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Sample records for allele frequency shifts

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

    PubMed Central

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

    2015-01-01

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. PMID:26560341

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  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. Frequency-Shift Hearing Aid

    NASA Technical Reports Server (NTRS)

    Weinstein, Leonard M.

    1994-01-01

    Proposed hearing aid maps spectrum of speech into band of lower frequencies at which ear remains sensitive. By redirecting normal speech frequencies into frequency band from 100 to 1,500 Hz, hearing aid allows people to understand normal conversation, including telephone calls. Principle operation of hearing aid adapted to other uses such as, clearing up noisy telephone or radio communication. In addition, loud-speakers more easily understood in presence of high background noise.

  13. Frequency shift by optical coherent control

    SciTech Connect

    Ignesti, Emilio; Buffa, Roberto; Fini, Lorenzo; Sali, Emiliano; Cavalieri, Stefano; Tognetti, Marco V.

    2010-02-15

    We report the experimental observation of an optically controllable shift of the central frequency of a laser pulse, using a scheme based on dynamical electromagnetically induced transparency. This is evidence of frequency shift controllable by a coherent process. Original theoretical results are in agreement with the experimental data.

  14. 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.

  15. 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

  16. 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.

  17. Broadband frequency demodulator for detecting small frequency shifts

    NASA Astrophysics Data System (ADS)

    Weyand, K.; Simon, E.

    1980-03-01

    A technique is presented that enables the indication of the smallest frequency-modulation shifts over a wide carrier-frequency range. Through coil-less modulation following conversion of the carrier-frequency, and subsequent phase-sensitive rectification of the low-frequency signal, it is possible to achieve high linearity and resolution over a frequency range of 20 kHz through 4 MHz. It is noted that the smallest frequency shift that can still be detected is 10 to the -4th Hz.

  18. Frequency shifts in gravitational resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Baeßler, S.; Nesvizhevsky, V. V.; Pignol, G.; Protasov, K. V.; Rebreyend, D.; Kupriyanova, E. A.; Voronin, A. Yu.

    2015-02-01

    Quantum states of ultracold neutrons in a gravitational field are characterized through gravitational resonance spectroscopy. This paper discusses systematic effects that appear in the spectroscopic measurements. The discussed frequency shifts—which we call the Stern-Gerlach shift, interference shift, and spectator-state shift—appear in conceivable measurement schemes and have general importance. These shifts have to be taken into account in precision experiments.

  19. 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

  20. 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.

  1. 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

  2. Data for phase angle shift with frequency

    PubMed Central

    Paul, T.; Banerjee, D.; Kargupta, K.

    2016-01-01

    Phase angle shift between the current and voltage with frequency has been reported for a single phosphoric acid fuel cell in the cell temperature from 100 °C to 160 °C and the humidifier temperature from 40 °C to 90 °C. An electrochemical workbench is employed to find the shift. The figure of phase angle shift shows a peak in high humidifier temperatures. The peak in phase angle shift directs to lower frequency side with decreasing humidifier temperature. The estimation of electrochemical reaction time is also evaluated in the humidifier temperature zone from 50 °C to 90 °C. PMID:27158655

  3. 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

  4. 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.

  5. 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

  6. 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

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

    PubMed Central

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

  8. 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

  9. Wideband Doppler frequency shift measurement and direction ambiguity resolution using optical frequency shift and optical heterodyning.

    PubMed

    Lu, Bing; Pan, Wei; Zou, Xihua; Yan, Xianglei; Yan, Lianshan; Luo, Bin

    2015-05-15

    A photonic approach for both wideband Doppler frequency shift (DFS) measurement and direction ambiguity resolution is proposed and experimentally demonstrated. In the proposed approach, a light wave from a laser diode is split into two paths. In one path, the DFS information is converted into an optical sideband close to the optical carrier by using two cascaded electro-optic modulators, while in the other path, the optical carrier is up-shifted by a specific value (e.g., from several MHz to hundreds of MHz) using an optical-frequency shift module. Then the optical signals from the two paths are combined and detected by a low-speed photodetector (PD), generating a low-frequency electronic signal. Through a subtraction between the specific optical frequency shift and the measured frequency of the low-frequency signal, the value of DFS is estimated from the derived absolute value, and the direction ambiguity is resolved from the derived sign (i.e., + or -). In the proof-of-concept experiments, DFSs from -90 to 90 kHz are successfully estimated for microwave signals at 10, 15, and 20 GHz, where the estimation errors are lower than ±60  Hz. The estimation errors can be further reduced via the use of a more stable optical frequency shift module.

  10. 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.

  11. 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)

  12. Reduction of frequency noise and frequency shift by phase shifting elements in frequency modulation atomic force microscopy

    SciTech Connect

    Kobayashi, Kei; Yamada, Hirofumi; Matsushige, Kazumi

    2011-03-15

    We recently reported the analysis of the frequency noise in the frequency modulation atomic force microscopy (FM-AFM) both in high-Q and low-Q environments [Rev. Sci. Instrum. 80, 043708 (2009)]. We showed in the paper that the oscillator noise, the frequency fluctuation of the oscillator, becomes prominent in the modulation frequency lower than f{sub 0}/2Q, where f{sub 0} and Q are the resonance frequency and Q-factor. The magnitude of the oscillator noise is determined by the slope of the phase versus frequency curve of the cantilever at f{sub 0}. However, in actual FM-AFM in liquids, the phase versus frequency curve may not be always ideal because of the existence of various phase shifting elements (PSEs). For example, the spurious resonance peaks caused by the acoustic excitation and a band-pass filter in the self-oscillation loop increase the slope of the phase versus frequency curve. Due to those PSEs, the effective Q-factor is often increased from the intrinsic Q-factor of the cantilever. In this article, the frequency noise in the FM-AFM system with the PSEs in the self-oscillation loop is analyzed to show that the oscillator noise is reduced by the increase of the effective Q-factor. It is also shown that the oscillation frequency deviates from the resonance frequency due to the increase of the effective Q-factor, thereby causing the reduction in the frequency shift signal with the same factor. Therefore the increase of the effective Q-factor does not affect the signal-to-noise ratio in the frequency shift measurement, but it does affect the quantitativeness of the measured force in the FM-AFM. Furthermore, the reduction of the frequency noise and frequency shift by the increase of the effective Q-factor were confirmed by the experiments.

  13. 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

  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. 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).

  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. Quantitative Measurement of the Doppler Shift at an Ultrasonic Frequency

    ERIC Educational Resources Information Center

    Nerbun, R. C.; Leskovec, R. A.

    1976-01-01

    Discussed is a Doppler shift laboratory experiment for an introductory college physics course. Ultrasonic transducers and a digital phase detector circuit "black box" are used to overcome room noise and "standing waves" and to produce an observable frequency shift. (SL)

  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. 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

  1. s-Wave collisional frequency shift of a fermion clock.

    PubMed

    Hazlett, Eric L; Zhang, Yi; Stites, Ronald W; Gibble, Kurt; O'Hara, Kenneth M

    2013-04-19

    We report an s-wave collisional frequency shift of an atomic clock based on fermions. In contrast to bosons, the fermion clock shift is insensitive to the population difference of the clock states, set by the first pulse area in Ramsey spectroscopy, θ(1). The fermion shift instead depends strongly on the second pulse area θ(2). It allows the shift to be canceled, nominally at θ(2)=π/2, but correlations perturb the null to slightly larger θ(2). The frequency shift is relevant for optical lattice clocks and increases with the spatial inhomogeneity of the clock excitation field, naturally larger at optical frequencies. PMID:23679589

  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. 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.

  4. 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.

  5. About the p-mode frequency shifts in HD 49933

    NASA Astrophysics Data System (ADS)

    Salabert, D.; Régulo, C.; Ballot, J.; García, R. A.; Mathur, S.

    2011-06-01

    We study the frequency dependence of the frequency shifts of the low-degree p modes measured in the F5V star HD 49933, by analyzing the second run of observations collected by the CoRoT satellite. The 137-day light curve is divided into two subseries corresponding to periods of low and high stellar activity. The activity-frequency relationship is obtained independently from the analysis of the mode frequencies extracted by both a local and a global peak-fitting analyses, and from a cross-correlation technique in the frequency range between 1450 μHz and 2500 μHz. The three methods return consistent results. We show that the frequency shifts measured in HD 49933 present a frequency dependence with a clear increase with frequency, reaching a maximal shift of about 2 μHz around 2100 μHz. Similar variations are obtained between the l = 0 and l = 1 modes. At higher frequencies, the frequency shifts show indications of a downturn followed by an upturn, consistent between the l = 0 and 1 modes. We show that the frequency variation of the p-mode frequency shifts of the solar-like oscillating star HD 49933 has a comparable shape to the one observed in the Sun, which is understood to arise from changes in the outer layers due to its magnetic activity.

  6. 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.

  7. Quantum interference of biphotons with a Doppler frequency shift

    NASA Astrophysics Data System (ADS)

    Lariontsev, E. G.

    2016-08-01

    We report a theoretical study of transformation of a biphoton state of light under Bragg diffraction on a travelling sound wave in an acousto-optic modulator (AOM). It is shown that the diffraction of AOM biphotons emitted during the collinear parametric scattering of light leads to a shift of the carrier frequency of a biphoton wave packet, which exceeds twice the Doppler frequency shift for the classical field. A method is proposed for measuring the Doppler frequency shift of a biphoton, which is based on interference between independent biphotons.

  8. 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.

  9. Atomic frequency standard relativistic Doppler shift experiment

    NASA Technical Reports Server (NTRS)

    Peters, H. E.; Reinhardt, V. S.

    1974-01-01

    An experiment has been performed to measure possible space anisotropy as it would effect the frequency of a cesium atomic beam standard clock in a laboratory on earth due to motion relative to external coordinate frames. The cesium frequency was measured as a function of orientation with respect to an atomic hydrogen maser standard. Over a period of 34 days 101 measurements were made. The results are consistent with a conclusion that no general orientation dependance attributable to spacial anisotropy was observed. It is shown that both the airplane clock results, and the null results for the atomic beam clock, are consistent with Einstein general or special relativity, or with the Lorentz transformations alone.

  10. 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

  11. [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.

  12. Frequency Shift During Mass Properties Testing Using Compound Pendulum Method

    NASA Technical Reports Server (NTRS)

    Wolfe, David; Regan, Chris

    2012-01-01

    During mass properties testing on the X-48B Blended Wing Body aircraft (The Boeing Company, Chicago, Illinois) at the National Aeronautics and Space Administration Dryden Flight Research Center, Edwards, California, large inertia measurement errors were observed in results from compound pendulum swings when compared to analytical models. By comparing periods of oscillations as measured from an average over the test period versus the period of each oscillation, it was noticed that the frequency of oscillation was shifting significantly throughout the test. This phenomenon was only noticed during compound pendulum swings, and not during bifilar pendulum swings. The frequency shift was only visible upon extensive data analysis of the frequency for each oscillation, and did not appear in averaged frequency data over the test period. Multiple test articles, test techniques, and hardware setups were used in attempts to eliminate or identify the cause of the frequency shift. Plotting the frequency of oscillation revealed a region of minimal shift that corresponded to a larger amplitude range. This region of minimal shift provided the most accurate results compared to a known test article; however, the amplitudes that produce accurate inertia measurements are amplitudes larger than those generally accepted in mass properties testing. This paper examines two case studies of the frequency shift, using mass properties testing performed on a dummy test article, and on the X-48B Blended Wing Body aircraft.

  13. 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

  14. Single-Sideband Frequency Shifting In Birefringent Optical Fiber

    NASA Astrophysics Data System (ADS)

    Risk, W. P.; Youngquist, R. C.; Kino, G. S.; Shaw, H. J.

    1984-09-01

    Single-sideband frequency shifting has been demonstrated in birefringent fiber by using a traveling acoustic wave to couple the two orthogonal polarizations of the fiber. Both surface and bulk acoustic waves have been used. Frequency shifts as high as 15 MHz have been observed, with carrier and unwanted sideband suppressions of 25-30 dB, using acoustic powers of a few watts.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. Lattice-induced nonadiabatic frequency shifts in optical lattice clocks

    SciTech Connect

    Beloy, K.

    2010-09-15

    We consider the frequency shift in optical lattice clocks which arises from the coupling of the electronic motion to the atomic motion within the lattice. For the simplest of three-dimensional lattice geometries this coupling is shown to affect only clocks based on blue-detuned lattices. We have estimated the size of this shift for the prospective strontium lattice clock operating at the 390-nm blue-detuned magic wavelength. The resulting fractional frequency shift is found to be on the order of 10{sup -18} and is largely overshadowed by the electric quadrupole shift. For lattice clocks based on more complex geometries or other atomic systems, this shift could potentially be a limiting factor in clock accuracy.

  2. Bandwidth extension for IR detectors through spatial-frequency shifting.

    PubMed

    Lettington, A H; Hong, Q H; Tzimopoulou, S

    1996-09-10

    We describe a new scheme for extending the bandwidth of IR detectors by the employment of a reticle that shifts the higher spatial-frequency content of the scene onto the lower-frequency region. Then all the spatial-frequency information can pass through the bandwidth of the detector system, so that a high-resolution image may be reconstructed from a series of pictures obtained with the reticle in a number of predetermined positions. PMID:21127517

  3. 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).

  4. 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

  5. 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

  6. Cancellation of the Collisional Frequency Shift in Caesium Fountain Clocks

    SciTech Connect

    Szymaniec, K.; Chalupczak, W.; Tiesinga, E.; Williams, C. J.; Weyers, S.; Wynands, R.

    2007-04-13

    We have observed that the collisional frequency shift in primary caesium fountain clocks varies with the clock state population composition and, in particular, is zero for a given fraction of the |F=4,m{sub F}=0> atoms, depending on the initial cloud parameters. We present a theoretical model explaining our observations. The possibility of the collisional shift cancellation implies an improvement in the performance of caesium fountain standards and a simplification in their operation.

  7. Collisional frequency shifts in 133Cs fountain clocks.

    PubMed

    Leo, P J; Julienne, P S; Mies, F H; Williams, C J

    2001-04-23

    We present a theoretical analysis of the density dependent frequency shift in Cs fountain clocks using the highly constrained binary collision model described by Leo et al. [Phys. Rev. Lett. 85, 2721 (2000)]. We predict a reversal in the clock shift at temperatures near 0.08 microK. Our results show that s waves dominate the collision process. However, as a consequence of the large scattering lengths in Cs the clock shift is strongly temperature dependent and does not reach a constant Wigner-law value until temperatures are less than 0.1 nK.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Frequency-shift vs phase-shift characterization of in-liquid quartz crystal microbalance applications

    SciTech Connect

    Montagut, Y. J.; Garcia, J. V.; Jimenez, Y.; Arnau, A.; March, C.; Montoya, A.

    2011-06-15

    The improvement of sensitivity in quartz crystal microbalance (QCM) applications has been addressed in the last decades by increasing the sensor fundamental frequency, following the increment of the frequency/mass sensitivity with the square of frequency predicted by Sauerbrey. However, this sensitivity improvement has not been completely transferred in terms of resolution. The decrease of frequency stability due to the increase of the phase noise, particularly in oscillators, made impossible to reach the expected resolution. A new concept of sensor characterization at constant frequency has been recently proposed. The validation of the new concept is presented in this work. An immunosensor application for the detection of a low molecular weight contaminant, the insecticide carbaryl, has been chosen for the validation. An, in principle, improved version of a balanced-bridge oscillator is validated for its use in liquids, and applied for the frequency shift characterization of the QCM immunosensor application. The classical frequency shift characterization is compared with the new phase-shift characterization concept and system proposed.

  17. Frequency-shift vs phase-shift characterization of in-liquid quartz crystal microbalance applications.

    PubMed

    Montagut, Y J; García, J V; Jiménez, Y; March, C; Montoya, A; Arnau, A

    2011-06-01

    The improvement of sensitivity in quartz crystal microbalance (QCM) applications has been addressed in the last decades by increasing the sensor fundamental frequency, following the increment of the frequency/mass sensitivity with the square of frequency predicted by Sauerbrey. However, this sensitivity improvement has not been completely transferred in terms of resolution. The decrease of frequency stability due to the increase of the phase noise, particularly in oscillators, made impossible to reach the expected resolution. A new concept of sensor characterization at constant frequency has been recently proposed. The validation of the new concept is presented in this work. An immunosensor application for the detection of a low molecular weight contaminant, the insecticide carbaryl, has been chosen for the validation. An, in principle, improved version of a balanced-bridge oscillator is validated for its use in liquids, and applied for the frequency shift characterization of the QCM immunosensor application. The classical frequency shift characterization is compared with the new phase-shift characterization concept and system proposed. PMID:21721715

  18. Frequency-shift vs phase-shift characterization of in-liquid quartz crystal microbalance applications

    NASA Astrophysics Data System (ADS)

    Montagut, Y. J.; García, J. V.; Jiménez, Y.; March, C.; Montoya, A.; Arnau, A.

    2011-06-01

    The improvement of sensitivity in quartz crystal microbalance (QCM) applications has been addressed in the last decades by increasing the sensor fundamental frequency, following the increment of the frequency/mass sensitivity with the square of frequency predicted by Sauerbrey. However, this sensitivity improvement has not been completely transferred in terms of resolution. The decrease of frequency stability due to the increase of the phase noise, particularly in oscillators, made impossible to reach the expected resolution. A new concept of sensor characterization at constant frequency has been recently proposed. The validation of the new concept is presented in this work. An immunosensor application for the detection of a low molecular weight contaminant, the insecticide carbaryl, has been chosen for the validation. An, in principle, improved version of a balanced-bridge oscillator is validated for its use in liquids, and applied for the frequency shift characterization of the QCM immunosensor application. The classical frequency shift characterization is compared with the new phase-shift characterization concept and system proposed.

  19. Shifting fundamental frequency in simulated electric-acoustic listening

    PubMed Central

    Brown, Christopher A.; Scherrer, Nicole M.; Bacon, Sid P.

    2010-01-01

    Previous experiments have shown significant improvement in speech intelligibility under both simulated [Brown, C. A., and Bacon, S. P. (2009a). J. Acoust. Soc. Am. 125, 1658–1665; Brown, C. A., and Bacon, S. P. (2010). Hear. Res. 266, 52–59] and real [Brown, C. A., and Bacon, S. P. (2009b). Ear Hear. 30, 489–493] electric-acoustic stimulation when the target speech in the low-frequency region was replaced with a tone modulated in frequency to track the changes in the target talker’s fundamental frequency (F0), and in amplitude with the amplitude envelope of the target speech. The present study examined the effects in simulation of applying these cues to a tone lower in frequency than the mean F0 of the target talker. Results showed that shifting the frequency of the tonal carrier downward by as much as 75 Hz had no negative impact on the benefit to intelligibility due to the tone, and that even a shift of 100 Hz resulted in a significant benefit over simulated electric-only stimulation when the sensation level of the tone was comparable to that of the tones shifted by lesser amounts. PMID:20815462

  20. 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.

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

    PubMed

    Fazeli, Zahra; Vallian, Sadeq

    2012-12-01

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

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

    PubMed

    Cowell, Robert

    2016-07-01

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

  3. Soliton Self-Frequency Shift: Experimental Demonstrations and Applications

    PubMed Central

    Lee, Jennifer H.; van Howe, James; Liu, Xiang; Xu, Chris

    2012-01-01

    Soliton self-frequency shift (SSFS), a consequence of Raman self-pumping that continuously red-shifts a soliton pulse, has been widely studied recently for applications to fiber-based sources and signal processing. In this paper, the fundamentals of SSFS are reviewed. Various fiber platforms for SSFS (single-mode fiber, microstructured fiber, and higher order mode fiber) are presented and experimental SSFS demonstrations in these fibers are discussed. Observation of Cerenkov radiation in fibers exhibiting SSFS is also presented. A number of interesting applications of SSFS, such as wavelength-agile lasers, analog-to-digital conversion, and slow light, are briefly discussed. PMID:23055656

  4. Soliton Self-Frequency Shift: Experimental Demonstrations and Applications.

    PubMed

    Lee, Jennifer H; van Howe, James; Liu, Xiang; Xu, Chris

    2008-01-01

    Soliton self-frequency shift (SSFS), a consequence of Raman self-pumping that continuously red-shifts a soliton pulse, has been widely studied recently for applications to fiber-based sources and signal processing. In this paper, the fundamentals of SSFS are reviewed. Various fiber platforms for SSFS (single-mode fiber, microstructured fiber, and higher order mode fiber) are presented and experimental SSFS demonstrations in these fibers are discussed. Observation of Cerenkov radiation in fibers exhibiting SSFS is also presented. A number of interesting applications of SSFS, such as wavelength-agile lasers, analog-to-digital conversion, and slow light, are briefly discussed.

  5. Dynamics of a semiconductor laser with frequency shifted feedback

    NASA Astrophysics Data System (ADS)

    Noblet, Yoann; Toomey, Joshua P.; Kane, Deborah M.

    2014-03-01

    Dynamics of the output of a semiconductor laser with frequency-shifted optical feedback system is systematically analyzed. Results from experimental studies using an 830 nm, QW, Fabry-Perot cavity, semiconductor laser are reported. The dynamics are mapped as a function of the level of frequency shifted feedback (FSF) and the injection current. The frequency shift of the optical feedback is the fundamental or a sub-harmonic of the external cavity frequency in the experiments. Multi-GHz-bandwidth real time data collection and analysis is used to investigate the temporal and spectral behaviour of the output power of the nonlinear system. The results are contrasted with those from conventional semiconductor laser with optical feedback systems. Three fundamentally different regimes of operation are identified for the FSF system corresponding to low, medium and high levels of FSF. The low and medium level FSF regimes are consistent with those found in the semiconductor with conventional optical feedback system. It is only when high levels of FSF are used that the output gives a noisy, near periodic output which is similar to the pulsed comb of mode output observed in analogous FSF laser systems using solid state gain media when the FSF is resonant.

  6. Investigation of the resonance frequency shift in parts with cracks

    NASA Astrophysics Data System (ADS)

    Zahariev, Krasimir; Kin, Yulian; Sutin, Alexander

    2005-09-01

    It is known that development of crack in various parts leads to resonance frequency variation and that phenomena can be used for crack detection and remaining lifetime prediction. We have investigated this effect on a steel specimen (25×150×6 mm). The crack was initiated at the root of preliminary machined notch and propagated under cycling loading on fatigue machine. The finite-element analysis was applied for calculation of frequency shift for three flexural modes of vibration and it was observed that the frequency shift increases with the increase of crack size. The maximum detected frequency shift was 3.8% for the crack size 23% of a sample width. The experimental measurements were conducted by measurements of sound produced by free vibration of the sample after impact excitation (impact resonance acoustic spectroscopy). The relative difference between acoustical measurements and FEA results did not exceed 1%. The conducted research provides a good basis for development of the remaining life prediction methods, for example, by Paris formulation. Parameters of the formulation for our case were determined experimentally. [Research supported by 21 Century Fund of Indiana.

  7. 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.

  8. 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

  9. 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.

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

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

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

  11. 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...

  12. 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

  13. Modeling of Doppler frequency shift in multipath radiochannels

    NASA Astrophysics Data System (ADS)

    Penzin, Maksim; Iyin, Nikolay

    2016-06-01

    We discuss the modeling of propagation of a quasi-monochromatic radio signal, represented by a coherent pulse sequence, in a non-stationary multipath radio channel. In such a channel, signal propagation results in the observed frequency shift for each ray (Doppler effect). The modeling is based on the assumption that during propagation of a single pulse a channel can be considered stationary. A phase change in the channel transfer function is shown to cause the observed frequency shift in the received signal. Thus, instead of measuring the Doppler frequency shift, we can measure the rate of change in the mean phase of one pulse relative to another. The modeling is carried out within the framework of the method of normal waves. The method enables us to model the dynamics of the electromagnetic field at a given point with the required accuracy. The modeling reveals that a local change in ionospheric conditions more severely affects the rays whose reflection region is in the area where the changes occur.

  14. Direct Derivation of the Gravitational Red Shift (Einstein Shift) with the frequency dependent Gall metric

    NASA Astrophysics Data System (ADS)

    Gall, Clarence A.

    1999-05-01

    When an electromagnetic radiation (EMR) source is in uniform motion with respect to an observer, a spectral (Doppler) shift in frequency is seen (blue as it approaches, red as it recedes). Since special relativity is limited to coordinate systems in uniform relative motion, this theory should be subject to this condition. On the other hand, the gravitational red shift (Einstein; Relativity: The Special and the General Theory, Crown,(1961), p.129) claims that EMR frequency decreases as the gravitational field, where the source is located, increases. As a gravitational effect, one would expect its derivation from a solution of the general relativistic field equations (R_μσ=0). Up to now, it has only been possible to derive it indirectly, by comparing the gravitational field to a (centrifugal) field produced by coordinate systems in relative rotational motion as an approximation of special relativity. Since rotation implies acceleration, it does not meet the conditions of special relativity so this is unsatisfactory. This work shows that the problem lies in the Schwarzschild metric which is independent of EMR frequency. By contrast it is easy to deduce the gravitational red shift from the frequency dependent Gall metric (Gall in AIP Conference Proceedings 308, The Evolution of X-Ray Binaries,(1993), p. 87).

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

    PubMed

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

    2013-08-01

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

  16. 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.

  17. 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

  18. 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.

  19. 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

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

    NASA Astrophysics Data System (ADS)

    Agarwal, Aditi

    2016-07-01

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

  1. Removing the depth-degeneracy in optical frequency domain imaging with frequency shifting

    PubMed Central

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

    2009-01-01

    A novel technique using an acousto-optic frequency shifter in optical frequency domain imaging (OFDI) is presented. The frequency shift eliminates the ambiguity between positive and negative differential delays, effectively doubling the interferometric ranging depth while avoiding image cross-talk. A signal processing algorithm is demonstrated to accommodate nonlinearity in the tuning slope of the wavelength-swept OFDI laser source. PMID:19484034

  2. 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

  3. Using Tensor Light Shifts to Measure and Cancel a Cell's Quadruopolar Frequency Shift

    NASA Astrophysics Data System (ADS)

    Hunter, Larry; Peck, Stephen; Lane, Nathanael; Ang, Daniel

    2016-05-01

    We have developed a new technique that uses the tensor light shift to measure and cancel the frequency shift produced by the quadrupolar anisotropy of a vapor cell. We demonstrate the technique on the 6 S1/2, F = 4 level of Cs using the D1 transition. The method extends our ability to study quadrupolar wall interactions beyond diamagnetic atoms. We have deduced the twist angle per wall adhesion for cesium on an alkene coating to be about 1.4 mrad. This value is about 37 times larger than the twist angle observed in 131 Xe, suggesting that it is not produced by the interaction of the nuclear quadrupole moment with a collisional electric-field gradient. Alternative mechanisms that may be responsible for the observed quadrupolar frequency shifts are discussed. By cancelling the cell-induced quadrupole shift we have extended our cells' effective spin-relaxation times by as much as a factor of two. This cancellation improves magnetometer sensitivity in highly anisotropic cells and could reduce systematic uncertainties in some precision measurements. This work was supported by NSF Grant No. PHY1205824 and No. PHY1519265.

  4. 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.

  5. Spin-exchange frequency shift in alkali-metal-vapor cell frequency standards

    SciTech Connect

    Micalizio, Salvatore; Godone, Aldo; Levi, Filippo; Vanier, Jacques

    2006-03-15

    In this paper we calculate the effect of spin-exchange collisions in alkali-metal vapors. In the framework of the high-energy approximation, we evaluate the spin-exchange cross sections related to the line broadening and to the frequency shift of the ground state hyperfine transition. We do the calculation for the four isotopes, {sup 23}Na, {sup 39}K, {sup 87}Rb, and {sup 133}Cs. The results are used in particular to evaluate the spin-exchange frequency shift in Rb vapor cell frequency standards used in many applications. It turns out that, due to possible fluctuations in the atomic density, spin exchange may affect significantly the medium and long term frequency stability of the frequency standard.

  6. 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

  7. 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

  8. 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

  9. 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.

  10. Frequency shifting approach towards textual transcription of heartbeat sounds.

    PubMed

    Arvin, Farshad; Doraisamy, Shyamala; Safar Khorasani, Ehsan

    2011-10-04

    Auscultation is an approach for diagnosing many cardiovascular problems. Automatic analysis of heartbeat sounds and extraction of its audio features can assist physicians towards diagnosing diseases. Textual transcription allows recording a continuous heart sound stream using a text format which can be stored in very small memory in comparison with other audio formats. In addition, a text-based data allows applying indexing and searching techniques to access to the critical events. Hence, the transcribed heartbeat sounds provides useful information to monitor the behavior of a patient for the long duration of time. This paper proposes a frequency shifting method in order to improve the performance of the transcription. The main objective of this study is to transfer the heartbeat sounds to the music domain. The proposed technique is tested with 100 samples which were recorded from different heart diseases categories. The observed results show that, the proposed shifting method significantly improves the performance of the transcription.

  11. [Theory study on glycine linear oligopeptide vibrational spectrum frequency shift].

    PubMed

    Ye, Zhi-Peng; Li, Xin; Yang, Meng-Shi; Chen, Liang; Xu, Can; Chu, Xiu-Xiang

    2014-04-01

    By using the density functional theory, glycine linear oligopeptide of different lengths was geometrically optimized on the 6-31G (d) basis set level, their growth processes were simulated, and the average binding energy and vibration frequency were calculated with geometry. The results showed that the average binding energies tend to change in a regular pattern and stabilize with the number of residues increasing; With the oligopeptide chain bond length analysis it was found that the chain to the radial direction there is a opposite trend for chain and radial direction, which is anisotropic. It was found by the IR spectrum analysis that red shifts and blue shifts occur respectively when the same group of peptide bond vibrate, which is anisotropic; These phenomena originate from that quasi one-dimensional nanostructures lead to the anisotropy of the bond length; the induced effects, coupling effects and hydrogen bonding etc. between the same groups lead to the vibration frequency red shifts and blue shifts. The authors conclude that the growth of glycine linear oligopeptide is conducive to stability of the structure, and the authors infer that the oligopeptide has the tendency of self-assembled growth; Through the conformation and spectrum, the authors infer that there is a size effect in physical and chemical properties. The physical and chemical properties of peptide chain end group are extremely stable and unaffected by the impact of the oligopeptide chain length The results are significant to measuring the length and the number of residue of peptide, and to manufacturing the special features oligopeptide chain.

  12. 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.

  13. 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

  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. PMID:25867025

  15. Raman frequency shifts calculated from the volume data in naphthalene

    NASA Astrophysics Data System (ADS)

    Özdemir, H.; Yurtseven, H.

    2015-06-01

    The Raman frequencies for modes of symmetry Ag and Bg are calculated as functions of temperature (at atmospheric pressure) and pressure (at room temperature) using the observed volume data from the literature through the mode Grüneisen parameters in naphthalene. By determining the temperature and pressure dependence of the isobaric (γP) and isothermal (γT) mode Grüneisen parameters, respectively, the Raman frequencies of the modes which were calculated, are in good agreement with the observed frequencies considered in naphthalene. Our results show that the Raman frequencies for the modes studied, can be predicted from the volume data by means of the mode Grüneisen parameters. This also leads to predicting the temperature dependence of the thermal expansion (αP) and the pressure dependence of the isothermal compressibility (κT) from the frequency shifts, (1/ϑ)(∂ϑ/∂T)P, and (1/ϑ)(∂ϑ/∂P)T, respectively, which can be measured accurately in naphthalene.

  16. Cardiac frequency throughout a working shift in coal miners.

    PubMed

    Montoliu, M A; Gonzalez, V; Palenciano, L

    1995-06-01

    Despite the ever-increasing mechanization of industrial activities, coal mining still remains a physically demanding occupation as it is not always possible to extensively mechanize the extraction process. To estimate the physical effort necessary to sustain coal mining activities in a poorly-mechanized mine, cardiac frequency (fc) was measured throughout the working shift with a Sport-Tester PE3000 (Polar Electro OY, Finland) in a representative sample of 73 Asturian miners engaged in a full spectrum of underground work. The mean +/- SD of the overall fc values measured in miners working at the coal face (Group 1, 33 subjects, mean age 32.7 years, age range 21-48 years) was 106.5 +/- 18.2 beats.min-1. In other miners (Group 2, 40 subjects, mean age 34.6 years, age range 23-48 years) corresponding figures were 103.1 +/- 17.7 beats.min-1 (p < 0.05). Subjects' average working shift fc (beats.min-1) was not related to age, measured (treadmill) VO2 max nor VO2 max.kg body weight-1, while average working-shift fc (%fc max) was weakly related to age (r = 0.396, p < 0.05), VO2 max (r = -0.295, p < 0.05) and VO2 max.kg body weight-1 (r = -0.352, p < 0.05). Working-shift peak fc (beats.min-1) was negatively related to age (r = -0.334, p < 0.05). Our study has provided the distribution of the overall fc values likely to be found in subjects working in these poorly-mechanized mines. However, average working-shift fc differs considerably from subject to subject and is largely unpredictable.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. Observations of frequency shift associated with schooling fish

    NASA Astrophysics Data System (ADS)

    Diachok, Orest

    2003-04-01

    The number of sardines per school, N, is nominally 10000 and the separation between sardines in school, s, is nominally 1 fish length, L.s is much smaller than the wavelength at f (the resonance frequency of individuals), which suggests that schools may exhibit acoustic properties of bubble clouds. Long-term, broadband transmission loss measurements at a shallow-water site in the Gulf of Lion revealed absorption lines due to dispersed sardines at 1.3 kHz at 20 m at night and 2.7 kHz at 65 m at dawn. Temporal changes in observed values of f were consistent with concurrent echo sounder observations of the vertical migration of sardines, and theoretical computations based on laboratory measurements of swim bladder dimensions. The measured resonance frequency of sardines in schools during daytime, 1.7 kHz at 65 m, was 0.6f at the same depth at dawn. The observed frequency shift is consistent with a hybrid model of the fundamental resonance frequency of a bubble cloud, which is based on theories developed by Feuillade, Nero, and Love (1996) and dAgostino and Brennan (1988), and s=0.8 L and N=5000 fish per school. [Work supported by ONR.

  2. Blackbody radiation shift in the {sup 87}Rb frequency standard

    SciTech Connect

    Safronova, M. S.; Jiang Dansha; Safronova, U. I.

    2010-08-15

    The operation of atomic clocks is generally carried out at room temperature, whereas the definition of the second refers to the clock transition in an atom at absolute zero. This implies that the clock transition frequency should be corrected in practice for the effect of finite temperature, of which the leading contributor is the blackbody radiation (BBR) shift. Experimental measurements of the BBR shifts are difficult. In this work, we have calculated the blackbody radiation shift of the ground-state hyperfine microwave transition in {sup 87}Rb using the relativistic all-order method and carried out a detailed evaluation of the accuracy of our final value. Particular care is taken to accurately account for the contributions from highly excited states. Our predicted value for the Stark coefficient, k{sub S}=-1.240(4)x10{sup -10} Hz/(V/m){sup 2}, is three times more accurate than the previous calculation [E. J. Angstman, V. A. Dzuba, and V. V. Flambaum, Phys. Rev. A 74, 023405 (2006)].

  3. 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

  4. 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

  5. Frequency-Shift Detectors Bind Binaural as Well as Monaural Frequency Representations

    ERIC Educational Resources Information Center

    Carcagno, Samuele; Semal, Catherine; Demany, Laurent

    2011-01-01

    Previous psychophysical work provided evidence for the existence of automatic frequency-shift detectors (FSDs) that establish perceptual links between successive sounds. In this study, we investigated the characteristics of the FSDs with respect to the binaural system. Listeners were presented with sound sequences consisting of a chord of pure…

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. Spin waves and collisional frequency shifts of a trapped-atom clock.

    PubMed

    Maineult, Wilfried; Deutsch, Christian; Gibble, Kurt; Reichel, Jakob; Rosenbusch, Peter

    2012-07-13

    We excite spin waves with spatially inhomogeneous Ramsey pulses and study the resulting frequency shifts of a chip-scale atomic clock of trapped 87Rb. The density-dependent frequency shifts of the hyperfine transition simulate the s-wave collisional frequency shifts of fermions, including those of optical lattice clocks. As the spin polarizations oscillate in the trap, the frequency shift reverses and it depends on the area of the second Ramsey pulse, exhibiting a predicted beyond mean-field frequency shift. Numerical and analytic models illustrate these observed behaviors. PMID:23030137

  14. 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

  15. Frequency shifts in a rubidium frequency standard due to coupling to another standard

    NASA Technical Reports Server (NTRS)

    Jaduszliwer, Bernardo; Cook, R. A.; Frueholz, R. P.

    1990-01-01

    Highly reliable timing system, such as used on board satellites, may incorporate a hot standby atomic clock besides the active one. RF couplings between them may affect the performance of the active clock. The effect of such couplings between two rubidium atomic clocks was investigated, and it was found that they will add an oscillatory term to the Allan Variance of the active clock, degrading its frequency stability, and that under certain circumstances they may also shift the active clock's operating frequency. These two effects are discussed in detail, and the level of isolation required to render them negligible is established.

  16. Elimination of the light shift in rubidium gas cell frequency standards using pulsed optical pumping

    NASA Technical Reports Server (NTRS)

    English, T. C.; Jechart, E.; Kwon, T. M.

    1978-01-01

    Changes in the intensity of the light source in an optically pumped, rubidium, gas cell frequency standard can produce corresponding frequency shifts, with possible adverse effects on the long-term frequency stability. A pulsed optical pumping apparatus was constructed with the intent of investigating the frequency stability in the absence of light shifts. Contrary to original expectations, a small residual frequency shift due to changes in light intensity was experimentally observed. Evidence is given which indicates that this is not a true light-shift effect. Preliminary measurements of the frequency stability of this apparatus, with this small residual pseudo light shift present, are presented. It is shown that this pseudo light shift can be eliminated by using a more homogeneous C-field. This is consistent with the idea that the pseudo light shift is due to inhomogeneity in the physics package (position-shift effect).

  17. Next-generation sequencing analysis of off-ladder alleles due to migration shift caused by sequence variation at D12S391 locus.

    PubMed

    Fujii, Koji; Watahiki, Haruhiko; Mita, Yusuke; Iwashima, Yasuki; Miyaguchi, Hajime; Kitayama, Tetsushi; Nakahara, Hiroaki; Mizuno, Natsuko; Sekiguchi, Kazumasa

    2016-09-01

    In short tandem repeat (STR) analysis, length polymorphisms are detected by capillary electrophoresis (CE). At most STR loci, mobility shift due to sequence variation in the repeat region was thought not to affect the typing results. In our recent population studies of 1501 Japanese individuals, off-ladder calls were observed at the D12S391 locus using PowerPlex Fusion in nine samples for allele 22, one sample for allele 25, and one sample for allele 26. However, these samples were typed as ordinary alleles within the bins using GlobalFiler. In this study, next-generation sequencing analysis using MiSeq was performed for the D12S391 locus from the 11 off-ladder samples and 33 other samples, as well as the allelic ladders of PowerPlex Fusion and GlobalFiler. All off-ladder allele 22 in the nine samples had [AGAT]11[AGAC]11 as a repeat structure, while the corresponding allele was [AGAT]15[AGAC]6[AGAT] for the PowerPlex Fusion ladder, and [AGAT]13[AGAC]9 for the GlobalFiler ladder. Overall, as the number of [AGAT] in the repeat structure decreased at the D12S391 locus, the peak migrated more slowly using PowerPlex Fusion, the reverse strand of which was labeled, and it migrated more rapidly using GlobalFiler, the forward strand of which was labeled. The allelic ladders of both STR kits were reamplified with our small amplicon D12S391 primers and their mobility was also examined. In conclusion, off-ladder observations of allele 22 at the D12S391 locus using PowerPlex Fusion were mainly attributed to a relatively large difference of the repeat structure between its allelic ladder and off-ladder allele 22. PMID:27591542

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

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

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

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

  6. Controllable Raman soliton self-frequency shift in nonlinear metamaterials

    SciTech Connect

    Xiang Yuanjiang; Wen Shuangchun; Guo Jun; Fan Dianyuan

    2011-09-15

    Controllable and dispersive magnetic permeability in the metamaterials (MMs) provides us more freedom to harness the propagation of ultrashort electromagnetic pulses at will. Here we discuss the controllability of the Raman soliton self-frequency shift (SSFS) in the MMs with a nonlinear electric polarization. First, we derive a generalized nonlinear Schroedinger equation suitable for few-cycle pulse propagation in the MMs with delayed Raman response, and demonstrate the Raman effect, high-order Raman-related nonlinearity, and high-order nonlinear dispersion terms occurring in this equation. Second, we present a theoretical investigation on the controllability of the Raman SSFS in the MMs. In particular, we identify the combined effects of the anomalous self-steepening (SS), third-order dispersion (TOD), and Raman effect on SSFS. It is shown that the positive SS effect suppresses SSFS; however, the negative SS effect enhances SSFS, and the positive TOD leads to the deceleration of SSFS. Finally, the effects of SS on the SSFS of the second-order soliton are also discussed.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Frequency-shifted interferometry for fiber-optic sensing

    NASA Astrophysics Data System (ADS)

    Ye, Fei

    This thesis studies frequency-shifted interferometry (FSI), a useful and versatile technique for fiber-optic sensing. I first present FSI theory by describing practical FSI configurations and discussing the parameters that affect system performance. Then, I demonstrate the capabilities of FSI in fiber-optic sensor multiplexing and high sensitivity chemical analysis. We implemented a cryogenic liquid level sensing system in which an array of 3 fiber Bragg grating (FBG) based sensors was interrogated by FSI. Despite sensors' spectral overlap, FSI is able to separate sensor signals according to their spatial locations and to measure their spectra, from which whether a sensor is in liquid or air can be unambiguously determined. I showed that a broadband source paired with a fast tunable filter can be used in FSI systems as the light source. An array of 9 spectrally overlapping FBGs was successfully measured by such a system, indicating the potential of system cost reduction as well as measurement speed improvement. I invented the the FSI-CRD technique, a highly sensitive FSI-based fiber cavity ring-down (CRD) method capable of deducing minuscule loss change in a fiber cavity from the intensity decay rate of continuous-wave light circulating in the cavity. As a proof-of-principle experiment, I successfully measured the fiber bend loss introduced in the fiber cavity with FSI-CRD, which was found to be 0.172 dB/m at a bend radius of 12.5 mm. We then applied FSI-CRD to evanescent-field sensing. We incorporated fiber tapers as the sensor head in the system and measured the concentration of 1-octyne solutions. A minimum detectable 1-octyne concentration of 0.29% was achieved with measurement sensitivity of 0.0094 dB/% 1-octyne. The same system also accurately detected the concentration change of sodium chloride (NaCl) and glucose solutions. Refractive index sensitivity of 1 dB/RIU with a measurement error of 1x10-4 dB was attined for NaCl solutions. Finally, I proposed a

  14. 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

  15. Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Allelic Variants Relate to Shifts in Faecal Microbiota of Cystic Fibrosis Patients

    PubMed Central

    Santangelo, Floriana; Gagliardi, Antonella; De Biase, Riccardo Valerio; Stamato, Antonella; Bertasi, Serenella; Lucarelli, Marco

    2013-01-01

    Introduction In this study we investigated the effects of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene variants on the composition of faecal microbiota, in patients affected by Cystic Fibrosis (CF). CFTR mutations (F508del is the most common) lead to a decreased secretion of chloride/water, and to mucus sticky secretions, in pancreas, respiratory and gastrointestinal tracts. Intestinal manifestations are underestimated in CF, leading to ileum meconium at birth, or small bowel bacterial overgrowth in adult age. Methods Thirty-six CF patients, fasting and under no-antibiotic treatment, were CFTR genotyped on both alleles. Faecal samples were subjected to molecular microbial profiling through Temporal Temperature Gradient Electrophoresis and species-specific PCR. Ecological parameters and multivariate algorithms were employed to find out if CFTR variants could be related to the microbiota structure. Results Patients were classified by two different criteria: 1) presence/absence of F508del mutation; 2) disease severity in heterozygous and homozygous F508del patients. We found that homozygous-F508del and severe CF patients exhibited an enhanced dysbiotic faecal microbiota composition, even within the CF cohort itself, with higher biodiversity and evenness. We also found, by species-specific PCR, that potentially harmful species (Escherichia coli and Eubacterium biforme) were abundant in homozygous-F508del and severe CF patients, while beneficial species (Faecalibacterium prausnitzii, Bifidobacterium spp., and Eubacterium limosum) were reduced. Conclusions This is the first report that establishes a link among CFTR variants and shifts in faecal microbiota, opening the way to studies that perceive CF as a ‘systemic disease’, linking the lung and the gut in a joined axis. PMID:23613805

  16. Frequency-shifted feedback amplifier for broadband laser cooling

    NASA Astrophysics Data System (ADS)

    Lim, Michael; van Kooy, Alexander; Yanakas, Michael

    2014-03-01

    We have developed a compact, all-solid state laser amplifier for generating asymmetric sidebands with controlled number and spacing of optical frequencies. The gain element is a tapered semiconductor amplifier, used in conjunction with an acousto-optic modulator that generates red-detuned feedback frequencies. This results in asymmetric sidebands that are all lower in optical frequency than the narrowband seed laser frequency. The output laser spectrum has a well-defined edge (the input laser frequency) and multiple sidebands whose number, frequency spacing, and power are fully controlled by the seed laser characteristics and a single radio frequency input. The number of sidebands can be varied in a controlled way, and the output optical power is variable up to the Watt level of the amplifier chip. The system will be used for broadband laser cooling.

  17. Frequency Shift of Carbon-Nanotube-Based Mass Sensor Using Nonlocal Elasticity Theory

    NASA Astrophysics Data System (ADS)

    Lee, Haw-Long; Hsu, Jung-Chang; Chang, Win-Jin

    2010-11-01

    The frequency equation of carbon-nanotube-based cantilever sensor with an attached mass is derived analytically using nonlocal elasticity theory. According to the equation, the relationship between the frequency shift of the sensor and the attached mass can be obtained. When the nonlocal effect is not taken into account, the variation of frequency shift with the attached mass on the sensor is compared with the previous study. According to this study, the result shows that the frequency shift of the sensor increases with increasing the attached mass. When the attached mass is small compared with that of the sensor, the nonlocal effect is obvious and increasing nonlocal parameter decreases the frequency shift of the sensor. In addition, when the location of the attached mass is closer to the free end, the frequency shift is more significant and that makes the sensor reveal more sensitive. When the attached mass is small, a high sensitivity is obtained.

  18. 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

  19. 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

  20. Scattering of cold-atom coherences by hot atoms: frequency shifts from background-gas collisions.

    PubMed

    Gibble, Kurt

    2013-05-01

    Frequency shifts from background-gas collisions currently contribute significantly to the inaccuracy of atomic clocks. Because nearly all collisions with room-temperature background gases that transfer momentum eject the cold atoms from the clock, the interference between the scattered and unscattered waves in the forward direction dominates these frequency shifts. We show they are ≈ 10 times smaller than in room-temperature clocks and that van der Waals interactions produce the cold-atom background-gas shift. General considerations allow the loss of the Ramsey fringe amplitude to bound this frequency shift. PMID:23683186

  1. Increased frequency shifts in high aspect ratio terahertz split ring resonators

    NASA Astrophysics Data System (ADS)

    Chiam, Sher-Yi; Singh, Ranjan; Gu, Jianqiang; Han, Jiaguang; Zhang, Weili; Bettiol, Andrew A.

    2009-02-01

    The resonance of split ring resonators (SRRs) is known to shift upon the addition of a dielectric overlayer, a feature useful for practical applications. Here, we demonstrate that the frequency shift is enlarged by increasing the SRR height, thereby potentially enhancing sensitivity and tunability. We fabricated SRRs resonating at terahertz frequencies using a focused proton beam. This resulted in SRRs nearly 10 μm high, with smooth and vertical sidewalls. Terahertz time domain spectroscopy was used for characterization. Upon applying a dielectric overlayer (ɛ =2.7), a resonance located at 640 GHz shifted by nearly 120 GHz. Simulations also indicate a widening frequency shift as SRR height increases.

  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. Frequency shift measurement in shock-compressed materials

    DOEpatents

    Moore, D.S.; Schmidt, S.C.

    1984-02-21

    A method is disclosed for determining molecular vibrational frequencies in shock-compressed transparent materials. A single laser beam pulse is directed into a sample material while the material is shock-compressed from a direction opposite that of the incident laser beam. A Stokes beam produced by stimulated Raman scattering is emitted back along the path of the incident laser beam, that is, in the opposite direction to that of the incident laser beam. The Stokes beam is separated from the incident beam and its frequency measured. The difference in frequency between the Stokes beam and the incident beam is representative of the characteristic frequency of the Raman active mode of the sample. Both the incident beam and the Stokes beam pass perpendicularly through the stock front advancing through the sample, thereby minimizing adverse effects of refraction.

  4. Frequency shift measurement in shock-compressed materials

    DOEpatents

    Moore, David S.; Schmidt, Stephen C.

    1985-01-01

    A method for determining molecular vibrational frequencies in shock-compressed transparent materials. A single laser beam pulse is directed into a sample material while the material is shock-compressed from a direction opposite that of the incident laser beam. A Stokes beam produced by stimulated Raman scattering is emitted back along the path of the incident laser beam, that is, in the opposite direction to that of the incident laser beam. The Stokes beam is separated from the incident beam and its frequency measured. The difference in frequency between the Stokes beam and the incident beam is representative of the characteristic frequency of the Raman active mode of the sample. Both the incident beam and the Stokes beam pass perpendicularly through the shock front advancing through the sample, thereby minimizing adverse effects of refraction.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Optical correlation of spatial-frequency-shifted images in a photorefractive BSO correlator.

    PubMed

    Tavassoli, Abtine; Becker, Michael F

    2004-03-10

    The optical cross correlation of an image with another image that was spatial-frequency shifted in one dimension was demonstrated in a photorefractive VanderLugt correlator. The first image was stored as a Fourier-transform hologram in a photorefractive Bi12SiO20 crystal (BSO) and was successively correlated with different spatial-frequency-shifted versions of a second image. We implemented the spatial-frequency shift by rotating a galvanometer mirror in an image plane, causing the Fourier transform to be shifted laterally in the BSO. We verified that the resulting operation in the BSO was an accurate complex multiplication of the shifted and the stored Fourier transforms. As many as 20 successive readouts were conducted without measurable erasure of the stored hologram. The dynamic range, saturation behavior, and other performance parameters were measured and are discussed. PMID:15046173

  15. 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

  16. Protein-induced water 1H MR frequency shifts: Contributions from magnetic susceptibility and exchange effects

    NASA Astrophysics Data System (ADS)

    Luo, Jie; He, Xiang; d'Avignon, D. Andre'; Ackerman, Joseph J. H.; Yablonskiy, Dmitriy A.

    2010-01-01

    Defining the biophysics underlying the remarkable MRI phase contrast reported in high field MRI studies of human brain would lead to more quantitative image analysis and more informed pulse sequence development. Toward this end, the dependence of water 1H resonance frequency on protein concentration was investigated using bovine serum albumin (BSA) as a model system. Two distinct mechanisms were found to underlie a water 1H resonance frequency shift: (i) a protein-concentration-induced change in bulk magnetic susceptibility, causing a shift to lower frequency, and (ii) exchange of water between chemical-shift distinct environments, i.e., free (bulk water) and protein-associated ("bound") water, including freely exchangeable 1H sites on proteins, causing a shift to higher frequency. At 37 °C the amplitude of the exchange effect is roughly half that of the susceptibility effect.

  17. Multi-pulse frequency shifted (MPFS) multiple access modulation for ultra wideband

    DOEpatents

    Nekoogar, Faranak; Dowla, Farid U.

    2012-01-24

    The multi-pulse frequency shifted technique uses mutually orthogonal short duration pulses o transmit and receive information in a UWB multiuser communication system. The multiuser system uses the same pulse shape with different frequencies for the reference and data for each user. Different users have a different pulse shape (mutually orthogonal to each other) and different transmit and reference frequencies. At the receiver, the reference pulse is frequency shifted to match the data pulse and a correlation scheme followed by a hard decision block detects the data.

  18. Doppler compensation by shifting transmitted object frequency within limits

    NASA Technical Reports Server (NTRS)

    Laughlin, C. R., Jr.; Hollenbaugh, R. C.; Allen, W. K. (Inventor)

    1973-01-01

    A system and method are disclosed for position locating, deriving centralized air traffic control data, and communicating via voice and digital signals between a multiplicity of remote aircraft, including supersonic transports, and a central station. Such communication takes place through a synchronous satellite relay station. Side tone ranging patterns, as well as the digital and voice signals, are modulated on a carrier transmitted from the central station and received on all of the supersonic transports. Each aircraft communicates with the ground stations via a different frequency multiplexed spectrum. Supersonic transport position is derived from a computer at the central station and supplied to a local air traffic controller. Position is determined in response to variable phase information imposed on the side tones at the aircrafts. Common to all of the side tone techniques is Doppler compensation for the supersonic transport velocity.

  19. Frequency shift of the Bragg and Non-Bragg backscattering from periodic water wave

    NASA Astrophysics Data System (ADS)

    Wen, Biyang; Li, Ke

    2016-08-01

    Doppler effect is used to measure the relative speed of a moving target with respect to the radar, and is also used to interpret the frequency shift of the backscattering from the ocean wave according to the water-wave phase velocity. The widely known relationship between the Doppler shift and the water-wave phase velocity was deduced from the scattering measurements data collected from actual sea surface, and has not been verified under man-made conditions. Here we show that this ob- served frequency shift of the scattering data from the Bragg and Non-Bragg water wave is not the Doppler shift corresponding to the water-wave phase velocity as commonly believed, but is the water-wave frequency and its integral multiple frequency. The power spectrum of the backscatter from the periodic water wave consists of serials discrete peaks, which is equally spaced by water wave frequency. Only when the water-wave length is the integer multiples of the Bragg wave, and the radar range resolution is infinite, does the frequency shift of the backscattering mathematically equal the Doppler shift according to the water-wave phase velocity.

  20. Frequency shift of the Bragg and Non-Bragg backscattering from periodic water wave.

    PubMed

    Wen, Biyang; Li, Ke

    2016-01-01

    Doppler effect is used to measure the relative speed of a moving target with respect to the radar, and is also used to interpret the frequency shift of the backscattering from the ocean wave according to the water-wave phase velocity. The widely known relationship between the Doppler shift and the water-wave phase velocity was deduced from the scattering measurements data collected from actual sea surface, and has not been verified under man-made conditions. Here we show that this ob- served frequency shift of the scattering data from the Bragg and Non-Bragg water wave is not the Doppler shift corresponding to the water-wave phase velocity as commonly believed, but is the water-wave frequency and its integral multiple frequency. The power spectrum of the backscatter from the periodic water wave consists of serials discrete peaks, which is equally spaced by water wave frequency. Only when the water-wave length is the integer multiples of the Bragg wave, and the radar range resolution is infinite, does the frequency shift of the backscattering mathematically equal the Doppler shift according to the water-wave phase velocity. PMID:27531469

  1. Frequency shift of the Bragg and Non-Bragg backscattering from periodic water wave

    PubMed Central

    Wen, Biyang; Li, Ke

    2016-01-01

    Doppler effect is used to measure the relative speed of a moving target with respect to the radar, and is also used to interpret the frequency shift of the backscattering from the ocean wave according to the water-wave phase velocity. The widely known relationship between the Doppler shift and the water-wave phase velocity was deduced from the scattering measurements data collected from actual sea surface, and has not been verified under man-made conditions. Here we show that this ob- served frequency shift of the scattering data from the Bragg and Non-Bragg water wave is not the Doppler shift corresponding to the water-wave phase velocity as commonly believed, but is the water-wave frequency and its integral multiple frequency. The power spectrum of the backscatter from the periodic water wave consists of serials discrete peaks, which is equally spaced by water wave frequency. Only when the water-wave length is the integer multiples of the Bragg wave, and the radar range resolution is infinite, does the frequency shift of the backscattering mathematically equal the Doppler shift according to the water-wave phase velocity. PMID:27531469

  2. Frequency shift of the Bragg and Non-Bragg backscattering from periodic water wave.

    PubMed

    Wen, Biyang; Li, Ke

    2016-08-17

    Doppler effect is used to measure the relative speed of a moving target with respect to the radar, and is also used to interpret the frequency shift of the backscattering from the ocean wave according to the water-wave phase velocity. The widely known relationship between the Doppler shift and the water-wave phase velocity was deduced from the scattering measurements data collected from actual sea surface, and has not been verified under man-made conditions. Here we show that this ob- served frequency shift of the scattering data from the Bragg and Non-Bragg water wave is not the Doppler shift corresponding to the water-wave phase velocity as commonly believed, but is the water-wave frequency and its integral multiple frequency. The power spectrum of the backscatter from the periodic water wave consists of serials discrete peaks, which is equally spaced by water wave frequency. Only when the water-wave length is the integer multiples of the Bragg wave, and the radar range resolution is infinite, does the frequency shift of the backscattering mathematically equal the Doppler shift according to the water-wave phase velocity.

  3. Simultaneous generation of a frequency-multiplied and phase-shifted microwave signal with large tunability.

    PubMed

    Feng, Danqi; Xie, Heng; Chen, Guodong; Qian, Lifen; Sun, Junqiang

    2014-07-28

    We demonstrate a photonic approach to simultaneously realize a frequency-multiplied and phase-shifted microwave signal based on the birefringence effects in the high nonlinear fiber. The phase shift caused by asymmetric variations in refractive indexes of fiber between two orthogonal polarization states is introduced into two coherent harmonic of the modulated signals. By beating the phase-modulated sidebands, a frequency-multiplied microwave signal is generated and its phase can be adjusted by simply controlling the pump power. A microwave signal at doubled- or quadrupled-frequency with a full 2π phase shift is obtained over a frequency range from 10 GHz to 30 GHz. The proposed approach has the potential applications in the system with larger-broadband, higher-frequency and -data-rate system, even to handle a multi-wavelength operation.

  4. Filter-less frequency-doubling microwave signal generator with tunable phase shift

    NASA Astrophysics Data System (ADS)

    Li, Yueqin; Pei, Li; Li, Jing; Wang, Yiqun; Yuan, Jin

    2016-07-01

    A prototype for frequency-doubling microwave signal generator with tunable phase shift based on a filter-less architecture is proposed and analyzed. In the proposal, one dual parallel polarization modulator is used as the key component to generate two ±1st order sidebands along the orthogonal polarization directions with suppressed carrier. Then the polarization states of the two sidebands are aligned with the principal axes of an electro-optical phase modulator (EOPM). Tunable phase shift is implemented by controlling the direct current voltage applied to the EOPM. Without using any filters or wavelength-dependent components, the system possesses good frequency tunability and it can be applied to multi-wavelength operation. Taking advantage of the ability of frequency multiplication, the frequency tuning range can be wider than the operation bandwidth of the modulator. By theoretical analyses and simulated verifications, a frequency-doubling microwave signal ranging from 22 to 40 GHz with full range phase shift is achieved.

  5. 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

  6. Thermal frequency shift and tunable microwave absorption in BiFeO3 family

    NASA Astrophysics Data System (ADS)

    Li, Yong; Fang, Xiaoyong; Cao, Maosheng

    2016-04-01

    Tunable frequency is highly sought-after task of researcher, because of the potential for applications in selecting frequency, absorber, imaging and biomedical diagnosis. Here, we report the original observation of thermal frequency shift of dielectric relaxation in La/Nd doped BiFeO3 (BFO) in X-band from 300 to 673 K. It exhibits an unexpected result: the relaxation shifts to lower frequency with increasing temperature. The relaxation maximally shifts about a quarter of X-band. The nonlinear term of lattice vibration plays an important role in the frequency shift. The frequency shift leads to tuning microwave absorption, which almost covers the whole X-band by changing temperature. Meanwhile, the great increase of dielectric loss of La/Nd doped BFO due to thermal excited electron hopping enhances microwave absorption above ~460 and ~480 K, respectively. The microwave absorption of La/Nd doped BFO surpasses -20 dB at 673 K, and the minimum reflection loss of La doped BFO reaches -39 dB. These results open a new pathway to develop BFO-based materials in electromagnetic functional materials and devices for tunable frequency, stealth and thermal imaging at long wavelength.

  7. Thermal frequency shift and tunable microwave absorption in BiFeO3 family

    PubMed Central

    Li, Yong; Fang, Xiaoyong; Cao, Maosheng

    2016-01-01

    Tunable frequency is highly sought-after task of researcher, because of the potential for applications in selecting frequency, absorber, imaging and biomedical diagnosis. Here, we report the original observation of thermal frequency shift of dielectric relaxation in La/Nd doped BiFeO3 (BFO) in X-band from 300 to 673 K. It exhibits an unexpected result: the relaxation shifts to lower frequency with increasing temperature. The relaxation maximally shifts about a quarter of X-band. The nonlinear term of lattice vibration plays an important role in the frequency shift. The frequency shift leads to tuning microwave absorption, which almost covers the whole X-band by changing temperature. Meanwhile, the great increase of dielectric loss of La/Nd doped BFO due to thermal excited electron hopping enhances microwave absorption above ~460 and ~480 K, respectively. The microwave absorption of La/Nd doped BFO surpasses −20 dB at 673 K, and the minimum reflection loss of La doped BFO reaches −39 dB. These results open a new pathway to develop BFO-based materials in electromagnetic functional materials and devices for tunable frequency, stealth and thermal imaging at long wavelength. PMID:27093897

  8. Thermal frequency shift and tunable microwave absorption in BiFeO3 family.

    PubMed

    Li, Yong; Fang, Xiaoyong; Cao, Maosheng

    2016-04-20

    Tunable frequency is highly sought-after task of researcher, because of the potential for applications in selecting frequency, absorber, imaging and biomedical diagnosis. Here, we report the original observation of thermal frequency shift of dielectric relaxation in La/Nd doped BiFeO3 (BFO) in X-band from 300 to 673 K. It exhibits an unexpected result: the relaxation shifts to lower frequency with increasing temperature. The relaxation maximally shifts about a quarter of X-band. The nonlinear term of lattice vibration plays an important role in the frequency shift. The frequency shift leads to tuning microwave absorption, which almost covers the whole X-band by changing temperature. Meanwhile, the great increase of dielectric loss of La/Nd doped BFO due to thermal excited electron hopping enhances microwave absorption above ~460 and ~480 K, respectively. The microwave absorption of La/Nd doped BFO surpasses -20 dB at 673 K, and the minimum reflection loss of La doped BFO reaches -39 dB. These results open a new pathway to develop BFO-based materials in electromagnetic functional materials and devices for tunable frequency, stealth and thermal imaging at long wavelength.

  9. On the contribution of sunspots to the observed frequency shifts of solar acoustic modes

    NASA Astrophysics Data System (ADS)

    Santos, A. R. G.; Cunha, M. S.; Avelino, P. P.; Chaplin, W. J.; Campante, T. L.

    2016-09-01

    Activity-related variations in the solar oscillation properties have been known for 30 years. However, the relative importance of the different contributions to the observed variations is not yet fully understood. Our goal is to estimate the relative contribution from sunspots to the observed activity-related variations in the frequencies of the acoustic modes. We use a variational principle to relate the phase differences induced by sunspots on the acoustic waves to the corresponding changes in the frequencies of the global acoustic oscillations. From the sunspot properties (area and latitude as a function of time), we are able to estimate the spot-induced frequency shifts. These are then combined with a smooth frequency shift component, associated with long-term solar-cycle variations, and the results compared with the frequency shifts derived from the Global Oscillation Network Group data. The result of this comparison is consistent with a sunspot contribution to the observed frequency shifts of roughly 30 per cent, with the remaining 70 per cent resulting mostly from a global, non-stochastic variation, possibly related to the changes in the overall magnetic field. Moreover, analysis of the residuals obtained after the subtraction of the model frequency shifts from the observations indicates the presence of a 1.5-yr periodicity in the data in phase with the quasi-biennial variations reported in the literature.

  10. Thermal frequency shift and tunable microwave absorption in BiFeO3 family.

    PubMed

    Li, Yong; Fang, Xiaoyong; Cao, Maosheng

    2016-01-01

    Tunable frequency is highly sought-after task of researcher, because of the potential for applications in selecting frequency, absorber, imaging and biomedical diagnosis. Here, we report the original observation of thermal frequency shift of dielectric relaxation in La/Nd doped BiFeO3 (BFO) in X-band from 300 to 673 K. It exhibits an unexpected result: the relaxation shifts to lower frequency with increasing temperature. The relaxation maximally shifts about a quarter of X-band. The nonlinear term of lattice vibration plays an important role in the frequency shift. The frequency shift leads to tuning microwave absorption, which almost covers the whole X-band by changing temperature. Meanwhile, the great increase of dielectric loss of La/Nd doped BFO due to thermal excited electron hopping enhances microwave absorption above ~460 and ~480 K, respectively. The microwave absorption of La/Nd doped BFO surpasses -20 dB at 673 K, and the minimum reflection loss of La doped BFO reaches -39 dB. These results open a new pathway to develop BFO-based materials in electromagnetic functional materials and devices for tunable frequency, stealth and thermal imaging at long wavelength. PMID:27093897

  11. Measurement of the rotational Doppler frequency shift of a spinning object using a radio frequency orbital angular momentum beam.

    PubMed

    Zhao, Mingyang; Gao, Xinlu; Xie, Mutong; Zhai, Wensheng; Xu, Wenjing; Huang, Shanguo; Gu, Wanyi

    2016-06-01

    An indirect approach based on phase measurement is proposed to measure the rotational Doppler frequency shift, which takes full advantage of the phase structure of orbital angular momentum (OAM) beams in radio domain, using a vector network analyzer (VNA) as a phase discriminator. A proof-of-concept experiment is established by an optical-controlled system with the OAM state of 1. By analyzing the experiment's results, the rotational Doppler frequency shift is measured as 24.83 Hz (max error rate 0.67%) at 50π rad/s rotational velocity, deducing the rotational velocity as 50.18π (average error rate 0.36%). PMID:27244411

  12. 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.

  13. 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

  14. Does the light shift drive frequency aging in the rubidium atomic clock?

    PubMed

    Camparo, James

    2005-07-01

    Frequency aging in the rubidium (Rb) vapor-cell atomic clock plays a significant role in the device's timekeeping ability. Though many researchers have speculated on the physical mechanism(s) driving the linear, deterministic frequency change (i.e., deltaf(t)/fo = At), there is little unambiguous experimental data regarding the phenomenon. Here, long-term data were used from on-orbit global positioning system (GPS) Rb clocks to examine one postulated mechanism for frequency aging (i.e., the light-shift effect). Defining the light shift of the clock's fractional frequency as alphaI/Io, where alpha is the light-shift coefficient, we find that temporal variations of the relative light intensity, I/Io, cannot account for frequency aging. However, for the population of clocks considered here, we obtain the intriguing result that alpha/A = 1.7 +/- 1.5. Thus, it may be that frequency aging is driven by the light-shift effect through temporal variations of the light-shift coefficient.

  15. Controlling dipole-dipole frequency shifts in a lattice-based optical atomic clock

    SciTech Connect

    Chang, D.E.; Lukin, M.D.; Ye Jun

    2004-02-01

    Motivated by the ideas of using cold alkaline-earth atoms trapped in an optical lattice for realization of optical atomic clocks, we investigate theoretically the perturbative effects of atom-atom interactions on a clock transition frequency. These interactions are mediated by the dipole fields associated with the optically excited atoms. We predict resonancelike features in the frequency shifts when constructive interference among atomic dipoles occur. We theoretically demonstrate that by fine tuning the coherent dipole-dipole couplings in appropriately designed lattice geometries, the undesirable frequency shifts can be greatly suppressed.

  16. Physical origin of the frequency shifts in cesium beam frequency standards: Related environmental sensitivity

    NASA Technical Reports Server (NTRS)

    Audoin, Claude; Dimarcq, N.; Giordano, V.; Viennet, J.

    1990-01-01

    When observed in a cesium beam frequency standard, the hyperfine transition frequency of the atoms differs slightly from the invariant transition frequency of the unperturbed atoms at rest. The various physical and technical origins of the frequency offsets are stated. They relate to fundamental physical effects, to the method of probing the atomic resonance and to the frequency control of the slaved oscillator. The variation of the frequency offsets under a change of the value of the internal operating characteristics is considered. The sensitivity to a change of the magnetic induction, the microwave power, and the temperature is given. A comparison is made of the sensitivity of cesium beam frequency standards of the commercially available type, making use of magnetic state selection, and of devices under study, in which the state preparation and detection is accomplished optically. The pathways between the external stimuli and the physical origin of the frequency offsets are specified.

  17. 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

  18. The concept of direct orthometric height determination based on frequency shift equation

    NASA Astrophysics Data System (ADS)

    Shen, WenBin; Ning, Jinsheng; Li, Jiancheng; Liu, Jingnan; Chao, Dingbo

    2008-12-01

    The orthometric height system plays a key role in geodesy, and it has broad applications in various fields and activities. On an arbitrary equigeopotential surface, there does not exist the frequency shift of an electromagnetic wave signal. However, between arbitrary two different equigeopotential surfaces, there exists the frequency shift of the signal. Just due to this principle of nature, one can determine the geopotential difference as well as the orthometric height difference between two separated points P and Q using electromagnetic wave signals, especially the GPS signals. GPS signals with a definite frequency f are emitted and two receivers at P and Q on ground receive the signals coming from the emitter simultaneously. The frequencies of the signals are recorded by receivers at P and Q, and consequently the frequency difference (shift) between the received frequencies of the signals at P and Q is determined. Then, the geopotential difference between these two points is determined based on the geopotential frequency shift equation, and the corresponding orthometric height difference is further determined based on the Bruns' formula. Further, using this approach a unified world height datum could be realized, because P and Q could be chosen quite arbitrarily, e.g., they are located on two separated continents or islands.

  19. Derivative of the light frequency shift as a measure of spacetime curvature for gravitational wave detection

    NASA Astrophysics Data System (ADS)

    Congedo, Giuseppe

    2015-04-01

    The measurement of frequency shifts for light beams exchanged between two test masses nearly in free fall is at the heart of gravitational-wave detection. It is envisaged that the derivative of the frequency shift is in fact limited by differential forces acting on those test masses. We calculate the derivative of the frequency shift with a fully covariant, gauge-independent and coordinate-free method. This method is general and does not require a congruence of nearby beams' null geodesics as done in previous work. We show that the derivative of the parallel transport is the only means by which gravitational effects shows up in the frequency shift. This contribution is given as an integral of the Riemann tensor—the only physical observable of curvature—along the beam's geodesic. The remaining contributions are the difference of velocities, the difference of nongravitational forces, and finally fictitious forces, either locally at the test masses or nonlocally integrated along the beam's geodesic. As an application relevant to gravitational-wave detection, we work out the frequency shift in the local Lorentz frame of nearby geodesics.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. Nonlinear modification of the laser noise power spectrum induced by frequency-shifted optical feedback

    NASA Astrophysics Data System (ADS)

    Lacot, Eric; Houchmandzadeh, Bahram; Girardeau, Vadim; Hugon, Olivier; Jacquin, Olivier

    2016-09-01

    In this article, we study the nonlinear coupling between the stationary (i.e., the beating modulation signal) and transient (i.e., the laser quantum noise) dynamics of a laser subjected to frequency-shifted optical feedback. We show how the noise power spectrum and more specifically the relaxation oscillation frequency of the laser are modified under different optical feedback conditions. Specifically we study the influence of (i) the amount of light returning to the laser cavity and (ii) the initial detuning between the frequency shift and intrinsic relaxation frequency. The present work shows how the relaxation frequency is related to the strength of the beating signal, and the shape of the noise power spectrum gives an image of the transfer modulation function (i.e., of the amplification gain) of the nonlinear-laser dynamics. The theoretical predictions, confirmed by numerical resolutions, are in good agreement with the experimental data.

  5. Frequency shifts and modulation effects due to solenoidal magnetic field inhomogeneities in ion cyclotron mass spectrometry

    NASA Astrophysics Data System (ADS)

    Mitchell, Dale W.; Rockwood, Alan L.; Smith, Richard D.

    1995-02-01

    Solenoidal (i.e. axially symmetric) magnetic field inhomogeneities, which in addition have symmetry under the operation z --> -z are the most important to Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry since they introduce frequency shifts at first-order in perturbation theory. Frequency shifts for all three fundamental modes are derived for the leading second-order and fourth-order solenoidal inhomogeneities without any restrictions on the initial conditions. The analytical frequency shifts agree very well with frequency shifts obtained from numerical trajectory calculations using the exact classical equations of motion. The effect of the inhomogeneity on the ion trajectory is solved analytically. For a strong magnetic bottle field, the cyclotron motion is frequency modulated at twice the z-oscillation frequency resulting in sidebands. However, the amplitude of these sidebands is negligibly small for typical inhomogeneity strengths. The effect of a magnetized ICR trap on the homogeneity of the magnetic field is studied by analytical methods. We find that the leading magnetic bottle field decreases as d-3, where d is the cylindrical ion trap diameter.

  6. Frequency shift between coherent superposition states induced by the Berry phase evolving linearly in time

    NASA Astrophysics Data System (ADS)

    Morinaga, Atsuo; Hasegawa, Yasushi

    2015-07-01

    The frequency shift induced by the Berry phase between two coherent superposition states with m'=-1 and m =1 was demonstrated under constant rotation of a magnetic field with frequency f for angle θ from the rotation axis. It was found that the frequency shift is v =2 f -2 f cosθ for 0 ≤θ ≤π /3 , v =-2 f cosθ for π /3 <θ <2 π /3 , and v =-2 f -2 f cosθ for 2 π /3 ≤θ ≤π in the case of the right-handed rotation. For the left-handed rotation, the frequency changes in the opposite sign. The frequency shift is zero at θ =0 ,π /2 , and π , and it jumps by 2 f in the vicinity of θ =π /3 and 2 π /3 . We confirm that the frequency shift is given by the time derivative of the Berry phase which does not depend on the sign of the g factor.

  7. Multiple soliton self-frequency shift cancellations in a temporally tailored photonic crystal fiber

    SciTech Connect

    Liu, Lai; Kang, Zhe; Li, Qing; Gao, Xuejian; Qin, Guanshi E-mail: wpqin@jlu.edu.cn; Qin, Weiping E-mail: wpqin@jlu.edu.cn; Liao, Meisong; Hu, Lili; Ohishi, Yasutake

    2014-11-03

    We report the generation of multiple soliton self-frequency shift cancellations in a temporally tailored tellurite photonic crystal fiber (PCF). The temporally regulated group velocity dispersion (GVD) is generated in the fiber by soliton induced optical Kerr effect. Two red-shifted dispersive waves spring up when two Raman solitons meet their own second zero-dispersion-wavelengths in the PCF. These results show how, through temporally tailored GVD, nonlinearities can be harnessed to generate unexpected effects.

  8. 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.

  9. Frequency shifts in distortion-product otoacoustic emissions evoked by swept tones.

    PubMed

    Shera, Christopher A; Abdala, Carolina

    2016-08-01

    When distortion-product otoacoustic emissions (DPOAEs) are evoked using stimuli whose instantaneous frequencies change rapidly and continuously with time (swept tones), the oscillatory interference pattern known as distortion-product fine structure shifts slightly along the frequency axis in the same direction as the sweep. By analogy with the temporal mechanisms thought to underlie the differing efficacies of up- and down-swept stimuli as perceptual maskers (e.g., Schroeder-phase complexes), fine-structure shifts have been ascribed to the phase distortion associated with dispersive wave propagation in the cochlea. This paper tests an alternative hypothesis and finds that the observed shifts arise predominantly as a methodological side effect of the analysis procedures commonly used to extract delayed emissions from the measured time waveform. Approximate expressions for the frequency shifts of DPOAE distortion and reflection components are derived, validated with computer simulations, and applied to account for DPOAE fine-structure shifts measured in human subjects. Component magnitudes are shown to shift twice as much as component phases. Procedures for compensating swept-tone measurements to obtain estimates of the total DPOAE and its components measured at other sweep rates or in the sinusoidal steady state are presented. PMID:27586726

  10. Accurate measurements of transition frequencies and isotope shifts of laser-trapped francium.

    PubMed

    Sanguinetti, S; Calabrese, R; Corradi, L; Dainelli, A; Khanbekyan, A; Mariotti, E; de Mauro, C; Minguzzi, P; Moi, L; Stancari, G; Tomassetti, L; Veronesi, S

    2009-04-01

    An interferometric method is used to improve the accuracy of the 7S-7P transition frequencies of three francium isotopes by 1 order of magnitude. The deduced isotope shifts for 209-211Fr confirm the ISOLDE data. The frequency of the D2 transition of 212Fr--the accepted reference for all Fr isotope shifts--is revised, and a significant difference with the ISOLDE value is found. Our results will be a benchmark for the accuracy of the theory of Fr energy levels, a necessary step to investigate fundamental symmetries. PMID:19340162

  11. Continuous wave operation of quantum cascade lasers with frequency-shifted feedback

    NASA Astrophysics Data System (ADS)

    Lyakh, A.; Barron-Jimenez, R.; Dunayevskiy, I.; Go, R.; Tsvid, G.; Patel, C. Kumar N.

    2016-01-01

    Operation of continuous wave quantum cascade lasers with a frequency-shifted feedback provided by an acousto-optic modulator is reported. Measured linewidth of 1.7 cm-1 for these devices, under CW operating conditions, was in a good agreement with predictions of a model based on frequency-shifted feedback seeded by spontaneous emission. Linewidth broadening was observed for short sweep times, consistent with sound wave grating period variation across the illuminated area on the acousto-optic modulator. Standoff detection capability of the AOM-based QCL setup was demonstrated for several solid materials.

  12. 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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  15. 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

  16. Experimental investigation on electron cyclotron absorption at down-shifted frequency in the PLT tokamak

    SciTech Connect

    Mazzucato, E.; Fidone, I.; Cavallo, A.; von Goeler, S.; Hsuan, H.

    1986-05-01

    The absorption of 60 GHz electron cyclotron waves, with the extraordinary mode and an oblique angle of propagation, has been investigated in the PLT tokamak in the regime of down-shifted frequencies. The production of energetic electrons, with energies of up to 300 to 400 keV, peaks at values of toroidal field (approx. =29 kG) for which the wave frequency is significantly smaller than the electron cyclotron frequency in the whole plasma region. The observations are consistent with the predictions of the relativistic theory of electron cyclotron damping at down-shifted frequency. Existing rf sources make this process a viable method for assisting the current ramp-up, and for heating the plasma of present large tokamaks.

  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. Realization of fiber-based laser Doppler vibrometer with serrodyne frequency shifting.

    PubMed

    Li, Yanlu; Meersman, Stijn; Baets, Roel

    2011-06-10

    We demonstrate a laser Doppler vibrometer (LDV) based on the serrodyne frequency shifting technique. A proof-of-principle system is implemented on the basis of fiber-optic components but opens the way toward an ultracompact integrated LDV system on a silicon chip. With a low laser power of 50  μW, the serrodyne LDV was able to measure submicrometer vibrations with frequencies in the audio range.

  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. The detection of brain oedema with frequency-dependent phase shift electromagnetic induction.

    PubMed

    González, César A; Rubinsky, Boris

    2006-06-01

    The spectroscopic distribution of inductive phase shift in the brain as a function of the relative volume of oedema was evaluated with theoretical and experimental methods in the frequency range 1 to 8 MHz. The theoretical study employed a simple mathematical model of electromagnetic induction in tissue and brain tissue data available from the literature to calculate the phase shift as a function of oedema in the bulk of the brain. Experimental data were generated from bulk measurements of ex vivo homogenized pig brain tissue mixed with various volumes of physiological saline in a volume sample typical of the human brain. There is good agreement between the analytical and the experimental results. Detectable changes in phase shift begin from a frequency of about 3 MHz to 4 MHz in the tested compositions and volume. The phase shift increases with frequency and fluid content. The results suggest that measuring phase shift in the bulk of the brain has the potential for becoming a robust means for non-contact detection of oedema in the brain.

  2. Note: Laser frequency shifting by using two novel triple-pass acousto-optic modulator configurations

    SciTech Connect

    Carlos-Lopez, E. de; Lopez, J. M.; Lopez, S.; Espinosa, M. G.; Lizama, L. A.

    2012-11-15

    We report the design of two novel triple-pass acousto-optic modulator systems. These designs are extensions of the well known acousto-optic modulator (AOM) double-pass configuration, which eliminates the angle dependence of the diffracted beam with respect to the modulation frequency. In a triple-pass system, however, the frequency dependence of the angle does not disappear but the frequency shift is larger, spanning 3 times the AOM central frequency. In some applications, such as optically pumped Cesium-beam frequency standards, the frequencies of the two laser beams remain fixed and a triple-pass optical system can be used to reduce to one the number of lasers used in such atomic clocks. The two triple-pass configurations use either a retro-reflecting mirror, or a right angle prism to pass for third time the laser beam through the AOM, obtaining diffraction efficiencies of about 27% and 44%, respectively.

  3. Note: laser frequency shifting by using two novel triple-pass acousto-optic modulator configurations.

    PubMed

    de Carlos-López, E; López, J M; López, S; Espinosa, M G; Lizama, L A

    2012-11-01

    We report the design of two novel triple-pass acousto-optic modulator systems. These designs are extensions of the well known acousto-optic modulator (AOM) double-pass configuration, which eliminates the angle dependence of the diffracted beam with respect to the modulation frequency. In a triple-pass system, however, the frequency dependence of the angle does not disappear but the frequency shift is larger, spanning 3 times the AOM central frequency. In some applications, such as optically pumped Cesium-beam frequency standards, the frequencies of the two laser beams remain fixed and a triple-pass optical system can be used to reduce to one the number of lasers used in such atomic clocks. The two triple-pass configurations use either a retro-reflecting mirror, or a right angle prism to pass for third time the laser beam through the AOM, obtaining diffraction efficiencies of about 27% and 44%, respectively. PMID:23206109

  4. Spontaneous cortical DC-potential shifts: modulation stereotypy; relationships to higher EEG-frequencies.

    PubMed

    Etlinger, S C; Guttmann, G; Bauer, H

    1986-07-01

    A description of scalp-recorded, spontaneous, cerebral DC-potential shifts is given independent of other variables (shift stereotypy), in relationship to higher frequencies (theta, alpha 1, alpha 2: 4-13 Hz) and as analyzed pairwise across the median sagittal line (Fz, Cz, Pz) separately according to frequency and condition (relaxation and moderate mental load). Spontaneous DC-shifts are shown to behave unpredictably. Whether measured jointly (up to triads) or as dyad and triad context entropy, the frontal DC-shifts are calculated as being random, whereby their definition as such within the context of the Principle Component Analysis is supported by the analysis of longitudinal registrations. Cross-correlation analysis of the cerebral slow potential's relationship to each of the higher frequencies (theta, alpha 1, alpha 2) reveals it to be highly independent, the highest correlation accounting for merely 11% of the common variance, the average being 9% (R congruent to 0.3). By matching the conjoint activity of the DC-potential between Fz-Cz, Cz-Pz, and Fz-Pz to that of theta, alpha 1, alpha 2 at the same paired sites, the DC-activity is shown to be operating at higher levels of synchronous activity than the higher frequencies, regardless of pairing and/or condition, although the general level of synchronous activity (DC, theta, alpha 1, alpha 2) is remarkably high along the median sagittal line, 75% of the correlation averages of all analysis-pairings being above 0.60.

  5. Blackbody radiation shift of the {sup 133}Cs hyperfine transition frequency

    SciTech Connect

    Micalizio, Salvatore; Godone, Aldo; Calonico, Davide; Levi, Filippo; Lorini, Luca

    2004-05-01

    We report the theoretical evaluations of the static scalar polarizability of the {sup 133}Cs ground state and of the blackbody radiation shift induced on the transition frequency between the two hyperfine levels with m{sub F}=0. This shift is of fundamental importance in the evaluation of the accuracy of the primary frequency standards based on atomic fountains and is employed in the realization of the SI second in the International Atomic Time scale at the level of 1x10{sup -15}. Our computed value for the polarizability is {alpha}{sub 0}=(6.600{+-}0.016)x10{sup -39}C m{sup 2}/V in agreement at the level of 1x10{sup -3} with recent theoretical and experimental values. As regards the blackbody radiation shift we find for the relative hyperfine transition frequency {beta}=(-1.49{+-}0.07)x10{sup -14} at T=300 K in agreement with frequency measurements reported by our group and by Bauch and Schroeder [Phys. Rev. Lett. 78, 622 (1997)]. This value is lower by 2x10{sup -15} than that obtained with measurements based on the dc Stark shift and than the value commonly accepted up to now.

  6. Numerical study of relativistic frequency shift for the cold-atom clock experiment in space

    NASA Astrophysics Data System (ADS)

    Le Poncin-Lafitte, C.; Lambert, S. B.

    2007-02-01

    This paper is motivated by the development of several space missions using an Earth-orbit laser-cooled atomic clock, providing a time-keeping accuracy of the order of 10-16 10-18 in fractional frequency. We focus here on a particular part of the future data processing, namely the relativistic effects on frequency shift. These effects appear to be numerous and intricate, and it is important to precisely quantify their order of magnitude. Obviously, at this level of accuracy, a detailed analysis of all natural or artificial potential sources of error is required, and such a study is still missing at this time. We present here a numerical study of one-way relativistic frequency shifts of orders 1/c2, 1/c3 and 1/c4. These shifts are computed in the case of the ACES mission, i.e. a clock aboard the International Space Station and passing above a mid-latitude observing site. We obtain orders of magnitude for all interesting relativistic effects. We show that the influence on frequency shift of the mass quadrupole moment J2 of the Earth at the order 1/c3 has an amplitude around 10-18, below the expected sensitivity of ACES but close to the one of future missions such as RACE.

  7. Investigation of the Phonon Frequency Shifts in ZnO Quantum Dots

    NASA Astrophysics Data System (ADS)

    Alim, Khan A.

    2005-03-01

    Nanostructures made of ZnO have recently attracted attention due to their proposed applications in low-voltage and short-wavelength electro-optical devices. However, the origin of the observed phonon frequency shifts in such nanostructures is not always understood. We carried out both resonant and non-resonant Raman measurements for 20 nm-diameter ZnO quantum dots (QDs) and bulk ZnO reference samples [1]. A comparison with a recently developed theory [2], allowed us to clarify the origin of the phonon frequency shifts in ZnO QDs. It was found that the phonon confinement results in phonon frequency shifts of only few cm-1. At the same time, the UV laser heating of the QD ensemble was found to induce a large red shift of phonon frequencies for up to 14 cm-1. The authors acknowledge the support of MARCO and its Functional Engineered Nano Architectonics (FENA) Focus Center. [1] K.A. Alim, V.A. Fonoberov, and A.A. Balandin, Appl. Phys. Lett., in review (2004). [2] V.A. Fonoberov and A.A. Balandin, Phys. Stat. Solidi C 1, 2650 (2004); cond-mat/0405681; cond-mat/0411742.

  8. 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

  9. 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

  10. 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.

  11. Raman Self-Frequency Shift of Dissipative Kerr Solitons in an Optical Microresonator.

    PubMed

    Karpov, Maxim; Guo, Hairun; Kordts, Arne; Brasch, Victor; Pfeiffer, Martin H P; Zervas, Michail; Geiselmann, Michael; Kippenberg, Tobias J

    2016-03-11

    The formation of temporal dissipative Kerr solitons in microresonators driven by a continuous-wave laser enables the generation of coherent, broadband, and spectrally smooth optical frequency combs as well as femtosecond pulse sources with compact form factors. Here we report the observation of a Raman-induced soliton self-frequency shift for a microresonator dissipative Kerr soliton also referred to as the frequency-locked Raman soliton. In amorphous silicon nitride microresonator-based single soliton states the Raman effect manifests itself by a spectrum that is sech^{2} in shape and whose center is spectrally redshifted from the continuous wave pump laser. The shift is theoretically described by the first-order shock term of the material's Raman response, and we infer a Raman shock time of ∼20  fs for amorphous silicon nitride. Moreover, we observe that the Raman-induced frequency shift can lead to a cancellation or overcompensation of the soliton recoil caused by the formation of a coherent dispersive wave. The observations are in agreement with numerical simulations based on the Lugiato-Lefever equation with a Raman shock term. Our results contribute to the understanding of Kerr frequency combs in the soliton regime, enable one to substantially improve the accuracy of modeling, and are relevant to the understanding of the fundamental timing jitter of microresonator solitons.

  12. Prediction of spectral shifts proportional to source distances by time-varying frequency or wavelength selection

    NASA Astrophysics Data System (ADS)

    Guruprasad, V.

    2008-08-01

    Any frequency selective device with an ongoing drift will cause observed spectra to be variously and simultaneously scaled in proportion to their source distances. The reason is that detectors after the drifting selection will integrate instantaneous electric or magnetic field values from successive sinusoids, and these sinusoids would differ in both frequency and phase. Phase differences between frequencies are ordinarily irrelevant, and recalibration procedures at most correct for frequency differences. With drifting selection, however, each integrated field value comes from the sinusoid of the instantaneously selected frequency at its instantaneous received phase, hence the waveform constructed by the integration will follow the drifting selection with a phase acceleration given by the drift rate times the slope of the received phase spectrum. A phase acceleration is literally a frequency shift, and the phase spectrum slope of a received waveform is an asymptotic measure of the source distance, as the path delay presents phase offsets proportional to frequency times the distance, and eventually exceeding all initial phase differences. Tunable optics may soon be fast enough for realizing such shifts by Fourier switching, and could lead to pocket X-ray devices; sources continuously variable from RF to gamma rays; capacity multiplication with jamming and noise immunity in both fibre and radio channels, passive ranging from ground to deep space; etc.

  13. Harmonic generation at high field strengths - Frequency shifts and saturation phenomena. [optical mixing technique

    NASA Technical Reports Server (NTRS)

    Stappaerts, E. A.

    1975-01-01

    Optical harmonic generation and mixing in the gas phase has been proposed as a technique for the generation of coherent radiation in the vacuum ultraviolet and soft X-ray spectral region. At the high field strengths required by these processes the interaction between atoms and the electromagnetic field shows intensity-dependent resonances. In this paper we modify harmonic generation theory to include the effect of these frequency shifts. Closed-form expressions for generated dipole moment, absorption probability, and coherence length are presented. The most important consequences of frequency shifts on resonantly enhanced processes are that the pump laser must be tuned away from the small-field resonance frequency, that the conversion efficiency may saturate, and that the dispersion of the medium may change sign. As an example, the generation of 198-A radiation by a five-photon mixing process in Li(+) is considered.

  14. The resonance frequency shift characteristic of Terfenol-D rods for magnetostrictive actuators

    NASA Astrophysics Data System (ADS)

    Jin, Ke; Kou, Yong; Zheng, Xiaojing

    2012-04-01

    This paper focuses on the resonance frequency shift characteristic of Terfenol-D rods for magnetostrictive actuators. A 3D nonlinear dynamic model to describe the magneto-thermo-elastic coupling behavior of actuators is proposed based on a nonlinear constitutive model. The coupled interactions among stress- and magnetic-field-dependent variables for actuators are solved iteratively using the finite element method. The model simulations show a good correlation with the experimental data, which demonstrates that this model can capture the coupled resonance frequency shift features for magnetostrictive actuators well. Moreover, a comprehensive description for temperature, pre-stress and bias field dependences of resonance frequency is discussed in detail. These essential and important investigations will be of significant benefit to both theoretical research and the applications of magnetostrictive materials in smart or intelligent structures and systems.

  15. 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.

  16. Dynamic phase measurement based on spatial carrier-frequency phase-shifting method.

    PubMed

    Huang, Linbo; Lu, Xiaoxu; Li, Jiaosheng; Zhou, Yunfei; Xiong, Jiaxiang; Tian, Jindong; Zhong, Liyun

    2016-06-27

    Combining spatial carrier-frequency phase-shifting (SCPS) technique and Fourier transform method, from one-frame spatial carrier-frequency interferogram (SCFI), a novel phase retrieval method is proposed and applied to dynamic phase measurement. First, using the SCPS technique, four-frame phase-shifting sub-interferograms can be constructed from one-frame SCFI. Second, using Fourier transform method, the accurate phase-shifts of four sub-interferograms can be extracted rapidly, so there is no requirement of calibration for the carrier-frequency in advance compared to most existing SCPS methods. Third, the wrapped phase can be retrieved with the least-squares algorithm through using the above phase-shifts. Finally, the phase variations of a water droplet evaporation and a Jurkat cell apoptosis induced by a drug are presented with the proposed method. Both the simulation and experimental results demonstrate that in addition to maintaining high accuracy of the SCPS method, the proposed method reveals more rapid processing speed of phase retrieval, and this will greatly facilitate its application in dynamic phase measurement. PMID:27410538

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  4. Mercury species induced frequency-shift of molecular orientational transformation based on SERS.

    PubMed

    Chen, Lei; Zhao, Yue; Wang, Yaxin; Zhang, Yongjun; Liu, Yang; Han, Xiao Xia; Zhao, Bing; Yang, Jinghai

    2016-08-01

    We proposed a novel readout method based on a peculiar phenomenon in which the vibrational frequencies of a SERS-active probe (dimethyldithiocarbamic acid sodium salt, DASS) can be affected when there is mercury species. Compared to the SERS intensity-dependent quantitative determination method, SERS frequency-shift-based methods have several advantages: smaller standard deviation, perfect linear relationship, and higher accuracy and sensitivity. In addition, the SERS frequency-shift-based method was not affected by irreproducible aggregation of the SERS substrate and instrumental factors, which greatly improved the application prospect of SERS-based detection. The DASS-modified silver nanoparticles produced a highly sensitive sensor specific to mercury species. Upon the addition of a solution of mercury species to the chip, the mercury species specifically binds to the sulfur atoms, which induces a frequency shift of the band at 1374 cm(-1). The detection limit of the proposed method for Hg(2+) is as low as 10(-8) M. In addition, the proposed method exhibited the same phenomenon for organic mercury. Moreover, these results suggest that the proposed platform possesses the potential for sensitive, selective, and high-throughput on-site mercury pollution monitoring in resource-constrained settings. PMID:27273584

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

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

    2015-01-01

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

  7. Electromobility Shift Assay Reveals Evidence in Favor of Allele-Specific Binding of RUNX1 to the 5' Hypersensitive Site 4-Locus Control Region.

    PubMed

    Dehghani, Hossein; Ghobakhloo, Sepideh; Neishabury, Maryam

    2016-08-01

    In our previous studies on the Iranian β-thalassemia (β-thal) patients, we identified an association between the severity of the β-thal phenotype and the polymorphic palindromic site at the 5' hypersensitive site 4-locus control region (5'HS4-LCR) of the β-globin gene cluster. Furthermore, a linkage disequilibrium was observed between this region and XmnI-HBG2 in the patient population. Based on this data, it was suggested that the well-recognized phenotype-ameliorating role assigned to positive XmnI could be associated with its linked elements in the LCR. To investigate the functional significance of polymorphisms at the 5'HS4-LCR, we studied its influence on binding of transcription factors. Web-based predictions of transcription factor binding revealed a binding site for runt-related transcription factor 1 (RUNX1), when the allele at the center of the palindrome (TGGGG(A/G)CCCCA) was A but not when it was G. Furthermore, electromobility shift assay (EMSA) presented evidence in support of allele-specific binding of RUNX1 to 5'HS4. Considering that RUNX1 is a well-known regulator of hematopoiesis, these preliminary data suggest the importance of further studies to confirm this interaction and consequently investigate its functional and phenotypical relevance. These studies could help us to understand the molecular mechanism behind the phenotype modifying role of the 5'HS4-LCR polymorphic palindromic region (rs16912979), which has been observed in previous studies. PMID:27492765

  8. The Coefficient of the Voltage Induced Frequency Shift Measurement on a Quartz Tuning Fork

    PubMed Central

    Hou, Yubin; Lu, Qingyou

    2014-01-01

    We have measured the coefficient of the voltage induced frequency shift (VIFS) of a 32.768 KHz quartz tuning fork. Three vibration modes were studied: one prong oscillating, two prongs oscillating in the same direction, and two prongs oscillating in opposite directions. They all showed a parabolic dependence of the eigen-frequency shift on the bias voltage applied across the fork, due to the voltage-induced internal stress, which varies as the fork oscillates. The average coefficient of the VIFS effect is as low as several hundred nano-Hz per millivolt, implying that fast-response voltage-controlled oscillators and phase-locked loops with nano-Hz resolution can be built. PMID:25414971

  9. Lattice-Induced Frequency Shifts in Sr Optical Lattice Clocks at the 10{sup -17} Level

    SciTech Connect

    Westergaard, P. G.; Lodewyck, J.; Lecallier, A.; Millo, J.; Lemonde, P.; Lorini, L.; Burt, E. A.; Zawada, M.

    2011-05-27

    We present a comprehensive study of the frequency shifts associated with the lattice potential in a Sr lattice clock by comparing two such clocks with a frequency stability reaching 5x10{sup -17} after a 1 h integration time. We put the first experimental upper bound on the multipolar M1 and E2 interactions, significantly smaller than the recently predicted theoretical upper limit, and give a 30-fold improved upper limit on the effect of hyperpolarizability. Finally, we report on the first observation of the vector and tensor shifts in a Sr lattice clock. Combining these measurements, we show that all known lattice related perturbations will not affect the clock accuracy down to the 10{sup -17} level, even for lattices as deep as 150 recoil energies.

  10. Perturbing Open Cavities: Anomalous Resonance Frequency Shifts in a Hybrid Cavity-Nanoantenna System.

    PubMed

    Ruesink, Freek; Doeleman, Hugo M; Hendrikx, Ruud; Koenderink, A Femius; Verhagen, Ewold

    2015-11-13

    The influence of a small perturbation on a cavity mode plays an important role in fields like optical sensing, cavity quantum electrodynamics, and cavity optomechanics. Typically, the resulting cavity frequency shift directly relates to the polarizability of the perturbation. Here, we demonstrate that particles perturbing a radiating cavity can induce strong frequency shifts that are opposite to, and even exceed, the effects based on the particles' polarizability. A full electrodynamic theory reveals that these anomalous results rely on a nontrivial phase relation between cavity and nanoparticle radiation, allowing backaction via the radiation continuum. In addition, an intuitive model based on coupled mode theory is presented that relates the phenomenon to retardation. Because of the ubiquity of dissipation, we expect these findings to benefit the understanding and engineering of a wide class of systems. PMID:26613442

  11. Improved accuracy of the NPL-CsF2 primary frequency standard: evaluation of distributed cavity phase and microwave lensing frequency shifts

    NASA Astrophysics Data System (ADS)

    Li, Ruoxin; Gibble, Kurt; Szymaniec, Krzysztof

    2011-10-01

    We evaluate the distributed cavity phase (DCP) and microwave lensing frequency shifts, which were the two largest sources of uncertainty for the NPL-CsF2 caesium fountain clock. We report measurements that confirm a detailed theoretical model of the microwave cavity fields and the frequency shifts of the clock that they produce. The model and measurements significantly reduce the DCP uncertainty to 1.1 × 10-16. We derive the microwave lensing frequency shift for a cylindrical cavity with circular apertures. An analytic result with reasonable approximations is given, in addition to a full calculation that indicates a shift of 6.2 × 10-17. The measurements and theoretical models we report, along with improved evaluations of collisional and microwave leakage induced frequency shifts, reduce the frequency uncertainty of the NPL-CsF2 standard to 2.3 × 10-16, nearly a factor of two lower than its most recent complete evaluation.

  12. Phase-sensitive laser detection by frequency-shifted optical feedback

    SciTech Connect

    Lacot, E.; Hugon, O.

    2004-11-01

    For further interferometric application on diffusive target, the phase fluctuation of a solid-state laser submitted to frequency shifted optical feedback is analyzed both theoretically and experimentally. As a drawback of the laser high sensitivity to optical feedback, the phase fluctuations induced by a strong phase-amplitude coupling noise are several orders of magnitude higher than the standard interferometric phase noise induced by the laser frequency width (Schawlow-Townes limit). Nevertheless, by sending a few milliwatts output power microchip laser beam on a diffusive target with an effective reflectivity of 10{sup -9}, a target displacement precision of 0.1 A/{radical}(Hz) has been experimentally determined.

  13. Frequency-dependent polarization-angle-phase-shift in the microwave-induced magnetoresistance oscillations

    SciTech Connect

    Liu, Han-Chun; Ye, Tianyu; Mani, R. G.; Wegscheider, W.

    2015-02-14

    Linear polarization angle, θ, dependent measurements of the microwave radiation-induced oscillatory magnetoresistance, R{sub xx}, in high mobility GaAs/AlGaAs 2D electron devices have shown a θ dependence in the oscillatory amplitude along with magnetic field, frequency, and extrema-dependent phase shifts, θ{sub 0}. Here, we suggest a microwave frequency dependence of θ{sub 0}(f) using an analysis that averages over other smaller contributions, when those contributions are smaller than estimates of the experimental uncertainty.

  14. Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2013-04-01

    The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm-1 for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm-1. These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra.

  15. New method for moisture content measurement using phase shifts at two microwave frequencies.

    PubMed

    Okamura, S; Zhang, Y

    2000-01-01

    A new method to measure moisture content of material is described in this paper. The method is based on two phase shifts of transmitted microwave signal at two different frequencies. The result using this method for moisture measurement of timber indicates this method being effective. The maximum error and mean value of error in moisture range from 2 to 30% on dry basis are 4.1% and 1.9%, respectively. PMID:11098442

  16. Control of the soliton self-frequency shift dynamics using topographic optical fibers.

    PubMed

    Bendahmane, A; Vanvincq, O; Mussot, A; Kudlinski, A

    2013-09-01

    We demonstrate that the dynamics of the soliton self-frequency shift can be accurately controlled by using tapered optical fibers with optimized longitudinal profile shape (that we term topographic fibers). The tapering profiles tailored for a targeted soliton spectral trajectory through dispersion and nonlinearity management are determined by an inverse algorithm. This control is demonstrated experimentally with topographic photonic crystal fibers fabricated directly on a drawing tower.

  17. 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

  18. Intimin subtyping of atypical enteropathogenic Escherichia coli isolated from children with and without diarrhea: a possible temporal shift in the distribution of intimin alleles.

    PubMed

    Franco, Roger T; Araújo, Lizandra D R; Penna, Francisco J; Magalhães, Paula P; Mendes, Edilberto N

    2012-09-01

    Intimins of atypical EPEC strains from children with and without diarrhea were genotyped. κ was not found and β was the most common. η- and ζ-alleles prevailed in strains from children without diarrhea and ι-allele among children older than 13 months. ε-allele emerged in 2006 and was the most common in 2007.

  19. Proposal of a truncated atomic beam fountain for reduction of collisional frequency shift

    SciTech Connect

    Takamizawa, A.; Yanagimachi, S.; Ikegami, T.; Shirakawa, Y.

    2010-07-15

    We propose an atomic fountain clock with a truncated cold atomic beam to achieve both a low collisional frequency shift and high frequency stability. In this clock, the launching velocity of a cold atomic beam can be swept to reduce the atomic density in the interrogation region for the Ramsey resonance and to increase the atomic density in the detection region. Before the top of the beam arrives at the interrogation region, the cold atomic beam is truncated by turning off the cooling laser beams to remove the unnecessary light shift. The atomic density in the interrogation region is theoretically evaluated to be 0.04 times that in an ordinary atomic fountain with optical molasses for the same number of detected atoms. The frequency stability limit due to quantum projection noise is calculated to reach 6.4x10{sup -14} in 1 s from the number of detected atoms while the fractional collisional shift is estimated to be {approx}{sup -}2x10{sup -16}.

  20. Dynamics of suspended microchannel resonators conveying opposite internal fluid flow: Stability, frequency shift and energy dissipation

    NASA Astrophysics Data System (ADS)

    Zhang, Wen-Ming; Yan, Han; Jiang, Hui-Ming; Hu, Kai-Ming; Peng, Zhi-Ke; Meng, Guang

    2016-04-01

    In this paper, the dynamics of suspended microchannel resonators which convey internal flows with opposite directions are investigated. The fluid-structure interactions between the laminar fluid flow and oscillating cantilever are analyzed by comprehensively considering the effects of velocity profile, flow viscosity and added flowing particle. A new model is developed to characterize the dynamic behavior of suspended microchannel resonators with the fluid-structure interactions. The stability, frequency shift and energy dissipation of suspended microchannel resonators are analyzed and discussed. The results demonstrate that the frequency shifts induced by the added flowing particle which are obtained from the new model have a good agreement with the experimental data. The steady mean flow can cause the frequency shift and influence the stability of the dynamic system. As the flow velocity reaches the critical value, the coupled-mode flutter occurs via a Hamiltonian Hopf bifurcation. The perturbation flow resulted from the vibration of the microcantilever leads to energy dissipation, while the steady flow does not directly cause the damping which increases with the increasing of the flow velocity predicted by the classical model. It can also be found that the steady flow firstly changes the mode shape of the cantilever and consequently affects the energy dissipation.

  1. 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.

  2. The Contribution of Chemical Exchange to MRI Frequency Shifts in Brain Tissue

    PubMed Central

    Shmueli, Karin; Dodd, Stephen J.; Li, Tie-Qiang; Duyn, Jeff H.

    2010-01-01

    Recent high-field MRI studies based on resonance frequency contrast have revealed brain structure with unprecedented detail. Although subtle magnetic susceptibility variations caused by iron and myelin seem to be important to this contrast, recent research on protein solutions suggests that chemical exchange between water and macromolecular protons may contribute substantially to the observed gray-white matter frequency contrast. To investigate this, we performed spectroscopic MRI experiments at 14 Tesla on samples of fixed human visual cortex and fresh pig brain. To allow direct observation of any exchange-induced frequency shifts, these samples were soaked in reference chemicals (TSP and dioxane) that are assumed not to be involved in exchange. For both fresh and fixed tissues and with both reference chemicals, substantial negative exchange-induced gray-white matter frequency contrast (−6.3 to −13.5 ppb) was found, whereas intra-cortical contrast was negligible. The sign of the gray-white matter exchange-induced frequency difference was opposite to the overall gray-white matter frequency difference observed in vivo. This suggests that exchange contributes to, but is not sufficient to explain, the frequency contrast in vivo, and that tissue susceptibility differences may have a greater contribution than previously thought. The exchange-dependent contribution may report on tissue chemical composition and pH. PMID:20928888

  3. Frequency of spontaneous BOLD signal shifts during infancy and correlates with cognitive performance.

    PubMed

    Alcauter, Sarael; Lin, Weili; Smith, J Keith; Goldman, Barbara D; Reznick, J Steven; Gilmore, John H; Gao, Wei

    2015-04-01

    Numerous studies have been conducted to delineate the early development of different functional networks, based on measuring the temporal synchronization of spontaneous blood oxygenation level-dependent (BOLD) signals acquired using resting state functional MRI (rsfMRI). However, little attention has been paid to the change of the frequency properties of these signals during early brain development. Such frequency properties may reflect important physiological changes and potentially have significant cognitive consequences. In this study, leveraging a large (N=86 subjects), longitudinal sample of human infants scanned during the first two years of life, we aimed to specifically delineate the developmental changes of the frequency characteristics of spontaneous BOLD signals. Both whole-brain and network-level examinations were carried out and the frequency-behavior relationship was explored. Our results revealed a clear right-ward shift of BOLD signal frequency during the first year of life. Moreover, the power at the peak-frequency for sensorimotor and lateral visual networks correlates with domain-specific Mullen Scales in 1-year-olds, suggesting the behavioral significance of the BOLD signal frequency during infancy. Findings from this study shed light into early functional brain development and provide a new perspective for future searches for functional developmental abnormalities.

  4. Direct measurement of laser-induced frequency shift rate of ultracold cesium molecules by analyzing losses of trapped atoms

    SciTech Connect

    Zhang Yichi; Ma Jie; Li Yuqing; Wu Jizhou; Zhang Linjie; Chen Gang; Wang Lirong; Zhao Yanting; Xiao Liantuan; Jia Suotang

    2012-09-24

    We report on a quantitative experimental determination of the laser-induced frequency shift rate of the ultracold cesium molecules formed via photoassociation (PA) by means of the trap loss measurement of the losses of trapped atoms in a standard magneto-optical trap. The experiment was directly performed by varying the photoassociation laser intensity without any additional frequency monitor technologies. Our experimental method utilized dependences of the losses on the laser-induced frequency shift rate based on the conditions of the identified photoassociation spectral shape. We demonstrated that the method is sensitive enough to determine small frequency shifts of rovibrational levels of ultracold cesium molecules.

  5. Frequency-shift low-pass filtering and least mean square adaptive filtering for ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Wang, Shanshan; Li, Chunyu; Ding, Mingyue; Yuchi, Ming

    2016-04-01

    Ultrasound image quality enhancement is a problem of considerable interest in medical imaging modality and an ongoing challenge to date. This paper investigates a method based on frequency-shift low-pass filtering (FSLF) and least mean square adaptive filtering (LMSAF) for ultrasound image quality enhancement. FSLF is used for processing the ultrasound signal in the frequency domain, while LMSAPF in the time domain. Firstly, FSLF shifts the center frequency of the focused signal to zero. Then the real and imaginary part of the complex data are filtered respectively by finite impulse response (FIR) low-pass filter. Thus the information around the center frequency are retained while the undesired ones, especially background noises are filtered. Secondly, LMSAF multiplies the signals with an automatically adjusted weight vector to further eliminate the noises and artifacts. Through the combination of the two filters, the ultrasound image is expected to have less noises and artifacts and higher resolution, and contrast. The proposed method was verified with the RF data of the CIRS phantom 055A captured by SonixTouch DAQ system. Experimental results show that the background noises and artifacts can be efficiently restrained, the wire object has a higher resolution and the contrast ratio (CR) can be enhanced for about 12dB to 15dB at different image depth comparing to delay-and-sum (DAS).

  6. Beam-loaded frequency shift study in an over-sized backward wave oscillator

    SciTech Connect

    Li, Zhenghong; Zhou, Zhigang; Qiu, Rong

    2014-10-15

    The oversized backward wave oscillator (BWO) can significantly decreases the internal rf electric field in the device. The beam-loaded effect is obvious in such devices and its performance is also significantly affected. Based on the characteristics of the oversized BWO, a self-consistent equation is developed to study its beam-loaded frequency shift together with particle in cell (PIC) simulations. The mechanism whereby the output rf frequency is affected by the beam's parameters and the device's structure is theoretically studied. The frequency's dependence on the drift tube length between the reflector and SWS (slow wave structures) in the device is deduced in the paper and the theoretical results agree with those obtained in PIC simulations.

  7. FREQUENCY SHIFTS OF RESONANT MODES OF THE SUN DUE TO NEAR-SURFACE CONVECTIVE SCATTERING

    SciTech Connect

    Bhattacharya, J.; Hanasoge, S.; Antia, H. M.

    2015-06-20

    Measurements of oscillation frequencies of the Sun and stars can provide important independent constraints on their internal structure and dynamics. Seismic models of these oscillations are used to connect structure and rotation of the star to its resonant frequencies, which are then compared with observations, the goal being that of minimizing the difference between the two. Even in the case of the Sun, for which structure models are highly tuned, observed frequencies show systematic deviations from modeled frequencies, a phenomenon referred to as the “surface term.” The dominant source of this systematic effect is thought to be vigorous near-surface convection, which is not well accounted for in both stellar modeling and mode-oscillation physics. Here we bring to bear the method of homogenization, applicable in the asymptotic limit of large wavelengths (in comparison to the correlation scale of convection), to characterize the effect of small-scale surface convection on resonant-mode frequencies in the Sun. We show that the full oscillation equations, in the presence of temporally stationary three-dimensional (3D) flows, can be reduced to an effective “quiet-Sun” wave equation with altered sound speed, Brünt–Väisäla frequency, and Lamb frequency. We derive the modified equation and relations for the appropriate averaging of 3D flows and thermal quantities to obtain the properties of this effective medium. Using flows obtained from 3D numerical simulations of near-surface convection, we quantify their effect on solar oscillation frequencies and find that they are shifted systematically and substantially. We argue therefore that consistent interpretations of resonant frequencies must include modifications to the wave equation that effectively capture the impact of vigorous hydrodynamic convection.

  8. LOOP- SIMULATION OF THE AUTOMATIC FREQUENCY CONTROL SUBSYSTEM OF A DIFFERENTIAL MINIMUM SHIFT KEYING RECEIVER

    NASA Technical Reports Server (NTRS)

    Davarian, F.

    1994-01-01

    The LOOP computer program was written to simulate the Automatic Frequency Control (AFC) subsystem of a Differential Minimum Shift Keying (DMSK) receiver with a bit rate of 2400 baud. The AFC simulated by LOOP is a first order loop configuration with a first order R-C filter. NASA has been investigating the concept of mobile communications based on low-cost, low-power terminals linked via geostationary satellites. Studies have indicated that low bit rate transmission is suitable for this application, particularly from the frequency and power conservation point of view. A bit rate of 2400 BPS is attractive due to its applicability to the linear predictive coding of speech. Input to LOOP includes the following: 1) the initial frequency error; 2) the double-sided loop noise bandwidth; 3) the filter time constants; 4) the amount of intersymbol interference; and 5) the bit energy to noise spectral density. LOOP output includes: 1) the bit number and the frequency error of that bit; 2) the computed mean of the frequency error; and 3) the standard deviation of the frequency error. LOOP is written in MS SuperSoft FORTRAN 77 for interactive execution and has been implemented on an IBM PC operating under PC DOS with a memory requirement of approximately 40K of 8 bit bytes. This program was developed in 1986.

  9. Shifting of wrapped phase maps in the frequency domain using a rational number

    NASA Astrophysics Data System (ADS)

    Gdeisat, Munther A.; Burton, David R.; Lilley, Francis; Arevalillo-Herráez, Miguel; Abushakra, Ahmad; Qaddoura, Maen

    2016-10-01

    The number of phase wraps in an image can be either reduced, or completely eliminated, by transforming the image into the frequency domain using a Fourier transform, and then shifting the spectrum towards the origin. After this, the spectrum is transformed back to the spatial domain using the inverse Fourier transform and finally the phase is extracted using the arctangent function. However, it is a common concern that the spectrum can be shifted only by an integer number, meaning that the phase wrap reduction is often not optimal. In this paper we propose an algorithm than enables the spectrum to be frequency shifted by a rational number. The principle of the proposed method is confirmed both by using an initial computer simulation and is subsequently validated experimentally on real fringe patterns. The technique may offer in some cases the prospects of removing the necessity for a phase unwrapping process altogether and/or speeding up the phase unwrapping process. This may be beneficial in terms of potential increases in signal recovery robustness and also for use in time-critical applications.

  10. 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.

  11. 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

  12. Cancelation of thermally induced frequency shifts in bimaterial cantilevers by nonlinear optomechanical interactions

    NASA Astrophysics Data System (ADS)

    Vy, Nguyen Duy; Tri Dat, Le; Iida, Takuya

    2016-08-01

    Bimaterial cantilevers have recently been used in, for example, the calorimetric analysis with picowatt resolution in microscopic space based on state-of-the-art atomic force microscopes. However, thermally induced effects usually change physical properties of the cantilevers, such as the resonance frequency, which reduce the accuracy of the measurements. Here, we propose an approach to circumvent this problem that uses an optical microcavity formed between a metallic layer coated on the back of the cantilever and one coated at the end of an optical fiber irradiating the cantilever. In addition to increasing the sensitivity, the optical rigidity of this system diminishes the thermally induced frequency shift. For a coating thickness of several tens of nanometers, the input power is 5-10 μW. These values can be evaluated from parameters derived by directly irradiating the cantilever in the absence of the microcavity. The system has the potential of using the cantilever both as a thermometer without frequency shifting and as a sensor with nanometer-controlled accuracy.

  13. Near- and far-field scattering resonance frequency shift in dielectric and perfect electric conducting cylinders.

    PubMed

    Yuffa, Alex J; Gutierrez, Yael; Sanz, Juan M; Alcaraz de la Osa, Rodrigo; Saiz, José M; González, Francisco; Moreno, Fernando; Videen, Gorden

    2016-03-01

    The ability to infer near-field scattering properties from far-field measurements is of paramount importance in nano-optics. Recently we derived an approximate formula for predicting the frequency shift between near- and far-field intensity peaks in the case of a dielectric sphere. In this work we demonstrate that almost an identical formula can be used to predict the resonance shift of a dielectric cylinder and a perfectly conducting cylinder. We find the redshift of the resonance peak of the perfect electric conducting cylinder to be approximately 2 orders of magnitude greater than for the dielectric cylinder. The errors in our approximate analytic formula for predicting the redshift are approximately only twice as great. Furthermore, we apply the redshift formula to a silicon cylinder and discuss its magneto-dielectric properties, which may be of interest in design of metamaterials. PMID:26974908

  14. Linear ion trap for second-order Doppler shift reduction in frequency standard applications

    NASA Technical Reports Server (NTRS)

    Prestage, John D.; Janik, Gary R.; Dick, G. John; Maleki, Lute

    1990-01-01

    The authors have designed and are presently testing a novel linear ion trap that permits storage of a large number of ions with reduced susceptibility to the second-order Doppler effect caused by the RF confining fields. This new trap should store about 20 times the number of ions as a conventional RF trap with no corresponding increase in second-order Doppler shift from the confining field. In addition, the sensitivity of this shift to trapping parameters, i.e., RF voltage, RF frequency, and trap size, is greatly reduced. The authors have succeeded in trapping mercury ions and xenon ions in the presence of helium buffer gas. Trap times as long as 2000 s have been measured.

  15. [Research on explosive temperature network monitoring system based on the linear frequency shift of spectrum].

    PubMed

    Wen, Qiang; Lian, Su-Jie; Zhang, Chen; Zhao, Hui; Zhao, Yu; Wang, Gao; Xu, De-Gang; Yao, Jian-Quan

    2014-03-01

    In order to obtain the different position temperature changes in the process of explosive casting accurate, stability and comprehensive, we designed the temperature monitoring system based on fiber Bragg grating spectral shift. Through the fiberoptic network, the system can monitor the different point temperature of melt-cast explosive real-time. According to the function of linear frequency shift of fiber Bragg grating wavelength with the grating of temperature, we get the temperature of different positions. Four channels share a broadband light source with a coupler. The Bragg wavelengths of the 5 gratings of each fiber are separated from each other. Using the gratings designed, spliced and packaged by our own, we can obtain temperature data through the demodulator. The temperature data was processed by the Origin to draw diagram time-temperature curve. The results show that the measured temperature data of the fiber Bragg grating can meet the requirements of experiment.

  16. The effects and inhibition of frequency offset on differential phase-shift keying detection

    NASA Astrophysics Data System (ADS)

    Guo, Hao; Zhou, Jing; Su, Shaojing; Pan, Zhongming

    2015-10-01

    Differential phase-shift keying (DPSK) has been widely implemented and developed in high-speed optical communication systems. The low error rate detection at high access rate is one of the considerable issues in practical engineering application. Balanced detection based on fiber Mach-Zehnder delay interferometer (MZDI) is the typical optical DPSK signal detecting method. It requires that the free spectrum range (FSR) of the MZDI equals the reciprocal of symbol period of the DPSK signal. For the reasons of ambient temperature variation and nonlinear phase noise, a dynamic frequency offset always exists between the FSR and the reciprocal of symbol period. That may introduce some optical signal-to-noise ratio (OSNR) costs and fault detections. Therefore, it is significant to inhibit the frequency offset on DPSK detection. In this paper, firstly, we discuss the effects of frequency offset on DPSK detection, and realize the conclusion that frequency offset is virtually equivalent to an additional phase difference between adjacent symbols. Secondly, through simulation, we analyze the feasibility of DPSK detection in the presence of a definite range of frequency offset, and present the quantitative computation of effective coverage, duty cycle, and optimal sampling time of symbol interference. Some issues which should be considered in practical implementation are also discussed. Finally, according to the relationship among phase difference, temperature and voltage, we propose a phase difference compensation scheme which can automatically adjust the voltage for optimal detections, and dynamically track the changing of ambient temperature and nonlinear phase noise. Furthermore, we ascertain the performance of the voltage requested for implementing the scheme. The scheme can be also developed to quadrature phase-shift keying (QPSK) and differential QPSK (DQPSK) modulation situations.

  17. 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

  18. 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

  19. Excitation-induced frequency shifts and frequency-dependent dephasing in Eu 3+:Y 2O 3

    NASA Astrophysics Data System (ADS)

    Huang, Jin; Zhang, J. M.; Mossberg, T. W.

    1990-02-01

    Using photon echo techniques and working on the 7F 0- 5D 0 transition of Eu 3+ in Eu 3+:Y 2O 3, we have studied the dependence of the homogeneous dephasing time on spectral position within the transition's inhomogeneous absorption profile. In agreement with previous observations [R.M. Macfarlane and R.M. Shelby, Optics Comm. 39 (1981) 169], a strong variation is observed. Interestingly, however, we find that the variation in linewidth is excitation-pulse-intensity dependent, becoming less pronounced the smaller the excitation intensity. Our observation are consistent with the notion that the variation in dephasing time is attributable, in large part, to the presence of excitation-induced optical frequency shifts in this system.

  20. 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.

  1. Rigorous intensity and phase-shift manipulation in optical frequency conversion.

    PubMed

    Yang, Bo; Yue, Yang-Yang; Lu, Rong-Er; Hong, Xu-Hao; Zhang, Chao; Qin, Yi-Qiang; Zhu, Yong-Yuan

    2016-01-01

    A simple method is employed to investigate the nonlinear frequency conversion in optical superlattices (OSL) with pump depletion. Four rigorous phase-matching conditions for different purposes are obtained directly from the nonlinear coupled equations, and the resulting OSL domain structures are generally aperiodic rather than periodic. With this method, not only the intensity but also the phase-shift of the harmonic waves can be manipulated at will. The second-harmonic generation of Gaussian beam is further investigated. This work may provide a guidance for the practical applications of designing nonlinear optical devices with high conversion efficiency. PMID:27272308

  2. Rigorous intensity and phase-shift manipulation in optical frequency conversion

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Yue, Yang-Yang; Lu, Rong-Er; Hong, Xu-Hao; Zhang, Chao; Qin, Yi-Qiang; Zhu, Yong-Yuan

    2016-06-01

    A simple method is employed to investigate the nonlinear frequency conversion in optical superlattices (OSL) with pump depletion. Four rigorous phase-matching conditions for different purposes are obtained directly from the nonlinear coupled equations, and the resulting OSL domain structures are generally aperiodic rather than periodic. With this method, not only the intensity but also the phase-shift of the harmonic waves can be manipulated at will. The second-harmonic generation of Gaussian beam is further investigated. This work may provide a guidance for the practical applications of designing nonlinear optical devices with high conversion efficiency.

  3. Rigorous intensity and phase-shift manipulation in optical frequency conversion

    PubMed Central

    Yang, Bo; Yue, Yang-Yang; Lu, Rong-er; Hong, Xu-Hao; Zhang, Chao; Qin, Yi-Qiang; Zhu, Yong-Yuan

    2016-01-01

    A simple method is employed to investigate the nonlinear frequency conversion in optical superlattices (OSL) with pump depletion. Four rigorous phase-matching conditions for different purposes are obtained directly from the nonlinear coupled equations, and the resulting OSL domain structures are generally aperiodic rather than periodic. With this method, not only the intensity but also the phase-shift of the harmonic waves can be manipulated at will. The second-harmonic generation of Gaussian beam is further investigated. This work may provide a guidance for the practical applications of designing nonlinear optical devices with high conversion efficiency. PMID:27272308

  4. Multiplication of the frequency shift of optical radiation by means of cascade acousto-optic interaction

    SciTech Connect

    Kotov, V M

    2000-04-30

    A method for increasing the frequency shift of optical radiation by means of cascade acousto-optic diffraction of light is proposed and studied. The method is based on special features of anisotropic diffraction in an anisotropic medium and optical properties of gyrotropic media. Five-cascade diffraction of radiation from a He - Ne laser ({lambda}=0.633 {mu}m) in a TeO{sub 2} single crystal with an efficiency of 8% was obtained experimentally. (laser applications and other topics in quantum electronics)

  5. 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.

  6. Multipoint sensing with a low-coherence source using single-arm frequency-shifted interferometry.

    PubMed

    Zhang, Yiwei; Ye, Fei; Qi, Bing; Qian, Li

    2016-07-20

    We demonstrate that multiple-site sensing along an optical fiber can be done with incoherent continuous-wave light. Using a broadband low-coherence noise source, a slow detector, and an optical modulator, we construct a single-arm frequency-shifted interferometer (SA-FSI) capable of simultaneously sensing multiple weak-reflection sites distributed either in parallel or in series along fiber links. By scanning the driving frequency of an electro-optic amplitude modulator in the range of 2.7-3.2 GHz at steps of 41.7 KHz, we demonstrate a spatial resolution of 0.3 m and a measurement range of over 1 km. PMID:27463900

  7. Acoustic attenuation logging using centroid frequency shift and amplitude ratio methods: A numerical study

    SciTech Connect

    Quan, Y.; Harris, J.M.; Chen, X.

    1994-12-31

    The centroid frequency shift method is proposed to estimate seismic attenuation from full waveform acoustic logs. This approach along with the amplitude ratio method is applied to investigate the attenuation properties of the P head wave in fluid-filled boreholes. The generalized reflection and transmission coefficients method is used to perform forward modeling. The authors suggest an empirical formula to describe the frequency-dependent geometrical spreading of the P-wave in a borehole. They simulate a more realistic borehole by including a mudcake and an invaded zone which are modeled by a large number of radially symmetric thin layers. The numerical tests show that this invaded zone exhibits very strong influence on the attenuation measurement.

  8. Frequency-Shifted Interferometry — A Versatile Fiber-Optic Sensing Technique

    PubMed Central

    Ye, Fei; Zhang, Yiwei; Qi, Bing; Qian, Li

    2014-01-01

    Fiber-optic sensing is a field that is developing at a fast pace. Novel fiber-optic sensor designs and sensing principles constantly open doors for new opportunities. In this paper, we review a fiber-optic sensing technique developed in our research group called frequency-shifted interferometry (FSI). This technique uses a continuous-wave light source, an optical frequency shifter, and a slow detector. We discuss the operation principles of several FSI implementations and show their applications in fiber length and dispersion measurement, locating weak reflections along a fiber link, fiber-optic sensor multiplexing, and high-sensitivity cavity ring-down measurement. Detailed analysis of FSI system parameters is also presented. PMID:24955943

  9. 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

  10. 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

  11. 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

  12. FM echolocating bats shift frequencies to avoid broadcast-echo ambiguity in clutter.

    PubMed

    Hiryu, Shizuko; Bates, Mary E; Simmons, James A; Riquimaroux, Hiroshi

    2010-04-13

    Sonar broadcasts are followed by echoes at different delays from objects at different distances. When broadcasts are emitted rapidly in cluttered surroundings, echo streams from successive broadcasts overlap and cause ambiguity in matching echoes to corresponding broadcasts. To identify reactions to ambiguity in clutter, echolocating bats that emit multiple-harmonic FM sounds were trained to fly into a dense, extended array of obstacles (multiple rows of vertically hanging chains) while the sonar sounds the bat emitted were recorded with a miniature radio microphone carried by the bat. Flight paths were reconstructed from thermal-infrared video recordings. Successive rows of chains extended more than 6 m in depth, so each broadcast was followed by a series of echoes from multiple rows of chains that lasted up to 40 ms. Bats emitted sounds in pairs ("strobe groups") at short (20-40 ms) interpulse intervals (IPIs) alternating with longer IPIs (>50 ms). For many short IPIs, the stream of echoes from the first broadcast was still arriving when the second broadcast was emitted. This overlap caused ambiguity about matching echoes with broadcasts. Bats shifted frequencies of the first sound in each strobe group upward and the second sound downward by 3-6 kHz. When overlap and ambiguity ceased, frequency shifts ceased also. Frequency differences were small compared with the total broadcast band, which was 75-80 kHz wide, but the harmonic structure of echoes enhances the differences in spectrograms. Bats could use time-frequency comparisons of echoes with broadcasts to assign echoes to the corresponding broadcasts and thus avoid ambiguity.

  13. FM echolocating bats shift frequencies to avoid broadcast–echo ambiguity in clutter

    PubMed Central

    Hiryu, Shizuko; Bates, Mary E.; Simmons, James A.; Riquimaroux, Hiroshi

    2010-01-01

    Sonar broadcasts are followed by echoes at different delays from objects at different distances. When broadcasts are emitted rapidly in cluttered surroundings, echo streams from successive broadcasts overlap and cause ambiguity in matching echoes to corresponding broadcasts. To identify reactions to ambiguity in clutter, echolocating bats that emit multiple-harmonic FM sounds were trained to fly into a dense, extended array of obstacles (multiple rows of vertically hanging chains) while the sonar sounds the bat emitted were recorded with a miniature radio microphone carried by the bat. Flight paths were reconstructed from thermal-infrared video recordings. Successive rows of chains extended more than 6 m in depth, so each broadcast was followed by a series of echoes from multiple rows of chains that lasted up to 40 ms. Bats emitted sounds in pairs (“strobe groups”) at short (20–40 ms) interpulse intervals (IPIs) alternating with longer IPIs (>50 ms). For many short IPIs, the stream of echoes from the first broadcast was still arriving when the second broadcast was emitted. This overlap caused ambiguity about matching echoes with broadcasts. Bats shifted frequencies of the first sound in each strobe group upward and the second sound downward by 3–6 kHz. When overlap and ambiguity ceased, frequency shifts ceased also. Frequency differences were small compared with the total broadcast band, which was 75–80 kHz wide, but the harmonic structure of echoes enhances the differences in spectrograms. Bats could use time–frequency comparisons of echoes with broadcasts to assign echoes to the corresponding broadcasts and thus avoid ambiguity. PMID:20351291

  14. Green pulsed lidar-radar emitter based on a multipass frequency-shifting external cavity.

    PubMed

    Zhang, Haiyang; Brunel, Marc; Romanelli, Marco; Vallet, Marc

    2016-04-01

    This paper investigates the radio frequency (RF) up-conversion properties of a frequency-shifting external cavity on a laser beam. We consider an infrared passively Q-switched pulsed laser whose intensity modulation results from the multiple round-trips in the external cavity, which contains a frequency shifter. The output beam undergoes optical second-harmonic generation necessary to reach the green wavelength. We model the pulse train using a rate-equation model to simulate the laser pulses, together with a time-delayed interference calculation taking both the diffraction efficiency and the Gaussian beam propagation into account. The predictions are verified experimentally using a diode-pumped Nd:YAG laser passively Q-switched by Cr4+:YAG whose pulse train makes multiple round-trips in a mode-matched external cavity containing an acousto-optic frequency shifter driven at 85 MHz. Second-harmonic generation is realized in a KTP crystal, yielding RF-modulated pulses at 532 nm with a modulation contrast of almost 100%. RF harmonics up to the 6th order (1.020 GHz) are observed in the green output pulses. Such a RF-modulated green laser may find applications in underwater detection and ranging.

  15. Frequency Shift of a Rotating Mass-Imbalance Immersed in an Acoustic Fluid

    SciTech Connect

    Stephen R. Novascone; David M. Weinberg; Michael J. Anderson

    2005-08-01

    In this paper, we describe a physical mechanism that relates a measurable behavior of a vibrating device to the physical properties of a surrounding acoustic medium. The vibrating device under consideration is a rotating imbalance immersed in an unbounded acoustic fluid. It is assumed that the rotating imbalance is driven by an electromagnetic motor excited by a given DC voltage. If nonlinearities are ignored, the steady state operational frequency of such a device is determined by a balance between the applied electromagnetic and opposing frictional torque on the rotating imbalance. If nonlinearities are retained, it is shown that under certain circumstances, the surrounding acoustic medium exerts an additional time-averaged opposing torque on the rotating imbalance that reduces the operational frequency of the device. Consequently, the operational frequency of the device becomes linked to the physical properties of the surrounding medium. Analytical calculations showed that the radiative resistance of an acoustic fluid caused the opposing torque. The shift in frequency is proportional to the radiative resistance and the square of the rotating eccentricity, but inversely proportional the total transducer mass and the damping effect of the DC motor.

  16. Green pulsed lidar-radar emitter based on a multipass frequency-shifting external cavity.

    PubMed

    Zhang, Haiyang; Brunel, Marc; Romanelli, Marco; Vallet, Marc

    2016-04-01

    This paper investigates the radio frequency (RF) up-conversion properties of a frequency-shifting external cavity on a laser beam. We consider an infrared passively Q-switched pulsed laser whose intensity modulation results from the multiple round-trips in the external cavity, which contains a frequency shifter. The output beam undergoes optical second-harmonic generation necessary to reach the green wavelength. We model the pulse train using a rate-equation model to simulate the laser pulses, together with a time-delayed interference calculation taking both the diffraction efficiency and the Gaussian beam propagation into account. The predictions are verified experimentally using a diode-pumped Nd:YAG laser passively Q-switched by Cr4+:YAG whose pulse train makes multiple round-trips in a mode-matched external cavity containing an acousto-optic frequency shifter driven at 85 MHz. Second-harmonic generation is realized in a KTP crystal, yielding RF-modulated pulses at 532 nm with a modulation contrast of almost 100%. RF harmonics up to the 6th order (1.020 GHz) are observed in the green output pulses. Such a RF-modulated green laser may find applications in underwater detection and ranging. PMID:27139644

  17. Electric dipole moment searches: Effect of linear electric field frequency shifts induced in confined gases

    SciTech Connect

    Barabanov, A. L.; Golub, R.; Lamoreaux, S. K.

    2006-11-15

    The search for particle electric dipole moments (EDM's) represents a most promising way to search for physics beyond the standard model. A number of groups are planning a new generation of experiments using stored gases of various kinds. In order to achieve the target sensitivities it will be necessary to deal with the systematic error resulting from the interaction of the well-known v-vectorxE-vector field with magnetic field gradients which is often referred to as the geometric phase effect [E. D. Commins, Am. J. Phys. 59, 1077 (1991); J. M. Pendlebury et al., Phys. Rev. A 70, 032102 (2004)]. This interaction produces a frequency shift linear in the electric field, mimicking an EDM. In this work we introduce an analytic form for the velocity autocorrelation function which determines the velocity-position correlation function which in turn determines the behavior of the frequency shift [S. K. Lamoreaux and R. Golub, Phys. Rev A 71, 032104 (2005)] and show how it depends on the operating conditions of the experiment. We also discuss some additional issues.

  18. Cahokia's emergence and decline coincided with shifts of flood frequency on the Mississippi River.

    PubMed

    Munoz, Samuel E; Gruley, Kristine E; Massie, Ashtin; Fike, David A; Schroeder, Sissel; Williams, John W

    2015-05-19

    Here we establish the timing of major flood events of the central Mississippi River over the last 1,800 y, using floodwater sediments deposited in two floodplain lakes. Shifts in the frequency of high-magnitude floods are mediated by moisture availability over midcontinental North America and correspond to the emergence and decline of Cahokia--a major late prehistoric settlement in the Mississippi River floodplain. The absence of large floods from A.D. 600 to A.D. 1200 facilitated agricultural intensification, population growth, and settlement expansion across the floodplain that are associated with the emergence of Cahokia as a regional center around A.D. 1050. The return of large floods after A.D. 1200, driven by waning midcontinental aridity, marks the onset of sociopolitical reorganization and depopulation that culminate in the abandonment of Cahokia and the surrounding region by A.D. 1350. Shifts in the frequency and magnitude of flooding may be an underappreciated but critical factor in the formation and dissolution of social complexity in early agricultural societies.

  19. Cahokia’s emergence and decline coincided with shifts of flood frequency on the Mississippi River

    PubMed Central

    Munoz, Samuel E.; Gruley, Kristine E.; Massie, Ashtin; Fike, David A.; Schroeder, Sissel; Williams, John W.

    2015-01-01

    Here we establish the timing of major flood events of the central Mississippi River over the last 1,800 y, using floodwater sediments deposited in two floodplain lakes. Shifts in the frequency of high-magnitude floods are mediated by moisture availability over midcontinental North America and correspond to the emergence and decline of Cahokia—a major late prehistoric settlement in the Mississippi River floodplain. The absence of large floods from A.D. 600 to A.D. 1200 facilitated agricultural intensification, population growth, and settlement expansion across the floodplain that are associated with the emergence of Cahokia as a regional center around A.D. 1050. The return of large floods after A.D. 1200, driven by waning midcontinental aridity, marks the onset of sociopolitical reorganization and depopulation that culminate in the abandonment of Cahokia and the surrounding region by A.D. 1350. Shifts in the frequency and magnitude of flooding may be an underappreciated but critical factor in the formation and dissolution of social complexity in early agricultural societies. PMID:25941363

  20. Cahokia's emergence and decline coincided with shifts of flood frequency on the Mississippi River.

    PubMed

    Munoz, Samuel E; Gruley, Kristine E; Massie, Ashtin; Fike, David A; Schroeder, Sissel; Williams, John W

    2015-05-19

    Here we establish the timing of major flood events of the central Mississippi River over the last 1,800 y, using floodwater sediments deposited in two floodplain lakes. Shifts in the frequency of high-magnitude floods are mediated by moisture availability over midcontinental North America and correspond to the emergence and decline of Cahokia--a major late prehistoric settlement in the Mississippi River floodplain. The absence of large floods from A.D. 600 to A.D. 1200 facilitated agricultural intensification, population growth, and settlement expansion across the floodplain that are associated with the emergence of Cahokia as a regional center around A.D. 1050. The return of large floods after A.D. 1200, driven by waning midcontinental aridity, marks the onset of sociopolitical reorganization and depopulation that culminate in the abandonment of Cahokia and the surrounding region by A.D. 1350. Shifts in the frequency and magnitude of flooding may be an underappreciated but critical factor in the formation and dissolution of social complexity in early agricultural societies. PMID:25941363

  1. Phase-Shifted Based Numerical Method for Modeling Frequency-Dependent Effects on Seismic Reflections

    NASA Astrophysics Data System (ADS)

    Chen, Xuehua; Qi, Yingkai; He, Xilei; He, Zhenhua; Chen, Hui

    2016-08-01

    The significant velocity dispersion and attenuation has often been observed when seismic waves propagate in fluid-saturated porous rocks. Both the magnitude and variation features of the velocity dispersion and attenuation are frequency-dependent and related closely to the physical properties of the fluid-saturated porous rocks. To explore the effects of frequency-dependent dispersion and attenuation on the seismic responses, in this work, we present a numerical method for seismic data modeling based on the diffusive and viscous wave equation (DVWE), which introduces the poroelastic theory and takes into account diffusive and viscous attenuation in diffusive-viscous-theory. We derive a phase-shift wave extrapolation algorithm in frequencywavenumber domain for implementing the DVWE-based simulation method that can handle the simultaneous lateral variations in velocity, diffusive coefficient and viscosity. Then, we design a distributary channels model in which a hydrocarbon-saturated sand reservoir is embedded in one of the channels. Next, we calculated the synthetic seismic data to analytically and comparatively illustrate the seismic frequency-dependent behaviors related to the hydrocarbon-saturated reservoir, by employing DVWE-based and conventional acoustic wave equation (AWE) based method, respectively. The results of the synthetic seismic data delineate the intrinsic energy loss, phase delay, lower instantaneous dominant frequency and narrower bandwidth due to the frequency-dependent dispersion and attenuation when seismic wave travels through the hydrocarbon-saturated reservoir. The numerical modeling method is expected to contribute to improve the understanding of the features and mechanism of the seismic frequency-dependent effects resulted from the hydrocarbon-saturated porous rocks.

  2. Shift in cytotype frequency and niche space in the invasive plant Centaurea maculosa.

    PubMed

    Treier, Urs A; Broennimann, Olivier; Normand, Signe; Guisan, Antoine; Schaffner, Urs; Steinger, Thomas; Müller-Schärer, Heinz

    2009-05-01

    Polyploidy is often assumed to increase the spread and thus the success of alien plant species, but few empirical studies exist. We tested this hypothesis with Centaurea maculosa Lam., a species native to Europe and introduced into North America approximately 120 years ago where it became highly invasive. We analyzed the ploidy level of more than 2000 plants from 93 native and 48 invasive C. maculosa populations and found a pronounced shift in the relative frequency of diploid and tetraploid cytotypes. In Europe diploid populations occur in higher frequencies than tetraploids and only four populations had both cytotypes, while in North America diploid plants were found in only one mixed population and thus tetraploids clearly dominated. Our results showed a pronounced shift in the climatic niche between tetraploid populations in the native and introduced range toward drier climate in North America and a similar albeit smaller shift between diploids and tetraploids in the native range. The field data indicate that diploids have a predominately monocarpic life cycle, while tetraploids are often polycarpic. Additionally, the polycarpic life-form seems to be more prevalent among tetraploids in the introduced range than among tetraploids in the native range. Our study suggests that both ploidy types of C. maculosa were introduced into North America, but tetraploids became the dominant cytotype with invasion. We suggest that the invasive success of C. maculosa is partly due to preadaptation of the tetraploid cytotype in Europe to drier climate and possibly further adaptation to these conditions in the introduced range. The potential for earlier and longer seed production associated with the polycarpic life cycle constitutes an additional factor that may have led to the dominance of tetraploids over diploids in the introduced range.

  3. On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes.

    PubMed

    Wang, Weizhou; Zhang, Yu; Ji, Baoming; Tian, Anmin

    2011-06-14

    The C-Hal (Hal = Cl, Br, or I) bond-length change and the corresponding vibrational frequency shift of the C-Hal stretch upon the C-Hal···Y (Y is the electron donor) halogen bond formation have been determined by using density functional theory computations. Plots of the C-Hal bond-length change versus the corresponding vibrational frequency shift of the C-Hal stretch all give straight lines. The coefficients of determination range from 0.94366 to 0.99219, showing that the correlation between the C-Hal bond-length change and the corresponding frequency shift is very good in the halogen-bonded complexes. The possible effects of vibrational coupling, computational method, and anharmonicity on the bond-length change-frequency shift correlation are discussed in detail.

  4. On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes

    NASA Astrophysics Data System (ADS)

    Wang, Weizhou; Zhang, Yu; Ji, Baoming; Tian, Anmin

    2011-06-01

    The C-Hal (Hal = Cl, Br, or I) bond-length change and the corresponding vibrational frequency shift of the C-Hal stretch upon the C-Hal ⋯Y (Y is the electron donor) halogen bond formation have been determined by using density functional theory computations. Plots of the C-Hal bond-length change versus the corresponding vibrational frequency shift of the C-Hal stretch all give straight lines. The coefficients of determination range from 0.94366 to 0.99219, showing that the correlation between the C-Hal bond-length change and the corresponding frequency shift is very good in the halogen-bonded complexes. The possible effects of vibrational coupling, computational method, and anharmonicity on the bond-length change-frequency shift correlation are discussed in detail.

  5. Regime shifts in annual maximum rainfall across Australia - implications for intensity-frequency-duration (IFD) relationships

    NASA Astrophysics Data System (ADS)

    Verdon-Kidd, D. C.; Kiem, A. S.

    2015-12-01

    Rainfall intensity-frequency-duration (IFD) relationships are commonly required for the design and planning of water supply and management systems around the world. Currently, IFD information is based on the "stationary climate assumption" that weather at any point in time will vary randomly and that the underlying climate statistics (including both averages and extremes) will remain constant irrespective of the period of record. However, the validity of this assumption has been questioned over the last 15 years, particularly in Australia, following an improved understanding of the significant impact of climate variability and change occurring on interannual to multidecadal timescales. This paper provides evidence of regime shifts in annual maximum rainfall time series (between 1913-2010) using 96 daily rainfall stations and 66 sub-daily rainfall stations across Australia. Furthermore, the effect of these regime shifts on the resulting IFD estimates are explored for three long-term (1913-2010) sub-daily rainfall records (Brisbane, Sydney, and Melbourne) utilizing insights into multidecadal climate variability. It is demonstrated that IFD relationships may under- or over-estimate the design rainfall depending on the length and time period spanned by the rainfall data used to develop the IFD information. It is recommended that regime shifts in annual maximum rainfall be explicitly considered and appropriately treated in the ongoing revisions of the Engineers Australia guide to estimating and utilizing IFD information, Australian Rainfall and Runoff (ARR), and that clear guidance needs to be provided on how to deal with the issue of regime shifts in extreme events (irrespective of whether this is due to natural or anthropogenic climate change). The findings of our study also have important implications for other regions of the world that exhibit considerable hydroclimatic variability and where IFD information is based on relatively short data sets.

  6. The second post-Newtonian light propagation and its astrometric measurement in the Solar System: Light time and frequency shift

    NASA Astrophysics Data System (ADS)

    Deng, Xue-Mei

    2016-05-01

    The light time equation and frequency shift are worked out in the framework of a second parametrized post-Newtonian (2PPN) formalism in the Solar System barycentric reference system (SSBRS) developed in a recently published paper. Effects of each body’s oblateness, spin and translational motion are taken into account for the light propagation. It is found that, at the second post-Newtonian (2PN) approximation, the light time and frequency shift depend on the parameter η only.

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

    PubMed

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

    2011-01-01

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

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

    PubMed

    Sulcebe, Genc; Shyti, Erkena

    2016-08-01

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

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

    PubMed Central

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

    2015-01-01

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

  10. Frequency Shift and Sub-band Effect in Pair-Production Process Under Adiabatic Closing the External Field

    NASA Astrophysics Data System (ADS)

    Song, Xinfang; Wang, Wenyuan; Fu, Libin

    2016-09-01

    Oscillating electric field is chosen to investigate the electron-positron pair production process by using a quantum kinetic theory and the effective mass model [Phys. Rev. Lett. 112, 050402 (2014)]. The particle yield exhibits a characteristic oscillatory structure which is related to the multi-photon thresholds. The true peak positions are typically slightly above the naive threshold estimate, which is defined as frequency shift. During the numerical calculations, we find the frequency shift can be affected by the system parameters under adiabatic closing the external field, it is worthwhile to study in detail. In this paper, we investigate the frequency shift and the sub-band effect in electron-positron pair production with oscillating electric field. First, a quantum kinetic theory and the effective mass are presented to obtain the frequency shift, the results are fitted very well. And we find the frequency shift and the sub-band effect can be influenced by pulse duration, photon number, and strength of the external field. The frequency shift becomes evident as increases of photon number and the external field strength. The sub-band width is relatively lower at longer pulse duration, higher photon number region, and weaker external field. The results shown in the paper are helpful for understanding multi-photon pair production process in the strong field.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  13. Diversified pulse generation from frequency shifted feedback Tm-doped fibre lasers

    NASA Astrophysics Data System (ADS)

    Chen, He; Chen, Sheng-Ping; Jiang, Zong-Fu; Hou, Jing

    2016-05-01

    Pulsed fibre lasers operating in the eye-safe 2 μm spectral region have numerous potential applications in areas such as remote sensing, medicine, mid-infrared frequency conversion, and free-space communication. Here, for the first time, we demonstrate versatile 2 μm ps-ns pulses generation from Tm-based fibre lasers based on frequency shifted feedback and provide a comprehensive report of their special behaviors. The lasers are featured with elegant construction and the unparalleled capacity of generating versatile pulses. The self-starting mode-locking is initiated by an intra-cavity acousto-optical frequency shifter. Diversified mode-locked pulse dynamics were observed by altering the pump power, intra-cavity polarization state and cavity structure, including as short as 8 ps single pulse sequence, pulse bundle state and up to 12 nJ, 3 ns nanosecond rectangular pulse. A reflective nonlinear optical loop mirror was introduced to successfully shorten the pulses from 24 ps to 8 ps. Beside the mode-locking operation, flexible Q-switching and Q-switched mode-locking operation can also be readily achieved in the same cavity. Up to 78 μJ high energy nanosecond pulse can be generated in this regime. Several intriguing pulse dynamics are characterized and discussed.

  14. Diversified pulse generation from frequency shifted feedback Tm-doped fibre lasers

    PubMed Central

    Chen, He; Chen, Sheng-Ping; Jiang, Zong-Fu; Hou, Jing

    2016-01-01

    Pulsed fibre lasers operating in the eye-safe 2 μm spectral region have numerous potential applications in areas such as remote sensing, medicine, mid-infrared frequency conversion, and free-space communication. Here, for the first time, we demonstrate versatile 2 μm ps-ns pulses generation from Tm-based fibre lasers based on frequency shifted feedback and provide a comprehensive report of their special behaviors. The lasers are featured with elegant construction and the unparalleled capacity of generating versatile pulses. The self-starting mode-locking is initiated by an intra-cavity acousto-optical frequency shifter. Diversified mode-locked pulse dynamics were observed by altering the pump power, intra-cavity polarization state and cavity structure, including as short as 8 ps single pulse sequence, pulse bundle state and up to 12 nJ, 3 ns nanosecond rectangular pulse. A reflective nonlinear optical loop mirror was introduced to successfully shorten the pulses from 24 ps to 8 ps. Beside the mode-locking operation, flexible Q-switching and Q-switched mode-locking operation can also be readily achieved in the same cavity. Up to 78 μJ high energy nanosecond pulse can be generated in this regime. Several intriguing pulse dynamics are characterized and discussed. PMID:27193213

  15. Diversified pulse generation from frequency shifted feedback Tm-doped fibre lasers.

    PubMed

    Chen, He; Chen, Sheng-Ping; Jiang, Zong-Fu; Hou, Jing

    2016-01-01

    Pulsed fibre lasers operating in the eye-safe 2 μm spectral region have numerous potential applications in areas such as remote sensing, medicine, mid-infrared frequency conversion, and free-space communication. Here, for the first time, we demonstrate versatile 2 μm ps-ns pulses generation from Tm-based fibre lasers based on frequency shifted feedback and provide a comprehensive report of their special behaviors. The lasers are featured with elegant construction and the unparalleled capacity of generating versatile pulses. The self-starting mode-locking is initiated by an intra-cavity acousto-optical frequency shifter. Diversified mode-locked pulse dynamics were observed by altering the pump power, intra-cavity polarization state and cavity structure, including as short as 8 ps single pulse sequence, pulse bundle state and up to 12 nJ, 3 ns nanosecond rectangular pulse. A reflective nonlinear optical loop mirror was introduced to successfully shorten the pulses from 24 ps to 8 ps. Beside the mode-locking operation, flexible Q-switching and Q-switched mode-locking operation can also be readily achieved in the same cavity. Up to 78 μJ high energy nanosecond pulse can be generated in this regime. Several intriguing pulse dynamics are characterized and discussed. PMID:27193213

  16. Simple analytical expression for the peak-frequency shifts of plasmonic resonances for sensing.

    PubMed

    Yang, Jianji; Giessen, Harald; Lalanne, Philippe

    2015-05-13

    We derive a closed-form expression that accurately predicts the peak frequency shift and broadening induced by tiny perturbations of plasmonic nanoresonators without critically relying on repeated electrodynamic simulations of the spectral response of nanoresonator for various locations, sizes, or shapes of the perturbing objects. In comparison with other approaches of the same kind, the force of the present approach is that the derivation is supported by a mathematical formalism based on a rigorous normalization of the resonance modes of nanoresonators consisting of lossy and dispersive materials. Accordingly, accurate predictions are obtained for a large range of nanoparticle shapes and sizes used in various plasmonic nanosensors even beyond the quasistatic limit. The expression gives quantitative insight and, combined with an open-source code, provides accurate and fast predictions that are ideally suited for preliminary designs or for interpretation of experimental data. It is also valid for photonic resonators with large mode volumes. PMID:25844813

  17. Few-mode fiber based distributed curvature sensor through quasi-single-mode Brillouin frequency shift.

    PubMed

    Wu, Hao; Wang, Ruoxu; Liu, Deming; Fu, Songnian; Zhao, Can; Wei, Huifeng; Tong, Weijun; Shum, Perry Ping; Tang, Ming

    2016-04-01

    We proposed and demonstrated a few-mode fiber (FMF) based optical-fiber sensor for distributed curvature measurement through quasi-single-mode Brillouin frequency shift (BFS). By central-alignment splicing FMF and single-mode fiber (SMF) with a fusion taper, a SMF-components-compatible distributed curvature sensor based on FMF is realized using the conventional Brillouin optical time-domain analysis system. The distributed BFS change induced by bending in FMF has been theoretically and experimentally investigated. The precise BFS response to the curvature along the fiber link has been calibrated. A proof-of-concept experiment is implemented to validate its effectiveness in distributed curvature measurement. PMID:27192275

  18. Fine structures of organic photovoltaic thin films probed by frequency-shift electrostatic force microscopy

    NASA Astrophysics Data System (ADS)

    Araki, Kento; Ie, Yutaka; Aso, Yoshio; Matsumoto, Takuya

    2016-07-01

    The localized charge and electrostatic properties of organic photovoltaic thin films are predominating factors for controlling energy conversion efficiency. The surface potential and electrostatic structures of organic photovoltaic thin films were investigated by frequency shift mode Kelvin force microscopy (KFM) and electrostatic force microscopy (EFM). The KFM images of a poly[2-methoxy-5-(3‧,7‧-dimethyloctyloxy)-1,4-phenylene vinylene]/phenyl-C61-butyric-acid-methyl ester (PCBM) blend thin film reveals that the PCBM domains precipitate as the topmost layer on the thin films. We find fine structures that were not observed in the topography and KFM images. The bias dependence of the EFM images suggests that the EFM contrast reflects the field-induced polarization, indicating the presence of charge trapping sites.

  19. Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus.

    PubMed

    Herruzo, Elena T; Garcia, Ricardo

    2012-01-01

    Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip-surface forces such as the Lennard-Jones and Derjaguin-Muller-Toporov forces. PMID:22496992

  20. Correction of Proton Resonance Frequency Shift Temperature Maps for Magnetic Field Disturbances Caused by Breathing

    NASA Astrophysics Data System (ADS)

    Shmatukha, Andriy V.; Bakker, Chris J. G.

    2006-05-01

    Respiratory Induced Resonance Offset (RIRO) is a periodic disturbance of the magnetic field due to breathing. Such disturbances handicap the accuracy of the Proton Resonance Frequency Shift (PRFS) method of MRI temperature mapping in anatomies situated nearby the lungs and chest wall. In this work, we propose a method capable of minimizing errors caused by RIRO in PRFS temperature maps. In this method, a set of baseline images characterizing RIRO at a variety of respiratory cycle instants is acquired before the thermal treatment starts. During the treatment, the temperature evolution is found from two successive images. Then, the calculated temperature changes are corrected for the additional contribution caused by RIRO using the pre-treatment baseline images acquired at the identical instances of the respiratory cycle. Our method is shown to improve the accuracy and stability of PRFS temperature maps in the presence of RIRO and motion in phantom and volunteer experiments.

  1. Self-precession and frequency shift for electromagnetic waves in homogeneous plasmas

    NASA Technical Reports Server (NTRS)

    Arons, J.; Max, C. E.

    1974-01-01

    The nonlinear propagation of an arbitrarily polarized electromagnetic wave in a uniform plasma is studied. It is shown that nonlinear effects cause precession of the polarization ellipse as the wave propagates. The ellipticity remains constant, but the orientation of the principal axes is rotated relative to its initial value. A relativistic Vlasov model is used to study nonlinear frequency shifts as well as self-precession, in a plasma of arbitrary temperature. Even when the electron temperature is much greater than the product of the electron mass times the square of the velocity of light, the qualitative nature of these two processes remains unchanged, although their dependence on the plasma density is altered in significant ways. Implications of these effects for plasma instabilities driven by strong electromagnetic waves are briefly discussed.

  2. Infrared Frequency Selective Surfaces Fabricated using Optical Lithography and Phase-Shift Masks

    SciTech Connect

    S.J. Spector; D.K. Astolfi; S.P. Doran; T.M. Lyszczarz; J.E. Raynolds

    2001-06-15

    A frequency selective surface (FSS) structure has been fabricated for use in a thermophotovoltaic system. The FSS provides a means for reflecting the unusable light below the bandgap of the thermophotovoltaic cell while transmitting the usable light above the bandgap. This behavior is relatively independent of the light's incident angle. The fabrication of the FSS was done using optical lithography and a phase-shift mask. The FSS cell consisted of circular slits spaced by 1100 nm. The diameters and widths of the circular slits were 870 nm and 120 nm, respectively. The FSS was predicted to pass wavelengths near 7 {micro}m and reflect wavelengths outside of this pass-band. The FSSs fabricated performed as expected with a pass-band centered near 5 {micro}m.

  3. Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus.

    PubMed

    Herruzo, Elena T; Garcia, Ricardo

    2012-01-01

    Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip-surface forces such as the Lennard-Jones and Derjaguin-Muller-Toporov forces.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. Using noncontact AFM frequency shifts to determine stereocilia bundle stiffness and tension in the developing cochlear sensory epithelium

    NASA Astrophysics Data System (ADS)

    Chadwick, Richard S.; Cartagena-Rivera, Alexander X.

    2015-12-01

    Measurement of frequency shifts of cantilevers having an attached microsphere oscillating at acoustic frequencies can be used to assess mechanical properties of cochlear structures. The method has already been reported for measuring elastic and viscous properties of the tectorial membrane. We describe here how the method can be used to examine other cochlear structures. Theory and formulas for relating hair bundle stiffness and tension in the developing cochlear sensory epithelium to measured frequency shifts are given to estimate the expected frequency shifts and show feasibility of the measurements. We show through a molecular model of myosin II located along the edges of confluent hexagons that myosin contractile forces are balanced by isotropic tension in the developing confluent sheet of cells.

  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. Vibrational dephasing and frequency shifts of hydrogen-bonded pyridine-water complexes.

    PubMed

    Kalampounias, A G; Tsilomelekis, G; Boghosian, S

    2015-01-25

    In this paper we present the picosecond vibrational dynamics and Raman shifts of hydrogen-bonded pyridine-water complexes present in aqueous solutions in a wide concentration range from dense to extreme dilute solutions. We studied the vibrational dephasing and vibrational frequency modulation by calculating time correlation functions of vibrational relaxation by fits in the frequency domain. The concentration induced variations in bandwidths, band frequencies and characteristic dephasing times have been estimated and interpreted as effects due to solute-solvent interactions. The time-correlation functions of vibrational dephasing were obtained for the ring breathing mode of both "free" and hydrogen-bonded pyridine molecules and it was found that sufficiently deviate from the Kubo model. There is a general agreement in the whole concentration range with the modeling proposed by the Rothschild approach, which applies to complex liquids. The results have shown that the reorientation of pyridine aqueous solutions is very slow and hence in both scattering geometries only vibrational dephasing is probed. It is proposed that the spectral changes depend on the perturbations induced by the dynamics of the water molecules in the first hydration cell and water in bulk, while at extreme dilution conditions, the number of bulk water molecules increases and the interchange between molecules belonging to the first hydration cell may not be the predominant modulation mechanism. The evolution of several parameters, such as the characteristic times, the percentage of Gaussian character in the peak shape and the a parameter are indicative of drastic variations at extreme dilution revealing changes in the vibrational relaxation of the pyridine complexes in the aqueous environment. The higher dilution is correlated to diffusion of water molecules into the reference pyridine system in agreement with the jump diffusion model, while at extreme dilutions, almost all pyridine molecules are

  14. Vibrational dephasing and frequency shifts of hydrogen-bonded pyridine-water complexes

    NASA Astrophysics Data System (ADS)

    Kalampounias, A. G.; Tsilomelekis, G.; Boghosian, S.

    2015-01-01

    In this paper we present the picosecond vibrational dynamics and Raman shifts of hydrogen-bonded pyridine-water complexes present in aqueous solutions in a wide concentration range from dense to extreme dilute solutions. We studied the vibrational dephasing and vibrational frequency modulation by calculating time correlation functions of vibrational relaxation by fits in the frequency domain. The concentration induced variations in bandwidths, band frequencies and characteristic dephasing times have been estimated and interpreted as effects due to solute-solvent interactions. The time-correlation functions of vibrational dephasing were obtained for the ring breathing mode of both "free" and hydrogen-bonded pyridine molecules and it was found that sufficiently deviate from the Kubo model. There is a general agreement in the whole concentration range with the modeling proposed by the Rothschild approach, which applies to complex liquids. The results have shown that the reorientation of pyridine aqueous solutions is very slow and hence in both scattering geometries only vibrational dephasing is probed. It is proposed that the spectral changes depend on the perturbations induced by the dynamics of the water molecules in the first hydration cell and water in bulk, while at extreme dilution conditions, the number of bulk water molecules increases and the interchange between molecules belonging to the first hydration cell may not be the predominant modulation mechanism. The evolution of several parameters, such as the characteristic times, the percentage of Gaussian character in the peak shape and the a parameter are indicative of drastic variations at extreme dilution revealing changes in the vibrational relaxation of the pyridine complexes in the aqueous environment. The higher dilution is correlated to diffusion of water molecules into the reference pyridine system in agreement with the jump diffusion model, while at extreme dilutions, almost all pyridine molecules are

  15. 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.

  16. 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

  17. Measuring the spin polarization of alkali-metal atoms using nuclear magnetic resonance frequency shifts of noble gases

    SciTech Connect

    Liu, X. H.; Luo, H.; Qu, T. L. Yang, K. Y.; Ding, Z. C.

    2015-10-15

    We report a novel method of measuring the spin polarization of alkali-metal atoms by detecting the NMR frequency shifts of noble gases. We calculated the profile of {sup 87}Rb D1 line absorption cross sections. We then measured the absorption profile of the sample cell, from which we calculated the {sup 87}Rb number densities at different temperatures. Then we measured the frequency shifts resulted from the spin polarization of the {sup 87}Rb atoms and calculated its polarization degrees at different temperatures. The behavior of frequency shifts versus temperature in experiment was consistent with theoretical calculation, which may be used as compensative signal for the NMRG closed-loop control system.

  18. Quantum Monte Carlo Simulation of Vibrational Frequency Shifts of CO in Solid para-HYDROGEN

    NASA Astrophysics Data System (ADS)

    Wang, Lecheng; Le Roy, Robert; Roy, Pierre-Nicholas

    2014-06-01

    Stimulated by Fajardo's remarkable study of the rovibrational spectra of CO isotopologues trapped in solid para-hydrogen, we have performed quantum Monte Carlo simulations to predict his observed vibrational frequency shifts and inertial rotational constants using 2-body potentials based on the best available models for the pH_2-pH_2 and CO-pH_2, potential energy functions. We started by fitting an analytic `Morse/Long-Range' (MLR) function to the 1D ``adiabaic hindered rotor" version of Hinde's 5D pH_2-pH_2 potential developed by Faruk et al. We then modified it to take account of many-body effects by scaling it until it yielded the correct equilibrium lattice parameters for the fcc and hcp structures of pure solid para-hydrogen. A CO molecule was then placed at different interstitial or substitution sites in large equilibrated fcc or hcp para-hydrogen lattices, and the structural and dynamical behaviors of the micro-solvation environment around CO were simulated with a PIMC algorithm using a 2D effective pH_2-CO potential based on the 5D H_2--CO potential energy surface recently reported by Li et al., with a lattice sum of values of the 2D CO vibrational difference potential being use to predict the vibrational frequency shift. The effective rotational constants Beff for CO in different solid para-hydrogen structures were also calculated and compared with the experimental observations and with predicted Beff values for CO in large-sized para-hydrogen--CO clusters. M. E. Fajardo, J. Phys. Chem. A 117, 13504 (2013). R. Hinde, J. Chem. Phys., 128, 154308 (2008). H. Li, X-L. Zhang, R.J. Le Roy, and P.-N. Roy, J. Chem. Phys. 139, 164315 (2013). R.J. Le Roy, C.C. Haugen, J. Tao and Hui Li, Mol. Phys., 109, 435 (2011) N. Faruk, R.J. Le Roy, and P.-N. Roy, J. Chem. Phys. (submitted December 2013). Y. Mizumoto and Y. Ohtsuki, Chem. Phys. Lett. 501, 304 (2011).

  19. Analytical calculation of the frequency shift in phase oscillators driven by colored noise: implications for electrical engineering and neuroscience.

    PubMed

    Galán, Roberto F

    2009-09-01

    We provide an analytical expression for the mean frequency shift in phase oscillators as a function of the standard deviation, sigma and the autocorrelation time, tau of small random perturbations. We show that the frequency shift is negative and proportional to sigma;{2} . Its absolute value increases monotonically with tau , approaching an asymptote determined by the L2 -norm of the phase-response curve. We validate our theoretical predictions with computer simulations and discuss their implications for the design of electronic oscillators and for the encoding of information in biological neural networks.

  20. A laser-cooled cesium fountain frequency standard and a measurement of the frequency shift due to ultra-cold collisions

    NASA Technical Reports Server (NTRS)

    Gibble, Kurt; Kasapi, Steven; Chu, Steven

    1993-01-01

    A frequency standard based on an atomic fountain of cesium atoms may have an accuracy of 10(exp -16) due to longer interaction times and smaller anticipated systematic errors. All of the known systematic effects that now limit the accuracy of the Cs frequency standard increase either linearly or as some higher power of the atom's velocity. The one systematic frequency shift which is dramatically different is the frequency shift due to the collisions between the laser cooled atoms. At a temperature of a few micro-K, the de Broglie wavelength (lambda(sub deB) = h/p, where h is Planck's constant and p is the momentum of the atom) is much larger than the scale of the interatomic potential. Under these conditions the collision cross sections can be as large as (lambda(sub deB)(sup 2))/Pi and the frequency shift due to these collisions was recently calculated. In our Cs atomic fountain, we laser cooled and trapped 10(exp 10) Cs atoms in 0.4 s. By shifting the frequencies of the laser beams, the atoms were launched upwards at 2.5 m/s and a fraction of the atoms were optically pumped into the F=3 ground state. The unwanted atoms in the F=4 ground state were removed from the fountain with radiation pressure from a laser beam tuned to excite only those atoms. The Cs atoms in the F=3 state traveled ballistically upwards, were excited by the microwave cavity, and then returned back through the same cavity in the atomic fountain configuration. By varying the cold atom density, a density dependent shift of -12.9 +/- 0.7 mHz or -1.4 x 10-12 for an average fountain density of (2.7 +/- 1.5) 10(exp 9) atoms/cm(sup 3) was measured.

  1. Description of the suppression of the soliton self-frequency shift by bandwidth-limited amplification.

    PubMed

    Uzunov, Ivan M

    2010-12-01

    A perturbation study of the suppression of the soliton self-frequency shift by the bandwidth-limited optical amplification is proposed. The stability of the equilibrium point for the soliton amplitude and velocity identified by the adiabatic approximation of the soliton perturbation theory (SPT) is analyzed by a numerical solution of a linearized system in the neighborhood of the equilibrium point. The obtained analytical expressions for the eigenvalues of the linearized system allow the determination of the values of pulse and material parameters for which the equilibrium point is stable. A perturbation approach that leads to the research of the equation of strongly nonlinear Duffing-Van der Pol oscillator is suggested. The last equation is explored by two different methods. First, the recently obtained results for this equation by the hyperbolic perturbation method are used. Next, the hyperbolic Lindstedt-Poincare perturbation method is applied to the exploration of this equation. The equilibrium velocity of the perturbed stationary solution was calculated as a critical value of the control parameter in both methods. It turned out that the coupling of the equilibrium velocity and the amplitude of the perturbed stationary solution in both methods is similar to the relation between the soliton amplitude and velocity derived by the adiabatic approximation of SPT. The change in the form of the perturbed stationary solution has also been identified by means of the hyperbolic Lindstedt-Poincare perturbation method. PMID:21230747

  2. Optimal spectral filtering in soliton self-frequency shift for deep-tissue multiphoton microscopy

    NASA Astrophysics Data System (ADS)

    Wang, Ke; Qiu, Ping

    2015-05-01

    Tunable optical solitons generated by soliton self-frequency shift (SSFS) have become valuable tools for multiphoton microscopy (MPM). Recent progress in MPM using 1700 nm excitation enabled visualizing subcortical structures in mouse brain in vivo for the first time. Such an excitation source can be readily obtained by SSFS in a large effective-mode-area photonic crystal rod with a 1550-nm fiber femtosecond laser. A longpass filter was typically used to isolate the soliton from the residual in order to avoid excessive energy deposit on the sample, which ultimately leads to optical damage. However, since the soliton was not cleanly separated from the residual, the criterion for choosing the optimal filtering wavelength is lacking. Here, we propose maximizing the ratio between the multiphoton signal and the n'th power of the excitation pulse energy as a criterion for optimal spectral filtering in SSFS when the soliton shows dramatic overlapping with the residual. This optimization is based on the most efficient signal generation and entirely depends on physical quantities that can be easily measured experimentally. Its application to MPM may reduce tissue damage, while maintaining high signal levels for efficient deep penetration.

  3. 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.

  4. 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

  5. Effect of Irregularities in the Earth's Rotation on Relativistic Shifts in Frequency and Time of Earthbound Atomic Clocks

    NASA Astrophysics Data System (ADS)

    Fateev, V. F.; Kopeikin, S. M.; Pasynok, S. L., S. L.

    2015-10-01

    The effect of irregularities in the earth's rotation (precession and nutation of the earth's axis of rotation, oscillations in the modulus of the angular velocity, periodic deviations in the line of the poles, and the angular momentum of the globe) on the frequency and time of high-stability atomic clocks are examined in terms of the theory of relativity. It is shown that the relative shift in frequency and time owing to these effects can exceed 5×10-16.

  6. Photonic generation of microwave frequency shift keying signal using a single-drive Mach-Zehnder modulator.

    PubMed

    Cao, Pan; Hu, Xiaofeng; Zhang, Liang; Wu, Jiayang; Jiang, Xinhong; Su, Yikai

    2014-06-16

    We propose and experimentally demonstrate a new scheme for photonic generation of microwave frequency shift keying (FSK) signal by employing one single-drive Mach-Zehnder modulator (MZM). In the proposed method, an electrical signal with different radio frequency (RF) amplitudes and direct current (DC) components for bit '0' and bit '1' is generated. After amplification, the signal is fed into a single-drive MZM which is biased at the quadrature and null points of its transmission curve for bit '0' and bit '1', respectively. Due to the different RF amplitudes, a microwave FSK signal can be obtained after photodetection, where the space frequency is the same as the RF frequency and the mark frequency is twice as large as the RF frequency. The feasibility of the proposed scheme is verified by a proof-of-concept experiment. 5/10-GHz and 10/20-GHz microwave FSK signals with different bit rates are successfully demonstrated.

  7. Phase and amplitude dynamics in large systems of coupled oscillators: growth heterogeneity, nonlinear frequency shifts, and cluster states.

    PubMed

    Lee, Wai Shing; Ott, Edward; Antonsen, Thomas M

    2013-09-01

    This paper addresses the behavior of large systems of heterogeneous, globally coupled oscillators each of which is described by the generic Landau-Stuart equation, which incorporates both phase and amplitude dynamics of individual oscillators. One goal of our paper is to investigate the effect of a spread in the amplitude growth parameter of the oscillators and of the effect of a homogeneous nonlinear frequency shift. Both of these effects are of potential relevance to recently reported experiments. Our second goal is to gain further understanding of the macroscopic system dynamics at large coupling strength, and its dependence on the nonlinear frequency shift parameter. It is proven that at large coupling strength, if the nonlinear frequency shift parameter is below a certain value, then there is a unique attractor for which the oscillators all clump at a single amplitude and uniformly rotating phase (we call this a single-cluster "locked state"). Using a combination of analytical and numerical methods, we show that at higher values of the nonlinear frequency shift parameter, the single-cluster locked state attractor continues to exist, but other types of coexisting attractors emerge. These include two-cluster locked states, periodic orbits, chaotic orbits, and quasiperiodic orbits.

  8. 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.

  9. 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

  10. 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

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

    PubMed 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

  12. 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.

  13. A calibration concept for passive MW imaging using beam steering by frequency shift and aperture synthesis

    NASA Astrophysics Data System (ADS)

    Schreiber, Eric; Peichl, Markus; Jirousek, Matthias

    2013-10-01

    Passive microwave (MW) remote sensing is used in Earth observation missions for example to estimate the salinity of oceans or the soil moisture of landscapes. In these cases the absolute brightness temperature numbers are important for sufficient accuracy of the estimated geo-physical parameters. Consequently a suitable system calibration network is required. At DLR a radiometric demonstrator for fully-electronic MW imaging was set up at Ka-band, which is based on a combination of beam steering by frequency shift using a broadband slotted-waveguide antenna for one scanning direction, and the application of aperture synthesis for the other direction. Aperture synthesis is well known from radio astronomy, but it is still a new imaging principle for Earth observation or security applications. Hence as well new calibration techniques have to be developed for this kind of scanning mechanism. In this paper a novel approach for a noise-source based calibration method taking into account the antenna losses will be introduced. When using aperture synthesis techniques to determine the absolute brightness temperature values, it is very important, among other things, to know the exact phase transfer function of the system in order to achieve the desired radiometric resolution. Consequently our approach enables phase calibration as well. The paper outlines a proof of concept for this calibration method using a two-element interferometer called VESAS (Voll Elektronischer Scanner mit AperturSynthese) as a demonstrator. The functionality of the demonstrator and the proof of concept of the imaging principle mentioned before are written in detail in [1].

  14. Propagating Neural Source Revealed by Doppler Shift of Population Spiking Frequency

    PubMed Central

    Zhang, Mingming; Shivacharan, Rajat S.; Chiang, Chia-Chu; Gonzalez-Reyes, Luis E.

    2016-01-01

    Electrical activity in the brain during normal and abnormal function is associated with propagating waves of various speeds and directions. It is unclear how both fast and slow traveling waves with sometime opposite directions can coexist in the same neural tissue. By recording population spikes simultaneously throughout the unfolded rodent hippocampus with a penetrating microelectrode array, we have shown that fast and slow waves are causally related, so a slowly moving neural source generates fast-propagating waves at ∼0.12 m/s. The source of the fast population spikes is limited in space and moving at ∼0.016 m/s based on both direct and Doppler measurements among 36 different spiking trains among eight different hippocampi. The fact that the source is itself moving can account for the surprising direction reversal of the wave. Therefore, these results indicate that a small neural focus can move and that this phenomenon could explain the apparent wave reflection at tissue edges or multiple foci observed at different locations in neural tissue. SIGNIFICANCE STATEMENT The use of novel techniques with an unfolded hippocampus and penetrating microelectrode array to record and analyze neural activity has revealed the existence of a source of neural signals that propagates throughout the hippocampus. The source itself is electrically silent, but its location can be inferred by building isochrone maps of population spikes that the source generates. The movement of the source can also be tracked by observing the Doppler frequency shift of these spikes. These results have general implications for how neural signals are generated and propagated in the hippocampus; moreover, they have important implications for the understanding of seizure generation and foci localization. PMID:27013678

  15. Allelic Spectra of Risk SNPs Are Different for Environment/Lifestyle Dependent versus Independent Diseases

    PubMed Central

    Amos, Christopher I.

    2015-01-01

    Genome-wide association studies (GWAS) have generated sufficient data to assess the role of selection in shaping allelic diversity of disease-associated SNPs. Negative selection against disease risk variants is expected to reduce their frequencies making them overrepresented in the group of minor (<50%) alleles. Indeed, we found that the overall proportion of risk alleles was higher among alleles with frequency <50% (minor alleles) compared to that in the group of major alleles. We hypothesized that negative selection may have different effects on environment (or lifestyle)-dependent versus environment (or lifestyle)-independent diseases. We used an environment/lifestyle index (ELI) to assess influence of environmental/lifestyle factors on disease etiology. ELI was defined as the number of publications mentioning “environment” or “lifestyle” AND disease per 1,000 disease-mentioning publications. We found that the frequency distributions of the risk alleles for the diseases with strong environmental/lifestyle components follow the distribution expected under a selectively neutral model, while frequency distributions of the risk alleles for the diseases with weak environmental/lifestyle influences is shifted to the lower values indicating effects of negative selection. We hypothesized that previously selectively neutral variants become risk alleles when environment changes. The hypothesis of ancestrally neutral, currently disadvantageous risk-associated alleles predicts that the distribution of risk alleles for the environment/lifestyle dependent diseases will follow a neutral model since natural selection has not had enough time to influence allele frequencies. The results of our analysis suggest that prediction of SNP functionality based on the level of evolutionary conservation may not be useful for SNPs associated with environment/lifestyle dependent diseases. PMID:26201053

  16. 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

  17. 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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

    Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

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

  20. 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

  1. 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

  2. The effect of classical and quantum dynamics on vibrational frequency shifts of H{sub 2} in clathrate hydrates

    SciTech Connect

    Plattner, Nuria; Meuwly, Markus

    2014-01-14

    Vibrational frequency shifts of H{sub 2} in clathrate hydrates are important to understand the properties and elucidate details of the clathrate structure. Experimental spectra of H{sub 2} in clathrate hydrates have been measured for different clathrate compositions, temperatures, and pressures. In order to establish reliable relationships between the clathrate structure, dynamics, and observed frequencies, calculations of vibrational frequency shifts in different clathrate environments are required. In this study, a combination of classical molecular dynamics simulations, electronic structure calculations, and quantum dynamical simulation is used to calculate relative vibrational frequencies of H{sub 2} in clathrate hydrates. This approach allows us to assess dynamical effects and simulate the change of vibrational frequencies with temperature and pressure. The frequency distributions of the H{sub 2} vibrations in the different clathrate cage types agree favorably with experiment. Also, the simulations demonstrate that H{sub 2} in the 5{sup 12} cage is more sensitive to the details of the environment and to quantum dynamical effects, in particular when the cage is doubly occupied. We show that for the 5{sup 12} cage quantum effects lead to frequency increases and double occupation is unlikely. This is different for the 5{sup 12}6{sup 4} cages for which higher occupation numbers than one H{sub 2} per cage are likely.

  3. The Effect of Doppler Frequency Shift, Frequency Offset of the Local Oscillators, and Phase Noise on the Performance of Coherent OFDM Receivers

    NASA Technical Reports Server (NTRS)

    Xiong, Fuqin; Andro, Monty

    2001-01-01

    This paper first shows that the Doppler frequency shift affects the frequencies of the RF carrier, subcarriers, envelope, and symbol timing by the same percentage in an Orthogonal Frequency Division Multiplexing (OFDM) signal or any other modulated signals. Then the SNR degradation of an OFDM system due to Doppler frequency shift, frequency offset of the local oscillators and phase noise is analyzed. Expressions are given and values for 4-, 16-, 64-, and 256-QAM OFDM systems are calculated and plotted. The calculations show that the Doppler shift of the D3 project is about 305 kHz, and the degradation due to it is about 0.01 to 0.04 dB, which is negligible. The degradation due to frequency offset and phase noise of local oscillators will be the main source of degradation. To keep the SNR degradation under 0.1 dB, the relative frequency offset due to local oscillators must be below 0.01 for the 16 QAM-OFDM. This translates to an offset of 1.55 MHz (0.01 x 155 MHz) or a stability of 77.5 ppm (0.01 x 155 MHz/20 GHz) for the DI project. To keep the SNR degradation under 0.1 dB, the relative linewidth (0) due to phase noise of the local oscillators must be below 0.0004 for the 16 QAM-OFDM. This translates to a linewidth of 0.062 MHz (0.0004 x 155 MHz) of the 20 GHz RIF carrier. For a degradation of 1 dB, beta = 0.04, and the linewidth can be relaxed to 6.2 MHz.

  4. Ambient noise induces independent shifts in call frequency and amplitude within the Lombard effect in echolocating bats.

    PubMed

    Hage, Steffen R; Jiang, Tinglei; Berquist, Sean W; Feng, Jiang; Metzner, Walter

    2013-03-01

    The Lombard effect, an involuntary rise in call amplitude in response to masking ambient noise, represents one of the most efficient mechanisms to optimize signal-to-noise ratio. The Lombard effect occurs in birds and mammals, including humans, and is often associated with several other vocal changes, such as call frequency and duration. Most studies, however, have focused on noise-dependent changes in call amplitude. It is therefore still largely unknown how the adaptive changes in call amplitude relate to associated vocal changes such as frequency shifts, how the underlying mechanisms are linked, and if auditory feedback from the changing vocal output is needed. Here, we examined the Lombard effect and the associated changes in call frequency in a highly vocal mammal, echolocating horseshoe bats. We analyzed how bandpass-filtered noise (BFN; bandwidth 20 kHz) affected their echolocation behavior when BFN was centered on different frequencies within their hearing range. Call amplitudes increased only when BFN was centered on the dominant frequency component of the bats' calls. In contrast, call frequencies increased for all but one BFN center frequency tested. Both amplitude and frequency rises were extremely fast and occurred in the first call uttered after noise onset, suggesting that no auditory feedback was required. The different effects that varying the BFN center frequency had on amplitude and frequency rises indicate different neural circuits and/or mechanisms underlying these changes.

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

    PubMed Central

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

    2010-01-01

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

  6. Oxygen-induced frequency shifts in hyperoxia: a significant component of BOLD signal.

    PubMed

    Song, Youngkyu; Cho, Gyunggoo; Chun, Song-I; Baek, Jin Hee; Cho, HyungJoon; Kim, Young Ro; Park, Sung Bin; Kim, Jeong Kon

    2014-07-01

    In comparison to the well-documented significance of intravascular deoxyhemoglobin (deoxyHgb), the effects of dissolved oxygen on the blood-oxygen-level-dependent (BOLD) signal have not been widely reported. Based on the fact that the prolonged inspiration of high oxygen fraction gas can result in up to a sixfold increase of the baseline tissue oxygenation, the current study focused on the influence of dissolved oxygen on the BOLD signal during hyperoxia. As results, our in vitro study revealed that the r1 and r2 (relaxivities) of the oxygen-treated serum were 0.22 mM(-1) · s(-1) and 0.19 mM(-1) · s(-1) , respectively. In an in vivo experiment, hyperoxic respiration induced negative BOLD contrast (i.e. signal decrease) in 18-42% of measured brain regions, voxels with accompanying significant decreases in both the T(*)2 (-12.1% to -19.4%) and T1 (-5.8% to -3.3%) relaxation times. In contrast, the T(*)2 relaxation time significantly increased (11.2% to 14.0%) for the voxels displaying positive BOLD contrast (in 41-50% of the measured brain), which reflected a hyperoxygenation-induced reduction in tissue deoxyHgb concentration. These data imply that hyperoxia-driven BOLD signal changes are primarily determined by the counteracting effects of extravascular oxygen and intravascular deoxyHgb. Oxygen-induced magnetic susceptibility was further demonstrated by the study of 1 min hypoxia, which induced BOLD signal changes opposite to those under hyperoxia. Vasoconstriction was more common in voxels with negative BOLD contrast than in voxels with positive contrast (% change of blood volume, -9.8% to -12.8% versus 2.0% to 2.2%), which further suggests that negative BOLD contrast is mainly evoked by an increase in extravascular oxygen concentration. Conclusively, frequency shifts, which are induced by the accumulation of oxygen molecules and associated magnetic field inhomogeneity, are a significant source of the negative BOLD contrast during hyperoxia.

  7. Frequency Shift of Polar Whispering Gallery Modes Caused by Uniaxial Stress

    NASA Astrophysics Data System (ADS)

    Wagner, H.-P.; Schmitzer, H.; Lutti, J.; Borri, P.; Langbein, W.

    2010-03-01

    Optical whispering gallery modes in small spheres -so called microcavity optical resonators- have been investigated in the past years because they are promising as single virus or single bacterium detectors and as pressure sensors for microfluidic applications. Due to high Q-factors whispering gallery modes are very sensitive to changes of the shape and the refractive index of the sphere. Both can be caused by mechanical stress. A small exerted compressive force will therefore lead to an energy shift of the resonant modes. The relationship between this energy shift and the exerted force depends on the geometry of the experimental setup. We investigated the energy shift of polar modes in polystyrene beads of 45 micron diameter applying an uniaxial force. With increasing force we find a shift to higher energy for resonator modes with different mode order n and number l. The observed results will be compared with model calculations.

  8. [Evaluation of the Effect of Adiabatic Pulse and B1 Shim to the Radio Frequency Homogeneity in Chemical Shift Imaging].

    PubMed

    Kikuchi, Chie; Inoue, Mitsuhiro; Okawa, Kohei; Taguchi, Jyunichi; Hirota, Yoshifumi; Yanagiya, Yohei

    2016-04-01

    It is considered that the enhancement of chemical shift and the elevation of signal-to-noise ratio (SNR) induced by high magnetic fields are useful for the evaluation of metabolism using magnetic resonance spectroscopy (MRS). However, the reduction of the localization in MRS seems to be caused by the decreased homogeneity of radio frequency (RF) pulses, especially in chemical shift imaging (CSI). To search the influence of B1 shim mode and the significance of adiabatic pulses, we have examined the changes of RF homogeneity using 3 T magnetic resonance imaging (MRI) with the water phantom and the metabolites phantom (containing acetate and lactate) in CSI. The RF homogeneity and chemical shift artifact were obviously improved using the adiabatic pulses. Improvement of the homogeneity of RF pulses was observed when B1 shim was used. These results suggest the usefulness of CSI using adiabatic pulses and B1 shim when small amount of metabolites of target is measured in MRS. PMID:27097994

  9. Frequency shift and mode coupling of the collective modes of superfluid Fermi gases in the BCS-BEC crossover

    SciTech Connect

    Zhou Yu; Wen Wen; Huang Guoxiang

    2008-03-01

    We investigate the dynamical behavior of large-amplitude collective modes in a superfluid Fermi gas in the crossover from Bardeen-Cooper-Schrieffer (BCS) superfluid to Bose-Einstein condensate (BEC) based on a hydrodynamic approach. We first solve the superfluid hydrodynamic equations that describe the time evolution of fermionic condensates in the BCS-BEC crossover and calculate explicitly the frequency shifts of the collective modes induced by nonlinear effects using the Lindstedt-Poincare method. The result shows that the frequency shifts display different features in different superfluid regimes. We then study the second-harmonic generation of the collective modes under a phase-matching condition, which can be fulfilled by choosing appropriate parameters of the system. The analytical results obtained are checked by numerical simulations and good agreement is found.

  10. Evaluation of the systematic shifts of a single-{sup 40}Ca{sup +}-ion frequency standard

    SciTech Connect

    Huang, Yao; Liu, Qu; Cao, Jian; Liu, Peiliang; Ou, Baoquan; Guan, Hua; Huang, Xueren; Gao, Kelin

    2011-11-15

    Progress on the evaluation of systematic frequency shifts is described in the development of the optical frequency standard based on single-trapped {sup 40}Ca{sup +} with a ''clock'' transition at 729 nm. The overall systematic uncertainty of the 4s {sup 2} S{sub 1/2}-3d {sup 2} D{sub 5/2} clock resonance has been characterized to be 7.8 x 10{sup -16}. This uncertainty is at a level similar to the Cs fountain primary standard, while the potential stability for the {sup 40}Ca{sup +} clock exceeds that of Cs.

  11. Nonlinear frequency shift of electrostatic waves in general collisionless plasma: Unifying theory of fluid and kinetic nonlinearities

    SciTech Connect

    Liu, Chang; Dodin, Ilya Y.

    2015-08-15

    The nonlinear frequency shift is derived in a transparent asymptotic form for intense Langmuir waves in general collisionless plasma. The formula describes both fluid and kinetic effects simultaneously. The fluid nonlinearity is expressed, for the first time, through the plasma dielectric function, and the kinetic nonlinearity accounts for both smooth distributions and trapped-particle beams. Various known limiting scalings are reproduced as special cases. The calculation avoids differential equations and can be extended straightforwardly to other nonlinear plasma waves.

  12. Frequency-modulated atomic force microscopy operation by imaging at the frequency shift minimum: The dip-df mode

    NASA Astrophysics Data System (ADS)

    Rode, Sebastian; Schreiber, Martin; Kühnle, Angelika; Rahe, Philipp

    2014-04-01

    In frequency modulated non-contact atomic force microscopy, the change of the cantilever frequency (Δf) is used as the input signal for the topography feedback loop. Around the Δf(z) minimum, however, stable feedback operation is challenging using a standard proportional-integral-derivative (PID) feedback design due to the change of sign in the slope. When operated under liquid conditions, it is furthermore difficult to address the attractive interaction regime due to its often moderate peakedness. Additionally, the Δf signal level changes severely with time in this environment due to drift of the cantilever frequency f0 and, thus, requires constant adjustment. Here, we present an approach overcoming these obstacles by using the derivative of Δf with respect to z as the input signal for the topography feedback loop. Rather than regulating the absolute value to a preset setpoint, the slope of the Δf with respect to z is regulated to zero. This new measurement mode not only makes the minimum of the Δf(z) curve directly accessible, but it also benefits from greatly increased operation stability due to its immunity against f0 drift. We present isosurfaces of the Δf minimum acquired on the calcite CaCO3(10overline{1}4) surface in liquid environment, demonstrating the capability of our method to image in the attractive tip-sample interaction regime.

  13. Frequency-modulated atomic force microscopy operation by imaging at the frequency shift minimum: The dip-df mode

    SciTech Connect

    Rode, Sebastian; Schreiber, Martin; Kühnle, Angelika; Rahe, Philipp

    2014-04-15

    In frequency modulated non-contact atomic force microscopy, the change of the cantilever frequency (Δf) is used as the input signal for the topography feedback loop. Around the Δf(z) minimum, however, stable feedback operation is challenging using a standard proportional-integral-derivative (PID) feedback design due to the change of sign in the slope. When operated under liquid conditions, it is furthermore difficult to address the attractive interaction regime due to its often moderate peakedness. Additionally, the Δf signal level changes severely with time in this environment due to drift of the cantilever frequency f{sub 0} and, thus, requires constant adjustment. Here, we present an approach overcoming these obstacles by using the derivative of Δf with respect to z as the input signal for the topography feedback loop. Rather than regulating the absolute value to a preset setpoint, the slope of the Δf with respect to z is regulated to zero. This new measurement mode not only makes the minimum of the Δf(z) curve directly accessible, but it also benefits from greatly increased operation stability due to its immunity against f{sub 0} drift. We present isosurfaces of the Δf minimum acquired on the calcite CaCO{sub 3}(101{sup ¯}4) surface in liquid environment, demonstrating the capability of our method to image in the attractive tip-sample interaction regime.

  14. Vibrational frequency shifts as a probe of hydrogen bonds: thermal expansion and glass transition of myoglobin in mixed solvents.

    PubMed

    Demmel, F; Doster, W; Petry, W; Schulte, A

    1997-01-01

    The contribution of hydrogen bonds to protein-solvent interactions and their impact on structural flexibility and dynamics of myoglobin are discussed. The shift of vibrational peak frequencies with the temperature of myoglobin in sucrose/water and glycerol/water solutions is used to probe the expansion of the hydrogen bond network. We observe a characteristic change in the temperature slope of the O-H stretching frequency at the glass transition which correlates with the discontinuity of the thermal expansion coefficient. The temperature-difference spectra of the amide bands show the same tendency, indicating that stronger hydrogen bonding in the bulk affects the mainchain solvent interactions in parallel. However, the hydrogen bond strength decreases relative to the bulk solvent with increasing cosolvent concentration near the protein surface, which suggests preferential hydration. Weaker and/or fewer hydrogen bonds are observed at low degrees of hydration. The central O-H stretching frequency of protein hydration water is red-shifted by 40 cm-1 relative to the bulk. The shift increases towards lower temperatures, consistent with contraction and increasing strength of the protein-water bonds. The temperature slope shows a discontinuity near 180 K. The contraction of the network has reached a critical limit which leads to frozen-in structures. This effect may represent the molecular mechanism underlying the dynamic transition observed for the mean square displacements of the protein atoms and the heme iron of myoglobin. PMID:9378100

  15. Multivariate analysis of spectral data with frequency shifts: application to temperature dependent infrared spectra of peptides and proteins.

    PubMed

    Kubelka, Jan

    2013-10-15

    Changes in the amide I' IR band with temperature are widely used for elucidation of peptide and protein conformational transitions and folding equilibria. Since amide I' exhibits inherent temperature dependent frequency shifts, standard mixture analysis methods are not applicable. To reliably extract the true thermodynamic states, frequency shifts of the component spectra must be explicitly taken into account. For this purpose, new methods termed shifted multivariate spectra analysis (SMSA) and parametric SMSA (pSMSA) are developed and tested on sets of synthetic data as well as real experimental amide I' spectra for thermal unfolding of an α-helical peptide. SMSA uses no specific functional form for the transition (soft modeling), while the parametric variant (pSMSA) assumes a thermodynamic model (hard modeling). The implementation is optimized specifically for amide I' IR in that it takes advantage of known, linear dependence of the frequencies as well as intensities on temperature. The synthetic data tests demonstrate the robustness of the methods; the initial test parameters are recovered with a high degree of reliability, although the nonparameteric SMSA is subject to the rotational ambiguity. Application to the peptide experimental amide I' data illustrates additional complications encountered with the analysis of real systems, such as correction for the side-chain spectra and interference of spectral shape changes. Nevertheless, the results are in excellent agreement with the independent control using circular dichroism (CD) data. The general applicability and limitations of the methods are discussed along with potential extensions.

  16. PHYSICAL BASIS OF QUANTUM ELECTRONICS: Frequency shift of radiation of an atom near a cluster of two perfectly conducting spherical nanoparticles

    NASA Astrophysics Data System (ADS)

    Guzatov, D. V.

    2005-10-01

    Expressions for the frequency shift of radiation of an atom located near a cluster of two perfectly conducting spherical nanoparticles are obtained within the framework of a classical model. The asymptotic expression is found for the radiation frequency shift of an atom located between spheres approaching each other.

  17. Dipolar dynamic frequency shifts in multiple-quantum spectra of methyl groups in proteins: correlation with side-chain motion.

    PubMed

    Tugarinov, Vitali; Ollerenshaw, Jason E; Kay, Lewis E

    2006-07-01

    Small deviations from the expected relative positions of multiplet components in double- and zero-quantum 1H-13C methyl correlation maps have been observed in spectra recorded on a 7-kDa protein. These dynamic frequency shifts (DFS) are the result of dipolar cross-correlations that derive from fields produced by the spins within the methyl groups. The shifts have been quantified and compared with values calculated from a Redfield analysis. Good agreement is noted between the signs of the predicted and experimentally observed relative shifts of lines in both F1 and F2 dimensions of spectra, as well as between the magnitudes of the calculated and observed shifts in the F2 (1H) dimension. The experimental DFS values show a reasonable correlation with 2H relaxation-derived measures of methyl side-chain dynamics, as expected from theory. This suggests that in cases where such shifts can be quantified, they can serve as qualitative measures of motion. PMID:16826549

  18. Proton-resonance frequency shift MR thermometry is affected by changes in the electrical conductivity of tissue.

    PubMed

    Peters, R D; Henkelman, R M

    2000-01-01

    The proton-resonance frequency (PRF) shift method of MR thermometry provides an easy and practical means of quantitatively monitoring in vivo temperatures for MR image-guided thermal-coagulation therapy. However, reported discrepancies in the numerical value of the PRF-thermal coefficient persist, when measured in a variety of experimental conditions and in different tissue types, both ex vivo and in vivo. In this report, a potential source of variation in the PRF-shift method of thermometry is identified that manifests as a constant incremental phase shift per unit change in temperature that is independent of the echo-time setting, when constructing temperature-sensitive phase images from a gradient-echo pulse sequence. It is proposed that this confounding phase-shift offset arises from thermally induced changes in the electrical conductivity of the material. To this end, it is demonstrated that the MR-derived temperature changes could be in error by as much as 28%, as measured from a simple calibration experiment on freshly excised cow liver. A simple method of overcoming this phase-shift offset is described.

  19. Microwave photonic filter using multiwavelength Brillouin-erbium fiber laser with double-Brillouin-frequency shift

    SciTech Connect

    Loh, K. K.; Yeo, K. S.; Shee, Y. G.

    2015-04-24

    A microwave photonic filter based on double-Brillouin-frequency spaced multiwavelength Brillouin-erbium fiber laser (BEFL) is experimentally demonstrated. The filter selectivity can be easily adjusted by tuning and apodizing the optical taps generated from the multiwavelength BEFL. Reconfiguration of different frequency responses are demonstrated.

  20. Shifts in frequency-modulated pulses recorded during an encounter with Blainville's beaked whales (Mesoplodon densirostris).

    PubMed

    Keating, Jennifer L; Barlow, Jay; Rankin, Shannon

    2016-08-01

    Echolocation signals produced by beaked whales (family: Ziphiidae) include frequency-modulated (FM) pulses that appear to have species-specific characteristics. To date there has been no established evidence that a single species of beaked whale might produce more than one type of FM pulse. In 2014 a group of Blainville's beaked whales (Mesoplodon densirostris) were sighted off of Southern California; recordings included FM pulses with significant increases in peak frequency, center frequency, and -10 dB bandwidth relative to FM pulses previously attributed to this species. This research suggests there may be greater variation in received beaked whale FM pulses than previously understood. PMID:27586775

  1. Complex hydrologic changes in frequency-magnitude response due to shifting agricultural practices in the Midwestern U.S.

    NASA Astrophysics Data System (ADS)

    Takbiri, Z.; Czuba, J. A.; Foufoula-Georgiou, E.

    2014-12-01

    Hydrologic change is occurring in many basins throughout the Midwestern U.S. not only in the mean annual streamflow but across a spectrum of magnitudes and frequencies. Disentangling the causative mechanisms responsible for these changes such as anthropogenic factors, e.g., artificial drainage to increase agricultural productivity, and climatic shifts in precipitation patterns is important for planning effective mitigation strategies. We have begun unraveling these changes in a human impacted agricultural landscape in the Midwestern U.S., specifically two subbasins of the Minnesota River Basin in Minnesota: the Redwood and Whetstone River Basins, where there has been a shift in agriculture from small grains to soybeans. This shift occurred at different times for each basin (1976 and 1991, respectively) and when soy covered about 20% of the basin area an apparent shift in the hydrologic regime also occurred as evidence by visual inspection of the hydrographs. Precisely quantifying the nature of this hydrologic regime shift however is a challenge and this work adds in this direction. Using Copulas and the joint probability distribution of daily precipitation and streamflow, we quantified a significantly higher dependence between precipitation and streamflow increments in the mid-quantiles (0.1-0.6; attributed to the artificial drainage to the stream rather than the slower infiltration and subsurface runoff) and no significant change for high quantiles (because for extreme storms the artificially fast drainage does not differ much hydrologically from the naturally fast overland flow). We further performed a multi-scale analysis of streamflow increments via wavelets to quantify the changes in the magnitude and frequency of the rising and falling limbs of hydrographs, confirming the above findings. Since precipitation changes were confirmed not to be significant, it is suggested that streamflow changes are largely driven by a change in land use and not climate in these

  2. 3D absolute shape measurement of live rabbit hearts with a superfast two-frequency phase-shifting technique

    PubMed Central

    Wang, Yajun; Laughner, Jacob I.; Efimov, Igor R.; Zhang, Song

    2013-01-01

    This paper presents a two-frequency binary phase-shifting technique to measure three-dimensional (3D) absolute shape of beating rabbit hearts. Due to the low contrast of the cardiac surface, the projector and the camera must remain focused, which poses challenges for any existing binary method where the measurement accuracy is low. To conquer this challenge, this paper proposes to utilize the optimal pulse width modulation (OPWM) technique to generate high-frequency fringe patterns, and the error-diffusion dithering technique to produce low-frequency fringe patterns. Furthermore, this paper will show that fringe patterns produced with blue light provide the best quality measurements compared to fringe patterns generated with red or green light; and the minimum data acquisition speed for high quality measurements is around 800 Hz for a rabbit heart beating at 180 beats per minute. PMID:23482151

  3. Pattern segmentation with activity dependent natural frequency shift and sub-threshold resonance

    NASA Astrophysics Data System (ADS)

    Shtrahman, E.; Zochowski, M.

    2015-03-01

    Understanding the mechanisms underlying distributed pattern formation in brain networks and its content driven dynamical segmentation is an area of intense study. We investigate a theoretical mechanism for selective activation of diverse neural populations that is based on dynamically shifting cellular resonances in functionally or structurally coupled networks. We specifically show that sub-threshold neuronal depolarization from synaptic coupling or external input can shift neurons into and out of resonance with specific bands of existing extracellular oscillations, and this can act as a dynamic readout mechanism during information storage and retrieval. We find that this mechanism is robust and suggest it as a general coding strategy that can be applied to any network with oscillatory nodes.

  4. Possible origins of a time-resolved frequency shift in Raman plasma amplifiers

    SciTech Connect

    Turnbull, D.; Li, S.; Morozov, A.; Suckewer, S.

    2012-07-15

    Raman amplification is a resonant process in which the energy of a long pump pulse is transferred to a short seed pulse by a plasma wave. There has been a significant effort to identify a window in parameter space within which the interaction is expected to be highly efficient and not degraded by competing instabilities or excessive damping. However, experimental results have thus far failed to approach the theoretical limits. Recent amplified signal spectra display a characteristic blue shift, which evolves within the seed pulse duration and suggests that the mechanism responsible for this shift is also limiting amplification in these experiments. We present the evidence and explore different hypotheses for the origins of the shift-namely localization in density minima along the axis of laser propagation induced by an ion acoustic wave that could arise from the Langmuir decay instability, filamentation which could also modulate the plasma density but in the plane transverse to laser propagation, particle trapping, and additional ionization induced by the amplified seed field.

  5. Red-shifted cyanide stretching frequencies in cyanide-bridged transition metal donor-acceptor complexes. Support for vibronic coupling

    SciTech Connect

    Watzky, M.A.; Endicott, J.F.; Song, X.

    1996-06-05

    Patterns in the cyanide stretching frequencies have been examined in several series of monometal- and CN{sup {minus}} bridged transition metal complexes. Metal-to-cyanide back-bonding can be identified as a major factor contributing to red shifts of v{sub CN} in monometal complexes. This effect is complicated in cyanide-bridged complexes in two ways: (a) when both metals can back-bond to cyanide, the net interaction is repulsive and results in a blue shift of v{sub CN}: and (b) when a donor and acceptor are bridged, V{sub CN} undergoes a substantial red shift (sometimes more than 60 cm{sup {minus}1} lower in energy than the parent monometal complex). These effects can be described by simple perturbational models for the electronic interactions. Monometal cyanide complexes and CN{sup {minus}}-bridged backbonding metals can be treated in terms of their perturbations of the CN{sup {minus}} {pi} and {pi}* orbitals by using a simple, Hueckel-like, three-center perturbational treatment of electronic interactions. However, bridged donor-acceptor pairs are best described by a vibronic model in which it is assumed that the extent of electronic delocalization is in equilibrium with variations of some nuclear coordinates. Consistent with this approach, it is found that (a) the oscillator strength of the donor-acceptor charge transfer (DACT) absorption is roughly proportional to the red shift of v{sub CN} and (b) there are strong symmetry constraints on the coupling.

  6. The results of determining the gravity potential difference on the measurement of the relativistic frequency shift of the mobile frequency standard

    NASA Astrophysics Data System (ADS)

    Gienko, Elena; Kanushin, Vadim; Tolstikov, Alexander; Karpik, Alexander; Kosarev, Nikolay; Ganagina, Irina

    2016-04-01

    In 2015 in the research on the grant of the Russian science Foundation No. 14-27-00068 was experimentally confirmed the possibility of measuring the gravity potential difference on relativistic frequency shift of the mobile hydrogen standard CH1-1006 (relative frequency instability of the order 10E-14). Hydrogen frequency standard CH1-1006 was calibrated in the system of secondary standard WET 1-19 (SNIIM, Novosibirsk, Russia) and transported to the place of experiment (a distance of 550 km, the Russian Federation, Republic of Altai), where it moved between the measured points at a distance of 35 km with a height difference of 850 meters. To synchronize spatially separated standard CH1-1006 and secondary standard WET 1-19 was applied the method "CommonView", based on the processing results of pseudorange phase GNSS measurements at the point of placement hours. Changing the frequency standard CH1-1006, measured in the system of secondary standard WET 1-19 and associated with his movement between points and the change of gravitational potential, was equal to 7.98•10E-14. Evaluation of root-mean-square two-sample frequency deviation of the standard at the time interval of the experiment was equal to the value of 7.27•10E-15. To control the results of the frequency determination of the gravity potential difference between the points were made high precision gravimetric measurements with an error of 6 MkGal and GNSS measurements for the coordinate determinations in ITRF2008 with an accuracy of 2-5 cm. The difference between the results of the frequency determination of the gravity potential difference with control data from GNSS and gravimetric measurements was estimated 16% of the total value that corresponds to the error of frequency measurement in the experiment. The possibility of using a single moveable frequency standard to determine the gravity potential difference at spaced points using the method of "CommonView", without the use of optical communications

  7. Measurement of air-refractive-index fluctuation from laser frequency shift with uncertainty of order 10-9

    NASA Astrophysics Data System (ADS)

    Banh Quoc, Tuan; Ishige, Masashi; Ohkubo, Yuria; Aketagawa, Masato

    2009-12-01

    In the previous work (Ishige et al 2009 Meas. Sci. Technol. 20 084019), we presented a method of measuring the relative air-refractive-index fluctuation (Δnair) from the laser frequency shift with the measurement uncertainty of order 10-8 using a phase modulation homodyne interferometer (Basile et al 1991 Metrologia 28 455), which was supported by an ultralow thermal expansion material (ULTEM) and an external cavity laser diode (ECLD). In this paper, an improvement in the uncertainty of the Δnair measurement is presented. The improvement method is based on a Fabry-Perot cavity constructed on the ULTEM, which has a thermal expansion coefficient of 2 × 10-8 K-1 and an ECLD. The Pound-Drever-Hall method (Drever et al 1983 Appl. Phys. B 31 97) is also used to control the ECLD frequency to track the resonance of the cavity. Δnair can be derived from the ECLD frequency shift. The estimated measurement uncertainty of Δnair for a short time (~150 s) in the experiment is of order 2.5 × 10-9 or less.

  8. Level-dependent auditory tuning: Transducer-based active processes in hearing and best-frequency shifts.

    PubMed

    Nadrowski, Björn; Göpfert, Martin C

    2009-01-01

    Ears boost their sensitivity by means of active, force-generating processes that augment the minute vibrations induced by soft sounds. These processes can alter auditory frequency-tuning in a level-dependent way. In the antennal hearing organ of Drosophila, for example, the active process shifts the best frequency (BF) of the antennal sound receiver when the sound intensity is varied, tuning the receiver to conspecific songs. Here we show that this level-dependent tuning can be reproduced by an active transduction model as proposed for vertebrate hair cells and the Drosophila ear. We further show that the direction of the frequency shift depends on the system to which the molecular modules for auditory transduction connect: If this system is mass-less such as the sensory hair bundles of bullfrog saccular hair cells, the BF of the displacement response will increase as the sound intensity declines. Conversely, BF will decrease with declining intensity if the transduction modules couple to inertial systems such as the fly's antennal sound receiver or cupulae in the fish lateral line. PMID:19704854

  9. Magnetic activity cycles in solar-like stars: The cross-correlation technique of p-mode frequency shifts

    NASA Astrophysics Data System (ADS)

    Régulo, C.; García, R. A.; Ballot, J.

    2016-05-01

    Aims: We set out to study the use of cross-correlation techniques to infer the frequency shifts that are induced by changing magnetic fields in p-mode frequencies and to provide a precise estimation of error bars. Methods: This technique and the calculation of the associated errors is first tested and validated on the Sun where p-mode magnetic behaviour is very well known. These validation tests are performed on 6000-day time series of Sun-as-a-star observations delivered by the SoHO spacecraft. Errors of the frequency shifts are quantified through Monte Carlo simulations. The same methodology is then applied to three solar-like oscillating stars: HD 49933, observed by CoRoT, as well as KIC 3733735 and KIC 7940546, observed by Kepler. Results: We first demonstrate the reliability of the error bars computed with the Monte Carlo simulations using the Sun. From the three stars analyzed, we confirm the presence of a magnetic activity cycle in HD 49933 with this methodology and we unveil the seismic signature of ongoing magnetic variations in KIC 3733735. Finally, the third star, KIC 7940546, seems to be in a quiet regime.

  10. Widely tunable mid-infrared fiber laser source based on soliton self-frequency shift in microstructured tellurite fiber.

    PubMed

    Koptev, M Yu; Anashkina, E A; Andrianov, A V; Dorofeev, V V; Kosolapov, A F; Muravyev, S V; Kim, A V

    2015-09-01

    A turnkey fiber laser source generating high-quality pulses with a spectral sech shape and Fourier transform-limited duration of order 100 fs widely tunable in the 1.6-2.65 μm range is presented. It is based on Raman soliton self-frequency shifting in the suspended-core microstructured TeO2-WO3-La2O3 glass fiber pumped by a hybrid Er/Tm fiber system. Detailed experimental and theoretical studies, which are in a very good agreement, of nonlinear pulse dynamics in the tellurite fiber with carefully measured and calculated parameters are reported. A quantitatively verified numerical model is used to show Raman soliton shift in the range well beyond 3 μm for increased pump energy.

  11. Definition of Shifts of Optical Transitions Frequencies due to Pulse Perturbation Action by the Photon Echo Signal Form

    NASA Astrophysics Data System (ADS)

    Lisin, V. N.; Shegeda, A. M.; Samartsev, V. V.

    2015-09-01

    A relative phase shift between the different groups of excited dipoles, which appears as result of its frequency splitting due to action of a pulse of electric or magnetic fields, depends on a time, if the pulse overlaps in time with echo-pulse. As а consequence, the echo waveform is changed. The echo time form is modulated. The inverse modulation period well enough approximates Zeeman and pseudo-Stark splitting in the cases of magnetic and, therefore, electrical fields. Thus the g-factors of ground 4I15/2 and excited 4F9/2 optical states of Er3+ ion in LuLiF4 and YLiF4 have been measured and pseudo-Stark shift of R1 line in ruby has been determined.

  12. Signal processing method based on group delay calculation for distributed Bragg wavelength shift in optical frequency domain reflectometry.

    PubMed

    Wada, Daichi; Igawa, Hirotaka; Murayama, Hideaki; Kasai, Tokio

    2014-03-24

    A signal processing method based on group delay calculations is introduced for distributed measurements of long-length fiber Bragg gratings (FBGs) based on optical frequency domain reflectometry (OFDR). Bragg wavelength shifts in interfered signals of OFDR are regarded as group delay. By calculating group delay, the distribution of Bragg wavelength shifts is obtained with high computational efficiency. We introduce weighted averaging process for noise reduction. This method required only 3.5% of signal processing time which was necessary for conventional equivalent signal processing based on short-time Fourier transform. The method also showed high sensitivity to experimental signals where non-uniform strain distributions existed in a long-length FBG.

  13. Collisional Losses, Decoherence, and Frequency Shifts in Optical Lattice Clocks with Bosons

    SciTech Connect

    Lisdat, Ch.; Winfred, J. S. R. Vellore; Middelmann, T.; Riehle, F.; Sterr, U.

    2009-08-28

    We have quantified collisional losses, decoherence and the collision shift in a one-dimensional optical lattice clock on the highly forbidden transition {sup 1}S{sub 0}-{sup 3}P{sub 0} at 698 nm with bosonic {sup 88}Sr. We were able to distinguish two loss channels: inelastic collisions between atoms in the upper and lower clock state and atoms in the upper clock state only. Based on the measured coefficients, we determine the operation parameters at which a 1D-lattice clock with {sup 88}Sr shows no degradation due to collisions on the fractional uncertainty level of 10{sup -16}.

  14. Center of Mass Estimation for a Spinning Spacecraft Using Doppler Shift of the GPS Carrier Frequency

    NASA Technical Reports Server (NTRS)

    Sedlak, Joseph E.

    2016-01-01

    A sequential filter is presented for estimating the center of mass (CM) of a spinning spacecraft using Doppler shift data from a set of onboard Global Positioning System (GPS) receivers. The advantage of the proposed method is that it is passive and can be run continuously in the background without using commanded thruster firings to excite spacecraft dynamical motion for observability. The NASA Magnetospheric Multiscale (MMS) mission is used as a test case for the CM estimator. The four MMS spacecraft carry star cameras for accurate attitude and spin rate estimation. The angle between the spacecraft nominal spin axis (for MMS this is the geometric body Z-axis) and the major principal axis of inertia is called the coning angle. The transverse components of the estimated rate provide a direct measure of the coning angle. The coning angle has been seen to shift slightly after every orbit and attitude maneuver. This change is attributed to a small asymmetry in the fuel distribution that changes with each burn. This paper shows a correlation between the apparent mass asymmetry deduced from the variations in the coning angle and the CM estimates made using the GPS Doppler data. The consistency between the changes in the coning angle and the CM provides validation of the proposed GPS Doppler method for estimation of the CM on spinning spacecraft.

  15. Spin relaxation and linear-in-electric-field frequency shift in an arbitrary, time-independent magnetic field

    SciTech Connect

    Clayton, Steven Michael

    2010-12-03

    A method is presented to calculate the spin relaxation times T{sub 1}, T{sub 2} due to a nonuniform magnetic field, and the linear-in-electric-field precession frequency shift {delta}{omega}{sub E} when an electric field is present, in the diffusion approximation for spins confined to a rectangular cell. It is found that the rectangular cell geometry admits of a general result for T{sub 1}, T{sub 2}, and {delta}{omega}{sub E} in terms of the spatial cosine-transform components of the magnetic field.

  16. Non-mechanical scanning laser Doppler velocimetry with sensitivity to direction of transverse velocity component using optical serrodyne frequency shifting

    NASA Astrophysics Data System (ADS)

    Maru, Koichi; Watanabe, Kento

    2014-05-01

    This paper proposes a non-mechanical axial scanning laser Doppler velocimeter (LDV) with sensitivity to the direction of the transverse velocity component using optical serrodyne frequency shifting. Serrodyne modulation via the electro-optic effect of a LiNbO3 (LN) phase shifter is employed to discriminate the direction of the transverse velocity component. The measurement position is scanned without any moving mechanism in the probe by changing the wavelength of the light input to the probe. The experimental results using a sensor probe setup indicate that both the scan of the measurement position and the introduction of directional sensitivity are successfully demonstrated.

  17. 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.

  18. Compensating for frequency shifts in modulation transfer spectroscopy caused by residual amplitude modulation

    NASA Astrophysics Data System (ADS)

    Jaatinen, Esa; Hopper, David J.

    2008-01-01

    Residual amplitude modulation (RAM) distorts saturated absorption signals, limiting the accuracy of optical frequency references based on modulation transfer spectroscopy (MTS). Described here are two independent means by which RAM is produced in these references: (1) by the modulator and (2) when the overlap of the optical fields in the saturable absorber is asymmetric. Methods to vary RAM generated by either mechanism will be outlined and these will be used to show how RAM arising from one effect can be cancelled by the other. A theoretical treatment of MTS signals in references containing RAM is given and used to evaluate the level of signal distortion allowing the conditions for RAM cancellation to be determined. This technique is applied to improve the frequency accuracy of a reference by an order of magnitude.

  19. 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

  20. Method of shifting and fixing optical frequency of an optical resonator, and optical resonator made by same

    NASA Technical Reports Server (NTRS)

    Savchenkov, Anatoliy A. (Inventor); Strekalov, Dmitry V. (Inventor); Maleki, Lute (Inventor); Matsko, Andrey B. (Inventor); Iltchenko, Vladimir S. (Inventor); Martin, Jan M. (Inventor)

    2010-01-01

    A method of shifting and fixing an optical frequency of an optical resonator to a desired optical frequency, and an optical resonator made by such a method are provided. The method includes providing an optical resonator having a surface and a refractive index, and obtaining a coating composition having a predetermined concentration of a substance and having a refractive index that is substantially similar to the refractive index of the optical resonator. The coating composition inherently possesses a thickness when it is applied as a coating. The method further includes determining a coating ratio for the surface of the optical resonator and applying the coating composition onto a portion of the surface of the optical resonator based upon the determined coating ratio.

  1. Resonance frequency shifts due to quantized electronic states in atomically thin NEMS

    NASA Astrophysics Data System (ADS)

    Chen, Changyao; Deshpande, Vikram; Koshino, Mikito; Lee, Sunwoo; Gondarenko, Alexander; MacDonald, Allan; Kim, Philip; Hone, James

    The classic picture of the force exerted on a parallel plate capacitor assumes infinite density of states (DOS), which implies identical electrochemical and electrostatic potential. However, such assumption can breakdown in low-dimensional devices where the DOS is finite or quantized. Here we consider the mechanical resonance shift of a nanoelectromechanical (NEMS) resonator with small DOS, actuated and detected capacitively at fixed electrochemical potential. We found three leading correction terms to the classical picture: the first term leads to the modulation of static force due to the variation in chemical potential, and the second and third terms are related to the static and dynamic changes in spring constants, caused by quantum capacitance. The theory agrees well with recent experimental findings from graphene resonator in quantum Hall regimes, where the chemical potential and quantum capacitance are tuned by magnetic field, while the gate voltage is kept constant.

  2. Frequency-shift free optical phase conjugation using counter-propagating dual pump four-wave mixing in fiber

    NASA Astrophysics Data System (ADS)

    Anchal, Abhishek; K, Pradeep Kumar; Landais, Pascal

    2016-03-01

    We propose and numerically verify a novel scheme of frequency-shift free optical phase conjugation by counter-propagating dual pump four-wave mixing in nonlinear fiber. The two counter-propagating pumps create a Bragg grating inside the fiber, which diffracts the forward propagating signal and generates a backward propagating idler wave whose phase is conjugate of signal phase. The two pump frequencies are placed symmetrically about signal frequency to ensure that idler wave will have same frequency as that of signal wave. Since the signal and idler waves appear at opposite ends, the idler is easily filtered out from the rest of the spectrum. Using nonlinear Schrödinger equation, we derive equations of signal and idler evolution. We obtain expressions for idler phase and show that perfect phase conjugation is achieved at an optimum length of fiber for a given pump power. We study the effect of fiber length and pump power on phase conjugation. Simulation results show the perfect phase conjugation at optimum fiber length under lossless conditions and small phase-offset when fiber loss and self and cross phase modulations are included. The small phase-offset is avoided by choosing fiber length smaller than optimum fiber length. Simulation results exhibit close agreement to theoretical values, which validates our simulations.

  3. Electron cyclotron heating of a tokamak reactor at down-shifted frequencies

    SciTech Connect

    Fidone, I.; Giruzzi, G.; Mazzucato, E.

    1985-01-01

    The absorption of electron cyclotron waves in a hot and dense tokamak plasma is investigated for the case of the extraordinary mode for outside launching. It is shown that, for electron temperatures T/sub e/ greater than or equal to 5 keV, strong absorption occurs for oblique propagation at frequencies significantly below the electron gyrofrequency at the plasma center. A new density dependence of the wave absorption is found which is more favorable for plasma heating than the familiar n/sub e//sup -1/ scaling.

  4. Method of hybrid multiplexing for fiber-optic Fabry-Perot sensors utilizing frequency-shifted interferometry.

    PubMed

    Ou, Yiwen; Zhou, Ciming; Zheng, Angui; Cheng, Chunfu; Fan, Dian; Yin, Jiadi; Tian, Hui; Li, Mengmeng; Lu, Ying

    2014-12-10

    Experimental and theoretical research on hybrid multiplexing for fiber-optic Fabry-Perot (F-P) sensors based on frequency-shifted interferometry is presented. Four F-P sensors multiplexed in a hybrid configuration were experimentally investigated. The location of each multiplexed sensor was retrieved by performing the fast Fourier transform, and the reflection spectrum of each sensor was also obtained in spite of the spectral overlap, which was consistent with the results measured by an optical spectrum analyzer. With theoretical modeling, the maximum sensor number of a two-channel hybrid multiplexing system reaches 26 with crosstalk of less than -50  dB and a maximum frequency-domain signal-to-noise ratio (SNR) of ∼25  dB, when the source power is 2 mW and the sensor separation is optimal, i.e., 40 m. And the sensor number is almost twice that multiplexed by a serial system under the same conditions. An SNR improvement of 3.9 dB can be achieved by using a Hamming window in a noise-free system compared with a Hanning window. In addition, we applied the experimental multiplexing system to a strain sensing test. The cavity lengths and cavity-length shifts of the four F-P sensors were demodulated, which was consistent with the actual situation. It provides a new feasible method to multiplex F-P sensors at large scale. PMID:25608081

  5. Dynamic Universe Model predicts frequency shifting in electromagnetic radiation near gravitating masses

    NASA Astrophysics Data System (ADS)

    Naga Parameswara Gupta, Satyavarapu

    2016-07-01

    In this paper, Dynamic Universe Model studies the light rays and other electromagnetic radiation passing grazingly near any gravitating mass. This change in frequency will depend on relative direction of movement between mass and radiation. Change in frequency depends on relative direction between ray and the Gravitating mass. Here in this paper we will mathematically derive the results and show these predictions. Dynamic Universe Model uses a new type of Tensor. There are no differential or integral equations here. No singularities and body to body collisions in this model. Many papers were published in USA and CANADA. See Dynamic Universe Model Blog for further details and papers Dynamic Universe Model never reduces to General relativity on any condition. It uses a different type of mathematics based on Newtonian physics. This mathematics used here is simple and straightforward. As there are no differential equations present in Dynamic Universe Model, the set of equations give single solution in x y z Cartesian coordinates for every point mass for every time step Keywords: Dynamic Universe Model, Hubble Space telescope (HST), SITA simulations , singularity-free cosmology,

  6. Electron cyclotron heating at down-shifted frequencies in existing tokamak devices

    SciTech Connect

    Mazzucato, E.; Fidone, I.; Giruzzi, G.; Krivenski, V.

    1985-06-01

    Plasma heating in existing tokamak devices by electron cyclotron waves with frequency (f) significantly smaller than the electron gyrofrequency (f/sub c/) is investigated for the case of Maxwellian plasmas. It is shown that for central electron temperatures larger than 3 keV, strong absorption of extraordinary waves can occur at values of toroidal field for which the condition f = f/sub c/ is not satisfied in the plasma region. The cases of f = 60 GHz and f = 100 GHz are discussed for the PLT and TFTR devices as representative of medium (approx. =30 kG) and high (approx. =50 kG) magnetic field tokamaks, respectively. Numerical calculations with a ray tracing code indicate that most of the rf energy is absorbed in a central plasma region. These results are of practical interest because they significantly simplify the main technical problem of ECH in a tokamak reactor, i.e., the development of high frequency and high power microwave sources.

  7. Relativistic Tennis with Photons: Frequency Up-Shifting, Light Intensification and Ion Acceleration with Flying Mirrors

    SciTech Connect

    Bulanov, S. V.; Esirkepov, T. Zh.; Kando, M.; Koga, J. K.; Pirozhkov, A. S.; Rosanov, N. N.; Zhidkov, A. G.

    2011-01-04

    We formulate the Flying Mirror Concept for relativistic interaction of ultra-intense electromagnetic waves with plasmas, present its theoretical description and the results of computer simulations and laboratory experiments. In collisionless plasmas, the relativistic flying mirrors are thin and dense electron or electron-ion layers accelerated by the high intensity electromagnetic waves up to velocity close to the speed of light in vacuum; in nonlinear-media and in nonlinear vacuum they are the ionization fronts and the refraction index modulations induced by a strong electromagnetic wave. The reflection of the electromagnetic wave at the relativistic mirror results in its energy and frequency change due to the double Doppler effect. In the co-propagating configuration, in the radiation pressure dominant regime, the energy of the electromagnetic wave is transferred to the ion energy providing a highly efficient acceleration mechanism. In the counter-propagation configuration the frequency of the reflected wave is multiplied by the factor proportional to the gamma-factor squared. If the relativistic mirror performs an oscillatory motion as in the case of the electron motion at the plasma-vacuum interface, the reflected light spectrum is enriched with high order harmonics.

  8. Relativistic Tennis with Photons: Frequency Up-Shifting, Light Intensification and Ion Acceleration with Flying Mirrors

    NASA Astrophysics Data System (ADS)

    Bulanov, S. V.; Esirkepov, T. Zh.; Kando, M.; Koga, J. K.; Pirozhkov, A. S.; Rosanov, N. N.; Zhidkov, A. G.

    2011-01-01

    We formulate the Flying Mirror Concept for relativistic interaction of ultra-intense electromagnetic waves with plasmas, present its theoretical description and the results of computer simulations and laboratory experiments. In collisionless plasmas, the relativistic flying mirrors are thin and dense electron or electron-ion layers accelerated by the high intensity electromagnetic waves up to velocity close to the speed of light in vacuum; in nonlinear-media and in nonlinear vacuum they are the ionization fronts and the refraction index modulations induced by a strong electromagnetic wave. The reflection of the electromagnetic wave at the relativistic mirror results in its energy and frequency change due to the double Doppler effect. In the co-propagating configuration, in the radiation pressure dominant regime, the energy of the electromagnetic wave is transferred to the ion energy providing a highly efficient acceleration mechanism. In the counter-propagation configuration the frequency of the reflected wave is multiplied by the factor proportional to the gamma-factor squared. If the relativistic mirror performs an oscillatory motion as in the case of the electron motion at the plasma-vacuum interface, the reflected light spectrum is enriched with high order harmonics.

  9. Study of a mode-locked erbium-doped frequency-shifted-feedback fiber laser incorporating a broad bandpass filter: Experimental results

    NASA Astrophysics Data System (ADS)

    Vazquez-Zuniga, Luis Alonso; Jeong, Yoonchan

    2013-10-01

    We present rigorous experimental studies on the spectral and temporal behaviors of an erbium-doped frequency-shifted-feedback fiber laser (FSFL), with respect to various parameters of the laser cavity, including the direction of the frequency-shift mechanism, the quantity of frequency-shift, and the output coupling ratio (OCR) of the cavity. We show that if the filter bandwidth is much broader than the laser linewidth, the laser spectrum tends to split and form a secondary spectral band (SSB) on the shorter or longer wavelength side of the primary spectrum, depending on whether the direction of the frequency-shift mechanism is upward or downward, respectively. We found that the SSB forms a parasitic pulse with much lower peak power traveling on the leading or trailing edge of the primary pulse, which leads to a significant asymmetry in the whole pulse formation in the time domain.

  10. Broadband tunable Raman soliton self-frequency shift to mid-infrared band in a highly birefringent microstructure fiber

    NASA Astrophysics Data System (ADS)

    Wei, Wang; Xin-Ying, Bi; Jun-Qi, Wang; Yu-Wei, Qu; Ying, Han; Gui-Yao, Zhou; Yue-Feng, Qi

    2016-07-01

    Raman soliton self-frequency shifted to mid-infrared band (λ > 2 μm) has been achieved in an air-silica microstructure fiber (MF). The MF used in our experiment has an elliptical core with diameters of 1.08 and 2.48 μm for fast and slow axis. Numerical simulation shows that each fundamental orthogonal polarization mode has two wide-spaced λ ZDW and the λ ZDW pairs located at 701/2110 nm and 755/2498 nm along the fast and slow axis, respectively. Using 810-nm Ti:sapphire femtosecond laser as pump, when the output power varies from 0.3 to 0.5 W, the furthest red-shift Raman solitons in both fast and slow axis shift from near-infrared band to mid-infrared band, reaching as far as 2030 and 2261 nm. Also, mid-infrared Raman solitons can always be generated for pump wavelength longer than 790 nm if output pump power reaches 0.5 W. Specifically, with pump power at 0.5 W, the mid-infrared soliton in slow axis shifts from 2001 to 2261 nm when the pump changes from 790 nm to 810 nm. This means only a 20 nm change of pump results in 260 nm tunability of a mid-infrared soliton. Project supported by the National Natural Science Foundation of China (Grant Nos. 61405172, 61405173, and 61275093), the Natural Science Foundation of Hebei Province, China (Grant No. F2014203194), the College Science Research Program of Hebei Province, China (Grant No. QN20131044), and the Program of Independent Research for the Young Teachers of Yanshan University of China (Grant No. 13LGB017).

  11. Method and apparatus for determining pressure-induced frequency-shifts in shock-compressed materials

    DOEpatents

    Moore, D.S.; Schmidt, S.C.

    1983-12-16

    A method and an apparatus for conducting coherent anti-Stokes Raman scattering spectroscopy in shock-compressed materials are disclosed. The apparatus includes a sample vessel having an optically transparent wall and an opposing optically reflective wall. Two coherent laser beams, a pump beam and a broadband Stokes beam, are directed through the window and focused on a portion of the sample. In the preferred embodiment, a projectile is fired from a high-pressure gas gun to impact the outside of the reflective wall, generating a planar shock wave which travels through the sample toward the window. The pump and Stokes beams result in the emission from the shock-compressed sample of a coherent anti-Stokes beam, which is emitted toward the approaching reflective wall of the vessel and reflected back through the window. The anti-Stokes beam is folded into a spectrometer for frequency analysis. The results of such analysis are useful for determining chemical and physical phenomena which occur during the shock-compression of the sample.

  12. Method and apparatus for determining pressure-induced frequency-shifts in shock-compressed materials

    DOEpatents

    Moore, David S.; Schmidt, Stephen C.

    1985-01-01

    A method and an apparatus for conducting coherent anti-Stokes Raman scattering spectroscopy in shock-compressed materials are disclosed. The apparatus includes a sample vessel having an optically transparent wall and an opposing optically reflective wall. Two coherent laser beams, a pump beam and a broadband Stokes beam, are directed through the window and focused on a portion of the sample. In the preferred embodiment, a projectile is fired from a high-pressure gas gun to impact the outside of the reflective wall, generating a planar shock wave which travels through the sample toward the window. The pump and Stokes beams result in the emission from the shock-compressed sample of a coherent anti-Stokes beam, which is emitted toward the approaching reflective wall of the vessel and reflected back through the window. The anti-Stokes beam is folded into a spectrometer for frequency analysis. The results of such analysis are useful for determining chemical and physical phenomena which occur during the shock-compression of the sample.

  13. Temporary threshold shift in military pilots measured using conventional and extended high-frequency audiometry after one flight.

    PubMed

    Kuronen, Pentti; Sorri, Martti J; Pääkkönen, Rauno; Muhli, Arto

    2003-01-01

    Noise of such a high level that it can result in hearing deterioration is an inherent characteristic of military flying. Susceptibility to hearing impairment was studied using 51 Finnish Air Force military personnel as subjects. The test persons flew missions on a British Aerospace Hawk 51 advanced jet trainer, Boeing F-18 Hornet, Mikoyan & Gurevich MiG-21bis and Saab 35 Draken interceptors, and a Valmet Redigo turboprop liaison aircraft. The duration of noise exposure was one flight mission, which varied from 30 to 60 min. Noise doses and levels were measured using a miniature microphone at the inlet of the ear canal, while a second microphone was located at the level of the subject's shoulder. Hearing thresholds were measured before each flight using conventional (0.125-8 kHz) and extended high-frequency (EHF) (8.20 kHz) audiometry. The measurements were repeated as soon as possible after the flight. The study showed that the pre-flight threshold levels of the subjects were good. Both conventional and EHF audiometry revealed statistically significant temporary threshold shifts (TTS) at several frequencies and with all aircraft types involved. The changes were, however, minor. The risk of noise-induced hearing impairment at the studied exposure levels is, in all probability, rather small. The role of extended high-frequency audiometry would be in research, and it might be performed for flying personnel upon entering service and every fifth year thereafter. PMID:12564513

  14. A QSPR study on the solvent-induced frequency shifts of acetone and dimethyl sulfoxide in organic solvents

    NASA Astrophysics Data System (ADS)

    Ou, Yu Heng; Chang, Chia Ming; Chen, Ying Shao

    2016-06-01

    In this study, solvent-induced frequency shifts (SIFS) in the infrared spectrum of acetone and dimethyl sulfoxide in organic solvents were investigated by using four types of quantum-chemical reactivity descriptors. The results showed that the SIFS of acetone is mainly affected by the electron-acceptance chemical potential and the maximum nucleophilic condensed local softness of organic solvents, which represent the electron flow and the polarization between acetone and solvent molecules. On the other hand, the SIFS of dimethyl sulfoxide changes with the maximum positive charge of hydrogen atom and the inverse of apolar surface area of solvent molecules, showing that the electrostatic and hydrophilic interactions are main mechanisms between dimethyl sulfoxide and solvent molecules. The introduction of the four-element theory model-based quantitative structure-property relationship approach improved the assessing quality and provided a basis for interpreting the solute-solvent interactions.

  15. A QSPR study on the solvent-induced frequency shifts of acetone and dimethyl sulfoxide in organic solvents.

    PubMed

    Ou, Yu Heng; Chang, Chia Ming; Chen, Ying Shao

    2016-06-01

    In this study, solvent-induced frequency shifts (SIFS) in the infrared spectrum of acetone and dimethyl sulfoxide in organic solvents were investigated by using four types of quantum-chemical reactivity descriptors. The results showed that the SIFS of acetone is mainly affected by the electron-acceptance chemical potential and the maximum nucleophilic condensed local softness of organic solvents, which represent the electron flow and the polarization between acetone and solvent molecules. On the other hand, the SIFS of dimethyl sulfoxide changes with the maximum positive charge of hydrogen atom and the inverse of apolar surface area of solvent molecules, showing that the electrostatic and hydrophilic interactions are main mechanisms between dimethyl sulfoxide and solvent molecules. The introduction of the four-element theory model-based quantitative structure-property relationship approach improved the assessing quality and provided a basis for interpreting the solute-solvent interactions. PMID:26994584

  16. Asynchronous, all-optical signal processing based on the self-frequency shift of a gigahertz Raman soliton.

    PubMed

    Kato, Masao; Fujiura, Kazuo; Kurihara, Takashi

    2005-03-10

    Ultrafast asynchronous all-optical signal processing is experimentally demonstrated. It is based on the intensity-dependent, self-frequency shift of a gigahertz Raman soliton. We demonstrate error-free, asynchronous, all-optical, bit-by-bit, self-signal recognition and demultiplexing from contended optical packets without use of an optical buffer, control pulse, or bit-phase synchronization. Fourfold, contended, 9.95-Gbit/s optical packets are transmitted through a conventional repeater span of 80 km and simultaneously demultiplexed to multiwavelength 9.95-Gbit/s optical packets with 0.5-dB processing sensitivity. Furthermore, we successfully accomplish demultiplexing from overlapping signals in contended optical packets with better than 3-dB recognition sensitivity. We confirm the capability of realizing a 3x cascade operation from bit-error-rate measurements.

  17. Three-dimensional surface imaging by multi-frequency phase shift profilometry with angle and pattern modeling for system calibration

    NASA Astrophysics Data System (ADS)

    Wang, Zhenzhou

    2016-08-01

    In this paper, we present a 3D surface imaging system based on the well-known phase shift profilometry. To yield the analytical solutions, four shifted phases and three high carrier frequencies are used to compute the phase map and reduce the noises that are caused by the inherent optical aberrations and external influences, e.g. different illumination light sources, uneven intensity distribution and automatic image processing algorithms. To reduce the system noise, we propose to model the pattern of the calibration grid in a virtual space. To obtain the modeled pattern, we use a plane to intercept the rays that are modeled by the proposed angle modeling method. In the world coordinate system, the angle and the pattern are computed based on the calibration data. A registration method is used to transform the modeled pattern in the virtual space to the ideal pattern in the world coordinate system by computing the least squared errors between the true points in the modeled pattern and the measured points in the practical pattern. The modeled (true) points are used for re-calibration of the 3D imaging system. Experimental results showed that the measurement accuracy increases considerably and the MSE is reduced from 0.95 mm to 0.65 mm (32% average error decrease) after replacing the measured points with the true points for calibration.

  18. Large dynamic Stokes shift of DNA intercalation dye Thiazole Orange has contribution from a high-frequency mode.

    PubMed

    Karunakaran, Venugopal; Pérez Lustres, J Luis; Zhao, Lijuan; Ernsting, Nikolaus P; Seitz, Oliver

    2006-03-01

    Fluorescence of the cyanine dye Thiazole Orange (TO) is quenched by intramolecular twisting in the excited state. In polypeptide nucleic acids, a vibrational progression in a 1400 cm(-1) mode depends on base pairing, from which follows that the high-frequency displacement is coupled to the twist coordinate. The coupling is intrinsic to TO. This is shown by femtosecond fluorescence upconversion and transient absorption spectroscopy with the dye in methanol solution. Narrow emission from the Franck-Condon state shifts to the red and broadens within 100 fs. The radiative rate does not decrease during this process. Vibrational structure builds up on a 200 fs time scale; it is assigned to asymmetric stretching activity in the methine bridge. Further Stokes shift and decay are observed over 2 ps. Emission from the global S(1) minimum is discovered in an extremely wide band around 12 000 cm(-1). As the structure twists away from the Franck-Condon region, the mode becomes more displaced and overlap with increasingly higher vibrational wave functions of the electronic ground state is achieved. Twisting motion is thus leveraged into a fast-shrinking effective energy gap between the two electronic states, and internal conversion ensues.

  19. 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

  20. 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...

  1. Elimination of the Stark shift from the vibrational transition frequency of optically trapped {sup 174}Yb{sup 6}Li molecules

    SciTech Connect

    Kajita, Masatoshi; Gopakumar, Geetha; Abe, Minori; Hada, Masahiko

    2011-08-15

    Transition frequencies of cold molecules must be accurately evaluated to test the variance in the proton-to-electron mass ratio. Measuring the X {sup 2}{Sigma}(v,N)=(0,0){yields}(1,0) transition frequency of optically trapped {sup 174}Yb{sup 6}Li molecules is a promising method for achieving this goal. The Stark shifts induced by trap and probe (for the Raman transition) lasers are eliminated by choosing appropriate frequencies (magic frequencies) during the construction of the optical lattice. In the far-off resonance region, the Stark shift is found to be less than 10{sup -16} even when the laser frequencies are detuned from the magic frequencies by {approx}1 MHz.

  2. Large-capacity multiplexing of near-identical weak fiber Bragg gratings using frequency-shifted interferometry.

    PubMed

    Ou, Yiwen; Zhou, Ciming; Qian, Li; Fan, Dian; Cheng, Chunfu; Guo, Huiyong

    2015-11-30

    We demonstrate interrogation of a large-capacity sensor array with nearly identical weak fiber Bragg gratings (FBGs) based on frequency-shifted interferometry (FSI). In contrast to time-division multiplexing, FSI uses continuous-wave light and therefore requires no pulse modulation or high-speed detection/acquisition. FSI utilizes a frequency shifter in the Sagnac interferometer to encode sensor location information into the relative phase between the clock-wise and counter-clockwise propagating lightwaves. Sixty-five weak FBGs with reflectivities in the range of -31 ~-34 dB and with near identical peak reflection wavelengths around 1555 nm at room temperature were interrogated simultaneously. Temperature sensing was conducted and the average measurement accuracy of the peak wavelengths was ± 3.9 pm, corresponding to a temperature resolution of ± 0.4 °C. Our theoretical analysis taking into account of detector noise, fiber loss, and sensor cross-talk noise shows that there exists an optimal reflectivity that maximizes multiplexing capacity. The multiplexing capacity can reach 3000 with the corresponding sensing range of 30 km, when the peak reflectivity of each grating is -40 dB, the sensor separation 10 m and the source power 14 mW. Experimental results and theoretical analysis reveal that FSI has distinct cost and speed advantages in multiplexing large-scale FBG networks. PMID:26698773

  3. Large-capacity multiplexing of near-identical weak fiber Bragg gratings using frequency-shifted interferometry.

    PubMed

    Ou, Yiwen; Zhou, Ciming; Qian, Li; Fan, Dian; Cheng, Chunfu; Guo, Huiyong

    2015-11-30

    We demonstrate interrogation of a large-capacity sensor array with nearly identical weak fiber Bragg gratings (FBGs) based on frequency-shifted interferometry (FSI). In contrast to time-division multiplexing, FSI uses continuous-wave light and therefore requires no pulse modulation or high-speed detection/acquisition. FSI utilizes a frequency shifter in the Sagnac interferometer to encode sensor location information into the relative phase between the clock-wise and counter-clockwise propagating lightwaves. Sixty-five weak FBGs with reflectivities in the range of -31 ~-34 dB and with near identical peak reflection wavelengths around 1555 nm at room temperature were interrogated simultaneously. Temperature sensing was conducted and the average measurement accuracy of the peak wavelengths was ± 3.9 pm, corresponding to a temperature resolution of ± 0.4 °C. Our theoretical analysis taking into account of detector noise, fiber loss, and sensor cross-talk noise shows that there exists an optimal reflectivity that maximizes multiplexing capacity. The multiplexing capacity can reach 3000 with the corresponding sensing range of 30 km, when the peak reflectivity of each grating is -40 dB, the sensor separation 10 m and the source power 14 mW. Experimental results and theoretical analysis reveal that FSI has distinct cost and speed advantages in multiplexing large-scale FBG networks.

  4. 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.

  5. The functional importance of sequence versus expression variability of MHC alleles in parasite resistance.

    PubMed

    Axtner, Jan; Sommer, Simone

    2012-12-01

    Understanding selection processes driving the pronounced allelic polymorphism of the major histocompatibility complex (MHC) genes and its functional associations to parasite load have been the focus of many recent wildlife studies. Two main selection scenarios are currently debated which explain the susceptibility or resistance to parasite infections either by the effects of (1) specific MHC alleles which are selected frequency-dependent in space and time or (2) a heterozygote or divergent allele advantage. So far, most studies have focused only on structural variance in co-evolutionary processes although this might not be the only trait subject to natural selection. In the present study, we analysed structural variance stretching from exon1 through exon3 of MHC class II DRB genes as well as genotypic expression variance in relation to the gastrointestinal helminth prevalence and infection intensity in wild yellow-necked mice (Apodemus flavicollis). We found support for the functional importance of specific alleles both on the sequence and expression level. By resampling a previously investigated study population we identified specific MHC alleles affected by temporal shifts in parasite pressure and recorded associated changes in allele frequencies. The allele Apfl-DRB*23 was associated with resistance to infections by the oxyurid nematode Syphacia stroma and at the same time with susceptibility to cestode infection intensity. In line with our expectation, MHC mRNA transcript levels tended to be higher in cestode-infected animals carrying the allele Apfl-DRB*23. However, no support for a heterozygote or divergent allele advantage on the sequence or expression level was detected. The individual amino acid distance of genotypes did not explain individual differences in parasite loads and the genetic distance had no effect on MHC genotype expression. For ongoing studies on the functional importance of expression variance in parasite resistance, allele

  6. 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

  7. 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...

  8. 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

  9. 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.

  10. 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.

  11. New Seasonal Shift in In-Stream Diurnal Nitrate Cycles Identified by Mining High-Frequency Data.

    PubMed

    Aubert, Alice H; Breuer, Lutz

    2016-01-01

    The recent development of in-situ monitoring devices, such as UV-spectrometers, makes the study of short-term stream chemistry variation relevant, especially the study of diurnal cycles, which are not yet fully understood. Our study is based on high-frequency data from an agricultural catchment (Studienlandschaft Schwingbachtal, Germany). We propose a novel approach, i.e. the combination of cluster analysis and Linear Discriminant Analysis, to mine from these data nitrate behavior patterns. As a result, we observe a seasonality of nitrate diurnal cycles, that differs from the most common cycle seasonality described in the literature, i.e. pre-dawn peaks in spring. Our cycles appear in summer and the maximum and minimum shift to a later time in late summer/autumn. This is observed both for water- and energy-limited years, thus potentially stressing the role of evapotranspiration. This concluding hypothesis on the role of evapotranspiration on nitrate stream concentration, which was obtained through data mining, broadens the perspective on the diurnal cycling of stream nitrate concentrations. PMID:27073838

  12. Investigation of the mechanical bending and frequency shift induced by adsorption and temperature using micro- and nanocantilever sensors

    NASA Astrophysics Data System (ADS)

    Feng, Lu; Gao, Fengling; Liu, Meihua; Wang, Shibin; Li, Linan; Shen, Min; Wang, Zhiyong

    2012-07-01

    The marked progress in MEMS/NEMS technology has demanded the development of a fundamental understanding of cantilever-based sensing principles. One of the challenges of cantilever-based detection is identifying and discerning the most influenced parameters responsible for the observed changes in the cantilever response. For example, effects of various force fields such as those induced by atom/molecular adsorption and variations in temperature may occur simultaneously, increasing the number of parameters that need to be concurrently measured to ensure the reliability of sensors. In this paper, we, therefore, systematically investigate the interplay between these two distinctly different mechanisms and attendant mechanical response. To this end, a theory model is proposed to predict the mechanical bending and resonance frequency shift of micro- and nanocantilevers taking into account atom/molecular adsorption and variations in temperature at the same time. The adsorption induced mechanical responses of microcantilevers are modeled for the van der Waals interaction in presence of surface effect. Thermal effects addressed here include the thermal mismatch between the substrate and coating layer owing to different thermal expansion coefficients and the temperature-dependent material properties. The theoretical and computational model developed here will allow one to gain an insight into not only the mechanical responses observed experimentally but also the fundamental, novel detection principles for sensing applications.

  13. New Seasonal Shift in In-Stream Diurnal Nitrate Cycles Identified by Mining High-Frequency Data

    PubMed Central

    2016-01-01

    The recent development of in-situ monitoring devices, such as UV-spectrometers, makes the study of short-term stream chemistry variation relevant, especially the study of diurnal cycles, which are not yet fully understood. Our study is based on high-frequency data from an agricultural catchment (Studienlandschaft Schwingbachtal, Germany). We propose a novel approach, i.e. the combination of cluster analysis and Linear Discriminant Analysis, to mine from these data nitrate behavior patterns. As a result, we observe a seasonality of nitrate diurnal cycles, that differs from the most common cycle seasonality described in the literature, i.e. pre-dawn peaks in spring. Our cycles appear in summer and the maximum and minimum shift to a later time in late summer/autumn. This is observed both for water- and energy-limited years, thus potentially stressing the role of evapotranspiration. This concluding hypothesis on the role of evapotranspiration on nitrate stream concentration, which was obtained through data mining, broadens the perspective on the diurnal cycling of stream nitrate concentrations. PMID:27073838

  14. 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

  15. 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

  16. Evaluation of trap-induced systematic frequency shifts for a multi-ion optical clock at the 10‑19 level

    NASA Astrophysics Data System (ADS)

    Keller, J.; Burgermeister, T.; Kalincev, D.; Kiethe, J.; Mehlstäubler, T. E.

    2016-06-01

    In order to improve the short-term stability of trapped-ion optical clocks, we are developing a frequency standard based on 115In+ / 172Yb+ Coulomb crystals. For this purpose, we have developed scalable segmented Paul traps which allow a high level of control for multiple ion ensembles. In this article, we detail on our recent results regarding the reduction of the leading sources of frequency uncertainty introduced by the ion trap: 2nd-order Doppler shifts due to micromotion and the heating of secular motion, as well as the black-body radiation shift due to warming of the trap. We show that the fractional frequency uncertainty due to each of these effects can be reduced to well below 10-19.

  17. Evaluation of trap-induced systematic frequency shifts for a multi-ion optical clock at the 10-19 level

    NASA Astrophysics Data System (ADS)

    Keller, J.; Burgermeister, T.; Kalincev, D.; Kiethe, J.; Mehlstäubler, T. E.

    2016-06-01

    In order to improve the short-term stability of trapped-ion optical clocks, we are developing a frequency standard based on 115In+ / 172Yb+ Coulomb crystals. For this purpose, we have developed scalable segmented Paul traps which allow a high level of control for multiple ion ensembles. In this article, we detail on our recent results regarding the reduction of the leading sources of frequency uncertainty introduced by the ion trap: 2nd-order Doppler shifts due to micromotion and the heating of secular motion, as well as the black-body radiation shift due to warming of the trap. We show that the fractional frequency uncertainty due to each of these effects can be reduced to well below 10-19.

  18. 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

  19. Characterization of light shift below 10(-15) in a cesium fountain frequency standard operated without the use of mechanical shutters.

    PubMed

    Enzer, Daphna G; Klipstein, William M

    2006-09-01

    We characterize the light shift in the interaction region of a laser-cooled frequency standard and demonstrate an approach for its mitigation without the use of mechanical shutters. The light shift is confirmed to be below 10-15 and expected to be orders of magnitude lower. This technique makes use of a master-slave laser configuration where cutting the injection power to a slave laser causes it to lase at its free-running wavelength, often two or more nanometers off from the atomic resonance.

  20. Doppler-shifting effects on frequency spectra of gravity waves observed near the summer mesopause at high latitude

    NASA Technical Reports Server (NTRS)

    Fritts, David C.; Wang, Ding-Yi

    1991-01-01

    Results are presented of radar observations of horizontal and vertical velocities near the summer mesopause at Poker Flat (Alaska), showing that the observed vertical velocity spectra were influenced strongly by Doppler-shifting effects. The horizontal velocity spectra, however, were relatively insensitive to horizontal wind speed. The observed spectra are compared with predicted spectra for various models of the intrinsic motion spectrum and degrees of Doppler shifting.

  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. Residual compressive stress induced infrared-absorption frequency shift of hexagonal boron nitride in cubic boron nitride films prepared by plasma-enhanced chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Liu, Yong; Jin, Panpan; Chen, Aili; Yang, Hangsheng; Xu, Yabo

    2012-09-01

    The effects of compressive stress on the TO phonon frequencies of hexagonal boron nitride (hBN) in cubic BN (cBN) films were investigated using infrared absorption spectroscopy, showing that the B-N stretching vibration of hBN at 1380 cm-1 shifted to high wavenumbers under biaxial compressive stress with the rate 2.65 cm-1 per GPa, while the B-N-B bending vibration near 780 cm-1 shifted to low wavenumbers with the rate -3.45 cm-1/GPa. The density functional perturbation theoretical calculation was carried out to check the above phonon frequencies under stress for two typical orientations of hBN crystallite. The results are shown to be in fair agreement with the experimental data. Our results suggest that the residual compressive stress accumulated in cBN films can be evaluated from the IR peak position near 780 cm-1.

  3. Mitigation of nonlinear effects through frequency shift free mid-span spectral inversion using counter-propagating dual pumped FWM in fiber

    NASA Astrophysics Data System (ADS)

    Anchal, Abhishek; Kumar, Pradeep; Landais, Pascal

    2016-10-01

    We propose and numerically verify a scheme of frequency-shift free mid-span spectral inversion (MSSI) for nonlinearity mitigation in an optical transmission system. Spectral inversion is accomplished by optical phase conjugation, realized by counter-propagating dual pumped four-wave mixing in a highly nonlinear fiber. We examine the performance of MSSI due to critical parameters such as nonlinear fiber length, pump and signal power. We demonstrate the near complete nonlinearity mitigation of 40 Gbps DQPSK modulated data transmitted over 1000 km standard single mode fiber using our method of MSSI. We perform simulation of bit-error rate as a function of optical signal to noise ratio to corroborate the effect of frequency-shift free MSSI.

  4. 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

  5. Absolute frequency of the {sup 88}Sr{sup +} 5s {sup 2}S{sub 1/2}-4d {sup 2}D{sub 5/2} reference transition at 445 THz and evaluation of systematic shifts

    SciTech Connect

    Madej, A.A.; Bernard, J.E.; Dube, P.; Marmet, L.; Windeler, R.S.

    2004-07-01

    A Cs referenced optical frequency comb system has been used to measure the center frequency of the 5s {sup 2}S{sub 1/2}-4d {sup 2}D{sub 5/2} transition at 445 THz in a single, trapped, and laser-cooled {sup 88}Sr{sup +} ion. The transition frequency {nu}{sub SD}=444 779 044 095 510 Hz{+-}50 Hz (1{sigma}) is obtained, when corrected for systematic shifts. A detailed calculation of the estimated systematic shifts is presented which yields improved values for the various shift parameters including blackbody and electric quadrupole moment shifts.

  6. Finite element analysis and frequency shift studies for the bridge coupler of the coupled cavity linear accelerator of the spallation neutron source.

    SciTech Connect

    Chen, Z.

    2001-01-01

    The Spallation Neutron Source (SNS) is an accelerator-based neutron scattering research facility. The linear accelerator (linac) is the principal accelerating structure and divided into a room-temperature linac and a superconducting linac. The normal conducting linac system that consists of a Drift Tube Linac (DTL) and a Coupled Cavity Linac (CCL) is to be built by Los Alamos National Laboratory. The CCL structure is 55.36-meters long. It accelerates H- beam from 86.8 Mev to 185.6 Mev at operating frequency of 805 MHz. This side coupled cavity structure has 8 cells per segment, 12 segments and 11 bridge couplers per module, and 4 modules total. A 5-MW klystron powers each module. The number 3 and number 9 bridge coupler of each module are connected to the 5-MW RF power supply. The bridge coupler with length of 2.5 {beta}{gamma} is a three-cell structure and located between the segments and allows power flow through the module. The center cell of each bridge coupler is excited during normal operation. To obtain a uniform electromagnetic filed and meet the resonant frequency shift, the RF induced heat must be removed. Thus, the thermal deformation and frequency shift studies are performed via numerical simulations in order to have an appropriate cooling design and predict the frequency shift under operation. The center cell of the bridge coupler also contains a large 4-inch slug tuner and a tuning post that used to provide bulk frequency adjustment and field intensity adjustment, so that produce the proper total field distribution in the module assembly.

  7. The doppler frequency shift caused by the inhomogeneities of a medium induced by pulses of intense laser radiation

    NASA Astrophysics Data System (ADS)

    Rozanov, N. N.; Kiselev, Al. S.; Kiselev, An. S.

    2008-08-01

    Self-reflection of pulses of intense laser radiation from an inhomogeneity induced by them in a medium with fast optical nonlinearity is analyzed. The reflected radiation is characterized by a considerable Doppler shift and by a signal magnitude that is sufficient for experimental detection.

  8. Reply to Comment on ‘Roles of interbasin frequency changes in the poleward shifts of maximum intensity location of tropical cyclones’

    NASA Astrophysics Data System (ADS)

    Moon, Il-Ju; Kim, Sung-Hun; Klotzbach, Phil; Chan, Johnny C. L.

    2016-06-01

    Recently a pronounced global poleward shift in the latitude at which the maximum intensities of tropical cyclones (TC) occur has been identified. Moon et al (2015 Environ. Res. Lett. 10 104004) reported that the poleward migration is significantly influenced by changes in interbasin frequency. These frequency changes are a larger contributor to the poleward shift than the intrabasin migration component. The strong role of interbasin frequency changes in the poleward migration also suggest that the poleward trend could be changed to an opposite equatorward trend in the future due to multi-decadal variability that significantly impacts Northern Hemisphere TC frequency. In the accompanying comment, Kossin et al (2016 Environ. Res. Lett. 11 068001) questioned the novelty and robustness of our results by raising issues associated with subsampling, contributions from some basins to poleward migration, and data dependency. Here, we explain the originality and importance of our main findings, which are different from those of Kossin et al (2014 Nature 509 349–52) and reaffirm that our conclusions are maintained regardless of the issues that were raised.

  9. Vibrational frequency shifts of fluid nitrogen fundamental and hot band transitions as a function of pressure and temperature

    SciTech Connect

    Schmidt, S.C.; Schiferl, D.; Zinn, A.S.; Ragan, D.D.; Moore, D.S.

    1989-01-01

    Coherent anti-Stokes Raman scattering (CARS) and spontaneous Raman spectroscopy have been used to obtain vibrational spectra of shock-compressed and static high-pressure fluid nitrogen, respectively. Vibrational frequencies were obtained from the CARS data using a semiclassical model for these spectra. Spontaneous Raman vibrational frequencies were determined by fitting data using a Lorentz shape line. A functional form was found for the dependence of the vibrational frequency on pressure and temperature to 40 GPa and 5000 K, respectively. The result is compared to a recent theoretical model. 6 refs., 2 figs., 1 tab.

  10. 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.

  11. 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.

  12. 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.

  13. Wearable Multi-Frequency and Multi-Segment Bioelectrical Impedance Spectroscopy for Unobtrusively Tracking Body Fluid Shifts during Physical Activity in Real-Field Applications: A Preliminary Study

    PubMed Central

    Villa, Federica; Magnani, Alessandro; Maggioni, Martina A.; Stahn, Alexander; Rampichini, Susanna; Merati, Giampiero; Castiglioni, Paolo

    2016-01-01

    Bioelectrical Impedance Spectroscopy (BIS) allows assessing the composition of body districts noninvasively and quickly, potentially providing important physiological/clinical information. However, neither portable commercial instruments nor more advanced wearable prototypes simultaneously satisfy the demanding needs of unobtrusively tracking body fluid shifts in different segments simultaneously, over a broad frequency range, for long periods and with high measurements rate. These needs are often required to evaluate exercise tests in sports or rehabilitation medicine, or to assess gravitational stresses in aerospace medicine. Therefore, the aim of this work is to present a new wearable prototype for monitoring multi-segment and multi-frequency BIS unobtrusively over long periods. Our prototype guarantees low weight, small size and low power consumption. An analog board with current-injecting and voltage-sensing electrodes across three body segments interfaces a digital board that generates square-wave current stimuli and computes impedance at 10 frequencies from 1 to 796 kHz. To evaluate the information derivable from our device, we monitored the BIS of three body segments in a volunteer before, during and after physical exercise and postural shift. We show that it can describe the dynamics of exercise-induced changes and the effect of a sit-to-stand maneuver in active and inactive muscular districts separately and simultaneously. PMID:27187389

  14. Wearable Multi-Frequency and Multi-Segment Bioelectrical Impedance Spectroscopy for Unobtrusively Tracking Body Fluid Shifts during Physical Activity in Real-Field Applications: A Preliminary Study.

    PubMed

    Villa, Federica; Magnani, Alessandro; Maggioni, Martina A; Stahn, Alexander; Rampichini, Susanna; Merati, Giampiero; Castiglioni, Paolo

    2016-01-01

    Bioelectrical Impedance Spectroscopy (BIS) allows assessing the composition of body districts noninvasively and quickly, potentially providing important physiological/clinical information. However, neither portable commercial instruments nor more advanced wearable prototypes simultaneously satisfy the demanding needs of unobtrusively tracking body fluid shifts in different segments simultaneously, over a broad frequency range, for long periods and with high measurements rate. These needs are often required to evaluate exercise tests in sports or rehabilitation medicine, or to assess gravitational stresses in aerospace medicine. Therefore, the aim of this work is to present a new wearable prototype for monitoring multi-segment and multi-frequency BIS unobtrusively over long periods. Our prototype guarantees low weight, small size and low power consumption. An analog board with current-injecting and voltage-sensing electrodes across three body segments interfaces a digital board that generates square-wave current stimuli and computes impedance at 10 frequencies from 1 to 796 kHz. To evaluate the information derivable from our device, we monitored the BIS of three body segments in a volunteer before, during and after physical exercise and postural shift. We show that it can describe the dynamics of exercise-induced changes and the effect of a sit-to-stand maneuver in active and inactive muscular districts separately and simultaneously. PMID:27187389

  15. Developmental shifts in frequency distribution of polysomal mRNA and their posttranscriptional regulation in the sea urchin embryo.

    PubMed

    Shepherd, G W; Nemer, M

    1980-08-01

    The frequency distributions of polyadenylylated RNAs from the polysomes of sea urchin blastulae and gastrulae were estimated from their kinetics of hybridization with complementary DNA. Developmental decreases in complexity were observed among abundant, intermediate, and rare frequency classes. The class of highest abundance in the blastula polysomes had a complexity of 5.6 X 10(4) nucleotides and contained about 30 mRNA species, which divided into subsets according to developmental fate. Studies with purified DNA complementary to this abundant class revealed that five of these mRNA species remained abundant in the gastrula, wherein each comprised 2% of the polyadenylylated RNA in the polysomes. Approximately 5 species decreased to a nearly rare frequency and 20 were absent or at the limits of detection in polyadenylylated RNA of gastrula polysomes. These distinctly different developmental fates suggest distinct modes of regulation of mRNA concentration for different subsets. Focusing on the small number of abundant blastula mRNAs, we ascertained that those which were absent from gastrula polysomes were nevertheless represented in the gastrula nuclear RNA. Therefore, the appearance of abundant mRNA species in polysomes can be regulated by posttranscriptional processes. PMID:6933514

  16. Specific heat related to the Raman frequency shifts for the rotatory mode in ammonia solid I close to the melting point

    NASA Astrophysics Data System (ADS)

    Karaçalı, H.; Yurtseven, H.

    2006-03-01

    This study gives an evidence for the validity of our spectroscopic modification of the Pippard relation as applied to ammonia solid I close to the melting point. We use our calculated frequencies for the rotatory lattice (librational) mode in ammonia solid I for the pressures of 0, 1.93 and 3.07 kbars. We obtain that the specific heat Cp varies linearly with the frequency shifts 1/ν(∂ν/∂T) for this Raman mode at those pressures studied in this crystalline system. Our values of the slope dP/dT that we deduced from the linear plots, are not in satisfactory agreement with the experimental values in ammonia solid I near the melting point.

  17. Identification of the third/extra allele for forensic application in cases with TPOX tri-allelic pattern.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; da Motta, Carlos Henrique Ares Silveira; Rodenbusch, Rodrigo; Gusmão, Leonor; Alho, Clarice Sampaio

    2015-05-01

    Genotyping of polymorphic short tandem repeats (STRs) loci is widely used in forensic DNA analysis. STR loci eventually present tri-allelic pattern as a genotyping irregularity and, in that situation, the doubt about the tri-allele locus frequency calculation can reduce the analysis strength. In the TPOX human STR locus, tri-allelic genotypes have been reported with a widely varied frequency among human populations. We investigate whether there is a single extra allele (the third allele) in the TPOX tri-allelic pattern, what it is, and where it is, aiming to understand its genomic anatomy and to propose the knowledge of this TPOX extra allele from genetic profile, thus preserving the two standard TPOX alleles in forensic analyses. We looked for TPOX tri-allelic subjects in 75,113 Brazilian families. Considering only the parental generation (mother+father) we had 150,226 unrelated subjects evaluated. From this total, we found 88 unrelated subjects with tri-allelic pattern in the TPOX locus (0.06%; 88/150,226). Seventy three of these 88 subjects (73/88; 83%) had the Clayton's original Type 2 tri-allelic pattern (three peaks of even intensity). The remaining 17% (15/88) show a new Type 2 derived category with heterozygote peak imbalance (one double dose peak plus one regular sized peak). In this paper we present detailed data from 66 trios (mother+father+child) with true biological relationships. In 39 of these families (39/66; 59%) the extra TPOX allele was transmitted either from the mother or from the father to the child. Evidences indicated the allele 10 as the extra TPOX allele, and it is on the X chromosome. The present data, which support the previous Lane hypothesis, improve the knowledge about tri-allelic pattern of TPOX CODIS' locus allowing the use of TPOX profile in forensic analyses even when with tri-allelic pattern. This evaluation is now available for different forensic applications.

  18. Effect of strong phonon-phonon coupling on the temperature dependent structural stability and frequency shift of 2D hexagonal boron nitride.

    PubMed

    Anees, P; Valsakumar, M C; Panigrahi, B K

    2016-01-28

    The temperature dependent structural stability, frequency shift and linewidth of 2D hexagonal boron nitride (h-BN) are studied using a combination of lattice dynamics (LD) and molecular dynamics (MD) simulations. The in-plane lattice parameter shows a negative thermal expansion in the whole computed temperature range (0-2000 K). When the in-plane lattice parameter falls below the equilibrium value, the quasi-harmonic bending (ZA) mode frequency becomes imaginary along the Γ-M direction in the Brillouin zone, leading to a structural instability of the 2D sheet. The ZA mode is seen to be stabilized in the dispersion obtained from MD simulations, due to the automatic incorporation of higher order phonon scattering processes in MD, which are absent in a quasi-harmonic dispersion. The mode resolved phonon spectra computed with a quasi-harmonic method predict a blueshift of the longitudinal and transverse (LO/TO) optic mode frequencies with an increase in temperature. On the other hand, both canonical (NVT) and isobaric-isothermal (NPT) ensembles predict a redshift with an increase in temperature, which is more prominent in the NVT ensemble. The strong phonon-phonon coupling dominates over the thermal contraction effect and leads to a redshift in LO/TO mode frequency in the NPT ensemble simulations. The out-of-plane (ZO) optic mode quasi-harmonic frequencies are redshifted due to a membrane effect. The phonon-phonon coupling effects in the NVT and NPT ensemble simulations lead to a further reduction in the ZO mode frequencies. The linewidth of the LO/TO and ZO mode frequencies increases in a monotonic fashion. The temperature dependence of acoustic modes is also analyzed. The quasi-harmonic calculations predict a redshift of ZA mode, and at the same time the TA (transverse acoustic) and LA (longitudinal acoustic) mode frequencies are blueshifted. The strong phonon-phonon coupling in MD simulations causes a redshift of the LA and TA mode frequencies, while the ZA mode

  19. Inferring the age of a fixed beneficial allele.

    PubMed

    Ormond, Louise; Foll, Matthieu; Ewing, Gregory B; Pfeifer, Susanne P; Jensen, Jeffrey D

    2016-01-01

    Estimating the age and strength of beneficial alleles is central to understanding how adaptation proceeds in response to changing environmental conditions. Several haplotype-based estimators exist for inferring the age of segregating beneficial mutations. Here, we develop an approximate Bayesian-based approach that rather estimates these parameters for fixed beneficial mutations in single populations. We integrate a range of existing diversity, site frequency spectrum, haplotype- and linkage disequilibrium-based summary statistics. We show that for strong selective sweeps on de novo mutations the method can estimate allele age and selection strength even in nonequilibrium demographic scenarios. We extend our approach to models of selection on standing variation, and co-infer the frequency at which selection began to act upon the mutation. Finally, we apply our method to estimate the age and selection strength of a previously identified mutation underpinning cryptic colour adaptation in a wild deer mouse population, and compare our findings with previously published estimates as well as with geological data pertaining to the presumed shift in selective pressure. PMID:26576754

  20. Time dependent Doppler shifts in high-order harmonic generation in intense laser interactions with solid density plasma and frequency chirped pulses

    SciTech Connect

    Welch, E. C.; Zhang, P.; He, Z.-H.; Dollar, F.; Krushelnick, K.; Thomas, A. G. R.

    2015-05-15

    High order harmonic generation from solid targets is a compelling route to generating intense attosecond or even zeptosecond pulses. However, the effects of ion motion on the generation of harmonics have only recently started to be considered. Here, we study the effects of ion motion in harmonics production at ultrahigh laser intensities interacting with solid density plasma. Using particle-in-cell simulations, we find that there is an optimum density for harmonic production that depends on laser intensity, which scales linearly with a{sub 0} with no ion motion but with a reduced scaling if ion motion is included. We derive a scaling for this optimum density with ion motion and also find that the background ion motion induces Doppler red-shifts in the harmonic structures of the reflected pulse. The temporal structure of the Doppler shifts is correlated to the envelope of the incident laser pulse. We demonstrate that by introducing a frequency chirp in the incident pulse we are able to eliminate these Doppler shifts almost completely.

  1. A novel femtosecond-gated, high-resolution, frequency-shifted shearing interferometry technique for probing pre-plasma expansion in ultra-intense laser experiments

    SciTech Connect

    Feister, S. Orban, C.; Nees, J. A.; Morrison, J. T.; Frische, K. D.; Chowdhury, E. A.; Roquemore, W. M.

    2014-11-15

    Ultra-intense laser-matter interaction experiments (>10{sup 18} W/cm{sup 2}) with dense targets are highly sensitive to the effect of laser “noise” (in the form of pre-pulses) preceding the main ultra-intense pulse. These system-dependent pre-pulses in the nanosecond and/or picosecond regimes are often intense enough to modify the target significantly by ionizing and forming a plasma layer in front of the target before the arrival of the main pulse. Time resolved interferometry offers a robust way to characterize the expanding plasma during this period. We have developed a novel pump-probe interferometry system for an ultra-intense laser experiment that uses two short-pulse amplifiers synchronized by one ultra-fast seed oscillator to achieve 40-fs time resolution over hundreds of nanoseconds, using a variable delay line and other techniques. The first of these amplifiers acts as the pump and delivers maximal energy to the interaction region. The second amplifier is frequency shifted and then frequency doubled to generate the femtosecond probe pulse. After passing through the laser-target interaction region, the probe pulse is split and recombined in a laterally sheared Michelson interferometer. Importantly, the frequency shift in the probe allows strong plasma self-emission at the second harmonic of the pump to be filtered out, allowing plasma expansion near the critical surface and elsewhere to be clearly visible in the interferograms. To aid in the reconstruction of phase dependent imagery from fringe shifts, three separate 120° phase-shifted (temporally sheared) interferograms are acquired for each probe delay. Three-phase reconstructions of the electron densities are then inferred by Abel inversion. This interferometric system delivers precise measurements of pre-plasma expansion that can identify the condition of the target at the moment that the ultra-intense pulse arrives. Such measurements are indispensable for correlating laser pre-pulse measurements

  2. Detailed discussion of a linear electric field frequency shift induced in confined gases by a magnetic field gradient: Implications for neutron electric-dipole-moment experiments

    NASA Astrophysics Data System (ADS)

    Lamoreaux, S. K.; Golub, R.

    2005-03-01

    The search for particle electric dipole moments (EDM’s) is one of the best places to look for physics beyond the standard model of electroweak interaction because the size of time reversal violation predicted by the standard model is incompatible with present ideas concerning the creation of the baryon-antibaryon asymmetry. As the sensitivity of these EDM searches increases more subtle systematic effects become important. We develop a general analytical approach to describe a systematic effect recently observed in an electric dipole moment experiment using stored particles [J. M. Pendlebury , Phys. Rev. A 70, 032102 (2004)]. Our approach is based on the relationship between the systematic frequency shift and the velocity autocorrelation function of the resonating particles. Our results, when applied to well-known limiting forms of the correlation function, are in good agreement with both the limiting cases studied in recent work that employed a numerical and heuristic analysis. Our general approach explains some of the surprising results observed in that work and displays the rich behavior of the shift for intermediate frequencies, which has not been studied previously.

  3. Spectroscopic and Ab Initio Investigation of C-H⋅⋅⋅N Hydrogen-Bonded Complexes of Fluorophenylacetylenes: Frequency Shifts and Correlations.

    PubMed

    Dey, Arghya; Mondal, Sohidul Islam; Sen, Saumik; Patwari, G Naresh

    2016-08-18

    The C-H⋅⋅⋅N hydrogen-bonded complexes of several fluorophenyacetylenes with ammonia and methylamine were characterized by a redshift in the acetylenic C-H stretching vibration of the phenylacetylene moiety. These redshifts were linearly correlated with the stabilization energies calculated at the CCSD(T)/CBS//MP2-aug-cc-pVDZ level. Analysis of various components of the interaction energy indicated that the observed redshifts were weakly correlated with the electrostatic component. The weaker linear correlation between the frequency shifts and the electrostatic component between two data sets can perhaps be attributed to the marginal differences in the Stark tuning rate and zero-field shifts. The induction and exchange-repulsion components were linearly correlated. However, the dispersion component depends on the nature of the hydrogen-bond acceptor and shows a quantum jump when the hydrogen-bond acceptor is changed from ammonia to methylamine. The observed linear correlation between the redshifts in the C-H stretching frequencies and the total stabilization energies is due to mutual cancellation of deviations from linearity between various components. PMID:27146197

  4. Fluid nonlinear frequency shift of nonlinear ion acoustic waves in multi-ion species plasmas in the small wave number region.

    PubMed

    Feng, Q S; Xiao, C Z; Wang, Q; Zheng, C Y; Liu, Z J; Cao, L H; He, X T

    2016-08-01

    The properties of the nonlinear frequency shift (NFS), especially the fluid NFS from the harmonic generation of the ion-acoustic wave (IAW) in multi-ion species plasmas, have been researched by Vlasov simulation. Pictures of the nonlinear frequency shift from harmonic generation and particle trapping are shown to explain the mechanism of NFS qualitatively. The theoretical model of the fluid NFS from harmonic generation in multi-ion species plasmas is given, and the results of Vlasov simulation are consistent with the theoretical result of multi-ion species plasmas. When the wave number kλ_{De} is small, such as kλ_{De}=0.1, the fluid NFS dominates in the total NFS and will reach as large as nearly 15% when the wave amplitude |eϕ/T_{e}|∼0.1, which indicates that in the condition of small kλ_{De}, the fluid NFS dominates in the saturation of stimulated Brillouin scattering, especially when the nonlinear IAW amplitude is large. PMID:27627405

  5. Unified Electrostatic Understanding on the Solvation-Induced Changes in the CN Stretching Frequency and the NMR Chemical Shifts of a Nitrile.

    PubMed

    Torii, Hajime

    2016-09-15

    Understanding on the spectroscopic properties of a functional group is essential to use it to detect changes in the structural and/or dynamical properties through the situations of intermolecular interactions. The present study is devoted to elucidating the factors that control the solvation-induced changes in the C≡N stretching frequency and the (13)C and (15)N NMR chemical shifts of the nitrile group. It is shown that the nonelectrostatic contribution of the hydration-induced changes in the C≡N stretching frequency as previously thought, as well as the specific effect of hydrogen bonding on the (13)C and (15)N chemical shifts, actually originate from the spatially inhomogeneous nature of the electrostatic situation generated by the hydrogen-bond donating water molecule, especially by the OH bond dipole. On this basis, a unified electrostatic interaction model that encompasses the cases of both hydration and dipolar solvation is constructed. The responses of electrons in these two cases are also discussed. PMID:27547990

  6. Fluid nonlinear frequency shift of nonlinear ion acoustic waves in multi-ion species plasmas in the small wave number region

    NASA Astrophysics Data System (ADS)

    Feng, Q. S.; Xiao, C. Z.; Wang, Q.; Zheng, C. Y.; Liu, Z. J.; Cao, L. H.; He, X. T.

    2016-08-01

    The properties of the nonlinear frequency shift (NFS), especially the fluid NFS from the harmonic generation of the ion-acoustic wave (IAW) in multi-ion species plasmas, have been researched by Vlasov simulation. Pictures of the nonlinear frequency shift from harmonic generation and particle trapping are shown to explain the mechanism of NFS qualitatively. The theoretical model of the fluid NFS from harmonic generation in multi-ion species plasmas is given, and the results of Vlasov simulation are consistent with the theoretical result of multi-ion species plasmas. When the wave number k λD e is small, such as k λD e=0.1 , the fluid NFS dominates in the total NFS and will reach as large as nearly 15 % when the wave amplitude |e ϕ / Te|˜0.1 , which indicates that in the condition of small k λD e , the fluid NFS dominates in the saturation of stimulated Brillouin scattering, especially when the nonlinear IAW amplitude is large.

  7. Phase Shift of a Coplanar Waveguide by Bias Voltage on Thick Lead Zirconate Titanate Film at Microwave Frequency

    NASA Astrophysics Data System (ADS)

    Shibata, Kouji; Iijima, Takashi; Masuda, Yoichiro

    2008-09-01

    A coplanar waveguide was fabricated by depositing a 1-µm-thick Au film on a multilayer dielectric, consisting of a 2-µm-thick lead zirconate titanate (PZT) film over an Al2O3 substrate, through etching. Following this, the reflection constant, transmission constant, and phase variation were measured for this transmission line as bias voltage was varied from 30 to 50 V. As a result, it was confirmed that the phase variation becomes about 15° at a 50 V bias at a frequency of 10 GHz. We then confirmed the basic input-output characteristics of this type of structure in the microwave band. Finally, the relative permittivity of a PZT thick film as a coplanar waveguide was estimated using the measurement results of relative permittivity according to the split cavity resonator method, and phase variation under the condition in which a bias voltage was applied.

  8. Impact of longer-term modest climate shifts on architecture of high-frequency sequences (Cyclothems), Pennsylvanian of midcontinent U.S.A

    USGS Publications Warehouse

    Feldman, H.R.; Franseen, E.K.; Joeckel, R.M.; Heckel, P.H.

    2005-01-01

    Pennsylvanian glacioeustatic cyclothems exposed in Kansas and adjacent areas provide a unique opportunity to test models of the impact of relative sea level and climate on stratal architecture. A succession of eight of these high-frequency sequences, traced along dip for 500 km, reveal that modest climate shifts from relatively dry-seasonal to relatively wet-seasonal with a duration of several sequences (???600,000 to 1 million years) had a dominant impact on facies, sediment dispersal patterns, and sequence architecture. The climate shifts documented herein are intermediate, both in magnitude and duration, between previously documented longer-term climate shifts throughout much of the Pennsylvanian and shorter-term shifts described within individual sequences. Climate indicators are best preserved at sequence boundaries and in incised-valley fills of the lowstand systems tracts (LST). Relatively drier climate indicators include high-chroma paleosols, typically with pedogenic carbonates, and plant assemblages that are dominated by gymnosperms, mostly xerophytic walchian conifers. The associated valleys are small (4 km wide and >20 m deep), and dominated by quartz sandstones derived from distant source areas, reflecting large drainage networks. Transgressive systems tracts (TST) in all eight sequences gen erally are characterized by thin, extensive limestones and thin marine shales, suggesting that the dominant control on TST facies distribution was the sequestration of siliciclastic sediment in updip positions. Highstand systems tracts (HST) were significantly impacted by the intermediate-scale climate cycle in that HSTs from relatively drier climates consist of thin marine shales overlain by extensive, thick regressive limestones, whereas HSTs from relatively wetter climates are dominated by thick marine shales. Previously documented relative sea-level changes do not track the climate cycles, indicating that climate played a role distinct from that of relative sea

  9. 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...

  10. 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

  11. RbTiOPO4 cascaded Raman operation with multiple Raman frequency shifts derived by Q-switched Nd:YAlO3 laser

    PubMed Central

    Duan, Yanmin; Zhu, Haiyong; Zhang, Yaoju; Zhang, Ge; Zhang, Jian; Tang, Dingyuan; Kaminskii, A. A.

    2016-01-01

    An intra-cavity RbTiOPO4 (RTP) cascade Raman laser was demonstrated for efficient multi-order Stokes emission. An acousto-optic Q-switched Nd:YAlO3 laser at 1.08 μm was used as the pump source and a 20-mm-long x-cut RTP crystal was used as the Raman medium to meet the X(Z,Z)X Raman configuration. Multi-order Stokes with multiple Raman shifts (~271, ~559 and ~687 cm−1) were achieved in the output. Under an incident pump power of 9.5 W, a total average output power of 580 mW with a pulse repetition frequency of 10 kHz was obtained. The optical conversion efficiency is 6.1%. The results show that the RTP crystal can enrich laser spectral lines and generate high order Stokes light. PMID:27666829

  12. Frequency shift of the propagating ultraintense field in a plasma with a fraction of electron-positron pairs under the conditions of response saturation

    SciTech Connect

    Shiryaev, O. B.

    2013-05-15

    A model is derived from the Maxwell and fluid dynamics equations to describe the interactions between a relativistically intense electromagnetic wave and a cold unmagnetized plasma composed of an electron-ion background and a fraction of electron-positron pairs. Combining the envelope approximation for the propagating field and the quasistatic treatment of the plasma dynamics, the model sustains fully nonlinear plane-wave solutions and shows that saturation of the plasma response occurs at ultrarelativistic intensities of the incident field even for pair concentrations far below those of the electron-ion background. Stability of the electromagnetic wave under the saturation conditions is demonstrated and an expression is derived to link its interaction-induced frequency shift to the concentration of the electron-positron pairs.

  13. Long-lived frequency shifts observed in a magnetic resonance force microscope experiment following microwave irradiation of a nitroxide spin probe

    SciTech Connect

    Chen, Lei; Longenecker, Jonilyn G.; Moore, Eric W.; Marohn, John A.

    2013-04-01

    We introduce a spin-modulation protocol for force-gradient detection of magnetic resonance that enables the real-time readout of longitudinal magnetization in an electron spin resonance experiment involving fast-relaxing spins. We applied this method to observe a prompt change in longitudinal magnetization following the microwave irradiation of a nitroxide-doped perdeuterated polystyrene film having an electron spin-lattice relaxation time of T{sub 1}{approx}1ms. The protocol allowed us to discover a large, long-lived cantilever frequency shift. Based on its magnitude, lifetime, and field dependence, we tentatively attribute this persistent signal to deuteron spin magnetization created via transfer of polarization from nitroxide spins.

  14. High efficiency production of germ-line transgenic Japanese medaka (Oryzias latipes) by electroporation with direct current-shifted radio frequency pulses.

    PubMed

    Hostetler, Heather A; Peck, Stephanie L; Muir, William M

    2003-08-01

    Although there have been several studies showing the production of transgenic fish through electroporation techniques, success rates have been low and few studies show germ-line integration and expression. When electroporation has been successful, the device used is no longer commercially available. The goal of this experiment was to find an alternative efficient method of generating transgenic Japanese medaka (Oryzias latipes) using a commercially available electroporation device. The Gene Pulser II and RF module (Bio-Rad Laboratories, USA), along with two reporter gene constructs, were used. In contrast to other electroporation devices, which are based on a single pulse with exponential decay or square wave technology, the Gene Pulser II incorporates a direct current (DC)-shifted radio frequency (RF) signal. With this technique, over 1000 embryos can be electroporated in less than 30 min. The plasmid pCMV-SPORT-beta-gal (Invitrogen, USA) was used in the supercoiled form to optimize parameters for gene transfer into single-celled embryos, and resulted in up to 100% somatic gene transfer. Similar conditions were used to generate fish transgenic for both the pCMV-EGFP plasmid (Clontech, USA) and a cytomegalovirus (CMV) driven phytase-EGFP construct. The conditions used were a voltage of 25 V, a percent modulation of 100%, a radio frequency of 35 kHz, a burst duration of 10 ms, 3 bursts, and a burst interval of 1.0 s. Seventy percent of the embryos electroporated with the pCMV-EGFP construct survived to sexual maturity, and of those, 85% were capable of passing the transgene on to their offspring. Transgenic second generation back-crossed (BC2) fry were subjected to Southern blot analysis, which confirmed germ-line integration, and observation for green fluorescence protein, which confirmed protein expression. DC-shifted RF pulses are effective and efficient in the production of transgenic medaka, and germ-line integration and expression can be achieved without

  15. Comparison of particle-in-cell simulations with experimentally observed frequency shifts between ions of the same mass-to-charge in Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Leach, Franklin E; Kharchenko, Andriy; Heeren, Ron M A; Nikolaev, Eugene; Amster, I Jonathan

    2010-02-01

    It has been previously observed that the measured frequency of ions in a Fourier transform mass spectrometry experiment depend upon the number of trapped ions, even for populations consisting exclusively of a single mass-to-charge. Since ions of the same mass-to-charge are thought not to exert a space-charge effect among themselves, the experimental observation of such frequency shifts raises questions about their origin. To determine the source of such experimentally observed frequency shifts, multiparticle ion trajectory simulations have been conducted on monoisotopic populations of Cs(+) ranging from 10(2) ions to 10(6) ions. A close match to experimental behavior is observed. By probing the effect of ion number and orbital radius on the shift in the cyclotron frequency, it is shown that for a monoisotopic population of ions, the frequency shift is caused by the interaction of ions with their image-charge. The addition of ions of a second mass-to-charge to the simulation allows the comparison of the magnitude of the frequency shift resulting from space-charge (ion-ion) effects versus ion interactions with their image charge.

  16. Exploration of MR-guided head and neck hyperthermia by phantom testing of a modified prototype applicator for use with proton resonance frequency shift thermometry.

    PubMed

    Numan, Wouter C M; Hofstetter, Lorne W; Kotek, Gyula; Bakker, Jurriaan F; Fiveland, Eric W; Houston, Gavin C; Kudielka, Guido; Yeo, Desmond T B; Paulides, Margarethus M

    2014-05-01

    Magnetic resonance thermometry (MRT) offers non-invasive temperature imaging and can greatly contribute to the effectiveness of head and neck hyperthermia. We therefore wish to redesign the HYPERcollar head and neck hyperthermia applicator for simultaneous radio frequency (RF) heating and magnetic resonance thermometry. In this work we tested the feasibility of this goal through an exploratory experiment, in which we used a minimally modified applicator prototype to heat a neck model phantom and used an MR scanner to measure its temperature distribution. We identified several distorting factors of our current applicator design and experimental methods to be addressed during development of a fully MR compatible applicator. To allow MR imaging of the electromagnetically shielded inside of the applicator, only the lower half of the HYPERcollar prototype was used. Two of its antennas radiated a microwave signal (150 W, 434 MHz) for 11 min into the phantom, creating a high gradient temperature profile (ΔTmax = 5.35 °C). Thermal distributions were measured sequentially, using drift corrected proton resonance frequency shift-based MRT. Measurement accuracy was assessed using optical probe thermometry and found to be about 0.4 °C (0.1-0.7 °C). Thermal distribution size and shape were verified by thermal simulations and found to have a good correlation (r(2 )= 0.76). PMID:24773040

  17. An estimation of the influence of force decrease on the mean power spectral frequency shift of the EMG during repetitive maximum dynamic knee extensions.

    PubMed

    Karlsson, J S; Ostlund, N; Larsson, B; Gerdle, B

    2003-10-01

    Frequency analysis of myoelectric (ME) signals, using the mean power spectral frequency (MNF), has been widely used to characterize peripheral muscle fatigue during isometric contractions assuming constant force. However, during repetitive isokinetic contractions performed with maximum effort, output (force or torque) will decrease markedly during the initial 40-60 contractions, followed by a phase with little or no change. MNF shows a similar pattern. In situations where there exist a significant relationship between MNF and output, part of the decrease in MNF may per se be related to the decrease in force during dynamic contractions. This study estimated force effects on the MNF shifts during repetitive dynamic knee extensions. Twenty healthy volunteers participated in the study and both surface ME signals (from the right vastus lateralis, vastus medialis, and rectus femoris muscles) and the biomechanical signals (force, position, and velocity) of an isokinetic dynamometer were measured. Two tests were performed: (i) 100 repetitive maximum isokinetic contractions of the right knee extensors, and (ii) five gradually increasing static knee extensions before and after (i). The corresponding ME signal time-frequency representations were calculated using the continuous wavelet transform. Compensation of the MNF variables of the repetitive contractions was performed with respect to the individual MNF-force relation based on an average of five gradually increasing contractions. Whether or not compensation was necessary was based on the shape of the MNF-force relationship. A significant compensation of the MNF was found for the repetitive isokinetic contractions. In conclusion, when investigating maximum dynamic contractions, decreases in MNF can be due to mechanisms similar to those found during sustained static contractions (force-independent component of fatigue) and in some subjects due to a direct effect of the change in force (force-dependent component of fatigue

  18. In the pursuit of small "red shift" of C-H stretching vibrational frequency of C-H...pi interactions for benzene dimer: How to amend MP2 calculations to reproduce the experimental results.

    PubMed

    Dinadayalane, T C; Leszczynski, Jerzy

    2009-02-28

    For the bent T-shaped benzene dimer, the vibrational frequencies at the MP2/aug-cc-pVDZ level with counterpoise correction reproduce experimental results of the small "red shifts" of C-H stretching, while those without counterpoise correction yield considerable "blue shift." Counterpoise correction also affects the C-H bond distances of C-H...pi interactions as well as intermoiety distances.

  19. 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

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

    PubMed

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

    2014-08-01

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

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

    PubMed

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

    2014-08-01

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

  2. Distribution of HLA-B alleles in Mexican Amerindian populations.

    PubMed

    Vargas-Alarcón, Gilberto; Hernández-Pacheco, Guadalupe; Zuñiga, Joaquín; Rodríguez-Pérez, José Manuel; Pérez-Hernández, Nonanzit; Rangel, Carlos; Villarreal-Garza, Cynthia; Martínez-Laso, Jorge; Granados, Julio; Arnaiz-Villena, Antonio

    2003-02-01

    In the present study we analyzed by PCR-SSO technique the HLA-B gene frequencies in 281 healthy individuals from four Mexican Amerindian populations (66 Mayos, 90 Mazatecans, 72 Nahuas and 53 Teenek). The most frequent alleles in all studied populations were HLA-B35, HLA-B39, and HLA-B40; however, some differences were observed between populations. The HLA-B35 allele was the most frequent in three of the four populations studied (Mayos, Nahuas and Teenek), whereas in Mazatecans the most frequent allele was HLA-B39. HLA-B40 presented frequencies higher than 10% in all groups. On the other hand, only Mayos presented an HLA-B51 gene frequency higher than 10%. When comparisons were made, important differences between groups were observed. The Teenek group presented an increased frequency of HLA-B35 when compared to Mazatecans and the HLA-B52 allele was increased in Nahuas and Teenek when compared to Mayos. An increased frequency of HLA-B39 was observed in Mazatecans when compared to Nahuas, Mayos and Teenek. Also, an increased frequency of HLA-B51 was observed in Mayos when compared to Mazatecans and Nahuas. These data corroborate the restricted polymorphism of HLA-B alleles and the high frequency of HLA-B35, HLA-B39 and HLA-B40 alleles in autochthonous American populations. In spite of the restriction in this polymorphism, differences in frequencies of HLA-B alleles could be helpful in distinguishing each of these populations.

  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. PMID:25549886

  4. Orthorhombic -Ca(HCOO)2 and monoclinic LiH2C6H4SO3 . H2O crystals - new materials for Raman lasers with large frequency shifts

    NASA Astrophysics Data System (ADS)

    Kaminskii, A. A.; Haussühl, E.; Haussühl, S.; Eichler, H. J.; Rhee, H.

    2006-02-01

    We report on the first observation of (3)-nonlinear lasing effects - efficient high-order stimulated Raman scattering (SRS) in LiH2C6H4SO3 . H2O and -Ca(HCOO)2 single crys- tals. We classify these materials as promising SRS-media for Raman laser converters with many large frequency shifts.

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

    PubMed Central

    Caballero, Armando; García-Dorado, Aurora

    2013-01-01

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

  6. Characterization of 12 silent alleles of the human butyrylcholinesterase (BCHE) gene.

    PubMed Central

    Primo-Parmo, S. L.; Bartels, C. F.; Wiersema, B.; van der Spek, A. F.; Innis, J. W.; La Du, B. N.

    1996-01-01

    The silent phenotype of human butyrylcholinesterase (BChE), present in most human populations in frequencies of approximately 1/100,000, is characterized by the complete absence of BChE activity or by activity <10% of the average levels of the usual phenotype. Heterogeneity in this phenotype has been well established at the phenotypic level, but only a few silent BCHE alleles have been characterized at the DNA level. Twelve silent alleles of the human butyrylcholinesterase gene (BCHE) have been identified in 17 apparently unrelated patients who were selected by their increased sensitivity to the muscle relaxant succinylcholine. All of these alleles are characterized by single nucleotide substitutions or deletions leading to distinct changes in the structure of the BChE enzyme molecule. Nine of the nucleotide substitutions result in the replacement of single amino acid residues. Three of these variants, BCHE*33C, BCHE*198G, and BCHE*201T, produce normal amounts of immunoreactive but enzymatically inactive BChE protein in the plasma. The other six amino acid substitutions, encoded by BCHE*37S, BCHE*125F, BCHE*170E, BCHE*471R, and BCHE*518L, seem to cause reduced expression of BChE protein, and their role in determining the silent phenotype was confirmed by expression in cell culture. The other four silent alleles, BCHE*271STOP, BCHE*500STOP, BCHE*FS6, and BCHE*I2E3-8G, encode BChES truncated at their C-terminus because of premature stop codons caused by nucleotide substitutions, a frame shift, or altered splicing. The large number of different silent BCHE alleles found within a relatively small number of patients shows that the heterogeneity of the silent BChE phenotype is high. The characterization of silent BChE variants will be useful in the study of the structure/function relationship for this and other closely related enzymes. Images Figure 2 PMID:8554068

  7. Allelic loss in colorectal carcinoma

    SciTech Connect

    Kern, S.E.; Fearon, E.R.; Tersmette, K.W.F.; Enterline, J.P.; Vogelstein, B.; Hamilton, S.R. ); Leppert, M.; Nakamura, Yusuke; White, R. )

    1989-06-02

    Clinical and pathological associations with molecular genetic alterations were studied in colorectal carcinomas from 83 patients. Fractional allelic loss, a measure of allelic deletions throughout the genome, and allelic deletions of specific chromosomal arms (the short arm of 17 and long arm of 18) each provided independent prognostic information by multivariate analysis when considered individually with Dukes' classification. Distant metastasis was significantly associated with high fractional allelic loss and with deletions of 17p and 18q. Mutations of ras proto-oncogenes and deletions of 5q had no prognostic importance. Statistically significant associations were also found between allelic losses and a family history of cancer, left-sided tumor location, and absence of extracellular tumor mucin. Allelic deletion analysis thus identified subsets of colorectal carcinoma with increased predilection for distant metastasis and cancer-related death. Further studies may define a subset of genetic alterations that can be used clinically to help assess prognosis.

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

    PubMed

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

    2005-12-01

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

  9. Estimating Relatedness in the Presence of Null Alleles.

    PubMed

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

    2016-01-01

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

  10. Anomalous phase shifts in drift wave fluctuations

    NASA Astrophysics Data System (ADS)

    Diallo, Ahmed; Skiff, Fred

    2003-10-01

    Ion phase space density fluctuation measurements are performed in a linearly magnetized device using Laser Induced Fluorescence(LIF). An ICP source produces an 8cm diameter plasma column that drifts in a cylindrical vessel whose diameter and length are 40 cm and 3 m, respectively. These experiments are performed using a CW singly ionized Argon plasma that is immersed in a 1kG magnetic field along the axis of the cylinder. A density of the order of 10^9 cm-3 is obtained under a regulated neutral background pressure of 2.× 10-4 torr. The electron and ion temperature are respectively 2 eV and 0.1 eV. LIF is carried out by pumping the Ar II metastable (3d^1)^2G_9/2, using a CW tunable laser centered at 611.6653 nm scanned over 6 GHz, to metastable (4p^1)F_7/2, and then detecting the 460nm photons emitted from its transition to (4s^1)^2F_5/2. This collection is made possible using two low f-umber periscopes that are directed to PMTs. Here we present measurements of the complex two-point correlation function < f(v_i_allel),z_1,ω)f(v_i_allel,z_2,ω)> as a function of the spatial separation of two LIF detection systems Δ d = z_2-z_1, the ion parallel velocity v_i_allel and the frequency ω. Preliminary results show ion particle velocity dependent phase shifts at the drift wave frequency.

  11. On the correlation between bond-length change and vibrational frequency shift in hydrogen-bonded complexes: a computational study of Y...HCl dimers (Y = N2, CO, BF).

    PubMed

    McDowell, Sean A C; Buckingham, A David

    2005-11-01

    The H-Cl bond-length change and the harmonic vibrational frequency shift of the H-Cl stretch on formation of the linear isoelectronic Y...H-Cl complexes (Y = N(2), CO, BF) have been determined by ab initio computations at different levels of theory. These shifts are in agreement with predictions from a model based on perturbation theory and involving the first and second derivatives of the interaction energy with respect to displacement of the H-Cl bond length from its equilibrium value in the isolated monomer. At the highest level of theory, blue shifts were obtained for BF...HCl and CO...HCl, while red shifts were obtained for FB...HCl, OC...HCl, and N(2)...HCl. These vibrational characteristics are rationalized by considering the balance between the interaction energy derivatives obtained from the perturbative model. The widely believed correlation between the bond-length change and the sign of the frequency shift obtained on complexation is discussed and found to be unreliable.

  12. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots

    PubMed Central

    Baker, Christopher L.; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M.; Paigen, Kenneth

    2015-01-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9 +/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. PMID:26368021

  13. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    PubMed

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. PMID:26368021

  14. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    PubMed

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape.

  15. Tri-allelic pattern at the TPOX locus: a familial study.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; Paskulin, Giorgio Adriano; Alvarez, Luís; Amorim, António; Batista Dos Santos, Sidney Emanuel; Alho, Clarice Sampaio

    2014-02-10

    Alleles at the TPOX STR locus have 6-14 different numbers of a four-nucleotide (AATG) repeat motif arranged in tandem. Although tri-allelic genotypes are generally rare, the TPOX tri-allelic pattern has a higher frequency, varying widely among populations. Despite this, there are few accurate reports to disclose the nature of the TPOX third allele. In this work we present data obtained from 45 individuals belonging to the same pedigree, in which there are cases of tri-allelic TPOX genotypes. The subjects were apparently healthy with a normal biological development. We noticed six tri-allelic cases in this family, and all of them were women. Karyotype analysis showed no occurrence of partial 2p trisomy. All the tri-allelic cases had the genotype 8-10-11, probably due to three copies of the TPOX STR sequence in all cells (Type 2 tri-allelic pattern). Based on previous data we assumed the allele 10 as the TPOX third allele. The pedigree analyses show evidences that the TPOX extra-allele was the allele10, it is placed far from the main TPOX locus, and that there is a potential linkage of the TPOX extra-allele-10 with Xq. This was the first study that included a large pedigree analysis in order to understand the nature TPOX tri-allelic pattern.

  16. Allelic Richness following Population Founding Events – A Stochastic Modeling Framework Incorporating Gene Flow and Genetic Drift

    PubMed Central

    Greenbaum, Gili; Templeton, Alan R.; Zarmi, Yair; Bar-David, Shirli

    2014-01-01

    Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing m