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

    PubMed Central

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

    1980-01-01

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

  3. 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.

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

    PubMed Central

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

    2012-01-01

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

  5. 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.

  6. 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).

  7. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

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

  8. Robust Identification of Local Adaptation from Allele Frequencies

    PubMed Central

    Günther, Torsten; Coop, Graham

    2013-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

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

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

    SciTech Connect

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

    1993-03-01

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

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

    PubMed

    van den Berg, Stéphanie M; Service, Susan K

    2012-12-01

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

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-01

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

  14. 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.

  15. 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.

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

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

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

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

    PubMed Central

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

    2007-01-01

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

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

    SciTech Connect

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

    1993-07-01

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

  19. 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).

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

    PubMed

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

    1999-09-01

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

  1. 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.

  2. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

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

    2009-04-01

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

  3. 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

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

    PubMed

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

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    Nussbaum, Francis, Jr.

    1988-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2007-03-01

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

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

    PubMed

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

    2008-12-01

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

  9. Range aliasing in frequency coherent geoacoustic inversion.

    PubMed

    Yardim, Caglar; Gerstoft, Peter; Hodgkiss, William S

    2011-10-01

    This paper discusses the effects of frequency selection on source localization and geoacoustic inversion methods that use frequency coherent objective functions. Matched-field processors based on frequency-coherent objective functions often have rapidly fluctuating range ambiguity surfaces. Insufficient sampling in frequency domain results in range aliasing terms that affect geoacoustic inversion. Range aliasing and its effects on source localization and environmental parameter inversion are demonstrated on data collected during the MAPEX2000 experiment. Guidance for frequency selection to avoid range aliasing is provided.

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

    PubMed Central

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

    1982-01-01

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

  11. 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

  12. 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.

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

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

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

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. Transponder System for High-Frequency Ranging

    NASA Technical Reports Server (NTRS)

    Lichtenberg, C. L.; Shores, P. W.; Kobayashi, H. S.

    1986-01-01

    Transponder system uses phase difference between transmitted and reflected high-frequency radio waves to measure distance to target. To suppress spurious measurements of reflections from objects near target at transmitted frequency and its harmonics, transponder at target generates return signal at half transmitted frequency. System useful in such applications as surveying, docking of ships, and short-range navigation.

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

    PubMed

    Ciesielka, M; Kozioł, P; Krajka, A

    1996-08-15

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

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

    PubMed

    Fung, Tak; Keenan, Kevin

    2014-01-01

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

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

    PubMed

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

    1994-08-15

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

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

    PubMed Central

    Trotter, Meredith V.; Spencer, Hamish G.

    2013-01-01

    Frequency-dependent selection (FDS) remains a common heuristic explanation for the maintenance of genetic variation in natural populations. The pairwise-interaction model (PIM) is a well-studied general model of frequency-dependent selection, which assumes that a genotype’s fitness is a function of within-population intergenotypic interactions. Previous theoretical work indicated that this type of model is able to sustain large numbers of alleles at a single locus when it incorporates recurrent mutation. These studies, however, have ignored the impact of the distribution of fitness effects of new mutations on the dynamics and end results of polymorphism construction. We suggest that a natural way to model mutation would be to assume mutant fitness is related to the fitness of the parental allele, i.e., the existing allele from which the mutant arose. Here we examine the numbers and distributions of fitnesses and alleles produced by construction under the PIM with mutation from parental alleles and the impacts on such measures due to different methods of generating mutant fitnesses. We find that, in comparison with previous results, generating mutants from existing alleles lowers the average number of alleles likely to be observed in a system subject to FDS, but produces polymorphisms that are highly stable and have realistic allele-frequency distributions. PMID:23852384

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

    PubMed

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

    2010-09-01

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

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

    PubMed

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

    2015-05-01

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

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

    PubMed

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

    2014-01-01

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

  6. 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.

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

    PubMed

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

    2016-05-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2006-12-01

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

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

    PubMed

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

    2014-10-01

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

  11. 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

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

    PubMed

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

    2003-01-01

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

  13. Frequency of CCR5Δ32 allele in healthy Bosniak population.

    PubMed

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

    2014-08-28

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

  14. Frequency of CCR5Δ32 allele in healthy Bosniak population

    PubMed Central

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

    2014-01-01

    Recent evidence has demonstrated the role of CCR5Δ32 in a variety of human diseases: from infectious and inflammatory diseases to cancer. Several studies have confirmed that genetic variants in chemokine receptor CCR5 gene are correlated with susceptibility and resistance to HIV infection. A 32-nucleotide deletion within the CCR5 reading frame is associated with decreased susceptibility to HIV acquisition and a slower progression to AIDS. Mean frequency of CCR5Δ32 allele in Europe is approximately 10%. The highest allele frequency is observed among Nordic populations (about 12%) and the lowest in the regions of Southeast Mediterranean (about 5%). Although the frequency of CCR5Δ32 was determined in numerous European populations, there is a lack of studies on this variant in the Bosnia and Herzegovina population. Therefore, the aim of our study was to assess the frequency of CCR5Δ32 allele in the cohort of Bosniaks and compare the results with European reports. CCR5Δ32 was detected by sequence-specific PCR in a sample of 100 healthy Bosniaks (DNA collected 2011-2013). Mean age of the cohort being 58.8 (±10.7) years, with 82% of women. We identified 17 heterozygotes and one mutant homozygote in study group, with mean ∆32 allele frequency of 9.5%. CCR5∆32 allele frequency among Bosniaks is comparable to that found in Caucasian populations and follows the pattern of the north-southern gradient observed for Europe. Further studies on larger cohorts with adequate female-to-male ratio are necessary. PMID:25172974

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

    PubMed

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

    2016-03-01

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

  16. 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.

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

    PubMed Central

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

    1981-01-01

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

  18. 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

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

    PubMed

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

    2002-01-23

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

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

    PubMed

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

    2000-01-01

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

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

    PubMed Central

    Slatkin, M; Muirhead, C A

    2000-01-01

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

  2. 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.

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

    PubMed

    Kofler, Robert; Nolte, Viola; Schlötterer, Christian

    2016-01-01

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

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

    PubMed

    Cassar, M; Farrugia, C; Vidal, C

    2008-05-01

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

  5. 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

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

    PubMed

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

    2016-03-01

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

  7. 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.

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

    PubMed

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

    1998-04-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2007-03-01

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

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525..., which may include the fundamental and/or one or more higher frequencies, which lie within the...

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

    PubMed

    Fazeli, Zahra; Vallian, Sadeq

    2012-12-01

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

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

    PubMed

    Cowell, Robert

    2016-07-01

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

  14. 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.

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

    PubMed Central

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

    1980-01-01

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

  16. 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...

  17. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Frequency range of measurements. 18.309 Section... MEDICAL EQUIPMENT Technical Standards § 18.309 Frequency range of measurements. (a) For field strength measurements: Frequency band in which device operates (MHz) Range of frequency measurements Lowest...

  18. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Frequency range of measurements. 18.309 Section... MEDICAL EQUIPMENT Technical Standards § 18.309 Frequency range of measurements. (a) For field strength measurements: Frequency band in which device operates (MHz) Range of frequency measurements Lowest...

  19. Linear allele-specific long-range amplification: a novel method of long-range molecular haplotyping.

    PubMed

    Wu, Wei-Ming; Tsai, Hsiang-Ju; Pang, Jong-Hwei S; Wang, Tzu-Hao; Wang, Hsin-Shih; Hong, Hong-Shang; Lee, Yun-Shien

    2005-10-01

    Haplotypes have been repeatedly shown to be more powerful than collections of single-locus markers in gene-mapping studies. Various haplotyping methods including statistical estimation are employed but molecular haplotyping, the acquisition of information directly on physical DNA sequences, has been in demand for its accuracy and independence from family pedigrees. We investigated the allelic specificity of long-range PCR, which was successful for long-range haplotyping in recent reports, and found problems of initial mispriming and crossover amplification significantly confounded its application. Based on these observations, we designed a novel method based on linear amplification of a hemizygous DNA segment with a single phosphorothioate-modified oligonucleotide. Our results revealed, with a single nucleotide polymorphism as the discriminative marker, downstream haplotypes of 14-15 kb DNA segment could be confidently scored. With two rounds of the method and five single nucleotide polymorphisms, molecular haplotypes of 29.3 kb spanning the HCR and CDSN genes, two genes associated with the susceptibility of psoriasis, of 11 members, belonging to a CEPH family, were revealed. Clear Mendelian segregation of 35 highly heterozygous SNPs confirmed the accuracy of the method. Problems of low specificity associated with long-range PCR were not observed. The simplicity, along with long-sequence accessibility and feasibility of a single nucleotide difference as the discriminative marker indicated our method holds promise for future gene-mapping studies.

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

    PubMed Central

    2013-01-01

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

  1. 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

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

    PubMed

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

    2013-08-01

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

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

    PubMed

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

    2009-01-01

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

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

    PubMed

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

    2016-05-01

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

  5. 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.

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

    PubMed Central

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

    2011-01-01

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

  7. 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

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

    PubMed

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

    2013-06-01

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

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

    PubMed Central

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

    2003-01-01

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

  10. 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.

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

    PubMed

    Verhulst, Brad; Neale, Michael C

    2016-09-01

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

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

    PubMed

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

    2015-10-21

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

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

    PubMed

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

    2013-07-10

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

  14. 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.

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

    PubMed Central

    Ramasamy, Thirumurugan; Ayyavoo, Jayachitra

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  17. 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.

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

    PubMed

    Racimo, Fernando

    2016-02-01

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

  19. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  2. 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...

  3. 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...

  4. 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...

  5. 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...

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Mork, J.; Sundnes, G.

    1985-03-01

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

  8. 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

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

    PubMed

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

    2016-01-01

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

  10. 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

  11. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 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 carrier... used in the device, without going below 9 kHz (25 MHz for CB receivers), up to the frequency shown...

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 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 carrier... used in the device, without going below 9 kHz (25 MHz for CB receivers), up to the frequency shown...

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

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 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 carrier... used in the device, without going below 9 kHz (25 MHz for CB receivers), up to the frequency shown...

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

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 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 carrier... used in the device, without going below 9 kHz (25 MHz for CB receivers), up to the frequency shown...

  15. 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

  16. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Frequency range of measurements. 18.309 Section 18.309 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL INDUSTRIAL, SCIENTIFIC, AND MEDICAL EQUIPMENT Technical Standards § 18.309 Frequency range of measurements. (a) For field...

  17. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Frequency range of measurements. 18.309 Section 18.309 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL INDUSTRIAL, SCIENTIFIC, AND MEDICAL EQUIPMENT Technical Standards § 18.309 Frequency range of measurements. (a) For field...

  18. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Frequency range of measurements. 18.309 Section 18.309 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL INDUSTRIAL, SCIENTIFIC, AND MEDICAL EQUIPMENT Technical Standards § 18.309 Frequency range of measurements. (a) For field...

  19. 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.

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

    PubMed

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

    1994-04-01

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

  1. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Lin, Wan-Yu; Liu, Nianjun

    2012-01-01

    The presence of missing single-nucleotide polymorphism (SNP) genotypes is common in genetic studies. For studies with low-density SNPs, the most commonly used approach to dealing with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is valid only when the missingness is random. However, a given assay often has a different capability in genotyping heterozygotes and homozygotes, causing the phenomenon of "differential dropout" in the sense that the missing rates of heterozygotes and homozygotes are different. In practice, differential dropout among genotypes exists in even carefully designed studies, such as the data from the HapMap project and the Wellcome Trust Case Control Consortium. Under the assumption of Hardy-Weinberg equilibrium and no genotyping error, we here propose a statistical method to model the differential dropout among different genotypes. Compared with the naïve method, our method provides more accurate allele frequency estimates when the differential dropout is present. To demonstrate its practical use, we further apply our method to the HapMap data and a scleroderma data set. PMID:22719749

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

    PubMed

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

    2012-01-01

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

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

    PubMed

    Pickrell, Joseph K; Pritchard, Jonathan K

    2012-01-01

    Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com. PMID:23166502

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

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

    Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and “ancient” Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com. PMID:23166502

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

    PubMed

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

    2009-12-01

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

  8. 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. PMID:27309543

  9. 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

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

    PubMed

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

    2013-12-01

    We previously documented the lowest frequency of CYP2C9*2 in Mexican indigenous Tepehuanos followed by Mestizos and Mexican-Americans populations, suggesting a negative correlation between the CYP2C9*2 frequency and the degree of Asian ancestry in indigenous Americans. We determined the influence of ethnic admixture components on the CYP2C9 allele distribution in 505 Amerindian from eight indigenous populations through genotyping CYP2C9*2, *3 and *6 alleles by real-time PCR and molecular evaluation of ancestry. The frequencies for CYP2C9*2 were 0.026 in Seris and 0.057 in Mayos, being higher than in Asians (P<0.001). CYP2C9*3 was found in Tarahumaras (0.104), Mayos (0.091), Tepehuanos (0.075), Guarijíos (0.067), Huicholes (0.033) and Coras (0.037), with East Asians having lower frequencies than the former three groups (P<0.001). CYP2C9*6 was not found. The frequency of CYP2C9*2 was lower in Amerindians than in European populations, and higher than their Asian ancestors. The presence of this allele in ethnic groups in Mexico can be explained by European admixture.

  11. Numerical simulation of carpet cloaking device in terahertz frequency range

    NASA Astrophysics Data System (ADS)

    Gill, V. V.; Vozianova, A. V.; Khodzitsky, M. K.

    2015-11-01

    This work is devoted to the numerical calculation of the effective constitutive parameters of the carpet cloaking device and to the numerical simulation of this cloak using finite element method (FEM) for the terahertz frequency range.

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

    PubMed Central

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

    1996-01-01

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

  13. 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.

  14. 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

  15. 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

  16. 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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  20. 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

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

    PubMed Central

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

    2012-01-01

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

  2. 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

  3. Coupled whispering gallery mode resonators in the Terahertz frequency range.

    PubMed

    Preu, S; Schwefel, H G L; Malzer, S; Döhler, G H; Wang, L J; Hanson, M; Zimmerman, J D; Gossard, A C

    2008-05-12

    We report on coupling of two whispering gallery mode resonators in the Terahertz frequency range. Due to the long wavelength in the millimeter to submillimeter range, the resonators can be macroscopic allowing for accurate size and shape control. This is necessary to couple specific modes of two or more resonators. Sets of polyethylene (PE) and quartz disk resonators are demonstrated, with medium (loaded) quality (Q)-factors of 40-800. Both exhibit coinciding resonance frequency spectra over more than ten times the free spectral range. Loading effects of single resonators are investigated which provide strong Q-factor degradation and red-shifts of the resonances in the 0.2% range. By coupling two resonators of the same size, we observe mode splitting, in very good agreement with our numerical calculations.

  4. Investigation of a slot nanoantenna in optical frequency range

    NASA Astrophysics Data System (ADS)

    Dinesh kumar, V.; Asakawa, Kiyoshi

    2009-11-01

    Following the analogy of radio frequency slot antenna and its complementary dipole, we propose the implementation of a slot nanoantenna (SNA) in the optical frequency range. Using finite-difference time-domain (FDTD) method, we investigate the electromagnetic (EM) properties of a SNA formed in a thin gold film and compare the results with the properties of a gold dipole nanoantenna (DNA) of the same dimension as the slot. It is found that the response of the SNA is very similar to the DNA, like their counterparts in the radio frequency (RF) range. The SNA can enhance the near field intensity of incident field which strongly depends on its feedgap dimension. The resonance of the SNA is influenced by its slot length; for the increasing slot length, resonant frequency decreases whereas the sharpness of resonance increases. Besides, the resonance of the SNA is found sensitive to the thickness of metal film, when the latter is smaller than the skin depth. The effect of polarization of incident field on the EM response of the SNA was examined; the field enhancement is optimum when polarization is parallel to the feedgap. Finally, we calculate the radiation patterns of the DNA and SNA and compare them with those of the RF dipole antenna. The radiation pattern of the SNA is found to be independent of its slot length when excited at resonant frequency. To the best of our knowledge, this is the first study on a slot antenna in the optical frequency.

  5. 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.

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

    PubMed

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

    2016-04-01

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

  7. 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.

  8. 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.

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

    PubMed Central

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

    2015-01-01

    It has been 12 years since the Allele Frequency Net Database (AFND; http://www.allelefrequencies.net) was first launched, providing the scientific community with an online repository for the storage of immune gene frequencies in different populations across the world. There have been a significant number of improvements from the first version, making AFND a primary resource for many clinical and scientific areas including histocompatibility, immunogenetics, pharmacogenetics and anthropology studies, among many others. The most widely used part of AFND stores population frequency data (alleles, genes or haplotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex class I chain-related genes (MIC) and a number of cytokine gene polymorphisms. AFND now contains >1400 populations from more than 10 million healthy individuals. Here, we report how the main features of AFND have been updated to include a new section on ‘HLA epitope’ frequencies in populations, a new section capturing the results of studies identifying HLA associations with adverse drug reactions (ADRs) and one for the examination of infectious and autoimmune diseases associated with KIR polymorphisms—thus extending AFND to serve a new user base in these growing areas of research. New criteria on data quality have also been included. PMID:25414323

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

    PubMed Central

    2012-01-01

    Background The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. Results In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952) of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612) were intronic and 9% (n = 464) were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS). Significant (P < 0.01) mean allele frequency differentials between the low and high fertility groups were observed for 720 SNPs (58 NSS). Allele frequencies for 43 of the SNPs were also determined by genotyping the 150 individual animals (Sequenom® MassARRAY). No significant differences (P > 0.1) were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total). Conclusions The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post

  11. Frequency stability requirements for two way range rate tracking

    NASA Technical Reports Server (NTRS)

    Reinhardt, V.

    1975-01-01

    Accuracy limitations to two way range rate Doppler tracking due to master (reference) oscillator frequency instabilities are discussed. Theory is developed to treat both the effects of random and nonrandom oscillator instabilities. The nonrandom instabilities treated are drift, environmental effects, and coherent phase modulation. The effects of random instabilities on range rate accuracy are shown to be describable in terms of sigma y (2, T, tau). For the typical noise processes encountered in precision oscillators, range rate error is related to the more familiar sigma y (tau) and script L (f). Three examples are discussed to show how to determine range rate error from given sigma y (tau) or script L (f) curves, and approximations are developed to simplify the treatment of complex systems. An error analysis of range determined from rate data is also given.

  12. Modeling of long range frequency sweeping for energetic particle modes

    SciTech Connect

    Nyqvist, R. M.; Breizman, B. N.

    2013-04-15

    Long range frequency sweeping events are simulated numerically within a one-dimensional, electrostatic bump-on-tail model with fast particle sources and collisions. The numerical solution accounts for fast particle trapping and detrapping in an evolving wave field with a fixed wavelength, and it includes three distinct collisions operators: Drag (dynamical friction on the background electrons), Krook-type collisions, and velocity space diffusion. The effects of particle trapping and diffusion on the evolution of holes and clumps are investigated, and the occurrence of non-monotonic (hooked) frequency sweeping and asymptotically steady holes is discussed. The presented solution constitutes a step towards predictive modeling of frequency sweeping events in more realistic geometries.

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

    PubMed

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

    2001-04-01

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

  14. 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.

  15. A broadband multifocal metalens in the terahertz frequency range

    NASA Astrophysics Data System (ADS)

    Hashemi, Mahdieh; Moazami, Amin; Naserpour, Mahin; Zapata-Rodríguez, Carlos J.

    2016-07-01

    Metasurfaces, the 2D form of metamaterials with their ability in phase, amplitude and polarization manipulation are widely used in designing optical devices. Efforts to find proper photonic components in the terahertz (THz) range of frequency lead us to adopt metasurfaces as their constituent elements. Here, we conceived a broadband THz lens with an adjustable number and arrangement of focal points. To have a full control over the lens functionality, we used a metasurface with the capability of simultaneously modulating the amplitude and phase of the incident wave. C-shaped ring resonators (CSRRs) with different geometry and orientation capable of simultaneously manipulating phase and amplitude of the scattered fields, are proper choice to design the lens. We show that the introduced lens in a one-dimensional layout has a wide range of working frequencies within the THz spectrum, which can be used in a plethora of applications.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  18. Atmospheric range correction for two-frequency SLR measurements

    NASA Astrophysics Data System (ADS)

    Wijaya, Dudy D.; Brunner, Fritz K.

    2011-09-01

    It has been widely known that the use of two-frequency Satellite Laser Ranging (SLR) system is limited by stringent precision requirements of the range measurements and the proper atmospheric model. Owing to the stringent requirements, this SLR system is impractical for the current requirement of SLR measurements within the framework of global geodetic observing system (GGOS). If in the future this stringent requirement could be met, this SLR system would be an attractive tool to reduce atmospheric propagation effects of SLR and would be of great benefit for the next generation of GGOS design. To anticipate possible future developments of the two-frequency SLR systems, we have developed a new atmospheric correction formula for the two-frequency SLR measurements. The new formula eliminates the total atmospheric density effect including its gradient and provides two terms to calculate the curvature effect and the water vapor distribution effect. While the curvature effect can be calculated by an accurate model, the required information about the water vapor distribution along the propagation path can be calculated using previous developments of optical delay modeling or alternatively using results from microwave measurements. Theoretical simulations using the two-frequency systems of the Graz and TIGO-Concepción stations shows that the new formula completely reduces all propagation effects at any elevation angle above 3° with an accuracy better than 1 mm. However, the required precision for the difference of the two-frequency SLR measurements, i.e. better than 45 μm for a single epoch, exceeds the capability of the current state of the art SLR systems.

  19. Ionospheric Coherence Bandwidth Measurements in the Lower VHF Frequency Range

    NASA Astrophysics Data System (ADS)

    Suszcynsky, D. M.; Light, M. E.; Pigue, M. J.

    2015-12-01

    The United States Department of Energy's Radio Frequency Propagation (RFProp) experiment consists of a satellite-based radio receiver suite to study various aspects of trans-ionospheric signal propagation and detection in four frequency bands, 2 - 55 MHz, 125 - 175 MHz, 365 - 415 MHz and 820 - 1100 MHz. In this paper, we present simultaneous ionospheric coherence bandwidth and S4 scintillation index measurements in the 32 - 44 MHz frequency range collected during the ESCINT equatorial scintillation experiment. 40-MHz continuous wave (CW) and 32 - 44 MHz swept frequency signals were transmitted simultaneously to the RFProp receiver suite from the Reagan Test Site at Kwajalein Atoll in the Marshall Islands (8.7° N, 167.7° E) in three separate campaigns during the 2014 and 2015 equinoxes. Results show coherence bandwidths as small as ~ 1 kHz for strong scintillation (S4 > 0.7) and indicate a high degree of ionospheric variability and irregularity on 10-m spatial scales. Spread-Doppler clutter effects arising from preferential ray paths to the satellite due to refraction off of isolated density irregularities are also observed and are dominant at low elevation angles. The results are compared to previous measurements and available scaling laws.

  20. 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

  1. 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.

  2. A wide range sigma—delta fractional-N frequency synthesizer with adaptive frequency calibration

    NASA Astrophysics Data System (ADS)

    Jianjun, Wei; Hanjun, Jiang; Lingwei, Zhang; Jingjing, Dong; Fule, Li; Zhihua, Wang; Chun, Zhang

    2013-06-01

    A wide range fractional-N frequency synthesizer in 0.18 μm RF CMOS technology is implemented. A switched-capacitors bank LC-tank VCO and an adaptive frequency calibration technique are used to expand the frequency range. A 16-bit third-order sigma—delta modulator with dither is used to randomize the fractional spur. The active area is 0.6 mm2. The experimental results show the proposed frequency synthesizer consumes 4.3 mA from a single 1.8 V supply voltage except for buffers. The frequency range is 1.44-2.11 GHz and the frequency resolution is less than 0.4 kHz. The phase noise is -94 dBc/Hz @ 100 kHz and -121 dBc/Hz @ 1 MHz at the output of the prescaler with a loop bandwidth of approximately 120 kHz. The performance meets the requirements for the multi-band and multi-mode transceiver applications.

  3. 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.

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

    PubMed

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

    2016-10-01

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

  5. 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.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro

    2014-06-01

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

  9. 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.

  10. 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.

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

    PubMed

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

    2014-01-01

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

  12. 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

  13. 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.

  14. 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. PMID:26361047

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

    PubMed

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

    2008-12-01

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

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

    PubMed

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

    1997-01-01

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

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

    PubMed

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

    1999-01-01

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

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

    PubMed

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

    2010-05-24

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

  19. 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

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

    PubMed Central

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

    2013-01-01

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

  1. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 5000. Above 1000 5th harmonic of the highest frequency or 40 GHz, whichever is lower. (2) A... below 10 GHz: to the tenth harmonic of the highest fundamental frequency or to 40 GHz, whichever is... harmonic of the highest fundamental frequency or to 100 GHz, whichever is lower. (3) If the...

  2. Allele frequencies and haplotypes for 28 Y-STRs in Ovambo population.

    PubMed

    Fujihara, Junko; Yuasa, Isao; Muro, Tomonori; Iida, Reiko; Tsubota, Etsuko; Nakamura, Hiroaki; Imamura, Shinji; Yasuda, Toshihiro; Takeshita, Haruo

    2009-07-01

    Y-chromosomal 28 short tandem repeat (STR) loci were investigated in unrelated healthy individuals of the Ovambo population from Namibia (n=54). Sixteen Y-chromosome short tandem repeat (Y-STR) polymorphic loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, GATAH4, DYS437, DYS438, and DYS448) were analyzed using AmpFISTR Yfiler Polymerase Chain Reaction (PCR) Amplification Kit. DYS441-445 and DYS446, DYS447, DYS449, DYS450, DYS459a/b, DYS463 and DYS464a/b/c/d were investigated using a multiplex PCR system. Fifty-one haplotypes were identified in 54 Ovambos. The STR diversity values for Y-STRs loci ranged from 0.036 (DYS392) to 0.900 (DYS 385). PMID:19442559

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

    PubMed

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

    2004-08-01

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

  4. 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.

  5. 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.

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

    PubMed

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

    2015-11-01

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

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

    PubMed

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

    2014-06-01

    Human haplotypes include essential information about SNPs, which in turn provide valuable information for such studies as finding relationships between some diseases and their potential genetic causes, e.g., for Genome Wide Association Studies. Due to expensiveness of directly determining haplotypes and recent progress in high throughput sequencing, there has been an increasing motivation for haplotype assembly, which is the problem of finding a pair of haplotypes from a set of aligned fragments. Although the problem has been extensively studied and a number of algorithms have already been proposed for the problem, more accurate methods are still beneficial because of high importance of the haplotypes information. In this paper, first, we develop a probabilistic model, that incorporates the Minor Allele Frequency (MAF) of SNP sites, which is missed in the existing maximum likelihood models. Then, we show that the probabilistic model will reduce to the Minimum Error Correction (MEC) model when the information of MAF is omitted and some approximations are made. This result provides a novel theoretical support for the MEC, despite some criticisms against it in the recent literature. Next, under the same approximations, we simplify the model to an extension of the MEC in which the information of MAF is used. Finally, we extend the haplotype assembly algorithm HapSAT by developing a weighted Max-SAT formulation for the simplified model, which is evaluated empirically with positive results. PMID:24491253

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

    PubMed Central

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

    2015-01-01

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

  9. 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

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

    PubMed

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

    1991-06-01

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

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

    PubMed

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

    2016-03-01

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

  13. 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

  14. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Section 15.202 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES... is defined as a device operating in a mode in which it has the capability to transmit without receiving an enabling signal. In this mode it is able to select a channel and initiate a network by...

  15. Airborne Gravity Gradiometry Resolves a Full Range of Gravity Frequencies

    NASA Astrophysics Data System (ADS)

    Mataragio, J.; Brewster, J.; Mims, J.

    2007-12-01

    Airborne Full Tensor Gradiometry (Air\\-FTGR) was flown at high altitude coincident with Airborne Gravity (AG) flown in 2003 in West Arnhem Land, Australia. A preliminary analysis of two data sets indicates that the Air\\-FTGR system has the capability of resolving intermediate to long wavelengths features that may be associated with relatively deeper geological structures. A comparison of frequency filtered slices and power spectral density (PSD) for both data sets using the short (> 5 km), intermediate (10 km) and long (20 km) wavelengths reveals that high altitude Air\\-FTGR data show greater response in high frequency anomalies than a conventional Airborne Gravity and matches well with the AG even at the longest wavelengths anomalies. The effect of line spacing and target resolution was examined between the two data sets. Reprocessed gradient and AG data at 2, 4 and 6 km line spacing suggest that Air\\-FTGR could be effectively flown at a comparatively wider line spacing to resolve similar targets the AG would resolve with tighter line spacing. Introduction Airborne Full Tensor Gradiometry (Air\\-FTGR) data have been available to the mining industry since 2002 and their use for geologic applications is well established. However, Air\\-FTGR data has been mostly considered and used in mapping and delineation of near surface geological targets. This is due to the fact that gravity gradiometer measurements are well suited to capture the high frequency signal associated with near\\-surface targets ( Li, 2001). This is possible because the gradiometer signal strength falls off with the cube of the distance to the target. Nonetheless, in recent years there has been an increasing demand from the mining, oil, and gas industry in utilizing Full Tensor Gravity Gradiometer as a mapping tool for both regional and prospect level surveys. Air\\-FTGR as a Regional Mapping Tool Several, relatively low altitude surveys have been successfully flown in Brazil, Canada and Australia

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

    PubMed

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

    1994-09-16

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

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

    PubMed

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

    1997-04-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    Arango, Eliana; Carmona-Fonseca, Jaime

    2013-01-01

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

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

    PubMed

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

    2016-09-01

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

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

    SciTech Connect

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

    1993-01-01

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

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

    PubMed

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

    1996-06-01

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

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

    PubMed

    Dandré, F; Cassaigne, A; Iron, A

    1995-06-01

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

  4. 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})

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

    PubMed

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

    2011-01-01

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

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

    PubMed

    Sulcebe, Genc; Shyti, Erkena

    2016-08-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  10. 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.

  11. Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka).

    PubMed

    McClelland, Erin K; Ming, Tobi J; Tabata, Amy; Kaukinen, Karia H; Beacham, Terry D; Withler, Ruth E; Miller, Kristina M

    2013-09-01

    The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non-neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of FST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations. PMID:24033436

  12. 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.

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

    PubMed

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

    2007-04-01

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

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

    PubMed

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

    2015-04-01

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

  15. 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.

  16. 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

  17. 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

  18. 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.

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

    PubMed

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

    2015-10-01

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

  20. 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.

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

    PubMed

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

    2016-03-01

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

  2. Improvement spatial resolution of frequency modulated continuous wave laser ranging system by splicing equal optical frequency interval sampled signal

    NASA Astrophysics Data System (ADS)

    Shi, Guang; Zhang, Fumin; Qu, Xinghua

    2015-02-01

    A dual interferometry FMCW laser ranging system is presented. The auxiliary interferometer for generating the clock pulses at equally spaced optical frequencies is incorporated into the main interferometer to simplify the system configuration and to compensate the tuning linearity of the laser source. The need of widely tunable laser limits the practical application of the FMCW laser ranging for precision industrial measurement. Splicing sampled signal method is proposed to break though the tuning range of the laser source limitation against the special resolution. In the experiments, 50 μm range resolution at 8.7 m is demonstrated, and this resolution is maintained over the entire measuring range. The measuring range depending on the power and coherence length of the source can reach more than 20 m. The system structure is simple, and the requirement on the tuning range of laser source is reduced in this system.

  3. Buried Object Detection Method Using Optimum Frequency Range in Extremely Shallow Underground

    NASA Astrophysics Data System (ADS)

    Sugimoto, Tsuneyoshi; Abe, Touma

    2011-07-01

    We propose a new detection method for buried objects using the optimum frequency response range of the corresponding vibration velocity. Flat speakers and a scanning laser Doppler vibrometer (SLDV) are used for noncontact acoustic imaging in the extremely shallow underground. The exploration depth depends on the sound pressure, but it is usually less than 10 cm. Styrofoam, wood (silver fir), and acrylic boards of the same size, different size styrofoam boards, a hollow toy duck, a hollow plastic container, a plastic container filled with sand, a hollow steel can and an unglazed pot are used as buried objects which are buried in sand to about 2 cm depth. The imaging procedure of buried objects using the optimum frequency range is given below. First, the standardized difference from the average vibration velocity is calculated for all scan points. Next, using this result, underground images are made using a constant frequency width to search for the frequency response range of the buried object. After choosing an approximate frequency response range, the difference between the average vibration velocity for all points and that for several points that showed a clear response is calculated for the final confirmation of the optimum frequency range. Using this optimum frequency range, we can obtain the clearest image of the buried object. From the experimental results, we confirmed the effectiveness of our proposed method. In particular, a clear image of the buried object was obtained when the SLDV image was unclear.

  4. 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.

  5. 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.

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

    PubMed

    Levine, J E; Yang, S Y

    1995-11-01

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

  7. 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

  8. High-resolution frequency-modulated continuous-wave laser ranging for precision distance metrology applications

    NASA Astrophysics Data System (ADS)

    Shi, Guang; Zhang, Fumin; Qu, Xinghua; Meng, Xiangsong

    2014-12-01

    Frequency-modulated continuous wave (FMCW) laser ranging is one of the most interesting techniques for precision distance metrology. In order to ensure the theoretical measurement range and precision, a narrow linewidth external cavity tunable laser with large tuning range is chosen. In practical situations, the tuning nonlinearity of the laser reduces the measurement precision, hence an auxiliary interferometer is used to measure the laser tuning rate and linearize the frequency ramp. Then, fast Fourier transform algorithm is applied to the resampled signal of the main interferometer, and the full-width at half maximum of the frequency spectrum is narrowed. In the end, the experiments are carried out using the FMCW laser ranging system and demonstrate 50-μm range resolution at 8.7 m.

  9. 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

  10. Widely tunable laser frequency offset lock with 30 GHz range and 5 THz offset.

    PubMed

    Biesheuvel, J; Noom, D W E; Salumbides, E J; Sheridan, K T; Ubachs, W; Koelemeij, J C J

    2013-06-17

    We demonstrate a simple and versatile method to greatly extend the tuning range of optical frequency shifting devices, such as acousto-optic modulators (AOMs). We use this method to stabilize the frequency of a tunable narrow-band continuous-wave (CW) laser to a transmission maximum of an external Fabry-Perot interferometer (FPI) with a tunable frequency offset. This is achieved through a servo loop which contains an in-loop AOM for simple radiofrequency (RF) tuning of the optical frequency over the full 30 GHz mode-hop-free tuning range of the CW laser. By stabilizing the length of the FPI to a stabilized helium-neon (HeNe) laser (at 5 THz offset from the tunable laser) we simultaneously transfer the ~ 1 MHz absolute frequency stability of the HeNe laser to the entire 30 GHz range of the tunable laser. Thus, our method allows simple, wide-range, fast and reproducible optical frequency tuning and absolute optical frequency measurements through RF electronics, which is here demonstrated by repeatedly recording a 27-GHz-wide molecular iodine spectrum at scan rates up to 500 MHz/s. General technical aspects that determine the performance of the method are discussed in detail.

  11. Dielectric response of transformer oil based ferrofluid in low frequency range

    NASA Astrophysics Data System (ADS)

    Rajnak, M.; Kurimsky, J.; Dolnik, B.; Marton, K.; Tomco, L.; Taculescu, A.; Vekas, L.; Kovac, J.; Vavra, I.; Tothova, J.; Kopcansky, P.; Timko, M.

    2013-07-01

    In this article, our experimental study of the dynamic dielectric behaviour of transformer oil-based ferrofluid with magnetite nanoparticles is presented. Frequency-dependent dielectric permittivity and dissipation factor were measured within the frequency range from 20 Hz to 2 MHz by a capacitance method. The ferrofluid samples were placed in a liquid crystal cell, and experiments were carried out in an electromagnetically anechoic chamber. Two polarization processes and corresponding relaxations were revealed within the applied frequency range. Schwarz theory of electric double layer polarization is used to explain the low frequency relaxation maximum. Moreover, the shift of the maximum position towards higher frequencies is observed as the magnetic volume fraction in the ferrofluid increases. The related decrease in relaxation time due to higher counterion mobility is analysed. Reduced electric field intensity due to depolarization field, which is dependent on the particle concentration, is proposed as the reason for the maxima shift. This assumption is wholly supported by a complementary experiment.

  12. Development of Acceleration Sensor and Acceleration Evaluation System for Super-Low-Range Frequencies

    NASA Astrophysics Data System (ADS)

    Asano, Shogo; Matsumoto, Hideki

    2001-05-01

    This paper describes the development process for acceleration sensors used on automobiles and an acceleration evaluation system designed specifically for acceleration at super-low-range frequencies. The features of the newly developed sensor are as follows. 1) Original piezo-bimorph design based on a disc-center-fixed structure achieves pyroeffect cancelling and stabilization of sensor characteristics and enables the detection of the acceleration of 0.0009 G at the super-low-range-frequency of 0.03 Hz. 2) The addition of a self-diagnostic function utilizing the characteristics of piezoceramics enables constant monitoring of sensor failure. The frequency range of acceleration for accurate vehicle motion control is considered to be from DC to about 50 Hz. However, the measurement of acceleration in the super-low-range frequency near DC has been difficult because of mechanical and electrical noise interruption. This has delayed the development of the acceleration sensor for automotive use. We have succeeded in the development of an acceleration evaluation system for super-low-range frequencies from 0.015 Hz to 2 Hz with detection of the acceleration range from 0.0002 G (0.2 gal) to 1 G, as well as the development of a piezoelectric-type acceleration sensor for automotive use.

  13. Numerical analysis of radio-frequency sheath-plasma interactions in the ion cyclotron range of frequencies

    SciTech Connect

    Kohno, H.; Myra, J. R.; D'Ippolito, D. A.

    2012-01-15

    A new finite element numerical scheme for analyzing self-consistent radio-frequency (RF) sheath-plasma interaction problems in the ion cyclotron range of frequencies is applied to various problems represented by simplified models for the tokamak scrape-off layer. The present code incorporates a modified boundary condition, which is called a sheath boundary condition, that couples the radio-frequency waves and sheaths at the material boundaries by treating the sheath as a thin vacuum layer. A series of numerical analyses in one- and two-dimensional domains show several important physical properties, such as the existence of multiple roots, hysteresis effects, presence and characteristics of the sheath-plasma waves, and the phase shift of a reflected slow wave, some of which are newly identified by introducing a spatially varying plasma density and background magnetic field.

  14. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

    2012-01-01

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

  18. 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

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2015-01-01

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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Ultrawideband temperature-dependent dielectric properties of animal liver tissue in the microwave frequency range.

    PubMed

    Lazebnik, Mariya; Converse, Mark C; Booske, John H; Hagness, Susan C

    2006-04-01

    The development of ultrawideband (UWB) microwave diagnostic and therapeutic technologies, such as UWB microwave breast cancer detection and hyperthermia treatment, is facilitated by accurate knowledge of the temperature- and frequency-dependent dielectric properties of biological tissues. To this end, we characterize the temperature-dependent dielectric properties of a representative tissue type-animal liver-from 0.5 to 20 GHz. Since discrete-frequency linear temperature coefficients are impractical and inappropriate for applications spanning wide frequency and temperature ranges, we propose a novel and compact data representation technique. A single-pole Cole-Cole model is used to fit the dielectric properties data as a function of frequency, and a second-order polynomial is used to fit the Cole-Cole parameters as a function of temperature. This approach permits rapid estimation of tissue dielectric properties at any temperature and frequency.

  8. Leg stiffness of older and younger individuals over a range of hopping frequencies.

    PubMed

    Hobara, Hiroaki; Kobayashi, Yoshiyuki; Yoshida, Eiichi; Mochimaru, Masaaki

    2015-04-01

    The purpose of this study was to compare spring-mass behavior between older and younger individuals at a range of hopping frequencies. A total of 14 elderly and 14 young subjects performed in-place hopping in time with a metronome at frequencies of 2.2, 2.6, and 3.0 Hz. Using a spring-mass model, leg stiffness was calculated as the ratio of maximum ground reaction force to maximum center of mass displacement at the middle of the stance phase during ground contact. The lower extremities of both groups behaved like a simple spring-mass system at all three hopping frequencies. Further, statistical analysis revealed the existence of a significant interaction between hopping frequency and age group on leg stiffness. These results suggest that the sensitivity of leg stiffness to accommodate for variations in hopping frequency is likely to differ between elderly and young individuals. PMID:25716326

  9. 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.

  10. 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. PMID:26133825

  11. 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.

  12. 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.

  13. Leg stiffness adjustment for a range of hopping frequencies in humans.

    PubMed

    Hobara, Hiroaki; Inoue, Koh; Muraoka, Tetsuro; Omuro, Kohei; Sakamoto, Masanori; Kanosue, Kazuyuki

    2010-02-10

    The purpose of the present study was to determine how humans adjust leg stiffness over a range of hopping frequencies. Ten male subjects performed in place hopping on two legs, at three frequencies (1.5, 2.2, and 3.0Hz). Leg stiffness, joint stiffness and touchdown joint angles were calculated from kinetic and/or kinematics data. Electromyographic activity (EMG) was recorded from six leg muscles. Leg stiffness increased with an increase in hopping frequency. Hip and knee stiffnesses were significantly greater at 3.0Hz than at 1.5Hz. There was no significant difference in ankle stiffness among the three hopping frequencies. Although there were significant differences in EMG activity among the three hopping frequencies, the largest was the 1.5Hz, followed by the 2.2Hz and then 3.0Hz. The subjects landed with a straighter leg (both hip and knee were extended more) with increased hopping frequency. These results suggest that over the range of hopping frequencies we evaluated, humans adjust leg stiffness by altering hip and knee stiffness. This is accomplished by extending the touchdown joint angles rather than by altering neural activity.

  14. 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...

  15. 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

  16. Absolute frequency measurement for the emission transitions of molecular iodine in the 982 - 985 nm range

    SciTech Connect

    Matyugin, Yu A; Ignatovich, S M; Kuznetsov, Sergei A; Nesterenko, M I; Okhapkin, M V; Pivtsov, V S; Skvortsov, Mikhail N; Bagaev, Sergei N

    2012-03-31

    We report high-precision frequency measurements of the separate hyperfine structure (HFS) components of the emission B - X system transitions of {sup 127}I{sub 2} molecules in the 982 - 985 nm range. To resolve the HFS of the emission lines, advantage was taken of the method of three-level laser spectroscopy. The function of exciting radiation was fulfilled by the second harmonic of a cw Nd : YAG laser, and the probe radiation in the 968 - 998 nm range was generated by an external-cavity diode laser. The output Nd : YAG laser frequency was locked to an HFS component of the absorption transition and the probing laser radiation to the emission transition component. When both frequencies were locked to HFS components with a common upper level, the output diode laser frequency was precisely equal to the emission transition frequency. The output frequency of the thus stabilised diode laser was measured with the help of a femtosecond optical frequency synthesiser based on a Ti : sapphire laser. We present the results of the absolute frequency measurements of 20 HFS components belonging to six vibrational - rotational transitions of the B - X system of iodine [R56(32 - 48)a1, P58(32 - 48)a1, P85(33 - 48)a1, R87(33 - 48a1, R88(33 - 48)a10] and all 15 components of the R86(33 - 48) line. The relative measurement uncertainty is equal to 7 Multiplication-Sign 10{sup -10} and is determined by the frequency instability of the diode laser radiation.

