Science.gov

Sample records for allele frequency estimation

  1. High throughput automated allele frequency estimation by pyrosequencing.

    PubMed

    Doostzadeh, Julie; Shokralla, Shadi; Absalan, Farnaz; Jalili, Roxana; Mohandessi, Sharareh; Langston, James W; Davis, Ronald W; Ronaghi, Mostafa; Gharizadeh, Baback

    2008-01-01

    Pyrosequencing is a DNA sequencing method based on the principle of sequencing-by-synthesis and pyrophosphate detection through a series of enzymatic reactions. This bioluminometric, real-time DNA sequencing technique offers unique applications that are cost-effective and user-friendly. In this study, we have combined a number of methods to develop an accurate, robust and cost efficient method to determine allele frequencies in large populations for association studies. The assay offers the advantage of minimal systemic sampling errors, uses a general biotin amplification approach, and replaces dTTP for dATP-apha-thio to avoid non-uniform higher peaks in order to increase accuracy. We demonstrate that this newly developed assay is a robust, cost-effective, accurate and reproducible approach for large-scale genotyping of DNA pools. We also discuss potential improvements of the software for more accurate allele frequency analysis. PMID:18628978

  2. High Throughput Automated Allele Frequency Estimation by Pyrosequencing

    PubMed Central

    Absalan, Farnaz; Jalili, Roxana; Mohandessi, Sharareh; Langston, James W.; Davis, Ronald W.; Ronaghi, Mostafa; Gharizadeh, Baback

    2008-01-01

    Pyrosequencing is a DNA sequencing method based on the principle of sequencing-by-synthesis and pyrophosphate detection through a series of enzymatic reactions. This bioluminometric, real-time DNA sequencing technique offers unique applications that are cost-effective and user-friendly. In this study, we have combined a number of methods to develop an accurate, robust and cost efficient method to determine allele frequencies in large populations for association studies. The assay offers the advantage of minimal systemic sampling errors, uses a general biotin amplification approach, and replaces dTTP for dATP-apha-thio to avoid non-uniform higher peaks in order to increase accuracy. We demonstrate that this newly developed assay is a robust, cost-effective, accurate and reproducible approach for large-scale genotyping of DNA pools. We also discuss potential improvements of the software for more accurate allele frequency analysis. PMID:18628978

  3. Effects of allele frequency estimation on genomic predictions and inbreeding coefficients

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic calculations often require estimating allele frequencies, which differ across time due to selection and drift. Data were 50,000 simulated markers and 39,985 actual markers for 2391 genotyped Holstein bulls. Gene content of relatives and gene frequencies in the base (founder) population were ...

  4. 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. PMID:26607217

  5. 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

  6. 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

  7. Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model

    PubMed Central

    Yin, Bin-Cheng; Li, Honghua; Ye, Bang-Ce

    2008-01-01

    Background High throughput genotyping of single nucleotide polymorphisms (SNPs) for genome-wide association requires technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. In this work, we have developed a theoretical approach to estimate allele frequency in pooled DNA samples, based on the physical principles of DNA immobilization and hybridization on solid surface using the Langmuir kinetic model and quantitative analysis of the allelic signals. Results This method can successfully distinguish allele frequencies differing by 0.01 in the actual pool of clinical samples, and detect alleles with a frequency as low as 2%. The accuracy of measuring known allele frequencies is very high, with the strength of correlation between measured and actual frequencies having an r2 = 0.9992. These results demonstrated that this method could allow the accurate estimation of absolute allele frequencies in pooled samples of DNA in a feasible and inexpensive way. Conclusion We conclude that this novel strategy for quantitative analysis of the ratio of SNP allelic sequences in DNA pools is an inexpensive and feasible alternative for detecting polymorphic differences in candidate gene association studies and genome-wide linkage disequilibrium scans. PMID:19087310

  8. A Generalized Approach for Estimating Effective Population Size from Temporal Changes in Allele Frequency

    PubMed Central

    Waples, R. S.

    1989-01-01

    The temporal method for estimating effective population size (N(e)) from the standardized variance in allele frequency change (F) is presented in a generalized form. Whereas previous treatments of this method have adopted rather limiting assumptions, the present analysis shows that the temporal method is generally applicable to a wide variety of organisms. Use of a revised model of gene sampling permits a more generalized interpretation of N(e) than that used by some other authors studying this method. It is shown that two sampling plans (individuals for genetic analysis taken before or after reproduction) whose differences have been stressed by previous authors can be treated in a uniform way. Computer simulations using a wide variety of initial conditions show that different formulas for computing F have much less effect on N(e) than do sample size (S), number of generations between samples (t), or the number of loci studied (L). Simulation results also indicate that (1) bias of F is small unless alleles with very low frequency are used; (2) precision is typically increased by about the same amount with a doubling of S, t, or L; (3) confidence intervals for N(e) computed using a χ(2) approximation are accurate and unbiased under most conditions; (4) the temporal method is best suited for use with organisms having high juvenile mortality and, perhaps, a limited effective population size. PMID:2731727

  9. Evaluation of DNA pooling for the estimation of microsatellite allele frequencies: a case study using striped bass (Morone saxatilis).

    PubMed

    Skalski, Garrick T; Couch, Charlene R; Garber, Amber F; Weir, Bruce S; Sullivan, Craig V

    2006-06-01

    Using striped bass (Morone saxatilis) and six multiplexed microsatellite markers, we evaluated procedures for estimating allele frequencies by pooling DNA from multiple individuals, a method suggested as cost-effective relative to individual genotyping. Using moment-based estimators, we estimated allele frequencies in experimental DNA pools and found that the three primary laboratory steps, DNA quantitation and pooling, PCR amplification, and electrophoresis, accounted for 23, 48, and 29%, respectively, of the technical variance of estimates in pools containing DNA from 2-24 individuals. Exact allele-frequency estimates could be made for pools of sizes 2-8, depending on the locus, by using an integer-valued estimator. Larger pools of size 12 and 24 tended to yield biased estimates; however, replicates of these estimates detected allele frequency differences among pools with different allelic compositions. We also derive an unbiased estimator of Hardy-Weinberg disequilibrium coefficients that uses multiple DNA pools and analyze the cost-efficiency of DNA pooling. DNA pooling yields the most potential cost savings when a large number of loci are employed using a large number of individuals, a situation becoming increasingly common as microsatellite loci are developed in increasing numbers of taxa. PMID:16582444

  10. 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

  11. Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping.

    PubMed

    Gautier, Mathieu; Foucaud, Julien; Gharbi, Karim; Cézard, Timothée; Galan, Maxime; Loiseau, Anne; Thomson, Marian; Pudlo, Pierre; Kerdelhué, Carole; Estoup, Arnaud

    2013-07-01

    Molecular markers produced by next-generation sequencing (NGS) technologies are revolutionizing genetic research. However, the costs of analysing large numbers of individual genomes remain prohibitive for most population genetics studies. Here, we present results based on mathematical derivations showing that, under many realistic experimental designs, NGS of DNA pools from diploid individuals allows to estimate the allele frequencies at single nucleotide polymorphisms (SNPs) with at least the same accuracy as individual-based analyses, for considerably lower library construction and sequencing efforts. These findings remain true when taking into account the possibility of substantially unequal contributions of each individual to the final pool of sequence reads. We propose the intuitive notion of effective pool size to account for unequal pooling and derive a Bayesian hierarchical model to estimate this parameter directly from the data. We provide a user-friendly application assessing the accuracy of allele frequency estimation from both pool- and individual-based NGS population data under various sampling, sequencing depth and experimental error designs. We illustrate our findings with theoretical examples and real data sets corresponding to SNP loci obtained using restriction site-associated DNA (RAD) sequencing in pool- and individual-based experiments carried out on the same population of the pine processionary moth (Thaumetopoea pityocampa). NGS of DNA pools might not be optimal for all types of studies but provides a cost-effective approach for estimating allele frequencies for very large numbers of SNPs. It thus allows comparison of genome-wide patterns of genetic variation for large numbers of individuals in multiple populations. PMID:23730833

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

    PubMed Central

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

    1999-01-01

    Polymorphic enzyme and minisatellite loci were used to estimate the degree of inbreeding in experimentally bottlenecked populations of the butterfly, Bicyclus anynana (Satyridae), three generations after founding events of 2, 6, 20, or 300 individuals, each bottleneck size being replicated at least four times. Heterozygosity fell more than expected, though not significantly so, but this traditional measure of the degree of inbreeding did not make full use of the information from genetic markers. It proved more informative to estimate directly the probability distribution of a measure of inbreeding, sigma2, the variance in the number of descendants left per gene. In all bottlenecked lines, sigma2 was significantly larger than in control lines (300 founders). We demonstrate that this excess inbreeding was brought about both by an increase in the variance of reproductive success of individuals, but also by another process. We argue that in bottlenecked lines linkage disequilibrium generated by the small number of haplotypes passing through the bottleneck resulted in hitchhiking of particular marker alleles with those haplotypes favored by selection. In control lines, linkage disequilibrium was minimal. Our result, indicating more inbreeding than expected from demographic parameters, contrasts with the findings of previous (Drosophila) experiments in which the decline in observed heterozygosity was slower than expected and attributed to associative overdominance. The different outcomes may both be explained as a consequence of linkage disequilibrium under different regimes of inbreeding. The likelihood-based method to estimate inbreeding should be of wide applicability. It was, for example, able to resolve small differences in sigma2 among replicate lines within bottleneck-size treatments, which could be related to the observed variation in reproductive viability. PMID:10049922

  13. 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

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

    PubMed Central

    2013-01-01

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

  15. Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

    PubMed Central

    Boitard, Simon; Kofler, Robert; Françoise, Pierre; Robelin, David; Schlötterer, Christian; Futschik, Andreas

    2013-01-01

    Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/. PMID:23311589

  16. Bayesian Inference of Natural Selection from Allele Frequency Time Series.

    PubMed

    Schraiber, Joshua G; Evans, Steven N; Slatkin, Montgomery

    2016-05-01

    The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We developed a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in nonequilibrium populations. We introduce a novel path augmentation approach, in which we use Markov chain Monte Carlo to integrate over the space of allele frequency trajectories consistent with the observed data. Using simulations, we show that this approach has good power to estimate selection coefficients and allele age. Moreover, when applying our approach to data on horse coat color, we find that ignoring a relevant demographic history can significantly bias the results of inference. Our approach is made available in a C++ software package. PMID:27010022

  17. 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

  18. 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.

  19. Fast spatial ancestry via flexible allele frequency surfaces

    PubMed Central

    Rañola, John Michael; Novembre, John; Lange, Kenneth

    2014-01-01

    Motivation: Unique modeling and computational challenges arise in locating the geographic origin of individuals based on their genetic backgrounds. Single-nucleotide polymorphisms (SNPs) vary widely in informativeness, allele frequencies change non-linearly with geography and reliable localization requires evidence to be integrated across a multitude of SNPs. These problems become even more acute for individuals of mixed ancestry. It is hardly surprising that matching genetic models to computational constraints has limited the development of methods for estimating geographic origins. We attack these related problems by borrowing ideas from image processing and optimization theory. Our proposed model divides the region of interest into pixels and operates SNP by SNP. We estimate allele frequencies across the landscape by maximizing a product of binomial likelihoods penalized by nearest neighbor interactions. Penalization smooths allele frequency estimates and promotes estimation at pixels with no data. Maximization is accomplished by a minorize–maximize (MM) algorithm. Once allele frequency surfaces are available, one can apply Bayes’ rule to compute the posterior probability that each pixel is the pixel of origin of a given person. Placement of admixed individuals on the landscape is more complicated and requires estimation of the fractional contribution of each pixel to a person’s genome. This estimation problem also succumbs to a penalized MM algorithm. Results: We applied the model to the Population Reference Sample (POPRES) data. The model gives better localization for both unmixed and admixed individuals than existing methods despite using just a small fraction of the available SNPs. Computing times are comparable with the best competing software. Availability and implementation: Software will be freely available as the OriGen package in R. Contact: ranolaj@uw.edu or klange@ucla.edu Supplementary information: Supplementary data are available at

  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 Central

    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

    2014-01-01

    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. PMID:24752137

  2. 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

    2014-01-01

    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. PMID:24752137

  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. Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies

    PubMed Central

    Ackermann, Marit; Beyer, Andreas

    2012-01-01

    Epistatic genetic interactions are key for understanding the genetic contribution to complex traits. Epistasis is always defined with respect to some trait such as growth rate or fitness. Whereas most existing epistasis screens explicitly test for a trait, it is also possible to implicitly test for fitness traits by searching for the over- or under-representation of allele pairs in a given population. Such analysis of imbalanced allele pair frequencies of distant loci has not been exploited yet on a genome-wide scale, mostly due to statistical difficulties such as the multiple testing problem. We propose a new approach called Imbalanced Allele Pair frequencies (ImAP) for inferring epistatic interactions that is exclusively based on DNA sequence information. Our approach is based on genome-wide SNP data sampled from a population with known family structure. We make use of genotype information of parent-child trios and inspect 3×3 contingency tables for detecting pairs of alleles from different genomic positions that are over- or under-represented in the population. We also developed a simulation setup which mimics the pedigree structure by simultaneously assuming independence of the markers. When applied to mouse SNP data, our method detected 168 imbalanced allele pairs, which is substantially more than in simulations assuming no interactions. We could validate a significant number of the interactions with external data, and we found that interacting loci are enriched for genes involved in developmental processes. PMID:22346757

  5. Statistics of Natural Populations. II. Estimating an Allele Probability in Families Descended from Cryptic Mothers

    PubMed Central

    Arnold, Jonathan; Morrison, Melvin L.

    1985-01-01

    In population studies, adults are frequently difficult or inconvenient to identify for genotype, but a family profile of genotypes can be obtained from an unidentified female crossed with a single unidentified male. The problem is to estimate an allele frequency in the cryptic parental gene pool from the observed family profiles. For example, a worker may wish to estimate inversion frequencies in Drosophila; inversion karyotypes are cryptic in adults but visible in salivary gland squashes from larvae. A simple mixture model, which assumes the Hardy-Weinberg law, Mendelian laws and a single randomly chosen mate per female, provides the vehicle for studying three competing estimators of an allele frequency. A simple, heuristically appealing estimator called the Dobzhansky estimator is compared with the maximum likelihood estimator and a close relative called the grouped profiles estimator. The Dobzhansky estimator is computationally simple, consistent and highly efficient and is recommended in practice over its competitors. PMID:17246258

  6. 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

  7. 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

    2015-01-01

    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. PMID:25966202

  8. Estimating allelic diversity generated by excision of different transposon types.

    PubMed

    Nordborg, M; Walbot, V

    1995-05-01

    Methods are presented for calculating the number and type of different DNA sequences generated by base excision and insertion events at a given site in a known DNA sequence. We calculate, for example, that excision of the Mu1 transposon from the bz1::Mu1 allele of maize should generate more than 500,000 unique alleles given the extent of base deletion (up to 34 bases removed) and base insertion (0-5 bases) observed thus far in sequenced excision alleles. Analysis of this universe of potential alleles can, for example, be used to predict the frequency of creation of stop codons or repair-generated duplications. In general, knowledge of the distribution of alleles can be used to evaluate models of both excision and repair by determining whether particular events occur more frequently than expected. Such quantitative analysis complements the qualitative description provided by the DNA sequence of individual events. Similar methods can be used to evaluate the outcome of other cases of DNA breakage and repair such as programmed V(D)J recombination in immunoglobin genes. PMID:24172918

  9. 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

  10. Frequency of Bt resistance alleles in H. armigera during 2006-2008 in Northern China.

    PubMed

    Gao, Yulin; Wu, Kongming; Gould, Fred

    2009-08-01

    Helicoverpa armigera is an important lepidopteran pest of cotton in China. From 2002, the frequency of Bt resistance alleles and quantitative shifts in larval Cry1Ac tolerance of field H. armigera population were monitored using bioassays of F(1) and F(2) offspring of isofemale lines from Xiajin County of Shandong Province (an intensive Bt cotton planting area) and Anci County of Hebei Province (a multiple-crop system including corn, soybean, peanut, and Bt cotton) in northern China. During 2006-2008, a total of 2,306 isofemale lines from the Xiajin population and a total of 1,270 isofemale lines from the Anci population were successfully screened on Cry1Ac diets. For each year, it was estimated that the major resistance gene frequency in Xiajin population in 2006, 2007, and 2008 was 0, 0.00022, and 0.00033, respectively. No major alleles conferring resistance to Cry1Ac were found in the Anci population; the frequency of resistance alleles for Cry1Ac was 0. Based on the relative average development rates (RADRs) of H. armigera larvae in F(1) tests, no substantial increase in Cry1Ac tolerance was found in either location over the 3-yr period. There were also significantly positive correlations between RADR of lines in the F(1) generation and the RADR of their F(2) offspring, indicating genetic variation in response to toxin. The low frequency of resistance alleles found in this study and in our previous results from 2002 to 2005 suggest the frequency of resistance alleles has remained low and that natural refugia resistance management strategy maybe effective for delaying resistance evolution in H. armigera to Bt cotton in northern China. PMID:19689916

  11. 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

  12. 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

  13. 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)

  14. 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

  15. Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size.

    PubMed

    Garza, J C; Slatkin, M; Freimer, N B

    1995-07-01

    The distributions of allele sizes at eight simple-sequence repeat (SSR) or microsatellite loci in chimpanzees are found and compared with the distributions previously obtained from several human populations. At several loci, the differences in average allele size between chimpanzees and humans are sufficiently small that there might be a constraint on the evolution of average allele size. Furthermore, a model that allows for a bias in the mutation process shows that for some loci a weak bias can account for the observations. Several alleles at one of the loci (Mfd 59) were sequenced. Differences between alleles of different lengths were found to be more complex than previously assumed. An 8-base-pair deletion was present in the nonvariable region of the chimpanzee locus. This locus contains a previously unrecognized repeated region, which is imperfect in humans and perfect in chimpanzees. The apparently greater opportunity for mutation conferred by the two perfect repeat regions in chimpanzees is reflected in the higher variance in repeat number at Mfd 59 in chimpanzees than in humans. These data indicate that interspecific differences in allele length are not always attributable to simple changes in the number of repeats. PMID:7659015

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

    PubMed Central

    2010-01-01

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

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

    PubMed Central

    Salvadori, Luana de Cassia; Santana, Fabiana Covolo de Souza; Marcos, Elaine Valim Camarinha

    2014-01-01

    Background HLA allele identification is used in bone marrow transplant programs as HLA compatibility between the donor and recipient may prevent graft rejection. Objective This study aimed to estimate the frequency of alleles and haplotypes of the HLA system in the region of Bauru and compare these with the frequencies found in other regions of the country. Methods HLA-A*, HLA-B*, and HLA-DRB1* allele frequencies and haplotypes were analyzed in a sample of 3542 volunteer donors at the National Registry of Voluntary Bone Marrow Donors (REDOME) in Bauru. HLA low resolution typing was performed using reverse line blot with the Dynal Reli™ SSO-HLA Typing Kit and automated Dynal AutoReli™48 device (Invitrogen, USA). Results Twenty, 36, and 13 HLA-A*, HLA-B*, and HLA-DRB1* allele groups, respectively, were identified. The most common alleles for each locus were HLA-A*02, HLA-B*35, and HLA-DRB1*07. The most frequent haplotype was A*01-B*08-DRB1*03. Allele and haplotype frequencies were compared to other regions in Brazil and the similarities and differences among populations are shown. Conclusion The knowledge of the immunogenic profile of a population contributes to the comprehension of the historical and anthropological aspects of different regions. Moreover, this helps to find suitable donors quickly, thereby shortening waiting lists for transplants and thus increasing survival rates among recipients.

  18. Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data

    PubMed Central

    Brandt, Débora Y. C.; Aguiar, Vitor R. C.; Bitarello, Bárbara D.; Nunes, Kelly; Goudet, Jérôme; Meyer, Diogo

    2015-01-01

    Next-generation sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the human leukocyte antigen (HLA) genes. Because accurate genotype calls and allele frequency estimations are crucial to population genomics analyses, it is important to assess the reliability of NGS data. Here, we evaluate the reliability of genotype calls and allele frequency estimates of the single-nucleotide polymorphisms (SNPs) reported by 1000G (phase I) at five HLA genes (HLA-A, -B, -C, -DRB1, and -DQB1). We take advantage of the availability of HLA Sanger sequencing of 930 of the 1092 1000G samples and use this as a gold standard to benchmark the 1000G data. We document that 18.6% of SNP genotype calls in HLA genes are incorrect and that allele frequencies are estimated with an error greater than ±0.1 at approximately 25% of the SNPs in HLA genes. We found a bias toward overestimation of reference allele frequency for the 1000G data, indicating mapping bias is an important cause of error in frequency estimation in this dataset. We provide a list of sites that have poor allele frequency estimates and discuss the outcomes of including those sites in different kinds of analyses. Because the HLA region is the most polymorphic in the human genome, our results provide insights into the challenges of using of NGS data at other genomic regions of high diversity. PMID:25787242

  19. 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

  20. 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).

  1. 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

  2. Genotype and allele frequencies of isoniazid-metabolizing enzymes NAT2 and GSTM1 in Latvian tuberculosis patients.

    PubMed

    Igumnova, Viktorija; Capligina, Valentina; Krams, Alvils; Cirule, Andra; Elferts, Didzis; Pole, Ilva; Jansone, Inta; Bandere, Dace; Ranka, Renate

    2016-07-01

    Pharmacogenomic testing of tuberculosis drug-metabolizing enzyme genes was proposed as a strategy to identify patients at risk for suboptimal responses to medications. However, variations of the genotype frequencies among ethnic groups exist and new alleles are been identified. The aim of this study was to identify polymorphisms of genes encoding metabolic enzymes NAT2 and GSTM1 in tuberculosis patients in Latvia and to estimate the frequency of NAT2 slow acetylator and GSTM1 null genotypes. In total, 85 DNA samples were genotyped, all individuals were Caucasian. An ethnic heterogeneity reflecting the multiethnic population of the country was observed. 49 patients were Latvians, 30 were Russians and 6 of other ethnicity. In total, 7 NAT2 alleles were identified: *4, *5, *6, *7, *11, *12, * and *13. The most frequent was the slow acetylation allele NAT2*6 (frequency 0.388) followed by the slow acetylation allele NAT2*5 and the rapid acetylation allele NAT2*4 (frequencies 0.306 and 0.194, respectively). The predominance of slow (51.8%) and intermediate (43.5%) acetylators compared with rapid acetylators (4.7%) was observed. The GSTM1 null genotype was detected in 48.2% of tuberculosis patients. When subgroup analysis was performed according to ethnicity, the results showed that neither NAT2 allele frequencies nor GSTM1 null genotype frequency did not differ significantly in TB patients of Latvian or Russian ethnicity. Overall, genotyping results were similar with previous reports of a NAT2 gene variation and GSTM1 null genotype frequency in Caucasians. Our findings have a contribution for the pharmacogenetics-based tuberculosis therapy in Latvia in future. PMID:27236516

  3. The Equilibrium Allele Frequency Distribution for a Population with Reproductive Skew

    PubMed Central

    Der, Ricky; Plotkin, Joshua B.

    2014-01-01

    We study the population genetics of two neutral alleles under reversible mutation in a model that features a skewed offspring distribution, called the Λ-Fleming–Viot process. We describe the shape of the equilibrium allele frequency distribution as a function of the model parameters. We show that the mutation rates can be uniquely identified from this equilibrium distribution, but the form of the offspring distribution cannot itself always be so identified. We introduce an estimator for the mutation rate that is consistent, independent of the form of reproductive skew. We also introduce a two-allele infinite-sites version of the Λ-Fleming–Viot process, and we use it to study how reproductive skew influences standing genetic diversity in a population. We derive asymptotic formulas for the expected number of segregating sites as a function of sample size and offspring distribution. We find that the Wright–Fisher model minimizes the equilibrium genetic diversity, for a given mutation rate and variance effective population size, compared to all other Λ-processes. PMID:24473932

  4. Comparison of Prion Allele Frequency found in Suffolk and Targhee Sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Scrapie is a class of Transmissible Spongiform Encephalopathy that affects sheep and goats. The objective of this study was to compare genotypic and allelic frequencies among USSES Targhee and Suffolk sheep. A total of 122 sheep were genotyped for codon 171 with allele specific primers in 2 separate...

  5. 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

  6. 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. PMID:25467111

  7. 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

  8. HLA-B27 allele frequency in Sri Lankan patients with spondyloarthritides.

    PubMed

    Kidnapillai, S; Sirisena, N D; Dissanayake, V H

    2016-06-01

    This preliminary study aims to describe the HLA-B27 allele frequency in Sri Lankan patients with spondyloarthritides (SA). An anonymised database of 373 Sri Lankan patients with SA referred for HLA-B27 testing was retrospectively analysed. Eighty five (22.8%) patients were positive for the HLA-B27 allele. A male preponderance was observed among the positives. The HLA-B27 allele frequency in this sample of patients with SA was relatively low compared to published studies in other populations. Further research is needed to identify the predominant subtypes of the allele to determine which subtypes are the most prevalent in a larger sample of Sri Lankan patients with SA, and to define their association with the specific types of SA. PMID:27423748

  9. 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

  10. 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

  11. Natural Selection VS. Random Drift: Evidence from Temporal Variation in Allele Frequencies in Nature

    PubMed Central

    Mueller, Laurence D.; Barr, Lorraine G.; Ayala, Francisco J.

    1985-01-01

    We have obtained monthly samples of two species, Drosophila pseudoobscura and Drosophila persimilis, in a natural population from Napa County, California. In each species, about 300 genes have been assayed by electrophoresis for each of seven enzyme loci in each monthly sample from March 1972 to June 1975. Using statistical methods developed for the purpose, we have examined whether the allele frequencies at different loci vary in a correlated fashion. The methods used do not detect natural selection when it is deterministic (e.g., overdominance or directional selection), but only when alleles at different loci vary simultaneously in response to the same environmental variations. Moreover, only relatively large fitness differences (of the order of 15%) are detectable. We have found strong evidence of correlated allele frequency variation in 13–20% of the cases examined. We interpret this as evidence that natural selection plays a major role in the evolution of protein polymorphisms in nature. PMID:4054608

  12. Determination of permethrin resistance allele frequency of human head louse populations by quantitative sequencing.

    PubMed

    Kwon, Deok Ho; Yoon, Kyong Sup; Strycharz, Joseph P; Clark, J Marshall; Lee, Si Hyeock

    2008-09-01

    A quantitative sequencing (QS) protocol that detects the frequencies of sodium channel mutations (M815I, T917I, and L920F) responsible for knockdown resistance in permethrin-resistant head lice (Pediculus humanus capitis De Geer) was tested as a population genotyping method for use as a preliminary resistance monitoring tool. Genomic DNA fragments of the sodium channel a-subunit gene that encompass the three mutation sites were polymerase chain reaction (PCR)-1 amplified from individual head lice with either resistant or susceptible genotypes, and combined in various ratios to generate standard DNA template mixtures for QS. After sequencing, the signal ratios between resistant and susceptible nucleotides were calculated and plotted against the corresponding resistance allele frequencies. Quadratic regression coefficients of the plots were close to 1, demonstrating that the signal ratios are highly correlated with the resistance allele frequencies. Resistance allele frequencies predicted by QS, using either "pooled DNA" (DNA extracted from individual louse specimens and pooled) or "pooled specimen DNA" (DNA simultaneously extracted from multiple louse specimens), agreed well with those determined by individual sequencing, confirming the reliability and accuracy of QS as a population genotyping method and validating our approach of using the pooled specimen DNA as the DNA template for QS. Our protocol for QS was determined to be highly reliable for the prediction of resistance allele frequencies higher than approximately 7.4% at the 95% confidence level. According to the resistance allele frequencies determined by QS, pyrethroid resistance varies substantially among different geographical regions, emphasizing the importance of early resistance detection and proper management strategies. PMID:18826035

  13. 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

  14. Genotype and allelic frequencies of a newly identified mutation causing blindness in jordanian awassi sheep flocks.

    PubMed

    Jawasreh, K I Z; Ababneh, H; Awawdeh, F T; Al-Massad, M A; Al-Majali, A M

    2012-01-01

    A total of 423 blood samples were collected (during 2009 and 2010) from all the ram holdings at three major Jordanian governmental Awassi breeding stations (Al-Khanasry, Al-Mushairfa and Al-Fjaje) and two private flocks. All blood samples were screened for the presence of mutations at the CNGA3 gene (responsible for day blindness in Awassi sheep) using RFLP-PCR. The day blindness mutation was detected in all studied flocks. The overall allele and genotype frequencies of all studied flocks of the day blindness mutation were 0.088 and 17.49%, respectively. The genotype and allele frequencies were higher in station flocks than the farmer flocks (0.121, 24.15 and 0.012, 2.32, respectively). Al-Mushairfa and Al-Khanasry stations have the highest genotype and allele frequencies for the day blindness mutation that were 27.77, 30.00% and 0.14, 0.171, respectively. The investigated farmer flocks have low percentages (0.03, 5.88% at Al-Shoubak and 0.005 and 1.05%, at Al-Karak, respectively for genotype and allele frequencies) compared with the breeding stations. Ram culling strategy was applied throughout the genotyping period in order to gradually eradicate this newly identified day blindness mutation from Jordanian Breeding station, since they annually distribute a high percentage of improved rams to farmer's flocks. PMID:25049475

  15. Genotype and Allelic Frequencies of a Newly Identified Mutation Causing Blindness in Jordanian Awassi Sheep Flocks

    PubMed Central

    Jawasreh, K. I. Z.; Ababneh, H.; Awawdeh, F. T.; Al-Massad, M. A.; Al-Majali, A. M.

    2012-01-01

    A total of 423 blood samples were collected (during 2009 and 2010) from all the ram holdings at three major Jordanian governmental Awassi breeding stations (Al-Khanasry, Al-Mushairfa and Al-Fjaje) and two private flocks. All blood samples were screened for the presence of mutations at the CNGA3 gene (responsible for day blindness in Awassi sheep) using RFLP-PCR. The day blindness mutation was detected in all studied flocks. The overall allele and genotype frequencies of all studied flocks of the day blindness mutation were 0.088 and 17.49%, respectively. The genotype and allele frequencies were higher in station flocks than the farmer flocks (0.121, 24.15 and 0.012, 2.32, respectively). Al-Mushairfa and Al-Khanasry stations have the highest genotype and allele frequencies for the day blindness mutation that were 27.77, 30.00% and 0.14, 0.171, respectively. The investigated farmer flocks have low percentages (0.03, 5.88% at Al-Shoubak and 0.005 and 1.05%, at Al-Karak, respectively for genotype and allele frequencies) compared with the breeding stations. Ram culling strategy was applied throughout the genotyping period in order to gradually eradicate this newly identified day blindness mutation from Jordanian Breeding station, since they annually distribute a high percentage of improved rams to farmer’s flocks. PMID:25049475

  16. Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

    PubMed Central

    Rellstab, Christian; Zoller, Stefan; Tedder, Andrew; Gugerli, Felix; Fischer, Martin C.

    2013-01-01

    Sequencing of pooled samples (Pool-Seq) using next-generation sequencing technologies has become increasingly popular, because it represents a rapid and cost-effective method to determine allele frequencies for single nucleotide polymorphisms (SNPs) in population pools. Validation of allele frequencies determined by Pool-Seq has been attempted using an individual genotyping approach, but these studies tend to use samples from existing model organism databases or DNA stores, and do not validate a realistic setup for sampling natural populations. Here we used pyrosequencing to validate allele frequencies determined by Pool-Seq in three natural populations of Arabidopsis halleri (Brassicaceae). The allele frequency estimates of the pooled population samples (consisting of 20 individual plant DNA samples) were determined after mapping Illumina reads to (i) the publicly available, high-quality reference genome of a closely related species (Arabidopsis thaliana) and (ii) our own de novo draft genome assembly of A. halleri. We then pyrosequenced nine selected SNPs using the same individuals from each population, resulting in a total of 540 samples. Our results show a highly significant and accurate relationship between pooled and individually determined allele frequencies, irrespective of the reference genome used. Allele frequencies differed on average by less than 4%. There was no tendency that either the Pool-Seq or the individual-based approach resulted in higher or lower estimates of allele frequencies. Moreover, the rather high coverage in the mapping to the two reference genomes, ranging from 55 to 284x, had no significant effect on the accuracy of the Pool-Seq. A resampling analysis showed that only very low coverage values (below 10-20x) would substantially reduce the precision of the method. We therefore conclude that a pooled re-sequencing approach is well suited for analyses of genetic variation in natural populations. PMID:24244686

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

    PubMed Central

    2010-01-01

    Background The extreme polymorphism that is observed in major histocompatibility complex (MHC) genes, which code for proteins involved in recognition of non-self oligopeptides, is thought to result from a pressure exerted by parasites because parasite antigens are more likely to be recognized by MHC heterozygotes (heterozygote advantage) and/or by rare MHC alleles (negative frequency-dependent selection). The Ewens-Watterson test (EW) is often used to detect selection acting on MHC genes over the recent history of a population. EW is based on the expectation that allele frequencies under balancing selection should be more even than under neutrality. We used computer simulations to investigate whether this expectation holds for selection exerted by parasites on host MHC genes under conditions of heterozygote advantage and negative frequency-dependent selection acting either simultaneously or separately. Results In agreement with simple models of symmetrical overdominance, we found that heterozygote advantage acting alone in populations does, indeed, result in more even allele frequency distributions than expected under neutrality, and this is easily detectable by EW. However, under negative frequency-dependent selection, or under the joint action of negative frequency-dependent selection and heterozygote advantage, distributions of allele frequencies were less predictable: the majority of distributions were indistinguishable from neutral expectations, while the remaining runs resulted in either more even or more skewed distributions than under neutrality. Conclusions Our results indicate that, as long as negative frequency-dependent selection is an important force maintaining MHC variation, the EW test has limited utility in detecting selection acting on these genes. PMID:20979635

  18. HLA-A, -B, -C, -DRB1 Allele and Haplotype Frequencies Distinguish Eastern European Americans from the General European American Population

    PubMed Central

    Mack, Steven J.; Tu, Bin; Lazaro, Ana; Yang, Ruyan; Lancaster, Alex K.; Cao, Kai; Ng, Jennifer; Hurley, Carolyn Katovich

    2012-01-01

    Sequence based typing was used to identify HLA-A,B,C,DRB1 alleles from 558 consecutively recruited U.S. volunteers with Eastern European ancestry for an unrelated hematopoietic stem cell registry. Four of the 31 HLA-A alleles, 29 -C alleles, 59 -B alleles, and 42 -DRB1 alleles identified (A*0325, B*440204, Cw*0332, and *0732N) are novel. The HLA-A*02010101g allele was observed at a frequency of 0.28. Two-, three- and four-locus haplotypes were estimated using the expectation maximization algorithm. The highest-frequency extended haplotypes (A*010101g-Cw*070101g-B*0801g-DRB1*0301 and A*03010101g-Cw*0702-B*0702-DRB1*1501) were observed at frequencies of 0.04 and 0.03, respectively. Linkage disequilibrium values (D’ij) of the constituent 2-locus haplotypes were highly significant for both extended haplotypes (p-values were less than 8 × 10−10), but were consistently higher for the more frequent haplotype. Balancing selection was inferred to be acting on all four loci, with the strongest evidence of balancing selection observed for the HLA-C locus. Comparisons of the A-C-B haplotype and DRB1 frequencies in this population to those for African, European and western Asian populations revealed high degrees of identity with Czech, Polish, and Slovenian populations and significant differences from the general European American population. PMID:19000140

  19. 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

  20. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

    PubMed Central

    Falush, Daniel; Stephens, Matthew; Pritchard, Jonathan K

    2003-01-01

    We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu. PMID:12930761

  1. 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

  2. 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

  3. 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

  4. 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. PMID:26517173

  5. Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data.

    PubMed

    Dos Santos, Eduardo Jose Melos; McCabe, Antony; Gonzalez-Galarza, Faviel F; Jones, Andrew R; Middleton, Derek

    2016-03-01

    The Allele Frequencies Net Database (AFND) is a freely accessible database which stores population frequencies for alleles or genes of the immune system in worldwide populations. Herein we introduce two new tools. We have defined new classifications of data (gold, silver and bronze) to assist users in identifying the most suitable populations for their tasks. The gold standard datasets are defined by allele frequencies summing to 1, sample sizes >50 and high resolution genotyping, while silver standard datasets do not meet gold standard genotyping resolution and/or sample size criteria. The bronze standard datasets are those that could not be classified under the silver or gold standards. The gold standard includes >500 datasets covering over 3 million individuals from >100 countries at one or more of the following loci: HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1 and -DRB1 - with all loci except DPA1 present in more than 220 datasets. Three out of 12 geographic regions have low representation (the majority of their countries having less than five datasets) and the Central Asia region has no representation. There are 18 countries that are not represented by any gold standard datasets but are represented by at least one dataset that is either silver or bronze standard. We also briefly summarize the data held by AFND for KIR genes, alleles and their ligands. Our second new component is a data submission tool to assist users in the collection of the genotypes of the individuals (raw data), facilitating submission of short population reports to Human Immunology, as well as simplifying the submission of population demographics and frequency data. PMID:26585775

  6. 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

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

    PubMed Central

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

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

    PubMed

    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

  9. 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

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

    PubMed Central

    Rujirojindakul, Pairaya; Chongsuvivatwong, Virasakdi; Limprasert, Pornprot

    2015-01-01

    Background. The objective of this study was to investigate the association of the ABO blood group phenotype and allele frequency with CHIK fever. Methods. A rural community survey in Southern Thailand was conducted in August and September 2010. A total of 506 villagers were enrolled. Cases were defined as individuals having anti-CHIK IgG by hemagglutination ≥1 : 10. Results. There were 314 cases (62.1%) with CHIK seropositivity. Females were less likely to have positive anti-CHIK IgG with odds ratio (OR) (95% CI) of 0.63 (0.43, 0.93). All samples tested were Rh positive. Distribution of CHIK seropositivity versus seronegativity (P value) in A, B, AB, and O blood groups was 80 versus 46 (0.003), 80 versus 48 (0.005), 24 versus 20 (0.55), and 130 versus 78 (<0.001), respectively. However, chi-square test between ABO and CHIK infection showed no statistical significance (P = 0.76). Comparison of the ABO blood group allele frequency between CHIK seropositivity and seronegativity was not statistically significant. Conclusion. This finding demonstrated no association of the ABO blood group phenotypes and allele frequencies with CHIK infection. PMID:25977691

  11. HLA-G allele and haplotype frequencies in a healthy population of Iran.

    PubMed

    Kuroshli, Zahra; Gourabi, Hamid; Bazrgar, Masoud; Sanati, Mohammad Hossein; Bahraminejad, Elmira; Anisi, Khadije

    2014-06-01

    The human leukocyte antigen (HLA)-G molecule is expressed in cytotrophoblast cells, adult thymic epithelial cells, erythroblasts, pancreatic islets and mesenchymal stem cells. Although, HLA-G expression in allotransplanted patients is correlated with a better allograft acceptance, it is associated with an advanced grade of the tumor in cancer. In addition to the role on the immune system, HLA-G is also involved in successful pregnancy through the embryo implantation, fetal survival and the initial steps of hematopoiesis and angiogenesis. The aim of this study was determination of HLA-G allele frequencies in a healthy population of Iran. In this research, we selected 100 samples from healthy Iranian individuals and henceforth, we used polymerase chain reaction (PCR) followed by sequencing technique for exon 2, 3, 4 and intron 2 of the gene for evaluating the HLA-G alleles frequencies. Investigation of intronic (intron 2) variation is the novelty of our study. The obtained results indicated thirteen alleles of HLA-G in Iranian individuals including G*01:01:01:01, G*01:06, G*01:01:01:06, G*01:01:02, G*01:01:03, G*01:01:05, G*01:01:06, G*01:01:07, G*01:01:08, G*01:03, G*01:04:01, G*01:04:03, and G*01:04:04. According to this study, the most prevalent alleles in the Iranian population were G*01:01:01:01 (52.5%), G*01:01:02 (16%) and G*01:04:03 (14.5%) and also the lowest alleles regarding the frequency were G*01:01:01:06 (0.5%) and G*01:03 (0.5%). The results of G*01:01:01:01 and G*01:04:01 frequencies showed some similarities with the polish population. Our results were similar to the north Indian population for the frequencies of G*01:06 and G*01:01:02. PMID:24659125

  12. Investigator HDplex markers: allele frequencies and mutational events in a North Italian population.

    PubMed

    Turrina, Stefania; Ferrian, Melissa; Caratti, Stefano; De Leo, Domenico

    2015-07-01

    Autosomal short tandem repeats (STRs) analysis represents the method of election in forensic genetics and up to now, 23 STRs are available for these purposes. However, in particular circumstances such as human identification or complex kinship cases, examination of additional STRs may be required in order to obtain reliable conclusions. For this purpose, a new multiplex STR system, namely Investigator® HDplex kit (QIAGEN) that coamplifies a set of 12 autosomal loci, 9 of which, represents novel supplementary STRs, was recently developed. A population sample of 359 unrelated healthy subjects residing in North Italy was typed to determine allele frequencies, forensic parameters and genetic distances among European populations. Furthermore, to evaluate the suitability of the HDplex kit as an auxiliary tool for paternity testing, mutation rates were estimated on 84 confirmed family trios. The 12 loci resulted highly informative with a combined power of discrimination of 0.999998 and no departures from Hardy-Weinberg equilibrium were observed with the sole exception of locus D4S2366. From the comparison of our population sample and European reference populations, a single significant difference was revealed with the Poland population at D4S2366 locus. With regard to the mutation rate study, on a total of 2,016 meioses considered, six single-step mutational events were observed and the average mutation rate calculated was of 2.94 × 10(-3) per locus per generation (95% confidence interval, 1.08 × 10(-3)-6.39 × 10(-3)). PMID:25205546

  13. 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...

  14. Factors Influencing Ascertainment Bias of Microsatellite Allele Sizes: Impact on Estimates of Mutation Rates

    PubMed Central

    Li, Biao; Kimmel, Marek

    2013-01-01

    Microsatellite loci play an important role as markers for identification, disease gene mapping, and evolutionary studies. Mutation rate, which is of fundamental importance, can be obtained from interspecies comparisons, which, however, are subject to ascertainment bias. This bias arises, for example, when a locus is selected on the basis of its large allele size in one species (cognate species 1), in which it is first discovered. This bias is reflected in average allele length in any noncognate species 2 being smaller than that in species 1. This phenomenon was observed in various pairs of species, including comparisons of allele sizes in human and chimpanzee. Various mechanisms were proposed to explain observed differences in mean allele lengths between two species. Here, we examine the framework of a single-step asymmetric and unrestricted stepwise mutation model with genetic drift. Analysis is based on coalescent theory. Analytical results are confirmed by simulations using the simuPOP software. The mechanism of ascertainment bias in this model is a tighter correlation of allele sizes within a cognate species 1 than of allele sizes in two different species 1 and 2. We present computations of the expected average allele size difference, given the mutation rate, population sizes of species 1 and 2, time of separation of species 1 and 2, and the age of the allele. We show that when the past demographic histories of the cognate and noncognate taxa are different, the rate and directionality of mutations affect the allele sizes in the two taxa differently from the simple effect of ascertainment bias. This effect may exaggerate or reverse the effect of difference in mutation rates. We reanalyze literature data, which indicate that despite the bias, the microsatellite mutation rate estimate in the ancestral population is consistently greater than that in either human or chimpanzee and the mutation rate estimate in human exceeds or equals that in chimpanzee with the rate

  15. 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

  16. 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

  17. Determination of the allelic frequency in Smith-Lemli-Opitz syndrome by analysis of massively parallel sequencing data sets.

    PubMed

    Cross, J L; Iben, J; Simpson, C L; Thurm, A; Swedo, S; Tierney, E; Bailey-Wilson, J E; Biesecker, L G; Porter, F D; Wassif, C A

    2015-06-01

    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 nucleotide polymorphism (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

  18. 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. PMID:19458791

  19. Semantic Web-Based Integration of Cancer Pathways and Allele Frequency Data

    PubMed Central

    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. PMID:19458791

  20. Allele frequency distribution of 13 X-chromosomal STR loci in Pakistani population.

    PubMed

    Tariq, Muhammad Akram; Ullah, Obaid; Riazuddin, S Amer; Riazuddin, Sheikh

    2008-11-01

    Short tandem repeat (STR) markers are extensively being used for human identification as well as paternity and forensic case work. X-chromosome STR (X-STR) markers are a powerful complementary system especially in deficiency paternity testing. Many X-linked microsatellites have been evaluated but further studies are required to determine population specific statistics. Here, we report allele frequencies of 13 X-linked microsatellites (DXS8378, DXS9902, DXS6810, DXS7132, DXS981, DXS6793, DXS6801, DXS6789, GATA172D05, HPRTB, GATA31E08, DXS8377, and DXS7423) in the Pakistani population. Blood samples were collected from individuals representing all major ethnic groups of the Pakistan population. A total of 5-18 alleles were observed for each locus and altogether 109 alleles for all 13 X-STR loci. Heterozygosity in females ranged from 0.524 to 0.884. No significant deviation was observed from Hardy-Weinberg equilibrium for all 13 microsatellites. In addition, there was no evidence of linkage disequilibrium in any pairs of these markers. These results strongly suggest that the X-linked microsatellites described here can potentially serve as an extension to autosomal systems currently used in parentage analysis and forensic case work. PMID:18629532

  1. Allelic frequencies and statistical data obtained from 15 STR loci in a population of the Goiás State.

    PubMed

    Vieira, T C; Silva, D M; Gigonzac, M A D; Ferreira, V L; Gonçalves, M W; da Cruz, A D

    2013-01-01

    Due to the miscegenation of the Brazilian population, the central region of Brazil was colonized by internal migration of individuals from different origins, who contributed to the genetic diversity existing in this population. The purpose of this study was to estimate population parameters based on the allele frequencies for 15 polymorphic autosomal short-tandem repeat (STR) loci present in the population of the State of Goiás in the central region of Brazil, and to compare the results with those of others from different Brazilian populations. DNA was obtained from a sample of 986 unrelated individuals by a commercial reagent kit and was quantified by spectrometry for later amplification in the thermocycler. These loci, commonly used in forensics and paternity testing, reflected Hardy-Weinberg equilibrium in this population. The D18S51 and Penta E loci had the highest number of alleles, while the observed heterozygosity reached the highest rates in FGA (0.920), D7S820 (0.870), and vWA (0.867) markers. Genetic diversity reached the highest levels in Penta E (0.906), Penta D (0.873), and D18S51 (0.860) markers, and the investigated forensic parameters showed high average values, with 93% power of discrimination, polymorphism information content of 78%, gene diversity of 79%, and observed heterozygosity of 79%. Similar to the other populations of Brazil, the population of the Midwest is derived from the admixture of 3 main parental groups: Amerindian, European, particularly Portuguese, and Africans from sub-Saharan Africa. In this context, the overall distribution of allele frequencies in the STR markers of various Brazilian populations is quite similar to the data obtained in this study. PMID:23359020

  2. 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

  3. 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

  4. 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

  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. 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

  7. Estimating copy numbers of alleles from population-scale high-throughput sequencing data

    PubMed Central

    2015-01-01

    Background With the recent development of microarray and high-throughput sequencing (HTS) technologies, a number of studies have revealed catalogs of copy number variants (CNVs) and their association with phenotypes and complex traits. In parallel, a number of approaches to predict CNV regions and genotypes are proposed for both microarray and HTS data. However, only a few approaches focus on haplotyping of CNV loci. Results We propose a novel approach to infer copy unit alleles and their numbers in each sample simultaneously from population-scale HTS data by variational Bayesian inference on a generative probabilistic model inspired by latent Dirichlet allocation, which is a well studied model for document classification problems. In simulation studies, we evaluated concordance between inferred and true copy unit alleles for lower-, middle-, and higher-copy number dataset, in which precision and recall were ≥ 0.9 for data with mean coverage ≥ 10× per copy unit. We also applied the approach to HTS data of 1123 samples at highly variable salivary amylase gene locus and a pseudogene locus, and confirmed consistency of the estimated alleles within samples belonging to a trio of CEPH/Utah pedigree 1463 with 11 offspring. Conclusions Our proposed approach enables detailed analysis of copy number variations, such as association study between copy unit alleles and phenotypes or biological features including human diseases. PMID:25707811

  8. Determination of knockdown resistance allele frequencies in global human head louse populations using the serial invasive signal amplification reaction

    PubMed Central

    Hodgdon, Hilliary E.; Yoon, Kyong Sup; Previte, Domenic J.; Kim, Hyo Jeong; Aboelghar, Gamal E.; Lee, Si Hyeock; Clark, J. Marshall

    2010-01-01

    BACKGROUND Pediculosis is the most prevalent parasitic infestation of humans. Resistance to pyrethrin- and pyrethroid-based pediculicides is due to knockdown (kdr)-type point mutations in the voltage-sensitive sodium channel α-subunit gene. Early detection of resistance is crucial for the selection of effective management strategies. RESULTS Kdr allele frequencies of lice from 14 countries were determined using serial invasive signal amplification reaction. Lice collected from Uruguay, UK and Australia had kdr allele frequencies of 100% while lice from Ecuador, Papua New Guinea, South Korea and Thailand had kdr allele frequencies of 0%. The remaining 7 countries investigated, including seven US populations, two Argentina, Brazil, Denmark, Czech Republic, Egypt and Israel, displayed variable kdr allele frequencies, ranging from 11% to 97%. CONCLUSION The newly developed and validated SISAR method is suitable for accurate monitoring of kdr allele frequencies in head lice. Proactive management is needed where kdr-type resistance is not yet saturated. Based on sodium channel insensitivity and its occurrence in louse populations resistant to pyrethrin- and pyrethroid-based pediculicides, the T917I mutation appears a key marker for resistance. Results from the Egyptian population, however, indicate that phenotypic resistance of lice with single or double mutations (M815I and/or L920F) should also be determined. PMID:20564731

  9. Population-ethnic group specific genome variation allele frequency data: a querying and visualization journey.

    PubMed

    Viennas, Emmanouil; Gkantouna, Vassiliki; Ioannou, Marina; Georgitsi, Marianthi; Rigou, Maria; Poulas, Konstantinos; Patrinos, George P; Tzimas, Giannis

    2012-08-01

    National/ethnic mutation databases aim to document the genetic heterogeneity in various populations and ethnic groups worldwide. We have previously reported the development and upgrade of FINDbase (www.findbase.org), a database recording causative mutations and pharmacogenomic marker allele frequencies in various populations around the globe. Although this database has recently been upgraded, we continuously try to enhance its functionality by providing more advanced visualization tools that would further assist effective data querying and comparisons. We are currently experimenting in various visualization techniques on the existing FINDbase causative mutation data collection aiming to provide a dynamic research tool for the worldwide scientific community. We have developed an interactive web-based application for population-based mutation data retrieval. It supports sophisticated data exploration allowing users to apply advanced filtering criteria upon a set of multiple views of the underlying data collection and enables browsing the relationships between individual datasets in a novel and meaningful way. PMID:22659238

  10. 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

  11. Utilizing Ethnic-Specific Differences in Minor Allele Frequency to Recategorize Reported Pathogenic Deafness Variants

    PubMed Central

    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.

    2014-01-01

    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

  12. Population genetics of nine short tandem repeat loci: allele frequency distribution in a Brazilian population sample.

    PubMed

    Soares-Vieira, José Arnaldo; Billerbeck, Ana Elisa C; Pinto, Emília Modolo; Iwamura, Edna S M; Bilharinho de Mendonça, Berenice; Otto, Paulo A

    2002-06-01

    Gene and genotype frequencies in relation to the D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, and D7S820 loci were determined in a sample of 290 unrelated individuals (204 Caucasians and 86 mulattoes) living in the city of São Paulo, Brazil. The sex test Amelogenin was also performed in all subjects from our sample, revealing the expected sex in all instances. Allele frequency data obtained from the analysis of these samples were in the usual range of other population groups with similar racial background. In the sample of Caucasian individuals, panmictic proportions were ruled out in relation to TPOX and CSF1PO loci, but only in the latter was the overall frequency of heterozygotes significantly less than expected. In the sample of mulattoes, Hardy-Weinberg proportions were rejected in relation to FGA and CSF1PO loci, but in no instance were the overall numbers of heterozygotes different from the corresponding expected ones under panmixia. Taking into account all this and also the number of tests performed, the degree of genetic heterogeneity of Brazilian populations, and the critical level reached by the significant results (1% < alpha<5%), the departures from panmixia here observed can be considered to be negligible in altering significantly biologic relationship odds calculated under the assumption of random matings. PMID:12040266

  13. Knockdown resistance allele frequencies in North American head louse (Anoplura: Pediculidae) populations.

    PubMed

    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

    2014-03-01

    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

  14. 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

  15. Detection of MPLW515L/K Mutations and Determination of Allele Frequencies with a Single-Tube PCR Assay

    PubMed Central

    Takei, Hiraku; Morishita, Soji; Araki, Marito; Edahiro, Yoko; Sunami, Yoshitaka; Hironaka, Yumi; Noda, Naohiro; Sekiguchi, Yuji; Tsuneda, Satoshi; Ohsaka, Akimichi; Komatsu, Norio

    2014-01-01

    A gain-of-function mutation in the myeloproliferative leukemia virus (MPL) gene, which encodes the thrombopoietin receptor, has been identified in patients with essential thrombocythemia and primary myelofibrosis, subgroups of classic myeloproliferative neoplasms (MPNs). The presence of MPL gene mutations is a critical diagnostic criterion for these diseases. Here, we developed a rapid, simple, and cost-effective method of detecting two major MPL mutations, MPLW515L/K, in a single PCR assay; we termed this method DARMS (dual amplification refractory mutation system)-PCR. DARMS-PCR is designed to produce three different PCR products corresponding to MPLW515L, MPLW515K, and all MPL alleles. The amplicons are later detected and quantified using a capillary sequencer to determine the relative frequencies of the mutant and wild-type alleles. Applying DARMS-PCR to human specimens, we successfully identified MPL mutations in MPN patients, with the exception of patients bearing mutant allele frequencies below the detection limit (5%) of this method. The MPL mutant allele frequencies determined using DARMS-PCR correlated strongly with the values determined using deep sequencing. Thus, we demonstrated the potential of DARMS-PCR to detect MPL mutations and determine the allele frequencies in a timely and cost-effective manner. PMID:25144224

  16. Estimating urban flood-frequency characteristics

    USGS Publications Warehouse

    Jennings, M.E.; Atkins, J.B.; Inman, E.J.

    1989-01-01

    Methods in use by the U.S. Geological Survey to estimate flood-frequency characteristics for urban watersheds are compared with estimates based on the Soil Conservation Service TR-55 model. Data from four small urban watersheds in Georgia are used in the flood-peak and hydrograph comparisons.

  17. Component external leakage and rupture frequency estimates

    SciTech Connect

    Eide, S.A.; Khericha, S.T.; Calley, M.B.; Johnson, D.A.; Marteeny, M.L.

    1991-11-01

    In order to perform detailed internal flooding risk analyses of nuclear power plants, external leakage and rupture frequencies are needed for various types of components - piping, valves, pumps, flanges, and others. However, there appears to be no up-to-date, comprehensive source for such frequency estimates. This report attempts to fill that void. Based on a comprehensive search of Licensee Event Reports (LERs) contained in Nuclear Power Experience (NPE), and estimates of component populations and exposure times, component external leakage and rupture frequencies were generated. The remainder of this report covers the specifies of the NPE search for external leakage and rupture events, analysis of the data, a comparison with frequency estimates from other sources, and a discussion of the results.

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

    PubMed Central

    Field, Wesley; Hershberg, Ruth

    2015-01-01

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

  19. 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

  20. Allelic frequency and genotypes of prion protein at codon 136 and 171 in Iranian Ghezel sheep breeds

    PubMed Central

    Zadeh, Reza Ashrafi; Omrani, Mir Davood; Ramezani, Fatemeh; Amniattalab, Amir

    2011-01-01

    PrP genotypes at codons 136 and 171 in 120 Iranian Ghezel sheep breeds were studied using allele-specific PCR amplification and compared with the well-known sheep breeds in North America, the United States and Europe. The frequency of V allele and VV genotype at codon 136 of Ghezel sheep breed was significantly lower than AA and AV. At codon 171, the frequency of allele H was significantly lower than Q and R. Despite the similarities of PrP genotypes at codons 136 and 171 between Iranian Ghezel sheep breeds and some of the studied breeds, significant differences were found with others. Planning of effective breeding control and successful eradication of susceptible genotypes in Iranian Ghezel sheep breeds will not be possible unless the susceptibility of various genotypes in Ghezel sheep breeds to natural or experimental scrapie has been elucidated. PMID:21778818

  1. 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

  2. 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.

  3. Molecular analysis of human leukocyte antigen class I and class II allele frequencies and haplotype distribution in Pakistani population

    PubMed Central

    Moatter, T.; Aban, M.; Tabassum, S.; Shaikh, U.; Pervez, S.

    2010-01-01

    AIM: Distribution of HLA class I and II alleles and haplotype was studied in Pakistani population and compared with the data reported for Caucasoid, Africans, Orientals and Arab populations. MATERIALS AND METHODS: HLA class I and II polymorphisms in 1000 unrelated Pakistani individuals was studied using sequence-specific primers and polymerase chain reaction and assay. RESULTS: The most frequent class I alleles observed were A*02, B*35 and CW*07, with frequencies of 19.2, 13.7 and 20%, respectively. Fifteen distinct HLA-DRB1 alleles and eight HLA-DQB1 alleles were recognized. The most frequently observed DRB1 alleles which represented more than 60% of the subjects were DRB1 *03, *07, *11 and *15. The rare DRB1 alleles detected in this study were HLADRB1 *08 and *09, having frequencies of 0.9 and 1.7%, respectively. In addition, at DRB1-DQB1 loci there were 179 different haplotypes and 285 unique genotypes and the most common haplotype was DRB1*15-DQB1*06 which represented 17% of the total DRB1-DQB1 haplotypes. In our population, haplotype A*33-B*58-Cw*03 comprised 2.8% of the total class I haplotypes observed. This haplotype was seen only in the oriental populations and has not been reported in the African or European Caucasoid. CONCLUSION: Our study showed a close similarity of HLA class I and II alleles with that of European Caucasoid and Orientals. In Pakistani population, two rare loci and three haplotypes were identified, whereas haplotypes characteristic of Caucasians, Africans and Orientals were also found, suggesting an admixture of different races due to migration to and from this region. PMID:21206703

  4. Impact of TP53 mutation variant allele frequency on phenotype and outcomes in myelodysplastic syndromes.

    PubMed

    Sallman, D A; Komrokji, R; Vaupel, C; Cluzeau, T; Geyer, S M; McGraw, K L; Al Ali, N H; Lancet, J; McGinniss, M J; Nahas, S; Smith, A E; Kulasekararaj, A; Mufti, G; List, A; Hall, J; Padron, E

    2016-03-01

    Although next-generation sequencing has allowed for the detection of somatic mutations in myelodysplastic syndromes (MDS), the clinical relevance of variant allele frequency (VAF) for the majority of mutations is unknown. We profiled TP53 and 20 additional genes in our training set of 219 patients with MDS or secondary acute myeloid leukemia with findings confirmed in a validation cohort. When parsed by VAF, TP53 VAF predicted for complex cytogenetics in both the training (P=0.001) and validation set (P<0.0001). MDS patients with a TP53 VAF > 40% had a median overall survival (OS) of 124 days versus an OS that was not reached in patients with VAF <20% (hazard ratio (HR), 3.52; P=0.01) with validation in an independent cohort (HR, 4.94, P=0.01). TP53 VAF further stratified distinct prognostic groups independent of clinical prognostic scoring systems (P=0.0005). In multivariate analysis, only a TP53 VAF >40% was an independent covariate (HR, 1.61; P<0.0001). In addition, SRSF2 VAF predicted for monocytosis (P=0.003), RUNX1 VAF with thrombocytopenia (P=0.01) and SF3B1 with ringed sideroblasts (P=0.001). Together, our study indicates that VAF should be incorporated in patient management and risk stratification in MDS. PMID:26514544

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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. PMID:26755614

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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.

  15. Frequency of HLA-DRB1 gene alleles in patients with multiple sclerosis in a Lithuanian population.

    PubMed

    Balnytė, Renata; Rastenytė, Daiva; Mickevičienė, Dalia; Vaitkus, Antanas; Skrodenienė, Erika; Vitkauskienė, Astra

    2012-01-01

    The aim of the present study was to investigate the influence of HLA-DRB1 alleles on the genetic susceptibility to multiple sclerosis in the Lithuanian population. MATERIAL AND METHODS. A total of 120 patients with multiple sclerosis and 120 unrelated healthy controls were enrolled in this case-control study. Allelic frequencies were compared between the groups. HLA-DRB1 alleles were genotyped using the polymerase chain reaction. RESULTS. HLA-DRB1*15 was present in 55.8% of the patients with multiple sclerosis and 10.0% of the controls (OR, 5.58; 95% CI, 3.19-9.77; P<0.0001). The protective alleles that were found to be more prevalent among the controls compared with the patients with multiple sclerosis were HLA-DRB1*01 (26.7% vs. 7.5%, P<0.0001), *03 (17.5% vs. 8.3%, P=0.034), and *16 (11.7% vs. 3.3%, P=0.014). HLA-DRB1*15 was more common among the female patients with multiple sclerosis than among the male patients (68.4% vs. 34.1%; OR, 4.18; 95%, CI 1.90-9.22; P=0.001). The heterozygous inheritance of HLA-DRB1*15 allele was more common in the patients with a history of maternal multiple sclerosis than in those with a history of paternal multiple sclerosis (29.4% vs. 9.8%; P=0.045). CONCLUSIONS. HLA-DRB1*15 was found to be associated with multiple sclerosis in the Lithuanian population. This allele was more prevalent among the female patients with multiple sclerosis. Maternal multiple sclerosis was more common than paternal multiple sclerosis, but the relationship with HLA-DRB1*15 allele was not established. HLA-DRB1*01, *03, and *16 appeared to be the protective alleles in this series. PMID:22370504

  16. Frequency of alleles conferring resistance to the Bt toxins Cry1Ac and Cry2Ab in Australian populations of Helicoverpa armigera (Lepidoptera: Noctuidae).

