none has concentrated specifically on early-onset (aged 50 and younger) breast cancer. The objectives of this study was to examine (in a Puerto Rican population) the differences in the relative frequency of occurrence of apoE4 in non-breast cancer versus breast cancer patients and to examine, as well, the potential differences of same in early- versus late-onset patients. We found an increased frequency of apoE4 (odds ratio 2.15) only in early-onset breast cancer survivors, which is similar to the findings of those studies that combined or adjusted for age as well as for an association between apoE4 and decreased tumor size. ApoE is also a potential risk factor for long-term cognitive effects after chemotherapy and affects response to hormone replacement. Our data supports the theory that knowing the apoE genotype of women who are at risk of developing breast cancer may be beneficial, as such knowledge would aid in the prediction of tumor size and the development of treatment regimens.

  8. Variation in Meiotic Recombination Frequencies Between Allelic Transgenes Inserted at Different Sites in the Drosophila melanogaster Genome

    PubMed Central

    McMahan, Susan; Kohl, Kathryn P.; Sekelsky, Jeff

    2013-01-01

    Meiotic crossovers are distributed nonrandomly across the genome. Classic studies in Drosophila suggest that the position of a gene along a chromosome arm can affect the outcome of the recombination process, with proximity to the centromere being associated with lower crossing over. To examine this phenomenon molecularly, we developed an assay that measures meiotic crossovers and noncrossover gene conversions between allelic transgenes inserted into different genomic positions. To facilitate collecting a large number of virgin females, we developed a useful genetic system that kills males and undesired classes of females. We found that the recombination frequency at a site in the middle of the X chromosome, where crossovers are normally frequent, was similar to the frequency at the centromere-proximal end of the euchromatin, where crossovers are normally infrequent. In contrast, we recovered no recombinants—crossovers or noncrossovers—at a site on chromosome 4 and at a site toward the distal end of the X chromosome. These results suggest that local sequence or chromatin features have a stronger impact on recombination rates in this transgene assay than position along the chromosome arm. PMID:23797104

  9. Frequencies of allele groups HLA-A, HLA-B and HLA-DRB1 in a population from the northwestern region of São Paulo State, Brazil.

    PubMed

    Ayo, C M; da Silveira Camargo, A V; Xavier, D H; Batista, M F; Carneiro, O A; Brandão de Mattos, C C; Ricci, O; de Mattos, L C

    2015-02-01

    The aim of this study was to estimate the HLA-A, HLA-B and HLA-DRB1 allele groups frequencies in a population of 1559 volunteer bone marrow donors from the northwestern region of São Paulo State grouped according to ethnicity. An additional objective was to compare the allele frequencies of the current study with data published for other Brazilian populations. The allele groups were characterized by the PCR-rSSO method using Luminex(®) technology. Twenty HLA-A, 32 HLA-B and 13 HLA-DRB1 allele groups were identified. The most common allele groups in European descent and mixed African and European descent samples were HLA-A*02, HLA-B*35 and HLA-DRB1*13, while HLA-A*02, HLA-B*35 and HLA-DRB1*11 were more common in African descent samples. The HLA-A*23, HLA-A*36, HLA-B*58 and HLA-B*81 allele groups were more common in sample from African descent than European descent, and the HLA-DRB1*08 was more common in mixed African and European descent than in European descent. Allele group frequencies were compared with samples from other Brazilian regions. The HLA-A*30 and HLA-A*23 were more common in this study than in the populations of Rio Grande do Sul and Paraná; and the HLA-A*01, HLA-B*18, HLA-B*57 and HLA-DRB1*11 were more common in this study than in the population of Piauí. The least frequent allele groups were HLA-A*31, HLA-B*15, HLA-B*40 and HLA-DRB1*08 for the population of Piauí, HLA-A*01 and HLA-A*11 for Parana, HLA-A*02 and -A*03 for Rio Grande do Sul and HLA-DRB1*04 for Paraná, Rio Grande do Sul and Piauí. These data provide an overview on the knowledge on HLA diversity in the population of the northwestern region of São Paulo State and show that the genes of this system are useful to distinguish different ethnic groups.

  10. Allele and genotype frequencies of CYP2C9, CYP2C19 and CYP2D6 in an Italian population.

    PubMed

    Scordo, Maria Gabriella; Caputi, Achille P; D'Arrigo, Concetta; Fava, Giuseppina; Spina, Edoardo

    2004-08-01

    The polymorphic cytochrome P450 isoenzymes (CYPs) 2C9, 2C19 and 2D6 metabolise many important drugs, as well as other xenobiotics. Their polymorphism gives rise to important interindividual and interethnic variability in the metabolism and disposition of several therapeutic agents and may cause differences in the clinical response to these drugs. In this study, we determined the genotype profile of a random Italian population in order to compare the CYP2C9, CYP2C19 and CYP2D6 allele frequencies among Italians with previous findings in other Caucasian populations. Frequencies for the major CYP2C9, CYP2C19 and CYP2D6 mutated alleles and genotypes have been evaluated in 360 unrelated healthy Italian volunteers (210 males and 150 females, aged 19-52 years). Genotyping has been carried out on peripheral leukocytes DNA by molecular biology techniques (PCR, RFLP, long-PCR). CYP2C9, CYP2C19 and CYP2D6 allele and genotype frequencies resulted in equilibrium with the Hardy-Weinberg equation. One hundred and fourteen subjects (31.7%) carried one and 23 subjects (6.4%) carried two CYP2C9 mutated alleles. Sixty-eight (18.9%) volunteers were found to be heterozygous and six (1.7%) homozygous for the CYP2C19*2, while no CYP2C19*3 was detected in the evaluated population. Volunteers could be divided into four CYP2D6 genotypes groups: 192 subjects (53.3%) with no mutated alleles (homozygous extensive metabolisers, EM), 126 (35.0%) with one mutated allele (heterozygous EM), 12 (3.4%) with two mutated alleles (poor metabolisers, PM) and 30 (8.3%) with extracopies of a functional gene (ultrarapid metabolisers, UM). Frequencies of both CYP2C9 and CYP2C19 allelic variants, as well as CYP2D6 detrimental alleles, in Italian subjects were similar to those of other Caucasian populations. Conversely, the prevalence of CYP2D6 gene duplication among Italians resulted very high, confirming the higher frequency of CYP2D6 UM in the Mediterranean area compared to Northern Europe. PMID:15177309

  11. Using Internet search engines to estimate word frequency.

    PubMed

    Blair, Irene V; Urland, Geoffrey R; Ma, Jennifer E

    2002-05-01

    The present research investigated Internet search engines as a rapid, cost-effective alternative for estimating word frequencies. Frequency estimates for 382 words were obtained and compared across four methods: (1) Internet search engines, (2) the Kucera and Francis (1967) analysis of a traditional linguistic corpus, (3) the CELEX English linguistic database (Baayen, Piepenbrock, & Gulikers, 1995), and (4) participant ratings of familiarity. The results showed that Internet search engines produced frequency estimates that were highly consistent with those reported by Kucera and Francis and those calculated from CELEX, highly consistent across search engines, and very reliable over a 6-month period of time. Additional results suggested that Internet search engines are an excellent option when traditional word frequency analyses do not contain the necessary data (e.g., estimates for forenames and slang). In contrast, participants' familiarity judgments did not correspond well with the more objective estimates of word frequency. Researchers are advised to use search engines with large databases (e.g., AltaVista) to ensure the greatest representativeness of the frequency estimates.

  12. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China*

    PubMed Central

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng

    2013-01-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population’s genetic background, for individual identification, and for paternity testing in forensic practice. PMID:23733431

  13. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China.

    PubMed

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng

    2013-06-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background, for individual identification, and for paternity testing in forensic practice.

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

    PubMed

    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, P<0.001) highest than the Delta 32 mean value, indicating that probably the Vikings 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.

  15. Evaluation of Piloted Inputs for Onboard Frequency Response Estimation

    NASA Technical Reports Server (NTRS)

    Grauer, Jared A.; Martos, Borja

    2013-01-01

    Frequency response estimation results are presented using piloted inputs and a real-time estimation method recently developed for multisine inputs. A nonlinear simulation of the F-16 and a Piper Saratoga research aircraft were subjected to different piloted test inputs while the short period stabilator/elevator to pitch rate frequency response was estimated. Results show that the method can produce accurate results using wide-band piloted inputs instead of multisines. A new metric is introduced for evaluating which data points to include in the analysis and recommendations are provided for applying this method with piloted inputs.

  16. A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis.

    PubMed

    Mimee, Benjamin; Duceppe, Marc-Olivier; Véronneau, Pierre-Yves; Lafond-Lapalme, Joël; Jean, Martine; Belzile, François; Bélair, Guy

    2015-11-01

    Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species.

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

    PubMed

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

    2014-06-01

    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. PMID:24491253

  18. Variant allele frequency enrichment analysis in vitro reveals sonic hedgehog pathway to impede sustained temozolomide response in GBM

    PubMed Central

    Biswas, Nidhan K.; Chandra, Vikas; Sarkar-Roy, Neeta; Das, Tapojyoti; Bhattacharya, Rabindra N.; Tripathy, Laxmi N.; Basu, Sunandan K.; Kumar, Shantanu; Das, Subrata; Chatterjee, Ankita; Mukherjee, Ankur; Basu, Pryiadarshi; Maitra, Arindam; Chattopadhyay, Ansuman; Basu, Analabha; Dhara, Surajit

    2015-01-01

    Neoplastic cells of Glioblastoma multiforme (GBM) may or may not show sustained response to temozolomide (TMZ) chemotherapy. We hypothesize that TMZ chemotherapy response in GBM is predetermined in its neoplastic clones via a specific set of mutations that alter relevant pathways. We describe exome-wide enrichment of variant allele frequencies (VAFs) in neurospheres displaying contrasting phenotypes of sustained versus reversible TMZ-responses in vitro. Enrichment of VAFs was found on genes ST5, RP6KA1 and PRKDC in cells showing sustained TMZ-effect whereas on genes FREM2, AASDH and STK36, in cells showing reversible TMZ-effect. Ingenuity pathway analysis (IPA) revealed that these genes alter cell-cycle, G2/M-checkpoint-regulation and NHEJ pathways in sustained TMZ-effect cells whereas the lysine-II&V/phenylalanine degradation and sonic hedgehog (Hh) pathways in reversible TMZ-effect cells. Next, we validated the likely involvement of the Hh-pathway in TMZ-response on additional GBM neurospheres as well as on GBM patients, by extracting RNA-sequencing-based gene expression data from the TCGA-GBM database. Finally, we demonstrated TMZ-sensitization of a TMZ non-responder neurosphere in vitro by treating them with the FDA-approved pharmacological Hh-pathway inhibitor vismodegib. Altogether, our results indicate that the Hh-pathway impedes sustained TMZ-response in GBM and could be a potential therapeutic target to enhance TMZ-response in this malignancy. PMID:25604826

  19. Beyond orchids and dandelions: Testing the 5HTT “risky” allele for evidence of phenotypic capacitance and frequency dependent selection

    PubMed Central

    Conley, Dalton; Rauscher, Emily; Siegal, Mark L.

    2013-01-01

    The persistence of behaviorally deleterious genes in the human population poses an interesting question for population genetics: If certain alleles at these loci are deleterious, why have they survived in the population? We consider evidence for phenotypic capacitance and/or frequency dependent selection for an allele that has been putatively shown to have negative associations with human behaviors (the “short” 5-HTT promoter region allele) yet which has persisted in human and non-human primate populations. Using National Longitudinal Study of Adolescent Health data, we compare sibling and twin variation in depression by 5-HTT genotype (specified in several ways) and investigate sibship-level cross-person gene-gene interactions. In support of the “orchid / dandelion” hypothesis, we find evidence that the short allele increases variation in phenotypes in response to environmental (or genetic) differences (i.e. acts as a perturbation of a phenotypic capacitor). Further, we also find some evidence that the effects of allelic variation at this locus are moderated by the genetic environment of the sibship unit (i.e. may be susceptible to frequency dependent selection). We discuss implications of these findings for genetic models in general, specifically with respect to stable unit treatment value assumption violations (i.e. non-independence of units of analysis). PMID:23701535

  20. Relationship between allozymes, heterozygosity and morphological characters in red deer (Cervus elaphus), and the influence of selective hunting on allele frequency distribution.

    PubMed

    Hartl, G B; Lang, G; Klein, F; Willing, R

    1991-06-01

    Morphological characters in red deer (Cervus elaphus), which serve as criteria for selective hunting, were examined in relation to electrophoretic variation in three populations from the Vosges in eastern France. From the polymorphic loci examined, certain alleles at Idh-2, Me-1 and Acp-1 showed significant associations with a special development of body and antler characters selected for by hunters. Idh-2(125) was associated with larger hind foot length in females and a higher number of antler points in males. Me-1(90) and Acp-1(100) were associated with small spikes. The populations studied differed from one another in the duration and intensity of selective hunting and the increase or decrease in the respective allele frequencies could be explained by selection for large body size, a high number of antler points and against small spikes in yearlings, rather than by genetic drift. Among other morphological characters examined, the length of the main beam was significantly associated with the allele Acp-2(100). In contrast, no associations could be detected between overall heterozygosity and the development or the degree of asymmetry (in paired structures) of any of the morphological traits in question. Although no obvious differences in the overall values of polymorphism or heterozygosity were found between the populations, selective hunting leads towards a change in allele frequencies and eventually to the loss of one or the other rare allele. PMID:1880046

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

    PubMed Central

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

    2015-01-01

    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. PMID:26560341

  2. Estimation of recombination frequency in bi-parental genetic populations.

    PubMed

    Sun, Ziqi; Li, Huihui; Zhang, Luyan; Wang, Jiankang

    2012-06-01

    Summary Linkage analysis plays an important role in genetic studies. In linkage analysis, accurate estimation of recombination frequency is essential. Many bi-parental populations have been used, and determining an appropriate population is of great importance in precise recombination frequency. In this study, we investigated the estimation efficiency of recombination frequency in 12 bi-parental populations. The criteria that we used for comparison were LOD score in testing linkage relationship, deviation between estimated and real recombination frequency, standard error (SE) of estimates and the least theoretical population size (PS) required to observe at least one recombinant and to declare the statistically significant linkage relationship. Theoretical and simulation results indicated that larger PS and smaller recombination frequency resulted in higher LOD score and smaller deviation. Lower LOD score, higher deviation and higher SE for estimating the recombination frequency in the advanced backcrossing and selfing populations are larger than those in backcross and F2 populations, respectively. For advanced backcrossing and selfing populations, larger populations were needed in order to observe at least one recombinant and to declare significant linkage. In comparison, in F2 and F3 populations higher LOD score, lower deviation and SE were observed for co-dominant markers. A much larger population was needed to observe at least one recombinant and to detect loose linkage for dominant and recessive markers. Therefore, advanced backcrossing and selfing populations had lower precision in estimating the recombination frequency. F2 and F3 populations together with co-dominant markers represent the ideal situation for linkage analysis and linkage map construction.

  3. Real-Time Parameter Estimation in the Frequency Domain

    NASA Technical Reports Server (NTRS)

    Morelli, Eugene A.

    1999-01-01

    A method for real-time estimation of parameters in a linear dynamic state space model was developed and studied. The application is aircraft dynamic model parameter estimation from measured data in flight for indirect adaptive or reconfigurable control. Equation error in the frequency domain was used with a recursive Fourier transform for the real-time data analysis. Linear and nonlinear simulation examples and flight test data from the F-18 High Alpha Research Vehicle HARV) were used to demonstrate that the technique produces accurate model parameter estimates with appropriate error bounds. Parameter estimates converged in less than 1 cycle of the dominant dynamic mode natural frequencies, using control surface inputs measured in flight during ordinary piloted maneuvers. The real-time parameter estimation method has low computational requirements, and could be implemented aboard an aircraft in real time.

  4. cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms.

    PubMed

    Ali, Sajid; Soubeyrand, Samuel; Gladieux, Pierre; Giraud, Tatiana; Leconte, Marc; Gautier, Angélique; Mboup, Mamadou; Chen, Wanquan; de Vallavieille-Pope, Claude; Enjalbert, Jérôme

    2016-07-01

    Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecology and evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a new and accurate method, cloncase, for estimating both the rate of sexual vs. asexual reproduction and the effective population size, based on the frequency of clonemate resampling across generations. Simulations showed that our method provides reliable estimates of sex frequency and effective population size for a wide range of parameters. The cloncase method was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an important wheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using two temporally spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e. three-quarter of individuals being sexually derived during the yearly sexual cycle), indicating strong contribution of sexual reproduction to the life cycle of the pathogen in this area. The inferred effective population size of this partially clonal organism (Nc  = 998) was in good agreement with estimates obtained using methods based on temporal variations in allelic frequencies. The cloncase estimator presented herein is the first method allowing accurate inference of both sex frequency and effective population size from population data without knowledge of recombination or mutation rates. cloncase can be applied to population genetic data from any organism with cyclical parthenogenesis and should in particular be very useful for improving our understanding of pest and microbial population biology. PMID:26858112

  5. Real-time PCR genotyping assay for canine progressive rod-cone degeneration and mutant allele frequency in Toy Poodles, Chihuahuas and Miniature Dachshunds in Japan.

    PubMed

    Kohyama, Moeko; Tada, Naomi; Mitsui, Hiroko; Tomioka, Hitomi; Tsutsui, Toshihiko; Yabuki, Akira; Rahman, Mohammad Mahbubur; Kushida, Kazuya; Mizukami, Keijiro; Yamato, Osamu

    2016-03-01

    Canine progressive rod-cone degeneration (PRCD) is a middle- to late-onset, autosomal recessive, inherited retinal disorder caused by a substitution (c.5G>A) in the canine PRCD gene that has been identified in 29 or more purebred dogs. In the present study, a TaqMan probe-based real-time PCR assay was developed and evaluated for rapid genotyping and large-scale screening of the mutation. Furthermore, a genotyping survey was carried out in a population of the three most popular breeds in Japan (Toy Poodles, Chihuahuas and Miniature Dachshunds) to determine the current mutant allele frequency. The assay separated all the genotypes of canine PRCD rapidly, indicating its suitability for large-scale surveys. The results of the survey showed that the mutant allele frequency in Toy Poodles was high enough (approximately 0.09) to allow the establishment of measures for the prevention and control of this disorder in breeding kennels. The mutant allele was detected in Chihuahuas for the first time, but the frequency was lower (approximately 0.02) than that in Toy Poodles. The mutant allele was not detected in Miniature Dachshunds. This assay will allow the selective breeding of dogs from the two most popular breeds (Toy Poodle and Chihuahua) in Japan and effective prevention or control of the disorder. PMID:26549343

  6. Real-time PCR genotyping assay for canine progressive rod-cone degeneration and mutant allele frequency in Toy Poodles, Chihuahuas and Miniature Dachshunds in Japan

    PubMed Central

    KOHYAMA, Moeko; TADA, Naomi; MITSUI, Hiroko; TOMIOKA, Hitomi; TSUTSUI, Toshihiko; YABUKI, Akira; RAHMAN, Mohammad Mahbubur; KUSHIDA, Kazuya; MIZUKAMI, Keijiro; YAMATO, Osamu

    2015-01-01

    Canine progressive rod-cone degeneration (PRCD) is a middle- to late-onset, autosomal recessive, inherited retinal disorder caused by a substitution (c.5G>A) in the canine PRCD gene that has been identified in 29 or more purebred dogs. In the present study, a TaqMan probe-based real-time PCR assay was developed and evaluated for rapid genotyping and large-scale screening of the mutation. Furthermore, a genotyping survey was carried out in a population of the three most popular breeds in Japan (Toy Poodles, Chihuahuas and Miniature Dachshunds) to determine the current mutant allele frequency. The assay separated all the genotypes of canine PRCD rapidly, indicating its suitability for large-scale surveys. The results of the survey showed that the mutant allele frequency in Toy Poodles was high enough (approximately 0.09) to allow the establishment of measures for the prevention and control of this disorder in breeding kennels. The mutant allele was detected in Chihuahuas for the first time, but the frequency was lower (approximately 0.02) than that in Toy Poodles. The mutant allele was not detected in Miniature Dachshunds. This assay will allow the selective breeding of dogs from the two most popular breeds (Toy Poodle and Chihuahua) in Japan and effective prevention or control of the disorder. PMID:26549343

  7. A Simple Joint Estimation Method of Residual Frequency Offset and Sampling Frequency Offset for DVB Systems

    NASA Astrophysics Data System (ADS)

    Kwon, Ki-Won; Cho, Yongsoo

    This letter presents a simple joint estimation method for residual frequency offset (RFO) and sampling frequency offset (STO) in OFDM-based digital video broadcasting (DVB) systems. The proposed method selects a continual pilot (CP) subset from an unsymmetrically and non-uniformly distributed CP set to obtain an unbiased estimator. Simulation results show that the proposed method using a properly selected CP subset is unbiased and performs robustly.

  8. Frequencies of 23 Functionally Significant Variant Alleles Related with Metabolism of Antineoplastic Drugs in the Chilean Population: Comparison with Caucasian and Asian Populations

    PubMed Central

    Roco, Ángela; Quiñones, Luis; Agúndez, José A. G.; García-Martín, Elena; Squicciarini, Valentina; Miranda, Carla; Garay, Joselyn; Farfán, Nancy; Saavedra, Iván; Cáceres, Dante; Ibarra, Carol; Varela, Nelson

    2012-01-01

    Cancer is a leading cause of death worldwide. The cancer incidence rate in Chile is 133.7/100,000 inhabitants and it is the second cause of death, after cardiovascular diseases. Most of the antineoplastic drugs are metabolized to be detoxified, and some of them to be activated. Genetic polymorphisms of drug-metabolizing enzymes can induce deep changes in enzyme activity, leading to individual variability in drug efficacy and/or toxicity. The present research describes the presence of genetic polymorphisms in the Chilean population, which might be useful in public health programs for personalized treatment of cancer, and compares these frequencies with those reported for Asian and Caucasian populations, as a contribution to the evaluation of ethnic differences in the response to chemotherapy. We analyzed 23 polymorphisms in a group of 253 unrelated Chilean volunteers from the general population. The results showed that CYP2A6*2, CYP2A6*3, CYP2D6*3, CYP2C19*3, and CYP3A4*17 variant alleles are virtually absent in Chileans. CYP1A1*2A allele frequency (0.37) is similar to that of Caucasians and higher than that reported for Japanese people. Allele frequencies for CYP3A5*3(0.76) and CYP2C9*3(0.04) are similar to those observed in Japanese people. CYP1A1*2C(0.32), CYP1A2*1F(0.77), CYP3A4*1B(0.06), CYP2D6*2(0.41), and MTHFR T(0.52) allele frequencies are higher than the observed either in Caucasian or in Japanese populations. Conversely, CYP2C19*2 allelic frequency (0.12), and genotype frequencies for GSTT1 null (0.11) and GSTM1 null (0.36) are lower than those observed in both populations. Finally, allele frequencies for CYP2A6*4(0.04), CYP2C8*3(0.06), CYP2C9*2(0.06), CYP2D6*4(0.12), CYP2E1*5B(0.14), CYP2E1*6(0.19), and UGT2B7*2(0.40) are intermediate in relation to those described in Caucasian and in Japanese populations, as expected according to the ethnic origin of the Chilean population. In conclusion, our findings support the idea that ethnic variability must be

  9. Increased frequency of co-existing JAK2 exon-12 or MPL exon-10 mutations in patients with low JAK2(V617F) allelic burden.

    PubMed

    Nussenzveig, Roberto H; Pham, Ha T; Perkins, Sherrie L; Prchal, Josef T; Agarwal, Archana M; Salama, Mohamed E

    2016-01-01

    The frequency of co-existing JAK2(V617F)/MPL and JAK2(V617F)/JAK2 exon-12 mutations has not been previously investigated in MPNs. Poor survival was reported in primary myelofibrosis with low JAK2(V617F) allelic burden. However, mutational status of JAK2 exon-12 or MPL were not reported in these patients. This study developed a cost-effective multiplex high resolution melt assay that screens for mutations in JAK2 gene exons-12 and -14 ((V617F)) and MPL gene exon-10. Co-existing mutations with JAK2(V617F) were detected in 2.9% (6/208; two JAK2 exon-12 and four MPL exon-10) patient specimens with known JAK2(V617F) (allelic-burden range: 0.1-96.8%). Co-existing mutations were detected in specimens with < 12% JAK2(V617F) allelic burden. Current WHO guidelines do not recommend further testing once JAK2(V617F) mutation is detected in MPNs. The findings, however, indicate that quantification of JAK2(V617F) allele burden may be clinically relevant in MPNs and in those with low allelic burden additional testing for JAK2 exon-12 and MPL exon-10 mutation should be pursued.

  10. Modal vector estimation for closely spaced frequency modes

    NASA Technical Reports Server (NTRS)

    Craig, R. R., Jr.; Chung, Y. T.; Blair, M.

    1982-01-01

    Techniques for obtaining improved modal vector estimates for systems with closely spaced frequency modes are discussed. In describing the dynamical behavior of a complex structure modal parameters are often analyzed: undamped natural frequency, mode shape, modal mass, modal stiffness and modal damping. From both an analytical standpoint and an experimental standpoint, identification of modal parameters is more difficult if the system has repeated frequencies or even closely spaced frequencies. The more complex the structure, the more likely it is to have closely spaced frequencies. This makes it difficult to determine valid mode shapes using single shaker test methods. By employing band selectable analysis (zoom) techniques and by employing Kennedy-Pancu circle fitting or some multiple degree of freedom (MDOF) curve fit procedure, the usefulness of the single shaker approach can be extended.

  11. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome projects routinely produce draft sequences for species from diverse evolutionary clades, but generally do not create single nucleotide polymorphism (SNP) resources. We present an approach for de novo SNP discovery based on short-read sequencing of reduced representation libraries (RRL) to ge...

  12. Robust and Efficient Frequency Estimator for Undersampled Waveforms Based on Frequency Offset Recognition

    PubMed Central

    Huang, Xiangdong; Bai, Ruipeng; Jin, Xukang; Fu, Haipeng

    2016-01-01

    This paper proposes an efficient frequency estimator based on Chinese Remainder Theorem for undersampled waveforms. Due to the emphasis on frequency offset recognition (i.e., frequency shift and compensation) of small-point DFT remainders, compared to estimators using large-point DFT remainders, it can achieve higher noise robustness in low signal-to-noise ratio (SNR) cases and higher accuracy in high SNR cases. Numerical results show that, by incorporating a remainder screening method and the Tsui spectrum corrector, the proposed estimator not only lowers the SNR threshold of detection, but also provides a higher accuracy than the large-point DFT estimator when the DFT size decreases to 1/90 of the latter case. PMID:27701456

  13. A reassessment of frequency estimates of PvuII-generated VNTR profiles in a Finnish, an Italian, and a general U.S. Caucasian database: no evidence for ethnic subgroups affecting forensic estimates.

    PubMed

    Budowle, B; Monson, K L; Giusti, A M

    1994-09-01

    Recently, Krane et al. addressed the effect of estimating various target DNA profile frequencies in Finnish, Italian, and general U.S. Caucasian databases. They observed that, when using an "inappropriate ethnic," or noncognate, database (e.g., a Finnish target profile frequency estimated in an Italian database, and vice versa), estimates were less common than when the target profile frequencies were estimated using their own ethnic, or cognate, database, and these estimates differed by more than one order of magnitude. These differences were attributed to the effects of subgroups. We demonstrate that the differences can be ascribed to statistical artifacts that induce large biases and correlations. Additionally, we show that the differences of estimates of any specific DNA profile frequency based on allelic size frequencies from different databases become smaller when the fixed-bin rather than a +/- 2.5% floating-bin approach is used. PMID:7915881

  14. A microsatellite polymorphism in the von Willebrand factor gene: comparison of allele frequencies in different population samples and evaluation for forensic medicine.

    PubMed

    Sajantila, A; Pacek, P; Lukka, M; Syvänen, A C; Nokelainen, P; Sistonen, P; Peltonen, L; Budowle, B

    1994-09-16

    The allele frequencies at the tetranucleotide repeat (TCTA) vWA locus in the vWF gene were determined in the general Finnish population, in a population representing an internal isolate of Finland, in the Vologda-Russian population, and in US Black population samples. The allele and genotype frequencies from these population samples were compared with each other and with those reported from Spanish and British population samples. Statistically significant differences were demonstrated between most of the different groups (Finns vs. Vologda-Russians, Finns vs. US Blacks, Finns vs. Spanish, Vologda-Russians vs. US Blacks, Vologda-Russians vs. Spanish, US Blacks vs. Spanish and US Blacks vs. British Caucasians), but not between the two Caucasoid population samples from Finland and Great Britain, nor between or within the subpopulation samples from Finland and those from Vologda-Russia. In addition, the vWA marker was evaluated and demonstrated to be reliable for forensic purposes and paternity testing.

  15. Real-Time Parameter Estimation in the Frequency Domain

    NASA Technical Reports Server (NTRS)

    Morelli, Eugene A.

    2000-01-01

    A method for real-time estimation of parameters in a linear dynamic state-space model was developed and studied. The application is aircraft dynamic model parameter estimation from measured data in flight. Equation error in the frequency domain was used with a recursive Fourier transform for the real-time data analysis. Linear and nonlinear simulation examples and flight test data from the F-18 High Alpha Research Vehicle were used to demonstrate that the technique produces accurate model parameter estimates with appropriate error bounds. Parameter estimates converged in less than one cycle of the dominant dynamic mode, using no a priori information, with control surface inputs measured in flight during ordinary piloted maneuvers. The real-time parameter estimation method has low computational requirements and could be implemented

  16. Good-Turing frequency estimation in a finite population.

    PubMed

    Hwang, Wen-Han; Lin, Chih-Wei; Shen, Tsung-Jen

    2015-03-01

    Good-Turing frequency estimation (Good, ) is a simple, effective method for predicting detection probabilities of objects of both observed and unobserved classes based on observed frequencies of classes in a sample. The method has been used widely in several disciplines, such as information retrieval, computational linguistics, text recognition, and ecological diversity estimation. Nevertheless, existing studies assume sampling with replacement or sampling from an infinite population, which might be inappropriate for many practical applications. In light of this limitation, this article presents a modification of the Good-Turing estimation method to account for finite population sampling. We provide three practical extensions of the modified method, and we examine performance of the modified method and its extensions in simulation experiments.

  17. Allele Frequencies of the Single Nucleotide Polymorphisms Related to the Body Burden of Heavy Metals in the Korean Population and Their Ethnic Differences

    PubMed Central

    Eom, Sang-Yong; Lim, Ji-Ae; Kim, Yong-Dae; Choi, Byung-Sun; Hwang, Myung Sil; Park, Jung-Duck; Kim, Heon; Kwon, Ho-Jang

    2016-01-01

    This study was performed to select single nucleotide polymorphisms (SNPs) related to the body burden of heavy metals in Koreans, to provide Korean allele frequencies of selected SNPs, and to assess the difference in allele frequencies with other ethnicities. The candidate-gene approach method and genome-wide association screening were used to select SNPs related to the body burden of heavy metals. Genotyping analysis of the final 192 SNPs selected was performed on 1,483 subjects using the VeraCode Goldengate assay. Allele frequencies differences and genetic differentiations between the Korean population and Chinese (CHB), Japanese (JPT), Caucasian (CEU), and African (YIR) populations were tested by Fisher’s exact test and fixation index (FST), respectively. The Korean population was genetically similar to the CHB and JPT populations (FST < 0.05, for all SNPs in both populations). However, a significant difference in the allele frequencies between the Korean and CEU and YIR populations were observed in 99 SNPs (60.7%) and 120 SNPs (73.6%), respectively. Ten (6.1%) and 26 (16.0%) SNPs had genetic differentiation (FST > 0.05) among the Korean-CEU and Korean-YIR comparisons, respectively. The SNP with the largest FST value between the Korean and African populations was cystathionine-β-synthase rs234709 (FST: KOR-YIR, 0.309; KOR-CEU, 0.064). Our study suggests that interethnic differences exist in SNPs associated with heavy metals of Koreans, and it should be considered in future studies that address ethnic differences in heavy-metal concentrations in the body and genetic susceptibility to the body burden of heavy metals. PMID:27437086

  18. Status of allele frequency and diversity of Plasmodium falciparum msp1, msp2 and glurp before implementation of an artemisinin-based combined therapy in Northwestern Colombia.

    PubMed Central

    Arango, Eliana; Carmona-Fonseca, Jaime

    2013-01-01

    Introduction: The status of msp1, msp2 and glurp allele frequency and the diversity of Plasmodium falciparum in Northwestern Colombia before the implementation of an artemisinin-combined therapy have been explored only by a few authors and in a relatively small number of samples from this highly endemic region. Objective: To evaluate the frequency of msp1, msp2, and glurp alleles and the diversity of P. falciparum in two Colombian regions before the use of an artemisinin-combined therapy. Methods: This study was part of a major anti-malarial efficacy trial designed as a random, clinically-controlled study for which 224 subjects were recruited. Region 2 of msp1 and msp2 (central region) were amplified by a nested PCR; glurp (region R2) was amplified by a semi-nested PCR. Results: For msp1, five genotypes were observed, representing the K1, MAD20, and RO33 allelic families. All samples corresponded to a MAD20 150 bp allele. For msp2 (IC family), two alleles were detected and for glurp, eight were observed. A total 33 haplotypes were detected. Conclusions: Analysis of glurpcan be used to successfully genotype parasite populations in the new studies in Colombia aimed at exploring Plasmodium spp population dynamics. In addition, analysis of msp1 and msp2 can also be of value for comparisons with past studies, but not when the objective is to study parasites obtained from the same patient in a reduced period of time; for instance, during treatment efficacy studies. PMID:24892236

  19. Allele frequencies of the major milk proteins in the Finnish Ayrshire and detection of a new kappa-casein variant.

    PubMed

    Ikonen, T; Ruottinen, O; Erhardt, G; Ojala, M

    1996-06-01

    A total of 20990 Finnish Ayrshire cows were phenotyped for the major milk proteins by isoelectric focusing in polyacrylamide gels. The predominant alleles in the Finnish Ayrshire were alpha S1-casein B (0.999), alpha S2-casein A (0.991), beta-casein A1 (0.509) and alpha 2 (0.490), kappa-casein A (0.612) and beta-lactoglobulin B (0.716). The kappa-casein E allele (0.307) was also rather common in the Finnish Ayrshire. A new kappa-casein variant (kappa-casein F) was demonstrated in two Finnish Ayrshire cows, a dam and a daughter.

  20. The frequency of the mitochondrial aldehyde dehydrogenase I2 (atypical) allele in Caucasian, Oriental and African black populations determined by the restriction profile of PCR-amplified DNA.

    PubMed

    Dandré, F; Cassaigne, A; Iron, A

    1995-06-01

    The aldehyde dehydrogenase I (ALDH I) gene codes for a mitochondrial enzyme which plays a major role in hepatic alcohol detoxication. It has been related to alcohol flushing in Orientals bearing the atypical ALDH I2 gene. The variant protein results from a lysine for glutamate substitution at position 487 (G-->A change in exon 12). A procedure for ALDH I2 detection consisting in a differentiation between the 'atypical' allele and the 'wild' allele has been improved through PCR and subsequent MboII digestion. Blood samples collected on anticoagulant or directly absorbed on blotting paper were used for DNA amplification in the presence of two specific oligonucleotidic primers, each one able to incorporate a restriction site in the amplimer. After MboII digestion, PCR products were separated by polyacrylamide gel electrophoresis and then visualized with ethidium bromide. This technique permits a rapid and non-radioactive detection of atypical ALDH I2 on a PCR product without the use of allele specific oligonucleotides. It was applied to the study of ALDH I2 allele frequency in random population samples of three ethnic groups: Caucasians, Orientals and African blacks.

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

    PubMed

    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

  2. Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe

    PubMed Central

    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

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

    PubMed

    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

  4. RegScan: a GWAS tool for quick estimation of allele effects on continuous traits and their combinations

    PubMed Central

    Kals, Mart; Esko, Tõnu; Mägi, Reedik; Fischer, Krista

    2015-01-01

    Genome-wide association studies are becoming computationally more demanding with the growing amounts of data. Combinatorial traits can increase the data dimensions beyond the computational capabilities of the current tools. We addressed this issue by creating an application for quick association analysis that is ten to hundreds of times faster than the leading fast methods. Our tool (RegScan) is designed for performing basic linear regression analysis with continuous traits maximally fast on large data sets. RegScan specifically targets association analysis of combinatorial traits in metabolomics. It can both generate and analyze the combinatorial traits efficiently. RegScan is capable of analyzing any number of traits together without the need to specify each trait individually. The main goal of the article is to show that RegScan can be the preferred analytical tool when large amounts of data need to be analyzed quickly using the allele frequency test. Availability: Precompiled RegScan (all major platforms), source code, user guide and examples are freely available at www.biobank.ee/regscan. Requirements: Qt 4.4.3 or newer for dynamic compilations. PMID:24008273

  5. Generalized flood-frequency estimates for urban areas in Missouri

    USGS Publications Warehouse

    Gann, Ector Eugene

    1971-01-01

    A method is presented for estimating flood-frequency information for urban areas in Missouri. Flood-frequency relations are presented which provide an estimate of the flood-peak discharge for floods with recurrence intervals from 2.33 to 100 years for basins with various degrees of existing or projected urban development. Drainage area sizes for which the relations are applicable range from 0.1 to 50 square miles. These generalized relations will be useful to the urban planner and designer until more comprehensive studies are completed for the individual urban areas within the State. The relations will also be of use in the definition of flood-hazard areas in Missouri.

  6. Estimating correlations of neighbouring frequencies in ambient seismic noise

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Ben-Zion, Yehuda

    2016-08-01

    Extracting accurate empirical Green's functions from the ambient seismic noise field requires the noise to be fully diffuse and that different frequency components are not correlated. Calculating a matrix of correlation coefficients of power spectral samples can be used to estimate deviations from a fully diffuse random noise field in the analysed frequency range. A fully diffuse field has correlations only in a narrow region around the diagonal of the matrix, with frequency resolution inversely proportional to length of the used time window. Analysis of low-frequency data (0.005-0.6 Hz) recorded by three broad-band stations of the southern California seismic network reveals three common types of correlations, manifested in the correlation coefficient matrix as square, diagonal halo and correlated stripes. Synthetic calculations show that these types of signatures in the correlation coefficient matrix can result from certain combinations of cross-frequency correlated random components and diffuse field. The analysis of observed data indicates that the secondary microseismic peak around 0.15 Hz is correlated with its neighbouring frequencies, while the primary peak around 0.06 Hz is more diffuse. This suggests that the primary and secondary peaks may be associated with somewhat different physical origins. In addition, significant correlation of frequencies below that of the primary microseismic peak suggests that the very low frequencies noise is less scattered during propagation. The power spectra recorded by a station close to the edge of the Los Angeles basin is higher compared to data recorded by stations outside the basin perhaps because of enhanced basin reverberations and/or closer proximity to the ocean. This and other regional variations should be tested further using data from many more stations.

  7. Allele frequencies and population data for 17 Y-STR loci (The AmpFlSTR® Y-filer™) in Casablanca resident population.

    PubMed

    Laouina, Adil; El Houate, Brahim; Yahia, Hakima; Azeddoug, Houssine; Boulouiz, Redouane; Chbel, Faiza

    2011-01-01

    Allele frequencies and population data for 17 Y-STR loci included in the AmpFlSTR® Y-filer™ PCR amplification kit (Applied Biosystems, Foster City, USA), that permit the simultaneous amplification of all the markers included in the actually used European "extended haplotype", DYS19, DYS189I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II, DYS438, DYS439 and also DYS437, DYS448, DYS456, DYS458, DYS635 and Y GATA H4, were obtained from a sample of 166 healthy unrelated males resident in Casablanca (from Morocco). A total of 166 haplotypes were identified, of which 142 were unique. The overall haplotype diversity for the 17 Y-STR loci reached 0.9974, and a discrimination capacity was 0.855. We report some non-standard situations, including duplications and microvariant alleles. PMID:21126935

  8. HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in a population of 432 healthy unrelated individuals from Albania.

    PubMed

    Sulcebe, Genc; Shyti, Erkena

    2016-08-01

    This paper reports the HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype polymorphism in a population of 432 healthy individuals from Albania. First-field HLA genotyping was performed by polymerase chain reaction sequence-specific priming and/or oligonucleotide methods. The data were analyzed statistically using gene counting and Arlequin software packages. No deviation from Hardy Weinberg Equilibrium was detected at any of the loci studied. The HLA genotypic data of the population sample reported here are available publicly in the Allele Frequencies Net Database and they can serve as a reference database for further HLA-based population genetics studies including the Albanian population. PMID:27262454

  9. Allele and Haplotype Frequencies of Human Leukocyte Antigen-A, -B, -C, -DRB1, and -DQB1 From Sequence-Based DNA Typing Data in Koreans

    PubMed Central

    In, Ji Won; Roh, Eun Youn; Oh, Sohee; Shin, Sue; Park, Kyoung Un

    2015-01-01

    Background Data on allele frequencies (AFs) and haplotype frequencies (HFs) of HLA-C and -DQB1 are limited in Koreans. We investigated AFs and HFs of HLA-A, -B, -C, -DRB1, and -DQB1 in Koreans by high-resolution sequence-based typing (SBT). Methods Hematopoietic stem cells were obtained from 613 healthy, unrelated donors to analyze HLA-A, -B, -C, -DRB1, and -DQB1 genotypes by using AlleleSEQR HLA-A, -B, -C, -DRB1, and -DQB1 SBT kits (Abbott Molecular, USA), respectively. Alleles belonging to HLA-C*07:01/07:06 group were further discriminated by using PCR-sequence specific primer analysis. AFs and HFs were calculated by direct counting and maximum likelihood method, respectively. Results In all, 24 HLA-A, 46 HLA-B, 24 HLA-C, 29 HLA-DRB1, and 15 HLA-DQB1 alleles were identified. AFs and HFs of HLA-A, -B, and -DRB1 were similar to those reported previously. For the HLA-C locus, C*01:02 was the most common allele, followed by C*03:03, C*03:04, C*14:02, C*03:02, and C*07:02 (AF ≥7%). AFs of C*07:01 and C*07:06 were 0.16% and 3.18%, respectively. For the HLA-DQB1 locus, DQB1*03:01 was the most common allele, followed by DQB1*03:03, *03:02, *06:01, *05:01, *04:01, and *06:02 (AF ≥7%). AFs of DQB1*02:01 and DQB1*02:02 were 2.12% and 6.69%, respectively. HFs of A*33:03-C*07:06 and C*07:06-B*44:03 were 3.09% and 3.10%, respectively, while those of DRB1*07:01-DQB1*02:02 and DRB1*03:01-DQB1*02:01 were 6.61% and 2.04%, respectively. Conclusions This study reported AFs and HFs of HLA, including HLA-C and -DQB1, in Koreans by using high-resolution SBT. These data can be used to resolve ambiguous results of HLA typing for organ and hematopoietic stem cell transplantations. PMID:26131415

  10. Frequency of thermostability variants: estimation of total rare variant frequency in human populations

    SciTech Connect

    Mohrenweiser, H.W.; Neel, J.V.

