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Sample records for allele frequency ranged

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

    PubMed

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

    2009-01-01

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

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

    PubMed

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

    2015-04-30

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

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

    PubMed

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

    2014-04-22

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

  4. Frequency of FCGR3B Alleles in Thai Blood Donors

    PubMed Central

    Kaset, Chollanot; Leetrakool, Nipapan; Intharanut, Kamphon

    2013-01-01

    Background Human neutrophil antigens (HNAs) are involved in autoimmune and alloimmune neutropenia and transfusion-related acute lung injury. The HNA-1 system is important in immunogenetics, and allele frequencies have been described in different populations. This study investigated the frequency of FCGR3B alleles encoding HNA-1a, HNA-1b, and HNA-1c among Thai blood donors and compared these frequencies with those previously reported for other populations. Methods Eight hundred DNA samples obtained from unrelated healthy blood donors at the National Blood Centre, Thai Red Cross Society, Bangkok, and the Blood Bank, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand, were included. Samples were simultaneously typed for each FCGR3B allele using an in-house polymerase chain reaction with sequence-specific primer (PCR-SSP) technique. Results The frequencies of FCGR3B*1, FCGR3B*2, and FCGR3B*3 alleles in central Thai blood donors were 0.548, 0.452, and 0.004, respectively; only FCGR3B*1 and FCGR3B*2 alleles were found in northern Thai blood donors (0.68 and 0.32, respectively). Compared with other Asian populations, central Thais had higher frequencies of the FCGR3B*2 allele (P<0.001), while the frequencies of the FCGR3B*1 and FCGR3B*2 alleles in northern Thais were similar to those previously reported in Taiwanese and Japanese populations. In contrast, the frequencies of the FCGR3B*1 and FCGR3B*2 alleles in the northern Thai population were statistically different from those observed in central Thai, Korean, German, and Turkish populations. Conclusions FCGR3B allele frequencies were significantly different between central and northern Thai blood donors. Our in-house PCR-SSP method is a simple, cost-effective, and convenient method for FCGR3B allele detection. PMID:24205492

  5. 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).

  6. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

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

  7. Allele Frequencies at Microsatellite Loci: The Stepwise Mutation Model Revisited

    PubMed Central

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

    1993-01-01

    We 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. We 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. We show 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. PMID:8454213

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-02

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

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

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2010-12-01

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

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

    PubMed

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

    2013-01-01

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

  11. 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

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

    PubMed

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

    2014-03-01

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

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

    SciTech Connect

    Sachse, C.; Brockmoeller, J.; Bauer, S.; Roots, I.

    1997-02-01

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

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

    PubMed Central

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

    2011-01-01

    Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft’s PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding. PMID:21113021

  15. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

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

    2009-04-01

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

  16. Non-Equilibrium Allele Frequency Spectra Via Spectral Methods

    PubMed Central

    Hey, Jody; Chen, Kevin

    2011-01-01

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

  17. Recovering frequencies of known haplotype blocks from single-nucleotide polymorphism allele frequencies.

    PubMed Central

    Pe'er, Itsik; Beckmann, Jacques S

    2004-01-01

    Prospects for large-scale association studies rely on economical methods and powerful analysis. Representing available SNPs by small subsets and measuring allele frequencies on pooled DNA samples each improve genotyping cost effectiveness, while haplotype analysis may highlight associations in otherwise underpowered studies. This manuscript provides the mathematical framework to integrate these methodologies. PMID:15126415

  18. Distribution of BoLA-DRB3 allelic frequencies and identification of two new alleles in Iranian buffalo breed.

    PubMed

    Mosafer, J; Heydarpour, M; Manshad, E; Russell, G; Sulimova, G E

    2012-01-01

    The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found.

  19. Distribution of BoLA-DRB3 Allelic Frequencies and Identification of Two New Alleles in Iranian Buffalo Breed

    PubMed Central

    Mosafer, J.; Heydarpour, M.; Manshad, E.; Russell, G.; Sulimova, G. E.

    2012-01-01

    The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found. PMID:22454612

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

    PubMed

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

    2009-11-01

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

  1. 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

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

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

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

  3. 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

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

    PubMed

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

    2011-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2014-10-01

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

  7. 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...

  8. Determination of allele frequency in pooled DNA: comparison of three PCR-based methods.

    PubMed

    Wilkening, Stefan; Hemminki, Kari; Thirumaran, Ranjit Kumar; Bermejo, Justo Lorenzo; Bonn, Stefan; Försti, Asta; Kumar, Rajiv

    2005-12-01

    Determination of allele frequency in pooled DNA samples is a powerful and efficient tool for large-scale association studies. In this study, we tested and compared three PCR-based methods for accuracy, reproducibility, cost, and convenience. The methods compared were: (i) real-time PCR with allele-specific primers, (ii) real-time PCR with allele-specific TaqMan probes, and (iii) quantitative sequencing. Allele frequencies of three single nucleotide polymorphisms in three different genes were estimated from pooled DNA. The pools were made of genomic DNA samples from 96 cases with basal cell carcinoma of the skin and 96 healthy controls with known genotypes. In this study, the allele frequency estimation made by real-time PCR with allele-specific primers had the smallest median deviation (MD) from the real allele frequency with 1.12% (absolute percentage points) and was also the cheapest method. However; this method required the most time for optimization and showed the highest variation between replicates (SD = 6.47%). Quantitative sequencing, the simplest method, was found to have intermediate accuracies (MD = 1.44%, SD = 4.2%). Real-time PCR with TaqMan probes, a convenient but very expensive method, had an MD of 1.47% and the lowest variation between replicates (SD = 3.18%).

  9. Frequency of the delta ccr5 deletion allele in the urban Brazilian population.

    PubMed

    Passos, G A; Picanço, V P

    1998-04-01

    Studies on screening genes conferring resistance to HIV-1 and AIDS onset have shown a direct relationship between a 32 base pair (bp) deletion in the CCR5 beta-chemokine receptor gene (delta ccr5 mutant allele) and long survival of HIV-1 infected individuals bearing this mutation. These findings led to an interest in studies of delta ccr5 allele distribution in human populations. In the present study, polymerase chain reactions (PCR) in genomic DNA samples, using specific CCR5 oligonucleotide primers surrounding the breakpoint deletion, detected a 193-bp product from the normal CCR5 allele and a 161-bp product from the 32-bp deletion allele. In an investigation of the urban Brazilian population we detected a 93% frequency of normal CCR5/CCR5 homozygous individuals and a 7% frequency of CCR5/delta ccr5 heterozygous individuals. The frequency of the delta ccr5 mutant allele in this population is 0.035; however, no homozygous delta ccr5 individual has been detected thus far. This is the first evidence for the contribution of the delta ccr5 allele to the genetic background of the urban Brazilian population, which is characterized by intense ethnic admixture. These findings open perspectives for further studies on the relationship between delta ccr5 allele frequency and AIDS onset in high-risk HIV-1 exposures individuals.

  10. Estimating Selection Coefficients in Spatially Structured Populations from Time Series Data of Allele Frequencies

    PubMed Central

    Mathieson, Iain; McVean, Gil

    2013-01-01

    Inferring the nature and magnitude of selection is an important problem in many biological contexts. Typically when estimating a selection coefficient for an allele, it is assumed that samples are drawn from a panmictic population and that selection acts uniformly across the population. However, these assumptions are rarely satisfied. Natural populations are almost always structured, and selective pressures are likely to act differentially. Inference about selection ought therefore to take account of structure. We do this by considering evolution in a simple lattice model of spatial population structure. We develop a hidden Markov model based maximum-likelihood approach for estimating the selection coefficient in a single population from time series data of allele frequencies. We then develop an approximate extension of this to the structured case to provide a joint estimate of migration rate and spatially varying selection coefficients. We illustrate our method using classical data sets of moth pigmentation morph frequencies, but it has wide applications in settings ranging from ecology to human evolution. PMID:23307902

  11. High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR

    PubMed Central

    Germer, Søren; Holland, Michael J.; Higuchi, Russell

    2000-01-01

    We have developed an accurate, yet inexpensive and high-throughput, method for determining the allele frequency of biallelic polymorphisms in pools of DNA samples. The assay combines kinetic (real-time quantitative) PCR with allele-specific amplification and requires no post-PCR processing. The relative amounts of each allele in a sample are quantified. This is performed by dividing equal aliquots of the pooled DNA between two separate PCR reactions, each of which contains a primer pair specific to one or the other allelic SNP variant. For pools with equal amounts of the two alleles, the two amplifications should reach a detectable level of fluorescence at the same cycle number. For pools that contain unequal ratios of the two alleles, the difference in cycle number between the two amplification reactions can be used to calculate the relative allele amounts. We demonstrate the accuracy and reliability of the assay on samples with known predetermined SNP allele frequencies from 5% to 95%, including pools of both human and mouse DNAs using eight different SNPs altogether. The accuracy of measuring known allele frequencies is very high, with the strength of correlation between measured and known frequencies having an r2 = 0.997. The loss of sensitivity as a result of measurement error is typically minimal, compared with that due to sampling error alone, for population samples up to 1000. We believe that by providing a means for SNP genotyping up to thousands of samples simultaneously, inexpensively, and reproducibly, this method is a powerful strategy for detecting meaningful polymorphic differences in candidate gene association studies and genome-wide linkage disequilibrium scans. PMID:10673283

  12. Statistical Inference in the Wright-Fisher Model Using Allele Frequency Data.

    PubMed

    Tataru, Paula; Simonsen, Maria; Bataillon, Thomas; Hobolth, Asger

    2016-08-02

    The Wright-Fisher model provides an elegant mathematical framework for understanding allele frequency data. In particular, the model can be used to infer the demographic history of species and identify loci under selection. A crucial quantity for inference under the Wright-Fisher model is the distribution of allele frequencies (DAF). Despite the apparent simplicity of the model, the calculation of the DAF is challenging. We review and discuss strategies for approximating the DAF, and how these are used in methods that perform inference from allele frequency data. Various evolutionary forces can be incorporated in the Wright-Fisher model, and we consider these in turn. We begin our review with the basic bi-allelic Wright-Fisher model where random genetic drift is the only evolutionary force. We then consider mutation, migration, and selection. In particular, we compare diffusion-based and moment-based methods in terms of accuracy, computational efficiency, and analytical tractability. We conclude with a brief overview of the multi-allelic process with a general mutation model. [Allele frequency, diffusion, inference, moments, selection, Wright-Fisher.].

  13. Predictive long-range allele-specific mapping of regulatory variants and target transcripts.

    PubMed

    Lee, Kibaick; Lee, Seulkee; Bang, Hyoeun; Choi, Jung Kyoon

    2017-01-01

    Genome-wide association studies (GWASs) have identified a large number of noncoding associations, calling for systematic mapping to causal regulatory variants and their distal target genes. A widely used method, quantitative trait loci (QTL) mapping for chromatin or expression traits, suffers from sample-to-sample experimental variation and trans-acting or environmental effects. Instead, alleles at heterozygous loci can be compared within a sample, thereby controlling for those confounding factors. Here we introduce a method for chromatin structure-based allele-specific pairing of regulatory variants and target transcripts. With phased genotypes, much of allele-specific expression could be explained by paired allelic cis-regulation across a long range. This approach showed approximately two times greater sensitivity than QTL mapping. There are cases in which allele imbalance cannot be tested because heterozygotes are not available among reference samples. Therefore, we employed a machine learning method to predict missing positive cases based on various features shared by observed allele-specific pairs. We showed that only 10 reference samples are sufficient to achieve high prediction accuracy with a low sampling variation. In conclusion, our method enables highly sensitive fine mapping and target identification for trait-associated variants based on a small number of reference samples.

  14. Frequency of the arylsulphatase A pseudodeficiency allele in the Spanish population.

    PubMed

    Chabás, A; Castellvi, S; Bayés, M; Balcells, S; Grinberg, D; Vilageliu, L; Marfany, G; Lissens, W; Gonzàlez-Duarte, R

    1993-12-01

    Pseudodeficiency in arylsulphatase A (ASA) is a relatively frequent condition in healthy individuals. It produces a reduction in enzyme activity similar to that found in metachromatic leukodystrophy (MLD). Unambiguous discrimination between the two conditions cannot be achieved through conventional enzyme activity assays. A PCR method has been developed which detects the pseudodeficiency (pd) allele using a single pair of primers encompassing the mutation site and hair follicles as the source of DNA. The frequency of this allele in the Spanish population has been evaluated and correlations between different genotypes and ASA activity levels have been established. Ten out of 55 individuals were heterozygous for the ASA pd allele, while two were homozygous. The allele frequency was thus 12.7%.

  15. 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 ...

  16. 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.

  17. HLA-DRB1 and -DRB3 allele frequencies and haplotypic associations in Koreans.

    PubMed

    Song, Eun Young; Park, Hyejin; Roh, Eun Youn; Park, Myoung Hee

    2004-03-01

    We have investigated the frequencies of human leukocyte antigen-DRB1 (HLA-DRB1) and -DRB3 alleles and DRB1-DRB3 haplotypic associations in 800 Koreans. DRB1 genotyping was done using polymerase chain reaction-sequence-specific oligonucleotide (PCR-SSO) and PCR-single strand conformation polymorphism (SSCP) methods. DRB3 genotyping was done on 447 samples carrying DRB3-associated DRB1 alleles (DRB1*03, *11, *12, *13, and *14) using PCR-SSCP method. The allele frequencies of DRB3*0101, DRB3*0202, and DRB3*0301 were 0.073, 0.136, and 0.120, respectively, and we found one case of a probable new allele (DRB3*01new, 0.001). DRB1-DRB3 haplotypes with frequency (HF) > 0.005 exhibited strong associations between DRB3*0101 and DRB1*1201, *1301, and *1403; between DRB3*0301 and DRB1*1202 and *1302; between DRB3*0202 and DRB1*0301, *1101, *1401, *1405, and *1406 alleles. Most of the DRB1 alleles with frequency > 0.005 were exclusively associated with particular DRB3 alleles with relative linkage disequilibrium values of 1.0, except for DRB1*1201, *1202 and *1301; the rare presence (HF < 0.005) of DRB3*0202 associations were observed for these DRB1 alleles. We also investigated and presented rare DRB1-DRB3 associations in additional 6000 Koreans. Comparison with other ethnic groups revealed that DRB1*0301 and *1301 related DRB1-DRB3 haplotypes vary among different populations, in that Koreans and other Asian populations show less diversity compared with Caucasoids or African Americans.

  18. Frequency Specific Effects of ApoE ε4 Allele on Resting-State Networks in Nondemented Elders

    PubMed Central

    Liang, Ying; Li, Zhenzhen; Neuroimaging Initiative, Alzheimer's Disease

    2017-01-01

    We applied resting-state functional magnetic resonance imaging (fMRI) to examine the Apolipoprotein E (ApoE) ε4 allele effects on functional connectivity of the default mode network (DMN) and the salience network (SN). Considering the frequency specific effects of functional connectivity, we decomposed the brain network time courses into two bands: 0.01–0.027 Hz and 0.027–0.08 Hz. All scans were acquired by the Alzheimer's Disease Neuroscience Initiative (ADNI). Thirty-two nondemented subjects were divided into two groups based on the presence (n = 16) or absence (n = 16) of the ApoE ε4 allele. We explored the frequency specific effects of ApoE ε4 allele on the default mode network (DMN) and the salience network (SN) functional connectivity. Compared to ε4 noncarriers, the DMN functional connectivity of ε4 carriers was significantly decreased while the SN functional connectivity of ε4 carriers was significantly increased. Many functional connectivities showed significant differences at the lower frequency band of 0.01–0.027 Hz or the higher frequency band of 0.027–0.08 Hz instead of the typical range of 0.01–0.08 Hz. The results indicated a frequency dependent effect of resting-state signals when investigating RSNs functional connectivity.

  19. 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

  20. Using maximum likelihood to estimate population size from temporal changes in allele frequencies.

    PubMed Central

    Williamson, E G; Slatkin, M

    1999-01-01

    We develop a maximum-likelihood framework for using temporal changes in allele frequencies to estimate the number of breeding individuals in a population. We use simulations to compare the performance of this estimator to an F-statistic estimator of variance effective population size. The maximum-likelihood estimator had a lower variance and smaller bias. Taking advantage of the likelihood framework, we extend the model to include exponential growth and show that temporal allele frequency data from three or more sampling events can be used to test for population growth. PMID:10353915

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

    PubMed Central

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

    2009-01-01

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

  2. Allele and genotype frequencies of CYP2B6 in a Turkish population.

    PubMed

    Yuce-Artun, Nazan; Kose, Gulcin; Suzen, H Sinan

    2014-06-01

    Increasing interest in cytochrome P450 2B6 (CYP2B6) genetic polymorphism was stimulated by revelations of a specific CYP2B6 genotype significantly affecting the metabolism of various drugs in common clinical use in terms of increasing drug efficacy and avoiding adverse drug reactions. The present study aimed to determine the frequencies of CYP2B6*4 CYP2B6*5, CYP2B6*6, CYP2B6*7 and CYP2B6*9 alleles in healthy Turkish individuals (n = 172). Frequencies of three single nucleotide polymorphisms were 516G>T (28%), 785A>G (33%), and 1459C>T (12%). The frequencies of CYP2B6*1, *4, *5, *6, *7, and *9 alleles were 54.3 (95% CI 49.04-59.56), 6.4% (95% CI 3.81-8.99), 11% (95% CI 7.69-14.31), 25.3% (95% CI 20.71-29.89), 0.87% (95% CI -0.11-1.85) and 2.0% (95% CI 0.52-3.48), respectively. Allele *6 was more frequent (25.3%) than the other variant alleles in Turkish subjects. The frequencies of CYP2B6*4, *5, *6, *7, and *9 alleles were similar to European populations but significantly different from that reported for Asian populations. This is the first study to document the frequencies of the CYP2B6*4, *5, *6, *7, *9 alleles in the healthy Turkish individuals and our results could provide clinically useful information on drug metabolism by CYP2B6 in Turkish population.

  3. HLA-DRB and HLA-DQB Allele and Haplotype Frequencies in Iranian Patients with Recurrent Aphthous Stomatitis.

    PubMed

    Najafi, Shamsolmoulouk; Mohammadzadeh, Mahsa; Zare Bidoki, Alireza; Meighani, Ghasem; Aslani, Saeed; Mahmoudi, Mahdi; Rezaei, Nima

    Recurrent aphthous stomatitis (RAS) is known as the most common chronic disease of the oral cavity, which affects a range of 5-25% of the population. RAS appears to be associated with some human leukocyte antigen (HLA) class II alleles and haplotypes. This study attempts to survey the distribution of HLA-DRB and -DQB alleles among Iranian RAS patients and healthy controls. In order to evaluate the association of HLA-DR and DQ alleles and haplotypes, 54 patients with RAS and 100 unrelated healthy subjects as control group were investigated. Our data indicated that DRB1*13:17, DRB1*15:01, and DRB5*01 were significantly more frequent in RAS patients in comparison to controls. However, DRB3:01allele frequency was higher in the controls compared to the patients. The significantly frequent allele in the patients compared with the healthy subjects was HLA-DQB1*03:02. However, both HLA-DQB1*02:01 and HLA-DQB1*03:01 alleles were most frequent in the healthy individuals rather than the patients. The DRB*04/DQB1*03:01 and DRB*01:01/DQB1*02:01 haplotypes were significantly distributed in healthy subjects compared with patients. However, DRB*07:01/DQB1*03:02 haplotype was found to be significantly frequent in patients than controls. In respect of HLA genes, factors are involved in the incidence of RAS; various HLA-DRB and HLA-DQB1 alleles and the related haplotypes are suggested to be the three main RAS susceptibility factors in our population study.

  4. Resistance allele frequency to bt cotton in field populations of helicoverpa armigera (Lepidoptera: Noctuidae) in China.

    PubMed

    Liu, Fengyi; Xu, Zhiping; Chang, Juhua; Chen, Jin; Meng, Fengxia; Zhu, Yu Cheng; Shen, Jinliang

    2008-06-01

    Resistance evolution in target insects to Bacillus thurningiensis (Bt) cotton, Gossypium hirsutum L., is a main threat to Bt cotton technology. An increasing trend of population density of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) has been observed since 2001 in Qiuxian County (Hebei, China), where Bt cotton has been planted dominantly since 1998. This region was selected in 2006 and 2007 for estimating frequency of gene alleles conferring resistance to Bt cotton by screening the F1 progeny from single-pair cross between field-collected male and laboratory female of the Bt-resistant strain of H. armigera (F1 screen). F1 offspring from each single-pair line were screened for resistance alleles based on larval growth, development, and survival on Bt cotton leaves for 5 d. Two-year results indicated that approximately equal to 20% of field-collected males carried resistance alleles. The conservative estimate of the resistance allele frequency was 0.094 (95% CI, 0.044-0.145) for 2006 and 0.107 (95% CI, 0.055-0.159) for 2007. This is the first report of resistance allele frequency increase to such a high level in the field in China. Long-term adoption of Bt sprays, dominant planting of single-toxin-producing Bt cotton, and lack of conventional cotton refuge system might accelerate the resistance evolution in the region.

  5. 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

  6. Estimation of the frequency of hexosaminidase a variant alleles in the American Jewish population.

    PubMed

    Greenberg, D A; Kaback, M M

    1982-05-01

    There appear to be several alleles of the hexosaminidase A (HEX A) gene that lead to different clinical syndromes. In addition to the infantile-onset Tay-Sachs disease (TSD), there is a juvenile-onset and an adult-onset form, which are also characterized by low HEX A levels. There are also apparently healthy adults with low HEX A activity. Based primarily on data from population screening for TSD carrier status, we estimate the allele frequency of the combined variant alleles for which data are available to be about 4.5 x 10(-4) and the frequency of adults showing zero HEX A levels (when tested using artificial substrate) to be about 1:67,000. The implications for population screening and prenatal diagnosis are discussed.

  7. Monooxygenase Levels and Knockdown Resistance (kdr) Allele Frequencies in Anopheles gambiae and Anopheles arabiensis in Kenya

    PubMed Central

    Chen, Hong; Githeko, Andrew K; Githure, John I; Mutunga, James; Zhou, Guofa; Yan, Guiyun

    2013-01-01

    Pyrethroid-treated bed nets and indoor spray are important components of malaria control strategies in Kenya. Information on resistance to pyrethroid insecticides in Anopheles gambiae and An. arabiensis populations is essential to the selection of appropriate insecticides and the management of insecticide resistance. Monooxygenase activity and knockdown resistance (kdr) allele frequency are biochemical and molecular indicators of mosquito resistance to pyrethroids. This study determined baseline information on monooxygenase activity and kdr allele frequency in anopheline mosquitoes in the western region, the Great Rift Valley-central province region, and the coastal region of Kenya. A total of 1990 field-collected individuals, representing 12 An. gambiae and 22 An. arabiensis populations was analyzed. We found significant among-population variation in monooxygenase activity in An. gambiae and An. arabiensis and substantial variability among individuals within populations. Nine out of 12 An. gambiae populations exhibited significantly higher average monooxygenase activity than the susceptible Kisumu reference strain. The kdr alleles (L1014S) were detected in three An. gambiae populations, and one An. arabiensis population in western Kenya, but not in the Rift Valley-central region and the coastal Kenya region. All genotypes with the kdr alleles were heterozygous, and the conservative estimation of kdr allele frequency was below 1% in these four populations. Information on monooxygenase activity and kdr allele frequency reported in this study provided baseline data for monitoring insecticide resistance changes in Kenya during the era when large-scale insecticide-treated bednet and indoor residual spray campaigns were being implemented. PMID:18402140

  8. Genome Wide Allele Frequency Fingerprints (GWAFFs) of Populations via Genotyping by Sequencing

    PubMed Central

    Byrne, Stephen; Czaban, Adrian; Studer, Bruno; Panitz, Frank; Bendixen, Christian; Asp, Torben

    2013-01-01

    Genotyping-by-Sequencing (GBS) is an excellent tool for characterising genetic variation between plant genomes. To date, its use has been reported only for genotyping of single individuals. However, there are many applications where resolving allele frequencies within populations on a genome-wide scale would be very powerful, examples include the breeding of outbreeding species, varietal protection in outbreeding species, monitoring changes in population allele frequencies. This motivated us to test the potential to use GBS to evaluate allele frequencies within populations. Perennial ryegrass is an outbreeding species, and breeding programs are based upon selection on populations. We tested two restriction enzymes for their efficiency in complexity reduction of the perennial ryegrass genome. The resulting profiles have been termed Genome Wide Allele Frequency Fingerprints (GWAFFs), and we have shown how these fingerprints can be used to distinguish between plant populations. Even at current costs and throughput, using sequencing to directly evaluate populations on a genome-wide scale is viable. GWAFFs should find many applications, from varietal development in outbreeding species right through to playing a role in protecting plant breeders’ rights. PMID:23469194

  9. 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

    2016-03-08

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

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

    PubMed

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

    2012-05-01

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

  11. The genetic signature of rapid range expansions: How dispersal, growth and invasion speed impact heterozygosity and allele surfing.

    PubMed

    Goodsman, Devin W; Cooke, Barry; Coltman, David W; Lewis, Mark A

    2014-12-01

    As researchers collect spatiotemporal population and genetic data in tandem, models that connect demography and dispersal to genetics are increasingly relevant. The dominant spatiotemporal model of invasion genetics is the stepping-stone model which represents a gradual range expansion in which individuals jump to uncolonized locations one step at a time. However, many range expansions occur quickly as individuals disperse far from currently colonized regions. For these types of expansion, stepping-stone models are inappropriate. To more accurately reflect wider dispersal in many organisms, we created kernel-based models of invasion genetics based on integrodifference equations. Classic theory relating to integrodifference equations suggests that the speed of range expansions is a function of population growth and dispersal. In our simulations, populations that expanded at the same speed but with spread rates driven by dispersal retained more heterozygosity along axes of expansion than range expansions with rates of spread that were driven primarily by population growth. To investigate surfing we introduced mutant alleles in wave fronts of simulated range expansions. In our models based on random mating, surfing alleles remained at relatively low frequencies and surfed less often compared to previous results based on stepping-stone simulations with asexual reproduction.

  12. Distribution of BoLA-DRB3 allelic frequencies and identification of a new allele in the iranian cattle breed sistani (Bos indicus).

    PubMed

    Mohammadi, A; Nassiry, M R; Mosafer, J; Mohammadabadi, M R; Sulimova, G E

    2009-02-01

    The distribution of the frequencies of BoLA-DRB3 gene alleles in the Iranian cattle breed Sistani was studied by the PCR-RFLP ("hemi-nested") assay using restriction endonucleases RsaI, HaeIII and BstYI. In the examined cattle breed (65 animals) 32 alleles have been identified one of which being described for the first time (6.15% frequency). The nucleotide sequence of the polymorphic region of exon 2 of this allele has been determined and submitted in the GeneBank database under accession number DQ486519. The submitted sequence has maximum homology (92%) with the previously described sequence DRB3-mRNA from Bos indicus (AccN X79346) and differs from it by 24 nucleotide substitutions which result in 16 amino acid substitutions. The peptide (on the basis of the reconstructed amino acid sequence) has 89% identity to the sequence encoded by the BIDRBF 188 locus (Bos indicus). The results obtained permit the sequence described by us to be considered as a new allele of the BoLA-DRB3 gene (DRB3.2**X). The total frequency of the main six alleles (DRB3.2*X, *10, *11, *20, *34 and *X) occurring with a frequency of over 5% is about 60% in Iranian Sistani cattle. Fifteen alleles have <1% frequency. The highest frequency was observed for DRB3.2*8 allele (21.54%) like in other previously described breeds of Bos indicus (up to 23.07%). The Iranian breed Sistani has a high level of similarity by the spectrum of BoLA-DRB3 alleles and their frequencies to other Bos indicus breeds and significantly differs by these criteria from the Bos taurus breeds. The Iranian Sistani herd under study includes alleles associated with to resistance to leukemia (DRB3.2*ll and *23) and to different forms of mastitis (DRB3.2*2, *7, *11, *23 and *24) although their frequencies are low (from 0.77 to 5.37%). On the whole, a high level of diversity of BoLA-DRB3 gene alleles and the availability of alleles associated with resistance to different diseases makes this breed of interest for breeding practice.

  13. Determination of arylsulfatase A pseudodeficiency allele and haplotype frequency in the Tunisian population.

    PubMed

    Ben Halim, Nizar; Dorboz, Imen; Kefi, Rym; Kharrat, Najla; Eymard-Pierre, Eleonore; Nagara, Majdi; Romdhane, Lilia; Ben Alaya-Bouafif, Nissaf; Rebai, Ahmed; Miladi, Najoua; Boespflug-Tanguy, Odile; Abdelhak, Sonia

    2016-03-01

    Arylsulfatase A (ASA) is a lysosomal enzyme involved in the catabolism of cerebroside sulfate. ASA deficiency is associated with metachromatic leukodystrophy (MLD). Low ASA activities have also been reported in a more common condition with no apparent clinical consequences termed ASA pseudo-deficiency (ASA-PD) which is associated with two linked mutations in the ASA gene (c.1049A>G and c.*96A>G). This study aimed to investigate the frequency of the two ASA-PD variants and their linkage disequilibrium (LD) among Tunisians. ASA-PD variants were detected in 129 healthy Tunisians and their frequencies were compared to those described worldwide. The frequency of the PD allele was estimated at 17.4% for the overall sample, with c.1049A>G and c.*96A>G frequencies of 25.6 and 17.4%, respectively. This study also revealed a high LD between the two ASA-PD variants (r(2) = 0.61). Inter-population analysis revealed similarities in the ASA-PD genetic structure between Tunisians and populations from Middle East with c.*96A>G frequencies being the highest in the world. A significant North vs. South genetic differentiation in the ASA-PD frequency was also observed in Tunisian population who seems genetically intermediate between Africans, Middle-Easterners and Europeans. This is the first report on the allele frequency of the ASA-PD in North Africa, revealing a relatively high frequency of the PD allele among Tunisians. This study gives also evidence on the importance of discriminating ASA-PD allele from pathological mutations causing MLD and supporting enzymatic activity testing with both sulfatiduria determination and genetic testing in the differential diagnosis of MLD in the Tunisian population.

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

    PubMed Central

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

    2016-01-01

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

  15. Allele specific-PCR and melting curve analysis showed relatively high frequency of β-casein gene A1 allele in Iranian Holstein, Simmental and native cows.

    PubMed

    Gholami, M; Hafezian, S H; Rahimi, G; Farhadi, A; Rahimi, Z; Kahrizi, D; Kiani, S; Karim, H; Vaziri, S; Muhammadi, S; Veisi, F; Ghadiri, K; Shetabi, H; Zargooshi, J

    2016-10-31

    There are two allelic forms of A1 and A2 of β-casein gene in dairy cattle. Proteolytic digestion of bovine β-casein A1 type produces bioactive peptide of β-casomorphin-7 known as milk devil. β-casomorphin-7 causes many diseases, including type 1 diabetes, cardiovascular disease syndrome, sudden death and madness. The aim of the present study was to determine the different allelic forms of β-casein gene in Iranian Holstein, Simmental and native cattle in order to identify A1 and A2 variants. The blood samples were collected randomly and DNA was extracted using modified salting out method. An 854 bp fragment including part of exon 7 and part of intron 6 of β-casein gene was amplified by allele specific polymerase chain reaction (AS-PCR). Also, the accuracy of AS-PCR genotyping has been confirmed by melting temperature curve analysis using Real-time PCR machinery. The comparison of observed allele and genotype frequency among the studied breeds was performed using the Fisher exact and Chi-squared test, respectively by SAS program. Obtained results showed the A1 allele frequencies of 50, 51.57, 54.5, 49.4 and 46.6% in Holstein, Simmental, Sistani, Taleshi and Mazandarani cattle populations, respectively. The chi-square test was shown that no any populations were in Hardy-Weinberg equilibrium for studied marker locus. Comparison and analysis of the test results for allelic frequency showed no any significant differences between breeds (P>0.05). The frequency of observed genotypes only differs significantly between Holstein and Taleshi breeds but no any statistically significant differences were found for other breeds (P>0.05). A relatively high frequency of β-casein A1 allele was observed in Iranian native cattle. Therefore, determine the genotypes and preference alleles A2 in these native and commercial cattle is recommended.

  16. Allele frequencies of microsatellite loci for genetic characterization of a Sicilian bovine population.

    PubMed

    Cosenza, M; Reale, S; Lupo, T; Vitale, F; Caracappa, S

    2015-01-30

    Short tandem repeats are used as an effective method to trace DNA markers in genotyping. Using a standardized kit, we tested 11 microsatellite markers recommended by the International Society for Animal Genetics (ISAG) in a sample of 495 Sicilian cattle. The aim of this study was to investigate the allele frequencies in the Sicilian cattle population to provide a reference database and at the same time to assess the use of the ISAG microsatellite panel for pedigree analysis. DNA samples were collected from blood and amplified in an 11-plex polymerase chain reaction (PCR); PCR products were injected in a 3130 Genetic Analyzer. All loci showed high mean polymorphism information content (0.768), and the observed mean heterozygosity was less than the expected value (0.732 vs 0.794, respectively). The exact test for Hardy-Weinberg proportions, allele number, and inbreeding coefficient were calculated. Our results indicated that equilibrium was not always maintained. The observed mean homozygote value exceeded the expected value (132.81 vs 102.14), but no evidence for allele dropout was found. These results could be explained by a non-random mating; further studies using a larger number of animals could confirm or invalidate this hypothesis. The probability of identity and exclusion of a locus were also estimated and proved to be useful in paternity testing. The ISAG microsatellite panel is useful to screen the Sicilian bovine kinship. Currently, an allele frequency database is being constructed.

  17. Allele frequency of antiretroviral host factor TRIMCyp in wild-caught cynomolgus macaques (Macaca fascicularis)

    PubMed Central

    Saito, Akatsuki; Kawamoto, Yoshi; Higashino, Atsunori; Yoshida, Tomoyuki; Ikoma, Tomoko; Suzaki, Yuriko; Ami, Yasushi; Shioda, Tatsuo; Nakayama, Emi E.; Akari, Hirofumi

    2012-01-01

    A recent study showed that the frequency of an antiretroviral factor TRIM5 gene-derived isoform, TRIMCyp, in cynomolgus macaques (Macaca fascicularis) varies widely according to the particular habitat examined. However, whether the findings actually reflect the prevalence of TRIMCyp in wild cynomolgus macaques is still uncertain because the previous data were obtained with captive monkeys in breeding and rearing facilities. Here, we characterized the TRIM5 gene in cynomolgus macaques captured in the wild, and found that the frequency of the TRIMCyp allele was comparable to those in captive monkeys. This suggests that the previous results with captive monkeys do indeed reflect the natural allele frequency and that breeding and rearing facilities may not affect the frequency of TRIM5 alleles. Interestingly, the prevalence of a minor haplotype of TRIMCyp in wild macaques from the Philippines was significantly lower than in captive ones, suggesting that it is advantageous for wild monkeys to possess the major haplotype of TRIMCyp. Overall, our results add to our understanding of the geographic and genetic prevalence of cynomolgus macaque TRIMCyp. PMID:22969754

  18. 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.

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

    PubMed Central

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

    2016-01-01

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction. PMID:26903642

  20. Investigating the relationship between FMR1 allele length and cognitive ability in children: a subtle effect of the normal allele range on the normal ability range?

    PubMed

    Loat, C S; Craig, G; Plomin, R; Craig, I W

    2006-09-01

    The FMR1 gene contains a trinucleotide repeat tract which can expand from a normal size of around 30 repeats to over 200 repeats, causing mental retardation (Fragile X Syndrome). Evidence suggests that premutation males (55-200 repeats) are susceptible to a late-onset tremor/ataxia syndrome and females to premature ovarian failure, and that intermediate alleles ( approximately 41-55 repeats) and premutations may be in excess in samples with special educational needs. We explored the relationship between FMR1 allele length and cognitive ability in 621 low ability and control children assessed at 4 and 7 years, as well as 122 students with high IQ. The low and high ability and control samples showed no between-group differences in incidence of longer alleles. In males there was a significant negative correlation between allele length and non-verbal ability at 4 years (p = 0.048), academic achievement in maths (p = 0.003) and English (p = 0.011) at 7 years, and IQ in the high ability group (p = 0.018). There was a significant negative correlation between allele length and a standardised score for IQ and general cognitive ability at age 7 in the entire male sample (p = 0.002). This suggests that, within the normal spectrum of allele length, increased repeat numbers may have a limiting influence on cognitive performance.

  1. The joint allele frequency spectrum of multiple populations: a coalescent theory approach.

    PubMed

    Chen, Hua

    2012-03-01

    The allele frequency spectrum is a series of statistics that describe genetic polymorphism, and is commonly used for inferring population genetic parameters and detecting natural selection. Population genetic theory on the allele frequency spectrum for a single population has been well studied using both coalescent theory and diffusion equations. Recently, the theory was extended to the joint allele frequency spectrum (JAFS) for three populations using diffusion equations and was shown to be very useful in inferring human demographic history. In this paper, I show that the JAFS can be analytically derived with coalescent theory for a basic model of two isolated populations and then extended to multiple populations and various complex scenarios, such as those involving population growth and bottleneck, migration, and positive selection. Simulation study is used to demonstrate the accuracy and applicability of the theoretical model. The coalescent theory-based approach for the JAFS can characterize the demographic history with comprehensive statistical models as the diffusion approach does, and in addition gains several novel advantages: the computational complexity of calculating the JAFS with coalescent theory is reduced, and thus it is feasible to analytically obtain the JAFS for multiple populations; the hitchhiking effect can be efficiently modeled in coalescent theory, enabling the development of methodologies for detecting selection via multi-population polymorphism data. As an alternative to the diffusion approximation approach, the coalescent theory for the JAFS also provides a foundation for population genetic inference with the advent of large-scale genomic polymorphism data.

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

    PubMed

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

    2014-11-01

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

  3. QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

    PubMed Central

    Whitney, Kenneth D.; Broman, Karl W.; Kane, Nolan C.; Hovick, Stephen M.; Randell, Rebecca A.; Rieseberg, Loren H.

    2014-01-01

    The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 SNP markers, and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological, and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favored in the wild. QTL for a number of other ecophysiological, phenological, and architectural traits co-localized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence. PMID:25522096

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

    PubMed

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

    2014-04-01

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

  5. Analysis of HLA DQ alpha allele and genotype frequencies in populations from Florida.

    PubMed

    Crouse, C A; Feuer, W J; Nippes, D C; Hutto, S C; Barnes, K S; Coffman, D; Livingston, S H; Ginsberg, L; Glidewell, D E

    1994-05-01

    HLA DQ alpha allele and genotype frequencies for Caucasian, African American, Haitian, and Hispanic populations in Florida have been estimated. The Florida laboratories involved in these studies collected donor samples from a variety of sites including clinical laboratories, victim and suspect standards, blood banks, county jail detainees, and laboratory personnel. We have determined that the Caucasian and African American DQ alpha genotype frequencies do not deviate significantly from Hardy-Weinberg expectations and as a result of this heterogeneity analyses, data from the four Florida Caucasian populations may be combined and data from the four Florida African American populations may be combined to form two large HLA DQ alpha genotype frequency databanks. Further, data from the Florida Haitian population may be combined with the Florida African American population. Comparison of the combined Florida Caucasian populations, combined Florida African American populations, the Palm Beach Sheriff's Office (PBSO) Hispanic, and PBSO Haitian population with other databases does not support combination because allele frequency distributions are heterogeneous.

  6. Upper bounds on FST in terms of the frequency of the most frequent allele and total homozygosity: the case of a specified number of alleles.

    PubMed

    Edge, Michael D; Rosenberg, Noah A

    2014-11-01

    FST is one of the most frequently-used indices of genetic differentiation among groups. Though FST takes values between 0 and 1, authors going back to Wright have noted that under many circumstances, FST is constrained to be less than 1. Recently, we showed that at a genetic locus with an unspecified number of alleles, FST for two subpopulations is strictly bounded from above by functions of both the frequency of the most frequent allele (M) and the homozygosity of the total population (HT). In the two-subpopulation case, FST can equal one only when the frequency of the most frequent allele and the total homozygosity are 1/2. Here, we extend this work by deriving strict bounds on FST for two subpopulations when the number of alleles at the locus is specified to be I. We show that restricting to I alleles produces the same upper bound on FST over much of the allowable domain for M and HT, and we derive more restrictive bounds in the windows M∈[1/I,1/(I-1)) and HT∈[1/I,I/(I(2)-1)). These results extend our understanding of the behavior of FST in relation to other population-genetic statistics.

  7. 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...

  8. 33 CFR 86.01 - Frequencies and range of audibility.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Frequencies and range of... Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525 Hz. The range of audibility of the signal from a whistle shall be determined by those...

  9. 33 CFR 86.01 - Frequencies and range of audibility.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Frequencies and range of... Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525 Hz. The range of audibility of the signal from a whistle shall be determined by those...

  10. 33 CFR 86.01 - Frequencies and range of audibility.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Frequencies and range of... Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525 Hz. The range of audibility of the signal from a whistle shall be determined by those...

  11. 33 CFR 86.01 - Frequencies and range of audibility.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Frequencies and range of... Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525 Hz. The range of audibility of the signal from a whistle shall be determined by those...

  12. 33 CFR 86.01 - Frequencies and range of audibility.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Frequencies and range of... Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525 Hz. The range of audibility of the signal from a whistle shall be determined by those...

  13. 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

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

    PubMed

    Sala, A; Penacino, G; Corach, D

    1998-10-01

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

  15. Characteristics of different frequency ranges in scanning electron microscope images

    SciTech Connect

    Sim, K. S. Nia, M. E.; Tan, T. L.; Tso, C. P.; Ee, C. S.

    2015-07-22

    We demonstrate a new approach to characterize the frequency range in general scanning electron microscope (SEM) images. First, pure frequency images are generated from low frequency to high frequency, and then, the magnification of each type of frequency image is implemented. By comparing the edge percentage of the SEM image to the self-generated frequency images, we can define the frequency ranges of the SEM images. Characterization of frequency ranges of SEM images benefits further processing and analysis of those SEM images, such as in noise filtering and contrast enhancement.

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

    PubMed Central

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

    2013-01-01

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

  17. Lower Frequency of HLA-DRB1 Type 1 Diabetes Risk Alleles in Pediatric Patients with MODY

    PubMed Central

    López-Euba, Tamara; Velayos, Teresa; Martínez de LaPiscina, Idoia; Bilbao, José Ramón; Rica, Itxaso; Castaño, Luis

    2017-01-01

    Objective The aim of this study was to determine the frequency of susceptible HLA-DRB1 alleles for type 1 diabetes in a cohort of pediatric patients with a confirmed genetic diagnosis of MODY. Materials and Methods 160 families with a proband diagnosed with type 1 diabetes and 74 families with a molecular diagnosis of MODY (61 GCK-MODY and 13 HNF1A-MODY) were categorized at high definition for HLA-DRB1 locus. According to the presence or absence of the susceptible HLA-DRB1 alleles for type 1 diabetes, we considered three different HLA-DRB1 genotypes: 0 risk alleles (no DR3 no DR4); 1 risk allele (DR3 or DR4); 2 risk alleles (DR3 and/or DR4). Results Compared with type 1 diabetes, patients with MODY carried higher frequency of 0 risk alleles, OR 22.7 (95% CI: 10.7–48.6) and lower frequency of 1 or 2 risk alleles, OR 0.53 (95% CI: 0.29–0.96) and OR 0.06 (95% CI: 0.02–0.18), respectively. Conclusions The frequency of HLA-DRB1 risk alleles for type 1 diabetes is significantly lower in patients with MODY. In children and adolescents with diabetes, the presence of 2 risk alleles (DR3 and/or DR4) reduces the probability of MODY diagnosis, whereas the lack of risk alleles increases it. Therefore, we might consider that HLA-DRB1 provides additional information for the selection of patients with high probability of monogenic diabetes. PMID:28052112

  18. 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

  19. Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans

    PubMed Central

    Pritchard, Jonathan K.

    2016-01-01

    The site frequency spectrum (SFS) has long been used to study demographic history and natural selection. Here, we extend this summary by examining the SFS conditional on the alleles found at the same site in other species. We refer to this extension as the “phylogenetically-conditioned SFS” or cSFS. Using recent large-sample data from the Exome Aggregation Consortium (ExAC), combined with primate genome sequences, we find that human variants that occurred independently in closely related primate lineages are at higher frequencies in humans than variants with parallel substitutions in more distant primates. We show that this effect is largely due to sites with elevated mutation rates causing significant departures from the widely-used infinite sites mutation model. Our analysis also suggests substantial variation in mutation rates even among mutations involving the same nucleotide changes. In summary, we show that variable mutation rates are key determinants of the SFS in humans. PMID:27977673

  20. 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.

  1. Frequency detection of imidacloprid resistance allele in Aphis gossypii field populations by real-time PCR amplification of specific-allele (rtPASA).

    PubMed

    Zhang, Jing; Cui, Li; Xu, Xibao; Rui, Changhui

    2015-11-01

    The Aphis gossypii Glover (Hemiptera: Aphididae) is one of the most serious pests worldwide, and imidacloprid has been widely used to control this insect pest. Just like other classes of insecticides, the resistance to imidacloprid has been found in A. gossypii. An amino acid mutation (R81T) in the nicotinic acetylcholine receptor (nAChR) beta1 subunit was detected in the imidacloprid-resistant A. gossypii collected from Langfang (LF) and Dezhou (DZ) cities. To estimate the R81T mutation frequency of A. gossypii field populations, a simple, rapid and accurate rtPASA (real-time PCR amplification of specific allele) protocol was developed. The performance of the rtPASA protocol was evaluated by comparing with the data generated by a cPASA (competitive PCR amplification of specific allele) method from 50 individual genotypes. The R81T allele frequencies of the LF population (34.7%±1.3%) and DZ population (45.2%±5.2%) estimated by the rtPASA protocol matched the frequencies (LF 38.1%, DZ 48.2%) deduced by the cPASA method in specimens. The results indicated that the rtPASA format was applicable for the detection of mutation associated with imidacloprid resistance and will allow rapid and efficient monitoring of A. gossypii resistance in field populations in a high throughput format.

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

    PubMed Central

    Racimo, Fernando

    2016-01-01

    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

  3. 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.

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

    PubMed

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

    2012-06-01

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

  5. Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6

    PubMed Central

    Smith, Leslie; Montagna, Christina; Thayer, Mathew J.

    2013-01-01

    Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encodes a large intergenic non-coding RNA gene named Asynchronous replication and Autosomal RNA on chromosome 6, or ASAR6. Disruption of ASAR6 results in delayed replication, delayed mitotic chromosome condensation, and activation of the previously silent alleles of mono-allelic genes on chromosome 6. The ASAR6 gene resides within an ∼1.2 megabase domain of asynchronously replicating DNA that is coordinated with other random asynchronously replicating loci along chromosome 6. In contrast to other nearby mono-allelic genes, ASAR6 RNA is expressed from the later-replicating allele. ASAR6 RNA is synthesized by RNA Polymerase II, is not polyadenlyated, is restricted to the nucleus, and is subject to random mono-allelic expression. Disruption of ASAR6 leads to the formation of bridged chromosomes, micronuclei, and structural instability of chromosome 6. Finally, ectopic integration of cloned genomic DNA containing ASAR6 causes delayed replication of entire mouse chromosomes. PMID:23593023

  6. 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.

  7. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Certified operating frequency range. 15.202 Section 15.202 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.202 Certified operating frequency range. Client devices that operate in a...

  8. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Certified operating frequency range. 15.202 Section 15.202 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.202 Certified operating frequency range. Client devices that operate in a...

  9. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Certified operating frequency range. 15.202 Section 15.202 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.202 Certified operating frequency range. Client devices that operate in a...

  10. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Certified operating frequency range. 15.202 Section 15.202 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.202 Certified operating frequency range. Client devices that operate in a...

  11. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Certified operating frequency range. 15.202 Section 15.202 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.202 Certified operating frequency range. Client devices that operate in a...

  12. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... lowest frequency for which a radiated emission limit is specified, up to the frequency shown in the... level of radiated emissions within the frequency range 9 kHz to 30 MHz, such as a CB receiver or a device designed to conduct its radio frequency emissions via connecting wires or cables, e.g., a...

  13. Allele and genotype frequencies of polymorphisms in cytokine genes in ethnic Russian individuals from Moscow, Russia.

    PubMed

    Shadrina, Alexandra; Voronina, Elena; Zolotukhin, Igor; Filipenko, Maxim

    2017-02-01

    Two hundred and twenty eight ethnic Russian individuals from Moscow, Russia, were genotyped at 14 single nucleotide polymorphisms CCL2 A-2578G; VEGFA C-2578A, G-634C, and C+936T; TNF G+419A and G-308A; IL1A G-889A; IL1RN T+1018C; IL6G-174C and G-572C; IFNG T+874A; IL1B C-511T; IL10 A+1082G; TGFB1 C-509T. Genotypes were determined using real-time polymerase chain reaction with TaqMan probes and polymerase chain reaction followed by melting analysis of dual-labeled probe. Genotype distribution was in accordance with Hardy-Weinberg equilibrium for all studied polymorphisms. Genotype data are available in the Allele Frequencies Net Database under identifier AFND 3367 and the population name "Russia Moscow Cytokine".

  14. 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.

  15. Analysis and frequency of bovine lymphocyte antigen (BoLA-DRB3) alleles in Iranian Holstein cattle.

    PubMed

    Nassiry, M R; Shahroodi, F Eftekhar; Mosafer, J; Mohammadi, A; Manshad, E; Ghazanfari, S; Mohammad Abadi, M R; Sulimova, G E

    2005-06-01

    The bovine lymphocyte antigen (BoLA-DRB3) gene encodes cell surface glycoproteins that initiate immune response by presenting processed antigenic peptides to CD4 T helper cells. DRB3 is the most polymorphic bovine MHC class II gene which encodes the peptide-binding groove. DRB3 gene has been extensively evaluated as a candidate marker for association with various bovine diseases and immunological traits. This study describes genetic variability in the BoLA-DRB3 in Iranian Holstein cattle. This is the first study of the DNA polymorphism of the BoLA-DRB3 gene in Iranian Holstein cattle. Hemi-nested PCR-RFLP method is used for identification the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the studied herd (26 alleles). Almost 67% of the alleles were accounted for four alleles (BoLA-DRB3.2*8, *24, *11 and *16) in Iranian Holstein cattle. The DRB3.2*8 allele frequency (26.6%) was higher than the others. The frequencies of the DRB3.2*54, *37, *36, *28, *25, *14, *13, *10, *1 alleles were lower than 1%. Significant distinctions have been found between Iranian Holstein cattle and other cattle breeds studied. In Iranian Holstein cattle the alleles (BoLA-DRB3.2*22, *2 and *16) associated with a lower risk of cystic ovarian disease in Holstein cattle are found. The alleles associated with the resistance to mastitis and to bovine leukemia virus infection BoLA-DRB3.2*11 and *23 are detected with the frequencies 10.4% and 4.4%, respectively. Thus in the Iranian Holstein cows studied are found alleles which are associated with resistance to various diseases. The method of DNA-typing of animals can be used in agricultural practice for BoLA-DRB3 allele genotyping of cattle in order to reduce spreading of alleles providing susceptibility to mastitis or leukemia in cattle herds.