    PubMed

    Mahon, R J; Olsen, K M; Downes, S; Addison, S

    2007-12-01

    Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) is an important lepidopteran pest of cotton (Gossypium spp.) in Australia and the Old World. From 2002, F2 screens were used to examine the frequency of resistance alleles in Australian populations of H. armigera to Bacillus thuringiensis (Bt) CrylAc and Cry2Ab, the two insecticidal proteins present in the transgenic cotton Bollgard II. At that time, Ingard (expressing Cry1Ac) cotton had been grown in Australia for seven seasons, and Bollgard II was about to be commercially released. The principal objective of our study was to determine whether sustained exposure caused an elevated frequency of alleles conferring resistance to Cry1Ac in a species with a track record of evolving resistance to conventional insecticides. No major alleles conferring resistance to Cry1Ac were found. The frequency of resistance alleles for Cry1Ac was <0.0003, with a 95% credibility interval between 0 and 0.0009. In contrast, alleles conferring resistance to Cry2Ab were found at a frequency of 0.0033 (0.0017, 0.0055). The first isolation of this allele was found before the widespread deployment of Bollgard II. For both toxins the experiment-wise detection probability was 94.4%. Our results suggest that alleles conferring resistance to Cry1Ac are rare and that a relatively high baseline frequency of alleles conferring resistance to Cry2Ab existed before the introduction of Bt cotton containing this toxin. PMID:18232402

  17. High Frequency of Pathogenic Rearrangements in SPG11 and Extensive Contribution of Mutational Hotspots and Founder Alleles.

    PubMed

    Günther, Sven; Elert-Dobkowska, Ewelina; Soehn, Anne S; Hinreiner, Sophie; Yoon, Grace; Heller, Raoul; Hellenbroich, Yorck; Hübner, Christian A; Ray, Peter N; Hehr, Ute; Bauer, Peter; Sulek, Anna; Beetz, Christian

    2016-07-01

    Biallelic loss-of-function mutations in SPG11 cause a wide spectrum of recessively inherited, neurodegenerative disorders including hereditary spastic paraplegia (HSP), amyotrophic lateral sclerosis, and Charcot-Marie-Tooth disease. By comprehensive screening of three large cohorts of HSP index patients, we identified 83 alleles with "small" mutations and 13 alleles that carry large genomic rearrangements. Including relevant data from previous studies, we estimate that copy number variants (CNVs) account for ∼19% of pathogenic SPG11 alleles. The breakpoints for all novel and some previously reported CNVs were determined by long-range PCR and sequencing. This revealed several Alu-associated recombination hotspots. We also found evidence for additional mutational mechanisms, including for a two-step event in which an Alu retrotransposition preceded the actual rearrangement. Apparently independent samples with identical breakpoints were analyzed by microsatellite PCRs. The resulting haplotypes suggested the existence of two rearrangement founder alleles. Our findings widen the spectra of mutations and mutational mechanisms in SPG11, underscore the pivotal role played by Alus, and are of high diagnostic relevance for a wide spectrum of clinical phenotypes including the most frequent form of recessive HSP. PMID:27071356

  18. 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. PMID:26249527

  19. Genotype and allele frequencies of drug-metabolizing enzymes and drug transporter genes affecting immunosuppressants in the Spanish white population.

    PubMed

    Bosó, Virginia; Herrero, María J; Buso, Enrique; Galán, Juan; Almenar, Luis; Sánchez-Lázaro, Ignacio; Sánchez-Plumed, Jaime; Bea, Sergio; Prieto, Martín; García, María; Pastor, Amparo; Sole, Amparo; Poveda, José Luis; Aliño, Salvador F

    2014-04-01

    Interpatient variability in drug response can be widely explained by genetically determined differences in metabolizing enzymes, drug transporters, and drug targets, leading to different pharmacokinetic and/or pharmacodynamic behaviors of drugs. Genetic variations affect or do not affect drug responses depending on their influence on protein activity and the relevance of such proteins in the pathway of the drug. Also, the frequency of such genetic variations differs among populations, so the clinical relevance of a specific variation is not the same in all of them. In this study, a panel of 33 single nucleotide polymorphisms in 14 different genes (ABCB1, ABCC2, ABCG2, CYP2B6, CYP2C19, CYP2C9, CYP3A4, CYP3A5, MTHFR, NOD2/CARD15, SLCO1A2, SLCO1B1, TPMT, and UGT1A9), encoding for the most relevant metabolizing enzymes and drug transporters relating to immunosuppressant agents, was analyzed to determine the genotype profile and allele frequencies in comparison with HapMap data. A total of 570 Spanish white recipients and donors of solid organ transplants were included. In 24 single nucleotide polymorphisms, statistically significant differences in allele frequency were observed. The largest differences (>100%) occurred in ABCB1 rs2229109, ABCG2 rs2231137, CYP3A5 rs776746, NOD2/CARD15 rs2066844, TPMT rs1800462, and UGT1A9 rs72551330. In conclusion, differences were recorded between the Spanish and other white populations in terms of allele frequency and genotypic distribution. Such differences may have implications in relation to dose requirements and drug-induced toxicity. These data are important for further research to help explain interindividual pharmacokinetic and pharmacodynamic variability in response to drug therapy. PMID:24232128

  20. ACTN3 Allele Frequency in Humans Covaries with Global Latitudinal Gradient

    PubMed Central

    Lek, Monkol; North, Kathryn N.; Organ, Chris L.

    2013-01-01

    A premature stop codon in ACTN3 resulting in α-actinin-3 deficiency (the ACTN3 577XX genotype) is common in humans and reduces strength, muscle mass, and fast-twitch fiber diameter, but increases the metabolic efficiency of skeletal muscle. Linkage disequilibrium data suggest that the ACTN3 R577X allele has undergone positive selection during human evolution. The allele has been hypothesized to be adaptive in environments with scarce resources where efficient muscle metabolism would be selected. Here we test this hypothesis by using recently developed comparative methods that account for evolutionary relatedness and gene flow among populations. We find evidence that the ACTN3 577XX genotype evolved in association with the global latitudinal gradient. Our results suggest that environmental variables related to latitudinal variation, such as species richness and mean annual temperature, may have influenced the adaptive evolution of ACTN3 577XX during recent human history. PMID:23359641

  1. 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.

  2. Allelic frequencies for the HLA-DQA1, D1S80, HUMTHO1, HUMTPOX, HUMCSF1PO and HUMVWA loci in Cantabria (middle north Spain).

    PubMed

    Sánchez-Molina, I; Calvet, R

    2000-01-01

    Allele frequencies for six DNA polymorphisms have been studied in a population sample from Cantabria (middle north Spain) using the polymerase chain reaction. The HLA-DQA1 locus was analyzed by the reverse dot-blot technique and the other five by polyacrylamide gel electrophoresis followed by silver staining. Six alleles were found for HLA-DQA1. 15 alleles for D1S80, 6 alleles for HUMTHO1 and HUMCSF1PO, 7 for HUMTPOX and 8 alleles for HUMVWA. The 21 repeat allele in HUMVWA had not previously been reported in a Spanish population. The genotype distributions met Hardy-Weinberg expectations for all the systems and some statistical parameters of forensic interest were calculated. Comparisons with other populations revealed significant differences for HLA-DQA1, HUMVWA and HUMTHO1, with interracial differences being more pronounced than between Spanish populations. The HUMVWA system showed the highest forensic efficiency of the six polymorphisms studied. PMID:10641932

  3. High frequency of the apolipoprotein E *4 allele in African pygmies and most of the African populations in sub-Saharan Africa.

    PubMed

    Zekraoui, L; Lagarde, J P; Raisonnier, A; Gérard, N; Aouizérate, A; Lucotte, G

    1997-08-01

    Apolipoprotein E genotypes (alleles *2, *3, and *4) have been determined in 70 Aka Pygmies and 470 unrelated African sub-Saharan subjects. Allele frequencies for Pygmies are 5.7% for APOE*2, 53.6% for APOE*3, and 40.7% for APOE*4, and the global proportions for sub-Saharan subjects are 11.6% for APOE*2, 70.6% for APOE*3, and 17.8% for APOE*4. The frequencies in some ethnic groups are statistically different from the overall mean in the Afar and the Isa, the Ewe (Togo), the Malinke (Guinea), and the Mossi; three ethnic groups have a higher allele frequency of APOE*4 (Fon, 29.4%; Zairians, 33.3%; Tutsi, 38.5%). The APOE*4 allele is considered the ancestral form because of its high frequency in African Pygmies and other aboriginal populations. PMID:9198315

  4. Skewed allele frequencies of an Mx gene mutation with potential resistance to avian influenza virus in different chicken populations.

    PubMed

    Li, X Y; Qu, L J; Yao, J F; Yang, N

    2006-07-01

    The Mx gene is considered to confer positive antiviral responses to the orthomyxovirus in many organisms. In the chicken, 1 nonsynonymous single nucleotide polymorphism (G to A) at position 2,032 of Mx cDNA was demonstrated to confer positive antiviral activity in vitro to avian influenza virus in a previous study. In the current study, 15 Chinese native chicken breeds, 4 highly selected commercial lines, and the Red Jungle Fowl were selected to detect allele frequencies of the Mx mutation. The frequencies of the favorable allele A in native breeds were 0.7241 to 0.9554, which were much higher than those (0.0565 to 0.2742) found in the commercial populations. Whereas most native breeds were in Hardy-Weinberg equilibrium at this locus (P > 0.01), 3 out of 4 commercial populations were not in Hardy-Weinberg equilibrium (P < 0.01). Selection, environment, and negative correlations between production and disease resistant traits could contribute to highly skewed frequencies of the mutation among native breeds and commercial populations. The results suggested that further studies are needed with regard to the genetic resistance to avian influenza in different populations with various domestication background and selection history. PMID:16830876

  5. 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.

  6. [Distribution and frequency of HLA alleles and haplotypes in Brazilians with type 1 diabetes mellitus].

    PubMed

    Alves, Crésio; Meyer, Isadora; Vieira, Nara; Toralles, Maria Betânia P; LeMaire, Denise

    2006-06-01

    The genetic predisposition to type 1 diabetes (DM1) is associated with genes of the human leukocyte antigen (HLA) system, specially the HLA-DR and -DQ. In Caucasians, the HLA-DR3 and -DR4 antigens are associated with susceptibility and the -DR2, with protection. In Brazil, a country with a large miscegenation of European Caucasians, Native Amerindians and African Blacks, the genetic basis of DM1 has not been adequately studied. The aim of this paper is to present a critical review of articles indexed in the MEDLINE and LILACS-BIREME data basis about the association of HLA with DM1 in Brazilians. Eight papers, all of them from the Southeast region, were found. Immunogenetic susceptibility to DM1 in Brazilians was associated with HLA-DRB1*03, -DRB*04, -DQB1*0201, -DQB1*0302 alleles, and protection against DM1 was associated with HLA-DQB1*0602, -DQB1*0301 alleles and -DR2 and -DR7 antigens. Since the Brazilian population is not racially homogeneous, it is not possible to extrapolate studies from a single region to the remainder of the country. It is necessary to study populations from different regions to identify new associations or to strengthen associations with the ones already identified. This knowledge will contribute to future prophylactic or therapeutic interventions in the group of Brazilians at risk of developing DM1. PMID:16936983

  7. A prospective evaluation of the transthyretin Ile122 allele frequency in an African-American population.

    PubMed

    Yamashita, Taro; Hamidi Asl, Kamran; Yazaki, Masahide; Benson, Merrill D

    2005-06-01

    Transthyretin Val122Ile is one of greater than 80 mutations in transthyretin (TTR) that are associated with hereditary amyloidosis. Retrospective studies have shown a prevalence of this mutation as high as 3.9% in African-Americans. The present study was undertaken to determine in a prospective fashion the prevalence of the TTR Val122Ile allele in African-Americans in a Midwestern American city. DNA was isolated from cord bloods collected at the time of birth in the County hospital of Indianapolis, Indiana. Samples were identified only as to ethnic origin of the mother. Analysis was performed by PCR amplification of TTR exon 4 followed by SSCP and RFLP. Cord bloods from 1,973 children born at the County hospital were analyzed. Thirty of 1,000 DNA samples from African-American newborns were positive for TTR Val122Ile (3%). Two of 453 DNA samples from Caucasian newborns were positive (0.44%). Zero of 490 DNA samples from newborns of Hispanic mothers and 0 of 30 from newborns with mothers classified as other (including Asian) were positive. This prospective study demonstrates that 3% of newborns of African-American women in an urban population have the TTR Val122Ile mutation which is associated with late-onset cardiomyopathy. The degree of penetrance of this mutation at the clinical level has not yet been determined. PMID:16011990

  8. 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.

  9. 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

  10. Impact of harmonics on the interpolated DFT frequency estimator

    NASA Astrophysics Data System (ADS)

    Belega, Daniel; Petri, Dario; Dallet, Dominique

    2016-01-01

    The paper investigates the effect of the interference due to spectral leakage on the frequency estimates returned by the Interpolated Discrete Fourier Transform (IpDFT) method based on the Maximum Sidelobe Decay (MSD) windows when harmonically distorted sine-waves are analyzed. The expressions for the frequency estimation error due to both the image of the fundamental tone and harmonics, and the frequency estimator variance due to the combined effect of both the above disturbances and wideband noise are derived. The achieved expressions allow us to identify which harmonics significantly contribute to frequency estimation uncertainty. A new IpDFT-based procedure capable to compensate all the significant effects of harmonics on the frequency estimation accuracy is then proposed. The derived theoretical results are verified through computer simulations. Moreover, the accuracy of the proposed procedure is compared with those of other state-of-the-art frequency estimation methods by means of both computer simulations and experimental results.

  11. 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

  12. Frequency of Bt resistance alleles in Helicoverpa armigera in the Xinjiang cotton-planting region of China.

    PubMed

    Li, Guoping; Feng, Hongqiang; Gao, Yulin; Wyckhuys, Kris A G; Wu, Kongming

    2010-10-01

    Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) is a key insect pest of cotton in Xinjiang cotton-planting region of northwest China. In this region, cotton is grown on average ≈ 1.65 million ha (1.53 ≈ 1.80 million ha) annually in largely monoculture agricultural landscapes, similarly to cropping systems in the United States or Australia. Under such cropping regimes, naturally occurring refuges (with non-Bt crops) may be insufficient to prevent H. armigera resistance development to Bt toxins. Therefore, we assessed frequency of alleles conferring resistance to Cry1Ac toxin of F(1) and F(2) offspring of H. armigera isofemale lines from two distinct localities in the region during 2005-2009. More specifically, a total of 224 isofemale lines was collected from Korla County (≈ 70% Bt cotton adoption) and 402 lines from Shache County (≈ 5% Bt cotton planting). Subsequent offspring was screened on Cry1Ac artificial diet. From 2005 to 2009, resistance gene frequency in Korla fluctuated between 0.0000 and 0.0040, while being 0.0000-0.0008 in individuals collected from Shache, and there were no significant increases in both counties from 2005 to 2009. Relative average development rates (RADRs) of larvae in F(1) tests showed significant increases from Korla, but not in Shache. RADR of F(1) larvae is significantly correlated with RADR of F(2) offspring, indicating genetic variation in response to toxin in field H. armigera population. Although the occurrence of Cry1Ac resistance alleles was low in Xinjiang cotton-planting region of China, particular attention should be given to H. armigera resistance development in Korla County. PMID:22546469

  13. Allelic frequency determination of the 24-bp chitotriosidase duplication in the Portuguese population by real-time PCR.

    PubMed

    Rodrigues, M R; Sá Miranda, M C; Amaral, O

    2004-01-01

    Chitotriosidase is a human chitinase produced by macrophages. Its enzymatic activity is markedly elevated in serum of patients suffering from lysosomal storage disorders, as well as other diseases in which macrophages are activated. Therefore, it is a useful tool as a secondary marker in the diagnosis of several disorders including Gaucher disease type 1 and Niemann-Pick disease. The determination of chitotriosidase levels as a diagnosis complement in some lysosomal storage disorders and in enzyme replacement therapy follow-up of Gaucher disease patients is of great importance. However, the fact that a mutation caused by a 24-bp duplication in the CHIT1 gene resulting in deficiency of plasma chitotriosidase activity is very frequent makes the establishment of the frequency of this mutation in different population groups necessary. Furthermore, in order to validate the use of chitotriosidase activity as a marker, it is indispensable to screen individuals for this particular mutation. In this work, we present the results of a study where the allelic frequency of the above mentioned CHIT1 gene mutation was determined in the Portuguese population by real-time PCR. The frequency of carriers encountered in this sample of Portuguese individuals was of 37%. PMID:15528158

  14. Tidal frequency estimation for closed basins

    NASA Technical Reports Server (NTRS)

    Eades, J. B., Jr.

    1978-01-01

    A method was developed for determining the fundamental tidal frequencies for closed basins of water, by means of an eigenvalue analysis. The mathematical model employed, was the Laplace tidal equations.

  15. 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

  16. 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

  17. 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

  18. 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

  19. Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency.

    PubMed

    Hancock, Angela M; Witonsky, David B; Ehler, Edvard; Alkorta-Aranburu, Gorka; Beall, Cynthia; Gebremedhin, Amha; Sukernik, Rem; Utermann, Gerd; Pritchard, Jonathan; Coop, Graham; Di Rienzo, Anna

    2010-05-11

    Human populations use a variety of subsistence strategies to exploit an exceptionally broad range of ecoregions and dietary components. These aspects of human environments have changed dramatically during human evolution, giving rise to new selective pressures. To understand the genetic basis of human adaptations, we combine population genetics data with ecological information to detect variants that increased in frequency in response to new selective pressures. Our approach detects SNPs that show concordant differences in allele frequencies across populations with respect to specific aspects of the environment. Genic and especially nonsynonymous SNPs are overrepresented among those most strongly correlated with environmental variables. This provides genome-wide evidence for selection due to changes in ecoregion, diet, and subsistence. We find particularly strong signals associated with polar ecoregions, with foraging, and with a diet rich in roots and tubers. Interestingly, several of the strongest signals overlap with those implicated in energy metabolism phenotypes from genome-wide association studies, including SNPs influencing glucose levels and susceptibility to type 2 diabetes. Furthermore, several pathways, including those of starch and sucrose metabolism, are enriched for strong signals of adaptations to a diet rich in roots and tubers, whereas signals associated with polar ecoregions are overrepresented in genes associated with energy metabolism pathways. PMID:20445095

  20. How Metastrategic Considerations Influence the Selection of Frequency Estimation Strategies

    ERIC Educational Resources Information Center

    Brown, Norman R.

    2008-01-01

    Prior research indicates that enumeration-based frequency estimation strategies become increasingly common as memory for relevant event instances improves and that moderate levels of context memory are associated with moderate rates of enumeration [Brown, N. R. (1995). Estimation strategies and the judgment of event frequency. Journal of…

  1. 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.

  2. 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.

  3. 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.

  4. Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker effects and interactions cannot be accurately estimated when minor marker allele frequencies (MAF) are low. To increase the accuracy of estimation for three marker systems in commercial use, an Angus population at USMARC was subjected to marker assisted-selection for multiple years t...

  5. 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.

  6. Efficient Blind Estimation of MC-CDMA Carrier Frequency Offset

    NASA Astrophysics Data System (ADS)

    Chang, Ann-Chen; Hsu, Chun; Su, Ing-Jiunn

    This letter presents an efficient blind carrier frequency offset (CFO) estimate approach for multicarrier-code division multiple access (MC-CDMA) system. It can reduce the searching grids required and improve the CFO estimating accuracy compared with conventional searching-based algorithms. Simulation results are provided for illustrating the effectiveness of the proposed blind estimate approach.

  7. The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations.

    PubMed Central

    Marth, Gabor T; Czabarka, Eva; Murvai, Janos; Sherry, Stephen T

    2004-01-01

    We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American samples. For this analysis we derived a simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories. The direct calculation generates the spectrum orders of magnitude faster than coalescent simulations do and allows us to generate spectra for a large number of alternative histories on a multidimensional parameter grid. Model-fitting experiments using this grid reveal significant population-specific differences among the demographic histories that best describe the observed allele frequency spectra. European and Asian spectra show a bottleneck-shaped history: a reduction of effective population size in the past followed by a recent phase of size recovery. In contrast, the African-American spectrum shows a history of moderate but uninterrupted population expansion. These differences are expected to have profound consequences for the design of medical association studies. The analytical methods developed for this study, i.e., a closed mathematical formulation for the allele frequency spectrum, correcting the ascertainment bias introduced by shallow SNP sampling, and dealing with variable sample sizes provide a general framework for the analysis of public variation data. PMID:15020430

  8. 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. PMID:12798016

  9. 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

  10. 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

  11. 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. PMID:25846829

  12. 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

  13. Allele frequency-based analyses robustly map sequence sites under balancing selection in a malaria vaccine candidate antigen.

    PubMed Central

    Polley, Spencer D; Chokejindachai, Watcharee; Conway, David J

    2003-01-01

    The Plasmodium falciparum apical membrane antigen 1 (AMA1) is a leading candidate for a malaria vaccine. Here, within-population analyses of alleles from 50 Thai P. falciparum isolates yield significant evidence for balancing selection on polymorphisms within the disulfide-bonded domains I and III of the surface accessible ectodomain of AMA1, a result very similar to that seen previously in a Nigerian population. Studying the frequency of nucleotide polymorphisms in both populations shows that the between-population component of variance (F(ST)) is significantly lower in domains I and III compared to the intervening domain II and compared to 11 unlinked microsatellite loci. A nucleotide site-by-site analysis shows that sites with exceptionally high or low F(ST) values cluster significantly into serial runs, with four runs of low values in domain I and one in domain III. These runs may map the sequences that are consistently under the strongest balancing selection from naturally acquired immune responses. PMID:14573469

  14. Regional differences of HFE (C282Y, H63D) allele frequencies in the Netherlands A model case illustrating the significance of genographics and prehistorical population migration.

    PubMed

    Cobbaert, C M; Delanghe, J; Boer, J M A; Feskens, E J M

    2012-01-01

    We investigated HFE C282Y and H63D allele frequencies in three Dutch towns in the Netherlands, as well as their association with cardiovascular disease (CVD) mortality. Study subjects were selected from participants of the Monitoring Project on Cardiovascular Disease Risk Factors in the Netherlands carried out in Amsterdam, Doetinchem and Maastricht among > 35000 subjects, 20-59 years of age. Mortality follow-up lasted 9 to 13 years. A random sample of the cohort (n = 1075) provided information on the total study population. The random sample and all CVD deaths (n = 301) were genotyped for the C282Y and H63D mutation. Adjusted hazard ratios (HR) for CVD mortality were calculated per genotype. C282Y allele frequencies differed significantly between the towns investigated (p = 0.017), whereas the allele frequencies of H63D were similar (p = 0.141) across towns. In Maastricht we found a C282Y allele frequency of 0.086 compared to 0.055 in Amsterdam and 0.054 in Doetinchem. C282Y and H63D heterozygosity did not predict fatal CVD in either men or women, whereas homozygosity for the H63D mutation increased fatal CVD in women (adjusted HR = 8.5; 95% CI = 2.3-31.1). The unexpected high C282Y allele frequency in Maastricht is in line with the recent evidence of a Celtic origin of citizens from the former southern Netherlands and with prehistorical population migrations revealed in the context of the international Genographic Project, a landmark study of prehistorical human migrations around the globe. We recommend that when designing national screening programmes and national registries for genetic disorders, potential regional prevalence differences should be taken into account. PMID:23340149

  15. 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

  16. 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

  17. 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

  18. 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. PMID:12109025

  19. Frequencies of 23 functionally significant variant alleles related with metabolism of antineoplastic drugs in the chilean population: comparison with caucasian and asian populations.

    PubMed

    Roco, Angela; 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

  20. 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

  1. Frequency of streptococcal upper respiratory tract infections and HLA-Cw*06 allele in 70 patients with guttate psoriasis from northern Poland

    PubMed Central

    Szczerkowska-Dobosz, Aneta; Rębała, Krzysztof; Wysocka, Joanna; Roszkiewicz, Jadwiga; Szczerkowska, Zofia; Placek, Waldemar

    2015-01-01

    Introduction The association of guttate psoriasis with a streptococcal throat infection and HLA-Cw*06 allele is well established in different populations. Nevertheless, only few studies on this form of disease have been performed in the Polish population. Aim To analyze the frequencies of streptococcal-induced guttate psoriasis and HLA-Cw*06 allele in 70 patients with guttate psoriasis originating from northern Poland. Material and methods Seventy patients with guttate psoriasis and 24 healthy volunteers were enrolled into the study. Both groups were sex- and age-matched. The evidence of streptococcal infection was based on the positive throat swabs and/or elevated ASO titers. The modified method, including PCR-SSP and PCR-RFLP, was applied to HLA-Cw*06 genotyping. Results HLA-Cw*06 allele was confirmed in 49 (70%) out of 70 patients, which is significantly higher than in the control population (30%) (p = 0.001). Evidence for streptococcal infection was found in 34 (48.5%) subjects with psoriasis. Twenty-seven of them (79%) carried HLA-Cw*06 allele. In 36 individuals in whom no evidence of streptococcal infection was found, 14 (39%) did not carry HLA-Cw*06 allele. Conclusions Our data confirm that HLA-Cw*06 is a major, but not imperative, genetic determinant for guttate psoriasis. PMID:26755910

  2. 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.

  3. 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

  4. 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...

  5. 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.

  6. 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.

  7. 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 and allele frequencies.

    PubMed

    Tait, R G; Shackelford, S D; Wheeler, T L; King, D A; Casas, E; Thallman, R M; Smith, T P L; Bennett, G L

    2014-02-01

    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 and mode of inheritance for previously reported SNP on targeted beef carcass quality traits; 2) estimate effects of previously reported SNP on nontarget performance traits; and 3) evaluate tenderness SNP specific residual variance models compared to a single residual variance model for tenderness. Divergent haplotypes within µ-calpain (CAPN1), and SNP within calpastatin (CAST) and growth hormone receptor (GHR) were successfully selected to increase their frequencies. Traits evaluated were birth BW, weaning BW, final BW, fat thickness, LM area, USDA marbling score, yield grade, slice shear force (SSF), and visible and near infrared predicted slice shear force. Both CAPN1 and CAST exhibited additive (P < 0.001) modes of inheritance for SSF and neither exhibited dominance (P ≥ 0.19). Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P = 0.55). Estimated additive effects of CAPN1 (1.049 kg) and CAST (1.257 kg) on SSF were large in this study. Animals homozygous for tender alleles at both CAPN1 and CAST would have 4.61 kg lower SSF (38.6% of the mean) than animals homozygous tough for both markers. There was also an effect of CAST on yield grade (P < 0.02). The tender CAST allele was associated with more red meat yield and less trimmable fat. There were no significant effects (P ≥ 0.23) for GHR on any of the traits evaluated in this study. Furthermore, CAST specific residual variance models were found to fit significantly better (P < 0.001) than single residual variance models for SSF, with the tougher genotypes having larger residual variance. Thus, the risk of a tough steak from the undesired CAST genotype is increased through both an

  8. 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

  9. 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

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

    PubMed

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

    2012-01-01

    P-glycoprotein, encoded by the MDR1 or ABCB1 gene, is an integral component of the blood-brain barrier as an efflux pump for xenobiotics crucial in limiting drug uptake into the central nervous system. Dogs homozygous for a 4-base pair deletion of the canine MDR1 gene show altered expression or function of P-glycoprotein, resulting in neurotoxicosis after administration of the substrate drugs. In the present study, the usefulness of microchip electrophoresis for genotyping assays detecting this deletion mutation was evaluated. Mutagenically separated polymerase chain reaction (MS-PCR) and real-time PCR assays were newly developed and evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies dogs in Japan to determine the allele frequency in this breed. Microchip electrophoresis showed advantages in detection sensitivity and time saving over other modes of electrophoresis. The MS-PCR assay clearly discriminated all genotypes. Real-time PCR assay was most suitable for a large-scale survey due to its high throughput and rapidity. The genotyping survey demonstrated that the carrier and mutant allele frequencies were 0.49% and 0.25%, respectively, suggesting that the mutant allele frequency in Border Collies is markedly low compared to that in the susceptible dog breeds such as rough and smooth Collies. PMID:22362942

  11. 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 Central

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

    1994-01-01

    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

  12. 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

  13. Brillouin frequency shift estimation in BOTDA via subpixel processing

    NASA Astrophysics Data System (ADS)

    Ruiz-Lombera, R.; Mirapeix, J.; Laarossi, I.; Rodríguez-Cobo, L.; Lopez-Higuera, J. M.

    2016-05-01

    In this paper we propose the employment of sub-pixel algorithms for the estimation of the central frequency of the Brillouin Gain Spectrum in a Brillouin Optical Time Domain Analyzer. The experimental results will show that the proposed solution shows a good performance when the chosen frequency step for the required frequency sweep is high. If the improved computational efficiency in comparison to the traditional Lorentzian fitting is also considered, it can be concluded that this approach may be of great interest for dynamic measurement scenarios.

  14. Adaptive frequency estimation by MUSIC (Multiple Signal Classification) method

    NASA Astrophysics Data System (ADS)

    Karhunen, Juha; Nieminen, Esko; Joutsensalo, Jyrki

    During the last years, the eigenvector-based method called MUSIC has become very popular in estimating the frequencies of sinusoids in additive white noise. Adaptive realizations of the MUSIC method are studied using simulated data. Several of the adaptive realizations seem to give in practice equally good results as the nonadaptive standard realization. The only exceptions are instantaneous gradient type algorithms that need considerably more samples to achieve a comparable performance. A new method is proposed for constructing initial estimates to the signal subspace. The method improves often dramatically the performance of instantaneous gradient type algorithms. The new signal subspace estimate can also be used to define a frequency estimator directly or to simplify eigenvector computation.

  15. 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.

  16. Estimating the Upper Tail of Flood Frequency Distributions

    NASA Astrophysics Data System (ADS)

    Smith, James A.