  17. On radio frequency current drive in the ion cyclotron range of frequencies in DEMO and large ignited plasmas

    NASA Astrophysics Data System (ADS)

    Brambilla, Marco; Bilato, Roberto

    2015-02-01

    To explore the possibility of efficient fast wave current drive in an ignited plasma in the ion cyclotron (IC) range of frequency in spite of competition from absorption by ions, we have added to the full-wave toroidal code TORIC a set of subroutines which evaluate absorption by these particles at IC harmonic resonances, using a realistic ‘slowing-down’ distribution function, and taking into account that their Larmor radius is comparable or even larger than the fast wave wavelength. The thermalized population of α-particles is not a serious competitor for power absorption as long as their number density is compatible with maintenance of ignition. By contrast, the energetic slowing down fraction, in spite of its even greater dilution, can absorb from the waves a substantial amount of power at the cyclotron resonance and its harmonics. An extensive exploration both in frequency and in toroidal wavenumbers using the parameters of one of the European versions of DEMO shows that three frequency windows exist in which damping is nevertheless predominantly on the electrons. Designing an antenna capable of shaping the launched spectrum to optimize current drive, however, will not be straightforward. Only in a narrow range when the first IC harmonic of tritium is deep inside the plasma on the high-field side of the magnetic axis, and that of deuterium and helium is still outside on the low-field side, it appears possible to achieve a satisfactory current drive efficiency with a conventional multi-strap antenna, preferentially located in the upper part of the vessel. Exploiting the other two windows at quite low and quite high frequencies is either impossible on first principles, or will demand novel ideas in antenna design.

  18. 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.

  19. Rolling estimations of long range dependence volatility for high frequency S&P500 index

    NASA Astrophysics Data System (ADS)

    Cheong, Chin Wen; Pei, Tan Pei

    2015-10-01

    This study evaluates the time-varying long range dependence behaviors of the S&P500 volatility index using the modified rescaled adjusted range (R/S) statistic. For better computational result, a high frequency rolling bipower variation realized volatility estimates are used to avoid possible abrupt jump. The empirical analysis findings allow us to understand better the informationally market efficiency before and after the subprime mortgage crisis.

  20. 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.

  1. Computerized J-H loop tracer for soft magnetic thick films in the audio frequency range

    NASA Astrophysics Data System (ADS)

    Loizos, G.; Niarchos, D.

    2014-07-01

    A computerized J-H loop tracer for soft magnetic thick films in the audio frequency range is described. It is a system built on a PXI platform combining PXI modules for control signal generation and data acquisition. The physiscal signals are digitized and the respective data strems are processed, presented and recorded in LabVIEW 7.0.

  2. Obtaining eigensolutions for multiple frequency ranges in a single NASTRAN execution

    NASA Technical Reports Server (NTRS)

    Pamidi, P. R.; Brown, W. K.

    1990-01-01

    A novel and general procedure for obtaining eigenvalues and eigenvectors for multiple frequency ranges in a single NASTRAN execution is presented. The scheme is applicable to normal modes analyzes employing the FEER and Inverse Power methods of eigenvalue extraction. The procedure is illustrated by examples.

  3. Semiannual Status Report. [excitation of electromagnetic waves in the whistler frequency range

    NASA Technical Reports Server (NTRS)

    1994-01-01

    During the last six months, we have continued our study of the excitation of electromagnetic waves in the whistler frequency range and the role that these waves will play in the acceleration of electrons and ions in the auroral region. A paper entitled 'Electron Beam Excitation of Upstream Waves in the Whistler Mode Frequency Range' was listed in the Journal of Geophysical Research. In this paper, we have shown that an anisotropic electron beam (or gyrating electron beam) is capable of generating both left-hand and right-hand polarized electromagnetic waves in the whistler frequency range. Since right-hand polarized electromagnetic waves can interact with background electrons and left-hand polarized waves can interact with background ions through cyclotron resonance, it is possible that these beam generated left-hand and right-hand polarized electromagnetic waves can accelerate either ions or electrons (or both), depending on the physical parameters under consideration. We are currently carrying out a comprehensive study of the electromagnetic whistler and lower hybrid like waves observed in the auroral zone using both wave and particle data. Our first task is to identify these wave modes and compare it with particle observations. Using both the DE-1 particle and wave measurements, we can positively identify those electromagnetics lower hybrid like waves as fast magnetosonic waves and the upper cutoff of these waves is the local lower hybrid frequency. From the upper cutoff of the frequency spectrum, one can infer the particle density and the result is in very good agreement with the particle data. Since these electromagnetic lower hybrid like waves can have frequencies extended down to the local ion cyclotron frequency, it practically confirms that they are not whistler waves.

  4. AC electric field induced dielectrophoretic assembly behavior of gold nanoparticles in a wide frequency range

    NASA Astrophysics Data System (ADS)

    Liu, Weiyu; Wang, Chunhui; Ding, Haitao; Shao, Jinyou; Ding, Yucheng

    2016-05-01

    In this work, we focus on frequency-dependence of pearl chain formations (PCF) of gold nanoparticles driven by AC dielectrophoresis (DEP), especially in a low field-frequency range, where induced double-layer charging effect at ideally polarizable surfaces on particle DEP behavior and surrounding liquid motion need not be negligible. As field frequency varies, grown features of DEP assembly structures ranging from low-frequency non-bridged gap to high-frequency single gold nanoparticle-made nanowires bridging the electrodes are demonstrated experimentally. Specifically, at 10 kHz, a kind of novel channel-like structure with parallel opposing banks is formed at the center of interelectrode gap. In stark contrast, at 1 MHz, thin PCF with diameter of 100 nm is created along the shortest distance of the isolation spacing. Moreover, a particular conductive path of nanoparticle chains is produced at 1 MHz in a DEP device embedded with multiple floating electrodes. A theoretical framework taking into account field-induced double-layer polarization at both the particle/electrolyte and electrode/electrolyte interface is developed to correlate these experimental observations with induced-charge electrokinetic (ICEK) phenomenon. And a RC circuit model is helpful in accounting for the formation of this particular non-bridged channel-like structure induced by a low-frequency AC voltage. As compared to thin PCF formed at high field frequency that effectively short circuits the electrode pair, though it is difficult for complete PCF bridging to occur at low frequency, the non-bridged conducting microstructure has potential to further miniaturize the size of electrode gap fabricated by standard micromachining process and may find useful application in biochemical sensing.

  5. The influence of flight speed on the ranging performance of bats using frequency modulated echolocation pulses

    NASA Astrophysics Data System (ADS)

    Boonman, Arjan M.; Parsons, Stuart; Jones, Gareth

    2003-01-01

    Many species of bat use ultrasonic frequency modulated (FM) pulses to measure the distance to objects by timing the emission and reception of each pulse. Echolocation is mainly used in flight. Since the flight speed of bats often exceeds 1% of the speed of sound, Doppler effects will lead to compression of the time between emission and reception as well as an elevation of the echo frequencies, resulting in a distortion of the perceived range. This paper describes the consequences of these Doppler effects on the ranging performance of bats using different pulse designs. The consequences of Doppler effects on ranging performance described in this paper assume bats to have a very accurate ranging resolution, which is feasible with a filterbank receiver. By modeling two receiver types, it was first established that the effects of Doppler compression are virtually independent of the receiver type. Then, used a cross-correlation model was used to investigate the effect of flight speed on Doppler tolerance and range-Doppler coupling separately. This paper further shows how pulse duration, bandwidth, function type, and harmonics influence Doppler tolerance and range-Doppler coupling. The influence of each signal parameter is illustrated using calls of several bat species. It is argued that range-Doppler coupling is a significant source of error in bat echolocation, and various strategies bats could employ to deal with this problem, including the use of range rate information are discussed.

  6. 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.

  7. [Study of the dielectric permeability in the superhigh frequency range of a degraded polyoxybutyrate biopolymer].

    PubMed

    Beliaev, G A; Volova, T G; Drokin, N A; Shepov, V N

    2000-01-01

    The dielectric permeability of the degradable biopolymer polyhydroxybutyrate synthesized by hydrogen-oxidizing bacteria Alcaligenes eutrophus was investigated by the resonance method using original highly sensitive microstrip sensors. For the first time, a linear growth of dielectric permeability (delta epsilon/delta T = 7 x 10(-4) degree-1) due to the flexibility of the polymer chain in the temperature range from 10 to 70 degrees C was revealed. The energy of a bend of the nearest fragments was evaluated (E = 392 K), and its correspondence to the energies of bends of the alcyl groups of low-molecular substances like liquid crystals was established. It was shown that at low values of dielectric permeability in the high-frequency range (epsilon' = 2.25 +/- 0.02), which are stable, in a wide range of frequencies of the electromagnetic field (1 MHz - 1 Hz), polyoxybutyrate can be used in the microwave equipment.

  8. 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.

  9. Observation of harmonically related solar radio zebra patterns in the 1-4 GHz frequency range

    NASA Astrophysics Data System (ADS)

    Sawant, H. S.; Karlický, M.; Fernandes, F. C. R.; Cecatto, J. R.

    2002-12-01

    A unique case of two zebra patterns related harmonically with ratio of ~ 1:2 was observed by distant radio telescopes at São José dos Campos and Ondřejov Observatories. Accompanied zebras show that the ratio of frequencies of the neighboring zebra lines is in the range of 1.009-1.037. There is a tendency of a decrease of this ratio with decreasing frequency within the specific zebra pattern. Both facts speak in favour of plasma emission models for the zebra pattern fine structure in radio burst continua.

  10. Excitation of azimuthal surface modes by relativistic flows of electrons in the high-frequency range

    SciTech Connect

    Girka, V. O.; Girka, I. O.; Pavlenko, I. V.

    2011-05-15

    Excitation of extraordinarily polarized azimuthal surface eigenwaves is shown to be possible in the frequency range above the upper hybrid resonance in waveguides with metal walls which are partially filled by cold magnetoactive plasma. Interaction of these waves with flows of electrons which rotate around the plasma column in the narrow gap separating the plasma from the wall of the waveguide is studied. Conditions of resonant interaction of the beam with the mentioned high-frequency azimuthal surface waves are shown by numerical methods to be reachable ones in the case of enough strong external magnetic fields without passing to the field of ultra-relativistic velocities of the beam.

  11. 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).

  12. 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).

  13. Evaluation of frequency dependent non-linear optical property using long-range correction method

    NASA Astrophysics Data System (ADS)

    Yokoi, Yukina; Ishimaru, Hiroki; Kamiya, Muneaki; Sekino, Hideo

    2015-02-01

    We for the first time performed a systematic evaluation of dynamic second hyperpolarizabilities corresponding to all the third-order Nonlinear Optical (NLO) processes using Time Dependent Density Functional Theory (TDDFT) with exchange functional corrected for long-range interaction. We develop a program system which quantitatively evaluate the frequency dependent non-linear optical property of molecules, and apply to the polyene molecules of different lengths. The dispersion curves obtained for each NLO processes have divergence at the frequency corresponding to the one predicted by Sum Over State (SOS) interpretation of the property.

  14. Fundamental Frequency Range in Japanese and English: The Case of Simultaneous Bilinguals.

    PubMed

    Graham, Calbert

    2014-01-01

    This article reports an experiment to test whether Japanese and English speakers vary their fundamental frequency (f0) range as a function of the language spoken. Speech samples of Japanese-(American) English simultaneous bilinguals (5 males, 5 females; all undergraduates at UC Berkeley) performing comparable reading tasks in their two native languages were analysed. The study builds on a relatively new approach to measuring f0 range that computes its high and low points from tonal targets in the intonational phonology. Unlike in most previous studies where f0 range is traditionally treated as a one-dimensional measure, f0 range in this study is measured along two quasi-independent dimensions: level and span. Findings revealed statistically significant crosslanguage differences between Japanese and English in both dimensions. This provides new insights into the relation between prosodic structure and f0 range in these two typologically different prosodic systems. PMID:25997935

  15. Fundamental Frequency Range in Japanese and English: The Case of Simultaneous Bilinguals.

    PubMed

    Graham, Calbert

    2014-01-01

    This article reports an experiment to test whether Japanese and English speakers vary their fundamental frequency (f0) range as a function of the language spoken. Speech samples of Japanese-(American) English simultaneous bilinguals (5 males, 5 females; all undergraduates at UC Berkeley) performing comparable reading tasks in their two native languages were analysed. The study builds on a relatively new approach to measuring f0 range that computes its high and low points from tonal targets in the intonational phonology. Unlike in most previous studies where f0 range is traditionally treated as a one-dimensional measure, f0 range in this study is measured along two quasi-independent dimensions: level and span. Findings revealed statistically significant crosslanguage differences between Japanese and English in both dimensions. This provides new insights into the relation between prosodic structure and f0 range in these two typologically different prosodic systems.

  16. Clock signal requirement for high-frequency, high dynamic range acquisition systems

    SciTech Connect

    Viscor, Ivo; Halamek, Josef; Villa, Marco

    2005-11-15

    Analog-to-digital converters (ADC's) are increasingly replacing mixers in frequency conversion schemes. To achieve superior performances, in terms of bandwidth and dynamic range, a nearly ideal ADC clock is needed, with a spectral purity higher than the reference signal of the classical mixing scheme. These requirements of spectral purity for the ADC clock are discussed by analyzing in detail the nonuniform sampling process and by characterizing an actual acquisition system. The effect of clock phase imperfections on the output is proportional to the input frequency over sampling frequency ratio. Moreover, at the output we may have a multiple folding of the phase jitter spectrum. These effects are illustrated by three sets of measurements performed using our system: transfer of spurious clock components, aliasing of these components, and transfer of clock phase noise.

  17. Propagation in a shearing plasma. II - Turbulence and the frequency range of pulsar microstructure

    NASA Technical Reports Server (NTRS)

    Harding, A. K.; Tademaru, E.

    1980-01-01

    Numerical calculations are presented which explore the propagation of radio waves and pulses through a turbulent shearing plasma. A stochastic model is used to describe the turbulent velocity field, in which random fluctuations are superposed on a mean profile. Both Gaussian wave packets and shot-noise pulses polarized in the plane of shearing acquire quasi-periodic intensity modulations above the rest-frame plasma frequency. The frequency range over which these modulations appear is shown to depend on the spatial correlation length of the turbulent fluctuations and on their standard deviation from the mean velocity. The period of the modulations is variable from one realization of the random process to the next, and the average period is frequency dependent. The results of these calculations lend further support to a model for pulsar microstructure in which periodic micropulses are pure temporal modulations of the emitted radiation due to propagation effects in magnetospheric shearing regions. It is shown that turbulence on a scale of approximately 10 cm can produce these quasi-periodic modulations over a frequency range comparable to that of observed microstructure.

  18. Design and optimization of an ultra-wide frequency range CMOS divide-by-two circuit

    NASA Astrophysics Data System (ADS)

    Bo, Lu; Niansong, Mei; Hu, Chen; Zhiliang, Hong

    2010-11-01

    A novel toggled flip-flop (TFF) divide-by-two circuit (DTC) and its optimization method based on a large-signal analysis approach are proposed. By reducing the output RC constant in tracking mode and making it large in latching mode, compressing the internal signal swing as well as compensating the current leaked in the latching mode, the operating frequency range is greatly expanded. Implemented in a SMIC 0.13 μm RF CMOS process with a 1.2 V power supply, it can work under an ultra-wide frequency band ranging from 320 MHz to 29.6 GHz. Experimental results show that two phase-locked loops (PLLs) with the proposed DTC can achieve in-band phase noise of -94 dBc/Hz @ 10 kHz under 4224 MHz operating frequency and -84 dBc/Hz @ 10 kHz under 10 GHz operating frequency, respectively. The power consumption of the proposed DTC is reduced by almost 50% compared with the conventional counterparts.

  19. 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.

  20. 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.

  1. [Immunotropic effects of electromagnetic fields in the range of radio- and microwave frequencies].

    PubMed

    Dabrowski, M P; Stankiewicz, W; Sobiczewska, E; Szmigielski, S

    2001-11-01

    On the grounds of reviewed literature and the results of own experiments, the authors present current views on the possible immunotropic influence of low energy electromagnetic fields, in the range of radio- and microwave frequencies. They conclude, that a more systematic and multidisciplinary investigations should be undertaken, comprising the wide spectrum of immune homeostatic tasks, including defensive, immunoregulatory and pro-regenerative capabilities of immune system exposed to rapid environmental spread of different electromagnetic emitters.

  2. 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.

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

    PubMed

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

    2016-01-01

    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. PMID:27388587

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

    PubMed Central

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

    2016-01-01

    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. PMID:27388587

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

    PubMed

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

    2016-07-08

    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.

  6. 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.

  7. Serially homologous ears perform frequency range fractionation in the praying mantis, Creobroter (Mantodea, Hymenopodidae).

    PubMed

    Yager, D D

    1996-04-01

    Unlike most praying mantises that have a single region of auditory sensitivity, species in the genus Creobroter have equally sensitive hearing at 2-4 and at 25-50 kHz and and are relatively insensitivity at 10-15 kHz- they have a W-shaped audiogram. Ultrasonic sensitivity originates from an auditory organ in the ventral midline of the metathorax that closely resembles the ear of other mantises. Ablation experiments demonstrate that low frequency sensitivity derives from a serially homologous mesothoracic auditory organ. Extracellular recordings suggest that these two ears operate largely, if not entirely, independently of one another in the thorax. The low frequency response has a longer latency, more action potentials per stimulus, and different patterns of change with increasing SPL than the high frequency response. Separate interneurons mediate responses in the two frequency ranges, but our evidence suggests that they are two serially homologous sets of cells. Neither auditory organ shows any physiological evidence of directional sensitivity. Ultrasound triggers a set of behaviors in flying hymenopodid mantises much like those in other mantises, but the behavioral significance of low frequency hearing in these animals is still unknown. PMID:8847662

  8. Compensation of laser frequency tuning nonlinearity of a long range OFDR using deskew filter.

    PubMed

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

    2013-02-11

    We present a simple and effective method to compensate the optical frequency tuning nonlinearity of a tunable laser source (TLS) in a long range optical frequency-domain reflectometry (OFDR) by using the deskew filter, where a frequency tuning nonlinear phase obtained from an auxiliary interferometer is used to compensate the nonlinearity effect on the beating signals generated from a main OFDR interferometer. The method can be applied to the entire spatial domain of the OFDR signals at once with a high computational efficiency. With our proposed method we experimentally demonstrated a factor of 93 times improvement in spatial resolution by comparing the results of an OFDR system with and without nonlinearity compensation. In particular we achieved a measurement range of 80 km and a spatial resolution of 20 cm and 1.6 m at distances of 10 km and 80 km, respectively with a short signal processing time of less than 1 s for 5 × 10(6) data points. The improved performance of the OFDR with a high spatial resolution, a long measurement range and a short process time will lead to practical applications in the real-time monitoring, test and measurement of fiber optical communication networks and sensing systems.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. Boosting brain excitability by transcranial high frequency stimulation in the ripple range

    PubMed Central

    Moliadze, Vera; Antal, Andrea; Paulus, Walter

    2010-01-01

    Alleviating the symptoms of neurological diseases by increasing cortical excitability through transcranial stimulation is an ongoing scientific challenge. Here, we tackle this issue by interfering with high frequency oscillations (80–250 Hz) via external application of transcranial alternating current stimulation (tACS) over the human motor cortex (M1). Twenty-one subjects participated in three different experimental studies and they received on separate days tACS at three frequencies (80 Hz, 140 Hz and 250 Hz) and sham stimulation in a randomized order. tACS with 140 Hz frequency increased M1 excitability as measured by transcranial magnetic stimulation-generated motor evoked potentials (MEPs) during and for up to 1 h after stimulation. Control experiments with sham and 80 Hz stimulation were without any effect, and 250 Hz stimulation was less efficient with a delayed excitability induction and reduced duration. After-effects elicited by 140 Hz stimulation were robust against inversion of test MEP amplitudes seen normally under activation. Stimulation at 140 Hz reduced short interval intracortical inhibition, but left intracortical facilitation, long interval cortical inhibition and cortical silent period unchanged. Implicit motor learning was not facilitated by 140 Hz stimulation. High frequency stimulation in the ripple range is a new promising non-invasive brain stimulation protocol to increase human cortical excitability during and after the end of stimulation. PMID:20962008

  15. Dielectric dispersion of water in the frequency range from 10 mHz to 30 MHz.

    PubMed

    Batalioto, F; Duarte, A R; Barbero, G; Neto, A M F

    2010-03-18

    We investigate the dielectric dispersion of water, specially in the low-frequency range, by using the impedance spectroscopy technique. The frequency dependencies of the real R and imaginary chi parts of the impedance could not be explained by means of the usual description of the dielectric properties of the water as an insulating liquid containing ions. This is due to the incomplete knowledge of the parameters entering in the fundamental equations describing the evolution of the system, and on the mechanisms regulating the exchange of charge of the cell with the external circuit. We propose a simple description of our experimental data based on the model of Debye, by invoking a dc conductivity of the cell, related to the nonblocking character of the electrodes. A discussion on the electric circuits able to simulate the cell under investigation, based on bulk and surface elements, is also reported. We find that the simple circuit formed by a series of two parallels of resistance and capacitance is able to reproduce the experimental data concerning the real and imaginary part of the electrical impedance of the cell for frequency larger than 1 Hz. According to this description, one of the parallels takes into account the electrical properties of interface between the electrode and water, and the other of the bulk. For frequency lower than 1 Hz, a good agreement with the experimental data is obtained by simulating the electrical properties of the interface by means of the constant phase element.

  16. Boosting brain excitability by transcranial high frequency stimulation in the ripple range.

    PubMed

    Moliadze, Vera; Antal, Andrea; Paulus, Walter

    2010-12-15

    Alleviating the symptoms of neurological diseases by increasing cortical excitability through transcranial stimulation is an ongoing scientific challenge. Here, we tackle this issue by interfering with high frequency oscillations (80–250 Hz) via external application of transcranial alternating current stimulation (tACS) over the human motor cortex (M1). Twenty-one subjects participated in three different experimental studies and they received on separate days tACS at three frequencies (80 Hz, 140 Hz and 250 Hz) and sham stimulation in a randomized order. tACS with 140 Hz frequency increased M1 excitability as measured by transcranial magnetic stimulation-generated motor evoked potentials (MEPs) during and for up to 1 h after stimulation. Control experiments with sham and 80 Hz stimulation were without any effect, and 250 Hz stimulation was less efficient with a delayed excitability induction and reduced duration. After-effects elicited by 140 Hz stimulation were robust against inversion of test MEP amplitudes seen normally under activation. Stimulation at 140 Hz reduced short interval intracortical inhibition, but left intracortical facilitation, long interval cortical inhibition and cortical silent period unchanged. Implicit motor learning was not facilitated by 140 Hz stimulation. High frequency stimulation in the ripple range is a new promising non-invasive brain stimulation protocol to increase human cortical excitability during and after the end of stimulation.