  16. Controlling for P-value inflation in allele frequency change in experimental evolution and artificial selection experiments.

    PubMed

    Kemppainen, Petri; Rønning, Bernt; Kvalnes, Thomas; Hagen, Ingerid J; Ringsby, Thor Harald; Billing, Anna M; Pärn, Henrik; Lien, Sigbjørn; Husby, Arild; Saether, Bernt-Erik; Jensen, Henrik

    2016-11-04

    Experimental evolution studies can be used to explore genomic response to artificial and natural selection. In such studies, loci that display larger allele frequency change than expected by genetic drift alone are assumed to be directly or indirectly associated with traits under selection. However, such studies report surprisingly many loci under selection, suggesting that current tests for allele frequency change may be subject to P-value inflation and hence be anticonservative. One factor known from genomewide association (GWA) studies to cause P-value inflation is population stratification, such as relatedness among individuals. Here, we suggest that by treating presence of an individual in a population after selection as a binary response variable, existing GWA methods can be used to account for relatedness when estimating allele frequency change. We show that accounting for relatedness like this effectively reduces false-positives in tests for allele frequency change in simulated data with varying levels of population structure. However, once relatedness has been accounted for, the power to detect causal loci under selection is low. Finally, we demonstrate the presence of P-value inflation in allele frequency change in empirical data spanning multiple generations from an artificial selection experiment on tarsus length in two free-living populations of house sparrow and correct for this using genomic control. Our results indicate that since allele frequencies in large parts of the genome may change when selection acts on a heritable trait, such selection is likely to have considerable and immediate consequences for the eco-evolutionary dynamics of the affected populations.

  17. Length of FMR1 repeat alleles within the normal range does not substantially affect the risk of early menopause

    PubMed Central

    Ruth, Katherine S.; Bennett, Claire E.; Schoemaker, Minouk J.; Weedon, Michael N.; Swerdlow, Anthony J.; Murray, Anna

    2016-01-01

    STUDY QUESTION Is the length of FMR1 repeat alleles within the normal range associated with the risk of early menopause? SUMMARY ANSWER The length of repeat alleles within the normal range does not substantially affect risk of early menopause. WHAT IS KNOWN ALREADY There is a strong, well-established relationship between length of premutation FMR1 alleles and age at menopause, suggesting that this relationship could continue into the normal range. Within the normal range, there is conflicting evidence; differences in ovarian reserve have been identified with FMR1 repeat allele length, but a recent population-based study did not find any association with age at menopause as a quantitative trait. STUDY DESIGN, SIZE, DURATION We analysed cross-sectional baseline survey data collected at recruitment from 2004 to 2010 from a population-based, prospective epidemiological cohort study of >110 000 women to investigate whether repeat allele length was associated with early menopause. PARTICIPANTS/MATERIALS, SETTING, METHOD We included 4333 women from the Breakthrough Generations Study (BGS), of whom 2118 were early menopause cases (menopause under 46 years) and 2215 were controls. We analysed the relationship between length of FMR1 alleles and early menopause using logistic regression with allele length as continuous and categorical variables. We also conducted analyses with the outcome age at menopause as a quantitative trait as well as appropriate sensitivity and exploratory analyses. MAIN RESULTS AND THE ROLE OF CHANCE There was no association of the shorter or longer FMR1 allele or their combined genotype with the clinically relevant end point of early menopause in our main analysis. Likewise, there were no associations with age at menopause as a quantitative trait in our secondary analysis. LIMITATIONS, REASONS FOR CAUTION Women with homozygous alleles in the normal range may have undetected FMR1 premutation alleles, although there was no evidence to suggest this. We

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

    PubMed Central

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

    2016-01-01

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

  19. 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

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

    PubMed

    Field, Wesley; Hershberg, Ruth

    2015-05-26

    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.

  1. 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

  2. Inferring microevolutionary patterns from allele-size frequency distributions of minisatellite loci: a worldwide study of the APOB 3' hypervariable region polymorphism.

    PubMed

    Destro-Bisol, G; Capelli, C; Belledi, M

    2000-10-01

    The availability of numerous population and molecular data makes the apolipoprotein B 3' hypervariable region (APOB 3' HVR) polymorphism ideal for a pilot study of the relationships between the allele-size frequency distributions (referred to as allele-size distributions) of minisatellite loci and the microevolutionary processes underlying their present-day polymorphism in human populations. In this paper, we present a worldwide APOB 3' HVR study, based on published and unpublished data, which refers to 36 populations. We systematically compare APOB 3' HVR within-group diversity (in terms of heterozygosity, number of alleles, and allele-size variance) in numerous human populations, including African, European, Asian, Amerindian, Australomelanesian, and Polynesian groups. Overall, our analyses indicate a greater APOB 3' HVR diversity in Africans than non-Africans. Then, we compare APOB 3' HVR allele-size distributions. The APOB 3' HVR allele-size distribution is found to be quasi-unimodal in Africans and bimodal or nonunimodal in non-African populations. The analysis of the distribution of pairwise comparisons suggests that Africans expanded earlier and/or that their ancestral population was larger than other continental groups. As a final step, we examine APOB 3' HVR interpopulational relationships by using three genetic distances. The F(ST) genetic distance, which assumes genetic drift as being the agent that differentiates populations, provides results that are more congruent with established anthropological knowledge than mutation-based distances (D(SW) and R(ST)). We hypothesize that the ancestral population was characterized by a high heterozygosity, an extended range of allele size, and a quasi-unimodal allele-size distribution centered on allele *37, features persisting in examined African populations. Sampling processes during "out-of-Africa" migrations would be responsible for the decrease in APOB 3' HVR gene diversity and the nonunimodal allele

  3. 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.

  4. Allele frequencies of D21S11, FGA, TH01, and VWA in populations of the Balkans.

    PubMed

    Huckenbeck, W; Scheil, H G; Schmidt, H D; Efremovska, L; Mikerezi, I

    2004-12-01

    This study is part of an extensive investigation of the genetic relationship between Balkan populations, especially the Aromuns. Allele frequencies of four STRs (D21S11, FGA, TH01, VWA) from Macedonians (Skopje), Gramostian Aromuns from the Stip region (Macedonia), Moskopolian Aromuns from Krusevo (Macedonia), and Musequiar Aromuns from Dukasi (Albania) are presented.

  5. 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.

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

    PubMed

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

    2015-01-01

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

  7. Genotypic and allelic frequencies of gene polymorphisms associated with meat tenderness in Nellore beef cattle.

    PubMed

    Carvalho, M E; Eler, J P; Bonin, M N; Rezende, F M; Biase, F H; Meirelles, F V; Regitano, L C A; Coutinho, L L; Balieiro, J C C; Ferraz, J B S

    2017-02-16

    The objectives of this study were to characterize the allelic and genotypic frequencies of polymorphisms in the µ-calpain and calpastatin genes, and to assess their association with meat tenderness and animal growth in Nellore cattle. We evaluated 605 Nellore animals at 24 months of age, on average, at slaughter. The polymorphisms were determined for the molecular markers CAPN316, CAPN530, CAPN4751, CAPN4753, and UOGACAST1. Analyses of meat tenderness at 7, 14, and 21 days of maturation were performed in samples of longissimus thoracis obtained between the 12th and 13th rib and sheared using a Warner Bratzler Shear Force. Significant effects were observed for meat tenderness at days 7, 14, and 21 of maturation for the marker CAPN4751, at day 21 for the marker CAPN4753, and at days 14 and 21 for the marker UOGCAST1. For genotypic combinations of markers, the results were significant for the combination CAPN4751/UOGCAST1 in the three maturation periods and CAPN4753/UOGCAST1 at days 14 and 21 of maturation.

  8. Allele frequencies of three factor VIII gene polymorphisms in Iranian populations and their application in hemophilia A carrier detection.

    PubMed

    Azimifar, S Babak; Seyedna, S Yoosef; Zeinali, Sirous

    2006-05-01

    Hemophilia A is an X-linked recessive bleeding disorder caused by a quantitative or qualitative deficiency of blood coagulation factor VIII (FVIII). ARMS (amplification refractory mutation system) primers were designed to determine allele frequencies of three FVIII gene linked markers, IVS7 nt 27 G/A SNP, BclI/intron 18, and HindIII/intron 19 among 85 normal Iranian women from unrelated families. Then same method was applied to perform carrier detection for hemophilia A families. The allele frequencies of IVS7 nt 27 "G"/"A" allele, BclI "T"/"A" allele, and HindIII "C"/"T" allele among normal women were 0.88/0.12, 0.52/0.48, and 0.48/0.52, respectively. The three polymorphisms were found to be in strong linkage disequilibrium, which decreased the overall heterozygosity to 51%. Twenty-one women from 15 unrelated hemophilia A families were referred to us for hemophilia A carrier detection. Taking advantage of these three biallelic polymorphisms in conjunction with multiallelic St14 VNTR (locus DXS52), IVS13 (CA)n STR, and IVS22 (CA)n STR, carrier status was determined in 16 women (16/21 or 76% of the at-risk women) from 11 families (11/15 or 73% of the families). The used ARMS methods are rapid and can easily be applied in conjunction with other FVIII gene linked polymorphisms for indirect mutation detection of hemophilia A where they are informative.

  9. Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species.

    PubMed

    Titze, Ingo; Riede, Tobias; Mau, Ted

    2016-06-01

    Vocal folds are used as sound sources in various species, but it is unknown how vocal fold morphologies are optimized for different acoustic objectives. Here we identify two main variables affecting range of vocal fold vibration frequency, namely vocal fold elongation and tissue fiber stress. A simple vibrating string model is used to predict fundamental frequency ranges across species of different vocal fold sizes. While average fundamental frequency is predominantly determined by vocal fold length (larynx size), range of fundamental frequency is facilitated by (1) laryngeal muscles that control elongation and by (2) nonlinearity in tissue fiber tension. One adaptation that would increase fundamental frequency range is greater freedom in joint rotation or gliding of two cartilages (thyroid and cricoid), so that vocal fold length change is maximized. Alternatively, tissue layers can develop to bear a disproportionate fiber tension (i.e., a ligament with high density collagen fibers), increasing the fundamental frequency range and thereby vocal versatility. The range of fundamental frequency across species is thus not simply one-dimensional, but can be conceptualized as the dependent variable in a multi-dimensional morphospace. In humans, this could allow for variations that could be clinically important for voice therapy and vocal fold repair. Alternative solutions could also have importance in vocal training for singing and other highly-skilled vocalizations.

  10. Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species

    PubMed Central

    Titze, Ingo; Riede, Tobias; Mau, Ted

    2016-01-01

    Vocal folds are used as sound sources in various species, but it is unknown how vocal fold morphologies are optimized for different acoustic objectives. Here we identify two main variables affecting range of vocal fold vibration frequency, namely vocal fold elongation and tissue fiber stress. A simple vibrating string model is used to predict fundamental frequency ranges across species of different vocal fold sizes. While average fundamental frequency is predominantly determined by vocal fold length (larynx size), range of fundamental frequency is facilitated by (1) laryngeal muscles that control elongation and by (2) nonlinearity in tissue fiber tension. One adaptation that would increase fundamental frequency range is greater freedom in joint rotation or gliding of two cartilages (thyroid and cricoid), so that vocal fold length change is maximized. Alternatively, tissue layers can develop to bear a disproportionate fiber tension (i.e., a ligament with high density collagen fibers), increasing the fundamental frequency range and thereby vocal versatility. The range of fundamental frequency across species is thus not simply one-dimensional, but can be conceptualized as the dependent variable in a multi-dimensional morphospace. In humans, this could allow for variations that could be clinically important for voice therapy and vocal fold repair. Alternative solutions could also have importance in vocal training for singing and other highly-skilled vocalizations. PMID:27309543

  11. Contraction of fully expanded FMR1 alleles to the normal range: predisposing haplotype or rare events?

    PubMed

    Maia, Nuno; Loureiro, Joana R; Oliveira, Bárbara; Marques, Isabel; Santos, Rosário; Jorge, Paula; Martins, Sandra

    2017-02-01

    Fragile X syndrome (FXS), the most common cause of inherited intellectual disability, is due to the expansion over 200 CGGs and methylation of this polymorphic region, in the 5'-UTR (untranslated region) of FMR1 (Xq27.3). We have identified four FXS mosaic males: M1-(CGG)35/(CGG)>200; M2-(CGG)26/(CGG)>200; M3-(CGG)39/(CGG)>200; and M4-(CGG)18/(CGG)125/(CGG)>200. After genotyping their respective mothers, we suggested that normal alleles of these patients resulted from post-zygotic contractions of full expansions. The detection of these four rare independent cases led us to hypothesize the existence of a large-contraction predisposing haplotype in our population. Next, we questioned whether other normal pure CGGs would have arisen through similar contractions from fully expanded alleles. To address these questions, we identified stable single-nucleotide polymorphism (SNP) lineages and related short tandem repeat (STR) haplotypes (DXS998-DXS548-FRAXAC1-FRAXAC2) of the four mosaics, 123 unrelated FXS patients and 212 controls. An extended flanking haplotype (34-44-38-336) shared by mosaics from lineage A suggested a risk lineage-specific haplotype more prone to large contractions. Other normal pure FMR1 alleles from this SNP background also shared phylogenetically close STR haplotypes, although a single (CGG)exp>(CGG)24 contraction or the loss of AGG interruptions may explain their origin. In both scenarios, multistep FMR1 mutations involving the gain or loss of several CGGs seem to underlie the evolution of the repeat.

  12. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... § 15.33 Frequency range of radiated measurements. (a) For an intentional radiator, the spectrum shall... kHz, up to at least the frequency shown in this paragraph: (1) If the intentional radiator operates... lower. (2) If the intentional radiator operates at or above 10 GHz and below 30 GHz: to the...

  13. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... § 15.33 Frequency range of radiated measurements. (a) For an intentional radiator, the spectrum shall... kHz, up to at least the frequency shown in this paragraph: (1) If the intentional radiator operates... lower. (2) If the intentional radiator operates at or above 10 GHz and below 30 GHz: to the...

  14. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... § 15.33 Frequency range of radiated measurements. (a) For an intentional radiator, the spectrum shall... kHz, up to at least the frequency shown in this paragraph: (1) If the intentional radiator operates... lower. (2) If the intentional radiator operates at or above 10 GHz and below 30 GHz: to the...

  15. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... § 15.33 Frequency range of radiated measurements. (a) For an intentional radiator, the spectrum shall... kHz, up to at least the frequency shown in this paragraph: (1) If the intentional radiator operates... lower. (2) If the intentional radiator operates at or above 10 GHz and below 30 GHz: to the...

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

    PubMed Central

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

    2016-01-01

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

  17. No differences of butyrylcholinesterase protein activity and allele frequency in Lewy body diseases.

    PubMed

    Maetzler, Walter; Keller, Stefanie; Michelis, Joan; Koehler, Niklas; Stransky, Elke; Becker, Clemens; Schulte, Claudia; Melms, Arthur; Gasser, Thomas; Berg, Daniela

    2009-08-01

    Butyrylcholinesterase (BChE) genotypes and protein (BuChE) activity, especially in combination with Apolipoprotein E4 (ApoE4), have been investigated as risk factors for developing Alzheimer disease (AD) and may be associated with the rate of progression of cognitive decline. Despite similar pathologic (e.g. amyloid deposition) and neurochemical (e.g. cholinergic deficits) aspects between AD and Lewy body diseases (LBD), scarce data is obtainable about BChE genotypes and BuChE activity in LBD. We measured BuChE activity levels in serum and cerebrospinal fluid (CSF) of 114 LBD subjects (59 of them were demented) and 31 elderly controls. We found higher CSF BuChE activity in males compared to females, and a negative correlation of serum BuChE activity with age and cognitive function. Demented LBD patients, non-demented LBD patients and controls did not differ significantly with regard to serum and CSF BuChE activity. Furthermore, BChE K variant and ApoE4 allele frequencies were determined. The BChE K variant was significantly associated with lower serum activity; the same trend was observable in CSF. The subgroups did not differ significantly with regard to BChE K/ApoE4 occurrence. These data confirm and extend previous results on the relationship between BChE gene and BuChE activity, and argue rather against a major impact of BuChE on LBD-associated pathologies.

  18. 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

  19. 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.

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

    PubMed Central

    Kiesler, Kevin M.; Vallone, Peter M.

    2013-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  2. 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.

  3. Technique for extending the frequency range of digital dividers

    NASA Technical Reports Server (NTRS)

    Long, W. C.; Middleton, J. H. (Inventor)

    1973-01-01

    A technique for extending the frequency range of a presettable digital divider is described. The conventional digital divider consists of several counter stages with the count of each stage compared to a preselected number. When the counts for all stages are equal to the preselected numbers, an output pulse is generated and all stages are reset. For high input frequencies, the least significant stage of the divider has to be reset in a very short time. This limits the frequency that can be handled by the conventional digital divider. This invention provides a technique in which the second least significant and higher stages are reset and the least significant stage is permitted to free-run. Hence, the time in which the reset operation can be performed is increased thereby extending the frequency range of the divider.

  4. A multi-frequency method for ultrasonic ranging.

    PubMed

    Queirós, Ricardo; Corrêa Alegria, Francisco; Silva Girão, Pedro; Cruz Serra, António

    2015-12-01

    This paper presents a method for ultrasonic ranging based on the cross-correlation of two multi-frequency signals. The stimulus signal is composed by multiple sine-wave bursts/segments, each containing a different frequency and an integer number of periods. The frequency of each sine-wave burst is different from that of the adjacent bursts, but it is very close to the transducer resonant frequency. The time-of-flight (TOF) is estimated by finding the maximum of the cross-correlation. Interpolation is used to increase the measurement resolution. The experimental error corresponding to two standard deviations, for a range up to 1 m, is less than 0.3 mm.

  5. 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

  6. Polymorphism and predictability at the alpha-glycerophosphate dehydrogenase locus in Colias butterflies: gradients in allele frequency within single populations.

    PubMed

    Johnson, G B

    1976-06-01

    Heterozygosity at the alpha-glycerophosphate dehydrogenase locus of five species of Colias butterflies is widespread in montane populations; alpine and lowland populations are not heterozygous. Within a single demographically characterized population of C. meadii where the population extends from alpine down into montane habitats, a marked cline in allele frequency is seen. Such within-population clines suggest the involvement of strong selection across the marked ecological interface. Thermal factors are the most likely causative agents, but associative overdominance is not excluded.

  7. Insecticide Resistance Allele Frequencies in Anopheles gambiae before and after Anti-Vector Interventions in Continental Equatorial Guinea

    PubMed Central

    Reddy, Michael R.; Godoy, Adrian; Dion, Kirstin; Matias, Abrahan; Callender, Kevin; Kiszewski, Anthony E.; Kleinschmidt, Immo; Ridl, Frances C.; Powell, Jeffrey R.; Caccone, Adalgisa; Slotman, Michel A.

    2013-01-01

    Anti-malaria interventions that rely on insecticides can be compromised by insecticide-resistance alleles among malaria vectors. We examined frequency changes of resistance alleles at two loci, knockdown resistance (kdr) and acetylcholinesterase-1 (ace-1), which confer resistance to pyrethroids and DDT, and carbamates, respectively. A total of 7,059 Anopheles gambiae sensu stricto mosquitoes were analyzed from multiple sites across continental Equatorial Guinea. A subset of sites included samples collected pre-intervention (2007) and post-intervention (2009–2011). Both L1014S and L1014F resistance alleles were observed in almost all pre-intervention collections. In particular, L1014F was already at substantial frequencies in M form populations (17.6–74.6%), and at high frequencies (> 50%) in all but two S form populations. Comparison before and throughout anti-vector interventions showed drastic increases in L1014F, presumably caused by intensified selection pressure imposed by pyrethroids used in vector control efforts. In light of these findings, inclusion of other insecticide classes in any anti-vector intervention can be considered prudent. PMID:23438768

  8. Allelic and genotype frequencies of catechol-O-methyltransferase (Val158Met) and CYP2D6*10 (Pro34Ser) single nucleotide polymorphisms in the Philippines

    PubMed Central

    Baclig, Michael O; Predicala, Rey Z; Mapua, Cynthia A; Lozano-Kühne, Jingky P; Daroy, Maria Luisa G; Natividad, Filipinas F; Javier, Francis O

    2012-01-01

    A hospital-based cross-sectional study was conducted to determine the allelic and genotype frequencies in the genes encoding for catechol-O-methyltransferase and CYP2D6*10 among healthy volunteers and patients clinically diagnosed with cancer pain. PCR-RFLP was used to identify COMT and CYP2D6*10 genotypes. Allelic frequencies among healthy volunteer Filipinos were 0.83 and 0.17 for the COMT Val and COMT Met alleles, respectively. Calculated frequencies in Hardy-Weinberg equilibrium (HWE) were 73% for COMT Val/Val, 26% for COMT Val/Met, and 1% for COMT Met/Met genotype. For CYP2D6*10, allelic frequencies in HWE among volunteers were 0.46 for the C allele and 0.54 for the T allele. Twenty percent were identified as homozygous for the wild-type C/C genotype, 56% were identified as heterozygous for the C/T genotype, and 24% were identified as homozygous for the T/T variant genotype. No significant differences in COMT and CYP2D6*10 allele frequencies between cancer patients and healthy volunteers were noted. Our data demonstrated that the allele frequencies of COMT and CYP2D6*10 in the Filipino healthy volunteers were similar with other Asians but markedly different from Caucasian populations. PMID:22724048

  9. Allelic and genotype frequencies of catechol-O-methyltransferase (Val158Met) and CYP2D6*10 (Pro34Ser) single nucleotide polymorphisms in the Philippines.

    PubMed

    Baclig, Michael O; Predicala, Rey Z; Mapua, Cynthia A; Lozano-Kühne, Jingky P; Daroy, Maria Luisa G; Natividad, Filipinas F; Javier, Francis O

    2012-01-01

    A hospital-based cross-sectional study was conducted to determine the allelic and genotype frequencies in the genes encoding for catechol-O-methyltransferase and CYP2D6*10 among healthy volunteers and patients clinically diagnosed with cancer pain. PCR-RFLP was used to identify COMT and CYP2D6*10 genotypes. Allelic frequencies among healthy volunteer Filipinos were 0.83 and 0.17 for the COMT Val and COMT Met alleles, respectively. Calculated frequencies in Hardy-Weinberg equilibrium (HWE) were 73% for COMT Val/Val, 26% for COMT Val/Met, and 1% for COMT Met/Met genotype. For CYP2D6*10, allelic frequencies in HWE among volunteers were 0.46 for the C allele and 0.54 for the T allele. Twenty percent were identified as homozygous for the wild-type C/C genotype, 56% were identified as heterozygous for the C/T genotype, and 24% were identified as homozygous for the T/T variant genotype. No significant differences in COMT and CYP2D6*10 allele frequencies between cancer patients and healthy volunteers were noted. Our data demonstrated that the allele frequencies of COMT and CYP2D6*10 in the Filipino healthy volunteers were similar with other Asians but markedly different from Caucasian populations.

  10. 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

  11. Increase of TCR V beta accessibility within E beta regulatory region influences its recombination frequency but not allelic exclusion.

    PubMed

    Senoo, Makoto; Wang, Lili; Suzuki, Daisuke; Takeda, Naoki; Shinkai, Yoichi; Habu, Sonoko

    2003-07-15

    Seventy percent of the murine TCRbeta locus (475 kb) was deleted to generate a large deleted TCRbeta (beta(LD)) allele to investigate a possible linkage between germline transcription, recombination frequency, and allelic exclusion of the TCR Vbeta genes. In these beta(LD/LD) mice, the TCRbeta gene locus contained only four Vbeta genes at the 5' side of the locus, and consequently, the Vbeta10 gene was located in the original Dbeta1-Jbeta1cluster within the Ebeta regulatory region. We showed that the frequency of recombination and expression of the Vbeta genes are strongly biased to Vbeta10 in these mutant mice even though the proximity of the other three 5'Vbeta genes was also greatly shortened toward the Dbeta-Jbeta cluster and the Ebeta enhancer. Accordingly, the germline transcription of the Vbeta10 gene in beta(LD/LD) mice was exceptionally enhanced in immature double negative thymocytes compared with that in wild-type mice. During double negative-to-double positive transition of thymocytes, the level of Vbeta10 germline transcription was prominently increased in beta(LD/LD) recombination activating gene 2-deficient mice receiving anti-CD3epsilon Ab in vivo. Interestingly, however, despite the increased accessibility of the Vbeta10 gene in terms of transcription, allelic exclusion of this Vbeta gene was strictly maintained in beta(LD/LD) mice. These results provide strong evidence that increase of Vbeta accessibility influences frequency but not allelic exclusion of the TCR Vbeta rearrangement if the Vbeta gene is located in the Ebeta regulatory region.

  12. Experimental Limits on Gravitational Waves in the MHz frequency Range

    SciTech Connect

    Lanza, Robert Jr.

    2015-03-01

    This thesis presents the results of a search for gravitational waves in the 1-11MHz frequency range using dual power-recycled Michelson laser interferometers at Fermi National Accelerator Laboratory. An unprecedented level of sensitivity to gravitational waves in this frequency range has been achieved by cross-correlating the output fluctuations of two identical and colocated 40m long interferometers. This technique produces sensitivities better than two orders of magnitude below the quantum shot-noise limit, within integration times of less than 1 hour. 95% confidence level upper limits are placed on the strain amplitude of MHz frequency gravitational waves at the 10-21 Hz-1/2 level, constituting the best direct limits to date at these frequencies. For gravitational wave power distributed over this frequency range, a broadband upper limit of 2.4 x 10-21Hz-1/2 at 95% confidence level is also obtained. This thesis covers the detector technology, the commissioning and calibration of the instrument, the statistical data analysis, and the gravitational wave limit results. Particular attention is paid to the end-to-end calibration of the instrument’s sensitivity to differential arm length motion, and so to gravitational wave strain. A detailed statistical analysis of the data is presented as well.

  13. 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.

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

    PubMed

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

    2008-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-11-01

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

  16. Improving range resolution with a frequency-hopping technique

    NASA Technical Reports Server (NTRS)

    Stitt, G. R.; Bowhill, S. A.

    1986-01-01

    Range resolution of a conventional pulsed Doppler radar is determined by the scattering volume defined by the transmitted pulse shape. To increase the resolution, the length of the pulse must be reduced. Reducing the pulse length also reduces the transmitted power and hense the signal to noise ratio unless the peak power capability of the transmitter is greatly increased. Improved range resolution may also be attained through the use of various pulse coding methods, but such methods are sometimes difficult to implement from a hardware standpoint. The frequency-hopping (F-H) technique described increases the range resolution of pulse Doppler MST (mesosphere stratosphere troposphere) radar without the need for extensive modifications to the radar transmitter. This technique consists of sending a repeated sequence of pulses, each pulse in the sequence being transmitted at a unique radio frequency that is under the control of a microcomputer. This technique is discussed along with other radar parameters.

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

    PubMed

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

    2008-05-01

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

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

    PubMed

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

    2015-01-01

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

  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.

  20. Description and Power Analysis of Two Tests for Detecting Recent Population Bottlenecks from Allele Frequency Data

    PubMed Central

    Cornuet, J. M.; Luikart, G.

    1996-01-01

    When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed. PMID:8978083

  1. Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower.

    PubMed

    Whitney, Kenneth D; Broman, Karl W; Kane, Nolan C; Hovick, Stephen M; Randell, Rebecca A; Rieseberg, Loren H

    2015-05-01

    The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 single nucleotide polymorphism (SNP) markers and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favoured in the wild. QTL for a number of other ecophysiological, phenological and architectural traits colocalized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence.

  2. Maximum-likelihood and markov chain monte carlo approaches to estimate inbreeding and effective size from allele frequency changes.

    PubMed Central

    Laval, Guillaume; SanCristobal, Magali; Chevalet, Claude

    2003-01-01

    Maximum-likelihood and Bayesian (MCMC algorithm) estimates of the increase of the Wright-Malécot inbreeding coefficient, F(t), between two temporally spaced samples, were developed from the Dirichlet approximation of allelic frequency distribution (model MD) and from the admixture of the Dirichlet approximation and the probabilities of fixation and loss of alleles (model MDL). Their accuracy was tested using computer simulations in which F(t) = 10% or less. The maximum-likelihood method based on the model MDL was found to be the best estimate of F(t) provided that initial frequencies are known exactly. When founder frequencies are estimated from a limited set of founder animals, only the estimates based on the model MD can be used for the moment. In this case no method was found to be the best in all situations investigated. The likelihood and Bayesian approaches give better results than the classical F-statistics when markers exhibiting a low polymorphism (such as the SNP markers) are used. Concerning the estimations of the effective population size all the new estimates presented here were found to be better than the F-statistics classically used. PMID:12871924

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

    PubMed

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

    2007-10-01

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

  4. Beta-thalassemia mutations in Rome. A high frequency of the IVSII-745 allele in subjects of latium origin.

    PubMed

    Massa, A; Cianciulli, P; Cianetti, L; Iazzone, R; Cenci, A; Sorrentino, F; Franco, G; Pecci, G; Papa, G; Peschle, C

    1994-01-01

    We studied the molecular bases of beta-thalassemia in Rome, a city centrally located in Latium, which is a region with a low incidence of beta-carriers. People also come to Rome from other regions for specific or prenatal diagnostic assessment. Only 11 patients (20%) out of 62 characterized beta-thalassemia subjects were of Latium family origin. They presented five mutations with an uncommonly high frequency of the IVSII-745 allele, that was found in homozygosis in 4 unrelated patients from a southeastern area in the province of Frosinone. These data may indicate a founder effect.

  5. Range-azimuth decouple beamforming for frequency diverse array with Costas-sequence modulated frequency offsets

    NASA Astrophysics Data System (ADS)

    Wang, Zhe; Wang, Wen-Qin; Shao, Huaizong

    2016-12-01

    Different from the phased-array using the same carrier frequency for each transmit element, the frequency diverse array (FDA) uses a small frequency offset across the array elements to produce range-angle-dependent transmit beampattern. FDA radar provides new application capabilities and potentials due to its range-dependent transmit array beampattern, but the FDA using linearly increasing frequency offsets will produce a range and angle coupled transmit beampattern. In order to decouple the range-azimuth beampattern for FDA radar, this paper proposes a uniform linear array (ULA) FDA using Costas-sequence modulated frequency offsets to produce random-like energy distribution in the transmit beampattern and thumbtack transmit-receive beampattern. In doing so, the range and angle of targets can be unambiguously estimated through matched filtering and subspace decomposition algorithms in the receiver signal processor. Moreover, random-like energy distributed beampattern can also be utilized for low probability of intercept (LPI) radar applications. Numerical results show that the proposed scheme outperforms the standard FDA in focusing the transmit energy, especially in the range dimension.

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

    PubMed Central

    Mattei, Josiemer; Parnell, Laurence D; Lai, Chao-Qiang; Garcia-Bailo, Bibiana; Adiconis, Xian; Shen, Jian; Arnett, Donna; Demissie, Serkalem; Tucker, Katherine L; Ordovas, Jose M

    2009-01-01

    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 pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs) in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n = 969, ages 45–75 years) and compared them to similarly aged non-Hispanic whites (NHW) (n = 597). Results Minor allele frequency (MAF) distributions for 45.5% of the SNPs assessed in Puerto Ricans were significantly different from those of NHW. Puerto Ricans carried risk alleles in higher frequency and protective alleles in lower frequency than NHW. Patterns of population differentiation showed that Puerto Ricans had SNPs with exceptional FST values in intronic, non-synonymous and promoter regions. NHW had exceptional FST values in intronic and promoter region SNPs only. Conclusion These observations may serve to explain and broaden studies on the impact of gene polymorphisms on chronic diseases affecting Puerto Ricans. PMID:19682384

  7. The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large-effect alleles can allow range expansion.

    PubMed

    Gilbert, K J; Whitlock, M C

    2017-03-01

    Range expansions are complex evolutionary and ecological processes. From an evolutionary standpoint, a populations' adaptive capacity can determine the success or failure of expansion. Using individual-based simulations, we model range expansion over a two-dimensional, approximately continuous landscape. We investigate the ability of populations to adapt across patchy environmental gradients and examine how the effect sizes of mutations influence the ability to adapt to novel environments during range expansion. We find that genetic architecture and landscape patchiness both have the ability to change the outcome of adaptation and expansion over the landscape. Adaptation to new environments succeeds via many mutations of small effect or few of large effect, but not via the intermediate between these cases. Higher genetic variance contributes to increased ability to adapt, but an alternative route of successful adaptation can proceed from low genetic variance scenarios with alleles of sufficiently large effect. Steeper environmental gradients can prevent adaptation and range expansion on both linear and patchy landscapes. When the landscape is partitioned into local patches with sharp changes in phenotypic optimum, the local magnitude of change between subsequent patches in the environment determines the success of adaptation to new patches during expansion.

  8. Ranging with frequency-shifted feedback lasers: from μm-range accuracy to MHz-range measurement rate

    NASA Astrophysics Data System (ADS)

    Kim, J. I.; Ogurtsov, V. V.; Bonnet, G.; Yatsenko, L. P.; Bergmann, K.

    2016-12-01

    We report results on ranging based on frequency-shifted feedback (FSF) lasers with two different implementations: (1) An Ytterbium-fiber system for measurements in an industrial environment with accuracy of the order of 1 μm, achievable over a distance of the order of meters with potential to reach an accuracy of better than 100 nm; (2) A semiconductor laser system for a high rate of measurements with an accuracy of 2 mm @ 1 MHz or 75 μm @ 1 kHz and a limit of the accuracy of ≥10 μm. In both implementations, the distances information is derived from a frequency measurement. The method is therefore insensitive to detrimental influence of ambient light. For the Ytterbium-fiber system, a key feature is the injection of a single-frequency laser, phase modulated at variable frequency Ω, into the FSF-laser cavity. The frequency Ω_{max} at which the detector signal is maximal yields the distance. The semiconductor FSF-laser system operates without external injection seeding. In this case, the key feature is frequency counting that allows convenient choice of either accuracy or speed of measurements simply by changing the duration of the interval during which the frequency is measured by counting.

  9. Inheritance of Cry1F resistance, cross-resistance and frequency of resistant alleles in Spodoptera frugiperda (Lepidoptera: Noctuidae).

    PubMed

    Vélez, A M; Spencer, T A; Alves, A P; Moellenbeck, D; Meagher, R L; Chirakkal, H; Siegfried, B D

    2013-12-01

    Transgenic maize, Zea maize L., expressing the Cry1F protein from Bacillus thuringiensis has been registered for Spodoptera frugiperda (J. E. Smith) control since 2003. Unexpected damage to Cry1F maize was reported in 2006 in Puerto Rico and Cry1F resistance in S. frugiperda was documented. The inheritance of Cry1F resistance was characterized in a S. frugiperda resistant strain originating from Puerto Rico, which displayed >289-fold resistance to purified Cry1F. Concentration-response bioassays of reciprocal crosses of resistant and susceptible parental populations indicated that resistance is recessive and autosomal. Bioassays of the backcross of the F1 generation crossed with the resistant parental strain suggest that a single locus is responsible for resistance. In addition, cross-resistance to Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry2Aa and Vip3Aa was assessed in the Cry1F-resistant strain. There was no significant cross-resistance to Cry1Aa, Cry1Ba and Cry2Aa, although only limited effects were observed in the susceptible strain. Vip3Aa was highly effective against susceptible and resistant insects indicating no cross-resistance with Cry1F. In contrast, low levels of cross-resistance were observed for both Cry1Ab and Cry1Ac. Because the resistance is recessive and conferred by a single locus, an F1 screening assay was used to measure the frequency of Cry1F-resistant alleles from populations of Florida and Texas in 2010 and 2011. A total frequency of resistant alleles of 0.13 and 0.02 was found for Florida and Texas populations, respectively, indicating resistant alleles could be found in US populations, although there have been no reports of reduced efficacy of Cry1F-expressing plants.

  10. Multimode VCSEL model for wide frequency-range RIN simulation

    NASA Astrophysics Data System (ADS)

    Perchoux, Julien; Rissons, Angélique; Mollier, Jean-Claude

    2008-01-01

    In this paper, we present an equivalent circuit model for oxide-confined AlGaAs/GaAs VCSEL with the noise contribution adapted to optomicrowave links applications. This model is derived from the multimode rate equations. In order to understand the modal competition process, we restrain our description to a two-modes rate equations system affected by the spectral hole-burning. The relative intensity noise (RIN) measurements which were achieved on a prober in Faraday cage confirm the low frequency enhancement described by the model. We validate our model for a wide frequency-range [1 MHz-10 GHz] and high bias level up to six times the threshold current.

  11. Heating by waves in the ion cyclotron frequency range

    SciTech Connect

    Koch, R.

    1996-03-01

    The main aspects of heating with the fast wave in the ion cyclotron range of frequencies (ICRF) are reviewed. First, the ion cyclotron resonance mechanism, fundamental and harmonics, is examined. Then the properties of fast wave dispersion are reviewed, and the principles of minority and higher cylcotron harmonic heating are discussed. An elementary coupling model is worked out in order to outline the computation of the electrical properties of ICRF antennas. Using the simple model, the antenna radiation pattern inside the plasma is computed and the effect of phasing on the k spectrum and on the antenna radiation properties is illustrated. The quasi linear-Fokker-Planck computation of the deformation of distribution functions due to Radio-Frequency (RF) and tail formation are briefly discussed. 11 refs., 5 figs.

  12. Comprehensive genetic testing with ethnic-specific filtering by allele frequency in a Japanese hearing-loss population

    PubMed Central

    Moteki, Hideaki; Azaiez, Hela; Booth, Kevin T; Shearer, A Eliot; Sloan, Christina M; Kolbe, Diana L; Nishio, Shin-ya; Hattori, Mitsuru; Usami, Shin-ichi; Smith, Richard J H

    2016-01-01

    Recent advances in targeted genomic enrichment with massively parallel sequencing (TGE+MPS) have made comprehensive genetic testing for non-syndromic hearing loss (NSHL) possible. After excluding NSHL subjects with causative mutations in GJB2 and the MT-RNR1 (1555A>G) variant by Sanger sequencing, we completed TGE+MPS on 194 probands with presumed NSHL identified across Japan. We used both publicly available minor allele frequency (MAF) datasets and ethnic-specific MAF filtering against an in-house database of 200 normal-hearing Japanese controls. Ethnic-specific MAF filtering allowed us to re-categorize as common 203 variants otherwise annotated as rare or novel in non-Japanese ethnicities. This step minimizes false-positive results and improves the annotation of identified variants. Causative variants were identified in 27% of probands with solve rates of 35%, 35% and 19% for dominant, recessive and sporadic NSHL, respectively. Mutations in MYO15A and CDH23 follow GJB2 as the frequent causes of recessive NSHL; copy number variations in STRC are a major cause of mild-to-moderate NSHL. Ethnic-specific filtering by allele frequency is essential to optimize the interpretation of genetic data. PMID:26346818

  13. Positive Selection of Deleterious Alleles through Interaction with a Sex-Ratio Suppressor Gene in African Buffalo: A Plausible New Mechanism for a High Frequency Anomaly

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-08-01

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

  16. [Spectral analysis of nitrofurantoin in the terahertz frequency range].

    PubMed

    Kang, Xu-Sheng; Hou, Di-Bo; Zhang, Guang-Xin; Chen, Xi-Ai; Yue, Fei-Heng; Huang, Ping-Jie; Zhou, Ze-Kui

    2012-07-01

    The present article measured the absorption coefficient spectra and refractive index spectra of nitrofurantoin original drug, which is one kind of nitrofuran drugs, in the terahertz frequency range from 0.2 to 1.8 THz using terahertz time-domain spectroscopy. The results showed that there exist a number of characteristic absorption peaks of nitrofurantoin with different intensity in the range and the absorption coefficient spectra can be used to identify nitrofurantoin. The article also simulated absorption coefficient spectra of nitrofurantoin molecule within 0.2 - 1.8 THz using density functional theory by Gaussian software, and vibrational modes of some peaks in the experimental absorption coefficient spectra were analyzed and identified. The results show that the experimental absorption peaks at 1.25 and 1.60 THz correspond with the theoretical peaks at 1.30 and 1.67 THz, and these experimental peaks were caused by intramolecular vibrational modes of nitrofurantoin.

  17. Dielectric permittivity of biological tissues in the microwave frequency range

    NASA Astrophysics Data System (ADS)

    Behari, J.; Alex, Z. C.; Zaidi, Zahid H.

    1994-09-01

    The accurate knowledge of complex dielectric behavior of biological tissues at microwave frequency is of great importance in the biomedical field for its diagnostic and therapeutic uses. This information is also essential for studying the mechanism underlying the absorption of electromagnetic energy and also the emission by tissues. In the present work, in vitro complex dielectric permittivity of liver and muscle were measured in the frequency range 0.6 GHz to 1.2 GHz using a network analyzer. An open ended coaxial cable method was used and the complex dielectric permittivity was measured from the actual terminal admittance of the sample. The system was calibrated with three standard samples. The measurements were conducted at room temperature. The calculated values of (Epsilon) ' varied from 53 to 48 for liver and from 49 to 46 for muscle. The corresponding (Epsilon) ' varied from 29 to 38 and 30 to 34 respectively. The relaxation frequency and degree of dispersion were also calculated and estimation of bound water content made in each case.

  18. Wide tracking range, auto ranging, low jitter phase lock loop for swept and fixed frequency systems

    DOEpatents

    Kerner, Thomas M.

    2001-01-01

    The present invention provides a wide tracking range phase locked loop (PLL) circuit that achieves minimal jitter in a recovered clock signal, regardless of the source of the jitter (i.e. whether it is in the source or the transmission media). The present invention PLL has automatic harmonic lockout detection circuitry via a novel lock and seek control logic in electrical communication with a programmable frequency discriminator and a code balance detector. (The frequency discriminator enables preset of a frequency window of upper and lower frequency limits to derive a programmable range within which signal acquisition is effected. The discriminator works in combination with the code balance detector circuit to minimize the sensitivity of the PLL circuit to random data in the data stream). In addition, the combination of a differential loop integrator with the lock and seek control logic obviates a code preamble and guarantees signal acquisition without harmonic lockup. An adaptive cable equalizer is desirably used in combination with the present invention PLL to recover encoded transmissions containing a clock and/or data. The equalizer automatically adapts to equalize short haul cable lengths of coaxial and twisted pair cables or wires and provides superior jitter performance itself. The combination of the equalizer with the present invention PLL is desirable in that such combination permits the use of short haul wires without significant jitter.

  19. A Frequency Domain Approach to Pretest Analysis Model Correlation and Model Updating for the Mid-Frequency Range

    DTIC Science & Technology

    2009-02-01

    range of modal analysis and the high frequency region of statistical energy analysis , is referred to as the mid-frequency range. The corresponding...frequency range of modal analysis and the high frequency region of statistical energy analysis , is referred to as the mid-frequency range. The...predictions. The averaging process is consistent with the averaging done in statistical energy analysis for stochastic systems. The FEM will always

  20. Highly Connected Populations and Temporal Stability in Allelic Frequencies of a Harvested Crab from the Southern Pacific Coast.

    PubMed

    Rojas-Hernandez, Noemi; Veliz, David; Riveros, Marcela P; Fuentes, Juan P; Pardo, Luis M

    2016-01-01

    For marine invertebrates with a benthic adult form and a planktonic larva phase, the connectivity among populations is mainly based on larval dispersal. While an extended larval phase will promote gene flow, other factors such as an intensive fishery and geographical barriers could lead to changes in genetic variability. In this study, the population genetic structure of the commercial crab Metacarcinus edwardsii was analyzed along 700 km of the Chilean coast. The analysis, based on eight microsatellite loci genotyped from megalopae and adult crabs, considered temporal and spatial patterns of genetic variation. The results showed no evidence of spatial patterns in genetic structure, suggesting high connectivity among the sampling sites. The temporal analysis showed no evidence of changes in allele frequencies and no evidence of a recent bottleneck. The lack of spatial structure and allele variation over time could be explained by the interaction of factors such as i) low reproductive variance due to the capability of females to store sperm in the seminal receptacle, which can be used for successive broods, ii) high larval dispersal and iii) high individual reproductive output. Using our data as priors, a genetic modelling approach coincided, predicting this temporal and spatial stability. The same analysis showed that a reduction in population size leads to the loss of genetic variability in populations, as well as of the genetic cohesiveness between populations, pointing out the importance management for species under exploitation, such as M. edwardsii.

  1. Genetic Diversity and Allelic Frequency of Glutamate-Rich Protein (GLURP) in Plasmodium falciparum Isolates from Sub-Saharan Africa

    PubMed Central

    Duru, Kimberley C; Thomas, Bolaji N

    2014-01-01

    Glutamate-rich protein is a Plasmodium falciparum (Pf) antigen found in all stages of the parasite and has been reported to induce clinical immunity. The R0 and R2 regions have been found to exhibit a high degree of conservation, therefore serving as a good vaccine design material. We assayed the genetic diversity of Pf glurp genes in the R0 and R2 regions, as well as evaluated the role of seasonality on allelic frequency. A total of 402 genomic DNA samples, extracted from filter paper blood samples, were screened by nested polymerase chain reaction (PCR) analysis of Pf glurp R0 and R2 regions, in addition to fragment analysis of the polymorphic regions to identify allelic diversity of the parasite population. We found an extensive heterogeneity in the R2 region in general, and this heterogeneity is seasonally dependent, indicative of region plasticity. The R0 region displayed genetic conservation, as expected. We conclude that positive genotyping results with glurp R0 region should be seen as indicative of an active Pf infection, requiring adequate treatment. In addition, we advocate extending the possibility that an R0 region genotypic positivity could serve as diagnostic tool, thereby reducing cases of untreated or poorly treated infection, contributory to recrudescence or treatment failure. PMID:25452699

  2. Highly Connected Populations and Temporal Stability in Allelic Frequencies of a Harvested Crab from the Southern Pacific Coast

    PubMed Central

    Rojas-Hernandez, Noemi; Veliz, David; Riveros, Marcela P; Fuentes, Juan P.; Pardo, Luis M.

    2016-01-01

    For marine invertebrates with a benthic adult form and a planktonic larva phase, the connectivity among populations is mainly based on larval dispersal. While an extended larval phase will promote gene flow, other factors such as an intensive fishery and geographical barriers could lead to changes in genetic variability. In this study, the population genetic structure of the commercial crab Metacarcinus edwardsii was analyzed along 700 km of the Chilean coast. The analysis, based on eight microsatellite loci genotyped from megalopae and adult crabs, considered temporal and spatial patterns of genetic variation. The results showed no evidence of spatial patterns in genetic structure, suggesting high connectivity among the sampling sites. The temporal analysis showed no evidence of changes in allele frequencies and no evidence of a recent bottleneck. The lack of spatial structure and allele variation over time could be explained by the interaction of factors such as i) low reproductive variance due to the capability of females to store sperm in the seminal receptacle, which can be used for successive broods, ii) high larval dispersal and iii) high individual reproductive output. Using our data as priors, a genetic modelling approach coincided, predicting this temporal and spatial stability. The same analysis showed that a reduction in population size leads to the loss of genetic variability in populations, as well as of the genetic cohesiveness between populations, pointing out the importance management for species under exploitation, such as M. edwardsii. PMID:27814382

  3. The frequency of different CGG-repeat alleles in the FMR-1 gene in the general population and special populations

    SciTech Connect

    Holden, J.J.A. |; Chalifoux, M.; Wing, M.

    1994-09-01

    The fragile X (FRAXA) syndrome is the most common inherited form of developmental disability and was the first genetic disorder in which the mechanism of mutation is triplet repeat expansion. The normal fragile X mental retardation-1 gene has 6-52 copies of the CGG-repeat; affected males have extensive amplification, coupled with methylation and gene inactivation; and carriers have between about 55 and 200 copies. There is some overlap in the 45-55 repeat range, with some alleles showing stable and othres unstable transmission. There have been several estimates of the incidence of the FRAXA syndrome, based on testing of special populations using chromosome analysis and the range is 1/750-1/2000. Because of the high burden associated with this syndrome, and in the face of discussions about population screening, it is important to know the actual incidence of mutations in this gene, as well as the distribution of unstable repeats above 45 copes. We have initiated a general population screening to examine 50,000 newborn samples using PCR, and have developed a rapid, inexpensive and reliable method for amplifying the CGG-repeat from Guthrie spots. In the first 1600 samples examined, we found 15 alleles with greater than 45 CGG-repeats, with the highest being 61 repeats.

  4. An analysis of HLA-A, -B, and -DRB1 allele and haplotype frequencies of 21,918 residents living in Liaoning, China.

    PubMed

    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.

  5. Transport induced by ion cyclotron range of frequencies waves

    SciTech Connect

    Zhang, Debing Xu, Yingfeng; Wang, Shaojie

    2014-11-15

    The Vlasov equation, which includes the effect of the ion cyclotron range of frequencies (ICRF) waves, can be written as the Fokker-Planck equation which describes the quasilinear transport in phase space by using the Lie-transform method. The radial transport fluxes of particle, energy and parallel momentum driven by ICRF waves in the slab geometry have been derived. The results show that the ICRF-induced radial redistributions of particle, energy and parallel momentum are driven by the inhomogeneity in energy of the equilibrium distribution function, and related to the correlation between the excursion in the real space and the excursion in energy. For the case with strong asymmetry of k{sub y} spectrum, the ICRF-induced radial transport driven by the energy inhomogeneity dominates the ICRF-induced radial transport driven by the spatial inhomogeneity.

  6. High precision spectroscopy and imaging in THz frequency range

    NASA Astrophysics Data System (ADS)

    Vaks, Vladimir L.

    2014-03-01

    Application of microwave methods for development of the THz frequency range has resulted in elaboration of high precision THz spectrometers based on nonstationary effects. The spectrometers characteristics (spectral resolution and sensitivity) meet the requirements for high precision analysis. The gas analyzers, based on the high precision spectrometers, have been successfully applied for analytical investigations of gas impurities in high pure substances. These investigations can be carried out both in absorption cell and in reactor. The devices can be used for ecological monitoring, detecting the components of chemical weapons and explosive in the atmosphere. The great field of THz investigations is the medicine application. Using the THz spectrometers developed one can detect markers for some diseases in exhaled air.

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

    PubMed

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

    2007-05-24

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

  8. Allele frequencies of the new European Standard Set (ESS) loci in a population of Apulia (Southern Italy).

    PubMed

    Piglionica, M; Baldassarra, S Lonero; Giardina, E; Tonino Marsella, L; Resta, N; Dell'Erba, A

    2013-02-01

    Allele frequencies of five miniSTRs loci (D1S1656, D2S441, D12S391, D10S1248 and D22S1045) included in the new European Standard Set (ESS) were calculated from a sample of 150 unrelated individuals from Apulia, a Region of Southern Italy. Two different PCR Amplification Kits were used, in order to evaluate the concordance of the genotypes. The results obtained with the two kits showed no differences in all genotype profiles. No deviation from Hardy-Weinberg expectations was detected at either locus. Moreover genetic analysis using Fst estimation showed no evidence for differentiation at the five new loci between Apulia and Italian populations. The high levels of polymorphisms of the analyzed markers in the Apulian population allow to confirm that these markers are useful tools in paternity and forensic analysis from degraded DNA samples.

  9. POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface.

    PubMed

    Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro

    2010-04-01

    Currently, there is a demand for software to analyze polymorphism data such as microsatellite DNA and single nucleotide polymorphism with easily accessible interface in many fields of research. In this article, we would like to make an announcement of POPTREE2, a computer program package, that can perform evolutionary analyses of allele frequency data. The original version (POPTREE) was a command-line program that runs on the Command Prompt of Windows and Unix. In POPTREE2 genetic distances (measures of the extent of genetic differentiation between populations) for constructing phylogenetic trees, average heterozygosities (H) (a measure of genetic variation within populations) and G(ST) (a measure of genetic differentiation of subdivided populations) are computed through a simple and intuitive Windows interface. It will facilitate statistical analyses of polymorphism data for researchers in many different fields. POPTREE2 is available at http://www.med.kagawa-u.ac.jp/ approximately genomelb/takezaki/poptree2/index.html.

  10. Range and Frequency of Africanized Honey Bees in California (USA)

    PubMed Central

    Kono, Yoshiaki; Kohn, Joshua R.

    2015-01-01

    Africanized honey bees entered California in 1994 but few accounts of their northward expansion or their frequency relative to European honey bees have been published. We used mitochondrial markers and morphometric analyses to determine the prevalence of Africanized honeybees in San Diego County and their current northward progress in California west of the Sierra Nevada crest. The northernmost African mitotypes detected were approximately 40 km south of Sacramento in California’s central valley. In San Diego County, 65% of foraging honey bee workers carry African mitochondria and the estimated percentage of Africanized workers using morphological measurements is similar (61%). There was no correlation between mitotype and morphology in San Diego County suggesting Africanized bees result from bidirectional hybridization. Seventy percent of feral hives, but only 13% of managed hives, sampled in San Diego County carried the African mitotype indicating that a large fraction of foraging workers in both urban and rural San Diego County are feral. We also found a single nucleotide polymorphism at the DNA barcode locus COI that distinguishes European and African mitotypes. The utility of this marker was confirmed using 401 georeferenced honey bee sequences from the worldwide Barcode of Life Database. Future censuses can determine whether the current range of the Africanized form is stable, patterns of introgression at nuclear loci, and the environmental factors that may limit the northern range of the Africanized honey bee. PMID:26361047

  11. Range and Frequency of Africanized Honey Bees in California (USA).

    PubMed

    Kono, Yoshiaki; Kohn, Joshua R

    2015-01-01

    Africanized honey bees entered California in 1994 but few accounts of their northward expansion or their frequency relative to European honey bees have been published. We used mitochondrial markers and morphometric analyses to determine the prevalence of Africanized honeybees in San Diego County and their current northward progress in California west of the Sierra Nevada crest. The northernmost African mitotypes detected were approximately 40 km south of Sacramento in California's central valley. In San Diego County, 65% of foraging honey bee workers carry African mitochondria and the estimated percentage of Africanized workers using morphological measurements is similar (61%). There was no correlation between mitotype and morphology in San Diego County suggesting Africanized bees result from bidirectional hybridization. Seventy percent of feral hives, but only 13% of managed hives, sampled in San Diego County carried the African mitotype indicating that a large fraction of foraging workers in both urban and rural San Diego County are feral. We also found a single nucleotide polymorphism at the DNA barcode locus COI that distinguishes European and African mitotypes. The utility of this marker was confirmed using 401 georeferenced honey bee sequences from the worldwide Barcode of Life Database. Future censuses can determine whether the current range of the Africanized form is stable, patterns of introgression at nuclear loci, and the environmental factors that may limit the northern range of the Africanized honey bee.

  12. 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

  13. dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.

    PubMed

    Tahira, Tomoko; Baba, Shingo; Higasa, Koichiro; Kukita, Yoji; Suzuki, Yutaka; Sugano, Sumio; Hayashi, Kenshi

    2005-08-01

    We present a database, dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/), that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5' ends of full-length cDNA clones. We searched for the SNPs in these regions by sequencing or single-strand conformation polymorphism (SSCP) analysis. The allele frequencies of the identified SNPs in two ethnic groups were quantified by SSCP analyses of pooled DNA samples. The accuracy of our estimation is supported by strong correlations between the frequencies in our data and those in other databases for the same ethnic groups. The frequencies vary considerably between the two ethnic groups studied, suggesting the need for population-based collections and allele frequency determination of SNPs, in, e.g., association studies of diseases. We show profiles of SNP densities that are characteristic of transcription start site regions. A fraction of the SNPs revealed a significantly different allele frequency between the groups, suggesting differential selection of the genes involved.

  14. Role of the B Allele of Influenza A Virus Segment 8 in Setting Mammalian Host Range and Pathogenicity

    PubMed Central

    Turnbull, Matthew L.; Wise, Helen M.; Nicol, Marlynne Q.; Smith, Nikki; Dunfee, Rebecca L.; Beard, Philippa M.; Jagger, Brett W.; Ligertwood, Yvonne; Hardisty, Gareth R.; Xiao, Haixia; Benton, Donald J.; Coburn, Alice M.; Paulo, Joao A.; Gygi, Steven P.; McCauley, John W.; Taubenberger, Jeffery K.; Lycett, Samantha J.; Weekes, Michael P.; Dutia, Bernadette M.

    2016-01-01

    ABSTRACT Two alleles of segment 8 (NS) circulate in nonchiropteran influenza A viruses. The A allele is found in avian and mammalian viruses, but the B allele is viewed as being almost exclusively found in avian viruses. This might reflect the fact that one or both of its encoded proteins (NS1 and NEP) are maladapted for replication in mammalian hosts. To test this, a number of clade A and B avian virus-derived NS segments were introduced into human H1N1 and H3N2 viruses. In no case was the peak virus titer substantially reduced following infection of various mammalian cell types. Exemplar reassortant viruses also replicated to similar titers in mice, although mice infected with viruses with the avian virus-derived segment 8s had reduced weight loss compared to that achieved in mice infected with the A/Puerto Rico/8/1934 (H1N1) parent. In vitro, the viruses coped similarly with type I interferons. Temporal proteomics analysis of cellular responses to infection showed that the avian virus-derived NS segments provoked lower levels of expression of interferon-stimulated genes in cells than wild type-derived NS segments. Thus, neither the A nor the B allele of avian virus-derived NS segments necessarily attenuates virus replication in a mammalian host, although the alleles can attenuate disease. Phylogenetic analyses identified 32 independent incursions of an avian virus-derived A allele into mammals, whereas 6 introductions of a B allele were identified. However, A-allele isolates from birds outnumbered B-allele isolates, and the relative rates of Aves-to-Mammalia transmission were not significantly different. We conclude that while the introduction of an avian virus segment 8 into mammals is a relatively rare event, the dogma of the B allele being especially restricted is misleading, with implications in the assessment of the pandemic potential of avian influenza viruses. IMPORTANCE Influenza A virus (IAV) can adapt to poultry and mammalian species, inflicting a

  15. Allele and genotype frequencies of CYP2B6 and CYP2C19 polymorphisms in Egyptian agricultural workers.

    PubMed

    Ellison, Corie A; Abou El-Ella, Soheir S; Tawfik, Maha; Lein, Pamela J; Olson, James R

    2012-01-01

    Genetic variability in cytochrome P-450 (CYP) has the potential to modify pharmacological and toxicological responses to many chemicals. Both CYP2B6 and CYP2C19 are pharmacologically and toxicologically relevant due to their ability to metabolize multiple drugs and environmental contaminants, including the organophosphorus (OP) pesticide chlorpyrifos. The aim of this study was to determine the prevalence of CYP2B6 and CYP2C19 variants in an indigenous Egyptian population (n = 120) that was shown to be occupationally exposed to chlorpyrifos. Further, the genotyping data was compared for Egyptians with previously studied populations to determine between population differences. Allelic frequencies were CYP2B6 1459C > T (3.8%), CYP2B6 785A > G (30.4%), CYP2B6 516G > T (28.8%), CYP2C19 681G > A (3.8%), and CYP2C19 431G > A (0%). The most prevalent CYP2B6 genotype combinations were CYP2B6 *1/*1 (44%), *1/*6 (38%), *6/*6 (8%), and *1/*5 (6%). The frequency of the CYP2C19 genotype combinations were CYP2C19 *1/*1 (93%), *1/*2 (6%), and *2/*2 (1%). The frequency of the CYP2B6 516G > T and CYP2B6 785A > G polymorphisms in this Egyptian cohort is similar to that found North American and European populations but significantly different from that reported for West African populations, while that of CYP2B6 1459C > T is similar to that found in Africans and African Americans. The observed frequency of CYP2C19 681G > A in Egyptians is similar to that of African pygmies but significantly different from other world populations, while CYP2C19 431 G > A was significantly different from that of African pygmies but similar to other world populations.

  16. Long range ultra-high frequency (UHF) radio frequency identification (RFID) antenna design

    NASA Astrophysics Data System (ADS)

    Reynolds, Nathan D.

    There is an ever-increasing demand for radio frequency identification (RFID) tags that are passive, long range, and mountable on multiple surfaces. Currently, RFID technology is utilized in numerous applications such as supply chain management, access control, and public transportation. With the combination of sensory systems in recent years, the applications of RFID technology have been extended beyond tracking and identifying. This extension includes applications such as environmental monitoring and healthcare applications. The available sensory systems usually operate in the medium or high frequency bands and have a low read range. However, the range limitations of these systems are being overcome by the development of RFID sensors focused on utilizing tags in the ultra-high frequency (UHF) band. Generally, RFID tags have to be mounted to the object that is being identified. Often the objects requiring identification are metallic. The inherent properties of metallic objects have substantial effects on nearby electromagnetic radiation; therefore, the operation of the tag antenna is affected when mounted on a metallic surface. This outlines one of the most challenging problems for RFID systems today: the optimization of tag antenna performance in a complex environment. In this research, a novel UHF RFID tag antenna, which has a low profile, long range, and is mountable on metallic surfaces, is designed analytically and simulated using a 3-D electromagnetic simulator, ANSYS HFSS. A microstrip patch antenna is selected as the antenna structure, as patch antennas are low profile and suitable for mounting on metallic surfaces. Matching and theoretical models of the microstrip patch antenna are investigated. Once matching and theory of a microstrip patch antenna is thoroughly understood, a unique design technique using electromagnetic band gap (EBG) structures is explored. This research shows that the utilization of an EBG structure in the patch antenna design yields

  17. Variation in meiotic recombination frequencies between allelic transgenes inserted at different sites in the Drosophila melanogaster genome.

    PubMed

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

    2013-08-07

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

  18. Polymorphism of the bovine POU1F1 gene: allele frequencies and effects on milk production in three Iranian native breeds and Holstein cattle of Iran.

    PubMed

    Zakizadeh, S; Reissmann, M; Rahimi, G; Javaremi, A Nejati; Reinecke, P; Mirae-Ashtiani, S R; Shahrbabak, M Moradi

    2007-08-01

    The aim of this study was to estimate the allele frequencies in polymorphic site of exon six of POU1F1 gene in three Iranian native and Holstein cattle. Genomic DNA was extracted from 3 Iranian native cattle breeds, including 97 Mazandarani, 87 Sarabi, 112 Golpaygani and also 110 Holstein cattle. A 451 bp fragment of intron 5 and exon 6 were amplified and digested with HinfI restriction enzyme. Frequencies of allele A were 0.37, 0.27, 0.34 and 0.21 for Mazandarani, Sarabi, Golpaygani and Holstein cattle, respectively. Significant differences in genotype frequencies were found between Mazandarani or Golpaygani and Holstein cattle. No significant differences in genotype frequencies were found between Sarabi and Holstein cattle. Transition A to G in nucleotide 1256 is responsible for HinfI(-) allele. No significant association was observed between POU1F1 polymorphism and milk production. Differences in allelic frequency between native Bos indicus breeds (Mazandarani, Golpaygani) and Holstein at the present study might be due to differences in origin breeds, low number of samples and/or as the effect of natural selection in native breeds.

  19. A wide-frequency-range air-jet shaker

    NASA Technical Reports Server (NTRS)

    Herr, Robert W

    1957-01-01

    This paper presents a description of a simple air-jet shaker. Its force can be calibrated statically and appears to be constant with frequency. It is relatively easy to use, and it has essentially massless characteristics. This shaker is applied to define the unstable branch of a frequency-response curve obtained for a nonlinear spring with a single degree of freedom.

  20. 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.

  1. OutLyzer: software for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice

    PubMed Central

    Muller, Etienne; Goardon, Nicolas; Brault, Baptiste; Rousselin, Antoine; Paimparay, Germain; Legros, Angelina; Fouillet, Robin; Bruet, Olivia; Tranchant, Aurore; Domin, Florian; San, Chankannira; Quesnelle, Céline; Frebourg, Thierry; Ricou, Agathe; Krieger, Sophie; Vaur, Dominique; Castera, Laurent

    2016-01-01

    Highlighting tumoral mutations is a key step in oncology for personalizing care. Considering the genetic heterogeneity in a tumor, software used for detecting mutations should clearly distinguish real tumor events of interest that could be predictive markers for personalized medicine from false positives. OutLyzer is a new variant-caller designed for the specific and sensitive detection of mutations for research and diagnostic purposes. It is based on statistic and local evaluation of sequencing background noise to highlight potential true positive variants. 130 previously genotyped patients were sequenced after enrichment by capturing the exons of 22 genes. Sequencing data were analyzed by HaplotypeCaller, LofreqStar, Varscan2 and OutLyzer. OutLyzer had the best sensitivity and specificity with a fixed limit of detection for all tools of 1% for SNVs and 2% for Indels. OutLyzer is a useful tool for detecting mutations of interest in tumors including low allele-frequency mutations, and could be adopted in standard practice for delivering targeted therapies in cancer treatment. PMID:27825131

  2. Phenol sulphotransferase SULT1A1 polymorphism: molecular diagnosis and allele frequencies in Caucasian and African populations.

    PubMed Central

    Coughtrie, M W; Gilissen, R A; Shek, B; Strange, R C; Fryer, A A; Jones, P W; Bamber, D E

    1999-01-01

    Sulphation, catalysed by members of the sulphotransferase (SULT) enzyme family, is an important component of the body's chemical defence mechanism, but also acts to bioactivate mutagens such as hydroxylated aryl and heterocyclic amines. A major human sulphotransferase, SULT1A1 (P-PST), metabolizes and/or bioactivates many drugs, iodothyronines and hydroxylated aromatic amines. The enzyme activity varies widely within the population and is under genetic control. We have developed an assay detecting a G-->A transition in SULT1A1 that causes an Arg213-->His substitution associated with low SULT activity and altered enzyme properties, and have used it to assess the SULT1A1 genotype in Caucasian (n=293) and African (Nigerian, n=52) populations. We show that the mutant SULT1A1*2 allele is present at frequencies of 0.321 and 0.269 in the Caucasian and African populations respectively. We also demonstrate a significant age-related difference in SULT1A1 genotype within our Caucasian population, with increasing incidence of SULT1A1*1 homozygosity and decreasing incidence of SULT1A1*2 homozygosity with increasing age, indicating a potential association of SULT1A1*1 allozyme(s) with protection against cell and/or tissue damage during aging. PMID:9854023

  3. 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

  4. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... frequency generated in the device or 25 MHz, whichever is lower Tenth harmonic or 1,000 MHz, whichever is... harmonic. Above 1,000 ......do Tenth harmonic or highest detectable emission. (b) For conducted...

  5. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... frequency generated in the device or 25 MHz, whichever is lower Tenth harmonic or 1,000 MHz, whichever is... harmonic. Above 1,000 ......do Tenth harmonic or highest detectable emission. (b) For conducted...

  6. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... frequency generated in the device or 25 MHz, whichever is lower Tenth harmonic or 1,000 MHz, whichever is... harmonic. Above 1,000 ......do Tenth harmonic or highest detectable emission. (b) For conducted...

  7. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... frequency generated in the device or 25 MHz, whichever is lower Tenth harmonic or 1,000 MHz, whichever is... harmonic. Above 1,000 ......do Tenth harmonic or highest detectable emission. (b) For conducted...

  8. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... frequency generated in the device or 25 MHz, whichever is lower Tenth harmonic or 1,000 MHz, whichever is... harmonic. Above 1,000 ......do Tenth harmonic or highest detectable emission. (b) For conducted...

  9. Fundamental factors affecting the optimum frequency range for SETI

    NASA Astrophysics Data System (ADS)

    Oliver, Bernard M.

    1993-08-01

    There is little doubt that confirmation of the existence of extraterrestrial intelligent life will be obtained from electromagnetic waves generated by our counterparts. The best frequency regions in which to expect such signals depends upon the free-space loss, the background noise, the spectral purity obtainable, and the power required as a function of frequency. This paper will discuss the rationale that led to the selection of the microwave window for the NASA SETI Program.

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

    PubMed

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

    2015-11-11

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

  11. 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

  12. The Frequency of HLA-A, HLA-B, and HLA-DRB1 Alleles in Patients with Acute Lymphoblastic Leukemia in the Turkish Population: A Case-Control Study

    PubMed Central

    Patıroğlu, Türkan; Akar, H. Haluk

    2016-01-01

    We studied the frequencies of human leukocyte antigen alleles (A, B, and DRB1) in 90 patients with acute lymphoblastic leukemia (ALL) and then compared them with 126 controls in this study. Although the frequencies of the A*03 allele, the DRB1*03 allele, the DRB1*04 allele, the A*02/B*35/DRB1*13 haplotype, and homozygosity of A*02 were higher in patients (p=0.006, p=0.003, p=0.002, p=0.01, and p=0.02, respectively), the frequencies of the A*23, B*13, B*40, and DRB1*13 alleles were lower (p=0.002, p=0.07, p=0.002, and p=0.003, respectively) in patients than controls. The frequencies of the DRB1*04 and DRB1*07 alleles were higher in patients in the high-risk group and standard-risk group, respectively (p=0.009 and p=0.007, respectively). This study indicated that the frequency of the A*03 allele, the DRB1*03 allele, the DRB1*04 allele, the A*02/B*35/DRB1*13 haplotype, and A*02 homozygosity may play a predisposing role in patients with ALL in the Turkish population. The frequency of the DRB1*04 and DRB1*07 alleles may also be associated with high risk and standard risk in patients with ALL, respectively. PMID:27095065

  13. The Frequency of HLA-A, HLA-B, and HLA-DRB1 Alleles in Patients with Acute Lymphoblastic Leukemia in the Turkish Population: A Case-Control Study.

    PubMed

    Patıroğlu, Türkan; Akar, H Haluk

    2016-12-01

    We studied the frequencies of human leukocyte antigen alleles (A, B, and DRB1) in 90 patients with acute lymphoblastic leukemia (ALL) and then compared them with 126 controls in this study. Although the frequencies of the A*03 allele, the DRB1*03 allele, the DRB1*04 allele, the A*02/B*35/DRB1*13 haplotype, and homozygosity of A*02 were higher in patients (p=0.006, p=0.003, p=0.002, p=0.01, and p=0.02, respectively), the frequencies of the A*23, B*13, B*40, and DRB1*13 alleles were lower (p=0.002, p=0.07, p=0.002, and p=0.003, respectively) in patients than controls. The frequencies of the DRB1*04 and DRB1*07 alleles were higher in patients in the high-risk group and standard-risk group, respectively (p=0.009 and p=0.007, respectively). This study indicated that the frequency of the A*03 allele, the DRB1*03 allele, the DRB1*04 allele, the A*02/B*35/DRB1*13 haplotype, and A*02 homozygosity may play a predisposing role in patients with ALL in the Turkish population. The frequency of the DRB1*04 and DRB1*07 alleles may also be associated with high risk and standard risk in patients with ALL, respectively.

  14. 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

  15. Allelic frequencies of 3' Ig heavy chain locus enhancer HS1,2-A associated with Ig levels in patients with schizophrenia and healthy control subjects

    PubMed Central

    Frezza, Domenico; Giambra, Vincenzo; Mattioli, Claudia; Piccoli, Katia; Massoud, Renato; Siracusano, Alberto; Giannantonio, Massimo Di; Birshtein, Barbara K.; Rubino, I. Alex

    2009-01-01

    Infectious and autoimmune pathogenic hypotheses of schizophrenia have been proposed, prompting searches for antibodies against viruses or brain structures, and for altered levels of immunoglobulins. Previous experiments have shown that allele frequencies of the Ig heavy chain 3' enhancer HS1,2*A are associated with several autoimmune diseases, suggesting a possible correlation between HS1,2 alleles and Ig production. To test this, we analyzed levels of serum Igs and HS1,2*A genotypes in two independent cohorts, one of 88 schizophrenic inpatients (24 women) and a second of 133 healthy subjects (59 women). Both groups were similar in the frequency of individuals with altered serum concentration of Ig classes and IgG subclasses (schizophrenia panel-80%; controls-68%). With the possible exception of a stabilizing effect of olanzapine, no psychopharmacological drug consumed during the month prior to serum sampling in the schizophrenia group significantly affected Ig levels. In both patient and control cohorts, an increased frequency of the HS1,2 *2A allele corresponded to increased Ig plasma levels, while an increased frequency of the HS1,2*1A allele corresponded to decreased Ig plasma levels. EMSA analysis with nuclear extracts from human B cells showed that the transcription factor SP1 bound to the polymorphic region of both HS1,2*1A and HS1,2*2A while NF-κB bound only to the HS1,2*2A. We predict that differences in transcription factor binding sites in the two allelic variants of the 3' IgH enhancer HS1,2 may provide a mechanism by which differences in Ig expression are affected. PMID:19309558

  16. Tremor suppression orthoses for parkinson's patients: a frequency range perspective.

    PubMed

    Rahimi, Fariborz; Almeida, Quincy J; Wang, David; Janabi-Sharifi, Farrokh

    2009-01-01

    While the majority of tremor-afflicted Parkinso-nian (PD) patients suffer from rest tremors, which is not considered highly disabling, a portion of these PD patients also demonstrate action tremors that interfere with their daily lives. Two main considerations in designing an orthosis that aims at suppressing the tremor, are the frequency bands of the tremor and the joints tremor affects. Nine subjects, which included six healthy people, two PD patients with typical tremor afflictions, and a PD patient with severe tremor of not only in her fingers and wrist, but also in her elbow, participated in this study. The highly afflicted patient displayed the need for tremor suppression in action as well as when in rest. The study focuses on uncommon elbow tremors and demonstrates that, for typically afflicted patients, tremor amplitudes are comparable to healthy subjects, but the frequency distribution of the tremors are different at high levels of elbow torque. For the highly afflicted patient, both tremor amplitude and its frequency distribution are different at all levels of elbow torque. The study further investigates the tremors in two bands of frequency on both hands of the highly troubled patient before, and after medication. The two bands are those of classical Parkinsonian tremor (4-6 Hz) and physiological (or enhanced physiological) tremor (8-12 Hz). Power spectrum and tremor amplitude comparisons reveal that, for part of tremulous PD patients, both tremors coexist and, depending on the level of affliction, the designed orthosis needs to suppress tremors in both bands, even at more proximal joints, such as the elbow.

  17. 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

  18. Allelic and genotypic frequencies in polymorphic Booroola fecundity gene and their association with multiple birth and postnatal growth in Chhotanagpuri sheep

    PubMed Central

    Oraon, Thanesh; Singh, D. K.; Ghosh, Mayukh; Kullu, S. S.; Kumar, Rajesh; Singh, L. B.

    2016-01-01

    Aim: Chhotanagpuri breed of sheep reared for mutton in Jharkhand, India, having problem of low litter size and body weight. The response of genetic improvement for traits with low heritability through traditional selection method is time-consuming. Therefore, marker-assisted selection based on a polymorphism study of suitable candidate gene can response quickly. Thus, this study was aimed at identification of different allelic and genotypic frequencies of Booroola fecundity (FecB) gene and its association with multiple birth and postnatal growth in Chhotanagpuri sheep. Materials and Methods: DNA isolation and gene-specific amplification of FecB gene was performed from blood samples of from 92 Chhotanagpuri lambs maintained under similar feeding and management conditions. Custom nucleotide sequencing and single-strand conformational polymorphism analysis were performed to identify different genotypes with respect to the target gene. Statistical analysis was performed for determination of allelic and genotypic frequencies of FecB gene polymorphisms and its association with multiple birth and postnatal growth of lambs from birth to 52 weeks age. Results: “AA,” “AB,” and “BB” genotypes were found at locus-1 as it is polymorphic for FecB gene while locus-2 was found to be monomorphic for FecB gene. Higher frequency of “A” allele at locus-1 was found in single born lambs, whereas “B” allele was predominant among multiple born lambs. The lambs having “BB” genotype weighed significantly (p≤0.01) heavier than those of “AB” and “AA” genotype at 52 weeks of age. Conclusion: “BB” genotype has emerged as favored genotype for multiple births and better growth indicator. Therefore, homozygous lambs for “B” allele should be selected and utilized in breeding program for better growth rate. PMID:27956784

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

    PubMed

    Williams, R C; McAuley, J E

    1992-01-01

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

  20. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

    PubMed Central

    Chang, Hsiao-Han; Worby, Colin J.; Yeka, Adoke; Nankabirwa, Joaniter; Kamya, Moses R.; Staedke, Sarah G.; Hubbart, Christina; Amato, Roberto; Kwiatkowski, Dominic P.

    2017-01-01

    As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings. PMID

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

    PubMed

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

    2016-05-01

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

  2. Genotype prevalence and allele frequencies of 5,10-methylenetetrahydrofolate reductase (MTHFR) C677T mutation in two caste groups of India.

    PubMed

    Rai, V; Yadav, U; Kumar, P

    2012-06-15

    The aim of the present study was to investigate the distribution of 5,10-methylenetetrahydrofolate reductase (MTHFR) polymorphism in two caste group populations of eastern Uttar Pradesh. This mutation has been suggested to be positively associated with the risk of several congenital and multifactorial disorders. Frequency of mutant T allele differs in various ethnic and geographical populations of the world. MTHFR C677T mutation analysis was carried out by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) method and the samples studied were randomly selected from the healthy individuals belonging to two caste populations. In Brahmin samples, genotype frequencies of CC, CT and TT were 0.727, 0.25 and 0.023 respectively whereas in Rajput samples, CC genotype was observed in 88 samples, CT genotype in 25 and TT genotype was found in 2 samples. Frequency of mutant T allele was found to be 0.147 in Brahmin and 0.126 in Rajput populations. The percentage of CT genotype and C allele were high in both the populations.

  3. 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.

  4. Frequency distribution of Q188R, N314D, Duarte 1, and Duarte 2 GALT variant alleles in an Indian galactosemia population.

    PubMed

    Singh, Ramandeep; Thapa, Babu R; Kaur, Gurjit; Prasad, Rajendra

    2012-12-01

    Classical galactosemia is a genetic disorder caused by mutations in the galactose-1-phosphate uridyltransferase (GALT) gene. The Q188R and N314D mutations are the most frequently cited GALT gene mutations. N314D is further associated with two variants, Duarte 1 and Duarte 2. Nevertheless, no reports are available on the clinical and molecular spectrum of galactosemia from the Indian population. The present study was designed to establish the frequency of these two most common mutations and their variants in Indian galactosemia patients so as to determine a single most common mutation/polymorphism for establishing the DNA-based diagnosis of galactosemia. Three alleles were found to be present at a frequency of 0.036 (Q188R), 0.40 (N314D), and 0.39 (D2); no D1 alleles were found. A significantly higher frequency of the Duarte 2 allele in our population suggests the presence of a milder form of galactosemia, which can be well managed by early diagnosis and dietary management.

  5. Estimation of the 6-digit level allele and haplotype frequencies of HLA-A, -B, and -C in Koreans using ambiguity-solving DNA typing.

    PubMed

    Jun, J-H; Hwang, K; Kim, S-K; Oh, H-B; Cho, M-C; Lee, K-J

    2014-09-01

    Because Korean society is fast becoming multi-ethnic, the determination of ambiguous human leukocyte antigen (HLA) types using HLA allele frequencies is becoming less applicable. In this study, we focused on the development of new technical methods to directly resolve the ambiguities arising from HLA genotyping. One hundred and fifty unrelated healthy Korean adults were included in this study. All alleles from each HLA locus were first divided into 2-4 groups, with each group amplified in a single PCR tube (multi-group-specific amplification, MGSA). To resolve phase ambiguities, some allele groups were also amplified separately in small group-specific amplification (SGSA) tubes. In order to then resolve incomplete sequence ambiguities, primers for MGSA and SGSA were initially designed to cover additional exons. If needed, a heterozygous ambiguity resolving primer (HARP) or sequence specific primer (SSP) was also used. When MGSA and SGSA methods were applied, the rate of phase ambiguity was greatly reduced to an average of 6% (1.3% in HLA-A, 15.7% in -B, and 2.0% in -C). Additional HARP and SSP methods could resolve all the phase ambiguities. Using our proposed method, we also detected three alleles that have not been previously reported in Korea, C*04:82, C*07:18, and C*08:22, and report 6-digit level HLA allele and haplotype frequencies among Koreans. In conclusion, the use of MGSA/SGSA for the initial amplification step is a cost-effective method facilitating timely and accurate reporting, given the continuing increase in the ethnic diversity of the Korean population. The MGSA described here can be applicable to various populations and thus could be shared by the majority of HLA typing laboratories. However, efforts to solve HLA ambiguity should continue, because SGSA, HARPs and SSPs would be specific to a particular population.

  6. Somatic homologous recombination in planta: the recombination frequency is dependent on the allelic state of recombining sequences and may be influenced by genomic position effects.

    PubMed

    Swoboda, P; Hohn, B; Gal, S

    1993-02-01

    We have previously described a non-selective method for scoring somatic recombination in the genome of whole plants. The recombination substrate consists of a defective partial dimer of Cauliflower Mosaic Virus (CaMV) sequences, which can code for production of viable virus only upon homologous recombination; this leads to disease symptoms on leaves. Brassica napus plants (rapeseed) harbouring the recombination substrate as a transgene were used to examine the time in plant development at which recombination takes place. The analysis of three transgene loci revealed recombination frequencies specific for each locus. Recombination frequencies were increased if more than one transgene locus was present per genome, either in allelic (homozygosity of the transgene locus) or in non-allelic positions. In both cases, the overall recombination frequency was found to be elevated to approximately the sum of the frequencies for the individual transgene loci or slightly higher, suggesting that the respective transgene loci behave largely independently of each other. For all plants tested (single locus, two or multiple loci) maximal recombination frequencies were of the order of 10(-6) events per cell division.

  7. Allele frequencies and genetic diversity in two groups of wild tufted capuchin monkeys (Cebus apella nigritus) living in an urban forest fragment.

    PubMed

    Amaral, Jeanne Margareth Jimenes; Simões, Aguinaldo Luiz; De Jong, David

    2005-12-30

    There have been numerous studies genetically characterizing Old World Primates using microsatellites. However, few studies have been made of New World species and none on free-ranging Cebus apella, even though it is probably the most widely distributed species of monkey in the New World. The paucity of studies is due, in part, to the lack of polymorphisms described for this species. We studied two groups of wild tufted capuchins, Cebus apella nigritus, which inhabit Mata Santa Teresa, the Ecological Reserve of Ribeirão Preto, a 158-ha forest fragment in a semi-urban zone of Ribeirão Preto, SP, Brazil. Group 1 had about 60 animals, 35 of which were sampled, and group 2 had about 40 animals, 20 of which were sampled. These group sizes are much larger than the published reports of 6-30 for this species, despite, or perhaps due to the isolation and the size of the forest fragment. Allele PEPC59*1 was the most frequent of all alleles at all loci in both groups (55.7 and 55%), allele PEPC8*1 was the most common allele in group 2 (46.9%) and PEPC8*4 in group 1 (41.1%), allele PEPC3*2 was the most common in group 1 (35.7%) and allele PEPC3*4 in group 2 (31.6%). The genetic diversity, considering each locus in each group, varied from 61.9% at locus PEPC59 to 78.6% at locus PEPC3, both in group 1. The mean genetic diversity (H(S)), considering both groups for all of the loci, was 71.1%. The inter-group diversity (F(ST)) was 1.9%, indicating that these groups belong to the same population. These groups apparently have a high genetic diversity, despite their isolation in a limited forest fragment, although more data are needed to adequately characterize this population.

  8. An optical beam frequency reference with 10{sup -14} range frequency instability

    SciTech Connect

    McFerran, J. J.; Hartnett, J. G.; Luiten, A. N.

    2009-07-20

    The authors report on a thermal beam optical frequency reference with a fractional frequency instability of 9.2x10{sup -14} at 1 s reducing to 2.0x10{sup -14} at 64 s before slowly rising. The {sup 1}S{sub 0}{r_reversible}{sup 3}P{sub 1} intercombination line in neutral {sup 40}Ca is used as a frequency discriminator. A diode laser at 423 nm probes the ground state population after a Ramsey-Borde sequence of 657 nm light-field interactions on the atoms. The measured fractional frequency instability is an order of magnitude improvement on previously reported thermal beam optical clocks. The photon shot-noise of the read-out produces a limiting square root {lambda}-variance of 7x10{sup -14}/{radical}({tau})

  9. Neonatal screening for hereditary fructose intolerance: frequency of the most common mutant aldolase B allele (A149P) in the British population.

    PubMed

    James, C L; Rellos, P; Ali, M; Heeley, A F; Cox, T M

    1996-10-01

    Hereditary fructose intolerance (HFI) causes severe and sometimes fatal metabolic disturbances in infants and children but responds to dietary treatment. To determine the practicability of screening newborn infants for HFI, we have investigated the frequency of the most common and widespread mutant allele of aldolase B, A149P, in the neonatal population. The polymerase chain reaction was used to amplify aldolase B exon 5 genomic sequences in DNA present in dried blood specimens preserved on Guthrie cards. The A149P mutation was identified by discriminatory hybridisation to allele specific oligonucleotides and confirmed independently by digestion with the restriction endonuclease BsaHI. Twenty-seven A149P heterozygotes were identified by the molecular analysis of aldolase B genes in blood samples obtained from a random cohort of 2050 subjects born in 1994 and 1995, 1.32 +/- 0.49% (95% confidence level). Although no A149P homozygotes were identified, the data allow the frequency of 1 in 23,000 homozygotes for this allele to be predicted. Our findings have implications for establishing an interventional mass screening programme to identify newborn infants with HFI in the UK.

  10. Performance analysis of single-frequency MPPSK integrated system for ranging applications.

    PubMed

    Yao, Yu; Wu, Lenan

    2014-01-01

    The dual-frequency MPPSK-MODEM is a flexible platform. When ranging accuracy request is low or platform is particularly limited by power, the platform would perform both data transmission and range measurement with single-frequency modes. In this paper, the ranging resolution of MPPSK pulse waveforms with the match filter and impacting filter processing are discussed, respectively. Also, the parameter selection of MPPSK modulator for ranging is considered. In particular, requirements that allow for employing such special parameter values for range measurements with high accuracy and high range are investigated. Moreover, high repetition frequency (HRF) biphase code MPPSK pulse train base on m sequence is presented, and the ranging accuracy of the proposed signal with the match filter processing is deduced. In addition to theoretical considerations, the paper presents system simulations and measurement results of single-frequency MPPSK integrated systems, demonstrating the high-performance of ranging applications.

  11. Performance Analysis of Single-Frequency MPPSK Integrated System for Ranging Applications

    PubMed Central

    Wu, Lenan

    2014-01-01

    The dual-frequency MPPSK-MODEM is a flexible platform. When ranging accuracy request is low or platform is particularly limited by power, the platform would perform both data transmission and range measurement with single-frequency modes. In this paper, the ranging resolution of MPPSK pulse waveforms with the match filter and impacting filter processing are discussed, respectively. Also, the parameter selection of MPPSK modulator for ranging is considered. In particular, requirements that allow for employing such special parameter values for range measurements with high accuracy and high range are investigated. Moreover, high repetition frequency (HRF) biphase code MPPSK pulse train base on m sequence is presented, and the ranging accuracy of the proposed signal with the match filter processing is deduced. In addition to theoretical considerations, the paper presents system simulations and measurement results of single-frequency MPPSK integrated systems, demonstrating the high-performance of ranging applications. PMID:25140340

  12. Association between a high-expressing interferon-gamma allele and a lower frequency of kidney angiomyolipomas in TSC2 patients.

    PubMed

    Dabora, Sandra L; Roberts, Penelope; Nieto, Andres; Perez, Ron; Jozwiak, Sergiusz; Franz, David; Bissler, John; Thiele, Elizabeth A; Sims, Katherine; Kwiatkowski, David J

    2002-10-01

    Tuberous sclerosis complex (TSC) is a familial hamartoma syndrome in which renal involvement is common and, at times, life threatening. We have investigated the potential effect of a non-TSC gene on renal disease in a cohort of 172 TSC patients with TSC2 mutations. Patients were genotyped for an interferon-gamma (IFN-gamma) microsatellite polymorphism, within intron 1, for which one common allele (allele 2, with 12 CA repeats) has been shown to have a higher expression of IFN-gamma. A chi(2) analysis was used to examine the association between IFN-gamma allele 2 and the development of kidney angiomyolipomas (KAMLs) in this TSC2 cohort. Because of the age-dependent development of KAMLs in TSC, we initially focused on the 127 patients who were >5 years old. Additional subgroup analyses were done to investigate the influence of age and gender. The transmission/disequilibrium test (TDT) was also performed in a subset of this cohort (46 probands) for whom parent and/or sibling samples were available for analysis. Both chi(2) analysis and TDT suggested an association between IFN-gamma allele 2 and the absence of KAMLs in patients who have known TSC2 mutations. Among the 127 patients who were >5 years old, KAMLs were present in 95 (75%) and were absent in 32 (25%). In the group with KAML present, the frequency of IFN-gamma allele 2 was 56%; in the group with KAML absent, the frequency of IFN-gamma allele 2 was significantly higher, at 78% (P=.02, by chi(2) analysis). The family-based TDT analysis gave similar results, with a TDT statistic (TDT chi2=5.45) corresponding to a P value of.02. Subgroup analyses show that both age and gender may influence the impact of this association. Although these results should be replicated in other populations with TSC, the present study suggests that modifier genes play a role in the variable expression of TSC and also suggests a potential therapy for KAMLs in patients with TSC.

  13. Numerical Analysis of Stochastic Dynamical Systems in the Medium-Frequency Range

    DTIC Science & Technology

    2003-02-01

    frequency vibration analysis such as the statistical energy analysis (SEA), the traditional modal analysis (well-suited for high and low: frequency...that the first few structural normal modes primarily constitute the total response. In the higher frequency range, the statistical energy analysis (SEA

  14. Polymorphisms and allele frequencies of glutathione S-transferases A1 and P1 genes in the Polish population.

    PubMed

    Skrzypczak-Zielinska, M; Zakerska-Banaszak, O; Tamowicz, B; Sobieraj, I; Drweska-Matelska, N; Szalata, M; Slomski, R; Mikstacki, A

    2015-03-31

    Glutathione S-transferases (GST) A1 and P1 are crucial enzymes involved in the biotransformation of drugs, carcinogens, and toxins, and their activity may influence drug response, susceptibility to diseases, and carcinogenesis. The genes encoding these enzymes, GSTA1 and GSTP1, have been examined in many studies because of their genetic variability, which may affect enzymatic activity. The goal of this study was to determine the distribution of the alleles GSTA1*A/*B and GSTP1*A, *B, and *C in the Polish population. A total of 160 subjects from the Polish population were genotyped for 2 polymorphisms (I105V and A114V) in the GSTP1 gene using pyrosequencing. The promoter region of the GSTA1 gene was screened using sequencing. The detected variants were subjected to haplotype analysis. We found that the distribution of the alleles GSTA1*A/*B and GSTP1*A, *B, and *C in the Polish population correspond to the results of studies in Caucasians. Furthermore, we identified additional single nucleotide polymorphisms, excluding 3 well-known changes (G-52A, C-69T, T-567G), which are linked to alleles GSTA1*A/*B, that affect enzyme activity. A total of 4 haplotypes were identified in 160 Polish individuals.

  15. 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

  16. Frequency-dependent conductivity contrast for tissue characterization using a dual-frequency range conductivity mapping magnetic resonance method.

    PubMed

    Kim, Dong-Hyun; Chauhan, Munish; Kim, Min-Oh; Jeong, Woo Chul; Kim, Hyung Joong; Sersa, Igor; Kwon, Oh In; Woo, Eung Je

    2015-02-01

    Electrical conductivities of biological tissues show frequency-dependent behaviors, and these values at different frequencies may provide clinically useful diagnostic information. MR-based tissue property mapping techniques such as magnetic resonance electrical impedance tomography (MREIT) and magnetic resonance electrical property tomography (MREPT) are widely used and provide unique conductivity contrast information over different frequency ranges. Recently, a new method for data acquisition and reconstruction for low- and high-frequency conductivity images from a single MR scan was proposed. In this study, we applied this simultaneous dual-frequency range conductivity mapping MR method to evaluate its utility in a designed phantom and two in vivo animal disease models. Magnetic flux density and B(1)(+) phase map for dual-frequency conductivity images were acquired using a modified spin-echo pulse sequence. Low-frequency conductivity was reconstructed from MREIT data by the projected current density method, while high-frequency conductivity was reconstructed from MREPT data by B(1)(+) mapping. Two different conductivity phantoms comprising varying ion concentrations separated by insulating films with or without holes were used to study the contrast mechanism of the frequency-dependent conductivities related to ion concentration and mobility. Canine brain abscess and ischemia were used as in vivo models to evaluate the capability of the proposed method to identify new electrical properties-based contrast at two different frequencies. The simultaneous dual-frequency range conductivity mapping MR method provides unique contrast information related to the concentration and mobility of ions inside tissues. This method has potential to monitor dynamic changes of the state of disease.

  17. New range of vectors with a stringent 5-fluoroorotic acid-based counterselection system for generating mutants by allelic replacement in Staphylococcus aureus.

    PubMed

    Redder, Peter; Linder, Patrick

    2012-06-01

    We have developed a range of vectors for allelic replacements in Staphylococcus aureus to facilitate genetic work in this opportunistic pathogen. The central feature of the vector range is a selection/counterselection system that takes advantage of the 5-fluoroorotic acid (FOA) resistance and pyrimidine prototrophy caused by the loss and gain, respectively, of the pyrF and pyrE genes. This system allows for stringent counterselection of the vectors during the second homologous recombination of a classic allelic replacement. The basic vector pRLY2, which contains the pyrFE genes from Bacillus subtilis, was combined with chloramphenicol, erythromycin, and tetracycline resistance genes and four different versions of nonreplicative or conditionally replicative origins of replication. The choice between these 12 different pRLY vectors allows for high versatility and ensures that the vectors can be used in virtually any genetic background. Finally, as proof of concept, we present six deletions or modifications of components in the S. aureus degradosome as well as the operon containing the cshB DEAD box helicase.

  18. Short communication: The combined use of linkage disequilibrium-based haploblocks and allele frequency-based haplotype selection methods enhances genomic evaluation accuracy in dairy cattle.

    PubMed

    Jónás, Dávid; Ducrocq, Vincent; Croiseau, Pascal

    2017-04-01

    The construction and use of haploblocks [adjacent single nucleotide polymorphisms (SNP) in strong linkage disequilibrium] for genomic evaluation is advantageous, because the number of effects to be estimated can be reduced without discarding relevant genomic information. Furthermore, haplotypes (the combination of 2 or more SNP) can increase the probability of capturing the quantitative trait loci effect compared with individual SNP markers. With regards to haplotypes, the allele frequency parameter is also of interest, because as a selection criterion, it allows the number of rare alleles to be reduced, and the effects of those alleles are usually difficult to estimate. We have proposed a simple pipeline that simultaneously incorporates linkage disequilibrium and allele frequency information in genomic evaluation, and here we present the first results obtained with this procedure. We used a population of 2,235 progeny-tested bulls from the Montbéliarde breed for the tests. Phenotype data were available in the form of daughter yield deviations on 5 production traits, and genotype data were available from the 50K SNP chip. We conducted a classical validation study by splitting the population into training (80% oldest animals) and validation (20% youngest animals) sets to emulate a real-life scenario in which the selection candidates had no available phenotype data. We measured all reported parameters for the validation set. Our results proved that the proposed method was indeed advantageous, and that the accuracy of genomic evaluation could be improved. Compared with results from a genomic BLUP analysis, correlations between daughter yield deviations (a proxy for true) and genomic estimated breeding values increased by an average of 2.7 percentage points for the 5 traits. Inflation of the genomic evaluation of the selection candidates was also significantly reduced. The proposed method outperformed the other SNP and haplotype-based tests we had evaluated in a

  19. 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. PMID:27879769

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2015-04-01

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

  2. 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

  3. 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

  4. Contemporary evolution of sea urchin gamete-recognition proteins: experimental evidence of density-dependent gamete performance predicts shifts in allele frequencies over time.

    PubMed

    Levitan, Don R

    2012-06-01

    Species whose reproductive strategies evolved at one density regime might be poorly adapted to other regimes. Field and laboratory experiments on the sea urchin Strongylocentrotus franciscanus examined the influences of the two most common sperm-bindin alleles, which differ at two amino acid sites, on fertilization success. In the field experiment, the arginine/glycine (RG) genotype performed best at low densities and the glycine/arginine (GR) genotype at high densities. In the laboratory experiment, the RG genotype had a higher affinity with available eggs, whereas the GR genotype was less likely to induce polyspermy. These sea urchins can reach 200 years of age. The RG allele dominates in larger/old sea urchins, whereas smaller/younger sea urchins have near-equal RG and GR allele frequencies. A latitudinal cline in RG and GR genotypes is consistent with longer survival of sea urchins in the north and with predominance of RG genotypes in older individuals. The largest/oldest sea urchins were likely conceived at low densities, before sea-urchin predators, such as sea otters, were overharvested and sea-urchin densities exploded off the west coast of North America. Contemporary evolution of gamete-recognition proteins might allow species to adapt to shifts in abundances and reduces the risk of reproductive failure in altered populations.

  5. The effect of duty cycle and frequency on muscle torque production using kilohertz frequency range alternating current.

    PubMed

    Ward, Alex R; Robertson, Valma J; Ioannou, Harry

    2004-09-01

    We investigated the frequency and duty cycle dependence of maximal electrically induced torque (MEIT) of the wrist extensors. Fifty hertz burst modulated sinusoidal alternating current (AC) in the frequency range 0.5-20 kHz was used, with duty cycles ranging from a minimum (one cycle) to maximum (continuous AC). MEITs were similar at low frequencies but decreased markedly above 2.5 kHz. MEITs also decreased markedly above a 20% duty cycle. Subjective reports of discomfort were fewest at 4 kHz and at duty cycles in the range 20-25%. Our conclusion is that for maximum torque production, a frequency of 1 kHz and a duty cycle of 20% are indicated. When comfort is a major consideration, a frequency of 2.5 kHz provides an acceptable trade-off between MEIT and comfort. The findings also suggest that low duty cycle, burst modulated AC stimulation may be more effective than stimulation using conventional low-frequency pulsed current.

  6. Mutant allele frequencies among domestic cats in some eastern areas of Canada: regional homogeneity of factors in Canadian Atlantic Provinces and the French colony of Saint Pierre.

    PubMed

    Todd, N B; Todd, L M

    1976-01-01

    Surveys to determine mutant allele frequencies in domestic cats of the Canadian Atlantic Provinces (Halifax, Nova Scotia; Fredericton, New Brunswick; Charlottetown, Prince Edward Island; St. John's Newfoundland) and the French colony of Saint Pierre, Saint Pierre et Miquelon, reveal a general regional homogeneity for most factors. Despite diverse historical patterns of settlement, a strong common component of origin is indicated. This is tentatively identified as late 18th and early 19th century British. One mutant, polydactyly, which is of New England origin appears to have been distributed largely by loyalist refugees from New England at the time of the American Rebellion. No elements of a specific Acadian (French) character have yet been identified. Siamese cats have been "introduced" to the region in recent years and are now so abundant that they will undoubtedly cause a significant change in some mutant allele frequencies over the next few decades. Interregional exchanges of cats no doubt are contributing to homogenizing the populations of the area, but the practice of sterilization of pets offsets this to some degree.

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

    PubMed

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

    2015-07-03

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

  8. Optimal frequency range for medical radar measurements of human heartbeats using body-contact radar.

    PubMed

    Brovoll, Sverre; Aardal, Øyvind; Paichard, Yoann; Berger, Tor; Lande, Tor Sverre; Hamran, Svein-Erik

    2013-01-01

    In this paper the optimal frequency range for heartbeat measurements using body-contact radar is experimentally evaluated. A Body-contact radar senses electromagnetic waves that have penetrated the human body, but the range of frequencies that can be used are limited by the electric properties of the human tissue. The optimal frequency range is an important property needed for the design of body-contact radar systems for heartbeat measurements. In this study heartbeats are measured using three different antennas at discrete frequencies from 0.1 - 10 GHz, and the strength of the received heartbeat signal is calculated. To characterize the antennas, when in contact with the body, two port S-parameters(†) are measured for the antennas using a pork rib as a phantom for the human body. The results shows that frequencies up to 2.5 GHz can be used for heartbeat measurements with body-contact radar.

  9. 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.

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

    PubMed

    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.

  11. 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

  12. Dielectric Properties of Birch Wood in the High-Frequency Range

    NASA Astrophysics Data System (ADS)

    Goreshnev, M. A.; Litvishko, E. S.; Lopatin, V. V.

    2016-01-01

    Results of measurement of dielectric properties of birch wood in the radio-frequency range depending on its humidity are presented. The dependences obtained indicate strong influence of wood anisotropy especially at low frequencies. It is shown that it is irrational to use the wood for insulation if its humidity exceeds 15-20%.

  13. Simulation of polarizer based on chiral medium for terahertz frequency range

    NASA Astrophysics Data System (ADS)

    Korolenko, S. Yu; Grebenchukov, A. N.; Masyukov, M. S.; Vozianova, A. V.; Khodzitsky, M. K.

    2016-08-01

    The work is devoted to development of the polarizer for terahertz frequency range. Chiral medium was simulated using the software package CST Microwave Studio by the method of Finite-Differences in Frequency Domain. The influence of geometry of chiral unit cell on the polarization of incident plane wave was investigated.

  14. Electron-beam buncher to operate over the frequency range 1-4 GHz

    SciTech Connect

    Goldberg, D.A.; Arthur, A.A.; Flood, W.S.; Voelker, F.

    1983-03-01

    We present a description of an electron buncher to be installed in the terminal of a Van de Graaff, which is to produce a modulated beam over the frequency range 1-4 GHz. The modulator geometry has been optimized so that the modulation amplitude should be nearly constant over the frequency ranges 1-2 GHz and 2-4 GHz. Preliminary results indicate the device works as predicted.