    1987-08-01

    Procedures for estimating recurrence intervals of extreme floods are developed. Estimation procedures proposed in this paper differ from standard procedures in that only the largest 10-20% of flood peaks are explicitly used to estimate flood quantiles. Quantile estimation procedures are developed for both annual peak and seasonal flood frequency distributions. The underlying model of flood peaks is a marked point process ?, where ? represents time of occurrence of the jth flood during year i and the mark ? represents magnitude of the flood peak. Results from extreme value theory are used to parameterize the upper tail of flood peak distributions. Quantile estimation procedures are applied to the 92-year record of flood peaks from the Potomac River. Results suggest that Potomac flood peaks are bounded above. The estimated upper bound is only 20% larger than the flood of record.

  17. On estimating the exponent of power-law frequency distributions.

    PubMed

    White, Ethan P; Enquist, Brian J; Green, Jessica L

    2008-04-01

    Power-law frequency distributions characterize a wide array of natural phenomena. In ecology, biology, and many physical and social sciences, the exponents of these power laws are estimated to draw inference about the processes underlying the phenomenon, to test theoretical models, and to scale up from local observations to global patterns. Therefore, it is essential that these exponents be estimated accurately. Unfortunately, the binning-based methods traditionally used in ecology and other disciplines perform quite poorly. Here we discuss more sophisticated methods for fitting these exponents based on cumulative distribution functions and maximum likelihood estimation. We illustrate their superior performance at estimating known exponents and provide details on how and when ecologists should use them. Our results confirm that maximum likelihood estimation outperforms other methods in both accuracy and precision. Because of the use of biased statistical methods for estimating the exponent, the conclusions of several recently published papers should be revisited. PMID:18481513

  18. 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

  19. 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

  20. Frequency of HLA-DRB1 and HLA-DQB1 Alleles and Haplotype Association in Syrian Population.

    PubMed

    Jazairi, Batoul; Khansaa, Issam; Ikhtiar, Adnan; Murad, Hossam

    2016-02-01

    The study of Human Leukocyte Antigen (HLA) system is very important in health and diseases. As the HLA loci are the most polymorphic in the human genome, it plays a very important role in the immune responses to self and nonself antigens. In the light of the growing importance of typing the HLA alleles in transplantation, autoimmune diseases, cancer, and many other diseases, we studied 225 unrelated healthy Syrian subjects for their HLA class II genotypes in an attempt to reveal the distribution of the HLA (DRB1-DQB1) alleles in the general Syrian population. Our results revealed that the most common alleles for the DRB1 locus were DRB1*11 (26.4%), DRB1*04 (14%), and DRB1*07 (12%). However, the most frequent alleles for the DQB1 locus were DQB1*03 (40.9%) and DQB1*05 (25.1%). The frequent of two-locus haplotypes carry the most frequent alleles at these loci. The most frequently detected class II ''haplotypes'' are DRB1*11-DQB1*03 (8.9%), DRB1*01-DQB1*05 (3.6%), and DRB1*04-DQB1*03 (2.7%). Compared with other populations, our result, deduced from the analysis of genetic distances and the construction of neighbor-joining (NJ) dendrogram, and principal component analysis (PCA) indicates that Syrians are related to Middle Eastern populations. Our data about the Syrian population will aid researchers in studying the relation of HLA class II with different diseases in a Syrian population and will add to the available international literature associated with these loci. PMID:26853713

  1. Robust estimation of the motile cilia beating frequency.

    PubMed

    Meste, O; Brau, F; Guyon, A

    2015-10-01

    The estimation of the cilia beating frequency (CBF) is of great interest in understanding how the CBF modulates liquid fluxes and how it is controlled by the ciliated cell intra- and/or extracellular medium composition in physiological processes. Motion artifacts and camera defaults may hinder the computation of the frequency variations during long-lasting experiments. We have developed a new analysis approach consisting of a preliminary corrective step (removal of a grid pattern on the image sequence and shift compensation), followed by a harmonic model of the observed cilia using a maximum likelihood estimator framework. It is shown that a more accurate estimation of the frequency can be obtained by averaging the squared Fourier transform of individual pixels followed by a particular summation over the different frequencies, namely the compressed spectrum. Robustness of the proposed method over traditional approaches is shown by several examples and simulations. The method is then applied to images of samples containing ciliated ependymal cells located in the third cerebral ventricle of mouse brains, showing that even small variations in CBF in response to changes in the amount of oxygenation, pH or glucose were clearly visible in the computed frequencies. As a conclusion, this method reveals a fine metabolic tuning of the cilia beating in ependimocytes lining the third cerebral ventricle. Such regulations are likely to participate in homeostatic mechanisms regulating CSF movements and brain energy supply. PMID:26215519

  2. The effects of the nonstationarity on the regional frequency estimates

    NASA Astrophysics Data System (ADS)

    Nam, W.; Jang, H.; Choi, W.; Heo, J. H.

    2014-12-01

    Regional frequency analysis (RFA) is widely used to estimate more reliable quantiles of extreme hydro-meteorological events. This approach requires the assumption of stationarity. In this paper, index flood method was used to analyze the nonstationary 24-hour rainfall maxima of 9 virtual sites in a region. Monte Carlo simulation was used to generate the nonstationary data based on the generalized extreme value (GEV) model with time varying location/scale parameters. To analyze the temporal change of regional frequency estimates such as index flood, growth curve, quantile, and the heterogeneity measure, the accumulation of the data from the given time step and moving window concept were applied. Results indicated that the stationarity of the data had more effects on the index flood than the growth curve. There was little effects of the shape parameter of GEV distribution on the temporal pattern of the regional frequency estimates. Temporal change of the heterogeneity measure was not significant. These results showed that the time varying parameters of the nonstationary GEV model need to be formed considering the temporal pattern of the regional frequency estimates.

  3. Vestibular function is associated with residual low-frequency hearing loss in patients with bi-allelic mutations in the SLC26A4 gene.

    PubMed

    Jung, Jinsei; Seo, Young Wook; Choi, Jae Young; Kim, Sung Huhn

    2016-05-01

    DFNB4 is non-syndromic, autosomal recessive type of hearing loss with an enlarged vestibular aqueduct (EVA) caused by mutations in SLC26A4/pendrin. Although the characteristics of hearing loss are well known in DFNB4, vestibular function remains inconclusive. We evaluated the vestibular function of 31 patients with bi-allelic mutations in SLC26A4/pendrin and analyzed genetic, radiological, and audiological correlations with vestibular function. In a caloric test, unilateral and bilateral vestibulopathies were detected in 45.2% and 6.4% of patients, respectively; however, only 22.6% had subjective vertigo symptoms. While vestibular phenotype was not significantly associated with specific mutations in genetic alleles or the sizes of the endolymphatic sac and vestibular aqueduct, a residual hearing threshold at a low frequency (500 Hz) was definitely correlated with vestibular function in DFNB4 (p = 0.005). These findings may indicate that vestibular function in DFNB4 deteriorates unilaterally in ears when hearing loss occurs. In conclusion, DFNB4 shows vestibular dysfunction, which is strongly linked to hearing loss at low frequencies without any allelic or anatomical predisposing factor. PMID:26900070

  4. Frequency of alleles conferring resistance to Bt maize in French and US corn belt populations of the European corn borer, Ostrinia nubilalis.

    PubMed

    Bourguet, D; Chaufaux, J; Séguin, M; Buisson, C; Hinton, J L; Stodola, T J; Porter, P; Cronholm, G; Buschman, L L; Andow, D A

    2003-05-01

    Farmers, industry, governments and environmental groups agree that it would be useful to manage transgenic crops producing insecticidal proteins to delay the evolution of resistance in target pests. The main strategy proposed for delaying resistance to Bacillus thuringiensis ( Bt) toxins in transgenic crops is the high-dose/refuge strategy. This strategy is based on the unverified assumption that resistance alleles are initially rare (<10(-3)). We used an F(2) screen on >1,200 isofemale lines of Ostrinia nubilalis Hübner (Lepidoptera: Crambidae) collected in France and the US corn belt during 1999-2001. In none of the isofemale lines did we detect alleles conferring resistance to Bt maize producing the Cry1Ab toxin. A Bayesian analysis of the data indicates that the frequency of resistance alleles in France was <9.20 x 10(-4) with 95% probability, and a detection probability of >80%. In the northern US corn belt, the frequency of resistance to Bt maize was <4.23 x 10(-4) with 95% probability, and a detection probability of >90%. Only 95 lines have been screened from the southern US corn belt, so these data are still inconclusive. These results suggest that resistance is probably rare enough in France and the northern US corn belt for the high-dose plus refuge strategy to delay resistance to Bt maize. PMID:12748773

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. Phenotype-Genotype Correlations and Estimated Carrier Frequencies of Primary Hyperoxaluria.

    PubMed

    Hopp, Katharina; Cogal, Andrea G; Bergstralh, Eric J; Seide, Barbara M; Olson, Julie B; Meek, Alicia M; Lieske, John C; Milliner, Dawn S; Harris, Peter C

    2015-10-01

    Primary hyperoxaluria (PH) is a rare autosomal recessive disease characterized by oxalate accumulation in the kidneys and other organs. Three loci have been identified: AGXT (PH1), GRHPR (PH2), and HOGA1 (PH3). Here, we compared genotype to phenotype in 355 patients in the Rare Kidney Stone Consortium PH registry and calculated prevalence using publicly available whole-exome data. PH1 (68.4% of families) was the most severe PH type, whereas PH3 (11.0% of families) showed the slowest decline in renal function but the earliest symptoms. A group of patients with disease progression similar to that of PH3, but for whom no mutation was detected (11.3% of families), suggested further genetic heterogeneity. We confirmed that the AGXT p.G170R mistargeting allele resulted in a milder PH1 phenotype; however, other potential AGXT mistargeting alleles caused more severe (fully penetrant) disease. We identified the first PH3 patient with ESRD; a homozygote for two linked, novel missense mutations. Population analysis suggested that PH is an order of magnitude more common than determined from clinical cohorts (prevalence, approximately 1:58,000; carrier frequency, approximately 1:70). We estimated PH to be approximately three times less prevalent among African Americans than among European Americans because of a limited number of common European origin alleles. PH3 was predicted to be as prevalent as PH1 and twice as common as PH2, indicating that PH3 (and PH2) cases are underdiagnosed and/or incompletely penetrant. These results highlight a role for molecular analyses in PH diagnostics and prognostics and suggest that wider analysis of the idiopathic stone-forming population may be beneficial. PMID:25644115

  11. Segmentation and frequency domain ML pitch estimation of speech signals

    NASA Astrophysics Data System (ADS)

    Hanna, Salim A.

    The rate of oscillation of the vocal cords and its inverse value, the pitch period, are important speech features that are useful for speech analysis/synthesis, speech recognition, and speech coding. An automatic approach for the estimation of the pitch period in continuous speech is presented. The proposed approach considers the segmentation of the speech signal into homogeneous regions and the detection of segments that are generated by vocal cord oscillations prior to pitch estimation. The pitch period of voiced segments is estimated in the frequency domain using a maximum likelihood (ML) procedure. The estimated pitch period is chosen to maximize a likelihood function over the range of expected pitch periods. An efficient simplified realization of the generalized likelihood ratio segmentation method is also described.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. Digital frequency estimation in burst mode QPSK transmission

    NASA Astrophysics Data System (ADS)

    Bellini, S.; Molinari, C.; Tartara, G.

    1990-07-01

    In burst digital transmission using PSK modulation with coherent detection, the recovery of the carrier reference phase and the symbol clock is a key aspect. If all users have a common clock synchronization, symbol timing needs not to be recovered in each burst. A digital processor for carrier recovery without preambles, in the presence of frequency offset, is considered. As an example, a 2 Mb/s QPSK transmission system is considered in which Eb/No = 10 dB, and the burst and estimation interval length L = 15. Using the algorithm described and averaging eight successive estimated frequency offsets, in order to eliminate anomalous errors, the bit-error-rate degradation is equal to 0.14 dB when Delta-f = 20 kHz.

  17. Estimating correlations of neighboring frequencies in ambient seismic noise

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Ben-Zion, Yehuda

    2016-05-01

    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 analyzed 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 broadband 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 neighboring 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 Angles 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.

  18. 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.

  19. Sampling frequency affects estimates of annual nitrous oxide fluxes

    NASA Astrophysics Data System (ADS)

    Barton, L.; Wolf, B.; Rowlings, D.; Scheer, C.; Kiese, R.; Grace, P.; Stefanova, K.; Butterbach-Bahl, K.

    2015-11-01

    Quantifying nitrous oxide (N2O) fluxes, a potent greenhouse gas, from soils is necessary to improve our knowledge of terrestrial N2O losses. Developing universal sampling frequencies for calculating annual N2O fluxes is difficult, as fluxes are renowned for their high temporal variability. We demonstrate daily sampling was largely required to achieve annual N2O fluxes within 10% of the ‘best’ estimate for 28 annual datasets collected from three continents—Australia, Europe and Asia. Decreasing the regularity of measurements either under- or overestimated annual N2O fluxes, with a maximum overestimation of 935%. Measurement frequency was lowered using a sampling strategy based on environmental factors known to affect temporal variability, but still required sampling more than once a week. Consequently, uncertainty in current global terrestrial N2O budgets associated with the upscaling of field-based datasets can be decreased significantly using adequate sampling frequencies.

  20. Sampling frequency affects estimates of annual nitrous oxide fluxes.

    PubMed

    Barton, L; Wolf, B; Rowlings, D; Scheer, C; Kiese, R; Grace, P; Stefanova, K; Butterbach-Bahl, K

    2015-01-01

    Quantifying nitrous oxide (N2O) fluxes, a potent greenhouse gas, from soils is necessary to improve our knowledge of terrestrial N2O losses. Developing universal sampling frequencies for calculating annual N2O fluxes is difficult, as fluxes are renowned for their high temporal variability. We demonstrate daily sampling was largely required to achieve annual N2O fluxes within 10% of the 'best' estimate for 28 annual datasets collected from three continents--Australia, Europe and Asia. Decreasing the regularity of measurements either under- or overestimated annual N2O fluxes, with a maximum overestimation of 935%. Measurement frequency was lowered using a sampling strategy based on environmental factors known to affect temporal variability, but still required sampling more than once a week. Consequently, uncertainty in current global terrestrial N2O budgets associated with the upscaling of field-based datasets can be decreased significantly using adequate sampling frequencies. PMID:26522228

  1. Threshold Frequency Estimation for the Russian River, CA

    NASA Astrophysics Data System (ADS)

    Pelle, A.; Tootle, G. A.; Johnson, L. E.; Cifelli, R.; Hsu, C.

    2014-12-01

    The National Weather Service (NWS) Office of Hydrologic Development (OHD) has developed a distributed hydrologic model which incorporates the concept of threshold frequency (TF). The TF represents flood flows for each grid translated to their equivalent flood frequency, or recurrence interval. It is intended to provide a more understandable representation of the criticality of the flows in terms that forecasters and the general public can better understand. The OHD has developed procedures for estimating the TF values which involve long term simulations of surface runoff using gridded precipitation data sets. This approach requires extensive data compilation and computer processing which can be difficult and time consuming. This study addresses a quick way to derive the gridded TF estimates using the US Geological Survey (USGS) flood frequency estimation approach based on regional regression analysis of basin characteristics (Gotvald et al 2012). The USGS approach used generalized least squares regression to develop a set of equations for estimating flows with 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities for ungaged basins in California. These equations for the North Coast region of California were applied to each grid of the RDHM model, each of which has a drainage area and mean annual precipitation value. Simulated flows for each grid output from the RDHM for a moderate flood event in December 2012 were then translated to the corresponding flow frequency to generate a time series of TF for the event. The approach applied is considered a feasible and efficient way to generate the TF values for any location where the USGS regression analyses have been developed.

  2. Estimation of skin conductance at low frequencies using measurements at higher frequencies for EDA applications.

    PubMed

    Nordbotten, Bernt J; Tronstad, Christian; Martinsen, Ørjan G; Grimnes, Sverre

    2014-06-01

    Using low-frequency (LF) alternating current skin conductance (SC) has recently been recommended for electrodermal activity (EDA) measurement, but the method may imply some limitations in sampling rate, which are insufficient for capturing the complete SC waveform. The aim of this study was to assess whether LF SC can be estimated based on skin admittance (SA) measurements at higher frequencies allowing higher sampling rates. SA measurements from 1 Hz to 70 kHz were gathered from 20 healthy human participants, and an interval from 500 Hz to 10 kHz was used to fit a Cole model to the measured SA by means of the nonlinear least squares method. The LF extrapolation of this fit was used to estimate the LF SC at 1, 10, 22 and 30 Hz. The method produced an overestimation of SC by approximately 20%, and the variation in LF SC was preserved by approximately 95%. The overestimation is most likely due to different frequency dependence behavior (dispersion) of SC at the lowest frequencies, which is not accounted for by a single dispersion model. In conclusion, the SA method using high frequency is unsuitable for estimation of the LF SC level, but can probably be used in EDA measurements, which are scored based on the variations in SC. PMID:24844405

  3. SLC40A1 Q248H allele frequencies and Q248H-associated risk of non-HFE iron overload in persons of sub-Saharan African descent.

    PubMed

    Barton, James C; Acton, Ronald T; Lee, Pauline L; West, Carol

    2007-01-01

    The ferroportin polymorphism SLC40A1 Q248H (exon 6, cDNA 744G-->T; Gln248His) occurs in persons of sub-Saharan African descent with and without iron overload, and is associated with elevated serum ferritin concentrations (SF). However, the risk of iron overload associated with Q248H has not been defined. We tabulated previously reported Q248H allele frequency estimates in African-Americans and Native Africans, and computed the risk of iron overload associated with Q248H in subjects who lacked HFE C282Y. The aggregate Q248H allele frequency in 1038 African-Americans in two cohorts from Alabama and one cohort each from Washington, DC and California was 0.0525 (95% CI: 0.0451, 0.0652); there was no significant difference in frequencies across these cohorts. The aggregate frequency in 259 Natives from southeast Africa in two cohorts was 0.0946 (95% CI: 0.0694, 0.1198); the difference between the frequencies of these cohorts was not significant. The aggregate Q248H frequencies in African-Americans and Native Africans differed significantly (0.0525 vs. 0.0946, respectively; p=0.0021). There were reports of 24 unrelated African-Americans and 15 unrelated Native Africans without HFE C282Y who had iron overload. In African-Americans, the odds ratio (OR) of Q248H-associated risk of iron overload using 610 C282Y-negative control subjects unselected for SF was 1.57 (95% CI: 0.52, 4.72; p=0.29). In Native Africans, the OR using 208 control subjects unselected for SF was 1.05 (95% CI: 0.28, 3.90; p=0.58). We conclude that the frequency of SLC40A1 Q248H is significantly lower in African-Americans than in Native Africans. Although OR estimates of iron overload in African-Americans and Native Africans with Q248H were greater than unity, the increased OR were not statistically significant. PMID:17490902

  4. 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.

  5. 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. PMID:25066278

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

    PubMed Central

    Sun, Hao; Yang, Zhaoqing; Lin, Keqin; Liu, Shuyuan; Huang, Kai; Wang, Xiuyun; Chu, Jiayou; Huang, Xiaoqin

    2015-01-01

    Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency. PMID:26230582

  7. 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.

  8. 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.

  9. Convergence of oscillator spectral estimators for counted-frequency measurements.

    NASA Technical Reports Server (NTRS)

    Tausworthe, R. C.

    1972-01-01

    A common intermediary connecting frequency-noise calibration or testing of an oscillator to useful applications is the spectral density of the frequency-deviating process. In attempting to turn test data into predicts of performance characteristics, one is naturally led to estimation of statistical values by sample-mean and sample-variance techniques. However, sample means and sample variances themselves are statistical quantities that do not necessarily converge (in the mean-square sense) to actual ensemble-average means and variances, except perhaps for excessively large sample sizes. This is especially true for the flicker noise component of oscillators. This article shows, for the various types of noises found in oscillators, how sample averages converge (or do not converge) to their statistical counterparts. The convergence rate is shown to be the same for all oscillators of a given spectral type.

  10. HLA-A, B and DRB1 allele and haplotype frequencies in volunteer bone marrow donors from the north of Parana State

    PubMed Central

    Bardi, Marlene Silva; Jarduli, Luciana Ribeiro; Jorge, Adylson Justino; Camargo, Rossana Batista Oliveira Godoy; Carneiro, Fernando Pagotto; Gelinski, Jair Roberto; Silva, Roseclei Assunção Feliciano; Lavado, Edson Lopes

    2012-01-01

    Background Knowledge of allele and haplotype frequencies of the human leukocyte antigen (HLA) system is important in the search for unrelated bone marrow donors. The Brazilian population is very heterogeneous and the HLA system is highly informative of populations because of the high level of polymorphisms. Aim The aim of this study was to characterize the immunogenetic profile of ethnic groups (Caucasians, Afro-Brazilians and Asians) in the north of Parana State. Methods A study was carried out of 3978 voluntary bone marrow donors registered in the Brazilian National Bone Marrow Donor Registry and typed for the HLA-A, B and DRB1 (low resolution) loci. The alleles were characterized by the polymerase chain reaction sequence-specific oligonucleotides method using the LabType SSO kit (One Lambda, CA, USA). The ARLEQUIN v.3.11 computer program was used to calculate allele and haplotype frequencies Results The most common alleles found in Caucasians were HLA-A*02, 24, 01; HLA-B*35, 44, 51; DRB1*11, 13, 07; for Afro-Brazilians they were HLA-A*02, 03, 30; HLA-B*35, 15, 44; DRB1*13, 11, 03; and for Asians they were: HLA-A*24, 02, 26; HLA-B*40, 51, 52; DRB1*04, 15, 09. The most common haplotype combinations were: HLA-A*01, B*08, DRB1*03 and HLA-A*29, B*44, DRB1*07 for Caucasians; HLA-A*29, B*44, DRB1*07 and HLA-A*01, B*08 and DRB1*03 for Afro-Brazilians; and HLA-A*24, B*52, DRB1*15 and HLA-A*24, B*40 and DRB1*09 for Asians. Conclusion There is a need to target and expand bone marrow donor campaigns in the north of Parana State. The data of this study may be used as a reference by the Instituto Nacional de Cancer/Brazilian National Bone Marrow Donor Registry to evaluate the immunogenetic profile of populations in specific regions and in the selection of bone marrow donors PMID:23049380

  11. Estimation of modal parameters using bilinear joint time frequency distributions

    NASA Astrophysics Data System (ADS)

    Roshan-Ghias, A.; Shamsollahi, M. B.; Mobed, M.; Behzad, M.

    2007-07-01

    In this paper, a new method is proposed for modal parameter estimation using time-frequency representations. Smoothed Pseudo Wigner-Ville distribution which is a member of the Cohen's class distributions is used to decouple vibration modes completely in order to study each mode separately. This distribution reduces cross-terms which are troublesome in Wigner-Ville distribution and retains the resolution as well. The method was applied to highly damped systems, and results were superior to those obtained via other conventional methods.

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

    PubMed

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

    2011-11-01

    Neuronal ceroid lipofuscinosis (NCL) constitutes a group of recessively inherited lysosomal storage diseases that primarily affect neuronal cells. Such diseases share certain clinical and pathologic features in human beings and animals. Neuronal ceroid lipofuscinosis in Border Collie dogs was first detected in Australia in the 1980s, and the pathogenic mutation was shown to be a nonsense mutation (c.619C>T) in exon 4 in canine CLN5 gene. In the present study, novel rapid genotyping assays including polymerase chain reaction (PCR)-restriction fragment length polymorphism, PCR primer-induced restriction analysis, mutagenically separated PCR, and real-time PCR with TaqMan minor groove binder probes, were developed. The utility of microchip electrophoresis was also evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies in Japan using these assays to determine the current allele frequency in Japan, providing information to control and prevent this disease in the next stage. All assays developed in the current study are available to discriminate these genotypes, and microchip electrophoresis showed a timesaving advantage over agarose gel electrophoresis. Of all assays, real-time PCR was the most suitable for large-scale examination because of its high throughput. The genotyping survey demonstrated that the carrier frequency was 8.1%. This finding suggested that the mutant allele frequency of NCL in Border Collies is high enough in Japan that measures to control and prevent the disease would be warranted. The genotyping assays developed in the present study could contribute to the prevention of NCL in Border Collies. PMID:22362793

  13. 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. PMID:10646230

  14. 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

  15. 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

  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 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

  17. 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.

  18. 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…

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

    PubMed Central

    Akala, Hoseah M; Achieng, Angela O; Eyase, Fredrick L; Juma, Dennis W; Ingasia, Luiser; Cheruiyot, Agnes C; Okello, Charles; Omariba, Duke; Owiti, Eunice A; Muriuki, Catherine; Yeda, Redemptah; Andagalu, Ben; Johnson, Jacob D; Kamau, Edwin

    2014-01-01

    Background The renewed malaria eradication efforts require an understanding of the seasonal patterns of frequency of polymorphic variants in order to focus limited funds productively. Although cross-sectional studies in holoendemic areas spanning a single year could be useful in describing parasite genotype status at a given point, such information is inadequate in describing temporal trends in genotype polymorphisms. For Plasmodium falciparum isolates from Kisumu District Hospital, Plasmodium falciparum chloroquine-resistance transporter gene (Pfcrt-K76T) and P. falciparum multidrug resistance gene 1 (PfMDR1-N86Y), were analyzed for polymorphisms and parasitemia changes in the 53 months from March 2008 to August 2012. Observations were compared with prevailing climatic factors, including humidity, rainfall, and temperature. Methods Parasitemia (the percentage of infected red blood cells per total red blood cells) was established by microscopy for P. falciparum malaria-positive samples. P. falciparum DNA was extracted from whole blood using a Qiagen DNA Blood Mini Kit. Single nucleotide polymorphism identification at positions Pfcrt-K76T and PfMDR1-N86Y was performed using real-time polymerase chain reaction and/or sequencing. Data on climatic variables were obtained from http://www.tutiempo.net/en/. Results A total of 895 field isolates from 2008 (n=169), 2009 (n=161), 2010 (n=216), 2011 (n=223), and 2012 (n=126) showed large variations in monthly frequency of PfMDR1-N86Y and Pfcrt-K76T as the mutant genotypes decreased from 68.4%±15% and 38.1%±13% to 29.8%±18% and 13.3%±9%, respectively. The mean percentage of parasitemia was 2.61%±1.01% (coefficient of variation 115.86%; n=895). There was no correlation between genotype or parasitemia and climatic factors. Conclusion This study shows variability in the frequency of Pfcrt-K76T and PfMDR1-N86Y polymorphisms during the study period, bringing into focus the role of cross-sectional studies in describing temporal

  20. Global patterns of variation in allele and haplotype frequencies and linkage disequilibrium across the CYP2E1 gene

    PubMed Central

    Lee, Mi-Young; Mukherjee, Namita; Pakstis, Andrew J.; Khaliq, Shagufta; Mohyuddin, Aisha; Mehdi, S. Qasim; Speed, William C.; Kidd, Judith R.; Kidd, Kenneth K.

    2009-01-01

    Cytochrome P450 2E1, gene symbol CYP2E1, is one of a family of enzymes with a central role in activating and detoxifying xenobiotics and endogenous compounds. Genetic variation at this gene has been reported in different human populations, and some association studies have reported increased risk for cancers and other diseases. To the best of our knowledge, multi-SNP haplotypes and linkage disequilibrium (LD) have not been systematically studied for CYP2E1 in multiple populations. Haplotypes can greatly increase the power both to identify patterns of genetic variation relevant for gene expression as well as to detect disease-related susceptibility mutations. We present frequency and LD data and analyses for 11 polymorphisms and their haplotypes that we have studied on over 2,600 individuals from 50 human population samples representing the major geographical regions of the world. The diverse patterns of haplotype variation found in the different populations we have studied show that ethnicity may be an important variable helping to explain inconsistencies that have been reported by association studies. More studies clearly are needed of the variants we have studied, especially those in the 5′ region, such as the VNTR, as well as studies of additional polymorphisms known for this gene to establish evidence relating any systematic differences in gene expression that exist to the haplotypes at this gene. PMID:18663376

  1. 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

  2. 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

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

    PubMed

    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

  4. 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

  5. Flood frequency estimation by hydrological continuous simulation and classical methods

    NASA Astrophysics Data System (ADS)

    Brocca, L.; Camici, S.; Melone, F.; Moramarco, T.; Tarpanelli, A.

    2009-04-01

    In recent years, the effects of flood damages have motivated the development of new complex methodologies for the simulation of the hydrologic/hydraulic behaviour of river systems, fundamental to direct the territorial planning as well as for the floodplain management and risk analysis. The valuation of the flood-prone areas can be carried out through various procedures that are usually based on the estimation of the peak discharge for an assigned probability of exceedence. In the case of ungauged or scarcely gauged catchments this is not straightforward, as the limited availability of historical peak flow data induces a relevant uncertainty in the flood frequency analysis. A possible solution to overcome this problem is the application of hydrological simulation studies in order to generate long synthetic discharge time series. For this purpose, recently, new methodologies based on the stochastic generation of rainfall and temperature data have been proposed. The inferred information can be used as input for a continuous hydrological model to generate a synthetic time series of peak river flow and, hence, the flood frequency distribution at a given site. In this study stochastic rainfall data have been generated via the Neyman-Scott Rectangular Pulses (NSRP) model characterized by a flexible structure in which the model parameters broadly relate to underlying physical features observed in rainfall fields and it is capable of preserving statistical properties of a rainfall time series over a range of time scales. The peak river flow time series have been generated through a continuous hydrological model aimed at flood prediction and developed for the purpose (hereinafter named MISDc) (Brocca, L., Melone, F., Moramarco, T., Singh, V.P., 2008. A continuous rainfall-runoff model as tool for the critical hydrological scenario assessment in natural channels. In: M. Taniguchi, W.C. Burnett, Y. Fukushima, M. Haigh, Y. Umezawa (Eds), From headwater to the ocean

  6. 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…

  7. A frequency-domain estimator for use in adaptive control systems

    NASA Technical Reports Server (NTRS)

    Lamaire, Richard O.; Valavani, Lena; Athans, Michael; Stein, Gunter

    1991-01-01

    This paper presents a frequency-domain estimator that can identify both a parametrized nominal model of a plant as well as a frequency-domain bounding function on the modeling error associated with this nominal model. This estimator, which we call a robust estimator, can be used in conjunction with a robust control-law redesign algorithm to form a robust adaptive controller.

  8. A frequency-domain estimator for use in adaptive control systems

    NASA Technical Reports Server (NTRS)

    Lamaire, Richard O.; Valavani, Lena; Athans, Michael; Stein, Gunter

    1987-01-01

    The paper presents a frequency-domain estimator which can identify both a nominal model of a plant as well as a frequency-domain bounding function on the modeling error associated with this nominal model. This estimator, which is called a robust estimator, can be used in conjunction with a robust control-law redesign algorithm to form a robust adaptive controller.

  9. Allele frequency-based and polymorphism-versus-divergence indices of balancing selection in a new filtered set of polymorphic genes in Plasmodium falciparum.

    PubMed

    Ochola, Lynette Isabella; Tetteh, Kevin K A; Stewart, Lindsay B; Riitho, Victor; Marsh, Kevin; Conway, David J

    2010-10-01

    Signatures of balancing selection operating on specific gene loci in endemic pathogens can identify candidate targets of naturally acquired immunity. In malaria parasites, several leading vaccine candidates convincingly show such signatures when subjected to several tests of neutrality, but the discovery of new targets affected by selection to a similar extent has been slow. A small minority of all genes are under such selection, as indicated by a recent study of 26 Plasmodium falciparum merozoite-stage genes that were not previously prioritized as vaccine candidates, of which only one (locus PF10_0348) showed a strong signature. Therefore, to focus discovery efforts on genes that are polymorphic, we scanned all available shotgun genome sequence data from laboratory lines of P. falciparum and chose six loci with more than five single nucleotide polymorphisms per kilobase (including PF10_0348) for in-depth frequency-based analyses in a Kenyan population (allele sample sizes >50 for each locus) and comparison of Hudson-Kreitman-Aguade (HKA) ratios of population diversity (π) to interspecific divergence (K) from the chimpanzee parasite Plasmodium reichenowi. Three of these (the msp3/6-like genes PF10_0348 and PF10_0355 and the surf(4.1) gene PFD1160w) showed exceptionally high positive values of Tajima's D and Fu and Li's F indices and have the highest HKA ratios, indicating that they are under balancing selection and should be prioritized for studies of their protein products as candidate targets of immunity. Combined with earlier results, there is now strong evidence that high HKA ratio (as well as the frequency-independent ratio of Watterson's /K) is predictive of high values of Tajima's D. Thus, the former offers value for use in genome-wide screening when numbers of genome sequences within a species are low or in combination with Tajima's D as a 2D test on large population genomic samples. PMID:20457586

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

    PubMed

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

    2009-04-01

    Helicoverpa punctigera and Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) are important pests of field and horticultural crops in Australia. The former is endemic to the continent, whereas the latter is also distributed in Africa and Asia. Although H. armigera rapidly developed resistance to virtually every group of insecticide used against it, there is only one report of resistance to an insecticide in H. punctigera. In 1996 the Australian cotton industry adopted Ingard, which expresses the Bacillus thuringiensis (Bt) toxin gene cry1Ac. In 2004/2005, Bollgard II (which expresses Cry1Ac and Cry2Ab) replaced Ingard and has subsequently been grown on 80% of the area planted to cotton, Gossypium hirsutum L. From 2002/2003 to 2006/2007, F2 screens were used to detect resistance to Cry1Ac or Cry2Ab. We detected no alleles conferring resistance to Cry1Ac; the frequency was < 0.0005 (n = 2,180 alleles), with a 95% credibility interval between 0 and 0.0014. However, during the same period, we detected alleles that confer resistance to Cry2Ab at a frequency of 0.0018 (n = 2,192 alleles), with a 95% credibility interval between 0.0005 and 0.0040. For both toxins, the experiment-wise detection probability was 94%, i.e., if there actually was a resistance allele in any tested lines, we would have detected it 94% of the time. The first isolation of Cry2Ab resistance in H. punctigera was before the widespread deployment of Bollgard II. This finding supports our published notion for H. armigera that alleles conferring resistance to Cry2Ab may be present at detectable frequencies in populations before selection by transgenic crops. PMID:19449655

  11. The Use of Film Subtitles to Estimate Word Frequencies

    ERIC Educational Resources Information Center

    New, Boris; Brysbaert, Marc; Veronis, Jean; Pallier, Christophe

    2007-01-01

    We examine the use of film subtitles as an approximation of word frequencies in human interactions. Because subtitle files are widely available on the Internet, they may present a fast and easy way to obtain word frequency measures in language registers other than text writing. We compiled a corpus of 52 million French words, coming from a variety…

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

    PubMed

    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

  13. 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

  14. 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

  15. Performance Analysis of the Blind Minimum Output Variance Estimator for Carrier Frequency Offset in OFDM Systems

    NASA Astrophysics Data System (ADS)

    Yang, Feng; Li, Kwok H.; Teh, Kah C.

    2006-12-01

    Carrier frequency offset (CFO) is a serious drawback in orthogonal frequency division multiplexing (OFDM) systems. It must be estimated and compensated before demodulation to guarantee the system performance. In this paper, we examine the performance of a blind minimum output variance (MOV) estimator. Based on the derived probability density function (PDF) of the output magnitude, its mean and variance are obtained and it is observed that the variance reaches the minimum when there is no frequency offset. This observation motivates the development of the proposed MOV estimator. The theoretical mean-square error (MSE) of the MOV estimator over an AWGN channel is obtained. The analytical results are in good agreement with the simulation results. The performance evaluation of the MOV estimator is extended to a frequency-selective fading channel and the maximal-ratio combining (MRC) technique is applied to enhance the MOV estimator's performance. Simulation results show that the MRC technique significantly improves the accuracy of the MOV estimator.

  16. 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.

  17. Semantic priming increases word frequency judgments: Evidence for the role of memory strength in frequency estimation.

    PubMed

    Woltz, Dan J; Gardner, Michael K

    2015-09-01

    Previous research has demonstrated a systematic, nonlinear relationship between word frequency judgments and values from word frequency norms. This relationship could reflect a perceptual process similar to that found in the psychophysics literature for a variety of sensory phenomena. Alternatively, it could reflect memory strength differences that are expected for words of varying levels of prior exposure. Two experiments tested the memory strength explanation by semantically priming words prior to frequency judgments. Exposure to related word meanings produced a small but measurable increase in target word frequency ratings. Repetition but not semantic priming had a greater impact on low compared to high frequency words. These findings are consistent with a memory strength view of frequency judgments that assumes a distributed network with lexical and semantic levels of representation. PMID:26253593

  18. Tetra-allelic SNPs: Informative forensic markers compiled from public whole-genome sequence data.

    PubMed

    Phillips, C; Amigo, J; Carracedo, Á; Lareu, M V

    2015-11-01

    Multiple-allele single nucleotide polymorphisms (SNPs) are potentially useful for forensic DNA analysis as they can provide more discrimination power than normal binary SNPs. In addition, the presence in a profile of more than two alleles per marker provides a clearer indication of mixed DNA than assessments of imbalanced signals in the peak pairs of binary SNPs. Using the 1000 Genomes Phase III human variant data release of 2014 as the starting point, this study collated 961 tetra-allelic SNPs that pass minimum sequence quality thresholds and where four separate nucleotide substitution alleles were detected. Although most of these loci had three of the four alleles in combined frequencies of 2% or less, 160 had high heterozygosities with 50 exceeding those of 'ideal' 0.5:0.5 binary SNPs. From this set of most polymorphic tetra-allelic SNPs, we identified markers most informative for forensic purposes and explored these loci in detail. Subsets of the most polymorphic tetra-allelic SNPs will make useful additions to current panels of forensic identification SNPs and ancestry-informative SNPs. The 24 most discriminatory tetra-allelic SNPs were estimated to detect more than two alleles in at least one marker per profile in 99.9% of mixtures of African contributors. In European contributor mixtures 99.4% of profiles would show multiple allele patterns, but this drops to 92.6% of East Asian contributor mixtures due to reduced levels of polymorphism for the 24 SNPs in this population group. PMID:26209763

  19. Estimation of Soil Moisture With Dual-Frequency-PALS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The purpose of this study is to evaluate whether the NASA/JPL dual frequency airborne system, Passive Active L-band and S-band (PALS), can provide a reliable soil moisture measurements so that they can be integrated to provide soil moisture data at the scales of the spaceborne coarse resolutions. Th...

  20. 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.

  1. Estimation of Electron Temperature and Frequency Components in a Dual Frequency Capacitively-Coupled Plasma Processing Reactor

    NASA Astrophysics Data System (ADS)

    Ito, Toru; Mo, Yun; Masahiro, Horigome

    2008-10-01

    The measurement of electron temperature in RF plasma sources with Langmuir probes is difficult because of the influence of rf noise. We attempted to estimate the electron temperature in a capacitively-coupled plasma processing reactor with a Surface Wave Probe [1] which employs microwaves. We also estimated the frequency spectrum with the sensitive PAP [1, 2]. We measured the harmonics which appeared in the bulk plasma for various experimental conditions in the dual-frequency [60 MHz and 2MHz] capacitively-coupled plasma processing reactor. We estimated RF power spectra for several experimental conditions like RF power [500-2000W], gas pressure [3-20Pa], and gas species [Ar, CF4]. The measurement results suggest the existence of energy transport among several frequency spectrum. [1ex] [1] K. Nakamura, M. Ohata, and H. Sugai: J. Vac. Sci. Technol. A 21, 325 (2003). [0pt] [2] T. Shirakawa and H. Sugai : Jpn. J. Appl. Phys. 32, 5129 (1993).

  2. Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

    PubMed Central

    Gadala-Maria, Daniel; Yaari, Gur; Uduman, Mohamed; Kleinstein, Steven H.

    2015-01-01

    Individual variation in germline and expressed B-cell immunoglobulin (Ig) repertoires has been associated with aging, disease susceptibility, and differential response to infection and vaccination. Repertoire properties can now be studied at large-scale through next-generation sequencing of rearranged Ig genes. Accurate analysis of these repertoire-sequencing (Rep-Seq) data requires identifying the germline variable (V), diversity (D), and joining (J) gene segments used by each Ig sequence. Current V(D)J assignment methods work by aligning sequences to a database of known germline V(D)J segment alleles. However, existing databases are likely to be incomplete and novel polymorphisms are hard to differentiate from the frequent occurrence of somatic hypermutations in Ig sequences. Here we develop a Tool for Ig Genotype Elucidation via Rep-Seq (TIgGER). TIgGER analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles, and also constructs a personalized germline database containing the specific set of alleles carried by a subject. This information is then used to improve the initial V segment assignments from existing tools, like IMGT/HighV-QUEST. The application of TIgGER to Rep-Seq data from seven subjects identified 11 novel V segment alleles, including at least one in every subject examined. These novel alleles constituted 13% of the total number of unique alleles in these subjects, and impacted 3% of V(D)J segment assignments. These results reinforce the highly polymorphic nature of human Ig V genes, and suggest that many novel alleles remain to be discovered. The integration of TIgGER into Rep-Seq processing pipelines will increase the accuracy of V segment assignments, thus improving B-cell repertoire analyses. PMID:25675496

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. Detection, estimation, and discrimination of frequency diverse targets in ultra-wideband synthetic aperture radar data

    NASA Astrophysics Data System (ADS)

    Miller, Timothy R.

    New ultra-wideband radar imaging systems developed for ground-penetrating and foliage-penetrating applications are a departure from traditional, higher frequency radar systems. The assumption that targets are ideal point scatterers with impulsive responses is no longer acceptable. Target responses are frequency dependent and thus spread in time. The research outlined in this dissertation addresses target detection, estimation, and discrimination issues involved with processing frequency-dependent scattering returns. Frequency dependence is exploited in prescreening algorithms, new imaging algorithms and processing techniques to estimate time-domain target responses, and discrimination techniques based upon multiuser communications approaches. We present results and discuss the contributions of these studies.

  8. Multi-constrained fault estimation observer design with finite frequency specifications for continuous-time systems

    NASA Astrophysics Data System (ADS)

    Zhang, Ke; Jiang, Bin; Shi, Peng; Xu, Jinfa

    2014-08-01

    The design of a multi-constrained full-order fault estimation observer (FFEO) with finite frequency specifications is studied for continuous-time systems. By constructing an augmented system, a multi-constrained FFEO in finite frequency domain is proposed to achieve fault estimation. Meanwhile, the presented FFEO can avoid the overdesign problem generated by the entire frequency domain by the generalised Kalman-Yakubovich-Popov lemma. Furthermore, by introducing slack variables, improved results on FFEO design in different frequency domains are obtained such that different Lyapunov matrices can be separately designed for each constraint. Simulation results are presented to demonstrate the effectiveness and potentials of the proposed techniques.

  9. 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

  10. 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...

  11. 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

  12. 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

  13. 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.

  14. 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

  15. Structure-aware Bayesian compressive sensing for frequency-hopping spectrum estimation

    NASA Astrophysics Data System (ADS)

    Liu, Shengheng; Zhang, Yimin D.; Shan, Tao; Qin, Si; Amin, Moeness G.

    2016-05-01

    Frequency-hopping (FH) is one of the commonly used spread spectrum techniques that finds wide applications in communications and radar systems due to its capability of low probability of intercept, reduced interference, and desirable ambiguity property. In this paper, we consider the blind estimation of the instantaneous FH spectrum without the knowledge of hopping patterns. The FH signals are analyzed in the joint time-frequency domain, where FH signals manifest themselves as sparse entries, thus inviting compressive sensing and sparse reconstruction techniques for FH spectrum estimation. In particular, the signals' piecewise-constant frequency characteristics are exploited in the reconstruction of sparse quadratic time-frequency representations. The Bayesian compressive sensing methods are applied to provide high-resolution frequency estimation. The FH spectrum characteristics are used in the design of signal-dependent kernel within the framework of structure-aware sparse reconstruction.

  16. Subtitle-based word frequencies as the best estimate of reading behavior: the case of greek.

    PubMed

    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

  17. 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 ...

  18. Techniques for estimating flood-frequency discharges for streams in Iowa

    USGS Publications Warehouse

    Eash, David A.

    2001-01-01

    Techniques for estimating flood-frequency discharges for streams in Iowa are presented for determining (1) regional regression estimates for ungaged sites on ungaged streams; (2) weighted estimates for gaged sites; and (3) weighted estimates for ungaged sites on gaged streams. The technique for determining regional regression estimates for ungaged sites on ungaged streams requires determining which of four possible examples applies to the location of the stream site and its basin. Illustrations for determining which example applies to an ungaged stream site and for applying both the one-variable and multi-variable regression equations are provided for the estimation techniques.

  19. Uncommon breeding birds in North Dakota: Population estimates and frequencies of occurrence

    USGS Publications Warehouse

    Igl, L.D.; Johnson, D.H.; Kantrud, H.A.

    1999-01-01

    Breeding bird populations were surveyed on 128 randomly selected quarter-sections throughout North Dakota in 1967, 1992, and 1993. Population estimates and frequencies of occurrence are reported for 92 uncommon breeding bird species with statewide frequencies of less than 10%.

  20. Single channel speech separation in modulation frequency domain based on a novel pitch range estimation method

    NASA Astrophysics Data System (ADS)

    Mahmoodzadeh, Azar; Abutalebi, Hamid Reza; Soltanian-Zadeh, Hamid; Sheikhzadeh, Hamid

    2012-12-01

    Computational Auditory Scene Analysis (CASA) has been the focus in recent literature for speech separation from monaural mixtures. The performance of current CASA systems on voiced speech separation strictly depends on the robustness of the algorithm used for pitch frequency estimation. We propose a new system that estimates pitch (frequency) range of a target utterance and separates voiced portions of target speech. The algorithm, first, estimates the pitch range of target speech in each frame of data in the modulation frequency domain, and then, uses the estimated pitch range for segregating the target speech. The method of pitch range estimation is based on an onset and offset algorithm. Speech separation is performed by filtering the mixture signal with a mask extracted from the modulation spectrogram. A systematic evaluation shows that the proposed system extracts the majority of target speech signal with minimal interference and outperforms previous systems in both pitch extraction and voiced speech separation.

  1. High frequency of allelic imbalance at chromosome region 16q22-23 in human breast cancer: correlation with high PgR and low S phase.

    PubMed

    Skirnisdottir, S; Eiriksdottir, G; Baldursson, T; Barkardottir, R B; Egilsson, V; Ingvarrson, S

    1995-04-21

    The loss of genetic material from a specific chromosome region in tumors suggests that presence of tumor-suppressor genes. Loss of heterozygosity (LOH) or allelic imbalance (AI) on the long arm of chromosome 16 is a known event in sporadic breast cancer. To locate the commonly deleted regions, and therefore (a) candidate tumor-suppressor gene(s), a deletion map of chromosome 16 was made, using 10 microsatellite markers on 150 sporadic breast tumors. The 3 smallest regions of overlap (SRO) were detected on the long arm of chromosome 16. Allelic imbalance was observed with at least one marker in 67% of the tumors. One marker, D16S421, at the 16q22-23 region, showed the highest allelic imbalance, 58%. Tumors with and without AI on 16q were tested for correlation with clinico-pathological features of the tumors such as estrogen- and progesterone-receptor content (ER and PgR), age at diagnosis, tumor size, node status, histological type, S-phase fraction, AI on chromosome 3p, and ploidy. A correlation was found between AI on 16q and high PgR content, also low S-phase fraction (99% confidence limits). A comparison of tumors with and without AI at the D16S421 marker locus revealed a slight correlation with high PgR content. The survival data showed no difference between patients with AI on 16q and those with a normal allele pattern on the long arm of chromosome 16. PMID:7615353

  2. Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes

    PubMed Central

    2014-01-01

    Background Pathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright’s FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright’s FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex. Methods We have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright’s FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles. Results We show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents. Conclusion Our

  3. 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...

  4. 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

  5. Range and Velocity Estimation of Moving Targets Using Multiple Stepped-frequency Pulse Trains

    PubMed Central

    Li, Gang; Meng, Huadong; Xia, Xiang-Gen; Peng, Ying-Ning

    2008-01-01

    Range and velocity estimation of moving targets using conventional stepped-frequency pulse radar may suffer from the range-Doppler coupling and the phase wrapping. To overcome these problems, this paper presents a new radar waveform named multiple stepped-frequency pulse trains and proposes a new algorithm. It is shown that by using multiple stepped-frequency pulse trains and the robust phase unwrapping theorem (RPUT), both of the range-Doppler coupling and the phase wrapping can be robustly resolved, and accordingly, the range and the velocity of a moving target can be accurately estimated.

  6. Rapid estimation of frequency response functions by close-range photogrammetry

    NASA Technical Reports Server (NTRS)

    Tripp, J. S.

    1985-01-01

    The accuracy of a rapid method which estimates the frequency response function from stereoscopic dynamic data is computed. It is shown that reversal of the order of the operations of coordinate transformation and Fourier transformation, which provides a significant increase in computational speed, introduces error. A portion of the error, proportional to the perturbation components normal to the camera focal planes, cannot be eliminated. The remaining error may be eliminated by proper scaling of frequency data prior to coordinate transformation. Methods are developed for least squares estimation of the full 3x3 frequency response matrix for a three dimensional structure.

  7. 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.

  8. 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…

  9. 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)

  10. Maximum likelihood method for estimating airplane stability and control parameters from flight data in frequency domain

    NASA Technical Reports Server (NTRS)

    Klein, V.

    1980-01-01

    A frequency domain maximum likelihood method is developed for the estimation of airplane stability and control parameters from measured data. The model of an airplane is represented by a discrete-type steady state Kalman filter with time variables replaced by their Fourier series expansions. The likelihood function of innovations is formulated, and by its maximization with respect to unknown parameters the estimation algorithm is obtained. This algorithm is then simplified to the output error estimation method with the data in the form of transformed time histories, frequency response curves, or spectral and cross-spectral densities. The development is followed by a discussion on the equivalence of the cost function in the time and frequency domains, and on advantages and disadvantages of the frequency domain approach. The algorithm developed is applied in four examples to the estimation of longitudinal parameters of a general aviation airplane using computer generated and measured data in turbulent and still air. The cost functions in the time and frequency domains are shown to be equivalent; therefore, both approaches are complementary and not contradictory. Despite some computational advantages of parameter estimation in the frequency domain, this approach is limited to linear equations of motion with constant coefficients.

  11. 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

  12. On the use of radar-based quantitative precipitation estimates for precipitation frequency analysis

    NASA Astrophysics Data System (ADS)

    Eldardiry, Hisham; Habib, Emad; Zhang, Yu

    2015-12-01

    The high spatio-temporal resolutions of radar-based multi-sensor Quantitative Precipitation Estimates (QPEs) makes them a potential complement to the gauge records for engineering design purposes, such as precipitation frequency analysis. The current study investigates three fundamental issues that arise when radar-based QPE products are used in frequency analysis: (a) Effect of sample size due to the typically short records of radar products; (b) Effect of uncertainties present in radar-rainfall estimation algorithms; and (c) Effect of the frequency estimation approach adopted. The study uses a 13-year dataset of hourly, 4 × 4 km2 radar-based over a domain that covers Louisiana, USA. Data-based investigations, as well as synthetic simulations, are performed to quantify the uncertainties associated with the radar-based derived frequencies, and to gain insight into the relative contributions of short record lengths and those from conditional biases in the radar product. Three regional estimation procedures were tested and the results indicate the sensitivity of the radar frequency estimates to the selection of the estimation approach and the impact on the uncertainties of the derived extreme quantiles. The simulation experiments revealed that the relatively short radar records explained the majority of the uncertainty associated with the radar-based quantiles; however, they did not account for any tangible contribution to the systematic underestimation observed between radar- and gauge-based frequency estimates. This underestimation was mostly attributable to the conditional bias inherent in the radar product. Addressing such key outstanding problems in radar-rainfall products is necessary before they can be fully and reliably used for frequency analysis applications.

  13. Similarities between Line Fishing and Baited Stereo-Video Estimations of Length-Frequency: Novel Application of Kernel Density Estimates

    PubMed Central

    Langlois, Timothy J.; Fitzpatrick, Benjamin R.; Fairclough, David V.; Wakefield, Corey B.; Hesp, S. Alex; McLean, Dianne L.; Harvey, Euan S.; Meeuwig, Jessica J.

    2012-01-01

    Age structure data is essential for single species stock assessments but length-frequency data can provide complementary information. In south-western Australia, the majority of these data for exploited species are derived from line caught fish. However, baited remote underwater stereo-video systems (stereo-BRUVS) surveys have also been found to provide accurate length measurements. Given that line fishing tends to be biased towards larger fish, we predicted that, stereo-BRUVS would yield length-frequency data with a smaller mean length and skewed towards smaller fish than that collected by fisheries-independent line fishing. To assess the biases and selectivity of stereo-BRUVS and line fishing we compared the length-frequencies obtained for three commonly fished species, using a novel application of the Kernel Density Estimate (KDE) method and the established Kolmogorov–Smirnov (KS) test. The shape of the length-frequency distribution obtained for the labrid Choerodon rubescens by stereo-BRUVS and line fishing did not differ significantly, but, as predicted, the mean length estimated from stereo-BRUVS was 17% smaller. Contrary to our predictions, the mean length and shape of the length-frequency distribution for the epinephelid Epinephelides armatus did not differ significantly between line fishing and stereo-BRUVS. For the sparid Pagrus auratus, the length frequency distribution derived from the stereo-BRUVS method was bi-modal, while that from line fishing was uni-modal. However, the location of the first modal length class for P. auratus observed by each sampling method was similar. No differences were found between the results of the KS and KDE tests, however, KDE provided a data-driven method for approximating length-frequency data to a probability function and a useful way of describing and testing any differences between length-frequency samples. This study found the overall size selectivity of line fishing and stereo-BRUVS were unexpectedly similar. PMID

  14. Similarities between line fishing and baited stereo-video estimations of length-frequency: novel application of Kernel Density Estimates.

    PubMed

    Langlois, Timothy J; Fitzpatrick, Benjamin R; Fairclough, David V; Wakefield, Corey B; Hesp, S Alex; McLean, Dianne L; Harvey, Euan S; Meeuwig, Jessica J

    2012-01-01

    Age structure data is essential for single species stock assessments but length-frequency data can provide complementary information. In south-western Australia, the majority of these data for exploited species are derived from line caught fish. However, baited remote underwater stereo-video systems (stereo-BRUVS) surveys have also been found to provide accurate length measurements. Given that line fishing tends to be biased towards larger fish, we predicted that, stereo-BRUVS would yield length-frequency data with a smaller mean length and skewed towards smaller fish than that collected by fisheries-independent line fishing. To assess the biases and selectivity of stereo-BRUVS and line fishing we compared the length-frequencies obtained for three commonly fished species, using a novel application of the Kernel Density Estimate (KDE) method and the established Kolmogorov-Smirnov (KS) test. The shape of the length-frequency distribution obtained for the labrid Choerodon rubescens by stereo-BRUVS and line fishing did not differ significantly, but, as predicted, the mean length estimated from stereo-BRUVS was 17% smaller. Contrary to our predictions, the mean length and shape of the length-frequency distribution for the epinephelid Epinephelides armatus did not differ significantly between line fishing and stereo-BRUVS. For the sparid Pagrus auratus, the length frequency distribution derived from the stereo-BRUVS method was bi-modal, while that from line fishing was uni-modal. However, the location of the first modal length class for P. auratus observed by each sampling method was similar. No differences were found between the results of the KS and KDE tests, however, KDE provided a data-driven method for approximating length-frequency data to a probability function and a useful way of describing and testing any differences between length-frequency samples. This study found the overall size selectivity of line fishing and stereo-BRUVS were unexpectedly similar. PMID

  15. 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

  16. Subtlex-pl: subtitle-based word frequency estimates for Polish.

    PubMed

    Mandera, Paweł; Keuleers, Emmanuel; Wodniecka, Zofia; Brysbaert, Marc

    2015-06-01

    We present SUBTLEX-PL, Polish word frequencies based on movie subtitles. In two lexical decision experiments, we compare the new measures with frequency estimates derived from another Polish text corpus that includes predominantly written materials. We show that the frequencies derived from the two corpora perform best in predicting human performance in a lexical decision task if used in a complementary way. Our results suggest that the two corpora may have unequal potential for explaining human performance for words in different frequency ranges and that corpora based on written materials severely overestimate frequencies for formal words. We discuss some of the implications of these findings for future studies comparing different frequency estimates. In addition to frequencies for word forms, SUBTLEX-PL includes measures of contextual diversity, part-of-speech-specific word frequencies, frequencies of associated lemmas, and word bigrams, providing researchers with necessary tools for conducting psycholinguistic research in Polish. The database is freely available for research purposes and may be downloaded from the authors' university Web site at http://crr.ugent.be/subtlex-pl . PMID:24942246

  17. Robust k-mer frequency estimation using gapped k-mers

    PubMed Central

    Ghandi, Mahmoud; Mohammad-Noori, Morteza

    2013-01-01

    Oligomers of fixed length, k, commonly known as k-mers, are often used as fundamental elements in the description of DNA sequence features of diverse biological function, or as intermediate elements in the constuction of more complex descriptors of sequence features such as position weight matrices. k-mers are very useful as general sequence features because they constitute a complete and unbiased feature set, and do not require parameterization based on incomplete knowledge of biological mechanisms. However, a fundamental limitation in the use of k-mers as sequence features is that as k is increased, larger spatial correlations in DNA sequence elements can be described, but the frequency of observing any specific k-mer becomes very small, and rapidly approaches a sparse matrix of binary counts. Thus any statistical learning approach using k-mers will be susceptible to noisy estimation of k-mer frequencies once k becomes large. Because all molecular DNA interactions have limited spatial extent, gapped k-mers often carry the relevant biological signal. Here we use gapped k-mer counts to more robustly estimate the ungapped k-mer frequencies, by deriving an equation for the minimum norm estimate of k-mer frequencies given an observed set of gapped k-mer frequencies. We demonstrate that this approach provides a more accurate estimate of the k-mer frequencies in real biological sequences using a sample of CTCF binding sites in the human genome. PMID:23861010

  18. 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).

  19. 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.

  20. Estimation of gene frequency and test for Hardy-Weinberg equilibrium in the HLA system.

    PubMed Central

    Matsuura, M; Eguchi, S

    1990-01-01

    This paper concerns the testing for Hardy-Weinberg equilibrium and the estimation of gene frequency in the human leukocyte antigens (HLA) system. An extensive simulation study for both testing and estimation is given for investigating the performance of the projection method by Eguchi and Matsuura, which has a closed form, and the method is asymptotically equivalent to the maximum likelihood method. We compare our projection test statistic with the likelihood ratio test and the single degree of freedom chi-square test suggested by Nam and Gart. Actual mean square errors of the projection estimator of gene frequency under the Hardy-Weinberg equilibrium are compared with the maximum likelihood estimator and some other estimators recently discussed by Nam. PMID:2269220

  1. Vast Volatility Matrix Estimation using High Frequency Data for Portfolio Selection.

    PubMed

    Fan, Jianqing; Li, Yingying; Yu, Ke

    2012-01-01

    Portfolio allocation with gross-exposure constraint is an effective method to increase the efficiency and stability of portfolios selection among a vast pool of assets, as demonstrated in Fan et al. (2011). The required high-dimensional volatility matrix can be estimated by using high frequency financial data. This enables us to better adapt to the local volatilities and local correlations among vast number of assets and to increase significantly the sample size for estimating the volatility matrix. This paper studies the volatility matrix estimation using high-dimensional high-frequency data from the perspective of portfolio selection. Specifically, we propose the use of "pairwise-refresh time" and "all-refresh time" methods based on the concept of "refresh time" proposed by Barndorff-Nielsen et al. (2008) for estimation of vast covariance matrix and compare their merits in the portfolio selection. We establish the concentration inequalities of the estimates, which guarantee desirable properties of the estimated volatility matrix in vast asset allocation with gross exposure constraints. Extensive numerical studies are made via carefully designed simulations. Comparing with the methods based on low frequency daily data, our methods can capture the most recent trend of the time varying volatility and correlation, hence provide more accurate guidance for the portfolio allocation in the next time period. The advantage of using high-frequency data is significant in our simulation and empirical studies, which consist of 50 simulated assets and 30 constituent stocks of Dow Jones Industrial Average index. PMID:23264708

  2. 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

  3. Estimation of Resonant Frequency of a Circular Microstrip Antenna Using Artificial Neural Network

    NASA Astrophysics Data System (ADS)

    Singh, Jagtar; Singh, A. P.; Kamal, T. S.

    2012-03-01

    In recent years the art of using artificial neural networks for wireless communication engineers has been gaining momentum. In this paper a general procedure is suggested for estimating the resonant frequency of circular microstrip patch antenna using artificial neural networks. The method of moments (MOM) based IE3D software was used to generate data dictionary for training and validation set of ANN. The proposed technique uses multilayer feed-forward back-propagation artificial neural network with one hidden layers for estimating the resonant frequency of a circular microstrip antenna. A relative performance of the different training algorithms is carried out for estimating the resonant frequency with particular attention paid to the speed of computation and accuracy achieved. This type of performance comparison has not been attempted so far.

  4. Joint Entropy for Space and Spatial Frequency Domains Estimated from Psychometric Functions of Achromatic Discrimination

    PubMed Central

    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

  5. 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

  6. Weighted interframe averaging-based channel estimation for orthogonal frequency division multiplexing passive optical network

    NASA Astrophysics Data System (ADS)

    Lin, Bangjiang; Li, Yiwei; Zhang, Shihao; Tang, Xuan

    2015-10-01

    Weighted interframe averaging (WIFA)-based channel estimation (CE) is presented for orthogonal frequency division multiplexing passive optical network (OFDM-PON), in which the CE results of the adjacent frames are directly averaged to increase the estimation accuracy. The effectiveness of WIFA combined with conventional least square, intrasymbol frequency-domain averaging, and minimum mean square error, respectively, is demonstrated through 26.7-km standard single-mode fiber transmission. The experimental results show that the WIFA method with low complexity can significantly enhance transmission performance of OFDM-PON.

  7. Next-generation sequencing of ABCA4: High frequency of complex alleles and novel mutations in patients with retinal dystrophies from Central Europe.

    PubMed

    Ścieżyńska, Aneta; Oziębło, Dominika; Ambroziak, Anna M; Korwin, Magdalena; Szulborski, Kamil; Krawczyński, Maciej; Stawiński, Piotr; Szaflik, Jerzy; Szaflik, Jacek P; Płoski, Rafał; Ołdak, Monika

    2016-04-01

    Variation in the ABCA4 locus has emerged as the most prevalent cause of monogenic retinal diseases. The study aimed to discover causative ABCA4 mutations in a large but not previously investigated cohort with ABCA4-related diseases originating from Central Europe and to refine the genetic relevance of all identified variants based on population evidence. Comprehensive clinical studies were performed to identify patients with Stargardt disease (STGD, n = 76) and cone-rod dystrophy (CRD, n = 16). Next-generation sequencing targeting ABCA4 was applied for a widespread screening of the gene. The results were analyzed in the context of exome data from a corresponding population (n = 594) and other large genomic databases. Our data disprove the pathogenic status of p.V552I and provide more evidence against a causal role of four further ABCA4 variants as drivers of the phenotype under a recessive paradigm. The study identifies 12 novel potentially pathogenic mutations (four of them recurrent) and a novel complex allele p.[(R152*; V2050L)]. In one third (31/92) of our cohort we detected the p.[(L541P; A1038V)] complex allele, which represents an unusually high level of genetic homogeneity for ABCA4-related diseases. Causative ABCA4 mutations account for 79% of STGD and 31% of CRD cases. A combination of p.[(L541P; A1038V)] and/or a truncating ABCA4 mutation always resulted in an early disease onset. Identification of ABCA4 retinopathies provides a specific molecular diagnosis and justifies a prompt introduction of simple precautions that may slow disease progression. The comprehensive, population-specific study expands our knowledge on the genetic landscape of retinal diseases. PMID:26593885

  8. 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

  9. Estimating Cell Concentration in Three-Dimensional Engineered Tissues using High Frequency Quantitative Ultrasound

    PubMed Central

    Mercado, Karla P.; Helguera, Marίa; Hocking, Denise C.; Dalecki, Diane

    2015-01-01

    Histology and biochemical assays are standard techniques for estimating cell concentration in engineered tissues. However, these techniques are destructive and cannot be used for longitudinal monitoring of engineered tissues during fabrication processes. The goal of this study was to develop high-frequency quantitative ultrasound techniques to nondestructively estimate cell concentration in three-dimensional (3-D) engineered tissue constructs. High-frequency ultrasound backscatter measurements were obtained from cell-embedded, 3-D agarose hydrogels. Two broadband single-element transducers (center frequencies of 30 and 38 MHz) were employed over the frequency range of 13 to 47 MHz. Agarose gels with cell concentrations ranging from 1×104 to 1×106 cells mL−1 were investigated. The integrated backscatter coefficient (IBC), a quantitative ultrasound spectral parameter, was calculated and used to estimate cell concentration. Accuracy and precision of this technique were analyzed by calculating the percent error and coefficient of variation of cell concentration estimates. The IBC increased linearly with increasing cell concentration. Axial and lateral dimensions of regions of interest that resulted in errors of less than 20% were determined. Images of cell concentration estimates were employed to visualize quantitatively regional differences in cell concentrations. This ultrasound technique provides the capability to rapidly quantify cell concentration within 3-D tissue constructs noninvasively and nondestructively. PMID:24627179

  10. 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.

  11. 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.

  12. 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).

  13. 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

  14. 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.

  15. 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

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

    PubMed

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

    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

  17. 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

  18. Methods for estimating magnitude and frequency of floods in Montana based on data through 1983

    USGS Publications Warehouse

    Omang, R.J.; Parrett, Charles; Hull, J.A.

    1986-01-01

    Equations are presented for estimating flood magnitudes for ungaged sites in Montana based on data through 1983. The State was divided into eight regions based on hydrologic conditions, and separate multiple regression equations were developed for each region. These equations relate annual flood magnitudes and frequencies to basin characteristics and are applicable only to natural flow streams. In three of the regions, equations also were developed relating flood magnitudes and frequencies to basin characteristics and channel geometry measurements. The standard errors of estimate for an exceedance probability of 1% ranged from 39% to 87%. Techniques are described for estimating annual flood magnitude and flood frequency information at ungaged sites based on data from gaged sites on the same stream. Included are curves relating flood frequency information to drainage area for eight major streams in the State. Maximum known flood magnitudes in Montana are compared with estimated 1 %-chance flood magnitudes and with maximum known floods in the United States. Values of flood magnitudes for selected exceedance probabilities and values of significant basin characteristics and channel geometry measurements for all gaging stations used in the analysis are tabulated. Included are 375 stations in Montana and 28 nearby stations in Canada and adjoining States. (Author 's abstract)

  19. Methods for Estimating Magnitude and Frequency of Peak Flows for Natural Streams in Utah

    USGS Publications Warehouse

    Kenney, Terry A.; Wilkowske, Chris D.; Wright, Shane J.

    2007-01-01

    Estimates of the magnitude and frequency of peak streamflows is critical for the safe and cost-effective design of hydraulic structures and stream crossings, and accurate delineation of flood plains. Engineers, planners, resource managers, and scientists need accurate estimates of peak-flow return frequencies for locations on streams with and without streamflow-gaging stations. The 2-, 5-, 10-, 25-, 50-, 100-, 200-, and 500-year recurrence-interval flows were estimated for 344 unregulated U.S. Geological Survey streamflow-gaging stations in Utah and nearby in bordering states. These data along with 23 basin and climatic characteristics computed for each station were used to develop regional peak-flow frequency and magnitude regression equations for 7 geohydrologic regions of Utah. These regression equations can be used to estimate the magnitude and frequency of peak flows for natural streams in Utah within the presented range of predictor variables. Uncertainty, presented as the average standard error of prediction, was computed for each developed equation. Equations developed using data from more than 35 gaging stations had standard errors of prediction that ranged from 35 to 108 percent, and errors for equations developed using data from less than 35 gaging stations ranged from 50 to 357 percent.

  20. Application of a tri-axial accelerometer to estimate jump frequency in volleyball.

    PubMed

    Jarning, Jon M; Mok, Kam-Ming; Hansen, Bjørge H; Bahr, Roald

    2015-03-01

    Patellar tendinopathy is prevalent among athletes, and most likely associated with a high jumping load. If methods for estimating jump frequency were available, this could potentially assist in understanding and preventing this condition. The objective of this study was to explore the possibility of using peak vertical acceleration (PVA) or peak resultant acceleration (PRA) measured by an accelerometer to estimate jump frequency. Twelve male elite volleyball players (22.5 ± 1.6 yrs) performed a training protocol consisting of seven typical motion patterns, including jumping and non-jumping movements. Accelerometer data from the trial were obtained using a tri-axial accelerometer. In addition, we collected video data from the trial. Jump-float serving and spike jumping could not be distinguished from non-jumping movements using differences in PVA or PRA. Furthermore, there were substantial inter-participant differences in both the PVA and the PRA within and across movement types (p < 0.05). These findings suggest that neither PVA nor PRA measured by a tri-axial accelerometer is an applicable method for estimating jump frequency in volleyball. A method for acquiring real-time estimates of jump frequency remains to be verified. However, there are several alternative approaches, and further investigations are needed. PMID:25902964

  1. 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

  2. Delay Estimation Using Instantaneous Frequency and Phase Difference-Simulation Study.

    PubMed

    Liu, Paul; Liu, Dong

    2016-03-01

    We propose a time-domain delay estimator that takes the slope of the best fit line crossing the origin in the instantaneous frequency-phase difference plane as the delay estimate. This formulation differs from existing phase-based estimators in two respects. First, we find the instantaneous frequency at all individual sample points, including large and abrupt spikes caused by destructive interference in the coherent scattering process. This differs from Loupas which finds a smoothed-out center frequency estimate within an observation window. We show that under high signal-to-noise ratio (SNR), the information from these spikes can be properly used. Second, we show that error ought to be considered as the deviation of the phase difference from the best fit line rather than deviation from the averaged phase difference. Without considering instantaneous frequency, phase-based estimators make the following two errors: samples with phase difference far away from the center frequency need not be errors as they naturally have large phase difference when their instantaneous frequency is large; samples with phase difference close to the center frequency may in fact be errors if their instantaneous frequency is large. We derive the Gauss-Markov least-squares best fit line and then propose an iterative variant that removes samples from the line-fitting process if its deviation from the best fit line is sufficiently large. The iterative version can reduce the effect of aliasing for larger delays and also further reduce the root-mean-square error (RMSE) of the estimate. Simulation studies using various bandwidth, SNR, and delay parameters indicate that iterative phase least squares (PLS) begins to outperform correlation phase Loupas at between SNR of 30 dB (for larger bandwidths and larger delays) and 60 dB (for smaller bandwidths and smaller delays). As SNR increases, iterative PLS can reach a 30- to 50-dB increase in performance over correlation phase Loupas with respect to

  3. 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. PMID:18255527

  4. Direct Rotor-Position Estimation Method for Salient Pole PM Motor by Using High-Frequency Voltage

    NASA Astrophysics Data System (ADS)

    Ito, Masato; Kinpara, Yoshihiko

    Recently, a number of methods have been proposed for estimating the rotor position of a salient pole PM motor, and methods using a high-frequency voltage can estimate the rotor position accurately, even at low speeds. In the conventional method, the rotor position is estimated indirectly by minimizing the position error signal associated with the difference between the estimated position and the real one. This paper proposes a novel direct rotor-position estimation method for salient pole PM motors. In this method, a rotating high-frequency voltage is supplied to the motor, and the rotor position is estimated directly from the high-frequency current in the motor.

  5. 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...

  6. 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

  7. 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

  8. 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

  9. Ultrasonic frequency analysis for estimating pH in albumin-rich biofluids.

    PubMed

    Rackov, Andrien A; Burns, David H

    2016-03-01

    Ultrasound is known as a non-invasive imaging modality capable of propagating through highly scattering media such as tissue, blood, and other biological fluids, yet currently provides little chemical information. We have developed a straightforward and rapid methodology for estimating pH in albumin-rich biofluids based on analysis of ultrasonic frequencies. Albumin is the most abundant protein in serum and undergoes conformational changes with pH. It was shown that when ultrasound propagated through albumin solutions, the attenuation of collected ultrasound signals increased with pH. By measuring the ultrasound frequency spectra at several albumin concentrations and pH values, the pH of the solutions could be determined by multilinear regression. Differences in absolute protein content contributed to signal differences in the frequency profiles and were minimized through normalization of each spectrum by the sum of all its frequency intensities. This strategy was applied to human serum samples from multiple donors, for which a multilinear regression model was developed with a coefficient of determination (R(2)) of 0.93 and a standard error of estimate (SEE) of 0.08 pH units. The use of albumin as a pH indicator opens the doors for estimations in other albumin-rich media, such as amniotic fluid and cerebrospinal fluid. PMID:26717815

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. How does sampling frequency control accuracy of fluvial suspended particulate matter flux estimates?

    NASA Astrophysics Data System (ADS)

    Coynel, A.; Hurtrez, J. E.; Schäfer, J.; Etcheber, H.; Blanc, G.

    2003-04-01

    Climatic change and anthropogenic actions greatly affect the environment: impacts of these factors on erosion and Suspended Particulate Matter (SPM) transport have been studied in different watersheds of southwest France with heterogeneous flood characteristics, vegetal cover and land use. The influence of sampling frequency on annual SPM flux estimates was analysed in two contrasted watersheds: the Garonne basin, a large plain river system (55 000 km^2), and the Nivelle basin, a small Pyrenean mountainous river system (238 km^2). Data banks derived from long-term high resolution sampling in both basins allowed to determine seasonal variations of the relation between water discharge and SPM concentrations during individual floods. High resolution diagrams of SPM concentrations versus discharge show clockwise and anti-clockwise hysteresis loops that were attributed to different sediment sources. Annual SPM fluxes were calculated for the Garonne River (La Réole) in 1994-1998, and for the Nivelle River (Saint Pée-sur-Nivelle) in 1996 by addition of daily fluxes and 30-minute fluxes, respectively. The annual SPM fluxes derived from the most complete dataset derived are considered as reference fluxes. Then, different fixed period strategies (e.g. monthly, semi-monthly, weekly, daily) corresponding to lower sampling frequencies were simulated by randomly extracting individual SPM. and water discharge data from the data base. For each simulation, the reduced dataset was used to estimate maximum and minimum annual SPM fluxes in order to determine the confidence level generated for a given sampling strategy. To obtain a reliable estimate of the SPM flux with less than 20 % error, the minimum sampling frequency is every three days for the Garonne River, whereas for the Nivelle River the minimum sampling frequency for reliable SPM flux estimation is every six hours. This difference in minimum sampling frequency between the two watersheds appears to depend rather on flow

  15. Estimating Loss-of-Coolant Accident Frequencies for the Standardized Plant Analysis Risk Models

    SciTech Connect

    S. A. Eide; D. M. Rasmuson; C. L. Atwood

    2008-09-01

    The U.S. Nuclear Regulatory Commission maintains a set of risk models covering the U.S. commercial nuclear power plants. These standardized plant analysis risk (SPAR) models include several loss-of-coolant accident (LOCA) initiating events such as small (SLOCA), medium (MLOCA), and large (LLOCA). All of these events involve a loss of coolant inventory from the reactor coolant system. In order to maintain a level of consistency across these models, initiating event frequencies generally are based on plant-type average performance, where the plant types are boiling water reactors and pressurized water reactors. For certain risk analyses, these plant-type initiating event frequencies may be replaced by plant-specific estimates. Frequencies for SPAR LOCA initiating events previously were based on results presented in NUREG/CR-5750, but the newest models use results documented in NUREG/CR-6928. The estimates in NUREG/CR-6928 are based on historical data from the initiating events database for pressurized water reactor SLOCA or an interpretation of results presented in the draft version of NUREG-1829. The information in NUREG-1829 can be used several ways, resulting in different estimates for the various LOCA frequencies. Various ways NUREG-1829 information can be used to estimate LOCA frequencies were investigated and this paper presents two methods for the SPAR model standard inputs, which differ from the method used in NUREG/CR-6928. In addition, results obtained from NUREG-1829 are compared with actual operating experience as contained in the initiating events database.

  16. 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.

  17. Estimation of the turbulent boundary layer pressure wavenumber-frequency spectrum using a fixed probe pair

    NASA Technical Reports Server (NTRS)

    Mathur, Gopal P.; Cannon, Mark R.

    1990-01-01

    The turbulent boundary layer (TBL) pressure fluctuations represent a dominant source of aircraft interior noise during cruise. The wavenumber-frequency characteristics of the TBL pressure field become important when determining its coupling with the aircraft structure and the resulting sound radiation into the interior of the aircraft. A technique is presented to estimate the TBL pressure wavenumber-frequency spectrum using a fixed probe pair consisting of two microphones. Flight test data from the McDonnel Douglas Ultra High Bypass Demonstrator aircraft were used to estimate the TBL pressure wavenumber-frequency spectra. These data were compared with selected wall pressure prediction models based on the existing wind tunnel data. The estimated in-flight spectral levels for the Demonstrator aircraft were in good agreement with the TBL wall pressure prediction models in the medium wavenumber range. The estimated TBL wavenumber spectral levels were found to be on the higher side in the low wavenumber region when compared with the predicted levels.

  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. PMID:24990677

  19. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

    PubMed Central

    Hodgson, Jason A.; Pickrell, Joseph K.; Pearson, Laurel N.; Quillen, Ellen E.; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D.; Perry, George H.

    2014-01-01

    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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. Inversion to estimate ocean wave directional spectrum from high-frequency radar

    NASA Astrophysics Data System (ADS)

    Hisaki, Yukiharu

    2015-04-01

    An high-frequency (HF) radar observes ocean surface currents and waves by radiating HF radio waves to the sea surface and analyzing the backscattered signals. Ocean wave spectrum is estimated from the first- and the second-order scattering of Doppler spectra by the inversion. The estimation of ocean surface currents is robust, because the surface currents can be derived from the peak Doppler frequency of the first-order scattering in the Doppler spectrum. The method to estimate ocean wave spectra is complicated and the second-order scattering in the Doppler spectrum is fragile, which is affected by the noise in the Doppler spectrum. A new method to estimate ocean wave spectra from HF radar is developed. This method is the extension of Hisaki (1996, 2005, 2006, 2009, 2014). The new method can be applied to both the single radar and dual radar array case, while the previous methods can be applied only the single radar case (Hisaki, 2005, 2006, 2009, 2014) or dual radar case (Hisaki, 1996). Ocean wave spectra are estimated in the regular grid cells, while wave spectra are estimated on the polar grids points with the origin of the radar position in the previous method for single radar case. The governing equations for wave estimation are the integral equations which relate the wave spectrum to the Doppler spectrum, and the energy balance equation under the assumption of stationarity. The regularization constraints in the horizontal space and the wave frequency-direction space are also used for the estimation. The unknowns, which are spectral values, surface wind speeds and directions, are estimated by seeking the minimum of the objective function, which is defined as the sum of weighted squares of the equations. The signal to noise ratio in the Doppler spectrum for wave estimation must be high. We selected the Doppler spectra using the SOM (Self organization map ) analysis method. The method will be demonstrated by comparing with in-situ observed data, in which only

  6. 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.

  7. Technique for estimating magnitude and frequency of peak flows in Maryland

    USGS Publications Warehouse

    Dillow, Jonathan J.A.

    1996-01-01

    Methods are presented for estimating peak-flow magnitudes of selected frequencies for drainage basins in Maryland. The methods were developed by generalized least-squares regression techniques using data from 219 streamflow-gaging stations in and near Maryland, and apply to peak flows with recurrence intervals of 2, 5, 10, 25, 50, 100, and 500 years. The State is divided into five hydrologic regions: the Appalachian Plateaus and Allegheny Ridges region, the Blue Ridge and Great Valley region, the Piedmont region, the Western Coastal Plain region, and the Eastern Coastal Plain region. Sets of equations for calculating peak discharges based on physical basin characteristics and their associated standard errors of prediction are provided for each of the five hydrologic regions. Basin characteristics and flood-frequency characteristics are tabulated for 236 streamflow- gaging stations in Maryland and surrounding States. Methods of estimating peak flows at sites in Maryland for ungaged and gaged sites are presented.

  8. 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. PMID:27410875

  9. Technique for estimating flood-peak discharges and frequencies on rural streams in Illinois

    USGS Publications Warehouse

    Curtis, G.W.

    1987-01-01

    Flood-peak discharges and frequencies are presented for 394 gaged sites in Illinois, Indiana, and Wisconsin for recurrence intervals ranging from 2 to 100 years. A technique is presented for estimating flood-peak discharges at recurrence intervals ranging from 2 to 500 years for nonregulated streams in Illinois with drainage areas ranging from 0.02 to 10,000 square miles. Multiple-regression analyses, using basin characteristics and peak streamflow data from 268 of the 394 gaged sites, were used to define the flood-frequency relation. The most significant independent variables for estimating flood-peak discharge are drainage area, slope, rainfall intensity and a regional factor. Examples are given to show a step-by-step procedure in calculating a 50-year flood for a site on an ungaged stream, a site at a gaged location, and a site near a gaged location. (USGS)

  10. 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

  11. Documentary evidence of past floods in Europe and their utility in flood frequency estimation

    NASA Astrophysics Data System (ADS)

    Kjeldsen, T. R.; Macdonald, N.; Lang, M.; Mediero, L.; Albuquerque, T.; Bogdanowicz, E.; Brázdil, R.; Castellarin, A.; David, V.; Fleig, A.; Gül, G. O.; Kriauciuniene, J.; Kohnová, S.; Merz, B.; Nicholson, O.; Roald, L. A.; Salinas, J. L.; Sarauskiene, D.; Šraj, M.; Strupczewski, W.; Szolgay, J.; Toumazis, A.; Vanneuville, W.; Veijalainen, N.; Wilson, D.

    2014-09-01

    This review outlines the use of documentary evidence of historical flood events in contemporary flood frequency estimation in European countries. The study shows that despite widespread consensus in the scientific literature on the utility of documentary evidence, the actual migration from academic to practical application has been limited. A detailed review of flood frequency estimation guidelines from different countries showed that the value of historical data is generally recognised, but practical methods for systematic and routine inclusion of this type of data into risk analysis are in most cases not available. Studies of historical events were identified in most countries, and good examples of national databases attempting to collate the available information were identified. The conclusion is that there is considerable potential for improving the reliability of the current flood risk assessments by harvesting the valuable information on past extreme events contained in the historical data sets.

  12. 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.

  13. Frequencies and Flutter Speed Estimation for Damaged Aircraft Wing Using Scaled Equivalent Plate Analysis

    NASA Technical Reports Server (NTRS)

    Krishnamurthy, Thiagarajan

    2010-01-01

    Equivalent plate analysis is often used to replace the computationally expensive finite element analysis in initial design stages or in conceptual design of aircraft wing structures. The equivalent plate model can also be used to design a wind tunnel model to match the stiffness characteristics of the wing box of a full-scale aircraft wing model while satisfying strength-based requirements An equivalent plate analysis technique is presented to predict the static and dynamic response of an aircraft wing with or without damage. First, a geometric scale factor and a dynamic pressure scale factor are defined to relate the stiffness, load and deformation of the equivalent plate to the aircraft wing. A procedure using an optimization technique is presented to create scaled equivalent plate models from the full scale aircraft wing using geometric and dynamic pressure scale factors. The scaled models are constructed by matching the stiffness of the scaled equivalent plate with the scaled aircraft wing stiffness. It is demonstrated that the scaled equivalent plate model can be used to predict the deformation of the aircraft wing accurately. Once the full equivalent plate geometry is obtained, any other scaled equivalent plate geometry can be obtained using the geometric scale factor. Next, an average frequency scale factor is defined as the average ratio of the frequencies of the aircraft wing to the frequencies of the full-scaled equivalent plate. The average frequency scale factor combined with the geometric scale factor is used to predict the frequency response of the aircraft wing from the scaled equivalent plate analysis. A procedure is outlined to estimate the frequency response and the flutter speed of an aircraft wing from the equivalent plate analysis using the frequency scale factor and geometric scale factor. The equivalent plate analysis is demonstrated using an aircraft wing without damage and another with damage. Both of the problems show that the scaled

  14. Short pulse multi-frequency phase-based time delay estimation.

    PubMed

    Assous, Said; Hopper, Clare; Lovell, Mike; Gunn, Dave; Jackson, Peter; Rees, John

    2010-01-01

    An approach for time delay estimation, based on phase difference detection, is presented. A multiple-frequency short continuous wave pulse is used to solve the well-known phase ambiguity problem when the maximum distance exceeds a full wavelength. Within an unambiguous range defined with the lowest frequency difference between components, the corresponding phase difference is unique and any distance within this range can be determined. Phase differences between higher frequency components are used to achieve a finer resolution. The concept will be presented and the effectiveness of the approach will be investigated through theoretical and practical examples. The method will be validated using underwater acoustic measurements, simulating noisy environments, demonstrating resolutions better than a 50th of a wavelength, even in the presence of high levels (-5 dB) of additive Gaussian noise. Furthermore, the algorithm is simple to use and can be easily implemented, being based on phase detection using the discrete Fourier transform. PMID:20058978

  15. Estimation of the Doppler frequency and direction of arrival of the ionospherically propagated HF signals

    NASA Astrophysics Data System (ADS)

    Su, Hongtao; Liu, Hongwei; Shui, Penglang; Bao, Zheng

    2009-08-01

    High-frequency (HF) signals reflected from different points within each ionospheric layer may have slightly different Doppler frequencies and angles of arrival. The superposition of these signals leads to time varying and nonplanar wavefronts. Investigation of temporal and spatial characteristics of the ionospherically propagated HF signals plays an important role in designing the signal processing algorithms for the HF over-the-horizon radar (OTHR). A cost-efficient superresolution algorithm for simultaneously estimating the Doppler frequencies and angles of arrival of the ionospherically propagated HF signals is proposed in this paper. The effectiveness of the proposed algorithm is verified by the experimental data from a trial HF OTHR. Furthermore, the superposition model with the HF signal reflected by a smooth ionospheric layer consisting of a number of submode signals is also confirmed by the experimental data processing results.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Contributions of contour frequency, amplitude, and luminance to the watercolor effect estimated by conjoint measurement.

    PubMed

    Gerardin, Peggy; Devinck, Frédéric; Dojat, Michel; Knoblauch, Kenneth

    2014-01-01

    The watercolor effect is a long-range, assimilative, filling-in phenomenon induced by a pair of distant, wavy contours of different chromaticities. Here, we measured joint influences of the contour frequency and amplitude and the luminance of the interior contour on the strength of the effect. Contour pairs, each enclosing a circular region, were presented with two of the dimensions varying independently across trials (luminance/frequency, luminance/amplitude, frequency/amplitude) in a conjoint measurement paradigm (Luce & Tukey, 1964). In each trial, observers judged which of the stimuli evoked the strongest fill-in color. Control stimuli were identical except that the contours were intertwined and generated little filling-in. Perceptual scales were estimated by a maximum likelihood method (Ho, Landy, & Maloney, 2008). An additive model accounted for the joint contributions of any pair of dimensions. As shown previously using difference scaling (Devinck & Knoblauch, 2012), the strength increases with luminance of the interior contour. The strength of the phenomenon was nearly independent of the amplitude of modulation of the contour but increased with its frequency up to an asymptotic level. On average, the strength of the effect was similar along a given dimension regardless of the other dimension with which it was paired, demonstrating consistency of the underlying estimated perceptual scales. PMID:24722563

  1. 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

  2. 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.

  3. An improved Q estimation approach: the weighted centroid frequency shift method

    NASA Astrophysics Data System (ADS)

    Li, Jingnan; Wang, Shangxu; Yang, Dengfeng; Dong, Chunhui; Tao, Yonghui; Zhou, Yatao

    2016-06-01

    Seismic wave propagation in subsurface media suffers from absorption, which can be quantified by the quality factor Q. Accurate estimation of the Q factor is of great importance for the resolution enhancement of seismic data, precise imaging and interpretation, and reservoir prediction and characterization. The centroid frequency shift method (CFS) is currently one of the most commonly used Q estimation methods. However, for seismic data that contain noise, the accuracy and stability of Q extracted using CFS depend on the choice of frequency band. In order to reduce the influence of frequency band choices and obtain Q with greater precision and robustness, we present an improved CFS Q measurement approach—the weighted CFS method (WCFS), which incorporates a Gaussian weighting coefficient into the calculation procedure of the conventional CFS. The basic idea is to enhance the proportion of advantageous frequencies in the amplitude spectrum and reduce the weight of disadvantageous frequencies. In this novel method, we first construct a Gauss function using the centroid frequency and variance of the reference wavelet. Then we employ it as the weighting coefficient for the amplitude spectrum of the original signal. Finally, the conventional CFS is adopted for the weighted amplitude spectrum to extract the Q factor. Numerical tests of noise-free synthetic data demonstrate that the WCFS is feasible and efficient, and produces more accurate results than the conventional CFS. Tests for noisy synthetic data indicate that the new method has better anti-noise capability than the CFS. The application to field vertical seismic profile (VSP) data further demonstrates its validity5.

  4. 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.

  5. 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.

  6. 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

  7. A new auditory threshold estimation technique for low frequencies: Proof of concept

    PubMed Central

    Lichtenhan, Jeffery T.; Cooper, Nigel P.; Guinan, John J.

    2012-01-01

    Objectives Presently available non-behavioral methods to estimate auditory thresholds perform less well at frequencies below 1 kHz than at 1 kHz and above. For many uses, such as providing accurate infant hearing aid amplification for low-frequency vowels, we need an accurate non-behavioral method to estimate low-frequency thresholds. Here we develop a novel technique to estimate low-frequency cochlear thresholds based on the use of a previously-reported waveform. We determine how well the method works by comparing the resulting thresholds to thresholds from onset-response compound action potentials (CAPs) and single auditory-nerve (AN) fibers in cats. A long-term goal is to translate this technique for use in humans. Design An electrode near the cochlea records a combination of cochlear microphonic (CM) and neural responses. In response to low-frequency, near threshold-level tones, the CM is almost sinusoidal while the neural responses occur preferentially at one phase of the tone. If the tone is presented again but with its polarity reversed, the neural response keeps the same shape, but shifts ½ cycle in time. Averaging responses to tones presented separately at opposite polarities overlaps and interleaves the neural responses and yields a waveform in which the CM is cancelled and the neural response appears twice each tone cycle, i.e. the resulting neural response is mostly at twice the tone frequency. We call the resultant waveform “the auditory nerve overlapped waveform” (ANOW). ANOW level functions were measured in anesthetized cats from 10 to 80 dB SPL in 10 dB steps using tones between 0.3 and 1 kHz. As a response metric, we calculated the magnitude of the ANOW component at twice the tone frequency (ANOW2f). The ANOW threshold was the sound level where the interpolated ANOW2f crossed a statistical criterion that was higher than 95% of the noise floor distribution. ANOW thresholds were compared to onset-CAP thresholds from the same recordings and

  8. Stochastic modeling of triple-frequency BeiDou signals: estimation, assessment and impact analysis

    NASA Astrophysics Data System (ADS)

    Li, Bofeng

    2016-03-01

    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

  9. 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

  10. CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC III) was subjected to marker assisted selection for multiple years to equalize specific marker frequencies to 1) estimate effect size an...

  11. Estimation of size and number density of microbubbles based on analysis of frequency-dependent attenuation

    NASA Astrophysics Data System (ADS)

    Yoshida, Kenji; Tamura, Kazuki; Yamaguchi, Tadashi

    2016-07-01

    A method of estimating the size and number density of microbubbles in suspension is proposed, which matches the theoretically calculated frequency dependent attenuation coefficient with the experimental data. Assuming that the size distribution of bubbles is given by a log-normal function, three parameters (expected value and standard deviation of radius and the number density of bubbles) of Sonazoid® in the steady flow were estimated. Bubbles are exposed to ultrasound with a center frequency of 5 MHz and mechanical indices of 0.4, 0.5, 0.7, and 1.1. The expected value and standard deviation for the size distribution were estimated to be 70–85 and 45–60% of the reference values in the case of a lower mechanical index, respectively. The number density was estimated to be 20–30 times smaller than the reference values. This fundamental examination indicates that the number density of bubbles can be qualitatively evaluated by the proposed method.

  12. 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.

  13. 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. PMID:21870117

  14. 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

  15. 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

  16. 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

  17. Baseline Micronuclei Frequency in Children: Estimates from Meta- and Pooled Analyses

    PubMed Central

    Neri, Monica; Ceppi, Marcello; Knudsen, Lisbeth E.; Merlo, Domenico Franco; Barale, Roberto; Puntoni, Riccardo; Bonassi, Stefano

    2005-01-01

    The number of studies evaluating the effect of environmental exposure to genotoxic agents in children has rapidly increased in the last few years. The frequency of micronuclei (MN) in peripheral blood lymphocytes determined with the cytokinesis block assay is among the most popular biomarkers used for this purpose, although large inter- and intralaboratory variability of this end point has been observed in population studies. The availability of reference measures is therefore necessary for laboratories to validate protocols and analytical procedures, and for molecular epidemiologists, as well, to estimate the statistical power of studies and to assess the quality of data. In this article, we provide estimates of the baseline frequency of MN in children, conducting a meta-analysis of MN frequency reported by field studies in children and a pooled analysis of individual data [available from published studies and from the Human Micronucleus International Collaborative Study (HUMN) database]. Thirteen articles were selected for meta-analysis, and individual data included in the pooled analysis were retrieved from the databases of 12 laboratories. Overall means of 4.48 [95% confidence interval (CI), 3.35–5.98] and 5.70 (95% CI, 4.29–7.56) MN per 1,000 binucleated cells were estimated by the meta- and pooled analysis, respectively. A clear effect of age was detected, even within the restricted range of pediatric age considered, with significantly lower frequency values in newborns. No influence of sex was found. The study showed the advantage of using data from large collaborative studies and suggested a synergistic use of meta- and pooled analysis. PMID:16140632

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. Estimation of tensile force in tie-rods using a frequency-based identification method

    NASA Astrophysics Data System (ADS)

    Amabili, M.; Carra, S.; Collini, L.; Garziera, R.; Panno, A.

    2010-05-01

    A technique is developed to identify in-situ the tensile force in tie-rods which are used in ancient monumental masonry buildings to eliminate the lateral load exercised by the vaults and arcs. The technique is based on a frequency-based identification method that allows to minimize the measurement error and that is of simple execution. In particular, the first natural frequencies of the tie-rods are experimentally identified by measuring the frequency response functions (FRFs) with instrumented hammer excitation; four to six natural frequencies can be easily identified with a simple test. Then, a numerical model, based on the Rayleigh-Ritz method, is developed for the axially loaded tie-rod by using the Timoshenko beam theory retaining shear deformation and rotary inertia. Non-uniform section of the rod is considered since this is often the case for hand-made tie-rods in old buildings. The part of the tie-rod inserted inside the masonry wall is also modeled and a simple support is assumed at the extremities inside the walls. The constraints given to the part of the tie-rod inserted inside the masonry structure are assumed to be elastic foundations. The tensile force and the stiffness of the foundation are the unknowns. In some cases, the length of the rod inside the masonry wall can be also assumed as unknown. The numerical model is used to calculate the natural frequencies for a given set of unknowns. Then, a weighted difference between the calculated and identified natural frequencies is calculated and this difference is minimized in order to identify the unknowns, and in particular the tensile force. An estimation of the error in the identification of the force is given. The technique has been tested on five tie-rods at the ground floor of the famous castle of Fontanellato, Italy.

  4. 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.

  5. Haplotype reconstruction and estimation of haplotype frequencies from nuclear families with only one parent available.

    PubMed

    Ding, Xiangdong; Zhang, Qin; Flury, Christine; Simianer, Henner

    2006-01-01

    Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families can be an alternative strategy in determining the linkage phase. In this paper, haplotype reconstruction and estimation of haplotype frequencies via expectation maximization (EM) algorithm including nuclear families with only one parent available is proposed. Parent and his (her) child are treated as parent-child pair with one shared haplotype. This reduces the number of potential haplotype pairs for both parent and child separately, resulting in a higher accuracy of the estimation. In a series of simulations, the comparisons of PHASE, GENEHUNTER, EM-based approach for complete nuclear families and our approach are carried out. In all situations, EM-based approach for trio data is comparable but slightly worse error rate than PHASE, our approach is slightly better and much faster than PHASE for incomplete trios, the performance of GENEHUNTER is very bad in simple nuclear family settings and dramatically decreased with the number of markers being increased. On the other hand, the comparison result of different sampling designs demonstrates that sampling trios is the most efficient design to estimate haplotype frequencies in populations under same genotyping cost. PMID:16954697

  6. 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

  7. 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

  8. On the behavior of instantaneous frequency estimators implemented on Doppler flow imagers.

    PubMed

    Nowicki, A; Reid, J; Pedersen, P C; Schmidt, A W; Oung, H

    1990-01-01

    Analytical and experimental results have been used to examine the behavior of the "autocorrelator" or instantaneous frequency detector (IFD) applied to color-coded Doppler flow mapping. Two effects were studied. The first was the influence of noise, as modified by a stationary echo canceler, on the Doppler frequency detector. Our theoretical considerations predict that uncorrelated input noise signals become partially correlated after cancellation, and bias the response to flow signals. This effect was confirmed by experiment. The canceler introduces a constant negative bias into the denominator of the algorithm implemented by the estimator, thus changing the indicated frequency. The second phenomenon, examined through processing computer simulated Doppler signals added to real noise, is related to the possible ambiguity, called aliasing, of measurements of the mean frequency for wide-band Doppler spectra. We show that aliasing cannot be observed with these spectra unless the signal is first processed by a canceler. Thus, regions of apparent reversed flow direction on two-dimensional flow images of turbulence must usually be due to real reversal of the flow direction. PMID:2238257

  9. 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

  10. 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

  11. 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.

  12. Estimation of cable tension force using the frequency-based system identification method

    NASA Astrophysics Data System (ADS)

    Kim, Byeong Hwa; Park, Taehyo

    2007-07-01

    This work proposes a new technique to estimate cable tension force from measured natural frequencies. The proposed method is able to simultaneously identify tension force, flexural rigidity, and axial rigidity of a cable system. Firstly, a finite element model that can consider both sag-extensibility and flexural rigidity is constructed for a target cable system. Next, a frequency-based sensitivity-updating algorithm is applied to identify the model. The proposed approach is applicable to a wide range of a cable system that is beyond the applicable limits of the existing methods. From the experimental works, it is seen that the tension force is determined with an accuracy of 3% by the proposed approach. Furthermore, it is observed that the flexural rigidity of cable with high bending stiffness is proportional to the applied tension force.

  13. Estimating an appropriate sampling frequency for monitoring ground water well contamination

    SciTech Connect

    Tuckfield, R.C.

    1994-09-01

    Nearly 1,500 ground water wells at the Savannah River Site (SRS) are sampled quarterly to monitor contamination by radionuclides and other hazardous constituents from nearby waste sites. Some 10,000 water samples were collected in 1993 at a laboratory analysis cost of $10,000,000. No widely accepted statistical method has been developed, to date, for estimating a technically defensible ground water sampling frequency consistent and compliant with federal regulations. Such a method is presented here based on the concept of statistical independence among successively measured contaminant concentrations in time.

  14. Transfer-function-parameter estimation from frequency response data: A FORTRAN program

    NASA Technical Reports Server (NTRS)

    Seidel, R. C.

    1975-01-01

    A FORTRAN computer program designed to fit a linear transfer function model to given frequency response magnitude and phase data is presented. A conjugate gradient search is used that minimizes the integral of the absolute value of the error squared between the model and the data. The search is constrained to insure model stability. A scaling of the model parameters by their own magnitude aids search convergence. Efficient computer algorithms result in a small and fast program suitable for a minicomputer. A sample problem with different model structures and parameter estimates is reported.

  15. 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

  16. 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

  17. Experimental determination of frequency response function estimates for flexible joint industrial manipulators with serial kinematics

    NASA Astrophysics Data System (ADS)

    Saupe, Florian; Knoblach, Andreas

    2015-02-01

    Two different approaches for the determination of frequency response functions (FRFs) are used for the non-parametric closed loop identification of a flexible joint industrial manipulator with serial kinematics. The two applied experiment designs are based on low power multisine and high power chirp excitations. The main challenge is to eliminate disturbances of the FRF estimates caused by the numerous nonlinearities of the robot. For the experiment design based on chirp excitations, a simple iterative procedure is proposed which allows exploiting the good crest factor of chirp signals in a closed loop setup. An interesting synergy of the two approaches, beyond validation purposes, is pointed out.

  18. Allele-specific disparity in breast cancer

    PubMed Central

    2011-01-01

    Background In a cancer cell the number of copies of a locus may vary due to amplification and deletion and these variations are denoted as copy number alterations (CNAs). We focus on the disparity of CNAs in tumour samples, which were compared to those in blood in order to identify the directional loss of heterozygosity. Methods We propose a numerical algorithm and apply it to data from the Illumina 109K-SNP array on 112 samples from breast cancer patients. B-allele frequency (BAF) and log R ratio (LRR) of Illumina were used to estimate Euclidian distances. For each locus, we compared genotypes in blood and tumour for subset of samples being heterozygous in blood. We identified loci showing preferential disparity from heterozygous toward either the A/B-allele homozygous (allelic disparity). The chi-squared and Cochran-Armitage trend tests were used to examine whether there is an association between high levels of disparity in single nucleotide polymorphisms (SNPs) and molecular, clinical and tumour-related parameters. To identify pathways and network functions over-represented within the resulting gene sets, we used Ingenuity Pathway Analysis (IPA). Results To identify loci with a high level of disparity, we selected SNPs 1) with a substantial degree of disparity and 2) with substantial frequency (at least 50% of the samples heterozygous for the respective locus). We report the overall difference in disparity in high-grade tumours compared to low-grade tumours (p-value < 0.001) and significant associations between disparity in multiple single loci and clinical parameters. The most significantly associated network functions within the genes represented in the loci of disparity were identified, including lipid metabolism, small-molecule biochemistry, and nervous system development and function. No evidence for over-representation of directional disparity in a list of stem cell genes was obtained, however genes appeared to be more often altered by deletion than by

  19. Estimation of accuracy of earth-rotation parameters in different frequency bands

    NASA Astrophysics Data System (ADS)

    Vondrak, J.

    1986-11-01

    The accuracies of earth-rotation parameters as determined by five different observational techniques now available (i.e., optical astrometry /OA/, Doppler tracking of satellites /DTS/, satellite laser ranging /SLR/, very long-base interferometry /VLBI/ and lunar laser ranging /LLR/) are estimated. The differences between the individual techniques in all possible combinations, separated by appropriate filters into three frequency bands, were used to estimate the accuracies of the techniques for periods from 0 to 200 days, from 200 to 1000 days and longer than 1000 days. It is shown that for polar motion the most accurate results are obtained with VLBI anad SLR, especially in the short-period region; OA and DTS are less accurate, but with longer periods the differences in accuracy are less pronounced. The accuracies of UTI-UTC as determined by OA, VLBI and LLR are practically equivalent, the differences being less than 40 percent.

  20. ESTIMATING LOW-FLOW FREQUENCIES OF UNGAGED STREAMS IN NEW ENGLAND.

    USGS Publications Warehouse

    Wandle, S. William, Jr.

    1987-01-01

    Equations to estimate low flows were developed using multiple-regression analysis with a sample of 48 river basins, which were selected from the U. S. Geological Survey's network of gaged river basins in Massachusetts, New Hampshire, Rhode Island, Vermont, and southwestern Maine. Low-flow characteristics are represented by the 7Q2 and 7Q10 (the annual minimum 7-day mean low flow at the 2- and 10-year recurrence intervals). These statistics for each of the 48 basins were determined from a low-flow frequency analysis of streamflow records for 1942-71, or from a graphical or mathematical relationship if the record did not cover this 30-year period. Estimators for the mean and variance of the 7-day low flows at the index and short-term sites were used for two stations where discharge measurements of base flow were available and for two sites where the graphical technique was unsatisfactory.

  1. 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.

  2. 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

  3. 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

  4. Negative Selection on BRCA1 Susceptibility Alleles Sheds Light on the Population Genetics of Late-Onset Diseases and Aging Theory

    PubMed Central

    Pavard, Samuel; Metcalf, C. Jessica E.

    2007-01-01

    The magnitude of negative selection on alleles involved in age-specific mortality decreases with age. This is the foundation of the evolutionary theory of senescence. Because of this decrease in negative selection with age, and because of the absence of reproduction after menopause, alleles involved in women's late-onset diseases are generally considered evolutionarily neutral. Recently, genetic and epidemiological data on alleles involved in late onset-diseases have become available. It is therefore timely to estimate selection on these alleles. Here, we estimate selection on BRCA1 alleles leading to susceptibility to late-onset breast and ovarian cancer. For this, we integrate estimates of the risk of developing a cancer for BRCA1-carriers into population genetics frameworks, and calculate selection coefficients on BRCA1 alleles for different demographic scenarios varying across the extent of human demography. We then explore the magnitude of negative selection on alleles leading to a diverse range of risk patterns, to capture a variety of late-onset diseases. We show that BRCA1 alleles may have been under significant negative selection during human history. Although the mean age of onset of the disease is long after menopause, variance in age of onset means that there are always enough cases occurring before the end of reproductive life to compromise the selective value of women carrying a susceptibility allele in BRCA1. This seems to be the case for an extended range of risk of onset functions varying both in mean and variance. This finding may explain the distribution of BRCA1 alleles' frequency, and also why alleles for many late-onset diseases, like certain familial forms of cancer, coronary artery diseases and Alzheimer dementia, are typically recent and rare. Finally, we discuss why the two most popular evolutionary theories of aging, mutation accumulation and antagonistic pleiotropy, may underestimate the effect of selection on survival at old ages. PMID

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Formant frequency estimation of high-pitched vowels using weighted linear prediction.

    PubMed

    Alku, Paavo; Pohjalainen, Jouni; Vainio, Martti; Laukkanen, Anne-Maria; Story, Brad H

    2013-08-01

    All-pole modeling is a widely used formant estimation method, but its performance is known to deteriorate for high-pitched voices. In order to address this problem, several all-pole modeling methods robust to fundamental frequency have been proposed. This study compares five such previously known methods and introduces a technique, Weighted Linear Prediction with Attenuated Main Excitation (WLP-AME). WLP-AME utilizes temporally weighted linear prediction (LP) in which the square of the prediction error is multiplied by a given parametric weighting function. The weighting downgrades the contribution of the main excitation of the vocal tract in optimizing the filter coefficients. Consequently, the resulting all-pole model is affected more by the characteristics of the vocal tract leading to less biased formant estimates. By using synthetic vowels created with a physical modeling approach, the results showed that WLP-AME yields improved formant frequencies for high-pitched sounds in comparison to the previously known methods (e.g., relative error in the first formant of the vowel [a] decreased from 11% to 3% when conventional LP was replaced with WLP-AME). Experiments conducted on natural vowels indicate that the formants detected by WLP-AME changed in a more regular manner between repetitions of different pitch than those computed by conventional LP. PMID:23927127

  11. Combining corpus-derived sense profiles with estimated frequency information to disambiguate clinical abbreviations.

    PubMed

    Xu, Hua; Stetson, Peter D; Friedman, Carol

    2012-01-01

    Abbreviations are widely used in clinical notes and are often ambiguous. Word sense disambiguation (WSD) for clinical abbreviations therefore is a critical task for many clinical natural language processing (NLP) systems. Supervised machine learning based WSD methods are known for their high performance. However, it is time consuming and costly to construct annotated samples for supervised WSD approaches and sense frequency information is often ignored by these methods. In this study, we proposed a profile-based method that used dictated discharge summaries as an external source to automatically build sense profiles and applied them to disambiguate abbreviations in hospital admission notes via the vector space model. Our evaluation using a test set containing 2,386 annotated instances from 13 ambiguous abbreviations in admission notes showed that the profile-based method performed better than two baseline methods and achieved a best average precision of 0.792. Furthermore, we developed a strategy to combine sense frequency information estimated from a clustering analysis with the profile-based method. Our results showed that the combined approach largely improved the performance and achieved a highest precision of 0.875 on the same test set, indicating that integrating sense frequency information with local context is effective for clinical abbreviation disambiguation. PMID:23304376

  12. Spatially smooth regional estimation of the flood frequency curve (with uncertainty)

    NASA Astrophysics Data System (ADS)

    Laio, F.; Ganora, D.; Claps, P.; Galeati, G.

    2011-09-01

    SummaryIdentification of the flood frequency curve in ungauged basins is usually performed by means of regional models based on the grouping of data recorded at various gauging stations. The present work aims at implementing a regional procedure that overcomes some of the limitations of the standard approaches and adds a clearer representation of the uncertainty components of the estimation. The information in the sample records is summarized in a set of sample L-moments, that become the variables to be regionalized. To transfer the information to ungauged basins we adopt a regional model for each of the L-moments, based on a comprehensive multiple regression approach. The independent variables of the regression are selected among a large number of geomorpholoclimatic catchment descriptors. Each model is calibrated on the entire dataset of stations using non-standard least-squares techniques accounting for the sample variability of L-moments, without resorting to any grouping procedure to create sub-regions. In this way, L-moments are allowed to vary smoothly from site to site in the descriptor space, following the variation of the descriptors selected in the regression models. This approach overcomes the subjectivity affecting the techniques for the definition and verification of the homogeneous regions. In addition, the method provides accurate confidence bands for the frequency curves estimated in ungauged basins. The procedure has been applied to a vast region in North-Western Italy (about 30,000 km 2). Cross-validation techniques are used to assess the efficiency of this approach in reconstructing the flood frequency curves, demonstrating the feasibility and the robustness of the approach.

  13. Distribution of HLA-DRB1 and HLA-DQB1 alleles in Lak population of Iran.

    PubMed

    Varzi, Ali Mohammad; Shahsavar, Farhad; Tarrahi, Mohammad Javad

    2016-07-01

    Human leukocyte antigen (HLA) genes are the most polymorphic loci in the human genome and encode the highly polymorphic molecules critically involved in immune responses. Anthropological studies based on highly polymorphic HLA genes provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine the HLA-DRB1 and HLA-DQB1 allele frequencies in 100 unrelated Lak individuals from Lorestan province of Iran. Finally, we compared the results with those previously described in four other Iranian populations. Commercial HLA-Type kits were used for determination of the HLA-DRB1 and HLA-DQB1 allele frequencies. Differences between populations in the distribution of HLA-DRB1 and HLA-DQB1 alleles were estimated by χ2 test with Yate's correction and Fisher's exact test. The most frequent HLA-DRB1 alleles were (*)1103=4 (23%), (*)1502 (9.5%), (*)0701 (9%), (*)0301 (8.5%), (*)1101 (7.5%) and (*)1501 (6%) while HLA-DQB1(*)0301 (40%), (*)0201 (15%), (*)0502 (10.5%), (*)0303 (10%), (*)0602=3 (9.5%), and (*)0501 (7.5%) were the most frequent alleles in Lak population. HLA-DRB1(*)0409, (*)0804, (*)1102, (*)1112, (*)1405, and HLA-DQB1(*)0503, (*)0604 were the least observed frequencies in Lak population. Our results based on HLA-DRB1 and HLA-DQB1 allele frequencies showed that the Lak population possesses the previously reported general features of the Lur and Kurd populations but still with unique, decreased or increased frequencies of several alleles. In other words, the Lak population is close to Lurs Khorramabadi and Kurd but far from Lurs Kohkiloyeh/Boyerahmad and Bakhtiari. PMID:27189628

  14. Pilot-aided sampling frequency offset estimation and compensation using DSP technique in DD-OOFDM systems

    NASA Astrophysics Data System (ADS)

    Chen, Ming; He, Jing; Tang, Jin; Chen, Lin

    2014-06-01

    To improve the outage performance of an optical orthogonal frequency-division multiplexing (OFDM) system under the frequency offset between the sampling clocks in the transmitter and receiver, a pilot-aided sampling frequency offset (SFO) estimation and compensation scheme for the optical OFDM system with intensity-modulation and direct-detection (DD-OOFDM) is experimentally demonstrated. The experimental and simulated results show that the scheme can work effectively even with large sampling frequency offsets. In addition, it can achieve a good bit error rate (BER) performance without the sampling clock frequency synchronization in the receiver.

  15. 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

  16. 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.

  17. 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...

  18. Estimation of the Fundamental Frequency of the Speech Signal Compressed by G.723.1 Algorithm Applying PCC Interpolation

    NASA Astrophysics Data System (ADS)

    Milivojević, Zoran N.; Brodić, Darko

    2011-07-01

    In this paper the results of the estimation of the fundamental frequency of the speech signal modeled by the G.723.1 method are analyzed. The estimation of the fundamental frequency was performed by the Peaking-Peaks algorithm with the implemented Parametric Cubic Convolution (PCC) interpolation. The efficiency of PCC was tested for Keys, Greville and Greville two-parametric kernel. Depending on MSE a window that gives optimal results was chosen.

  19. Anthelmintic resistance in Swedish sheep flocks based on a comparison of the results from the faecal egg count reduction test and resistant allele frequencies of the beta-tubulin gene.

    PubMed

    Höglund, Johan; Gustafsson, Katarina; Ljungström, Britt-Louise; Engström, Annie; Donnan, Alison; Skuce, Philip

    2009-04-01

    A faecal egg count reduction test (FECRT) survey was conducted during the grazing season 2006 and 2007 to provide an updated indication of the prevalence of anthelmintic resistance in sheep flocks in Sweden. A total of 1330 faecal samples from 90 flocks on 45 farms, with a minimum of 20 ewes each, was collected by local sheep veterinarians. Per treatment group, approximately 15 lambs were dewormed either with oral suspensions of ivermectin (Ivomec vet.) or albendazole (Valbazen vet.). The efficacy on each farm was investigated either in 2006 or 2007 by faecal egg counts collected on the day of treatment and in a new sample from the same animals 7-10 days later. Third-stage larvae (L3) were initially identified morphologically from pooled cultures. These were then used as the source of genomic DNA template for two molecular tests. The first was a PCR-based test for specific identification of Haemonchus contortus, and the second was a Pyrosequencing assay for the analysis of benzimidazole (BZ) resistance targeting the P200 mutation in the parasite's beta-tubulin gene. Larval cultures indicated that Teladorsagia and Trichostrongylus were the predominant genera, but Haemonchus was diagnosed in 37% of the flocks. The PCR results revealed an almost 100% agreement with those farms that had previously been shown to have Haemonchus present, even when the % prevalence was low (approximately 3%). Only two (4%) of the surveyed farms showed evidence of BZ-resistant worm populations, with H. contortus being the species implicated according to post-treatment larval culture results. The Pyrosequencing assay detected BZ resistant allele frequencies of >40% in the Haemonchus-positive farms and 100% resistant alleles in the clinically most resistant farms. These preliminary results suggest that the FECRT is less sensitive than the molecular test at detecting BZ resistance. However, both tests need to be interpreted carefully, bearing in mind the relative proportions of species

  20. Techniques for estimating peak-streamflow frequency for unregulated streams and streams regulated by small floodwater retarding structures in Oklahoma

    USGS Publications Warehouse

    Tortorelli, Robert L.

    1997-01-01

    Statewide regression equations for Oklahoma were determined for estimating peak discharge and flood frequency for selected recurrence intervals from 2 to 500 years for ungaged sites on natural unregulated streams. The most significant independent variables required to estimate peak-streamflow frequency for natural unregulated streams in Oklahoma are contributing drainage area, main-channel slope, and mean-annual precipitation. The regression equations are applicable for watersheds with drainage areas less than 2,510 square miles that are not affected by regulation from manmade works. Limitations on the use of the regression relations and the reliability of regression estimates for natural unregulated streams are discussed. Log-Pearson Type III analysis information, basin and climatic characteristics, and the peak-stream-flow frequency estimates for 251 gaging stations in Oklahoma and adjacent states are listed. Techniques are presented to make a peak-streamflow frequency estimate for gaged sites on natural unregulated streams and to use this result to estimate a nearby ungaged site on the same stream. For ungaged sites on urban streams, an adjustment of the statewide regression equations for natural unregulated streams can be used to estimate peak-streamflow frequency. For ungaged sites on 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 frequency. The statewide regression equations are adjusted by substituting the drainage area below the floodwater retarding structures, or drainage area that represents the percentage of the unregulated basin, in the contributing drainage area parameter to obtain peak-streamflow frequency estimates.

  1. 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

  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. 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.

  4. Estimating surface electromagnetic properties and corresponding effects on radio frequency signatures

    NASA Astrophysics Data System (ADS)

    Bole, M. Kate; Bole, Dan; Anklam, Sean; Janaskie, Justin

    2010-04-01

    Estimates of surface terrain electromagnetic properties can be utilized by Computational Electromagnetic Modeling (CEM) software to predict radio signal propagation loss between a transmitter and receiver. This paper will examine the variability of the dielectric properties of surface soils as a function of composition, moisture content, and frequency using a semi-empirical model from literature. Using the CEM software the signal path loss will be calculated and the effects of the variability in the dielectric constant of soil examined. High resolution remote sensing imagery will be considered as a data source for soil composition and moisture content information. This topic has implications on using modeling and simulation to understand and predict the performance of RF ground sensors and systems.

  5. Estimation of peak-frequency relations, flood hydrographs, and volume-duration-frequency relations of ungaged small urban streams in Ohio

    USGS Publications Warehouse

    Sherwood, J.M.

    1993-01-01

    Methods are presented to estimate peak-frequency relations, flood hydrographs, and volume-duration-frequency relations of urban streams in Ohio with drainage areas less than 6.5 square miles. The methods were developed to assist planners in the design of hydraulic structures for which hydrograph routing is required or where the temporary storage of water is an important element of the design criteria. Examples of how to use the methods also are presented. The data base for the analyses consisted of 5-minute rainfall-runoff data collected for a period of 5 to 8 years at 62 small drainage basins distributed throughout Ohio. The U.S. Geological Survey rainfall-runoff model A634 was used and was calibrated for each site. The calibrayed models were used in conjunction with long-term (66-87 years) rainfall and evaporation records to synthesize a long-term series of flood-hydrograph records at each site. A method was developed and used to increase the variance of the synthetic flood characterictics in order to make them more representative of observed flood characteristics. Multiple-regression equations were developed to estimate peak discharges having recurrence intervals of 2, 5, 10, 25, 50, and 100 years. The explanatory variables in the peak-discharge equations are drainage area, average annual precipitation, and basin development factor. Average standard errors of prediction for the peak-frequency equations range from ? 34 to ? 40 percent. A method is presented to estimate flood hydrographs by applying a specific peak discharge and basin lagtime to a dimensionless hydrograph. An equation was developed to estimate basin lagtime in which main-channel length divided by the square root of the main-channel slope (L/SL) and basin-development factor are the explanatory variables and the average standard error of prediction is ? 53 percent. A dimensional hydrograph originally developed by the U.S. Geological Survey for use in Georgia was verified for use in urban areas of

  6. How Do College Students Estimate Their Drinking? Comparing Consumption Patterns among Quantity-Frequency, Graduated Frequency, and Timeline Follow-Back Methods

    ERIC Educational Resources Information Center

    Fishburne, John W.; Brown, Janice M.

    2006-01-01

    This exploratory study was designed to compare several commonly used measures of alcohol use among college students in order to appreciate how estimations of college drinking may be affected by the type of assessment tool used. Consumption patterns of 42 college student drinkers were compared using a quantity-frequency measure, a graduated…

  7. Estimating the magnitude and frequency of floods for streams in west-central Florida, 2001

    USGS Publications Warehouse

    Hammett, Kathleen M.; DelCharco, Michael J.

    2005-01-01

    Flood discharges were estimated for recurrence intervals of 2, 5, 10, 25, 50, 100, 200, and 500 years for 94 streamflow stations in west-central Florida. Most of the stations are located within the 10,000 square-mile, 16-county area that forms the Southwest Florida Water Management District. All stations had at least 10 years of homogeneous record, and none have flood discharges that are significantly affected by regulation or urbanization. Guidelines established by the U.S. Water Resources Council in Bulletin 17B were used to estimate flood discharges from gaging station records. Multiple linear regression analysis was then used to mathematically relate estimates of flood discharge for selected recurrence intervals to explanatory basin characteristics. Contributing drainage area, channel slope, and the percent of total drainage area covered by lakes (percent lake area) were the basin characteristics that provided the best regression estimates. The study area was subdivided into four geographic regions to further refine the regression equations. Region 1 at the northern end of the study area includes large rivers that are characteristic of the rolling karst terrain of northern Florida. Only a small part of Region 1 lies within the boundaries of the Southwest Florida Water Management District. Contributing drainage area and percent lake area were the most statistically significant basin characteristics in Region 1; the prediction error of the regression equations varied with the recurrence interval and ranged from 57 to 69 percent. In the three other regions of the study area, contributing drainage area, channel slope, and percent lake area were the most statistically significant basin characteristics, and are the three characteristics that can be used to best estimate the magnitude and frequency of floods on most streams within the Southwest Florida Water Management District. The Withlacoochee River Basin dominates Region 2; the prediction error of the regression

  8. 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.

  9. 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. PMID:25310505

  10. 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.

  11. 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

  12. 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.

  13. Fatigue level estimation of monetary bills based on frequency band acoustic signals with feature selection by supervised SOM

    NASA Astrophysics Data System (ADS)

    Teranishi, Masaru; Omatu, Sigeru; Kosaka, Toshihisa

    Fatigued monetary bills adversely affect the daily operation of automated teller machines (ATMs). In order to make the classification of fatigued bills more efficient, the development of an automatic fatigued monetary bill classification method is desirable. We propose a new method by which to estimate the fatigue level of monetary bills from the feature-selected frequency band acoustic energy pattern of banking machines. By using a supervised self-organizing map (SOM), we effectively estimate the fatigue level using only the feature-selected frequency band acoustic energy pattern. Furthermore, the feature-selected frequency band acoustic energy pattern improves the estimation accuracy of the fatigue level of monetary bills by adding frequency domain information to the acoustic energy pattern. The experimental results with real monetary bill samples reveal the effectiveness of the proposed method.

  14. 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.

  15. Estimating one-dimensional models from frequency-domain electromagnetic data using modular neural networks

    SciTech Connect

    Poulton, M.M.; Birken, R.A.

    1998-03-01

    An artificial neural network interpretation system is being used to interpret data from a frequency-domain electromagnetic (EM) geophysical system in near real time. The interpretation system integrates 45 separate networks in a data visualization shell. The networks produce interpretations at three different transmitter-receiver (Tx-Rx) separations for half-space and layered-earth interpretations. Modular neural networks (MNN`s) were found to be the only paradigm that could successfully perform the layered-earth interpretations. An MNN with 16 inputs, five local experts, each with seven hidden processing elements, and three outputs was trained on 4795 patterns for 200 epochs. For two-layer models with a resistivity contrast greater than 2:1, resistivity estimates had greater than 96% accuracy for the first-layer resistivity, greater than 98% for the second-layer resistivity, and greater than 96% for the thickness of the first layer. If the contrast is less than 2:1, the resistivity accuracies are unaffected but thickness estimates for layers less than 2 m are unreliable. A Tx-Rx separation of 16 m with maximum depth of penetration of 8 m was assumed for the example cited.

  16. Floods in Kansas and techniques for estimating their magnitude and frequency on unregulated streams

    USGS Publications Warehouse

    Clement, R.W.

    1987-01-01

    Techniques are presented for generalizing the skewness coefficient of log-Pearson Type III distributions of annual maximum discharges and for flood magnitudes that have selected recurrence intervals from 2 to 100 yr. A weighted least-square (WLS) regression model was used to generalize the coefficients of station skewness that resulted in a root-mean-sq error of prediction of 0.35 compared to 0.55 for the skewness map published in Bulletin 17B of the U.S. Water Resources Council. Estimates of generalized skewness were computed for each of 245 streamflow gaging stations with a minimum of 10 years of record and a contributing drainage area of < 20,000 sq mi. The WLS regression model also was used to develop equations for estimating flood magnitude for selected recurrence intervals for ungaged stream locations by using data from 218 of the 245 streamflow gaging stations that had contributing-drainage areas of less than 10,000 sq mi. The errors of prediction of the most reliable WLS equations ranged from 28 to 42%. The WLS equations were compared statistically to previous developed equations and were determined to be different and more accurate than previously published equations. Flood magnitudes and frequencies for 245 streamflow gaging stations, based on data collected through the 1983 water year, are presented along with a summary of the seasonal distribution of annual maximum discharges and an analysis of the maximum observed discharges. (Author 's abstract)

  17. Individual estimation of exposures to extremely low frequency magnetic fields in jobs commonly held by women.

    PubMed

    Deadman, J E; Infante-Rivard, C

    2002-02-15

    Exposures to extremely low frequency (ELF) magnetic fields have not been documented extensively in occupations besides the work environments of electric or telephone utilities. A 1980-1993 study of childhood acute lymphoblastic leukemia (ALL) in Québec, Canada, gathered detailed information about the occupations of 491 mothers of ALL cases and mothers of a similar number of healthy controls. This information was combined with published data on the intensities of ELF magnetic fields associated with sources or work environments to estimate ELF magnetic field exposures for a wide range of jobs commonly held by women. Estimated exposures for 61 job categories ranged from 0.03 to 0.68 microT; the 25th, 50th, and 75th percentiles were 0.135, 0.17, and 0.23 microT, respectively. By job category, the most highly exposed jobs (>0.23 microT) included bakery worker, cashier, cook and kitchen worker, electronics worker, residential and industrial sewing machine operator, and textile machine operator. By work environment, the most highly exposed job categories were electronics worker in an assembly plant (0.70 microT) and sewing machine operators in a textile factory (0.68 microT) and shoe factory (0.66 microT). These results provide new information on expected levels of exposure in a wide range of jobs commonly held by women. PMID:11836202

  18. 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

  19. 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

  20. 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)

  1. 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

  2. HLA alleles and haplotypes among the Lakota Sioux: report of the ASHI minority workshops, part III.

    PubMed

    Leffell, Mary S; Fallin, M Daniele; Hildebrand, William H; Cavett, Joshua W; Iglehart, Brian A; Zachary, Andrea A

    2004-01-01

    Human leukocyte antigen (HLA) class I and II alleles were defined for 302 Lakota Sioux American Indians as part of the American Society for Histocompatibility and Immunogenetics coordinated studies on minority populations. The study group was comprised of adult volunteers from the Cheyenne River and Ogala Sioux tribes residing, respectively, on the Cheyenne River and Pine Ridge Reservations in South Dakota. Of the participants, 263 (87%) claimed full American Indian ancestry through both maternal and paternal grandparents. The study group included 25 nuclear families that were informative for genotyping. HLA phenotypes from 202 adults with no other known first-degree relative included in the study were used for calculation of allele and haplotype frequencies by maximum likelihood estimation. HLA-A, -B, and -Cw alleles were found to be in Hardy Weinberg equilibrium. Deviation from equilibrium was observed for DRB1 alleles (p=0.01), but could be attributed to the sample size and the occurrence of some genotypes with low expected frequencies. Polymorphism among the Sioux was limited with four to seven alleles comprising >80% of those observed at each locus. Several alleles were found at high frequency (0.05-0.30) among the Sioux that are also prevalent in other Native Americans and Alaska Natives, including: A*2402, *3101, and *0206; B*3501,*3901, *5101, and *2705; Cw*0702, *0404, and *03041; DRB1*0407, *0404, *1402, and *16021; and DQB1*0301, *0302, and *0402. DRB1*0811, which has been only previously described in Navajo and Tlingit Indians, was found to occur at a frequency of 0.119 among the Sioux. Two new alleles were defined among the Sioux: Cw*0204 and DRB1*040703, which were found in two and four individuals, respectively. In the haplotype analyses, significant linkage disequilibrium (p<0.00001) was seen in all pairwise comparisons of loci and numerous two and three locus haplotypes were found to have strong, positive linkage disequilibrium values. The two most

  3. 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

  4. Estimation of rockfall frequency from simulated trajectories and observed tree impacts

    NASA Astrophysics Data System (ADS)

    Monnet, Jean-Matthieu; Bourrier, Franck; Lopez Saez, Jérôme; Corona, Christophe

    2014-05-01

    While significant progress has been achieved regarding the modeling of rockfall propagation, including the interaction with forest cover, the estimation of the spatial distribution of rockfall frequency in release areas remains a challenging task. Indeed, the very low number of observed events makes any statistical modeling difficult, so that estimations are generally based on expert knowledge regarding the rock structure of start zone and a few recorded events. Meanwhile, recent dendrochronological studies have shown that trees, as silent witnesses of numerous events, bring information about the spatial distribution of rockfall trajectories. This data can be compared to simulated trajectories in order to reconstruct the most probable start zones. This study presents a methodological framework for the resolution of this problem and a real-case example. Consider a forest patch f located below a cliff with Ns potential rockfall start points. The expected value of the number of impacts in this forest patch during lapse T can be calculated as (1) : δΣNs Impacts(f) = T × (pstart(i)× ppropagation(i,f)) i=1 (1) with pstart(i) the probability of rockfall for the start point i, ppropagation(i,f) the probability that a rockfall from start point i impacts at least one tree in the forest patch f . The matrix formulation for the whole forest divided in Nf forest patches is (2): Impact1×Nf = T × P start1×Nf ×P propagationNs×Nf (2) Ppropagation can be estimated with numerical simulations, by taking into account the current state of the forest stand if trees are measured and georeferenced, and if the volume of rockfall is known. Impact can be also be observed on the field. Under the assumption that the forest stand and the start frequencies do not change during lapse T , the equation system (2) can be solved for the Nf coefficients of Pstart. This framework was tested on a rockfall area located in Valdrôme, France, where more than 1000 trees were measured and geolocated

  5. 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.

  6. Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern.

    PubMed

    Trask, Amanda E; Bignal, Eric M; McCracken, Davy I; Monaghan, Pat; Piertney, Stuart B; Reid, Jane M

    2016-07-01

    Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However

  7. 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

  8. Optimal Estimation of Rain-Rate Profiles from Single-Frequency Radar Echoes

    NASA Technical Reports Server (NTRS)

    Haddad, Ziad S.; Im, Eastwood; Durden, Stephen L.

    1996-01-01

    The significant ambiguities inherent in the determination of a particular vertical rain intensity profile from a given time profile of radar echo powers measured by a downward-looking (spaceborne or airborne) radar at a single attenuating frequency are well documented. Indeed, one already knows that by appropriately varying the parameters of the reflectivity-rain rate (Z-R) and/or attenuation-rain rate (k- R) relationships one can produce several substantially different rain-rate profiles that would produce the same radar power profile. Imposing the additional constraint that the path-averaged rain rate be a given fixed number does reduce the ambiguities but falls far short of eliminating them. While formulas to generate all mutually ambiguous rain-rate profiles from a given profile of received radar reflectivities have already been derived, there remains to be produced a quantitative measure to assess how likely each of these profiles is, what the appropriate "average" profile should be, and what the "variance" of these multiple solutions is. To do this, one needs to spell out the stochastic constraints that can allow us to make sense of the words "average" and "variance" in a mathematically rigorous way. Such a quantitative approach would be particularly well suited for such systems as the planned precipitation radar of the Tropical Rainfall Measuring Mission (TRMM). Indeed, one would then be able to use the radar reflectivities measured by the TRMM radar to estimate the rain-rate profile that would most likely have produced the measurements, as well as the uncertainty in the estimated rain rates as a function of range. Such an optimal approach is described in this paper.

  9. Optimal Estimation of Rain Rate Profiles from Single-Frequency Radar Echoes

    NASA Technical Reports Server (NTRS)

    Haddad, Ziad S.; Im, Eastwood

    1992-01-01

    The significant ambiguities inherent in the determination of a particular vertical rain intensity profile from a given time profile of radar echo powers measured by a downward-looking (spaceborne or airborne) radar at a single attenuating frequency are well-documented. Indeed, one already knows that by appropriately varying the parameters of the reflectivity-rain-rate (Z - R) and/or attenuation-rain-rate (k - R) relationships, one can produce several substantially different hypothetical rain rate profiles which would have the same radar power profile. Imposing the additional constraint that the path-averaged rain-rate be a given fixed number does reduce the ambiguities but falls far short of eliminating them. While we now know how to generate as many mutually ambiguous rain-rate profiles from a given profile of received radar reflectivities as we like, there remains to produce a quantitative measure to assess how likely each of these profiles is, what the appropriate 'average' profile should be, and what the 'variance' of these multiple solutions is. Of course, in order to do this, one needs to spell out the stochastic constraints that can allow us to make sense of the words 'average' and 'variance' in a mathematically rigorous way. Such a quantitative approach would be particularly well-suited for such systems as the proposed Precipitation Radar of the Tropical Rainfall Measuring Mission (TRMM). Indeed, one would then be able to use the radar reflectivities measured by the TRMM radar from one particular look in order to estimate the most likely rain-rate profile that would have produced the measurements, as well as the uncertainty in the estimated rain-rates as a function of range. Such an optimal approach is described in this paper.

  10. 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. PMID:2130371

  11. 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

  12. 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

  13. Frequencies of cytotoxic T lymphocyte precursor estimate in three different populations.

    PubMed

    Haque, K; Truman, C; Dittmer, I; Denning-Kendall, P; Hows, J; Bradley, B

    1999-06-01

    There is speculation that high cytotoxic T lymphocyte precursor frequencies (CTLpf) correlate with poor clinical outcome of bone marrow/organ transplantation. It is also believed that human umbilical cord blood is immunologically naive, and, therefore cord blood T cells may be less able to mediate graft versus host disease than marrow-derived T cells. CTLpf were determined in peripheral blood mononuclear cells collected from healthy adults, human umbilical cord blood and renal dialysis patients who were randomly selected and entered into this study. A highly sensitive non-radioactive Europium release cytotoxicity assay was optimized and modified to carry out the CTLpf estimation by using the principle of limiting dilution analysis. The results of CTLpf in healthy adults ranged from 1/694 to 1/66,666, median 1/7,339 (n=10); cord blood ranged from 1/1,562 to 1/35,714, median 1/10,162 (n=6) and dialysis patients ranged from 1/1,054 to 1/17,857 median 1/5,208 (n=9). The results demonstrated that there is little difference of CTLpf median values between the groups, but there is a wide variation of CTLpf between individuals within a population. It suggests that this variation should be taken into account when considering CTLpf assay as pre-transplantation cross-match procedure. PMID:10466544

  14. 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

  15. Population Dynamics of Sex-Determining Alleles in Honey Bees and Self-Incompatibility Alleles in Plants

    PubMed Central

    Yokoyama, Shozo; Nei, Masatoshi

    1979-01-01

    Mathematical theories of the population dynamics of sex-determining alleles in honey bees are developed. It is shown that in an infinitely large population the equilibrium frequency of a sex allele is 1/n, where n is the number of alleles in the population, and the asymptotic rate of approach to this equilibrium is 2/(3n) per generation. Formulae for the distribution of allele frequencies and the effective and actual numbers of alleles that can be maintained in a finite population are derived by taking into account the population size and mutation rate. It is shown that the allele frequencies in a finite population may deviate considerably from 1/n. Using these results, available data on the number of sex alleles in honey bee populations are discussed. It is also shown that the number of self-incompatibility alleles in plants can be studied in a much simpler way by the method used in this paper. A brief discussion about general overdominant selection is presented. PMID:17248901

  16. 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...

  17. The effect of deleterious alleles on adaptation in asexual populations.

    PubMed Central

    Johnson, Toby; Barton, Nick H

    2002-01-01

    We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles. PMID:12242249

  18. The Use of Multi-Sensor Quantitative Precipitation Estimates for Deriving Extreme Precipitation Frequencies with Application in Louisiana

    NASA Astrophysics Data System (ADS)

    El-Dardiry, Hisham Abd El-Kareem

    The Radar-based Quantitative Precipitation Estimates (QPE) is one of the NEXRAD products that are available in a high temporal and spatial resolution compared with gauges. Radar-based QPEs have been widely used in many hydrological and meteorological applications; however, a few studies have focused on using radar QPE products in deriving of Precipitation Frequency Estimates (PFE). Accurate and regionally specific information on PFE is critically needed for various water resources engineering planning and design purposes. This study focused first on examining the data quality of two main radar products, the near real-time Stage IV QPE product, and the post real-time RFC/MPE product. Assessment of the Stage IV product showed some alarming data artifacts that contaminate the identification of rainfall maxima. Based on the inter-comparison analysis of the two products, Stage IV and RFC/MPE, the latter was selected for the frequency analysis carried out throughout the study. The precipitation frequency analysis approach used in this study is based on fitting Generalized Extreme Value (GEV) distribution as a statistical model for the hydrologic extreme rainfall data that based on Annual Maximum Series (AMS) extracted from 11 years (2002-2012) over a domain covering Louisiana. The parameters of the GEV model are estimated using method of linear moments (L-moments). Two different approaches are suggested for estimating the precipitation frequencies; Pixel-Based approach, in which PFEs are estimated at each individual pixel and Region-Based approach in which a synthetic sample is generated at each pixel by using observations from surrounding pixels. The region-based technique outperforms the pixel based estimation when compared with results obtained by NOAA Atlas 14; however, the availability of only short record of observations and the underestimation of radar QPE for some extremes causes considerable reduction in precipitation frequencies in pixel-based and region

  19. 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

  20. Associations of HLA-A, HLA-B and HLA-C alleles frequency with prevalence of herpes simplex virus infections and diseases across global populations: implication for the development of an universal CD8+ T-cell epitope-based vaccine.

    PubMed

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

    2014-08-01

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

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

    PubMed Central

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

    2014-01-01

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

  2. HLA-B alleles of the Cayapa of Ecuador: New B39 and B15 alleles

    SciTech Connect

    Garber, T.L.; Butler, L.M.; Watkins, D.I.

    1995-05-01

    Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B*3905, HLA-B*3906, HLA-B*3907, and HLA-B*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles. 70 refs., 2 figs., 2 tabs.

  3. 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...

  4. 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...

  5. 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...

  6. 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. PMID:21444083

  7. 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. PMID:25549886

  8. 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.

  9. 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.

  10. On the source-frequency dependence of fracture-orientation estimates from shear-wave transmission experiments

    NASA Astrophysics Data System (ADS)

    Santos, Leo K.; de Figueiredo, J. J. S.; Omoboya, Bode; Schleicher, Jörg; Stewart, Robert R.; Dyaur, Nikolay

    2015-03-01

    Shear-wave propagation through anisotropic fractured or cracked media can provide valuable information about these fracture swarms and their orientations. The main goal of this work is to recover information about fracture orientation based on the shear waveforms (S-waveforms). For this study, we carried out ultrasonic S-wave measurements in a synthetic physical model made of epoxy resin (isotropic matrix proxy), with small cylindrical rubber strips as inclusions (artificial cracks) inserted in it to simulate a homogeneous anisotropic medium. In these experiments, we used low, intermediate, and high frequency shear-wave sources, with frequencies 90, 431, and 840 kHz. We integrated and interpreted the resulting S-wave seismograms, cross-correlation panels and anisotropic parameter-analysis curves. We were able to estimate the crack orientation in single-orientation fracture zones. The high frequency peaks associated with scattered S-waves provided interpretable information about the fracture orientations when the propagation direction was parallel to the fracture plane. The analysis was possible utilizing results from frequency-versus-polarization-angle curves. Moreover, we applied a bandpass filtering process to the intermediate and high frequency seismograms in order to obtain low frequency seismograms. A spectral analysis using frequency-wavenumber (F-K) spectra supports this filtering process. The results obtained using an analysis of cross-correlograms and the Thomsen parameter γ extracted from filtered high-frequency data were quite similar to those obtained using a low-frequency source. This highlighted the possibility of using less expensive high-frequency sources to recover information about the fracture set.

  11. 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

  12. 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

  13. A Maximum-Likelihood Method for the Estimation of Pairwise Relatedness in Structured Populations

    PubMed Central

    Anderson, Amy D.; Weir, Bruce S.

    2007-01-01

    A maximum-likelihood estimator for pairwise relatedness is presented for the situation in which the individuals under consideration come from a large outbred subpopulation of the population for which allele frequencies are known. We demonstrate via simulations that a variety of commonly used estimators that do not take this kind of misspecification of allele frequencies into account will systematically overestimate the degree of relatedness between two individuals from a subpopulation. A maximum-likelihood estimator that includes FST as a parameter is introduced with the goal of producing the relatedness estimates that would have been obtained if the subpopulation allele frequencies had been known. This estimator is shown to work quite well, even when the value of FST is misspecified. Bootstrap confidence intervals are also examined and shown to exhibit close to nominal coverage when FST is correctly specified. PMID:17339212

  14. 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

  15. 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 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

  16. Combining non-precise historical information with instrumental measurements for flood frequency estimation: a fuzzy Bayesian approach

    NASA Astrophysics Data System (ADS)

    Salinas, Jose Luis; Kiss, Andrea; Viglione, Alberto; Blöschl, Günter

    2016-04-01

    Efforts of the historical environmental extremes community during the last decades have resulted in the obtention of long time series of historical floods, which in some cases range longer than 500 years in the past. In hydrological engineering, historical floods are useful because they give additional information which improves the estimates of discharges with low annual exceedance probabilities, i.e. with high return periods, and additionally might reduce the uncertainty in those estimates. In order to use the historical floods in formal flood frequency analysis, the precise value of the peak discharges would ideally be known, but in most of the cases, the information related to historical floods is given, quantitatively, in a non-precise manner. This work presents an approach on how to deal with the non-precise historical floods, by linking the descriptions in historical records to fuzzy numbers representing discharges. These fuzzy historical discharges are then introduced in a formal Bayesian inference framework, taking into account the arithmetics of non-precise numbers modelled by fuzzy logic theory, to obtain a fuzzy version of the flood frequency curve combining the fuzzy historical flood events and the instrumental data for a given location. Two case studies are selected from the historical literature, representing different facets of the fuzziness present in the historical sources. The results from the cases studies are given in the form of the fuzzy estimates of the flood frequency curves together with the fuzzy 5% and 95% Bayesian credibility bounds for these curves. The presented fuzzy Bayesian inference framework provides a flexible methodology to propagate in an explicit way the imprecision from the historical records into the flood frequency estimate, which allows to assess the effect that the incorporation of non-precise historical information can have in the flood frequency regime.

  17. High-precision coseismic displacement estimation with a single-frequency GPS receiver

    NASA Astrophysics Data System (ADS)

    Guo, Bofeng; Zhang, Xiaohong; Ren, Xiaodong; Li, Xingxing

    2015-07-01

    To improve the performance of Global Positioning System (GPS) in the earthquake/tsunami early warning and rapid response applications, minimizing the blind zone and increasing the stability and accuracy of both the rapid source and rupture inversion, the density of existing GPS networks must be increased in the areas at risk. For economic reasons, low-cost single-frequency receivers would be preferable to make the sparse dual-frequency GPS networks denser. When using single-frequency GPS receivers, the main problem that must be solved is the ionospheric delay, which is a critical factor when determining accurate coseismic displacements. In this study, we introduce a modified Satellite-specific Epoch-differenced Ionospheric Delay (MSEID) model to compensate for the effect of ionospheric error on single-frequency GPS receivers. In the MSEID model, the time-differenced ionospheric delays observed from a regional dual-frequency GPS network to a common satellite are fitted to a plane rather than part of a sphere, and the parameters of this plane are determined by using the coordinates of the stations. When the parameters are known, time-differenced ionospheric delays for a single-frequency GPS receiver could be derived from the observations of those dual-frequency receivers. Using these ionospheric delay corrections, coseismic displacements of a single-frequency GPS receiver can be accurately calculated based on time-differenced carrier-phase measurements in real time. The performance of the proposed approach is validated using 5 Hz GPS data collected during the 2012 Nicoya Peninsula Earthquake (Mw 7.6, 2012 September 5) in Costa Rica. This shows that the proposed approach improves the accuracy of the displacement of a single-frequency GPS station, and coseismic displacements with an accuracy of a few centimetres are achieved over a 10-min interval.

  18. Estimation of the whole-body averaged SAR of grounded human models for plane wave exposure at respective resonance frequencies.

    PubMed

    Hirata, Akimasa; Yanase, Kazuya; Laakso, Ilkka; Chan, Kwok Hung; Fujiwara, Osamu; Nagaoka, Tomoaki; Watanabe, Soichi; Conil, Emmanuelle; Wiart, Joe

    2012-12-21

    According to the international guidelines, the whole-body averaged specific absorption rate (WBA-SAR) is used as a metric of basic restriction for radio-frequency whole-body exposure. It is well known that the WBA-SAR largely depends on the frequency of the incident wave for a given incident power density. The frequency at which the WBA-SAR becomes maximal is called the 'resonance frequency'. Our previous study proposed a scheme for estimating the WBA-SAR at this resonance frequency based on an analogy between the power absorption characteristic of human models in free space and that of a dipole antenna. However, a scheme for estimating the WBA-SAR in a grounded human has not been discussed sufficiently, even though the WBA-SAR in a grounded human is larger than that in an ungrounded human. In this study, with the use of the finite-difference time-domain method, the grounded condition is confirmed to be the worst-case exposure for human body models in a standing posture. Then, WBA-SARs in grounded human models are calculated at their respective resonant frequencies. A formula for estimating the WBA-SAR of a human standing on the ground is proposed based on an analogy with a quarter-wavelength monopole antenna. First, homogenized human body models are shown to provide the conservative WBA-SAR as compared with anatomically based models. Based on the formula proposed here, the WBA-SARs in grounded human models are approximately 10% larger than those in free space. The variability of the WBA-SAR was shown to be ±30% even for humans of the same age, which is caused by the body shape. PMID:23202273

  19. Multiple Input Design for Real-Time Parameter Estimation in the Frequency Domain

    NASA Technical Reports Server (NTRS)

    Morelli, Eugene

    2003-01-01

    A method for designing multiple inputs for real-time dynamic system identification in the frequency domain was developed and demonstrated. The designed inputs are mutually orthogonal in both the time and frequency domains, with reduced peak factors to provide good information content for relatively small amplitude excursions. The inputs are designed for selected frequency ranges, and therefore do not require a priori models. The experiment design approach was applied to identify linear dynamic models for the F-15 ACTIVE aircraft, which has multiple control effectors.

  20. Time-Frequency Mixed-Norm Estimates: Sparse M/EEG imaging with non-stationary source activations

    PubMed Central

    Gramfort, A.; Strohmeier, D.; Haueisen, J.; Hämäläinen, M.; Kowalski, M.

    2013-01-01

    Magnetoencephalography (MEG) and electroencephalography (EEG) allow functional brain imaging with high temporal resolution. While solving the inverse problem independently at every time point can give an image of the active brain at every millisecond, such a procedure does not capitalize on the temporal dynamics of the signal. Linear inverse methods (Minimum-norm, dSPM, sLORETA, beamformers) typically assume that the signal is stationary: regularization parameter and data covariance are independent of time and the time varying signal-to-noise ratio (SNR). Other recently proposed non-linear inverse solvers promoting focal activations estimate the sources in both space and time while also assuming stationary sources during a time interval. However such an hypothesis only holds for short time intervals. To overcome this limitation, we propose time-frequency mixed-norm estimates (TF-MxNE), which use time-frequency analysis to regularize the ill-posed inverse problem. This method makes use of structured sparse priors defined in the time-frequency domain, offering more accurate estimates by capturing the non-stationary and transient nature of brain signals. State-of-the-art convex optimization procedures based on proximal operators are employed, allowing the derivation of a fast estimation algorithm. The accuracy of the TF-MxNE is compared to recently proposed inverse solvers with help of simulations and by analyzing publicly available MEG datasets. PMID:23291276

  1. Full Bayes Poisson gamma, Poisson lognormal, and zero inflated random effects models: Comparing the precision of crash frequency estimates.

    PubMed

    Aguero-Valverde, Jonathan

    2013-01-01

    In recent years, complex statistical modeling approaches have being proposed to handle the unobserved heterogeneity and the excess of zeros frequently found in crash data, including random effects and zero inflated models. This research compares random effects, zero inflated, and zero inflated random effects models using a full Bayes hierarchical approach. The models are compared not just in terms of goodness-of-fit measures but also in terms of precision of posterior crash frequency estimates since the precision of these estimates is vital for ranking of sites for engineering improvement. Fixed-over-time random effects models are also compared to independent-over-time random effects models. For the crash dataset being analyzed, it was found that once the random effects are included in the zero inflated models, the probability of being in the zero state is drastically reduced, and the zero inflated models degenerate to their non zero inflated counterparts. Also by fixing the random effects over time the fit of the models and the precision of the crash frequency estimates are significantly increased. It was found that the rankings of the fixed-over-time random effects models are very consistent among them. In addition, the results show that by fixing the random effects over time, the standard errors of the crash frequency estimates are significantly reduced for the majority of the segments on the top of the ranking. PMID:22633143

  2. Estimation of ground range on the sweep frequency backscatter leading edge

    NASA Astrophysics Data System (ADS)

    Su, Fanfan; Zhao, Zhengyu; Deng, Feng; Li, Shipeng

    2011-04-01

    The high frequency management system with backscatter radar supplies the real time ionosphere channel conditions to high frequency users, which leads to the demand for the ground range between the radar location and the scatters on the distant ground. The ionosphere electron density profile is usually inversed to obtain the ground range. An inversion algorithm, with which the ground range on the leading edge of the backscatter ionograms can be obtained without electron density, is presented in this paper. The ray path geometry of the backscatter sounding and the change in the group path on the leading edge with operating frequency are used to derive the ground range. Synthesized backscatter ionogram and experimental backscatter ionograms are processed to validate the algorithm. The results indicate that the algorithm is usable for high frequency management system.

  3. Estimation of Failure Frequency for Type I and II High Level Waste Tanks

    SciTech Connect

    Subramanian, K.H.

    2001-05-15

    The failure frequency of Type I and Type II High Level Waste tanks was calculated. The degradation mechanism that could lead to large break failure and the credits taken for steps taken to prevent large break failure were considered.

  4. Shear Wave Splitting Analysis to Estimate Fracture Orientation and Frequency Dependent Anisotropy

    NASA Astrophysics Data System (ADS)

    Gholami, Raoof; Moradzadeh, Ali; Rasouli, Vamegh; Hanachi, Javid

    2016-02-01

    Shear wave splitting is a well-known method for indication of orientation, radius, and length of fractures in subsurface layers. In this paper, a three component near offset VSP data acquired from a fractured sandstone reservoir in southern part of Iran was used to analyse shear wave splitting and frequency-dependent anisotropy assessment. Polarization angle obtained by performing rotation on radial and transverse components of VSP data was used to determine the direction of polarization of fast shear wave which corresponds to direction of fractures. It was shown that correct implementation of shear wave splitting analysis can be used for determination of fracture direction. During frequency-dependent anisotropy analysis, it was found that the time delays in shear-waves decrease as the frequency increases. It was clearly demonstrated throughout this study that anisotropy may have an inverse relationship with frequency. The analysis presented in this paper complements the studied conducted by other researchers in this field of research.

  5. Improved frequency and time of arrival estimation methods in search and rescue system based on MEO satellites

    NASA Astrophysics Data System (ADS)

    Lin, Mo; Li, Rui; Li, Jilin

    2007-11-01

    This paper deals with several key points including parameter estimation such as frequency of arrival (FOA), time of arrival (TOA) estimation algorithm and signal processing techniques in Medium-altitude Earth Orbit Local User Terminals (MEOLUT) based on Cospas-Sarsat Medium-altitude Earth Orbit Search and Rescue system (MEOSAR). Based on an analytical description of distress beacon, improved TOA and FOA estimation methods have been proposed. An improved FOA estimation method which integrates bi-FOA measurement, FFT method, Rife algorithm and Gaussian window is proposed to improve the accuracy of FOA estimation. In addition, TPD algorithm and signal correlation techniques are used to achieve a high performance of TOA estimation. Parameter estimation problems are solved by proposed FOA/TOA methods under quite poor Carrier-to-Noise (C/N0). A number of simulations are done to show the improvements. FOA and TOA estimation error are lower than 0.1Hz and 11μs respectively which is very high system requirement for MEOSAR system MEOLUT.

  6. Power spectral density estimation by spline smoothing in the frequency domain

    NASA Technical Reports Server (NTRS)

    Defigueiredo, R. J. P.; Thompson, J. R.

    1972-01-01

    An approach, based on a global averaging procedure, is presented for estimating the power spectrum of a second order stationary zero-mean ergodic stochastic process from a finite length record. This estimate is derived by smoothing, with a cubic smoothing spline, the naive estimate of the spectrum obtained by applying FFT techniques to the raw data. By means of digital computer simulated results, a comparison is made between the features of the present approach and those of more classical techniques of spectral estimation.

  7. Power spectral density estimation by spline smoothing in the frequency domain.

    NASA Technical Reports Server (NTRS)

    De Figueiredo, R. J. P.; Thompson, J. R.

    1972-01-01

    An approach, based on a global averaging procedure, is presented for estimating the power spectrum of a second order stationary zero-mean ergodic stochastic process from a finite length record. This estimate is derived by smoothing, with a cubic smoothing spline, the naive estimate of the spectrum obtained by applying Fast Fourier Transform techniques to the raw data. By means of digital computer simulated results, a comparison is made between the features of the present approach and those of more classical techniques of spectral estimation.-

  8. Dynamics of Neutral and Selected Alleles When the Offspring Distribution Is Skewed

    PubMed Central

    Der, Ricky; Epstein, Charles; Plotkin, Joshua B.

    2012-01-01

    We analyze the dynamics of two alternative alleles in a simple model of a population that allows for large family sizes in the distribution of offspring number. This population model was first introduced by Eldon and Wakeley, who described the backward-time genealogical relationships among sampled individuals, assuming neutrality. We study the corresponding forward-time dynamics of allele