  17. Dielectric dispersion of water in the frequency range from 10 mHz to 30 MHz.

    PubMed

    Batalioto, F; Duarte, A R; Barbero, G; Neto, A M F

    2010-03-18

    We investigate the dielectric dispersion of water, specially in the low-frequency range, by using the impedance spectroscopy technique. The frequency dependencies of the real R and imaginary chi parts of the impedance could not be explained by means of the usual description of the dielectric properties of the water as an insulating liquid containing ions. This is due to the incomplete knowledge of the parameters entering in the fundamental equations describing the evolution of the system, and on the mechanisms regulating the exchange of charge of the cell with the external circuit. We propose a simple description of our experimental data based on the model of Debye, by invoking a dc conductivity of the cell, related to the nonblocking character of the electrodes. A discussion on the electric circuits able to simulate the cell under investigation, based on bulk and surface elements, is also reported. We find that the simple circuit formed by a series of two parallels of resistance and capacitance is able to reproduce the experimental data concerning the real and imaginary part of the electrical impedance of the cell for frequency larger than 1 Hz. According to this description, one of the parallels takes into account the electrical properties of interface between the electrode and water, and the other of the bulk. For frequency lower than 1 Hz, a good agreement with the experimental data is obtained by simulating the electrical properties of the interface by means of the constant phase element. PMID:20178324

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Morfology of SEE spectral features in a wide pump wave frequency range

    NASA Astrophysics Data System (ADS)

    Sergeev, E. N.; Frolov, V. L.; Grach, S. M.; Kotov, P. V.

    Systematic study of stimulated electromagnetic emission (SEE) stationary spectrum dependence on the pump wave (PW) frequency f_0 was continued. Investigations were performed at the SURA facility for the PW frequency range 4.3≤ f_0 ≤ 9.5 MHz with stepping of ≈ 5-50 kHz including the vicinities of the electron gyroharmonics nfce from n=4 to n=7 for most prominent SEE features like downshifted maximum (DM) and its satellites, narrow and broad continua (NC and BC), upshifted maximum (UM), broad upshifted maximum (BUM), and broad upshifted structure (BUS) (for references see, e.g., Leyser et al., J. Geophys. Res., 1993, v. 98, p. 17597, 1994, Frolov et al., Geophys. Res. Lett., 2001, v. 28, p. 3103). Main attention was paid to maximal and integral intensities of the SEE features and their frequency shifts Δ f from f_0. The results can be summarized as follows. (i) While the SEE qualitative behaviour periodically repeats between successive gyroharmonics, maximal intensity for all of the SEE features is observed for 4fce5fce (except of narrow range below 6 and 7fce) the BC is replaced by a set of DM satellites in the SEE spectrum. (iii) DM intensity decreases with f_0 and DM peak frequency shift increases with f_0 as Δ fDM ˜ 2 f_0\\cdot10-3 across the whole f_0 frequency range, except of narrow ranges near f_0 ≃ nfce, where the DM intensity falls up to the noise level, and Δ fDM decreases up to ≈ 9 kHz. (iv) The UM behaviour is similar for the DM one, but for f_0≃ nfce the maximal UM and minimal DM intensities occur for the same f_0, while the minimal UM is observed for f_0 less by 10-20 kHz in comparison with f_0 for the minimal DM. (v) Maximal BUM intensity is observed for f_0 just above nfce where the frequency shift of BUM peak Δ fBUM ≃ 20 kHz; for f_0 ≳ nfce+30 kHz Δ f

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

    PubMed Central

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

    2015-01-01

    Inosine triphosphatase (ITPA) single nucleotide polymorphisms (SNPs) are strongly associated with protection against ribavirin (RBV)-induced anaemia in European, American and Asian patients; however, there is a paucity of data for Brazilian patients. The aim of this study was to evaluate the ITPA SNP (rs7270101/rs1127354) frequency in healthy and hepatitis C virus (HCV)-infected patients from Brazil and the association with the development of severe anaemia during antiviral therapy. ITPA SNPs were determined in 200 HCV infected patients and 100 healthy individuals by sequencing. Biochemical parameters and haemoglobin (Hb) levels were analysed in 97 patients who underwent antiviral therapy. A combination of AArs7270101+CCrs1127354 (100% ITPase activity) was observed in 236/300 individuals. Anaemia was observed in 87.5% and 86.2% of treated patients with AA (rs7270101) and CC genotypes (rs1127354), respectively. Men with AA (rs7270101) showed a considerable reduction in Hb at week 12 compared to those with AC/CC (p = 0.1475). In women, there was no influence of genotype (p = 0.5295). For rs1127354, men with the CC genotype also showed a sudden reduction in Hb compared to those with AC. Allelic distribution of rs7270101 and rs1127354 shows high rates of the genotypes AA and CC, respectively, suggesting that the study population had a great propensity for developing RBV-induced anaemia. A progressive Hb reduction during treatment was observed; however, this reduction was greater in men at week 12 than in women. PMID:26154744

  4. Spectral investigation of nematic liquid crystals with high optical anisotropy at THz frequency range

    NASA Astrophysics Data System (ADS)

    Chodorow, U.; Parka, J.; Garbat, K.; Pałka, N.; Czupryński, K.

    2012-04-01

    Liquid crystals (LCs) with high optical anisotropy are very desirable for different applications in devices, such as filters, phase shifters, or phase gratings [T. Göbel, P. Meissner, A. Gaebler, M. Koeberle, S. Mueller, and R. Jakoby, Dual-Frequency Switching Liquid Crystal Based Tunable THz Filter, CLEO, Baltimore, MD, 2009; C.-Y. Chen, T.-R. Tsai, C.-L. Pan, and R.-P. Pan, Room temperature terahertz phase shifter based on magnetically controlled birefringence in liquid crystals, Appl. Phys. Lett. 83 (2003), pp. 4497-4499; and C.-J. Lin, C.-H. Lin, Y.-T. Li, R.-P. Pan, and C.-L. Pan, Electrically controlled liquid crystal phase grating for terahertz waves, IEEE Photon. Technol. Lett. 21 (2009), pp. 730-732]. We present spectral studies of LCs with large optical anisotropy in the range from 0.3 to 3 THz. Nematic LC mixtures which have Δn > 0.30 for visible frequency range, i.e., 1825 (Δn = 0.42 at 633 nm) were measured. Properties of LC materials like birefringence, absorption coefficients, and refractive indices for ordinary and extraordinary polarization in THz range were obtained. Orientation of LC was done by a high electric field. Measurements were performed using a TDS spectra 3000 spectrometer.

  5. Optimization of the signal processing in frequency modulated continuous wave laser ranging system

    NASA Astrophysics Data System (ADS)

    Meng, Xiangsong; Zhang, Fumin; Qu, Xinghua

    2015-02-01

    Based on a dual interferometry frequency modulated wave laser (FMCW) laser ranging system, three steps to optimize the signal processing is proposed in this paper. The first step is signal re-sampling, by which the sampling signal is turned to be equal optical frequency intervals. The second step is splicing the re-sampled signal, by which can break though the tuning range of the laser source limitation. The last step is the all-phase pretreatment of the signal, its means that the all-phase Fast Fourier Transformation (apFFT) is used to handle the re-sampled signal, which could reduce the phase error of the signal. The experiments shows that the noise effect due to the tuning nonlinearity of laser can be reduced by re-sampling the signal, 50μm range resolution can be easily obtained by this method, the apFFT is more reliable and effective than FFT in the processing to reduce the phase error and improve the speed of operation.

  6. Nanostructured composite layers for electromagnetic shielding in the GHz frequency range

    NASA Astrophysics Data System (ADS)

    Suchea, M.; Tudose, I. V.; Tzagkarakis, G.; Kenanakis, G.; Katharakis, M.; Drakakis, E.; Koudoumas, E.

    2015-10-01

    We report on preliminary results regarding the applicability of nanostructured composite layers for electromagnetic shielding in the frequency range of 4-20 GHz. Various combinations of materials were employed including poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS), polyaniline, graphene nanoplatelets, carbon nanotubes, Cu nanoparticles and Poly(vinyl alcohol). As shown, paint-like nanocomposite layers consisting of graphene nanoplatelets, polyaniline PEDOT:PSS and Poly(vinyl alcohol) can offer quite effective electromagnetic shielding, similar or even better than that of commercial products, the response strongly depending on their thickness and resistivity.

  7. Comments on finite Larmor radius models for ion cyclotron range of frequencies heating in tokamaks

    SciTech Connect

    Phillips, C.K.; Wilson, J.R.; Hosea, J.C.; Majeski, R.; Smithe, D.N.

    1994-06-01

    The accuracy of standard finite Larmor radius (FLR) models for wave propagation in the ion cyclotron range of frequencies (ICRF) is compared against full hot plasma models. For multiple ion species plasmas, the FLR model is shown to predict the presence of a spurious second harmonic ion-ion type resonance between the second harmonic cyclotron layers of two ion species. It is shown explicitly here that the spurious resonance is an artifact of the FLR models and that no absorption occurs in the plasma as a result of this ``resonance.``

  8. 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.

  9. Range-resolved frequency-agile CO2 lidar measurements of smokestack vapor effluents

    NASA Astrophysics Data System (ADS)

    D'Amico, Francis M.; Vanderbeek, Richard G.; Warren, Russell E.

    1999-11-01

    Range-resolved lidar measurements of chemical vapor output from a smokestack were conducted using a moderate-power (100 millijoules per pulse) frequency-agile CO2 differential absorption lidar (DIAL) system. A 70-foot non-industrial smokestack, erected for the purpose of studying effluent emissions, was used in the experiment. These measurements were conducted for the purpose of obtaining real data to support development of advanced chemical and biological (CB) range- resolved vapor detection algorithms. Plume transmission measurements were made using natural atmospheric backscatter from points at the mouth of the stack and several positions downwind. Controlled releases of triethyl-phosphate (TEP), dimethyl-methylphosphonate (DMMP), and sulfur-hexaflouride (SF6) were performed. Test methodology and experimental results are presented. Effective application of ground-based lidar to the monitoring of smokestack effluents, without the use of fixed targets, is discussed.

  10. 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.

  11. Nonlinear magneto-optical rotation with frequency-modulated light in the geophysical field range

    NASA Astrophysics Data System (ADS)

    Acosta, V.; Ledbetter, M. P.; Rochester, S. M.; Budker, D.; Jackson Kimball, D. F.; Hovde, D. C.; Gawlik, W.; Pustelny, S.; Zachorowski, J.; Yashchuk, V. V.

    2006-05-01

    Recent work investigating resonant nonlinear magneto-optical rotation (NMOR) related to long-lived (τrel˜1s) ground-state atomic coherences has demonstrated potential magnetometric sensitivities exceeding 10-11G/Hz for small (≲1μG ) magnetic fields. In the present work, NMOR using frequency-modulated light (FM NMOR) is studied in the regime where the longitudinal magnetic field is in the geophysical range (˜500mG) , of particular interest for many applications. In this regime a splitting of the FM NMOR resonance due to the nonlinear Zeeman effect is observed. At sufficiently high light intensities, there is also a splitting of the FM NMOR resonances due to ac Stark shifts induced by the optical field, as well as evidence of alignment-to-orientation conversion type processes. The consequences of these effects for FM-NMOR-based atomic magnetometry in the geophysical field range are considered.

  12. 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

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

    PubMed

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

    2014-08-01

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

  14. 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.

  15. 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…

  16. 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.

  17. 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.

  18. 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...

  19. 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. PMID:27307400

  20. 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.

  1. Magnetic relaxation for Mn-based compounds exhibiting the Larmor precession at THz wave range frequencies

    NASA Astrophysics Data System (ADS)

    Mizukami, S.; Iihama, S.; Sasaki, Y.; Sugihara, A.; Ranjbar, R.; Suzuki, K. Z.

    2016-10-01

    Mn-based hard magnets are potentially suitable for advanced ultra-high frequency spintronics applications because they exhibit the Larmor precession of magnetization at THz wave-range frequencies with low magnetic relaxation. However, the low magnetic relaxation properties are not well understood; thus, a more detailed study is necessary. In this study, magnetization precessions in L10 Mn1.54Ga, D022 Mn2.12Ga, and C38 MnAlGe epitaxial films grown on MgO substrates were investigated using an all-optical pump-probe method under a magnetic field of ˜20 kOe. The coherent magnetization precessions at frequencies of more than 0.1, 0.2, and 0.3 THz for the C38 MnAlGe, L10 Mn1.54Ga, and D022 Mn2.12Ga films, respectively, were clearly measured. The effective damping constant for the C38 MnAlGe film was smaller than the previously reported value measured at 10 kOe by a factor of 2, whereas those showed a large angular dependence. The effective damping constants for the L10 Mn1.54Ga and D022 Mn2.12Ga films were independent of the field angle and approximately identical to the values measured at 10 kOe. Thus, it was concluded that the values for the Gilbert damping constant, α, were 0.008 and 0.012 for the L10 Mn1.54Ga and D022 Mn2.12Ga films, respectively. The possible origin of the discrepancy between the experimental and theoretical α values for these films is discussed.

  2. 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

  3. Frequency-division multiplexing in the terahertz range using a leaky-wave antenna

    NASA Astrophysics Data System (ADS)

    Karl, Nicholas J.; McKinney, Robert W.; Monnai, Yasuaki; Mendis, Rajind; Mittleman, Daniel M.

    2015-11-01

    The idea of using radiation in the 0.1-1.0 THz range as carrier waves for free-space wireless communications has attracted growing interest in recent years, due to the promise of the large available bandwidth. Recent research has focused on system demonstrations, as well as the exploration of new components for modulation, beam steering and polarization control. However, the multiplexing and demultiplexing of terahertz signals remains an unaddressed challenge, despite the importance of such capabilities for broadband networks. Using a leaky-wave antenna based on a metal parallel-plate waveguide, we demonstrate frequency-division multiplexing and demultiplexing over more than one octave of bandwidth. We show that this device architecture offers a unique method for controlling the spectrum allocation, by variation of the waveguide plate separation. This strategy, which is distinct from those previously employed in either the microwave or optical regimes, enables independent control of both the centre frequency and bandwidth of multiplexed terahertz channels.

  4. 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.

  5. 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.

  6. Absolute distance measurement with extension of nonambiguity range using the frequency comb of a femtosecond laser

    NASA Astrophysics Data System (ADS)

    Jang, Yoon-Soo; Lee, Keunwoo; Han, Seongheum; Lee, Joohyung; Kim, Young-Jin; Kim, Seung-Woo

    2014-12-01

    We revisit the method of synthetic wavelength interferometry (SWI) for absolute measurement of long distances using the radio-frequency harmonics of the pulse repetition rate of a mode-locked femtosecond laser. Our intention here is to extend the nonambiguity range (NAR) of the SWI method using a coarse virtual wavelength synthesized by shifting the pulse repetition rate. The proposed concept of NAR extension is experimentally verified by measuring a ˜13-m distance with repeatability of 9.5 μm (root-mean-square). The measurement precision is estimated to be 31.2 μm in comparison with an incremental He-Ne laser interferometer. This extended SWI method is found to be well suited for long-distance measurements demanded in the fields of large-scale precision engineering, geodetic survey, and future space missions.

  7. Fiber optic probe of free electron evanescent fields in the optical frequency range

    SciTech Connect

    So, Jin-Kyu MacDonald, Kevin F.; Zheludev, Nikolay I.

    2014-05-19

    We introduce an optical fiber platform which can be used to interrogate proximity interactions between free-electron evanescent fields and photonic nanostructures at optical frequencies in a manner similar to that in which optical evanescent fields are sampled using nanoscale aperture probes in scanning near-field microscopy. Conically profiled optical fiber tips functionalized with nano-gratings are employed to couple electron evanescent fields to light via the Smith-Purcell effect. We demonstrate the interrogation of medium energy (30–50 keV) electron fields with a lateral resolution of a few micrometers via the generation and detection of visible/UV radiation in the 700–300 nm (free-space) wavelength range.

  8. 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.

  9. 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.

  10. Transformation and pp60v-src autophosphorylation correlate with SHC-GRB2 complex formation in rat and chicken cells expressing host-range and kinase-active, transformation-defective alleles of v-src.

    PubMed Central

    Verderame, M F; Guan, J L; Woods Ignatoski, K M

    1995-01-01

    The biochemical properties of several pp60v-src substrates believed to participate in src-mediated transformation were examined in cells expressing a kinase-active, transformation-defective v-src allele (v-src-F172 delta/Y416F) and its parental allele, v-src-F172 delta, a host-range--dependent allele that transforms chicken cells to a fusiform morphology, but does not transform rat cells. Because pp60v-src-F172 delta is dependent on autophosphorylation for transforming ability, these alleles provide a unique opportunity to examine the role of pp60v-src autophosphorylation in regulating substrate interactions. Increased pp125FAK tyrosine phosphorylation and high levels of pp60v-src-associated phosphotidylinositol-3' kinase activity were detected specifically in chicken cells exhibiting round, refractile transformation but not in cells transformed to a fusiform morphology. Increased pp125FAK kinase activity, but not increased pp125FAK tyrosine-phosphorylation correlated with pp60v-src autophosphorylation and increased anchorage-independent growth. Thus, pp125FAK and PI3'K may participate in morphological transformation by v-src. Furthermore, association of phosphorylated SHC with the adapter GRB2 correlated with increased anchorage-independent growth (and autophosphorylation) in both rat and chicken cells independent of the morphological phenotype induced. Therefore, host-range dependence for transformation may be regulated through association of SHC with GRB2, thus implicating SHC as a crucial substrate for src-dependent transformation. Images PMID:7579711

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

    PubMed Central

    2011-01-01

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

  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. 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.

  14. 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.

  15. 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.

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

    PubMed

    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. PMID:27575226

  17. 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.

  18. 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.

  19. 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.

  20. Time-frequency analysis of acoustic signals in the audio-frequency range generated during Hadfield's steel friction

    NASA Astrophysics Data System (ADS)

    Dobrynin, S. A.; Kolubaev, E. A.; Smolin, A. Yu.; Dmitriev, A. I.; Psakhie, S. G.

    2010-07-01

    Time-frequency analysis of sound waves detected by a microphone during the friction of Hadfield’s steel has been performed using wavelet transform and window Fourier transform methods. This approach reveals a relationship between the appearance of quasi-periodic intensity outbursts in the acoustic response signals and the processes responsible for the formation of wear products. It is shown that the time-frequency analysis of acoustic emission in a tribosystem can be applied, along with traditional approaches, to studying features in the wear and friction process.

  1. The possible meaning of the upper and lower alpha frequency ranges for cognitive and creative tasks.

    PubMed

    Petsche, H; Kaplan, S; von Stein, A; Filz, O

    1997-06-01

    This study is aimed at verifying the functional independence of two frequency bands within the alpha range. It is based on experiments that examined the role of these two hands with regard to the amount of local electrogenesis (amplitude) and the cooperation of brain areas (coherence) in mental tasks concerning: (1) visual perception and imagery; (2) listening to and composing music; (3) verbal and visual creativity; and (4) aspects of mood. In all experiments EEG were recorded for at least 1 min during each task, separated one from another by at rest periods of at least equal lengths. EEG electrodes were pasted according to the 10/20 system (averaged ear lobes as reference). After FFT power was calculated for all 19 electrodes, coherence was estimated for all possible electrode pairs (i.e. 171). This was done for six frequency ranges between 1.5 and 31.5 Hz, the alpha range having been divided into two (7.5-9 Hz and 9.5-12.5 Hz). The spectral parameters obtained during each task were compared with those of the merged EEG at rest, significant changes (P < or = 0.01-P < or = 0.05) were entered into schematic maps of the brain. Generally, fewer differences were found for amplitude than for coherence. In all four tasks concerning visual perception the clearest differences were found in single person studies. But also in group studies more or less distinct differences were found between alpha 1 and 2. Also in the series with music the two alpha bands did not behave uniformly, nor were uniform features found in the two series of musically trained and untrained subjects. Distinct discrepancies were also found in a verbal and visual imagery task. With respect to mood, only elevated mood was correlated with a decrease of coherence in alpha 2 and an increase of amplitude in alpha 1. This study though hinting at a different functional significance of these two alpha bands, however, does not allow to draw any conclusions as to their distinct functional meanings. Generally

  2. 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.

  3. 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. PMID:9770314

  4. 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.

  5. 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.

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

    PubMed

    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.

  7. 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

  8. Allelic variation in the squirrel monkey x-linked color vision gene: biogeographical and behavioral correlates.

    PubMed

    Cropp, Susan; Boinski, Sue; Li, Wen-Hsiung

    2002-06-01

    Most Neotropical primate species possess a polymorphic X-linked and a monomorphic autosomal color vision gene. Consequently, populations are composed of both dichromatics and trichromatics. Most theories on the maintenance of this genetic system revolve around possible advantages for foraging ecology. To examine the issue from a different angle, we compared the numbers and relative frequencies of alleles at the X-linked locus among three species of Saimiri representing a wide range of geographical and behavioral variation in the genus. Exons 3, 4, and 5 of the X-linked opsin gene were sequenced for a large number of X chromosomes for all three species. Several synonymous mutations were detected in exons 4 and 5 for the originally reported alleles but only a single nonsynonymous change was detected. Two alleles were found that appeared to be the result of recombination events. The low occurrence of recombinant alleles and absence of mutations in the amino acids critical for spectral tuning indicates that stabilizing selection acts to maintain the combinations of critical sites specific to each allele. Allele frequencies were approximately the same for all Saimiri species, with a slight but significant difference between S. boliviensis and S. oerstedii. No apparent correlation exists between allele frequencies and behavioral or biogeographical differences between species, casting doubt on the speculation that the spectral sensitivities of the alleles have been maintained because they are specifically well-tuned to Saimiri visual ecology. Rather, the spectral tuning peaks might have been maintained because they are as widely spaced as possible within the limited range of middlewave to longwave spectra useful to all primates. This arrangement creates a balance between maximizing the distance between spectral tuning peaks (allowing the color opponency of the visual system to distinguish between peaks) and maximizing the number of alleles within a limited range (yielding

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. An obliquely propagating electromagnetic drift instability in the lower hybrid frequency range

    NASA Astrophysics Data System (ADS)

    Ji, Hantao; Kulsrud, Russell; Fox, William; Yamada, Masaaki

    2005-08-01

    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) wave in the electron frame and the forward propagating sound (slow) wave 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 a 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.

