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

    PubMed

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

    2010-05-11

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

  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. PMID:25728575

  4. Broadband optical serrodyne frequency shifting.

    PubMed

    Johnson, D M S; Hogan, J M; Chiow, S-w; Kasevich, M A

    2010-03-01

    We demonstrate serrodyne frequency shifting of light from 200 MHz to 1.2 GHz with an efficiency of better than 60%. The frequency shift is imparted by an electro-optic phase modulator driven by a high-frequency high-fidelity sawtooth waveform that is passively generated by a commercially available nonlinear transmission line. We also implement a push-pull configuration using two serrodyne-driven phase modulators, allowing for continuous tuning between -1.6 GHz and +1.6 GHz. Compared with competing technologies, this technique is simple and robust, and it offers the largest available tuning range in this frequency band. PMID:20195339

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

    PubMed Central

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

    2014-01-01

    The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency. PMID:24752137

  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

    2014-01-01

    The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency. PMID:24752137

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

    PubMed

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

    2016-05-01

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

  8. 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

  9. 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.

  10. Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies

    PubMed Central

    Ackermann, Marit; Beyer, Andreas

    2012-01-01

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

  11. 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.

  12. 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

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

    PubMed

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

    2015-01-01

    Pernambuco is one of the 27 federal units of Brazil, ranking seventh in the number of inhabitants. We examined the allele frequencies of 13 short tandem repeat loci (CFS1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, vWA, and TPOX), the minimum recommended by the Federal Bureau of Investigation and commonly used in forensic genetics laboratories in Brazil, in a sample of 609 unrelated individuals from all geographic regions of Pernambuco. The allele frequencies ranged from 5 to 47.2%. No significant differences for any loci analyzed were observed compared with other publications in other various regions of Brazil. Most of the markers observed were in Hardy-Weinberg equilibrium. The occurrence of the allele 47.2 (locus FGA) and alleles 35.1 and 39 (locus D21S11), also described in a single study of the Brazilian population, was observed. The other forensic parameters analyzed (matching probability, power of discrimination, polymorphic information content, paternity exclusion, complement factor I, observed heterozygosity, expected heterozygosity) indicated that the studied markers are very informative for human forensic identification purposes in the Pernambuco population. PMID:25966202

  14. High throughput automated allele frequency estimation by pyrosequencing.

    PubMed

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

    2008-01-01

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

  15. High Throughput Automated Allele Frequency Estimation by Pyrosequencing

    PubMed Central

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

    2008-01-01

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

  16. Fast spatial ancestry via flexible allele frequency surfaces

    PubMed Central

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

    2014-01-01

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

  17. Frequency shifts of high frequency p-modes

    NASA Technical Reports Server (NTRS)

    Jain, Rekha

    1995-01-01

    Frequency shifts of high frequency p-modes during the solar cycle are calculated for a non-magnetic polytrope convection zone model. An isothermal chromospheric atmosphere threaded by a uniform horizontal magnetic field is correlated to this model. The relevant observations of such frequency changes are discussed. The calculated simultaneous changes in the field strength and chromospheric temperature result in the frequency shifts that are similar to those of the observations.

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

    PubMed

    Gao, Yulin; Wu, Kongming; Gould, Fred

    2009-08-01

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

  19. Data for phase angle shift with frequency.

    PubMed

    Paul, T; Banerjee, D; Kargupta, K

    2016-06-01

    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

  20. 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

  1. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

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

    2009-04-01

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

  2. 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

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

    PubMed Central

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

    2016-01-01

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

  4. Damage detection using frequency shift path

    NASA Astrophysics Data System (ADS)

    Wang, Longqi; Lie, Seng Tjhen; Zhang, Yao

    2016-01-01

    This paper introduces a novel concept called FREquency Shift (FRESH) path to describe the dynamic behavior of structures with auxiliary mass. FRESH path combines the effects of frequency shifting and amplitude changing into one space curve, providing a tool for analyzing structure health status and properties. A damage index called FRESH curvature is then proposed to detect local stiffness reduction. FRESH curvature can be easily adapted for a particular problem since the sensitivity of the index can be adjusted by changing auxiliary mass or excitation power. An algorithm is proposed to adjust automatically the contribution from frequency and amplitude in the method. Because the extraction of FRESH path requires highly accurate frequency and amplitude estimators; therefore, a procedure based on discrete time Fourier transform is introduced to extract accurate frequency and amplitude with the time complexity of O (n log n), which is verified by simulation signals. Moreover, numerical examples with different damage sizes, severities and damping are presented to demonstrate the validity of the proposed damage index. In addition, applications of FRESH path on two steel beams with different damages are presented and the results show that the proposed method is valid and computational efficient.

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

    ERIC Educational Resources Information Center

    Nussbaum, Francis, Jr.

    1988-01-01

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

  6. 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. PMID:26393729

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

    PubMed

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

    1995-07-01

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

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

    PubMed Central

    2010-01-01

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

  9. Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers.

    PubMed

    Bradshaw, H D; Schemske, Douglas W

    2003-11-13

    The role of major mutations in adaptive evolution has been debated for more than a century. The classical view is that adaptive mutations are nearly infinite in number with infinitesimally small phenotypic effect, but recent theory suggests otherwise. To provide empirical estimates of the magnitude of adaptive mutations in wild plants, we conducted field studies to determine the adaptive value of alternative alleles at a single locus, YELLOW UPPER (YUP). YUP controls the presence or absence of yellow carotenoid pigments in the petals of pink-flowered Mimulus lewisii, which is pollinated by bumblebees, and its red-flowered sister species M. cardinalis, which is pollinated by hummingbirds. We bred near-isogenic lines (NILs) in which the YUP allele from each species was substituted into the other. M. cardinalis NILs with the M. lewisii YUP allele had dark pink flowers and received 74-fold more bee visits than the wild type, whereas M. lewisii NILs with the M. cardinalis yup allele had yellow-orange flowers and received 68-fold more hummingbird visits than the wild type. These results indicate that an adaptive shift in pollinator preference may be initiated by a single major mutation. PMID:14614505

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

    SciTech Connect

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

    1994-09-01

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

  11. Frequency shifting with a solid-state switching capacitor

    NASA Technical Reports Server (NTRS)

    Mattauch, R. J.; Viola, T. J., Jr.

    1973-01-01

    Frequency shifting, commonly used in electronic signal processing, is applied in tuning, automatic frequency control, antenna element switching, phase shifting, etc. Frequency shifting can be accomplished economically and reliably with simple circuit comprising conventional resistor and solid-state switching device which can be equivalent to two capacitors, depending on switching state.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  13. A frequency-shifted bispectrum for rolling element bearing diagnosis

    NASA Astrophysics Data System (ADS)

    Dong, Guangming; Chen, Jin; Zhao, Fagang

    2015-03-01

    This paper is in the field of vibration based fault diagnosis for rolling element bearings, where one major issue is the ability to detect faults as early as possible. Bispectrum analysis has been applied in bearing diagnosis. In this paper, a frequency-shifted bispectrum is studied for bearing diagnosis. It is found that the frequency-shifted bispectrum is more suitable for analyzing amplitude modulated and frequency modulated signals than the bispectrum, when choosing the carrier frequency as the specific frequency shift value. For bearing vibration signals with amplitude modulation characteristics, in which the carrier frequencies are structural resonant frequencies, one of the structural resonances can be chosen as the specific frequency shift value for the frequency-shifted bispectrum analysis. To increase diagnostic ability of the frequency-shifted bispectrum for bearing faults, firstly, the frequency resolution is increased in the frequency-shifted bispectrum analysis through band pass filtering and frequency zooming; secondly, integration of the frequency-shifted bispectrum along one frequency variable is used to produce a one-dimensional spectral representation. Numerical simulation and experimental results show the feasibility of the proposed method for qualitatively and quantitatively diagnosing bearing faults.

  14. 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)

  15. 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

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

    PubMed

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

    2016-06-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2016-05-01

    Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high-throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty-ADU), which complicates the calculation of important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high-throughput sequencing data in the form of read counts. We bridge the gap from data collection (using restriction enzyme based techniques [e.g. GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's performance and to help guide the collection of empirical data. We also provide an implementation of our model in the R package polyfreqs and demonstrate its use with two example analyses that investigate (i) levels of expected and observed heterozygosity and (ii) model adequacy. Our simulations show that the number of individuals sampled from a population has a greater impact on estimation error than sequencing coverage. The example analyses also show that our model and software can be used to make inferences beyond the estimation of allele frequencies for autopolyploids by providing assessments of model adequacy and estimates of heterozygosity. PMID:26607217

  19. 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

  20. 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

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

    PubMed Central

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

    1985-01-01

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

  2. 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.

  3. Laser frequency stabilization and shifting by using modulation transfer spectroscopy

    NASA Astrophysics Data System (ADS)

    Cheng, Bing; Wang, Zhao-Ying; Wu, Bin; Xu, Ao-Peng; Wang, Qi-Yu; Xu, Yun-Fei; Lin, Qiang

    2014-10-01

    The stabilizing and shifting of laser frequency are very important for the interaction between the laser and atoms. The modulation transfer spectroscopy for the 87Rb atom with D2 line transition F = 2 → F' = 3 is used for stabilizing and shifting the frequency of the external cavity grating feedback diode laser. The resonant phase modulator with electro—optical effect is used to generate frequency sideband to lock the laser frequency. In the locking scheme, circularly polarized pump- and probe-beams are used. By optimizing the temperature of the vapor, the pump- and probe-beam intensity, the laser linewidth of 280 kHz is obtained. Furthermore, the magnetic field generated by a solenoid is added into the system. Therefore the system can achieve the frequency locking at any point in a range of hundreds of megahertz frequency shifting with very low power loss.

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

    PubMed

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

    2008-09-01

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

  5. 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

  6. 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.

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  9. Shift of the shadow boundary in high frequency scattering

    NASA Astrophysics Data System (ADS)

    Zworski, Maciej

    1991-02-01

    The microlocal theory of diffraction is used to establish the conjecture of Keller and Rubinow relating the shift of the shadow boundary in high frequency scattering to the directional curvatures of a strictly convex obstacle.

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

    PubMed Central

    2010-01-01

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

  11. 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

  12. 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.

  13. Edge technique for measurement of laser frequency shifts including the Doppler shift

    NASA Technical Reports Server (NTRS)

    Korb, Larry (Inventor)

    1991-01-01

    A method is disclosed for determining the frequency shift in a laser system by transmitting an outgoing laser beam. An incoming laser beam having a frequency shift is received. A first signal is acquired by transmitting a portion of the incoming laser beam to an energy monitor detector. A second signal is acquired by transmitting a portion of the incoming laser beam through an edge filter to an edge detector, which derives a first normalized signal which is proportional to the transmission of the edge filter at the frequency of the incoming laser beam. A second normalized signal is acquired which is proportional to the transmission of the edge filter at the frequency of the outgoing laser beam. The frequency shift is determined by processing the first and second normalized signals.

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

    PubMed

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

    2016-01-01

    Evolutionary and cultural history can affect the genetic characteristics of a population and influences the frequency of different variants at a particular genetic marker (allele frequency). These characteristics directly influence the strength of forensic DNA evidence and make the availability of suitable allele frequency information for every discrete country or jurisdiction highly relevant. Population sub-structure within Indonesia has not been well characterised but should be expected given the complex geographical, linguistic and cultural architecture of the Indonesian population. Here we use forensic short tandem repeat (STR) markers to identify a number of distinct genetic subpopulations within Indonesia and calculate appropriate population sub-structure correction factors. This data represents the most comprehensive investigation of population sub-structure within Indonesia to date using these markers. The results demonstrate that significant sub-structure is present within the Indonesian population and must be accounted for using island specific allele frequencies and corresponding sub-structure correction factors in the calculation of forensic DNA match statistics. PMID:26517173

  15. Frequency shifts of ionospheric nfH resonances.

    NASA Technical Reports Server (NTRS)

    Benson, R. F.

    1972-01-01

    New observational data are analyzed to interpret mechanisms responsible for large positive frequency shifts of Alouette II plasma resonances (corresponding to the first and second electron cyclotron harmonics) relative to frequency values expected from model magnetic field calculations. It is shown that the frequency shifts can be consistently explained by plasma wave dispersion effects combined with sounder transmitter frequency deviation (positive offset of several kilohertz) and a negative offset (several tens of gammas) in the geomagnetic field relative to the model field. Plasma wave dispersion effects are observed on the electron cyclotron second harmonic resonance when it is in the vicinity of the resonance observed near the upper hybrid frequency. The observations suggest that an oblique echo model may be required for interpretation of the electron cyclotron second harmonic resonance.

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

    PubMed

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

    2016-03-01

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

  17. 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.

  18. Enhanced two-frequency phase-shifting method.

    PubMed

    Hyun, Jae-Sang; Zhang, Song

    2016-06-01

    One of the major challenges of employing a two-frequency (or two-wavelength) phase-shifting algorithm for absolute three-dimensional shape measurement is its sensitivity to noise. Therefore, three- or more-frequency phase-shifting algorithms are often used in lieu of a two-frequency phase-shifting algorithm for applications where the noise is severe. This paper proposes a method to use geometric constraints of digital fringe projection system to substantially reduce the noise impact by allowing the use of more than one period of equivalent phase map for temporal phase unwrapping. Experiments successfully verified the enhanced performance of the proposed method without increasing the number of patterns. PMID:27411193

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

    PubMed

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

    2016-01-01

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

  20. 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

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

    PubMed Central

    Rujirojindakul, Pairaya; Chongsuvivatwong, Virasakdi; Limprasert, Pornprot

    2015-01-01

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

  2. Nonlinear Pressure Shifts of ^133Cs Hyperfine Frequencies

    NASA Astrophysics Data System (ADS)

    Gong, Fei; Jau, Yuan-Yu; Happer, William

    2007-06-01

    The hyperfine (microwave) magnetic-resonance frequencies of optically pumped alkali-metal atoms in buffer-gas have long been used in compact, portable frequency standards. The buffer gas is needed to slow down the diffusion of optically pumped atoms to the cell walls, and to eliminate Doppler broadening of the microwave resonances. Van der Waals molecules, consisting of an alkali-metal atom loosely bound to a buffer gas atom, can form in such vapor cells. The molecules strongly affect the spin relaxation of alkali metal atoms in Ar, Kr and Xe gases at pressures of a few Torr. The hyperfine-shift interaction, δAI.S, the modification a nearby buffer-gas atom makes to the Fermi contact interaction between S and the nuclear spin I of the alkali atom, can contribute to the width of the microwave resonance line, and it is responsible for the pressure shifts of the hyperfine resonance frequencies that are so important for clocks. Our experiments show that Van der Waals molecules also modify the effects of the hyperfine-shift interaction δAI.S. For Ar pressures of a few tens of Torr or less, the shift of the microwave resonance frequency of ^133Cs in Ar buffer gas is not linear in the buffer gas pressure. This occurs because the contribution to the pressure shift from molecules is suppressed when τδA I > h.

  3. Frequency shift of hyperfine transitions due to blackbody radiation

    SciTech Connect

    Angstmann, E. J.; Dzuba, V. A.; Flambaum, V. V.

    2006-08-15

    We have performed calculations of the size of the frequency shift induced by a static electric field on the clock transition frequencies of the hyperfine splitting in Yb{sup +}, Rb, Cs, Ba{sup +}, and Hg{sup +}. The calculations are used to find the frequency shifts due to blackbody radiation which are needed for accurate frequency measurements and improvements of the limits on variation of the fine-structure constant {alpha}. Our result for Cs [{delta}{nu}/E{sup 2}=-2.26(2)x10{sup -10}Hz/(V/m){sup 2}] is in good agreement with early measurements and ab initio calculations. We present arguments against recent claims that the actual value might be smaller. The difference ({approx}10%) is due to the contribution of the continuum spectrum in the sum over intermediate states.

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

    PubMed

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

    2014-06-01

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

  5. 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

  6. 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.

  7. 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

  8. Nonlinear Pressure Shifts of ^133Cs Hyperfine Frequencies

    NASA Astrophysics Data System (ADS)

    Gong, Fei; Jau, Yuan-Yu; Happer, William

    2008-05-01

    The hyperfine (microwave) magnetic-resonance frequencies of optically pumped alkali-metal atoms in buffer-gas have long been used in compact, portable frequency standards. Van der Waals molecules, consisting of an alkali-metal atom loosely bound to a buffer gas atom, can form in such vapor cells. The molecules strongly affect the spin relaxation of alkali metal atoms in Ar, Kr and Xe gases at pressures of a few Torr, where the collisionally limited lifetime of the molecules is comparable to the characteristic period of the spin-rotation interaction between the rotational angular momentum N of the molecule and the electron spin S of the alkali-metal atom. The hyperfine-shift interaction, the modification a nearby buffer-gas atom makes to the Fermi contact interaction between S and the nuclear spin I of the alkali atom, can contribute to the width of the microwave resonance line, and it is responsible for the pressure shifts of the hyperfine resonance frequencies that are so important for clocks. Major improvements have been done to the apparatus and the process of data taking since last time. The experimental results show that Van der Waals molecules also modify the effects of the hyperfine-shift interaction. For Ar or Kr pressures of a few tens of Torr or less, the shift of the microwave resonance frequency of Cs is not linear in the buffer gas pressure.

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

    PubMed Central

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

    2008-01-01

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

  10. 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...

  11. 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

  12. 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

  13. 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

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

    PubMed

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

    2009-01-01

    We demonstrate the use of Semantic Web technology to integrate the ALFRED allele frequency database and the Starpath pathway resource. The linking of population-specific genotype data with cancer-related pathway data is potentially useful given the growing interest in personalized medicine and the exploitation of pathway knowledge for cancer drug discovery. We model our data using the Web Ontology Language (OWL), drawing upon ideas from existing standard formats BioPAX for pathway data and PML for allele frequency data. We store our data within an Oracle database, using Oracle Semantic Technologies. We then query the data using Oracle's rule-based inference engine and SPARQL-like RDF query language. The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions. Among the possibilities is the ability to identify genetic variants which are associated with cancer pathways and whose frequency varies significantly between ethnic groups. This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine. It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies. PMID:19458791

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

    PubMed Central

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

    2009-01-01

    We demonstrate the use of Semantic Web technology to integrate the ALFRED allele frequency database and the Starpath pathway resource. The linking of population-specific genotype data with cancer-related pathway data is potentially useful given the growing interest in personalized medicine and the exploitation of pathway knowledge for cancer drug discovery. We model our data using the Web Ontology Language (OWL), drawing upon ideas from existing standard formats BioPAX for pathway data and PML for allele frequency data. We store our data within an Oracle database, using Oracle Semantic Technologies. We then query the data using Oracle’s rule-based inference engine and SPARQL-like RDF query language. The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions. Among the possibilities is the ability to identify genetic variants which are associated with cancer pathways and whose frequency varies significantly between ethnic groups. This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine. It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies. PMID:19458791

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

    PubMed Central

    Der, Ricky; Plotkin, Joshua B.

    2014-01-01

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

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

    PubMed

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

    2008-11-01

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

  18. Matched Pair of AOTFs with Net Zero Frequency-shift

    NASA Astrophysics Data System (ADS)

    Ward, J. D.; Pannell, C. N.

    Acousto-Optic Tunable Filters are used in many applications where their fast agile tuning characteristics can be used to advantage. In addition, their ability to conserve spatial-coherence is useful in specialist applications, for example with single-mode optical fibres. Since, as is common with most AO devices, AOTFs generally use a travelling acoustic wave, the diffracted beam is frequency-shifted by an amount that is essentially equal to the RF drive frequency. This can be inconvenient, especially in applications where the AOTF is deployed in a multi pass configuration such as a recirculating-ring or laser-cavity. Often in such configurations a second AO device (usually similar to the first) is deployed in such a way so as to compensate for the frequency-shift. For an AO device using the isotropic AO interaction this is relatively straightforward since there is a symmetry about the device and interaction. However, an AOTF uses the anisotropic interaction which is asymmetric, and this is frequently further complicated by the inclusion of pointing-stability compensation. This compensation is usually achieved by cutting an appropriate angled wedge on the back (exit) face of the AOTF. We describe and characterise a pair of matched AOTFs operating in opposite quadrants of the "K-space" diagram that when combined have true reciprocity and give a net zero frequency shift whilst maintaining excellent pointing-stability. Any minor deviations in manufacture are self-compensated making these components ideal for use within a single-mode fibre network, or laser cavity. Furthermore, small controlled frequency-shifts (up to about 10 kHz) may be introduced with little or no detriment to the alignment of the system, or indeed the throughput when pigtailed between two single mode optical fibres.

  19. 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

  20. Global Doppler frequency shift detection with near-resonant interferometry

    NASA Astrophysics Data System (ADS)

    Landolt, Andrin; Roesgen, Thomas

    2009-10-01

    The recent development in measuring 2D Doppler shift distributions for flow velocimetry using the dispersive properties of atomic line filters is presented. On the basis of velocity field measurements on a subsonic jet flow and a tip vortex flow in a medium-sized wind tunnel, the technique was assessed. Atomic line filters near a resonant transition combine imaging capabilities with a sharp frequency cutoff and an associated region of strong anomalous dispersion. While conventional Doppler global velocimetry relies on the absorption of the filter to convert frequency shifts to intensity variations, near-resonant interferometry uses its dispersion to detect frequency shifts as phase changes in an interference pattern. In the present setup, an iodine vapor cell in an imaging Michelson interferometer is used. With the illuminating laser frequency tuned near a resonant transition, the cell’s dispersion converts the frequency content of the field of view into a distortion of the carrier-fringe pattern recorded at the image plane of the interferometer. The phase distribution in the fringe images is reconstructed by filtering the individual images with a 2D Gabor filter pair tuned to the spatial frequencies of the basic carrier-fringe pattern. The post-processing is concluded with subsequent phase-unwrapping and subtraction of the carrier reference fringe phase. The method and the setup were demonstrated and calibrated experimentally on a rotating disc. The capability of the technique to operate in a real experimental environment was validated in a free subsonic jet and a tip vortex flow behind a wing section in a medium-sized wind tunnel facility. The measurements were found to be in generally good agreement with the theoretically predicted system characteristics and the reference measurements. As with other Doppler global techniques, the stability of the pulsed laser system and the secondary scattering in the test volume were identified as the main error sources.

  1. Cold Collision Frequency Shift in Two-Dimensional Atomic Hydrogen

    SciTech Connect

    Ahokas, J.; Jaervinen, J.; Vasiliev, S.

    2007-01-26

    We report a measurement of the cold collision frequency shift in atomic hydrogen gas adsorbed on the surface of superfluid {sup 4}He at T(less-or-similar sign)90 mK. Using two-photon electron and nuclear magnetic resonance in 4.6 T field we separate the resonance line shifts due to the dipolar and exchange interactions, both proportional to surface density {sigma}. We find the clock shift {delta}{nu}{sub c}=-1.0(1)x10{sup -7} Hz cm{sup -2}x{sigma}, which is about 100 times smaller than the value predicted by the mean field theory and known scattering lengths in the three-dimensional case.

  2. Cyclotron Mode Frequency Shifts in Multi-Species Ion Plasmas

    NASA Astrophysics Data System (ADS)

    Affolter, Matthew

    2014-10-01

    Plasmas exhibit a variety of cyclotron modes, which are used in a broad range of devices to manipulate and diagnose charged particles. Here we discuss cyclotron modes in trapped plasmas with a single sign of charge. Collective effects and electric fields shift these cyclotron mode frequencies away from the ``bare'' cyclotron frequencies Ωs ≡ qB /ms c for each species s. These electric fields may arise from applied trap potentials, from space charge including collective effects, and from image charge in the trap walls. We will describe a new laser-thermal cyclotron spectroscopy technique, applied to well-diagnosed pure ion plasmas. This technique enables detailed observations of cos (mθ) surface cyclotron modes with m = 0 , 1, and 2 in near rigid-rotor multi-species ion plasmas. For each species s, we observe cyclotron mode frequency shifts which are dependent on the plasma density through the E × B rotation frequency, and on the charge concentration of species s, in close agreement with recent theory. This includes the novel m = 0 radial ``breathing'' mode, which generates no external electric field except at the plasma ends. These cyclotron frequencies can be used to determine the plasma E × B rotation frequency and the species charge concentrations, in close agreement with our laser diagnostics. Here, this plasma characterization permits a determination of the ``bare'' cyclotron frequencies to an accuracy of 2 parts in 104. These new results give a physical basis for the ``space charge'' and ``amplitude'' calibration equations of cyclotron mass spectroscopy, widely used in molecular chemistry and biology. Also, at high temperatures there is preliminary evidence that radially-standing electrostatic Bernstein waves couple to the surface cyclotron modes, producing new resonant frequencies. Supported by NSF/DOE Partnership grants PHY-0903877 and DE-SC0002451.

  3. 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.

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

    PubMed Central

    Waples, R. S.

    1989-01-01

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

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

    PubMed

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

    2015-10-21

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

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

    PubMed

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

    2007-03-01

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

  8. 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

  9. 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

  10. 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

  11. Using tensor light shifts to measure and cancel a cell's quadrupolar frequency shift

    NASA Astrophysics Data System (ADS)

    Peck, S. K.; Lane, N.; Ang, D. G.; Hunter, L. R.

    2016-02-01

    We have developed a 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 θCs -alkene=1.4 mrad . This value is about 37 times larger than the twist angle observed in 131Xe, 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 canceling the cell-induced quadrupole shift we have extended our cells' effective spin-relaxation times by as much as a factor of 2. This cancellation improves magnetometer sensitivity in highly anisotropic cells and could reduce systematic uncertainties in some precision measurements.

  12. 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.

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

    PubMed Central

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

    2014-01-01

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

  14. 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

  15. 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

  16. 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.

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

    PubMed

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

    2011-01-01

    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. PMID:21970368

  18. 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

  19. 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.

  20. 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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2012-08-01

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

  3. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2016-07-01

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

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

    PubMed

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

    2002-06-01

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

  7. 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.

  8. 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)].

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

    PubMed

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

    2014-03-01

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

  10. 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

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

    PubMed

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

    2006-06-01

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

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

    PubMed Central

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

    2014-01-01

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

  14. 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…

  15. Operating principle, saturable loss, and self-frequency shift in Kerr-shift mode-locked lasers

    NASA Astrophysics Data System (ADS)

    Herrmann, J.; Müller, M.

    1995-01-01

    The operating principle of a recently demonstrated new Kerr-induced ultrashort-pulse-generation technique called Kerr-shift mode locking is analyzed. It is shown that in Kerr-shift mode-locked lasers an intensity-dependent red shift of the central laser frequency is caused by the combined action of the self-phase modulation that is due to the nonlinear index laser host medium and the Lorentzian-shaped profile of the homogeneously broadened gain. The introduction of a long-pass wavelength filter (knife-edge) transforms this intensity-dependent frequency shift into fast self-amplitude modulation (SAM), which is accompanied by an additional linear red shift of the central laser frequency. The SAM parameter and the linear frequency shift are calculated and compared with the experimental results.

  16. 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

  17. Ionospheric nf sub H resonances: Frequency shifts versus plasma conditions

    NASA Technical Reports Server (NTRS)

    Benson, R. F.

    1971-01-01

    The Alouette 2 resonances observed near the harmonics of the electron cyclotron frequency f sub H reveal frequency shifts (relative to the n(f sub H) values derived from model field calculations) which can be interpreted in terms of plasma wave dispersion effects. These effects are observed on the 2(f sub H) resonance when it is near the resonance observed close to the upper hybrid frequency f sub T. The observations suggest that an oblique echo model may be required to give a proper interpretation of the 2(f sub H) resonance. Cyclotron damping can be ignored only when the angle between the propagation vector and the direction perpendicular to the earth's magnetic field B is less than a few degrees for the 2(f sub H) wave, and less than a few tenths of a degree for the n(f sub H) waves with n 2. The negative offset of the absolute value of B inferred from the plasma resonance observations is consistent with expectations based on recent OGO 3 and OGO 5 rubidium magnetometer observations at higher altitudes in the equatorial regions.

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

    PubMed Central

    Field, Wesley; Hershberg, Ruth

    2015-01-01

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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  1. 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.

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

    PubMed Central

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

    2010-01-01

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

  3. 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

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

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

    2003-01-01

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

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

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

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

  7. 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

  8. 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).

  9. Frequency shifts in NIST Cs primary frequency standards due to transverse rf field gradients

    NASA Astrophysics Data System (ADS)

    Ashby, Neil; Barlow, Stephan; Heavner, Thomas; Jefferts, Steven

    2015-03-01

    A single-particle Green's function (propagator) is introduced to study the deflection of laser-cooled cesium atoms in an atomic fountain due to microwave magnetic field gradients in the Ramsey TE011 cavity. The deflection results in a state-dependent loss of atoms at apertures in the physics package, resulting in a frequency bias. A model accounting only for motion in one dimension transverse to the symmetry axis of the fountain is discussed in detail and then generalized to two transverse dimensions. Results for fractional frequency shifts due to transverse field gradients are computed for NIST-F1 and NIST-F2 cesium fountains. The shifts are found to be negligible except in cases of higher rf power applied to the cavities.

  10. 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.

  11. 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

  12. 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.

  13. Coding for slow frequency hopped differential phase shift keying

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Gulliver, T. A.; Mason, Lloyd J.; Blake, Ian F.

    The performance of Reed-Solomon (RS) error-correcting codes with slow frequency hopped (SFH) differential phase shift keying (DPSK) signaling is analyzed and evaluated under worst-case partial-band noise (PBN) and worst-case multitone (MT) jamming. The results of a study of the bit error rate (BER) performance of this coded system are presented. A representative set of the performance curves is shown. SFH is used because the differential signaling required only the phase of the previous received signal as a reference. Using DPSK eliminates the need to establish a phase reference for the hop, as with coherent signaling. From the results it is clear that the number of codeword symbols per hop must be small in order for the RS code to provide protection against jamming. Otherwise, no improvement over uncoded DPSK is gained. Lowering the symbols per hop can be achieved either by reducing the number of bits per hop, or interleaving the RS codewords to a depth determined by the hop length and RS code parameters.

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

    PubMed

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

    2015-07-01

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

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

    PubMed

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

    2016-02-13

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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2007-12-01

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

  4. 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.

  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. PMID:26249527

  6. A Protein Concentration Measurement System Using a Flexural Plate-Wave Frequency-Shift Readout Technique

    PubMed Central

    Wang, Chua-Chin; Sung, Tzu-Chiao; Hsu, Chia-Hao; Tsai, Yue-Da; Chen, Yun-Chi; Lee, Ming-Chih; Huang, I-Yu

    2013-01-01

    A protein concentration measurement system with two-port flexural plate-wave (FPW) biosensors using a frequency-shift readout technique is presented in this paper. The proposed frequency-shift readout method employs a peak detecting scheme to measure the amount of resonant frequency shift. The proposed system is composed of a linear frequency generator, a pair of peak detectors, two registers, and a subtractor. The frequency sweep range of the linear frequency generator is limited to 2 MHz to 10 MHz according to the characteristics of the FPW biosensors. The proposed frequency-shift readout circuit is carried out on silicon using a standard 0.18 μm CMOS technology. The sensitivity of the peak detectors is measured to be 10 mV. The power consumption of the proposed protein concentration measurement system is 48 mW given a 0.1 MHz system clock. PMID:23344375

  7. 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

  8. Photonic radio frequency phase-shift amplification by radio frequency interferometry.

    PubMed

    Ayun, Moshe Ben; Schwarzbaum, Arye; Rosenberg, Seva; Pinchas, Monika; Sternklar, Shmuel

    2015-11-01

    We present a new technique for radio frequency (RF) phase-shift amplification based on RF interferometry and demonstrate it in an optical system. A striking feature of this amplifier is that the input phase noise is not amplified together with the input phase signal, so the phase sensitivity improves with higher phase amplification. We also predict that in the case of correlated amplitude noise, the sensitivity is not affected by the amplitude noise. With 600 MHz of modulated light and a phase amplification of 100, we demonstrate a phase resolution of 0.2 mrad, giving a distance resolution of 8 μm. We postulate that nanometric distance resolution can be achieved with sub-gigahertz modulation. PMID:26512469

  9. Precise laser frequency scanning using frequency-synthesized optical frequency sidebands - Application to isotope shifts and hyperfine structure of mercury

    NASA Technical Reports Server (NTRS)

    Rayman, M. D.; Aminoff, C. G.; Hall, J. L.

    1989-01-01

    Based on an efficient broadband electrooptic modulator producing RF optical sidebands locked to a stable cavity, a tunable dye laser can be scanned under computer control with frequency-synthesizer precision. Cavity drift is suppressed in software by using a strong feature in the spectrum for stabilization. Mercury isotope shifts are measured with a reproducibility of about 50 kHz. This accuracy of about 1/300 of the linewidth illustrates the power of the technique. Derived hyperfine-structure constants are compared with previous atomic-beam data.

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

    PubMed

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

    2014-04-01

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

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

    PubMed Central

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

    2013-01-01

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

  12. Microwave lensing frequency shift of the PHARAO laser-cooled microgravity atomic clock

    NASA Astrophysics Data System (ADS)

    Peterman, Phillip; Gibble, Kurt; Laurent, Phillipe; Salomon, Christophe

    2016-04-01

    We evaluate the microwave lensing frequency shift of the microgravity laser-cooled caesium clock PHARAO. We find microwave lensing frequency shifts of δν/ν  =  11  ×  10-17 to 13  ×  10-17, larger than the shift of typical fountain clocks. The shift has a weak dependence on PHARAO parameters, including the atomic temperature, size of the atomic cloud, detection laser intensities, and the launch velocity. We also find the lensing frequency shift to be insensitive to selection and detection spatial inhomogeneities and the expected low-frequency vibrations. We conservatively assign a nominal microwave lensing frequency uncertainty of  ±4  ×  10-17.

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

    PubMed Central

    2012-01-01

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

  14. Brillouin frequency shift estimation in BOTDA via subpixel processing

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

    Sánchez-Molina, I; Calvet, R

    2000-01-01

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

  16. 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.

  17. 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.

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

    PubMed

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

    1997-08-01

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

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

    PubMed

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

    2013-07-01

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

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

    PubMed

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

    2006-07-01

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

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

    PubMed Central

    2013-01-01

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

  2. 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.

  3. Semilinear coherent optical oscillator with frequency shifted feedback.

    PubMed

    Rebhi, Riadh; Mathey, Pierre; Jauslin, Hans Rudolf; Odoulov, Serguey

    2007-12-10

    It is shown that the saw-tooth variation of the cavity length in a photorefractive semilinear coherent oscillator can suppress the instability in the frequency domain and prevent a bifurcation in the oscillation spectrum. To achieve such a suppression the frequency of the cavity length modulation should be chosen appropriately. It depends on the photorefractive crystal parameters (electrooptic properties, photoconductivity, dimensions) and on the experimental conditions (pump intensity ratio, orientation of the pump and oscillation waves with respect to the crystallographic axes, polarization of the pump waves, etc. ). It depends also strongly on a possible misalignment of the two pump waves. On the other hand, within a certain range of the experimental parameters the mirror vibration may lead to a further frequency splitting in the already existing two-mode oscillation spectrum. PMID:19551007

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

    PubMed

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

    2006-06-01

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

  5. Asymmetric polarization-based frequency shifting interferometer for microelectronics

    NASA Astrophysics Data System (ADS)

    Lee, Seung Hyun; Kim, Min Young

    2014-05-01

    Frequency Scanning Interferometry(FSI) generally results in superior optical performance comparing with other 3-dimensional measuring methods as its hardware structure is fixed in operation and only the light frequency is scanned in a specific spectral band without vertical scanning of the target surface or the objective lens. However, it still suffers from optical noise due to polarization characteristic of target surfaces and relatively long processing time due to the number of images acquired in frequency scanning phase. First, a Polarization-based Frequency Scanning Interferometry(PFSI) is proposed for optical noise robustness. It consists of tunable laser for light source, λ/4 plate in front of reference mirror, λ /4 plate in front of target object, polarizing beam splitter, polarizer in front of image sensor, polarizer in front of the fiber coupled light source, λ/2 plate between PBS and polarizer of the light source. Using the proposed system, we can solve the problem of fringe image with low contrast by using polarization technique. Also, we can control light distribution of object beam and reference beam. Second the signal processing acceleration method is proposed for PFSI, based on parallel processing architecture, which consists of parallel processing hardware and software such as Graphic Processing Unit(GPU) and Compute Unified Device Architecture(CUDA). Finally, the proposed system is evaluated in terms of accuracy and processing speed through a series of experiment and the obtained results show the effectiveness of the proposed system and method.

  6. Electric Quadrupole Shift Cancellation in Single-Ion Optical Frequency Standards

    SciTech Connect

    Dube, P.; Madej, A.A.; Bernard, J.E.; Marmet, L.; Boulanger, J.-S.; Cundy, S.

    2005-07-15

    The electric quadrupole shift is presently the most significant source of uncertainty on the systematic shifts for several single-ion optical frequency standards. We present a simple method for canceling this shift based on measurements of the Zeeman spectrum of the clock transition. This method is easy to implement and yields very high cancellation levels. A fractional uncertainty of 5x10{sup -18} for the canceled quadrupole shift is estimated for a measurement of the absolute frequency of the 5s {sup 2}S{sub 1/2}-4d {sup 2}D{sub 5/2} clock transition of {sup 88}Sr{sup +}.

  7. Development of high-precision high-frequency phase-shifting circuit

    NASA Astrophysics Data System (ADS)

    Ye, Shuliang; Song, Jiaying; Zhang, Baowu; Qiu, Jian

    2010-08-01

    Phase-locked frequency multiplying technology is utilized to amplify 10MHz signal to 640MHz. Pulse inhibition method is then exploited to make high-frequency signal have a phase shift of 2π. 20MHz signal with 2π / 32 phase shift is output after 5 times flip frequency division. In order to optimize electromagnetic compatibility, signal integrity and power integrity of a high-speed circuit, system simulation is performed using HyperLynx, a specially EDA simulation software. A whole printed circuit board (PCB) was made under the guide of optimized simulation results. Phase-shift experiments show that the output of high-frequency phase-shifting circuit system is two-way signals with a frequency of 20.0001 MHz with 1.8ns time difference, i.e. two signals with 12.96°phase difference are obtained.

  8. Comment on ``Ramsey spectroscopy, matter-wave interferometry, and the microwave-lensing frequency shift''

    NASA Astrophysics Data System (ADS)

    Jefferts, S. R.; Heavner, T. P.; Barlow, S. E.; Ashby, N.

    2015-06-01

    The theory of a frequency shift in primary frequency standards due to microwave lensing in Gibble [Phys. Rev. A 90, 015601 (2014), 10.1103/PhysRevA.90.015601] contains a number of problems that undermine its validity. Furthermore, because the exposition of the theory has multiple errors and because the shift has never been experimentally observed, we believe this possible shift should not be included as a correction to primary frequency standards contributing to international atomic time. Although the theory may describe the basic mechanisms of a possible frequency shift, we argue it is not possible to use this theory to make reliable corrections to a primary frequency standard at the δ f /f ˜10-16 level.

  9. Simulation of a programmed frequency shift near extraction from the Fermilab Booster

    SciTech Connect

    Lucas, P.; Kerns, Q.

    1987-03-01

    The longitudinal phase space program ESME has been used to simulate the effects of a linear shift in RF frequency away from that appropriate for the accelerator guide field. This shift takes place in the new Booster low level RF and is used to position the particle bunches in Main Ring buckets in a reproducible fashion. Shifts in frequency are found to generate synchrotron oscillations; however, the simulations show that these can be reduced to acceptable levels by introduction of jumps in RF phase preceding the programmed frequency changes. Lowering the RF voltage near extraction from the Booster, a desirable operational feature, has also been investigated.

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

    PubMed

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

    2013-01-01

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

  11. 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

  12. 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

  13. 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.

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

    PubMed Central

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

    2013-01-01

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

  15. Effects of frequency shifts and visual gender information on vowel category judgments

    NASA Astrophysics Data System (ADS)

    Glidden, Catherine; Assmann, Peter F.

    2003-10-01

    Visual morphing techniques were used together with a high-quality vocoder to study the audiovisual contribution of talker gender to the identification of frequency-shifted vowels. A nine-step continuum ranging from ``bit'' to ``bet'' was constructed from natural recorded syllables spoken by an adult female talker. Upward and downward frequency shifts in spectral envelope (scale factors of 0.85 and 1.0) were applied in combination with shifts in fundamental frequency, F0 (scale factors of 0.5 and 1.0). Downward frequency shifts generally resulted in malelike voices whereas upward shifts were perceived as femalelike. Two separate nine-step visual continua from ``bit'' to ``bet'' were also constructed, one from a male face and the other a female face, each producing the end-point words. Each step along the two visual continua was paired with the corresponding step on the acoustic continuum, creating natural audiovisual utterances. Category boundary shifts were found for both acoustic cues (F0 and formant frequency shifts) and visual cues (visual gender). The visual gender effect was larger when acoustic and visual information were matched appropriately. These results suggest that visual information provided by the speech signal plays an important supplemental role in talker normalization.

  16. Applying Echoes Mean Frequency Shift for Attenuation Imaging in Tissue

    NASA Astrophysics Data System (ADS)

    Litniewski, J.; Klimonda, Z.; Nowicki, A.

    The purpose of this study was to develop the attenuation parametric imaging technique and to apply it for in vivo characterization of tissue. Local attenuation coefficient was determined by evaluating the frequency downshift that encounters the amplitude spectrum of the interrogating ultrasonic pulse during propagation in the absorbing tissue. Operation and accuracy of the processing methods were verified by assessing the size-independent region of interest (ROI) for attenuation determination and calculating the attenuation coefficient distribution for experimentally recorded tissue-phantom scattered waveforms. The Siemens Antares scanner equipped with Ultrasound Research Interface unit allowing for direct radiofrequency (RF) signals recording was used for B-scan imaging of the tissue- mimicking phantom in vitro and liver in vivo. RF data were processed to determine attenuation coefficient along the B-scan lines. Also, the preliminary studies of backscattered signals from skin recorded using a skin scanner were performed to calculate parametric-attenuation images.

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

    PubMed Central

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

    2012-01-01

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

  18. 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

  19. 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

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

    PubMed

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

    2005-06-01

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

  1. Multi-channel multi-carrier generation using multi-wavelength frequency shifting recirculating loop.

    PubMed

    Li, Xinying; Yu, Jianjun; Dong, Ze; Zhang, Junwen; Shao, Yufeng; Chi, Nan

    2012-09-24

    We propose and experimentally demonstrate a novel scheme to generate optical frequency-locked multi-channel multi-carriers (MCMC), using a recirculating frequency shifter (RFS) loop based on multi-wavelength frequency shifting single side band (MWFS-SSB) modulation. In this scheme, optical subcarriers with multiple wavelengths can be generated each round. Furthermore, the generated MCMC are frequency- and phase-locked within each channel, and therefore can be effectively used for WDM superchannel. Dual-wavelength frequency shifting SSB modulation is carried out with dual-wavelength optical seed source in our experimental demonstration. Using this scheme, we successfully generate dual-channel multi-carriers, and one channel has 28 subcarriers while the other has 29 ones with 25-GHz subcarrier spacing. We also experimentally demonstrate that this kind of source can be used to carry 50-Gb/s optical polarization-division-multiplexing quadrature phase shift keying (PDM-QPSK) signal. PMID:23037333

  2. 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.

  3. 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

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

    PubMed

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

    2015-06-01

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

  5. 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.

  6. 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

  7. 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.

    2016-06-01

    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 (GONG) data. The result of this comparison is consistent with a sunspot contribution to the observed frequency shifts of roughly 30%, with the remaining 70% 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.

  8. 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.

  9. 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

  10. 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

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

    PubMed Central

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

    1999-01-01

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

  12. 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

  13. Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths

    NASA Astrophysics Data System (ADS)

    Gu, Quanli; Trindle, Carl; Knee, J. L.

    2012-09-01

    Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

  14. 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

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

    PubMed

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

    2010-10-01

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

  16. 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.

  17. 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.

  18. Effects of frequency-shifted auditory feedback on voice F0 contours in syllables

    NASA Astrophysics Data System (ADS)

    Donath, Thomas M.; Natke, Ulrich; Kalveram, Karl Th.

    2002-01-01

    Previous studies have shown that, during continuous vocalization, voice fundamental frequency (voice F0) is modified by frequency-shifted auditory feedback. In this study, the effects of frequency-shifted auditory feedback on voice F0 contours were determined for the first two syllables of the nonsense word [tatatas]. Results show that voice F0 is auditorily controlled with a long latency and responses are not interrupted by the onset and offset of phonation itself. Furthermore, after-effects were found in voice F0 in trials after the termination of the frequency shift, which indicates that the response persists for several seconds. It is argued that the purpose of the auditory-vocal system is not to control voice F0 precisely within single syllables, but rather on a supra-segmental level in the context of prosody.

  19. Collision-induced frequency shifts in bright matter-wave solitons and soliton molecules

    NASA Astrophysics Data System (ADS)

    Martin, A. D.

    2016-02-01

    A recent experiment has detected collision-induced frequency shifts in bright matter-wave solitons [J. H. V. Nguyen et al., Nat. Phys. 10, 918 (2014), 10.1038/nphys3135]. Using a particle model, we derive the frequency shift for two solitons in a harmonic trap, and compare it to the recent experimental results and reported theoretical approximation. We find regimes where the frequency shift is much smaller than previously predicted, and propose experiments to test these findings. We also predict that reducing the experimental trap frequency will reveal soliton molecules or soliton bound states in a cold-atom system. The bound-state dynamics are found to be both highly phase dependent and sensitive to the residual 3D nature of the experiment.

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

    PubMed

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

    2004-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  2. 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.

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

    PubMed Central

    Faure, Eric

    2008-01-01

    Background In Europe, the north-south downhill cline frequency of the chemokine receptor CCR5 allele with a 32-bp deletion (CCR5-Δ32) raises interesting questions for evolutionary biologists. We had suggested first that, in the past, the European colonizers, principally Romans, might have been instrumental of a progressively decrease of the frequencies southwards. Indeed, statistical analyses suggested strong negative correlations between the allele frequency and historical parameters including the colonization dates by Mediterranean civilisations. The gene flows from colonizers to native populations were extremely low but colonizers are responsible of the spread of several diseases suggesting that the dissemination of parasites in naive populations could have induced a breakdown rupture of the fragile pathocenosis changing the balance among diseases. The new equilibrium state has been reached through a negative selection of the null allele. Results Most of the human diseases are zoonoses and cat might have been instrumental in the decrease of the allele frequency, because its diffusion through Europe was a gradual process, due principally to Romans; and that several cat zoonoses could be transmitted to man. The possible implication of a feline lentivirus (FIV) which does not use CCR5 as co-receptor is discussed. This virus can infect primate cells in vitro and induces clinical signs in macaque. Moreover, most of the historical regions with null or low frequency of CCR5-Δ32 allele coincide with historical range of the wild felid species which harbor species-specific FIVs. Conclusion We proposed the hypothesis that the actual European CCR5 allelic frequencies are the result of a negative selection due to a disease spreading. A cat zoonosis, could be the most plausible hypothesis. Future studies could provide if CCR5 can play an antimicrobial role in FIV pathogenesis. Moreover, studies of ancient DNA could provide more evidences regarding the implications of

  4. 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

  5. Local time distribution of the SSC-associated HF-Doppler frequency shifts

    NASA Technical Reports Server (NTRS)

    Kikuchi, T.; Sugiuchi, H.; Ishimine, T.

    1985-01-01

    The HF-Doppler frequency shift observed at the storm's sudden commencement is composed of a frequency increase (+) and decrease (-), and classified into four types, SCF(+ -), SCF(- +), SCF(+) and SCF(-). Since the latter two types are special cases of the former two types, two different kinds of electrical field exist in the F region and cause the ExB drift motion of plasma. HUANG (1976) interpreted the frequency increase of SCF(+ -) as due to the westward induction electric field proportional to delta H/ delta t and the succeeding frequency decrease due to the eastward conduction electric field which produces ionospheric currents responsible for the magnetic increase on the ground. In spite of his success in interpreting the SCF(+ -), some other interpretations are needed for the explanation of the whole set of SCF's, particularly SCF(- +). Local time distributions of the SCF's are derived from 41 SCF's which are observed on the HF standard signal (JJY) as received in Okinawa (path length =1600 km) and Kokubunji (60 km). It is shown that the SCF(+ -) appears mainly during the day, whereas the SCF(- +) is observed during the night. The results indicate that the preliminary frequency shift (+) of SCF(+ -) and (-) of SCF(- +) is caused by a westward electric field in the dayside hemisphere, while by an eastward electric field in the nightside hemisphere. The main frequency shift (-) of SCF(+ -) and (+) of SCF(- +) is caused by the reversed electric field. Consequently, the preliminary frequency shift is caused by the dusk-to-dawn electric field, while the main frequency shift by the dawn-to-dusk electric field.

  6. 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.

  7. Dark resonances in the field of frequency-shifted feedback laser radiation

    NASA Astrophysics Data System (ADS)

    Romanenko, V. I.; Romanenko, A. V.; Yatsenko, L. P.; Kazakov, G. A.; Litvinov, A. N.; Matisov, B. G.; Rozhdestvensky, Yu V.

    2010-11-01

    We present a theory of dark resonances in fluorescence of a three-level atom gas interacting with a polychromatic field of a frequency-shifted feedback laser. We show that conditions for the resonance observation are optimal when the phase relations between the laser spectral components provide generation of a light pulse train. We study analytically the field broadening and the light shift of the resonances.

  8. 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

  9. 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.

  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. Wideband signal upconversion and phase shifting based on a frequency tunable optoelectronic oscillator

    NASA Astrophysics Data System (ADS)

    Liu, Shifeng; Zhu, Dan; Pan, Shilong

    2014-03-01

    A wideband signal upconversion and phase shifting scheme based on a frequency tunable optoelectronic oscillator (OEO) are proposed and demonstrated. The OEO performs simultaneously tunable high-quality local oscillator (LO) signal generation, wideband frequency upconversion, and phase shifting within the whole 2π range. With the generated LO tuning from 9.549 to 11.655 GHz, wideband square signals are successfully upconverted to the X band. The phase of the upconverted signal is tuned from 0 to 360 deg. The phase noise of the oscillation signal is about -104 dBc/Hz at 10 kHz offset with or without the injected baseband signal.

  12. Phase-shift effect in capacitively coupled plasmas with two radio frequency or very high frequency sources

    SciTech Connect

    Xu Xiang; Zhao Shuxia; Zhang Yuru; Wang Younian

    2010-08-15

    A two-dimensional fluid model was built to study the argon discharge in a capacitively coupled plasma reactor and the full set of Maxwell equations is included in the model to understand the electromagnetic effect in the capacitive discharge. Two electrical sources are applied to the top and bottom electrodes in our simulations and the phase-shift effect is focused on. We distinguish the difference of the phase-shift effect on the plasma uniformity in the traditional radio frequency discharge and in the very high frequency discharge where the standing wave effect dominates. It is found that in the discharges with frequency 13.56 MHz, the control of phase difference can less the influence of the electrostatic edge effect, and it gets the best radial uniformity of plasma density at the phase difference {pi}. But in the very high frequency discharges, the standing wave effect plays an important role. The standing wave effect can be counteracted at the phase difference 0, and be enhanced at the phase difference {pi}. The standing wave effect and the edge effect are balanced at some phase-shift value between 0 and {pi}, which is determined by discharge parameters.

  13. 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.

  14. A frequency shift maximum frequency follower Doppler demodulator with amplitude correction.

    PubMed

    Follett, D H

    1981-11-01

    A commonly used maximum-frequency follower Doppler demodulator uses a variable-frequency voltage controlled filter that requires two good quality multipliers and can be difficult to set up and stabilise. An alternative presented here has the advantage of cheapness, easy setting-up and amplitude independence over about 25 dB giving the potential for quantitative as well as qualitative results. A switching modulator is first used to convert the Doppler spectrum into a pair of sidebands disposed about the modulating frequency. The modulation frequency is continually adjusted so that the lower sideband edge, representing the highest Doppler frequency, just passes the skirt of a low pass filter. The filter output, after rectification and smoothing, provides drive to the voltage controlled oscillator (VCO) generating the modulation frequency and also forms the flow signal output. The fixed low pass filter results in a stable feed-back loop in which high loop gain can be used so that linearity depends mostly on the VCO. The characteristic slope is independent of signal amplitude above a threshold, but increasing signal causes an increasing offset voltage. A simple signal rectifier enables this offset to be largely cancelled, giving amplitude independence. PMID:6765877

  15. Frequency-multiplying microwave photonic phase shifter for independent multichannel phase shifting.

    PubMed

    Zhang, Yamei; Pan, Shilong

    2016-03-15

    A frequency-multiplying microwave photonic phase shifter with independent multichannel phase shifting capability is proposed and demonstrated using an integrated polarization division multiplexing dual-parallel Mach-Zehnder modulator (PDM-DPMZM) and a polarizer. By building a proper power distribution network to drive the PDM-DPMZM, two sidebands along two orthogonal polarization directions are generated with a spacing of two or four times the frequency of the driving signal. Leading the signal to a polarizer and a photodetector, a frequency-doubled or frequency-quadrupled signal with its phase adjusted by the polarization direction of the polarizer is achieved. The magnitude of the signal remains almost unchanged when the phase is adjusted. The proposed approach features compact configuration, scalable independent phase-shift channels and wide bandwidth, which can find applications in beam forming and analog signal processing for millimeter-wave or terahertz applications. PMID:26977684

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

    PubMed Central

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

    2004-01-01

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

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

    PubMed

    Lucotte, Gérard

    2002-05-01

    The CCR5 gene encodes for the co-receptor for the major macrophage-tropics strains of human immunodeficiency virus (HIV-1), and a mutant allele of this gene (Delta 32) provide to homozygotes a strong resistance against infection by HIV. The frequency of the Delta 32 allele was investigated in 40 populations of 8842 non-infected subjects coming from Europe, the Middle-East and North Africa. A clear north-south decreasing gradient was evident for Delta 32 frequencies, with a significant correlation coefficient (r=0.83). The main frequency value of Delta 32 for Sweden, Norway, Denmark, Finland and Iceland (0.134) is significantly (chi(2)=63.818, P<0.001) highest than the Delta 32 mean value, indicating that probably the Vikings might have been instrumental in disseminating the Delta 32 allele during the eighth to the tenth centuries during historical times. Possibly variola virus has discriminated the Delta 32 carriers in Europe since the eighth century AD, explaining the high frequency of the Delta 32 allele in Europe today. PMID:12798016

  18. 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

  19. 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.

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

    PubMed

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

    1991-06-01

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

  1. 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. 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.

  3. Relaxation and frequency shifts in the ground state of Rb-85

    NASA Technical Reports Server (NTRS)

    Vanier, J.; Simard, J.-F.; Boulanger, J.-S.

    1974-01-01

    Results are presented on the relaxation and frequency shifts measured for the 0-0 transition of the ground state of Rb-85 at 3.03 GHz in various physical environments. These results include data on spin-exchange, buffer-gas, and wall interactions.

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

    PubMed

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

    2015-11-01

    Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species. PMID:25846829

  5. 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

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

    PubMed Central

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

    2003-01-01

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

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

    PubMed

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

    2012-01-01

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

  8. Phase-Shift Control of Resonant Frequencies of Magnetostatic Wave Resonators

    NASA Astrophysics Data System (ADS)

    Koike, Takuro; Nakazawa, Hiroaki

    1994-05-01

    We discuss a possible technique to control the resonant frequencies of a straight-edge magnetostatic wave (MSW) resonator without changing the external applied magnetic field and the circuit parameters of a feedback load circuit. The method is to use two additional microstrip electrodes at the edges of the resonator and two varactor diodes connected in series. Upon varying the bias voltages to the varactor diodes, the input admittance at the center electrode can be changed. Theoretical investigation reveals that very large resonant frequency shifts can be obtained by changing only the bias voltage change to the varactor diodes, which may be useful in mobile telephone applications in the gigaherz frequency range.

  9. Accurate quantification of water-macromolecule exchange induced frequency shift: effects of reference substance.

    PubMed

    Leutritz, Tobias; Hilfert, Liane; Smalla, Karl-Heinz; Speck, Oliver; Zhong, Kai

    2013-01-01

    Water-macromolecule exchange induces a bulk water frequency shift contributing to the contrast in phase imaging. For separating the effects of the water-macromolecule exchange and the macromolecule susceptibility, appropriate internal or external references are needed. In this study, two internal reference compounds, 2,2,3,3-tetradeuterio-3-trimethylsilyl-propionate (TMSP) and 1,4-dioxane, were used to study the macromolecule-dependent water frequency shift in a bovine serum albumin (BSA)-water system in detail. For TMSP, the water-macromolecule exchange shift depended on both the BSA and the reference concentration and stabilized to a value of 0.025 ppm/mM (298 K, TMSP concentrations > 30 mM). For dioxane, the dependency of the water-macromolecule exchange shift on the BSA concentration is independent of dioxane at low concentrations. The resulting shift was smaller (0.009 ppm/mM) when compared with using higher TMSP concentrations as reference. This discrepancy might be due to additional dioxane-water interactions. Measurements with an external chloroform reference in a coaxial geometry showed a shift of -0.013 ppm/mM resulting from the opposing effects of macromolecules in water exchange-induced shift and diamagnetic susceptibility shift. All these effects should be considered in the interpretation of tissue phase contrast. From the experimental data, the equilibrium binding constant between BSA and TMSP has been quantified to be K(d) = 1.3 ± 0.4, and the estimated number of interaction sites for BSA is 12.7 ± 2.6. PMID:22374834

  10. 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. PMID:27015482

  11. Differential Stark shift measurement of clock states of Yb+ using an optical frequency comb

    NASA Astrophysics Data System (ADS)

    Quraishi*, Qudsia; Hayes, David; Hucul, David; Matsukevich, Dzmitry; Debnath, Shantanu; Clark, Susan; Monroe, Chris

    2011-03-01

    Quantum information processing with trapped ions has traditionally involved state preparation, manipulation (eg. quantum gates) and detection using CW lasers. Quantum gates implemented with ions typically involve optical Raman transitions between two atomic levels. An optical frequency comb, emitted by a pulsed laser, is an excellent tool for bridging atomic frequency differences. Previously, we demonstrated quantum gates and separately, ultrafast spin manipulation, using pulsed lasers [1,2]. Unlike the CW case, employing pulsed lasers has the marked advantage of both low spontaneous emission and low AC Stark shifts, because the high powers available from pulsed lasers allow for larger detunings from optical resonance. Here, we show both experimentally and theoretically the scaling of the differential Stark shift with detuning (6 THz to 20 THz) of the Raman fields, achieving values of 10-3 of the Rabi frequency.

  12. Analysis of frequency shifting in seismic signals using Gabor-Wigner transform

    NASA Astrophysics Data System (ADS)

    Kumar, Roshan; Sumathi, P.; Kumar, Ashok

    2015-12-01

    A hybrid time-frequency method known as Gabor-Wigner transform (GWT) is introduced in this paper for examining the time-frequency patterns of earthquake damaged buildings. GWT is developed by combining the Gabor transform (GT) and Wigner-Ville distribution (WVD). GT and WVD have been used separately on synthetic and recorded earthquake data to identify frequency shifting due to earthquake damages, but GT is prone to windowing effect and WVD involves ambiguity function. Hence to obtain better clarity and to remove the cross terms (frequency interference), GT and WVD are judiciously combined and the resultant GWT used to identify frequency shifting. Synthetic seismic response of an instrumented building and real-time earthquake data recorded on the building were investigated using GWT. It is found that GWT offers good accuracy for even slow variations in frequency, good time-frequency resolution, and localized response. Presented results confirm the efficacy of GWT when compared with GT and WVD used separately. Simulation results were quantified by the Renyi entropy measures and GWT shown to be an adequate technique in identifying localized response for structural damage detection.

  13. 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

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

    PubMed Central

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

    2015-01-01

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

  15. 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

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

    PubMed

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

    2012-01-01

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

  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. Orthogonal modulation system with Manchester-coded payload and frequency-shift keying label

    NASA Astrophysics Data System (ADS)

    Yang, Liu; Luo, Fengguang

    2016-04-01

    We propose an orthogonal modulation scheme with 40 Gb/s Manchester-coded (MC) payload and 2.5 Gb/s frequency-shift keying (FSK) label. The high-speed FSK label is generated by an FSK modulator, which consists of two modulators, while MC payload is generated by an intensity modulator. Simulation results show that the available extinction ratio of FSK and amplitude-shift keying with MC payload can improve from 5.1 to 11.2 dB, compared with the traditional not-return-to-zero payload. The receiver sensitivities of both MC payload and FSK label show a remarkable improvement.

  19. 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

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

    PubMed Central

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

    2015-01-01

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

  1. Frequency domain phase retrieval of simultaneous multi-wavelength phase-shifting interferometry

    NASA Astrophysics Data System (ADS)

    Yin, Zhenxing; Zhong, Liyun; Xu, Xiaofei; Zhang, Wangping; Tian, Jindong; Lu, Xiaoxu

    2016-05-01

    In simultaneous multi-wavelength phase-shifting interferometry, we propose a novel frequency domain phase retrieval (FDPR) algorithm. First, using only a one-time phase-shifting operation, a sequence of simultaneous multi-wavelength phase-shifting interferograms (SPSMWIs) are captured by a monochrome charge-coupled device. Second, by performing a Fourier transform for each pixel of SPSMWIs, the wrapped phases of each wavelength can be retrieved from the complex amplitude located in the spectral peak of each wavelength. Finally, the phase of the synthetic wavelength can be obtained by the subtraction between the wrapped phases of a single wavelength. In this study, the principle and the application condition of the proposed approach are discussed. Both the simulation and the experimental result demonstrate the simple and convenient performance of the proposed FDPR approach.

  2. 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.

  3. 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

  4. Theory and measurement of the soliton self-frequency shift and efficiency in optical microcavities.

    PubMed

    Yi, Xu; Yang, Qi-Fan; Yang, Ki Youl; Vahala, Kerry

    2016-08-01

    Dissipative Kerr cavity solitons experience a so-called self-frequency shift (SFS) as a result of Raman interactions. The frequency shift has been observed in several microcavity systems. The Raman process has also been shown numerically to influence the soliton pumping efficiency. Here, a perturbed Lagrangian approach is used to derive simple analytical expressions for the SFS and the soliton efficiency. The predicted dependences of these quantities on soliton pulse width are compared with measurements in a high-Q silica microcavity. The Raman time constant in silica is also inferred. Analytical expressions for the Raman SFS and soliton efficiency greatly simplify the prediction of soliton behavior over a wide range of microcavity platforms. PMID:27472583

  5. 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

  6. 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.

  7. Position and frequency shifts induced by massive modes of the gravitational wave background in alternative gravity

    SciTech Connect

    Bellucci, Stefano; Capozziello, Salvatore; De Laurentis, Mariafelicia; Faraoni, Valerio

    2009-05-15

    Alternative theories of gravity predict the presence of massive scalar, vector, and tensor gravitational wave modes in addition to the standard massless spin 2 graviton of general relativity. The deflection and frequency shift effects on light from distant sources propagating through a stochastic background of gravitational waves, containing such modes, differ from their counterparts in general relativity. Such effects are considered as a possible signature for alternative gravity in attempts to detect deviations from Einstein's gravity by astrophysical means.

  8. 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.

  9. Spin-mediated dissipation and frequency shifts of a cantilever at milliKelvin temperatures

    NASA Astrophysics Data System (ADS)

    den Haan, A. M. J.; Wagenaar, J. J. T.; de Voogd, J. M.; Koning, G.; Oosterkamp, T. H.

    2015-12-01

    We measure the dissipation and frequency shift of a magnetically coupled cantilever in the vicinity of a silicon chip, down to 25 mK. The dissipation and frequency shift originates from the interaction with the unpaired electrons, associated with the dangling bonds in the native oxide layer of the silicon, which form a two-dimensional system of electron spins. We approach the sample with a 3.43 μ m -diameter magnetic particle attached to an ultrasoft cantilever and measure the frequency shift and quality factor as a function of temperature and the distance. Using a recent theoretical analysis [J. M. de Voogd et al., arXiv:1508.07972] of the dynamics of a system consisting of a spin and a magnetic resonator, we are able to fit the data and extract the relaxation time T1=0.39 ±0.08 ms and spin density σ =0.14 ±0.01 spins per nm 2. Our analysis shows that at temperatures ≤500 mK magnetic dissipation is an important source of noncontact friction.

  10. 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}.

  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. 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

  13. 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.

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

    PubMed

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

    2012-01-01

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

  15. 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

  16. 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).

  17. Predicting substrate resonance mode frequency shifts using conductive, through-substrate vias

    NASA Astrophysics Data System (ADS)

    Murray, Conal E.; Abraham, D. W.

    2016-02-01

    Through-substrate-vias (TSVs) provide conduction paths to allow for three-dimensional integration of microelectronic structures. It is also known that metallic TSVs can be used to suppress resonance modes within dielectric substrates by altering the propagation of electromagnetic waves. Numerical analyses of transmission through substrates containing metallic TSVs revealed that although resonance modes of the composite structure are shifted to higher frequencies, these frequencies are not solely dictated by the TSV periodicity. Simulations show that hybrid modes are formed through a convolution of the original substrate modes and a long-wavelength mode analogous to that found in a two-dimensional photonic crystal. An analytical formula is proposed that provides a simple relation between the intrinsic substrate mode frequencies and the long-wavelength mode that scales with the ratio of TSV radius to its periodicity.

  18. 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.

  19. Frequency Shifts of Resonant Modes of the Sun due to Near-Surface Convective Scattering

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  20. 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.

  1. Manipulation of Raman-induced frequency shift by use of asymmetric self-accelerating Airy pulse.

    PubMed

    Zhang, Lifu; Zhong, Haizhe; Li, Ying; Fan, Dianyuan

    2014-09-22

    We investigate the evolution of asymmetric self-accelerating finite energy Airy pulses (FEAP) in optical fibers with emphasis on the role of Raman scattering. We show that the Raman-induced frequency shift (RIFS) of soliton initiated by an asymmetric self-accelerating FEAP depends not only on the launched peak power but also on the truncation coefficient imposed on the asymmetric self-accelerating FEAP. We find that the RIFS of asymmetric self-accelerating FEAP increases with a decrease in the truncation coefficient, while the peak power and spectrum width of the outermost red shift of the shedding soliton spectrum are almost unchanged. The time and frequency shifts of the shedding soliton are found to be sensitive to the truncation coefficient when the truncation coefficient is in the range of 0 to 0.1. These excellent features would lead to the realization of a RIFS-based tunable light source by launching self-accelerating FEAP with different truncation coefficient into an optical fiber. PMID:25321729

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

    PubMed

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

    2016-01-01

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

  3. 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

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

    PubMed

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

    2016-07-01

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

  5. Exploring the sources of p-mode frequency shifts in the CoRoT target HD 49933

    NASA Astrophysics Data System (ADS)

    Liu, Zhi-E.; Bi, Shao-Lan; Yang, Wu-Ming; Li, Tan-Da; Liu, Kang; Tian, Zhi-Jia; Ge, Zhi-Shuai; Yu, Jie

    2014-06-01

    Oscillations of the solar-like star HD 49933 have been thoroughly observed by CoRot. Two dozen frequency shifts, which are closely related to the change in magnetic activity, have been measured. To explore the effects of magnetic activity on frequency shifts, we calculate frequency shifts for the radial and l = 1 p-modes of HD 49933 with the general variational method, which evaluates the shifts using a spatial integral of the product of a kernel and some sources. The theoretical frequency shifts reproduce the observation well. The magnitudes and positions of the sources are determined according to a χ2 criterion. We predict the source that contributes to both the l = 0 and l = 1 modes is located 0.48 - 0.62 Mm below the surface of the star. In addition, based on the assumption that A0 is proportional to the change in the MgII activity index ΔiMgII, we obtain that the change in MgII index between the minimum and maximum of the cycle during the period of HD 49933 is about 0.665. The magnitude of the frequency shifts compared to the Sun already demonstrates that HD 49933 is much more active than the Sun, which is further confirmed in this paper. Furthermore, our calculation of the frequency shifts for l = 1 modes indicates the variation of turbulent velocity in the stellar convective zone may be an important source for the l = 1 shifts.

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

    PubMed

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

    2016-02-01

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

  7. Low-frequency shift dispersive Raman spectroscopy for the analysis of respirable dosage forms.

    PubMed

    Wang, Hui; Boraey, Mohammed A; Williams, Lisa; Lechuga-Ballesteros, David; Vehring, Reinhard

    2014-07-20

    A high performance Raman system equipped with a CCD (charged coupled device) sensor and recently developed optical filter technology is described. It provides high sensitivity, high resolution, and access to low-frequency vibrations enabling resolution of spectral features due to lattice vibrational modes and internal vibrational modes, greatly improving the ability to detect small changes due to variations in the three dimensional molecular arrangement, e.g., during loss of crystallinity. Applications to solid state analysis, such as solid phase identification and differentiation of glycopyrronium bromide and formoterol fumarate in pharmaceutical powders, and identification of active pharmaceutical ingredients, e.g., salmeterol xinafoate, fluticasone propionate, mometasone furoate, and salbutamol sulphate, as well as excipients, e.g., amino acids, in different formulations, are presented. For the first time, low-frequency shift Raman spectra of mannitol polymorphs were measured and used for solid phase identification. Unambiguous identification of two similar bronchodilator metered dose inhalers, Ventolin(®) HFA and Airomir(®), was accomplished. The low-frequency shift Raman signals can be used for the analysis of crystallinity of small samples (<5mg) of respiratory dosage forms in a multi-component formulation matrix containing less than 3% by weight of the component of interest. PMID:24793839

  8. 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.

  9. 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.

  10. Blackbody-radiation shift in a {sup 43}Ca{sup +} ion optical frequency standard

    SciTech Connect

    Arora, Bindiya; Safronova, M. S.; Clark, Charles W.

    2007-12-15

    Motivated by the prospect of an optical frequency standard based on {sup 43}Ca{sup +}, we calculate the blackbody-radiation (BBR) shift of the 4s{sub 1/2}-3d{sub 5/2} clock transition, which is a major component of the uncertainty budget. The calculations are based on the relativistic all-order single-double method where all single and double excitations of the Dirac-Fock wave function are included to all orders of perturbation theory. Additional calculations are conducted for the dominant contributions in order to evaluate some omitted high-order corrections and estimate the uncertainties of the final results. The BBR shift obtained for this transition is 0.38(1) Hz. The tensor polarizability of the 3d{sub 5/2} level is also calculated and its uncertainty is evaluated as well. Our results are compared with other calculations.

  11. 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.

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2003-05-01

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

  14. 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

  15. 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.

  16. 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

  17. Shift of the interference extrema of low-frequency acoustic propagations near the axis of a deep sound channel

    NASA Astrophysics Data System (ADS)

    Lee, Seongwook; Na, Jungyul; Yoo, Jae Myung; Jurng, Moon-Sub; Oh, Suntaek

    2015-07-01

    Broadband interference patterns measured from acoustic propagations near the axis of a deep sound channel are interpreted. Analyses using mode theory for the waveguide with bilinear sound speed profiles show that the increase in sound speed without gradient variation shifts the positions of intensity maxima to higher frequencies in a fixed range whereas the increase in the gradient shifts the maxima to lower frequencies. Analytic results imply that the frequency shift of intensity extrema appearing in the measurements could be explained by the increase in the sound speed gradient above the axis of the deep sound channel.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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 87Rb D1 line absorption cross sections. We then measured the absorption profile of the sample cell, from which we calculated the 87Rb number densities at different temperatures. Then we measured the frequency shifts resulted from the spin polarization of the 87Rb 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.

  19. 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

  20. 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

  1. 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

  2. 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.

  3. Double Brillouin frequency shift through circulation of odd-order Stokes signal.

    PubMed

    Shee, Yu Gang; Al-Mansoori, Mohammed Hayder; Ismail, Alyani; Hitam, Salasiah; Mahdi, Mohd Adzir

    2010-07-10

    We demonstrate a simple configuration for generating a double Brillouin frequency shift through the circulation of an odd-order Brillouin Stokes signal. It is operated based on cascaded Brillouin scattering in single-mode optical fibers that behave as the Brillouin gain media. A four-port circulator is incorporated into the setup to circulate the odd-order Brillouin Stokes signal in the fiber. It thus initiates a higher order Brillouin Stokes signal, which is double Brillouin frequency downshifted from the input signal. For the 5 km long fiber, the Brillouin pump power at 23 mW gives a clean output spectrum with 30 dB sideband suppression ratio. The output signal is 0.174 nm or approximately 21.7 GHz downshifted from the input signal. PMID:20648173

  4. Response of microchip solid-state laser to external frequency-shifted feedback and its applications

    PubMed Central

    Tan, Yidong; Zhang, Shulian; Zhang, Song; Zhang, Yongqing; Liu, Ning

    2013-01-01

    The response of the microchip solid-state Nd:YAG laser, which is subjected to external frequency-shifted feedback, is experimentally and theoretically analysed. The continuous weak response of the laser to the phase and amplitude of the feedback light is achieved by controlling the feedback power level, and this system can be used to achieve contact-free measurement of displacement, vibration, liquid evaporation and thermal expansion with nanometre accuracy in common room conditions without precise environmental control. Furthermore, a strong response, including chaotic harmonic and parametric oscillation, is observed, and the spectrum of this response, as examined by a frequency-stabilised Nd:YAG laser, indicates laser spectral linewidth broadening. PMID:24105389

  5. 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

  6. Frequency-shifted interferometry--a versatile fiber-optic sensing technique.

    PubMed

    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

  7. 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

  8. 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

  9. 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

  10. Wavelength conversion through soliton self-frequency shift in tellurite microstructured fiber with picosecond pump pulse

    NASA Astrophysics Data System (ADS)

    Bi, Wanjun; Li, Xia; Xing, Zhaojun; Zhou, Qinling; Fang, Yongzheng; Gao, Weiqing; Xiong, Liangming; Hu, Lili; Liao, Meisong

    2016-01-01

    Wavelength conversion to the wavelength range that is not covered by commercially available lasers could be accomplished through the soliton self-frequency shift (SSFS) effect. In this study, the phenomenon of SSFS pumped by a picosecond-order pulse in a tellurite microstructured fiber is investigated both theoretically and experimentally. The balance between the dispersion and the nonlinearity achieved by a 1958 nm pump laser induces a distinct SSFS effect. Attributed to the large spectral distance between the pump pulse and the fiber zero-dispersion wavelength, the SSFS is not cancelled due to energy shedding from the soliton to the dispersive wave. Details about the physical mechanisms behind this phenomenon and the variations of the wavelength shift, the conversion efficiency are revealed based on numerical simulations. Owing to the large soliton number N, the pulse width of the first split fundamental soliton is approximately 40 fs, producing a pulse compression factor of ˜38, much higher than that pumped by a femtosecond pulse. Experiments were also conducted to confirm the validity of the simulation results. By varying the pump power, a continuous soliton shift from 1990 nm to 2264 nm was generated. The generation of SSFS in tellurite microstructured fibers with picosecond pump pulse can provide a new approach for wavelength conversion in the mid-infrared range and could be useful in medical and some other areas.

  11. 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.

  12. 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

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    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.

  15. 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

    2016-04-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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

    2016-04-01

    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.

  3. 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.

  4. Sheath Effects on Electron Density Measurements in Frequency Shift Probe and their Application to Electron Temperature Measurements

    NASA Astrophysics Data System (ADS)

    Nakamura, Keiji; Zhang, Qi; Sugai, Hideo

    2009-10-01

    Technologies of plasma monitoring are important for accurate plasma control. We have developed a frequency shift probe, and the probe enables us to measure an electron density from variation of resonance frequency of the probe head similarly to the hairpin probe. A plane structure of the probe head make it possible to minimizes disturbance to the processing plasma, and the probe is applicable to a reactive polymer-deposition plasmas since the polymer has no significant effects on the resonance frequency. The electron density is usually obtained from a plasma-induced shift of the probe resonance frequency, however influences of a sheath around the probe should been considered for more precise density measurements. In this work, sheath effects on the frequency shift probe were investigated, and the frequency shift probe was applied to measure a electron temperature using the sheath effects. As the sheath thickness increased, the resonance frequency decreased, and the sheath effect is enhanced depending on probe structure. Since the sheath width is proportional to Debye length, the probe resonance frequency depends on electron density and electron temperature, suggesting that resonance frequencies obtained in two probes having different sheath dependence gives an unique solution of the density and temperature of electrons.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. An accurate 3D inspection system using heterodyne multiple frequency phase-shifting algorithm

    NASA Astrophysics Data System (ADS)

    Xiao, Zhenzhong; Chee, Oichoo; Asundi, Anand

    This paper presents an accurate 3D inspection system for industrial applications, which uses digital fringe projection technology. The system consists of two CCD cameras and a DLP projector. The mathematical model of the 3D inspection system with 10 distortion parameters for each camera is proposed. A heterodyne multiple frequency phase-shifting algorithm is employed for overcoming the unwrapping problem of phase functions and for a reliable unwrapping procedure. The redundant phase information is used to increase the accuracy of the 3D reconstruction. To demonstrate the effectiveness of our system, a standard sphere was used for testing. The verification test for the 3D inspection systems are based on the VDI standard 2634. The result shows the proposed system can be used for industrial quality inspection with high measurement precision.

  10. 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.

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

    PubMed Central

    Herruzo, Elena T

    2012-01-01

    Summary 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

  12. 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.

  13. 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.

  14. 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

  15. Probe-controlled soliton frequency shift in the regime of optical event horizon.

    PubMed

    Gu, Jie; Guo, Hairun; Wang, Shaofei; Zeng, Xianglong

    2015-08-24

    In optical analogy of the event horizon, temporal pulse collision and mutual interactions are mainly between an intense solitary wave (soliton) and a dispersive probe wave. In such a regime, here we numerically investigate the probe-controlled soliton frequency shift as well as the soliton self-compression. In particular, in the dispersion landscape with multiple zero dispersion wavelengths, bi-directional soliton spectral tunneling effects is possible. Moreover, we propose a mid-infrared soliton self-compression to the generation of few-cycle ultrashort pulses, in a bulk of quadratic nonlinear crystals in contrast to optical fibers or cubic nonlinear media, which could contribute to the community with a simple and flexible method to experimental implementations. PMID:26368200

  16. An ultraviolet laser communication system using frequency-shift keying modulation scheme

    NASA Astrophysics Data System (ADS)

    Peng, Di-yong; Shi, Jun; Peng, Guang-hui; Xiao, Sha-li; Xu, Shan-he; Wang, Shan; Liu, Feng

    2015-01-01

    A communication system based on an ultraviolet (UV) laser at 266 nm is presented to improve the communication distance. The pulse frequency-shift keying (FSK) modulation scheme is studied and improved in order to reduce the bit error rate (BER), and is put into practice on a field programmable gate array (FPGA). The mathematical models of the modulation and demodulation are established. A test platform is set up to measure the energy density and pulse response under different distances and receiver elevation angles. It is shown that the omnibearing communication can be realized, and the bit rate is limited to 12.5 Mbit/s. The BER is estimated to be less than 10-7 at distance of 300 m in line-of-sight (LOS) communication model and to be less than 10-6 at distance of 80 m in non-line-of-sight (NLOS) communication model.

  17. Error detection and correction for a multiple frequency quaternary phase shift keyed signal

    NASA Astrophysics Data System (ADS)

    Hopkins, Kevin S.

    1989-06-01

    A multiple frequency quaternary phased shift (MFQPSK) signaling system was developed and experimentally tested in a controlled environment. In order to insure that the quality of the received signal is such that information recovery is possible, error detection/correction (EDC) must be used. Various EDC coding schemes available are reviewed and their application to the MFQPSK signal system is analyzed. Hamming, Golay, Bose-Chaudhuri-Hocquenghem (BCH), Reed-Solomon (R-S) block codes as well as convolutional codes are presented and analyzed in the context of specific MFQPSK system parameters. A computer program was developed in order to compute bit error probabilities as a function of signal to noise ratio. Results demonstrate that various EDC schemes are suitable for the MFQPSK signal structure, and that significant performance improvements are possible with the use of certain error correction codes.

  18. Evaluation of systematic shifts of the 88Sr+ single-ion optical frequency standard at the 10-17 level

    NASA Astrophysics Data System (ADS)

    Dubé, Pierre; Madej, Alan A.; Zhou, Zichao; Bernard, John E.