    1981-09-01

    Eight erythrocyte enzymes were examine for thermostability in an unselected sample of 100 newborn infants. Three thermolabile variants, one each of lactate dehydrogenase, glucosephosphate isomerase, and glucose-6-phosphate dehydrogenase, were identified, none of which was detectable as a variant by standard electrophoretic techniques. All were inherited. This frequency of 3.8 heritable thermostability variants per 1000 determinations is to be compared with a frequency of electrophoretically detectable variants of 1.1 per 1000 determinations, a frequency of 2.4 enzyme-deficiency variants per 1000 determinations, and a frequency of individuals with rare enzyme deficiency or electrophoretic or thermostability (or both) variants at these loci is 8.4 per 1000 determinations. A similar distribution and frequency is seen when the comparison is limited to the seven loci studied by all techniques. it is clear that not all of the electrophoretic and thermostability variants present in the population are detected by the techniques used in this study. Accordingly, it is estimated that the true frequency of carriers of a rare variant for each of these enzyme-coding loci averages greater than 10/1000. Some implications of these frequencies for human disease are discussed.

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

    PubMed

    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

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

    PubMed Central

    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

  13. Aircraft Fault Detection Using Real-Time Frequency Response Estimation

    NASA Technical Reports Server (NTRS)

    Grauer, Jared A.

    2016-01-01

    A real-time method for estimating time-varying aircraft frequency responses from input and output measurements was demonstrated. The Bat-4 subscale airplane was used with NASA Langley Research Center's AirSTAR unmanned aerial flight test facility to conduct flight tests and collect data for dynamic modeling. Orthogonal phase-optimized multisine inputs, summed with pilot stick and pedal inputs, were used to excite the responses. The aircraft was tested in its normal configuration and with emulated failures, which included a stuck left ruddervator and an increased command path latency. No prior knowledge of a dynamic model was used or available for the estimation. The longitudinal short period dynamics were investigated in this work. Time-varying frequency responses and stability margins were tracked well using a 20 second sliding window of data, as compared to a post-flight analysis using output error parameter estimation and a low-order equivalent system model. This method could be used in a real-time fault detection system, or for other applications of dynamic modeling such as real-time verification of stability margins during envelope expansion tests.

  14. Near-field scanning study for radio frequency interference estimation

    NASA Astrophysics Data System (ADS)

    Pan, Jingnan

    This dissertation discusses the novel techniques using near-fields scanning to do radio frequency interference (RFI) estimation. As the electronic products are becoming more and more complicated, the radio frequency (RF) receiver in the system is very likely interfered by multiple noise sources simultaneously. A method is proposed to identify the interference from different noise sources separately, even when they are radiating at the same time. This method is very helpful for engineers to identify the contribution of the coupling from different sources and further solve the electromagnetic interference issues efficiently. On the other hand, the equivalent dipole-moment models and a decomposition method based on reciprocity theory can also be used together to estimate the coupling from the noise source to the victim antennas. This proposed method provides convenience to estimate RFI issues in the early design stage and saves the time of RFI simulation and measurements. The finite element method and image theory can also predict the far fields of the radiation source, locating above a ground plane. This method applies the finite element method (FEM) to get the equivalent current sources from the tangential magnetic near fields. With the equivalent current sources, the far-field radiation can be calculated based on Huygens's Principle and image theory. By using only the magnetic near fields on the simplified Huygens's surface, the proposed method significantly saves measurement time and cost while also retaining good far-field prediction.

  15. Newtonized Orthogonal Matching Pursuit: Frequency Estimation Over the Continuum

    NASA Astrophysics Data System (ADS)

    Mamandipoor, Babak; Ramasamy, Dinesh; Madhow, Upamanyu

    2016-10-01

    We propose a fast sequential algorithm for the fundamental problem of estimating frequencies and amplitudes of a noisy mixture of sinusoids. The algorithm is a natural generalization of Orthogonal Matching Pursuit (OMP) to the continuum using Newton refinements, and hence is termed Newtonized OMP (NOMP). Each iteration consists of two phases: detection of a new sinusoid, and sequential Newton refinements of the parameters of already detected sinusoids. The refinements play a critical role in two ways: (1) sidestepping the potential basis mismatch from discretizing a continuous parameter space, (2) providing feedback for locally refining parameters estimated in previous iterations. We characterize convergence, and provide a Constant False Alarm Rate (CFAR) based termination criterion. By benchmarking against the Cramer Rao Bound, we show that NOMP achieves near-optimal performance under a variety of conditions. We compare the performance of NOMP with classical algorithms such as MUSIC and more recent Atomic norm Soft Thresholding (AST) and Lasso algorithms, both in terms of frequency estimation accuracy and run time.

  16. Frequency-dependent core shifts and parameter estimation in Blazars

    NASA Astrophysics Data System (ADS)

    Agarwal, Aditi

    2016-07-01

    We study the core shift effect in the parsec-scale jet of blazars using the 4.8-36.8 GHz radio light curves obtained from four decades of continuous monitoring. From a piecewise Gaussian fit to each flare, time lags between the observation frequencies and spectral indices (α) based on peak amplitudes (A) are determined. Index k is calculated and found to be ˜1, indicating equipartition between the magnetic field energy density and the particle energy density. A mean magnetic field strength at 1 pc (B1) and at the core (Bcore) are inferred which are found to be consistent with previous estimates. The measure of core position offset is also performed by averaging over all frequency pairs. Based on the statistical trend shown by the measured core radius as a function of frequency, we infer that the synchrotron opacity model may not be valid for all cases. A Fourier periodogram analysis yields power-law slopes in the range -1.6 to -3.5 describing the power spectral density shape and gives bend timescales. This result, and both positive and negative spectral indices, indicate that the flares originate from multiple shocks in a small region. Important objectives met in our study include: the demonstration of the computational efficiency and statistical basis of the piecewise Gaussian fit; consistency with previously reported results; evidence for the core shift dependence on observation frequency and its utility in jet diagnostics in the region close to the resolving limit of very long baseline interferometry observations.

  17. Some Bayesian statistical techniques useful in estimating frequency and density

    USGS Publications Warehouse

    Johnson, D.H.

    1977-01-01

    This paper presents some elementary applications of Bayesian statistics to problems faced by wildlife biologists. Bayesian confidence limits for frequency of occurrence are shown to be generally superior to classical confidence limits. Population density can be estimated from frequency data if the species is sparsely distributed relative to the size of the sample plot. For other situations, limits are developed based on the normal distribution and prior knowledge that the density is non-negative, which insures that the lower confidence limit is non-negative. Conditions are described under which Bayesian confidence limits are superior to those calculated with classical methods; examples are also given on how prior knowledge of the density can be used to sharpen inferences drawn from a new sample.

  18. SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

    PubMed

    Schunter, C; Garza, J C; Macpherson, E; Pascual, M

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are rapidly becoming the marker of choice in population genetics due to a variety of advantages relative to other markers, including higher genomic density, data quality, reproducibility and genotyping efficiency, as well as ease of portability between laboratories. Advances in sequencing technology and methodologies to reduce genomic representation have made the isolation of SNPs feasible for nonmodel organisms. RNA-seq is one such technique for the discovery of SNPs and development of markers for large-scale genotyping. Here, we report the development of 192 validated SNP markers for parentage analysis in Tripterygion delaisi (the black-faced blenny), a small rocky-shore fish from the Mediterranean Sea. RNA-seq data for 15 individual samples were used for SNP discovery by applying a series of selection criteria. Genotypes were then collected from 1599 individuals from the same population with the resulting loci. Differences in heterozygosity and allele frequencies were found between the two data sets. Heterozygosity was lower, on average, in the population sample, and the mean difference between the frequencies of particular alleles in the two data sets was 0.135 ± 0.100. We used bootstrap resampling of the sequence data to predict appropriate sample sizes for SNP discovery. As cDNA library production is time-consuming and expensive, we suggest that using seven individuals for RNA sequencing reduces the probability of discarding highly informative SNP loci, due to lack of observed polymorphism, whereas use of more than 12 samples does not considerably improve prediction of true allele frequencies.

  19. Allelic frequency of the MCP-1 promoter -2518 polymorphism in the Turkish population and in Turkish patients with juvenile rheumatoid arthritis.

    PubMed

    Ozyürek, A Ruhi; Gürses, Dolunay; Ulger, Zülal; Levent, Ertürk; Bakiler, A Rahmi; Berdeli, Afig

    2007-04-01

    Although genetic and environmental factors contribute to the pathogenesis of juvenile rheumathoid arthritis (JRA), the etiology and pathogenesis remain controversial. The objective of this study was to investigate genotypic and allelic frequencies of monocyte chemoattractant protein-1 (MCP-1) gene -2518 (G/A) polymorphism in the healthy Turkish population and patients with JRA. Genomic DNA was collected from 66 JRA patients and 150 healthy individuals. To evaluate the association of the -2518 (G/A) MCP-1 gene polymorphism with the outcome of JRA, we analyzed the types of JRA and the score on the childhood health assessment questionnaire (C-HAQ score). In the healthy Turkish population, the frequencies of A and G alleles were 71 and 29%, respectively. No significant difference was observed between the JRA patients and healthy subjects in the distribution allelic and genotypic frequencies of the -2518 (G/A) MCP-1 gene polymorphism (p>0.05). However, the AG genotype was found to be higher and the AA genotype was found to be lower in the patients with systemic type JRA compared to those with the other types of JRA (p=0.019). When the JRA patients were evaluated according to the C-HAQ score, we found that the -2518 (G/A) MCP-1 gene polymorphism did not relate the prognosis (p>0.05). AG genotype was found to be higher in the systemic type of JRA. The results indicate that MCP-1 gene polymorphism might slightly associate with patients with systemic JRA. Further studies are needed to elucidate the role of this polymorphism in the pathogenesis of JRA in various populations because this polymorphism has a functional significance and an ethnic difference.

  20. Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass.

    PubMed

    Renan, Sharon; Greenbaum, Gili; Shahar, Naama; Templeton, Alan R; Bouskila, Amos; Bar-David, Shirli

    2015-04-01

    Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited. PMID:25728575

  1. Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass.

    PubMed

    Renan, Sharon; Greenbaum, Gili; Shahar, Naama; Templeton, Alan R; Bouskila, Amos; Bar-David, Shirli

    2015-04-01

    Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.

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

    PubMed Central

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

    2016-01-01

    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. PMID:27602337

  3. Real-Time PCR Genotyping Assay for GM2 Gangliosidosis Variant 0 in Toy Poodles and the Mutant Allele Frequency in Japan

    PubMed Central

    RAHMAN, Mohammad Mahbubur; YABUKI, Akira; KOHYAMA, Moeko; MITANI, Sawane; MIZUKAMI, Keijiro; UDDIN, Mohammad Mejbah; CHANG, Hye-Sook; KUSHIDA, Kazuya; KISHIMOTO, Miori; YAMABE, Remi; YAMATO, Osamu

    2013-01-01

    ABSTRACT GM2 gangliosidosis variant 0 (Sandhoff disease, SD) is a fatal, progressive neurodegenerative lysosomal storage disease caused by mutations of the HEXB gene. In canine SD, a pathogenic mutation (c.283delG) of the canine HEXB gene has been identified in toy poodles. In the present study, a TaqMan probe-based real-time PCR genotyping assay was developed and evaluated for rapid and large-scale genotyping and screening for this mutation. Furthermore, a genotyping survey was carried out in a population of toy poodles in Japan to determine the current mutant allele frequency. The real-time PCR assay clearly showed all genotypes of canine SD. The assay was suitable for large-scale survey as well as diagnosis, because of its high throughput and rapidity. The genotyping survey demonstrated a carrier frequency of 0.2%, suggesting that the current mutant allele frequency is low in Japan. However, there may be population stratification in different places, because of the founder effect by some carriers. Therefore, this new assay will be useful for the prevention and control of SD in toy poodles. PMID:24161966

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

    PubMed Central

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

    2016-01-01

    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. Allele and haplotype frequencies of HLA-A, B, C, DRB1 and DQB1 genes in polytransfused patients in ethnically diverse populations from Brazil.

    PubMed

    Rodrigues, C; Macedo, L C; Bruder, A V; Quintero, F d C; de Alencar, J B; Sell, A M; Visentainer, J E L

    2015-10-01

    The red blood transfusion is a practice often used in patients with haematological and oncological diseases. However, the investigation of human leucocyte antigen (HLA) system frequency in these individuals is of great importance because multiple transfusions may lead to HLA alloimmunization. Brazil is a country that was colonized by many other ethnicities, leading to a mixed ethnicity and regionalized population. In view of the importance of HLA typing in these patients, the aim of this study was to investigate the allele and haplotype frequencies from polytransfused patients from three different regions from Brazil. HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 genotyping of 366 patients was performed by PCR-SSO, based on the Luminex technology (One Lambda(®) ), and the anti-HLA class I and class II antibodies were analysed using LabScreen Single Antigen Antibody Detection (One Lambda, Inc.). Allele and haplotype frequencies of polytransfused patients of three regions from Brazil were obtained using the Arlequin program. The most frequent allele frequencies observed were HLA-A*02, A*03, B*15, B*35, B*51, C*07, C*04, C*03, DRB1*13, DRB1*11, DRB1*07, DRB1*03, DRB1*01, DQB1*03, DQB1*02, DQB1*06 and DQB1*05. There were differences between the groups for allele variants HLA-B*57 (between Group 1 and Group 2) and HLA-C*12 (between Group 1 and Group 3). The most frequent haplotypes found in the sample were HLA-A*01B*08DRB1*03, DRBI*07DQB1*02, DRB1*01DQB1*05, DRB1*13DQB1*06 and A*02B*35. HLA class I and II antibodies were detected in 77.9% and 63.9% patients, respectively, while the both alloantibodies were detected in 62 (50.9%) patients. In conclusion, the HLA typing for polytransfused patients in each region has a great importance, as seen in this study; individuals from different regions from Brazil have HLA distribution not completely homogeneous.

  6. Instantaneous fault frequencies estimation in roller bearings via wavelet structures

    NASA Astrophysics Data System (ADS)

    Rodopoulos, Konstantinos I.; Antoniadis, Ioannis A.

    2016-11-01

    The main target of the current paper is the effective application of the method proposed in "Antoniadis et al. (2014) [17], in roller bearings under variable speed. For this reason, roller bearing model with slip and real data coming from a test rig has been used. The method extracts useful information from a complicated signal where the overlap among the harmonics can raise up to 30%. According to the proposed method, a set of wavelet transforms of the signal is first obtained, using a structure of Complex Shifted Morlet Wavelets. The center frequencies and the bandwidths of the individual wavelets, as well as the number of wavelets used, are associated with the characteristic fault frequency and its harmonic components. In this way, a set of complex signals result in the time domain, equal to the number of the wavelets used. Then, the instantaneous frequencies of the signals are estimated by applying an appropriate subspace algorithm (as for e.g. ESPRIT), to the entire set of the resulting complex wavelet transforms, exploiting the corresponding subspace rotational invariance property of this set of complex signals. The iterative procedure brings up accurate results from complicated signals, separating the fault associated signal components. Also, the spectrograms of the processed signals confirm the ability to match excited areas with specific faults.

  7. The deposit size frequency method for estimating undiscovered uranium deposits

    USGS Publications Warehouse

    McCammon, R.B.; Finch, W.I.

    1993-01-01

    The deposit size frequency (DSF) method has been developed as a generalization of the method that was used in the National Uranium Resource Evaluation (NURE) program to estimate the uranium endowment of the United States. The DSF method overcomes difficulties encountered during the NURE program when geologists were asked to provide subjective estimates of (1) the endowed fraction of an area judged favorable (factor F) for the occurrence of undiscovered uranium deposits and (2) the tons of endowed rock per unit area (factor T) within the endowed fraction of the favorable area. Because the magnitudes of factors F and T were unfamiliar to nearly all of the geologists, most geologists responded by estimating the number of undiscovered deposits likely to occur within the favorable area and the average size of these deposits. The DSF method combines factors F and T into a single factor (F??T) that represents the tons of endowed rock per unit area of the undiscovered deposits within the favorable area. Factor F??T, provided by the geologist, is the estimated number of undiscovered deposits per unit area in each of a number of specified deposit-size classes. The number of deposit-size classes and the size interval of each class are based on the data collected from the deposits in known (control) areas. The DSF method affords greater latitude in making subjective estimates than the NURE method and emphasizes more of the everyday experience of exploration geologists. Using the DSF method, new assessments have been made for the "young, organic-rich" surficial uranium deposits in Washington and idaho and for the solution-collapse breccia pipe uranium deposits in the Grand Canyon region in Arizona and adjacent Utah. ?? 1993 Oxford University Press.

  8. Allele frequencies of combined DNA index system (CODIS) and non-CODIS short tandem repeat loci in Goiás, Central Brazil.

    PubMed

    Rodovalho, R G; Santos, G S; Cavalcanti, L M; Moura, B F S M; Rodrigues, E L; Lima, P R; Gigonzac, M A D; Vieira, T C

    2015-07-03

    In studies of human identification, obtaining a high standard of outcomes and satisfactory conclusions are directly related to the use of highly polymorphic molecular markers. In addition to the combined DNA index system (CODIS) group, it is also important to implement non-CODIS markers into the analysis, as they increase the power of discrimination. During the identification process, it is essential to consider the genetic variation among distinct groups of populations, as the allele frequencies are directly associated with the power of discrimination. However, the population of Goiás, a State located in Central Brazil, is characterized by a highly mixed population due to its diverse ethnic origins. In this study, a survey of the allelic frequencies in the Goiás population was carried out using a molecular assembly composed of 21 autosomal loci both from and external to the CODIS group. The new data, for some of the markers used, were statistically similar to those from previous studies. This consistency means that the use of these markers might serve as a parameter for future population comparisons. The results from these analyses further our knowledge of the study of human identification.

  9. Real-time qPCR is a powerful assay to estimate the 171 R/Q alleles at the PrP locus directly in a flock's raw milk: a comparison with the targeted next-generation sequencing.

    PubMed

    Feligini, Maria; Bongioni, Graziella; Brambati, Eva; Amadesi, Alessandra; Cambuli, Caterina; Panelli, Simona; Bonacina, Cesare; Galli, Andrea

    2014-10-01

    The hazard to human health represented by transmissible spongiform encephalopathies in sheep is one of the major reasons for implementing the genetic selection plan to break down prion diseases. The problem is particularly important because of the risk of disease transmission from ewe to lamb via milk or colostrum. In order to establish an active and convenient monitoring of the flocks already undergone genetic selection and thus, indirectly increase consumers' security, the challenge of the work was quantifying the classical scrapie risk in bulk milk. A new quantitative real-time PCR assay for the estimation of the 171 R and Q allelic frequencies in a DNA pool representative of all the lactating ewes present in a flock was optimized and validated "in field". The repeatability range was 3.69-5.27 for R and 4.20-5.75 for Q. The ruggedness of the allele frequencies resulted 4.26 for R and 4.77 for Q. Regarding the validation "in field", none of the considered sources of variability (flock, month, number of genotyped animals and somatic cell count) showed a significant effect on flock and milk at the linear model. The targeted next-generation sequencing was also tested to evaluate its applicability in this context. Results show that the real-time PCR assay could represent a valid tool for the determination of 171 R/Q allele frequencies in bulk milk. The implementation of a service for breeder self-control along the production chain would aim to increase the production of high-security dairy products, while monitoring over time of the effects of genetic selection in the flocks.

  10. 'True' null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements.

    PubMed

    Dąbrowski, M J; Bornelöv, S; Kruczyk, M; Baltzer, N; Komorowski, J

    2015-05-01

    Null alleles are alleles that for various reasons fail to amplify in a PCR assay. The presence of null alleles in microsatellite data is known to bias the genetic parameter estimates. Thus, efficient detection of null alleles is crucial, but the methods available for indirect null allele detection return inconsistent results. Here, our aim was to compare different methods for null allele detection, to explain their respective performance and to provide improvements. We applied several approaches to identify the 'true' null alleles based on the predictions made by five different methods, used either individually or in combination. First, we introduced simulated 'true' null alleles into 240 population data sets and applied the methods to measure their success in detecting the simulated null alleles. The single best-performing method was ML-NullFreq_frequency. Furthermore, we applied different noise reduction approaches to improve the results. For instance, by combining the results of several methods, we obtained more reliable results than using a single one. Rule-based classification was applied to identify population properties linked to the false discovery rate. Rules obtained from the classifier described which population genetic estimates and loci characteristics were linked to the success of each method. We have shown that by simulating 'true' null alleles into a population data set, we may define a null allele frequency threshold, related to a desired true or false discovery rate. Moreover, using such simulated data sets, the expected null allele homozygote frequency may be estimated independently of the equilibrium state of the population.

  11. IQ Imbalance Estimation Scheme in the Presence of DC Offset and Frequency Offset in the Frequency Domain

    NASA Astrophysics Data System (ADS)

    Inamori, Mamiko; Takayama, Shuzo; Sanada, Yukitoshi

    Direct conversion receivers in orthogonal frequency division multiplexing (OFDM) systems suffer from direct current (DC) offset, frequency offset, and IQ imbalance. We have proposed an IQ imbalance estimation scheme in the presence of DC offset and frequency offset, which uses preamble signals in the time domain. In this scheme, the DC offset is eliminated by a differential filter. However, the accuracy of IQ imbalance estimation is deteriorated when the frequency offset is small. To overcome this problem, a new IQ imbalance estimation scheme in the frequency domain with the differential filter has been proposed in this paper. The IQ imbalance is estimated with pilot subcarriers. Numerical results obtained through computer simulation show that estimation accuracy and bit error rate (BER) performance can be improved even if the frequency offset is small.

  12. Allelic frequencies of the HLA-B17 antigen group: comparative analysis by serology, IEF and PCR-SSOP typing.

    PubMed

    Levine, J E; Yang, S Y

    1995-11-01

    Current typing technology for class I HLA antigens uses serological and/or isoelectric focusing gel electrophoresis. DNA typing for the HLA class I antigens can accurately identify the class I genotype of individuals and cell lines. Here, we report correlation of DNA typing results with serological and IEF results for the B17 group. The B17 antigens are relatively common, being carried by almost 9% of Caucasians and 28% of blacks. In this study, five 10th International Histocompatibility Workshop cell lines carrying B17 and 106 individuals in 61 families carrying B17 were DNA typed for B17 using B17-allele-specific amplification and sequence specific oligonucleotide probe hybridization pattern analysis. 38 (55.07%) out of 69 unrelated haplotypes had B*5701, 23 (33.33%) had B*5801, 6 (8.70%) had B*5702, and 2 (2.90%) had B*5802. DNA typing results correlated well with serological and isoelectric focusing results. In general, there was high degree of agreement between all three methods, although heterozygosity for B17 poses a particular problem for serological and IEF methodology. Both B*5701 and B*5801 have the same electrophoretic mobility on IEF gel, corresponding to B17.2, B*5702 corresponds to B17.1, while B*5802 corresponds to B17.3.

  13. A Modified Frequency Estimation Equating Method for the Common-Item Nonequivalent Groups Design

    ERIC Educational Resources Information Center

    Wang, Tianyou; Brennan, Robert L.

    2009-01-01

    Frequency estimation, also called poststratification, is an equating method used under the common-item nonequivalent groups design. A modified frequency estimation method is proposed here, based on altering one of the traditional assumptions in frequency estimation in order to correct for equating bias. A simulation study was carried out to…

  14. A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae

    PubMed Central

    Chu, Daniel B.; Burgess, Sean M.

    2016-01-01

    Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions. PMID:26747203

  15. A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae.

    PubMed

    Chu, Daniel B; Burgess, Sean M

    2016-03-01

    Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions. PMID:26747203

  16. Life satisfaction in the new country: a multilevel longitudinal analysis of effects of culture and 5-HTT allele frequency distribution in country of origin.

    PubMed

    Kashima, Emiko S; Kent, Stephen; Kashima, Yoshihisa

    2015-01-01

    Life satisfaction of migrants to Australia from 17 countries, assessed at 4-5 months, 16-17 months and 3½ years after arrival, was analyzed with a longitudinal, multilevel analysis. The results indicated that migrants were more satisfied, if the national average life satisfaction was higher in their country of origin, after adjustment for individual-level income, age, and sex and a linear temporal trend. Simultaneously, the migrants were also happier if people in their country of origin had a higher frequency of 5-HTT long allele, a genotype known to be associated with resilience under life stresses. These two relationships were independent, suggesting that both culture and gene matter in international transitions.

  17. Life satisfaction in the new country: a multilevel longitudinal analysis of effects of culture and 5-HTT allele frequency distribution in country of origin.

    PubMed

    Kashima, Emiko S; Kent, Stephen; Kashima, Yoshihisa

    2015-01-01

    Life satisfaction of migrants to Australia from 17 countries, assessed at 4-5 months, 16-17 months and 3½ years after arrival, was analyzed with a longitudinal, multilevel analysis. The results indicated that migrants were more satisfied, if the national average life satisfaction was higher in their country of origin, after adjustment for individual-level income, age, and sex and a linear temporal trend. Simultaneously, the migrants were also happier if people in their country of origin had a higher frequency of 5-HTT long allele, a genotype known to be associated with resilience under life stresses. These two relationships were independent, suggesting that both culture and gene matter in international transitions. PMID:24532702

  18. Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection

    PubMed Central

    2012-01-01

    Background Next generation sequencing provides clinical research scientists with direct read out of innumerable variants, including personal, pathological and common benign variants. The aim of resequencing studies is to determine the candidate pathogenic variants from individual genomes, or from family-based or tumor/normal genome comparisons. Whilst the use of appropriate controls within the experimental design will minimize the number of false positive variations selected, this number can be reduced further with the use of high quality whole genome reference data to minimize false positives variants prior to candidate gene selection. In addition the use of platform related sequencing error models can help in the recovery of ambiguous genotypes from lower coverage data. Description We have developed a whole genome database of human genetic variations, Huvariome, determined by whole genome deep sequencing data with high coverage and low error rates. The database was designed to be sequencing technology independent but is currently populated with 165 individual whole genomes consisting of small pedigrees and matched tumor/normal samples sequenced with the Complete Genomics sequencing platform. Common variants have been determined for a Benelux population cohort and represented as genotypes alongside the results of two sets of control data (73 of the 165 genomes), Huvariome Core which comprises 31 healthy individuals from the Benelux region, and Diversity Panel consisting of 46 healthy individuals representing 10 different populations and 21 samples in three Pedigrees. Users can query the database by gene or position via a web interface and the results are displayed as the frequency of the variations as detected in the datasets. We demonstrate that Huvariome can provide accurate reference allele frequencies to disambiguate sequencing inconsistencies produced in resequencing experiments. Huvariome has been used to support the selection of candidate cardiomyopathy

  19. Life satisfaction in the new country: a multilevel longitudinal analysis of effects of culture and 5-HTT allele frequency distribution in country of origin

    PubMed Central

    Kent, Stephen; Kashima, Yoshihisa

    2015-01-01

    Life satisfaction of migrants to Australia from 17 countries, assessed at 4–5 months, 16–17 months and 3½ years after arrival, was analyzed with a longitudinal, multilevel analysis. The results indicated that migrants were more satisfied, if the national average life satisfaction was higher in their country of origin, after adjustment for individual-level income, age, and sex and a linear temporal trend. Simultaneously, the migrants were also happier if people in their country of origin had a higher frequency of 5-HTT long allele, a genotype known to be associated with resilience under life stresses. These two relationships were independent, suggesting that both culture and gene matter in international transitions. PMID:24532702

  20. DNA-PCR system FGA (FIBRA)--genotype and allele frequencies in a sample of western Germany (Düsseldorf region).

    PubMed

    Huckenbeck, W; Scheil, H G; Kuntze, K

    1999-12-01

    Frequency data for the STR system FGA (HumFibra) were obtained from a Caucasoid German population sample (Düsseldorf area) of 424 unrelated individuals. PCR products were detected by horizontal polyacrylamid gel electrophoresis and a total of 16 alleles was identified by side-by-side comparison with a commercially available sequenced ladder. The observed genotype distribution showed no significant deviation from the Hardy-Weinberg equilibrium. The high information content (pooled German data: rate of heterozygosity = 0.8626; probability of match = 0.0344; mean exclusion chance = 0.7240) render this system a useful tool not only in forensic casework (criminal and paternity cases) but in population genetics too.

  1. Allelic Diversity and Its Implications for the Rate of Adaptation

    PubMed Central

    Caballero, Armando; García-Dorado, Aurora

    2013-01-01

    Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided. PMID:24121776

  2. Human Leukocyte Antigens-A, -B, -C, -DRB1 allele and haplotype frequencies in Americans originating from Southern Europe: Contrasting patterns of population differentiation between Italian and Spanish Americans

    PubMed Central

    Mack, Steven J.; Tu, Bin; Yang, Ruyan; Masaberg, Carly; Ng, Jennifer; Hurley, Carolyn Katovich

    2010-01-01

    High resolution DNA sequencing was used to identify the HLA-A, -B, -C, and -DRB1 alleles found in 552 individuals from the United States indicating Southern European (Italian or Spanish) heritage. A total of 46 HLA-A, 80 HLA-B, 32 HLA-C, and 50 DRB1 alleles were identified. Frequent alleles included A*02:01:01G (allele frequency = 0.26 in Italian Americans; 0.22 in Spanish Americans); B*07:02:01G (Italian Americans allele frequency = 0.11); B*44:03 (Spanish Americans allele frequency = 0.07); C*04:01:01G and C*07:01:01G (allele frequency = 0.13 and 0.16, respectively, in Italian Americans; 0.15 and 0.12, respectively, in Spanish Americans); and DRB1*07:01:01 (allele frequency = 0.12 in each population). The action of balancing selection was inferred at the HLA-B and -C loci in both populations. The A*01:01:01G-C*07:01:01G-B*08:01:01G-DRB1*03:01:01 haplotype was the most frequent A-C-B-DRB1 haplotype in Italian Americans (haplotype frequency = 0.049), and was the second most frequent haplotype in Spanish Americans (haplotype frequency = 0.021). A*29:02:01-C*16:01:01-B*44:03-DRB1*07:01:01 was the most frequent A-C-B-DRB1 haplotype in Spanish Americans (haplotype frequency = 0.023), and was observed at a frequency of 0.015 in Italian Americans. Pairwise F’st values measuring the degree of differentiation between these Southern European-American populations and European and European-American populations suggest that Spanish Americans constitute a distinct subset of the European-American population, most similar to Mexican Americans, whereas Italian Americans cannot be distinguished from the larger European-American population. PMID:20974205

  3. Situations Where It Is Appropriate to Use Frequency Estimation Equipercentile Equating

    ERIC Educational Resources Information Center

    Guo, Hongwen; Oh, Hyeonjoo J.; Eignor, Daniel

    2013-01-01

    In operational equating situations, frequency estimation equipercentile equating is considered only when the old and new groups have similar abilities. The frequency estimation assumptions are investigated in this study under various situations from both the levels of theoretical interest and practical use. It shows that frequency estimation…

  4. A fast and accurate frequency estimation algorithm for sinusoidal signal with harmonic components

    NASA Astrophysics Data System (ADS)

    Hu, Jinghua; Pan, Mengchun; Zeng, Zhidun; Hu, Jiafei; Chen, Dixiang; Tian, Wugang; Zhao, Jianqiang; Du, Qingfa

    2016-10-01

    Frequency estimation is a fundamental problem in many applications, such as traditional vibration measurement, power system supervision, and microelectromechanical system sensors control. In this paper, a fast and accurate frequency estimation algorithm is proposed to deal with low efficiency problem in traditional methods. The proposed algorithm consists of coarse and fine frequency estimation steps, and we demonstrate that it is more efficient than conventional searching methods to achieve coarse frequency estimation (location peak of FFT amplitude) by applying modified zero-crossing technique. Thus, the proposed estimation algorithm requires less hardware and software sources and can achieve even higher efficiency when the experimental data increase. Experimental results with modulated magnetic signal show that the root mean square error of frequency estimation is below 0.032 Hz with the proposed algorithm, which has lower computational complexity and better global performance than conventional frequency estimation methods.

  5. Estimating worker exposure to power-frequency magnetic fields

    SciTech Connect

    Wenzl, T.B.

    1992-01-01

    For a case-control study of brain cancer at a large automobile transmission plant, a strategy was developed to use two types of instruments to measure personal exposure to power-frequency magnetic fields. A representative group of 81 workers were asked to wear a data-logging dosimeter for one-half shift apiece. This instrument recorded 3-axis magnetic field values every 4 seconds. With little clarity about the biologic process which might connect these magnetic fields to cancer promotion, several indices summarizing exposure variability over time were computed. A new index of [open quotes]jaggedness[close quotes] was also computed, since some human studies suggest very uneven exposure profiles are the most biologically active, possibly via interference with melatonin synthesis in the pineal gland. Comparisons between the several exposure indices showed moderately high correlations between indices which were sensitive to peak exposures, but other indices were less well correlated. To test a simpler measurement strategy, a hand-held direct reading instrument was also used, with multiple measurements taken at the head and waist for most workstations. These were averaged and combined with time estimates to give[open quote] built-up[close quote] average exposures. Correlations were high (r = 0.8) between these built-up averages and averages derived from the datalogger records. It was possible to assign job titles to three distinct exposure categories based on measures of the central tendency of the distributions of measured exposures. By ranking job groups by their average exposures, electricians and non-production grinders were placed in a high exposure category, assemblers and material handlers were placed in a low category, and all other jobs were placed in a medium exposure category. Analysis of variance, with influence analysis, was used to determine that these categories had significant exposure differences from one another.

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

    PubMed Central

    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

  7. Joint Estimation of Time-Frequency Signature and DOA Based on STFD for Multicomponent Chirp Signals

    PubMed Central

    Zhao, Ziyue; Liu, Congfeng

    2014-01-01

    In the study of the joint estimation of time-frequency signature and direction of arrival (DOA) for multicomponent chirp signals, an estimation method based on spatial time-frequency distributions (STFDs) is proposed in this paper. Firstly, array signal model for multicomponent chirp signals is presented and then array processing is applied in time-frequency analysis to mitigate cross-terms. According to the results of the array processing, Hough transform is performed and the estimation of time-frequency signature is obtained. Subsequently, subspace method for DOA estimation based on STFD matrix is achieved. Simulation results demonstrate the validity of the proposed method. PMID:27382610

  8. Method for Estimating Low-Frequency Return Current of DC Electric Railcar

    NASA Astrophysics Data System (ADS)

    Hatsukade, Satoru

    The Estimation of the harmonic current of railcars is necessary for achieving compatibility between train signaling systems and railcar equipment. However, although several theoretical analyses methods for estimating the harmonic current of railcars using switching functions exist, there are no theoretical analysis methods estimating a low-frequency current at a frequency less than the power converter's carrier frequency. This paper describes a method for estimating the spectrum (frequency and amplitude) of the low-frequency return current of DC electric railcars. First, relationships between the return current and characteristics of the DC electric railcars, such as mass and acceleration, are determined. Then, the mathematical (not numerical) calculation results for low-frequency current are obtained from the time-current curve for a DC electric railcar by using Fourier series expansions. Finally, the measurement results clearly show the effectiveness of the estimation method development in this study.

  9. Joint angle and Doppler frequency estimation of coherent targets in monostatic MIMO radar

    NASA Astrophysics Data System (ADS)

    Cao, Renzheng; Zhang, Xiaofei

    2015-05-01

    This paper discusses the problem of joint direction of arrival (DOA) and Doppler frequency estimation of coherent targets in a monostatic multiple-input multiple-output radar. In the proposed algorithm, we perform a reduced dimension (RD) transformation on the received signal first and then use forward spatial smoothing (FSS) technique to decorrelate the coherence and obtain joint estimation of DOA and Doppler frequency by exploiting the estimation of signal parameters via rotational invariance techniques (ESPRIT) algorithm. The joint estimated parameters of the proposed RD-FSS-ESPRIT are automatically paired. Compared with the conventional FSS-ESPRIT algorithm, our RD-FSS-ESPRIT algorithm has much lower complexity and better estimation performance of both DOA and frequency. The variance of the estimation error and the Cramer-Rao Bound of the DOA and frequency estimation are derived. Simulation results show the effectiveness and improvement of our algorithm.

  10. The Potential of Water Vapor & Precipitation Estimation with a Differential-frequency Radar

    NASA Technical Reports Server (NTRS)

    Meneghini, Robert; Liao, Liang; Tian, Lin

    2006-01-01

    In the presence of rain, the radar return powers from a three-frequency radar, with center frequency at 22.235 GHz and upper and lower frequencies chosen with equal water vapor absorption coefficients, can be used to estimate water vapor density and parameters of the precipitation. A linear combination of differential measurements between the center and lower frequencies on one hand and the upper and lower frequencies on the other provide an estimate of differential water vapor absorption. Conversely, the difference in radar reflectivity factors (in dB) between the upper and lower frequencies is independent of water vapor absorption and can be used to estimate the median mass diameter of the hydrometeors. For a down-looking radar, path-integrated estimates of water vapor absorption may be possible under rain-free as well as raining conditions by using the surface returns at the three frequencies. Cross-talk or interference between the precipitation and water vapor estimates depends on the frequency separation of the channels as well as on the phase state and the median mass diameter of the hydrometeors. Simulations of the retrieval of water vapor absorption show that the largest source of variability arises from the variance in the measured radar return powers while the largest biases occur in the mixed-phase region. Use of high pulse repetition frequencies and signal whitening methods may be needed to obtain the large number of independent samples required. Measurements over a fractional bandwidth, defined as the ratio of the difference between the upper and lower frequencies to the center frequency, up to about 0.2 should be passible in a differential frequency mode, where a single transceiver and antenna are used. Difficulties in frequency allocation may require alternative choices of frequency where the water vapor absorptions at the low and high frequencies are unequal. We consider the degradation in the retrieval accuracy when the frequencies are not optimum.

  11. Flood frequency analysis: Confidence interval estimation by test inversion bootstrapping

    NASA Astrophysics Data System (ADS)

    Schendel, Thomas; Thongwichian, Rossukon

    2015-09-01

    A common approach to estimate extreme flood events is the annual block maxima approach, where for each year the peak streamflow is determined and a distribution (usually the generalized extreme value distribution (GEV)) is fitted to this series of maxima. Eventually this distribution is used to estimate the return level for a defined return period. However, due to the finite sample size, the estimated return levels are associated with a range of uncertainity, usually expressed via confidence intervals. Previous publications have shown that existing bootstrapping methods for estimating the confidence intervals of the GEV yield too narrow estimates of these uncertainty ranges. Therefore, we present in this article a novel approach based on the less known test inversion bootstrapping, which we adapted especially for complex quantities like the return level. The reliability of this approach is studied and its performance is compared to other bootstrapping methods as well as the Profile Likelihood technique. It is shown that the new approach improves significantly the coverage of confidence intervals compared to other bootstrapping methods and for small sample sizes should even be favoured over the Profile Likelihood.

  12. NOAA Atlas 14: Updated Precipitation Frequency Estimates for the United States

    NASA Astrophysics Data System (ADS)

    Pavlovic, S.; Perica, S.; Martin, D.; Roy, I.; StLaurent, M.; Trypaluk, C.; Unruh, D.; Yekta, M.; Bonnin, G. M.

    2013-12-01

    NOAA Atlas 14 precipitation frequency estimates, developed by the National Weather Service's Hydrometeorological Design Studies Center, serve as the de-facto standards for a wide variety of design and planning activities under federal, state, and local regulations. Precipitation frequency estimates are used in the design of drainage for highways, culverts, bridges, parking lots, as well as in sizing sewer and stormwater infrastructure. Water resources engineers use them to estimate the amount of runoff, to estimate the volume of detention basins and size detention-basin outlet structures, and to estimate the volume of sediment or the amount of erosion. They are also used by floodplain managers to delineate floodplains and regulate the development in floodplains, which is crucial for all communities in the National Flood Insurance Program. Hydrometeorological Design Studies Center now provides more than 35,000 downloads per month to its Precipitation Frequency Data Server. Precipitation frequency estimates are often used in engineering design without any understanding how these estimates have been developed or without any understanding of the uncertainties associated with these estimates. This presentation will describe novel tools and techniques that have being developed in the last years to determine precipitation frequency estimates in NOAA Atlas 14. Particular attention will be given to the regional frequency analysis approach based on L-moment statistics calculated from annual maximum series, selected statistics obtained in determining and parameterizing the probability distribution functions, and the potential implication for engineering design of recently published estimates.