  14. 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.

  15. Linearization of the frequency sweep of a frequency-modulated continuous-wave semiconductor laser radar and the resulting ranging performance.

    PubMed

    Karlsson, C J; Olsson, F A

    1999-05-20

    The performance of a frequency-modulated continuous-wave (FMCW) semiconductor laser radar has been examined. Frequency modulation (linear chirp) has been studied experimentally in detail. To create a linear frequency sweep, we modified the modulating function according to the measured frequency response of the laser, using an arbitrary function generator. The measurements indicate the possibility of achieving a spectral width of the signal peak that is transform limited rather than limited by the frequency modulation response of the laser, which permits the use of a narrow detection bandwidth. The narrow width results in a relatively high signal-to-noise ratio for low output power and thus also in relatively long-range and high-range accuracy. We have performed measurements of a diffuse target to determine the performance of a test laser radar system. The maximum range, range accuracy, and speed accuracy for a semiconductor laser with an output power of 10 mW and a linewidth of 400 kHz are presented. The influence of the laser's output power and coherence length on the performance of a semiconductor-laser-based FMCW laser radar is discussed. PMID:18319935

  16. 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...

  17. An acoustical assessment of pitch-matching accuracy in relation to speech frequency, speech frequency range, age and gender in preschool children

    NASA Astrophysics Data System (ADS)

    Trollinger, Valerie L.

    This study investigated the relationship between acoustical measurement of singing accuracy in relationship to speech fundamental frequency, speech fundamental frequency range, age and gender in preschool-aged children. Seventy subjects from Southeastern Pennsylvania; the San Francisco Bay Area, California; and Terre Haute, Indiana, participated in the study. Speech frequency was measured by having the subjects participate in spontaneous and guided speech activities with the researcher, with 18 diverse samples extracted from each subject's recording for acoustical analysis for fundamental frequency in Hz with the CSpeech computer program. The fundamental frequencies were averaged together to derive a mean speech frequency score for each subject. Speech range was calculated by subtracting the lowest fundamental frequency produced from the highest fundamental frequency produced, resulting in a speech range measured in increments of Hz. Singing accuracy was measured by having the subjects each echo-sing six randomized patterns using the pitches Middle C, D, E, F♯, G and A (440), using the solfege syllables of Do and Re, which were recorded by a 5-year-old female model. For each subject, 18 samples of singing were recorded. All samples were analyzed by the CSpeech for fundamental frequency. For each subject, deviation scores in Hz were derived by calculating the difference between what the model sang in Hz and what the subject sang in response in Hz. Individual scores for each child consisted of an overall mean total deviation frequency, mean frequency deviations for each pattern, and mean frequency deviation for each pitch. Pearson correlations, MANOVA and ANOVA analyses, Multiple Regressions and Discriminant Analysis revealed the following findings: (1) moderate but significant (p < .001) relationships emerged between mean speech frequency and the ability to sing the pitches E, F♯, G and A in the study; (2) mean speech frequency also emerged as the strongest

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2014-10-01

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

  20. 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.

  1. 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.

  2. 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…

  3. On the minimum electron transport coefficients in tokamaks in the range of low collision frequencies

    SciTech Connect

    Merezhkin, V. G.

    2009-06-15

    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 {tau}{sub E}(n-bar{sub e}) in the range of low values of n-bar{sub e} and <{nu}{sub e}{sup *}> {<=} 1. The similar character of electron energy confinement in this range, which expands with increasing magnetic field B{sub 0}, has stimulated the search for dimensionless parameters and simple physical models that would explain the experimentally observed dependences {chi}{sub e} {approx} 1/n{sub e} and {tau}{sub Ee} {approx} n-bar{sub e}. In 1987, T. Okhawa showed that the experimental data were satisfactorily described by the formula {chi}{sub eperpendicular} = (c{sup 2}/{omega}{sub pe}{sup 2}){nu}{sub 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 {nu}{sub e}/qR. In 2004, J. Callen took into account the decrease in the fraction of transient electrons with increasing toroidal ratio {epsilon} = r/R and corrected the coefficient c{sup 2}/{omega}{sub pe}{sup 2} in Okhawa equation by the factor {sigma}{sub ||} {sup Sp}/{sigma}{sub ||}{sup 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 {chi}{sub eperpendicular} will coincide with the T-11 scaling: {chi}{sub e}{sup an} {infinity} {epsilon}{sup 1.75}(T{sub e}/A{sub i}){sup 0.5}/(n{sub e}qR) at Ai = 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 {approx}(c/{omega}{sub pe})(m{sub i}/m{sub e}){sup 1/4}. In this case, the calculated coefficient

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

    PubMed

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

    2015-06-01

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

  5. Masking of low frequency information in short-range apparent motion.

    PubMed

    Cleary, R; Braddick, O J

    1990-01-01

    When an array of random dots is displaced, the ability to report the direction of apparent motion is subject to an upper spatial limit (dmax). Using spatially low-pass filtered random dot kinematograms we show that dmax is dependent on the upper cut-off frequency of the stimulus (Fh). The extent of this dependence is critically dependent on the size of the stimulus. Our results suggest a process whereby low spatial frequency motion information is masked by the presence of high spatial frequencies in the same region of the field, analogous to phenomena occurring in the perception of static form (e.g. the Abraham Lincoln effect). The effects of stimulus size on dmax, found for broad-band stimuli by ourselves and others, result from a loss of high frequency sensitivity at increased retinal eccentricities; this loss reduces the masking effect of high frequencies, as stimulus size increases.

  6. Frequency dependence of Q sub Lg and its relation to crustal anelasticity in the Basin and Range province

    SciTech Connect

    Mitchell, B.J. )

    1991-04-01

    The high observed frequency dependence of Q for 1-hz Lg waves (f{sup 0.4 - 0.6}) in the Basin and Range province can be explained by a frequency-independent layered model of intrinsic Q for shear waves (Q{sub mu}) which has very low values in the upper crust and rapidly increasing values at greater depths. By contrast, earlier work in the eastern United States indicated Q{sub mu} values in the upper crust which are high and which vary with frequency. The Q{mu} model which best explains reported values of Q{sub Lg} and its frequency dependence in the Basin-and-Range consists of an 8-km thick low-Q layer (60 or less) overlying Q values as high as 1,000 or more at mid-crustal depths. This Q{sub mu} distribution is best explained by an upper crust which contains fluids in interconnected cracks overlying a lower crust where higher lithostatic pressure has closed those cracks. These results indicate that whereas the frequency dependence of Q{mu} is an intrinsic property of crustal material, the frequency dependence of Q{sub Lg} arises from both the intrinsic frequency dependence of crustal material and its layered structure. A notation is suggested which distinguishes between the frequency dependence of Q{sub Lg} and Q{sub mu}.

  7. 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.

  8. Wide frequency range capacitive detection of loss in a metallic cantilever using resonance and relaxation modes.

    PubMed

    Richert, Ranko

    2007-05-01

    The impedance of a capacitor which embraces a charged cantilever is used to measure the mechanical properties of the cantilever material. The technique has been tested with an amorphous metallic specimen, but is applicable for many other solids. The material damping can be measured at the resonance frequency of the cantilever via the width of the resonance curve or by recording the ring-down behavior. Additionally, several decades in frequency are accessible below the resonance frequency, where values as low as nu=0.03 Hz are achieved easily. The data are analyzed with a single equation that captures the damping at all frequencies in terms of the material specific Young's modulus E and its loss angle tan delta=E"/E'.

  9. 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.

  10. Photonic chirped radio-frequency generator with ultra-fast sweeping rate and ultra-wide sweeping range.

    PubMed

    Wun, Jhih-Min; Wei, Chia-Chien; Chen, Jyehong; Goh, Chee Seong; Set, S Y; Shi, Jin-Wei

    2013-05-01

    A high-performance photonic sweeping-frequency (chirped) radio-frequency (RF) generator has been demonstrated. By use of a novel wavelength sweeping distributed-feedback (DFB) laser, which is operated based on the linewidth enhancement effect, a fixed wavelength narrow-linewidth DFB laser, and a wideband (dc to 50 GHz) photodiode module for the hetero-dyne beating RF signal generation, a very clear chirped RF waveform can be captured by a fast real-time scope. A very-high frequency sweeping rate (10.3 GHz/μs) with an ultra-wide RF frequency sweeping range (~40 GHz) have been demonstrated. The high-repeatability (~97%) in sweeping frequency has been verified by analyzing tens of repetitive chirped waveforms.

  11. 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.

  12. Detecting range expansions from genetic data

    PubMed Central

    Peter, Benjamin M; Slatkin, Montgomery

    2014-01-01

    We propose a method that uses genetic data to test for the occurrence of a recent range expansion and to infer the location of the origin of the expansion. We introduce a statistic ψ (the directionality index) that detects asymmetries in the two-dimensional allele frequency spectrum of pairs of population. These asymmetries are caused by the series of founder events that happen during an expansion and they arise because low frequency alleles tend to be lost during founder events, thus creating clines in the frequencies of surviving low-frequency alleles. Using simulations, we show that ψ is more powerful for detecting range expansions than both FST and clines in heterozygosity. We also show how we can adapt our approach to more complicated scenarios such as expansions with multiple origins or barriers to migration and we illustrate the utility of ψ by applying it to a data set from modern humans. PMID:24152007

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

    PubMed

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

    2016-09-01

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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. RHD allele distribution in Africans of Mali

    PubMed Central

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

    2003-01-01

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

  20. THz-range generation frequency growth in semiconductor superlattice coupled to external high-quality resonator

    NASA Astrophysics Data System (ADS)

    Makarov, Vladimir V.; Maksimenko, Vladimir A.; Khramova, Marina V.; Pavlov, Alexey N.; Hramov, Alexander E.

    2016-03-01

    We investigate effects of a linear resonator on spatial electron dynamics in semiconductor superlattice. We have shown that coupling the external resonant system to superlattice leads to occurrence of the additional area of negative differential conductance on the current-voltage characteristic, which does not occur in autonomous system. Furthermore, this region shows great increase of generation frequency, that contains practical interest.

  1. 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.

  2. 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.

  3. 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.

  4. Wide-range frequency selectivity in an acoustic sensor fabricated using a microbeam array with non-uniform thickness

    NASA Astrophysics Data System (ADS)

    Shintaku, Hirofumi; Kobayashi, Takayuki; Zusho, Kazuki; Kotera, Hidetoshi; Kawano, Satoyuki

    2013-11-01

    In this study, we have demonstrated the fabrication of a microbeam array (MBA) with various thicknesses and investigated the suitability it for an acoustic sensor with wide-range frequency selectivity. For this, an MBA composed of 64 beams, with thicknesses varying from 2.99-142 µm, was fabricated by using single gray-scale lithography and a thick negative photoresist. The vibration of the beams in air was measured using a laser Doppler vibrometer; the resonant frequencies of the beams were measured to be from 11.5 to 290 kHz. Lastly, the frequency range of the MBA with non-uniform thickness was 10.9 times that of the MBA with uniform thickness.

  5. 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.

  6. Cryocooled terahertz photoconductive detector system with background-limited performance in 1.5-4 THz frequency range.

    PubMed

    Aoki, Makoto; Hiromoto, Norihisa

    2015-10-01

    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(-14) W/Hz(1/2) in the frequency range from 1.5 to 4 THz even if the vibration noise of the mechanical refrigerator is present.

  7. 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.

  8. 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*∥∥.

  9. Measurement of ion motional heating rates over a range of trap frequencies and temperatures

    NASA Astrophysics Data System (ADS)

    Bruzewicz, C. D.; Sage, J. M.; Chiaverini, J.

    2015-04-01

    We present measurements of the motional heating rate of a trapped ion at different trap frequencies and temperatures between ˜0.6 and 1.5 MHz and ˜4 and 295 K. Additionally, we examine the possible effect of adsorbed surface contaminants with boiling points below ˜105 ∘C by measuring the ion heating rate before and after locally baking our ion trap chip under ultrahigh vacuum conditions. We compare the heating rates presented here to those calculated from available electric-field noise models. We can tightly constrain a subset of these models based on their expected frequency and temperature scaling interdependence. Discrepancies between the measured results and predicted values point to the need for refinement of theoretical noise models in order to more fully understand the mechanisms behind motional trapped-ion heating.

  10. Ion heating in the ion cyclotron range of frequencies in the Wisconsin Tokapole II

    SciTech Connect

    Biddle, A. P.

    1980-06-01

    Ion temperatures of 75 eV, a doubling of the ohmic heating temperature in a normal discharge, have been achieved using the fast magnetosonic wave heating at the second, third, and fourth harmonics of the cyclotron frequency in a single component hydrogen plasma. The wave launching structure is a single turn, shielded, insulated loop which constitutes the inductor of the rf source tank circuit. Power levels of 800 kW have been applied to the plasma for periods of up to 1.1 milliseconds. Good agreement has been found between theory and experiment for loading and wave propagation in the plasma for m = 0 and m = +1 modes. Eigenmodes have been observed by peaking of both the rf wave amplitude and the loading of the oscillator, as well as by oscillator frequency shifts imposed by their passage.

  11. Mechanical behavior of the fingertip in the range of frequencies and displacements relevant to touch.

    PubMed

    Wiertlewski, Michael; Hayward, Vincent

    2012-07-26

    It was previously suggested that the mechanical properties of the fingertip could be characterized by elasticity from dc to about 100Hz and by viscosity above this frequency. Using a specifically designed high mobility probe, we accurately measured the impedance of the fingertips of seven participants under a variety of conditions relevant to purposeful touch. Direct measurements vindicated previous indirect observations. We also characterized the dependency of the fingertip impedance upon normal load, orientation, and time.

  12. [The biological activity of a decameter-range electromagnetic field with a frequency of 24 MHz].

    PubMed

    Bezdol'naia, I S; Dumanskiĭ, Iu D; Smolia, A L

    1991-03-01

    A study of behavioural reactions indicates that the effect of 24 MHz frequencies of the electromagnetic field results in changes of the ratio of excitatory and inhibitory processes in the nervous system of white rats with prevalence of inhibitory processes. By the 90-th day of effect of the above factor all changes returned to the initial level. This indicates stability of the adaptative reactions of the integrative level of the nervous system to the acting factor. PMID:2042349

  13. [The mosaic structure of the high-frequency range of neocortical electrical activity in dogs].

    PubMed

    Dumenko, V N; Kozlov, M K

    2000-01-01

    The study was aimed to reveal the subbands of correlated changes in power spectral density of brain electrical activity (EA), including the low-voltage (up to 10 microV) high-frequency (HF) components (40-200 Hz) in dogs during instrumental conditioning by means of factor analysis. The values of the EA spectral density in interstimulus intervals calculated with a resolution of 1 Hz were used for subsequent factor analysis (the standard principle component technique with varimax rotation). Twenty factors could explain about 80% of total variance. The groups of frequencies which were presented by comparatively narrow peaks (2-3 points) of high loads (more than 0.6) of single factors ("stable" factors) were taken into consideration. In the process of conditioning the factor organization of the EA became substantially complicated, the number of the "stable" factors increased. It was originally shown that the high loads of these factors divided the HF band in comparatively narrow frequency subbands, which appear to reflect the functional mosaics in the neocortex.

  14. Distribution of interaural time difference in the barn owl's inferior colliculus in the low- and high-frequency ranges.

    PubMed

    Wagner, Hermann; Asadollahi, Ali; Bremen, Peter; Endler, Frank; Vonderschen, Katrin; von Campenhausen, Mark

    2007-04-11

    Interaural time differences are an important cue for azimuthal sound localization. It is still unclear whether the same neuronal mechanisms underlie the representation in the brain of interaural time difference in different vertebrates and whether these mechanisms are driven by common constraints, such as optimal coding. Current sound localization models may be discriminated by studying the spectral distribution of response peaks in tuning curves that measure the sensitivity to interaural time difference. The sound localization system of the barn owl has been studied intensively, but data that would allow discrimination between currently discussed models are missing from this animal. We have therefore obtained extracellular recordings from the time-sensitive subnuclei of the barn owl's inferior colliculus. Response peaks were broadly scattered over the physiological range of interaural time differences. A change in the representation of the interaural phase differences with frequency was not observed. In some neurons, response peaks fell outside the physiological range of interaural time differences. For a considerable number of neurons, the peak closest to zero interaural time difference was not the behaviorally relevant peak. The data are in best accordance with models suggesting that a place code underlies the representation of interaural time difference. The data from the high-frequency range, but not from the low-frequency range, are consistent with predictions of optimal coding. We speculate that the deviation of the representation of interaural time difference from optimal-coding models in the low-frequency range is attributable to the diminished importance of low frequencies for catching prey in this species. PMID:17428997

  15. Electron beam excitation of upstream waves in the whistler mode frequency range

    NASA Technical Reports Server (NTRS)

    Wong, Hung K.; Smith, Charles W.

    1994-01-01

    We examine whistler mode instabilities arising from electron beams in interplanetary space at 1 AU. Both parallel and obliquely propagating solutions are considered. We demonstrate that the generation of two simultaneous whistler mode waves is possible, and even reasonably likely, for beam parameters frequently encountered upstream of the Earth's bow shock and at interplanetary shocks. We also explore the generation of left-hand polarized waves at whistler mode frequencies under these same conditions. We offer both parametric variations derived from numerical solutions of the various instabilities as well as an analytical treatment of the problem which succeeds in unifying the various numerical results.

  16. 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.

  17. Improving Processes of Mechanized Pulsed Arc Welding of Low-Frequency Range Variation of Mode Parameters

    NASA Astrophysics Data System (ADS)

    Saraev, Yu N.; Solodskiy, S. A.; Ulyanova, O. V.

    2016-04-01

    A new technology of low-frequency modulation of the arc current in MAG and MIG welding is presented. The technology provides control of thermal and crystallization processes, stabilizes the time of formation and crystallization of the weld pool. Conducting theoretical studies allowed formulating the basic criteria for obtaining strong permanent joints for high-duty structures, providing conditions for more equilibrium structure of the deposited metal and the smaller width of the HAZ. The stabilization of time of the formation and crystallization of the weld pool improves the formation of the weld and increases productivity in welding thin sheet metal.

  18. High resolution kilometric range optical telemetry in air by radio frequency phase measurement.

    PubMed

    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.

  19. Motion artifacts in optical coherence tomography with frequency-domain ranging

    PubMed Central

    Yun, S. H.; Tearney, G. J.; de Boer, J. F.; Bouma, B. E.

    2009-01-01

    We describe results of theoretical and experimental investigations of artifacts that can arise in spectral-domain optical coherence tomography (SD-OCT) and optical frequency domain imaging (OFDI) as a result of sample or probe beam motion. While SD-OCT and OFDI are based on similar spectral interferometric principles, the specifics of motion effects are quite different because of distinct signal acquisition methods. These results provide an understanding of motion artifacts such as signal fading, spatial distortion and blurring, and emphasize the need for fast image acquisition in biomedical applications. PMID:19483816

  20. High resolution kilometric range optical telemetry in air by radio frequency phase measurement.

    PubMed

    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. PMID:27475593

  1. 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.

  2. 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.

  3. Plasma channel produced by femtosecond laser pulses as a medium for amplifying electromagnetic radiation of the subterahertz frequency range

    SciTech Connect

    Bogatskaya, A V; Volkova, E A; Popov, A M

    2013-12-31

    The electron energy distribution function in the plasma channel produced by a femtosecond laser pulse with a wavelength of 248 nm in atmospheric-pressure gases was considered. Conditions were determined whereby this channel may be employed for amplifying electromagnetic waves up to the terahertz frequency range over the energy spectrum relaxation time ∼10{sup -7} s. Gains were calculated as functions of time and radiation frequency. The effect of electron – electron collisions on the rate of relaxation processes in the plasma and on its ability to amplify the electromagnetic radiation was investigated. (interaction of laser radiation with matter)

  4. 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.

  5. Frontside-micromachined planar piezoresistive vibration sensor: Evaluating performance in the low frequency test range

    NASA Astrophysics Data System (ADS)

    Zhang, Lan; Lu, Jian; Takagi, Hideki; Maeda, Ryutaro

    2014-01-01

    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.

  6. 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.

  7. Observation of ICRF (ion cyclotron range of frequencies) wave-packet propagation in a tokamak plasma

    SciTech Connect

    Greene, G.J.; Gould, R.W.

    1987-11-01

    Experimental observation of ICRF wave-packet propagation in a tokamak plasma is reported. Studies were carried out in the Caltech Research Tokamak in a pure hydrogen plasma and in a regime where fast-wave damping was sufficiently small to permit multiple toroidal transits of the wave-packet. Waves were launched by exciting a small loop antenna with a short burst of rf current and were detected with shielded magnetic probes. Probe scans revealed a large increase in wave-packet amplitude at smaller minor radii, and the packet velocity was found to be independent of radial position. Measurement of the packet transit time yielded direct information about the wave group velocity. Packet velocity was investigated as a function of the fundamental excitation frequency, plasma density, and toroidal magnetic field. Results are compared with the predictions of a cold plasma model which includes a vacuum layer at the edge. 24 refs., 8 figs.

  8. Characterization of CVD graphene permittivity and conductivity in micro-/millimeter wave frequency range

    NASA Astrophysics Data System (ADS)

    Wu, Yunqiu; Wu, Yun; Kang, Kai; Chen, Yuanfu; Li, Yanrong; Chen, Tangsheng; Xu, Yuehang

    2016-09-01

    The permittivity and conductivity of chemical vapor deposited monolayer graphene are investigated up to 40 GHz. The characterization method is based on a coplanar waveguide transmission line structure that is fabricated on a multilayer substrate of Si/SiO2/graphene/Al2O3 from the bottom up. The effective relative permittivity of the coplanar waveguide transmission line is extracted using Thru-Reflect-Line calibration and scattering parameter measurements, and then the relative permittivity and corresponding conductivity of graphene are characterized using partial capacitance techniques. The results demonstrate that the conductivity and sheet resistance are remarkably frequency-dependent and that the complex relative permittivity is consistent with the Drude model.