  15. Outdoor stocking density in free-range laying hens: radio-frequency identification of impacts on range use.

    PubMed

    Campbell, D L M; Hinch, G N; Dyall, T R; Warin, L; Little, B A; Lee, C

    2017-01-01

    The number and size of free-range laying hen (Gallus gallus domesticus) production systems are increasing within Australia in response to consumer demand for perceived improvement in hen welfare. However, variation in outdoor stocking density has generated consumer dissatisfaction leading to the development of a national information standard on free-range egg labelling by the Australian Consumer Affairs Ministers. The current Australian Model Code of Practice for Domestic Poultry states a guideline of 1500 hens/ha, but no maximum density is set. Radio-frequency identification (RFID) tracking technology was used to measure daily range usage by individual ISA Brown hens housed in six small flocks (150 hens/flock - 50% of hens tagged), each with access to one of three outdoor stocking density treatments (two replicates per treatment: 2000, 10 000, 20 000 hens/ha), from 22 to 26, 27 to 31 and 32 to 36 weeks of age. There was some variation in range usage across the sampling periods and by weeks 32 to 36 individual hens from the lowest stocking density on average used the range for longer each day (P<0.001), with fewer visits and longer maximum durations per visit (P<0.001). Individual hens within all stocking densities varied in the percentage of days they accessed the range with 2% of tagged hens in each treatment never venturing outdoors and a large proportion that accessed the range daily (2000 hens/ha: 80.5%; 10 000 hens/ha: 66.5%; 20 000 hens/ha: 71.4%). On average, 38% to 48% of hens were seen on the range simultaneously and used all available areas of all ranges. These results of experimental-sized flocks have implications for determining optimal outdoor stocking densities for commercial free-range laying hens but further research would be needed to determine the effects of increased range usage on hen welfare.

  16. Full-range imaging of eye accommodation by high-speed long-depth range optical frequency domain imaging

    PubMed Central

    Furukawa, Hiroyuki; Hiro-Oka, Hideaki; Satoh, Nobuyuki; Yoshimura, Reiko; Choi, Donghak; Nakanishi, Motoi; Igarashi, Akihito; Ishikawa, Hitoshi; Ohbayashi, Kohji; Shimizu, Kimiya

    2010-01-01

    We describe a high-speed long-depth range optical frequency domain imaging (OFDI) system employing a long-coherence length tunable source and demonstrate dynamic full-range imaging of the anterior segment of the eye including from the cornea surface to the posterior capsule of the crystalline lens with a depth range of 12 mm without removing complex conjugate image ambiguity. The tunable source spanned from 1260 to 1360 nm with an average output power of 15.8 mW. The fast A-scan rate of 20,000 per second provided dynamic OFDI and dependence of the whole anterior segment change on time following abrupt relaxation from the accommodated to the relaxed status, which was measured for a healthy eye and that with an intraocular lens. PMID:21258564

  17. Multibeam single frequency synthetic aperture radar processor for imaging separate range swaths

    NASA Technical Reports Server (NTRS)

    Jain, A. (Inventor)

    1982-01-01

    A single-frequency multibeam synthetic aperture radar for large swath imaging is disclosed. Each beam illuminates a separate ""footprint'' (i.e., range and azimuth interval). The distinct azimuth intervals for the separate beams produce a distinct Doppler frequency spectrum for each beam. After range correlation of raw data, an optical processor develops image data for the different beams by spatially separating the beams to place each beam of different Doppler frequency spectrum in a different location in the frequency plane as well as the imaging plane of the optical processor. Selection of a beam for imaging may be made in the frequency plane by adjusting the position of an aperture, or in the image plane by adjusting the position of a slit. The raw data may also be processed in digital form in an analogous manner.

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

    PubMed Central

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

    2002-01-01

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

  19. 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.

  20. Multibeam single frequency synthetic aperture radar processor for imaging separate range swaths

    NASA Technical Reports Server (NTRS)

    Jain, A. (Inventor)

    1979-01-01

    A method and apparatus are described for single frequency multibeam imaging of multiple strips of range swath at high range intervals for those applications where it is desirable to cover a range swath much greater than is possible for a given interpulse interval. Data from a single frequency synthetic aperture radar (in which beam parameters are adjusted so that the return from each successive swath is received during successive interpulse periods) are separated in Dopple frequency for the return from each beam at the frequency plane of the processor. Alternatively, the image formed by each beam may be spatially separated in the azimuth direction and successively selected by positioning an appropriate slit in the recording plane of the processor.

  1. Frequency of the CCR5 delta 32 mutant allele in HIV-1-positive patients, female sex workers, and a normal population in Taiwan.

    PubMed

    Li, C; Yan, Y P; Shieh, B; Lee, C M; Lin, R Y; Chen, Y M

    1997-12-01

    A specific 32-nucleotide deletion mutant of the CCR5 gene (Accr5), the coreceptor gene for human immunodeficiency virus type 1 (HIV-1), can effectively suppress the transmission and pathogenesis of the virus. Individuals homozygous for the delta ccr5 allele resist primary macrophage-tropic HIV-1 infection, despite multiple high-risk sexual exposures. This gene deletion is relatively common among Caucasians but uncommon among Africans, Asians, and South Americans. We used polymerase chain reaction (PCR) technology to determine the frequency of the delta ccr5 allele in a Taiwanese population with diverse health status and social backgrounds. Subjects included 24 HIV-1-infected persons in the northern and southern parts of Taiwan; 131 HIV-1 high-risk, licensed female sex workers in the northern part of the island (21% of whom were aborigines); and 187 unrelated, healthy, HIV-1-negative individuals in southern Taiwan. PCR with primers encompassing the entire CCR5 gene was used to explore possible deletions at regions other than the 32-nucleotide area in the female sex workers. No ccr5 deletions were detected, indicating that they are rare or absent in the Taiwanese population. This finding implies that delta ccr5 is not likely to be part of the defense against the spread of HIV-1-infection in Taiwanese.

  2. 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.

  3. Drift Rather than Selection Dominates MHC Class II Allelic Diversity Patterns at the Biogeographical Range Scale in Natterjack Toads Bufo calamita

    PubMed Central

    Zeisset, Inga; Beebee, Trevor J. C.

    2014-01-01

    Study of major histocompatibility complex (MHC) loci has gained great popularity in recent years, partly due to their function in protecting vertebrates from infections. This is of particular interest in amphibians on account of major threats many species face from emergent diseases such as chytridiomycosis. In this study we compare levels of diversity in an expressed MHC class II locus with neutral genetic diversity at microsatellite loci in natterjack toad (Bufo (Epidalea) calamita) populations across the whole of the species’ biogeographical range. Variation at both classes of loci was high in the glacial refugium areas (REF) and much lower in postglacial expansion areas (PGE), especially in range edge populations. Although there was clear evidence that the MHC locus was influenced by positive selection in the past, congruence with the neutral markers suggested that historical demographic events were the main force shaping MHC variation in the PGE area. Both neutral and adaptive genetic variation declined with distance from glacial refugia. Nevertheless, there were also some indications from differential isolation by distance and allele abundance patterns that weak effects of selection have been superimposed on the main drift effect in the PGE zone. PMID:24937211

  4. Measurement of the dielectric properties of dispersive materials over a wide frequency range.

    SciTech Connect

    Molina, Luis Leroy; Salazar, Robert Austin; Bacon, Larry Donald; Lehr, Jane Marie

    2003-06-01

    The propagation of electromagnetic waves through dispersive media forms the basis for a wide variety of applications. Rapid advances in materials have produced new products with tailored responses across frequency bands. Many of these new materials, such as radar absorbing material and photonic crystals, are dispersive in nature. This, in turn, has opened up the possibility for the exploitation of these dispersive dielectric properties for a variety of applications. Thus, it is desirable to know the electromagnetic properties of both man-made and natural materials across a wide frequency range. With the advent of transient pulsers with sub-nanosecond risetimes and rates of voltage rise approaching 10**16 V/s, the frequencies of interest in the transient response extend to approximately the 2 GHz range. Although a network analyzer can provide either frequency- or time-domain data (by inverse transform), common TEM cells are only rated to 0.5 to 1.5 GHz--significantly below the maximum frequency of interest. To extend the frequency range to include 2 GHz, a TEM cell was characterized and a deembedding algorithm was applied to account, in part, for the limitations of the cell. The de-embedding technique is described along with such measurement issues such as clear time and sneak around. Measurements of complex permittivity of common drinking water are shown. This frequency extension will lead to more expansive testing of dielectric materials of interest.

  5. Acoustic Treatment Design Scaling Methods. Volume 2; Advanced Treatment Impedance Models for High Frequency Ranges

    NASA Technical Reports Server (NTRS)

    Kraft, R. E.; Yu, J.; Kwan, H. W.

    1999-01-01

    The primary purpose of this study is to develop improved models for the acoustic impedance of treatment panels at high frequencies, for application to subscale treatment designs. Effects that cause significant deviation of the impedance from simple geometric scaling are examined in detail, an improved high-frequency impedance model is developed, and the improved model is correlated with high-frequency impedance measurements. Only single-degree-of-freedom honeycomb sandwich resonator panels with either perforated sheet or "linear" wiremesh faceplates are considered. The objective is to understand those effects that cause the simple single-degree-of- freedom resonator panels to deviate at the higher-scaled frequency from the impedance that would be obtained at the corresponding full-scale frequency. This will allow the subscale panel to be designed to achieve a specified impedance spectrum over at least a limited range of frequencies. An advanced impedance prediction model has been developed that accounts for some of the known effects at high frequency that have previously been ignored as a small source of error for full-scale frequency ranges.

  6. Range compensation for backscattering measurements in the difference-frequency nearfield of a parametric sonar.

    PubMed

    Foote, Kenneth G

    2012-05-01

    Measurement of acoustic backscattering properties of targets requires removal of the range dependence of echoes. This process is called range compensation. For conventional sonars making measurements in the transducer farfield, the compensation removes effects of geometrical spreading and absorption. For parametric sonars consisting of a parametric acoustic transmitter and a conventional-sonar receiver, two additional range dependences require compensation when making measurements in the nonlinearly generated difference-frequency nearfield: an apparently increasing source level and a changing beamwidth. General expressions are derived for range compensation functions in the difference-frequency nearfield of parametric sonars. These are evaluated numerically for a parametric sonar whose difference-frequency band, effectively 1-6 kHz, is being used to observe Atlantic herring (Clupea harengus) in situ. Range compensation functions for this sonar are compared with corresponding functions for conventional sonars for the cases of single and multiple scatterers. Dependences of these range compensation functions on the parametric sonar transducer shape, size, acoustic power density, and hydrography are investigated. Parametric range compensation functions, when applied with calibration data, will enable difference-frequency echoes to be expressed in physical units of volume backscattering, and backscattering spectra, including fish-swimbladder-resonances, to be analyzed.

  7. Stable Allele Frequency Distribution of the Plasmodium falciparum clag Genes Encoding Components of the High Molecular Weight Rhoptry Protein Complex

    PubMed Central

    Alexandre, Jean Semé Fils; Xangsayarath, Phonepadith; Kaewthamasorn, Morakot; Yahata, Kazuhide; Sattabongkot, Jetsumon; Udomsangpetch, Rachanee; Kaneko, Osamu

    2012-01-01

    Plasmodium falciparum Clag protein is a candidate component of the plasmodial surface anion channel located on the parasite-infected erythrocyte. This protein is encoded by 5 separated clag genes and forms a RhopH complex with the other components. Previously, a signature of positive diversifying selection was detected on the hypervariable region of clag2 and clag8 by population-based analyses using P. falciparum originating from Thailand in 1988–1989. In this study, we obtained the sequence of this region of 3 clag genes (clag2, clag8, and clag9) in 2005 and evaluated the changes over time in the frequency distribution of the polymorphism of these gene products by comparison with the sequences obtained in 1988–1989. We found no difference in the frequency distribution of 18 putatively neutral loci between the 2 groups, evidence that the background of the parasite population structure has remained stable over 14 years. Although the frequency distribution of most of the polymorphic sites in the hypervariable region of Clag2, Clag8, and Clag9 was stable over 14 years, we found that a proportion of the major Clag2 group and one amino acid position of Clag8 changed significantly. This may be a response to a certain type of pressure. PMID:23264726

  8. Stable Allele Frequency Distribution of the Plasmodium falciparum clag Genes Encoding Components of the High Molecular Weight Rhoptry Protein Complex.

    PubMed

    Alexandre, Jean Semé Fils; Xangsayarath, Phonepadith; Kaewthamasorn, Morakot; Yahata, Kazuhide; Sattabongkot, Jetsumon; Udomsangpetch, Rachanee; Kaneko, Osamu

    2012-09-01

    Plasmodium falciparum Clag protein is a candidate component of the plasmodial surface anion channel located on the parasite-infected erythrocyte. This protein is encoded by 5 separated clag genes and forms a RhopH complex with the other components. Previously, a signature of positive diversifying selection was detected on the hypervariable region of clag2 and clag8 by population-based analyses using P. falciparum originating from Thailand in 1988-1989. In this study, we obtained the sequence of this region of 3 clag genes (clag2, clag8, and clag9) in 2005 and evaluated the changes over time in the frequency distribution of the polymorphism of these gene products by comparison with the sequences obtained in 1988-1989. We found no difference in the frequency distribution of 18 putatively neutral loci between the 2 groups, evidence that the background of the parasite population structure has remained stable over 14 years. Although the frequency distribution of most of the polymorphic sites in the hypervariable region of Clag2, Clag8, and Clag9 was stable over 14 years, we found that a proportion of the major Clag2 group and one amino acid position of Clag8 changed significantly. This may be a response to a certain type of pressure.

  9. Allele frequencies for 15 autosomal STR loci and haplotype data for 17 Y-STR loci in a population from Belize.

    PubMed

    Flores, Shahida; Sun, Jie; King, Jonathan; Eisenberg, Arthur; Budowle, Bruce

    2015-11-01

    Allele frequencies for 15 autosomal STR loci (N = 290) and haplotype data for 17 Y-STR loci (N = 157) were determined for an admixed population from Belize. There were no detectable departures from Hardy-Weinberg equilibrium expectations at any autosomal STR loci except for the D8S1179 locus (p = 0.002). The combined power of discrimination (PD) and combined power of exclusion (PE) were greater than 0.99999999 and 0.99999951, respectively. In addition, a total of 144 distinct Y-STR haplotypes were observed with 133 Y-STR haplotypes observed only once. The most common Y-STR haplotype was observed three times for two separate haplotypes. The various analyses of these forensically relevant STR loci showed that these markers are informative in the Belize population for forensic and parentage testing applications.

  10. 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.

  11. 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.

  12. 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

  13. Ionospheric frequency spread and its relationship with range spread in mid-latitude regions

    SciTech Connect

    Bowman, G.G. )

    1991-06-01

    The distinction between range spread and frequency spread as seen on mid-latitude ionograms is discussed. A classification of these two types of spread F is proposed in terms of different arrangements of the duplicate traces which provide the basic trace structures of mid-latitude spread F ionograms. Experimental results are presented to support the idea that frequency spread results from multiple ray paths (associated with a shallow ripple structure in the isoionic contours) close to the direction of the zenith position, so that each ray path has a range approximately equal to that of its neighbor. Furthermore, a horizontal gradient of maximum electron density is an additional requirement to create frequency spread. Atmospheric conditions (involving ionospheric F{sub 2} region heights and upper atmosphere neutral particle densities) which seem to favor the generation of frequency spread are discussed.

  14. Waves guided by density ducts in magnetoplasma in the nonresonant region of the whistler frequency range

    SciTech Connect

    Es’kin, V. A.; Zaboronkova, T. M.; Kudrin, A. V. Ostafiychuk, O. M.

    2015-03-15

    Guidance of azimuthally symmetric waves by cylindrical density ducts in magnetoplasma in the nonresonant region of the whistler frequency range is investigated. It is demonstrated that eigenmodes existing at the studied frequencies in ducts with enhanced plasma density allow simplified description that makes analysis of the features of their guided propagation much easier. The results of calculation of the dispersion characteristics and field structure of the whistler modes supported by such ducts are presented.

  15. 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

  16. 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

  17. 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

  18. Individual optimization of EEG channel and frequency ranges by means of genetic algorithm.

    PubMed

    Lee, Chungki; Jung, Jihee; Kwon, Gyuhyun; Kim, Laehyun

    2012-01-01

    It is well established that motor action/imagery provokes an event-related desynchronization (ERD) response at specific brain areas with specific frequency ranges, typically the sensory motor rhythm and beta bands. However, there are individual differences in both brain areas and frequency ranges which can be used to identify ERD. This often results in low classification accuracy of ERD, which makes it difficult to implement of BCI application such as the control of external devices and motor rehabilitation. To overcome this problem, an individually optimized solution may be desirable for enhancing the accuracy of detecting motor action/imagery with ERD rather than a global solution for all BCI users. This paper presents a method based on a genetic algorithm to find individually optimized brain areas and frequency ranges for ERD classification. To optimize these two components, we designed a chromosome consisting of 64-bit elements represented by a binary number and another 9-bit elements using 512 pre-defined frequency ranges (2^9). The average value of the significant level is set for the properties of the objective function for use in a t-test, (p < 0.01) depending on the random selection from a concurrent population. As a result, contralateral ERD responses in the spatial domain with individually optimized frequency ranges showed a significant difference between resting and motor action. The ERD responses for motor imagery, on the other hand, led to a bilateral pattern with a narrow frequency band compared to motor action. This study provides the possibility of selecting optimized electrode positions and frequency bands which can lead to high levels of ERD classification accuracy.

  19. Allele-dependent recombination frequency: homology requirement in meiotic recombination at the hot spot in the mouse major histocompatibility complex.

    PubMed

    Yoshino, M; Sagai, T; Lindahl, K F; Toyoda, Y; Moriwaki, K; Shiroishi, T

    1995-05-20

    Meiotic recombination break joints in the mouse major histocompatibility complex (MHC) are clustered within short segments known as hot spots. We systematically investigated the requirement for sequence homology between two chromosomes for recombination activity at the hot spot next to the Lmp2 gene. The results indicated that a high rate of recombination required a high degree of similarity of overall genome structure at the hot spot. In particular, the same copy number of repetitive sequences within the hot spot was essential for a high frequency of recombination, suggesting that recombination in mouse meiosis is more sensitive to heterozygous deletion or insertion of DNA than to mismatches of single-base substitutions.

  20. UTag: Long-range Ultra-wideband Passive Radio Frequency Tags

    SciTech Connect

    Dowla, F

    2007-03-14

    Long-range, ultra-wideband (UWB), passive radio frequency (RF) tags are key components in Radio Frequency IDentification (RFID) system that will revolutionize inventory control and tracking applications. Unlike conventional, battery-operated (active) RFID tags, LLNL's small UWB tags, called 'UTag', operate at long range (up to 20 meters) in harsh, cluttered environments. Because they are battery-less (that is, passive), they have practically infinite lifetimes without human intervention, and they are lower in cost to manufacture and maintain than active RFID tags. These robust, energy-efficient passive tags are remotely powered by UWB radio signals, which are much more difficult to detect, intercept, and jam than conventional narrowband frequencies. The features of long range, battery-less, and low cost give UTag significant advantage over other existing RFID tags.

  1. An atomic magnetometer with autonomous frequency stabilization and large dynamic range

    SciTech Connect

    Pradhan, S. E-mail: pradhans75@gmail.com; Poornima,; Dasgupta, K.; Mishra, S.; Behera, R.

    2015-06-15

    The operation of a highly sensitive atomic magnetometer using elliptically polarized resonant light is demonstrated. It is based on measurement of zero magnetic field resonance in degenerate two level systems using polarimetric detection. The transmitted light through the polarimeter is used for laser frequency stabilization, whereas reflected light is used for magnetic field measurement. Thus, the experimental geometry allows autonomous frequency stabilization of the laser frequency leading to compact operation of the overall device and has a preliminary sensitivity of <10 pT/Hz{sup 1/2} @ 1 Hz. Additionally, the dynamic range of the device is improved by feedback controlling the bias magnetic field without compromising on its sensitivity.

  2. An atomic magnetometer with autonomous frequency stabilization and large dynamic range.

    PubMed

    Pradhan, S; Mishra, S; Behera, R; Poornima; Dasgupta, K

    2015-06-01

    The operation of a highly sensitive atomic magnetometer using elliptically polarized resonant light is demonstrated. It is based on measurement of zero magnetic field resonance in degenerate two level systems using polarimetric detection. The transmitted light through the polarimeter is used for laser frequency stabilization, whereas reflected light is used for magnetic field measurement. Thus, the experimental geometry allows autonomous frequency stabilization of the laser frequency leading to compact operation of the overall device and has a preliminary sensitivity of <10 pT/Hz(1/2) @ 1 Hz. Additionally, the dynamic range of the device is improved by feedback controlling the bias magnetic field without compromising on its sensitivity.

  3. Note: Digital laser frequency auto-locking for inter-satellite laser ranging.

    PubMed

    Luo, Yingxin; Li, Hongyin; Yeh, Hsien-Chi

    2016-05-01

    We present a prototype of a laser frequency auto-locking and re-locking control system designed for laser frequency stabilization in inter-satellite laser ranging system. The controller has been implemented on field programmable gate arrays and programmed with LabVIEW software. The controller allows initial frequency calibrating and lock-in of a free-running laser to a Fabry-Pérot cavity. Since it allows automatic recovery from unlocked conditions, benefit derives to automated in-orbit operations. Program design and experimental results are demonstrated.

  4. Insecticide resistance in house flies from the United States: Resistance levels and frequency of pyrethroid resistance alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although insecticide resistance is a widespread problem for most insect pests, frequently the assessment of resistance occurs over a limited geographic range. Herein we report the first widespread survey of insecticide resistance ever undertaken for the house fly, Musca domestica, a major pest of a...

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

    PubMed Central

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

    2010-01-01

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

  6. Method of range profile for step frequency MMW radar based on wavelet transform power spectrum estimator

    NASA Astrophysics Data System (ADS)

    Li, Yuehua; Gao, Duntang; Shen, Qinghong; Li, Xingguo

    2001-11-01

    The method of range profile for step frequency MMW radar targets based on wavelet transform power spectrum estimator is studied. We show how the Fourier power spectrum can be detected by using the wavelet function coefficients (WFC) of the DWT. This method can successfully measure the power spectrum in samples for which traditional methods often fail because the sample are finite sized, have a complex geometry, or are varyingly sampled. We demonstrate that the spectrum features, such as the power law index, the magnitude, and the typical scales can be determined by the DWT reconstructed spectrum. We apply this method to the practical step frequency MMW radar target echo signals, and on the condition of the same sampling frequency and sampling data length, it can achieve one dimensional range profile with profile"s resolution superior to FFT"s, so the one dimensional range profile of targets can be analyzed with high resolution, the detail algorithm of range profiles spectrum estimation based on wavelet transforming multirange cells is proposed. Compare with FFT algorithm, using wavelet spectrum estimator of short data series, we can achieves high resolution, high accuracy, and low SNR threshold. The Experiment results make clear that the DWT estimator is a sensitive tool in range profile of step frequency MMW radar.

  7. Experiments and error analysis of laser ranging based on frequency-sweep polarization modulation

    NASA Astrophysics Data System (ADS)

    Gao, Shuyuan; Ji, Rongyi; Li, Yao; Cheng, Zhi; Zhou, Weihu

    2016-11-01

    Frequency-sweep polarization modulation ranging uses a polarization-modulated laser beam to determine the distance to the target, the modulation frequency is swept and frequency values are measured when transmitted and received signals are in phase, thus the distance can be calculated through these values. This method gets much higher theoretical measuring accuracy than phase difference method because of the prevention of phase measurement. However, actual accuracy of the system is limited since additional phase retardation occurs in the measuring optical path when optical elements are imperfectly processed and installed. In this paper, working principle of frequency sweep polarization modulation ranging method is analyzed, transmission model of polarization state in light path is built based on the theory of Jones Matrix, additional phase retardation of λ/4 wave plate and PBS, their impact on measuring performance is analyzed. Theoretical results show that wave plate's azimuth error dominates the limitation of ranging accuracy. According to the system design index, element tolerance and error correcting method of system is proposed, ranging system is built and ranging experiment is performed. Experiential results show that with proposed tolerance, the system can satisfy the accuracy requirement. The present work has a guide value for further research about system design and error distribution.

  8. A wide-range programmable frequency synthesizer based on a finite state machine filter

    NASA Astrophysics Data System (ADS)

    Alser, Mohammed H.; Assaad, Maher M.; Hussin, Fawnizu A.

    2013-11-01

    In this article, an FPGA-based design and implementation of a fully digital wide-range programmable frequency synthesizer based on a finite state machine filter is presented. The advantages of the proposed architecture are that, it simultaneously generates a high frequency signal from a low frequency reference signal (i.e. synthesising), and synchronising the two signals (signals have the same phase, or a constant difference) without jitter accumulation issue. The architecture is portable and can be easily implemented for various platforms, such as FPGAs and integrated circuits. The frequency synthesizer circuit can be used as a part of SERDES devices in intra/inter chip communication in system-on-chip (SoC). The proposed circuit is designed using Verilog language and synthesized for the Altera DE2-70 development board, with the Cyclone II (EP2C35F672C6) device on board. Simulation and experimental results are included; they prove the synthesizing and tracking features of the proposed architecture. The generated clock signal frequency of a range from 19.8 MHz to 440 MHz is synchronized to the input reference clock with a frequency step of 0.12 MHz.

  9. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province.

    PubMed

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  10. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province

    PubMed Central

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  11. Long-range vibration sensor based on correlation analysis of optical frequency-domain reflectometry signals.

    PubMed

    Ding, Zhenyang; Yao, X Steve; Liu, Tiegen; Du, Yang; Liu, Kun; Han, Qun; Meng, Zhuo; Chen, Hongxin

    2012-12-17

    We present a novel method to achieve a space-resolved long- range vibration detection system based on the correlation analysis of the optical frequency-domain reflectometry (OFDR) signals. By performing two separate measurements of the vibrated and non-vibrated states on a test fiber, the vibration frequency and position of a vibration event can be obtained by analyzing the cross-correlation between beat signals of the vibrated and non-vibrated states in a spatial domain, where the beat signals are generated from interferences between local Rayleigh backscattering signals of the test fiber and local light oscillator. Using the proposed technique, we constructed a standard single-mode fiber based vibration sensor that can have a dynamic range of 12 km and a measurable vibration frequency up to 2 kHz with a spatial resolution of 5 m. Moreover, preliminarily investigation results of two vibration events located at different positions along the test fiber are also reported.

  12. Frequencies of cystic fibrosis mutations in the Maine population: high proportion of unknown alleles in individuals of French-Canadian ancestry.

    PubMed

    Bayleran, J K; Yan, H; Hopper, C A; Simpson, E M

    1996-08-01

    Cystic fibrosis (CF) is one of the most common severe autosomal recessive disorders in Caucasian populations. A mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene causes this disorder. Reported here is the first analysis of CF mutations in the Maine population. We have screened 263 CF chromosomes for 16 previously reported mutations. Analysis of DNA from 124 apparently unrelated CF patients and 15 obligate carrier parents (whose partner and affected child were unavailable for study) resulted in the identification of 91% of the CF alleles and complete genotyping of 85% of the patients. The frequencies (%) of these mutations in the Maine population are delta F508 (75% of the chromosomes), G85E (0.76), R117H (0.76), I148T (1.1), 621 + 1G --> T (1.1), 711 + 1G --> T (3.0), A455E (1.1), 1717-1G --> A (1.1), G542X (1.9), G551D (1.9), R560T (0.76), Y1092X (0.38), W1282X (0.38), and N1303K (1.5). The exon 10 mutation, delta I507, and the exon 11 mutation, R553X, were not observed. Surprisingly, whereas only 5% of the alleles remain unidentified in the non-French population, the unidentified proportion in the French population is 19%. CF testing for the Maine population will be further improved as the as yet unidentified CF mutations in this population are characterized.

  13. Allelic frequencies of PRKAG3 in several pig breeds and its technological consequences on a Duroc × Landrace-Large White cross.

    PubMed

    Galve, A; Burgos, C; Varona, L; Carrodeguas, J A; Cánovas, Á; López-Buesa, P

    2013-10-01

    The allelic frequencies of PRKAG3 gene (the RN gene) have been investigated in several pig breeds. R200Q mutation appear only in Hampshire pigs, whereas V199I mutation is most abundant in Iberian, Porco Celta or Bizaro, and less in breeds selected for muscularity as Duroc, Landrace and Pietrain. A thorough study of phenotypic effects of V1991 has been performed in a Duroc × Landrace-Large White cross. 199I homozygous pigs show increased pH24 values in ham homogenates and loin (0.14 and 0.16 pH units, respectively) compared to 199V homozygous ones. Meat of 199I homozygous pigs exudates 42.6% less fluid and is darker (2.46 'L'-value units). 199I homozygous pigs are fatter (4.2 mm more backfat thickness) and contain less muscle mass in ham (1.0 percentage points) and shoulder (2.7 percentage points), than 199V homozygous ones. 199I homozygous pigs contain 7.3% less protein in the belly and 8.5% more fat in shoulder muscle mass than 199V homozygous pigs. 199I homozygous pigs have also superior functional properties: better gelling (22.8% larger G' value) and emulsion capacities (14 percentage points less of total exuded fluid), and higher curing yield in the belly (6 percentage points more). These data support the adipogenic character of the V199I mutation. The advantages and disadvantages of selecting any of the two PRKAG3 alleles for position 199 are discussed.

  14. Dual Cry2Ab and Vip3A resistant strains of Helicoverpa armigera and Helicoverpa punctigera (Lepidoptera: Noctuidae); testing linkage between loci and monitoring of allele frequencies.

    PubMed

    Walsh, T K; Downes, S J; Gascoyne, J; James, W; Parker, T; Armstrong, J; Mahon, R J

    2014-08-01

    Considerable attention has been given to delaying the evolution of insect resistance to toxins produced by transgenic crops. The major pests of cotton in Australia are the Lepidoptera Helicoverpa armigera (Hubner, 1805) and Helicoverpa punctigera (Wallengren), and the toxins deployed in current and imminent transgenic cotton varieties are Cry1Ac, Cry2Ab and Vip3A from Bacillus thuringiensis. In this study, lines that carry alleles conferring resistance to Cry2Ab and Vip3A were isolated using F2 tests. Extensive work on the Cry2Ab resistant lines, and preliminary work on the Vip3A resistant lines, suggested a single common resistance to each toxin in both species thereby justifying the use of more efficient F1 tests as the primary means for monitoring changes over time. A potential further efficiency could be gained by developing a single resistant line that carries both types of Bt resistance. Herein we report on work with both H. armigera and H. punctigera that tests whether dual Cry2Ab-Vip3A resistant lines can be developed and, if so, whether they can be used to effectively monitor resistance frequencies. Furthermore, the creation of dual resistant lines allowed linkage between the Cry2Ab and Vip3A resistances to be investigated for H. punctigera. We show that dual resistant lines can be used to increase the efficiency of the F1 screen for recessive alleles, and that in H. punctigera there is no linkage between Cry2Ab and Vip3A resistance.

  15. UWB micro-doppler radar for human gait analysis using joint range-time-frequency representation

    NASA Astrophysics Data System (ADS)

    Wang, Yazhou; Fathy, Aly E.

    2013-05-01

    In this paper, we present a novel, standalone ultra wideband (UWB) micro-Doppler radar sensor that goes beyond simple range or micro-Doppler detection to combined range-time-Doppler frequency analysis. Moreover, it can monitor more than one human object in both line-of-sight (LOS) and through wall scenarios, thus have full human objects tracking capabilities. The unique radar design is based on narrow pulse transceiver, high speed data acquisition module, and wideband antenna array. For advanced radar post-data processing, joint range-time-frequency representation has been performed. Characteristics of human walking activity have been analyzed using the radar sensor by precisely tracking the radar object and acquiring range-time-Doppler information simultaneously. The UWB micro-Doppler radar prototype is capable of detecting Doppler frequency range from -180 Hz to +180 Hz, which allows a maximum target velocity of 9 m/s. The developed radar sensor can also be extended for many other applications, such as respiration and heartbeat detection of trapped survivors under building debris.

  16. Application of generalized Snoek's law over a finite frequency range: A case study

    NASA Astrophysics Data System (ADS)

    Rozanov, Konstantin N.; Koledintseva, Marina Y.

    2016-02-01

    Generalized Snoek's law proposed in an integral form by Acher and coauthors is a useful tool for investigation of high-frequency properties of magnetic materials. This integral law referred to as Acher's law allows for evaluating the ultimate performance of RF and microwave devices which employ magnetic materials. It may also be helpful in obtaining useful information on the structure and morphology of the materials. The key factor in practical application of Acher's law is an opportunity to employ either measured or calculated data available over a finite frequency range. The paper uses simple calculations to check the applicability of Acher's law in cases when the frequency range is limited and the magnetic loss peak is comparatively wide and has a distorted shape. The cases of large magnetic damping, pronounced skin effect, and inhomogeneity of the material are considered. It is shown that in most cases calculation of the integral through fitting of actual magnetic frequency dispersion by the Lorentzian dispersion law results in accurate estimations of the ultimate high-frequency performance of magnetic materials.

  17. Development of gyrotrons for fusion with power exceeding 1 MW over a wide frequency range

    NASA Astrophysics Data System (ADS)

    Kariya, T.; Imai, T.; Minami, R.; Numakura, T.; Eguchi, T.; Kato, T.; Endo, Y.; Ichimura, M.; Shimozuma, T.; Kubo, S.; Takahashi, H.; Yoshimura, Y.; Igami, H.; Ito, S.; Mutoh, T.; Sakamoto, K.; Idei, H.; Zushi, H.; Nagasaki, K.; Sano, F.; Ono, M.; Mitsunaka, Y.

    2015-09-01

    Megawatt-class gyrotrons covering a wide frequency range (14 GHz-300 GHz) are in increasing demand for nuclear fusion. Recent electron cyclotron heating and electron cyclotron current drive experiments highlight a requirement of megawatt-scale gyrotrons at a relatively lower frequency (14-35 GHz) range of some plasma devices, like GAMMA 10/PDX of the University of Tsukuba, QUEST of Kyushu University, NSTX-U of Princeton Plasma Physics Laboratory, and Heliotron J of Kyoto University. Collaborative studies for designing a new 28 GHz/35 GHz dual-frequency gyrotron and a 14 GHz gyrotron have commenced. Operation above 1 MW of 28 GHz/35 GHz dual oscillation was demonstrated experimentally. Further in the design of dual-frequency gyrotron, operations with 2 MW 3 s and 0.4 MW CW (continuous wave) at 28 GHz, and power exceeding 1 MW for 3 s at 34.8 GHz have been shown to be feasible. The 14 GHz gyrotron is expected to operate above 1 MW. We are also developing higher frequency gyrotrons (77-300 GHz). The joint program of National Institute for Fusion Science and the University of Tsukuba developed two new 154 GHz gyrotrons for the large helical device after the demonstration of three 77 GHz gyrotrons. The 154 GHz gyrotrons achieved a maximum output power of 1.25 MW and quasi-CW operation of 0.35 MW for 30 min.

  18. Familial porphyria cutanea tarda: characterization of seven novel uroporphyrinogen decarboxylase mutations and frequency of common hemochromatosis alleles.

    PubMed Central

    Mendez, M; Sorkin, L; Rossetti, M V; Astrin, K H; del C Batlle, A M; Parera, V E; Aizencang, G; Desnick, R J

    1998-01-01

    Familial porphyria cutanea tarda (f-PCT) results from the half-normal activity of uroporphyrinogen decarboxylase (URO-D). Heterozygotes for this autosomal dominant trait are predisposed to photosensitive cutaneous lesions by various ecogenic factors, including iron overload and alcohol abuse. The 3.6-kb URO-D gene was completely sequenced, and a long-range PCR method was developed to amplify the entire gene for mutation analysis. Four missense mutations (M165R, L195F, N304K, and R332H), a microinsertion (g10insA), a deletion (g645Delta1053), and a novel exonic splicing defect (E314E) were identified. Expression of the L195F, N304K, and R332H polypeptides revealed significant residual activity, whereas reverse transcription-PCR and sequencing demonstrated that the E314E lesion caused abnormal splicing and exon 9 skipping. Haplotyping indicated that three of the four families with the g10insA mutation were unrelated, indicating that these microinsertions resulted from independent mutational events. Screening of nine f-PCT probands revealed that 44% were heterozygous or homozygous for the common hemochromatosis mutations, which suggests that iron overload may predispose to clinical expression. However, there was no clear correlation between f-PCT disease severity and the URO-D and/or hemochromatosis genotypes. These studies doubled the number of known f-PCT mutations, demonstrated that marked genetic heterogeneity underlies f-PCT, and permitted presymptomatic molecular diagnosis and counseling in these families to enable family members to avoid disease-precipitating factors. PMID:9792863

  19. Theoretical analysis of the EAST 4-strap ion cyclotron range of frequency antenna with variational theory

    NASA Astrophysics Data System (ADS)

    Zhang, Jia-Hui; Zhang, Xin-Jun; Zhao, Yan-Ping; Qin, Cheng-Ming; Chen, Zhao; Yang, Lei; Wang, Jian-Hua

    2016-08-01

    A variational principle code which can calculate self-consistently currents on the conductors is used to assess the coupling characteristic of the EAST 4-strap ion cyclotron range of frequency (ICRF) antenna. Taking into account two layers of antenna conductors without lateral frame but with slab geometry, the antenna impedances as a function of frequency and the structure of RF field excited inside the plasma in various phasing cases are discussed in this paper. Project supported by the National Magnetic Confinement Fusion Science Program, China (Grant No. 2015GB101001) and the National Natural Science Foundation of China (Grant Nos. 11375236 and 11375235).

  20. An impedance bridge measuring the capacitance ratio in the high frequency range up to 1 MHz

    NASA Astrophysics Data System (ADS)

    Bee Kim, Dan; Kew Lee, Hyung; Kim, Wan-Seop

    2017-02-01

    This paper describes a 2-terminal-pair impedance bridge, measuring the capacitance ratio in the high frequency range up to 1 MHz. The bridge was configured with two voltage sources and a phase control unit which enabled the bridge balance by synchronizing the voltage sources with an enhanced phase resolution. Without employing the transformers such as inductive voltage divider, injection and detection transformers, etc, the bridge system is quite simple to set up, and the balance procedure is quick and easy. Using this dual-source coaxial bridge, the 1:1 and 10:1 capacitance ratios were measured with 1 pF-1 nF capacitors in the frequency range from 1 kHz to 1 MHz. The measurement values obtained by the dual-source bridge were then compared with reference values measured using a commercial precision capacitance bridge of AH2700A, the Z-matrix method developed by ourselves, and the 4-terminal-pair coaxial bridge by the Czech Metrological Institute. All the measurements agreed within the reference uncertainty range of an order of 10-6-10-5, proving the bridge ability as a trustworthy tool for measuring the capacitance ratio in the high frequency range.

  1. Noise in any frequency range can enhance information transmission in a sensory neuron

    NASA Astrophysics Data System (ADS)

    Levin, Jacob E.

    1997-05-01

    The effect of noise on the neural encoding of broadband signals was investigated in the cricket cercal system, a mechanosensory system sensitive to small near-field air particle disturbances. Known air current stimuli were presented to the cricket through audio speakers in a controlled environment in a variety of background noise conditions. Spike trains from the second layer of neuronal processing, the primary sensory interneurons, were recorded with intracellular Electrodes and the performance of these neurons characterized with the tools of information theory. SNR, mutual information rates, and other measures of encoding accuracy were calculated for single frequency, narrowband, and broadband signals over the entire amplitude sensitivity range of the cells, in the presence of uncorrelated noise background also spanning the cells' frequency and amplitude sensitivity range. Significant enhancements of transmitted information through the addition of external noise were observed regardless of the frequency range of either the signal or noise waveforms, provided both were within the operating range of the cell. Considerable improvements in signal encoding were observed for almost an entire order of magnitude of near-threshold signal amplitudes. This included sinusoidal signals embedded in broadband white noise, broadband signals in broadband noise, and even broadband signals presented with narrowband noise in a completely non-overlapping frequency range. The noise related increases in mutual information rate for broadband signals were as high as 150%, and up to 600% increases in SNR were observed for sinusoidal signals. Additionally, it was shown that the amount of information about the signal carried, on average, by each spike was INCREASED for small signals when presented with noise—implying that added input noise can, in certain situations, actually improve the accuracy of the encoding process itself.

  2. Exploring the accessible frequency range of phase-resolved ferromagnetic resonance detected with x-rays

    NASA Astrophysics Data System (ADS)

    Warnicke, P.; Knut, R.; Wahlström, E.; Karis, O.; Bailey, W. E.; Arena, D. A.

    2013-01-01

    We present time- and element-resolved measurements of the magnetization dynamics in a ferromagnetic trilayer structure. A pump-probe scheme was utilized with a microwave magnetic excitation field phase-locked to the photon bunches and x-ray magnetic circular dichroism in transmission geometry. Using a relatively large photon bunch length with a full width at half maximum of 650 ps, the precessional motion of the magnetization was resolved up to frequencies of 2.5 GHz, thereby enabling sampling at frequencies significantly above the inverse bunch length. By simulating the experimental data with a numerical model based on a forced harmonic oscillator, we obtain good correlation between the two. The model, which includes timing jitter analysis, is used to predict the accessible frequency range of x-ray detected ferromagnetic resonance.

  3. Double Brillouin frequency spaced multiwavelength Brillouin-erbium fiber laser with 50 nm tuning range

    NASA Astrophysics Data System (ADS)

    Zhao, J. F.; Liao, T. Q.; Zhang, C.; Zhang, R. X.; Miao, C. Y.; Tong, Z. R.

    2012-09-01

    A 50 nm tuning range multiwavelength Brillouin-erbium fiber laser (MWBEFL) with double Brillouin frequency spacing is presented. Two separated gain blocks with symmetrical architecture, consisted by erbium-doped fiber amplifiers (EDFAs) and Brillouin gain media, are used to generate double Brillouin frequency spacing. The wider tuning range is realized by eliminating the self-lasing cavity modes existing in conventional MWBEFLs because of the absence of the physical mirrors at the ends of the linear cavity. The Brillouin pump (BP) is preamplified by the EDFA before entering the single-mode fiber (SMF), which leads to the reduction of threshold power and the generation enhancement of Brillouin Stokes (BS) signals. Four channels with 0.176 nm spacing are achieved at 2 mW BP power and 280 mW 980 nm pump power which can be tuned from 1525 to 1575 nm.

  4. A reduced order model for dielectric elastomer actuators over a range of frequencies and prestrains

    NASA Astrophysics Data System (ADS)

    Kiser, Jillian; Manning, Michael; Adler, David; Breuer, Kenneth

    2016-09-01

    The actuation strain of an equibiaxially prestrained dielectric elastomer membrane is studied as a function of driving frequency and prestrain. Experimental data are gathered on the membrane's creep and recovery following DC actuation, as well as the steady state amplitude and phase for AC driving voltages ranging from 2 to 40 Hz. The effect of prestretch on steady state actuation was also investigated, using membranes of both 250% and 300% prestretch. A three-element generalized Kelvin-Voigt model is developed to capture the transient and steady-state actuation responses as a function of frequency and prestrain. We show that, despite its relative simplicity, this model captures the relevant timescales for the membrane behavior with good fidelity and can be used to accurately predict the actuation magnitude and phase as a function of time over a range of actuation configurations and driving conditions.

  5. Artificial Temperature Anisotropy of Crystals in X-Ray Frequency Range

    SciTech Connect

    Mkrtchyan, Vahram P.; Gasparyan, Laura G.; Balyan, Minas K.

    2010-04-06

    The effect of artificial temperature anisotropy of crystals in X-ray frequency range was observed for the first time and an effort to theoretically interpret this effect in Bragg-Laue diffraction case was made. It was established that an isotropic crystal optically turns into an artificially anisotropic one with optical axis along the direction of applied external influence as a symmetry axis, giving rise to the double refraction.

  6. Determination of the dielectric constant of GaN in the kHz frequency range

    NASA Astrophysics Data System (ADS)

    Kane, M. J.; Uren, M. J.; Wallis, D. J.; Wright, P. J.; Soley, D. E. J.; Simons, A. J.; Martin, T.

    2011-08-01

    Capacitance techniques are used to show that the dielectric constant ɛ|| of GaN in the kHz frequency range is 10.6 ± 0.3. The data allow depth information to be accurately extracted using methods such as mercury probe capacitance profiling. The measurements complement the pre-existing data which are derived from infrared reflectivity and which give a value of 10.4 ± 0.3.

  7. Moment method analysis of microstrip antennas over a wide frequency range

    NASA Technical Reports Server (NTRS)

    Kwan, B. W.; Newman, E. H.

    1985-01-01

    Expressions for the self and mutual impedance between microstrip antenna modes on a grounded dielectric slab are presented. The mutual impedance between the microstrip modes and a vertical current filament in the dielectric is also presented. These are the quantities required in a method of moments analysis of the microstrip antenna. Entire domain expansion modes, suitable for representing the microstrip current over a broad frequency range, are used. Efficient methods for the evaluation of the mutual impedance elements are described.

  8. SS433: Evolution of Radio Structure in {L} and {C} Frequency Ranges

    NASA Astrophysics Data System (ADS)

    Chuprikov, A. A.; Guirin, I. A.

    2010-02-01

    We analyze results of data processing of observations of SS433 with the VLBA during more than 10 years. Data were processed with ASL for Windows software. The Multi Frequency Synthesis method was used for reconstruction of radio maps at 18- and 6-cm wavelength ranges (L and C ranges). High-quality images of SS433 for several epochs are presented. Evolution of its radio structure is demonstrated. Astrophysical parameters of the object and their temporal changes are discussed. Polarization phenomena were not taken into account. We present results of our data processing of RR polarization for all the observing sessions.

  9. High-Resolution Group Quantization Phase Processing Method in Radio Frequency Measurement Range

    NASA Astrophysics Data System (ADS)

    Du, Baoqing; Feng, Dazheng; Tang, Yaohua; Geng, Xin; Zhang, Duo; Cai, Chaofeng; Wan, Maoquan; Yang, Zhigang

    2016-07-01

    Aiming at the more complex frequency translation, the longer response time and the limited measurement precision in the traditional phase processing, a high-resolution phase processing method by group quantization higher than 100 fs level is proposed in radio frequency measurement range. First, the phase quantization is used as a step value to quantize every phase difference in a group by using the fixed phase relationships between different frequencies signals. The group quantization is formed by the results of the quantized phase difference. In the light of frequency drift mainly caused by phase noise of measurement device, a regular phase shift of the group quantization is produced, which results in the phase coincidence of two comparing signals which obtain high-resolution measurement. Second, in order to achieve the best coincidences pulse, a subtle delay is initiatively used to reduce the width of the coincidences fuzzy area according to the transmission characteristics of the coincidences in the specific medium. Third, a series of feature coincidences pulses of fuzzy area can be captured by logic gate to achieve the best phase coincidences information for the improvement of the measurement precision. The method provides a novel way to precise time and frequency measurement.

  10. Low-power wide-locking-range injection-locked frequency divider for OFDM UWB systems

    NASA Astrophysics Data System (ADS)

    Jiangwei, Yin; Ning, Li; Renliang, Zheng; Wei, Li; Junyan, Ren

    2009-05-01

    This paper describes a divide-by-two injection-locked frequency divider (ILFD) for frequency synthesizers as used in multiband orthogonal frequency division multiplexing (OFDM) ultra-wideband (UWB) systems. By means of dual-injection technique and other conventional tuning techniques, such as DCCA and varactor tuning, the divider demonstrates a wide locking range while consuming much less power. The chip was fabricated in the Jazz 0.18 μm RF CMOS process. The measurement results show that the divider achieves a locking range of 4.85 GHz (6.23 to 11.08 GHz) at an input power of 8 dBm. The core circuit without the test buffer consumes only 3.7 mA from a 1.8 V power supply and has a die area of 0.38 × 0.28 mm2. The wide locking range combined with low power consumption makes the ILFD suitable for its application in UWB systems.

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

    PubMed Central

    2009-01-01

    The CC chemokine receptor 5 (CCR5) molecule is an important co-receptor for HIV. The effect of the CCR5*D32 allele in susceptibility to HIV infection and AIDS disease is well known. Other alleles than CCR5*D32 have not been analysed before, neither in Amerindians nor in the majority of the populations all over the world. We investigated the distribution of the CCR5 coding region alleles in South Brazil and noticed a high CCR5*D32 frequency in the Euro-Brazilian population of the Paraná State (9.3%), which is the highest thus far reported for Latin America. The D32 frequency is even higher among the Euro-Brazilian Mennonites (14.2%). This allele is uncommon in Afro-Brazilians (2.0%), rare in the Guarani Amerindians (0.4%) and absent in the Kaingang Amerindians and the Oriental-Brazilians. R223Q is common in the Oriental-Brazilians (7.7%) and R60S in the Afro-Brazilians (5.0%). A29S and L55Q present an impaired response to β-chemokines and occurred in Afro- and Euro-Brazilians with cumulative frequencies of 4.4% and 2.7%, respectively. Two new non-synonymous alleles were found in Amerindians: C323F (g.3729G > T) in Guarani (1.4%) and Y68C (g.2964A > G) in Kaingang (10.3%). The functional characteristics of these alleles should be defined and considered in epidemiological investigations about HIV-1 infection and AIDS incidence in Amerindian populations. PMID:21637640

  12. 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.

  13. Frequency-Modulated, Continuous-Wave Laser Ranging Using Photon-Counting Detectors

    NASA Technical Reports Server (NTRS)

    Erkmen, Baris I.; Barber, Zeb W.; Dahl, Jason

    2014-01-01

    Optical ranging is a problem of estimating the round-trip flight time of a phase- or amplitude-modulated optical beam that reflects off of a target. Frequency- modulated, continuous-wave (FMCW) ranging systems obtain this estimate by performing an interferometric measurement between a local frequency- modulated laser beam and a delayed copy returning from the target. The range estimate is formed by mixing the target-return field with the local reference field on a beamsplitter and detecting the resultant beat modulation. In conventional FMCW ranging, the source modulation is linear in instantaneous frequency, the reference-arm field has many more photons than the target-return field, and the time-of-flight estimate is generated by balanced difference- detection of the beamsplitter output, followed by a frequency-domain peak search. This work focused on determining the maximum-likelihood (ML) estimation algorithm when continuous-time photoncounting detectors are used. It is founded on a rigorous statistical characterization of the (random) photoelectron emission times as a function of the incident optical field, including the deleterious effects caused by dark current and dead time. These statistics enable derivation of the Cramér-Rao lower bound (CRB) on the accuracy of FMCW ranging, and derivation of the ML estimator, whose performance approaches this bound at high photon flux. The estimation algorithm was developed, and its optimality properties were shown in simulation. Experimental data show that it performs better than the conventional estimation algorithms used. The demonstrated improvement is a factor of 1.414 over frequency-domainbased estimation. If the target interrogating photons and the local reference field photons are costed equally, the optimal allocation of photons between these two arms is to have them equally distributed. This is different than the state of the art, in which the local field is stronger than the target return. The optimal

  14. An Ultrasonic Multiple-Access Ranging Core Based on Frequency Shift Keying Towards Indoor Localization.

    PubMed

    Segers, Laurent; Van Bavegem, David; De Winne, Sam; Braeken, An; Touhafi, Abdellah; Steenhaut, Kris

    2015-07-30

    This paper describes a new approach and implementation methodology for indoor ranging based on the time difference of arrival using code division multiple access with ultrasound signals. A novel implementation based on a field programmable gate array using finite impulse response filters and an optimized correlation demodulator implementation for ultrasound orthogonal signals is developed. Orthogonal codes are modulated onto ultrasound signals using frequency shift keying with carrier frequencies of 24.5 kHz and 26 kHz. This implementation enhances the possibilities for real-time, embedded and low-power tracking of several simultaneous transmitters. Due to the high degree of parallelism offered by field programmable gate arrays, up to four transmitters can be tracked simultaneously. The implementation requires at most 30% of the available logic gates of a Spartan-6 XC6SLX45 device and is evaluated on accuracy and precision through several ranging topologies. In the first topology, the distance between one transmitter and one receiver is evaluated. Afterwards, ranging analyses are applied between two simultaneous transmitters and one receiver. Ultimately, the position of the receiver against four transmitters using trilateration is also demonstrated. Results show enhanced distance measurements with distances ranging from a few centimeters up to 17 m, while keeping a centimeter-level accuracy.