  13. NOAA Atlas 14: Updated Precipitation Frequency Estimates for the United States

    NASA Astrophysics Data System (ADS)

    Pavlovic, S.; Perica, S.; Martin, D.; Roy, I.; StLaurent, M.; Trypaluk, C.; Unruh, D.; Yekta, M.; Bonnin, G. M.

    2011-12-01

    NOAA Atlas 14 precipitation frequency estimates, developed by the National Weather Service's Hydrometeorological Design Studies Center, serve as the de-facto standards for a wide variety of design and planning activities under federal, state, and local regulations. Precipitation frequency estimates are used in the design of drainage for highways, culverts, bridges, parking lots, as well as in sizing sewer and stormwater infrastructure. Water resources engineers use them to estimate the amount of runoff, to estimate the volume of detention basins and size detention-basin outlet structures, and to estimate the volume of sediment or the amount of erosion. They are also used by floodplain managers to delineate floodplains and regulate the development in floodplains, which is crucial for all communities in the National Flood Insurance Program. Hydrometeorological Design Studies Center now provides more than 35,000 downloads per month to its Precipitation Frequency Data Server. Precipitation frequency estimates are often used in engineering design without any understanding how these estimates have been developed or without any understanding of the uncertainties associated with these estimates. This presentation will describe novel tools and techniques that have being developed in the last years to determine precipitation frequency estimates in NOAA Atlas 14. Particular attention will be given to the regional frequency analysis approach based on L-moment statistics calculated from annual maximum series, selected statistics obtained in determining and parameterizing the probability distribution functions, and the potential implication for engineering design of recently published estimates.

  14. Multivariate drought frequency estimation using copula method in Southwest China

    NASA Astrophysics Data System (ADS)

    Hao, Cui; Zhang, Jiahua; Yao, Fengmei

    2015-12-01

    Drought over Southwest China occurs frequently and has an obvious seasonal characteristic. Proper management of regional droughts requires knowledge of the expected frequency or probability of specific climate information. This study utilized k-means classification and copulas to demonstrate the regional drought occurrence probability and return period based on trivariate drought properties, i.e., drought duration, severity, and peak. A drought event in this study was defined when 3-month Standardized Precipitation Evapotranspiration Index (SPEI) was less than -0.99 according to the regional climate characteristic. Then, the next step was to classify the region into six clusters by k-means method based on annual and seasonal precipitation and temperature and to establish marginal probabilistic distributions for each drought property in each sub-region. Several copula types were selected to test the best fit distribution, and Student t copula was recognized as the best one to integrate drought duration, severity, and peak. The results indicated that a proper classification was important for a regional drought frequency analysis, and copulas were useful tools in exploring the associations of the correlated drought variables and analyzing drought frequency. Student t copula was a robust and proper function for drought joint probability and return period analysis, which is important for analyzing and predicting the regional drought risks.

  15. Estimating vehicle roadside encroachment frequency using accident prediction models

    SciTech Connect

    Miaou, S.-P.

    1996-07-01

    The existing data to support the development of roadside encroachment- based accident models are extremely limited and largely outdated. Under the sponsorship of the Federal Highway Administration and Transportation Research Board, several roadside safety projects have attempted to address this issue by providing rather comprehensive data collection plans and conducting pilot data collection efforts. It is clear from the results of these studies that the required field data collection efforts will be expensive. Furthermore, the validity of any field collected encroachment data may be questionable because of the technical difficulty to distinguish intentional from unintentional encroachments. This paper proposes an alternative method for estimating the basic roadside encroachment data without actually field collecting them. The method is developed by exploring the probabilistic relationships between a roadside encroachment event and a run-off-the-road event With some mild assumptions, the method is capable of providing a wide range of basic encroachment data from conventional accident prediction models. To illustrate the concept and use of such a method, some basic encroachment data are estimated for rural two-lane undivided roads. In addition, the estimated encroachment data are compared with the existing collected data. The illustration shows that the method described in this paper can be a viable approach to estimating basic encroachment data without actually collecting them which can be very costly.

  16. An estimator for the standard deviation of a natural frequency. II.

    NASA Technical Reports Server (NTRS)

    Schiff, A. J.; Bogdanoff, J. L.

    1971-01-01

    A method has been presented for estimating the variability of a system's natural frequencies arising from the variability of the system's parameters. The only information required to obtain the estimates is the member variability, in the form of second-order properties, and the natural frequencies and mode shapes of the mean system. It has also been established for the systems studied by means of Monte Carlo estimates that the specification of second-order properties is an adequate description of member variability.

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

    PubMed Central

    Delvaux, Nathália; da Costa, Vanessa Duarte; da Costa, Maristella Matos; Villar, Livia Melo; Coelho, Henrique Sérgio Moraes; Esberard, Eliane Bordalo Cathalá; Flores, Priscila Pollo; Brandão-Mello, Carlos Eduardo; Villela-Nogueira, Cristiane Alves; de Almeida, Adilson José; Lampe, Elisabeth

    2015-01-01

    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. PMID:26154744

  18. A comparative study of frequency offset estimations in real and complex OFDM systems using different algorithms

    NASA Astrophysics Data System (ADS)

    Sahu, Swagatika; Mohanty, Saumendra; Srivastav, Richa

    2013-01-01

    Orthogonal Frequency Division Multiplexing (OFDM) is an emerging multi-carrier modulation scheme, which has been adopted for several wireless standards such as IEEE 802.11a and HiperLAN2, etc. A well-known problem of OFDM is its sensitivity to frequency offset between the transmitted and received carrier frequencies. In (OFDM) system Carrier frequency offsets (CFOs) between the transmitter and the receiver destroy the orthogonality between carriers and degrade the system performance significantly. The main problem with frequency offset is that it introduces interference among the multiplicity of carriers in the OFDM signal.The conventional algorithms given by P. Moose and Schmidl describes how carrier frequency offset of an OFDM system can be estimated using training sequences. Simulation results show that the improved carrier frequency offset estimation algorithm which uses a complex training sequence for frequency offset estimation, performs better than conventional P. Moose and Schmidl algorithm, which can effectively improve the frequency estimation accuracy and provides a wide acquisition range for the carrier frequency offset with low complexity. This paper introduces the BER comparisons of different algorithms with the Improved Algorithms for different Real and Complex modulations schemes, considering random carrier offsets . This paper also introduces the BER performances with different CFOs for different Real and Complex modulation schemes for the Improved algorithm.

  19. Time-frequency and advanced frequency estimation techniques for the investigation of bat echolocation calls.

    PubMed

    Kopsinis, Yannis; Aboutanios, Elias; Waters, Dean A; McLaughlin, Steve

    2010-02-01

    In this paper, techniques for time-frequency analysis and investigation of bat echolocation calls are studied. Particularly, enhanced resolution techniques are developed and/or used in this specific context for the first time. When compared to traditional time-frequency representation methods, the proposed techniques are more capable of showing previously unseen features in the structure of bat echolocation calls. It should be emphasized that although the study is focused on bat echolocation recordings, the results are more general and applicable to many other types of signal. PMID:20136233

  20. Time-frequency and advanced frequency estimation techniques for the investigation of bat echolocation calls.

    PubMed

    Kopsinis, Yannis; Aboutanios, Elias; Waters, Dean A; McLaughlin, Steve

    2010-02-01

    In this paper, techniques for time-frequency analysis and investigation of bat echolocation calls are studied. Particularly, enhanced resolution techniques are developed and/or used in this specific context for the first time. When compared to traditional time-frequency representation methods, the proposed techniques are more capable of showing previously unseen features in the structure of bat echolocation calls. It should be emphasized that although the study is focused on bat echolocation recordings, the results are more general and applicable to many other types of signal.

  1. Fourier Spot Volatility Estimator: Asymptotic Normality and Efficiency with Liquid and Illiquid High-Frequency Data

    PubMed Central

    2015-01-01

    The recent availability of high frequency data has permitted more efficient ways of computing volatility. However, estimation of volatility from asset price observations is challenging because observed high frequency data are generally affected by noise-microstructure effects. We address this issue by using the Fourier estimator of instantaneous volatility introduced in Malliavin and Mancino 2002. We prove a central limit theorem for this estimator with optimal rate and asymptotic variance. An extensive simulation study shows the accuracy of the spot volatility estimates obtained using the Fourier estimator and its robustness even in the presence of different microstructure noise specifications. An empirical analysis on high frequency data (U.S. S&P500 and FIB 30 indices) illustrates how the Fourier spot volatility estimates can be successfully used to study intraday variations of volatility and to predict intraday Value at Risk. PMID:26421617

  2. Fourier Spot Volatility Estimator: Asymptotic Normality and Efficiency with Liquid and Illiquid High-Frequency Data.

    PubMed

    Mancino, Maria Elvira; Recchioni, Maria Cristina

    2015-01-01

    The recent availability of high frequency data has permitted more efficient ways of computing volatility. However, estimation of volatility from asset price observations is challenging because observed high frequency data are generally affected by noise-microstructure effects. We address this issue by using the Fourier estimator of instantaneous volatility introduced in Malliavin and Mancino 2002. We prove a central limit theorem for this estimator with optimal rate and asymptotic variance. An extensive simulation study shows the accuracy of the spot volatility estimates obtained using the Fourier estimator and its robustness even in the presence of different microstructure noise specifications. An empirical analysis on high frequency data (U.S. S&P500 and FIB 30 indices) illustrates how the Fourier spot volatility estimates can be successfully used to study intraday variations of volatility and to predict intraday Value at Risk. PMID:26421617

  3. A comparison of frequency estimation techniques for high-dynamic trajectories

    NASA Technical Reports Server (NTRS)

    Vilnrotter, V. A.; Hinedi, S.; Kumar, R.

    1988-01-01

    A comparison is presented for four different estimation techniques applied to the problem of continuously estimating the parameters of a sinusoidal Global Positioning System (GPS) signal, observed in the presence of additive noise, under extremely high-dynamic conditions. Frequency estimates are emphasized, although phase and/or frequency rate are also estimated by some of the algorithms. These parameters are related to the velocity, position, and acceleration of the maneuvering transmitter. Estimated performance at low carrier-to-noise ratios and high dynamics is investigated for the purpose of determining the useful operating range of an approximate Maximum Likelihood (ML) estimator, an Extended Kalman Filter (EKF), a Cross-Product Automatic Frequency Control (CPAFC) loop, and a digital phase-locked loop (PPL). Numerical simulations are used to evaluate performance while tracking a common trajectory exhibiting high dynamics.

  4. Subtitle-Based Word Frequencies as the Best Estimate of Reading Behavior: The Case of Greek

    PubMed Central

    Dimitropoulou, Maria; Duñabeitia, Jon Andoni; Avilés, Alberto; Corral, José; Carreiras, Manuel

    2010-01-01

    Previous evidence has shown that word frequencies calculated from corpora based on film and television subtitles can readily account for reading performance, since the language used in subtitles greatly approximates everyday language. The present study examines this issue in a society with increased exposure to subtitle reading. We compiled SUBTLEX-GR, a subtitled-based corpus consisting of more than 27 million Modern Greek words, and tested to what extent subtitle-based frequency estimates and those taken from a written corpus of Modern Greek account for the lexical decision performance of young Greek adults who are exposed to subtitle reading on a daily basis. Results showed that SUBTLEX-GR frequency estimates effectively accounted for participants’ reading performance in two different visual word recognition experiments. More importantly, different analyses showed that frequencies estimated from a subtitle corpus explained the obtained results significantly better than traditional frequencies derived from written corpora. PMID:21833273

  5. OPTIMIZING MINIRHIZOTRON SAMPLE FREQUENCY FOR ESTIMATING FINE ROOT PRODUCTION AND TURNOVER

    EPA Science Inventory

    The most frequent reason for using minirhizotrons in natural ecosystems is the determination of fine root production and turnover. Our objective is to determine the optimum sampling frequency for estimating fine root production and turnover using data from evergreen (Pseudotsuga ...

  6. Performance of mean-frequency estimators for Doppler radar and lidar

    NASA Technical Reports Server (NTRS)

    Frehlich, R. G.; Yadlowsky, M. J.

    1994-01-01

    The performance of mean-frequency estimators for Doppler radar and lidar measurements of winds is presented in terms of two basic parameters: Phi, the ratio of the average signal energy per estimate to the spectral noise level; and Omega, which is proportional to the number of independent samples per estimate. For fixed Phi and Omega, the Cramer-Rao bound (CRB) (theoretical best performance) for unbiased estimators of mean frequency (normalized by the spectral width of the signal), signal power, and spectral width are essentially independent of the number of data samples M. For large Phi, the estimators of mean frequency are unbiased and the performance is independent of M. The spectral domain estimators and covariance based estimators are bounded by the approximate period of M. The spectral domain estimators and covariance based estimators are bounded by the approximate periodogram CRB. The standard deviation of the maximum-likelihood estimator approaches the exact CRB, which can be more than a factor of 2 better than the performance of the spectral domain estimators or covariance-based estimators for typical Omega. For small Phi, the estimators are biased due to the effects of the uncorrelated noise (white noise), which results in uniformly distributed 'bad' estimates. The fraction of bad estimates is a function of Phi and M with weak dependence on the parameter Omega. Simple empirical models describe the standard deviation of the good estimates and the fraction of bad estimates. For Doppler lidar and for large Phi, better performance is obtained by using many low-energy pulses instead of one pulse with the same total energy. For small Phi, the converse is true.

  7. Techniques for estimating magnitude and frequency of floods on streams in Indiana

    USGS Publications Warehouse

    Glatfelter, D.R.

    1984-01-01

    A rainfall-runoff model was tlsed to synthesize long-term peak data at 11 gaged locations on small streams. Flood-frequency curves developed from the long-term synthetic data were combined with curves based on short-term observed data to provide weighted estimates of flood magnitude and frequency at the rainfall-runoff stations.

  8. Counting calories: partitioning energy intake estimates from a food frequency questionnaire.

    PubMed

    Flegal, K M; Larkin, F A; Metzner, H L; Thompson, F E; Guire, K E

    1988-10-01

    Differences in energy estimates between a food frequency questionnaire and a multi-day dietary record can be partitioned into distinct components due to differences in reported frequency of consumption and in reported serving size, and to differences in nutrient composition between the questionnaire standards and the foods reported on the records. The effect of each component on the relative validity of the questionnaire can be assessed by examining its contribution to the differences between the two methods in estimated group intake and in the relative ranking of individual respondents. This methodology was used for the 1984-1985 University of Michigan Food Frequency Study, in which the estimated energy intake from a quantitative food frequency questionnaire was compared with that from 16 days of food records collected over the course of a year from 228 white and black men and women aged 24-51 years. For all race-sex subgroups, mean energy intake estimated from the questionnaire was significantly greater than mean intake estimated from the record. Within race-sex subgroups, the correlations between estimates from the two methods were low, and agreement in classification by tertiles was poor. The differences in group mean energy intake between the methods were due to the effects of discrepancies in both serving size and frequency of consumption. However, the low correlations and poor agreement in classification for individual respondents were due principally to the effect of discrepancies in frequency. These results suggest that improving the accuracy of frequency estimation is a key element in increasing the relative validity of food frequency questionnaires used for epidemiologic research. PMID:3421241

  9. Estimating allele dropout probabilities by logistic regression: Assessments using Applied Biosystems 3500xL and 3130xl Genetic Analyzers with various commercially available human identification kits.

    PubMed

    Inokuchi, Shota; Kitayama, Tetsushi; Fujii, Koji; Nakahara, Hiroaki; Nakanishi, Hiroaki; Saito, Kazuyuki; Mizuno, Natsuko; Sekiguchi, Kazumasa

    2016-03-01

    Phenomena called allele dropouts are often observed in crime stain profiles. Allele dropouts are generated because one of a pair of heterozygous alleles is underrepresented by stochastic influences and is indicated by a low peak detection threshold. Therefore, it is important that such risks are statistically evaluated. In recent years, attempts to interpret allele dropout probabilities by logistic regression using the information on peak heights have been reported. However, these previous studies are limited to the use of a human identification kit and fragment analyzer. In the present study, we calculated allele dropout probabilities by logistic regression using contemporary capillary electrophoresis instruments, 3500xL Genetic Analyzer and 3130xl Genetic Analyzer with various commercially available human identification kits such as AmpFℓSTR® Identifiler® Plus PCR Amplification Kit. Furthermore, the differences in logistic curves between peak detection thresholds using analytical threshold (AT) and values recommended by the manufacturer were compared. The standard logistic curves for calculating allele dropout probabilities from the peak height of sister alleles were characterized. The present study confirmed that ATs were lower than the values recommended by the manufacturer in human identification kits; therefore, it is possible to reduce allele dropout probabilities and obtain more information using AT as the peak detection threshold.

  10. The National Flood Frequency Program, version 3 : a computer program for estimating magnitude and frequency of floods for ungaged sites

    USGS Publications Warehouse

    Ries, Kernell G.; Crouse, Michele Y.

    2002-01-01

    For many years, the U.S. Geological Survey (USGS) has been developing regional regression equations for estimating flood magnitude and frequency at ungaged sites. These regression equations are used to transfer flood characteristics from gaged to ungaged sites through the use of watershed and climatic characteristics as explanatory or predictor variables. Generally, these equations have been developed on a Statewide or metropolitan-area basis as part of cooperative study programs with specific State Departments of Transportation. In 1994, the USGS released a computer program titled the National Flood Frequency Program (NFF), which compiled all the USGS available regression equations for estimating the magnitude and frequency of floods in the United States and Puerto Rico. NFF was developed in cooperation with the Federal Highway Administration and the Federal Emergency Management Agency. Since the initial release of NFF, the USGS has produced new equations for many areas of the Nation. A new version of NFF has been developed that incorporates these new equations and provides additional functionality and ease of use. NFF version 3 provides regression-equation estimates of flood-peak discharges for unregulated rural and urban watersheds, flood-frequency plots, and plots of typical flood hydrographs for selected recurrence intervals. The Program also provides weighting techniques to improve estimates of flood-peak discharges for gaging stations and ungaged sites. The information provided by NFF should be useful to engineers and hydrologists for planning and design applications. This report describes the flood-regionalization techniques used in NFF and provides guidance on the applicability and limitations of the techniques. The NFF software and the documentation for the regression equations included in NFF are available at http://water.usgs.gov/software/nff.html.

  11. A Practical Guide for Estimating Dietary Fat and Fiber Using Limited Food Frequency Data.

    ERIC Educational Resources Information Center

    Neale, Anne Victoria; And Others

    1992-01-01

    A methodology is presented for estimating daily intake of dietary fat and fiber based on limited food frequency data. The procedure, which relies on National Food Consumption Survey data and daily consumption rates, can provide baseline estimates of dietary patterns for health promotion policymakers. (SLD)

  12. What to Do about Zero Frequency Cells when Estimating Polychoric Correlations

    ERIC Educational Resources Information Center

    Savalei, Victoria

    2011-01-01

    Categorical structural equation modeling (SEM) methods that fit the model to estimated polychoric correlations have become popular in the social sciences. When population thresholds are high in absolute value, contingency tables in small samples are likely to contain zero frequency cells. Such cells make the estimation of the polychoric…

  13. Sparse reconstruction for direction-of-arrival estimation using multi-frequency co-prime arrays

    NASA Astrophysics Data System (ADS)

    BouDaher, Elie; Ahmad, Fauzia; Amin, Moeness G.

    2014-12-01

    In this paper, multi-frequency co-prime arrays are employed to perform direction-of-arrival (DOA) estimation with enhanced degrees of freedom (DOFs). Operation at multiple frequencies creates additional virtual elements in the difference co-array of the co-prime array corresponding to the reference frequency. Sparse reconstruction is then used to fully exploit the enhanced DOFs offered by the multi-frequency co-array, thereby increasing the number of resolvable sources. For the case where the sources have proportional spectra, the received signal vectors at the different frequencies are combined to form an equivalent single measurement vector model corresponding to the multi-frequency co-array. When the sources have nonproportional spectra, a group sparsity-based reconstruction approach is used to determine the direction of signal arrivals. Performance evaluation of the proposed multi-frequency approach is performed using numerical simulations for both cases of proportional and nonproportional source spectra.

  14. Distribution of allele frequencies at TTN g.231054C > T, RPL27A g.3109537C > T and AKIRIN2 c.*188G > A between Japanese Black and four other cattle breeds with differing historical selection for marbling

    PubMed Central

    2011-01-01

    Background Marbling defined by the amount and distribution of intramuscular fat, so-called Shimofuri, is an economically important trait of beef cattle in Japan. Our previous study detected 3 single nucleotide polymorphisms (SNPs), g.231054C > T, g.3109537C > T and c.*188G > A, respectively, in the 5' flanking region of the titin (TTN), the 5' flanking region of the ribosomal protein L27a (RPL27A) and the 3' untranslated region of the akirin 2 genes (AKIRIN2), which have been considered as positional functional candidates for the genes responsible for marbling, and showed association of these SNPs with marbling in Japanese Black beef cattle. In the present study, we investigated the allele frequency distribution of the 3 SNPs among the 5 cattle breeds, Japanese Black, Japanese Brown, Japanese Shorthorn, Holstein and Brown Swiss breeds. Findings We genotyped the TTN g.231054C > T, RPL27A g.3109537C > T and AKIRIN2 c.*188G > A SNPs by polymerase chain reaction-restriction fragment length polymorphism method, using 101 sires and 1,705 paternal half sib progeny steers from 8 sires for Japanese Black, 86 sires and 27 paternal half sib progeny steers from 3 sires for Japanese Brown, 79 sires and 264 paternal half sib progeny steers from 14 sires for Japanese Shorthorn, 119 unrelated cows for Holstein, and 118 unrelated cows for Brown Swiss breeds. As compared to the frequencies of the g.231054C > T T, g.3109537C > T T and c.*188G > A A alleles, associated with high marbling, in Japanese Black breed that has been subjected to a strong selection for high marbling, those in the breeds, Japanese Shorthorn, Holstein and Brown Swiss breeds, that have not been selected for high marbling were null or lower. The Japanese Brown breed selected slightly for high marbling showed lower frequency than Japanese Black breed in the g.3109537C > T T allele, whereas no differences were detected between the 2 breeds in the frequencies of the g.231054C > T T and c.*188G > A A alleles

  15. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the...

  16. Local frequency estimation from intensity gradients in spatial carrier fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Ruihua; Guo, Hongwei

    2016-06-01

    Spatial carrier fringe pattern analysis is an effective tool in optical measurement, e.g. in interferometry and fringe projection technique. With it, the very large phase deformations in a spatial carrier fringe pattern may increases the bandwidth of fringe component thus leading to difficulties in retrieving its phase map. In order to overcome this problem, many local-adaptive methods have been developed for processing the spatial carrier fringe pattern with large phase variations, and in fact, the local spatial frequency estimation is central to these methods. This paper introduces a simple algorithm for estimating the local frequencies of a fringe pattern with spatial carrier. First, the intensity gradients of the fringe pattern are calculated, and then the standard deviations (SDs) of the intensity gradients at each pixel are estimated from its neighborhood. Finally the local frequencies are estimated from the SDs just calculated simply using an arccosine function. This algorithm is potential in developing effective techniques for retrieving phases from a spatial carrier fringe pattern with large phase variations. For example, we can recover the phase map by directly integrating the local frequencies or by use of an adaptive spatial carrier phase shifting algorithm (SCPS) with the local frequencies being the local phase shifts. It can also be used in Fourier transform method for exactly determining the carrier frequencies, or for extrapolating aperture in order to reduce the boundary effect. Combined with time-frequency techniques such as windowed Fourier transform and wavelet transform methods, it is helpful for alleviating the computational burdens.

  17. An adaptive filter-based method for robust, automatic detection and frequency estimation of whistles.

    PubMed

    Johansson, A Torbjorn; White, Paul R

    2011-08-01

    This paper proposes an adaptive filter-based method for detection and frequency estimation of whistle calls, such as the calls of birds and marine mammals, which are typically analyzed in the time-frequency domain using a spectrogram. The approach taken here is based on adaptive notch filtering, which is an established technique for frequency tracking. For application to automatic whistle processing, methods for detection and improved frequency tracking through frequency crossings as well as interfering transients are developed and coupled to the frequency tracker. Background noise estimation and compensation is accomplished using order statistics and pre-whitening. Using simulated signals as well as recorded calls of marine mammals and a human whistled speech utterance, it is shown that the proposed method can detect more simultaneous whistles than two competing spectrogram-based methods while not reporting any false alarms on the example datasets. In one example, it extracts complete 1.4 and 1.8 s bottlenose dolphin whistles successfully through frequency crossings. The method performs detection and estimates frequency tracks even at high sweep rates. The algorithm is also shown to be effective on human whistled utterances. PMID:21877804

  18. Effects of cigarette smoking on human in vivo somatic mutation: Longitudinal sampling of smokers demonstrates a decrease in glycophorin A (GPA) allele-loss variant cell frequencies following cessation

    SciTech Connect

    Bigbee, W.L.; Langlois, R.G. ); Grant, S.G.; Jensen, R.H. ); Mooney, L.M.; Perera, F.P. )

    1993-01-01

    The human in vivo glycophorin A (GPA) assay uses immunolabeling and flow cytometry to quantitate somatic variation in erythrocytes expressing GPA allele loss and allele-loss and duplication phenotypes in peripheral blood samples. The frequency of these variant erythrocytes (V[sub f]) presumably reflects the level of somatic mutation at this locus in the nucleated hematopoietic precursor cells of the bone marrow. We have previously shown that the GPA assay is a cumulative, integrating biodosimeter of accidental, medical, and occupational exposure to chemical mutagens and ionizing radiation. Surveys of otherwise unexposed populations point to an increased GPA allele loss V[sub f] in cigarette smokers compared to nonsmokers consistent with the induction of somatic mutation by mutagenic components of tobacco smoke. To further test this association, blood samples from active heavy smokers who entered a multi-endpoint Smokender study were obtained at enrollment and at 10 wks and 6 and 12 mo following smoking cessation. Results from the first 109 individuals reveal a decrease in the mean GPA allele loss V[sub f] ranging from 9.0 [+-] 1.0 [times] 10[sup [minus]6] (n = 109) for the active smoking samples, to 9.1 [+-] 1.8 [times] 10[sup [minus]6] (n = 46), 6.0 [+-] 0.7 [times] 10[sup [minus]6] (n = 15), and 5.8 [+-] 1.6 [times] 10[sup [minus]6] (n = 8) for the three postcessation samples, respectively. No change in the GPA allele loss and duplication V[sub f] was observed, thus confining the spectrum of mutational events induced by exposure to cigarette smoke. The observed decrease in the level of somatic mutation in smokers following cessation suggests limited persistence and/or repair of tobacco-smoke-induced genetic alterations consistent with epidemiologic findings of decreased cancer risk in smokers following cessation.

  19. Estimate of air carrier and air taxi crash frequencies from high altitude en route flight operations

    SciTech Connect

    Sanzo, D.; Kimura, C.Y.; Prassinos, P.G.

    1996-06-03

    In estimating the frequency of an aircraft crashing into a facility, it has been found convenient to break the problem down into two broad categories. One category estimates the aircraft crash frequency due to air traffic from nearby airports, the so-called near-airport environment. The other category estimates the aircraft crash frequency onto facilities due to air traffic from airways, jet routes, and other traffic flying outside the near-airport environment The total aircraft crash frequency is the summation of the crash frequencies from each airport near the facility under evaluation and from all airways, jet routes, and other traffic near the facility of interest. This paper will examine the problems associated with the determining the aircraft crash frequencies onto facilities outside the near-airport environment. This paper will further concentrate on the estimating the risk of aircraft crashes to ground facilities due to high altitude air carrier and air taxi traffic. High altitude air carrier and air taxi traffic will be defined as all air carrier and air taxi flights above 18,000 feet Mean Sea Level (MSL).

  20. Estimation of the running speed and bearing defect frequencies of an induction motor from vibration data

    NASA Astrophysics Data System (ADS)

    Ocak, Hasan; Loparo, Kenneth A.

    2004-05-01

    This paper presents two separate algorithms for estimating the running speed and the bearing key frequencies of an induction motor using vibration data. Bearing key frequencies are frequencies at which roller elements pass over a defect point. Most frequency domain-based bearing fault detection and diagnosis techniques (e.g. envelope analysis) rely on vibration measurements and the bearing key frequencies. Thus, estimation of the running speed and the bearing key frequencies are required for failure detection and diagnosis. The paper also incorporates the estimation algorithms with the most commonly used bearing fault detection technique, high-frequency demodulation, to detect bearing faults. Experimental data were used to verify the validity of the algorithms. Data were collected through an accelerometer measuring the vibration from the drive-end ball bearing of an induction motor (Reliance Electric 2HP IQPreAlert)-driven mechanical system. Both inner and outer race defects were artificially introduced to the bearing using electrical discharge machining. A linear vibration model was also developed for generating simulated vibration data. The simulated data were also used to validate the performance of the algorithms. The test results proved the algorithms to be very reliable.

  1. Methods for estimating the magnitude and frequency of peak streamflows for unregulated streams in Oklahoma

    USGS Publications Warehouse

    Lewis, Jason M.

    2010-01-01

    Peak-streamflow regression equations were determined for estimating flows with exceedance probabilities from 50 to 0.2 percent for the state of Oklahoma. These regression equations incorporate basin characteristics to estimate peak-streamflow magnitude and frequency throughout the state by use of a generalized least squares regression analysis. The most statistically significant independent variables required to estimate peak-streamflow magnitude and frequency for unregulated streams in Oklahoma are contributing drainage area, mean-annual precipitation, and main-channel slope. The regression equations are applicable for watershed basins with drainage areas less than 2,510 square miles that are not affected by regulation. The resulting regression equations had a standard model error ranging from 31 to 46 percent. Annual-maximum peak flows observed at 231 streamflow-gaging stations through water year 2008 were used for the regression analysis. Gage peak-streamflow estimates were used from previous work unless 2008 gaging-station data were available, in which new peak-streamflow estimates were calculated. The U.S. Geological Survey StreamStats web application was used to obtain the independent variables required for the peak-streamflow regression equations. Limitations on the use of the regression equations and the reliability of regression estimates for natural unregulated streams are described. Log-Pearson Type III analysis information, basin and climate characteristics, and the peak-streamflow frequency estimates for the 231 gaging stations in and near Oklahoma are listed. Methodologies are presented to estimate peak streamflows at ungaged sites by using estimates from gaging stations on unregulated streams. For ungaged sites on urban streams and streams regulated by small floodwater retarding structures, an adjustment of the statewide regression equations for natural unregulated streams can be used to estimate peak-streamflow magnitude and frequency.

  2. Estimate error of frequency-dependent Q introduced by linear regression and its nonlinear implementation

    NASA Astrophysics Data System (ADS)

    Li, Guofa; Huang, Wei; Zheng, Hao; Zhang, Baoqing

    2016-02-01

    The spectral ratio method (SRM) is widely used to estimate quality factor Q via the linear regression of seismic attenuation under the assumption of a constant Q. However, the estimate error will be introduced when this assumption is violated. For the frequency-dependent Q described by a power-law function, we derived the analytical expression of estimate error as a function of the power-law exponent γ and the ratio of the bandwidth to the central frequency σ . Based on the theoretical analysis, we found that the estimate errors are mainly dominated by the exponent γ , and less affected by the ratio σ . This phenomenon implies that the accuracy of the Q estimate can hardly be improved by adjusting the width and range of the frequency band. Hence, we proposed a two-parameter regression method to estimate the frequency-dependent Q from the nonlinear seismic attenuation. The proposed method was tested using the direct waves acquired by a near-surface cross-hole survey, and its reliability was evaluated in comparison with the result of SRM.

  3. Channel estimation for asymmetrically clipped optical orthogonal frequency division multiplexing communication system

    NASA Astrophysics Data System (ADS)

    Zhao, Hui; Li, Minghui; Wang, Ruyan; Wu, Dapeng

    2013-07-01

    The channel estimation problem for asymmetrically clipped optical orthogonal frequency division multiplexing wireless communication systems is investigated. In order to resolve the noise-sensitive problem of traditional least squares-based channel estimation method, a new channel estimation method which is based on superimposed training sequence and guarantees the linear minimum mean square error estimate is proposed. Cycle training sequence is added at variable power ratio to the information sequence at the transmitter prior to transmission. Then, statistical average method is employed to separate training and information sequences at the receiver. Simulation results show that the power ratio of training sequence needs to balance between the mean square error (MSE) of estimation and the error bit rate. Moreover, compared with the traditional least squares-based method, the proposed method has significantly improved the estimation performance under the condition of low signal-to-noise ratio, especially, when the MSE of the estimation reduces 1 to 2 orders.

  4. Utilization of accident databases and fuzzy sets to estimate frequency of HazMat transport accidents.

    PubMed

    Qiao, Yuanhua; Keren, Nir; Mannan, M Sam

    2009-08-15

    Risk assessment and management of transportation of hazardous materials (HazMat) require the estimation of accident frequency. This paper presents a methodology to estimate hazardous materials transportation accident frequency by utilizing publicly available databases and expert knowledge. The estimation process addresses route-dependent and route-independent variables. Negative binomial regression is applied to an analysis of the Department of Public Safety (DPS) accident database to derive basic accident frequency as a function of route-dependent variables, while the effects of route-independent variables are modeled by fuzzy logic. The integrated methodology provides the basis for an overall transportation risk analysis, which can be used later to develop a decision support system.

  5. An improved correlation method for amplitude estimation of gravitational background signal with time-varying frequency

    NASA Astrophysics Data System (ADS)

    Wu, Wei-Huang; Tian, Yuan; Luo, Jie; Shao, Cheng-Gang; Xu, Jia-Hao; Wang, Dian-Hong

    2016-09-01

    In the measurement of the gravitational constant G with angular acceleration method, the accurate estimation of the amplitude of the useful angular acceleration generated by source masses depends on the effective subtraction of the spurious gravitational signal caused by room fixed background masses. The gravitational background signal is of time-varying frequency, and mainly consists of the prominent fundamental frequency and second harmonic components. We propose an improved correlation method to estimate the amplitudes of the prominent components of the gravitational background signal with high precision. The improved correlation method converts a sinusoidal signal with time-varying frequency into a standard sinusoidal signal by means of the stretch processing of time. Based on Gaussian white noise model, the theoretical result shows the uncertainty of the estimated amplitude is proportional to /σ √{ N T } , where σ and N are the standard deviation of noise and the number of the useful signal period T, respectively.

  6. Utilization of accident databases and fuzzy sets to estimate frequency of HazMat transport accidents.

    PubMed

    Qiao, Yuanhua; Keren, Nir; Mannan, M Sam

    2009-08-15

    Risk assessment and management of transportation of hazardous materials (HazMat) require the estimation of accident frequency. This paper presents a methodology to estimate hazardous materials transportation accident frequency by utilizing publicly available databases and expert knowledge. The estimation process addresses route-dependent and route-independent variables. Negative binomial regression is applied to an analysis of the Department of Public Safety (DPS) accident database to derive basic accident frequency as a function of route-dependent variables, while the effects of route-independent variables are modeled by fuzzy logic. The integrated methodology provides the basis for an overall transportation risk analysis, which can be used later to develop a decision support system. PMID:19250750

  7. Joint entropy for space and spatial frequency domains estimated from psychometric functions of achromatic discrimination.

    PubMed

    Silveira, Vladímir de Aquino; Souza, Givago da Silva; Gomes, Bruno Duarte; Rodrigues, Anderson Raiol; Silveira, Luiz Carlos de Lima

    2014-01-01

    We used psychometric functions to estimate the joint entropy for space discrimination and spatial frequency discrimination. Space discrimination was taken as discrimination of spatial extent. Seven subjects were tested. Gábor functions comprising unidimensionalsinusoidal gratings (0.4, 2, and 10 cpd) and bidimensionalGaussian envelopes (1°) were used as reference stimuli. The experiment comprised the comparison between reference and test stimulithat differed in grating's spatial frequency or envelope's standard deviation. We tested 21 different envelope's standard deviations around the reference standard deviation to study spatial extent discrimination and 19 different grating's spatial frequencies around the reference spatial frequency to study spatial frequency discrimination. Two series of psychometric functions were obtained for 2%, 5%, 10%, and 100% stimulus contrast. The psychometric function data points for spatial extent discrimination or spatial frequency discrimination were fitted with Gaussian functions using the least square method, and the spatial extent and spatial frequency entropies were estimated from the standard deviation of these Gaussian functions. Then, joint entropy was obtained by multiplying the square root of space extent entropy times the spatial frequency entropy. We compared our results to the theoretical minimum for unidimensional Gábor functions, 1/4π or 0.0796. At low and intermediate spatial frequencies and high contrasts, joint entropy reached levels below the theoretical minimum, suggesting non-linear interactions between two or more visual mechanisms. We concluded that non-linear interactions of visual pathways, such as the M and P pathways, could explain joint entropy values below the theoretical minimum at low and intermediate spatial frequencies and high contrasts. These non-linear interactions might be at work at intermediate and high contrasts at all spatial frequencies once there was a substantial decrease in joint

  8. The Exponent of High-frequency Source Spectral Falloff and Contribution to Source Parameter Estimates

    NASA Astrophysics Data System (ADS)

    Kiuchi, R.; Mori, J. J.

    2015-12-01

    As a way to understand the characteristics of the earthquake source, studies of source parameters (such as radiated energy and stress drop) and their scaling are important. In order to estimate source parameters reliably, often we must use appropriate source spectrum models and the omega-square model is most frequently used. In this model, the spectrum is flat in lower frequencies and the falloff is proportional to the angular frequency squared. However, Some studies (e.g. Allmann and Shearer, 2009; Yagi et al., 2012) reported that the exponent of the high frequency falloff is other than -2. Therefore, in this study we estimate the source parameters using a spectral model for which the falloff exponent is not fixed. We analyze the mainshock and larger aftershocks of the 2008 Iwate-Miyagi Nairiku earthquake. Firstly, we calculate the P wave and SH wave spectra using empirical Green functions (EGF) to remove the path effect (such as attenuation) and site effect. For the EGF event, we select a smaller earthquake that is highly-correlated with the target event. In order to obtain the stable results, we calculate the spectral ratios using a multitaper spectrum analysis (Prieto et al., 2009). Then we take a geometric mean from multiple stations. Finally, using the obtained spectra ratios, we perform a grid search to determine the high frequency falloffs, as well as corner frequency of both of events. Our results indicate the high frequency falloff exponent is often less than 2.0. We do not observe any regional, focal mechanism, or depth dependencies for the falloff exponent. In addition, our estimated corner frequencies and falloff exponents are consistent between the P wave and SH wave analysis. In our presentation, we show differences in estimated source parameters using a fixed omega-square model and a model allowing variable high-frequency falloff.

  9. Regional equations for estimation of peak-streamflow frequency for natural basins in Texas

    USGS Publications Warehouse

    Asquith, William H.; Slade, Raymond M.

    1997-01-01

    Peak-streamflow frequency for 559 Texas stations with natural (unregulated and rural or nonurbanized) basins was estimated with annual peak-streamflow data through 1993. The peak-streamflow frequency and drainage-basin characteristics for the Texas stations were used to develop 16 sets of equations to estimate peak-streamflow frequency for ungaged natural stream sites in each of 11 regions in Texas. The relation between peak-streamflow frequency and contributing drainage area for 5 of the 11 regions is curvilinear, requiring that one set of equations be developed for drainage areas less than 32 square miles and another set be developed for drainage areas greater than 32 square miles. These equations, developed through multiple-regression analysis using weighted least squares, are based on the relation between peak-streamflow frequency and basin characteristics for streamflow-gaging stations. The regions represent areas with similar flood characteristics. The use and limitations of the regression equations also are discussed. Additionally, procedures are presented to compute the 50-, 67-, and 90-percent confidence limits for any estimation from the equations. Also, supplemental peak-streamflow frequency and basin characteristics for 105 selected stations bordering Texas are included in the report. This supplemental information will aid in interpretation of flood characteristics for sites near the state borders of Texas.

  10. Ehapp2: Estimate haplotype frequencies from pooled sequencing data with prior database information.

    PubMed

    Cao, Chang-Chang; Sun, Xiao

    2016-08-01

    To reduce the cost of large-scale re-sequencing, multiple individuals are pooled together and sequenced called pooled sequencing. Pooled sequencing could provide a cost-effective alternative to sequencing individuals separately. To facilitate the application of pooled sequencing in haplotype-based diseases association analysis, the critical procedure is to accurately estimate haplotype frequencies from pooled samples. Here we present Ehapp2 for estimating haplotype frequencies from pooled sequencing data by utilizing a database which provides prior information of known haplotypes. We first translate the problem of estimating frequency for each haplotype into finding a sparse solution for a system of linear equations, where the NNREG algorithm is employed to achieve the solution. Simulation experiments reveal that Ehapp2 is robust to sequencing errors and able to estimate the frequencies of haplotypes with less than 3% average relative difference for pooled sequencing of mixture of real Drosophila haplotypes with 50× total coverage even when the sequencing error rate is as high as 0.05. Owing to the strategy that proportions for local haplotypes spanning multiple SNPs are accurately calculated first, Ehapp2 retains excellent estimation for recombinant haplotypes resulting from chromosomal crossover. Comparisons with present methods reveal that Ehapp2 is state-of-the-art for many sequencing study designs and more suitable for current massive parallel sequencing. PMID:27216711

  11. Increasing long term response by selecting for favorable minor alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term response of genomic selection can be improved by considering allele frequencies of selected markers or quantitative trait loci (QTLs). A previous formula to weight allele frequency of favorable minor alleles was tested, and 2 new formulas were developed. The previous formula used nonlinear...

  12. Application of Model Based Parameter Estimation for RCS Frequency Response Calculations Using Method of Moments

    NASA Technical Reports Server (NTRS)

    Reddy, C. J.