  9. Range-resolved interferometric signal processing using sinusoidal optical frequency modulation.

    PubMed

    Kissinger, Thomas; Charrett, Thomas O H; Tatam, Ralph P

    2015-04-01

    A novel signal processing technique using sinusoidal optical frequency modulation of an inexpensive continuous-wave laser diode source is proposed that allows highly linear interferometric phase measurements in a simple, self-referencing setup. Here, the use of a smooth window function is key to suppress unwanted signal components in the demodulation process. Signals from several interferometers with unequal optical path differences can be multiplexed, and, in contrast to prior work, the optical path differences are continuously variable, greatly increasing the practicality of the scheme. In this paper, the theory of the technique is presented, an experimental implementation using three multiplexed interferometers is demonstrated, and detailed investigations quantifying issues such as linearity and robustness against instrument drift are performed.

  10. Beta and gamma frequency-range abnormalities in parkinsonian patients under cognitive sensorimotor task.

    PubMed

    Dushanova, Juliana; Philipova, Dolja; Nikolova, Gloria

    2010-06-15

    Parkinson's disease (PD) is a neurodegenerative disorder caused by a disruption of dopaminergic neurotransmission in the basal ganglia. Some of PD clinical symptoms are suggested to stem directly from the excessive synchrony between the basal ganglia and cortical circuits. Our present investigation explores the functional relationships between event-related desynchronization/synchronization (ERD/ERS) of beta and gamma band activity for idiopathic non-demented Parkinson's patients (PP) and control subjects (CS) during auditory discrimination tasks between two tone types (LT: 800 Hz, HT: 1000 Hz) within two post-stimulus intervals of 0-250 and 250-600 ms. Beta1 (13-20 Hz) ERD was found for both groups within both intervals more expressed in CS except for frontal beta1 synchronization in CS during the second interval. Beta2 (20-32 Hz) ERD was revealed in CS after both tones during both post-stimulus intervals. Beta2 ERS was only observed in PP. The most prominent beta2 ERS followed HT during the second interval. Gamma frequency (32-50 Hz) ERD was found in both groups except for fronto-parietal ERS for PP during the first interval after LT. During the second interval, either tone, we found prominent ERS for PP and ERD for CS everywhere except for a frontal ERS after HT. Deviations of the beta and gamma ERD/ERS for the PP compared with CS during the sensorimotor and cognitive processing are a clear evidence for disturbances in the temporal and regional integration of these frequency components and the relationships between cortical and the basal ganglia circuits in parkinsonism. PMID:20392453

  11. Active diagnostic of the eigenmode formation in the ion-cyclotron frequency range in the GAMMA10 central cell

    SciTech Connect

    Yamaguchi, Y.; Ichimura, M.; Higaki, H.; Kakimoto, S.; Nakagome, K.; Nemoto, K.; Katano, M.; Nakajima, H.; Fukuyama, A.; Cho, T.

    2006-10-15

    A wide-band radio-frequency (rf) probe system was constructed for the active diagnostic of the eigenmode formations in the ion-cyclotron range of frequency (ICRF) in GAMMA10. An antenna was installed in the peripheral region in the central cell. The low power rf pulse with the frequency sweep is applied to the antenna. The waves excited in the plasma are detected with a magnetic probe. The excitation of eigenmodes is described by using the antenna-plasma-probe transfer function. The transfer function can be obtained from the antenna current signal and the magnetic probe signal. When the real and imaginary parts of the transfer function are plotted on the complex plane, the resultant curves are approximately circular, indicating an eigenmode formation. The results of the measurement show that several eigenmodes can be excited in the present experimental condition.

  12. 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. PMID:23298019

  13. 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.

  14. 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

  15. Transitions between various diffuse discharge modes in atmospheric-pressure helium in the medium-frequency range

    NASA Astrophysics Data System (ADS)

    Boisvert, J.-S.; Margot, J.; Massines, F.

    2016-08-01

    In this paper, we investigate DBDs in the medium frequency range (MF, 0.3-3 MHz). More precisely, for a 2 inter-dielectric gap in helium at atmospheric pressure, the frequency is varied from 1.0 to 2.7 MHz. The generated discharge shows similarities with both the low-frequency atmospheric-pressure glow discharge (APGD) and the atmospheric pressure capacitively coupled radio-frequency (CCRF) discharge. In the frequency range under investigation, two diffuse discharge modes can be observed depending on the voltage applied between the electrodes. At low applied voltage, the discharge emissions are barely visible and are concentrated in the center of the gas gap similarly to CCRF discharges in the Ω mode where the electron density is concentrated in the bulk. Ohmic heating is the main power transfer mechanism. At higher applied voltage, the discharge emissions are 10 times more intense and are closer to the dielectric surfaces similarly to the more common radio-frequency α mode. These two discharge modes can be observed in the same experimental conditions with the amplitude of the applied voltage as sole control parameter. The gas temperature obtained from N2 impurities rotational spectrum increases from room temperature to about 500 K while the power density rises from 10-1 to 101 W cm-3 when the applied voltage is increased. In addition, when the discharge transits back and forth from the Ω to the α mode, a hysteresis is observed. The transition from the Ω to the α mode occurs abruptly with a large RMS current increase while the transition from the α to the Ω mode is rather smooth with no significant discontinuity in the RMS current.

  16. Transitions between various diffuse discharge modes in atmospheric-pressure helium in the medium-frequency range

    NASA Astrophysics Data System (ADS)

    Boisvert, J.-S.; Margot, J.; Massines, F.

    2016-08-01

    In this paper, we investigate DBDs in the medium frequency range (MF, 0.3–3 MHz). More precisely, for a 2 inter-dielectric gap in helium at atmospheric pressure, the frequency is varied from 1.0 to 2.7 MHz. The generated discharge shows similarities with both the low-frequency atmospheric-pressure glow discharge (APGD) and the atmospheric pressure capacitively coupled radio-frequency (CCRF) discharge. In the frequency range under investigation, two diffuse discharge modes can be observed depending on the voltage applied between the electrodes. At low applied voltage, the discharge emissions are barely visible and are concentrated in the center of the gas gap similarly to CCRF discharges in the Ω mode where the electron density is concentrated in the bulk. Ohmic heating is the main power transfer mechanism. At higher applied voltage, the discharge emissions are 10 times more intense and are closer to the dielectric surfaces similarly to the more common radio-frequency α mode. These two discharge modes can be observed in the same experimental conditions with the amplitude of the applied voltage as sole control parameter. The gas temperature obtained from N2 impurities rotational spectrum increases from room temperature to about 500 K while the power density rises from 10‑1 to 101 W cm‑3 when the applied voltage is increased. In addition, when the discharge transits back and forth from the Ω to the α mode, a hysteresis is observed. The transition from the Ω to the α mode occurs abruptly with a large RMS current increase while the transition from the α to the Ω mode is rather smooth with no significant discontinuity in the RMS current.

  17. Stroke frequency, but not swimming speed, is related to body size in free-ranging seabirds, pinnipeds and cetaceans

    PubMed Central

    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; Costa, Daniel P; Bost, Charles-André; Aoki, Kagari; Amano, Masao; Trathan, Phil; Shapiro, Ari; Naito, Yasuhiko

    2006-01-01

    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 (R2=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. PMID:17476766

  18. 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.

  19. Study and development of a six port network analyzer in the 1-18 GHz frequency range

    NASA Astrophysics Data System (ADS)

    Bergeault, Eric

    A theoretical and experimental study for the realization of a six port analyzer to calibrate the components of the verification kit, used to evaluate the measurement accuracy of automated network analyzers, is presented. The detection is performed at the frequency of use, and the scattering parameters are determined in magnitude and phase by means of power measurements. The six port accuracy, realized in the 1 to 18 GHz frequency range, is limited by uncertainties in the power measurements. The detection law of the Schottky diodes used as power detectors, that relates the incident power level and the diode output voltage, is performed in situ. The characterization requires only two reference unknown test loads without any power measurement. The procedure is shown to be rather stable with frequency, so that a midband characterization is generally sufficient to provide enough accuracy in the whole frequency range. The measurement uncertainties due to the variation of the detector reflection coefficients with power, are estimated by determining the variations of the six port parameters. The principle of the six port compared to that of the heteordyne network analyzers is simpler, and it makes modeling and correcting systematic errors easier. Good agreement is found between the measurement results obtained with the dual six port and the other operating systems. Generally, the amplitude measurements are within a few thousands, while the phase measurement errors are below or around one degree for the parameters being measured.

  20. Excitation, detection, and electrostatic manipulation of terahertz-frequency range plasmons in a two-dimensional electron system

    NASA Astrophysics Data System (ADS)

    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.

    2015-10-01

    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.

  1. Excitation, detection, and electrostatic manipulation of terahertz-frequency range plasmons in a two-dimensional electron system.

    PubMed

    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

  2. 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

  3. Dynamic Confinement of ITER Plasma by O-Mode Driver at Electron Cyclotron Frequency Range

    NASA Astrophysics Data System (ADS)

    Stefan, V. Alexander

    2009-05-01

    A low B-field side launched electron cyclotron O-Mode driver leads to the dynamic rf confinement, in addition to rf turbulent heating, of ITER plasma. The scaling law for the local energy confinement time τE is evaluated (τE ˜ 3neTe/2Q, where (3/2) neTe is the local plasma thermal energy density and Q is the local rf turbulent heating rate). The dynamics of unstable dissipative trapped particle modes (DTPM) strongly coupled to Trivelpiece-Gould (T-G) modes is studied for gyrotron frequency 170GHz; power˜24 MW CW; and on-axis B-field ˜ 10T. In the case of dynamic stabilization of DTPM turbulence and for the heavily damped T-G modes, the energy confinement time scales as τE˜(I0)-2, whereby I0(W/m^2) is the O-Mode driver irradiance. R. Prater et. al., Nucl. Fusion 48, No 3 (March 2008). E. P. Velikhov, History of the Russian Tokamak and the Tokamak Thermonuclear Fusion Research Worldwide That Led to ITER (Documentary movie; Stefan Studios Int'l, La Jolla, CA, 2008; E. P. Velikhov, V. Stefan.) M N Rosenbluth, Phys. Scr. T2A 104-109 1982 B. B. Kadomtsev and O. P. Pogutse, Nucl. Fusion 11, 67 (1971).

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

    NASA Technical Reports Server (NTRS)

    Hevizi, Laszlo G.; Walsh, E. J.; Mcintosh, Robert E.; Vandemark, Douglas; Hines, Donald E.; Swift, Robert N.; Scott, John F.

    1993-01-01

    Measurements of EM bias 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, are reported. 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. Recent tower, airborne, and satellite measurements exhibit a consistency in the characteristics of the wind speed dependence but suggest that there may be a height dependence in the determinations, with the bias decreasing with increasing altitude.

  5. 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.

  6. 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.

  7. 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.

  8. 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. PMID:19227068

  9. Wide range tuning of resonant frequency for a vortex core in a regular triangle magnet

    PubMed Central

    Yakata, Satoshi; Tanaka, Terumitsu; Kiseki, Kohei; Matsuyama, Kimihide; Kimura, Takashi

    2013-01-01

    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. PMID:24356511

  10. 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

  11. 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.

  12. 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.

  13. Optimal detection and concentration estimation of vapor materials using range-resolved lidar with frequency-agile lasers

    NASA Astrophysics Data System (ADS)

    Warren, Russell E.; Vanderbeek, Richard G.; D'Amico, Francis M.

    1999-10-01

    In previous work, we presented a methodology for optimally processing data from lidar with frequency-agile wavelength capability using techniques of multivariate statistics. Among the applications considered was the case of range- resolved lidar with short (delta function) transmitter pulses. This paper extends that analysis by deriving a method for estimating range-dependent vapor concentration for arbitrary pulse shapes. A Bayesian statistical approach leads to a MAP (maximum a posteriori) estimator for C(z), the concentration at range z. The estimates are computed iteratively for a given set of multiwavelength lidar return data using an approximation to the Gauss-Newton method. The concentration estimates are then used as the basis for a detection algorithm for the leading edge of the vapor plume based on the CUSUM approach. The detection and estimation approaches are illustrated on a combination of synthetic and field test data collected by SBCCOM at the Idaho National Engineering and Environmental Laboratory test site.

  14. Sequential detection and concentration estimation of chemical vapors using range-resolved lidar with frequency-agile lasers

    NASA Astrophysics Data System (ADS)

    Warren, Russell E.; Vanderbeek, Richard G.; D'Amico, Francis M.

    2000-07-01

    This paper extends our earlier work in developing statistically optimal algorithms for estimating the range- dependent concentration of multiple vapor materials using multiwavelength frequency-agile lidar with a fixed set of wavelength bursts to the case of a time series processor that recursively updates the estimates as new data become available. The concentration estimates are used to detect the presence of one or more vapor materials by a sequential approach that accumulates likelihood in time for each range cell. A Bayesian methodology is used to construct the concentration estimates with a prior concentration smoothness constraint chosen to produce numerically stable results at longer ranges having weak signal return. The approach is illustrated on synthetic and actual field test data collected by SBCCOM.

  15. 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.

  16. Absolute backscatter coefficient estimates of tissue-mimicking phantoms in the 5–50 MHz frequency range

    PubMed Central

    McCormick, Matthew M.; Madsen, Ernest L.; Deaner, Meagan E.; Varghese, Tomy

    2011-01-01

    Absolute backscatter coefficients in tissue-mimicking phantoms were experimentally determined in the 5–50 MHz frequency range using a broadband technique. A focused broadband transducer from a commercial research system, the VisualSonics Vevo 770, was used with two tissue-mimicking phantoms. The phantoms differed regarding the thin layers covering their surfaces to prevent desiccation and regarding glass bead concentrations and diameter distributions. Ultrasound scanning of these phantoms was performed through the thin layer. To avoid signal saturation, the power spectra obtained from the backscattered radio frequency signals were calibrated by using the signal from a liquid planar reflector, a water-brominated hydrocarbon interface with acoustic impedance close to that of water. Experimental values of absolute backscatter coefficients were compared with those predicted by the Faran scattering model over the frequency range 5–50 MHz. The mean percent difference and standard deviation was 54% ± 45% for the phantom with a mean glass bead diameter of 5.40 μm and was 47% ± 28% for the phantom with 5.16 μm mean diameter beads. PMID:21877789

  17. 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.

  18. A comparison of type 2 diabetes risk allele load between African Americans and European Americans.

    PubMed

    Keaton, Jacob M; Cooke Bailey, Jessica N; Palmer, Nicholette D; Freedman, Barry I; Langefeld, Carl D; Ng, Maggie C Y; Bowden, Donald W

    2014-12-01

    The prevalence of type 2 diabetes (T2D) is greater in populations of African descent compared to European-descent populations. Genetic risk factors may underlie the disparity in disease prevalence. Genome-wide association studies (GWAS) have identified >60 common genetic variants that contribute to T2D risk in populations of European, Asian, African and Hispanic descent. These studies have not comprehensively examined population differences in cumulative risk allele load. To investigate the relationship between risk allele load and T2D risk, 46 T2D single nucleotide polymorphisms (SNPs) in 43 loci from GWAS in European, Asian, and African-derived populations were genotyped in 1,990 African Americans (n = 963 T2D cases, n = 1,027 controls) and 1,644 European Americans (n = 719 T2D cases, n = 925 controls) ascertained and recruited using a common protocol in the southeast United States. A genetic risk score (GRS) was constructed from the cumulative risk alleles for each individual. In African American subjects, risk allele frequencies ranged from 0.024 to 0.964. Risk alleles from 26 SNPs demonstrated directional consistency with previous studies, and 3 SNPs from ADAMTS9, TCF7L2, and ZFAND6 showed nominal evidence of association (p < 0.05). African American individuals carried 38-67 (53.7 ± 4.0, mean ± SD) risk alleles. In European American subjects, risk allele frequencies ranged from 0.084 to 0.996. Risk alleles from 36 SNPs demonstrated directional consistency, and 10 SNPs from BCL11A, PSMD6, ADAMTS9, ZFAND3, ANK1, CDKN2A/B, TCF7L2, PRC1, FTO, and BCAR1 showed evidence of association (p < 0.05). European American individuals carried 38-65 (50.9 ± 4.4) risk alleles. African Americans have a significantly greater burden of 2.8 risk alleles (p = 3.97 × 10(-89)) compared to European Americans. However, GRS modeling showed that cumulative risk allele load was associated with risk of T2D in European Americans, but only marginally in African Americans. This result

  19. A Comparison of Type 2 Diabetes Risk Allele Load between African Americans and European Americans

    PubMed Central

    Keaton, Jacob M.; Cooke Bailey, Jessica N.; Palmer, Nicholette D.; Freedman, Barry I.; Langefeld, Carl D.; Ng, Maggie C. Y.; Bowden, Donald W.

    2014-01-01

    The prevalence of type 2 diabetes (T2D) is greater in populations of African descent compared to European-descent populations. Genetic risk factors may underlie the disparity in disease prevalence. Genome-wide association studies (GWAS) have identified >60 common genetic variants that contribute to T2D risk in populations of European, Asian, African, and Hispanic descent. These studies have not comprehensively examined population differences in cumulative risk allele load. To investigate the relationship between risk allele load and T2D risk, 46 T2D single nucleotide polymorphisms (SNPs) in 43 loci from GWAS in European, Asian, and African derived populations were genotyped in 1,990 African Americans (n=963 T2D cases, n=1,027 controls) and 1,644 European Americans (n=719 T2D cases, n=925 controls) ascertained and recruited using a common protocol in the southeast United States. A genetic risk score (GRS) was constructed from the cumulative risk alleles for each individual. In African American subjects, risk allele frequencies ranged from 0.024 to 0.964. Risk alleles from 26 SNPs demonstrated directional consistency with previous studies, and 3 SNPs from ADAMTS9, TCF7L2, and ZFAND6 showed nominal evidence of association (p<0.05). African American individuals carried 38–67 (53.7 ± 4.0, mean ± SD) risk alleles. In European American subjects, risk allele frequencies ranged from 0.084 to 0.996. Risk alleles from 36 SNPs demonstrated directional consistency, and 10 SNPs from BCL11A, PSMD6, ADAMTS9, ZFAND3, ANK1, CDKN2A/B, TCF7L2, PRC1, FTO, and BCAR1 showed evidence of association (p<0.05). European American individuals carried 38–65 (50.9 ± 4.4) risk alleles. African Americans have a significantly greater burden of 2.9 risk alleles (p=3.97×10−89) compared to European Americans. However, GRS modeling showed that cumulative risk allele load was associated with risk of T2D in European Americans, but only marginally in African Americans. This result suggests that

  20. Spectral features of stimulated electromagnetic emission, measured in the 4.3-9.5 MHz pump wave frequency range

    NASA Astrophysics Data System (ADS)

    Frolov, V. L.; Sergeev, E. N.; Ermakova, E. N.; Komrakov, G. P.; Stubbe, P.

    Steady state spectral features of stimulated electromagnetic emissions (SEEs) for their major emission components (DM, NC, BC, BUM, and BUS) are studied in a wide pump wave frequency range, from 4.3 to 9.5 MHz, i.e., from slightly above the 3rd to slightly above the 7th gyroharmonic frequency. Based on these systematic experimental data, new peculiarities in the behaviour of the SEE intensity and of the spectral properties, in relation to the gyroharmonic mode number, have been found. The experimental results, discussed in the paper, were collected during the years 1996-2000 at the Sura heating facility in Russia by modification of the ionospheric F region, using ordinary mode HF pump waves.

  1. 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.

  2. Vibroacoustics of the piano soundboard: (Non)linearity and modal properties in the low- and mid-frequency ranges

    NASA Astrophysics Data System (ADS)

    Ege, Kerem; Boutillon, Xavier; Rébillat, Marc

    2013-03-01

    The piano soundboard transforms the string vibration into sound and therefore, its vibrations are of primary importance for the sound characteristics of the instrument. An original vibro-acoustical method is presented to isolate the soundboard nonlinearity from that of the exciting device (here: a loudspeaker) and to measure it. The nonlinear part of the soundboard response to an external excitation is quantitatively estimated for the first time, at ≈-40 dB below the linear part at the ff nuance. Given this essentially linear response, a modal identification is performed up to 3 kHz by means of a novel high resolution modal analysis technique [K. Ege, X. Boutillon, B. David, High-resolution modal analysis, Journal of Sound and Vibration 325 (4-5) (2009) 852-869]. Modal dampings (which, so far, were unknown for the piano in this frequency range) are determined in the mid-frequency domain where FFT-based methods fail to evaluate them with an acceptable precision. They turn out to be close to those imposed by wood. A finite-element modelling of the soundboard is also presented. The low-order modal shapes and the comparison between the corresponding experimental and numerical modal frequencies suggest that the boundary conditions can be considered as blocked, except at very low frequencies. The frequency-dependency of the estimated modal densities and the observation of modal shapes reveal two well-separated regimes. Below ≈1 kHz, the soundboard vibrates more or less like a homogeneous plate. Above that limit, the structural waves are confined by ribs, as already noticed by several authors, and localised in restricted areas (one or a few inter-rib spaces), presumably due to a slightly irregular spacing of the ribs across the soundboard.

  3. 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

  4. Prediction of rain effects on earth-space communication links operating in the 10 to 35 GHz frequency range

    NASA Technical Reports Server (NTRS)

    Stutzman, Warren L.

    1989-01-01

    This paper reviews the effects of precipitation on earth-space communication links operating the 10 to 35 GHz frequency range. Emphasis is on the quantitative prediction of rain attenuation and depolarization. Discussions center on the models developed at Virginia Tech. Comments on other models are included as well as literature references to key works. Also included is the system level modeling for dual polarized communication systems with techniques for calculating antenna and propagation medium effects. Simple models for the calculation of average annual attenuation and cross-polarization discrimination (XPD) are presented. Calculation of worst month statistics are also presented.

  5. 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.