  15. An Ultrasonic Multiple-Access Ranging Core Based on Frequency Shift Keying Towards Indoor Localization

    PubMed Central

    Segers, Laurent; Van Bavegem, David; De Winne, Sam; Braeken, An; Touhafi, Abdellah; Steenhaut, Kris

    2015-01-01

    This paper describes a new approach and implementation methodology for indoor ranging based on the time difference of arrival using code division multiple access with ultrasound signals. A novel implementation based on a field programmable gate array using finite impulse response filters and an optimized correlation demodulator implementation for ultrasound orthogonal signals is developed. Orthogonal codes are modulated onto ultrasound signals using frequency shift keying with carrier frequencies of 24.5 kHz and 26 kHz. This implementation enhances the possibilities for real-time, embedded and low-power tracking of several simultaneous transmitters. Due to the high degree of parallelism offered by field programmable gate arrays, up to four transmitters can be tracked simultaneously. The implementation requires at most 30% of the available logic gates of a Spartan-6 XC6SLX45 device and is evaluated on accuracy and precision through several ranging topologies. In the first topology, the distance between one transmitter and one receiver is evaluated. Afterwards, ranging analyses are applied between two simultaneous transmitters and one receiver. Ultimately, the position of the receiver against four transmitters using trilateration is also demonstrated. Results show enhanced distance measurements with distances ranging from a few centimeters up to 17 m, while keeping a centimeter-level accuracy. PMID:26263986

  16. MEMS - Frequency Agile High Precision Ranging under the Dual Use Applications Program (DUAP)

    NASA Astrophysics Data System (ADS)

    Bauhahn, Paul

    2001-12-01

    The objective of this program was laboratory demonstration of a low cost, jamming resistant, precision ranging system (radar) for proximity fuze and short-range measurement systems. Two approaches were envisioned: (1) The baseline-a baseband system directly radiating and detecting a random sequence of short pulses and (2) A higher risk design based on a transmitter using high-speed modulation of a micro-electromechanical (MEM) oscillator to avoid low frequency antenna radiation requirements. Size constraints drive the design toward small, single-chip monocycle pulse radar implemented in CMOS (Complementary Metal Oxide Semiconductors). This device with two external capacitors, a battery and a miniature antenna for the baseline approach is described in Figure 1-1. Triggering ranges from several inches to more than 6feet were demonstrated. Fabrication of MEM components on gallium arsenide for the second approach will require additional work. While CMOS technology is almost ideal for the long time-constant, multiple pulse integration circuits in the precision ranging receiver and most of the transmitter circuits, it is insufficient for submunition sensor final output amplifiers. The issue is the small size of the submunition antenna. Either step recovery diode circuit or higher performance output transistors are needed to generate the high frequency spectrum required for efficient radiation from these antennas. Using a 0.5-micron BiCMOS/Si(3e process, recently available for prototyping at MOSIS,' all of the required CMOS and faster output devices could be implemented with trivial modifications of the existing circuits.

  17. [The normotensive carriers of the MTHFR 677T allele, displaying the increased risk of development of the abdominal aortic aneurysm (AAA), occur at the highest frequency among the smoking patients].

    PubMed

    Strauss, Ewa; Waliszewski, Krzysztof; Pawlak, Andrzej L

    2004-01-01

    Abdominal aortic aneurysm (AAA) presents itself as a progressive dilation of the abdominal aorta, leading--if untreated--to rupture. It is a common disease of the elderly, with a complex etiology. Smoking, hypertension and several genetic factors are recognized as relevant for the pathogenesis of AAA. We studied association between the polymorphism of the MTHFR (methylenetetrahydrofolate reductase) gene within the fourth exon (677C>T) and the occurrence of hypertension and smoking status in the group of 74 male patients with AAA. In the patients group, the smoking hypertensive persons represented the largest subgroup (43%). We determined the the MTHFR 677C>T polymorphism in AAA patients and compared it to that in 71 healthy normotensive males. The frequencies of the 677T allele and MTHFR 677C>T genotypes were similar in both groups, but the subgroup of normotensive AAA patients (n=29) displayed significantly increased frequencies of 677T allele (0.4) and of 677CT and TT genotypes (69%), as compared to those in the control group (0.28 and 46%, respectively). This corresponds to the 3.3-fold greater risk of AAA in normotensive subjects with the 677T allele of MTHFR, as compared to the homo-zygotes 677CC (p<0.03; 95% CI=1.2-9.2). The highest frequencies of MTHFR 677T allele (0.43) and 677CT and TT genotypes (73%) were found in the subgroup of normotensive smoking patients (n=22).

  18. Acoustic Behavior of Halobacterium salinarum Gas Vesicles in the High-Frequency Range: Experiments and Modeling.

    PubMed

    Cherin, Emmanuel; Melis, Johan M; Bourdeau, Raymond W; Yin, Melissa; Kochmann, Dennis M; Foster, F Stuart; Shapiro, Mikhail G

    2017-03-01

    Gas vesicles (GVs) are a new and unique class of biologically derived ultrasound contrast agents with sub-micron size whose acoustic properties have not been fully elucidated. In this study, we investigated the acoustic collapse pressure and behavior of Halobacterium salinarum gas vesicles at transmit center frequencies ranging from 12.5 to 27.5 MHz. The acoustic collapse pressure was found to be above 550 kPa at all frequencies, nine-fold higher than the critical pressure observed under hydrostatic conditions. We illustrate that gas vesicles behave non-linearly when exposed to ultrasound at incident pressure ranging from 160 kPa to the collapse pressure and generate second harmonic amplitudes of -2 to -6 dB below the fundamental in media with viscosities ranging from 0.89 to 8 mPa·s. Simulations performed using a Rayleigh-Plesset-type model accounting for buckling and a dynamic finite-element analysis suggest that buckling is the mechanism behind the generation of harmonics. We found good agreement between the level of second harmonic relative to the fundamental measured at 20 MHz and the Rayleigh-Plesset model predictions. Finite-element simulations extended these findings to a non-spherical geometry, confirmed that the acoustic buckling pressure corresponds to the critical pressure under hydrostatic conditions and support the hypothesis of limited gas flow across the GV shell during the compression phase in the frequency range investigated. From simulations, estimates of GV bandwidth-limited scattering indicate that a single GV has a scattering cross section comparable to that of a red blood cell. These findings will inform the development of GV-based contrast agents and pulse sequences to optimize their detection with ultrasound.

  19. Free-field reciprocity calibration of microphones in ultrasonic frequency range

    NASA Astrophysics Data System (ADS)

    Bouaoua, Nourreddine; Fedtke, Thomas; Mellert, Volker

    2005-09-01

    Exposure to airborne low-frequency ultrasound occurs in many industrial applications such as cleaning, welding plastics, measuring distances in buildings, and by using consumer devices such as camera rangefinders, automatic door openers, parametric ultrasound loudspeakers, etc. Exposure to ultrasound in air may be dangerous to the hearing and may have negative bio-effects on humans. Care should be taken in its use. In order to establish appropriate limits and to measure the output of ultrasound devices, there is a need to develop a sound-pressure standard in the frequency range from 20 kHz to about 160 kHz. A calibration project for quarter-inch microphones by the reciprocity method has been started in the PTB, and a new automated measurement setup for free-field reciprocity calibration of quarter-inch microphones has been established. A procedure for a free-field reciprocity calibration of quarter-inch microphones in the frequency range 20 to 160 kHz is described. First results of free-field calibration of quarter-inch microphones are presented, giving the sensitivities and the repeatability of results. The effects of reflections and cross talk on the accuracy of the measurements will be explained.

  20. Frequency dependence of electromagnetic bias in radar altimeter sea surface range measurements

    NASA Technical Reports Server (NTRS)

    Walsh, E. J.; Jackson, F. C.; Hines, D. E.; Piazza, C.; Hevizi, L. G.; Mclaughlin, D. J.; Mcintosh, R. E.; Swift, R. N.; Scott, J. F.; Yungel, J. K.

    1991-01-01

    Range measurements made by satellite radar altimeters experience a bias toward the troughs of ocean waves. A series of aircraft flights during February-April 1989 measured this electromagnetic (EM) bias at three radar frequencies and the UV under a variety of wind and wave conditions, and provided the first airborne open-ocean measurements at the 13.6-GHz and 5.3-GHz operating frequencies of the NASA altimeter on the TOPEX/Poseidon satellite. The data suggest that the mean EM bias decreases linearly with increasing radar frequency between 5.3 and 36 GHz, according to the expression: EM bias (percent of significant wave height) = (3.0-0.0617 F)(1 +/-0.5), where F is in gigahertz. EM bias is fairly constant over a mesoscale region on a given day but can fluctuate significantly from one day to another. It shows a strong increase at all radar frequencies with increasing wind speed, although other sea state conditions, such as the wind direction relative to the wave direction, are also factors.

  1. Mechanical properties of bulk polydimethylsiloxane for microfluidics over a large range of frequencies and aging times

    NASA Astrophysics Data System (ADS)

    Placet, V.; Delobelle, P.

    2015-03-01

    The dynamic mechanical characterization of polydimethylsiloxane (PDMS) over a large range of frequencies (10-2 < f < 105 Hz) and long aging times at room temperature (4 h < tv < ~60 000 h) has been presented. Three samples with different curing conditions have been studied and three different techniques, dynamic mechanical analysis at different temperatures, nano-indentation and scanning micro-deformation microscopy, have been used. Although the three techniques work at different scales and at different frequencies all the results match the same master curve. As expected, the storage and the loss moduli greatly increase with the frequency. Moreover, these moduli moderately increase with the aging time tv depending on the curing temperature. A simple model which takes the frequency and the aging time into account, and which is based on the Havriliak-Negami model, has been presented and identified. Hence, values of the relaxed and instantaneous moduli at tv = 0 and tv = ∞ are proposed. Only the relaxed moduli depend on the curing conditions and moreover it has been shown that the tangent of the phase lag is independent of the aging time and thus of the curing process.

  2. High-resolution frequency measurement method with a wide-frequency range based on a quantized phase step law.

    PubMed

    Du, Baoqiang; Dong, Shaofeng; Wang, Yanfeng; Guo, Shuting; Cao, Lingzhi; Zhou, Wei; Zuo, Yandi; Liu, Dan

    2013-11-01

    A wide-frequency and high-resolution frequency measurement method based on the quantized phase step law is presented in this paper. Utilizing a variation law of the phase differences, the direct different frequency phase processing, and the phase group synchronization phenomenon, combining an A/D converter and the adaptive phase shifting principle, a counter gate is established in the phase coincidences at one-group intervals, which eliminates the ±1 counter error in the traditional frequency measurement method. More importantly, the direct phase comparison, the measurement, and the control between any periodic signals have been realized without frequency normalization in this method. Experimental results show that sub-picosecond resolution can be easily obtained in the frequency measurement, the frequency standard comparison, and the phase-locked control based on the phase quantization processing technique. The method may be widely used in navigation positioning, space techniques, communication, radar, astronomy, atomic frequency standards, and other high-tech fields.

  3. Generation of High Resolution Radar Range Profiles and Range Profile Auto-Correlation Functions Using Stepped-Frequency Pulse Train

    DTIC Science & Technology

    1984-10-18

    resulting range resolution (of both the profile and itg auto- correlation function) is determined by the total bandwidth (i.e., the fre- quency spread...contrast provided by the resulting range profiles and range profile auto-correlation functions is determined. The target-to-clutter contrast provided by the...SIMULATION RESULTS FOR RANGE-PROFILES AND RANGE-PROFILE 86 AUTO -CORRELATION FIJNCTIONS OBTAINED BY PROCESSING RETURNS FROM FR9QUENCY-STEPPED PULSE

  4. Three-dimensional ray tracing of the Jovian magnetosphere in the low-frequency range

    NASA Astrophysics Data System (ADS)

    Menietti, J. D.; Green, J. L.; Gulkis, S.; Six, F.

    1984-03-01

    Three-dimensional ray tracing of the Jovian DAM emission has been performed utilizing the O-4 magnetic field model (Acuna and Ness, 1979) and a realistic plasma model. Minimal assumptions about the emission mechanism have been made that include radiation in the right-hand extraordinary mode, propagating nearly perpendicular to the field line at source points located just above the RX cutoff frequency along Io flux tubes. Ray tracing has been performed in the frequency range from 2-35 MHz from successive Io flux tubes separated by ten degrees of central meridian longitude for a full circumference of northern hemisphere sources. The results show unusual complexity in model arc spectra that is displayed in a constant Io phase format with many similarities to the Voyager PRA data. The results suggest much of the variation in observed DAM spectral features is a result of propagation effects rather than emission process differences.

  5. Three-dimensional ray tracing of the Jovian magnetosphere in the low-frequency range

    NASA Technical Reports Server (NTRS)

    Menietti, J. D.; Green, J. L.; Gulkis, S.; Six, F.

    1984-01-01

    Three-dimensional ray tracing of the Jovian DAM emission has been performed utilizing the O-4 magnetic field model (Acuna and Ness, 1979) and a realistic plasma model. Minimal assumptions about the emission mechanism have been made that include radiation in the right-hand extraordinary mode, propagating nearly perpendicular to the field line at source points located just above the RX cutoff frequency along Io flux tubes. Ray tracing has been performed in the frequency range from 2-35 MHz from successive Io flux tubes separated by ten degrees of central meridian longitude for a full circumference of northern hemisphere sources. The results show unusual complexity in model arc spectra that is displayed in a constant Io phase format with many similarities to the Voyager PRA data. The results suggest much of the variation in observed DAM spectral features is a result of propagation effects rather than emission process differences.

  6. Parallel PWMs Based Fully Digital Transmitter with Wide Carrier Frequency Range

    PubMed Central

    Zhou, Bo; Zhang, Kun; Zhou, Wenbiao; Zhang, Yanjun; Liu, Dake

    2013-01-01

    The carrier-frequency (CF) and intermediate-frequency (IF) pulse-width modulators (PWMs) based on delay lines are proposed, where baseband signals are conveyed by both positions and pulse widths or densities of the carrier clock. By combining IF-PWM and precorrected CF-PWM, a fully digital transmitter with unit-delay autocalibration is implemented in 180 nm CMOS for high reconfiguration. The proposed architecture achieves wide CF range of 2 M–1 GHz, high power efficiency of 70%, and low error vector magnitude (EVM) of 3%, with spectrum purity of 20 dB optimized in comparison to the existing designs. PMID:24223503

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

    PubMed

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

    2015-02-01

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

  8. A non-synonymous SNP with the allele frequency correlated with the altitude may contribute to the hypoxia adaptation of Tibetan chicken

    PubMed Central

    Wang, Yan; Yin, Huadong; Zhou, Lanyun; Zhong, Chengling

    2017-01-01

    The hypoxia adaptation to high altitudes is of considerable interest in the biological sciences. As a breed with adaptability to highland environments, the Tibetan chicken (Gallus gallus domestics), provides a biological model to search for genetic differences between high and lowland chickens. To address mechanisms of hypoxia adaptability at high altitudes for the Tibetan chicken, we focused on the Endothelial PAS domain protein 1 (EPAS1), a key regulatory factor in hypoxia responses. Detected were polymorphisms of EPAS1 exons in 157 Tibetan chickens from 8 populations and 139 lowland chickens from 7 breeds. We then designed 15 pairs of primers to amplify exon sequences by Sanger sequencing methods. Six single nucleotide polymorphisms (SNPs) were detected, including 2 missense mutations (SNP3 rs316126786 and SNP5 rs740389732) and 4 synonymous mutations (SNP1 rs315040213, SNP4 rs739281102, SNP6 rs739010166, and SNP2 rs14330062). There were negative correlations between altitude and mutant allele frequencies for both SNP6 (rs739010166, r = 0.758, p<0.001) and SNP3 (rs316126786, r = 0.844, P<0.001). We also aligned the EPAS1 protein with ortholog proteins from diverse vertebrates and focused that SNP3 (Y333C) was a conserved site among species. Also, SNP3 (Y333C) occurred in a well-defined protein domain Per-AhR-Arnt-Sim (PAS domain). These results imply that SNP3 (Y333C) is the most likely casual mutation for the high-altitude adaption in Tibetan chicken. These variations of EPAS1 provide new insights into the gene’s function. PMID:28222154

  9. Mutations of the GLA gene in Korean patients with Fabry disease and frequency of the E66Q allele as a functional variant in Korean newborns.

    PubMed

    Lee, Beom Hee; Heo, Sun Hee; Kim, Gu-Hwan; Park, Jung-Young; Kim, Woo-Shik; Kang, Duk-Hee; Choe, Kyung Hoon; Kim, Won-Ho; Yang, Song Hyun; Yoo, Han-Wook

    2010-08-01

    Fabry disease is caused by an alpha-galactosidase A (GLA) deficiency. In this study, we identified 28 unrelated Korean families with Fabry disease with 25 distinct mutations in the GLA gene including six novel mutations (p.W47X, p.C90X, p.D61EfsX32, IVS4(-11)T>A, p.D322E and p.W349). Notably, five subjects from four unrelated families carried the p.E66Q variant, previously known as a pathogenic mutation in atypical Fabry disease. Among these patients, only one had proteinuria and two had hypertrophic cardiomyopathy without any other systemic manifestation of Fabry disease. Substantial residual GLA activity was shown both in the leukocytes of p.E66Q patients (19.0-30.3% of normal activity) and in transiently overexpressed COS-7 cells (43.8 + or - 3.03% of normal activity). Although GLA harboring p.E66Q is unstable at neutral pH, the enzyme is efficiently expressed in the lysosomes of COS-7 cells. The location of p.E66 is distant from both the active site and the dimer interface, and has a more accessible surface area than have other mutations of atypical Fabry disease. In addition, the allele frequency of p.E66Q determined in 833 unrelated Korean individuals was remarkably high at 1.046% (95% confidence interval, 0.458-1.634%). These results indicate that p.E66Q is a functional polymorphism rather than a pathogenic mutation.

  10. Mid-frequency sound propagation through internal waves at short range with synoptic oceanographic observations.

    PubMed

    Rouseff, Daniel; Tang, Dajun; Williams, Kevin L; Wang, Zhongkang; Moum, James N

    2008-09-01

    Preliminary results are presented from an analysis of mid-frequency acoustic transmission data collected at range 550 m during the Shallow Water 2006 Experiment. The acoustic data were collected on a vertical array immediately before, during, and after the passage of a nonlinear internal wave on 18 August, 2006. Using oceanographic data collected at a nearby location, a plane-wave model for the nonlinear internal wave's position as a function of time is developed. Experimental results show a new acoustic path is generated as the internal wave passes above the acoustic source.

  11. A Robust Range Grating Lobe Suppression Method Based on Image Contrast for Stepped-Frequency SAR

    PubMed Central

    Gao, Wen-Bin; Long, Teng; Ding, Ze-Gang; Wu, Yi-Rong

    2016-01-01

    The magnitude error and phase error (MEPE) in the transfer function of a stepped-frequency synthetic aperture radar (SAR) system results in a periodic MEPE in the synthesized wideband waveform (SWW), which induces the grating lobes in the high-resolution range profile (HRRP). In this paper, a robust data-driven grating lobe suppression (GLS) method is proposed. Based on a contrast-based error estimation method and the grating lobes of the brightest scatterers in the SAR image, the periodic MEPE can be robustly estimated using the proposed method. By compensating the estimated periodic MEPE, the range grating lobes can be suppressed to the background level of the SAR image. Simulation results and real data processing have demonstrated the superiority of the proposed method. PMID:27929411

  12. Optical-fiber frequency domain interferometer with nanometer resolution and centimeter measuring range.

    PubMed

    Weng, Jidong; Tao, Tianjiong; Liu, Shenggang; Ma, Heli; Wang, Xiang; Liu, Cangli; Tan, Hua

    2013-11-01

    A new optical-fiber frequency domain interferometer (OFDI) device for accurate measurement of the absolute distance between two stationary objects, with centimeter measuring range and nanometer resolution, has been developed. Its working principle and on-line data processing method were elaborated. The new OFDI instrument was constructed all with currently available commercial communication products. It adopted the wide-spectrum amplified spontaneous emission light as the light source and optical-fiber tip as the test probe. Since this device consists of only fibers or fiber coupled components, it is very compact, convenient to operate, and easy to carry. By measuring the single-step length of a translation stage and the thickness of standard gauge blocks, its ability in implementing nanometer resolution and centimeter measuring range on-line measurements was validated.

  13. LTP in Hippocampal Area CA1 Is Induced by Burst Stimulation over a Broad Frequency Range Centered around Delta

    ERIC Educational Resources Information Center

    Grover, Lawrence M.; Kim, Eunyoung; Cooke, Jennifer D.; Holmes, William R.

    2009-01-01

    Long-term potentiation (LTP) is typically studied using either continuous high-frequency stimulation or theta burst stimulation. Previous studies emphasized the physiological relevance of theta frequency; however, synchronized hippocampal activity occurs over a broader frequency range. We therefore tested burst stimulation at intervals from 100…

  14. Alteration of frequency range for binaural beats in acute low-tone hearing loss.

    PubMed

    Karino, Shotaro; Yamasoba, Tatsuya; Ito, Ken; Kaga, Kimitaka

    2005-01-01

    The effect of acute low-tone sensorineural hearing loss (ALHL) on the interaural frequency difference (IFD) required for perception of binaural beats (BBs) was investigated in 12 patients with unilateral ALHL and 7 patients in whom ALHL had lessened. A continuous pure tone of 30 dB sensation level at 250 Hz was presented to the contralateral, normal-hearing ear. The presence of BBs was determined by a subjective yes-no procedure as the frequency of a loudness-balanced test tone was gradually adjusted around 250 Hz in the affected ear. The frequency range in which no BBs were perceived (FRNB) was significantly wider in the patients with ALHL than in the controls, and FRNBs became narrower in the recovered ALHL group. Specifically, detection of slow BBs with a small IFD was impaired in this limited (10 s) observation period. The significant correlation between the hearing level at 250 Hz and FRNBs suggests that FRNBs represent the degree of cochlear damage caused by ALHL.

  15. Absorption and modulus measurements in the seismic frequency and strain range on partially saturated sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Paffenholz, Josef; Burkhardt, Hans

    1989-07-01

    The absorptions 1/QE and 1/QS of partially water-saturated sedimentary rocks were determined from phase differences between stress and strain for longitudinal deformation frequencies between 0.03 and 300 Hz and torsional frequencies between 0.03 and 100 Hz. Both longitudinal and shear strain amplitudes were of the order of 10-6. For water saturation between 0 and 50%, Young's moduli and shear moduli were shown to decrease with increasing saturation. In this saturation range both 1/QE and 1/QS increased, but no distinguishable absorption maxima were observed. For saturation percentages greater than 50%, the moduli of the samples appeared independent of the water content. 1/QE increased until full saturation and showed a strong frequency dependence. 1/QS is much less affected by increasing water saturation and has no absorption maxima in general. Since the absorption and the moduli reduction show different saturation dependencies, two different mechanisms for these effects are proposed. The addition of water changes the interaction force between the molecules on opposite walls of thin cracks. This provides a mechanism for the modulus reduction. Calculations based on the Biot-Gardner theory (Gardner, 1962) indicate that part of the observed absorption may be caused by fluid flow due to the limited sample size as proposed by White (1986). Fluid-supported thermorelaxation is proposed, as a possible intrinsic absorption mechanism.

  16. Serotonin transporter protein (SLC6A4) allele and haplotype frequencies and linkage disequilibria in African- and European-American and Japanese populations and in alcohol-dependent subjects.

    PubMed

    Gelernter, J; Kranzler, H; Cubells, J F

    1997-12-01

    The SLC6A4 locus encodes the serotonin transporter, which in turn mediates the synaptic inactivation of the neurotransmitter serotonin. Two PCR-formatted polymorphisms at this locus have been described, the first of which is a variable number tandem repeat located in exon 2, and the second a repeat sequence polymorphism located in the promoter region. The latter polymorphism alters transcriptional activity of SLC6A4, and has been reported to be associated with anxiety and depression-related traits. We studied allele frequencies, and computed haplotype frequencies and linkage disequilibrium measures, for these two polymorphisms in European-American, African-American, and Japanese populations, and in a set of alcohol-dependent European-American subjects. Allele frequencies for both systems showed variation, with significant differences overall for each system, and significant differences between each pair of populations for both systems. Linkage disequilibrium also varied among the populations. There were no significant differences in allele or haplotype frequencies between the European-American population samples and alcohol-dependent subjects. The population differences demonstrate a potential for population stratification in association studies of either of these SLC6A4 polymorphisms. If genetic variation at this locus really is associated with behavioral variation, these results could reflect either different behavioral adaptations in different populations, or random genetic drift of a behaviorally important but selectively neutral polymorphism.

  17. Impaired Neural Synchrony in the Theta Frequency Range in Adolescents at Familial Risk for Schizophrenia

    PubMed Central

    Donkers, Franc C. L.; Schwikert, Shane R.; Evans, Anna M.; Cleary, Katherine M.; Perkins, Diana O.; Belger, Aysenil

    2011-01-01

    Puberty is a critical period for the maturation of the fronto-limbic and fronto-striate brain circuits responsible for executive function and affective processing. Puberty also coincides with the emergence of the prodromal signs of schizophrenia, which may indicate an association between these two processes. Time-domain analysis and wavelet based time–frequency analysis was performed on electroencephalographic (EEG) data of 30 healthy control (HC) subjects and 24 individuals at familial risk (FR) for schizophrenia. All participants were between the ages of 13 and 18 years and were carefully matched for age, gender, ethnicity, education, and Tanner Stage. Electrophysiological recordings were obtained from 32 EEG channels while participants performed a visual oddball task, where they identified rare visual targets among standard “scrambled” images and rare aversive and neutral distracter pictures. The time-domain analysis showed that during target processing the FR group showed smaller event-related potentials in the P2 and P3 range as compared to the HC group. In addition, EEG activity in the theta (4–8 Hz) frequency range was significantly reduced during target processing in the FR group. Inefficient cortical information processing during puberty may be an early indicator of altered brain function in adolescents at FR for schizophrenia and may represent a vulnerability marker for illness onset. Longitudinal assessments will have to determine their predictive value for illness onset in populations at FR for psychotic illness. PMID:21991257

  18. Characterization of a Prototype Radio Frequency Space Environment Path Emulator for Evaluating Spacecraft Ranging Hardware

    NASA Technical Reports Server (NTRS)

    Mitchell, Jason W.; Baldwin, Philip J.; Kurichh, Rishi; Naasz, Bo J.; Luquette, Richard J.

    2007-01-01

    The Formation Flying Testbed (FFTB) at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC) provides a hardware-in-the-loop test environment for formation navigation and control. The facility is evolving as a modular, hybrid, dynamic simulation facility for end-to-end guidance, navigation and control (GN&C) design and analysis of formation flying spacecraft. The core capabilities of the FFTB, as a platform for testing critical hardware and software algorithms in-the-loop, have expanded to include S-band Radio Frequency (RF) modems for interspacecraft communication and ranging. To enable realistic simulations that require RF ranging sensors for relative navigation, a mechanism is needed to buffer the RF signals exchanged between spacecraft that accurately emulates the dynamic environment through which the RF signals travel, including the effects of the medium, moving platforms, and radiated power. The Path Emulator for Radio Frequency Signals (PERFS), currently under development at NASA GSFC, provides this capability. The function and performance of a prototype device are presented.

  19. Frequency-Range Distribution of Boulders Around Cone Crater: Relevance to Landing Site Hazard Avoidance

    NASA Technical Reports Server (NTRS)

    Clegg-Watkins, R. N.; Jolliff, B. L.; Lawrence, S. J.

    2016-01-01

    Boulders represent a landing hazard that must be addressed in the planning of future landings on the Moon. A boulder under a landing leg can contribute to deck tilt and boulders can damage spacecraft during landing. Using orbital data to characterize boulder populations at locations where landers have safely touched down (Apollo, Luna, Surveyor, and Chang'e-3 sites) is important for determining landing hazard criteria for future missions. Additionally, assessing the distribution of boulders can address broader science issues, e.g., how far craters distribute boulders and how this distribution varies as a function of crater size and age. The availability of new Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images [1] enables the use of boulder size- and range frequency distributions for a variety of purposes [2-6]. Boulders degrade over time and primarily occur around young or fresh craters that are large enough to excavate bedrock. Here we use NAC images to analyze boulder distributions around Cone crater (340 m diameter) at the Apollo 14 site. Cone crater (CC) was selected because it is the largest crater where astronaut surface photography is available for a radial traverse to the rim. Cone crater is young (approximately 29 Ma [7]) relative to the time required to break down boulders [3,8], giving us a data point for boulder range-frequency distributions (BRFDs) as a function of crater age.

  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 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

  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

    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.

  2. Signature of forty years of artificial selection in U.S. Holstein cattle identified by long-range frequency analyses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three groups of U.S. Holstein cattle were analyzed for selection signature of artificial selection since 1964 using long-range frequency measures. The three groups included Holsteins unselected since 1964, contemporary Holsteins, and an elite line of contemporary Holsteins. Long-range frequencies in...

  3. Radio frequency interference survey over the 1.0-10.4 GHz frequency range at the Goldstone-Venus Development Station

    NASA Technical Reports Server (NTRS)

    Gulkis, S.; Olsen, E. T.; Klein, M. J.; Jackson, E. B.

    1989-01-01

    The results of a low sensitivity Radio Frequency Interference (RFI) survey carried out at the Venus Station of the Goldstone Communications Complex are reported. The data cover the spectral range from 1 GHz to 10.4 GHz with a 10-kHz instantaneous bandwidth. Frequency and power levels were observed using a sweep-frequency spectrum analyzer connected to a 1-m diameter antenna pointed at zenith. The survey was conducted from February 16, 1987 through February 24, 1987.

  4. The Multifractal Flood Frequency Analysis to Account Long Range Dependencies and the Clustering of Extremes

    NASA Astrophysics Data System (ADS)

    Tchiguirinskaia, I.; Schertzer, D. J.; Lovejoy, S.

    2012-12-01

    The classical quantile distributions in existing flood studies often rely on two hypotheses that are questionable: stationarity and independency of the components of the time series. We discuss how to better (statistically) predict the floods by using a physically based approach that accounts long range dependencies and the clustering of extremes often resulting in fat tailed (i.e., an algebraic type) probability distributions. It established on systems that respect a scale symmetry over a wide range of space-time scales to determine the relationship between flood magnitude and return period for a wide range of aggregation periods. The results were obtained during the CEATI Project "Multifractals and physically based estimates of extreme floods". The ambition of this project was to investigate very large data sets of reasonable quality (e.g., daily stream flow data recorded for at least 20 years for several thousands of gages distributed all over Canada and the USA). The multifractal parameters such as the mean intermittency parameter and the multifractality index were estimated on 8332 time series. Obtained results demonstrate that beyond the classical sampling of the extremes and its limitations, there is the possibility to eliminate long-range dependency by uncovering a stochastic process whose fractional integration would generate the observed long-range dependent process. The results confirm the dependence of parameter estimates on the length of available data. Then developing a metric for parameter estimation error became a principal step in uncertainty evaluation with respect to the multifractal estimates. A technique for estimating confidence intervals with the help of a Bayesian approach was developed. A detailed comparison of multifractal quantile plots and paleoflood data validates the forthcoming use of the multifractal flood frequency analysis.

  5. Graphics processing unit-based dispersion encoded full-range frequency-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Wang, Ling; Hofer, Bernd; Guggenheim, Jeremy A.; Považay, Boris

    2012-07-01

    Dispersion encoded full-range (DEFR) frequency-domain optical coherence tomography (FD-OCT) and its enhanced version, fast DEFR, utilize dispersion mismatch between sample and reference arm to eliminate the ambiguity in OCT signals caused by non-complex valued spectral measurement, thereby numerically doubling the usable information content. By iteratively suppressing asymmetrically dispersed complex conjugate artifacts of OCT-signal pulses the complex valued signal can be recovered without additional measurements, thus doubling the spatial signal range to cover the full positive and negative sampling range. Previously the computational complexity and low processing speed limited application of DEFR to smaller amounts of data and did not allow for interactive operation at high resolution. We report a graphics processing unit (GPU)-based implementation of fast DEFR, which significantly improves reconstruction speed by a factor of more than 90 in respect to CPU-based processing and thereby overcomes these limitations. Implemented on a commercial low-cost GPU, a display line rate of ~21,000 depth scans/s for 2048 samples/depth scan using 10 iterations of the fast DEFR algorithm has been achieved, sufficient for real-time visualization in situ.

  6. Allele surfing promotes microbial adaptation from standing variation.

    PubMed

    Gralka, Matti; Stiewe, Fabian; Farrell, Fred; Möbius, Wolfram; Waclaw, Bartlomiej; Hallatschek, Oskar

    2016-08-01

    The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from 'soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges.

  7. [Differences in allele frequency at the BAIB locus, determining the level of expression of beta-aminoisobutyric acid, in healthy donors and coronary artery atherosclerosis patients from Buryat and Lithuanian populations].

    PubMed

    Spitsyn, V A; Afanas'eva, I S

    2001-12-01

    Phenotype and allele frequencies of the genetically dimorphic system determining urinary excretion of beta-aminoisobutyric acid (BAIB) were studied in population samples of Buryats from the Aginskii Buryat Autonomous District and Lithuanians from Vilnius and in patients with coronary atherosclerosis (CA) from both populations. Frequency of allele BAIB*b, which determines high BAIB excretion, proved to be more than twice higher in Buryats compared with the population sample of Lithuanians (0.620 versus 0.289, respectively). The proportion of individuals with high BAIB excretion in CA patients of either ethnic sample was twice higher than in the corresponding control sample. Frequency of allele BAIB*b in CA patients and healthy individuals was 0.348 and 0.242, respectively, in the Lithuanian population and 0.775 and 0.557, respectively, in the Buryat population. Thus, assessment of urinary excretion of BAIB proved to be prognostically valuable. The method used to detect a variation in BAIB excretion is relatively inexpensive, simple, and suitable for mass screening of patients and healthy individuals (population control). After additional testing with representative samples, the method can be used as an accessory diagnostic test in patients with cardiovascular disorders.

  8. New creep-fatigue damage model based on the frequency modified strain range method

    SciTech Connect

    Kim, Y.J.; Seok, C.S.; Park, J.J.

    1996-12-01

    For mechanical systems operating at high temperature, damage due to the interaction effect of creep and fatigue plays an important role. The objective of this paper is to propose a modified creep-fatigue damage model which separately analyzes the pure creep damage due to the hold time and the creep-fatigue interaction damage during the startup and the shutdown period. The creep damage was calculated by the general creep damage equation and the creep-fatigue interaction damage was calculated by the modified equation which is based on the frequency modified strain range method with strain rate term. In order to verify the proposed model, a series of high temperature low cycle fatigue tests were performed. The test specimens were made from Inconel-718 superalloy and the test parameters were wave form and hold time. A good agreement between the predicted lives based on the proposed model and experimentally obtained ones was obtained.

  9. Filamentation instability of nonextensive current-driven plasma in the ion acoustic frequency range

    SciTech Connect

    Khorashadizadeh, S. M. Rastbood, E.; Niknam, A. R.

    2014-12-15

    The filamentation and ion acoustic instabilities of nonextensive current-driven plasma in the ion acoustic frequency range have been studied using the Lorentz transformation formulas. Based on the kinetic theory, the possibility of filamentation instability and its growth rate as well as the ion acoustic instability have been investigated. The results of the research show that the possibility and growth rate of these instabilities are significantly dependent on the electron nonextensive parameter and drift velocity. Besides, the increase of electrons nonextensive parameter and drift velocity lead to the increase of the growth rates of both instabilities. In addition, the wavelength region in which the filamentation instability occurs is more stretched in the presence of higher values of drift velocity and nonextensive parameter. Finally, the results of filamentation and ion acoustic instabilities have been compared and the conditions for filamentation instability to be dominant mode of instability have been presented.

  10. Stage-based frequency-modulated full-range complex Fourier-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Bian, Haiyi; Gao, Wanrong

    2015-10-01

    We propose a simple method to modulate spatial interferogram to achieve full-range complex imaging in Fourier-domain optical coherence tomography, in which a sample stage is employed which can be adjusted to introduce a constant carrier frequency into the interference signal during the B-scan by adjusting the stage angle with respect to the normal to the object under test. An additional phase, which is linearly related to the lateral position, is then induced in the A-scan. The in vivo images of human skin were generated which demonstrate that the method proposed can generate the cross-sectional image with the same quality with that obtained with other methods and with the advantage of the simplicity in implementation.

  11. Cosmic ray scintillations in the frequency range from 0.00001 to 0.01 Hz

    NASA Technical Reports Server (NTRS)

    Gehrels, N.; Lheureux, J.

    1978-01-01

    Power spectra of the flux variations in cosmic rays of energy greater than a few GeV are presented. The data were obtained at balloon altitudes (40-45 km) from two scintillation-type detectors flown for six hours from Palestine, Texas, on November 4, 1972. The large area detectors had effective count rates up to 2000 cps setting the Poisson noise level in the power spectra of the relative fluctuations at 0.001/Hz. The analysis was made on the singles rate of each of the counters as well as on the coincidence rates between them. In all cases, the spectra between 0.0001 and 0.002 Hz are power laws in frequency of the form f to the exponent negative gamma, where gamma is between 1.5 and 2.0. No significant peaks in the range 0.0001 to 0.01 Hz are observed.

  12. Fabrication and characterization of biotissue-mimicking phantoms in the THz frequency range

    NASA Astrophysics Data System (ADS)

    Liakhov, E.; Smolyanskaya, O.; Popov, A.; Odlyanitskiy, E.; Balbekin, N.; Khodzitsky, M.

    2016-08-01

    The study revealed the most promising candidates for phantoms mimicking different biological tissues in the terahertz frequency range. Closest to biological tissues in terms of the refractive index appeared to be gelatin-based gels; in terms of the absorption coefficient they were agar-based gels. Gelatin is more stable in time, but requires special storage conditions to limit water evaporation. The dense structure of the agar-based phantom allows its use without mold and risk of damage. However, agar is a nutrient medium for bacteria and its parameters degrade even when the phantom form and water content are retained. Use of liquid suspensions of lecithin and milk powder are found to be extremely limited.

  13. Experimental study of attenuation and dispersion over a broad frequency range: 1. The apparatus

    NASA Astrophysics Data System (ADS)

    Takei, Yasuko; Fujisawa, Kazuhiro; McCarthy, Christine

    2011-09-01

    We have developed a new experimental method to investigate the anelasticity of a polycrystalline solid at high homologous temperature (T/Tm = 0.6-0.7). By using a rock analogue (borneol polycrystals) and a partially molten rock analogue (borneol + melt) having low melting and eutectic temperatures (Tm = 204.5°C, Te = 43°C), respectively, testing high homologous temperature can occur near room temperature. An apparatus is described for cyclic compressive, Young's modulus type attenuation experiments over a wide range of frequencies (10-10-4 Hz) and at small strain amplitudes (10-6-10-5). Creep tests to measure steady state viscosity can also be performed. Details of the apparatus, including its piezoelectric actuator, dual laser displacement meters and trio of load cells, are discussed. Attenuation spectra and modulus dispersion measured for aluminum, acrylic plastic, and a rock analogue are presented to illustrate the accuracy of the method.

  14. Acoustic absorption measurement of human hair and skin within the audible frequency range.

    PubMed

    Katz, B F

    2000-11-01

    Utilizing the two-microphone impedance tube method, the acoustic absorption of human skin and hair is measured in the frequency range 1-6 kHz. Various locations on a number of human subjects are measured to determine if the presence of bone or an air pocket affects the acoustic absorption of human skin. The absorption coefficient of human hair is also measured. Additional techniques are utilized to minimize errors due to sample mounting methods. Techniques are employed to minimize potential errors in sensor and sample locations. The results of these measurements are compared to relevant historical papers on similar investigations. Results for skin measurements compare well with previous work. Measured hair absorption data do not agree with previous work in the area but do coincide with expected trends, which previous works do not.

  15. Global Low Frequency Protein Motions in Long-Range Allosteric Signaling

    NASA Astrophysics Data System (ADS)

    McLeish, Tom; Rogers, Thomas; Townsend, Philip; Burnell, David; Pohl, Ehmke; Wilson, Mark; Cann, Martin; Richards, Shane; Jones, Matthew

    2015-03-01

    We present a foundational theory for how allostery can occur as a function of low frequency dynamics without a change in protein structure. Elastic inhomogeneities allow entropic ``signalling at a distance.'' Remarkably, many globular proteins display just this class of elastic structure, in particular those that support allosteric binding of substrates (long-range co-operative effects between the binding sites of small molecules). Through multi-scale modelling of global normal modes we demonstrate negative co-operativity between the two cAMP ligands without change to the mean structure. Crucially, the value of the co-operativity is itself controlled by the interactions around a set of third allosteric ``control sites.'' The theory makes key experimental predictions, validated by analysis of variant proteins by a combination of structural biology and isothermal calorimetry. A quantitative description of allostery as a free energy landscape revealed a protein ``design space'' that identified the key inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, by analyzing naturally occurring CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. The methodology establishes the means to engineer allosteric mechanisms that are driven by low frequency dynamics.

  16. Harvesting Ambient Vibration Energy over a Wide Frequency Range for Self-Powered Electronics.

    PubMed

    Wang, Xiaofeng; Niu, Simiao; Yi, Fang; Yin, Yajiang; Hao, Chenglong; Dai, Keren; Zhang, Yue; You, Zheng; Wang, Zhong Lin

    2017-02-28

    Vibration is one of the most common energy sources in ambient environment. Harvesting vibration energy is a promising route to sustainably drive small electronics. This work introduces an approach to scavenge vibrational energy over a wide frequency range as an exclusive power source for continuous operation of electronics. An elastic multiunit triboelectric nanogenerator (TENG) is rationally designed to efficiently harvest low-frequency vibration energy, which can provide a maximum instantaneous output power density of 102 W·m(-3) at as low as 7 Hz and maintain its stable current outputs from 5 to 25 Hz. A self-charging power unit (SCPU) combining the TENG and a 10 mF supercapacitor gives a continuous direct current (DC) power delivery of 1.14 mW at a power management efficiency of 45.6% at 20 Hz. The performance of the SCPU can be further enhanced by a specially designed power management circuit, with a continuous DC power of 2 mW and power management efficiency of 60% at 7 Hz. Electronics such as a thermometer, hygrometer, and speedometer can be sustainably powered solely by the harvested vibration energy from a machine or riding bicycle. This approach has potential applications in self-powered systems for environment monitoring, machine safety, and transportation.

  17. Paternal kin recognition in the high frequency / ultrasonic range in a solitary foraging mammal

    PubMed Central

    2012-01-01

    Background Kin selection is a driving force in the evolution of mammalian social complexity. Recognition of paternal kin using vocalizations occurs in taxa with cohesive, complex social groups. This is the first investigation of paternal kin recognition via vocalizations in a small-brained, solitary foraging mammal, the grey mouse lemur (Microcebus murinus), a frequent model for ancestral primates. We analyzed the high frequency/ultrasonic male advertisement (courtship) call and alarm call. Results Multi-parametric analyses of the calls’ acoustic parameters and discriminant function analyses showed that advertisement calls, but not alarm calls, contain patrilineal signatures. Playback experiments controlling for familiarity showed that females paid more attention to advertisement calls from unrelated males than from their fathers. Reactions to alarm calls from unrelated males and fathers did not differ. Conclusions 1) Findings provide the first evidence of paternal kin recognition via vocalizations in a small-brained, solitarily foraging mammal. 2) High predation, small body size, and dispersed social systems may select for acoustic paternal kin recognition in the high frequency/ultrasonic ranges, thus limiting risks of inbreeding and eavesdropping by predators or conspecific competitors. 3) Paternal kin recognition via vocalizations in mammals is not dependent upon a large brain and high social complexity, but may already have been an integral part of the dispersed social networks from which more complex, kin-based sociality emerged. PMID:23198727

  18. Numerical Exposure Assessment Method for Low Frequency Range and Application to Wireless Power Transfer

    PubMed Central

    Kim, Minhyuk

    2016-01-01

    In this paper, a numerical exposure assessment method is presented for a quasi-static analysis by the use of finite-difference time-domain (FDTD) algorithm. The proposed method is composed of scattered field FDTD method and quasi-static approximation for analyzing of the low frequency band electromagnetic problems. The proposed method provides an effective tool to compute induced electric fields in an anatomically realistic human voxel model exposed to an arbitrary non-uniform field source in the low frequency ranges. The method is verified, and excellent agreement with theoretical solutions is found for a dielectric sphere model exposed to a magnetic dipole source. The assessment method serves a practical example of the electric fields, current densities, and specific absorption rates induced in a human head and body in close proximity to a 150-kHz wireless power transfer system for cell phone charging. The results are compared to the limits recommended by the International Commission on Non-Ionizing Radiation Protection (ICNIRP) and the IEEE standard guidelines. PMID:27898688

  19. Numerical Exposure Assessment Method for Low Frequency Range and Application to Wireless Power Transfer.

    PubMed

    Park, SangWook; Kim, Minhyuk

    2016-01-01

    In this paper, a numerical exposure assessment method is presented for a quasi-static analysis by the use of finite-difference time-domain (FDTD) algorithm. The proposed method is composed of scattered field FDTD method and quasi-static approximation for analyzing of the low frequency band electromagnetic problems. The proposed method provides an effective tool to compute induced electric fields in an anatomically realistic human voxel model exposed to an arbitrary non-uniform field source in the low frequency ranges. The method is verified, and excellent agreement with theoretical solutions is found for a dielectric sphere model exposed to a magnetic dipole source. The assessment method serves a practical example of the electric fields, current densities, and specific absorption rates induced in a human head and body in close proximity to a 150-kHz wireless power transfer system for cell phone charging. The results are compared to the limits recommended by the International Commission on Non-Ionizing Radiation Protection (ICNIRP) and the IEEE standard guidelines.

  20. Long range dependence in the high frequency USD/INR exchange rate

    NASA Astrophysics Data System (ADS)

    Kumar, Dilip

    2014-02-01

    Using high frequency data, this paper examines the long memory property in the unconditional and conditional volatility of the USD/INR exchange rate at different time scales using the Local Whittle (LW), the Exact Local Whittle (ELW) and the FIAPARCH models. Results indicate that the long memory property remains quite stable across different time scales for both unconditional and conditional volatility measures. Results from the non-overlapping moving window approach indicate that the extreme events (such as the subprime crisis and the European debt crisis) resulted in highly persistent behavior of the USD/INR exchange rate and thus lead to market inefficiency. This paper also examines the long memory property in the realized volatility based on different time scale data. Results indicate that the realized volatility measures based on different scales of the high frequency data exhibit a consistent and stable long memory property. However, the realized volatility measures based on daily data exhibit lower degree of long-range dependence. This study has implications for traders and investors (with different trading horizons) and can be helpful in predicting expected future volatility and in designing and implementing trading strategies at different time scales.

  1. Interaction of a relativistic electron beam with radiation in the THz frequency range

    NASA Astrophysics Data System (ADS)

    Sung, Chieh

    0.5-3 THz range with a maximum of ˜2 kW of peak power in a 200 ns pulse suitable as a seed for an FEL microbuncher. These sources represent the most powerful and the most energetic narrowband THz sources currently reported using nonlinear optical technique to our knowledge. During the FEL microbunching process, the wiggling electrons in the undulator also emit radiation coherently at the resonant frequency; as a result, the THz FEL microbuncher can double as a single pass THz amplifier tunable in the 0.5-3 THz range. It is shown that when seeded with a ˜1 kW THz pulse and driven by an electron beam with a peak current of 60A, a 2 m-long undulator can amplify the radiation power to ˜20MW. The frequency range can be further expanded to up to 9 THz via the High Gain Harmonic Generation (HGHG) FEL configuration. The results of these simulations are used as a guide in designing a single-pass THz FEL microbuncher/amplifier which is currently under construction. In order to study THz microbunching and amplification, several original techniques and diagnostics were also developed. Guiding a THz pulse through a hollow waveguide, filtering a short THz pulse using a Fabry-Perot interferometer and measuring the frequency components using a diffraction grating spectrometer were demonstrated.

  2. Opto-electronic device for frequency standard generation and terahertz-range optical demodulation based on quantum interference

    DOEpatents

    Georgiades, Nikos P.; Polzik, Eugene S.; Kimble, H. Jeff

    1999-02-02

    An opto-electronic system and technique for comparing laser frequencies with large frequency separations, establishing new frequency standards, and achieving phase-sensitive detection at ultra high frequencies. Light responsive materials with multiple energy levels suitable for multi-photon excitation are preferably used for nonlinear mixing via quantum interference of different excitation paths affecting a common energy level. Demodulation of a carrier with a demodulation frequency up to 100's THZ can be achieved for frequency comparison and phase-sensitive detection. A large number of materials can be used to cover a wide spectral range including the ultra violet, visible and near infrared regions. In particular, absolute frequency measurement in a spectrum from 1.25 .mu.m to 1.66 .mu.m for fiber optics can be accomplished with a nearly continuous frequency coverage.

  3. Opto-electronic device for frequency standard generation and terahertz-range optical demodulation based on quantum interference

    DOEpatents

    Georgiades, N.P.; Polzik, E.S.; Kimble, H.J.

    1999-02-02

    An opto-electronic system and technique for comparing laser frequencies with large frequency separations, establishing new frequency standards, and achieving phase-sensitive detection at ultra high frequencies are disclosed. Light responsive materials with multiple energy levels suitable for multi-photon excitation are preferably used for nonlinear mixing via quantum interference of different excitation paths affecting a common energy level. Demodulation of a carrier with a demodulation frequency up to 100`s THZ can be achieved for frequency comparison and phase-sensitive detection. A large number of materials can be used to cover a wide spectral range including the ultra violet, visible and near infrared regions. In particular, absolute frequency measurement in a spectrum from 1.25 {micro}m to 1.66 {micro}m for fiber optics can be accomplished with a nearly continuous frequency coverage. 7 figs.

  4. Optical conductivity of warm dense matter within a wide frequency range using quantum statistical and kinetic approaches

    NASA Astrophysics Data System (ADS)

    Veysman, M.; Röpke, G.; Winkel, M.; Reinholz, H.

    2016-07-01

    Fundamental properties of warm dense matter are described by the dielectric function, which gives access to the frequency-dependent electrical conductivity; absorption, emission, and scattering of radiation; charged particles stopping; and further macroscopic properties. Different approaches to the dielectric function and the related dynamical collision frequency are compared in a wide frequency range. The high-frequency limit describing inverse bremsstrahlung and the low-frequency limit of the dc conductivity are considered. Sum rules and Kramers-Kronig relation are checked for the generalized linear response theory and the standard approach following kinetic theory. The results are discussed in application to aluminum, xenon, and argon plasmas.

  5. Very-high-frequency dc-to-dc conversion and regulation in the low-megahertz range.

    NASA Technical Reports Server (NTRS)

    Feng, S. Y. M.; Wilson, T. G.; Sander, W. A., III

    1971-01-01

    Anticipated new mission requirements have motivated research on very-high-frequency (VHF) regulated dc-to-dc converters to operate at conversion frequencies in the low-megahertz range. State-of-the-art electronic components for VHF operation are discussed. Two different converter configurations, one using proportional control and having a conversion frequency of 0.1 MHz and the other using bistable control and having a conversion frequency of 3.8 MHz, are presented to indicate converter performance in this VHF region. Converter losses, which are of prime importance at these frequencies, are discussed and possible means of reducing these losses are suggested.

  6. Ion beam generated modes in the lower hybrid frequency range in a laboratory magnetoplasma

    NASA Astrophysics Data System (ADS)

    van Compernolle, Bart; Tripathi, Shreekrishna Kp; Gekelman, Walter; Pribyl, Patrick; Colestock, Patrick

    2012-10-01

    The interaction of a fast ion beam with a low β plasma has been studied in the laboratory. Experiments were performed at the LArge Plasma Device (LAPD) at UCLA. The experiments were done in a Helium plasma (n ˜10^12 cm-3, B0 = 1000 G - 1800 G, fpe/fce˜1 - 5, Te= 0.25 eV, vtevA). The ion beam is a Helium beam with energies ranging from 5 keV to 18 keV. The fast ion velocity is on the order of the Alfv'en velocity. The beam is injected from the end of the machine, and spirals down the linear device. Waves were observed below fci in the shear Alfv'en wave regime, and in a broad spectrum above fci in the lower hybrid frequency range, the focus of this paper. The wave spectra have distinct peaks close to ion cyclotron harmonics, extending out to the 100th harmonic in some cases. The wave generation was studied for various plasma parameters, as well as for different beam energies and pitch angles. The waves were measured with 3-axis electric and magnetic probes. Detailed measurements of the perpendicular mode structure will be shown. Langmuir probes were used to measure density and temperature evolution due to the beam-plasma interaction. Retarding field energy analyzers captured the ion beam profiles.

  7. Ion beam generated modes in the lower hybrid frequency range in a laboratory magnetoplasma

    NASA Astrophysics Data System (ADS)

    van Compernolle, Bart; Tripathi, Shreekrishna; Gekelman, Walter; Pribyl, Patrick

    2013-10-01

    The interaction of a fast ion beam with a low β plasma has been studied in the laboratory. Experiments were performed at the LArge Plasma Device (LAPD) at UCLA. The experiments were done in a Helium plasma (n ~=1012cm-3 , B0 = 1000 G - 1800 G, fpe /fce ~= 1 - 5 , Te ~= 4eV , vte <ranging from 5 keV to 18 keV. The fast ion velocity is on the order of the Alfvén velocity. The beam is injected from the end of the machine, and spirals down the linear device. Waves were observed below fci in the shear Alfvén wave regime, and in a broad spectrum above fci in the lower hybrid frequency range. The wave generation was studied for various plasma parameters, as well as for different beam energies and pitch angles. The waves were measured with 3-axis electric and magnetic probes. Detailed measurements of the 2D perpendicular mode structure will be shown. Progress on a theoretical framework of the wave generation by the ion beam will be presented along with comparisons to the measured wave properties. The work was performed at the LArge Plasma Device at the Basic Plasma Science Facility (BaPSF) at UCLA, funded by DOE/NSF.

  8. Development of a Radio Frequency Space Environment Path Emulator for Evaluating Spacecraft Ranging Hardware

    NASA Technical Reports Server (NTRS)

    Mitchell, Jason W.; Baldwin, Philip J.; Kurichh, Rishi; Naasz, Bo J.; Luquette, Richard J.

    2007-01-01

    The Formation Flying Testbed (FFTB) at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC) provides a hardware-in-the-loop test environment for formation navigation and control. The facility is evolving as a modular, hybrid, dynamic simulation facility for end-to-end guidance, navigation and. control (GN&C) design and analysis of formation flying spacecraft. The core capabilities of the FFTB, as a platform for testing critical hardware and software algorithms in-the-loop, have expanded to include S-band Radio Frequency (RF) modems for inter-spacecraft communication and ranging. To enable realistic simulations that require RF ranging sensors for relative navigation, a mechanism is needed to buffer the RF signals exchanged between spacecraft that accurately emulates the dynamic environment through which the RF signals travel, including the effects of medium, moving platforms, and radiated power. The Path Emulator for RF Signals (PERFS), currently under development at NASA GSFC, provides this capability. The function and performance of a prototype device are presented.

  9. Expanding Hardware-in-the-Loop Formation Navigation and Control with Radio Frequency Crosslink Ranging

    NASA Technical Reports Server (NTRS)

    Mitchell, Jason W.; Barbee, Brent W.; Baldwin, Philip J.; Luquette, Richard J.

    2007-01-01

    The Formation Flying Testbed (FFTB) at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC) provides a hardware-in-the-loop test environment for formation navigation and control. The facility continues to evolve as a modular, hybrid, dynamic simulation facility for end-to-end guidance, navigation, and control (GN&C) design and analysis of formation flying spacecraft. The core capabilities of the FFTB, as a platform for testing critical hardware and software algorithms in-the-loop, are reviewed with a focus on recent improvements. With the most recent improvement, in support of Technology Readiness Level (TRL) 6 testing of the Inter-spacecraft Ranging and Alarm System (IRAS) for the Magnetospheric Multiscale (MMS) mission, the FFTB has significantly expanded its ability to perform realistic simulations that require Radio Frequency (RF) ranging sensors for relative navigation with the Path Emulator for RF Signals (PERFS). The PERFS, currently under development at NASA GSFC, modulates RF signals exchanged between spacecraft. The RF signals are modified to accurately reflect the dynamic environment through which they travel, including the effects of medium, moving platforms, and radiated power.

  10. Wave Heating in Ion Cyclotron Ranges of Frequencies in RT-1

    NASA Astrophysics Data System (ADS)

    Nishiura, M.; Yoshida, Z.; Yano, Y.; Kawazura, Y.; Mushiake, T.; Saitoh, H.; Yamasaki, M.; Kashyap, A.; Takahashi, N.; Nakatsuka, M.; Fukuyama, A.

    2015-11-01

    The magnetosphere plasma device RT-1 has been developed for the studies on magnetosphere and advanced fusion plasmas. A levitated superconducting coil produces magnetic dipole fields that realize a high confinement state. The electron cyclotron resonance heating (ECRH) with 8.2 GHz and 50 kW produces the plasmas with hot electrons in a few ten keV range. We reported that the local electron beta exceeded 1 in RT-1 plasmas. In such situation, the ions still remain cold at a few ten eV. Heating ions is expected to access high ion beta state and to improve the plasma confinement theoretically. Therefore the ion cyclotron range of frequencies (ICRF) heating with 2-4 MHz and 10 kW is being prepared in RT-1. Based on the results of the TASK-WF2 code, the ∩ shape loop antenna was designed for a slow wave excitation, and was implemented in the RT-1. In the ICRF heating experiments, a base plasma was sustained by ECRH. We observed the clear increase in diamagnetic signals and impurity ion temperature (CIII) in helium plasmas at the neutral gas pressure of 3 mPa, if the ICRF power of 10 kW is comparable to the ECRH one. This result is the first time in a magnetosphere plasma device. The results related to the ICRF heating will be presented in detail. JSPS KAKENHI Grant Nos 23224014 and 24360384.

  11. Allele Frequencies of the Epidermal Growth Factor Receptors Polymorphism R521K in Colorectal Cancer Patients and Healthy Subjects Indicate a Risk-Reducing Effect of K521 in Syrian Population

    PubMed Central

    Mustafa, Ola Haj; Hamzeh, Abdul Rezzak; Ghabreau, Lina; Akil, Nizar; Almoustafa, Ala-Eddin; Alachkar, Amal

    2013-01-01

    Background: Colorectal cancer contributes heavily to cancer morbidity and mortality worldwide. Numerous therapies are currently in use, including monoclonal antibodies against cellular components involved in tumorigenesis such as epidermal growth factor receptors (EGFRs). Studies showed the polymorphism [R521K] GàA in the EGFR gene to be involved in both colorectal cancer susceptibility and clinical response to therapeutics (e.g., Cetuximab). Aim: We aimed at uncovering allele frequencies of this polymorphism among Syrian colorectal cancer patients and healthy individuals. Materials and Methods: Forty-seven patients with colorectal cancer were included in a case-control study along with 48 healthy subjects, all native Syrians. Individuals were genotyped using PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) and results were statistically analyzed to elucidate significant differences between the two groups. Results: Allele frequencies were 40.4% (G/G), 57.4% (G/A) and 2.1% (A/A) in colorectal cancer patients and 41.6% (G/G), 43.7% (G/A) and 14.5% (A/A) in healthy subjects. The A/A genotype was significantly lower in colorectal cancer patients than in the control group. Conclusions: Homozygosity for the A allele is linked to reducing the risk of developing colorectal cancer in Syrian patients. The lower prevalence of (A/A) locally may predict sub-optimal rates of clinical response to Cetuximab compared with populations with higher frequencies of the A allele. Larger scale investigations are needed for a stronger conclusion. PMID:23626956

  12. 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...

  13. Frequency-range discriminations: special and general abilities in zebra finches (Taeniopygia guttata) and humans (Homo sapiens).

    PubMed

    Weisman, R; Njegovan, M; Sturdy, C; Phillmore, L; Coyle, J; Mewhort, D

    1998-09-01

    The acoustic frequency ranges in birdsongs and human speech can provide important pitch cues for recognition. Zebra finches and humans were trained to sort contiguous frequencies into 3 or 8 ranges, based on associations between the ranges and reward. The 3-range task was conducted separately in 3 spectral regions. Zebra finches discriminated 3 ranges in the medium and high spectral regions faster than in the low region and discriminated 8 ranges with precision. Humans discriminated 3 ranges in all 3 spectral regions to the same modest standard and acquired only a crude discrimination of the lowest and highest of 8 ranges. The results indicate that songbirds have a special sensitivity to the pitches in conspecific songs and, relative to humans, have a remarkable general ability to sort pitches into ranges.

  14. Experimental Study of High-Range-Resolution Medical Acoustic Imaging for Multiple Target Detection by Frequency Domain Interferometry

    NASA Astrophysics Data System (ADS)

    Kimura, Tomoki; Taki, Hirofumi; Sakamoto, Takuya; Sato, Toru

    2009-07-01

    We employed frequency domain interferometry (FDI) for use as a medical acoustic imager to detect multiple targets with high range resolution. The phase of each frequency component of an echo varies with the frequency, and target intervals can be estimated from the phase variance. This processing technique is generally used in radar imaging. When the interference within a range gate is coherent, the cross correlation between the desired signal and the coherent interference signal is nonzero. The Capon method works under the guiding principle that output power minimization cancels the desired signal with a coherent interference signal. Therefore, we utilize frequency averaging to suppress the correlation of the coherent interference. The results of computational simulations using a pseudoecho signal show that the Capon method with adaptive frequency averaging (AFA) provides a higher range resolution than a conventional method. These techniques were experimentally investigated and we confirmed the effectiveness of the proposed method of processing by FDI.

  15. Effective conductivity and permittivity of unsaturated porous materials in the frequency range 1 mHz–1GHz

    PubMed Central

    Revil, A

    2013-01-01

    A model combining low-frequency complex conductivity and high-frequency permittivity is developed in the frequency range from 1 mHz to 1 GHz. The low-frequency conductivity depends on pore water and surface conductivities. Surface conductivity is controlled by the electrical diffuse layer, the outer component of the electrical double layer coating the surface of the minerals. The frequency dependence of the effective quadrature conductivity shows three domains. Below a critical frequency fp, which depends on the dynamic pore throat size Λ, the quadrature conductivity is frequency dependent. Between fp and a second critical frequency fd, the quadrature conductivity is generally well described by a plateau when clay minerals are present in the material. Clay-free porous materials with a narrow grain size distribution are described by a Cole-Cole model. The characteristic frequency fd controls the transition between double layer polarization and the effect of the high-frequency permittivity of the material. The Maxwell-Wagner polarization is found to be relatively negligible. For a broad range of frequencies below 1 MHz, the effective permittivity exhibits a strong dependence with the cation exchange capacity and the specific surface area. At high frequency, above the critical frequency fd, the effective permittivity reaches a high-frequency asymptotic limit that is controlled by the two Archie's exponents m and n like the low-frequency electrical conductivity. The unified model is compared with various data sets from the literature and is able to explain fairly well a broad number of observations with a very small number of textural and electrochemical parameters. It could be therefore used to interpret induced polarization, induction-based electromagnetic methods, and ground penetrating radar data to characterize the vadose zone. PMID:23576823

  16. Multicolor photoacoustic imaging by a single transducer with piezoelectric copolymer film in a wide frequency range

    NASA Astrophysics Data System (ADS)

    Ohmori, Tsutomu; Ishihara, Miya; Tsujita, Kazuhiro; Bansaku, Isao; Kikuchi, Makoto

    2010-02-01

    We built a photoacoustic tomographic (PAT) imaging system by scanning a single detector (φ 3.5 mm) made of piezoelectric copolymer poly(vinylidene difluoride-trifluoroethylene), P(VDF-TrFE), which had been fabricated for diagnostic photoacoustic measurement of cartilage tissues in our group. The PAT images of a phantom were obtained at two excitation wavelength of 687.5 nm and 795 nm. The phantom was made of agar including a black hair and agarose gels dissolving indocyanine green (ICG) and methylene blue (MB). Laser pulses (685-900 nm) were generated from a Ti:Sappire tunable laser to excite ICG and MB molecules. The PAT image at 687.5 nm shows signals due to all absorption sources. This is good agreement with dimension of the phantom. The PAT image at 795 nm shows a strong signal due to the ICG-dyed gel and almost no signal due to the MB-dyed gel. This result indicated that absorption sources were extracted by excitation wavelength according to their absorption spectra. The signal/noise ratio of the PAT images were compared between the P(VDF-TrFE) transducer in our group and a PZT transducer (Parametrics V309, 5 MHz, φ 12.7 mm) which is commercially available. The P(VDF-TrFE) transducer was more sensitive by 9 times (120 times per area) than the PZT transducer. By using this imaging system with a P(VDF-TrFE) transducer which is highly sensitive in a wide frequency range, we will achieve frequency analysis of the PAT images to associate photoacoustic waveforms with physical properties of sample tissues.

  17. Gravitational Wave Track in the Electromagnetic Field of the Earth in the Infra-Low Frequency Range

    NASA Astrophysics Data System (ADS)

    Grunskaya, L. V.; Isakevich, V. V.; Isakevich, D. V.; Luk'ianov, V. E.

    2017-01-01

    Signals in the infra-low frequency range in the electric and geomagnetic fields of the Earth have been detected, corresponding to frequencies of gravitational waves (GWs) emitted by a series of binary star systems (BSS). The coherence of the detected signals has been investigated. The amplitude characteristics of signals in the electric and geomagnetic fields at GW frequencies of BSS are estimated. The estimates of the amplitudes of the detected signals are in line with model estimates.

  18. Experimentally determined attenuation and modulus in Earth analogue materials over a wide range of frequency

    NASA Astrophysics Data System (ADS)

    McCarthy, C.; Fujisawa, K.; Takei, Y.; Hiraga, T.

    2009-12-01

    Seismic observations, particularly in areas of active tectonics, show large variations and can be affected by many variables, including temperature, composition, grain size, volatile content and the presence of small quantities of melt or other fluids. The understanding and interpretation of seismic wave dispersion and attenuation data can be significantly enhanced through improved knowledge of material dynamic response at the grain scale (and smaller). The organic binary system borneol-diphenylamine is a suitable analogue of melting in the Earth’s mantle. Not only does the solid phase deform through the same deformation mechanisms (diffusion creep, dislocation creep) observed in geologic materials, but the moderate and controllable dihedral angle (40° at 316 K) exhibited by this system provides an equilibrium melt-geometry very similar to that of the olivine + basalt system [Takei, 2000]. With a eutectic melting temperature (TE = 316 K at ambient pressure) just above room temperature, borneol-diphenylamine provides an attractive chemical analogue to study the properties of solid-melt interaction, obviating the difficulties associated with high-temperature, high-pressure experimentation. We have initiated compression-compression cyclic loading experiments on single phase (borneol; TM = 477 K) and multiphase (borneol-diphenylamine) aggregates. Our newly developed apparatus is able to apply and measure very small stress and strain amplitudes with high accuracy using a piezoelectric actuator and optical displacement meters, respectively. The planned experimental conditions are P = 1 atm, T = 298 - 333 K, strain amplitude <10-5, f = 10-4 - 102 Hz, and melt fraction φ = 0 - 0.1. The combination of low (sub seismic) frequency data obtained from these forced oscillation experiments and high-frequency data (f = 102 - 106) from ultrasonic wave transmission measurements allows us to explore the dissipation and Young’s modulus over a frequency range of some ten decades

  19. Blood optical properties at various glucose level values in THz frequency range

    NASA Astrophysics Data System (ADS)

    Gusev, S. I.; Borovkova, M. A.; Strepitov, M. A.; Khodzitsky, M. K.

    2015-07-01

    the patients. Most biomolecules have characteristic signature frequencies in the terahertz (THz) range, which can reveal their presence and determine the concentration. Therefore, this paper is intended to study the blood optical properties in the THz frequency range in order to determine THz radiation effect on blood. The main aim of this investigation is to determine the effect of blood glucose concentration on the blood optical properties. In the case if blood optical properties vary at different glucose concentrations having a proportional relationship between them, these results will confirm the possibility of development of non-invasive procedures for blood glucose level diagnostics.

  20. Co-analysis of Solar Microwave and Hard X-Ray Spectral Evolutions. I. In Two Frequency or Energy Ranges

    NASA Astrophysics Data System (ADS)

    Song, Qiwu; Huang, Guangli; Nakajima, Hiroshi

    2011-06-01

    Solar microwave and hard X-ray spectral evolutions are co-analyzed in the 2000 June 10 and 2002 April 10 flares, and are simultaneously observed by the Owens-Valley Solar Array in the microwave band and by Yohkoh/Hard X-ray Telescope or RHESSI in the hard X-ray band, with multiple subpeaks in their light curves. The microwave and hard X-ray spectra are fitted by a power law in two frequency ranges of the optical thin part and two photon energy ranges, respectively. Similar to an earlier event in Shao & Huang, the well-known soft-hard-soft pattern of the lower energy range changed to the hard-soft-hard (HSH) pattern of the higher energy range during the spectral evolution of each subpeak in both hard X-ray flares. This energy dependence is actually supported by a positive correlation between the overall light curves and spectral evolution in the lower energy range, while it becomes an anti-correlation in the higher energy range. Regarding microwave data, the HSH pattern appears in the spectral evolution of each subpeak in the lower frequency range, which is somewhat similar to Huang & Nakajima. However, it returns back to the well-known pattern of soft-hard-harder for the overall spectral evolution in the higher frequency range of both events. This frequency dependence is confirmed by an anti-correlation between the overall light curves and spectral evolution in the lower frequency range, but it becomes a positive correlation in the higher frequency range. The possible mechanisms are discussed, respectively, for reasons why hard X-ray and microwave spectral evolutions have different patterns in different energy and frequency intervals.

  1. Preferred Frequency Range, Technical Characteristics, and Interference Assessment for a Microwave Observatory of Subsurface and Subcanopy (MOSS) for 1 MHZ Bandwidth in the Frequency Range of 100-150 MHz

    NASA Technical Reports Server (NTRS)

    Honeycutt, Bryan L.

    2005-01-01

    This document presents rationale for the frequency band selection, technical and operational characteristics of active spaceborne sensors in the Earth Exploration-Satellite Service (active), and interference assessment for a 1 MHz bandwidth sensor in the 100-150 MHz frequency range. The active spaceborne sensors expected to be operating in the frequency range of 100-150 MHz is the synthetic aperture radar (SAR) such as the MOSS. The technical characteristics, mission objectives, orbital parameters, design parameters, antenna characteristics, and preliminary interference assessment are given for MOSS. The purpose of the document is to provide rationale for the frequency band selection, technical characteristics of the active spaceborne sensor Microwave Observatory of Subsurface and Subcanopy (MOSS) that can be used to analyze the compatibility of active spaceborne sensors and other systems of 1 MHz bandwidth in the 100-150 MHz frequency band.

  2. Ion beam generated modes in the lower hybrid frequency range in a laboratory magnetoplasma

    NASA Astrophysics Data System (ADS)

    Van Compernolle, B.; Tripathi, S.; Gekelman, W. N.; Colestock, P. L.; Pribyl, P.

    2012-12-01

    The generation of waves by ion ring distributions is of great importance in many instances in space plasmas. They occur naturally in the magnetosphere through the interaction with substorms, or they can be man-made in ionospheric experiments by photo-ionization of neutral atoms injected perpendicular to the earth's magnetic field. The interaction of a fast ion beam with a low β plasma has been studied in the laboratory. Experiments were performed at the LArge Plasma Device (LAPD) at UCLA. The experiments were done in a Helium plasma (n ≃ 1012 \\ cm-3, B0 = 1000 G - 1800 G, fpe}/f{ce ≃ 1 - 5, Te = 0.25\\ eV, vte ≤ vA). The ion beam \\cite{Tripathi_ionbeam} is a Helium beam with energies ranging from 5 keV to 18 keV. The fast ion velocity is on the order of the Alfvén velocity. The beam is injected from the end of the machine, and spirals down the linear device. Waves were observed below fci in the shear Alfvén wave regime, and in a broad spectrum above fci in the lower hybrid frequency range, the focus of this paper. The wave spectra have distinct peaks close to ion cyclotron harmonics, extending out to the 100th harmonic in some cases. The wave generation was studied for various magnetic fields and background plasma densities, as well as for different beam energies and pitch angles. The waves were measured with 3-axis electric and magnetic probes. Detailed measurements of the perpendicular mode structure will be shown. Langmuir probes were used to measure density and temperature evolution due to the beam-plasma interaction. Retarding field energy analyzers captured the ion beam profiles. The work was performed at the LArge Plasma Device at the Basic Plasma Science Facility (BaPSF) at UCLA, funded by DOE/NSF.

  3. Electromagnetic bias in sea surface range measurements at frequencies of the TOPEX/POSEIDON satellite

    SciTech Connect

    Hevizi, L.G.; McIntosh, R.E. ); Walsh, E.J.; Vandemark, D.; Hines, D.E.; Swift, R.N.; Scott, J.F. )

    1993-03-01

    Range measurements made by satellite radar altimeters experience an electromagnetic (EM) bias toward the troughs of ocean waves. This EM bias was measured at the 13.6 GHz and 5.3 GHz operating frequencies of the NASA altimeter on the TOPEX/POSEIDON satellite in a series of 11 aircraft flights from January 17, 1991, through March 4, 1991, during the Surface WAve Dynamics Experiment (SWADE). The data are consistent with an earlier set of airborne measurements and indicate that EM bias is slightly higher at 5.3 GHz than at 13.6 GHz, and that the magnitudes of both biases increase with increasing wind speed, as does their difference. With some exceptions, EM bias shows little variation over a mesoscale region on a given day or within 1 or 2 h, but it can change significantly over a 6-h period. An examination of recent tower, airborne, and satellite measurements shows a consistency in the characteristics of the wind speed dependence but suggests that there may be a height dependence in the determinations, with the bias decreasing with increasing altitude. The airborne measurements appear to be the most reasonable basis for correcting the NASA altimeter range data from the TOPEX/POSEIDON satellite. In addition, a preliminary analysis of a very limited amount of the data acquired at 20.3 m s[sup [minus]1] in Southern Ocean Waves Experiment (SOWEX) has given confidence that the quadratic models for the prelaunch EM bias corrections are more appropriate for wind speed dependence than are the linear models initially considered.

  4. An Obliquely Propagating Electromagnetic Drift Instability in the Lower Hybrid Frequency Range

    SciTech Connect

    Hantao Ji; Russell Kulsrud; William Fox; Masaaki Yamada

    2005-06-10

    By employing a local two-fluid theory, we investigate an obliquely propagating electromagnetic instability in the lower hybrid frequency range driven by cross-field current or relative drifts between electrons and ions. The theory self-consistently takes into account local cross-field current and accompanying pressure gradients. It is found that the instability is caused by reactive coupling between the backward propagating whistler (fast) waves in the moving electron frame, and the forward propagating sound (slow) waves in the ion frame when the relative drifts are large. The unstable waves we consider propagate obliquely to the unperturbed magnetic field and have mixed polarization with significant electromagnetic components. A physical picture of the instability emerges in the limit of large wave number characteristic of the local approximation. The primary positive feedback mechanism is based on reinforcement of initial electron density perturbations by compression of electron fluid via induced Lorentz force. The resultant waves are qualitatively consistent with the measured electromagnetic fluctuations in reconnecting current sheet in a laboratory plasma.

  5. Discriminating low frequency components from long range persistent fluctuations in daily atmospheric temperature variability

    NASA Astrophysics Data System (ADS)

    Lanfredi, M.; Simoniello, T.; Cuomo, V.; Macchiato, M.

    2009-07-01

    This study originated from recent results reported in literature, which support the existence of long-range (power-law) persistence in atmospheric temperature fluctuations on monthly and inter-annual scales. We investigated the results of Detrended Fluctuation Analysis (DFA) carried out on twenty-two historical daily time series recorded in Europe in order to evaluate the reliability of such findings in depth. More detailed inspections emphasized systematic deviations from power-law and high statistical confidence for functional form misspecification. Rigorous analyses did not support scale-free correlation as an operative concept for Climate modelling, as instead suggested in literature. In order to understand the physical implications of our results better, we designed a bivariate Markov process, parameterised on the basis of the atmospheric observational data by introducing a slow dummy variable. The time series generated by this model, analysed both in time and frequency domains, tallied with the real ones very well. They accounted for both the deceptive scaling found in literature and the correlation details enhanced by our analysis. Our results seem to evidence the presence of slow fluctuations from another climatic sub-system such as ocean, which inflates temperature variance up to several months. They advise more precise re-analyses of temperature time series before suggesting dynamical paradigms useful for Climate modelling and for the assessment of Climate Change.

  6. Discriminating low frequency components from long range persistent fluctuations in daily atmospheric temperature variability

    NASA Astrophysics Data System (ADS)

    Lanfredi, M.; Simoniello, T.; Cuomo, V.; Macchiato, M.

    2009-02-01

    This study originated from recent results reported in literature, which support the existence of long-range (power-law) persistence in atmospheric temperature fluctuations on monthly and inter-annual scales. We investigated the results of Detrended Fluctuation Analysis (DFA) carried out on twenty-two historical daily time series recorded in Europe in order to evaluate the reliability of such findings in depth. More detailed inspections emphasized systematic deviations from power-law and high statistical confidence for functional form misspecification. Rigorous analyses did not support scale-free correlation as an operative concept for Climate modelling, as instead suggested in literature. In order to understand the physical implications of our results better, we designed a bivariate Markov process, parameterised on the basis of the atmospheric observational data by introducing a slow dummy variable. The time series generated by this model, analysed both in time and frequency domains, tallied with the real ones very well. They accounted for both the deceptive scaling found in literature and the correlation details enhanced by our analysis. Our results seem to evidence the presence of slow fluctuations from another climatic sub-system such as ocean, which inflates temperature variance up to several months. They advise more precise re-analyses of temperature time series before suggesting dynamical paradigms useful for Climate modelling and for the assessment of Climate Change.

  7. Three dimensional ray tracing Jovian magnetosphere in the low frequency range

    NASA Technical Reports Server (NTRS)

    Menietti, J. D.

    1982-01-01

    Ray tracing of the Jovian magnetosphere in the low frequency range (1+40 MHz) has resulted in a new understanding of the source mechanism for Io dependent decametric radiation (DAM). Our three dimensional ray tracing computer code has provided model DAM arcs at 10 deg. intervals of Io longitude source positions for the full 360 deg of Jovian system III longitude. In addition, particularly interesting arcs were singled out for detailed study and modelling. Dependent decametric radiation arcs are categorized according to curvature--the higher curvature arcs are apparently due to wave stimulation at a nonconstant wave normal angle, psi. The psi(f) relationship has a signature that is common to most of the higher curvature arcs. The low curvature arcs, on the other hand, are adequately modelled with a constant wave normal angle of close to 90 deg. These results imply that for higher curvature arcs observed for from Jupiter (to diminish spacecraft motion effects) the electrons providing the gyroemission are relativistically beamed.

  8. Tuning the Polarization State of Light over a Broad Frequency Range with Metasurfaces

    NASA Astrophysics Data System (ADS)

    Wang, Mu; Jiang, Shang-Chi; Wang, Zheng-Han; Xiong, Xiang; Peng, Ru-Wen; Nanjing University Team

    Controlling the polarization state, the transmission direction and the phase of light within a confined space is an important issue in optics. By integrating metallic metastructure and dielectric interlayer, it is possible to realize the dispersion-free broadband device on sub-wavelength scale, where the strong response of the metallic structures helps to decrease the device size while the dielectric interlayer helps to eliminate the dispersion simultaneously in both the amplitude and the phase difference of the reflected/transmitted light. As an examples to apply this concept, a broadband quarter-wave plate and a half-wave plate are experimentally demonstrated. By carefully selecting the structural parameters, the polarization state of light can be freely tuned across a broad frequency range, and all of the polarization states on the Poincaré sphere can be realized dispersion free. Some contents of this talk can be found in the following references: [1] S.-C. Jiang, et al., High-efficiency generation of circularly polarized light via symmetry-induced anomalous reflection,Physical Review B 91, 125421 (2015), [2] S.-C. Jiang, et al., Controlling the Polarization State of Light with a Dispersion-Free Metastructure, Physical Review X 4, 021026 (2014), [3] X. Xiong, et al., Metallic stereostructured layer: an approach for broadband polarization state manipulation,Applied Physics Letters 105, 201105 (2014).

  9. Ray-tracing studies of fast waves in the lower hybrid range of frequencies

    NASA Astrophysics Data System (ADS)

    Dittman, A.; Pinsker, R. I.

    2016-10-01

    Fast waves in the lower-hybrid range of frequencies, also referred to as `whistlers' or `helicons', will be used in the DIII-D tokamak for off-axis non-inductive current drive. Ray-tracing studies have shown that the required off-axis deposition can be achieved in target plasmas that have been recently studied in DIII-D. We wish to characterize the sensitivity of the rf power deposition profile to details of the equilibrium, and are thereby motivated to re-examine the fundamentals of ray-tracing in this regime. We have studied ray-tracing in the vicinity of regular turning points (cut-offs) and mode-coupling points in simple geometries (slab, cylinder). Later phases of the work will use the GENRAY code to study the effect of strong magnetic shear in the outer region of the plasma on the shape of the ray trajectory in that region, and on wave accessibility to the core. The usual estimate of the accessibility limit on the parallel index of refraction of the wave (n∥), based on a slab model, is inaccurate under these conditions, which could lead to improved antenna/wave coupling by utilizing a lower n∥. Work supported in part by US DoE under the Science Undergraduate Laboratory Internship (SULI) program and under DE-FC02-04ER54698.

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

    PubMed

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

    2011-09-01

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

  11. Ion cyclotron range of frequencies heating of plasma with small impurity production

    DOEpatents

    Ohkawa, Tihiro

    1987-01-01

    Plasma including plasma ions is magnetically confined by a magnetic field. The plasma has a defined outer surface and is intersected by resonance surfaces of respective common ion cyclotron frequency of a predetermined species of plasma ions moving in the magnetic field. A radio frequency source provides radio frequency power at a radio frequency corresponding to the ion cyclotron frequency of the predetermined species of plasma ions moving in the field at a respective said resonance surface. RF launchers coupled to the radio frequency source radiate radio frequency energy at the resonance frequency onto the respective resonance surface within the plasma from a plurality of locations located outside the plasma at such respective distances from the intersections of the respective resonance surface and the defined outer surface and at such relative phases that the resulting interference pattern provides substantially null net radio frequency energy over regions near and including substantial portions of the intersections relative to the radio frequency energy provided thereby at other portions of the respective resonance surface within the plasma.

  12. The Influence of Fundamental Frequency and Sound Pressure Level Range on Breathing Patterns in Female Classical Singing

    ERIC Educational Resources Information Center

    Collyer, Sally; Thorpe, C. William; Callaghan, Jean; Davis, Pamela J.

    2008-01-01

    Purpose: This study investigated the influence of fundamental frequency (F0) and sound pressure level (SPL) range on respiratory behavior in classical singing. Method: Five trained female singers performed an 8-s messa di voce (a crescendo and decrescendo on one F0) across their musical F0 range. Lung volume (LV) change was estimated, and…

  13. Accurate displacement-measuring interferometer with wide range using an I2 frequency-stabilized laser diode based on sinusoidal frequency modulation

    NASA Astrophysics Data System (ADS)

    Vu, Thanh-Tung; Higuchi, Masato; Aketagawa, Masato

    2016-10-01

    We propose the use of the sinusoidal frequency modulation technique to improve both the frequency stability of an external cavity laser diode (ECLD) and the measurement accuracy and range of a displacement-measuring interferometer. The frequency of the ECLD was modulated at 300 kHz by modulating the injection current, and it was locked to the b21 hyperfine component of the transition 6-3, P(33), 127I2 (633 nm) by the null method. A relative frequency stability of 6.5  ×  10-11 was achieved at 100 s sampling time. The stabilized ECLD was then utilized as a light source for an unbalanced Michelson interferometer. In the interferometer, the displacement and direction of the target mirror can be determined using a Lissajous diagram based on two consecutive and quadrant-phase harmonics of the interference signal. Generally, the measurement range of the interferometer by the proposed method is limited by the modulation index and the signal-to-noise ratio of the harmonics. To overcome this drawback, suitable consecutive harmonic pairs were selected for the specific measurement ranges to measure the displacement. The displacements determined in the specific ranges by the proposed method were compared with those observed by a commercial capacitive sensor. From the comparison, the proposed method has high precision to determine the displacement. The measurement range was also extended up to 10 m by selecting a suitable modulation index and suitable consecutive pairs of harmonics.

  14. On the minimum electron transport coefficients in tokamaks in the range of low collision frequencies

    NASA Astrophysics Data System (ADS)

    Merezhkin, V. G.

    2009-06-01

    There are two close empirical scalings, namely, the T-11 and neo-Alcator ones, that provide correct estimates for the energy confinement time in tokamaks in ohmic heating regimes in the linear part of the dependence τ E ( bar n_e ) in the range of low values of bar n_e and <ν{/e *}> ≤ 1. The similar character of electron energy confinement in this range, which expands with increasing magnetic field B 0, has stimulated the search for dimensionless parameters and simple physical models that would explain the experimentally observed dependences χ e ˜ 1/ n e and τ Ee ˜ bar n_e . In 1987, T. Okhawa showed that the experimental data were satisfactorily described by the formula χ e⊥ = ( c 2/ω{/pe 2}) ν e / qR, in deriving of which the random spatial leap along the radius r on the electron trajectory was assumed to be the same as that in the coefficient of the poloidal field diffusion, while the repetition rate of these leaps was assumed to be ν e / qR. In 2004, J. Callen took into account the decrease in the fraction of transient electrons with increasing toroidal ratio ɛ = r/R and corrected the coefficient c 2/ω{/pe 2} in Okhawa equation by the factor σ{‖/Sp}/σ{‖/neo}. If one takes into account this correction and assumes that the frequency of the stochastic process is equal to the reciprocal of the half-period of rotation of a trapped electron along its banana trajectory, then the resulting expression for χ e⊥ will coincide with the T-11 scaling: χ{/e an} ∞ ɛ1.75( T e / A i )0.5/( n e qR) at A i = 1. If the same stochastic process also involves ions, it may result in the opening of the orbit of a trapped ion at the distance ˜( c/ω pe )( m i / m e )1/4. In this case, the calculated coefficient of electron and ion diffusion D is close to D an ≈ χ{/e an}/2.

  15. 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...

  16. Relationships between range access as monitored by radio frequency identification technology, fearfulness, and plumage damage in free-range laying hens.

    PubMed

    Hartcher, K M; Hickey, K A; Hemsworth, P H; Cronin, G M; Wilkinson, S J; Singh, M

    2016-05-01

    Severe feather-pecking (SFP), a particularly injurious behaviour in laying hens (Gallus gallus domesticus), is thought to be negatively correlated with range use in free-range systems. In turn, range use is thought to be inversely associated with fearfulness, where fearful birds may be less likely to venture outside. However, very few experiments have investigated the proposed association between range use and fearfulness. This experiment investigated associations between range use (time spent outside), fearfulness, plumage damage, and BW. Two pens of 50 ISA Brown laying hens (n=100) were fitted with radio frequency identification (RFID) transponders (contained within silicone leg rings) at 26 weeks of age. Data were then collected over 13 days. A total of 95% of birds accessed the outdoor run more than once per day. Birds spent an average duration of 6.1 h outside each day over 11 visits per bird per day (51.5 min per visit). The top 15 and bottom 15 range users (n=30), as determined by the total time spent on the range over 13 days, were selected for study. These birds were tonic immobility (TI) tested at the end of the trial and were feather-scored and weighed after TI testing. Birds with longer TI durations spent less time outside (P=0.01). Plumage damage was not associated with range use (P=0.68). The small group sizes used in this experiment may have been conducive to the high numbers of birds utilising the outdoor range area. The RFID technology collected a large amount of data on range access in the tagged birds, and provides a potential means for quantitatively assessing range access in laying hens. The present findings indicate a negative association between fearfulness and range use. However, the proposed negative association between plumage damage and range use was not supported. The relationships between range use, fearfulness, and SFP warrant further research.

  17. 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.

  18. The influence of human leukocyte antigen class I alleles and their population frequencies on human immunodeficiency virus type 1 control among African Americans.

    PubMed

    Lazaryan, Aleksandr; Song, Wei; Lobashevsky, Elena; Tang, Jianming; Shrestha, Sadeep; Zhang, Kui; McNicholl, Janet M; Gardner, Lytt I; Wilson, Craig M; Klein, Robert S; Rompalo, Anne; Mayer, Kenneth; Sobel, Jack; Kaslow, Richard A

    2011-04-01

    Populations of African ancestry continue to account for a disproportionate burden of the human immunodeficiency virus type 1 (HIV-1) epidemic in the United States. We investigated the effects of human leukocyte antigen (HLA) class I markers in association with virologic and immunologic control of HIV-1 infection among 338 HIV-1 subtype B-infected African Americans in 2 cohorts: Reaching for Excellence in Adolescent Care and Health (REACH) and HIV Epidemiology Research Study (HERS). One-year treatment-free interval measurements of HIV-1 RNA viral loads and CD4(+) T cells were examined both separately and combined to represent 3 categories of HIV-1 disease control (76 controllers, 169 intermediates, and 93 noncontrollers). Certain previously or newly implicated HLA class I alleles (A*32, A*36, A*74, B*14, B*1510, B*3501, B*45, B*53, B*57, Cw*04, Cw*08, Cw*12, and Cw*18) were associated with 1 or more of the endpoints in univariate analyses. After multivariable adjustments for other genetic and nongenetic risk factors of HIV-1 progression, the subset of alleles more strongly or consistently associated with HIV-1 disease control included A*32, A*74, B*14, B*45, B*53, B*57, and Cw*08. Carriage of infrequent HLA-B but not HLA-A alleles was associated with more favorable disease outcomes. Certain HLA class I associations with control of HIV-1 infection cross the boundaries of race and viral subtype, whereas others appear confined within one or the other of those boundaries.

  19. Effects of the gaseous and liquid water content of the atmosphere on range delay and Doppler frequency

    NASA Technical Reports Server (NTRS)

    Flock, W. L.

    1981-01-01

    When high precision is required for range measurement on Earth space paths, it is necessary to correct as accurately as possible for excess range delays due to the dry air, water vapor, and liquid water content of the atmosphere. Calculations based on representative values of atmospheric parameters are useful for illustrating the order of magnitude of the expected delays. Range delay, time delay, and phase delay are simply and directly related. Doppler frequency variations or noise are proportional to the time rate of change of excess range delay. Tropospheric effects were examined as part of an overall consideration of the capability of precision two way ranging and Doppler systems.

  20. 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.

  1. The influence of interlayer exchange coupling in giant-magnetoresistive devices on spin diode effect in wide frequency range

    SciTech Connect

    Ziętek, Sławomir Skowroński, Witold; Wiśniowski, Piotr; Czapkiewicz, Maciej; Stobiecki, Tomasz; Ogrodnik, Piotr; Barnaś, Józef

    2015-09-21

    Spin diode effect in a giant magnetoresistive strip is measured in a broad frequency range, including resonance and off-resonance frequencies. The off-resonance dc signal is relatively strong and also significantly dependent on the exchange coupling between magnetic films through the spacer layer. The measured dc signal is described theoretically by taking into account magnetic dynamics induced by Oersted field created by an ac current flowing through the system.

  2. Oscillating two stream instability of electromagnetic pump in the ion cyclotron range of frequency in a plasma

    SciTech Connect

    Ahmad, Nafis; Tripathi, V. K.; Rafat, M.; Husain, Mudassir M.

    2009-06-15

    An analytical formalism of oscillating two stream instability of a large amplitude electromagnetic wave in the ion cyclotron range of frequency in a plasma is developed. The instability produces electrostatic ion cyclotron sidebands and a driven low frequency mode. The nonlinear coupling arises primarily due to the motion of ions and is strong when the pump frequency is close to ion cyclotron frequency and the oscillatory ion velocity is a significant fraction of acoustic speed. For propagation perpendicular to the ambient magnetic field, the X-mode pump wave produces flute type perturbation with maximum growth rate at some specific wavelengths, which are three to four times larger than the ion Larmor radius. For propagation at oblique angles to ambient magnetic field, the ion cyclotron O-mode, the growth rate increases with the wave number of the low frequency mode.

  3. HIGH DYNAMIC RANGE OBSERVATIONS OF SOLAR CORONAL TRANSIENTS AT LOW RADIO FREQUENCIES WITH A SPECTRO-CORRELATOR

    SciTech Connect

    Hariharan, K.; Ramesh, R.; Kathiravan, C.; Rajalingam, M.; Abhilash, H. N.

    2016-02-15

    A new antenna system with a digital spectro-correlator that provides high temporal, spectral, and amplitude resolutions has been commissioned at the Gauribidanur Observatory near Bangalore in India. Presently, it is used for observations of the solar coronal transients in the scarcely explored frequency range ≈30–15 MHz. The details of the antenna system, the associated receiver setup, and the initial observational results are reported. Some of the observed transients exhibited quasi-periodicity in their time profiles at discrete frequencies. Estimates of the associated magnetic field strength (B) indicate that B ≈ 0.06–1 G at a typical frequency such as 19.5 MHz.

  4. 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

  5. Wide-frequency range, dynamic matching network and power system for the "Shoelace" radio frequency antenna on the Alcator C-Mod tokamak.

    PubMed

    Golfinopoulos, Theodore; LaBombard, Brian; Burke, William; Parker, Ronald R; Parkin, William; Woskov, Paul

    2014-04-01

    A wide-frequency range (50-300 kHz) power system has been implemented for use with a new RF antenna - the "Shoelace" antenna - built to drive coherent plasma fluctuations in the edge of the Alcator C-Mod tokamak. A custom, dynamically tunable matching network allows two commercial 1 kW, 50-Ω RF amplifiers to drive the low-impedance, inductive load presented by the antenna. This is accomplished by a discretely variable L-match network, with 81 independently selected steps available for each of the series and parallel legs of the matching configuration. A compact programmable logic device provides a control system that measures the frequency with better than 1 kHz accuracy and transitions to the correct tuning state in less than 1 ms. At least 85% of source power is dissipated in the antenna across the operational frequency range, with a minimum frequency slew rate of 1 MHz/s; the best performance is achieved in the narrower band from 80 to 150 kHz which is of interest in typical experiments. The RF frequency can be run with open-loop control, following a pre-programmed analog waveform, or phase-locked to track a plasma fluctuation diagnostic signal in real time with programmable phase delay; the amplitude control is always open-loop. The control waveforms and phase delay are programmed remotely. These tools have enabled first-of-a-kind measurements of the tokamak edge plasma system response in the frequency range and at the wave number at which coherent fluctuations regulate heat and particle transport through the plasma boundary.

  6. Wide-frequency range, dynamic matching network and power system for the "Shoelace" radio frequency antenna on the Alcator C-Mod tokamak

    NASA Astrophysics Data System (ADS)

    Golfinopoulos, Theodore; LaBombard, Brian; Burke, William; Parker, Ronald R.; Parkin, William; Woskov, Paul

    2014-04-01

    A wide-frequency range (50-300 kHz) power system has been implemented for use with a new RF antenna - the "Shoelace" antenna - built to drive coherent plasma fluctuations in the edge of the Alcator C-Mod tokamak. A custom, dynamically tunable matching network allows two commercial 1 kW, 50-Ω RF amplifiers to drive the low-impedance, inductive load presented by the antenna. This is accomplished by a discretely variable L-match network, with 81 independently selected steps available for each of the series and parallel legs of the matching configuration. A compact programmable logic device provides a control system that measures the frequency with better than 1 kHz accuracy and transitions to the correct tuning state in less than 1 ms. At least 85% of source power is dissipated in the antenna across the operational frequency range, with a minimum frequency slew rate of 1 MHz/s; the best performance is achieved in the narrower band from 80 to 150 kHz which is of interest in typical experiments. The RF frequency can be run with open-loop control, following a pre-programmed analog waveform, or phase-locked to track a plasma fluctuation diagnostic signal in real time with programmable phase delay; the amplitude control is always open-loop. The control waveforms and phase delay are programmed remotely. These tools have enabled first-of-a-kind measurements of the tokamak edge plasma system response in the frequency range and at the wave number at which coherent fluctuations regulate heat and particle transport through the plasma boundary.

  7. Wide-frequency range, dynamic matching network and power system for the “Shoelace” radio frequency antenna on the Alcator C-Mod tokamak

    SciTech Connect

    Golfinopoulos, Theodore LaBombard, Brian; Burke, William; Parker, Ronald R.; Parkin, William; Woskov, Paul

    2014-04-15

    A wide-frequency range (50–300 kHz) power system has been implemented for use with a new RF antenna – the “Shoelace” antenna – built to drive coherent plasma fluctuations in the edge of the Alcator C-Mod tokamak. A custom, dynamically tunable matching network allows two commercial 1 kW, 50-Ω RF amplifiers to drive the low-impedance, inductive load presented by the antenna. This is accomplished by a discretely variable L-match network, with 81 independently selected steps available for each of the series and parallel legs of the matching configuration. A compact programmable logic device provides a control system that measures the frequency with better than 1 kHz accuracy and transitions to the correct tuning state in less than 1 ms. At least 85% of source power is dissipated in the antenna across the operational frequency range, with a minimum frequency slew rate of 1 MHz/s; the best performance is achieved in the narrower band from 80 to 150 kHz which is of interest in typical experiments. The RF frequency can be run with open-loop control, following a pre-programmed analog waveform, or phase-locked to track a plasma fluctuation diagnostic signal in real time with programmable phase delay; the amplitude control is always open-loop. The control waveforms and phase delay are programmed remotely. These tools have enabled first-of-a-kind measurements of the tokamak edge plasma system response in the frequency range and at the wave number at which coherent fluctuations regulate heat and particle transport through the plasma boundary.

  8. Dielectric properties of skeletal muscle during ischemia in the frequency range from 50 Hz to 200 MHz.

    PubMed

    Schäfer, M; Kirlum, H J; Schlegel, C; Gebhard, M M

    1999-04-20

    The complex dielectric properties of canine skeletal muscles were measured at 25 degrees C during ischemia in the frequency range from 50 Hz to 200 MHz. The dielectric spectrum of skeletal muscle shows an alpha-dispersion below 1 kHz and a beta-dispersion with a relaxation frequency of about 100 kHz. The alpha-dispersion disappears between 450 and 500 min of ischemia time, the same time during which mechanical contraction was observed, and was restored later. During ischemia, the beta-dispersion is shifted continuously to higher frequencies; and at frequencies above 50 MHz, a decrease of the real part of the dielectric permittivity was measured. The dielectric loss factor decreases during ischemia at frequencies below 500 kHz, only interrupted by a short increase, coinciding with the disappearance of the alpha-dispersion. The principal processes that happen during ischemia inside the skeletal muscle tissues were studied with the help of a model especially designed to simulate membrane effects on the dielectric spectrum. The disappearance of the alpha-dispersion is explained by an increase of conductivity in the membrane of the sarcoplasmic reticulum. Shifting beta-dispersion to higher frequencies is a result of metabolically produced ions and therefore increasing conductivity of the intracellular medium. Decreasing dielectric permittivity at frequencies above 50 MHz and decreasing dielectric loss factor at low frequencies are caused by the cell edema.

  9. 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].

  10. Measurements of ICRF (ion cyclotron range of frequencies) loading with a ridged waveguide coupler on PLT

    SciTech Connect

    Greene, G.J.; Wilson, J.R.; Colestock, P.L.; Fortgang, C.M.; Hosea, J.C.; Hwang, D.Q.; Nagy, A.

    1987-11-01

    An ICRF ridged waveguide coupler has been installed on PLT for measurements of plasma loading. The coupler was partially filled with TiO/sub 2/ dielectric in order to sufficiently lower the cutoff frequency and utilized a tapered ridge for improved matching. Vacuum field measurements indicated a single propagating mode in the coupler and emphasized the importance of considering the fringing fields at the mouth of the waveguide. Low power experiments were carried out at 72.6 and 95.0 MHz without any external impedance matching network. Plasma loading increased rapidly as the face of the coupler approached the plasma, and, at fixed position, increased with line-averaged plasma density. At the lower frequency, the reflection coefficient exhibited a minimum (<8%) at a particular coupler position. At both frequencies, measurements indicated efficient power coupling to the plasma. Magnetic probe signals showed evidence of dense eigenmodes suggesting excitation of the fast wave. 24 refs., 13 figs.