    1998-01-01

    An implementation of the Model Based Parameter Estimation (MBPE) technique is presented for obtaining the frequency response of the Radar Cross Section (RCS) of arbitrarily shaped, three-dimensional perfect electric conductor (PEC) bodies. An Electric Field Integral Equation (EFTE) is solved using the Method of Moments (MoM) to compute the RCS. The electric current is expanded in a rational function and the coefficients of the rational function are obtained using the frequency derivatives of the EFIE. Using the rational function, the electric current on the PEC body is obtained over a frequency band. Using the electric current at different frequencies, RCS of the PEC body is obtained over a wide frequency band. Numerical results for a square plate, a cube, and a sphere are presented over a bandwidth. Good agreement between MBPE and the exact solution over the bandwidth is observed.

  13. Quantitative Sequencing for the Determination of Kdr-type Resistance Allele (V419L, L925I, I936F) Frequencies in Common Bed Bug (Hemiptera: Cimicidae) Populations Collected from Israel.

    PubMed

    Palenchar, Daniel J; Gellatly, Kyle J; Yoon, Kyong Sup; Mumcuoglu, Kosta Y; Shalom, Uri; Clark, J Marshall

    2015-09-01

    Human bed bug infestations have dramatically increased worldwide since the mid-1990s. A similar phenomenon was also observed in Israel since 2005, when infestations were reported from all over the country. Two single nucleotide polymorphisms (V419L and L925I) in the bed bug voltage-sensitive sodium channel confer kdr-type resistance to pyrethroids. Using quantitative sequencing (QS), the resistance allele frequencies of Israeli bed bug populations from across the country were determined. Genomic DNA was extracted from samples of 12 populations of bed bugs collected from Israel and DNA fragments containing the V419L or L925I and I936F mutations sites were PCR amplified. The PCR products were analyzed by QS and the nucleotide signal ratios calculated and used to predict the resistance allele frequencies of the unknown populations. Results of the genetic analysis show that resistant nucleotide signals are highly correlated to resistance allele frequencies for both mutations. Ten of the 12 tested populations had 100% of the L925I mutation and 0% of the V419L mutation. One population was heterogeneous for the L925I mutation and had 0% of the V419L mutation and another population was heterogeneous for the V419L mutation and had 100% of the L925I mutation. I936F occurred only at low levels. These results indicate that bed bugs in Israel are genetically resistant to pyrethroids. Thus, pyrethroids should only be used for bed bug management with caution using effective application and careful monitoring procedures. Additionally, new and novel-acting insecticides and nonchemical means of controlling bed bugs should be explored. PMID:26336243

  14. Frequencies of immune hypersensitivity reaction-associated HLA class I alleles in healthy South African Indian and mixed ancestry populations determined by a novel real-time PCR assay.

    PubMed

    Loubser, S; Paximadis, M; Gentle, N; Puren, A; Gray, C M; Tiemessen, C T

    2014-10-01

    We have determined the frequencies of human leucocyte antigen (HLA)-B*57:01, HLA-B*35:05, HLA-C*04 and HLA-C*08 in healthy individuals of South African Indian (SAI) ethnicity (n = 50) and South African mixed (SAM) ancestry (n = 50) using real-time allele-specific polymerase chain reaction (AS-PCR) assay. HLA-B*57:01 associates with immune hypersensitivity reaction (IHR) in individuals exposed to abacavir (ABC), while nevirapine (NVP) IHR associates with HLA-B*35:05, HLA-C*04 and HLA-C*08. Real-time AS-PCR assays typically use less DNA, are more cost-effective and rapid compared with conventional genotyping methods, such as sequence-based typing (SBT). The assay was developed using samples of known HLA class I genotype and subsequently applied to the SAI and SAM samples. HLA-B*57:01 was detected in SAM and SAI populations at frequencies of 8.0% and 12.0%, respectively, while HLA-B*35:05 was not found in SAI individuals, but was present in 6.0% of SAM individuals. HLA-C*04 was detected in 22.0% and 24.0% of SAM and SAI individuals, respectively, while 10.0% and 8.0% of SAM and SAI individuals, respectively, were HLA-C*08 positive. This study reports the development of a novel real-time AS-PCR assay to identify HLA class I alleles associated with ABC and NVP IHR and has established the frequencies of these alleles present in healthy SAI and SAM populations. Using South African demographic data, our hypothetical analysis suggests that a substantial number of individuals would benefit from the assay.

  15. Quantitative Sequencing for the Determination of Kdr-type Resistance Allele (V419L, L925I, I936F) Frequencies in Common Bed Bug (Hemiptera: Cimicidae) Populations Collected from Israel.

    PubMed

    Palenchar, Daniel J; Gellatly, Kyle J; Yoon, Kyong Sup; Mumcuoglu, Kosta Y; Shalom, Uri; Clark, J Marshall

    2015-09-01

    Human bed bug infestations have dramatically increased worldwide since the mid-1990s. A similar phenomenon was also observed in Israel since 2005, when infestations were reported from all over the country. Two single nucleotide polymorphisms (V419L and L925I) in the bed bug voltage-sensitive sodium channel confer kdr-type resistance to pyrethroids. Using quantitative sequencing (QS), the resistance allele frequencies of Israeli bed bug populations from across the country were determined. Genomic DNA was extracted from samples of 12 populations of bed bugs collected from Israel and DNA fragments containing the V419L or L925I and I936F mutations sites were PCR amplified. The PCR products were analyzed by QS and the nucleotide signal ratios calculated and used to predict the resistance allele frequencies of the unknown populations. Results of the genetic analysis show that resistant nucleotide signals are highly correlated to resistance allele frequencies for both mutations. Ten of the 12 tested populations had 100% of the L925I mutation and 0% of the V419L mutation. One population was heterogeneous for the L925I mutation and had 0% of the V419L mutation and another population was heterogeneous for the V419L mutation and had 100% of the L925I mutation. I936F occurred only at low levels. These results indicate that bed bugs in Israel are genetically resistant to pyrethroids. Thus, pyrethroids should only be used for bed bug management with caution using effective application and careful monitoring procedures. Additionally, new and novel-acting insecticides and nonchemical means of controlling bed bugs should be explored.

  16. High frequency and founder effect of the CYP3A4*20 loss-of-function allele in the Spanish population classifies CYP3A4 as a polymorphic enzyme.

    PubMed

    Apellániz-Ruiz, M; Inglada-Pérez, L; Naranjo, M E G; Sánchez, L; Mancikova, V; Currás-Freixes, M; de Cubas, A A; Comino-Méndez, I; Triki, S; Rebai, A; Rasool, M; Moya, G; Grazina, M; Opocher, G; Cascón, A; Taboada-Echalar, P; Ingelman-Sundberg, M; Carracedo, A; Robledo, M; Llerena, A; Rodríguez-Antona, C

    2015-06-01

    Cytochrome P450 3A4 (CYP3A4) is a key drug-metabolizing enzyme. Loss-of-function variants have been reported as rare events, and the first demonstration of a CYP3A4 protein lacking functional activity is caused by CYP3A4*20 allele. Here we characterized the world distribution and origin of CYP3A4*20 mutation. CYP3A4*20 was determined in more than 4000 individuals representing different populations, and haplotype analysis was performed using CYP3A polymorphisms and microsatellite markers. CYP3A4*20 allele was present in 1.2% of the Spanish population (up to 3.8% in specific regions), and all CYP3A4*20 carriers had a common haplotype. This is compatible with a Spanish founder effect and classifies CYP3A4 as a polymorphic enzyme. This constitutes the first description of a CYP3A4 loss-of-function variant with high frequency in a population. CYP3A4*20 results together with the key role of CYP3A4 in drug metabolism support screening for rare CYP3A4 functional alleles among subjects with adverse drug events in certain populations. PMID:25348618

  17. Inverse synthetic aperture radar processing using parametric time-frequency estimators Phase I

    SciTech Connect

    Candy, J.V., LLNL

    1997-12-31

    This report summarizes the work performed for the Office of the Chief of Naval Research (ONR) during the period of 1 September 1997 through 31 December 1997. The primary objective of this research was aimed at developing an alternative time-frequency approach which is recursive-in-time to be applied to the Inverse Synthethic Aperture Radar (ISAR) imaging problem discussed subsequently. Our short term (Phase I) goals were to: 1. Develop an ISAR stepped-frequency waveform (SFWF) radar simulator based on a point scatterer vehicular target model incorporating both translational and rotational motion; 2. Develop a parametric, recursive-in-time approach to the ISAR target imaging problem; 3. Apply the standard time-frequency short-term Fourier transform (STFT) estimator, initially to a synthesized data set; and 4. Initiate the development of the recursive algorithm. We have achieved all of these goals during the Phase I of the project and plan to complete the overall development, application and comparison of the parametric approach to other time-frequency estimators (STFT, etc.) on our synthesized vehicular data sets during the next phase of funding. It should also be noted that we developed a batch minimum variance translational motion compensation (TMC) algorithm to estimate the radial components of target motion (see Section IV). This algorithm is easily extended to recursive solution and will probably become part of the overall recursive processing approach to solve the ISAR imaging problem. Our goals for the continued effort are to: 1. Develop and extend a complex, recursive-in-time, time- frequency parameter estimator based on the recursive prediction error method (RPEM) using the underlying Gauss- Newton algorithms. 2. Apply the complex RPEM algorithm to synthesized ISAR data using the above simulator. 3. Compare the performance of the proposed algorithm to standard time-frequency estimators applied to the same data sets.

  18. Improved dichotomous search frequency offset estimator for burst-mode continuous phase modulation

    NASA Astrophysics Data System (ADS)

    Zhai, Wen-Chao; Li, Zan; Si, Jiang-Bo; Bai, Jun

    2015-11-01

    A data-aided technique for carrier frequency offset estimation with continuous phase modulation (CPM) in burst-mode transmission is presented. The proposed technique first exploits a special pilot sequence, or training sequence, to form a sinusoidal waveform. Then, an improved dichotomous search frequency offset estimator is introduced to determine the frequency offset using the sinusoid. Theoretical analysis and simulation results indicate that our estimator is noteworthy in the following aspects. First, the estimator can operate independently of timing recovery. Second, it has relatively low outlier, i.e., the minimum signal-to-noise ratio (SNR) required to guarantee estimation accuracy. Finally, the most important property is that our estimator is complexity-reduced compared to the existing dichotomous search methods: it eliminates the need for fast Fourier transform (FFT) and modulation removal, and exhibits faster convergence rate without accuracy degradation. Project supported by the National Natural Science Foundation of China (Grant No. 61301179), the Doctorial Programs Foundation of the Ministry of Education, China (Grant No. 20110203110011), and the Programme of Introducing Talents of Discipline to Universities, China (Grant No. B08038).

  19. Estimating uncertainty and change in flood frequency for an urban Swedish catchment

    NASA Astrophysics Data System (ADS)

    Westerberg, I.; Persson, T.

    2013-12-01

    Floods are extreme events that occur rarely, which means that there are relatively few data of weather and flow conditions during flooding episodes for estimation of flood frequency, and that such estimates are necessarily uncertain. There is even less data available for estimation of changes in flood frequency as a result of changes in land use, climate or the morphometry of the watercourse. In this study we used a combination of monitoring and modelling to overcome the lack of reliable discharge data and allow us to characterise the flooding problems in the highly urbanised Riseberga Creek catchment in eastern Malmö, Sweden, as well as investigating their potential change in the future. The study is part of the GreenClimeAdapt project, in which local stakeholders and researchers work with finding and demonstrating solutions to the present flooding problems in the catchment as well as adaptation to future change. A high-resolution acoustic doppler discharge gauge was installed in the creek and a hydrologic model was set up to extend this short record for estimation of flood frequency. Discharge uncertainty was estimated based on a stage-discharge analysis and accounted for in model calibration together with uncertainties in the model parameterisation. The model was first used to study the flow variability during the 16 years with available climate input data. Then it was driven with long-term climate realisations from a statistical weather generator to estimate flood frequency for present climate and for future climate and land-use scenarios through continuous simulation. The uncertainty in the modelled flood-frequency for present climate was found to be important, and could partly be reduced in the future using longer monitoring records containing additional and higher flood episodes. The climate and land-use change scenarios are mainly useful for sensitivity analysis of different adaptation measures that can be taken to reduce the flooding problems, for which

  20. Estimation of vibration frequency of loudspeaker diaphragm by parallel phase-shifting digital holography

    NASA Astrophysics Data System (ADS)

    Kakue, T.; Endo, Y.; Shimobaba, T.; Ito, T.

    2014-11-01

    We report frequency estimation of loudspeaker diaphragm vibrating at high speed by parallel phase-shifting digital holography which is a technique of single-shot phase-shifting interferometry. This technique records multiple phaseshifted holograms required for phase-shifting interferometry by using space-division multiplexing. We constructed a parallel phase-shifting digital holography system consisting of a high-speed polarization-imaging camera. This camera has a micro-polarizer array which selects four linear polarization axes for 2 × 2 pixels. We set a loudspeaker as an object, and recorded vibration of diaphragm of the loudspeaker by the constructed system. By the constructed system, we demonstrated observation of vibration displacement of loudspeaker diaphragm. In this paper, we aim to estimate vibration frequency of the loudspeaker diaphragm by applying the experimental results to frequency analysis. Holograms consisting of 128 × 128 pixels were recorded at a frame rate of 262,500 frames per second by the camera. A sinusoidal wave was input to the loudspeaker via a phone connector. We observed displacement of the loudspeaker diaphragm vibrating by the system. We also succeeded in estimating vibration frequency of the loudspeaker diaphragm by applying frequency analysis to the experimental results.

  1. Fast nearly ML estimation of Doppler frequency in GNSS signal acquisition process.

    PubMed

    Tang, Xinhua; Falletti, Emanuela; Lo Presti, Letizia

    2013-04-29

    It is known that signal acquisition in Global Navigation Satellite System (GNSS) field provides a rough maximum-likelihood (ML) estimate based on a peak search in a two-dimensional grid. In this paper, the theoretical mathematical expression of the cross-ambiguity function (CAF) is exploited to analyze the grid and improve the accuracy of the frequency estimate. Based on the simple equation derived from this mathematical expression of the CAF, a family of novel algorithms is proposed to refine the Doppler frequency estimate with respect to that provided by a conventional acquisition method. In an ideal scenario where there is no noise and other nuisances, the frequency estimation error can be theoretically reduced to zero. On the other hand, in the presence of noise, the new algorithm almost reaches the Cramer-Rao Lower Bound (CRLB) which is derived as benchmark. For comparison, a least-square (LS) method is proposed. It is shown that the proposed solution achieves the same performance of LS, but requires a dramatically reduced computational burden. An averaging method is proposed to mitigate the influence of noise, especially when signal-to-noise ratio (SNR) is low. Finally, the influence of the grid resolution in the search space is analyzed in both time and frequency domains.

  2. Fast Nearly ML Estimation of Doppler Frequency in GNSS Signal Acquisition Process

    PubMed Central

    Tang, Xinhua; Falletti, Emanuela; Presti, Letizia Lo

    2013-01-01

    It is known that signal acquisition in Global Navigation Satellite System (GNSS) field provides a rough maximum-likelihood (ML) estimate based on a peak search in a two-dimensional grid. In this paper, the theoretical mathematical expression of the cross-ambiguity function (CAF) is exploited to analyze the grid and improve the accuracy of the frequency estimate. Based on the simple equation derived from this mathematical expression of the CAF, a family of novel algorithms is proposed to refine the Doppler frequency estimate with respect to that provided by a conventional acquisition method. In an ideal scenario where there is no noise and other nuisances, the frequency estimation error can be theoretically reduced to zero. On the other hand, in the presence of noise, the new algorithm almost reaches the Cramer-Rao Lower Bound (CRLB) which is derived as benchmark. For comparison, a least-square (LS) method is proposed. It is shown that the proposed solution achieves the same performance of LS, but requires a dramatically reduced computational burden. An averaging method is proposed to mitigate the influence of noise, especially when signal-to-noise ratio (SNR) is low. Finally, the influence of the grid resolution in the search space is analyzed in both time and frequency domains. PMID:23628761

  3. Vertical normal modes of human ears: Individual variation and frequency estimation from pinna anthropometry.

    PubMed

    Mokhtari, Parham; Takemoto, Hironori; Nishimura, Ryouichi; Kato, Hiroaki

    2016-08-01

    Beyond the first peak of head-related transfer functions or pinna-related transfer functions (PRTFs) human pinnae are known to have two normal modes with "vertical" resonance patterns, involving two or three pressure anti-nodes in cavum, cymba, and fossa. However, little is known about individual variations in these modes, and there is no established model for estimating their center-frequencies from anthropometry. Here, with geometries of 38 pinnae measured, PRTFs were calculated and vertical modes visualized by numerical simulation. Most pinnae were found to have both Cavum-Fossa and Cavum-Cymba modes, with opposite-phase anti-nodes in cavum and either fossa or cymba, respectively. Nevertheless in both modes, fossa involvement varied substantially across pinnae, dependent on scaphoid fossa depth and cymba shallowness. Linear regression models were evaluated in mode frequency estimation, with 3322 measures derived from 31 pinna landmarks. The Cavum-Fossa normal mode frequency was best estimated [correlation coefficient r = 0.89, mean absolute error (MAE) = 257 Hz or 4.4%] by the distance from canal entrance to helix rim, and cymba horizontal depth. The Cavum-Cymba normal mode frequency was best estimated (r = 0.92, MAE = 247 Hz or 3.2%) by the sagittal-plane distance from concha floor to cymba anterior wall, and cavum horizontal depth. PMID:27586714

  4. Standardized Magnitude Estimations of Frequency and Amount for Use in Rating Extensivity.

    ERIC Educational Resources Information Center

    Bass, Bernard M.; And Others

    Magnitude estimation was employed to find the numerical equivalents of 39 expressions of frequency ranging from never to always, and 44 expressions of amount ranging from none to all. The results were generalizable across three age-education-occupation levels and unaffected by whether ratings were an important or unimportant issue. Geometric means…

  5. Estimating cochlear tuning dependence on stimulus level and frequency from the delay of otoacoustic emissions.

    PubMed

    Moleti, Arturo; Sisto, Renata

    2016-08-01

    An objective technique based on the time-frequency analysis of otoacoustic emissions is proposed to get fast and stable estimates of cochlear tuning. Time-frequency analysis allows one to get stable measurements of the delay/frequency function, which is theoretically expected to be a function of cochlear tuning. Theoretical considerations and numerical solutions of a nonlinear cochlear model suggest that the average phase-gradient delay of the otoacoustic emission single-reflection components, weighted, for each frequency, by the amplitude of the corresponding wavelet coefficients, approximately scales as the square root of the cochlear quality factor. The application of the method to human stimulus-frequency and transient-evoked otoacoustic emissions shows that tuning decreases approximately by a factor of 2, as the stimulus level increases by 30 dB in a moderate stimulus level range. The results also show a steady increase of tuning with increasing frequency, by a factor of 2 between 1 and 5 kHz. This last result is model-dependent, because it relies on the assumption that cochlear scale-invariance breaking is only due to the frequency dependence of tuning. The application of the method to the reflection component of distortion product otoacoustic emissions, separated using time-frequency filtering, is complicated by the necessity of effectively canceling the distortion component.

  6. Estimating cochlear tuning dependence on stimulus level and frequency from the delay of otoacoustic emissions.

    PubMed

    Moleti, Arturo; Sisto, Renata

    2016-08-01

    An objective technique based on the time-frequency analysis of otoacoustic emissions is proposed to get fast and stable estimates of cochlear tuning. Time-frequency analysis allows one to get stable measurements of the delay/frequency function, which is theoretically expected to be a function of cochlear tuning. Theoretical considerations and numerical solutions of a nonlinear cochlear model suggest that the average phase-gradient delay of the otoacoustic emission single-reflection components, weighted, for each frequency, by the amplitude of the corresponding wavelet coefficients, approximately scales as the square root of the cochlear quality factor. The application of the method to human stimulus-frequency and transient-evoked otoacoustic emissions shows that tuning decreases approximately by a factor of 2, as the stimulus level increases by 30 dB in a moderate stimulus level range. The results also show a steady increase of tuning with increasing frequency, by a factor of 2 between 1 and 5 kHz. This last result is model-dependent, because it relies on the assumption that cochlear scale-invariance breaking is only due to the frequency dependence of tuning. The application of the method to the reflection component of distortion product otoacoustic emissions, separated using time-frequency filtering, is complicated by the necessity of effectively canceling the distortion component. PMID:27586727

  7. High-frequency signal and noise estimates of CSR GRACE RL04

    NASA Astrophysics Data System (ADS)

    Bonin, Jennifer A.; Bettadpur, Srinivas; Tapley, Byron D.

    2012-12-01

    A sliding window technique is used to create daily-sampled Gravity Recovery and Climate Experiment (GRACE) solutions with the same background processing as the official CSR RL04 monthly series. By estimating over shorter time spans, more frequent solutions are made using uncorrelated data, allowing for higher frequency resolution in addition to daily sampling. Using these data sets, high-frequency GRACE errors are computed using two different techniques: assuming the GRACE high-frequency signal in a quiet area of the ocean is the true error, and computing the variance of differences between multiple high-frequency GRACE series from different centers. While the signal-to-noise ratios prove to be sufficiently high for confidence at annual and lower frequencies, at frequencies above 3 cycles/year the signal-to-noise ratios in the large hydrological basins looked at here are near 1.0. Comparisons with the GLDAS hydrological model and high frequency GRACE series developed at other centers confirm CSR GRACE RL04's poor ability to accurately and reliably measure hydrological signal above 3-9 cycles/year, due to the low power of the large-scale hydrological signal typical at those frequencies compared to the GRACE errors.

  8. Parameters estimation of sinusoidal frequency modulation signal with application in synthetic aperture radar imaging

    NASA Astrophysics Data System (ADS)

    Wang, Yong; Wang, Zhaofa; Zhao, Bin; Xu, Liang

    2016-04-01

    A method for estimating the parameters of the sinusoidal frequency modulation (SFM) signal is presented in this paper. Based on the modified discrete sinusoid frequency modulation transform (DSFMT), the SFM signal can be transformed into the DSFMT domain where it is energy-concentrated and then the parameters can be estimated by the global maximum. To search for the location of the global maximum with less computational load, particle swarm optimization is used in this paper. Then the algorithm is used in the synthetic aperture radar imaging with high frequency vibration of the platform, and the focus performance can be improved significantly. Simulation results demonstrate the effectiveness of the method proposed in this paper.

  9. Estimation of body resonances from a time-frequency analysis of violin vibrato

    NASA Astrophysics Data System (ADS)

    Mellody, Maureen; Wakefield, Gregory H.

    1999-11-01

    We present a signal-based technique for evaluating a pole-zero representation of the resonant response of a violin instrument. This technique combines time-frequency signal analysis with system identification techniques to determine the pole-zero function that would account for amplitude modulation observed on the partials of violin notes performed with vibrato. Violin vibrato signals are analyzed with the modal distribution to obtain values of instantaneous amplitude and frequency for each partial. From these, input and output functions are synthesized and used to estimate the violin body's impulse response using an infinite impulse response (IIR) system identification procedure. In each case, the input and output functions share the same instantaneous frequency of the measured partial. However, the rapid amplitude variations are present only on the output function. We report on the location and spacing of these estimated resonances and discuss their relationship to those obtained from theoretical predictions and other measurement procedures.

  10. Estimation and veering analysis of nonlinear resonant frequencies of cracked plates

    NASA Astrophysics Data System (ADS)

    Saito, A.; Castanier, M. P.; Pierre, C.

    2009-10-01

    In this paper, veering phenomena in the nonlinear vibration frequencies of a cantilevered cracked plate are investigated, and an efficient method for estimating these frequencies is proposed. Of particular interest is the vibration response in parameter regions where the natural frequency loci show veerings. For a representative finite element model, it is shown that the veerings due to crack length variation involve the switching of mode shapes and modal interactions. The nonlinearity caused by the crack closing effect is then introduced, and its effect on the vibration response near the veerings is discussed. The nonlinear forced response analysis is carried out using a hybrid frequency/time domain method, which is based on the method of harmonic balance. The nonlinear vibration response near loci veerings and crossings due to the variation of crack length is investigated in detail. Finally, a novel method for estimating the nonlinear resonant frequency is introduced by generalizing the concept of bilinear frequency approximation, and the method is validated with the results of nonlinear forced response analysis for several veering regions.

  11. Estimating the Radius of the Convective Core of Main-sequence Stars from Observed Oscillation Frequencies

    NASA Astrophysics Data System (ADS)

    Yang, Wuming

    2016-10-01

    The determination of the size of the convective core of main-sequence stars is usually dependent on the construction of models of stars. Here we introduce a method to estimate the radius of the convective core of main-sequence stars with masses between about 1.1 and 1.5 M ⊙ from observed frequencies of low-degree p-modes. A formula is proposed to achieve the estimation. The values of the radius of the convective core of four known stars are successfully estimated by the formula. The radius of the convective core of KIC 9812850 estimated by the formula is 0.140 ± 0.028 R ⊙. In order to confirm this prediction, a grid of evolutionary models was computed. The value of the convective-core radius of the best-fit model of KIC 9812850 is 0.149 R ⊙, which is in good agreement with that estimated by the formula from observed frequencies. The formula aids in understanding the interior structure of stars directly from observed frequencies. The understanding is not dependent on the construction of models.

  12. Motion estimation in the frequency domain using fuzzy c-planes clustering.

    PubMed

    Erdem, C E; Karabulut, G Z; Yanmaz, E; Anarim, E

    2001-01-01

    A recent work explicitly models the discontinuous motion estimation problem in the frequency domain where the motion parameters are estimated using a harmonic retrieval approach. The vertical and horizontal components of the motion are independently estimated from the locations of the peaks of respective periodogram analyses and they are paired to obtain the motion vectors using a procedure proposed. In this paper, we present a more efficient method that replaces the motion component pairing task and hence eliminates the problems of the pairing method described. The method described in this paper uses the fuzzy c-planes (FCP) clustering approach to fit planes to three-dimensional (3-D) frequency domain data obtained from the peaks of the periodograms. Experimental results are provided to demonstrate the effectiveness of the proposed method.

  13. Estimating the magnitude and frequency of floods in rural basins of North Carolina

    USGS Publications Warehouse

    Pope, Benjamin F.; Tasker, Gary D.; Robbins, Jeanne C.

    2001-01-01

    A statewide study was conducted to develop two methods for estimating the magnitude and frequency of floods in rural ungaged basins in North Carolina. Flood-frequency estimates for gaged sites in North Carolina were computed by fitting the annual peak flows for each site to a log-Pearson Type III distribution. As part of the computation of flood-frequency estimates for gaged sites, new values for generalized skew coefficients were developed. Basin characteristics for these gaged sites were computed by using a geographic information system and automated computer algorithms. Flood-frequency estimates and basin characteristics for 317 gaged sites were combined to form the data base that was used for this analysis. Regional regression analysis, using generalized least-squares regression, was used to develop a set of predictive equations that can be used to estimate the 2-, 5-, 10-, 25-, 50-, 100-, 200-, and 500-year recurrence interval discharges for rural ungaged basins in the Blue Ridge-Piedmont, Coastal Plain, and Sand Hills hydrologic areas. The predictive equations are all functions of drainage area. Average errors of prediction for these regression equations range from 36 to 65 percent. A region-of-influence method also was developed that interactively estimates recurrence interval discharges for rural ungaged basins in the Blue Ridge-Piedmont and Coastal Plain hydrologic areas of North Carolina. Regression techniques are used to develop a unique relation between flood discharge and basin characteristics for a subset of gaged sites with similar basin characteristics. This, then, can be used to estimate flood discharges at ungaged sites. Because the computations required for this method are somewhat complex, a computer application was developed that performs the computations and compares the predictive errors for this method. The computer application also includes the option of using the regression equations to compute estimated flood discharges and errors of

  14. The discrete Laplace exponential family and estimation of Y-STR haplotype frequencies.

    PubMed

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

    2013-07-21

    Estimating haplotype frequencies is important in e.g. forensic genetics, where the frequencies are needed to calculate the likelihood ratio for the evidential weight of a DNA profile found at a crime scene. Estimation is naturally based on a population model, motivating the investigation of the Fisher-Wright model of evolution for haploid lineage DNA markers. An exponential family (a class of probability distributions that is well understood in probability theory such that inference is easily made by using existing software) called the 'discrete Laplace distribution' is described. We illustrate how well the discrete Laplace distribution approximates a more complicated distribution that arises by investigating the well-known population genetic Fisher-Wright model of evolution by a single-step mutation process. It was shown how the discrete Laplace distribution can be used to estimate haplotype frequencies for haploid lineage DNA markers (such as Y-chromosomal short tandem repeats), which in turn can be used to assess the evidential weight of a DNA profile found at a crime scene. This was done by making inference in a mixture of multivariate, marginally independent, discrete Laplace distributions using the EM algorithm to estimate the probabilities of membership of a set of unobserved subpopulations. The discrete Laplace distribution can be used to estimate haplotype frequencies with lower prediction error than other existing estimators. Furthermore, the calculations could be performed on a normal computer. This method was implemented in the freely available open source software R that is supported on Linux, MacOS and MS Windows.

  15. Identification and characterization of variant alleles at CODIS STR loci.

    PubMed

    Allor, Catherine; Einum, David D; Scarpetta, Marco

    2005-09-01

    Short tandem repeat (STR) profiles from 32,671 individuals generated by the ABI Profiler Plus and Cofiler systems were screened for variant alleles not represented within manufacturer-provided allelic ladders. A total of 85 distinct variants were identified at 12 of the 13 CODIS loci, most of which involve a truncated tetranucleotide repeat unit. Twelve novel alleles, identified at D3S1358, FGA, D18S51, D5S818, D7S820 and TPOX, were confirmed by nucleotide sequence analysis and include both insertions and deletions involving the repeat units themselves as well as DNA flanking the repeat regions. Population genetic data were collected for all variants and frequencies range from 0.0003 (many single observations) to 0.0042 (D7S820 '10.3' in North American Hispanics). In total, the variant alleles identified in this study are carried by 1.6% of the estimated 1 million individuals tested annually in the U.S. for the purposes of parentage resolution. A paternity case involving a recombination event of paternal origin is presented and demonstrates how variant alleles can significantly strengthen the genetic evidence in troublesome cases. In such instances, increased costs and turnaround time associated with additional testing may be eliminated.

  16. Multiple linear regression to estimate time-frequency electrophysiological responses in single trials.

    PubMed

    Hu, L; Zhang, Z G; Mouraux, A; Iannetti, G D

    2015-05-01

    Transient sensory, motor or cognitive event elicit not only phase-locked event-related potentials (ERPs) in the ongoing electroencephalogram (EEG), but also induce non-phase-locked modulations of ongoing EEG oscillations. These modulations can be detected when single-trial waveforms are analysed in the time-frequency domain, and consist in stimulus-induced decreases (event-related desynchronization, ERD) or increases (event-related synchronization, ERS) of synchrony in the activity of the underlying neuronal populations. ERD and ERS reflect changes in the parameters that control oscillations in neuronal networks and, depending on the frequency at which they occur, represent neuronal mechanisms involved in cortical activation, inhibition and binding. ERD and ERS are commonly estimated by averaging the time-frequency decomposition of single trials. However, their trial-to-trial variability that can reflect physiologically-important information is lost by across-trial averaging. Here, we aim to (1) develop novel approaches to explore single-trial parameters (including latency, frequency and magnitude) of ERP/ERD/ERS; (2) disclose the relationship between estimated single-trial parameters and other experimental factors (e.g., perceived intensity). We found that (1) stimulus-elicited ERP/ERD/ERS can be correctly separated using principal component analysis (PCA) decomposition with Varimax rotation on the single-trial time-frequency distributions; (2) time-frequency multiple linear regression with dispersion term (TF-MLRd) enhances the signal-to-noise ratio of ERP/ERD/ERS in single trials, and provides an unbiased estimation of their latency, frequency, and magnitude at single-trial level; (3) these estimates can be meaningfully correlated with each other and with other experimental factors at single-trial level (e.g., perceived stimulus intensity and ERP magnitude). The methods described in this article allow exploring fully non-phase-locked stimulus-induced cortical

  17. Multiple linear regression to estimate time-frequency electrophysiological responses in single trials

    PubMed Central

    Hu, L.; Zhang, Z.G.; Mouraux, A.; Iannetti, G.D.

    2015-01-01

    Transient sensory, motor or cognitive event elicit not only phase-locked event-related potentials (ERPs) in the ongoing electroencephalogram (EEG), but also induce non-phase-locked modulations of ongoing EEG oscillations. These modulations can be detected when single-trial waveforms are analysed in the time-frequency domain, and consist in stimulus-induced decreases (event-related desynchronization, ERD) or increases (event-related synchronization, ERS) of synchrony in the activity of the underlying neuronal populations. ERD and ERS reflect changes in the parameters that control oscillations in neuronal networks and, depending on the frequency at which they occur, represent neuronal mechanisms involved in cortical activation, inhibition and binding. ERD and ERS are commonly estimated by averaging the time-frequency decomposition of single trials. However, their trial-to-trial variability that can reflect physiologically-important information is lost by across-trial averaging. Here, we aim to (1) develop novel approaches to explore single-trial parameters (including latency, frequency and magnitude) of ERP/ERD/ERS; (2) disclose the relationship between estimated single-trial parameters and other experimental factors (e.g., perceived intensity). We found that (1) stimulus-elicited ERP/ERD/ERS can be correctly separated using principal component analysis (PCA) decomposition with Varimax rotation on the single-trial time-frequency distributions; (2) time-frequency multiple linear regression with dispersion term (TF-MLRd) enhances the signal-to-noise ratio of ERP/ERD/ERS in single trials, and provides an unbiased estimation of their latency, frequency, and magnitude at single-trial level; (3) these estimates can be meaningfully correlated with each other and with other experimental factors at single-trial level (e.g., perceived stimulus intensity and ERP magnitude). The methods described in this article allow exploring fully non-phase-locked stimulus-induced cortical

  18. Multiple linear regression to estimate time-frequency electrophysiological responses in single trials.

    PubMed

    Hu, L; Zhang, Z G; Mouraux, A; Iannetti, G D

    2015-05-01

    Transient sensory, motor or cognitive event elicit not only phase-locked event-related potentials (ERPs) in the ongoing electroencephalogram (EEG), but also induce non-phase-locked modulations of ongoing EEG oscillations. These modulations can be detected when single-trial waveforms are analysed in the time-frequency domain, and consist in stimulus-induced decreases (event-related desynchronization, ERD) or increases (event-related synchronization, ERS) of synchrony in the activity of the underlying neuronal populations. ERD and ERS reflect changes in the parameters that control oscillations in neuronal networks and, depending on the frequency at which they occur, represent neuronal mechanisms involved in cortical activation, inhibition and binding. ERD and ERS are commonly estimated by averaging the time-frequency decomposition of single trials. However, their trial-to-trial variability that can reflect physiologically-important information is lost by across-trial averaging. Here, we aim to (1) develop novel approaches to explore single-trial parameters (including latency, frequency and magnitude) of ERP/ERD/ERS; (2) disclose the relationship between estimated single-trial parameters and other experimental factors (e.g., perceived intensity). We found that (1) stimulus-elicited ERP/ERD/ERS can be correctly separated using principal component analysis (PCA) decomposition with Varimax rotation on the single-trial time-frequency distributions; (2) time-frequency multiple linear regression with dispersion term (TF-MLRd) enhances the signal-to-noise ratio of ERP/ERD/ERS in single trials, and provides an unbiased estimation of their latency, frequency, and magnitude at single-trial level; (3) these estimates can be meaningfully correlated with each other and with other experimental factors at single-trial level (e.g., perceived stimulus intensity and ERP magnitude). The methods described in this article allow exploring fully non-phase-locked stimulus-induced cortical

  19. Estimation of peak-discharge frequency of urban streams in Jefferson County, Kentucky

    USGS Publications Warehouse

    Martin, Gary R.; Ruhl, Kevin J.; Moore, Brian L.; Rose, Martin F.

    1997-01-01

    An investigation of flood-hydrograph characteristics for streams in urban Jefferson County, Kentucky, was made to obtain hydrologic information needed for waterresources management. Equations for estimating peak-discharge frequencies for ungaged streams in the county were developed by combining (1) long-term annual peakdischarge data and rainfall-runoff data collected from 1991 to 1995 in 13 urban basins and (2) long-term annual peak-discharge data in four rural basins located in hydrologically similar areas of neighboring counties. The basins ranged in size from 1.36 to 64.0 square miles. The U.S. Geological Survey Rainfall- Runoff Model (RRM) was calibrated for each of the urban basins. The calibrated models were used with long-term, historical rainfall and pan-evaporation data to simulate 79 years of annual peak-discharge data. Peak-discharge frequencies were estimated by fitting the logarithms of the annual peak discharges to a Pearson-Type III frequency distribution. The simulated peak-discharge frequencies were adjusted for improved reliability by application of bias-correction factors derived from peakdischarge frequencies based on local, observed annual peak discharges. The three-parameter and the preferred seven-parameter nationwide urban-peak-discharge regression equations previously developed by USGS investigators provided biased (high) estimates for the urban basins studied. Generalized-least-square regression procedures were used to relate peakdischarge frequency to selected basin characteristics. Regression equations were developed to estimate peak-discharge frequency by adjusting peak-dischargefrequency estimates made by use of the threeparameter nationwide urban regression equations. The regression equations are presented in equivalent forms as functions of contributing drainage area, main-channel slope, and basin development factor, which is an index for measuring the efficiency of the basin drainage system. Estimates of peak discharges for streams

  20. Data on IL-6 c.-174 G>C genotype and allele frequencies in patients with coronary heart disease in dependence of cardiovascular outcome.

    PubMed

    Reichert, Stefan; Schlitt, Axel; Benten, Ann-Christin; Hofmann, Britt; Schaller, Hans-Günter; Schulz, Susanne

    2016-09-01

    In this data article we present data on the distribution of alleles and genotypes of the interleukin (IL)-6 c.-174 G>C polymorphism (rs 1800795) in patients with coronary heart disease (CHD) in dependence of the incidence of new cardiovascular events (combined endpoint: myocardial infarction, stroke/TIA, cardiac death, death according to stroke) within three years follow-up. Moreover, we investigated putative associations between individual expression of IL-6 genotypes and IL-6 serum level. This investigation is a subanalysis of the article entitled "The Interleukin 6 c.-174 CC genotype is a predictor for new cardiovascular events in patients with coronary heart disease within three years follow-up" (ClinicalTrials.gov identifier: NCT01045070) (Reichert et al., 2016) [1]. PMID:27570807

  1. Statistical Properties of Real-Time Amplitude Estimate of Harmonics Affected by Frequency Instability

    NASA Astrophysics Data System (ADS)

    Bellan, Diego; Pignari, Sergio A.

    2016-07-01

    This work deals with the statistical characterization of real-time digital measurement of the amplitude of harmonics affected by frequency instability. In fact, in modern power systems both the presence of harmonics and frequency instability are well-known and widespread phenomena mainly due to nonlinear loads and distributed generation, respectively. As a result, real-time monitoring of voltage/current frequency spectra is of paramount importance as far as power quality issues are addressed. Within this framework, a key point is that in many cases real-time continuous monitoring prevents the application of sophisticated algorithms to extract all the information from the digitized waveforms because of the required computational burden. In those cases only simple evaluations such as peak search of discrete Fourier transform are implemented. It is well known, however, that a slight change in waveform frequency results in lack of sampling synchronism and uncertainty in amplitude estimate. Of course the impact of this phenomenon increases with the order of the harmonic to be measured. In this paper an approximate analytical approach is proposed in order to describe the statistical properties of the measured magnitude of harmonics affected by frequency instability. By providing a simplified description of the frequency behavior of the windows used against spectral leakage, analytical expressions for mean value, variance, cumulative distribution function, and probability density function of the measured harmonics magnitude are derived in closed form as functions of waveform frequency treated as a random variable.

  2. Estimates of Flow Duration, Mean Flow, and Peak-Discharge Frequency Values for Kansas Stream Locations

    USGS Publications Warehouse

    Perry, Charles A.; Wolock, David M.; Artman, Joshua C.

    2004-01-01

    Streamflow statistics of flow duration and peak-discharge frequency were estimated for 4,771 individual locations on streams listed on the 1999 Kansas Surface Water Register. These statistics included the flow-duration values of 90, 75, 50, 25, and 10 percent, as well as the mean flow value. Peak-discharge frequency values were estimated for the 2-, 5-, 10-, 25-, 50-, and 100-year floods. Least-squares multiple regression techniques were used, along with Tobit analyses, to develop equations for estimating flow-duration values of 90, 75, 50, 25, and 10 percent and the mean flow for uncontrolled flow stream locations. The contributing-drainage areas of 149 U.S. Geological Survey streamflow-gaging stations in Kansas and parts of surrounding States that had flow uncontrolled by Federal reservoirs and used in the regression analyses ranged from 2.06 to 12,004 square miles. Logarithmic transformations of climatic and basin data were performed to yield the best linear relation for developing equations to compute flow durations and mean flow. In the regression analyses, the significant climatic and basin characteristics, in order of importance, were contributing-drainage area, mean annual precipitation, mean basin permeability, and mean basin slope. The analyses yielded a model standard error of prediction range of 0.43 logarithmic units for the 90-percent duration analysis to 0.15 logarithmic units for the 10-percent duration analysis. The model standard error of prediction was 0.14 logarithmic units for the mean flow. Regression equations used to estimate peak-discharge frequency values were obtained from a previous report, and estimates for the 2-, 5-, 10-, 25-, 50-, and 100-year floods were determined for this report. The regression equations and an interpolation procedure were used to compute flow durations, mean flow, and estimates of peak-discharge frequency for locations along uncontrolled flow streams on the 1999 Kansas Surface Water Register. Flow durations, mean

  3. Q estimation from reflection seismic data for hydrocarbon detection using a modified frequency shift method

    NASA Astrophysics Data System (ADS)

    Li, Fangyu; Zhou, Huailai; Jiang, Nan; Bi, Jianxia; Marfurt, Kurt J.