    2013-02-01

    An ion trap of the end-cap design was built recently at the National Research Council of Canada for improved control of the 88Sr+ single-ion optical frequency standard systematic shifts. The uncertainty on the micromotion-induced shifts is smaller by more than four orders of magnitude when compared to our previous trap system and reaches a fractional frequency uncertainty of 1×10-18. To obtain this low uncertainty level, the micromotion is minimized with trim electrodes and the trap is operated at a special frequency at which there is anticorrelation between the second-order Doppler and Stark shifts. This choice of operating frequency, determined by the differential scalar polarizability of the clock transition, yields a suppression by a factor of ≈28 in the combined micromotion shifts. Like many optical frequency standards, the dominant source of uncertainty in the new trap is the blackbody radiation shift. Its uncertainty has been reduced by an order of magnitude with a recent theoretical evaluation of the differential scalar polarizability of the clock transition. The fractional blackbody shift uncertainty, estimated using a model of the blackbody field at the ion, is 2.2×10-17. The otherwise dominant electric quadrupole shift is reduced to below the 3×10-19 level with a cancellation method based on the average frequency of several pairs of Zeeman components. This method also cancels the tensor Stark shift and simplifies the description of the frequency shifts that are quantization-axis dependent. This paper provides a detailed description of the 88Sr+ optical frequency standard uncertainty evaluation and the methods used to make the standard robust against changes in the trap environment. The total fractional frequency uncertainty of the 88Sr+ ion for our current system is estimated at 2.3×10-17. We also discuss the uncertainty evaluation of a recently reported measurement of the 88Sr+ S-D clock transition made over a 2-month period by comparison with a

  19. Analysis of fluorescence decay kinetics from variable-frequency phase shift and modulation data.

    PubMed Central

    Lakowicz, J R; Laczko, G; Cherek, H; Gratton, E; Limkeman, M

    1984-01-01

    Recently it has become possible to measure fluorescence phase-shift and modulation data over a wide range of modulation frequencies. In this paper we describe the analysis of these data by the method of nonlinear least squares to determine the values of the lifetimes and fractional intensities for a mixture of exponentially decaying fluorophores. Analyzing simulated data allowed us to determine those experimental factors that are most critical for successfully resolving the emissions from mixtures of fluorophores. The most critical factors are the accuracy of the experimental data, the relative difference of the individual decay times, and the inclusion of data measured at multiple emission wavelengths. After measuring at eight widely spaced modulation frequencies, additional measurements yielded only a modest increase in resolution. In particular, the uncertainty in the parameters decreased approximately as the reciprocal of the square root of the number of modulation frequencies. Our simulations showed that with presently available precision and data for one emission bandpass, two decay times could be accurately determined if their ratio were greater than or equal to 1.4. Three exponential decays could also be resolved, but only if the range of the lifetimes were fivefold or greater. To reliably determine closely-spaced decay times, the data were measured at multiple emission wavelengths so that the fractional intensities of the components could be varied. Also, independent knowledge of any of the parameters substantially increased the accuracy with which the remaining parameters could be determined. In the subsequent paper we present experimental results that broadly confirm the predicted resolving potential of variable-frequency phase-modulation fluorometry. PMID:6498264

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

    PubMed

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

    2016-03-01

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

  1. 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.

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

    PubMed Central

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

    2015-01-01

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

  3. 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

  4. 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

    2015-01-01

    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

  5. Carbon-donated hydrogen bonding: Electrostatics, frequency shifts, directionality, and bifurcation

    NASA Astrophysics Data System (ADS)

    Compaan, Katherine; Vergenz, Robert; Schleyer, Paul Von Rague; Arreguin, Isis

    Structure, energies, electrostatics, and vibrational modes were calculated ab initio for dimethyl sulfoxide (DMSO) and its 1:1 hydrogen bonded complex with chloride ion at the MP2/6-311+G** level. The interaction energy is -71.476 kJ/mole. On average, the C bond H stretching frequencies decreased by 35 cm-1, whereas their intensities increased by a factor of 19. Methyl torsion frequencies increased by 50-80 cm-1. We review the past and present understanding of hydrogen bonding, and apply these perspectives to analyze properties of the complex. The stretching shifts conform to the established spectral criteria for hydrogen bonding. The bifurcated geometry of the complex and its electrostatic character are fully consistent with trends observed in classically defined hydrogen bonds. All of the established definitions and criteria for identifying hydrogen bonding have been challenged. By any of the most well-established criteria, the DMSO/Cl- complex is hydrogen bonded. We propose a generally applicable working definition of hydrogen bonding to clarify and unify understanding of this interaction.

  6. Frequency shifts in the anterior default mode network and the salience network in chronic pain disorder

    PubMed Central

    2013-01-01

    Background Recent functional imaging studies on chronic pain of various organic etiologies have shown significant alterations in both the spatial and the temporal dimensions of the functional connectivity of the human brain in its resting state. However, it remains unclear whether similar changes in intrinsic connectivity networks (ICNs) also occur in patients with chronic pain disorder, defined as persistent, medically unexplained pain. Methods We compared 21 patients who suffered from chronic pain disorder with 19 age- and gender-matched controls using 3T-fMRI. All neuroimaging data were analyzed using both independent component analysis (ICA) and power spectra analysis. Results In patients suffering from chronic pain disorder, the fronto-insular ‘salience’ network (FIN) and the anterior default mode network (aDMN) predominantly oscillated at higher frequencies (0.20 - 0.24 Hz), whereas no significant differences were observed in the posterior DMN (pDMN) and the sensorimotor network (SMN). Conclusions Our results indicate that chronic pain disorder may be a self-sustaining and endogenous mental process that affects temporal organization in terms of a frequency shift in the rhythmical dynamics of cortical networks associated with emotional homeostasis and introspection. PMID:23497482

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2011-11-01

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

  9. 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

  10. 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.

  11. Research on double resonance peaks and abnormal frequency shift in permeability spectra of annealed FeCoB films

    NASA Astrophysics Data System (ADS)

    Liu, Bailin; Yang, Yi; Tang, Dongming; Zhang, Baoshan; Lu, Mu; Lu, Huaixian; Shi, Yi

    2011-02-01

    A FeCoB magnetic film was prepared by a magnetron sputtering method and then was divided into several small pieces for vacuum annealing at different temperatures. The dependence of the coercivity along the hard axis on the annealing temperature reveals a degeneration of softness with the growth of grain size when the annealing temperature is above 350 °C. In permeability spectra measurements, double resonance peaks and an abnormal positive shift in the resonance peak at higher frequency with the increase in annealing temperature are observed. The existence of two peaks is attributed to the double magnetic phases (Fe and FeCo) in the films. The positive shift in the resonance peak at higher frequency has been analyzed and ascribed to the enhanced internal stray fields with the annealing temperature. This phenomenon of positive frequency-shift is very fascinating and novel, which makes the ferromagnetic films more efficient for the applications in the noise absorbing area.

  12. 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).

  13. Cardiac frequency in miners recorded during four to five work shifts.

    PubMed

    Palenciano, L; Gonzalez, V; Santullano, L A; Rodriguez, B; Montoliu, M A

    1996-01-01

    Cardiac frequency (fc) was recorded in 101 coal-face miners [mean age 32.7 (range 21-49) years, mean height 169.6 (range 150-185) cm, mean body mass 76.9 (range 54-106) kg, mean maximal cardiac frequency (fcmax) 180.2 (range 154-197) beats min-1, mean maximal oxygen uptake (VO2max) 2.93 (range 1.9-4.0) 1.min-1] with a small-size, nonintrusive fc counter, during the five (n = 76) or at least four (n = 25) work-shifts in a week. The femax and VO2max were determined during a progressive test to exhaustion on a treadmill. Overall (four to five work-shifts) mean work-time fc(fc) was 97.7 (range 74.9-122.4) beats.min-1, resting fc (fcrest) 59.1 (range 50-75) beats.min-1, work-time increase in fc (fc-fcrest) 38.5 (range 21.1-55.8) beats.min-1 and percentage of fe reserve used (fcreserve = fcmax-fcrest) 32.0 (range 18.5-50.9). Multiple regression analysis showed that fc and fc-fcrest, as dependent variables, correlated with predicted percentage of CO lung diffusion capacity, (DLCOSB%) (r = - 0.334 and r = -0.273, respectively) but not with age, fcmax, VO2max, VO2max kg-1 body mass, effort test delta oxygen uptake/delta fe or percentage of forced expiratory volume in 1 s as independent variables. The percentage of fcreserve used as dependent variable, correlated with DLCOSB (r = -0.265) and fcmax (r = -0.227) but not with any of the other variables listed. Individual differences in worktime fc are thus large and virtually unpredictable. Other physiological variables not taken in account here (i.e. sense of effort, fatigue perception) as well as psychological ones (work satisfaction, motivation) may have played a role in those differences. At peaks of effort, some subjects reached fc values within the range of femax. PMID:8781871

  14. Coarse-Frequency-Comb Multiple-Beam Interferometry: Phase Assessment Using Common Phase Shifting Procedures

    NASA Astrophysics Data System (ADS)

    Schwider, J.

    2010-04-01

    interferometry in combination with frequency comb illumination. Through the use of a set of properly selected wavelengths the resulting interference pattern will become on the one hand more and more cosine-type with increasing enhancement factors and on the other hand it will be shown how the nonlinear relationship of the intensity distribution on the phase in the multiple beam interferometer can be overcome. Typical systematic errors show a periodicity with 4-times the fringe frequency of the interference pattern. By using the averaging of the measuring results of two measurements having a phase offset of π/4 it is possible to reduce this error by at least one order of magnitude. The impact of the nonlinear intensity profile of multiple beam fringes in transmitted light can in addition be reduced through inverted intensity values in the common phase shifting equations. It will be shown that in this way repeatability values can be obtained of 1.2 A˚ peak to valley and 0.12 A˚ rms.

  15. First observation of a (1,0) mode frequency shift of an electron plasma at antiproton beam injection.

    PubMed

    Kuroda, N; Mohri, A; Torii, H A; Nagata, Y; Shibata, M

    2014-07-11

    The frequency shift of the center-of-mass oscillation, known as the (1,0) mode, of a trapped electron plasma and, furthermore, its time evolution were observed during the cooling of an injected antiproton beam for the first time. Here, antiprotons mixed with the electrons did not follow faster electron oscillations but contributed to the modification of the effective potential. The time evolution of the plasma temperature, deduced from the frequency shift of the excited (3,0) mode, suggested that there was an abnormal energy deposition of the antiproton beam in the electron plasma before thermalization. PMID:25062195

  16. Positive frequency shifts observed upon adsorbing micron-sized solid objects to a quartz crystal microbalance from the liquid phase.

    PubMed

    Pomorska, Agata; Shchukin, Dmitry; Hammond, Richard; Cooper, Matthew A; Grundmeier, Guido; Johannsmann, Diethelm

    2010-03-15

    By specifically binding derivatized colloidal particles and physisorbing nonderivatized particles to the surface of a quartz crystal microbalance (QCM), we have observed positive shifts of frequency, Deltaf, in contrast to the negative frequency shifts typically found in adsorption experiments. Evidently, the Sauerbrey relation does not apply to this situation. A comparison of frequencies shifts and bandwidths on different overtones reveals a coupled resonance: at low overtones, Deltaf is negative, whereas it is positive at high overtones, with maximal resonance bandwidth observed at the crossover point. As predicted by the Dybwad model, the spheres bound to the surface form resonating systems on their own. A composite resonator is formed, consisting of a large crystal with resonance frequency omega and the adsorbed spheres with resonance frequency omega(S). In the case in which the resonance frequency of the small spheres (firmly attached to crystal), omega(S), is higher than the resonance frequency of the crystal, omega, Deltaf of the composite system is negative (leading to the Sauerbrey limit). In the opposite limit (that is, in the case of large adsorbed particles bound to the sensor surface via a sufficiently weak bridge) Deltaf is positive. Such a behavior is known from sphere-plate contacts in the dry state. Finite element calculation demonstrates that this phenomena is also plausible in liquid phase media, with Deltaf critically dependent on the strength of the sphere-plate contact. Operated in this mode, the QCM most likely probes the contact strength, rather than the mass of the particle. PMID:20166672

  17. 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.

  18. Radius dependent shift in surface plasmon frequency in large metallic nanospheres: Theory and experiment

    SciTech Connect

    Jacak, W.; Jacak, J.; Gonczarek, R.; Jacak, L.; Krasnyj, J.; Chepok, A.; Hu, D. Z.; Schaadt, D.

    2010-06-15

    Theoretical description of oscillations of electron liquid in large metallic nanospheres (with radius of few tens of nanometer) is formulated within random-phase-approximation semiclassical scheme in jellium model with retardation included via Lorentz friction. Spectrum of plasmons is determined including both surface and volume type excitations. It is demonstrated that only surface plasmons of dipole type can be excited by homogeneous dynamical electric field. The Lorentz friction due to irradiation of electromagnetic wave by plasmon oscillations is analyzed with respect to the sphere dimension. The resulting shift in resonance frequency turns out to be strongly sensitive to the sphere radius. The form of electromagnetic (e-m) response of the system of metallic nanospheres embedded in the dielectric medium is found. The theoretical predictions are verified by a measurement of extinction of light due to plasmon excitations in nanosphere colloidal water solutions, for Au and Ag metallic components with radius from 10 to 75 nm. Theoretical predictions and experiments clearly agree in the positions of surface plasmon resonances and in an emergence of the first volume plasmon resonance in the e-m response of the system for limiting big nanosphere radii, when dipole approximation is not exact.

  19. 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.

  20. Dependence of Brillouin frequency shift on water absorption ratio in polymer optical fibers

    NASA Astrophysics Data System (ADS)

    Minakawa, Kazunari; Koike, Kotaro; Hayashi, Neisei; Koike, Yasuhiro; Mizuno, Yosuke; Nakamura, Kentaro

    2016-06-01

    We studied the dependence of the Brillouin frequency shift (BFS) on the water-absorption ratio in poly(methyl methacrylate)-based polymer optical fibers (POFs) to clarify the effect of the humidity on POF-based Brillouin sensors. The BFS, deduced indirectly using an ultrasonic pulse-echo technique, decreased monotonically as the water absorption ratio increased, mainly because of the decrease in the Young's modulus. For the same water absorption ratio, the BFS change was larger at a higher temperature. The maximal BFS changes (absolute values) at 40, 60, and 80 °C were 158, 285, and 510 MHz, respectively (corresponding to the temperature changes of ˜9 °C, ˜16 °C, and ˜30 °C). Thus, some countermeasure against the humidity is indispensable in implementing strain/temperature sensors based on Brillouin scattering in POFs, especially at a higher temperature. On the other hand, Brillouin-based distributed humidity sensors might be developed by exploiting the BFS dependence on water absorption in POFs.

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

    PubMed

    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. PMID:25950644

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

    PubMed

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

    1999-12-01

    Frequency data for the STR system FGA (HumFibra) were obtained from a Caucasoid German population sample (Düsseldorf area) of 424 unrelated individuals. PCR products were detected by horizontal polyacrylamid gel electrophoresis and a total of 16 alleles was identified by side-by-side comparison with a commercially available sequenced ladder. The observed genotype distribution showed no significant deviation from the Hardy-Weinberg equilibrium. The high information content (pooled German data: rate of heterozygosity = 0.8626; probability of match = 0.0344; mean exclusion chance = 0.7240) render this system a useful tool not only in forensic casework (criminal and paternity cases) but in population genetics too. PMID:10646230

  3. 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

  4. 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

  5. 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

  6. Frequency shift of a crystal quartz resonator in thickness-shear modes induced by an array of hemispherical material units.

    PubMed

    Yuantai Hu; Huiliang Hu; Bin Luo; Huan Xue; Jiemin Xie; Ji Wang

    2013-08-01

    A two-dimensional model was established to study the dynamic characteristics of a quartz crystal resonator with the upper surface covered by an array of hemispherical material units. A frequency-dependent equivalent mass ratio was proposed to simulate the effect of the covered units on frequency shift of the resonator system. It was found that the equivalent mass ratio alternately becomes positive or negative with change of shear modulus and radius of each material unit, which indicates that the equivalent mass ratio is strongly related to the vibration mode of the covered loadings. The further numerical results show the cyclical feature in the relationship of frequency shift and shear modulus/radius as expected. The solutions are useful in the analysis of frequency stability of quartz resonators and acoustic wave sensors. PMID:25004547

  7. 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

  8. 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

  9. 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

  10. 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

  11. Stray-field-induced quadrupole shift and absolute frequency of the 688-THz {sup 171}Yb{sup +} single-ion optical frequency standard

    SciTech Connect

    Tamm, Chr.; Weyers, S.; Lipphardt, B.; Peik, E.

    2009-10-15

    We report experimental investigations of a single-ion optical frequency standard based on {sup 171}Yb{sup +}. The ion is confined in a cylindrically symmetric radiofrequency Paul trap. The reference transition is the {sup 2}S{sub 1/2}(F=0)-{sup 2}D{sub 3/2}(F{sup '}=2) electric quadrupole transition at 688 THz. Using a differential measurement scheme, we determine the shift of the reference transition frequency that occurs due to the interaction of the electric quadrupole moment of the {sup 2}D{sub 3/2} state with the gradient of the electrostatic stray field in the trap. We determine an upper limit for the instability of the quadrupole shift over times between 100 s to 20 h. We also observe the variations in the shift and in the applied stray-field compensation voltages that result from loading a new ion into the trap and during a subsequent storage period of 74 days. This information is utilized to measure the absolute frequency of the reference transition with an uncertainty that is a factor of 3 smaller than that of the previous measurement. Using a fiber laser based optical frequency comb generator and the cesium fountain clock CSF1 of PTB (Physikalisch-Technische Bundesanstalt), the frequency at 300 K temperature is determined as 688 358 979 309 306.62{+-}0.73 Hz.

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

    PubMed Central

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

    2014-01-01

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

  13. Non-linear Frequency Shifts, Mode Couplings, and Decay Instability of Plasma Waves

    NASA Astrophysics Data System (ADS)

    Affolter, Mathew; Anderegg, F.; Driscoll, C. F.; Valentini, F.

    2015-11-01

    We present experiments and theory for non-linear plasma wave decay to longer wavelengths, in both the oscillatory coupling and exponential decay regimes. The experiments are conducted on non-neutral plasmas in cylindrical Penning-Malmberg traps, θ-symmetric standing plasma waves have near acoustic dispersion ω (kz) ~kz - αkz2 , discretized by kz =mz (π /Lp) . Large amplitude waves exhibit non-linear frequency shifts δf / f ~A2 and Fourier harmonic content, both of which are increased as the plasma dispersion is reduced. Non-linear coupling rates are measured between large amplitude mz = 2 waves and small amplitude mz = 1 waves, which have a small detuning Δω = 2ω1 -ω2 . At small excitation amplitudes, this detuning causes the mz = 1 mode amplitude to ``bounce'' at rate Δω , with amplitude excursions ΔA1 ~ δn2 /n0 consistent with cold fluid theory and Vlasov simulations. At larger excitation amplitudes, where the non-linear coupling exceeds the dispersion, phase-locked exponential growth of the mz = 1 mode is observed, in qualitative agreement with simple 3-wave instability theory. However, significant variations are observed experimentally, and N-wave theory gives stunningly divergent predictions that depend sensitively on the dispersion-moderated harmonic content. Measurements on higher temperature Langmuir waves and the unusual ``EAW'' (KEEN) waves are being conducted to investigate the effects of wave-particle kinetics on the non-linear coupling rates. Department of Energy Grants DE-SC0002451and DE-SC0008693.

  14. 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.

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

    PubMed Central

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

    2009-01-01

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

  16. 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.

  17. [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

  18. Frequency of greatest temporary hearing threshold shift in harbor porpoises (Phocoena phocoena) depends on the noise level.

    PubMed

    Kastelein, Ronald A; Schop, Jessica; Gransier, Robin; Hoek, Lean

    2014-09-01

    Harbor porpoises may suffer hearing loss when they are exposed to high level sounds. After exposure for 60 min to a 6.5 kHz continuous tone at average received sound pressure levels (SPLav.re.) ranging from 118 to 154 dB re 1μPa, the temporary hearing threshold shifts (TTSs) of a harbor porpoise were quantified at the center frequency (6.5 kHz), at 0.5, 1.0, and 1.3 octaves above the center frequency (9.2, 13.0, and 16.0 kHz), and at a frequency assumed to be ecologically important for harbor porpoises (125 kHz, the center frequency of their echolocation signals) by means of a psychoacoustic technique. The hearing frequency at which the maximum TTS occurred depended on the SPLav.re. The higher the SPLav.re., the higher the TTS induced at frequencies higher than the exposure frequency; below 148 dB re 1 μPa, the maximum TTS was at 6.5 kHz, whereas above 148 dB re 1 μPa, the maximum TTS was at 9.2 kHz. The hearing threshold of the harbor porpoise for the center frequency of its echolocation signals (125 kHz) was not affected at the highest SPLav.re. to which the animal was exposed. PMID:25190414

  19. Experimental-Numerical Comparison of the Cantilever MEMS Frequency Shift in presence of a Residual Stress Gradient

    PubMed Central

    Ballestra, Alberto; Somà, Aurelio; Pavanello, Renato

    2008-01-01

    The dynamic characterization of a set of gold micro beams by electrostatic excitation in presence of residual stress gradient has been studied experimentally. A method to determine the micro-cantilever residual stress gradient by measuring the deflection and curvature and then identifying the residual stress model by means of frequency shift behaviour is presented. A comparison with different numerical FEM models and experimental results has been carried out, introducing in the model the residual stress of the structures, responsible for an initial upward curvature. Dynamic spectrum data are measured via optical interferometry and experimental frequency shift curves are obtained by increasing the dc voltage applied to the specimens. A good correspondence is pointed out between measures and numerical models so that the residual stress effect can be evaluated for different configurations.

  20. Reply to ``Comment on `Ramsey spectroscopy, matter-wave interferometry, and the microwave-lensing frequency shift' ''

    NASA Astrophysics Data System (ADS)

    Gibble, Kurt

    2015-06-01

    The Comment by Jefferts et al. [Phys. Rev. A 91, 067601 (2015), 10.1103/PhysRevA.91.067601] discusses the microwave-lensing frequency shift's possible dependence on the initial wave-packet size and two effects of wall interactions, the frequency shifts that they produce, and the nature of how dressed states are clipped by apertures. I identify conceptual errors in their criticisms, some of which are related to fundamental problems in their lensing treatment [Ashby et al., Phys. Rev. A 91, 033624 (2015), 10.1103/PhysRevA.91.033624] for the NIST-F1 and NIST-F2 atomic clocks [K. Gibble, arXiv:1505.00691]. Aside from typesetting errors that they note, the criticisms in the Comment are shown to be incorrect.

  1. 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.

  2. 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.

  3. 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.

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

    PubMed

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

    2010-10-01

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

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

    PubMed

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

    2009-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  7. 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.

  8. Shifted Coupling of EEG Driving Frequencies and fMRI Resting State Networks in Schizophrenia Spectrum Disorders

    PubMed Central

    Razavi, Nadja; Jann, Kay; Koenig, Thomas; Kottlow, Mara; Hauf, Martinus; Strik, Werner; Dierks, Thomas

    2013-01-01

    Introduction The cerebral resting state in schizophrenia is altered, as has been demonstrated separately by electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) resting state networks (RSNs). Previous simultaneous EEG/fMRI findings in healthy controls suggest that a consistent spatiotemporal coupling between neural oscillations (EEG frequency correlates) and RSN activity is necessary to organize cognitive processes optimally. We hypothesized that this coupling is disorganized in schizophrenia and related psychotic disorders, in particular regarding higher cognitive RSNs such as the default-mode (DMN) and left-working-memory network (LWMN). Methods Resting state was investigated in eleven patients with a schizophrenia spectrum disorder (n = 11) and matched healthy controls (n = 11) using simultaneous EEG/fMRI. The temporal association of each RSN to topographic spectral changes in the EEG was assessed by creating Covariance Maps. Group differences within, and group similarities across frequencies were estimated for the Covariance Maps. Results The coupling of EEG frequency bands to the DMN and the LWMN respectively, displayed significant similarities that were shifted towards lower EEG frequencies in patients compared to healthy controls. Conclusions By combining EEG and fMRI, each measuring different properties of the same pathophysiology, an aberrant relationship between EEG frequencies and altered RSNs was observed in patients. RSNs of patients were related to lower EEG frequencies, indicating functional alterations of the spatiotemporal coupling. Significance The finding of a deviant and shifted coupling between RSNs and related EEG frequencies in patients with a schizophrenia spectrum disorder is significant, as it might indicate how failures in the processing of internal and external stimuli, as commonly seen during this symptomatology (i.e. thought disorders, hallucinations), arise. PMID:24124576

  9. Correlates of the shift in heart rate variability with postures and walking by time-frequency analysis.

    PubMed

    Chan, Hsiao-Lung; Lin, Ming-An; Chao, Pei-Kuang; Lin, Chun-Hsien

    2007-05-01

    Heart rate (HR) variability derived from electrocardiogram (ECG) can be used to assess the function of the autonomic nervous system. HR exhibits various characteristics during different physical activities attributed to the altered autonomic mediation, where it is also beneficial to reveal the autonomic shift in response to physical-activity change. In this paper, the physical-activity-related HR behaviors were delineated using a portable ECG and body acceleration recorder based on a personal digital assistant and the smoothed pseudo Wigner-Ville distribution. The results based upon eighteen subjects performing four sequential 5-min physical activities (supine, sitting, standing and spontaneous walking) showed that the high-frequency heartbeat fluctuations during supine and sitting were significantly larger than during standing, and that the ratio of low- to high-frequency fluctuation during standing was significantly higher than during supine and sitting. This could be linked with the parasympathetic predominance during supine and sitting, and a shift to sympathetic dominance while standing. During spontaneous walking, the high-frequency fluctuation was significant lower than during supine. The low- to high-frequency ratio decreased significantly from standing to spontaneous walking, which may imply an increased vagal predominance (autonomic effect) or an increased respiratory activity (mechanical effect). PMID:17403552

  10. 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

  11. Frequency shift of spin waves in tunnel-junction spin-transfer nano-oscillators

    NASA Astrophysics Data System (ADS)

    Rodríguez-Suárez, R. L.; Matos-Abiague, A.; Azevedo, A.; Rezende, S. M.

    2010-10-01

    The excitations of microwave spin waves in magnetic tunnel junctions are theoretically investigated. An analytical approach which describes the dependence of the microwave precession frequency on the applied voltage is developed. It is shown that the spin-wave frequency is directly related to both the in-plane and perpendicular spin-transfer torques. In the low field regime the perpendicular torque can induce changes in the slope of the oscillation frequency versus applied voltage (df/dv) from negative (redshift) to positive (blueshift) values.

  12. 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

  13. 3D absolute shape measurement of live rabbit hearts with a superfast two-frequency phase-shifting technique.

    PubMed

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

    2013-03-11

    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

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. The role of excitation-pattern cues in the detection of frequency shifts in bandpass-filtered complex tones.

    PubMed

    Marmel, Frederic; Plack, Christopher J; Hopkins, Kathryn; Carlyon, Robert P; Gockel, Hedwig E; Moore, Brian C J

    2015-05-01

    One task intended to measure sensitivity to temporal fine structure (TFS) involves the discrimination of a harmonic complex tone from a tone in which all harmonics are shifted upwards by the same amount in hertz. Both tones are passed through a fixed bandpass filter centered on the high harmonics to reduce the availability of excitation-pattern cues and a background noise is used to mask combination tones. The role of frequency selectivity in this "TFS1" task was investigated by varying level. Experiment 1 showed that listeners performed more poorly at a high level than at a low level. Experiment 2 included intermediate levels and showed that performance deteriorated for levels above about 57 dB sound pressure level. Experiment 3 estimated the magnitude of excitation-pattern cues from the variation in forward masking of a pure tone as a function of frequency shift in the complex tones. There was negligible variation, except for the lowest level used. The results indicate that the changes in excitation level at threshold for the TFS1 task would be too small to be usable. The results are consistent with the TFS1 task being performed using TFS cues, and with frequency selectivity having an indirect effect on performance via its influence on TFS cues. PMID:25994700

  20. 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

  1. 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.

    2016-04-01

    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.

  2. Distributed magnetic field sensor based on magnetostriction using Rayleigh backscattering spectra shift in optical frequency-domain reflectometry

    NASA Astrophysics Data System (ADS)

    Du, Yang; Liu, Tiegen; Ding, Zhenyang; Liu, Kun; Feng, Bowen; Jiang, Junfeng

    2015-01-01

    We present a distributed optical-fiber magnetic-field sensor based on magnetostriction using the Rayleigh backscattering spectra (RBS) shift in optical frequency-domain reflectometry (OFDR). The magnetostrictive Fe-Co-V alloy thin films are attached to a 51-m single-mode fiber (SMF). We detect the strain coupled to the SMF caused by the magnetic field using the RBS shift. We measure the range of the magnetic field to be from 0 to 143.3 mT. The minimum measurable magnetic intensity variation is 12.9 mT when the spatial resolution is 4 cm, and it can be improved to 5.3 mT by deteriorating the spatial resolution to 14 cm.

  3. 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.

  4. 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}.

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

    NASA Astrophysics Data System (ADS)

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

    2012-07-01

    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.

  6. 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.

  7. Atomic Transition Frequencies, Isotope Shifts, and Sensitivity to Variation of the Fine Structure Constant for Studies of Quasar Absorption Spectra

    NASA Astrophysics Data System (ADS)

    Berengut, J. C.; Dzuba, V. A.; Flambaum, V. V.; King, J. A.; Kozlov, M. G.; Murphy, M. T.; Webb, J. K.

    Theories unifying gravity with other interactions suggest spatial and temporal variation of fundamental "constants" in the Universe. A change in the fine structure constant, α = {e}2/hslash c , could be detected via shifts in the frequencies of atomic transitions in quasar absorption systems. Recent studies using 140 absorption systems from the Keck telescope and 153 from the Very Large Telescope, suggest that α varies spatially (61). That is, in one direction on the sky α seems to have been smaller at the time of absorption, while in the opposite direction it seems to have been larger.

  8. 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.

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

    PubMed Central

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

    2015-01-01

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

  10. 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.

  11. 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.

  12. Automating the generation and collection of rate-frequency functions in a curve-shift brain stimulation reward paradigm.

    PubMed

    Ranaldi, R; Ferguson, S; Beninger, R J

    1994-08-01

    The electrical self-stimulation paradigm has proven to be very useful in research aimed at delineating the neural substrates involved in reward-related learning. Of the procedures currently employed the curve-shift method is among the more useful since it distinguishes between treatment effects on reward and performance. This method involves generating and plotting rate-frequency functions and quantifying the effects of experimental manipulations on reward by measuring the degree of lateral shift in these functions. We have designed a computerized system that automatically generates and collects descending rate-frequency functions from self-stimulating rats. The 3 main units of this system consisted of a 6809 micro-controller, a programmable timer logic board and a constant current source. The micro-controller and programmable timer operated on custom written software that monitored lever pressing in the operant chambers and controlled stimulation parameters to generate and record rate-frequency functions. The present report describes this system and presents some typical data collected from rats self-stimulating on ventral tegmental electrodes before and after the administration of intra-accumbens vehicle (0.5 microliter distilled H2O), (+)-amphetamine (20.0 micrograms/0.5 microliter), quinpirole (10.0 micrograms/0.5 microliter) and systemic quinpirole (1.0 mg/kg), all dopamine agonists. Stimulation consisting of 300-ms trains of cathodal rectangular pulses (0.1 ms) was available in 50-s trials. The number of pulses per train was decreased logarithmically from a value that sustained maximal responding to one that would not sustain responding. Self-stimulation thresholds were obtained by fitting the Gompertz growth model to the data and calculating the point of maximal acceleration of the sigmoidal curve. It was found that the present system generated and collected rate-frequency functions similar to those that have been obtained manually in previous experiments

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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,

  18. 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.

  19. 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.

  20. 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.

  1. 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).

  2. Waveguide elliptic polarizers for ECH at down-shifted frequencies on PLT

    SciTech Connect

    Doane, J.L.

    1986-01-01

    ECH experiments on PLT with resonance frequencies of 80 to 90 GHz at the plasma center use 60 GHz extraordinary mode (X-mode) propagation at 30/sup 0/ from the toroidal field. Efficient excitation of this mode requires elliptic polarization of the incident wave at the plasma edge. On PLT the elliptic polarization is achieved outside the vacuum vessel in an elliptically deformed section of circular waveguide propagating TM11, a mode that is intermediate between TE01 and HE11 (which has an ideal radiation pattern). The squeeze and orientation of the TM11 polarizer are adjusted to compensate both for the birefringence of a corrugated bend propagating HE11 and for a flat mirror inside PLT that reverses the sense of rotation of the polarization. 11 refs., 8 figs.

  3. 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

  4. 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

  5. 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...

  6. Temporary threshold shift in bottlenose dolphins (Tursiops truncatus) exposed to mid-frequency tones

    NASA Astrophysics Data System (ADS)

    Finneran, James J.; Carder, Donald A.; Schlundt, Carolyn E.; Ridgway, Sam H.

    2005-10-01

    A behavioral response paradigm was used to measure hearing thresholds in bottlenose dolphins before and after exposure to 3 kHz tones with sound exposure levels (SELs) from 100 to 203 dB re 1 μPa2 s. Experiments were conducted in a relatively quiet pool with ambient noise levels below 55 dB re 1 μPa2/Hz at frequencies above 1 kHz. Experiments 1 and 2 featured 1-s exposures with hearing tested at 4.5 and 3 kHz, respectively. Experiment 3 featured 2-, 4-, and 8-s exposures with hearing tested at 4.5 kHz. For experiment 2, there were no significant differences between control and exposure sessions. For experiments 1 and 3, exposures with SEL=197 dB re 1 μPa2 s and SEL>=195 dB re 1 μPa2 s, respectively, resulted in significantly higher TTS4 than control sessions. For experiment 3 at SEL=195 dB re 1 μPa2 s, the mean TTS4 was 2.8 dB. These data are consistent with prior studies of TTS in dolphins exposed to pure tones and octave band noise and suggest that a SEL of 195 dB re 1 μPa2 s is a reasonable threshold for the onset of TTS in dolphins and white whales exposed to midfrequency tones.

  7. 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.

  8. 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.

  9. 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.

  10. Unsplit complex frequency shifted perfectly matched layer for second-order wave equation using auxiliary differential equations.

    PubMed

    Gao, Yingjie; Zhang, Jinhai; Yao, Zhenxing

    2015-12-01

    The complex frequency shifted perfectly matched layer (CFS-PML) can improve the absorbing performance of PML for nearly grazing incident waves. However, traditional PML and CFS-PML are based on first-order wave equations; thus, they are not suitable for second-order wave equation. In this paper, an implementation of CFS-PML for second-order wave equation is presented using auxiliary differential equations. This method is free of both convolution calculations and third-order temporal derivatives. As an unsplit CFS-PML, it can reduce the nearly grazing incidence. Numerical experiments show that it has better absorption than typical PML implementations based on second-order wave equation. PMID:26723366

  11. Frequency shift in three-photon resonant four-wave mixing by internal atom-field interaction

    NASA Astrophysics Data System (ADS)

    de Melo, Natalia R.; Vianna, Sandra S.

    2015-11-01

    We report on experimental results of four-wave mixing processes in rubidium vapor where coherence is induced on the three-photon resonant transition from 5 s to 6 p states via intermediate Rydberg levels. It is shown that the use of two beams in a noncollinear configuration, i.e., θ ≠0 , and high atomic density unveil new features. First, the θ =0 (collinear configuration) odd-photon destructive interference between the incident and generated fields is strongly inhibited for θ ≠0 . Second, most importantly, the observed cooperative frequency shift of the three-photon transition is strongly enhanced for small, but nonzero, values of θ due to the factor (1-cosθ ) -1, which is not present if the generated radiation field is not considered self-consistently in the Maxwell-Bloch equations.

  12. 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.

  13. 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

  14. 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.

  15. 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.

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

    PubMed

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

    1995-04-21

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

  17. 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...

  18. 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

  19. GPR simulation based on complex frequency shifted recursive integration PML boundary of 3D high order FDTD

    NASA Astrophysics Data System (ADS)

    Li, Jing; Zeng, Zhaofa; Huang, Ling; Liu, Fengshan

    2012-12-01

    When applying the finite difference time domain (FDTD) method in Ground Penetrating Radar (GPR) simulation, the absorbing boundary conditions (ABC) are used to mitigate undesired reflection that can arise at the model's truncation boundaries. The classical PML boundary can make spurious reflection for the waves, such as reaching to the PML interface with near-grazing angles, low frequency waves or evanescent waves. The non-split complex frequency shifted PML which base on recursive integration (CFS-RIPML) has a good absorption effect for these interference waves. Meanwhile, the recursive integration, which does not need split field component, can overcome the shortcoming of CFS technique that needs more intermediate variable and large memory. In addition, the high-order FDTD can improve calculation accuracy and reduce the error caused by numerical dispersion effectively. In this paper, we derive the 3D high-order FDTD method with CFS-RIPML boundary and apply it in GPR simulation. The results show that the CFS-RIPML has significantly better absorption effect and lower reflections error than UPML and PML boundary. Compared with the two-order, the high-order FDTD can improve calculation accuracy effectively with the same grid size. Combination with CFS-RIPML boundary and high-order FDTD can improve the reliability and calculation accuracy of GPR and other geophysics numerical simulation.

  20. Dynamic shifts in the parameters of the traditional frequency range of the EEG during learning in dogs.

    PubMed

    Dumenko, V N

    1995-01-01

    The parameters of the electrical activity of various regions of the neocortex (NC) and the olfactory bulbs (OB) of dogs were studied by means of correlation-spectral analysis during the development of a food-dispenser paw pedal-pressing motor skill; a wide band of frequencies (1-100 Hz), which included both the traditional range (1-20 Hz) as well as high frequencies (HF), were used. Differences were demonstrated in the dynamics of the parameters in the NC and OB. The energy level of the potentials of the NC increased in the HF range (beta 3 and gamma), while in the OB it increased in the HF and alpha range. The coherence-phase characteristics of the NC potentials suggest that more stable (by comparison with resting wakefulness) temporal relationships between the oscillations not only within the limits of HF, but also in the alpha band, are formed in the presence of the developed skill. At the same time, greater phase shifts are characteristic for the interrelationships of the OB potentials and those of the NC, and the increase in coherence relates only to the HF range, whereas the oscillations of the traditional range are characterized by a decrease in coherence. The possible role of the alpha range (along with the HF) in the processing of information which supports appropriate behavior is stressed. PMID:8614481

  1. 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

  2. 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

  3. Absolute frequency and isotope shift of the magnesium (3 s2) 1S0→(3 s 3 d ) 1D2 two-photon transition by direct frequency-comb spectroscopy

    NASA Astrophysics Data System (ADS)

    Peters, E.; Reinhardt, S.; Hänsch, Th. W.; Udem, Th.

    2015-12-01

    We use a picosecond frequency-doubled mode-locked titanium sapphire laser to generate a frequency comb at 431 nm in order to probe the (3 s2) 1S0 →(3 s 3 d ) 1D2 transition in atomic magnesium. Using a second, self-referenced femtosecond frequency comb, the absolute transition frequency and the 24Mg and 26Mg isotope shift is determined relative to a global-positioning-system-referenced hydrogen maser. Our result for the transition frequency of the main isotope 24Mg of 1 391 128 606.14 (12 ) MHz agrees with previous measurements and reduces its uncertainty by four orders of magnitude. For the isotope shift we find δ ν26 ,24=3915.13 (39 ) MHz. Accurate values for transition frequencies in Mg are relevant in astrophysics and to test atomic structure calculations.

  4. Theoretical investigation of nonlinear damping and nonlinear phase shift of spin-electromagnetic waves propagating in infinite multiferroics at sub-terahertz frequencies

    NASA Astrophysics Data System (ADS)

    Ustinova, I. A.; Cherkasskii, M. A.; Ustinov, A. B.; Kalinikos, B. A.

    2015-12-01

    The nonlinear phase shift and nonlinear damping of spin-electromagnetic waves were theoretically studied for the first time in sub-terahertz frequency range in infinite homogeneous longitudinal magnetized multiferroics. The research was based on the solution of the Ginzburg-Landau equation. It is shown that the saturation of the phase shift occurs due to the nonlinear damping if the nonlinear damping coefficients exceed v1=108 s-1 and v2=109 s-1.

  5. μ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies.

    PubMed

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

    2014-02-01

    Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits; 2) estimate effects of previously reported SNP on nontarget performance traits; and 3) evaluate tenderness SNP specific residual variance models compared to a single residual variance model for tenderness. Divergent haplotypes within µ-calpain (CAPN1), and SNP within calpastatin (CAST) and growth hormone receptor (GHR) were successfully selected to increase their frequencies. Traits evaluated were birth BW, weaning BW, final BW, fat thickness, LM area, USDA marbling score, yield grade, slice shear force (SSF), and visible and near infrared predicted slice shear force. Both CAPN1 and CAST exhibited additive (P < 0.001) modes of inheritance for SSF and neither exhibited dominance (P ≥ 0.19). Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P = 0.55). Estimated additive effects of CAPN1 (1.049 kg) and CAST (1.257 kg) on SSF were large in this study. Animals homozygous for tender alleles at both CAPN1 and CAST would have 4.61 kg lower SSF (38.6% of the mean) than animals homozygous tough for both markers. There was also an effect of CAST on yield grade (P < 0.02). The tender CAST allele was associated with more red meat yield and less trimmable fat. There were no significant effects (P ≥ 0.23) for GHR on any of the traits evaluated in this study. Furthermore, CAST specific residual variance models were found to fit significantly better (P < 0.001) than single residual variance models for SSF, with the tougher genotypes having larger residual variance. Thus, the risk of a tough steak from the undesired CAST genotype is increased through both an

  6. 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

  7. 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

  8. 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

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

    PubMed

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

    2016-04-01

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

  10. Correlation of frequency shift discontinuity to atomic positions on a Si(111)7 × 7 surface by noncontact atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Morita, Seizo; Sugawara, Yasuhiro; Yokoyama, Kousuke; Uchihashi, Takayuki; Sugawara, Yasuhiro; Yokoyama, Kousuke

    2000-06-01

    We succeeded in obtaining site-dependent frequency-shift curves on an atomic scale as a function of the tip-sample surface distance between a clean Si(111)7×7 surface and a clean active Si tip with a dangling bond using noncontact atomic force microscopy (NC-AFM). As a result, we found a discontinuous jump in the frequency-shift curve measured above active Si adatoms with a dangling bond, in contrast to a continuous frequency-shift curve measured above gaps between adjacent Si adatoms. These results suggest the possibility that the NC-AFM can be developed into a kind of spectroscopic tool, i.e. atomic force spectroscopy, which can measure the three-dimensional force-related map with true atomic resolution. Furthermore, we succeeded in suppressing the discontinuous jump in the frequency-shift curve by replacing the clean active Si tip apex with an oxidized inactive Si tip apex. This result suggests the possibility that we can control the interaction force between the tip and sample atoms on an atomic scale by placing a suitable atom on the tip apex.

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

    PubMed

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

    2007-01-01

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

  12. 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.

  13. An electrostatic model for the frequency shifts in the carbonmonoxy stretching band of myoglobin: correlation of hydrogen bonding and the stark tuning rate.

    PubMed

    Franzen, Stefan

    2002-11-01

    The effect of internal and applied external electric fields on the vibrational stretching frequency for bound CO (nu(CO)) in myoglobin mutants was studied using density functional theory. Geometry optimization and frequency calculations were carried out for an imidazole-iron-porphine-carbonmonoxy adduct with various small molecule hydrogen-bonding groups. Over 70 vibrational frequency calculations of different model geometries and hydrogen-bonding groups were compared to derive overall trends in the C-O stretching frequency (nu(CO)) in terms of the C-O bond length and Mulliken charge. Simple linear functions were derived to predict the Stark tuning rate using an approach analogous to the vibronic theory of activation.(1) Potential energy calculations show that the strongest interaction occurs for C-H or N-H hydrogen bonding nearly perpendicular to the Fe-C-O bond axis. The calculated frequencies are compared to the structural data available from 18 myoglobin crystal structures, supporting the hypothesis that the vast majority of hydrogen-bonding interactions with CO occur from the side, rather than the end, of the bound CO ligand. The nu(CO) frequency shifts agree well with experimental frequency shifts for multiple bands, known as A states, and site-directed mutations in the distal pocket of myoglobin. The model calculations quantitatively explain electrostatic effects in terms of specific hydrogen-bonding interactions with bound CO in heme proteins. PMID:12405856

  14. Six-bit all-optical quantization using photonic crystal fiber with soliton self-frequency shift and pre-chirp spectral compression techniques

    NASA Astrophysics Data System (ADS)

    Kang, Zhe; Yuan, Jin-Hui; Li, Sha; Xie, Song-Lin; Yan, Bin-Bin; Sang, Xin-Zhu; Yu, Chong-Xiu

    2013-11-01

    In this paper, we propose an optical quantization scheme for all-optical analog-to-digital conversion that facilitates photonics integration. A segment of 10-m photonic crystal fiber with a high nonlinear coefficient of 62.8 W-1/km is utilized to realize large scale soliton self-frequency shift relevant to the power of the sampled optical signal. Furthermore, a 100-m dispersion-increasing fiber is used as the spectral compression module for further resolution enhancement. Simulation results show that 317-nm maximum wavelength shift is realized with 1550-nm initial wavelength and 6-bit quantization resolution is obtained with a subsequent spectral compression process.

  15. 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.

  16. 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.

  17. 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.

  18. Chirped femtosecond solitons and double-kink solitons in the cubic-quintic nonlinear Schroedinger equation with self-steepening and self-frequency shift

    SciTech Connect

    Alka,; Goyal, Amit; Gupta, Rama; Kumar, C. N.; Raju, Thokala Soloman

    2011-12-15

    We demonstrate that the competing cubic-quintic nonlinearity induces propagating solitonlike dark(bright) solitons and double-kink solitons in the nonlinear Schroedinger equation with self-steepening and self-frequency shift. Parameter domains are delineated in which these optical solitons exist. Also, fractional-transform solitons are explored for this model. It is shown that the nonlinear chirp associated with each of these optical pulses is directly proportional to the intensity of the wave and saturates at some finite value as the retarded time approaches its asymptotic value. We further show that the amplitude of the chirping can be controlled by varying the self-steepening term and self-frequency shift.

  19. Shifted dispersion-induced radio-frequency fading in microwave photonic filters using a dual-input Mach-Zehnder electro-optic modulator.

    PubMed

    Li, Liwei; Yi, Xiaoke; Huang, Thomas X H; Minasian, Robert A

    2013-04-01

    A simple microwave photonic processor structure with single passband response, and widely tunable capability, is demonstrated. It is based on the principle of shifted dispersion-induced radio-frequency (RF) fading by using a dual-input Mach-Zehnder electro-optic modulator (EOM) that is fed from a broadband optical source with unbalanced input fiber lengths into the upper and lower arms of the EOM, in combination with a dispersive medium. This topology consequently produces a spectral response equivalent to the curve of the dispersion-induced RF fading that is shifted from the conventional baseband location to high frequencies. Therefore, an equivalent single passband is formed without the requirement of the conventional tap coefficients. Experimental results verify the structure and demonstrate a continuously tunable microwave filter exhibiting shape invariance and a single passband. In addition, the filter response sidelobe suppression is also significantly improved by applying a Gaussian windowed profile to the broadband optical source. PMID:23546278

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Roles of interbasin frequency changes in the poleward shifts of the maximum intensity location of tropical cyclones

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    An observed poleward migration in the average latitude at which tropical cyclones (TCs) achieved their lifetime-maximum intensities (LMIs) was previously explained by changes in the mean meridional environments favorable to storm development linked to tropical expansion and anthropogenic warming. We show that the poleward migration is greatly influenced by basin-to-basin changes in TC frequency associated with multi-decadal variability, particularly for the Northern Hemisphere (NH). The contribution of the frequency changes to the poleward migration is comparable to that of the mean meridional environmental changes. A statistically significant global poleward trend can be identified simply from the frequency changes in each basin. An opposite trend exists in the frequency variations over the past 30 years between the North Atlantic and the eastern North Pacific where climatological mean latitudes of LMI are high (26.1°N) and low (16.5°N), respectively, which is the key factor in driving the frequency contribution. The strong roles of the interbasin frequency changes in the poleward migration also suggest that if the phase of multidecadal variability in the NH is reversed, as found in earlier TC records, the poleward trend could be changed to an opposite, equatorward, trend in the future.

  5. 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

  6. Studies on the shift in the frequency of the first Schumann resonance mode during a solar proton event

    NASA Astrophysics Data System (ADS)

    de, S. S.; de, B. K.; Bandyopadhyay, B.; Paul, Suman; Haldar, D. K.; Barui, S.

    2010-07-01

    The variation of the first Schumann resonance (SR) frequency spectra observed from the recorded data over Kolkata (22.56°N, 88.5°E) during a solar proton event (SPE) on July 14, 2000 has been presented. It shows increase in frequency during X-ray bursts and decrease during the period of occurrence of an SPE. The results from some other locations for the same event are also reported. The severe X-ray bursts recorded just before the proton event exhibit enhancement in frequency of the first mode due to enhancement of ionization in the D-region of the ionosphere. Some attempts are made to explain the observed variation during solar proton events in terms of the perturbations within the Earth-ionosphere waveguide on the basis of two-layer-model.

  7. 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

  8. 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

  9. Temperature and strain measurements using the power, line-width, shape, and frequency shift of the Brillouin loss spectrum

    NASA Astrophysics Data System (ADS)

    Bao, Xiaoyi; Smith, Jeffrey; Brown, Anthony W.

    2002-09-01

    A Brillouin scattering based fiber sensor system has been developed by our Fiber Optics Group for the structural monitoring and civil engineering related applications. In this paper, the Brillouin loss spectrum has been characterized in terms of its center frequency, peak power, line-width and shape. These parameters have been considered as a function of the input pump and probe laser powers, the pump pulse duration, strain and temperature. The measurement accuracy has been studied at different Brillouin frequency steps to study the uncertainty of the Brillouin frequency, line-width, peak power and shape factor vs. signal to noise ratio, so that we can optimize the system performance. Characterization of the Brillouin loss spectrum led to the development of an innovative technique to measure the strain and temperature simultaneously using the strain and temperature dependence on the peak power in conjunction with the Brillouin frequency for the single mode fiber with 3m spatial resolution, 3°C temperature resolution and 200 me (mm/m) strain accuracy.

  10. NONLINEAR OPTICAL PHENOMENA Frequency shift of Rayleigh line fine structure components in a water solution of 4-methylpyridine as a function of temperature, concentration, and light scattering angle

    NASA Astrophysics Data System (ADS)

    Bunkin, Nikolai F.; Gorelik, Vladimir S.; Sabirov, L. M.; Semenov, D. I.; Khaidarov, Kh S.

    2010-11-01

    The frequency shift Δv of the fine structure components of Rayleigh light scattering in 4-methylpyridine water solutions is studied in the ranges of 1 — 0.1 mole fraction concentrations and temperature 10 — 80 °C. The laws of Δv variation at different light scattering angles are discussed from the viewpoint of solution structural reorganisation under the varying temperature and concentration of nonelectrolyte in water. Existence of a continuous hydrogen-bond net in the solutions is experimentally proved in a certain range of temperatures and concentrations.

  11. 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.

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

    PubMed

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

    2009-04-01

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

  13. Increasing long-term response by selecting for favorable minor alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. Image-Guided Ultrasound Characterization of Volatile Sub-Micron Phase-Shift Droplets in the 20-40 MHz Frequency Range.

    PubMed

    Sheeran, Paul S; Daghighi, Yasaman; Yoo, Kimoon; Williams, Ross; Cherin, Emmanuel; Foster, F Stuart; Burns, Peter N

    2016-03-01

    Phase-shift perfluorocarbon droplets are designed to convert from the liquid to the gas state by the external application of acoustic or optical energy. Although droplet vaporization has been investigated extensively at ultrasonic frequencies between 1 and 10 MHz, few studies have characterized performance at the higher frequencies commonly used in small animal imaging. In this study, we use standard B-mode imaging sequences on a pre-clinical ultrasound platform to both image and activate sub-micron decafluorobutane droplet populations in vitro and in vivo at center frequencies in the range of 20-40 MHz. Results show that droplets remain stable against vaporization at low imaging pressures but are vaporized at peak negative pressures near 3.5 MPa at the three frequencies tested. This study also found that a small number of size outliers present in the distribution can greatly influence droplet performance. Removal of these outliers results in a more accurate assessment of the vaporization threshold and produces free-flowing microbubbles upon vaporization in the mouse kidney. PMID:26725168

  15. 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.

  16. Performance Evaluation of Tunable Channel-Selective Wavelength Shift by Cascaded Sum- and Difference-Frequency Generation in Periodically Poled Lithium Niobate Waveguides

    NASA Astrophysics Data System (ADS)

    Gao, Shiming; Yang, Changxi; Xiao, Xiaosheng; Tian, Yu; You, Zheng; Jin, Guofan

    2007-03-01

    We theoretically evaluate the performance of tunable channel-selective wavelength shift based on cascaded sum- and difference-frequency generation by the use of two pump lights in periodically poled lithium niobate waveguides. In double-pass configurations, the functions of wavelength add/drop and wavelength shift are easy to integrate in the same waveguide. Analysis shows that a longer waveguide more competently adapts narrower channel spacing in wavelength-division-multiplexed (WDM) systems. This wavelength shifter is flexible due to the almost separable operations of the two pumps: The channel is selected by setting the first pump, and the wavelength-shifting value is tuned by adjusting the second pump. This wavelength shifter has a very large dynamic region. For a 2.56-cm-long waveguide, the maximum dynamic region is as broad as 67 nm in a 0.4-nm channel-spacing WDM system. The dynamic region is mainly dominated by the limitation of multiple-channel crosstalk in a dense WDM system. However, it is dominated by the limitation of single-channel efficiency fluctuation in a coarse one.

  17. 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

  18. 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

  19. 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

  20. Shifting the Operating Point of Cochlear Amplification?:. Impact of Low Frequency Biasing and Contralateral Sound Stimulation on Dpoae

    NASA Astrophysics Data System (ADS)

    Wittekindt, Anna; Abel, Cornelius; Kössl, Manfred

    2009-02-01

    The mammalian efferent medial olivo-cochlear system is known to modulate active amplification of low-level sound in the cochlea. We investigated the effect of contralateral acoustic stimulation (CAS), known to elicit efferent activity, on distortion product otoacoustic emissions (DPOAEs) in the gerbil and, in second approach, biased the position of the cochlear partition and hence the operating point of the cochlear amplifier periodically by a low frequency tone (5 Hz). The study focussed on the quadratic distortion product f2-f1 that is sensitive to changes in the operating point of the amplifier transfer function. During CAS, a significant increase of the amplitude of f2-f1 was found while 2f1-f2 was less affected. Biasing by the low frequency tone resulted in a phase related amplitude modulation of f2-f1. This modulation pattern was changed pronouncedly during CAS, in dependence on the CAS-level. The current results suggest that efferent effects on DPOAEs might be produced by changes in the operating point of the cochlear amplifier and were in good agreement with a simple model based on a Boltzman function.

  1. 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

  2. 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

  3. 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.

  4. Widely tunable dispersive wave generation and soliton self-frequency shift in a tellurite microstructured optical fiber pumped near the zero dispersion wavelength

    NASA Astrophysics Data System (ADS)

    Zhang, Lei; Tuan, Tong-Hoang; Liu, Lai; Gao, Wei-Qing; Kawamura, Harutaka; Suzuki, Takenobu; Ohishi, Yasutake

    2015-12-01

    Widely tunable dispersive waves (DW) and Raman solitons are generated in a tellurite microstructured optical fiber (TMOF) by pumping in the anomalous dispersion regime, close to the zero dispersion wavelength (ZDW). The DW can be generated from 1518.3 nm to 1315.5 nm, and the soliton can be shifted from the pump wavelength of 1570 nm to 1828.7 nm, by tuning the average pump power from 3 dBm to 17.5 dBm. After the average pump power is increased to 18.8 dBm, two DW peaks (centered at 1323 nm and 1260 nm) and three soliton peaks (centered at 1762 nm, 1825 nm, and 1896 nm) can be observed simultaneously. When the average pump power is greater than 23.4 dBm, a flat and broadband supercontinuum (SC) can be formed by the combined nonlinear effects of soliton self-frequency shift (SSFS), DW generation, and cross phase modulation (XPM).

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

    PubMed Central

    Yokoyama, Shozo; Nei, Masatoshi

    1979-01-01

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

  6. 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

  7. 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

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

    SciTech Connect

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

    1995-05-01

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

  9. 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

  10. 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

  11. Hybrid bidirectional radio-over-fiber-based orthogonal frequency division multiple access-passive optical network supporting 60/120 GHz using offset quadrate phase shift keying

    NASA Astrophysics Data System (ADS)

    Zhang, Chongfu; Chen, Chen; Qiu, Kun

    2015-09-01

    A hybrid bidirectional orthogonal frequency division multiple access-passive optical network (OFDMA-PON) based on offset quadrate phase shift keying (OQPSK) to support 60- and 120-GHz radio-over-fiber system is proposed. The system can support wired/wireless applications and enable the dynamic bandwidth allocation according to a subscriber's application. It is successfully achieved by using the millimeter waves (MMWs) generation and the carrier-reuse technique. In the proposed scheme, the MMW bands used for downlink (DL) and uplink transmissions are generated at the optical line terminal by the dual-arm Mach-Zehnder modulators. Both 60- and 120-GHz MMWs are obtained for the transmission of the high bit-rate services in source-free optical network units (ONUs), only using a single 15-GHz sinusoidal wave source. The Rayleigh backscattering effect is considered in the proposed OQPSK-based OFDMA-PON. For DL transmission over a 30-km single-mode fiber, the power penalties are less than 0.8 and 1 dB for the OQPSK-OFDM wired data at 10 Gb/s and the OQPSK-OFDM wireless data at 5 Gb/s, respectively.

  12. Dispersion matching of sample and reference arms in optical frequency domain reflectometry-optical coherence tomography using a dispersion-shifted fiber

    NASA Astrophysics Data System (ADS)

    Asaka, Kota; Ohbayashi, Kohji

    2007-04-01

    We demonstrate dispersion matching of sample and reference arms in an optical frequency domain reflectometry-optical coherence tomography (OFDR-OCT) system with a discretely swept light source centered at 1550 nm, using a dispersion-shifted fiber (DSF) in the reference arm. By adjusting the optical length of the DSF so that it is equal to that of the free space in the sample arm, we achieve a high resolution of 27.2 μm (in air), which is very close to the theoretically expected value of 26.8 μm when we measure the reflective mirror. This improves the degraded resolution (36.1 μm ) in a system using a conventional single-mode fiber when the free-space length in the sample arm was 909 mm. We also demonstrate a clear interface between air and the enamel layer of an extracted human tooth with the discretely swept (DS) OFDR-OCT imaging due to the improved resolution provided by this technique. These results show the potential of our DS-OFDR-OCT system for a compact low-cost apparatus with a high axial resolution.

  13. Effects of delayed auditory feedback and frequency-shifted feedback on speech control and some potentials for future development of prosthetic aids for stammering

    PubMed Central

    Howell, Peter

    2007-01-01

    It has been known for at least a hundred years that the speech of a person who stammers becomes more fluent when alterations are made to the speaking environment. Alterations that lead to an improvement in fluency include a) noises that prevent a speaker hearing his or her own voice, and b) manipulations to the sound of a speaker's voice before it is heard. Examples of manipulations that have been made are introducing a delay, and shifting the voice up or down in frequency. The influences all these alterations have on fluent speakers and speakers who stammer, that have been established over the last century, are reviewed. In addition, the ways in which these phenomena have been explained for both fluent speaker and speakers who stammer are outlined. Several previous findings have potential significance for ways in which the fluency-enhancing effects of these alterations in speakers who stammer could be employed in clinical settings. These are highlighted and discussed, mainly in connection with the SpeechEasy™ prosthetic device for treating stammering. PMID:18259594

  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. PMID:26368021

  15. Fixation probability with multiple alleles and projected average allelic effect on selection.

    PubMed

    Lessard, Sabin; Lahaie, Philippe

    2009-06-01

    The first-order effect of selection on the probability of fixation of an allele, with respect to an intensity of selection s>0 in a diploid population of fixed finite size N, undergoing discrete, non-overlapping generations, is shown to be given by the sum of the average effects of that allele on the coefficient of selection in the current generation and all future generations, given the population state in the current generation. This projected average allelic effect is a weighted sum of average allelic effects in allozygous and autozygous offspring in the initial generation, with weights given in terms of expected coalescence times, under neutrality, for the lineages of two or three gametes chosen at random in the same generation. This is shown in the framework of multiple alleles at one locus, with genotypic values determining either viability or fertility differences, and with either multinomial or exchangeable reproduction schemes. In the limit of weak selection in a large population such that Ns tends to zero, the initial average allelic effects in allozygous offspring and autozygous offspring have the same weight on the fixation probability only in the domain of application of the Kingman coalescent. With frequency-dependent selection in a linear-game-theoretic context with two phenotypes determined by additive gene action, the first-order effect on the fixation probability is a combination of two effects of frequency-independent selection, one in a haploid population, the other in a diploid population. In the domain of application of the Kingman coalescent as the population size goes to infinity and Ns to zero, the first effect is three times more important than the second effect. This explains the one-third law of evolutionary dynamics in this domain, and shows how this law can be extended beyond this domain. PMID:19249322

  16. 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.

  17. Explaining the sawtooth: latitudinal periodicity in a circadian gene correlates with shifts in generation number.

    PubMed

    Levy, R C; Kozak, G M; Wadsworth, C B; Coates, B S; Dopman, E B

    2015-01-01

    Many temperate insects take advantage of longer growing seasons at lower latitudes by increasing their generation number or voltinism. In some insects, development time abruptly decreases when additional generations are fit into the season. Consequently, latitudinal 'sawtooth' clines associated with shifts in voltinism are seen for phenotypes correlated with development time, like body size. However, latitudinal variation in voltinism has not been linked to genetic variation at specific loci. Here, we show a pattern in allele frequency among voltinism ecotypes of the European corn borer moth (Ostrinia nubilalis) that is reminiscent of a sawtooth cline. We characterized 145 autosomal and sex-linked SNPs and found that period, a circadian gene that is genetically linked to a major QTL determining variation in post-diapause development time, shows cyclical variation between voltinism ecotypes. Allele frequencies at an unlinked circadian clock gene cryptochrome1 were correlated with period. These results suggest that selection on development time to 'fit' complete life cycles into a latitudinally varying growing season produces oscillations in alleles associated with voltinism, primarily through changes at loci underlying the duration of transitions between diapause and other life history phases. Correlations among clock loci suggest possible coupling between the circadian clock and the circannual rhythms for synchronizing seasonal life history. We anticipate that latitudinal oscillations in allele frequency will represent signatures of adaptation to seasonal environments in other insects and may be critical to understanding the ecological and evolutionary consequences of variable environments, including response to global climate change. PMID:25430782

  18. Apolipoprotein E alleles in women with severe pre-eclampsia.

    PubMed Central

    Nagy, B; Rigó, J; Fintor, L; Karádi, I; Tóth, T

    1998-01-01

    This study investigated the frequency of apolipoprotein E (apoE) alleles among women with severe pre-eclampsia. The presence of the three most common apoE alleles (epsilon 2, epsilon 3, epsilon 4) was determined by polymerase chain reaction-restriction fragment length polymorphism in three groups of white women: non-pregnant healthy (n = 101), pregnant healthy (n = 52), and pregnant with a diagnosis of severe pre-eclampsia (n = 54). The frequency of apo epsilon 2 was highest among women with severe pre-eclampsia (16.6%) followed by non-pregnant women (12.9%), and those experiencing a healthy pregnancy (10.6%). The higher frequency of the apo epsilon 2 allele detected among women with severe pre-eclampsia suggests that apoE may play a role in the development of pre-eclampsia. PMID:9659248

  19. What Is a Recessive Allele?

    ERIC Educational Resources Information Center

    American Biology Teacher, 1991

    1991-01-01

    Presents four misconceptions students have concerning the concepts of recessive and dominant alleles. Discusses the spectrum of dominant-recessive relationships, different levels of analysis between phenotype and genotype, possible causes of dominance, and an example involving wrinkled peas. (MDH)

  20. The frequency and distribution of spontaneous attention shifts between social and nonsocial stimuli in autistic, typically developing, and nonautistic developmentally delayed infants.

    PubMed

    Swettenham, J; Baron-Cohen, S; Charman, T; Cox, A; Baird, G; Drew, A; Rees, L; Wheelwright, S

    1998-07-01

    Spontaneous shifts of attention were observed in autistic, typically developing, and nonautistic developmentally delayed infants. Three types of attention shifting behaviour were observed; (1) between an object and another object, (2) between an object and a person, and (3) between a person and another person. The two control groups shifted attention more frequently between an object and a person than between an object and another object or between a person and another person. The infants with autism showed a different pattern, shifting attention between an object and another object more than any other type of shift. Furthermore, infants with autism showed fewer shifts of attention between an object and a person, and between person and person, than did the two control groups. They also spent less time overall looking at people and looked more briefly at people and for longer durations at objects, compared to the two control groups. These results indicate an abnormality in social orientation in autism even at the early age of 20 months. PMID:9690937

  1. Allele-specific MMP-3 transcription under in vivo conditions

    SciTech Connect

    Zhu Chaoyong; Odeberg, Jacob; Hamsten, Anders; Eriksson, Per . E-mail: Per.Eriksson@ki.se

    2006-09-29

    A common matrix metalloproteinases-3 (MMP-3) -1612 5A/6A promoter polymorphism is associated with risk for cardiovascular disease, rheumatoid arthritis, and other diseases. Here we used the haplotype chromatin immunoprecipitation method to study allele-specific MMP-3 expression under in vivo conditions in heterozygous THP-1 cells. Pyrosequencing was used to analyse the ratio of 5A-allele to 6A-allele after chromatin immunoprecipitation using an antibody against phosphorylated active RNA polymerase II. There was no allele-specific difference in transcriptional activity during basal conditions, i.e., in unstimulated monocytic THP-1 cells. However, after stimulation of MMP-3 expression by monocyte differentiation or incubation with IL-1{beta}, the haplotype containing the 5A-allele was associated with higher transcriptional activity compared with the 6A-containing haplotype. Electromobility shift assay demonstrated increased binding of nuclear proteins to the 5A-allele after monocyte differentiation. In conclusion, the common MMP-3 5A/6A promoter polymorphism appears to be functional only during specific environmental conditions involving inflammation.

  2. Shifting tools

    SciTech Connect

    Fisher, E.P.; Welch, W.R.

    1984-03-13

    An improved shifting tool connectable in a well tool string and useful to engage and position a slidable sleeve in a sliding sleeve device in a well flow conductor. The selectively profiled shifting tool keys provide better fit with and more contact area between keys and slidable sleeves. When the engaged slidable sleeve cannot be moved up and the shifting tool is not automatically disengaged, emergency disengagement means may be utilized by applying upward force to the shifting tool sufficient to shear pins and cause all keys to be cammed inwardly at both ends to completely disengage for removal of the shifting tool from the sliding sleeve device.

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

    PubMed

    Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T; Morgan, Alex A; Moreno-Estrada, Andres; Nilsen, Geoffrey B; Ruau, David; Lincoln, Stephen E; Bustamante, Carlos D; Butte, Atul J

    2012-01-01

    Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed

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

    PubMed Central

    Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T.; Morgan, Alex A.; Moreno-Estrada, Andres; Nilsen, Geoffrey B.; Ruau, David; Lincoln, Stephen E.; Bustamante, Carlos D.; Butte, Atul J.

    2012-01-01

    Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed

  5. alpha1-antitrypsin (PI) alleles as markers of Westeuropean influence in the Baltic Sea region.

    PubMed

    Beckman, L; Sikström, C; Mikelsaar, A; Krumina, A; Kucinskas, V; Beckman, G

    1999-01-01

    The distribution of alpha1-antitrypsin (PI) alleles was studied in an attempt to elucidate migrations and admixture between populations in the Baltic Sea region. The frequency of the PI Z allele, a typically Northwesteuropean marker gene, showed a highly significant regional variation in the Baltic Sea region. The highest frequency (4.5%) was found in the western part of Latvia (Courland). The PI S allele, another marker of Westeuropean influence, also showed an increased frequency in the Courland population. These results indicate that among the populations east of the Baltic Sea the Curonian population has the most pronounced Westeuropean influence. Archaeological data have shown that from the 7th century and for several hundreds of years Courland received immigrations from mainland Sweden and the island of Gotland. We speculate that the increased frequencies of the PI Z alleles and S alleles in Courland may have been caused by these migrations. PMID:9858859

  6. No association between an allele at the D sub 2 dopamine receptor gene (DRD2) and alcoholism

    SciTech Connect

    Gelernter, J.; Krystal, J.; Kennedy, J.L. West Haven Dept. of Veterans Affairs Medical Center, CT ); O'Malley, S.; Risch, N.; Merikangas, K.; Kidd, K.K. ); Kranzler, H.R. )

    1991-10-02

    The author attempted to replicate a positive allelic association between the A1 allele of DRD2 (the D{sub 2} dopamine receptor locus) and alcoholism that has been reported. They compared allele frequencies at the previously described Taq I restriction fragment length polymorphism system of DRD2 in alcoholics and random population controls.

  7. On the detection of acoustic-gravity waves generated by typhoon by use of real time HF Doppler frequency shift sounding system

    NASA Astrophysics Data System (ADS)

    Huang, Yinn-Nien; Cheng, Kang; Chen, Sen-Wen

    1985-07-01

    A development of a direct vision type high-frequency Doppler frequency sounder and a setup of HF Doppler frequency sounding array at the northern part of Taiwan Island were presented. By use of all typhoons that occurred in 1982 and 1983, the detectability of the typhoon-generated acoustic-gravity waves by use of this HF Doppler frequency sounding array was presented. The results show that the acoustic-gravity waves generated by a typhoon can be detected by this sounding array; however, the detectability is only 2 out of 12.

  8. Analysis of the distribution of HLA-A alleles in populations from five continents.

    PubMed

    Middleton, D; Williams, F; Meenagh, A; Daar, A S; Gorodezky, C; Hammond, M; Nascimento, E; Briceno, I; Perez, M P

    2000-10-01

    The variation and frequency of HLA-A genotypes were established by PCR-SSOP typing in diverse geographically distributed populations: Brazilian, Colombian Kogui, Cuban, Mexican, Omani, Singapore Chinese, and South African Zulu. HLA-A allelic families with only one allele were identified for HLA-A*01, -A*23, -A*25, -A*31, -A*32, -A*36, -A*43, -A*69, -A*80; and with two alleles for HLA-A*03, -A*11, -A*26, -A*29, -A*33, -A*34, and -A*66. Greater variation was detected for HLA-A*02, -A*24, and -A*68 allele families. Colombian Kogui and Mexican Seris showed the least diversity with respect to HLA-A alleles, albeit with small numbers tested, with only four and five HLA-A alleles identified, respectively. It would appear by their presence in all populations studied, either rural or indigenous, that certain alleles are very important in pathogen peptide presentation. PMID:11082518

  9. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis

    PubMed Central

    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-01-01

    Abstract Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5′- and 3′-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients. Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3′-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5′-UTR polymorphisms). For neither the 3′- nor the 5′-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance. The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold

  10. Absorption intensity changes and frequency shifts of fundamental and first overtone bands for OH stretching vibration of methanol upon methanol-pyridine complex formation in CCl4: analysis by NIR/IR spectroscopy and DFT calculations.

    PubMed

    Futami, Yoshisuke; Ozaki, Yasushi; Ozaki, Yukihiro

    2016-02-21

    Infrared (IR) and near infrared (NIR) spectra were measured for methanol and the methanol-pyridine complex in carbon tetrachloride. Upon the formation of the methanol-pyridine complex, the frequencies of both the fundamental and first overtone bands of the OH stretching vibration shifted to lower frequencies, and the absorption intensity of the fundamental increased significantly, while that of the first overtone decreased markedly. By using quantum chemical calculations, we estimated the absorption intensities and frequencies of the fundamental and first overtone bands for the OH stretching vibration based on the one-dimensional Schrödinger equation. The calculated results well reproduced the experimental results. The molecular vibration potentials and dipole moment functions of the OH stretching vibration modes were compared between methanol and the methanol-pyridine complex in terms of absorption intensity changes and frequency shifts. The large change in the dipole moment function was found to be the main cause for the variations in absorption intensity for the fundamental and first overtone bands. PMID:26862859

  11. Association of apolipoprotein E allele {epsilon}4 with late-onset sporadic Alzheimer`s disease

    SciTech Connect

    Lucotte, G.; David, F.; Berriche, S.

    1994-09-15

    Apolipoprotein E, type {epsilon}4 allele (ApoE {epsilon}4), is associated with late-onset sporadic Alzheimer`s disease (AD) in French patients. The association is highly significant (0.45 AD versus 0.12 controls for {epsilon}4 allele frequencies). These data support the involvement of ApoE {epsilon}4 allele as a very important risk factor for the clinical expression of AD. 22 refs., 1 fig., 3 tabs.

  12. Shifting Attention

    ERIC Educational Resources Information Center

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  13. Frequency noise in frequency swept fiber laser.

    PubMed

    Pedersen, Anders Tegtmeier; Rottwitt, Karsten

    2013-04-01

    This Letter presents a measurement of the spectral content of frequency shifted pulses generated by a lightwave synthesized frequency sweeper. We found that each pulse is shifted in frequency with very high accuracy. We also discovered that noise originating from light leaking through the acousto- optical modulators and forward propagating Brillouin scattering appear in the spectrum. PMID:23546253

  14. Investigation of broadening and shift of vapour absorption lines of H{sub 2}{sup 16}O in the frequency range 7184 – 7186 cm{sup -1}

    SciTech Connect

    Nadezhdinskii, A I; Pereslavtseva, A A; Ponurovskii, Ya Ya

    2014-10-31

    We present the results of investigation of water vapour absorption spectra in the 7184 – 7186 cm{sup -1} range that is of particular interest from the viewpoint of possible application of the data obtained for monitoring water vapour in the Earth's stratosphere. The doublet of H{sub 2}{sup 16}O near ν = 7185.596 cm{sup -1} is analysed. The coefficients of broadening and shift of water vapour lines are found in the selected range in mixtures with buffer gases and compared to those obtained by other authors. (laser spectroscopy)

  15. Apolipoprotein E alleles in Alzheimer`s and Parkinson`s patients

    SciTech Connect

    Poduslo, S.E.; Schwankhaus, J.D.

    1994-09-01

    A number of investigators have found an association between the apolipoprotein E4 allele and Alzheimer`s disease. The E4 allele appears at a higher frequency in late onset familial Alzheimer`s patients. In our studies we obtained blood samples from early and late onset familial and sporadic Alzheimer`s patients and spouses, as well as from Parkinson`s patients. The patients were diagnosed as probable Alzheimer`s patients after a neurological examination, extensive blood work, and a CAT scan. The diagnosis was made according to the NINCDS-ADRDA criteria. The apolipoprotein E4 polymorphism was detected after PCR amplification of genomic DNA, restriction enzyme digestion with Hhal, and polyacrylamide gel electrophoresis. Ethidium bromide-stained bands at 91 bp were designated as allele 3, at 83 bp as allele 2, and at 72 bp as allele 4. Of the 84 probable Alzheimer`s patients (all of whom were Caucasian), 47 were heterozygous and 13 were homozygous for the E4 allele. There were 26 early onset patients; 13 were heterozygous and 7 homozygous for the E4 allele. The frequencies for the E4 allele for late onset familial patients was 0.45 and for sporadic patients was 0.37. We analyzed 77 spouses with an average age of 71.9 {plus_minus} 7.4 years as controls, and 15 were heterozygous for the E4 allele for an E4 frequency of 0.097. Of the 53 Parkinson`s patients, 11 had the E4 allele for a frequency of 0.113. Thus our findings support the association of the ApoE4 allele with Alzheimer`s disease.

  16. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, Michael B.; Hargens, Alan R.; Dulchavsky, Scott A.; Ebert, Douglas J.; Lee, Stuart M. C.; Laurie, Steven S.; Garcia, Kathleen M.; Sargsyan, Ashot E.; Martin, David S.; Liu, John; Macias, Brandon R.; Arbeille, Philippe; Danielson, Richard; Chang, Douglas; Gunga, Hanns-Christian; Johnston, Smith L.; Westby, Christian M.; Ploutz-Snyder, Robert J.; Smith, Scott M.

    2016-01-01

    We hypothesize that microgravity-induced cephalad fluid shifts elevate intracranial pressure (ICP) and contribute to VIIP. We will test this hypothesis and a possible countermeasure in ISS astronauts.

  17. Allele Dependent Silencing of Collagen Type I Using Small Interfering RNAs Targeting 3'UTR Indels - a Novel Therapeutic Approach in Osteogenesis Imperfecta

    PubMed Central

    Lindahl, Katarina; Kindmark, Andreas; Laxman, Navya; Åström, Eva; Rubin, Carl-Johan; Ljunggren, Östen

    2013-01-01

    Osteogenesis imperfecta, also known as “brittle bone disease”, is a heterogeneous disorder of connective tissue generally caused by dominant mutations in the genes COL1A1 and COL1A2, encoding the α1 and α2 chains of type I (pro)collagen. Symptomatic patients are usually prescribed bisphosphonates, but this treatment is neither curative nor sufficient. A promising field is gene silencing through RNA interference. In this study small interfering RNAs (siRNAs) were designed to target each allele of 3'UTR insertion/deletion polymorphisms (indels) in COL1A1 (rs3840870) and COL1A2 (rs3917). For both indels, the frequency of heterozygous individuals was determined to be approximately 50% in Swedish cohorts of healthy controls as well as in patients with osteogenesis imperfecta. Cultures of primary human bone derived cells were transfected with siRNAs through magnet-assisted transfection. cDNA from transfected cells was sequenced in order to measure targeted allele/non-targeted allele ratios and the overall degree of silencing was assessed by quantitative PCR. Successful allele dependent silencing was observed, with promising results for siRNAs complementary to both the insertion and non-insertion harboring alleles. In COL1A1 cDNA the indel allele ratios were shifted from 1 to 0.09 and 0.19 for the insertion and non-insertion allele respectively while the equivalent resulting ratios for COL1A2 were 0.05 and 0.01. Reductions in mRNA abundance were also demonstrated; in cells treated with siRNAs targeting the COL1A1 alleles the average COL1A1 mRNA levels were reduced 65% and 78% compared to negative control levels and in cells treated with COL1A2 siRNAs the average COL1A2 mRNA levels were decreased 26% and 49% of those observed in the corresponding negative controls. In conclusion, allele dependent silencing of collagen type I utilizing 3'UTR indels common in the general population constitutes a promising mutation independent therapeutic approach for osteogenesis

  18. Allele surfing promotes microbial adaptation from standing variation.

    PubMed

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

    2016-08-01

    The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from 'soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges. PMID:27307400

  19. Pollution-tolerant allele in fingernail clams (Musculium transversum).

    PubMed

    Sloss, B L; Romano, M A; Anderson, R V

    1998-08-01

    For nearly 50 years, the fingernail clam (Musculium transversum) was believed to be virtually eliminated from the Illinois River. In 1991, workers began finding substantial populations of M. transversum in the Illinois River including several beds in and around the highly polluted Chicago Sanitary District. In order to determine if populations of M. transversum from polluted sites exhibited any genetic response to the high levels of toxins and to examine the genetic structure of several populations of M. transversum for any changes due to the population crash, starch-gel electrophoresis was performed on M. transversum from three Illinois River localities and four Mississippi River basin locations. The sampled populations produced an inbreeding coefficient (FIS) of 0.929, indicating that the populations were highly inbred. The results of a suspected founder effect due to a bottleneck was suggested by an FST = 0.442. The isozyme Glucose-6-phosphate isomerase-2 (Gpi-2) produced allelic frequency patterns that were consistent with expected patterns of a pollution-tolerant allele. Polluted sites exhibited elevated frequencies of Gpi-2(100) whereas nonpolluted sites exhibited elevated frequencies of Gpi-2(74). This frequency pattern suggested that natural selection was occurring in populations under severe toxic pressures, leading to an increase in the frequency of the allele Gpi-2(100). Therefore, Gpi-2(100) is a possible pollution-tolerant mutation in M. transversum. PMID:9680522

  20. Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles

    PubMed Central

    Lockhart, David W.; Listgarten, Jennifer; Maley, Stephen N.; Kadie, Carl; Learn, Gerald H.; Nickle, David C.; Heckerman, David E.; Deng, Wenjie; Brander, Christian; Ndung'u, Thumbi; Coovadia, Hoosen; Goulder, Philip J.R.; Korber, Bette T.; Walker, Bruce D.; Mullins, James I.

    2009-01-01

    Abstract HIV-1 can evolve HLA-specific escape variants in response to HLA-mediated cellular immunity. HLA alleles that are common in the host population may increase the frequency of such escape variants at the population level. When loss of viral fitness is caused by immune escape variation, these variants may revert upon infection of a new host who does not have the corresponding HLA allele. Furthermore, additional escape variants may appear in response to the nonconcordant HLA alleles. Because individuals with rare HLA alleles are less likely to be infected by a partner with concordant HLA alleles, viral populations infecting hosts with rare HLA alleles may undergo a greater amount of evolution than those infecting hosts with common alleles due to the loss of preexisting escape variants followed by new immune escape. This hypothesis was evaluated using maximum likelihood phylogenetic trees of each gene from 272 full-length HIV-1 sequences. Recent viral evolution, as measured by the external branch length, was found to be inversely associated with HLA frequency in nef (p < 0.02), env (p < 0.03), and pol (p ≤ 0.05), suggesting that rare HLA alleles provide a disproportionate force driving viral evolution compared to common alleles, likely due to the loss of preexisting escape variants during early stages postinfection. PMID:19327049