  11. Performances of a VLSI wide dynamic range current-to-frequency converter for strip ionization chambers

    NASA Astrophysics Data System (ADS)

    Bonazzola, G. C.; Cirio, R.; Donetti, M.; Marchetto, F.; Mazza, G.; Peroni, C.; Zampieri, A.

    1998-02-01

    In this paper we report on the design and test of a 14-channel VLSI chip to perform the current to frequency conversion for parallel plate strip ionization chambers. The chambers measure the intensity and the geometrical characteristics of a therapeutical beam.

  12. Three dimensional ray tracing of the Jovian magnetosphere in the low frequency range

    NASA Technical Reports Server (NTRS)

    Menietti, J. D.

    1984-01-01

    Ray tracing studies of Jovian low frequency emissions were studied. A comprehensive three-dimensional ray tracing computer code for examination of model Jovian decametric (DAM) emission was developed. The improvements to the computer code are outlined and described. The results of the ray tracings of Jovian emissions will be presented in summary form.

  13. Flat lensing in the visible frequency range by woodpile photonic crystals.

    PubMed

    Maigyte, L; Purlys, V; Trull, J; Peckus, M; Cojocaru, C; Gailevičius, D; Malinauskas, M; Staliunas, K

    2013-07-15

    We experimentally demonstrate full two-dimensional focalization of light beams at visible frequencies by a three-dimensional woodpile photonic crystal. The focalization (the flat lensing) with focal distances of the order of 50-70 μm is experimentally demonstrated. Experimental results are compared with numerical calculations and interpreted by harmonic expansion studies.

  14. New space research frequency band proposals in the 20- to 40.5-GHz range

    NASA Technical Reports Server (NTRS)

    Bishop, D. F.

    1991-01-01

    Future space research communications systems may require spectra above 20 GHz. Frequency bands above 20 GHz are identified that are suitable for space research. The selection of the proper bands depends on consideration of interference with other radio services, adequate bandwidths, link performance, and technical requirements for practical implementation.

  15. Extended parametric gain range in photonic crystal fibers with strongly frequency-dependent field distributions.

    PubMed

    Petersen, Sidsel R; Alkeskjold, Thomas T; Olausson, Christina B; Lægsgaard, Jesper

    2014-08-15

    The parametric gain range of a degenerate four-wave mixing process is determined in the undepleted pump regime. The gain range is considered with and without taking the mode field distributions of the four-wave mixing components into account. It is found that the mode field distributions have to be included to evaluate the parametric gain correctly in dispersion-tailored speciality fibers and that mode profile engineering can provide a way to increase the parametric gain range.

  16. [The peculiarities of the microwave in the frequency range of 51-52 GHz spectrum effects on E. coli cells].

    PubMed

    Ushakov, V L; Alipov, E D; Shcheglov, V S; Beliaev, I Ia

    2006-01-01

    The effects of microwaves on conformation of nucleoids in E. coli cells were studied by the method of anomalous viscosity time dependence (AVTD) at various frequencies in the range of 51-52 GHz and the power flux density of 100 microW/cm(2) . Linearly polarized microwaves resulted in significant effects within specific frequency windows of resonance type. The distances between frequency windows were in the range of 55-180 MHz. Only one of two possible circular polarizations, left-handed or right-handed, was shown to be effective at each frequency window. The sign of effective circular polarization alternated between frequency windows. We show that the effects of microwaves on E. coli cells as measured by the AVTD technique are not caused by adhesion of cells. The half-width of the 51.575 GHz resonance was measured to be 120+/-20 MHz. This value is very close to the half-width of the 51.755 GHz resonance as it has previously been determined at the same power flux density. The obtained data suggest similar targets for effects of microwaves at these two resonance frequencies and provide evidence for non-thermal nature of observed microwave effects.

  17. Measurement comparison among time-domain, FTIR and VNA-based spectrometers in the THz frequency range

    NASA Astrophysics Data System (ADS)

    Oberto, L.; Bisi, M.; Kazemipour, A.; Steiger, A.; Kleine-Ostmann, T.; Schrader, T.

    2017-02-01

    In this paper we present the outcome of the first international comparison in the terahertz frequency range among three different kinds of spectrometers. A Fourier-Transform infrared spectrometer, a vector network analyzer and a time-domain spectrometer have been employed for measuring the complex refractive index of three travelling standards made of selected dielectric materials in order to offer a wide enough range of parameters to be measured. The three spectrometers have been compared in terms of measurement capability and uncertainty.

  18. In vitro Neurons in Mammalian Cortical Layer 4 Exhibit Intrinsic Oscillatory Activity in the 10- to 50-Hz Frequency Range

    NASA Astrophysics Data System (ADS)

    Llinas, Rodolfo R.; Grace, Anthony A.; Yarom, Yosef

    1991-02-01

    We report here the presence of fast subthreshold oscillatory potentials recorded in vitro from neurons within layer 4 of the guinea pig frontal cortex. Two types of oscillatory neurons were recorded: (i) One type exhibited subthreshold oscillations whose frequency increased with membrane depolarization and encompassed a range of 10-45 Hz. Action potentials in this type of neuron demonstrated clear after-hyperpolarizations. (ii) The second type of neuron was characterized by narrow-frequency oscillations near 35-50 Hz. These oscillations often outlasted the initiating depolarizing stimulus. No calcium component could be identified in their action potential. In both types of cell the subthreshold oscillations were tetrodotoxin-sensitive, indicating that the depolarizing phase of the oscillation was generated by a voltage-dependent sodium conductance. The initial depolarizing phase was followed by a potassium conductance responsible for the falling phase of the oscillatory wave. In both types of cell, the subthreshold oscillation could trigger spikes at the oscillatory frequency, if the membrane was sufficiently depolarized. Combining intracellular recordings with Lucifer yellow staining showed that the narrow-frequency oscillatory activity was produced by a sparsely spinous interneuron located in layer 4 of the cortex. This neuron has extensive local axonal collaterals that ramify in layers 3 and 4 such that they may contribute to the columnar synchronization of activity in the 40- to 50-Hz range. Cortical activity in this frequency range has been proposed as the basis for the "conjunctive properties" of central nervous system networks.

  19. Cryocooled terahertz photoconductive detector system with background-limited performance in 1.5–4 THz frequency range

    SciTech Connect

    Aoki, Makoto; Hiromoto, Norihisa

    2015-10-15

    We describe a 4-K-cryocooled dual-band terahertz (THz) photoconductive detector system with background-limited performance. The detector system comprises two THz photoconductive detectors covering a response in a wide frequency range from 1.5 to 4 THz, low noise amplifiers, optical low-pass filters to eliminate input radiation of higher frequencies, and a mechanical 4 K Gifford-McMahon refrigerator that provides practical and convenient operation without a liquid He container. The electrical and optical performances of the THz detector system were evaluated at a detector temperature of 4 K under 300 K background radiation. We proved that the detector system can achieve background-limited noise-equivalent-power on the order of 10{sup −14} W/Hz{sup 1/2} in the frequency range from 1.5 to 4 THz even if the vibration noise of the mechanical refrigerator is present.

  20. Comment on "Mode Conversion of Waves In The Ion-Cyclotron Frequency Range in Magnetospheric Plasmas"

    SciTech Connect

    Kim, Eun; Johnson, J. R.

    2014-02-01

    Recently, Kazakov and Fulop [1] studied mode conversion (MC) at the ion-ion hybrid (IIH) resonance in planetary magnetospheric plasmas by simplifying the dispersion relation of the fast wave (FW) modes to describe a cutoff-resonance (CR) pair near the IIH resonance, which can be reduced to a Budden problem. They suggested that when the IIH resonance frequency (ωS) approaches the crossover frequency (ωcr), and the parallel wavenumber (k∥) is close to the critical wavenumber k* ∥(ωS = ωcr), MC can be efficient for arbitrary heavy ion density ratios. In this Comment, we argue that (a) the FW dispersion relation cannot be simplified to the CR pair especially near ωcr because in many parameter regimes there is a cutoff-resonance-cutoff (CRC) triplet that completely changes the wave absorption; and (b) the maximum MC efficiency does not always occur near k∥ ≈ k*∥∥.

  1. Influence of PDMS encapsulation on the sensitivity and frequency range of fiber-optic interferometer

    NASA Astrophysics Data System (ADS)

    Nedoma, Jan; Fajkus, Marcel; Vasinek, Vladimir

    2016-10-01

    Fiber-optic sensors are one of the dynamically developing areas of photonics and photonic applications. This group of sensors can also include fiber-optic interferometers which enable very sensitive sensing. They are entirely passive regarding power supply, and immune to electromagnetic interference. This type of sensor is dependent on the phase change. It mostly used in the field which requires high measurement accuracy. We can achieve a change of sensitivity in the order of 10-8. The fundamental problem of fiber-optic interferometry is a design and imposition (encapsulation) of the measuring arm and reference arm of the interferometer. Polydimethylsiloxane elastomer (PDMS) is one of the possibilities to encapsulation of the sensory arm. Two-component PDMS Sylgard 184 is used type. The article analyzes the effect of encapsulation into a PDMS of the measuring arm of the interferometer to frequency response and sensitivity of the Mach-Zehnder interferometer with the division of power in a ratio of 1:1 (measuring arm and reference arm). Input power set to a reference value of 1 mW, this value was constant for all performed experimental measurements. The generator of a harmonic signal with fixed amplitude signal used for analysis of the frequency characteristic of the interferometer. The application written in LabView development environment, evaluated the amplitude-frequency spectra of the signal. Repeated test of assembled prototype verified the measured results.

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

    PubMed

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

    2005-09-01

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

  3. Aerial low-frequency hearing in captive and free-ranging harbour seals (Phoca vitulina) measured using auditory brainstem responses.

    PubMed

    Lucke, Klaus; Hastie, Gordon D; Ternes, Kerstin; McConnell, Bernie; Moss, Simon; Russell, Deborah J F; Weber, Heike; Janik, Vincent M

    2016-12-01

    The hearing sensitivity of 18 free-ranging and 10 captive harbour seals (Phoca vitulina) to aerial sounds was measured in the presence of typical environmental noise through auditory brainstem response measurements. A focus was put on the comparative hearing sensitivity at low frequencies. Low- and mid-frequency thresholds appeared to be elevated in both captive and free-ranging seals, but this is likely due to masking effects and limitations of the methodology used. The data also showed individual variability in hearing sensitivity with probable age-related hearing loss found in two old harbour seals. These results suggest that the acoustic sensitivity of free-ranging animals was not negatively affected by the soundscape they experienced in the wild.

  4. Full-range swept source optical coherence tomography based on carrier frequency by transmissive dispersive optical delay line.

    PubMed

    Wu, Tong; Ding, Zhihua; Wang, Chuan; Chen, Minghui

    2011-12-01

    A high speed swept source optical coherence tomography (SS-OCT) system capable of full-range imaging is presented. Wave-number carrier frequency is introduced into the spectral interference signal by a transmissive dispersive optical delay line (TDODL). High carrier frequency in the spectral interference signal corresponding to an equivalent distance-shift is exploited to obtain full-range OCT imaging. Theoretical development is conducted with the instantaneous coherence function introduced for a complete description of a spectral interference signal. Performance advantage of the TDODL-based method over the conventional approach where only one side (positive or negative path length difference) is used for imaging to avoid overlaying mirror artifacts is confirmed by the measured envelopes of spectral interference signal. Feasibility of the proposed method for full-range imaging is validated in a custom-built SS-OCT system by in vivo imaging of a biological sample.

  5. Full-range swept source optical coherence tomography based on carrier frequency by transmissive dispersive optical delay line

    NASA Astrophysics Data System (ADS)

    Wu, Tong; Ding, Zhihua; Wang, Chuan; Chen, Minghui

    2011-12-01

    A high speed swept source optical coherence tomography (SS-OCT) system capable of full-range imaging is presented. Wave-number carrier frequency is introduced into the spectral interference signal by a transmissive dispersive optical delay line (TDODL). High carrier frequency in the spectral interference signal corresponding to an equivalent distance-shift is exploited to obtain full-range OCT imaging. Theoretical development is conducted with the instantaneous coherence function introduced for a complete description of a spectral interference signal. Performance advantage of the TDODL-based method over the conventional approach where only one side (positive or negative path length difference) is used for imaging to avoid overlaying mirror artifacts is confirmed by the measured envelopes of spectral interference signal. Feasibility of the proposed method for full-range imaging is validated in a custom-built SS-OCT system by in vivo imaging of a biological sample.

  6. Shielding properties of composite materials based on epoxy resin with graphene nanoplates in the microwave frequency range

    NASA Astrophysics Data System (ADS)

    Volynets, N. I.; Bychenok, D. S.; Lyubimov, A. G.; Kuzhir, P. P.; Maksimenko, S. A.; Baturkin, S. A.; Klochkov, A. Ya.; Mastrucci, M.; Micciulla, F.; Bellucci, S.

    2016-12-01

    Analysis of the electromagnetic properties of composite materials based on epoxy resin with the addition of 0.5 wt % graphene nanoplates in the frequency range of 26-37 GHz is performed. The influence of types of epoxy resin with different viscosities and the type of solvent used (ethanol, acetone) on the electromagnetic response in this frequency range are determined. It is established that the least viscous epoxy resin, Epikote 828, and solvent ethanol are most effective for creation of a shielding covering in the microwave range. Composite materials with optimal composition provide attenuation of the electromagnetic signal at a level at least 10 dB in power for a film thickness of 1.1 mm.

  7. High frequency of SLC22A12 variants causing renal hypouricemia 1 in the Czech and Slovak Roma population; simple and rapid detection method by allele-specific polymerase chain reaction.

    PubMed

    Gabrikova, Dana; Bernasovska, Jarmila; Sokolova, Jitka; Stiburkova, Blanka

    2015-10-01

    Renal hypouricemia is a rare heterogeneous inherited disorder characterized by impaired tubular uric acid transport with severe complications, such as acute kidney injury. Type 1 and 2 are caused by loss-of-function mutations in the SLC22A12 and SLC2A9 gene, respectively. A cohort of 881 randomly chosen ethnic Roma from two regions in Eastern Slovakia and two regions in the Czech Republic participated. Genomic DNA was isolated from buccal swabs and/or from blood samples. The c.1245_1253del and c.1400C>T genotypes were determined using polymerase chain reaction with allele-specific primers in a multiplex arrangement and/or direct sequencing of exon 7 and 9. Allele frequencies and genotypes were tested for Hardy-Weinberg equilibrium using the Chi-square test. 25 subjects were heterozygous and three were homozygous for the c.1245_1253del, while 92 subjects were heterozygous and two were homozygous for the c.1400C>T. Moreover, two participants were compound heterozygotes. Frequencies of the c.1245_1253del and c.1400C>T variants were 1.87 and 5.56 %, respectively. Our finding confirms an uneven geographical and ethnic distribution of SLC22A12 mutant variants. We found that the c.1245_1253del and c.1400C>T variants were present in the Czech and Slovak Roma population at unexpectedly high frequencies. Renal hypouricemia should be kept in mind during differential diagnostic on Roma patients with low serum uric acid concentrations.

  8. Retrieving sea-wave spectra using satellite-imagery spectra in a wide range of frequencies

    NASA Astrophysics Data System (ADS)

    Bondur, V. G.; Dulov, V. A.; Murynin, A. B.; Ignatiev, V. Yu.

    2016-11-01

    A method to register sea-wave spectra using optical aerospace imagery has been developed. The method is based on the use of retrieval operators both in areas of high and low spatial frequencies, including the areas of spectral maximum. The approach to adjust and validate the method developed using sea truth data obtained by string wave recorders has been suggested. This paper presents the results of using the suggested method to study sea-wave spectra using high-resolution satellite imagery for various water areas under different conditions of wave generation.

  9. High resolution kilometric range optical telemetry in air by radio frequency phase measurement

    NASA Astrophysics Data System (ADS)

    Guillory, Joffray; Šmíd, Radek; García-Márquez, Jorge; Truong, Daniel; Alexandre, Christophe; Wallerand, Jean-Pierre

    2016-07-01

    We have developed an optical Absolute Distance Meter (ADM) based on the measurement of the phase accumulated by a Radio Frequency wave during its propagation in the air by a laser beam. In this article, the ADM principle will be described and the main results will be presented. In particular, we will emphasize how the choice of an appropriate photodetector can significantly improve the telemeter performances by minimizing the amplitude to phase conversion. Our prototype, tested in the field, has proven its efficiency with a resolution better than 15 μm for a measurement time of 10 ms and distances up to 1.2 km.

  10. SSVEP-BCI implementation for 37-40 Hz frequency range.

    PubMed

    Müller, Sandra Mara Torres; Diez, Pablo F; Bastos-Filho, Teodiano Freire; Sarcinelli-Filho, Mário; Mut, Vicente; Laciar, Eric

    2011-01-01

    This work presents a Brain-Computer Interface (BCI) based on Steady State Visual Evoked Potentials (SSVEP), using higher stimulus frequencies (>30 Hz). Using a statistical test and a decision tree, the real-time EEG registers of six volunteers are analyzed, with the classification result updated each second. The BCI developed does not need any kind of settings or adjustments, which makes it more general. Offline results are presented, which corresponds to a correct classification rate of up to 99% and a Information Transfer Rate (ITR) of up to 114.2 bits/min.

  11. Dielectric properties of aluminum silver alloy thin films in optical frequency range

    SciTech Connect

    Yang Guang; Sun Jingbo; Zhou Ji

    2011-06-15

    The dielectric properties of direct current (dc) magnetron sputtering aluminum silver alloy films in optical frequency have been quantitatively studied by variable angle spectroscopic ellipsometry. The structure and surface topography of the alloy films were characterized using scanning probe microscopy and x-ray diffraction. The Drude-Lorentz model was used to simulate the dielectric function of Al-Ag alloy films. Meanwhile, the effective medium theory has been utilized for the treatment of surface roughness. We found that the interband transition around 1.5 eV can be shifted through a variable annealing temperature and a changeable silver percentage of Al-Ag alloys.

  12. Study of transmission line attenuation in broad band millimeter wave frequency range

    SciTech Connect

    Pandya, Hitesh Kumar B.; Austin, M. E.; Ellis, R. F.

    2013-10-15

    Broad band millimeter wave transmission lines are used in fusion plasma diagnostics such as electron cyclotron emission (ECE), electron cyclotron absorption, reflectometry and interferometry systems. In particular, the ECE diagnostic for ITER will require efficient transmission over an ultra wide band, 100 to 1000 GHz. A circular corrugated waveguide transmission line is a prospective candidate to transmit such wide band with low attenuation. To evaluate this system, experiments of transmission line attenuation were performed and compared with theoretical loss calculations. A millimeter wave Michelson interferometer and a liquid nitrogen black body source are used to perform all the experiments. Atmospheric water vapor lines and continuum absorption within this band are reported. Ohmic attenuation in corrugated waveguide is very low; however, there is Bragg scattering and higher order mode conversion that can cause significant attenuation in this transmission line. The attenuation due to miter bends, gaps, joints, and curvature are estimated. The measured attenuation of 15 m length with seven miter bends and eighteen joints is 1 dB at low frequency (300 GHz) and 10 dB at high frequency (900 GHz), respectively.

  13. Range Detection of the Extremely Low-Frequency Magnetic Field Produced by Laptop's AC Adapter

    NASA Astrophysics Data System (ADS)

    Brodić, Darko; Amelio, Alessia

    2017-02-01

    Human exposure to extremely low frequency magnetic field represents a risk to their health. This paper takes into consideration the level of an extremely low-frequency magnetic field between 30 and 300 Hz emitted by an AC laptop adapter. The experiment consists of testing 17 different AC adapters for laptops. During the testing, laptops are operated in a normal operating conditions as well as under heavy load. The magnetic field measurement is conducted in the area around the AC adapter. Obtained data is evaluated according to the critical level of the magnetic field proposed by safety standards. Furthermore, data is classified by a K-medians method in order to determine the critical levels of the magnetic field exposure in the nearby area of the AC adapter. Obtained classifications are evaluated according to safety standards, giving a critical analysis of magnetic field areas at risk. Due to emission of a very strong magnetic field in certain areas, a recommendation for safety use of the AC adapter is proposed.

  14. Inkjet Printed Wire-Grid Polarizers for the THz Frequency Range

    NASA Astrophysics Data System (ADS)

    Farid, A.; Laurita, N. J.; Tehrani, B.; Hester, J. G.; Tentzeris, M. M.; Armitage, N. P.

    2016-11-01

    We have investigated the use of inkjet printing technology for the production of THz range wire-grid polarizers using time-domain terahertz spectroscopy (TDTS). Such technology affords an inexpensive and reproducible way of quickly manufacturing THz range metamaterial structures. As a proof-of-concept demonstration, numerous thin silver-nanoparticle ink lines were printed using a Dimatix DMP-2831 printer. We investigated the optimal printing geometry of the polarizers by examining a number of samples with printed wires of varying thickness and spacing. We also investigated the polarization properties of multiply-stacked polarizers.

  15. Inkjet Printed Wire-Grid Polarizers for the THz Frequency Range

    NASA Astrophysics Data System (ADS)

    Farid, A.; Laurita, N. J.; Tehrani, B.; Hester, J. G.; Tentzeris, M. M.; Armitage, N. P.

    2017-03-01

    We have investigated the use of inkjet printing technology for the production of THz range wire-grid polarizers using time-domain terahertz spectroscopy (TDTS). Such technology affords an inexpensive and reproducible way of quickly manufacturing THz range metamaterial structures. As a proof-of-concept demonstration, numerous thin silver-nanoparticle ink lines were printed using a Dimatix DMP-2831 printer. We investigated the optimal printing geometry of the polarizers by examining a number of samples with printed wires of varying thickness and spacing. We also investigated the polarization properties of multiply-stacked polarizers.

  16. A novel allelic variant of the human TSG-6 gene encoding an amino acid difference in the CUB module. Chromosomal localization, frequency analysis, modeling, and expression.

    PubMed

    Nentwich, Hilke A; Mustafa, Zehra; Rugg, Marilyn S; Marsden, Brian D; Cordell, Martin R; Mahoney, David J; Jenkins, Suzanne C; Dowling, Barbara; Fries, Erik; Milner, Caroline M; Loughlin, John; Day, Anthony J

    2002-05-03

    Tumor necrosis factor-stimulated gene-6 (TSG-6) encodes a 35-kDa protein, which is comprised of contiguous Link and CUB modules. TSG-6 protein has been detected in the articular joints of osteoarthritis (OA) patients, with little or no constitutive expression in normal adult tissues. It interacts with components of cartilage matrix (e.g. hyaluronan and aggrecan) and thus may be involved in extracellular remodeling during joint disease. In addition, TSG-6 has been found to have anti-inflammatory properties in models of acute and chronic inflammation. Here we have mapped the human TSG-6 gene to 2q23.3, a region of chromosome 2 linked with OA. A single nucleotide polymorphism was identified that involves a non-synonymous G --> A transition at nucleotide 431 of the TSG-6 coding sequence, resulting in an Arg to Gln alteration in the CUB module (at residue 144 in the preprotein). Molecular modeling of the CUB domain indicated that this amino acid change might lead to functional differences. Typing of 400 OA cases and 400 controls revealed that the A(431) variant identified here is the major TSG-6 allele in Caucasians (with over 75% being A(431) homozygotes) but that this polymorphism is not a marker for OA susceptibility in the patients we have studied. Expression of the Arg(144) and Gln(144) allotypes in Drosophila Schneider 2 cells, and functional characterization, showed that there were no significant differences in the ability of these full-length proteins to bind hyaluronan or form a stable complex with inter-alpha-inhibitor.

  17. Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape.

    PubMed

    Delourme, R; Bousset, L; Ermel, M; Duffé, P; Besnard, A L; Marquer, B; Fudal, I; Linglin, J; Chadœuf, J; Brun, H

    2014-10-01

    Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for durability of major resistance genes. This was demonstrated in the Leptosphaeria maculans/Brassica napus pathosystem in a 5year recurrent selection field experiment on lines harboring the qualitative resistance gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of the virulent isolate population. In this study we continued this recurrent selection experiment in the same way to examine whether the pathogen population could adapt and render the major gene ineffective in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an effective approach for controlling the pathogen epidemics over time. This combination did not prevent isolates virulent against the major gene from amplifying in the long term but the quantitative resistance significantly delayed for 5years the loss of effectiveness of the qualitative resistance and disease severity was maintained at a low level on the genotype with both types of resistance after the fungus population had adapted to the major gene. We also showed that diversity of AvrLm6 virulence alleles was comparable in isolates recovered after the recurrent selection on lines carrying either the major gene alone or in combination with quantitative resistance: a single repeat-induced point mutation and deletion events were observed in both situations. Breeding varieties which combine qualitative and quantitative resistance can effectively contribute to disease control by increasing the potential for durability of major resistance genes.

  18. A new ionosphere-free ambiguity resolution method for long-range baseline with GNSS triple-frequency signals

    NASA Astrophysics Data System (ADS)

    Xu, Ying; Ji, Shengyue; Chen, Wu; Weng, Duojie

    2015-10-01

    New GNSS systems (i.e. GPS modernization, BeiDou, and Galileo) will provide multiple navigation signals for reliable navigation services. The triple or even multiple frequency signals are expected to bring great benefits to the ambiguity resolution (AR) over long-range baselines, which is always regarded as a huge challenge. Another issue in the long baseline AR is the unmodeled ionospheric delay, which is one of the major errors in ranging signals. A new triple-frequency, ionosphere-free technique for ambiguity resolution of long-range baseline is developed in this study. In this technique, the optimal observation combinations are chosen considering the effect of ionospheric delay. At the same time, using this technique, the double difference (DD) ionospheric delay is nullified in the ambiguity search process. The performance of the new technique is examined using the simulated GPS triple frequency data as well as the real BDS observation. Results show that the ambiguity can be fixed within 10 min for GPS and BDS long-range baselines with this new technique.

  19. Frontside-micromachined planar piezoresistive vibration sensor: Evaluating performance in the low frequency test range

    SciTech Connect

    Zhang, Lan; Lu, Jian Takagi, Hideki; Maeda, Ryutaro

    2014-01-15

    Using a surface piezoresistor diffusion method and front-side only micromachining process, a planar piezoresistive vibration sensor was successfully developed with a simple structure, lower processing cost and fewer packaging difficulties. The vibration sensor had a large sector proof mass attached to a narrow flexure. Optimization of the boron diffusion piezoresistor placed on the edge of the narrow flexure greatly improved the sensitivity. Planar vibration sensors were fabricated and measured in order to analyze the effects of the sensor dimensions on performance, including the values of flexure width and the included angle of the sector. Sensitivities of fabricated planar sensors of 0.09–0.46 mV/V/g were measured up to a test frequency of 60 Hz. The sensor functioned at low voltages (<3 V) and currents (<1 mA) with a high sensitivity and low drift. At low background noise levels, the sensor had performance comparable to a commercial device.

  20. Optical frequency domain imaging with a rapidly swept laser in the 815-870 nm range

    NASA Astrophysics Data System (ADS)

    Lim, H.; de Boer, J. F.; Park, B. H.; Lee, E. C.; Yelin, R.; Yun, S. H.

    2006-06-01

    Optical frequency domain imaging (OFDI) in the 800-nm biological imaging window is demonstrated by using a novel wavelength-swept laser source. The laser output is tuned continuously from 815 to 870 nm at a 43.2-kHz repetition rate with 7-mW average power. Axial resolution of 10-μm in biological tissue and peak sensitivity of 96 dB are achieved. In vivo imaging of Xenopus laevis is demonstrated with an acquisition speed of 84 frames per second (512 axial lines per frame). This new imaging technique may prove useful in comprehensive retinal screening for medical diagnosis and contrast-agent-based imaging for biological investigations.

  1. Low-frequency source for very long-range underwater communication.

    PubMed

    Mosca, Frédéric; Matte, Guillaume; Shimura, Takuya

    2013-01-01

    Very long-range underwater acoustic communication (UAC) is crucial for long cruising (>1000 km) autonomous underwater vehicles (AUVs). Very long-range UAC source for AUV must exhibit high electro-acoustic efficiency (>60%) and compactness. This paper describes the Janus-Hammer Bell (JHB) transducer that has been designed for this purpose and meets those requirements. The transducer works on the 450-550 Hz bandwidth and reaches source level above 200 dB (ref. 1 μPa at 1 m) with 1 kW excitation and full immersion capability. JHB source has been used for communication experiments by the Japanese institute for marine technology (Japan Agency for Marine-Earth Science and Technology) achieving a baud rate of 100 bits/s at 1000 km.

  2. Impact of high-frequency waves on the ocean altimeter range bias

    NASA Astrophysics Data System (ADS)

    Vandemark, D.; Chapron, B.; Elfouhaily, T.; Campbell, J. W.

    2005-11-01

    New aircraft observations are presented on the range determination error in satellite altimetry associated with ocean waves. Laser-based measurements of the cross correlation between the gravity wave slope and elevation are reported for the first time. These observations provide direct access to a long, O(10 m), gravity wave statistic central to nonlinear wave theory prediction of the altimeter sea state bias. Coincident Ka-band radar scattering data are used to estimate an electromagnetic (EM) range bias analogous to that in satellite altimetry. These data, along with ancillary wind and wave slope variance estimates, are used alongside existing theory to evaluate the extent of long- versus short-wave, O(cm), control of the bias. The longer wave bias contribution to the total EM bias is shown to range from 25 to as much as 100%. Moreover, on average the term is linearly related to wind speed and to the gravity wave slope variance, consistent with WNL theory. The EM bias associated with interactions between long and short waves is obtained assuming the effect is additive to the independently observed long-wave factor. This second component is also a substantial contributor, is observed to be quadratic in wind speed or wave slope, and dominates at moderate wind speeds. The behavior is shown to be consistent with EM bias prediction based in hydrodynamic modulation theory. Study implications for improved correction of the on-orbit satellite sea state bias are discussed.

  3. Excitation, detection, and electrostatic manipulation of terahertz-frequency range plasmons in a two-dimensional electron system

    PubMed Central

    Wu, Jingbo; Mayorov, Alexander S.; Wood, Christopher D.; Mistry, Divyang; Li, Lianhe; Muchenje, Wilson; Rosamond, Mark C.; Chen, Li; Linfield, Edmund H.; Davies, A. Giles; Cunningham, John E.

    2015-01-01

    Terahertz frequency time-domain spectroscopy employing free-space radiation has frequently been used to probe the elementary excitations of low-dimensional systems. The diffraction limit, however, prevents its use for the in-plane study of individual laterally-defined nanostructures. Here, we demonstrate a planar terahertz frequency plasmonic circuit in which photoconductive material is monolithically integrated with a two-dimensional electron system. Plasmons with a broad spectral range (up to ~ 400 GHz) are excited by injecting picosecond-duration pulses, generated and detected by a photoconductive semiconductor, into a high mobility two-dimensional electron system. Using voltage modulation of a Schottky gate overlying the two-dimensional electron system, we form a tuneable plasmonic cavity, and observe electrostatic manipulation of the plasmon resonances. Our technique offers a direct route to access the picosecond dynamics of confined electron transport in a broad range of lateral nanostructures. PMID:26487263

  4. Impact of major and minor mode on EEG frequency range activities of music processing as a function of expertise.

    PubMed

    Jenni, Raoul; Oechslin, Mathias S; James, Clara E

    2017-04-24

    Processing western tonal music may yield distinct brain responses depending on the mode of the musical compositions. Although subjective feelings in response to major and minor mode are well described, the underlying brain mechanisms and their development with increasing expertise have not been thoroughly examined. Using high-density electroencephalography, the present study investigated neuronal activities in the frequency domain in response to polyphone musical compositions in major and minor mode in non-musicians, amateurs and experts. During active listening decrease of theta- and gamma-frequency range activities occurred with increasing expertise in right posterior regions, possibly reflecting enhanced processing efficiency. Moreover, minor and major compositions distinctively modulated synchronization of neuronal activities in high frequency ranges (beta and gamma) in frontal regions, with increased activity in response to minor compositions in musicians and in experts in particular. These results suggest that high-frequency electroencephalographic (EEG) activities carry information about musical mode, showing gradual increase of processing efficiency and sensitivity with musical expertise.

  5. Stroke frequency, but not swimming speed, is related to body size in free-ranging seabirds, pinnipeds and cetaceans.

    PubMed

    Sato, Katsufumi; Watanuki, Yutaka; Takahashi, Akinori; Miller, Patrick J O; Tanaka, Hideji; Kawabe, Ryo; Ponganis, Paul J; Handrich, Yves; Akamatsu, Tomonari; Watanabe, Yuuki; Mitani, Yoko o; Costa, Daniel P; Bost, Charles-André; Aoki, Kagari; Amano, Masao; Trathan, Phil; Shapiro, Ari; Naito, Yasuhiko

    2007-02-22

    It is obvious, at least qualitatively, that small animals move their locomotory apparatus faster than large animals: small insects move their wings invisibly fast, while large birds flap their wings slowly. However, quantitative observations have been difficult to obtain from free-ranging swimming animals. We surveyed the swimming behaviour of animals ranging from 0.5 kg seabirds to 30 000 kg sperm whales using animal-borne accelerometers. Dominant stroke cycle frequencies of swimming specialist seabirds and marine mammals were proportional to mass(-0.29) (R(2)= 0.99, n = 17 groups), while propulsive swimming speeds of 1-2 m s(-1) were independent of body size. This scaling relationship, obtained from breath-hold divers expected to swim optimally to conserve oxygen, does not agree with recent theoretical predictions for optimal swimming. Seabirds that use their wings for both swimming and flying stroked at a lower frequency than other swimming specialists of the same size, suggesting a morphological trade-off with wing size and stroke frequency representing a compromise. In contrast, foot-propelled diving birds such as shags had similar stroke frequencies as other swimming specialists. These results suggest that muscle characteristics may constrain swimming during cruising travel, with convergence among diving specialists in the proportions and contraction rates of propulsive muscles.

  6. A MEMS Interface IC With Low-Power and Wide-Range Frequency-to-Voltage Converter for Biomedical Applications.

    PubMed

    Arefin, Md Shamsul; Redouté, Jean-Michel; Yuce, Mehmet Rasit

    2016-04-01

    This paper presents an interface circuit for capacitive and inductive MEMS biosensors using an oscillator and a charge pump based frequency-to-voltage converter. Frequency modulation using a differential crossed coupled oscillator is adopted to sense capacitive and inductive changes. The frequency-to-voltage converter is designed with a negative feedback system and external controlling parameters to adjust the sensitivity, dynamic range, and nominal point for the measurement. The sensitivity of the frequency-to-voltage converter is from 13.28 to 35.96 mV/MHz depending on external voltage and charging current. The sensitivity ranges of the capacitive and inductive interface circuit are 17.08 to 54.4 mV/pF and 32.11 to 82.88 mV/mH, respectively. A capacitive MEMS based pH sensor is also connected with the interface circuit to measure the high acidic gastric acid throughout the digestive tract. The sensitivity for pH from 1 to 3 is 191.4 mV/pH with 550 μV(pp) noise. The readout circuit is designed and fabricated using the UMC 0.18 μm CMOS technology. It occupies an area of 0.18 mm (2) and consumes 11.8 mW.

  7. Experimental study of attenuation and dispersion over a broad frequency range: 2. The universal scaling of polycrystalline materials

    NASA Astrophysics Data System (ADS)

    McCarthy, Christine; Takei, Yasuko; Hiraga, Takehiko

    2011-09-01

    In order to extend the range of conditions that can be obtained in experiments, we have measured the viscoelastic properties of polycrystalline organic borneol, as an analogue to mantle rock. Using a custom fabricated apparatus, the Young's modulus E and attenuation QE-1 were measured accurately over a broad frequency range (10-4 ≤ f (Hz) ≤ 2.15) and at low strain amplitude (10-5-10-6). Creep experiments were performed with the same apparatus to measure the steady state viscosity. Anelasticity and viscosity were measured at high homologous temperatures (T = 22-48°C; T/Tm = 0.61-0.67) and various grain sizes (3-22 μm), the growth of which was controlled by annealing. Using the measured viscosities η and the unrelaxed modulus EU determined from ultrasonic experiments, the frequency of the entire data set was normalized by the Maxwell frequency fM = EU/η, resulting in E and Q-1 master curves. The Q-1 data from previous studies on olivine-dominated samples also collapse onto the same curve when scaled by fM,, demonstrating the universality of anelasticity for polycrystalline materials. The similitude by the Maxwell frequency scaling indicates that the dominant mechanism for the anelasticity observed in this study and in previous studies is diffusionally accommodated grain boundary sliding. A generalized formulation for this similitude is provided to extrapolate the experimental data to velocity and attenuation of seismic shear waves.

  8. Genetic parameters and allele frequencies of five new European Standard Set STR loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in the population of Romania

    PubMed Central

    Stanciu, Florin; Vladu, Simona; Cuţăr, Veronica; Cocioabă, Daniela; Iancu, Florentina; Cotolea, Adnana; Stoian, Ionel Marius

    2013-01-01

    Aim To establish allele frequencies and genetic parameters for 5 new European Standard Set short tandem repeat (STR) loci in the population of Romania and to compare them with those in other populations. Methods DNA was isolated using QIAamp 96 DNA Swab BioRobot Kit and Chelex 100 methods. Polymerase chain reaction amplification was done using Investigator ESSplexPlus Kit (D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, and vWA). For DNA typing, Applied Biosystems 3500/3500xL Genetic Analyzer was used. Statistical analysis was done using Powerstats, GDA, and Arlequin software. Results Power of discrimination and polymorphism information content was highest for two new ESS loci, D1S1656 and D12S391. Comparison of allele frequencies for 5 new ESS loci in Romanian population with previously published population data showed significant differences for all compared populations, with the exception of Hungary. Geographically more distant populations, such as Spain, Sweden, United Kingdom, Germany, and Portugal differed more than closer populations. Conclusion New ESS STR loci are very useful for the analysis of forensic samples (persons or traces) due to their characteristics (shortness and high polymorphism). In comparisons with other common STR markers, they have a higher power of discrimination and also higher polymorphism information content, and could be used in any national DNA database. PMID:23771753

  9. SmEdA vibro-acoustic modelling in the mid-frequency range including the effect of dissipative treatments

    NASA Astrophysics Data System (ADS)

    Hwang, H. D.; Maxit, L.; Ege, K.; Gerges, Y.; Guyader, J.-L.

    2017-04-01

    Vibro-acoustic simulation in the mid-frequency range is of interest for automotive and truck constructors. The dissipative treatments used for noise and vibration control such as viscoelastic patches and acoustic absorbing materials must be taken into account in the problem. The Statistical modal Energy distribution Analysis (SmEdA) model consists in extending Statistical Energy Analysis (SEA) to the mid-frequency range by establishing power balance equations between the modes of the different subsystems. The modal basis of uncoupled-subsystems that can be estimated by the finite element method in the mid-frequency range is used as input data. SmEdA was originally developed by considering constant modal damping factors for each subsystem. However, this means that it cannot describe the local distribution of dissipative materials. To overcome this issue, a methodology is proposed here to take into account the effect of these materials. This methodology is based on the finite element models of the subsystems that include well-known homogenized material models of dissipative treatments. The Galerkin method with subsystem normal modes is used to estimate the modal damping loss factors. Cross-modal coupling terms which appear in the formulation due to the dissipative materials are assumed to be negligible. An approximation of the energy sharing between the subsystems damped by dissipative materials is then described by SmEdA. The different steps of the method are validated experimentally by applying it to a laboratory test case composed of a plate-cavity system with different configurations of dissipative treatments. The comparison between the experimental and the simulation results shows good agreement in the mid-frequency range.

  10. Efficiency improvement of heat exchangers by the rational choice of the range of frequencies of electromagnetic water treatment

    NASA Astrophysics Data System (ADS)

    Runov, D. M.; Laptev, A. G.

    2015-05-01

    The electromagnetic water treatment is considered as one of the reagentless methods to reduce the scaling and to improve the cooling efficiency of high-temperature gas flows. It is achieved by the rational choice of the frequency range under laboratory conditions. The choice is made by the lowest particle size distribution of the precipitated particles. The time analysis of the content of hardness salts in the treated water is carried out at the input to and output of the heat exchanger.

  11. The mechanism of modulation of geoacoustic emission intensity by weak electromagnetic fields in the audio-frequency range

    NASA Astrophysics Data System (ADS)

    Gavrilov, V. A.

    2016-07-01

    We propose a physical mechanism explaining the mechanism of modulation of the geoacoustic emission intensity by an external electromagnetic field in the audio-frequency range, which was previously revealed as a result of borehole measurements at the Petropavlovsk-Kamchatskii geodynamic testing area. It was established that electric double layers (EDL) at the interface between solid and liquid phases in a fluidsaturated geological medium play a key role in the mechanism proposed.

  12. An analysis of dielectric properties of synthetic ballast water at frequencies ranging from 300 to 3000 MHz.

    PubMed

    Boldor, Dorin; Ortego, Jeffrey; Rusch, Kelly A

    2008-01-01

    Ballast water presents an important vector for introduction of aquatic invasive species in the coastal waters around the world. Currently there are no established technologies proven to completely eliminate this problem due to the particularities of the ballasting and de-ballasting operations (extremely large volumes of water, efficiency at destroying macro and micro organisms, environmental issues associated with chemical treatments). Continuous microwave heating presents a potential solution to this problem, but the design of suitable applicators depends on the dielectric properties of the ballast water to be processed. The study presented in this paper is focused on the dielectric properties (dielectric constant--epsilon'; dielectric loss--epsilon") of synthetic ballast water inoculated with four organisms at seven different temperatures in the frequency range of 300 to 3000 MHz. The dielectric properties of the mixtures were determined using a network analyzer and a dielectric probe kit using the open-ended coaxial probe method. Numerical analysis was performed on data collected across all frequencies involved with an emphasis placed on F.C.C. allotted frequencies of 433, 915 and 2450 MHz. The dielectric constant was relatively independent of frequency and the organism used, but it showed a remarkable decrease with temperature. The dielectric loss showed an extreme decrease with increasing frequency, marked differences between the different organisms and between different growth stages of the same organism, and a large relatively linear increase with increasing temperature.

  13. An experimental investigation of thermoacoustic lasers operating in audible frequency range

    NASA Astrophysics Data System (ADS)

    Kolhe, Sanket Anil

    Thermoacoustic lasers convert heat from a high-temperature heat source into acoustic power while rejecting waste heat to a low temperature sink. The working fluids involved can be air or noble gases which are nontoxic and environmentally benign. Simple in construction due to absence of moving parts, thermoacoustic lasers can be employed to achieve generation of electricity at individual homes, water-heating for domestic purposes, and to facilitate space heating and cooling. The possibility of utilizing waste heat or solar energy to run thermoacoustic devices makes them technically promising and economically viable to generate large quantities of acoustic energy. The research presented in this thesis deals with the effects of geometric parameters (stack position, stack length, tube length) associated with a thermoacoustic laser on the output sound wave. The effects of varying input power on acoustic output were also studied. Based on the experiments, optimum operating conditions were identified and qualitative and/or quantitative explanations were provided to justify our observations. It was observed that the maximum sound pressure level was generated for the laser with the stack positioned at a distance of quarter lengths of a resonator from the closed end. Higher sound pressure levels were recorded for the laser with longer stack lengths and longer resonator lengths. Efforts were also made to develop high-frequency thermoacoustic lasers.

  14. Understanding and Utilizing Waveguide Invariant Range-frequency Striations in Ocean Acoustic Waveguides

    DTIC Science & Technology

    2011-02-01

    slope of the line connecting non-SRBR modes is sig- nif cantly different than the slope of the line connecting the SRBR modes. Thus, the non-SRBR modes...maximum range that one expects to see the source. All results presented in this chapter used Eqs. (3.8) and (3.9) with r = 5000 m, c1 = 1500 m/s, and c2...present work, ∆f was determined by using Eqs. (3.21) and (3.18) with c1 = 1500 m/s, c2 = 1800 m/s, r = 1000 meters, resulting in ∆f ≈ 81 Hz. ∆r was

  15. Perception of pitch location within a speaker's range: fundamental frequency, voice quality and speaker sex.

    PubMed

    Bishop, Jason; Keating, Patricia

    2012-08-01

    How are listeners able to identify whether the pitch of a brief isolated sample of an unknown voice is high or low in the overall pitch range of that speaker? Does the speaker's voice quality convey crucial information about pitch level? Results and statistical models of two experiments that provide answers to these questions are presented. First, listeners rated the pitch levels of vowels taken over the full pitch ranges of male and female speakers. The absolute f0 of the samples was by far the most important determinant of listeners' ratings, but with some effect of the sex of the speaker. Acoustic measures of voice quality had only a very small effect on these ratings. This result suggests that listeners have expectations about f0s for average speakers of each sex, and judge voice samples against such expectations. Second, listeners judged speaker sex for the same speech samples. Again, absolute f0 was the most important determinant of listeners' judgments, but now voice quality measures also played a role. Thus it seems that pitch level judgments depend on voice quality mostly indirectly, through its information about sex. Absolute f0 is the most important information for deciding both pitch level and speaker sex.

  16. Low-frequency predictability of the Dynamical Extended-Range Forecast Experiment

    NASA Technical Reports Server (NTRS)

    Nogues-Peagle, Julia; Rodgers, Dennis A.; Mo, Kingtse C.

    1992-01-01

    The objective of the study was to analyze data from the Dynamical Extended-Range Forecast Experiment conducted from January 1986 to March 1987, and to evaluate differences between analysis and forecasts with emphasis on the tropical 30-50-day oscillation. The diagnostic toll used is the projection of analysis and forecast data onto the normal modes of a primitive equation model. Examination of zonal-wind anomalies in the tropics shows that the forecast model predicts propagation of intraseasonal variations more accurately for slow propagation rates. The forecast amplitude is generally weaker than the analyzed amplitude. Analyzed kinetic energy and error fields exhibit similar horizontal scales for internal and external modes. External Rossby-mode components maximize in the extratropics while Rossby internal modes exhibit patterns that extend over the entire globe.

  17. Dielectric response of wurtzite gallium nitride in the terahertz frequency range

    NASA Astrophysics Data System (ADS)

    Hibberd, M. T.; Frey, V.; Spencer, B. F.; Mitchell, P. W.; Dawson, P.; Kappers, M. J.; Oliver, R. A.; Humphreys, C. J.; Graham, D. M.

    2016-12-01

    We report on the characterization of the intrinsic, anisotropic, dielectric properties of wurtzite gallium nitride in the spectral range of 0.5-11 THz, using terahertz time-domain spectroscopy. The ordinary (ε˜⊥) and extraordinary (ε˜∥) components of the complex dielectric function were determined experimentally for a semi-insulating, m-plane gallium nitride single crystal, providing measurements of the refractive indices (n⊥,∥) and absorption coefficients (α⊥,∥) . These material parameters were successfully modeled by considering the contribution of the optical phonon modes, measured using Raman spectroscopy, to the dielectric function, giving values for the relative static dielectric constants of ε0⊥ = 9.22 ± 0.02 and ε0∥ = 10.32 ± 0.03 for wurtzite gallium nitride.

  18. Wide range tuning of resonant frequency for a vortex core in a regular triangle magnet.

    PubMed

    Yakata, Satoshi; Tanaka, Terumitsu; Kiseki, Kohei; Matsuyama, Kimihide; Kimura, Takashi

    2013-12-20

    A magnetic vortex structure stabilized in a micron or nano-sized ferromagnetic disk has a strong potential as a unit cell for spin-based nano-electronic devices because of negligible magnetostatic interaction and superior thermal stability. Moreover, various intriguing fundamental physics such as bloch point reversal and symmetry breaking can be induced in the dynamical behaviors in the magnetic vortex. The static and dynamic properties of the magnetic vortex can be tuned by the disk dimension and/or the separation distance between the disks. However, to realize these modifications, the preparations of other devices with different sample geometries are required. Here, we experimentally demonstrate that, in a regular-triangle Permalloy dot, the dynamic properties of a magnetic vortex are greatly modified by the application of the in-plane magnetic field. The obtained wide range tunability based on the asymmetric position dependence of the core potential provides attractive performances in the microwave spintronic devices.

  19. Sub-frequency range stress wave factor NDE technique for assessing damage in fiber-epoxy composites

    NASA Astrophysics Data System (ADS)

    Hong, Gang

    This research aims at modifying, improving and calibrating the Stress Wave Factor Nondestructive Evaluation (SWF NDE) technique and applying it to a fiber epoxy composite material and other composite structures. In order to access the composite's integrity the Energy of SWF within a selected Sub Frequency Range (SFR) instead of the whole measured frequency range as of conventional SWF is used. This technique, introduced and examined herein and is termed the Sub Frequency Range Stress Wave Factors (SFR-SWF) and is tailored to improve the conventional SWF technique with respect to sensibility and accuracy. A series of controlled damage tests were performed, and relevant acousto-ultrasonic observations were conducted. The overall property of the composites subjected to hygrothermal degradation, the localized defects such as the surface crack and the historical damage were assessed with conventional SWF and SFR-SWF. The two methods are compared in detail. The hygrothermal degradation and surface crack experiments were also simulated using the finite element method. Dynamic numerical analysis was conducted to simulate the wave propagation process, both in time domain and frequency domain using the commercial finite element code ABAQUS. The numerical results were also evaluated via both SWF and SFR-SWF, and were compared with the results of experiments. Thus, the potential of SFR-SWF was evaluated. A general conclusion from this research is that the SFR-SWF has the better capability than that of the conventional SWF in assessing the composite's overall condition, localized defects and historical damage. Since there are still open questions regarding the physical understanding of the SWF and SFR-SWF, the finite element analysis provides confirmation for certain observed behaviors of the Acousto-Ultrasonic and SFR-SWF technique.

  20. A Constant Energy-Per-Cycle Ring Oscillator Over a Wide Frequency Range for Wireless Sensor Nodes

    PubMed Central

    Lee, Inhee; Sylvester, Dennis; Blaauw, David

    2016-01-01

    This paper presents an energy-efficient oscillator for wireless sensor nodes (WSNs). It avoids short-circuit current by minimizing the time spent in the input voltage range from Vthn to [Vdd − |Vthp|]. A current-feeding scheme with gate voltage control enables the oscillator to operate over a wide frequency range. A test chip is fabricated in a 0.18 μm CMOS process. The measurements show that the proposed oscillator achieves a constant energy-per-cycle (EpC) of 0.8 pJ/cycle over the 21–60 MHz frequency range and is more efficient than a conventional current-starved ring oscillator (CSRO) below 300 kHz at 1.8 V supply voltage. As an application example, the proposed oscillator is implemented in a switched-capacitor DC–DC converter. The converter is 11%–56% more efficient for load power values ranging from 583 pW to 2.9 nW than a converter using a conventional CSRO. PMID:27546899

  1. Excitation of the surface flute waves in electron cyclotron frequency range by internal rotating electron beam in a coaxial waveguide

    NASA Astrophysics Data System (ADS)

    Blednov, O.; Girka, I.; Girka, V.; Pavlenko, I.; Sydora, R.