  6. Numerical study on an equivalent source model for inhomogeneous magnetic field dosimetry in the low-frequency range.

    PubMed

    Nishizawa, Shinichiro; Ruoss, Hans-Oliver; Landstorfer, Friedrich M; Hashimoto, Osamu

    2004-04-01

    A new equivalent numerical source model is proposed for efficient dosimetric investigations in the low-frequency range. This approach allows the reproduction of complicated inhomogeneous magnetic field distributions around electronic appliances with full generality (i.e., supports three-dimensional vector fields). This paper investigates the accuracy of the equivalent source model using the geometry-based numerical reference model of a current loop to simulate the magnetic field distribution of a real electronic appliance. Good agreement between the equivalent source model and the reference is obtained with regard to the magnetic field distribution and the induced electric current density in a homogeneous human body model, respectively.

  7. 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.

  8. Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)

    PubMed Central

    Chen, Jun; Källman, Thomas; Ma, Xiaofei; Gyllenstrand, Niclas; Zaina, Giusi; Morgante, Michele; Bousquet, Jean; Eckert, Andrew; Wegrzyn, Jill; Neale, David; Lagercrantz, Ulf; Lascoux, Martin

    2012-01-01

    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 (FST = 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 FST. 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. PMID:22542968

  9. Microwave soft x-ray microscopy for nanoscale magnetization dynamics in the 5-10 GHz frequency range.

    PubMed

    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. PMID:26429444

  10. 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.

  11. Microwave soft x-ray microscopy for nanoscale magnetization dynamics in the 5–10 GHz frequency range

    DOE PAGES

    Bonetti, Stefano; Kukreja, Roopali; Chen, Zhao; Spoddig, Detlef; Ollefs, Katharina; Schöppner, Christian; Meckenstock, Ralf; Ney, Andreas; Pinto, Jude; Houanche, Richard; et al

    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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. The Digital Simulation of Synchronous Motors Fed by Voltage-Source Inverters Over Wide Speed and Frequency Ranges

    NASA Astrophysics Data System (ADS)

    Rowihal, Said Soliman

    Both voltage-source and current-source inverters are widely used for supplying three-phase power to induction motor drives, each having their advantages and disadvantages. For high power drives and applications requiring accurate speed and tracking coordination, the synchronous motors are the optimum choice. For constant speed applications of synchronous motor drives, current-source inverters tend to be favored as the motor can usually be operated in the overexcited leading power factor region, thus providing the inverter with sufficient electro-motive force to allow natural commutation. Generally speaking low speed operation of synchronous motors is not satisfactory from naturally commutated current-source inverters. To provide a dynamic range of speed and frequency would require expensive control circuitry and complicates the performance of the drive. The advantage of the voltage-source inverter for the wide range of speed and frequency control herein envisaged is that forced commutation is employed throughout the range and the commutating circuits have been well developed and established. On balance, voltage-source inverters represent a viable compromise for variable-speed three -phase synchronous motor drives including start-up. To investigate the transient response of the voltage -source fed-synchronous motor drives, a digital computer program is developed. The program is based on two models --machine model and inverter model. The machine is represented by a detailed two-axis model which includes the effects due to saliency, damper windings, and machine resistances. The inverter model represents a forced-commutated voltage-source inverter assuming ideal switching devices (thyristors and diodes). To cope with the wide variations of power factor during start-up, a thyristor with a reverse connected parallel diode are integrated as a bidirectional switch. The digital program provides the machine variables of interest (phase currents, field current, damper winding

  18. Study of the heating characteristics and mechanisms of magnetic nanoparticles over a wide range of frequencies and amplitudes of an alternating magnetic field

    NASA Astrophysics Data System (ADS)

    Seki, A.; Kita, E.; Isaka, D.; Kikuchi, Y.; Suzuki, K. Z.; Horiuchi, A.; Kishimoto, M.; Yanagihara, H.; Oda, T.; Ohkohchi, N.; Ikehata, H.; Nagano, I.

    2014-06-01

    An effective approach to gaining an understanding of the mechanism of heat generation for magnetic hyperthermia from nanomagnet suspensions is to perform heating tests over a wide frequency range. We constructed a heating test apparatus by using ferrite field cores with air gaps for low frequencies and solenoids for high frequencies. Magnetic field amplitudes up to 600 Oe (400 Oe) can be generated for frequencies lower than 500 kHz (800 kHz). Heat generation tests were performed for ferromagnetic nano-platelets and Co-doped Fe3O4 nanoparticles over a wide range of frequencies.

  19. 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. PMID:12919718

  20. 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.

  1. Viscoelastic behavior over a wide range of time and frequency in tin alloys: SnCd and SnSb

    SciTech Connect

    Quackenbush, J.; Brodt, M.; Lakes, R.S.

    1996-08-01

    All materials exhibit some viscoelastic response, which can manifest itself as creep, relaxation, or, if the load is sinusoidal in time, a phase angle {delta} between stress and strain. Recently, a study of pure elements with low melting points, Cd, In, Pb, and Sn disclosed that cadmium exhibited a substantial loss tangent of 0.03 to 0.04 over much of the audio range of frequencies, combined with a moderate stiffness G = 20.7 GPa. Lead, by contrast, exhibited tan {delta} of 0.005 to 0.016 in the audio range. Indium exhibited a high loss tangent exceeding 0.1 at very low frequency. A eutectic alloy of indium and tin was found to exhibit substantial damping exceeding 0.1 below 0.1 Hz, and this alloy was used to make a composite exhibiting high stiffness and high damping. It is the purpose of this communication to present viscoelastic properties of two additional low melting point alloys, SnCd and SnSb. Both InSn and SnSb are used as solders. Although the melting point of Sb is 630.74 C, T{sub H} > 0.55 at ambient temperature for the alloy of SnSb (95 wt% Sn/5 wt% Sb) which melts near 240 C. Eutectic SnCd melts at 177 C so T{sub H} {approx} 0.65 at room temperature.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. Design, performance, and grounding aspects of the International Thermonuclear Experimental Reactor ion cyclotron range of frequencies antenna

    NASA Astrophysics Data System (ADS)

    Durodié, F.; Dumortier, P.; Vrancken, M.; Messiaen, A.; Bamber, R.; Hancock, D.; Huygen, S.; Lockley, D.; Louche, F.; Maggiora, R.; Milanesio, D.; Nightingale, M. P. S.; Shannon, M.; Tigwell, P.; Van Schoor, M.; Vervier, M.; Wilson, D.; Winkler, K.

    2014-06-01

    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 RF

  7. 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).

  8. A detailed comparison of antenna impedance measurements on ASDEX Upgrade with the ion cyclotron range of frequencies antenna code TOPICA

    NASA Astrophysics Data System (ADS)

    Stepanov, I.; Noterdaeme, J.-M.; Bobkov, V.; Faugel, H.; Coster, D.; Milanesio, D.; Maggiora, R.; Siegl, G.; Bilato, R.; Brambilla, M.; Verdoolaege, G.; Braun, F.; Fünfgelder, H.; D'Inca, R.; Suttrop, W.; Kallenbach, A.; Schweinzer, J.; Wolfrum, E.; Fischer, R.; Mlynek, A.; Nikolaeva, V.; Guimarais, L.; the ASDEX Upgrade Team

    2015-09-01

    New antenna diagnostics on the ASDEX Upgrade, in the form of voltage and current probe pairs on the feeding lines of each ion cyclotron range of frequencies antenna, close to the input ports, have made it possible to study in detail the behavior of the ASDEX Upgrade two-strap antenna under changing loading conditions, and compare these measurements with the results of simulations using the TOPICA code. The present work extends previous studies by using the input impedance (more precisely, the complex voltage reflection coefficient Γ ) on each antenna port for comparison, instead of the more commonly used loading resistance or coupled power. The electron density profiles used for the simulation were reconstructed from the deuterium-carbon-nitrogen interferometer and lithium beam emission spectroscopy measurements, edge-localized mode-synchronized and averaged over time intervals from 10 to 200 ms depending on the case; 112 cases were compared from seven ASDEX Upgrade discharges with widely different plasma parameters and two operating frequencies (30 and 36.5 MHz). Very good agreement in \\vert Γ\\vert was found with the measurements on antenna 3 (<3% averaged over a shot), and good agreement was found with antennas 1 and 2 (<10%) the code reproduced the correct trend in loading resistance {{R}\\text{L}} in a significant majority of cases, although the discrepancies in the absolute values were rather high (up to  ˜50%) due to high reflection. Sources of discrepancy are discussed.

  9. Development and Applications of High—Frequency Gyrotrons in FIR FU Covering the sub-THz to THz Range

    NASA Astrophysics Data System (ADS)

    Idehara, Toshitaka; Sabchevski, Svilen Petrov

    2012-07-01

    Powerful sources of coherent radiation in the sub-terahertz and in the terahertz frequency range of the electromagnetic spectrum are necessary for a great and continuously expanding number of applications in the physical research and in various advanced technological processes as well as in radars, communication systems, for remote sensing and inspection etc.. In recent years, a spectacular progress in the development of various gyro-devices and in particular of the powerful high frequency (sub-terahertz and terahertz) gyrotron oscillators has demonstrated a remarkable potential for bridging the so-called terahertz power gap and stimulated many novel and prospective applications. In this review paper we outline two series of such devices, namely the Gyrotron FU Series which includes pulsed gyrotrons and Gyrotron FU CW Series which consist of tubes operated in a CW (continuous wave) or long pulse mode, both developed at the FIR FU Center. We present the most remarkable achievements of these devices and illustrate their applications by some characteristic examples. An outlook for the further extension of the Gyrotron FU CW Series is also provided.

  10. Low-frequency sound speed and attenuation in sandy seabottom from long-range broadband acoustic measurements.

    PubMed

    Wan, Lin; Zhou, Ji-Xun; Rogers, Peter H

    2010-08-01

    A joint China-U.S. underwater acoustics experiment was conducted in the Yellow Sea with a very flat bottom and a strong and sharp thermocline. Broadband explosive sources were deployed both above and below the thermocline along two radial lines up to 57.2 km and a quarter circle with a radius of 34 km. Two inversion schemes are used to obtain the seabottom sound speed. One is based on extracting normal mode depth functions from the cross-spectral density matrix. The other is based on the best match between the calculated and measured modal arrival times for different frequencies. The inverted seabottom sound speed is used as a constraint condition to extract the seabottom sound attenuation by three methods. The first method involves measuring the attenuation coefficients of normal modes. In the second method, the seabottom sound attenuation is estimated by minimizing the difference between the theoretical and measured modal amplitude ratios. The third method is based on finding the best match between the measured and modeled transmission losses (TLs). The resultant seabottom attenuation, averaged over three independent methods, can be expressed as alpha=(0.33+/-0.02)f(1.86+/-0.04)(dB/m kHz) over a frequency range of 80-1000 Hz.

  11. An algorithm for the calculation of 3-D ICRF (Ion Cyclotron Range of Frequencies) fields in tokamak geometry

    SciTech Connect

    Smithe, D.N.; Colestock, P.L.; Kashuba, R.J.; Kammash, T.

    1987-04-01

    A computational scheme is developed which permits tractable calculation of three-dimensional full-wave solutions to the Maxwell-Vlasov equations under typical Ion Cyclotron Range of Frequencies (ICRF) experimental conditions. The method is unique in that power deposition to the plasma is determined via the anti-Hermitian part of a truncated warm-plasma dielectric operator, rather than as the result of an assumed phenomenological collision frequency. The resulting computer code allows arbitrary variation of density, temperature, magnetic field, and minority concentration in the poloidal plane by performing a convolution of poloidal modes to produce a coupled system of differential equations in the radial variable. By assuming no inhomogeneity along the toroidal axis, an inverse transform over k/sub parallel/ is performed to yield the full three-dimensional field solutions. The application of the code to TFTR-like plasmas shows a mild resonance structure in antenna loading related to the changing number of wavelengths between antenna and the resonance layer. 48 figs.

  12. Adaptive three-dimensional range-crossrange-frequency filter processing string for sea mine classification in side scan sonar imagery

    NASA Astrophysics Data System (ADS)

    Aridgides, Tom; Fernandez, Manuel F.; Dobeck, Gerald J.

    1997-07-01

    An automatic, robust, adaptive clutter suppression, predetection level fusion, sea mine detection and classification processing string has been developed and applied to shallow water side-scan sonar imagery data. The overall processing string includes pre-processing string includes pre-processing, adaptive clutter filtering (ACF), 2D normalization, detection, feature extraction and classification processing blocks. The pre-processing block contains automatic gain control, data decimation and data alignment processing. The ACF is a multi-dimensional adaptive linear FIR filter, optimal in the least squares sense, for simultaneous background clutter suppression and preservation of an average peak target signature. After data alignment, using a 3D ACF enables simultaneous multiple frequency data fusion and clutter suppression in the composite frequency-range-crossrange domain. Following 2D normalization, the detection consists of thresholding, clustering of exceedances and limiting their number. Finally, features are extracted and a orthogonalization transformation is applied to the data, enabling an efficient application of the optimal log-likelihood-ratio-test (LLRT) classification rule. The utility of the overall processing string was demonstrated with two side-scan sonar data sets. The ACF, feature orthogonalization, LLRT-based classification processing string provided average probability of correct mine classification and false alarm rate performance exceeding the one obtained when utilizing an expert sonar operator. The overall processing string can be easily implemented in real-time using COTS technology.

  13. Optimization of electrode size for aluminum-nitride matrix ultrasonic transducers in the frequency range above 200 MHz.

    PubMed

    Wei, Yangjie; Herzog, Thomas; Heuer, Henning

    2013-03-01

    This paper describes an optimization method of the top electrode size for a thin film matrix ultrasonic transducer (M-UT) in the frequency range above 200 MHz. The goal of this work is to design an optimal top electrode size for an M-UT providing the maximal output peak-peak voltage (V(PP)) and the maximal signal-to-noise ratio (SNR) without additional electrical impedance matching. In order to reduce the complexity of the M-UT with more than 1000 elements, an intrinsic matching by electrode size variation is necessary. However, the size of a single element top electrode for an M-UT is related to the number of elements within a targeted sensor area, V(PP) and SNR of the transducer. In this paper, varying the active area of the top electrode from 0.09 to 25 mm(2) shows that for an Al-AlN-Al on silicon wafer configuration connected with a JSR Ultrasonics pulser/receiver (50 ohms), the optimal electrode size is 1 mm(2). With the optimal size electrode, the maximum output V(PP) of 0.08 V and the SNR of 42.93 dB are achieved at the resonance frequency of 225 MHz, and the bandwidth is 16.21 MHz.

  14. Photonic crystal fiber with a dual-frequency addressable liquid crystal: behavior in the visible wavelength range.

    PubMed

    Lorenz, A; Kitzerow, H-S; Schwuchow, A; Kobelke, J; Bartelt, H

    2008-11-10

    Wave-guiding in the visible spectral range is investigated for a micro-structured crystal fiber filled with a dual-frequency addressable nematic liquid crystal mixture. The fiber exhibits a solid core surrounded by just 4 rings of cylindrical holes. Control of the liquid crystal alignment by anchoring agents permits relatively low attenuation. Samples with different anchoring conditions at the interface of the silica glass and the liquid crystal show different transmission properties and switching behavior. Polarization dependent and independent fiber optic switching is observed. Due to a dualfrequency addressing scheme, active switching to both states with enhanced and reduced transmission becomes possible for planar anchoring. Even a non-perfect fiber shows reasonable transmission and a variety of interesting effects.

  15. A solar plasma stream measured by DRVID and dual-frequency range and Doppler radio metric data

    NASA Technical Reports Server (NTRS)

    Winn, F. B.; Wu, S. C.; Komarek, T. A.; Lam, V. W.; Royden, H. N.; Yip, K. B. W.

    1977-01-01

    S- and X-band DRVID, S- and X-band dual-frequency range (SX(p)), and Doppler (SX(p)) measured a 15-fold increase in the line-of-sight electron content of the solar plasma above the normal plasma background. A general increase in the plasma electron content continued for nearly 50 hours: it started about 12:00 (GMT) on 12 March 1976 and continued to grow until 17:00 (GMT) on 14 March. For the next 55 hours, between 17:00 (GMT) on 14 March to 00:54 (GMT) on 17 March, the plasma level diminished as the background level was approached. Not only were the temporal changes and absolute level of the plasma content measured but the measurements were also used to ascertain the mean-plasma-concentration location: it was estimated to be 4.1 light minutes from earth.

  16. 750 nm 1.5 W frequency-doubled semiconductor disk laser with a 44 nm tuning range.

    PubMed

    Saarinen, Esa J; Lyytikäinen, Jari; Ranta, Sanna; Rantamäki, Antti; Sirbu, Alexei; Iakovlev, Vladimir; Kapon, Eli; Okhotnikov, Oleg G

    2015-10-01

    We demonstrate 1.5 W of output power at the wavelength of 750 nm by intracavity frequency doubling a wafer-fused semiconductor disk laser diode-pumped at 980 nm. An optical-to-optical efficiency of 8.3% was achieved using a bismuth borate crystal. The wavelength of the doubled emission could be tuned from 720 to 764 nm with an intracavity birefringent plate. The beam quality parameter M2 of the laser output was measured to be below 1.5 at all pump powers. The laser is a promising tool for biomedical applications that can take advantage of the large penetration depth of light in tissue in the 700-800 nm spectral range.

  17. Photonic crystal fiber with a dual-frequency addressable liquid crystal: behavior in the visible wavelength range.

    PubMed

    Lorenz, A; Kitzerow, H-S; Schwuchow, A; Kobelke, J; Bartelt, H

    2008-11-10

    Wave-guiding in the visible spectral range is investigated for a micro-structured crystal fiber filled with a dual-frequency addressable nematic liquid crystal mixture. The fiber exhibits a solid core surrounded by just 4 rings of cylindrical holes. Control of the liquid crystal alignment by anchoring agents permits relatively low attenuation. Samples with different anchoring conditions at the interface of the silica glass and the liquid crystal show different transmission properties and switching behavior. Polarization dependent and independent fiber optic switching is observed. Due to a dualfrequency addressing scheme, active switching to both states with enhanced and reduced transmission becomes possible for planar anchoring. Even a non-perfect fiber shows reasonable transmission and a variety of interesting effects. PMID:19582031

  18. Microwave Absorption Properties of Ni-Foped SiC Powders in the 2-18 GHz Frequency Range

    NASA Astrophysics Data System (ADS)

    Jin, Hai-Bo; Li, Dan; Cao, Mao-Sheng; Dou, Yan-Kun; Chen, Tao; Wen, Bo; Simeon, Agathopoulos

    2011-03-01

    Ni-doped SiC powder with improved dielectric and microwave absorption properties was prepared by self-propagating high-temperature synthesis (SHS). The XRD analysis of the as-synthesized powders suggests that Ni is accommodated in the sites of Si in the lattice of SiC, which shrinks in the presence of Ni. The experimental results show an improvement in the dielectric properties of the Ni-doped SiC powder in the frequency range of 2-18 GHz. The bandwidth of the reflection loss below -10 dB is broadened from 3.04 (for pure SiC) to 4.56 GHz (for Ni-doped SiC), as well as the maximum reflection loss of produced powders from 13.34 to 22.57 dB, indicating that Ni-doped SiC could be used as an effective microwave absorption material.

  19. 750 nm 1.5 W frequency-doubled semiconductor disk laser with a 44 nm tuning range.

    PubMed

    Saarinen, Esa J; Lyytikäinen, Jari; Ranta, Sanna; Rantamäki, Antti; Sirbu, Alexei; Iakovlev, Vladimir; Kapon, Eli; Okhotnikov, Oleg G

    2015-10-01

    We demonstrate 1.5 W of output power at the wavelength of 750 nm by intracavity frequency doubling a wafer-fused semiconductor disk laser diode-pumped at 980 nm. An optical-to-optical efficiency of 8.3% was achieved using a bismuth borate crystal. The wavelength of the doubled emission could be tuned from 720 to 764 nm with an intracavity birefringent plate. The beam quality parameter M2 of the laser output was measured to be below 1.5 at all pump powers. The laser is a promising tool for biomedical applications that can take advantage of the large penetration depth of light in tissue in the 700-800 nm spectral range. PMID:26421536

  20. Synchronous waves of failed soft sweeps in the laboratory: remarkably rampant clonal interference of alleles at a single locus.

    PubMed

    Lee, Ming-Chun; Marx, Christopher J

    2013-03-01

    It has increasingly been recognized that adapting populations of microbes contain not one, but many lineages continually arising and competing at once. This process, termed "clonal interference," alters the rate and dynamics of adaptation and biases winning mutations toward those with the largest selective effect. Here we uncovered a dramatic example of clonal interference between multiple similar mutations occurring at the same locus within replicate populations of Methylobacterium extorquens AM1. Because these mutational events involved the transposition of an insertion sequence into a narrow window of a single gene, they were both readily detectable at low frequencies and could be distinguished due to differences in insertion sites. This allowed us to detect up to 17 beneficial alleles of this type coexisting in a single population. Despite conferring a large selective benefit, the majority of these alleles rose and then fell in frequency due to other lineages emerging that were more fit. By comparing allele-frequency dynamics to the trajectories of fitness gains by these populations, we estimated the fitness values of the genotypes that contained these mutations. Collectively across all populations, these alleles arose upon backgrounds with a wide range of fitness values. Within any single population, however, multiple alleles tended to rise and fall synchronously during a single wave of multiple genotypes with nearly identical fitness values. These results suggest that alleles of large benefit arose repeatedly in failed "soft sweeps" during narrow windows of adaptation due to the combined effects of epistasis and clonal interference. PMID:23307898

  1. Investigation of electrostatic waves in the ion cyclotron range of frequencies in L-4 and ACT-1

    SciTech Connect

    Ono, Masayuki.

    1993-05-01

    Electrostatic waves in the ion cyclotron range of frequencies (ICRF) were studied in the Princeton L-4 and ACT-1 devices for approximately ten years, from 1975 to 1985. The investigation began in the L-4 linear device, looking for the parametric excitation of electrostatic ion cyclotron waves in multi-ion-species plasmas. In addition, this investigation verified multi-ion-species effects on the electrostatic ion cyclotron wave dispersion religion including the ion-ion hybrid resonance. Finite-Larmor-radius modification of the wave dispersion relation was also observed, even for ion temperatures of T[sub i] [approx] 1/40 eV. Taking advantage of the relatively high field and long device length of L-4, the existence of the cold electrostatic ion cyclotron wave (CES ICW) was verified. With the arrival of the ACT-1 toroidal device, finite-Larmor-radius (FLR) waves were studied in a relatively collisionless warm-ion hydrogen plasma. Detailed investigations of ion Bernstein waves (IBW) included the verification of mode-transformation in their launching, their wave propagation characteristics, their absorption, and the resulting ion heating. This basic physics activity played a crucial role in developing a new reactor heating concept termed ion Bernstein wave heating. Experimental research in the lower hybrid frequency range confirmed the existence of FLR effects near the lower hybrid resonance, predicted by Stix in 1965. In a neon plasma with a carefully placed phased wave exciter, the neutralized ion Bernstein wave was observed for the first time. Using a fastwave ICRF antenna, two parasitic excitation processes for IBW -- parametric instability and density-gradient-driven excitation -- were also discovered. In the concluding section of this paper, a possible application of externally launched electrostatic waves is suggested for helium ash removal from fusion reactor plasmas.

  2. Investigation of electrostatic waves in the ion cyclotron range of frequencies in L-4 and ACT-1

    SciTech Connect

    Ono, Masayuki

    1993-05-01

    Electrostatic waves in the ion cyclotron range of frequencies (ICRF) were studied in the Princeton L-4 and ACT-1 devices for approximately ten years, from 1975 to 1985. The investigation began in the L-4 linear device, looking for the parametric excitation of electrostatic ion cyclotron waves in multi-ion-species plasmas. In addition, this investigation verified multi-ion-species effects on the electrostatic ion cyclotron wave dispersion religion including the ion-ion hybrid resonance. Finite-Larmor-radius modification of the wave dispersion relation was also observed, even for ion temperatures of T{sub i} {approx} 1/40 eV. Taking advantage of the relatively high field and long device length of L-4, the existence of the cold electrostatic ion cyclotron wave (CES ICW) was verified. With the arrival of the ACT-1 toroidal device, finite-Larmor-radius (FLR) waves were studied in a relatively collisionless warm-ion hydrogen plasma. Detailed investigations of ion Bernstein waves (IBW) included the verification of mode-transformation in their launching, their wave propagation characteristics, their absorption, and the resulting ion heating. This basic physics activity played a crucial role in developing a new reactor heating concept termed ion Bernstein wave heating. Experimental research in the lower hybrid frequency range confirmed the existence of FLR effects near the lower hybrid resonance, predicted by Stix in 1965. In a neon plasma with a carefully placed phased wave exciter, the neutralized ion Bernstein wave was observed for the first time. Using a fastwave ICRF antenna, two parasitic excitation processes for IBW -- parametric instability and density-gradient-driven excitation -- were also discovered. In the concluding section of this paper, a possible application of externally launched electrostatic waves is suggested for helium ash removal from fusion reactor plasmas.

  3. The Contribution of Microbunching Instability to Solar Flare Emission in the GHz to THz Range of Frequencies

    NASA Astrophysics Data System (ADS)

    Klopf, J. Michael; Kaufmann, Pierre; Raulin, Jean-Pierre; Szpigel, Sérgio

    2014-08-01

    Recent solar flare observations in the sub-terahertz range have provided evidence of a new spectral component with fluxes increasing for larger frequencies, separated from the well-known microwave emission that maximizes in the gigahertz range. Suggested interpretations explain the terahertz spectral component but do not account for the simultaneous microwave component. We present a mechanism for producing the observed "double spectra." Based on coherent enhancement of synchrotron emission at long wavelengths in laboratory accelerators, we consider how similar processes may occur within a solar flare. The instability known as microbunching arises from perturbations that produce electron beam density modulations, giving rise to broadband coherent synchrotron emission at wavelengths comparable to the characteristic size of the microbunch structure. The spectral intensity of this coherent synchrotron radiation (CSR) can far exceed that of the incoherent synchrotron radiation (ISR), which peaks at a higher frequency, thus producing a double-peaked spectrum. Successful CSR simulations are shown to fit actual burst spectral observations, using typical flaring physical parameters and power-law energy distributions for the accelerated electrons. The simulations consider an energy threshold below which microbunching is not possible because of Coulomb repulsion. Only a small fraction of the radiating charges accelerated to energies above the threshold is required to produce the microwave component observed for several events. The ISR/CSR mechanism can occur together with other emission processes producing the microwave component. It may bring an important contribution to microwaves, at least for certain events where physical conditions for the occurrence of the ISR/CSR microbunching mechanism are possible.

  4. The contribution of microbunching instability to solar flare emission in the GHz to THz range of frequencies

    SciTech Connect

    Klopf, J. Michael; Kaufmann, Pierre; Raulin, Jean-Pierre; Szpigel, Sergio

    2014-07-01

    Recent solar flare observations in the sub-terahertz range have provided evidence of a new spectral component with fluxes increasing for larger frequencies, separated from the well-known microwave emission that maximizes in the gigahertz range. Suggested interpretations explain the terahertz spectral component but do not account for the simultaneous microwave component. We present a mechanism for producing the observed "double spectra." Based on coherent enhancement of synchrotron emission at long wavelengths in laboratory accelerators, we consider how similar processes may occur within a solar flare. The instability known as microbunching arises from perturbations that produce electron beam density modulations, giving rise to broadband coherent synchrotron emission at wavelengths comparable to the characteristic size of the microbunch structure. The spectral intensity of this coherent synchrotron radiation (CSR) can far exceed that of the incoherent synchrotron radiation (ISR), which peaks at a higher frequency, thus producing a double-peaked spectrum. Successful CSR simulations are shown to fit actual burst spectral observations, using typical flaring physical parameters and power-law energy distributions for the accelerated electrons. The simulations consider an energy threshold below which microbunching is not possible because of Coulomb repulsion. Only a small fraction of the radiating charges accelerated to energies above the threshold is required to produce the microwave component observed for several events. The ISR/CSR mechanism can occur together with other emission processes producing the microwave component. It may bring an important contribution to microwaves, at least for certain events where physical conditions for the occurrence of the ISR/CSR microbunching mechanism are possible.

  5. Lattice dynamics and dielectric response of Mg-doped SrTiO3 ceramics in a wide frequency range

    NASA Astrophysics Data System (ADS)

    Tkach, A.; Vilarinho, P. M.; Kholkin, A. L.; Pashkin, A.; Samoukhina, P.; Pokorny, J.; Veljko, S.; Petzelt, J.

    2005-02-01

    Atomic substitutions in the SrTiO3 (ST) perovskite lattice are foreseen to modify the lattice vibration modes, which are apparently sensitive to the site at which the substitution occurs. In order to understand the effect of Mg substitution in the ST lattice, the dielectric properties of Sr1-xMgxTiO3 and SrTi1-yMgyO3-δ ceramics were investigated in radio frequency (rf), microwave, terahertz (THz), and infrared (IR) ranges. Micro-Raman spectroscopy and rf tunability measurements were also conducted on these samples. The micro-Raman spectra and the high-frequency dielectric properties of Sr1-xMgxTiO3, including rf tunability, do not differ considerably from the properties of undoped SrTiO3, confirming only slight (if any) incorporation of Mg into the Sr site of ST perovskite lattice. At the same time, Ti-site Mg doping results in significant stiffening of the soft lattice mode observed in IR reflectivity spectra. Dielectric permittivity and dielectric losses decrease in both rf and THz ranges accompanied by the decrease of the tunability, in accordance with the stiffened ferroelectric soft mode. The appearance in the Raman spectra of the forbidden polar modes TO4 at 545cm-1 and TO2 at 174cm-1 at room temperature and their strengthening on cooling, demonstrate the local loss of the inversion center and the breaking of the cubic symmetry by the substitution of Ti4+ by Mg2+ ions. These results confirm more favorable occupation of Mg at the Ti site of the ST lattice and show the possibility of using Ti-site Mg-doped ST as an active material for low-loss microwave waveguides and resonators.

  6. The contribution of microbunching instability to solar flare emission in the GHz to THz range of frequencies

    SciTech Connect

    Michael Klopf, J.; Kaufmann, Pierre; Raulin, Jean-Pierre; Szpigel, Sérgio

    2014-08-10

    Recent solar flare observations in the sub-terahertz range have provided evidence of a new spectral component with fluxes increasing for larger frequencies, separated from the well-known microwave emission that maximizes in the gigahertz range. Suggested interpretations explain the terahertz spectral component but do not account for the simultaneous microwave component. We present a mechanism for producing the observed 'double spectra'. Based on coherent enhancement of synchrotron emission at long wavelengths in laboratory accelerators, we consider how similar processes may occur within a solar flare. The instability known as microbunching arises from perturbations that produce electron beam density modulations, giving rise to broadband coherent synchrotron emission at wavelengths comparable to the characteristic size of the microbunch structure. The spectral intensity of this coherent synchrotron radiation (CSR) can far exceed that of the incoherent synchrotron radiation (ISR), which peaks at a higher frequency, thus producing a double-peaked spectrum. Successful CSR simulations are shown to fit actual burst spectral observations, using typical flaring physical parameters and power-law energy distributions for the accelerated electrons. The simulations consider an energy threshold below which microbunching is not possible because of Coulomb repulsion. Only a small fraction of the radiating charges accelerated to energies above the threshold is required to produce the microwave component observed for several events. The ISR/CSR mechanism can occur together with other emission processes producing the microwave component. It may bring an important contribution to microwaves, at least for certain events where physical conditions for the occurrence of the ISR/CSR microbunching mechanism are possible.

  7. Novel Reactor Relevant RF Actuator Schemes for the Lower Hybrid and the Ion Cyclotron Range of Frequencies

    NASA Astrophysics Data System (ADS)

    Bonoli, Paul

    2014-10-01

    This paper presents a fresh physics perspective on the onerous problem of coupling and successfully utilizing ion cyclotron range of frequencies (ICRF) and lower hybrid range of frequencies (LHRF) actuators in the harsh environment of a nuclear fusion reactor. The ICRF and LH launchers are essentially first wall components in a fusion reactor and as such will be subjected to high heat fluxes. The high field side (HFS) of the plasma offers a region of reduced heat flux together with a quiescent scrape off layer (SOL). Placement of the ICRF and LHRF launchers on the tokamak HFS also offers distinct physics advantages: The higher toroidal magnetic field makes it possible to couple faster phase velocity LH waves that can penetrate farther into the plasma core and be absorbed by higher energy electrons, thereby increasing the current drive efficiency. In addition, re-location of the LH launcher off the mid-plane (i.e., poloidal ``steering'') allows further control of the deposition location. Also ICRF waves coupled from the HFS couple strongly to mode converted ion Bernstein waves and ion cyclotron waves waves as the minority density is increased, thus opening the possibility of using this scheme for flow drive and pressure control. Finally the quiescent nature of the HFS scrape off layer should minimize the effects of RF wave scattering from density fluctuations. Ray tracing / Fokker Planck simulations will be presented for LHRF applications in devices such as the proposed Advanced Divertor Experiment (ADX) and extending to ITER and beyond. Full-wave simulations will also be presented which demonstrate the possible combinations of electron and ion heating via ICRF mode conversion. Work supported by the US DoE under Contract Numbers DE-FC02-01ER54648 and DE-FC02-99ER54512.

  8. Effects of sample size and sampling frequency on studies of brown bear home ranges and habitat use

    USGS Publications Warehouse

    Arthur, Steve M.; Schwartz, Charles C.

    1999-01-01

    We equipped 9 brown bears (Ursus arctos) on the Kenai Peninsula, Alaska, with collars containing both conventional very-high-frequency (VHF) transmitters and global positioning system (GPS) receivers programmed to determine an animal's position at 5.75-hr intervals. We calculated minimum convex polygon (MCP) and fixed and adaptive kernel home ranges for randomly-selected subsets of the GPS data to examine the effects of sample size on accuracy and precision of home range estimates. We also compared results obtained by weekly aerial radiotracking versus more frequent GPS locations to test for biases in conventional radiotracking data. Home ranges based on the MCP were 20-606 km2 (x = 201) for aerial radiotracking data (n = 12-16 locations/bear) and 116-1,505 km2 (x = 522) for the complete GPS data sets (n = 245-466 locations/bear). Fixed kernel home ranges were 34-955 km2 (x = 224) for radiotracking data and 16-130 km2 (x = 60) for the GPS data. Differences between means for radiotracking and GPS data were due primarily to the larger samples provided by the GPS data. Means did not differ between radiotracking data and equivalent-sized subsets of GPS data (P > 0.10). For the MCP, home range area increased and variability decreased asymptotically with number of locations. For the kernel models, both area and variability decreased with increasing sample size. Simulations suggested that the MCP and kernel models required >60 and >80 locations, respectively, for estimates to be both accurate (change in area <1%/additional location) and precise (CV < 50%). Although the radiotracking data appeared unbiased, except for the relationship between area and sample size, these data failed to indicate some areas that likely were important to bears. Our results suggest that the usefulness of conventional radiotracking data may be limited by potential biases and variability due to small samples. Investigators that use home range estimates in statistical tests should consider the

  9. Frequency conversion of molecular gas lasers in PbIn6Te10 crystal within mid-IR range.

    PubMed

    Ionin, A A; Kinyaevskiy, I O; Klimachev, Y M; Kotkov, A A; Badikov, V V; Mitin, K V

    2016-05-15

    PbIn6Te10 is a new mid-infrared (IR) nonlinear crystal with a very wide transparency range from 1.7 up to 31 μm. Calculated phase-matching angles show possibility of frequency conversion throughout the transparency range. Sum frequency generation of multiline carbon monoxide (CO) laser and difference frequency generation when mixing CO and carbon dioxide laser radiation were experimentally studied. Laser-induced damage threshold and frequency conversion efficiency under multiline CO laser pumping were measured.

  10. Frequency-range discriminations and absolute pitch in black-capped chickadees (Poecile atricapillus), mountain chickadees (Poecile gambeli), and zebra finches (Taeniopygia guttata).

    PubMed

    Lee, Tiffany T Y; Charrier, Isabelle; Bloomfield, Laurie L; Weisman, Ronald G; Sturdy, Christopher B

    2006-08-01

    The acoustic frequency ranges in birdsongs provide important absolute pitch cues for the recognition of conspecifics. Black-capped chickadees (Poecile atricapillus), mountain chickadees (Poecile gambeli), and zebra finches (Taeniopygia guttata) were trained to sort tones contiguous in frequency into 8 ranges on the basis of associations between response to the tones in each range and reward. All 3 species acquired accurate frequency-range discriminations, but zebra finches acquired the discrimination in fewer trials and to a higher standard than black-capped or mountain chickadees, which did not differ appreciably in the discrimination. Chickadees' relatively poorer accuracy was traced to poorer discrimination of tones in the higher frequency ranges. During transfer tests, the discrimination generalized to novel tones when the training tones were included, but not when they were omitted.

  11. Frequency-range discriminations and absolute pitch in black-capped chickadees (Poecile atricapillus), mountain chickadees (Poecile gambeli), and zebra finches (Taeniopygia guttata).

    PubMed

    Lee, Tiffany T Y; Charrier, Isabelle; Bloomfield, Laurie L; Weisman, Ronald G; Sturdy, Christopher B

    2006-08-01

    The acoustic frequency ranges in birdsongs provide important absolute pitch cues for the recognition of conspecifics. Black-capped chickadees (Poecile atricapillus), mountain chickadees (Poecile gambeli), and zebra finches (Taeniopygia guttata) were trained to sort tones contiguous in frequency into 8 ranges on the basis of associations between response to the tones in each range and reward. All 3 species acquired accurate frequency-range discriminations, but zebra finches acquired the discrimination in fewer trials and to a higher standard than black-capped or mountain chickadees, which did not differ appreciably in the discrimination. Chickadees' relatively poorer accuracy was traced to poorer discrimination of tones in the higher frequency ranges. During transfer tests, the discrimination generalized to novel tones when the training tones were included, but not when they were omitted. PMID:16893259

  12. A preliminary study on the prediction of damaged areas on ordinary concrete and lightweight concrete using electromechanical impedance technique with different frequency ranges

    NASA Astrophysics Data System (ADS)

    Cho, K. J.; Na, S.; Jang, J. G.; Lee, H. K.

    2014-03-01

    The electromechanical impedance (EMI) method for NDE uses a single piezoelectric material to act as an actuator and a sensor simultaneously, and the EMI method is suitable for structures with complex surfaces. However, this technique still has wide range of problems which needs to be investigated. For one, locating damaged areas on a host structure precisely is known to be extremely difficult as this non-model based technique heavily relies on the variations in the impedance signatures. In this study, an attempt to locate the damaged areas on an ordinary concrete panel and a lightweight concrete panel using bottom ash is carried out by using different frequency ranges. Since the sensing range decreases as the excitation frequency of piezoelectric material increases, one can possibly predict the damaged areas by analyzing the impedance signatures from different frequency ranges. Statistical analysis method such as root mean square deviation (RMSD) is applied to determine the changes of the experimental structures, and the RMSD values of low frequency range and high frequency range are compared to verify the relationship between the frequency range and sensing range. Furthermore, the applicability of this method to locating the damaged areas is investigated on various materials including the lightweight concrete.

  13. 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...

  14. Polymorphisms in the cytochrome P450 CYP1A2 gene (CYP1A2) in colorectal cancer patients and controls: allele frequencies, linkage disequilibrium and influence on caffeine metabolism

    PubMed Central

    Sachse, Christoph; Bhambra, Upinder; Smith, Gillian; Lightfoot, Tracy J; Barrett, Jennifer H; Scollay, Jenna; Garner, R Colin; Boobis, Alan R; Wolf, C Roland; Gooderham, Nigel J

    2003-01-01

    Aim Several single nucleotide polymorphisms (SNPs) of the cytochrome P450 enzyme 1A2 gene (CYP1A2) have been reported. Here, frequencies, linkage disequilibrium and phenotypic consequences of six SNPs are described. Methods From genomic DNA, 114 British Caucasians (49 colorectal cancer cases and 65 controls) were genotyped for the CYP1A2 polymorphisms −3858G→A (allele CYP1A2*1C), −2464T→delT (CYP1A2*1D), −740T→G (CYP1A2*1E and *1G), −164A→C (CYP1A2*1F), 63C→G (CYP1A2*2), and 1545T→C (alleles CYP1A2*1B, *1G, *1H and *3), using polymerase chain reaction–restriction fragment length polymorphism assays. All patients and controls were phenotyped for CYP1A2 by h.p.l.c. analysis of urinary caffeine metabolites. Results In 114 samples, the most frequent CYP1A2 SNPs were 1545T→C (38.2% of tested chromosomes), −164A→C (CYP1A2*1F, 33.3%) and −2464T→delT (CYP1A2*1D, 4.82%). The SNPs were in linkage disequilibrium: the most frequent constellations were found to be −3858G/−2464T/−740T/−164A/63C/1545T (61.8%), −3858G/−2464T/−740T/−164C/63C/1545C (33.3%), and −3858G/−2464delT/−740T/−164A/63C/1545C (3.51%), with no significant frequency differences between cases and controls. In the phenotype analysis, lower caffeine metabolic ratios were detected in cases than in controls. This was significant in smokers (n = 14, P = 0.020), and in a subgroup of 15 matched case-control pairs (P = 0.007), but it was not significant in nonsmokers (n = 100, P = 0.39). There was no detectable association between CYP1A2 genotype and caffeine phenotype. Conclusions (i) CYP1A2 polymorphisms are in linkage disequilibrium. Therefore, only −164A→C (CYP1A2*1F) and −2464T→delT (CYP1A2*1D) need to be analysed in the routine assessment of CYP1A2 genotype; (ii) in vivo CYP1A2 activity is lower in colorectal cancer patients than in controls, and (iii) CYP1A2 genotype had no effect on phenotype (based on the caffeine metabolite ratio). However, this

  15. Microstrip Antennas with Polarization Diversity across a Wide Frequency Range and Phased Array Antennas for Radar and Satellite Communications

    NASA Astrophysics Data System (ADS)

    Ho, Kevin Ming-Jiang

    The thesis comprises of 3 projects; an L-band microstrip antenna with frequency agility and polarization diversity, X-band phased array antennas incorporating commercially packaged RFIC phased array chips, and studies for Ku/Ka-band shared aperture antenna array. The first project features the use of commercially packaged RF-MEMS SPDT switches, that boasts of high reliability, high linearity, low losses, hermetically packaged and fully compatible for SMTA processes for mass-assembly and production. Using the switches in a novel manner for the feed network, microstrip antennas with polarization diversity are presented. Frequency agility is achieved with the use of tuning diodes to provide capacitive loading to the antenna element. Additional inductance effects from surface-mounted capacitors, and its impact, is introduced. Theoretical cross-polarization of probe-fed antenna elements is presented for both linear and circular polarized microstrip antennas. Designs and measurements are presented, for microstrip antennas with polarization diversity, wide frequency tuning range, and both features. Replacement of the tuning diodes with commercially-packaged high Q RF MEMS tunable capacitors will allow for significant improvements to the radiation efficiency. In another project, multi-channel CMOS RFIC phased-array receiver chips are assembled in QFN packages and directly integrated on the same multi-layered PCB stack-up with the antenna arrays. Problems of isolation from the PCB-QFN interface, and potential performance degradation on antenna array from the use of commercial-grade laminates for assembly requirements, namely potential scan blindness and radiation efficiency, are presented. Causes for apparent drift of dielectric constant for microstrip circuits, and high conductor losses observed in measurements, are introduced. Finally, studies are performed for the design of a Ku/Ka-Band shared aperture array. Different approaches for developing dual-band shared apertures

  16. Frequency range selection method of trans-impedance amplifier for high sensitivity lock-in amplifier used in the optical sensors

    NASA Astrophysics Data System (ADS)

    Park, Chang-In; Jeon, Su-Jin; Hong, Nam-Pyo; Choi, Young-Wan

    2016-03-01

    Lock-in amplifier (LIA) has been proposed as a detection technique for optical sensors because it can measure low signal in high noise level. LIA uses synchronous method, so the input signal frequency is locked to a reference frequency that is used to carry out the measurements. Generally, input signal frequency of LIA used in optical sensors is determined by modulation frequency of optical signal. It is important to understand the noise characteristics of the trans-impedance amplifier (TIA) to determine the modulation frequ