    2015-08-01

    As a powerfully diagnostic tool for structural interpretation, reservoir characterization, and hydrocarbon detection, quality factor Q provides useful information in seismic processing and interpretation. Popular methods, like the spectral ratio (SR) method, central frequency shift (CFS) method and peak frequency shift (PFS) method, have their respective limitations in dealing with field seismic data. The lack of a reliable method for estimating Q from reflection seismic data is an issue when utilizing the Q value for hydrocarbon detection. In this article, we derive an approximate equation and propose a dominant and central frequency shift (DCFS) method by combining the quality factor Q, the travel time, and dominant and central frequencies of two successive seismic signals along the wave propagating direction. Based on multi-layered analysis, we then proposed a method to obtain continuous volumetric Q estimation results. A test using synthetic data and statistical experiments showed the proposed method can achieve higher accuracy and robustness compared with existing methods. Application of field data also shows its potential and effectiveness to estimate seismic attenuation.

  4. Estimation of the auto frequency response function at unexcited points using dummy masses

    NASA Astrophysics Data System (ADS)

    Hosoya, Naoki; Yaginuma, Shinji; Onodera, Hiroshi; Yoshimura, Takuya

    2015-02-01

    If structures with complex shapes have space limitations, vibration tests using an exciter or impact hammer for the excitation are difficult. Although measuring the auto frequency response function at an unexcited point may not be practical via a vibration test, it can be obtained by assuming that the inertia acting on a dummy mass is an external force on the target structure upon exciting a different excitation point. We propose a method to estimate the auto frequency response functions at unexcited points by attaching a small mass (dummy mass), which is comparable to the accelerometer mass. The validity of the proposed method is demonstrated by comparing the auto frequency response functions estimated at unexcited points in a beam structure to those obtained from numerical simulations. We also consider random measurement errors by finite element analysis and vibration tests, but not bias errors. Additionally, the applicability of the proposed method is demonstrated by applying it to estimate the auto frequency response function of the lower arm in a car suspension.

  5. Rapid estimation of earthquake magnitude from the arrival time of the peak high‐frequency amplitude

    USGS Publications Warehouse

    Noda, Shunta; Yamamoto, Shunroku; Ellsworth, William L.

    2016-01-01

    We propose a simple approach to measure earthquake magnitude M using the time difference (Top) between the body‐wave onset and the arrival time of the peak high‐frequency amplitude in an accelerogram. Measured in this manner, we find that Mw is proportional to 2logTop for earthquakes 5≤Mw≤7, which is the theoretical proportionality if Top is proportional to source dimension and stress drop is scale invariant. Using high‐frequency (>2  Hz) data, the root mean square (rms) residual between Mw and MTop(M estimated from Top) is approximately 0.5 magnitude units. The rms residuals of the high‐frequency data in passbands between 2 and 16 Hz are uniformly smaller than those obtained from the lower‐frequency data. Top depends weakly on epicentral distance, and this dependence can be ignored for distances <200  km. Retrospective application of this algorithm to the 2011 Tohoku earthquake produces a final magnitude estimate of M 9.0 at 120 s after the origin time. We conclude that Top of high‐frequency (>2  Hz) accelerograms has value in the context of earthquake early warning for extremely large events.

  6. Estimation of flood-frequency characteristics of small urban streams in North Carolina

    USGS Publications Warehouse

    Robbins, J.C.; Pope, B.F.

    1996-01-01

    A statewide study was conducted to develop methods for estimating the magnitude and frequency of floods of small urban streams in North Carolina. This type of information is critical in the design of bridges, culverts and water-control structures, establishment of flood-insurance rates and flood-plain regulation, and for other uses by urban planners and engineers. Concurrent records of rainfall and runoff data collected in small urban basins were used to calibrate rainfall-runoff models. Historic rain- fall records were used with the calibrated models to synthesize a long- term record of annual peak discharges. The synthesized record of annual peak discharges were used in a statistical analysis to determine flood- frequency distributions. These frequency distributions were used with distributions from previous investigations to develop a database for 32 small urban basins in the Blue Ridge-Piedmont, Sand Hills, and Coastal Plain hydrologic areas. The study basins ranged in size from 0.04 to 41.0 square miles. Data describing the size and shape of the basin, level of urban development, and climate and rural flood charac- teristics also were included in the database. Estimation equations were developed by relating flood-frequency char- acteristics to basin characteristics in a generalized least-squares regression analysis. The most significant basin characteristics are drainage area, impervious area, and rural flood discharge. The model error and prediction errors for the estimating equations were less than those for the national flood-frequency equations previously reported. Resulting equations, which have prediction errors generally less than 40 percent, can be used to estimate flood-peak discharges for 2-, 5-, 10-, 25-, 50-, and 100-year recurrence intervals for small urban basins across the State assuming negligible, sustainable, in- channel detention or basin storage.

  7. SAR imagery of moving targets: application of time-frequency distributions for estimating motion parameters

    NASA Astrophysics Data System (ADS)

    Haimovich, Alexander M.; Peckham, C. D.; Teti, Joseph G., Jr.

    1994-06-01

    It is well known that targets moving along track within a Synthetic Aperture Radar (SAR) field of view are imaged as defocused objects. The SAR stripmap mode is tuned to stationary ground targets and the mismatch between the SAR processing parameters and the target motion parameters causes the energy to spill over to adjacent image pixels, thus not only hindering target feature extraction, but also reducing the probability of detection. The problem can be remedied by generating the image using a filter matched to the actual target motion parameters, effectively focusing the SAR image on the target. For a fixed rate of motion the target velocity can be estimated from the slope of the Doppler frequency characteristic. The processing is carried out on the range compressed data but before azimuth compression. The problem is similar to the classical problem of estimating the instantaneous frequency of a linear FM signal (chirp). This paper investigates the application of three different time-frequency analysis techniques to estimate the instantaneous Doppler frequency of range compressed SAR data. In particular, we compare the Wigner-Ville distribution, the Gabor expansion and the Short-Time Fourier transform with respect to their performance in noisy SAR data. Criteria are suggested to quantify the performance of each method in the joint time- frequency domain. It is shown that these methods exhibit sharp signal-to-noise threshold effects, i.e., a certain SNR below which the accuracy of the velocity estimation deteriorates rapidly. It is also shown that the methods differ with respect to their representation of the SAR data.

  8. RHD allele distribution in Africans of Mali

    PubMed Central

    Wagner, Franz F; Moulds, Joann M; Tounkara, Anatole; Kouriba, Bourema; Flegel, Willy A

    2003-01-01

    Background Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking. Results We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa) by evaluating 116 haplotypes. Only 69% could be attributed to standard RHD (55%) or the RHD deletion (14%). The aberrant RHD allele DAU-0 was predicted for 19%, RHDΨ for 7% and Ccdes for 4% of all haplotypes. DAU-3 and the new RHD allele RHD(L207F), dubbed DMA, were found in one haplotype each. A PCR-RFLP for the detection of the hybrid Rhesus box diagnostic for the RHD deletion in Europeans was false positive in 9 individuals, including all carriers of RHDΨ . Including two silent mutations and the RHD deletion, a total of 9 alleles could be differentiated. Conclusion Besides standard RHD and the RHD deletion, DAU-0, RHDΨ and Ccdes are major alleles in Mali. Our survey proved that the most frequent alleles of West Africans have been recognized allowing to devise reliable genotyping and phenotyping strategies. PMID:14505497

  9. Estimating flood-frequency curves with scarce data: a physically-based analytic approach

    NASA Astrophysics Data System (ADS)

    Basso, Stefano; Schirmer, Mario; Botter, Gianluca

    2016-04-01

    Predicting magnitude and frequency of floods is a key issue for hazard assessment and mitigation. While observations and statistical methods provide good estimates when long data series are available, their performances deteriorate with limited data. Moreover, the outcome of varying hydroclimatic drivers can hardly be evaluated by these methods. Physically-based approaches embodying mechanics of streamflow generation provide a valuable alternative that may improve purely statistical estimates and cope with human-induced alteration of climate and landscape. In this work, a novel analytic approach is proposed to derive seasonal flood-frequency curves, and to estimate the recurrence intervals of seasonal maxima. The method builds on a stochastic description of daily streamflows, arising from rainfall and soil moisture dynamics in the catchment. The limited number of parameters involved in the formulation embody climate and landscape attributes of the contributing catchment, and can be specified based on daily rainfall and streamflow data. The application to two case studies suggests the model ability to provide reliable estimates of seasonal flood-frequency curves in different climatic settings, and to mimic shapes of flood-frequency curves emerging in persistent and erratic flow regimes. The method is especially valuable when only short data series are available (e.g. newly or temporarily gauged catchments, modified climatic or landscape features). Indeed, estimates provided by the model for high flow events characterized by recurrence times greater than the available sample size do not deteriorate significantly, as compared to performance of purely statistical methods. The proposed physically-based analytic approach represent a first step toward a probabilistic characterization of extremes based on climate and landscape attributes, which may be especially valuable to assess flooding hazard in data scarce regions and support the development of reliable mitigation

  10. Non-identical smoothing operators for estimating time-frequency interdependence in electrophysiological recordings

    NASA Astrophysics Data System (ADS)

    Mehrkanoon, Saeid; Breakspear, Michael; Daffertshofer, Andreas; Boonstra, Tjeerd W.

    2013-12-01

    Synchronization of neural activity from distant parts of the brain is crucial for the coordination of cognitive activities. Because neural synchronization varies both in time and frequency, time-frequency (T-F) coherence is commonly employed to assess interdependences in electrophysiological recordings. T-F coherence entails smoothing the cross and power spectra to ensure statistical consistency of the estimate, which reduces its T-F resolution. This trade-off has been described in detail when the cross and power spectra are smoothed using identical smoothing operators, which may yield spurious coherent frequencies. In this article, we examine the use of non-identical smoothing operators for the estimation of T-F interdependence, i.e., phase synchronization is characterized by phase locking between signals captured by the cross spectrum and we may hence improve the trade-off by selectively smoothing the auto spectra. We first show that the frequency marginal density of the present estimate is bound within [0,1] when using non-identical smoothing operators. An analytic calculation of the bias and variance of present estimators is performed and compared with the bias and variance of standard T-F coherence using Monte Carlo simulations. We then test the use of non-identical smoothing operators on simulated data, whose T-F properties are known through construction. Finally, we analyze empirical data from eyes-closed surface electroencephalography recorded in human subjects to investigate alpha-band synchronization. These analyses show that selectively smoothing the auto spectra reduces the bias of the estimator and may improve the detection of T-F interdependence in electrophysiological data at high temporal resolution.

  11. An Improved Performance Frequency Estimation Algorithm for Passive Wireless SAW Resonant Sensors

    PubMed Central

    Liu, Boquan; Zhang, Chenrui; Ji, Xiaojun; Chen, Jing; Han, Tao

    2014-01-01

    Passive wireless surface acoustic wave (SAW) resonant sensors are suitable for applications in harsh environments. The traditional SAW resonant sensor system requires, however, Fourier transformation (FT) which has a resolution restriction and decreases the accuracy. In order to improve the accuracy and resolution of the measurement, the singular value decomposition (SVD)-based frequency estimation algorithm is applied for wireless SAW resonant sensor responses, which is a combination of a single tone undamped and damped sinusoid signal with the same frequency. Compared with the FT algorithm, the accuracy and the resolution of the method used in the self-developed wireless SAW resonant sensor system are validated. PMID:25429410

  12. The assessment of frequency estimates of Hae III-generated VNTR profiles in various reference databases.

    PubMed

    Budowle, B; Monson, K L; Giusti, A M; Brown, B L

    1994-03-01

    The likelihood of occurrence of 1964 Hae III-generated target DNA profiles was estimated using fixed bin frequencies from various regional and ethnic databases and the multiplication rule. The databases generally were from the following major categories: Black, Caucasian, Hispanic, Oriental, and American Indian. It was found that subdivision, either by ethnic group or by U.S. geographic region, within a major population group did not substantially affect forensic estimates of the likelihood of occurrence of a DNA profile. As expected, the greatest variation in estimates for within-group estimates was among American Indian databases. Because the greatest variation in statistical estimates occurs across-major population groups, in most cases, there will be no unfair bias applying general population database estimates. Therefore, based on empirical data, there is no demonstrable need for using alternate approaches, such as the ceiling approach, to derive statistical estimates. The current practice of using general population databases and the multiplication rule provides valid estimates of the likelihood of occurrence of a DNA profile. PMID:7910844

  13. Possibility of quantitative estimation of blood cell forms by the spatial-frequency spectrum analysis

    NASA Astrophysics Data System (ADS)

    Spiridonov, Igor N.; Safonova, Larisa P.; Samorodov, Andrey V.

    2000-05-01

    At present in hematology there are no quantitative estimates of such important for the cell classification parameters: cell form and nuclear form. Due to the absence of the correlation between morphological parameters and parameters measured by hemoanalyzers, both flow cytometers and computer recognition systems, do not provide the completeness of the clinical blood analysis. Analysis of the spatial-frequency spectra of blood samples (smears and liquid probes) permit the estimate the forms quantitatively. On the results of theoretical and experimental researches carried out an algorithm of the form quantitative estimation by means of SFS parameters has been created. The criteria of the quality of these estimates have been proposed. A test bench based on the coherent optical and digital processors. The received results could be applied for the automated classification of ether normal or pathological blood cells in the standard blood smears.

  14. Combined Radiometer-Radar Microphysical Profile Estimations with Emphasis on High Frequency Brightness Temperature Observations

    NASA Technical Reports Server (NTRS)

    Jackson, Gail Skofronick; Wang, James R.; Heymsfield, Gerald M.; Hood, Robbie; Manning, Will; Meneghini, Robert; Weinman, James A.; Hildebrand, Peter (Technical Monitor)

    2001-01-01

    Information about the vertical microphysical cloud structure is useful in many modeling and predictive practices. Radiometers and radars are used to observe hydrometeor properties. This paper describes an iterative retrieval algorithm that combines the use of airborne active and wideband (10 to 340 GHz) passive observations to estimate the vertical content and particle size distributions of liquid and frozen hydrometeors. The physically-based retrieval algorithm relies on the high frequencies (greater than 89 GHz) to provide details on the frozen hydrometeors. Neglecting the high frequencies yielded acceptable estimates of the liquid profiles, but the ice profiles were poorly retrieved. Airborne radar and radiometer observations from the third Convection and Moisture EXperiment (CAMEX-3) were used in the retrieval algorithm as constraints. Nadir profiles were estimated for a minute each of flight time (approximately 12.5 km along track) from an anvil, convection, and quasi- stratiform rain. The complex structure of the frozen hydrometeors required the most iterations for convergence for the anvil cloud type. The wideband observations were found to more than double the estimated frozen hydrometeor content as compared to retrievals using only 90-GHz and below. The convective and quasi-stratiform quickly reached convergence (minimized difference between observations and calculations using the estimated profiles). A qualitative validation using coincident in situ CAMEX-3 observations shows that the retrieved particle size distributions are well corroborated with independent measurements.

  15. Efficient methods for joint estimation of multiple fundamental frequencies in music signals

    NASA Astrophysics Data System (ADS)

    Pertusa, Antonio; Iñesta, José M.

    2012-12-01

    This study presents efficient techniques for multiple fundamental frequency estimation in music signals. The proposed methodology can infer harmonic patterns from a mixture considering interactions with other sources and evaluate them in a joint estimation scheme. For this purpose, a set of fundamental frequency candidates are first selected at each frame, and several hypothetical combinations of them are generated. Combinations are independently evaluated, and the most likely is selected taking into account the intensity and spectral smoothness of its inferred patterns. The method is extended considering adjacent frames in order to smooth the detection in time, and a pitch tracking stage is finally performed to increase the temporal coherence. The proposed algorithms were evaluated in MIREX contests yielding state of the art results with a very low computational burden.

  16. Theoretical optimal modulation frequencies for scattering parameter estimation and ballistic photon filtering in diffusing media.

    PubMed

    Panigrahi, Swapnesh; Fade, Julien; Ramachandran, Hema; Alouini, Mehdi

    2016-07-11

    The efficiency of using intensity modulated light for the estimation of scattering properties of a turbid medium and for ballistic photon discrimination is theoretically quantified in this article. Using the diffusion model for modulated photon transport and considering a noisy quadrature demodulation scheme, the minimum-variance bounds on estimation of parameters of interest are analytically derived and analyzed. The existence of a variance-minimizing optimal modulation frequency is shown and its evolution with the properties of the intervening medium is derived and studied. Furthermore, a metric is defined to quantify the efficiency of ballistic photon filtering which may be sought when imaging through turbid media. The analytical derivation of this metric shows that the minimum modulation frequency required to attain significant ballistic discrimination depends only on the reduced scattering coefficient of the medium in a linear fashion for a highly scattering medium.

  17. The effect of fine-scale sampling frequency on estimates of beach litter accumulation.

    PubMed

    Ryan, Peter G; Lamprecht, Annerie; Swanepoel, Debbie; Moloney, Coleen L

    2014-11-15

    The effect of sampling frequency on estimates of the rate of litter accumulation was determined for two South African sandy beaches. After initial cleaning, all manufactured items >10mm diameter were collected in alternating bouts of daily or weekly cleanups. Daily sampling collected 2.5 (range 2.1-3.4) times more litter items than weekly samples and 1.7 (1.3-2.3) times more litter by mass. Low density items such as foamed polystyrene showed a greater differential (4-5 times more items from daily sampling), presumably due to faster turnover of lightweight litter items. Variation in weekly samples was not consistently less than daily estimates, suggesting that less frequent samples only partly integrate short-term fluctuations in litter dynamics. Researchers using beach accumulation data to infer trends in nearshore marine litter, or to assess the efficacy of litter mitigation measures, need to ensure consistency in sampling frequency. PMID:25239099

  18. Inferring the age of a fixed beneficial allele.

    PubMed

    Ormond, Louise; Foll, Matthieu; Ewing, Gregory B; Pfeifer, Susanne P; Jensen, Jeffrey D

    2016-01-01

    Estimating the age and strength of beneficial alleles is central to understanding how adaptation proceeds in response to changing environmental conditions. Several haplotype-based estimators exist for inferring the age of segregating beneficial mutations. Here, we develop an approximate Bayesian-based approach that rather estimates these parameters for fixed beneficial mutations in single populations. We integrate a range of existing diversity, site frequency spectrum, haplotype- and linkage disequilibrium-based summary statistics. We show that for strong selective sweeps on de novo mutations the method can estimate allele age and selection strength even in nonequilibrium demographic scenarios. We extend our approach to models of selection on standing variation, and co-infer the frequency at which selection began to act upon the mutation. Finally, we apply our method to estimate the age and selection strength of a previously identified mutation underpinning cryptic colour adaptation in a wild deer mouse population, and compare our findings with previously published estimates as well as with geological data pertaining to the presumed shift in selective pressure. PMID:26576754

  19. Heart Instantaneous Frequency Based Estimation of HRV from Blood Pressure Waveforms

    NASA Astrophysics Data System (ADS)

    Lucena, Fausto; Barros, Allan Kardec; Takeuchi, Yoshinori; Ohnishi, Noboru

    The heart rate variability (HRV) is a measure based on the time position of the electrocardiogram (ECG) R-waves. There is a discussion whether or not we can obtain the HRV pattern from blood pressure (BP). In this paper, we propose a method for estimating HRV from a BP signal based on a HIF algorithm and carrying out experiments to compare BP as an alternative measurement of ECG to calculate HRV. Based on the hypotheses that ECG and BP have the same harmonic behavior, we model an alternative HRV signal using a nonlinear algorithm, called heart instantaneous frequency (HIF). It tracks the instantaneous frequency through a rough fundamental frequency using power spectral density (PSD). A novelty in this work is to use fundamental frequency instead of wave-peaks as a parameter to estimate and quantify beat-to-beat heart rate variability from BP waveforms. To verify how the estimate HRV signals derived from BP using HIF correlates to the standard gold measures, i.e. HRV derived from ECG, we use a traditional algorithm based on QRS detectors followed by thresholding to localize the R-wave time peak. The results show the following: 1) The spectral error caused by misestimation of time by R-peak detectors is demonstrated by an increase in high-frequency bands followed by the loss of time domain pattern. 2) The HIF was shown to be robust against noise and nuisances. 3) By using statistical methods and nonlinear analysis no difference between HIF derived from BP and HRV derived from ECG was observed.

  20. Rolling estimations of long range dependence volatility for high frequency S&P500 index

    NASA Astrophysics Data System (ADS)

    Cheong, Chin Wen; Pei, Tan Pei

    2015-10-01

    This study evaluates the time-varying long range dependence behaviors of the S&P500 volatility index using the modified rescaled adjusted range (R/S) statistic. For better computational result, a high frequency rolling bipower variation realized volatility estimates are used to avoid possible abrupt jump. The empirical analysis findings allow us to understand better the informationally market efficiency before and after the subprime mortgage crisis.

  1. An estimator for the standard deviation of a natural frequency. I.

    NASA Technical Reports Server (NTRS)

    Schiff, A. J.; Bogdanoff, J. L.

    1971-01-01

    A brief review of mean-square approximate systems is given. The case in which the masses are deterministic is considered first in the derivation of an estimator for the upper bound of the standard deviation of a natural frequency. Two examples presented include a two-degree-of-freedom system and a case in which the disorder in the springs is perfectly correlated. For purposes of comparison, a Monte Carlo simulation was done on a digital computer.

  2. Spectral analysis of GEOS-3 altimeter data and frequency domain collocation. [to estimate gravity anomalies

    NASA Technical Reports Server (NTRS)

    Eren, K.

    1980-01-01

    The mathematical background in spectral analysis as applied to geodetic applications is summarized. The resolution (cut-off frequency) of the GEOS 3 altimeter data is examined by determining the shortest wavelength (corresponding to the cut-off frequency) recoverable. The data from some 18 profiles are used. The total power (variance) in the sea surface topography with respect to the reference ellipsoid as well as with respect to the GEM-9 surface is computed. A fast inversion algorithm for matrices of simple and block Toeplitz matrices and its application to least squares collocation is explained. This algorithm yields a considerable gain in computer time and storage in comparison with conventional least squares collocation. Frequency domain least squares collocation techniques are also introduced and applied to estimating gravity anomalies from GEOS 3 altimeter data. These techniques substantially reduce the computer time and requirements in storage associated with the conventional least squares collocation. Numerical examples given demonstrate the efficiency and speed of these techniques.

  3. Ocean wave parameters and spectrum estimated from single and dual high-frequency radar systems

    NASA Astrophysics Data System (ADS)

    Hisaki, Yukiharu

    2016-09-01

    The high-frequency (HF) radar inversion algorithm for spectrum estimation (HIAS) can estimate ocean wave directional spectra from both dual and single radar. Wave data from a dual radar and two single radars are compared with in situ observations. The agreement of the wave parameters estimated from the dual radar with those from in situ observations is the best of the three. In contrast, the agreement of the wave parameters estimated from the single radar in which no Doppler spectra are observed in the cell closest to the in situ observation point is the worst among the three. Wave data from the dual radar and the two single radars are compared. The comparison of the wave heights estimated from the single and dual radars shows that the area sampled by the Doppler spectra for the single radar is more critical than the number of Doppler spectra in terms of agreement with the dual-radar-estimated wave heights. In contrast, the comparison of the wave periods demonstrates that the number of Doppler spectra observed by the single radar is more critical for agreement of the wave periods than the area of the Doppler spectra. There is a bias directed to the radar position in the single radar estimated wave direction.

  4. Estimating magnitude and frequency of floods using the PeakFQ 7.0 program

    USGS Publications Warehouse

    Veilleux, Andrea G.; Cohn, Timothy A.; Flynn, Kathleen M.; Mason, Jr., Robert R.; Hummel, Paul R.

    2014-01-01

    Flood-frequency analysis provides information about the magnitude and frequency of flood discharges based on records of annual maximum instantaneous peak discharges collected at streamgages. The information is essential for defining flood-hazard areas, for managing floodplains, and for designing bridges, culverts, dams, levees, and other flood-control structures. Bulletin 17B (B17B) of the Interagency Advisory Committee on Water Data (IACWD; 1982) codifies the standard methodology for conducting flood-frequency studies in the United States. B17B specifies that annual peak-flow data are to be fit to a log-Pearson Type III distribution. Specific methods are also prescribed for improving skew estimates using regional skew information, tests for high and low outliers, adjustments for low outliers and zero flows, and procedures for incorporating historical flood information. The authors of B17B identified various needs for methodological improvement and recommended additional study. In response to these needs, the Advisory Committee on Water Information (ACWI, successor to IACWD; http://acwi.gov/, Subcommittee on Hydrology (SOH), Hydrologic Frequency Analysis Work Group (HFAWG), has recommended modest changes to B17B. These changes include adoption of a generalized method-of-moments estimator denoted the Expected Moments Algorithm (EMA) (Cohn and others, 1997) and a generalized version of the Grubbs-Beck test for low outliers (Cohn and others, 2013). The SOH requested that the USGS implement these changes in a user-friendly, publicly accessible program.

  5. Effect of reference database on frequency estimates of polymerase chain reaction (PCR)-based DNA profiles.

    PubMed

    Monson, K L; Budowle, B

    1998-05-01

    A variety of general, regional, ancestral and ethnic databases is available for the polymerase chain reaction (PCR)-based loci LDLR, GYPA, HBGG, D7S8, Gc, DQA1, and D1S80. Generally, we observed greater differences in frequency estimations of DNA profiles between racial groups than between ethnic or geographic subgroups. Analysis revealed few forensically significant differences within ethnic subgroups, particularly within general United States groups, and multi-locus frequency estimates typically differ by less than a factor of ten. Using a database different from the one to which a target profile belongs tends to overestimate rarity. Implementation of the general correction of homozygote frequencies for a population substructure, advised by the 1996 National Research Council report, The Evaluation of Forensic DNA Evidence, has a minimal effect on profile frequencies. Even when it is known that both the suspect and all possible perpetrators must belong to the same isolated population, the special correction for inbreeding, which was proposed by the 1996 National Research Council report for this special case, has a relatively modest effect, typically a factor of two or less for 1% inbreeding. The effect becomes more substantial (exceeding a factor of ten) for inbreeding of 3% or more in multi-locus profiles rarer than about one in a million. PMID:9608687

  6. An EMG frequency-based test for estimating the neuromuscular fatigue threshold during cycle ergometry.

    PubMed

    Camic, Clayton L; Housh, Terry J; Johnson, Glen O; Hendrix, C Russell; Zuniga, Jorge M; Mielke, Michelle; Schmidt, Richard J

    2010-01-01

    The purposes of this investigation were twofold: (1) to determine if the model used for estimating the physical working capacity at the fatigue threshold (PWC(FT)) from electromyographic (EMG) amplitude data could be applied to the frequency domain of the signal to derive a new fatigue threshold for cycle ergometry called the mean power frequency fatigue threshold (MPF(FT)), and (2) to compare the power outputs associated with the PWC(FT), MPF(FT), ventilatory threshold (VT), and respiratory compensation point (RCP). Sixteen men [mean (SD) age = 23.4 (3.2) years] performed incremental cycle ergometer rides to exhaustion with bipolar surface EMG signals recorded from the vastus lateralis. There were significant (p < 0.05) mean differences for PWC(FT) [mean (SD) = 168 (36) W] versus MPF(FT) [208 (37) W] and VT [152 (33) W] versus RCP [205 (84) W], but no mean differences for PWC(FT) versus VT or MPF(FT) versus RCP. The mean difference between PWC(FT) and MPF(FT) may be due to the effects of specific metabolites that independently influence the time and frequency domains of the EMG signal. These findings indicated that the PWC(FT) model could be applied to the frequency domain of the EMG signal to estimate MPF(FT). Furthermore, the current findings suggested that the PWC(FT) may demarcate the moderate from heavy exercise domains, while the MPF(FT) demarcates heavy from severe exercise intensities.

  7. A maximum likelihood approach to jointly estimating seasonal and annual flood frequency distributions

    NASA Astrophysics Data System (ADS)

    Baratti, E.; Montanari, A.; Castellarin, A.; Salinas, J. L.; Viglione, A.; Blöschl, G.

    2012-04-01

    Flood frequency analysis is often used by practitioners to support the design of river engineering works, flood miti- gation procedures and civil protection strategies. It is often carried out at annual time scale, by fitting observations of annual maximum peak flows. However, in many cases one is also interested in inferring the flood frequency distribution for given intra-annual periods, for instance when one needs to estimate the risk of flood in different seasons. Such information is needed, for instance, when planning the schedule of river engineering works whose building area is in close proximity to the river bed for several months. A key issue in seasonal flood frequency analysis is to ensure the compatibility between intra-annual and annual flood probability distributions. We propose an approach to jointly estimate the parameters of seasonal and annual probability distribution of floods. The approach is based on the preliminary identification of an optimal number of seasons within the year,which is carried out by analysing the timing of flood flows. Then, parameters of intra-annual and annual flood distributions are jointly estimated by using (a) an approximate optimisation technique and (b) a formal maximum likelihood approach. The proposed methodology is applied to some case studies for which extended hydrological information is available at annual and seasonal scale.

  8. Estimation of LDA signal frequency using the autocovariance (ACV) lag ratio method

    NASA Astrophysics Data System (ADS)

    Matovic, D.; Tropea, C.

    1989-08-01

    An algorithm to realize the ACV lag ratio method is introduced and applied to real Doppler signals as acquired using a transient recorder, and processed on a digital computer. Measurements using other time domain and frequency domain estimation techniques are also performed on the same data sets and compared using basic statistical parameters. Results are presented for comparisons with an estimate based on the power spectral density, since the time domain estimates investigated are unable to achieve meaningful results for signals with high noise content. The prospects of implementing the ACV lag ratio method in a dedicated processor are discussed and the potential advantages of such a processor are summarized. For applications in phase/Doppler anemometry, the cross-correlation of the two Doppler signals rather than the autocorrelation can be computed without having to modify the algorithm for frequency determination. Once the frequency is known, the phase difference can be immediately computed by examining the shift of the cross-correlation function maximum away from lag time zero. Thus both particle velocity and size can be recovered with no additional computation.

  9. Estimating flood-peak discharge magnitudes and frequencies for rural streams in Illinois

    USGS Publications Warehouse

    Soong, David T.; Ishii, Audrey; Sharpe, Jennifer B.; Avery, Charles F.

    2004-01-01

    Flood-peak discharge magnitudes and frequencies at streamflow-gaging sites were developed with the annual maximum series (AMS) and the partial duration series (PDS) in this study. Regional equations for both flood series were developed for estimating flood-peak discharge magnitudes at specified recurrence intervals of rural Illinois streams. The regional equations are techniques for estimating flood quantiles at ungaged sites or for improving estimated flood quantiles at gaged sites with short records or unrepresentative data. Besides updating at-site floodfrequency estimates using flood data up to water year 1999, this study updated the generalized skew coefficients for Illinois to be used with the Log-Pearson III probability distribution for analyzing the AMS, developed a program for analyzing the partial duration series with the Generalized Pareto probability distribution, and applied the BASINSOFT program with digital datasets in soil, topography, land cover, and precipitation to develop a set of basin characteristics. The multiple regression analysis was used to develop the regional equations with subsets of the basin characteristics and the updated at-site flood frequencies. Seven hydrologic regions were delineated using physiographic and hydrologic characteristics of drainage basins of Illinois. The seven hydrologic regions were used for both the AMS and PDS analyses. Examples are presented to illustrate the use of the AMS regional equations to estimate flood quantiles at an ungaged site and to improve flood-quantile estimates at and near a gaged site. Flood-quantile estimates in four regulated channel reaches of Illinois also are approximated by linear interpolation. Documentation of the flood data preparation and evaluation, procedures for determining the flood quantiles, basin characteristics, generalized skew coefficients, hydrologic region delineations, and the multiple regression analyses used to determine the regional equations are presented in the

  10. µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype ... frequencies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size an...

  11. Stochastic modeling of triple-frequency BeiDou signals: estimation, assessment and impact analysis

    NASA Astrophysics Data System (ADS)

    Li, Bofeng

    2016-07-01

    Stochastic models are important in global navigation satellite systems (GNSS) estimation problems. One can achieve reliable ambiguity resolution and precise positioning only by use of a suitable stochastic model. The BeiDou system has received increased research focus, but based only on empirical stochastic models from the knowledge of GPS. In this paper, we will systematically study the estimation, assessment and impacts of a triple-frequency BeiDou stochastic model. In our estimation problem, a single-difference, geometry-free functional model is used to extract pure random noise. A very sophisticated structure of unknown variance matrix is designed to allow the estimation of satellite-specific variances, cross correlations between two arbitrary frequencies, as well as the time correlations for phase and code observations per frequency. In assessing the stochastic models, six data sets with four brands of BeiDou receivers on short and zero-length baselines are processed, and the results are compared. In impact analysis of stochastic model, the performance of integer ambiguity resolution and positioning are numerically demonstrated using a realistic stochastic model. The results from ultrashort (shorter than 10 m) and zero-length baselines indicate that BeiDou stochastic models are affected by both observation and receiver brands. The observation variances have been modeled by an elevation-dependent function, but the modeling errors for geostationary earth orbit (GEO) satellites are larger than for inclined geosynchronous satellite orbit (IGSO) and medium earth orbit (MEO) satellites. The stochastic model is governed by both the internal errors of the receiver and external errors at the site. Different receivers have different capabilities for resisting external errors. A realistic stochastic model is very important for achieving ambiguity resolution with a high success rate and small false alarm and for determining realistic variances for position estimates. To

  12. Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape.

    PubMed

    Delourme, R; Bousset, L; Ermel, M; Duffé, P; Besnard, A L; Marquer, B; Fudal, I; Linglin, J; Chadœuf, J; Brun, H

    2014-10-01

    Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for durability of major resistance genes. This was demonstrated in the Leptosphaeria maculans/Brassica napus pathosystem in a 5year recurrent selection field experiment on lines harboring the qualitative resistance gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of the virulent isolate population. In this study we continued this recurrent selection experiment in the same way to examine whether the pathogen population could adapt and render the major gene ineffective in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an effective approach for controlling the pathogen epidemics over time. This combination did not prevent isolates virulent against the major gene from amplifying in the long term but the quantitative resistance significantly delayed for 5years the loss of effectiveness of the qualitative resistance and disease severity was maintained at a low level on the genotype with both types of resistance after the fungus population had adapted to the major gene. We also showed that diversity of AvrLm6 virulence alleles was comparable in isolates recovered after the recurrent selection on lines carrying either the major gene alone or in combination with quantitative resistance: a single repeat-induced point mutation and deletion events were observed in both situations. Breeding varieties which combine qualitative and quantitative resistance can effectively contribute to disease control by increasing the potential for durability of major resistance genes.

  13. Compressed sensing theory-based channel estimation for optical orthogonal frequency division multiplexing communication system

    NASA Astrophysics Data System (ADS)

    Zhao, Hui; Li, Minghui; Wang, Ruyan; Liu, Yuanni; Song, Daiping

    2014-09-01

    Due to the spare multipath property of the channel, a channel estimation method, which is based on partial superimposed training sequence and compressed sensing theory, is proposed for line of sight optical orthogonal frequency division multiplexing communication systems. First, a continuous training sequence is added at variable power ratio to the cyclic prefix of orthogonal frequency division multiplexing symbols at the transmitter prior to transmission. Then the observation matrix of compressed sensing theory is structured by the use of the training symbols at receiver. Finally, channel state information is estimated using sparse signal reconstruction algorithm. Compared to traditional training sequences, the proposed partial superimposed training sequence not only improves the spectral efficiency, but also reduces the influence to information symbols. In addition, compared with classical least squares and linear minimum mean square error methods, the proposed compressed sensing theory based channel estimation method can improve both the estimation accuracy and the system performance. Simulation results are given to demonstrate the performance of the proposed method.

  14. Curved-region-based ridge frequency estimation and curved Gabor filters for fingerprint image enhancement.

    PubMed

    Gottschlich, Carsten

    2012-04-01

    Gabor filters (GFs) play an important role in many application areas for the enhancement of various types of images and the extraction of Gabor features. For the purpose of enhancing curved structures in noisy images, we introduce curved GFs that locally adapt their shape to the direction of flow. These curved GFs enable the choice of filter parameters that increase the smoothing power without creating artifacts in the enhanced image. In this paper, curved GFs are applied to the curved ridge and valley structures of low-quality fingerprint images. First, we combine two orientation-field estimation methods in order to obtain a more robust estimation for very noisy images. Next, curved regions are constructed by following the respective local orientation. Subsequently, these curved regions are used for estimating the local ridge frequency. Finally, curved GFs are defined based on curved regions, and they apply the previously estimated orientations and ridge frequencies for the enhancement of low-quality fingerprint images. Experimental results on the FVC2004 databases show improvements of this approach in comparison with state-of-the-art enhancement methods.

  15. Detection of main tidal frequencies using least squares harmonic estimation method

    NASA Astrophysics Data System (ADS)

    Mousavian, R.; Hossainali, M. Mashhadi

    2012-11-01

    In this paper the efficiency of the method of Least Squares Harmonic Estimation (LS-HE) for detecting the main tidal frequencies is investigated. Using this method, the tidal spectrum of the sea level data is evaluated at two tidal stations: Bandar Abbas in south of Iran and Workington on the eastern coast of the UK. The amplitudes of the tidal constituents at these two tidal stations are not the same. Moreover, in contrary to the Workington station, the Bandar Abbas tidal record is not an equispaced time series. Therefore, the analysis of the hourly tidal observations in Bandar Abbas and Workington can provide a reasonable insight into the efficiency of this method for analyzing the frequency content of tidal time series. Furthermore, applying the method of Fourier transform to the Workington tidal record provides an independent source of information for evaluating the tidal spectrum proposed by the LS-HE method. According to the obtained results, the spectrums of these two tidal records contain the components with the maximum amplitudes among the expected ones in this time span and some new frequencies in the list of known constituents. In addition, in terms of frequencies with maximum amplitude; the power spectrums derived from two aforementioned methods are the same. These results demonstrate the ability of LS-HE for identifying the frequencies with maximum amplitude in both tidal records.

  16. Estimating energetics in cetaceans from respiratory frequency: why we need to understand physiology

    PubMed Central

    Fahlman, A.; van der Hoop, J.; Moore, M. J.; Levine, G.; Rocho-Levine, J.; Brodsky, M.

    2016-01-01

    ABSTRACT The accurate estimation of field metabolic rates (FMR) in wild animals is a key component of bioenergetic models, and is important for understanding the routine limitations for survival as well as individual responses to disturbances or environmental changes. Several methods have been used to estimate FMR, including accelerometer-derived activity budgets, isotope dilution techniques, and proxies from heart rate. Counting the number of breaths is another method used to assess FMR in cetaceans, which is attractive in its simplicity and the ability to measure respiration frequency from visual cues or data loggers. This method hinges on the assumption that over time a constant tidal volume (VT) and O2 exchange fraction (ΔO2) can be used to predict FMR. To test whether this method of estimating FMR is valid, we measured breath-by-breath tidal volumes and expired O2 levels of bottlenose dolphins, and computed the O2 consumption rate (V̇O2) before and after a pre-determined duration of exercise. The measured V̇O2 was compared with three methods to estimate FMR. Each method to estimate V̇O2 included variable VT and/or ΔO2. Two assumption-based methods overestimated V̇O2 by 216-501%. Once the temporal changes in cardio-respiratory physiology, such as variation in VT and ΔO2, were taken into account, pre-exercise resting V̇O2 was predicted to within 2%, and post-exercise V̇O2 was overestimated by 12%. Our data show that a better understanding of cardiorespiratory physiology significantly improves the ability to estimate metabolic rate from respiratory frequency, and further emphasizes the importance of eco-physiology for conservation management efforts. PMID:26988759

  17. Estimating energetics in cetaceans from respiratory frequency: why we need to understand physiology.

    PubMed

    Fahlman, A; van der Hoop, J; Moore, M J; Levine, G; Rocho-Levine, J; Brodsky, M

    2016-01-01

    The accurate estimation of field metabolic rates (FMR) in wild animals is a key component of bioenergetic models, and is important for understanding the routine limitations for survival as well as individual responses to disturbances or environmental changes. Several methods have been used to estimate FMR, including accelerometer-derived activity budgets, isotope dilution techniques, and proxies from heart rate. Counting the number of breaths is another method used to assess FMR in cetaceans, which is attractive in its simplicity and the ability to measure respiration frequency from visual cues or data loggers. This method hinges on the assumption that over time a constant tidal volume (VT) and O2exchange fraction (ΔO2) can be used to predict FMR. To test whether this method of estimating FMR is valid, we measured breath-by-breath tidal volumes and expired O2levels of bottlenose dolphins, and computed the O2consumption rate (V̇O2 ) before and after a pre-determined duration of exercise. The measuredV̇O2 was compared with three methods to estimate FMR. Each method to estimateV̇O2 included variable VT and/or ΔO2 Two assumption-based methods overestimatedV̇O2 by 216-501%. Once the temporal changes in cardio-respiratory physiology, such as variation in VT and ΔO2, were taken into account, pre-exercise restingV̇O2 was predicted to within 2%, and post-exerciseV̇O2 was overestimated by 12%. Our data show that a better understanding of cardiorespiratory physiology significantly improves the ability to estimate metabolic rate from respiratory frequency, and further emphasizes the importance of eco-physiology for conservation management efforts.

  18. Estimating energetics in cetaceans from respiratory frequency: why we need to understand physiology.

    PubMed

    Fahlman, A; van der Hoop, J; Moore, M J; Levine, G; Rocho-Levine, J; Brodsky, M

    2016-01-01

    The accurate estimation of field metabolic rates (FMR) in wild animals is a key component of bioenergetic models, and is important for understanding the routine limitations for survival as well as individual responses to disturbances or environmental changes. Several methods have been used to estimate FMR, including accelerometer-derived activity budgets, isotope dilution techniques, and proxies from heart rate. Counting the number of breaths is another method used to assess FMR in cetaceans, which is attractive in its simplicity and the ability to measure respiration frequency from visual cues or data loggers. This method hinges on the assumption that over time a constant tidal volume (VT) and O2exchange fraction (ΔO2) can be used to predict FMR. To test whether this method of estimating FMR is valid, we measured breath-by-breath tidal volumes and expired O2levels of bottlenose dolphins, and computed the O2consumption rate (V̇O2 ) before and after a pre-determined duration of exercise. The measuredV̇O2 was compared with three methods to estimate FMR. Each method to estimateV̇O2 included variable VT and/or ΔO2 Two assumption-based methods overestimatedV̇O2 by 216-501%. Once the temporal changes in cardio-respiratory physiology, such as variation in VT and ΔO2, were taken into account, pre-exercise restingV̇O2 was predicted to within 2%, and post-exerciseV̇O2 was overestimated by 12%. Our data show that a better understanding of cardiorespiratory physiology significantly improves the ability to estimate metabolic rate from respiratory frequency, and further emphasizes the importance of eco-physiology for conservation management efforts. PMID:26988759

  19. Flood Frequency Estimates and Documented and Potential Extreme Peak Discharges in Oklahoma

    USGS Publications Warehouse

    Tortorelli, Robert L.; McCabe, Lan P.

    2001-01-01

    Knowledge of the magnitude and frequency of floods is required for the safe and economical design of highway bridges, culverts, dams, levees, and other structures on or near streams; and for flood plain management programs. Flood frequency estimates for gaged streamflow sites were updated, documented extreme peak discharges for gaged and miscellaneous measurement sites were tabulated, and potential extreme peak discharges for Oklahoma streamflow sites were estimated. Potential extreme peak discharges, derived from the relation between documented extreme peak discharges and contributing drainage areas, can provide valuable information concerning the maximum peak discharge that could be expected at a stream site. Potential extreme peak discharge is useful in conjunction with flood frequency analysis to give the best evaluation of flood risk at a site. Peak discharge and flood frequency for selected recurrence intervals from 2 to 500 years were estimated for 352 gaged streamflow sites. Data through 1999 water year were used from streamflow-gaging stations with at least 8 years of record within Oklahoma or about 25 kilometers into the bordering states of Arkansas, Kansas, Missouri, New Mexico, and Texas. These sites were in unregulated basins, and basins affected by regulation, urbanization, and irrigation. Documented extreme peak discharges and associated data were compiled for 514 sites in and near Oklahoma, 352 with streamflow-gaging stations and 162 at miscellaneous measurements sites or streamflow-gaging stations with short record, with a total of 671 measurements.The sites are fairly well distributed statewide, however many streams, large and small, have never been monitored. Potential extreme peak-discharge curves were developed for streamflow sites in hydrologic regions of the state based on documented extreme peak discharges and the contributing drainage areas. Two hydrologic regions, east and west, were defined using 98 degrees 15 minutes longitude as the

  20. A Technique for Estimating the Occlusion Effect for Frequencies Below 125 Hz

    PubMed Central

    Stone, Michael A.; Paul, Anna M.; Axon, Patrick; Moore, Brian C.J.

    2014-01-01

    Objectives The level of bone-conducted sound in the auditory meatus is increased at low frequencies by occlusion of the meatus, for example by the earmold of a hearing aid. Physical measures of this “occlusion effect” (OE) require vibration of the skull. In previous research, either self-voicing or audiometric bone-conduction vibrators have been used to produce this vibration, with the result that the OE could not be measured for frequencies below 125 Hz. However, frequencies below this can be important for music perception by hearing aid users. The objective was to develop and evaluate a method that gives a lower-bound estimate of the OE for frequencies below 125 Hz. Design A low-noise amplifier with extended low-frequency response was used to record the output of a miniature microphone inserted into the meatus of participants. The signal came from sounds of the heartbeat and blood flow of the participant, transmitted via bone-conduction through the walls of the meatus. A simultaneous recording was made of the carotid pulse to permit time-locked averaging (and hence noise reduction) of the microphone signal. Recordings were made from seven otologically and audiometrically normal participants, using clinical probe tips to produce the occlusion. Recordings were also made from an overlapping group of nine participants, using fast-setting impression material to provide a more consistent degree of occlusion. The difference in level of the recorded signal for unoccluded and occluded conditions provided a lower bound for the magnitude of the OE. Results The mean OE increased with decreasing frequency, reaching a plateau of about 40 dB for frequencies below 40 Hz. For some individual recordings, the OE reached 50 dB for frequencies below 20 Hz. With occlusion, the heartbeat became audible for most participants. Conclusions The OE can be very large at low frequencies. The use of hearing aids with closed fittings, which may be employed either to prevent acoustic

  1. A combined deterministic and probabilistic approach to estimate frequency of inadvertent criticality for a cask car lid drop event

    SciTech Connect

    Blanchard, A.

    2000-02-11

    This paper estimates the frequency of postulated accident scenarios in which combinations of equipment failures and/or human errors associated with the lifting and moving of the cask car lid during fuel bundle loading/unloading operations lead to conditions which produce a criticality. As noted in the paper, bounding values are used for values where uncertainty is large. However, in general best estimate values are used to determine the scenario frequencies. This is consistent with current methodology where best estimates are calculated for the frequency domain and conservative estimates are calculated for the consequence domain.

  2. Analysis and Design of Robust H∞ Fault Estimation Observer With Finite-Frequency Specifications for Discrete-Time Fuzzy Systems.

    PubMed

    Zhang, Ke; Jiang, Bin; Shi, Peng; Xu, Jinfa

    2015-07-01

    This paper addresses the problem of fault estimation observer design with finite-frequency specifications for discrete-time Takagi-Sugeno (T-S) fuzzy systems. First, for such T-S fuzzy models, an H∞ fault estimation observer with pole-placement constraint is proposed to achieve fault estimation. Based on the generalized Kalman-Yakubovich-Popov lemma, the given finite-frequency observer possesses less conservatism compared with the design of the entire-frequency domain. Furthermore, the performance of the presented fault estimation observer is further enhanced by adding the degree of freedom. Finally, two examples are presented to illustrate the effectiveness of the proposed strategy.

  3. Method of remotely estimating a rest or best lock frequency of a local station receiver using telemetry

    NASA Technical Reports Server (NTRS)

    Fielhauer, Karl B. (Inventor); Jensen, James R. (Inventor)

    2007-01-01

    A system includes a remote station and a local station having a receiver. The receiver operates in an unlocked state corresponding to its best lock frequency (BLF). The local station derives data indicative of a ratio of the BLF to a reference frequency of the receiver, and telemeters the data to the remote station. The remote station estimates the BLF based on (i) the telemetered data, and (ii) a predetermined estimate of the reference frequency.

  4. Complex demodulation in VLBI estimation of high frequency Earth rotation components

    NASA Astrophysics Data System (ADS)

    Böhm, S.; Brzeziński, A.; Schuh, H.

    2012-12-01

    The spectrum of high frequency Earth rotation variations contains strong harmonic signal components mainly excited by ocean tides along with much weaker non-harmonic fluctuations driven by irregular processes like the diurnal thermal tides in the atmosphere and oceans. In order to properly investigate non-harmonic phenomena a representation in time domain is inevitable. We present a method, operating in time domain, which is easily applicable within Earth rotation estimation from Very Long Baseline Interferometry (VLBI). It enables the determination of diurnal and subdiurnal variations, and is still effective with merely diurnal parameter sampling. The features of complex demodulation are used in an extended parameterization of polar motion and universal time which was implemented into a dedicated version of the Vienna VLBI Software VieVS. The functionality of the approach was evaluated by comparing amplitudes and phases of harmonic variations at tidal periods (diurnal/semidiurnal), derived from demodulated Earth rotation parameters (ERP), estimated from hourly resolved VLBI ERP time series and taken from a recently published VLBI ERP model to the terms of the conventional model for ocean tidal effects in Earth rotation recommended by the International Earth Rotation and Reference System Service (IERS). The three sets of tidal terms derived from VLBI observations extensively agree among each other within the three-sigma level of the demodulation approach, which is below 6 μas for polar motion and universal time. They also coincide in terms of differences to the IERS model, where significant deviations primarily for several major tidal terms are apparent. An additional spectral analysis of the as well estimated demodulated ERP series of the ter- and quarterdiurnal frequency bands did not reveal any significant signal structure. The complex demodulation applied in VLBI parameter estimation could be demonstrated a suitable procedure for the reliable reproduction of

  5. Uncertainty introduced by flood frequency analysis in the estimation of climate change impacts on flooding

    NASA Astrophysics Data System (ADS)

    Lawrence, Deborah

    2016-04-01

    Potential changes in extreme flooding under a future climate are of much interest in climate change adaptation work, and estimates for high flows with long return periods are often based on an application of flood frequency analysis methods. The uncertainty introduced by this estimation is, however, only rarely considered when assessing changes in flood magnitude. In this study, an ensemble of hydrological projections for each of 115 catchments distributed across Norway is analysed to derive an estimate for the percentage change in the magnitude of the 200-year flood under a future climate. This is the return level used for flood hazard mapping in Norway. The ensemble of projections is based on climate data from 10 EUROCORDEX GCM/RCM combinations, two bias correction methods (empirical quantile mapping and double gamma function), and 25 alternative parameterisations of the HBV hydrological model. For each hydrological simulation, the annual maximum series is used to estimate the 200-year flood for the reference period, 1971-2000 and a future period, 2071-2100, based on two and three-parameter GEV distributions. In addition, bootstrap resampling is used to estimate the 95% confidence levels for the extreme value estimates, and this range is incorporated into the ensemble estimates for each catchment. As has been shown in previous work based on earlier climate projections, there are large regional differences in the projected changes in the 200-year flood across Norway, with median ensemble projections ranging from 44% to +56% for the daily-averaged flood magnitude. These differences reflect the relative importance of rainfall vs. snowmelt as the dominant flood generating process in different regions, at differing altitudes and as a function of catchment area, in addition to dominant storm tracks. Variance decomposition is used to assess the relative contributions of the following components to the total spread (given by the 5 to 95% range) in the ensemble for each

  6. Genetic parameters and allele frequencies of five new European Standard Set STR loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in the population of Romania

    PubMed Central

    Stanciu, Florin; Vladu, Simona; Cuţăr, Veronica; Cocioabă, Daniela; Iancu, Florentina; Cotolea, Adnana; Stoian, Ionel Marius

    2013-01-01

    Aim To establish allele frequencies and genetic parameters for 5 new European Standard Set short tandem repeat (STR) loci in the population of Romania and to compare them with those in other populations. Methods DNA was isolated using QIAamp 96 DNA Swab BioRobot Kit and Chelex 100 methods. Polymerase chain reaction amplification was done using Investigator ESSplexPlus Kit (D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, and vWA). For DNA typing, Applied Biosystems 3500/3500xL Genetic Analyzer was used. Statistical analysis was done using Powerstats, GDA, and Arlequin software. Results Power of discrimination and polymorphism information content was highest for two new ESS loci, D1S1656 and D12S391. Comparison of allele frequencies for 5 new ESS loci in Romanian population with previously published population data showed significant differences for all compared populations, with the exception of Hungary. Geographically more distant populations, such as Spain, Sweden, United Kingdom, Germany, and Portugal differed more than closer populations. Conclusion New ESS STR loci are very useful for the analysis of forensic samples (persons or traces) due to their characteristics (shortness and high polymorphism). In comparisons with other common STR markers, they have a higher power of discrimination and also higher polymorphism information content, and could be used in any national DNA database. PMID:23771753

  7. Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure

    PubMed Central

    Chen, Hua; Slatkin, Montgomery

    2013-01-01

    It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144−0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories. PMID:23797107

  8. Estimation of the frequency of malformed sperm by slit scan flow cytometry

    SciTech Connect

    Halamka, J.; Gray, J.W.; Gledhill, B.L.; Lake, S.; Wyrobek, A.J.

    1984-01-01

    An investigation was made of the utility of Slit Scan Flow Cytometry (SSFCM) for measuring the frequencies of malformed sperm heads in control and mutagen treated B6C3F1/CRL mice. In SSFCM, fluorescence profiles of sperm heads stained with the DNA-specific fluorescent dye acriflavine were recorded for sperm flowing lengthwise through a 2.5-..mu..m-thick laser beam. Malformed sperm were detected as having fluorescence profiles that differed substantially from an average fluorescence profile for sperm from untreated mice. Fluorescence profiles were measured for 500 sperm per mouse from five control mice, five mice injected intraperitoneally daily for 5 days with a total of 375 mg/kg of body weight methyl methane sulfonate (MMS), and for 30 mice injected intraperitoneally daily for 5 days with total doses of procarbazine ranging from 125 mg/kg to 1250 mg/kg. Sperm were collected from the caudae epididymides 35 days after the last injection. Frequencies of malformed sperm in these samples were also estimated by visual analysis. All samples were analyzed in double blind fashion. The visual and SSFCM malformed sperm frequencies for the samples from control, MMS-treated, and procarbazine-treated mice were correlated. A dose effect was seen with both the visual and SSFCM estimates for the sperm from the procarbazine-treated mice. 8 references 3 figures.

  9. Estimation of magnitude and frequency of floods for streams in Puerto Rico : new empirical models

    USGS Publications Warehouse

    Ramos-Gines, Orlando

    1999-01-01

    Flood-peak discharges and frequencies are presented for 57 gaged sites in Puerto Rico for recurrence intervals ranging from 2 to 500 years. The log-Pearson Type III distribution, the methodology recommended by the United States Interagency Committee on Water Data, was used to determine the magnitude and frequency of floods at the gaged sites having 10 to 43 years of record. A technique is presented for estimating flood-peak discharges at recurrence intervals ranging from 2 to 500 years for unregulated streams in Puerto Rico with contributing drainage areas ranging from 0.83 to 208 square miles. Loglinear multiple regression analyses, using climatic and basin characteristics and peak-discharge data from the 57 gaged sites, were used to construct regression equations to transfer the magnitude and frequency information from gaged to ungaged sites. The equations have contributing drainage area, depth-to-rock, and mean annual rainfall as the basin and climatic characteristics in estimating flood peak discharges. Examples are given to show a step-by-step procedure in calculating a 100-year flood at a gaged site, an ungaged site, a site near a gaged location, and a site between two gaged sites.

  10. Methodology for Estimation of Flood Magnitude and Frequency for New Jersey Streams

    USGS Publications Warehouse

    Watson, Kara M.; Schopp, Robert D.

    2009-01-01

    Methodologies were developed for estimating flood magnitudes at the 2-, 5-, 10-, 25-, 50-, 100-, and 500-year recurrence intervals for unregulated or slightly regulated streams in New Jersey. Regression equations that incorporate basin characteristics were developed to estimate flood magnitude and frequency for streams throughout the State by use of a generalized least squares regression analysis. Relations between flood-frequency estimates based on streamflow-gaging-station discharge and basin characteristics were determined by multiple regression analysis, and weighted by effective years of record. The State was divided into five hydrologically similar regions to refine the regression equations. The regression analysis indicated that flood discharge, as determined by the streamflow-gaging-station annual peak flows, is related to the drainage area, main channel slope, percentage of lake and wetland areas in the basin, population density, and the flood-frequency region, at the 95-percent confidence level. The standard errors of estimate for the various recurrence-interval floods ranged from 48.1 to 62.7 percent. Annual-maximum peak flows observed at streamflow-gaging stations through water year 2007 and basin characteristics determined using geographic information system techniques for 254 streamflow-gaging stations were used for the regression analysis. Drainage areas of the streamflow-gaging stations range from 0.18 to 779 mi2. Peak-flow data and basin characteristics for 191 streamflow-gaging stations located in New Jersey were used, along with peak-flow data for stations located in adjoining States, including 25 stations in Pennsylvania, 17 stations in New York, 16 stations in Delaware, and 5 stations in Maryland. Streamflow records for selected stations outside of New Jersey were included in the present study because hydrologic, physiographic, and geologic boundaries commonly extend beyond political boundaries. The StreamStats web application was developed

  11. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis

    PubMed Central

    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-01-01

    Abstract Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5′- and 3′-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients. Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3′-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5′-UTR polymorphisms). For neither the 3′- nor the 5′-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance. The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold

  12. Estimation of Resolution of Shallow Layers by Frequency Domain Airborne Electromagnetic Measurements

    NASA Astrophysics Data System (ADS)

    Smith, B. D.; Minsley, B. J.; Kass, M. A.; Abraham, J. D.; Sams, J. I.; Veloski, G. A.; Esfahani, A.; Hodges, G.

    2012-12-01

    Helicopter frequency domain electromagnetic (HFDEM) that were conducted in two very different geoelectrical settings, permafrost and conductive alluvium, have been used to examine and quantify some aspects of the resolution of shallow layers (less than 5 meters). The surveys have used the Resolve system with six frequencies ranging from 400 Hz to 140 kHz. Though most discussion of the resolution of earth resistivity for airborne EM systems has concentrated on estimating the maximum depth of mapping or the resolution of deep layers, there are important applications for mapping shallow layers and it is useful to understand the capabilities and limitations of the HFDEM system in different environments. In permafrost terrains, mapping of the shallow active layer is important in understanding its distribution relative to surface processes such as thermal history, fires and carbon storage as well as in monitoring applications. Here the shallow active layer is a conductor relative to the very resistive permafrost. Mapping shallow layers in alluvial environments has been the focus of a study of subsurface drip irrigation in the Powder River of Wyoming. Here the focus of the HFDEM study has been in mapping the distribution of conductive clays and naturally occurring saline waters. Mapping of shallow layers in alluvial environments is important in agricultural applications to map recharge, soil salinity, and thickness of alluvium. Parameters for layered models (layer resistivity and thickness) have been estimated by inversion methods and the resolution of parameters has been evaluated using stochastic methods and an evaluation of linear estimates of resolution and uncertainty. Statistical estimates of resolution of parameters are compared with estimates from ground surveys.

  13. On Short-Time Estimation of Vocal Tract Length from Formant Frequencies

    PubMed Central

    Lammert, Adam C.; Narayanan, Shrikanth S.

    2015-01-01

    Vocal tract length is highly variable across speakers and determines many aspects of the acoustic speech signal, making it an essential parameter to consider for explaining behavioral variability. A method for accurate estimation of vocal tract length from formant frequencies would afford normalization of interspeaker variability and facilitate acoustic comparisons across speakers. A framework for considering estimation methods is developed from the basic principles of vocal tract acoustics, and an estimation method is proposed that follows naturally from this framework. The proposed method is evaluated using acoustic characteristics of simulated vocal tracts ranging from 14 to 19 cm in length, as well as real-time magnetic resonance imaging data with synchronous audio from five speakers whose vocal tracts range from 14.5 to 18.0 cm in length. Evaluations show improvements in accuracy over previously proposed methods, with 0.631 and 1.277 cm root mean square error on simulated and human speech data, respectively. Empirical results show that the effectiveness of the proposed method is based on emphasizing higher formant frequencies, which seem less affected by speech articulation. Theoretical predictions of formant sensitivity reinforce this empirical finding. Moreover, theoretical insights are explained regarding the reason for differences in formant sensitivity. PMID:26177102

  14. On Short-Time Estimation of Vocal Tract Length from Formant Frequencies.

    PubMed

    Lammert, Adam C; Narayanan, Shrikanth S

    2015-01-01

    Vocal tract length is highly variable across speakers and determines many aspects of the acoustic speech signal, making it an essential parameter to consider for explaining behavioral variability. A method for accurate estimation of vocal tract length from formant frequencies would afford normalization of interspeaker variability and facilitate acoustic comparisons across speakers. A framework for considering estimation methods is developed from the basic principles of vocal tract acoustics, and an estimation method is proposed that follows naturally from this framework. The proposed method is evaluated using acoustic characteristics of simulated vocal tracts ranging from 14 to 19 cm in length, as well as real-time magnetic resonance imaging data with synchronous audio from five speakers whose vocal tracts range from 14.5 to 18.0 cm in length. Evaluations show improvements in accuracy over previously proposed methods, with 0.631 and 1.277 cm root mean square error on simulated and human speech data, respectively. Empirical results show that the effectiveness of the proposed method is based on emphasizing higher formant frequencies, which seem less affected by speech articulation. Theoretical predictions of formant sensitivity reinforce this empirical finding. Moreover, theoretical insights are explained regarding the reason for differences in formant sensitivity. PMID:26177102

  15. Estimation of carrier frequencies of six autosomal-recessive Mendelian disorders in the Korean population.

    PubMed

    Song, Min-Jung; Lee, Seung-Tae; Lee, Mi-Kyung; Ji, Yongick; Kim, Jong-Won; Ki, Chang-Seok

    2012-02-01

    Although many studies have been performed to identify mutations in Korean patients with various autosomal-recessive Mendelian disorders (AR-MDs), little is known about the carrier frequencies of AR-MDs in the Korean population. Twenty common mutations from six AR-MDs, including Wilson disease (WD), non-syndromic hearing loss (NSHL), glycogen storage disease type Ia (GSD Ia), phenylketonuria (PKU), congenital hypothyroidism (CH), and congenital lipoid adrenal hyperplasia (CLAH) were selected to screen for based on previous studies. A total of 3057 Koreans were genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry followed by confirmation using the Sanger sequencing. We found 201 and 8 carriers with either one or two mutations in different genes, respectively, yielding a total carrier frequency of 1 in 15 (6.7%). Of the six AR-MDs, NSHL has the highest carrier frequency followed by WD, CH, CLAH, GSD Ia, and PKU. As carrier screening tests are becoming prevalent and the number of mutations known and tested is rising, a priori data on the carrier frequencies in different ethnic groups is mandatory to plan a population screening program and to estimate its efficiency. In light of this, the present results can be used as a basis to establish a screening policy for common AR-MRs in the Korean population. PMID:22170460

  16. Methods for estimating selected low-flow frequency statistics for unregulated streams in Kentucky

    USGS Publications Warehouse

    Martin, Gary R.; Arihood, Leslie D.

    2010-01-01

    This report provides estimates of, and presents methods for estimating, selected low-flow frequency statistics for unregulated streams in Kentucky including the 30-day mean low flows for recurrence intervals of 2 and 5 years (30Q2 and 30Q5) and the 7-day mean low flows for recurrence intervals of 5, 10, and 20 years (7Q2, 7Q10, and 7Q20). Estimates of these statistics are provided for 121 U.S. Geological Survey streamflow-gaging stations with data through the 2006 climate year, which is the 12-month period ending March 31 of each year. Data were screened to identify the periods of homogeneous, unregulated flows for use in the analyses. Logistic-regression equations are presented for estimating the annual probability of the selected low-flow frequency statistics being equal to zero. Weighted-least-squares regression equations were developed for estimating the magnitude of the nonzero 30Q2, 30Q5, 7Q2, 7Q10, and 7Q20 low flows. Three low-flow regions were defined for estimating the 7-day low-flow frequency statistics. The explicit explanatory variables in the regression equations include total drainage area and the mapped streamflow-variability index measured from a revised statewide coverage of this characteristic. The percentage of the station low-flow statistics correctly classified as zero or nonzero by use of the logistic-regression equations ranged from 87.5 to 93.8 percent. The average standard errors of prediction of the weighted-least-squares regression equations ranged from 108 to 226 percent. The 30Q2 regression equations have the smallest standard errors of prediction, and the 7Q20 regression equations have the largest standard errors of prediction. The regression equations are applicable only to stream sites with low flows unaffected by regulation from reservoirs and local diversions of flow and to drainage basins in specified ranges of basin characteristics. Caution is advised when applying the equations for basins with characteristics near the

  17. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

    PubMed

    Hodgson, Jason A; Pickrell, Joseph K; Pearson, Laurel N; Quillen, Ellen E; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D; Perry, George H

    2014-08-22

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa. PMID:24990677

  18. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

    PubMed

    Hodgson, Jason A; Pickrell, Joseph K; Pearson, Laurel N; Quillen, Ellen E; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D; Perry, George H

    2014-08-22

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa.

  19. Magnetic fields, plasma densities, and plasma beta parameters estimated from high-frequency zebra fine structures

    NASA Astrophysics Data System (ADS)

    Karlický, M.; Jiricka, K.

    2002-10-01

    Using the recent model of the radio zebra fine structures (Ledenev et al. 2001) the magnetic fields, plasma densities, and plasma beta parameters are estimated from high-frequency zebra fine structures. It was found that in the flare radio source of high-frequency (1-2 GHz) zebras the densities and magnetic fields vary in the intervals of (1-4)×1010 cm-3 and 40-230 G, respectively. Assuming then the flare temperature as about of 107K, the plasma beta parameters in the zebra radio sources are in the 0.05-0.81 interval. Thus the plasma pressure effects in such radio sources, especially in those with many zebra lines, are not negligible.

  20. Lower Bounds on the Frequency Estimation Error in Magnetically Coupled MEMS Resonant Sensors.

    PubMed

    Paden, Brad E

    2016-02-01

    MEMS inductor-capacitor (LC) resonant pressure sensors have revolutionized the treatment of abdominal aortic aneurysms. In contrast to electrostatically driven MEMS resonators, these magnetically coupled devices are wireless so that they can be permanently implanted in the body and can communicate to an external coil via pressure-induced frequency modulation. Motivated by the importance of these sensors in this and other applications, this paper develops relationships among sensor design variables, system noise levels, and overall system performance. Specifically, new models are developed that express the Cramér-Rao lower bound for the variance of resonator frequency estimates in terms of system variables through a system of coupled algebraic equations, which can be used in design and optimization. Further, models are developed for a novel mechanical resonator in addition to the LC-type resonators.

  1. Improved argument-FFT frequency offset estimation for QPSK coherent optical Systems

    NASA Astrophysics Data System (ADS)

    Han, Jilong; Li, Wei; Yuan, Zhilin; Li, Haitao; Huang, Liyan; Hu, Qianggao

    2016-02-01

    A frequency offset estimation (FOE) algorithm based on fast Fourier transform (FFT) of the signal's argument is investigated, which does not require removing the modulated data phase. In this paper, we analyze the flaw of the argument-FFT algorithm and propose a combined FOE algorithm, in which the absolute of frequency offset (FO) is accurately calculated by argument-FFT algorithm with a relatively large number of samples and the sign of FO is determined by FFT-based interpolation discrete Fourier transformation (DFT) algorithm with a relatively small number of samples. Compared with the previous algorithms based on argument-FFT, the proposed one has low complexity and can still effectively work with a relatively less number of samples.

  2. Estimating the magnitude and frequency of floods in urban basins in Missouri

    USGS Publications Warehouse

    Southard, Rodney E.

    2010-01-01

    Streamgage flood-frequency analyses were done for 35 streamgages on urban streams in and adjacent to Missouri for estimation of the magnitude and frequency of floods in urban areas of Missouri. A log-Pearson Type-III distribution was fitted to the annual series of peak flow data retrieved from the U.S. Geological Survey National Water Information System. For this report, the flood frequency estimates are expressed in terms of percent annual exceedance probabilities of 50, 20, 10, 4, 2, 1, and 0.2. Of the 35 streamgages, 30 are located in Missouri. The remaining five non-Missouri streamgages were added to the dataset to improve the range and applicability of the regression analyses from the streamgage frequency analyses. Ordinary least-squares was used to determine the best set of independent variables for the regression equations. Basin characteristics selected for independent variables into the ordinary least-squares regression analyses were based on theoretical relation to flood flows, literature review of possible basin characteristics, and the ability to measure the basin characteristics using digital datasets and geographic information system technology. Results of the ordinary least-squares were evaluated on the basis of Mallow's Cp statistic, the adjusted coefficient of determination, and the statistical significance of the independent variables. The independent variables of drainage area and percent impervious area were determined to be statistically significant and readily determined from existing digital datasets. The drainage area variable was computed using the best elevation data available, either from a statewide 10-meter grid or high-resolution elevation data from urban areas. The impervious area variable was computed from the National Land Cover Dataset 2001 impervious area dataset. The National Land Cover Dataset 2001 impervious area data for each basin was compared to historical imagery and 7.5-minute topographic maps to verify the national

  3. Accurate Estimation of Carotid Luminal Surface Roughness Using Ultrasonic Radio-Frequency Echo

    NASA Astrophysics Data System (ADS)

    Kitamura, Kosuke; Hasegawa, Hideyuki; Kanai, Hiroshi

    2012-07-01

    It would be useful to measure the minute surface roughness of the carotid arterial wall to detect the early stage of atherosclerosis. In conventional ultrasonography, the axial resolution of a B-mode image depends on the ultrasonic wavelength of 150 µm at 10 MHz because a B-mode image is constructed using the amplitude of the radio-frequency (RF) echo. Therefore, the surface roughness caused by atherosclerosis in an early stage cannot be measured using a conventional B-mode image obtained by ultrasonography because the roughness is 10-20 µm. We have realized accurate transcutaneous estimation of such a minute surface profile using the lateral motion of the carotid arterial wall, which is estimated by block matching of received ultrasonic signals. However, the width of the region where the surface profile is estimated depends on the magnitude of the lateral displacement of the carotid arterial wall (i.e., if the lateral displacement of the arterial wall is 1 mm, the surface profile is estimated in a region of 1 mm in width). In this study, the width was increased by combining surface profiles estimated using several ultrasonic beams. In the present study, we first measured a fine wire, whose diameter was 13 µm, using ultrasonic equipment to obtain an ultrasonic beam profile for determination of the optimal kernel size for block matching based on the correlation between RF echoes. Second, we estimated the lateral displacement and surface profile of a phantom, which had a saw tooth profile on its surface, and compared the surface profile measured by ultrasound with that measured by a laser profilometer. Finally, we estimated the lateral displacement and surface roughness of the carotid arterial wall of three healthy subjects (24-, 23-, and 23-year-old males) using the proposed method.

  4. Techniques for estimating the magnitude and frequency of floods in rural basins of South Carolina, 1999

    USGS Publications Warehouse

    Feaster, Toby D.; Tasker, Gary D.

    2002-01-01

    Data from 167 streamflow-gaging stations in or near South Carolina with 10 or more years of record through September 30, 1999, were used to develop two methods for estimating the magnitude and frequency of floods in South Carolina for rural ungaged basins that are not significantly affected by regulation. Flood frequency estimates for 54 gaged sites in South Carolina were computed by fitting the water-year peak flows for each site to a log-Pearson Type III distribution. As part of the computation of flood-frequency estimates for gaged sites, new values for generalized skew coefficients were developed. Flood-frequency analyses also were made for gaging stations that drain basins from more than one physiographic province. The U.S. Geological Survey, in cooperation with the South Carolina Department of Transportation, updated these data from previous flood-frequency reports to aid officials who are active in floodplain management as well as those who design bridges, culverts, and levees, or other structures near streams where flooding is likely to occur. Regional regression analysis, using generalized least squares regression, was used to develop a set of predictive equations that can be used to estimate the 2-, 5-, 10-, 25-, 50-, 100-, 200-, and 500-year recurrence-interval flows for rural ungaged basins in the Blue Ridge, Piedmont, upper Coastal Plain, and lower Coastal Plain physiographic provinces of South Carolina. The predictive equations are all functions of drainage area. Average errors of prediction for these regression equations ranged from -16 to 19 percent for the 2-year recurrence-interval flow in the upper Coastal Plain to -34 to 52 percent for the 500-year recurrence interval flow in the lower Coastal Plain. A region-of-influence method also was developed that interactively estimates recurrence- interval flows for rural ungaged basins in the Blue Ridge of South Carolina. The region-of-influence method uses regression techniques to develop a unique

  5. Defining the hundred year flood: A Bayesian approach for using historic data to reduce uncertainty in flood frequency estimates

    NASA Astrophysics Data System (ADS)

    Parkes, Brandon; Demeritt, David

    2016-09-01

    This paper describes a Bayesian statistical model for estimating flood frequency by combining uncertain annual maximum (AMAX) data from a river gauge with estimates of flood peak discharge from various historic sources that predate the period of instrument records. Such historic flood records promise to expand the time series data needed for reducing the uncertainty in return period estimates for extreme events, but the heterogeneity and uncertainty of historic records make them difficult to use alongside Flood Estimation Handbook and other standard methods for generating flood frequency curves from gauge data. Using the flow of the River Eden in Carlisle, Cumbria, UK as a case study, this paper develops a Bayesian model for combining historic flood estimates since 1800 with gauge data since 1967 to estimate the probability of low frequency flood events for the area taking account of uncertainty in the discharge estimates. Results show a reduction in 95% confidence intervals of roughly 50% for annual exceedance probabilities of less than 0.0133 (return periods over 75 years) compared to standard flood frequency estimation methods using solely systematic data. Sensitivity analysis shows the model is sensitive to 2 model parameters both of which are concerned with the historic (pre-systematic) period of the time series. This highlights the importance of adequate consideration of historic channel and floodplain changes or possible bias in estimates of historic flood discharges. The next steps required to roll out this Bayesian approach for operational flood frequency estimation at other sites is also discussed.

  6. Estimation of pseudo-2D shear-velocity section by inversion of high frequency surface waves

    USGS Publications Warehouse

    Luo, Y.; Liu, J.; Xia, J.; Xu, Y.; Liu, Q.

    2006-01-01

    A scheme to generate pseudo-2D shear-velocity sections with high horizontal resolution and low field cost by inversion of high frequency surface waves is presented. It contains six steps. The key step is the joint method of crossed correlation and phase shift scanning. This joint method chooses only two traces to generate image of dispersion curve. For Rayleigh-wave dispersion is most important for estimation of near-surface shear-wave velocity, it can effectively obtain reliable images of dispersion curves with a couple of traces. The result of a synthetic example shows the feasibility of this scheme. ?? 2005 Society of Exploration Geophysicists.

  7. Digital pilot aided carrier frequency offset estimation for coherent optical transmission systems.

    PubMed

    Zhao, Donghe; Xi, Lixia; Tang, Xianfeng; Zhang, Wenbo; Qiao, Yaojun; Zhang, Xiaoguang

    2015-09-21

    We present a digital pilot aided carrier frequency offset estimation (FOE) method for coherent optical transmission systems. Unlike the conventional pilot tone insertion scheme, the pilot of the proposed method is generated in a digital manner and can serve as a good FOE indicator. Aided by this kind of digital pilot, the FOE is implemented by determining the location of the digital pilot in the spectrum. Theoretical analysis and numerical simulations show that the proposed method has the advantages in wide range, high accuracy, modulation formats independent, no need to remove the modulation, and high tolerance to the residual chromatic dispersion (CD) and polarization mode dispersion (PMD).

  8. Estimation of flood frequency by SCHADEX method - in Nysa Kłodzka catchment

    NASA Astrophysics Data System (ADS)

    Osuch, M.; Romanowicz, R. J.; Paquet, E.; Garavaglia, F.

    2012-04-01

    Estimation of design flood using Continuous Simulation (CS) has emerged as a very active research topic across academic institutions in Europe. CS is based on the use of rainfall-runoff models, of various complexity, for transforming precipitation data into river flow. By coupling a rainfall-runoff model with a stochastic rainfall model, Monte Carlo simulations can generate long series of synthetic rainfall being transformed into river flow from which flood frequency characteristics can be deducted. This approach is favoured by politicians and water managers, as it allows the influence of water management and climatic changes to be taken into account during the estimation of flood frequency curves. The other approach to FFA is based on the available historical maximum annual or seasonal flow data and consists of fitting theoretical cumulative distributions to observations. These theoretical, parameterised distributions are used in practical applications to derive flow quantiles with a desired probability of exceedence for the purpose of water management. The aim of this work is an application of a continuous simulation approach to flood frequency analysis (FFA) using the Nysa Kłodzka catchment as a case study. The applied method is SCHADEX, a probabilistic method for extreme floods estimation which combines a weather pattern based rainfall probabilistic model and a conceptual rainfall-runoff model, within a stochastic event simulation framework. In that method, the distribution of areal precipitation is described by a compound probabilistic distribution based on weather patterns sub-sampling (MEWP distribution). These patterns represent synoptic situation and allow for disagreggation of heavy rainfall data into homogenous subsamples (Garavaglia et al. 2010 a and b). Extreme flood estimation is then achieved by stochastic simulation using MORDOR rainfall-runoff model. The resulting FFA curve is compared to an outcome of a seasonal maxima approach (recommended

  9. Surrogate measures for providing high frequency estimates of total phosphorus concentrations in urban watersheds.

    PubMed

    Viviano, Gaetano; Salerno, Franco; Manfredi, Emanuela Chiara; Polesello, Stefano; Valsecchi, Sara; Tartari, Gianni

    2014-11-01

    Until robust in situ sensors for total phosphorus (TP) are developed, continuous water quality measurements have the potential to be used as surrogates for generating high frequency estimates. Their use has widespread implications for water quality monitoring programmes considering that TP, in particular, is generally recognised as the limiting factor in the process of eutrophication. Surrogate measures for TP concentration, such as turbidity, have proved useful within natural and agricultural contexts, but their predictive capability for urban watersheds is considered more difficult, due to the different sources of TP, though a strict relationship with turbidity/suspended matter has been clearly described even for these environments. In this context, we investigated this still unresolved problem for high frequency estimation of TP concentration in urban environments by monitoring a medium-sized (71 km(2)) urban watershed (Lambro River watershed, north Italy) in which we detected 60 active combined sewer overflows, and an its natural sub-basin for comparison. We found two different relationships between turbidity and TP concentration in the investigated urban watershed that differently describe the prevalence of TP from point sources (domestic wastewaters) or diffuse origin (surface runoff). In this regard, we first characterise the prevailing sources of TP by using a marker for detecting domestic wastewater contamination (caffeine), then we describe the mutual relationships amongst the continuously monitored variables (in our case the occurrence of the First Flush and the clockwise turbidity/discharge hysteresis). Afterwards we discriminate, by observing variables that are continuously monitored (in our case, the discharge and the turbidity), amongst the continuous surrogate records according to their sources. In conclusion, we are able to apply the relevant turbidity/TP regression equations to each turbidity record and, thus, estimate the respective TP

  10. Techniques for estimating peak-flow frequency relations for North Dakota streams

    USGS Publications Warehouse

    Williams-Sether, Tara

    1992-01-01

    This report presents techniques for estimating peak-flow frequency relations for North Dakota streams. In addition, a generalized skew coefficient analysis was completed for North Dakota to test the validity of using the generalized skew coefficient map in Bulletin 17B of the Hydrology Subcommittee of the Interagency Advisory Committee on Water Data, 1982, 'Guidelines for Determining Flood Flow Frequency.' The analysis indicates that the generalized skew coefficient map in Bulletin 17B provides accurate estimates of generalized skew coefficient values for natural-flow streams in North Dakota. Peak-flow records through 1988 for 192 continuous- and partial-record streamflow gaging stations that had 10 or more years of record were used in a generalized least-squares regression analysis that relates peak flows for selected recurrence intervals to selected basin characteristics. Peak-flow equations were developed for recurrence intervals of 2, 10, 15, 25, 50, 100, and 500 years for three hydrologic regions in North Dakota. The peak-flow equations are applicable to natural-flow streams that have drainage areas of less than or equal to 1,000 square miles. The standard error of estimate for the three hydrologic regions ranges from 60 to 70 percent for the 100-year peak-flow equations. Methods are presented for transferring peak-flow data from gaging stations to ungaged sites on the same stream and for determining peak flows for ungaged sites on ungaged streams. Peak-flow relations, weighted estimates of peak flow, and selected basin characteristics are tabulated for the 192 gaging stations used in the generalized skew coefficient and regression analyses. Peak-flow relations also are provided for 63 additional gaging stations that were not used in the generalized skew coefficient and regression analyses. These 63 gaging stations generally represent streams that are significantly controlled by regulation and those that have drainage areas greater than 1,000 square miles.

  11. Estimating species - area relationships by modeling abundance and frequency subject to incomplete sampling.

    PubMed

    Yamaura, Yuichi; Connor, Edward F; Royle, J Andrew; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio

    2016-07-01

    Models and data used to describe species-area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species-area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species-area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density-area relationships and occurrence probability-area relationships can alter the form of species-area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied to a

  12. Estimating species - area relationships by modeling abundance and frequency subject to incomplete sampling.

    PubMed

    Yamaura, Yuichi; Connor, Edward F; Royle, J Andrew; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio

    2016-07-01

    Models and data used to describe species-area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species-area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species-area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density-area relationships and occurrence probability-area relationships can alter the form of species-area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied to a

  13. Estimating species – area relationships by modeling abundance and frequency subject to incomplete sampling

    USGS Publications Warehouse

    Yamaura, Yuichi; Connor, Edward F.; Royle, Andy; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio

    2016-01-01

    Models and data used to describe species–area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species–area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species–area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density–area relationships and occurrence probability–area relationships can alter the form of species–area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied

  14. A study of the association of childhood asthma with HLA alleles in the population of Siliguri, West Bengal, India.

    PubMed

    Lama, M; Chatterjee, M; Chaudhuri, T K

    2014-09-01

    Asthma is a heterogeneous disease for which a strong genetic basis is firmly established. It is a complex disorder influenced by gene-environment interaction. Human leukocyte antigen (HLA) genes have been shown to be consistently associated with asthma and its related phenotypes in various populations. The aim of this study was to determine the frequency of the selected HLA classes I and II allelic groups in asthmatic and control groups. HLA typing was performed using polymerase chain reaction-sequence-specific typing (PCR-SSP) method. The allele frequency was estimated by direct counting. Frequency of each HLA allelic group was compared between asthmatic group and control group using χ(2) test. P-value was corrected by multiplying with the number of the allelic groups studied. Odds ratio (OR) and its corresponding 95% confidence interval (CI) for each allelic group were calculated using graphpad instat 3.10. The results of this study showed a significantly higher frequency of HLA-DRB1*03 in asthmatics than in controls (11.43% vs 3.64%, OR = 3.78, 95% CI = 1.61-8.85, P = 0.0025, Pcorr  < 0.05). Analysis of HLA alleles in low and high total serum immunoglobulin E (IgE) level in asthmatics revealed no significant association. HLA-DRB1*03 may be implicated in the susceptibility to asthma in the pediatric population.

  15. Sequential detection and robust estimation of vapor concentration using frequency-agile lidar time series data

    NASA Astrophysics Data System (ADS)

    Warren, Russell E.; Vanderbeek, Richard G.; D'Amico, Francis M.; Ben-David, Avishai

    1999-01-01

    This paper extends an earlier optimal approach for frequency-agile lidar using fixed-size samples of data to include the time series aspect of data collection. The likelihood ratio test methodology for deterministic but unknown vapor concentration is replaced by a Bayesian formalism in which the path integral of vapor concentration CL evolves in time through a random walk model. The fixed- sample maximum likelihood estimates of CL derived earlier are replaced by Kalman filter estimates, and the log- likelihood ratio is generalized to a sequential test statistic written in terms of the Kalman estimates. In addition to the time series aspect, the earlier approach is generalized by (1) including the transmitted energy on a short-by-shot basis in a statistically optimum manner, (2) adding a linear slope component to the transmitter and received data models, and (3) replacing the nominal multivariate normal statistical assumption by a robust model in the Huber sensor for mitigating the effects of occasional data spikes caused by laser misfiring or EMI. The estimation and detection algorithms are compared with fixed-sample processing by the DIAL method on FAL data collected by ERDEC during vapor chamber testing at Dugway, Utah.

  16. Binary prefix for sampling frequency offset estimation in dispersive optical transmissions.

    PubMed

    Cheng, Lin; Liu, Xiang; Chand, Naresh; Effenberger, Frank; Chang, Gee-Kung

    2015-10-01

    We propose and experimentally demonstrate a method for sampling frequency offset (SFO) estimation in optical communication systems based on periodically inserted identical binary prefix. Different from conventional cyclic prefix, binary prefix provides not only high tolerance to chromatic dispersion in dispersive fiber transmission, but also the ability to estimate SFO by simple receiver-side digital signal processing. Moreover, this binary prefix based scheme is generally applicable to any advanced modulation formats. A proof-of-concept experiment is conducted to quantify the accuracy and tolerance of the scheme in estimating SFO. It is found that over a wide SFO range up to 341 ppm, the estimation error is kept under 20 ppb and signals are recovered with the same quality as with zero-offset sampling. The experimental results also confirm that this method is tolerant to link signal-to-noise ratio loss and dispersion, showing no additional penalty after transmission over a 40-km standard single-mode fiber at 1550 nm. PMID:26480132

  17. A method for estimating magnitude and frequency of floods in Montana

    USGS Publications Warehouse

    Johnson, M.V.; Omang, R.J.

    1976-01-01

    This report provides methods for estimating flood characteristics at most natural flow sites on rural streams in Montana. It also contains significant flood data and related information for many gaged sites on Montana streams. Frequency curves are provided for 442 gaged sites as defined by log-Pearson Type III analysis. To allow estimates at ungaged sites, mathematical equations relate the 2-, 5-, 10-, 25-, 50-, and 100-year flood magnitudes to basin characteristics. Drainage area, main channel slope, and mean annual precipitation were found to be the most significant estimating variables. Equations presented are limited to use on streams with drainage areas from about 0.1 to 2,600 square miles (0.3 to 6,700 square kilometres), with slope from about 5 to 1,200 feet per mile (1.5 to 366 metres per kilometre), and with precipitation from 10 to 100 inches (250 to 2,500 millimetres). Nomographs provide a simple graphical means of solving the estimating relations, and illustrative examples are presented.

  18. Real-Time Frequency Response Estimation Using Joined-Wing SensorCraft Aeroelastic Wind-Tunnel Data

    NASA Technical Reports Server (NTRS)

    Grauer, Jared A; Heeg, Jennifer; Morelli, Eugene A

    2012-01-01

    A new method is presented for estimating frequency responses and their uncertainties from wind-tunnel data in real time. The method uses orthogonal phase-optimized multi- sine excitation inputs and a recursive Fourier transform with a least-squares estimator. The method was first demonstrated with an F-16 nonlinear flight simulation and results showed that accurate short period frequency responses were obtained within 10 seconds. The method was then applied to wind-tunnel data from a previous aeroelastic test of the Joined- Wing SensorCraft. Frequency responses describing bending strains from simultaneous control surface excitations were estimated in a time-efficient manner.

  19. Knowledge of results for motor learning: relationship between error estimation and knowledge of results frequency.

    PubMed

    Guadagnoli, M A; Kohl, R M

    2001-06-01

    The authors of the present study investigated the apparent contradiction between early and more recent views of knowledge of results (KR), the idea that how one is engaged before receiving KR may not be independent of how one uses that KR. In a 2 ×: 2 factorial design, participants (N = 64) practiced a simple force-production task and (a) were required, or not required, to estimate error about their previous response and (b) were provided KR either after every response (100%) or after every 5th response (20%) during acquisition. A no-KR retention test revealed an interaction between acquisition error estimation and KR frequencies. The group that received 100% KR and was required to error estimate during acquisition performed the best during retention. The 2 groups that received 20% KR performed less well. Finally, the group that received 100% KR and was not required to error estimate during acquisition performed the poorest during retention. One general interpretation of that pattern of results is that motor learning is an increasing function of the degree to which participants use KR to test response hypotheses (J. A. Adams, 1971; R. A. Schmidt, 1975). Practicing simple responses coupled with error estimation may embody response hypotheses that can be tested with KR, thus benefiting motor learning most under a 100% KR condition. Practicing simple responses without error estimation is less likely to embody response hypothesis, however, which may increase the probability that participants will use KR to guide upcoming responses, thus attenuating motor learning under a 100% KR condition. The authors conclude, therefore, that how one is engaged before receiving KR may not be independent of how one uses KR. PMID:11404216

  20. Characterization of the treefrog null allele, 1991

    SciTech Connect

    Guttman, S.I.

    1992-04-01

    Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

  1. Characterization of the treefrog null allele

    SciTech Connect

    Guttman, S.I. . Dept. of Zoology)

    1990-12-01

    As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

  2. HLA-A, HLA-B, HLA-DRB1 allele and haplotype frequencies in 6384 umbilical cord blood units and transplantation matching and engraftment statistics in the Zhejiang cord blood bank of China.

    PubMed

    Wang, F; He, J; Chen, S; Qin, F; Dai, B; Zhang, W; Zhu, F M; Lv, H J

    2014-02-01

    Umbilical cord blood (UCB) is a widely accepted source of progenitor cells, and now, many cord blood banks were established. Here, we analysed the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies, HLA matching possibilities for searching potential donors and outcome of UCB transplantations in Zhejiang cord blood bank of China. A total of 6384 UCB units were characterized for 17 HLA-A, 30 HLA-B and 13 HLA-DRB1 alleles at the first field resolution level. Additionally, B*14, B*15 and B*40 were typed to the second field level. A total of 1372 distinct A-B-DRB1 haplotypes were identified. The frequencies of 7 haplotypes were more than 1%, and 439 haplotypes were <0.01%. A*02-B*46-DRB1*09, A*33-B*58-DRB1*03 and A*30-B*13-DRB1*07 were the most common haplotypes, with frequencies of 4.4%, 3.3%, and 2.9%, respectively. Linkage disequilibrium(LD) analysis showed that there were 83 A-B, 106 B-DRB1, 54 A-DRB1 haplotypes with positive LD, in which 51 A-B, 60 B-DRB1, 32 A-DRB1 haplotypes exhibited a significant LD (P < 0.05). In 682 search requests, 12.9%, 40.0% and 42.7% of patients were found to have 6 of 6, 5 of 6 and 4 of 6 HLA-A, HLA-B and HLA-DRB1 matching donors, respectively. A total of 30 UCB units were transplanted to 24 patients (3 patients not evaluated due to early death); 14 of 21 patients (66.7%) engrafted. This study reveals the HLA distribution and its transplantation application in the cord blood bank of Zhejiang province. These data can help to select potential UCB donors for transplantation and used to assess the scale of new cord blood banking endeavours.

  3. Left ventricle motion estimation based on signal-dependent time-frequency representation

    NASA Astrophysics Data System (ADS)

    Gutierrez, Marco A.; Weiderpass, Heinar A.; Furuie, Sergio S.

    2003-05-01

    In current clinical practice, the noninvasive assessment of left ventricular deformation can be determined using all the principal imaging modalities, including contrast angiography, echocardiography, cine computed tomography, single photon emission tomography and magnetic resonance imaging. However, since the heart undergoes complex motion, proper characterization of its motion still remains an open and challenging research problem. A number of approaches for nonrigid motion analysis have been studied in the literature. Much of the effort has confined to estimate the displacement vector for each image point or optical flow. This is a challenging problem in image analysis because of a wide range of possible motions and the presence of noise in the image sets. In this work, we present an algorithm for computation of optical flow based on a signal-dependent radially Gaussian kernel that adapts over time. The adaptive kernel obtained from the proposed algorithm is used to estimate a 3D-frequency spectrum for a given pixel in a series of images. The orientation of the spectrum in the frequency domain is totally governed by the pixel velocity. In a recent contribution, a linear regression model is used over the spectrum to obtain the velocity components that are proportional to the pixel movement.

  4. Radio Frequency Attenuation Length Estimates In Ice from Antarctic and Greenlandic Radar Depth Sounding Data

    NASA Astrophysics Data System (ADS)

    Stockham, Mark

    2014-03-01

    The balloon-borne Antarctic Impulsive Transient Antenna (ANITA) experiment is designed to detect in-ice neutrino collisions in Antarctica. These collisions produce radio waves that propagate upward to the suite of 32 horn antennas that constitute ANITA. The primary virtue of ANITA is the ability to simultaneously observe 1 million cubic kilometers of ice from its 38 kilometer altitude vantage point. The radio frequency signal strength observed at the balloon, however, depends on the radio frequency attenuation length of the ice through which the neutrino-generated signal must travel. Attenuation length is a location-specific ice property and varies mainly as a function of temperature and chemistry. The Center for Remote Sensing of Ice Sheets (CReSIS) project has data from many locations in Antarctica and Greenland produced by radar depth sounding. Using methods developed by analyzing the continuum signal in radar depth sounding data from Greenland, attenuation length estimates are compared to estimates derived from ice core data.

  5. Suspension parameter estimation in the frequency domain using a matrix inversion approach

    NASA Astrophysics Data System (ADS)

    Thite, A. N.; Banvidi, S.; Ibicek, T.; Bennett, L.

    2011-12-01

    The dynamic lumped parameter models used to optimise the ride and handling of a vehicle require base values of the suspension parameters. These parameters are generally experimentally identified. The accuracy of identified parameters can depend on the measurement noise and the validity of the model used. The existing publications on suspension parameter identification are generally based on the time domain and use a limited degree of freedom. Further, the data used are either from a simulated 'experiment' or from a laboratory test on an idealised quarter or a half-car model. In this paper, a method is developed in the frequency domain which effectively accounts for the measurement noise. Additional dynamic constraining equations are incorporated and the proposed formulation results in a matrix inversion approach. The nonlinearities in damping are estimated, however, using a time-domain approach. Full-scale 4-post rig test data of a vehicle are used. The variations in the results are discussed using the modal resonant behaviour. Further, a method is implemented to show how the results can be improved when the matrix inverted is ill-conditioned. The case study shows a good agreement between the estimates based on the proposed frequency-domain approach and measurable physical parameters.

  6. Practical methods for using vegetation patterns to estimate avalanche frequency and magnitude

    NASA Astrophysics Data System (ADS)

    Simonson, S.; Fassnacht, S. R.

    2011-12-01

    Practitioners working in avalanche terrain may never witness an extreme event, but understanding extreme events is important for categorizing avalanches that occur within a given season. Historical records of avalanche incidents and direct observations are the most reliable evidence of avalanche activity, but patterns in vegetation can be used to further quantify and map the frequency and magnitude of past events. We surveyed published literature to synthesize approaches for using vegetation sampling to characterize avalanche terrain, and developed examples to identify the benefits and caveats of using different practical field methods to estimate avalanche frequency and magnitude. Powerful avalanches can deposit massive piles of snow, rocks, and woody debris in runout zones. Large avalanches (relative to the path) can cut fresh trimlines, widening their tracks by uprooting, stripping, and breaking trees. Discs and cores can be collected from downed trees to detect signals of past avalanche disturbance recorded in woody plant tissue. Signals of disturbance events recorded in tree rings can include direct impact scars from the moving snow and wind blast, development of reaction wood in response to tilting, and abrupt variation in the relative width of annual growth rings. The relative ages of trees in avalanche paths and the surrounding landscape can be an indicator of the area impacted by past avalanches. Repeat photography can also be useful to track changes in vegetation over time. For Colorado, and perhaps elsewhere, several vegetation ecology methods can be used in combination to accurately characterize local avalanche frequency and magnitude.

  7. Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles.

    PubMed

    Hoffert, Jason D; Pisitkun, Trairak; Miller, R Lance

    2012-06-01

    Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially in the last 5-10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and the number of breeding rounds. Therefore, a well planned breeding strategy is critical for keeping costs to a minimum. However, designing a viable breeding strategy can be challenging. With so many different variables this would be an ideal task for a computer program. To facilitate this process, we created a Java-based program called Conditional Allele Mouse Planner (CAMP). CAMP is designed to provide an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. We provide a description of CAMP, how to use it, and offer it freely as an application.

  8. Towards Robust Estimation and Correction of Ionospheric TEC Signatures in Low Frequency Spaceborne SAR data

    NASA Astrophysics Data System (ADS)

    Liao, H.; Meyer, F. J.

    2013-12-01

    In the last decade, abundant research has proven the existence of ionospheric distortions in data acquired by spaceborne low-frequency Synthetic Aperture Radar (SAR) systems. The most prominent of these distortions are resolution degradation, distortions of the image geometry, biased phase information, and Faraday rotation, a rotation of the signal's polarization vector. For a given system, all these distortions are characterized by the ionospheric Total Electron Content (TEC). Hence, global correction of SAR would require accurate knowledge of TEC. While a variety of techniques for TEC estimation are available, the performance of these algorithms is limited as they do not exploit the entirety of ionosphere induced signatures available in a SAR data set. Instead, only a subset of information is selected by identifying the parameter of highest sensitivity for correcting a specific SAR observable. Therefore, more research is needed to improve the robustness and accuracy of ionospheric correction methods. The goal of our research is to improve ionospheric estimation performance through combining existing ionospheric correction methods with complementary strengths. Firstly, the implementational details of three ionospheric estimation methods will be presented. These include: (1) A Faraday rotation (FR)-based method where FR is first estimated from quad-polarized SAR data using the classical Bickel and Bates estimator. Ionospheric TEC is then derived from the FR measurements based on satellite observation geometry and a three-dimensional geomagnetic field model; (2) a second method exploits the fact that ionospheric group delay is dependent on the signal frequency. A lower and a higher-frequency sub-look image are firstly extracted from a wide-band SAR acquisition and ionosphere-induced range shifts between these sub-looks are then calculated using image cross-correlation methods. The advantage of this method is that it only requires a one-band image to determine

  9. Methods for estimating flood frequency in Montana based on data through water year 1998

    USGS Publications Warehouse

    Parrett, Charles; Johnson, Dave R.

    2004-01-01

    Annual peak discharges having recurrence intervals of 2, 5, 10, 25, 50, 100, 200, and 500 years (T-year floods) were determined for 660 gaged sites in Montana and in adjacent areas of Idaho, Wyoming, and Canada, based on data through water year 1998. The updated flood-frequency information was subsequently used in regression analyses, either ordinary or generalized least squares, to develop equations relating T-year floods to various basin and climatic characteristics, equations relating T-year floods to active-channel width, and equations relating T-year floods to bankfull width. The equations can be used to estimate flood frequency at ungaged sites. Montana was divided into eight regions, within which flood characteristics were considered to be reasonably homogeneous, and the three sets of regression equations were developed for each region. A measure of the overall reliability of the regression equations is the average standard error of prediction. The average standard errors of prediction for the equations based on basin and climatic characteristics ranged from 37.4 percent to 134.1 percent. Average standard errors of prediction for the equations based on active-channel width ranged from 57.2 percent to 141.3 percent. Average standard errors of prediction for the equations based on bankfull width ranged from 63.1 percent to 155.5 percent. In most regions, the equations based on basin and climatic characteristics generally had smaller average standard errors of prediction than equations based on active-channel or bankfull width. An exception was the Southeast Plains Region, where all equations based on active-channel width had smaller average standard errors of prediction than equations based on basin and climatic characteristics or bankfull width. Methods for weighting estimates derived from the basin- and climatic-characteristic equations and the channel-width equations also were developed. The weights were based on the cross correlation of residuals from the

  10. Estimating At-Sea Mortality of Marine Turtles from Stranding Frequencies and Drifter Experiments

    PubMed Central

    Koch, Volker; Peckham, Hoyt; Mancini, Agnese; Eguchi, Tomoharu

    2013-01-01

    Strandings of marine megafauna can provide valuable information on cause of death at sea. However, as stranding probabilities are usually very low and highly variable in space and time, interpreting the results can be challenging. We evaluated the magnitude and distribution of at-sea mortality of marine turtles along the Pacific coast of Baja California Sur, México during 2010–11, using a combination of counting stranded animals and drifter experiments. A total of 594 carcasses were found during the study period, with loggerhead (62%) and green turtles (31%) being the most common species. 87% of the strandings occurred in the southern Gulf of Ulloa, a known hotspot of loggerhead distribution in the Eastern Pacific. While only 1.8% of the deaths could be definitively attributed to bycatch (net marks, hooks), seasonal variation in stranding frequencies closely corresponded to the main fishing seasons. Estimated stranding probabilities from drifter experiments varied among sites and trials (0.05–0.8), implying that only a fraction of dead sea turtles can be observed at beaches. Total mortality estimates for 15-day periods around the floater trials were highest for PSL, a beach in the southern Gulf of Ulloa, ranging between 11 sea turtles in October 2011 to 107 in August 2010. Loggerhead turtles were the most numerous, followed by green and olive ridley turtles. Our study showed that drifter trials combined with beach monitoring can provide estimates for death at sea to measure the impact of small-scale fisheries that are notoriously difficult to monitor for by-catch. We also provided recommendations to improve the precision of the mortality estimates for future studies and highlight the importance of estimating impacts of small–scale fisheries on marine megafauna. PMID:23483880

  11. Carrier frequency offset estimation for an acoustic-electric channel using 16 QAM modulation

    NASA Astrophysics Data System (ADS)

    Cunningham, Michael T.; Anderson, Leonard A.; Wilt, Kyle R.; Chakraborty, Soumya; Saulnier, Gary J.; Scarton, Henry A.

    2016-05-01

    Acoustic-electric channels can be used to send data through metallic barriers, enabling communications where electromagnetic signals are ineffective. This paper considers an acoustic-electric channel that is formed by mounting piezoelectric transducers on metallic barriers that are separated by a thin water layer. The transducers are coupled to the barriers using epoxy and the barriers are positioned to axially-align the PZTs, maximizing energy transfer efficiency. The electrical signals are converted by the transmitting transducers into acoustic waves, which propagate through the elastic walls and water medium to the receiving transducers. The reverberation of the acoustic signals in these channels can produce multipath distortion with a significant delay spread that introduces inter-symbol interference (ISI) into the received signal. While the multipath effects can be severe, the channel does not change rapidly which makes equalization easier. Here we implement a 16-QAM system on this channel, including a method for obtaining accurate carrier frequency offset (CFO) estimates in the presence of the quasi-static multipath propagation. A raised-power approach is considered but found to suffer from excessive data noise resulting from the ISI. An alternative approach that utilizes a pilot tone burst at the start of a data packet is used for CFO estimation and found to be effective. The autocorrelation method is used to estimate the frequency of the received burst. A real-time prototype of the 16 QAM system that uses a Texas Instruments MSP430 microcontroller-based transmitter and a personal computer-based receiver is presented along with performance results.

  12. High frequency and allele-specific differences of BRCA1 founder mutations in breast cancer and ovarian cancer patients from Belarus.

    PubMed

    Bogdanova, N V; Antonenkova, N N; Rogov, Y I; Karstens, J H; Hillemanns, P; Dörk, T

    2010-10-01

    Breast cancer and ovarian cancer are common malignancies in Belarus accounting for about 3500 and 800 new cases per year, respectively. For breast cancer, the rates and age of onset appear to vary significantly in regions differentially affected by the Chernobyl accident. We assessed the frequency and distribution of three BRCA1 founder mutations 5382insC, 4153delA and Cys61Gly in two hospital-based series of 1945 unselected breast cancer patients and of 201 unselected ovarian cancer patients from Belarus as well as in 1019 healthy control females from the same population. Any of these mutations were identified in 4.4% of the breast cancer patients, 26.4% of the ovarian cancer patients and 0.5% of the controls. In the breast cancer patients, BRCA1 mutations were strongly associated with earlier age at diagnosis, with oestrogen receptor (ER) negative tumours and with a first-degree family history of breast cancer, although only 35% of the identified BRCA1 mutation carriers had such a family history. There were no marked differences in the regional distribution of BRCA1 mutations, so that the significant differences in age at diagnosis and family history of breast cancer patients from areas afflicted by the Chernobyl accident could not be explained by BRCA1. We next observed a higher impact and a shifted mutational spectrum of BRCA1 in the series of Byelorussian ovarian cancer patients where the three founder mutations accounted for 26.4% (53/201). While the Cys61Gly mutation appeared underrepresented in ovarian cancer as compared with breast cancer cases from the same population (p = 0.01), the 4153delA mutation made a higher contribution to ovarian cancer than to breast cancer (p < 0.01). BRCA1 mutations were significantly enriched among ovarian cancer cases with a first-degree family history of breast or ovarian cancer, whereas the median age at ovarian cancer diagnosis was not different between mutation carriers and non-carriers. Taken together, these results

  13. Relative validity and reproducibility of a food frequency questionnaire to estimate intake of dietary phylloquinone and menaquinones

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Several observational studies have investigated the relation of dietary phylloquinone and menaquinone intake with occurrence of chronic diseases. Most of these studies relied on food frequency questionnaires (FFQ) to estimate the intake of phylloquinone and menaquinones. However, none of...

  14. Curved-Region-Based Ridge Frequency Estimation and Curved Gabor Filters for Fingerprint Image Enhancement

    NASA Astrophysics Data System (ADS)

    Gottschlich, Carsten

    2012-04-01

    Gabor filters play an important role in many application areas for the enhancement of various types of images and the extraction of Gabor features. For the purpose of enhancing curved structures in noisy images, we introduce curved Gabor filters which locally adapt their shape to the direction of flow. These curved Gabor filters enable the choice of filter parameters which increase the smoothing power without creating artifacts in the enhanced image. In this paper, curved Gabor filters are applied to the curved ridge and valley structure of low-quality fingerprint images. First, we combine two orientation field estimation methods in order to obtain a more robust estimation for very noisy images. Next, curved regions are constructed by following the respective local orientation and they are used for estimating the local ridge frequency. Lastly, curved Gabor filters are defined based on curved regions and they are applied for the enhancement of low-quality fingerprint images. Experimental results on the FVC2004 databases show improvements of this approach in comparison to state-of-the-art enhancement methods.

  15. Instantaneous frequency-based ultrasonic temperature estimation during focused ultrasound thermal therapy.

    PubMed

    Liu, Hao-Li; Li, Meng-Lin; Shih, Tzu-Ching; Huang, Sheng-Min; Lu, I-Yeh; Lin, Deng-Yn; Lin, Shi-Ming; Ju, Kuen-Cheng

    2009-10-01

    Focused ultrasound thermal therapy relies on temperature monitoring for treatment guidance and assurance of targeting and dose control. One potential approach is to monitor temperature change through ultrasonic-backscattered signal processing. The current approach involves the detection of echo time-shifts based on cross-correlation processing from segmented radiofrequency (RF) data. In this study, we propose a novel ultrasonic temperature-measurement approach that detects changes in instantaneous frequency along the imaging beam direction. Focused ultrasound was used as the heating source, and the 1-D beamformed RF signals provided from an ultrasound imager were used to verify the proposed algorithm for temperature change estimation. For comparison, a conventional cross-correlation technique was also evaluated. Heating experiments testing tissue-mimicking phantoms and ex vivo porcine muscles were conducted. The results showed that temperature can be well estimated by the proposed algorithm in the temperature range, where the relationship of sound speed versus temperature is linear. Compared with the cross-correlation-based algorithm, the proposed new algorithm yields a six-fold increase in computational efficiency, along with comparable contrast-detection ability and precision. This new algorithm may serve as an alternative method for implementing temperature estimation into a clinical ultrasound imager for thermal therapy guidance. PMID:19643529

  16. Use of indexed historical floods in flood frequency estimation with Fuzzy Bayesian methods

    NASA Astrophysics Data System (ADS)

    Salinas, Jose; Viglione, Alberto; Kiss, Andrea; Bloeschl, Guenter

    2015-04-01

    Efforts of the historical environmental extremes community during the last decades have resulted in the existence of long time series of floods, for example in Central Europe and the Mediterranean region, which in some cases range longer than 500 years in the past. In most of the cases the flood time series are presented in terms of indices, representing a combination of socio-economic indicators for the flood impact, e.g. economic damage, flood duration and extension, ... In hydrological engineering, historical floods are very useful because they give additional information which will reduce the uncertainty in estimates of discharges with low annual exceedance probabilities, i.e. with high return periods. In order to use the historical floods in formal flood frequency analysis, the precise value of the peak discharges would ideally be known, but as commented, they are most usually given in term of indices. This work presents a novel method on how to obtain a prior distribution for the parameters of the annual peak discharges distribution from indexed historical floods time series. The prior distribution is incorporated in the flood frequency estimation via Bayesian methods (see e.g. Viglione et al., 2013) in order to reduce the uncertainties in the design flood estimates. The historical data used is subject to a high degree of uncertainty and unpreciseness. In this sense, a framework is presented where the discharge thresholds between flood indices are modeled as fuzzy numbers. These fuzzy thresholds will define a fuzzy prior distribution, which will requires to apply Fuzzy Bayesian Inference (Viertl, 2008ab) to obtain fuzzy credibility intervals for the design floods. Viertl, R. (2008a) Foundations of Fuzzy Bayesian Inference, Journal of Uncertain Systems, 2, 187-191. Viertl, R. (2008b) Fuzzy Bayesian Inference. In: Soft Methods For Handling Variability And Imprecision. Advances In Soft Computing. Vol. 48. Springer-Verlag Berlin, pp 10-15. Viglione, A., R. Merz

  17. Indoor location estimation with optical-based orthogonal frequency division multiplexing communications

    NASA Astrophysics Data System (ADS)

    Aminikashani, Mohammadreza; Gu, Wenjun; Kavehrad, Mohsen

    2016-05-01

    Visible light communication (VLC) using light-emitting diodes has been gaining increasing attention in recent years as it is appealing for a wide range of applications such as indoor positioning. Orthogonal frequency division multiplexing (OFDM) has been applied to indoor wireless optical communications in order to mitigate the effect of multipath distortion of the optical channel as well as increasing the data rate. An OFDM VLC system is proposed, which can be utilized for both communications and indoor positioning. A positioning algorithm based on power attenuation is used to estimate the receiver coordinates. We further calculate the positioning errors in all the locations of a room and compare them with those using single-carrier modulation schemes, i.e., on-off keying modulation. We demonstrate that our proposed OFDM positioning system outperforms by 74% its conventional counterpart. Finally, we investigate the impact of different system parameters on the positioning accuracy of the proposed OFDM VLC system.

  18. Lifetime estimation of moving subcellular objects in frequency-domain fluorescence lifetime imaging microscopy.

    PubMed

    Roudot, Philippe; Kervrann, Charles; Blouin, Cedric M; Waharte, Francois

    2015-10-01

    Fluorescence lifetime is usually defined as the average nanosecond-scale delay between excitation and emission of fluorescence. It has been established that lifetime measurements yield numerous indications on cellular processes such as interprotein and intraprotein mechanisms through fluorescent tagging and Förster resonance energy transfer. In this area, frequency-domain fluorescence lifetime imaging microscopy is particularly appropriate to probe a sample noninvasively and quantify these interactions in living cells. The aim is then to measure the fluorescence lifetime in the sample at each location in space from fluorescence variations observed in a temporal sequence of images obtained by phase modulation of the detection signal. This leads to a sensitivity of lifetime determination to other sources of fluorescence variations such as intracellular motion. In this paper, we propose a robust statistical method for lifetime estimation for both background and small moving structures with a focus on intracellular vesicle trafficking. PMID:26479936

  19. Synchronous waves of failed soft sweeps in the laboratory: remarkably rampant clonal interference of alleles at a single locus.

    PubMed

    Lee, Ming-Chun; Marx, Christopher J

    2013-03-01

    It has increasingly been recognized that adapting populations of microbes contain not one, but many lineages continually arising and competing at once. This process, termed "clonal interference," alters the rate and dynamics of adaptation and biases winning mutations toward those with the largest selective effect. Here we uncovered a dramatic example of clonal interference between multiple similar mutations occurring at the same locus within replicate populations of Methylobacterium extorquens AM1. Because these mutational events involved the transposition of an insertion sequence into a narrow window of a single gene, they were both readily detectable at low frequencies and could be distinguished due to differences in insertion sites. This allowed us to detect up to 17 beneficial alleles of this type coexisting in a single population. Despite conferring a large selective benefit, the majority of these alleles rose and then fell in frequency due to other lineages emerging that were more fit. By comparing allele-frequency dynamics to the trajectories of fitness gains by these populations, we estimated the fitness values of the genotypes that contained these mutations. Collectively across all populations, these alleles arose upon backgrounds with a wide range of fitness values. Within any single population, however, multiple alleles tended to rise and fall synchronously during a single wave of multiple genotypes with nearly identical fitness values. These results suggest that alleles of large benefit arose repeatedly in failed "soft sweeps" during narrow windows of adaptation due to the combined effects of epistasis and clonal interference. PMID:23307898

  20. Rainfall Intensity Estimation by Ground-Based Dual-Frequency Microwave Radiometers.

    NASA Astrophysics Data System (ADS)

    Liu, Gin-Rong; Liu, Chung-Chih; Kuo, Tsung-Hua

    2001-06-01

    Many investigators have used satellite data to derive rainfall intensity and to compare them with rain gauge data. However, there has always been a problem: what is the optimal time period for the two different types of data? A set of well-controlled data collected by ground-based dual-frequency microwave radiometers at the National Central University (24.9°N, 121.1°E) in Taiwan between January of 1996 and December of 1997 was used to find the answer. The results show that a 1-h interval would be the optimal time period and that hourly data will provide a better accuracy than other options (5, 10, or 30 min or 2 h). Two algorithms, the differential and the brightness temperature, were established to estimate rainfall intensity using ground-based dual-frequency microwave brightness temperature and rain gauge data. The results show that the root-mean-square error and the correlation coefficient are 0.63 mm h1 and 0.88, respectively, for the differential method, and 0.91 mm h1 and 0.71 for the brightness temperature method. The analysis also shows that because the atmospheric background and environmental influence in the continuous observations are identical, the changes in brightness temperature are only caused from the changes in liquid water content in the air. That probably made the differential method a better choice for rainfall intensity estimation than the brightness temperature method. Moreover, ground-based radiometers measure downwelling radiation from bottom up, and little ice-particle scattering or horizontal inhomogeneity is involved. The results can be compared with retrievals from satellite microwave radiometers for a better understanding of the physics of microwave emission and scattering due to raindrops or ice particles.

  1. A biophysical model for estimating the frequency of radiation-induced mutations resulting from chromosomal translocations

    NASA Astrophysics Data System (ADS)

    Wu, Honglu; Durante, Marco

    Gene mutations can be induced by radiation as a result of chromosomal translocations. A biophysical model is developed to estimate the frequency of this type of mutation induced by low-LET radiation. Mutations resulting from translocations are assumed to be formed by misrejoining of two DNA double strand breaks (DSB), one within the gene and one on a different chromosome. The chromosome containing the gene is assumed to occupy a spherical territory and does not overlap spatially with other chromosomes. Misrejoining between two DSB can occur only if the two DSB are closer than an interaction distance at the time of their induction. Applying the model to mutations of the hprt gene induced in G0 human lymphocyte cells by low-LET radiation, it is calculated that mutations resulting from translocations account for about 14% of the total mutations. The value of the interaction distance is determined to be 0.6 μm by comparing with the observed frequency of translocations in the X-chromosome.

  2. Mississippi River nitrate loads from high frequency sensor measurements and regression-based load estimation.

    PubMed

    Pellerin, Brian A; Bergamaschi, Brian A; Gilliom, Robert J; Crawford, Charles G; Saraceno, JohnFranco; Frederick, C Paul; Downing, Bryan D; Murphy, Jennifer C

    2014-11-01

    Accurately quantifying nitrate (NO3-) loading from the Mississippi River is important for predicting summer hypoxia in the Gulf of Mexico and targeting nutrient reduction within the basin. Loads have historically been modeled with regression-based techniques, but recent advances with high frequency NO3- sensors allowed us to evaluate model performance relative to measured loads in the lower Mississippi River. Patterns in NO3- concentrations and loads were observed at daily to annual time steps, with considerable variability in concentration-discharge relationships over the two year study. Differences were particularly accentuated during the 2012 drought and 2013 flood, which resulted in anomalously high NO3- concentrations consistent with a large flush of stored NO3- from soil. The comparison between measured loads and modeled loads (LOADEST, Composite Method, WRTDS) showed underestimates of only 3.5% across the entire study period, but much larger differences at shorter time steps. Absolute differences in loads were typically greatest in the spring and early summer critical to Gulf hypoxia formation, with the largest differences (underestimates) for all models during the flood period of 2013. In additional to improving the accuracy and precision of monthly loads, high frequency NO3- measurements offer additional benefits not available with regression-based or other load estimation techniques.

  3. Mississippi River nitrate loads from high frequency sensor measurements and regression-based load estimation

    USGS Publications Warehouse

    Pellerin, Brian A.; Bergamaschi, Brian A.; Gilliom, Robert J.; Crawford, Charles G.; Saraceno, John F.; Frederick, C. Paul; Downing, Bryan D.; Murphy, Jennifer C.

    2014-01-01

    Accurately quantifying nitrate (NO3–) loading from the Mississippi River is important for predicting summer hypoxia in the Gulf of Mexico and targeting nutrient reduction within the basin. Loads have historically been modeled with regression-based techniques, but recent advances with high frequency NO3– sensors allowed us to evaluate model performance relative to measured loads in the lower Mississippi River. Patterns in NO3– concentrations and loads were observed at daily to annual time steps, with considerable variability in concentration-discharge relationships over the two year study. Differences were particularly accentuated during the 2012 drought and 2013 flood, which resulted in anomalously high NO3– concentrations consistent with a large flush of stored NO3– from soil. The comparison between measured loads and modeled loads (LOADEST, Composite Method, WRTDS) showed underestimates of only 3.5% across the entire study period, but much larger differences at shorter time steps. Absolute differences in loads were typically greatest in the spring and early summer critical to Gulf hypoxia formation, with the largest differences (underestimates) for all models during the flood period of 2013. In additional to improving the accuracy and precision of monthly loads, high frequency NO3– measurements offer additional benefits not available with regression-based or other load estimation techniques.

  4. Estimation of Flood-Frequency Discharges for Rural, Unregulated Streams in West Virginia

    USGS Publications Warehouse

    Wiley, Jeffrey B.; Atkins, John T.

    2010-01-01

    Flood-frequency discharges were determined for 290 streamgage stations having a minimum of 9 years of record in West Virginia and surrounding states through the 2006 or 2007 water year. No trend was determined in the annual peaks used to calculate the flood-frequency discharges. Multiple and simple least-squares regression equations for the 100-year (1-percent annual-occurrence probability) flood discharge with independent variables that describe the basin characteristics were developed for 290 streamgage stations in West Virginia and adjacent states. The regression residuals for the models were evaluated and used to define three regions of the State, designated as Eastern Panhandle, Central Mountains, and Western Plateaus. Exploratory data analysis procedures identified 44 streamgage stations that were excluded from the development of regression equations representative of rural, unregulated streams in West Virginia. Regional equations for the 1.1-, 1.5-, 2-, 5-, 10-, 25-, 50-, 100-, 200-, and 500-year flood discharges were determined by generalized least-squares regression using data from the remaining 246 streamgage stations. Drainage area was the only significant independent variable determined for all equations in all regions. Procedures developed to estimate flood-frequency discharges on ungaged streams were based on (1) regional equations and (2) drainage-area ratios between gaged and ungaged locations on the same stream. The procedures are applicable only to rural, unregulated streams within the boundaries of West Virginia that have drainage areas within the limits of the stations used to develop the regional equations (from 0.21 to 1,461 square miles in the Eastern Panhandle, from 0.10 to 1,619 square miles in the Central Mountains, and from 0.13 to 1,516 square miles in the Western Plateaus). The accuracy of the equations is quantified by measuring the average prediction error (from 21.7 to 56.3 percent) and equivalent years of record (from 2.0 to 70

  5. Identification of the third/extra allele for forensic application in cases with TPOX tri-allelic pattern.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; da Motta, Carlos Henrique Ares Silveira; 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.

  6. A geographic information system tool to solve regression equations and estimate flow-frequency characteristics of Vermont Streams

    USGS Publications Warehouse

    Olson, Scott A.; Tasker, Gary D.; Johnston, Craig M.

    2003-01-01

    Estimates of the magnitude and frequency of streamflow are needed to safely and economically design bridges, culverts, and other structures in or near streams. These estimates also are used for managing floodplains, identifying flood-hazard areas, and establishing flood-insurance rates, but may be required at ungaged sites where no observed flood data are available for streamflow-frequency analysis. This report describes equations for estimating flow-frequency characteristics at ungaged, unregulated streams in Vermont. In the past, regression equations developed to estimate streamflow statistics required users to spend hours manually measuring basin characteristics for the stream site of interest. This report also describes the accompanying customized geographic information system (GIS) tool that automates the measurement of basin characteristics and calculation of corresponding flow statistics. The tool includes software that computes the accuracy of the results and adjustments for expected probability and for streamflow data of a nearby stream-gaging station that is either upstream or downstream and within 50 percent of the drainage area of the site where the flow-frequency characteristics are being estimated. The custom GIS can be linked to the National Flood Frequency program, adding the ability to plot peak-flow-frequency curves and synthetic hydrographs and to compute adjustments for urbanization.

  7. Estimating the frequency distributions of particulate matter and their metal elements in a temple.

    PubMed

    Lu, Hsin-Chung; Fang, Gour-Cheng; Wu, Yuh-Shen

    2006-07-01

    Air quality inside Asian temples is typically poor because of the burning of incense. This study measured and analyzed concentrations of fine (PM2.5) and coarse (PM2.5-10) particulate matter and their metal elements inside a temple in central Taiwan. Experimental results showed that the concentrations of metals Cd, Ni, Pb, and Cr inside the temple were higher than those at rural, suburban, urban, and industrial areas in other studies. Three theoretical parent distributions (lognormal, Weibull, and gamma) were used to fit the measured data. The lognormal distribution was the most appropriate distribution for representing frequency distributions of PM10, PM2.5, and their metal elements. Furthermore, the central limit theorem, H-statistic-based scheme, and parametric and nonparametric bootstrap methods were used to estimate confidence intervals for mean pollutant concentrations. The estimated upper confidence limits (UCLs) of means between different methods were very consistent, because the sample coefficient of variation (CV) was < 1. When the sample CV was > 1, the UCL based on H-statistical method tended to overestimate the UCLs when compared with other methods. Confidence intervals for pollutant concentrations at different percentiles were evaluated using parametric and nonparametric bootstrap methods. The probabilities of pollutants exceeding a critical concentration were also calculated.

  8. Tire-road friction coefficient estimation based on the resonance frequency of in-wheel motor drive system

    NASA Astrophysics Data System (ADS)

    Chen, Long; Bian, Mingyuan; Luo, Yugong; Qin, Zhaobo; Li, Keqiang

    2016-01-01

    In this paper, a resonance frequency-based tire-road friction coefficient (TRFC) estimation method is proposed by considering the dynamics performance of the in-wheel motor drive system under small slip ratio conditions. A frequency response function (FRF) is deduced for the drive system that is composed of a dynamic tire model and a simplified motor model. A linear relationship between the squared system resonance frequency and the TFRC is described with the FRF. Furthermore, the resonance frequency is identified by the Auto-Regressive eXogenous model using the information of the motor torque and the wheel speed, and the TRFC is estimated thereafter by a recursive least squares filter with the identified resonance frequency. Finally, the effectiveness of the proposed approach is demonstrated through simulations and experimental tests on different road surfaces.

  9. Towards in situ and high frequency estimates of suspended sediment properties

    NASA Astrophysics Data System (ADS)

    Martínez-Carreras, Núria; Schwab, Michael Peter; Klaus, Julian; Hissler, Christophe

    2016-04-01

    Sediment properties, including sediment-associated chemical constituents and sediment physical properties (as colour), can exhibit significant variations within and between storm runoff events. However, the number of samples included in suspended sediment studies is often limited by the time consuming and expensive laboratory procedures for suspended sediment analysis after stream water sampling. This, in turn, restricts high frequency sampling campaigns to a limited number of events and reduces accuracy when aiming to estimate fluxes and loads of sediment-associated chemical constituents. Our contribution addresses the potential for portable ultraviolet-visible (UV-VIS) light spectrometers (220-730 nm) to estimate suspended sediment properties in situ and at high temporal resolution. As far as we know, these instruments have primarily been developed and used to quantify solute concentrations (e.g. DOC and NO3-N), total concentrations of dissolved and particulate forms (e.g. TOC) and turbidity. Here we argue that light absorbance values can be calibrated to estimate solely sediment properties. For our proof-of-concept experiment, we measured light absorbance at 15-min intervals at the Weierbach catchment (NW Luxembourg, 0.46 km2) from December 2013 to January 2015. We then performed a local calibration using suspended sediment loss-on-ignition (LOI) measurements (n=34). We assessed the performance of several regression models that relate light absorbance measurements with the percentage weight LOI. The robust regression method presented the lowest standard error of prediction (0.48{%}) and was selected for calibration (adjusted r2 = 0.76 between observed and predicted values). This study demonstrates that spectrometers can be used to estimate suspended sediment properties at high temporal resolution and for long time spans in a simple, non-destructive and affordable manner. The advantages and disadvantages of the method compared to traditional approaches will be

  10. Floods in Georgia, magnitude and frequency : techniques for estimating the magnitude and frequency of floods in Georgia with compilation of flood data through 1974

    USGS Publications Warehouse

    Price, McGlone

    1979-01-01

    Regional relations are defined for estimating the magnitude and frequency of floods having recurrence intervals of 2, 5, 10, 25, 50, and 100 years on streams with natural flow in Georgia. Multiple-regression analyses were used to define the relationship between the flood-discharge frequency of annual peak discharges for streams draining 0.1 to 1,000 square miles and 10 climatological and physical basin characteristics. The analyses indicate that the drainage area of the basin is the most significant characteristic. Five regions having distinct flood-discharge frequency characteristics are delineated. Individual relations of flood magnitude and frequency to drainage area are given for parts of the main stems of the major rivers without significant regulation draining more than 1,000 square miles. (Kosco-USGS)

  11. Cross Time-Frequency Analysis for Combining Information of Several Sources: Application to Estimation of Spontaneous Respiratory Rate from Photoplethysmography

    PubMed Central

    Peláez-Coca, M. D.; Orini, M.; Lázaro, J.; Bailón, R.; Gil, E.

    2013-01-01

    A methodology that combines information from several nonstationary biological signals is presented. This methodology is based on time-frequency coherence, that quantifies the similarity of two signals in the time-frequency domain. A cross time-frequency analysis method, based on quadratic time-frequency distribution, has been used for combining information of several nonstationary biomedical signals. In order to evaluate this methodology, the respiratory rate from the photoplethysmographic (PPG) signal is estimated. The respiration provokes simultaneous changes in the pulse interval, amplitude, and width of the PPG signal. This suggests that the combination of information from these sources will improve the accuracy of the estimation of the respiratory rate. Another target of this paper is to implement an algorithm which provides a robust estimation. Therefore, respiratory rate was estimated only in those intervals where the features extracted from the PPG signals are linearly coupled. In 38 spontaneous breathing subjects, among which 7 were characterized by a respiratory rate lower than 0.15 Hz, this methodology provided accurate estimates, with the median error {0.00; 0.98} mHz ({0.00; 0.31}%) and the interquartile range error {4.88; 6.59} mHz ({1.60; 1.92}%). The estimation error of the presented methodology was largely lower than the estimation error obtained without combining different PPG features related to respiration. PMID:24363777

  12. Site-specific estimation of peak-streamflow frequency using generalized least-squares regression for natural basins in Texas

    USGS Publications Warehouse

    Asquith, William H.; Slade, R.M.

    1999-01-01

    The U.S. Geological Survey, in cooperation with the Texas Department of Transportation, has developed a computer program to estimate peak-streamflow frequency for ungaged sites in natural basins in Texas. Peak-streamflow frequency refers to the peak streamflows for recurrence intervals of 2, 5, 10, 25, 50, and 100 years. Peak-streamflow frequency estimates are needed by planners, managers, and design engineers for flood-plain management; for objective assessment of flood risk; for cost-effective design of roads and bridges; and also for the desin of culverts, dams, levees, and other flood-control structures. The program estimates peak-streamflow frequency using a site-specific approach and a multivariate generalized least-squares linear regression. A site-specific approach differs from a traditional regional regression approach by developing unique equations to estimate peak-streamflow frequency specifically for the ungaged site. The stations included in the regression are selected using an informal cluster analysis that compares the basin characteristics of the ungaged site to the basin characteristics of all the stations in the data base. The program provides several choices for selecting the stations. Selecting the stations using cluster analysis ensures that the stations included in the regression will have the most pertinent information about flooding characteristics of the ungaged site and therefore provide the basis for potentially improved peak-streamflow frequency estimation. An evaluation of the site-specific approach in estimating peak-streamflow frequency for gaged sites indicates that the site-specific approach is at least as accurate as a traditional regional regression approach.

  13. Population estimate of the preantral follicles and frequency of multioocyte follicles in prepubertal and adult bitches.

    PubMed

    Lunardon, N T; Silva-Santos, K C; Justino, R C; Dessunti, G T; Seneda, M M; Martins, M I M

    2015-04-01

    Oocytes from preantral follicles could be an alternative for in vitro maturation because most follicles are at the preantral stage. There are few studies that have sought to estimate the number of preantral follicles in bitches. Therefore, the aims of this study were to estimate the population of preantral follicles in the ovaries of small- and medium-sized prepubertal and adult bitches and compare the population of preantral follicles between the right and left ovaries and evaluate the frequency of multioocyte follicles (MOF). Eighty ovaries were collected by elective ovariohysterectomy from 40 healthy bitches. The bitches were divided into four groups: small-size prepubertal bitches (<10 kg, n = 20), medium-size prepubertal bitches (10-20 kg, n = 20), small-size adult bitches (<10 kg, n = 20), and medium-size adult bitches (10-20 kg, n = 20). Immediately after surgery, the ovaries were fixed in Bouin's solution and processed for histology. For each specimen, 70 histologic sections were cut and mounted on slides; then, the number of preantral follicles was estimated using a correction factor. The preantral follicles were classified according to the developmental stage. The data were analyzed using the Kruskal-Wallis test followed by Dunn's test for comparison between groups, and Fisher's exact test was used to evaluate the frequency of MOF (P ≤ 0.05). Considering the population of preantral follicles from the pair of ovaries, medium-size prepubertal bitches had the highest (P < 0.05) population of preantral follicles compared with the small and medium-size adult groups. There was a large variation in the numbers of preantral follicles among individuals of the same weight and within each group. There were differences between medium-size prepubertal and adult bitches regarding the population of preantral follicles in the right ovaries (145,482 ± 110,712 vs. 49,500 ± 44,821; P = 0.02); however, no differences were observed between the

  14. Estimating the Magnitude and Frequency of Floods in Small Urban Streams in South Carolina, 2001

    USGS Publications Warehouse

    Feaster, Toby D.; Guimaraes, Wladimir B.

    2004-01-01

    The magnitude and frequency of floods at 20 streamflowgaging stations on small, unregulated urban streams in or near South Carolina were estimated by fitting the measured wateryear peak flows to a log-Pearson Type-III distribution. The period of record (through September 30, 2001) for the measured water-year peak flows ranged from 11 to 25 years with a mean and median length of 16 years. The drainage areas of the streamflow-gaging stations ranged from 0.18 to 41 square miles. Based on the flood-frequency estimates from the 20 streamflow-gaging stations (13 in South Carolina; 4 in North Carolina; and 3 in Georgia), generalized least-squares regression was used to develop regional regression equations. These equations can be used to estimate the 2-, 5-, 10-, 25-, 50-, 100-, 200-, and 500-year recurrence-interval flows for small urban streams in the Piedmont, upper Coastal Plain, and lower Coastal Plain physiographic provinces of South Carolina. The most significant explanatory variables from this analysis were mainchannel length, percent impervious area, and basin development factor. Mean standard errors of prediction for the regression equations ranged from -25 to 33 percent for the 10-year recurrence-interval flows and from -35 to 54 percent for the 100-year recurrence-interval flows. The U.S. Geological Survey has developed a Geographic Information System application called StreamStats that makes the process of computing streamflow statistics at ungaged sites faster and more consistent than manual methods. This application was developed in the Massachusetts District and ongoing work is being done in other districts to develop a similar application using streamflow statistics relative to those respective States. Considering the future possibility of implementing StreamStats in South Carolina, an alternative set of regional regression equations was developed using only main channel length and impervious area. This was done because no digital coverages are currently

  15. solarFLAG hare and hounds: estimation of p-mode frequencies from Sun-as-star helioseismology data

    NASA Astrophysics Data System (ADS)

    Jiménez-Reyes, S. J.; Chaplin, W. J.; García, R. A.; Appourchaux, T.; Baudin, F.; Boumier, P.; Elsworth, Y.; Fletcher, S. T.; Lazrek, M.; Leibacher, J. W.; Lochard, J.; New, R.; Régulo, C.; Salabert, D.; Toutain, T.; Verner, G. A.; Wachter, R.

    2008-10-01

    We report on the results of the latest solarFLAG hare-and-hounds exercise, which was concerned with testing methods for extraction of frequencies of low-degree solar p modes from data collected by Sun-as-a-star observations. We have used the new solarFLAG simulator, which includes the effects of correlated mode excitation and correlations with background noise, to make artificial time-series data that mimic Doppler velocity observations of the Sun-as-a-star. The correlations give rise to asymmetry of mode peaks in the frequency power spectrum. 10 members of the group (the hounds) applied their `peak-bagging' codes to a 3456-d data set, and the estimated mode frequencies were returned to the hare (who was WJC) for comparison. Analysis of the results reveals a systematic bias in the estimated frequencies of modes above ~1.8mHz. The bias is negative, meaning the estimated frequencies systematically underestimate the input frequencies. We identify two sources that are the dominant contributions to the frequency bias. Both sources involve failure to model accurately subtle aspects of the observed power spectral density in the part (window) of the frequency power spectrum that is being fitted. One source of bias arises from a failure to account for the power spectral density coming from all those modes whose frequencies lie outside the fitting windows. The other source arises from a failure to account for the power spectral density of the weak l = 4 and 5 modes, which are often ignored in Sun-as-a-star analysis. The Sun-as-a-star peak-bagging codes need to allow for both sources, otherwise the frequencies are likely to be biased.

  16. Estimating Flow-Duration and Low-Flow Frequency Statistics for Unregulated Streams in Oregon

    USGS Publications Warehouse

    Risley, John; Stonewall, Adam J.; Haluska, Tana

    2008-01-01

    Flow statistical datasets, basin-characteristic datasets, and regression equations were developed to provide decision makers with surface-water information needed for activities such as water-quality regulation, water-rights adjudication, biological habitat assessment, infrastructure design, and water-supply planning and management. The flow statistics, which included annual and monthly period of record flow durations (5th, 10th, 25th, 50th, and 95th percent exceedances) and annual and monthly 7-day, 10-year (7Q10) and 7-day, 2-year (7Q2) low flows, were computed at 466 streamflow-gaging stations at sites with unregulated flow conditions throughout Oregon and adjacent areas of neighboring States. Regression equations, created from the flow statistics and basin characteristics of the stations, can be used to estimate flow statistics at ungaged stream sites in Oregon. The study area was divided into 10 regression modeling regions based on ecological, topographic, geologic, hydrologic, and climatic criteria. In total, 910 annual and monthly regression equations were created to predict the 7 flow statistics in the 10 regions. Equations to predict the five flow-duration exceedance percentages and the two low-flow frequency statistics were created with Ordinary Least Squares and Generalized Least Squares regression, respectively. The standard errors of estimate of the equations created to predict the 5th and 95th percent exceedances had medians of 42.4 and 64.4 percent, respectively. The standard errors of prediction of the equations created to predict the 7Q2 and 7Q10 low-flow statistics had medians of 51.7 and 61.2 percent, respectively. Standard errors for regression equations for sites in western Oregon were smaller than those in eastern Oregon partly because of a greater density of available streamflow-gaging stations in western Oregon than eastern Oregon. High-flow regression equations (such as the 5th and 10th percent exceedances) also generally were more accurate

  17. The internal clock: evidence for a temporal oscillator underlying time perception with some estimates of its characteristic frequency.

    PubMed

    Treisman, M; Faulkner, A; Naish, P L; Brogan, D

    1990-01-01

    Evidence for the proposition that human time perception is determined by an internal clock is largely indirect. It would strengthen the case for this hypothesis if a model for the internal clock were available from which predictions could be derived and tested, and if the basic parameter of such a model, the frequency at which the clock runs, could be estimated. A model for an internal temporal pacemaker is briefly described and its properties are explored by computer simulation. Results are obtained that provide a basis for predicting that, under appropriate conditions, interference between an imposed rhythm and the frequency of a temporal oscillator may cause perturbations in temporal judgment which are related to the characteristic frequency of that oscillator. Experimental data are reported which appear to demonstrate such an interference pattern. These results allow some estimates of the characteristic frequency of the temporal oscillator to be obtained.

  18. Joint Estimation of 2D-DOA and Frequency Based on Space-Time Matrix and Conformal Array

    PubMed Central

    Wan, Liang-Tian; Liu, Lu-Tao; Si, Wei-Jian; Tian, Zuo-Xi

    2013-01-01

    Each element in the conformal array has a different pattern, which leads to the performance deterioration of the conventional high resolution direction-of-arrival (DOA) algorithms. In this paper, a joint frequency and two-dimension DOA (2D-DOA) estimation algorithm for conformal array are proposed. The delay correlation function is used to suppress noise. Both spatial and time sampling are utilized to construct the spatial-time matrix. The frequency and 2D-DOA estimation are accomplished based on parallel factor (PARAFAC) analysis without spectral peak searching and parameter pairing. The proposed algorithm needs only four guiding elements with precise positions to estimate frequency and 2D-DOA. Other instrumental elements can be arranged flexibly on the surface of the carrier. Simulation results demonstrate the effectiveness of the proposed algorithm. PMID:24453856

  19. Runoff models and flood frequency statistics for design flood estimation in Austria - Do they tell a consistent story?

    NASA Astrophysics Data System (ADS)

    Rogger, M.; Kohl, B.; Pirkl, H.; Viglione, A.; Komma, J.; Kirnbauer, R.; Merz, R.; Blöschl, G.

    2012-08-01

    SummaryDesign floods for a given location at a stream can be estimated by a number of approaches including flood frequency statistics and the design storm method. If applied to the same catchment the two methods often yield quite different results. The aim of this paper is to contribute to understanding the reasons for these differences. A case study is performed for 10 alpine catchments in Tyrol, Austria, where the 100-year floods are estimated by (a) flood frequency statistics and (b) an event based runoff model. To identify the sources of the differences of the two methods, the 100-year floods are also estimated by (c) Monte Carlo simulations using a continuous runoff model. The results show that, in most catchments, the event based model gives larger flood estimates than flood frequency statistics. The reasons for the differences depend on the catchment characteristics and different rainfall inputs that were applied. For catchments with a high storage capacity the Monte Carlo simulations indicate a step change in the flood frequency curve when a storage threshold is exceeded which is not captured by flood frequency statistics. Flood frequency statistics therefore tends to underestimate the floods in these catchments. For catchments with a low storage capacity or significant surface runoff, no step change occurs, but in three catchments the design storms used were larger than those read from the IDF (intensity duration frequency) curve leading to an overestimation of the design floods. Finally, also the correct representation of flood dominating runoff components was shown to influence design flood results. Geologic information on the catchments was essential for identifying the reasons for the mismatch of the flood estimates.

  20. Estimation of rear-end vehicle crash frequencies in urban road tunnels.

    PubMed

    Meng, Qiang; Qu, Xiaobo

    2012-09-01

    According to The Handbook of Tunnel Fire Safety, over 90% (55 out of 61 cases) of fires in road tunnels are caused by vehicle crashes (especially rear-end crashes). It is thus important to develop a proper methodology that is able to estimate the rear-end vehicle crash frequency in road tunnels. In this paper, we first analyze the time to collision (TTC) data collected from two road tunnels of Singapore and conclude that Inverse Gaussian distribution is the best-fitted distribution to the TTC data. An Inverse Gaussian regression model is hence used to establish the relationship between the TTC and its contributing factors. We then proceed to introduce a new concept of exposure to traffic conflicts as the mean sojourn time in a given time period that vehicles are exposed to dangerous scenarios, namely, the TTC is lower than a predetermined threshold value. We further establish the relationship between the proposed exposure to traffic conflicts and crash count by using negative binomial regression models. Based on the limited data samples used in this study, the negative binomial regression models perform well although a further study using more data is needed. PMID:22664688

  1. Estimating the operating point of the cochlear transducer using low-frequency biased distortion products

    PubMed Central

    Brown, Daniel J.; Hartsock, Jared J.; Gill, Ruth M.; Fitzgerald, Hillary E.; Salt, Alec N.

    2009-01-01

    Distortion products in the cochlear microphonic (CM) and in the ear canal in the form of distortion product otoacoustic emissions (DPOAEs) are generated by nonlinear transduction in the cochlea and are related to the resting position of the organ of Corti (OC). A 4.8 Hz acoustic bias tone was used to displace the OC, while the relative amplitude and phase of distortion products evoked by a single tone [most often 500 Hz, 90 dB SPL (sound pressure level)] or two simultaneously presented tones (most often 4 kHz and 4.8 kHz, 80 dB SPL) were monitored. Electrical responses recorded from the round window, scala tympani and scala media of the basal turn, and acoustic emissions in the ear canal were simultaneously measured and compared during the bias. Bias-induced changes in the distortion products were similar to those predicted from computer models of a saturating transducer with a first-order Boltzmann distribution. Our results suggest that biased DPOAEs can be used to non-invasively estimate the OC displacement, producing a measurement equivalent to the transducer operating point obtained via Boltzmann analysis of the basal turn CM. Low-frequency biased DPOAEs might provide a diagnostic tool to objectively diagnose abnormal displacements of the OC, as might occur with endolymphatic hydrops. PMID:19354389

  2. Increasing long-term response by selecting for favorable minor alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term response of genomic selection can be improved by considering allele frequencies of selected markers or quantitative trait loci (QTLs). A previous formula to weight allele frequency of favorable minor alleles was tested, and 2 new formulas were developed. The previous formula used nonlinear...

  3. Polymorphisms in the cytochrome P450 CYP1A2 gene (CYP1A2) in colorectal cancer patients and controls: allele frequencies, linkage disequilibrium and influence on caffeine metabolism

    PubMed Central

    Sachse, Christoph; Bhambra, Upinder; Smith, Gillian; Lightfoot, Tracy J; Barrett, Jennifer H; Scollay, Jenna; Garner, R Colin; Boobis, Alan R; Wolf, C Roland; Gooderham, Nigel J

    2003-01-01

    Aim Several single nucleotide polymorphisms (SNPs) of the cytochrome P450 enzyme 1A2 gene (CYP1A2) have been reported. Here, frequencies, linkage disequilibrium and phenotypic consequences of six SNPs are described. Methods From genomic DNA, 114 British Caucasians (49 colorectal cancer cases and 65 controls) were genotyped for the CYP1A2 polymorphisms −3858G→A (allele CYP1A2*1C), −2464T→delT (CYP1A2*1D), −740T→G (CYP1A2*1E and *1G), −164A→C (CYP1A2*1F), 63C→G (CYP1A2*2), and 1545T→C (alleles CYP1A2*1B, *1G, *1H and *3), using polymerase chain reaction–restriction fragment length polymorphism assays. All patients and controls were phenotyped for CYP1A2 by h.p.l.c. analysis of urinary caffeine metabolites. Results In 114 samples, the most frequent CYP1A2 SNPs were 1545T→C (38.2% of tested chromosomes), −164A→C (CYP1A2*1F, 33.3%) and −2464T→delT (CYP1A2*1D, 4.82%). The SNPs were in linkage disequilibrium: the most frequent constellations were found to be −3858G/−2464T/−740T/−164A/63C/1545T (61.8%), −3858G/−2464T/−740T/−164C/63C/1545C (33.3%), and −3858G/−2464delT/−740T/−164A/63C/1545C (3.51%), with no significant frequency differences between cases and controls. In the phenotype analysis, lower caffeine metabolic ratios were detected in cases than in controls. This was significant in smokers (n = 14, P = 0.020), and in a subgroup of 15 matched case-control pairs (P = 0.007), but it was not significant in nonsmokers (n = 100, P = 0.39). There was no detectable association between CYP1A2 genotype and caffeine phenotype. Conclusions (i) CYP1A2 polymorphisms are in linkage disequilibrium. Therefore, only −164A→C (CYP1A2*1F) and −2464T→delT (CYP1A2*1D) need to be analysed in the routine assessment of CYP1A2 genotype; (ii) in vivo CYP1A2 activity is lower in colorectal cancer patients than in controls, and (iii) CYP1A2 genotype had no effect on phenotype (based on the caffeine metabolite ratio). However, this

  4. Joint Estimation of Carrier Frequency Offset and I/Q Imbalance in the Presence of Time-Varying DC Offset

    NASA Astrophysics Data System (ADS)

    Yunus, Umut; Lin, Hai; Yamashita, Katsumi

    Due to the importance of maintaining the orthogonality among subcarriers, the estimation of carrier frequency offset (CFO) is a crucial issue in orthogonal frequency division multiplexing (OFDM) systems. The CFO estimation becomes complicated in OFDM direct-conversion receivers (DCRs), where additional analog impairments such as I/Q imbalance and time-varying DC offset (TV-DCO) exist. In this paper, we propose a novel joint estimation method for CFO and I/Q imbalance in the presence of TV-DCO. By using the linear property of the TV-DCO and employing a periodic pilot sequence, the desired estimates can be obtained in closed-form. Simulation results confirm the validity of the proposed method.

  5. Main-channel slopes of selected streams in Iowa for estimation of flood-frequency discharges

    USGS Publications Warehouse

    Eash, David A.

    2003-01-01

    This report describes a statewide study conducted to develop main-channel slope (MCS) curves for 138 selected streams in Iowa with drainage areas greater than 100 square miles. MCS values determined from the curves can be used in regression equations for estimating floodfrequency discharges. Multivariable regression equations previously developed for two of the three hydrologic regions defined for Iowa require the measurement of MCS. Main-channel slope is a difficult measurement to obtain for large streams using 1:24,000-scale topographic maps. The curves developed in this report provide a simplified method for determining MCS values for sites located along large streams in Iowa within hydrologic Regions 2 and 3. The curves were developed using MCS values quantified for 2,058 selected sites along 138 selected streams in Iowa. A geographic information system (GIS) technique and 1:24,000-scale topographic data were used to quantify MCS values for the stream sites. The sites were selected at about 5-mile intervals along the streams. River miles were quantified for each stream site using a GIS program. Data points for river-mile and MCS values were plotted and a best-fit curve was developed for each stream. An adjustment was applied to all 138 curves to compensate for differences in MCS values between manual measurements and GIS quantifications. The multivariable equations for Regions 2 and 3 were developed using manual measurements of MCS. A comparison of manual measurements and GIS quantifications of MCS indicates that manual measurements typically produce greater values of MCS compared to GIS quantifications. Median differences between manual measurements and GIS quantifications of MCS are 14.8 and 17.7 percent for Regions 2 and 3, respectively. Comparisons of percentage differences between flood-frequency discharges calculated using MCS values of manual measurements and GIS quantifications indicate that use of GIS values of MCS for Region 3 substantially

  6. A robust and accurate center-frequency estimation (RACE) algorithm for improving motion estimation performance of SinMod on tagged cardiac MR images without known tagging parameters.

    PubMed

    Liu, Hong; Wang, Jie; Xu, Xiangyang; Song, Enmin; Wang, Qian; Jin, Renchao; Hung, Chih-Cheng; Fei, Baowei

    2014-11-01

    A robust and accurate center-frequency (CF) estimation (RACE) algorithm for improving the performance of the local sine-wave modeling (SinMod) method, which is a good motion estimation method for tagged cardiac magnetic resonance (MR) images, is proposed in this study. The RACE algorithm can automatically, effectively and efficiently produce a very appropriate CF estimate for the SinMod method, under the circumstance that the specified tagging parameters are unknown, on account of the following two key techniques: (1) the well-known mean-shift algorithm, which can provide accurate and rapid CF estimation; and (2) an original two-direction-combination strategy, which can further enhance the accuracy and robustness of CF estimation. Some other available CF estimation algorithms are brought out for comparison. Several validation approaches that can work on the real data without ground truths are specially designed. Experimental results on human body in vivo cardiac data demonstrate the significance of accurate CF estimation for SinMod, and validate the effectiveness of RACE in facilitating the motion estimation performance of SinMod.

  7. Bayesian Estimation of Fugitive Methane Point Source Emission Rates from a SingleDownwind High-Frequency Gas Sensor

    EPA Science Inventory

    Bayesian Estimation of Fugitive Methane Point Source Emission Rates from a Single Downwind High-Frequency Gas Sensor With the tremendous advances in onshore oil and gas exploration and production (E&P) capability comes the realization that new tools are needed to support env...

  8. A Study of Frequency Estimation Equipercentile Equating When There Are Large Ability Differences. Research Report. ETS RR-09-45

    ERIC Educational Resources Information Center

    Guo, Hongwen; Oh, Hyeonjoo J.

    2009-01-01

    In operational equating, frequency estimation (FE) equipercentile equating is often excluded from consideration when the old and new groups have a large ability difference. This convention may, in some instances, cause the exclusion of one competitive equating method from the set of methods under consideration. In this report, we study the…

  9. A Meta-Analysis of Children's Object-to-Mouth Frequency Data for Estimating Non-Dietary Ingestion Exposure

    EPA Science Inventory

    To improve estimates of non-dietary ingestion in probabilistic exposure modeling, a meta-analysis of children's object-to-mouth frequency was conducted using data from seven available studies representing 438 participants and ~ 1500 h of behavior observation. The analysis repres...

  10. The validity and reproducibility of food-frequency questionnaire–based total antioxidant capacity estimates in Swedish women

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Total antioxidant capacity (TAC) provides an assessment of antioxidant activity and synergistic interactions of redox molecules in foods and plasma. We investigated the validity and reproducibility of food frequency questionnaire (FFQ)–based TAC estimates assessed by oxygen radical absorbance capaci...

  11. Estimation and control of droplet size and frequency in projected spray mode of a gas metal arc welding (GMAW) process.

    PubMed

    Anzehaee, Mohammad Mousavi; Haeri, Mohammad

    2011-07-01

    New estimators are designed based on the modified force balance model to estimate the detaching droplet size, detached droplet size, and mean value of droplet detachment frequency in a gas metal arc welding process. The proper droplet size for the process to be in the projected spray transfer mode is determined based on the modified force balance model and the designed estimators. Finally, the droplet size and the melting rate are controlled using two proportional-integral (PI) controllers to achieve high weld quality by retaining the transfer mode and generating appropriate signals as inputs of the weld geometry control loop.

  12. An estimate of spherical impactor energy transfer for mechanical frequency up-conversion energy harvester

    NASA Astrophysics Data System (ADS)

    Corr, L. R.; Ma, D. T.

    2016-08-01

    Vibration energy harvesters, which use the impact mechanical frequency up-conversion technique, utilize an impactor, which gains kinetic energy from low frequency ambient environmental vibrations, to excite high frequency systems that efficiently convert mechanical energy to electrical energy. To take full advantage of the impact mechanical frequency up-conversion technique, it is prudent to understand the energy transfer from the low frequency excitations, to the impactor, and finally to the high frequency systems. In this work, the energy transfer from a spherical impactor to a multi degree of freedom spring / mass system, due to Hertzian impact, is investigated to gain insight on how best to design impact mechanical frequency up-conversion energy harvesters. Through this academic work, it is shown that the properties of the contact (or impact) area, i.e., radius of curvature and material properties, only play a minor role in energy transfer and that the equivalent mass of the target system (i.e., the spring / mass system) dictates the total amount of energy transferred during the impact. The novel approach of utilizing the well-known Hertzian impact methodology to gain an understanding of impact mechanical frequency up-conversion energy harvesters has made it clear that the impactor and the high frequency energy generating systems must be designed together as one system to ensure maximum energy transfer, leading to efficient ambient vibration energy harvesters.

  13. Optimal detection and concentration estimation of vapor materials using range-resolved lidar with frequency-agile lasers

    NASA Astrophysics Data System (ADS)

    Warren, Russell E.; Vanderbeek, Richard G.; D'Amico, Francis M.

    1999-10-01

    In previous work, we presented a methodology for optimally processing data from lidar with frequency-agile wavelength capability using techniques of multivariate statistics. Among the applications considered was the case of range- resolved lidar with short (delta function) transmitter pulses. This paper extends that analysis by deriving a method for estimating range-dependent vapor concentration for arbitrary pulse shapes. A Bayesian statistical approach leads to a MAP (maximum a posteriori) estimator for C(z), the concentration at range z. The estimates are computed iteratively for a given set of multiwavelength lidar return data using an approximation to the Gauss-Newton method. The concentration estimates are then used as the basis for a detection algorithm for the leading edge of the vapor plume based on the CUSUM approach. The detection and estimation approaches are illustrated on a combination of synthetic and field test data collected by SBCCOM at the Idaho National Engineering and Environmental Laboratory test site.

  14. Methods for Estimating Magnitude and Frequency of Floods in Rural Basins in the Southeastern United States: South Carolina

    USGS Publications Warehouse

    Feaster, Toby D.; Gotvald, Anthony J.; Weaver, J. Curtis

    2009-01-01

    For more than 50 years, the U.S. Geological Survey (USGS) has been developing regional regression equations that can be used to estimate flood magnitude and frequency at ungaged sites. Flood magnitude relates to the volume of flow that occurs over some period of time and usually is presented in cubic feet per second. Flood frequency relates to the probability of occurrence of a flood; that is, on average, what is the likelihood that a flood with a specified magnitude will occur in any given year (1 percent chance, 10 percent chance, 50 percent chance, and so on). Such flood estimates are needed for the efficient design of bridges, highway embankments, levees, and other structures near streams. In addition, these estimates are needed for the effective planning and management of land and water resources, to protect lives and property in flood-prone areas, and to determine flood-insurance rates.

  15. A second mutation associated with apparent [beta]-hexosaminidase A pseudodeficiency: Identification and frequency estimation

    SciTech Connect

    Cao, Z.; Chabot, T.; Triggs-Raine, B.L. ); Natowicz, M.R.; Prence, E.M. Harvard Medical School, Boston, MA ); Kaback, M.M.; Lim-Steele, S.T.; Brown, D. Univ. of California, San Diego, CA )

    1993-12-01

    Deficient activity of [beta]-hexosaminidase A (Hex A), resulting from mutations in the HEXA gene, typically causes Tay-Sachs disease. However, healthy individuals lacking Hex A activity against synthetic substrates (i.e., individuals who are pseudodeficient) have been described. Recently, an apparently benign C[sub 739]-to-T (Arg247Trp) mutation was found among individuals with Hex A levels indistinguishable from those of carriers of Tay-Sachs disease. This allele, when in compound heterozygosity with a second [open quotes]disease-causing[close quotes] allele, results in Hex A pseudodeficiency. The authors examined the HEXA gene of a healthy 42-year-old who was Hex A deficient but did not have the C[sub 739]-to-T mutation. The HEXA exons were PCR amplified, and the products were analyzed for mutations by using restriction-enzyme digestion or single-strand gel electrophoresis. A G[sub 805]-to-A (Gly269Ser) mutation associated with adult-onset G[sub m2] gangliosidosis was found on one chromosome. A new mutation, C[sub 745]-to-T (Arg 249Trp), was identified on the second chromosome. This mutation was detected in an additional 4/63 (6%) non-Jewish and 0/218 Ashkenazi Jewish enzyme-defined carriers. Although the Arg249Trp change may result in a late-onset form of G[sub M2] gangliosidosis, any phenotype must be very mild. This new mutation and the benign C[sub 739]-to-T mutation together account for [approximately]38% of non-Jewish enzyme-defined carriers. Because carriers of the C[sub 739]-to-T and C[sub 745]-to-T mutations cannot be differentiated from carriers of disease-causing alleles by using the classical biochemical screening approaches, DNA-based analyses for these mutations should be offered for non-Jewish enzyme-defined heterozygotes, before definitive counseling is provided. 46 refs., 5 figs., 2 tabs.

  16. Estimation of Frequency Noise in Semiconductor Lasers Due to Mechanical Thermal Noise

    NASA Technical Reports Server (NTRS)

    Numata, Kenji; Camp, Jordan

    2012-01-01

    We evaluate mechanical thermal noise in semiconductor lasers, applying a methodology developed for fixed-spacer cavities for laser frequency stabilization. Our simple model determines an underlying fundamental limit for the frequency noise of free-running semiconductor laser, and provides a framework: where the noise may be potentially reduced with improved design.

  17. Robust fundamental frequency estimation in sustained vowels: Detailed algorithmic comparisons and information fusion with adaptive Kalman filtering

    PubMed Central

    Tsanas, Athanasios; Zañartu, Matías; Little, Max A.; Fox, Cynthia; Ramig, Lorraine O.; Clifford, Gari D.

    2014-01-01

    There has been consistent interest among speech signal processing researchers in the accurate estimation of the fundamental frequency (F0) of speech signals. This study examines ten F0 estimation algorithms (some well-established and some proposed more recently) to determine which of these algorithms is, on average, better able to estimate F0 in the sustained vowel /a/. Moreover, a robust method for adaptively weighting the estimates of individual F0 estimation algorithms based on quality and performance measures is proposed, using an adaptive Kalman filter (KF) framework. The accuracy of the algorithms is validated using (a) a database of 117 synthetic realistic phonations obtained using a sophisticated physiological model of speech production and (b) a database of 65 recordings of human phonations where the glottal cycles are calculated from electroglottograph signals. On average, the sawtooth waveform inspired pitch estimator and the nearly defect-free algorithms provided the best individual F0 estimates, and the proposed KF approach resulted in a ∼16% improvement in accuracy over the best single F0 estimation algorithm. These findings may be useful in speech signal processing applications where sustained vowels are used to assess vocal quality, when very accurate F0 estimation is required. PMID:24815269

  18. Robust fundamental frequency estimation in sustained vowels: detailed algorithmic comparisons and information fusion with adaptive Kalman filtering.

    PubMed

    Tsanas, Athanasios; Zañartu, Matías; Little, Max A; Fox, Cynthia; Ramig, Lorraine O; Clifford, Gari D

    2014-05-01

    There has been consistent interest among speech signal processing researchers in the accurate estimation of the fundamental frequency (F(0)) of speech signals. This study examines ten F(0) estimation algorithms (some well-established and some proposed more recently) to determine which of these algorithms is, on average, better able to estimate F(0) in the sustained vowel /a/. Moreover, a robust method for adaptively weighting the estimates of individual F(0) estimation algorithms based on quality and performance measures is proposed, using an adaptive Kalman filter (KF) framework. The accuracy of the algorithms is validated using (a) a database of 117 synthetic realistic phonations obtained using a sophisticated physiological model of speech production and (b) a database of 65 recordings of human phonations where the glottal cycles are calculated from electroglottograph signals. On average, the sawtooth waveform inspired pitch estimator and the nearly defect-free algorithms provided the best individual F(0) estimates, and the proposed KF approach resulted in a ∼16% improvement in accuracy over the best single F(0) estimation algorithm. These findings may be useful in speech signal processing applications where sustained vowels are used to assess vocal quality, when very accurate F(0) estimation is required. PMID:24815269

  19. Efficiency of the inbreeding coefficient f and other estimators in detecting null alleles, as revealed by empirical data of locus oke3 across 65 populations of chum salmon Oncorhynchus keta

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Polymorphic DNA markers, e.g. mini- or microsatellite (SSR) loci, are often removed from data analyses if an excess of homozygosity, presumably an indication of null alleles, is observed. However, exclusion of such loci can reduce available information if multiple loci carry null alleles. Because nu...

  20. Development of Hierarchical Bayesian Model Based on Regional Frequency Analysis and Its Application to Estimate Areal Rainfall in South Korea

    NASA Astrophysics Data System (ADS)

    Kim, J.; Kwon, H. H.

    2014-12-01

    The existing regional frequency analysis has disadvantages in that it is difficult to consider geographical characteristics in estimating areal rainfall. In this regard, This study aims to develop a hierarchical Bayesian model based regional frequency analysis in that spatial patterns of the design rainfall with geographical information are explicitly incorporated. This study assumes that the parameters of Gumbel distribution are a function of geographical characteristics (e.g. altitude, latitude and longitude) within a general linear regression framework. Posterior distributions of the regression parameters are estimated by Bayesian Markov Chain Monte Calro (MCMC) method, and the identified functional relationship is used to spatially interpolate the parameters of the Gumbel distribution by using digital elevation models (DEM) as inputs. The proposed model is applied to derive design rainfalls over the entire Han-river watershed. It was found that the proposed Bayesian regional frequency analysis model showed similar results compared to L-moment based regional frequency analysis. In addition, the model showed an advantage in terms of quantifying uncertainty of the design rainfall and estimating the area rainfall considering geographical information. Acknowledgement: This research was supported by a grant (14AWMP-B079364-01) from Water Management Research Program funded by Ministry of Land, Infrastructure and Transport of Korean government.

  1. Bayesian Non-Stationary Flood Frequency Estimation at Ungauged Basins Using Climate Information and a Scaling Model

    NASA Astrophysics Data System (ADS)

    Lima, C. H.; Lall, U.

    2010-12-01

    Flood frequency statistical analysis most often relies on stationary assumptions, where distribution moments (e.g. mean, standard deviation) and associated flood quantiles do not change over time. In this sense, one expects that flood magnitudes and their frequency of occurrence will remain constant as observed in the historical information. However, evidence of inter-annual and decadal climate variability and anthropogenic change as well as an apparent increase in the number and magnitude of flood events across the globe have made the stationary assumption questionable. Here, we show how to estimate flood quantiles (e.g. 100-year flood) at ungauged basins without needing to consider stationarity. A statistical model based on the well known flow-area scaling law is proposed to estimate flood flows at ungauged basins. The slope and intercept scaling law coefficients are assumed time varying and a hierarchical Bayesian model is used to include climate information and reduce parameter uncertainties. Cross-validated results from 34 streamflow gauges located in a nested Basin in Brazil show that the proposed model is able to estimate flood quantiles at ungauged basins with remarkable skills compared with data based estimates using the full record. The model as developed in this work is also able to simulate sequences of flood flows considering global climate changes provided an appropriate climate index developed from the General Circulation Model is used as a predictor. The time varying flood frequency estimates can be used for pricing insurance models, and in a forecast mode for preparations for flooding, and finally, for timing infrastructure investments and location. Non-stationary 95% interval estimation for the 100-year Flood (shaded gray region) and 95% interval for the 100-year flood estimated from data (horizontal dashed and solid lines). The average distribution of the 100-year flood is shown in green in the right side.

  2. Error Analysis of Clay-Rock Water Content Estimation with Broadband High-Frequency Electromagnetic Sensors—Air Gap Effect

    PubMed Central

    Bore, Thierry; Wagner, Norman; Delepine Lesoille, Sylvie; Taillade, Frederic; Six, Gonzague; Daout, Franck; Placko, Dominique

    2016-01-01

    Broadband electromagnetic frequency or time domain sensor techniques present high potential for quantitative water content monitoring in porous media. Prior to in situ application, the impact of the relationship between the broadband electromagnetic properties of the porous material (clay-rock) and the water content on the frequency or time domain sensor response is required. For this purpose, dielectric properties of intact clay rock samples experimental determined in the frequency range from 1 MHz to 10 GHz were used as input data in 3-D numerical frequency domain finite element field calculations to model the one port broadband frequency or time domain transfer function for a three rods based sensor embedded in the clay-rock. The sensor response in terms of the reflection factor was analyzed in time domain with classical travel time analysis in combination with an empirical model according to Topp equation, as well as the theoretical Lichtenecker and Rother model (LRM) to estimate the volumetric water content. The mixture equation considering the appropriate porosity of the investigated material provide a practical and efficient approach for water content estimation based on classical travel time analysis with the onset-method. The inflection method is not recommended for water content estimation in electrical dispersive and absorptive material. Moreover, the results clearly indicate that effects due to coupling of the sensor to the material cannot be neglected. Coupling problems caused by an air gap lead to dramatic effects on water content estimation, even for submillimeter gaps. Thus, the quantitative determination of the in situ water content requires careful sensor installation in order to reach a perfect probe clay rock coupling. PMID:27096865

  3. Error Analysis of Clay-Rock Water Content Estimation with Broadband High-Frequency Electromagnetic Sensors--Air Gap Effect.

    PubMed

    Bore, Thierry; Wagner, Norman; Lesoille, Sylvie Delepine; Taillade, Frederic; Six, Gonzague; Daout, Franck; Placko, Dominique

    2016-01-01

    Broadband electromagnetic frequency or time domain sensor techniques present high potential for quantitative water content monitoring in porous media. Prior to in situ application, the impact of the relationship between the broadband electromagnetic properties of the porous material (clay-rock) and the water content on the frequency or time domain sensor response is required. For this purpose, dielectric properties of intact clay rock samples experimental determined in the frequency range from 1 MHz to 10 GHz were used as input data in 3-D numerical frequency domain finite element field calculations to model the one port broadband frequency or time domain transfer function for a three rods based sensor embedded in the clay-rock. The sensor response in terms of the reflection factor was analyzed in time domain with classical travel time analysis in combination with an empirical model according to Topp equation, as well as the theoretical Lichtenecker and Rother model (LRM) to estimate the volumetric water content. The mixture equation considering the appropriate porosity of the investigated material provide a practical and efficient approach for water content estimation based on classical travel time ana