    2014-12-01

    The initial stage of interaction between a gyrating beam of electrons, which move along Larmor orbits in a narrow gap between a cylindrical plasma layer and an internal screen of a metal coaxial waveguide and electromagnetic eigen waves, is studied theoretically. These waves are extraordinary polarized ones; they propagate along the azimuthal angle across an axial external steady magnetic field in the electron cyclotron frequency range. The numerical analysis shows that the excitation process is stable enough in respect to changing plasma waveguide parameters. The wider the plasma layer, the broader the range of plasma waveguide parameters within which effective wave excitation takes place. The main influence on the excitation of these modes is performed by the applied axial magnetic field, namely: its increase leads to an increase of growth rate and a broadening of the range of the waveguide parameters within which wave excitation is effective.

  2. A reconfigurable multi-mode multi-band transmitter with integrated frequency synthesizer for short-range wireless communication

    NASA Astrophysics Data System (ADS)

    Nan, Qi; Fan, Chen; Lingwei, Zhang; Xiaoman, Wang; Baoyong, Chi

    2013-09-01

    A reconfigurable multi-mode direct-conversion transmitter (TX) with integrated frequency synthesizer (FS) is presented. The TX as well as the FS is designed with a flexible architecture and frequency plan, which helps to support all the 433/868/915 MHz ISM band signals, with the reconfigurable bandwidth from 250 kHz to 2 MHz. In order to save power and chip area, only one 1.8 GHz VCO is adopted to cover the whole frequency range. All the operation modes can be regulated in real time by configuring the integrated register-bank through an SPI interface. Implemented in 180 nm CMOS, the FS achieves a frequency coverage of 320-460 MHz and 620-920 MHz. The lowest phase noise can be -107 dBc/Hz at a 100 kHz offset and -126 dBc/Hz at a 1 MHz offset. The transmitter features a + 10.2 dBm peak output power with a +9.5 dBm 1-dB-compression point and 250 kHz/500 kHz/1 MHz/2 MHz reconfigurable signal bandwidth.

  3. Temperature and frequency characteristics of low-loss MnZn ferrite in a wide temperature range

    NASA Astrophysics Data System (ADS)

    Sun, Ke; Lan, Zhongwen; Yu, Zhong; Xu, Zhiyong; Jiang, Xiaona; Wang, Zihui; Liu, Zhi; Luo, Ming

    2011-05-01

    A low-loss Mn0.7Zn0.24Fe2.06O4 ferrite has been prepared by a solid-state reaction method. The MnZn ferrite has a high initial permeability, μi (3097), a high saturation induction, Bs (526 mT), a high Curie temperature, Tc (220 °C), and a low core loss, PL (≤ 415 kW/m3) in a wide temperature (25-120 °C) and frequency (10-100 kHz) range. As the temperature increases, an initial decrease followed by a subsequent increase of hysteresis loss, Ph, and eddy current loss, Pe is observed. Both Ph and Pe increase with increasing frequency. When f ≥ 300 kHz, a residual loss, Pr, appears. Pe increases with increasing temperature and frequency. The temperature and frequency dependence of Ph can be explained by irreversible domain wall movements, Pe by the skin effect, and Pr by domain wall resonance, respectively.

  4. 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.

  5. 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.

  6. Digital predistortion of 75-110 GHz W-band frequency multiplier for fiber wireless short range access systems.

    PubMed

    Zhao, Ying; Deng, Lei; Pang, Xiaodan; Yu, Xianbin; Zheng, Xiaoping; Zhang, Hanyi; Monroy, Idelfonso Tafur

    2011-12-12

    We present a W-band fiber-wireless transmission system based on a nonlinear frequency multiplier for high-speed wireless short range access applications. By implementing a baseband digital signal predistortion scheme, intensive nonlinear distortions induced in a sextuple frequency multiplier can be effectively pre-compensated. Without using costly W-band components, a transmission system with 26 km fiber and 4 m wireless transmission operating at 99.6 GHz is experimentally validated. Adjacent-channel power ratio (ACPR) improvements for IQ-modulated vector signals are guaranteed and transmission performances for fiber and wireless channels are studied. This W-band predistortion technique is a promising candidate for applications in high capacity wireless-fiber access systems.

  7. HLA-A, HLA-B, HLA-DRB1 allele and haplotype frequencies in 6384 umbilical cord blood units and transplantation matching and engraftment statistics in the Zhejiang cord blood bank of China.

    PubMed

    Wang, F; He, J; Chen, S; Qin, F; Dai, B; Zhang, W; Zhu, F M; Lv, H J

    2014-02-01

    Umbilical cord blood (UCB) is a widely accepted source of progenitor cells, and now, many cord blood banks were established. Here, we analysed the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies, HLA matching possibilities for searching potential donors and outcome of UCB transplantations in Zhejiang cord blood bank of China. A total of 6384 UCB units were characterized for 17 HLA-A, 30 HLA-B and 13 HLA-DRB1 alleles at the first field resolution level. Additionally, B*14, B*15 and B*40 were typed to the second field level. A total of 1372 distinct A-B-DRB1 haplotypes were identified. The frequencies of 7 haplotypes were more than 1%, and 439 haplotypes were <0.01%. A*02-B*46-DRB1*09, A*33-B*58-DRB1*03 and A*30-B*13-DRB1*07 were the most common haplotypes, with frequencies of 4.4%, 3.3%, and 2.9%, respectively. Linkage disequilibrium(LD) analysis showed that there were 83 A-B, 106 B-DRB1, 54 A-DRB1 haplotypes with positive LD, in which 51 A-B, 60 B-DRB1, 32 A-DRB1 haplotypes exhibited a significant LD (P < 0.05). In 682 search requests, 12.9%, 40.0% and 42.7% of patients were found to have 6 of 6, 5 of 6 and 4 of 6 HLA-A, HLA-B and HLA-DRB1 matching donors, respectively. A total of 30 UCB units were transplanted to 24 patients (3 patients not evaluated due to early death); 14 of 21 patients (66.7%) engrafted. This study reveals the HLA distribution and its transplantation application in the cord blood bank of Zhejiang province. These data can help to select potential UCB donors for transplantation and used to assess the scale of new cord blood banking endeavours.

  8. Empirical dependence of acoustic transmission scintillation statistics on bandwidth, frequency, and range in New Jersey continental shelf.

    PubMed

    Andrews, Mark; Chen, Tianrun; Ratilal, Purnima

    2009-01-01

    The scintillation statistics of broadband acoustic transmissions are determined as a function of signal bandwidth B, center frequency f(c), and range with experimental data in the New Jersey continental shelf. The received signal intensity is shown to follow the Gamma distribution implying that the central limit theorem has led to a fully saturated field from independent multimodal propagation contributions. The Gamma distribution depends on the mean intensity and the number of independent statistical fluctuations or coherent cells micro of the received signal. The latter is calculated for the matched filter, the Parseval sum, and the bandpassed center frequency, all of which are standard ocean acoustic receivers. The number of fluctuations mu of the received signal is found to be an order of magnitude smaller than the time-bandwidth product TB of the transmitted signal, and to increase monotonically with relative bandwidth Bfc. A computationally efficient numerical approach is developed to predict the mean intensity and the corresponding broadband transmission loss of a fluctuating, range-dependent ocean waveguide by range and depth averaging the output of a time-harmonic stochastic propagation model. This model enables efficient and accurate estimation of transmission loss over wide areas, which has become essential in wide-area sonar imaging applications.

  9. Dynamic registration of the absorption spectrum of water in the SiO(2) nanopores in high-frequency range.

    PubMed

    Sinitsa, L N; Lugovskoy, A A

    2010-11-28

    The high-frequency region was used to record the absorption spectrum of water in nanoscale pores during vacuum pumping or injection of water. The wide spectral range, which included the vibration overtones, allowed to resolve the structure of the absorption bands with variation of water concentration in the pores of SiO(2). The absorption bands of water clusters in the 4570-5400 cm(-1) range consist of well-resolved sub-bands with interpeak intervals of up to 580 cm(-1). When the pore diameter is decreased from 11.8 to 2.6 nm, the absorption bands of clusters in this frequency range are shifted by 530 cm(-1) in the direction of the water monomer which indicates an increase of hydrogen bond strength in confined water with an increase of the pore diameter. The spectrum recorded during water pumping is extremely variable in time, and the cluster dynamics in large pores (11.8 nm) differs greatly from the dynamics in small pores (2.6 nm). While all types of water clusters are removed from small pores uniformly, in the case of large pores, the water clusters relating to strong hydrogen bonds are removed from the sample at the beginning of the vacuum pumping and the loosely coupled clusters are removed later. The rate of this process is not steady and varies throughout pumping.

  10. Human sympathetic outflows to skin and muscle target organs fluctuate concordantly over a wide range of time-varying frequencies.

    PubMed

    Bernjak, Alan; Cui, Jian; Iwase, Satoshi; Mano, Tadaaki; Stefanovska, Aneta; Eckberg, Dwain L

    2012-01-15

    Frequency-domain analyses of simultaneously recorded skin and muscle sympathetic nerve activities may yield unique information on otherwise obscure central processes governing human neural outflows. We used wavelet transform and wavelet phase coherence methods to analyse integrated skin and muscle sympathetic nerve activities and haemodynamic fluctuations, recorded from nine healthy supine young men. We tested two null hypotheses: (1) that human skin and muscle sympathetic nerve activities oscillate congruently; and (2) that whole-body heating affects these neural outflows and their haemodynamic consequences in similar ways. Measurements included peroneal nerve skin and tibial nerve muscle sympathetic activities; the electrocardiogram; finger photoplethysmographic arterial pressure; respiration (controlled at 0.25 Hz, and registered with a nasal thermistor); and skin temperature, sweating, and laser-Doppler skin blood flow. We made recordings at ∼27°C, for ∼20 min, and then during room temperature increases to ∼38°C, over 35 min. We analysed data with a wavelet transform, using the Morlet mother wavelet and wavelet phase coherence, to determine the frequencies and coherences of oscillations over time. At 27°C, skin and muscle nerve activities oscillated coherently, at ever-changing frequencies between 0.01 and the cardiac frequency (∼1 Hz). Heating significantly augmented oscillations of skin sympathetic nerve activity and skin blood flow, arterial pressure, and R-R intervals, over a wide range of low frequencies, and modestly reduced coordination between skin and muscle sympathetic oscillations. These results suggest that human skin and muscle sympathetic motoneurones are similarly entrained by external influences, including those of arterial baroreceptors, respiration, and other less well-defined brainstem oscillators. Our study provides strong support for the existence of multiple, time-varying central sympathetic neural oscillators in human subjects.

  11. Development of calibration techniques for ultrasonic hydrophone probes in the frequency range from 1 to 100 MHz

    NASA Astrophysics Data System (ADS)

    Umchid, Sumet

    The primary objective of this research was to develop and optimize the calibration techniques for ultrasonic hydrophone probes used in acoustic field measurements up to 100 MHz. A dependable, 100 MHz calibration method was necessary to examine the behavior of a sub-millimeter spatial resolution fiber optic (FO) sensor and assess the need for such a sensor as an alternative tool for high frequency characterization of ultrasound fields. Also, it was of interest to investigate the feasibility of using FO probes in high intensity fields such as those employed in HIFU (High Intensity Focused Ultrasound) applications. In addition to the development of a novel, 100 MHz calibration technique the innovative elements of this research include implementation of a prototype FO sensor with an active diameter of about 10 hum that exhibits uniform sensitivity over the considered frequency range and does not require any spatial averaging corrections up to about 75 MHz. The calibration technique provided the sensitivity of conventional, finite aperture piezoelectric hydrophone probes as a virtually continuous function of frequency and allowed the verification of the uniformity of the FO sensor frequency response. As anticipated, the overall uncertainty of the calibration was dependent on frequency and determined to be about +/-12% (+/-1 dB) up to 40 MHz, +/-20% (+/-1.5 dB) from 40 to 60 MHz and +/-25% (+/-2 dB) from 60 to 100 MHz. The outcome of this research indicates that once fully developed and calibrated, the combined acousto-optic system will constitute a universal reference tool in the wide, 100 MHz bandwidth.

  12. Allele frequencies in the VRN-A1, VRN-B1 and VRN-D1 vernalization response and PPD-B1 and PPD-D1 photoperiod sensitivity genes, and their effects on heading in a diverse set of wheat cultivars (Triticum aestivum L.).

    PubMed

    Kiss, Tibor; Balla, Krisztina; Veisz, Ottó; Láng, László; Bedő, Zoltán; Griffiths, Simon; Isaac, Peter; Karsai, Ildikó

    2014-01-01

    Heading of cereals is determined by complex genetic and environmental factors in which genes responsible for vernalization and photoperiod sensitivity play a decisive role. Our aim was to use diagnostic molecular markers to determine the main allele types in VRN-A1, VRN-B1, VRN-D1, PPD-B1 and PPD-D1 in a worldwide wheat collection of 683 genotypes and to investigate the effect of these alleles on heading in the field. The dominant VRN-A1, VRN-B1 and VRN-D1 alleles were present at a low frequency. The PPD-D1a photoperiod-insensitive allele was carried by 57 % of the cultivars and was most frequent in Asian and European cultivars. The PPD-B1 photoperiod-insensitive allele was carried by 22 % of the genotypes from Asia, America and Europe. Nine versions of the PPD-B1-insensitive allele were identified based on gene copy number and intercopy structure. The allele compositions in PPD-D1, PPD-B1 and VRN-D1 significantly influenced heading and together explained 37.5 % of the phenotypic variance. The role of gene model increased to 39.1 % when PPD-B1 intercopy structure was taken into account instead of overall PPD-B1 type (sensitive vs. insensitive). As a single component, PPD-D1 had the most important role (28.0 % of the phenotypic variance), followed by PPD-B1 (12.3 % for PPD-B1_overall, and 15.1 % for PPD-B1_intercopy) and VRN-D1 (2.2 %). Significant gene interactions were identified between the marker alleles within PPD-B1 and between VRN-D1 and the two PPD1 genes. The earliest heading genotypes were those with the photoperiod-insensitive allele in PPD-D1 and PPD-B1, and with the spring allele for VRN-D1 and the winter alleles for VRN-A1 and VRN-B1. This combination could only be detected in genotypes from Southern Europe and Asia. Late-heading genotypes had the sensitivity alleles for both PPD1 genes, regardless of the allelic composition of the VRN1 genes. There was a 10-day difference in heading between the earliest and latest groups under field conditions.

  13. Ultra-wideband coaxial hybrid coupler for load resilient ion cyclotron range of frequency heating at fusion plasmas

    SciTech Connect

    Kim, H. J.; Bae, Y. S.; Yang, H. L.; Kwak, J.-G.; Wang, S. J.; Kim, B. K.; Choi, J. J.

    2012-06-25

    We designed a high power and ultra-wideband two-section 3 dB coaxial hybrid coupler for load resilient ion cyclotron range of frequency heating by configuring asymmetric impedance matching using a three-dimensional simulation code, hfss. By adjusting the characteristic impedances of main and coupled lines of the hybrid coupler, we realized that the bandwidth of the proposed circuit is not only wider than that of a conventional three-section coupler, but also that the bandwidth is almost twice as wide compared to the conventional two-section hybrid coupler while maintaining the identical overall size.

  14. Numerical simulation of the electromagnetic fields excited by loop antennas in plasma in the whistler frequency range

    SciTech Connect

    Koldanov, V. A.; Korobkov, S. V.; Gushchin, M. E.; Kostrov, A. V.

    2011-08-15

    The electromagnetic fields excited by circular loop antennas in a magnetized plasma in the whistler frequency range are simulated by the finite-difference time-domain method. The spatial structure of quasi-monochromatic fields excited in the near- and far-field zones by an antenna with a harmonic current, as well as the dynamics of the electromagnetic field excited by an antenna with a current in the form of a single video pulse, is studied. Simulations performed for a uniform plasma and uniform ambient magnetic field agree well with the results of theoretical analysis and model laboratory experiments performed on large-scale plasma devices.

  15. Negative permittivity and permeability spectra of Cu/yttrium iron garnet hybrid granular composite materials in the microwave frequency range

    SciTech Connect

    Tsutaoka, Takanori Fukuyama, Koki; Kinoshita, Hideaki; Kasagi, Teruhiro; Yamamoto, Shinichiro; Hatakeyama, Kenichi

    2013-12-23

    The relative complex permittivity and permeability spectra of the coagulated copper and yttrium iron garnet (Cu/YIG) hybrid granular composite materials have been studied in the microwave range. The insulator to metal transition was observed at the percolation threshold of Cu particle content (φ{sub Cu} = 16.0 vol. %) in the electrical conductivity. In the percolation threshold, the low frequency plasmonic state caused by the metallic Cu particle networks was observed. The percolated Cu/YIG granular composites show simultaneous negative permittivity and permeability spectra under external magnetic fields.

  16. High frequency and allele-specific differences of BRCA1 founder mutations in breast cancer and ovarian cancer patients from Belarus.

    PubMed

    Bogdanova, N V; Antonenkova, N N; Rogov, Y I; Karstens, J H; Hillemanns, P; Dörk, T

    2010-10-01

    Breast cancer and ovarian cancer are common malignancies in Belarus accounting for about 3500 and 800 new cases per year, respectively. For breast cancer, the rates and age of onset appear to vary significantly in regions differentially affected by the Chernobyl accident. We assessed the frequency and distribution of three BRCA1 founder mutations 5382insC, 4153delA and Cys61Gly in two hospital-based series of 1945 unselected breast cancer patients and of 201 unselected ovarian cancer patients from Belarus as well as in 1019 healthy control females from the same population. Any of these mutations were identified in 4.4% of the breast cancer patients, 26.4% of the ovarian cancer patients and 0.5% of the controls. In the breast cancer patients, BRCA1 mutations were strongly associated with earlier age at diagnosis, with oestrogen receptor (ER) negative tumours and with a first-degree family history of breast cancer, although only 35% of the identified BRCA1 mutation carriers had such a family history. There were no marked differences in the regional distribution of BRCA1 mutations, so that the significant differences in age at diagnosis and family history of breast cancer patients from areas afflicted by the Chernobyl accident could not be explained by BRCA1. We next observed a higher impact and a shifted mutational spectrum of BRCA1 in the series of Byelorussian ovarian cancer patients where the three founder mutations accounted for 26.4% (53/201). While the Cys61Gly mutation appeared underrepresented in ovarian cancer as compared with breast cancer cases from the same population (p = 0.01), the 4153delA mutation made a higher contribution to ovarian cancer than to breast cancer (p < 0.01). BRCA1 mutations were significantly enriched among ovarian cancer cases with a first-degree family history of breast or ovarian cancer, whereas the median age at ovarian cancer diagnosis was not different between mutation carriers and non-carriers. Taken together, these results

  17. Plasma production and heating in a tandem mirror central cell by radio-frequency waves in the ion cyclotron frequency range

    NASA Astrophysics Data System (ADS)

    Golovato, S. N.; Brau, K.; Casey, J.; Coleman, J.; Gerver, M. J.; Guss, W.; Hallock, G.; Horne, S.; Irby, J.; Kumazawa, R.; Kesner, J.; Lane, B.; Machuzak, J.; Moran, T.; Myer, R.; Post, R. S.; Sevillano, E.; Smith, D. K.; Sullivan, J. D.; Torti, R.; Wang, L.; Yasaka, Y.; Yao, X. Z.; Zielinski, J.

    1988-12-01

    Plasma production and heating in the central cell of the Tara tandem mirror [Nucl. Fusion 22, 549 (1982); Plasma Physics and Controlled Nuclear Fusion Research, 1986, Proceedings of the 11th International Conference, Kyoto, Japan (IAEA, Vienna, 1987), Vol. 2, p. 251] have been studied. Using radio-frequency excitation by a slot antenna in the ion cyclotron frequency range (ICRF), plasmas with a peak β⊥ of 3%, density of 4×1012 cm-3, ion temperature of 800 eV, and electron temperature of 75-100 eV were routinely produced. The plasma radius decreased with increasing ICRF power, causing reduced ICRF coupling and saturation of the plasma beta. About 70% of the applied ICRF power can be accounted for in direct heating of both ions and electrons. Wave field measurements have identified the applied ICRF to be the slow, ion cyclotron wave. In operation without end plugging, the plasma parameters were limited by poor axial confinement and the requirements for maintenance of magnetohydrodynamic stability and microstability.

  18. Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies).

    PubMed

    Chen, Jun; Källman, Thomas; Ma, Xiaofei; Gyllenstrand, Niclas; Zaina, Giusi; Morgante, Michele; Bousquet, Jean; Eckert, Andrew; Wegrzyn, Jill; Neale, David; Lagercrantz, Ulf; Lascoux, Martin

    2012-07-01

    Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.

  19. Microwave soft x-ray microscopy for nanoscale magnetization dynamics in the 5–10 GHz frequency range

    SciTech Connect

    Bonetti, Stefano; Kukreja, Roopali; Chen, Zhao; Spoddig, Detlef; Ollefs, Katharina; Schöppner, Christian; Meckenstock, Ralf; Ney, Andreas; Pinto, Jude; Houanche, Richard; Frisch, Josef; Stöhr, Joachim; Dürr, Hermann A.; Ohldag, Hendrik

    2015-09-10

    In this study, we present a scanning transmission x-ray microscopy setup combined with a novel microwave synchronization scheme in order to study high frequency magnetization dynamics at synchrotron light sources. The sensitivity necessary to detect small changes of the magnetization on short time scales and nanometer spatial dimensions is achieved by combination of the developed excitation mechanism with a single photon counting electronics that is locked to the synchrotron operation frequency. The required mechanical stability is achieved by a compact design of the microscope. Our instrument is capable of creating direct images of dynamical phenomena in the 5-10 GHz range, with 35 nm resolution. When used together with circularly polarized x-rays, the above capabilities can be combined to study magnetic phenomena at microwave frequencies, such as ferromagnetic resonance (FMR) and spin waves. We demonstrate the capabilities of our technique by presenting phase resolved images of a –6 GHz nanoscale spin wave generated by a spin torque oscillator, as well as the uniform ferromagnetic precession with ~0.1° amplitude at –9 GHz in a micrometer-sized cobalt strip.

  20. Microwave absorption studies of Cr-doped Co-U type hexaferrites over 2-18 GHz frequency range

    NASA Astrophysics Data System (ADS)

    Kumar, Sandeep; Meena, Ram Swaroop; Chatterjee, Ratnamala

    2016-11-01

    The effect of Cr3+ ions doping on the electromagnetic (EM) properties of polycrystalline U-type hexaferrite samples: Ba4Co2-3xCr2xFe36O60 (0.0≤x≤0.60, in steps of 0.15) have been studied. The X-ray diffraction (XRD) studies confirmed the formation of single U-type hexaferrite phase in all the prepared samples. Le Bail refinement of XRD patterns was used to calculate the lattice parameters 'a' and 'c'. The room temperature M-H studies indicate that the saturation magnetization (Ms) decreases and coercivity (Hc) increases with increasing Cr3+ ions concentration. The complex permittivity (ε* = ε ‧ - i ε ″) and permeability (μ* = μ ‧ - i μ ″) measurement were carried out using vector network analyser (VNA) over 2-18 GHz frequency range. The complex permeability (μ* = μ ‧ - μ ″) spectra clearly observed the ferromagnetic resonance (FMR) phenomenon in all the prepared samples. The maximum microwave absorption (MWA) of 99.97% (or minimum reflection loss RLmin=-34.90 dB) was observed for Ba4Co1.1Cr0.6Fe36O60 sample at 8.2 GHz frequency with 1.7 mm absorber thickness. The RLmin peak was found to shift towards higher microwave (MW) frequency with increase in Cr3+ ions concentration.

  1. Frequency-based nanoparticle sensing over large field ranges using the ferromagnetic resonances of a magnetic nanodisc

    NASA Astrophysics Data System (ADS)

    Albert, Maximilian; Beg, Marijan; Chernyshenko, Dmitri; Bisotti, Marc-Antonio; Carey, Rebecca L.; Fangohr, Hans; Metaxas, Peter J.

    2016-11-01

    Using finite element micromagnetic simulations, we study how resonant magnetisation dynamics in thin magnetic discs with perpendicular anisotropy are influenced by magnetostatic coupling to a magnetic nanoparticle. We identify resonant modes within the disc using direct magnetic eigenmode calculations and study how their frequencies and spatial profiles are changed by the nanoparticle’s stray magnetic field. We demonstrate that particles can generate shifts in the resonant frequency of the disc’s fundamental mode which exceed resonance linewidths in recently studied spin torque oscillator devices. Importantly, it is shown that the simulated shifts can be maintained over large field ranges (here up to 1 T). This is because the resonant dynamics (the basis of nanoparticle detection here) respond directly to the nanoparticle stray field, i.e. detection does not rely on nanoparticle-induced changes to the magnetic ground state of the disc. A consequence of this is that in the case of small disc-particle separations, sensitivities to the particle are highly mode- and particle-position-dependent, with frequency shifts being maximised when the intense stray field localised directly beneath the particle can act on a large proportion of the disc’s spins that are undergoing high amplitude precession.

  2. Microwave soft x-ray microscopy for nanoscale magnetization dynamics in the 5–10 GHz frequency range

    SciTech Connect

    Bonetti, Stefano Chen, Zhao; Kukreja, Roopali; Spoddig, Detlef; Schöppner, Christian; Meckenstock, Ralf; Ollefs, Katharina; Ney, Andreas; Pinto, Jude; Houanche, Richard; Frisch, Josef; Stöhr, Joachim; Dürr, Hermann A.; Ohldag, Hendrik

    2015-09-15

    We present a scanning transmission x-ray microscopy setup combined with a novel microwave synchronization scheme for studying high frequency magnetization dynamics at synchrotron light sources. The sensitivity necessary to detect small changes in the magnetization on short time scales and nanometer spatial dimensions is achieved by combining the excitation mechanism with single photon counting electronics that is locked to the synchrotron operation frequency. Our instrument is capable of creating direct images of dynamical phenomena in the 5-10 GHz range, with high spatial resolution. When used together with circularly polarized x-rays, the above capabilities can be combined to study magnetic phenomena at microwave frequencies, such as ferromagnetic resonance (FMR) and spin waves. We demonstrate the capabilities of our technique by presenting phase resolved images of a ∼6 GHz nanoscale spin wave generated by a spin torque oscillator, as well as the uniform ferromagnetic precession with ∼0.1° amplitude at ∼9 GHz in a micrometer-sized cobalt strip.

  3. Microwave soft x-ray microscopy for nanoscale magnetization dynamics in the 5-10 GHz frequency range

    NASA Astrophysics Data System (ADS)

    Bonetti, Stefano; Kukreja, Roopali; Chen, Zhao; Spoddig, Detlef; Ollefs, Katharina; Schöppner, Christian; Meckenstock, Ralf; Ney, Andreas; Pinto, Jude; Houanche, Richard; Frisch, Josef; Stöhr, Joachim; Dürr, Hermann A.; Ohldag, Hendrik

    2015-09-01

    We present a scanning transmission x-ray microscopy setup combined with a novel microwave synchronization scheme for studying high frequency magnetization dynamics at synchrotron light sources. The sensitivity necessary to detect small changes in the magnetization on short time scales and nanometer spatial dimensions is achieved by combining the excitation mechanism with single photon counting electronics that is locked to the synchrotron operation frequency. Our instrument is capable of creating direct images of dynamical phenomena in the 5-10 GHz range, with high spatial resolution. When used together with circularly polarized x-rays, the above capabilities can be combined to study magnetic phenomena at microwave frequencies, such as ferromagnetic resonance (FMR) and spin waves. We demonstrate the capabilities of our technique by presenting phase resolved images of a ˜6 GHz nanoscale spin wave generated by a spin torque oscillator, as well as the uniform ferromagnetic precession with ˜0.1° amplitude at ˜9 GHz in a micrometer-sized cobalt strip.

  4. Microwave soft x-ray microscopy for nanoscale magnetization dynamics in the 5–10 GHz frequency range

    DOE PAGES

    Bonetti, Stefano; Kukreja, Roopali; Chen, Zhao; ...

    2015-09-10

    In this study, we present a scanning transmission x-ray microscopy setup combined with a novel microwave synchronization scheme in order to study high frequency magnetization dynamics at synchrotron light sources. The sensitivity necessary to detect small changes of the magnetization on short time scales and nanometer spatial dimensions is achieved by combination of the developed excitation mechanism with a single photon counting electronics that is locked to the synchrotron operation frequency. The required mechanical stability is achieved by a compact design of the microscope. Our instrument is capable of creating direct images of dynamical phenomena in the 5-10 GHz range,more » with 35 nm resolution. When used together with circularly polarized x-rays, the above capabilities can be combined to study magnetic phenomena at microwave frequencies, such as ferromagnetic resonance (FMR) and spin waves. We demonstrate the capabilities of our technique by presenting phase resolved images of a –6 GHz nanoscale spin wave generated by a spin torque oscillator, as well as the uniform ferromagnetic precession with ~0.1° amplitude at –9 GHz in a micrometer-sized cobalt strip.« less

  5. Dynamic Tensile Cracking in Slopes and the Possible Existence of Seismic Rayleigh Waves in a High Frequency Range

    NASA Astrophysics Data System (ADS)

    Uenishi, K.

    2011-12-01

    In the previous investigations (Earthq. Eng. Struct. Dyn. 2000, Int. J. Geomech. 2010, Rock Mech. Rock Eng. 2010) we have shown the possibility of evaluating the mechanical characteristics of relevant seismic waves from earthquake-induced dynamic structural failure patterns. Slopes are one of the typical structures that may experience mechanical destabilization by seismic waves and thus can be used as "sensors" to detect specific properties of the waves, some of which, especially those related to high frequencies, might be difficult to be identified by using ordinary seismological recordings. One notable example is the fill slopes in the Midorigaoka area in Sendai City, Japan, where the dynamic loading associated with the 1978 Miyagi-ken-oki earthquake (Japan Meteorological Agency Magnitude Mj = 7.4) generated crack openings in the top surface along the upper edge (crest). Although the slopes were reinforced by steel pipe piles after this 1978 event, tensile cracking was induced again along the upper edge by the off the Pacific coast of Tohoku earthquake in March, 2011 (moment magnitude Mw = 9.0). Similar tensile cracks were found not only in California after the 1906 and 1957 San Francisco and the 1989 Loma Prieta earthquakes but also in the South Island along the cliff edge at Redcliffs, Sumner and Sumner Head on the occasion of the February 2011 Christchurch, New Zealand, earthquake (Mw = 6.1). In this study, using the moving particle semi-implicit (MPS) method, we perform two-dimensional numerical simulations for body or Rayleigh surface wave interaction with an archetypal linear elastic slope. The results suggest, at least from the stress point of view, that in order to systematically explain the generation mechanism of the tensile cracking, it may be more reasonable to assume the existence of Rayleigh waves in a high frequency range. That is, body waves and low-frequency Rayleigh waves may not be able to generate such failure patterns. Further analysis shows

  6. Steady-state visual evoked potentials in the low frequency range in migraine: a study of habituation and variability phenomena.

    PubMed

    de Tommaso, Marina; Stramaglia, Sebastiano; Schoffelen, Jan Mathijs; Guido, Marco; Libro, Giuseppe; Losito, Luciana; Sciruicchio, Vittorio; Sardaro, Michele; Pellicoro, Mario; Puca, Franco Michele

    2003-08-01

    Previous studies have revealed that migraine patients display an increased photic driving to flash stimuli in the medium frequency range. The aim of this study was to perform a topographic analysis of steady-state visual evoked potentials (SVEPs) in the low frequency range (3-9 Hz), evaluating the temporal behaviour of the F1 amplitude by investigating habituation and variability phenomena. The main component of SVEPs, the F1, demonstrated an increased amplitude in several channels at 3 Hz. Behaviour of F1 amplitude was rather variable over time, and the wavelet-transform standard deviation was increased in migraine patients at a low stimulus rate. The discriminative value of the F1 mean amplitude and variability index, tested by both an artificial neural network classifier and a support vector machine, were high according to both methods. The increased photic driving in migraine should be subtended by a more generic abnormality of visual reactivity instead of a selective impairment of a visual subsystem. Temporal behaviour of SVEPs is not influenced by a clear tendency to habituation, but the F1 amplitude seemed to change in a complex way, which is better described by variability phenomena. An increased variability in response to flicker stimuli in migraine patients could be interpreted as an overactive regulation mechanism, prone to instability and consequently to headache attacks, whether spontaneous or triggered.

  7. Plasma density in discharge sustained in inhomogeneous gas flow by high-power radiation in the terahertz frequency range

    NASA Astrophysics Data System (ADS)

    Vodopyanov, A. V.; Glyavin, M. Yu.; Golubev, S. V.; Luchinin, A. G.; Razin, S. V.; Safronova, M. I.; Sidorov, A. V.; Fokin, A. P.

    2017-02-01

    We have measured the density of plasma (electron concentration) in discharge maintained in inhomogeneous argon flow under the action of high-power pulsed radiation of gyrotron (frequency, 0.67 THz; power 40 kW; pulse duration, 20-30 μs) in a range of background gas pressures in the discharge chamber from 10-3 to 300 Torr. The electron concentration at low pressures (10-3 to 7 Torr) was determined using Starkeffect induced broadening of the Hα atomic emission line (656.3 nm) of hydrogen present in discharge as a small impurity in residual gases. The maximum observed Stark broadening of the Hα line corresponded to a plasma density on the order of 2 × 1016 cm-3, which exceeded the critical value for the given frequency of radiation sustaining the discharge. At background pressures above 7 Torr, the plasma density was estimated from analysis of the spatiotemporal patterns and waveforms of discharge glow in the visible spectral range. These estimations gave electron concentrations on the level of (1-2) × 1015 cm-3.

  8. Optimal frequency ranges for extracting information on cardiovascular autonomic control from the blood pressure and pulse interval spectrograms in mice.

    PubMed

    Baudrie, Véronique; Laude, Dominique; Elghozi, Jean-Luc

    2007-02-01

    The analysis of blood pressure (BP) and heart rate (HR) variability by spectral methods has proven a useful tool in many animal species for the assessment of the vagal and sympathetic contributions to oscillations of BP and HR. Continuous BP measurements obtained in mice by telemetry were used to characterize the spectral bandwidths of autonomic relevance by using an approach with no a priori. The paradigm was based on the autonomic blockades obtained with conventional drugs (atropine, prazosin, atenolol). The spectral changes were estimated in all of the combinations of spectral bandwidths. The effect of hydralazine was also tested using the same systematic analysis, to detect the zones of sympathetic activation resulting reflexly from the vasodilatory action of the drug. Two zones of interest in the study of the autonomic control of BP and HR were observed. The first zone covered the 0.15-0.60 Hz range of the systolic BP spectrum and corresponds to the low-frequency zone (or Mayer waves). This zone reflects sympathetic control since the power spectral density of this zone was significantly reduced with alpha1-adrenoceptor blockade (prazosin), while it was significantly amplified as a result of a reflex sympathetic activation (hydralazine). The second zone covered the 2.5-5.0 Hz range of the pulse interval spectrum and corresponded to the high-frequency zone (respiratory sinus arrhythmia) under vagal control (blocked by atropine). These zones are recommended for testing the autonomic control of circulation in mice.

  9. High-sensitivity operation of single-beam optically pumped magnetometer in a kHz frequency range

    DOE PAGES

    Savukov, Igor Mykhaylovich; Kim, Y. J.; Shah, V.; ...

    2017-02-02

    Here, optically pumped magnetometers (OPM) can be used in various applications, from magnetoencephalography to magnetic resonance imaging and nuclear quadrupole resonance (NQR). OPMs provide high sensitivity and have the significant advantage of non-cryogenic operation. To date, many magnetometers have been demonstrated with sensitivity close to 1 fT, but most devices are not commercialized. Most recently, QuSpin developed a model of OPM that is low cost, high sensitivity, and convenient for users, which operates in a single-beam configuration. Here we developed a theory of single-beam (or parallel two-beam) magnetometers and showed that it is possible to achieve good sensitivity beyond theirmore » usual frequency range by tuning the magnetic field. Experimentally we have tested and optimized a QuSpin OPM for operation in the frequency range from DC to 1.7 kHz, and found that the performance was only slightly inferior despite the expected decrease due to deviation from the spin-exchange relaxation-free regime.« less

  10. High-sensitivity operation of single-beam optically pumped magnetometer in a kHz frequency range

    NASA Astrophysics Data System (ADS)

    Savukov, I.; Kim, Y. J.; Shah, V.; Boshier, M. G.

    2017-03-01

    Optically pumped magnetometers (OPM) can be used in various applications, from magnetoencephalography to magnetic resonance imaging and nuclear quadrupole resonance (NQR). OPMs provide high sensitivity and have the significant advantage of non-cryogenic operation. To date, many magnetometers have been demonstrated with sensitivity close to 1 fT, but most devices are not commercialized. Most recently, QuSpin developed a model of OPM that is low cost, high sensitivity, and convenient for users, which operates in a single-beam configuration. Here we developed a theory of single-beam (or parallel two-beam) magnetometers and showed that it is possible to achieve good sensitivity beyond their usual frequency range by tuning the magnetic field. Experimentally we have tested and optimized a QuSpin OPM for operation in the frequency range from DC to 1.7 kHz, and found that the performance was only slightly inferior despite the expected decrease due to deviation from the spin-exchange relaxation-free regime.

  11. The effects of sampling frequency on the climate statistics of the European Centre for Medium-Range Weather Forecasts

    SciTech Connect

    Phillips, T.J.; Gates, W.L. ); Arpe, K. )

    1992-12-20

    The effects of sampling frequency on the first- and second-moment statistics of selected European Centre for Medium-Range Weather Forecasts (ECMWF) model variables are investigated in a simulation of perpetual July' with a diurnal cycle included and with surface and atmospheric fields saved at hourly intervals. The shortest characteristic time scales are those of ground heat fluxes and temperatures, precipitation and runoff, convective processes, cloud properties, and atmospheric vertical motion, while the longest time scales are exhibited by soil temperature and moisture, surface pressure, and atmospheric specific humidity, temperature, and wind. The time scales of surface heat and momentum fluxes and of convective processes are substantially shorter over land than over oceans. An appropriate sampling frequency for each model variable is obtained by comparing the estimates of first- and second-moment statistics determined at intervals ranging from 2 to 24 hours with the best' estimates obtained from hourly sampling. Relatively accurate estimation of first- and second-moment climate statistics can be achieved by sampling a model variable at intervals that usually are longer than the bandwidth of its time series but that often are shorter than its characteristic time scale. The superior estimates of first-moment statistics are accompanied by inferior estimates of the variance of the daily means due to the presence of systematic biases, but these probably can be avoided by defining a different measure of low-frequency variability. Estimates of the intradiurnal variance of accumulated precipitation and surface runoff also are strongly impacted by the length of the storage interval. In light of these results, several alternative strategies for storage of the EMWF model variables are recommended. 20 refs., 9 figs., 1 tab.

  12. Cyclic loading experiments to measure material response over a broad frequency range: from tickling of rocks to squeezing of moons

    NASA Astrophysics Data System (ADS)

    McCarthy, C.; Takei, Y.; Cooper, R. F.; Savage, H. M.

    2014-12-01

    Seismology provides powerful methods for imaging the interior of the Earth, not only through differences in seismic velocities, but also through attenuation contrasts. As seismic waves travel through the Earth they are attenuated in accordance with the viscoelastic properties of the material through which they pass. With proper constraints, we will someday be able to use seismic attenuation data as a prospecting tool to determine the grain size, temperature, pressure, melt content, and water content of the material along the ray path. Furthermore, it should be possible to determine active deformation structure, such as crystallographic preferred orientations that form in response to far-field natural tectonic loading. Laboratory studies are striving to provide these needed constraints. Using analogues to mantle rock, we isolate and scrutinize the physics of how microstructural elements affect macroscopic properties of attenuation and steady-state viscosity. An organic analogue, borneol, was used to measure the effects of grain size, temperature, and melt content over a broad frequency range. In these experiments, grain boundary processes were found to play a major role. Polycrystalline ice, which can be considered a rock analogue, has been used to explore the effect of accumulated strain on attenuation, particularly in material that is actively deforming via dislocation creep. Here, defect concentration and substructure are important. I will discuss the use of cyclic loading experiments on borneol and on polycrystalline ice to probe material response from seismic to tidal frequencies, from 10 Hz to 10-4 Hz respectively. These experiments, then, inform our knowledge of viscoelastic behavior of geologic materials at not only seismic frequencies, but also the tidal forcing frequencies experienced by tidewater glaciers and icy satellites.

  13. Intermediate frequency band digitized high dynamic range radiometer system for plasma diagnostics and real-time Tokamak control

    SciTech Connect

    Bongers, W. A.; Beveren, V. van; Westerhof, E.; Goede, A. P. H.; Krijger, B.; Berg, M. A. van den; Graswinckel, M. F.; Schueller, F. C.; Thoen, D. J.; Nuij, P. J. W. M.; Baar, M. R. de; Donne, A. J. H.; Hennen, B. A.; Kantor, M.

    2011-06-15

    An intermediate frequency (IF) band digitizing radiometer system in the 100-200 GHz frequency range has been developed for Tokamak diagnostics and control, and other fields of research which require a high flexibility in frequency resolution combined with a large bandwidth and the retrieval of the full wave information of the mm-wave signals under investigation. The system is based on directly digitizing the IF band after down conversion. The enabling technology consists of a fast multi-giga sample analog to digital converter that has recently become available. Field programmable gate arrays (FPGA) are implemented to accomplish versatile real-time data analysis. A prototype system has been developed and tested and its performance has been compared with conventional electron cyclotron emission (ECE) spectrometer systems. On the TEXTOR Tokamak a proof of principle shows that ECE, together with high power injected and scattered radiation, becomes amenable to measurement by this device. In particular, its capability to measure the phase of coherent signals in the spectrum offers important advantages in diagnostics and control. One case developed in detail employs the FPGA in real-time fast Fourier transform (FFT) and additional signal processing. The major benefit of such a FFT-based system is the real-time trade-off that can be made between frequency and time resolution. For ECE diagnostics this corresponds to a flexible spatial resolution in the plasma, with potential application in smart sensing of plasma instabilities such as the neoclassical tearing mode (NTM) and sawtooth instabilities. The flexible resolution would allow for the measurement of the full mode content of plasma instabilities contained within the system bandwidth.

  14. Intermediate frequency band digitized high dynamic range radiometer system for plasma diagnostics and real-time Tokamak control.

    PubMed

    Bongers, W A; van Beveren, V; Thoen, D J; Nuij, P J W M; de Baar, M R; Donné, A J H; Westerhof, E; Goede, A P H; Krijger, B; van den Berg, M A; Kantor, M; Graswinckel, M F; Hennen, B A; Schüller, F C

    2011-06-01

    An intermediate frequency (IF) band digitizing radiometer system in the 100-200 GHz frequency range has been developed for Tokamak diagnostics and control, and other fields of research which require a high flexibility in frequency resolution combined with a large bandwidth and the retrieval of the full wave information of the mm-wave signals under investigation. The system is based on directly digitizing the IF band after down conversion. The enabling technology consists of a fast multi-giga sample analog to digital converter that has recently become available. Field programmable gate arrays (FPGA) are implemented to accomplish versatile real-time data analysis. A prototype system has been developed and tested and its performance has been compared with conventional electron cyclotron emission (ECE) spectrometer systems. On the TEXTOR Tokamak a proof of principle shows that ECE, together with high power injected and scattered radiation, becomes amenable to measurement by this device. In particular, its capability to measure the phase of coherent signals in the spectrum offers important advantages in diagnostics and control. One case developed in detail employs the FPGA in real-time fast Fourier transform (FFT) and additional signal processing. The major benefit of such a FFT-based system is the real-time trade-off that can be made between frequency and time resolution. For ECE diagnostics this corresponds to a flexible spatial resolution in the plasma, with potential application in smart sensing of plasma instabilities such as the neoclassical tearing mode (NTM) and sawtooth instabilities. The flexible resolution would allow for the measurement of the full mode content of plasma instabilities contained within the system bandwidth.

  15. Nucleotide variation and identification of novel blast resistance alleles of Pib by allele mining strategy.

    PubMed

    Ramkumar, G; Madhav, M S; Devi, S J S Rama; Prasad, M S; Babu, V Ravindra

    2015-04-01

    Pib is one of significant rice blast resistant genes, which provides resistance to wide range of isolates of rice blast pathogen, Magnaporthe oryzae. Identification and isolation of novel and beneficial alleles help in crop enhancement. Allele mining is one of the best strategies for dissecting the allelic variations at candidate gene and identification of novel alleles. Hence, in the present study, Pib was analyzed by allele mining strategy, and coding and non-coding (upstream and intron) regions were examined to identify novel Pib alleles. Allelic sequences comparison revealed that nucleotide polymorphisms at coding regions affected the amino acid sequences, while the polymorphism at upstream (non-coding) region affected the motifs arrangements. Pib alleles from resistant landraces, Sercher and Krengosa showed better resistance than Pib donor variety, might be due to acquired mutations, especially at LRR region. The evolutionary distance, Ka/Ks and phylogenetic analyzes also supported these results. Transcription factor binding motif analysis revealed that Pib (Sr) had a unique motif (DPBFCOREDCDC3), while five different motifs differentiated the resistance and susceptible Pib alleles. As the Pib is an inducible gene, the identified differential motifs helps to understand the Pib expression mechanism. The identified novel Pib resistant alleles, which showed high resistance to the rice blast, can be used directly in blast resistance breeding program as alternative Pib resistant sources.

  16. The effects of sampling frequency on the climate statistics of the European Centre for Medium-Range Weather Forecasts

    NASA Astrophysics Data System (ADS)

    Phillips, Thomas J.; Gates, W. Lawrence; Arpe, Klaus

    1992-12-01

    The effects of sampling frequency on the first- and second-moment statistics of selected European Centre for Medium-Range Weather Forecasts (ECMWF) model variables are investigated in a simulation of "perpetual July" with a diurnal cycle included and with surface and atmospheric fields saved at hourly intervals. The shortest characteristic time scales (as determined by the e-folding time of lagged autocorrelation functions) are those of ground heat fluxes and temperatures, precipitation and runoff, convective processes, cloud properties, and atmospheric vertical motion, while the longest time scales are exhibited by soil temperature and moisture, surface pressure, and atmospheric specific humidity, temperature, and wind. The time scales of surface heat and momentum fluxes and of convective processes are substantially shorter over land than over oceans. An appropriate sampling frequency for each model variable is obtained by comparing the estimates of first- and second-moment statistics determined at intervals ranging from 2 to 24 hours with the "best" estimates obtained from hourly sampling. Relatively accurate estimation of first- and second-moment climate statistics (10% errors in means, 20% errors in variances) can be achieved by sampling a model variable at intervals that usually are longer than the bandwidth of its time series but that often are shorter than its characteristic time scale. For the surface variables, sampling at intervals that are nonintegral divisors of a 24-hour day yields relatively more accurate time-mean statistics because of a reduction in errors associated with aliasing of the diurnal cycle and higher-frequency harmonics. The superior estimates of first-moment statistics are accompanied by inferior estimates of the variance of the daily means due to the presence of systematic biases, but these probably can be avoided by defining a different measure of low-frequency variability. Estimates of the intradiurnal variance of accumulated

  17. 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.

  18. Design, performance, and grounding aspects of the International Thermonuclear Experimental Reactor ion cyclotron range of frequencies antenna

    SciTech Connect

    Durodié, F. Dumortier, P.; Vrancken, M.; Messiaen, A.; Huygen, S.; Louche, F.; Van Schoor, M.; Vervier, M.; Winkler, K.

    2014-06-15

    ITER's Ion Cyclotron Range of Frequencies (ICRF) system [Lamalle et al., Fusion Eng. Des. 88, 517–520 (2013)] comprises two antenna launchers designed by CYCLE (a consortium of European associations listed in the author affiliations above) on behalf of ITER Organisation (IO), each inserted as a Port Plug (PP) into one of ITER's Vacuum Vessel (VV) ports. Each launcher is an array of 4 toroidal by 6 poloidal RF current straps specified to couple up to 20 MW in total to the plasma in the frequency range of 40 to 55 MHz but limited to a maximum system voltage of 45 kV and limits on RF electric fields depending on their location and direction with respect to, respectively, the torus vacuum and the toroidal magnetic field. A crucial aspect of coupling ICRF power to plasmas is the knowledge of the plasma density profiles in the Scrape-Off Layer (SOL) and the location of the RF current straps with respect to the SOL. The launcher layout and details were optimized and its performance estimated for a worst case SOL provided by the IO. The paper summarizes the estimated performance obtained within the operational parameter space specified by IO. Aspects of the RF grounding of the whole antenna PP to the VV port and the effect of the voids between the PP and the Blanket Shielding Modules (BSM) surrounding the antenna front are discussed. These blanket modules, whose dimensions are of the order of the ICRF wavelengths, together with the clearance gaps between them will constitute a corrugated structure which will interact with the electromagnetic waves launched by ICRF antennas. The conditions in which the grooves constituted by the clearance gaps between the blanket modules can become resonant are studied. Simple analytical models and numerical simulations show that mushroom type structures (with larger gaps at the back than at the front) can bring down the resonance frequencies, which could lead to large voltages in the gaps between the blanket modules and perturb the

  19. A wide range ultra-low power Phase-Locked Loop with automatic frequency setting in 130 nm CMOS technology for data serialisation

    NASA Astrophysics Data System (ADS)

    Firlej, M.; Fiutowski, T.; Idzik, M.; Moroń, J.; Świentek, K.

    2015-12-01

    The design and measurements results of a wide frequency range ultra-low power Phase-Locked Loop (PLL) for applications in readout systems of particle physics detectors are presented. The PLL was fabricated in a 130 nm CMOS technology. To allow the implementation of different data serialisation schemes multiple division factors (6, 8, 10, 16) were implemented in the PLL feedback loop. The main PLL block—VCO works in 16 frequency ranges/modes, switched either manually or automatically. A dedicated automatic frequency mode switching circuit was developed to allow simple frequency tuning. Although the PLL was designed and simulated for a frequency range of 30 MHz-3 GHz, due to the SLVS interface limits, the measurements were done only up to 1.3 GHz. The full PLL functionality was experimentally verified, confirming a very low and frequency scalable power consumption (0.7 mW at 1 GHz).

  20. Comparison of HLA allelic imputation programs.

    PubMed

    Karnes, Jason H; Shaffer, Christian M; Bastarache, Lisa; Gaudieri, Silvana; Glazer, Andrew M; Steiner, Heidi E; Mosley, Jonathan D; Mallal, Simon; Denny, Joshua C; Phillips, Elizabeth J; Roden, Dan M

    2017-01-01

    Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations.

  1. Comparison of HLA allelic imputation programs

    PubMed Central

    Shaffer, Christian M.; Bastarache, Lisa; Gaudieri, Silvana; Glazer, Andrew M.; Steiner, Heidi E.; Mosley, Jonathan D.; Mallal, Simon; Denny, Joshua C.; Phillips, Elizabeth J.; Roden, Dan M.

    2017-01-01

    Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles