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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

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

    2015-11-11

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

  2. 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

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

    PubMed

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

    2010-05-11

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

  4. 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.

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

    PubMed

    Levitan, Don R

    2012-06-01

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

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-02

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

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

    PubMed

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

    2014-04-22

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

  8. Frequency of FCGR3B Alleles in Thai Blood Donors

    PubMed Central

    Kaset, Chollanot; Leetrakool, Nipapan; Intharanut, Kamphon

    2013-01-01

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

  9. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

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

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

    PubMed Central

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

    1993-01-01

    We summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. We show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. We show that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size. PMID:8454213

  11. Frequency shifts in gravitational resonance spectroscopy

    DOE PAGES

    Baeßler, S.; Nesvizhevsky, V. V.; Pignol, G.; ...

    2015-02-25

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

  12. Frequency-Shift Hearing Aid

    NASA Technical Reports Server (NTRS)

    Weinstein, Leonard M.

    1994-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2015-04-30

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

  15. 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

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

    PubMed

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

    2016-03-08

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

  17. 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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2011-01-01

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

  20. 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.

  1. 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.

  2. Non-Equilibrium Allele Frequency Spectra Via Spectral Methods

    PubMed Central

    Hey, Jody; Chen, Kevin

    2011-01-01

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

  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; Lehtonen, Rainer; Hanski, Ilkka

    2016-01-01

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

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

    PubMed Central

    Pe'er, Itsik; Beckmann, Jacques S

    2004-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2010-12-01

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

  8. 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).

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2014-10-01

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

  11. 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)

  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. 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.

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

    PubMed

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

    2005-12-01

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

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

    PubMed

    Passos, G A; Picanço, V P

    1998-04-01

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

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

    PubMed Central

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

    2000-01-01

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

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

    PubMed

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

    2016-08-02

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

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

    PubMed

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

    1993-12-01

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

  19. 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 ...

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

    PubMed

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

    2004-03-01

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

  1. Quantum interference of biphotons with a Doppler frequency shift

    NASA Astrophysics Data System (ADS)

    Lariontsev, E. G.

    2016-08-01

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

  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. 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.

  5. Astrometric "Core-shifts" at the Highest Frequencies

    NASA Technical Reports Server (NTRS)

    Rioja, Maria; Dodson, Richard

    2010-01-01

    We discuss the application of a new VLBI astrometric method named "Source/Frequency Phase Referencing" to measurements of "core-shifts" in radio sources used for geodetic observations. We detail the reasons that astrometrical observations of 'core-shifts' have become critical in the era of VLBI2010. We detail how this new method allows the problem to be addressed at the highest frequencies and outline its superior compensation of tropospheric errors.

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

    PubMed Central

    Williamson, E G; Slatkin, M

    1999-01-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2014-06-01

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

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

    PubMed

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

    2008-06-01

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

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

    SciTech Connect

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

    1997-02-01

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

  11. 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.

  12. 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

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

    PubMed

    Greenberg, D A; Kaback, M M

    1982-05-01

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

  14. Lattice vibrational modes and their frequency shifts in semiconductor nanowires.

    PubMed

    Yang, Li; Chou, M Y

    2011-07-13

    We have performed first-principles calculations to study the lattice vibrational modes and their Raman activities in silicon nanowires (SiNWs). Two types of characteristic vibrational modes are examined: high-frequency optical modes and low-frequency confined modes. Their frequencies have opposite size dependence with a red shift for the optical modes and a blue shift for the confined modes as the diameter of SiNWs decreases. In addition, our calculations show that these vibrational modes can be detected by Raman scattering measurements, providing an efficient way to estimate the size of SiNWs.

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

    PubMed Central

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

    2013-01-01

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

  16. 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.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2012-05-01

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

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

    PubMed

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

    2009-02-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2014-03-01

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

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

    PubMed

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

    2016-10-31

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

  3. 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.

  4. Trapped electron cloud bolometer relying on frequency shift.

    PubMed Central

    Dehmelt, H

    1994-01-01

    An improved electron cloud bolometer is analyzed. In this device the cloud temperature is read out not via thermal noise induced by the electrons in a coupled LC circuit but via shift in their axial oscillation frequency in the Penning trap confining them. This shift occurs because as the electron cloud expands with increasing temperature, the average restoring force in the slightly anharmonic trap does change perceptibly. The scheme will be useful in exploring the microwave mode structure of the trap cavity and in locating magnetic field values for which the cavity-induced shift in the measured electron g factor disappears. PMID:11607480

  5. Trapped electron cloud bolometer relying on frequency shift.

    PubMed

    Dehmelt, H

    1994-07-05

    An improved electron cloud bolometer is analyzed. In this device the cloud temperature is read out not via thermal noise induced by the electrons in a coupled LC circuit but via shift in their axial oscillation frequency in the Penning trap confining them. This shift occurs because as the electron cloud expands with increasing temperature, the average restoring force in the slightly anharmonic trap does change perceptibly. The scheme will be useful in exploring the microwave mode structure of the trap cavity and in locating magnetic field values for which the cavity-induced shift in the measured electron g factor disappears.

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

    PubMed

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

    2015-01-30

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

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

    PubMed Central

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

    2012-01-01

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

  8. 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.

  9. Anomalously small BBR shift in Tl^+ frequency standard

    NASA Astrophysics Data System (ADS)

    Zuhrianda, Z.; Safronova, Marianna; Kozlov, Mikhail

    2012-06-01

    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. In the present work, we have used configuration interaction + coupled-cluster method to evaluate polarizabilities of the 6s^2 ^1S0 and 6s6p ^3P0 states of Tl^+; α0(^1S0)=19.5 a.u. and α0(^3P0)=21.4 a.u.. We find dynamic correction to the BBR shift to be negligible. The resulting BBR shift at 300 K is δνBBR=-0.0166(17) Hz. This result demonstrates that near cancelation of the ^1S0 and ^3P0 state polarizabilities in monovalent B^+, Al^+, In^+ ions of group 13 [Safronova et al., PRL 107, 143006 (2011)] continues for much heavier Tl^+, leading to anomalously small BBR shift for this system. The corresponding relative BBR shift at 300 K is |δνBBR/ν0|=1.1(1)x10-17. This calculation demonstrates that the BBR contribution to the fractional frequency uncertainty of the Tl^+ frequency standard at 300 K is 1x10-18.

  10. Light and buffer-gas frequency shifts in the Rb-85 maser frequency standard.

    NASA Technical Reports Server (NTRS)

    Stern, W. A.; Novick, R.

    1972-01-01

    The effect of buffer gas and pumping light on the output frequency of the Rb-85 maser is discussed. In contrast to a primary standard, these frequency shifts can be used to advantage when it is necessary to operate the maser at a frequency which differs from the ground-state hyperfine frequency by a few kilohertz. Using appropriate mixtures of buffer gas and carefully shaped lamp spectral profiles, it is also possible to operate the maser exactly at the ground-state hyperfine frequency. It is pointed out that the short-term phase stability of the maser is not impaired by these shifts.

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

    SciTech Connect

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

    2011-06-15

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

  12. Shifting fundamental frequency in simulated electric-acoustic listening.

    PubMed

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

    2010-09-01

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

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

    PubMed

    Chen, Hua

    2012-03-01

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

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

    PubMed

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

    2014-11-01

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

  15. Noble Gas Polarimetry Using Rb EPR Frequency Shifts

    NASA Astrophysics Data System (ADS)

    Ma, Z. L.; Jeong, K.; Houghtby, E.; Paskvan, T.; Limes, M. E.; Saam, B.

    2014-05-01

    EPR frequency shifts of optically polarized alkali-metal atoms can be exploited for polarimetry of noble-gas nuclei polarized by spin-exchange optical pumping. Our group recently measured the enhancement factor κ0 = 493 for Rb-129Xe, which characterizes the electron wave-function overlap during collisions and is crucial to the calibration of the frequency-shift for 129Xe polarimetry. This type of polarimetry is useful in several applications involving optically polarized 129Xe; our particular motivation is an in situ measurement of absolute 129Xe polarization within the optical pumping cell of a flow-through 129Xe polarizer. This application has some particular challenges, and we have initially observed some unexpected shifts in the 87Rb EPR frequency measurement on board the polarizer. In effort to disentangle these apparent systematic effects, we have constructed a separate experiment to characterize Rb EPR shifts for both 3He and 129Xe in sealed cells. We present results and analysis of these experiments and discuss implications for using this method in flow-through polarizers. NSF PHY-0855482

  16. 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

  17. 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.

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

    PubMed

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

    2009-11-01

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

  19. Blackbody radiation shift in ^87Rb frequency standard

    NASA Astrophysics Data System (ADS)

    Safronova, Marianna; Safronova, U. I.

    2010-03-01

    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 ^87Rb using the relativistic all-order method and evaluated the accuracy of our final value. Particular care is taken to accurately account for the contributions from highly-excited states. Various Rb atomic properties, including E1, E2, and E3 ground state polarizabilities, np and nd E1 polarizabilities, and hyperfine constants are also calculated. The results are compared with experiment and other theory where available.

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

    PubMed

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

    2014-04-01

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

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

    PubMed

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

    1994-05-01

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

  2. Anomalously small blackbody radiation shift in the Tl+ frequency standard

    NASA Astrophysics Data System (ADS)

    Zuhrianda, Z.; Safronova, M. S.; Kozlov, M. G.

    2012-02-01

    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. In the present work, we used configuration interaction + coupled-cluster method to evaluate polarizabilities of the 6s21S0 and 6s6p3P0 states of the Tl+ ion; we find α0(1S0)=19.6 a.u. and α0(3P0)=21.4 a.u. The resulting BBR shift of the 6s6p3P0-6s21S0 Tl+ transition at 300 K is ΔνBBR=-0.0157(16) Hz. This result demonstrates that near cancellation of the 1S0 and 3P0 state polarizabilities in divalent B+, Al+, and In+ ions of group IIIB [M. S. Safronova , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.107.143006 107, 143006 (2011)] continues for much heavier Tl+, leading to anomalously small BBR shift for this system. This calculation demonstrates that the BBR contribution to the fractional frequency uncertainty of the Tl+ frequency standard at 300 K is 1×10-18. We find that Tl+ has the smallest fractional BBR shift among all present or proposed frequency standards with the exception of Al+.

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

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

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

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

    PubMed

    Edge, Michael D; Rosenberg, Noah A

    2014-11-01

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

  5. 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.

  6. 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...

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

    NASA Astrophysics Data System (ADS)

    Agarwal, Aditi

    2016-07-01

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

  8. 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.

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

    PubMed

    Sala, A; Penacino, G; Corach, D

    1998-10-01

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

  10. Precision Calculation of Blackbody Radiation Shifts for Optical Frequency Metrology

    SciTech Connect

    Safronova, M. S.; Kozlov, M. G.; Clark, Charles W.

    2011-09-30

    We show that three group IIIB divalent ions, B{sup +}, Al{sup +}, and In{sup +}, have anomalously small blackbody radiation (BBR) shifts of the ns{sup 2} {sup 1}S{sub 0}-nsnp {sup 3}P{sub 0}{sup o} clock transitions. The fractional BBR shifts for these ions are at least 10 times smaller than those of any other present or proposed optical frequency standards at the same temperature, and are less than 0.3% of the Sr clock shift. We have developed a hybrid configuration-interaction + coupled-cluster method that provides accurate treatment of correlation corrections in such ions and yields a rigorous upper bound on the uncertainty of the final results. We reduce the BBR contribution to the fractional frequency uncertainty of the Al{sup +} clock to 4x10{sup -19} at T=300 K. We also reduce the uncertainties due to this effect at room temperature to 10{sup -18} level for B{sup +} and In{sup +} to facilitate further development of these systems for metrology and quantum sensing.

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

    PubMed Central

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

    2017-01-01

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

  12. 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

  13. 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.

  14. Predictions for collisional frequency shifts of ultracold rubidium atomic clocks

    NASA Astrophysics Data System (ADS)

    Kokkelmans, S. J. J. M. F.; Verhaar, B. J.; Heinzen, D. J.; Gibble, K.

    1997-04-01

    A few years ago atomic fountains using cold ^133Cs atoms led to a breakthrough in the field of atomic frequency standards(A. Clairon, C. Salomon, S. Guellati, and W. D. Phillips, Europhys. Lett. 16), 165 (1991); K. Gibble and S. Chu, Phys. Rev. Lett. 70, 1771 (1993).. It was soon found that the frequency shifts induced by collisions between atoms during their fountain orbit stand in the way to drawing the full benefits from this development. A possible way out is to switch to another atomic species(K. Gibble and B.J. Verhaar, Phys. Rev. A 52), 3370 (1995).. Recent experiments have made it possible to determine cold collision parameters for pairs of rubidium atoms with unprecedented accuracy(J.M. Vogels, C.C. Tsai, R.S. Freeland, S.J.J.M.F. Kokkelmans, B.J. Verhaar, and D.J. Heinzen (submitted).). Making use of these parameters we predict the collisional frequency shifts for a ^87Rb and a ^85Rb laser-cooled clock. Our results show the prospects for new atomic clocks based on ultracold rubidium to be promising.

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

    PubMed

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

    2014-04-01

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

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

    PubMed Central

    Mathieson, Iain; McVean, Gil

    2013-01-01

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

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

    PubMed Central

    Pritchard, Jonathan K.

    2016-01-01

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

  18. 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.

  19. Historical Shifts in Brazilian P. falciparum Population Structure and Drug Resistance Alleles

    PubMed Central

    Griffing, Sean M.; Viana, Giselle M. Rachid; Mixson-Hayden, Tonya; Sridaran, Sankar; Alam, Mohammad Tauqeer; de Oliveira, Alexandre Macedo; Barnwell, John W.; Escalante, Ananias A.; Povoa, Marinete Marins; Udhayakumar, Venkatachalam

    2013-01-01

    Previous work suggests that Brazilian Plasmodium falciparum has limited genetic diversity and a history of bottlenecks, multiple reintroductions due to human migration, and clonal expansions. We hypothesized that Brazilian P. falciparum would exhibit clonal structure. We examined isolates collected across two decades from Amapá, Rondônia, and Pará state (n = 190). By examining more microsatellites markers on more chromosomes than previous studies, we hoped to define the extent of low diversity, linkage disequilibrium, bottlenecks, population structure, and parasite migration within Brazil. We used retrospective genotyping of samples from the 1980s and 1990s to explore the population genetics of SP resistant dhfr and dhps alleles. We tested an existing hypothesis that the triple mutant dhfr mutations 50R/51I/108N and 51I/108N/164L developed in southern Amazon from a single origin of common or similar parasites. We found that Brazilian P. falciparum had limited genetic diversity and isolation by distance was rejected, which suggests it underwent bottlenecks followed by migration between sites. Unlike Peru, there appeared to be gene flow across the Brazilian Amazon basin. We were unable to divide parasite populations by clonal lineages and pairwise FST were common. Most parasite diversity was found within sites in the Brazilian Amazon, according to AMOVA. Our results challenge the hypothesis that triple mutant alleles arose from a single lineage in the Southern Amazon. SP resistance, at both the double and triple mutant stages, developed twice and potentially in different regions of the Brazilian Amazon. We would have required samples from before the 1980s to describe how SP resistance spread across the basin or describe the complex internal migration of Brazilian parasites after the colonization efforts of past decades. The Brazilian Amazon basin may have sufficient internal migration for drug resistance reported in any particular region to rapidly spread to

  20. 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)].

  1. Blackbody radiation shift in the Rb87 frequency standard

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

    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 Rb87 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, kS=-1.240(4)×10-10Hz/(V/m)2, is three times more accurate than the previous calculation [E. J. Angstman, V. A. Dzuba, and V. V. Flambaum, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.74.023405 74, 023405 (2006)].

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

    PubMed

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

    2015-11-01

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

  3. 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.

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

    PubMed Central

    Racimo, Fernando

    2016-01-01

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

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

    PubMed

    Racimo, Fernando

    2016-02-01

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

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

    PubMed

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

    2012-06-01

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

  7. 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…

  8. 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.

  9. 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

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

    PubMed

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

    2017-02-01

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

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

    PubMed Central

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

    2014-01-01

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

  12. Cryogenic fluid level sensors multiplexed by frequency-shifted interferometry.

    PubMed

    Ye, Fei; Chen, Tong; Xu, Di; Chen, Kevin P; Qi, Bing; Qian, Li

    2010-09-10

    We present a liquid level sensing system for cryogenic fluids based on an array of aluminum-coated fiber Bragg gratings written in high-attenuation fibers (HAFs) interrogated by frequency-shifted interferometry (FSI). The sensors are heated up optically through the absorption of light at the core of the HAF sections. The distinct thermal response of sensors in the liquid from that in the gas provides an unambiguous means to detect the liquid level. FSI allows the sensors to have overlapped spectral response, and, therefore, has the potential of accommodating a larger number of sensors in the array. The measurement of liquid nitrogen level using this system was experimentally demonstrated. The successful combination of aluminum-coated HAF Bragg grating sensors and the FSI technique promises a viable solution for liquid level sensor networks at cryogenic temperatures.

  13. 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.

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

    PubMed

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

    2005-06-01

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

  15. Postsynaptic membrane shifts during frequency potentiation of the hippocampal EPSP.

    PubMed

    Pitler, T A; Landfield, P W

    1987-10-01

    1. In some classes of central neurons, repetitive synaptic stimulation induces substantial changes in the postsynaptic membrane, in conjunction with robust frequency potentiation of the excitatory postsynaptic potential (EPSP). However, the nature and time course of these postsynaptic membrane shifts, or their possible contributions to EPSP frequency potentiation (e.g., by altering driving force or current pathways), have not been examined extensively. We therefore studied the simultaneous patterns of change in composite EPSP amplitude, postsynaptic input resistance (Rin), and postsynaptic membrane potential during a 4-min train of 10-Hz monosynaptic stimulation in CA1 neurons of hippocampal slices. Slices were maintained in media containing either control (4 mM) or high (6.5 mM) concentrations of K+. 2. Potentiation of the EPSP, hyperpolarization of the membrane, and a decline of Rin, all developed rapidly during 10-Hz synaptic stimulation; these responses reached maximal levels by 5-15 s of the stimulation train. In most cells, a membrane depolarization phase occurred between 15 and 45 s of stimulation, followed by rehyperpolarization by 1 min of stimulation. During the depolarization phase, both EPSP potentiation and the decline in Rin remained near maximal. No significant differences were seen as a function of K+ concentrations. 3. These results show that hyperpolarization is not invariably associated temporally with EPSP frequency potentiation. Moreover, if driving force and membrane conductance changes are assumed to be approximately similar in large dendrites and soma, then the increase in driving force due to membrane hyperpolarization was not sufficient to account for the three- and fourfold increases in EPSP amplitude seen during frequency potentiation. Further, based on similar assumptions and on dendritic models of EPSP attenuation, the decline in Rin should reduce EPSP amplitude at the dendritic synaptic site and, to a proportionately greater extent

  16. 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

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

    PubMed

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

    2011-01-01

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

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

    PubMed

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

    2016-11-04

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

  19. 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).

  20. 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.

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

    PubMed Central

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

    2016-01-01

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

  2. 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

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

    PubMed

    Field, Wesley; Hershberg, Ruth

    2015-05-26

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

  4. Frequency-shift vibro-acoustic modulation driven by low-frequency broadband excitations in a bistable cantilever oscillator

    NASA Astrophysics Data System (ADS)

    He, Qingbo; Xu, Yanyan; Lu, Siliang; Shao, Yong

    2017-03-01

    This paper reports a frequency-shift vibro-acoustic modulation (VAM) effect in a bistable microcracked cantilever oscillator. Low-frequency broadband excitations induced a VAM effect with a shifted modulation frequency through involving a microcracked metal beam in a bistable oscillator model. We used nonlinear dynamics equations and principles to describe the mechanism of a bistable oscillator whose natural frequency varied as the oscillation amplitude increased. We demonstrated this frequency-shift VAM effect using a prototype bistable oscillator model designed to efficiently detect microcracks in solid materials via the VAM effect using ambient vibration excitations.

  5. The perceived spatial frequency shift: evidence for frequency-selective neurones in the human brain

    PubMed Central

    Blakemore, Colin; Nachmias, Jacob; Sutton, Peter

    1970-01-01

    1. Prolonged observation of a high-contrast grating pattern causes an apparent shift in the spatial frequency of gratings subsequently viewed with the same retinal region. Gratings of higher and lower frequency than the adapting pattern seem, respectively, higher and lower than in fact they are. 2. There is no significant after-effect at the adapting frequency itself nor at frequencies more than two octaves away. 3. For very low adapting frequencies, the after-effect remains centred at about 3·0 c/deg and declines in strength as the adapting frequency is successively lowered. 4. The magnitude of the after-effect increases with the contrast of the adapting grating and the length of time spent in adaptation. It takes several hours to recover completely from 30 min adaptation. 5. The phenomenon is orientation-specific: a horizontal adapting grating has no effect on vertical test gratings. There is partial interocular transfer of the after-effect. 6. These findings provide further evidence that the visual system of man, like those of the cat and the monkey, contains neurones selectively sensitive to the orientation and dimensions of retinal images, and that these adaptable cells are actually involved in the encoding and perception of the size of simple patterns. PMID:5499822

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

    PubMed

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

    2004-12-01

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

  7. 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.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2017-02-16

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

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

    PubMed

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

    2006-05-01

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

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

    PubMed

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

    2009-01-01

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

  12. INTERACTION OF LASER RADIATION WITH MATTER. LASER PLASMA: Collision frequency shift of a short electromagnetic pulse

    NASA Astrophysics Data System (ADS)

    Chegotov, M. V.

    2004-03-01

    The frequency shift of a short electromagnetic pulse interaction with a plasma-like medium is discovered and studied. The shift is caused by elastic collisions of free electrons with ions or neutral particles.

  13. Influence of the intramolecular potential of adsorbed hydrogen on frequency shift calculations

    NASA Astrophysics Data System (ADS)

    Larin, Alexander V.

    1995-01-01

    The influence of the choice of the intramolecular potential on the resulting frequency shift of the fundamental vibrational transition in the dihydrogen molecule adsorbed on zeolite NaA is estimated. It is shown that an improved Morse potential and the potential calculated by Kołtsos and Wolniewicz lead to the same frequency shift value. Application of the Buckingham method for the frequency shift calculation to this case is discussed.

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2009-08-01

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

  18. Frequency-shifted interferometry for fiber-optic sensing

    NASA Astrophysics Data System (ADS)

    Ye, Fei

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

  19. 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

  20. 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.

  1. 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

  2. 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

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

    PubMed

    Johnson, G B

    1976-06-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-01-01

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

  7. 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.

  8. 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

  9. 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.

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

    PubMed

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

    2003-07-15

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

  11. 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.

  12. 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.

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

    PubMed

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

    2007-12-01

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

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

    PubMed

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

    2008-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-11-01

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

  16. Scheme for efficient extraction of low-frequency signal beyond the quantum limit by frequency-shift detection.

    PubMed

    Yang, R G; Zhang, J; Zhai, Z H; Zhai, S Q; Liu, K; Gao, J R

    2015-08-10

    Low-frequency (Hz~kHz) squeezing is very important in many schemes of quantum precision measurement. But it is more difficult than that at megahertz-frequency because of the introduction of laser low-frequency technical noise. In this paper, we propose a scheme to obtain a low-frequency signal beyond the quantum limit from the frequency comb in a non-degenerate frequency and degenerate polarization optical parametric amplifier (NOPA) operating below threshold with type I phase matching by frequency-shift detection. Low-frequency squeezing immune to laser technical noise is obtained by a detection system with a local beam of two-frequency intense laser. Furthermore, the low-frequency squeezing can be used for phase measurement in Mach-Zehnder interferometer, and the signal-to-noise ratio (SNR) can be enhanced greatly.

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

    PubMed

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

    2008-05-01

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

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

    PubMed

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

    2015-01-01

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

  19. 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.

  20. 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.

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

    PubMed Central

    Cornuet, J. M.; Luikart, G.

    1996-01-01

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

  2. Differential effects of frequency shifted feedback between child and adult stutterers.

    PubMed

    Howell, Peter; Sackin, Stevie; Williams, Roberta

    1999-01-01

    It has been reported previously that presentation of an altered form of the voice enhances the fluency of people who stutter. One of these forms of alteration is frequency shifted feedback. The effects of frequency shifted feedback was compared between two speaker groups that differed in age. The fluency enhancing effects of frequency shifted feedback was greater for adult speakers (mean age 21;3) than for children (mean age 9;11). The results are discussed in terms of their implications for theory and treatment.

  3. Labile cochlear tuning in the mustached bat. I. Concomitant shifts in biosonar emission frequency.

    PubMed

    Huffman, R F; Henson, O W

    1993-01-01

    The cochlea of the mustached bat (Pteronotus parnellii) has sharp tuning characteristics and pronounced resonance within a narrow band near the second harmonic, constant frequency (CF2) component of the animal's biosonar signals. That fine frequency discrimination occurs within this narrow band is evident from Doppler-shift compensation, whereby bats in flight lower the frequency of emitted CF2s to maintain returning echoes within this band. This study examined various factors capable of producing shifts in both the cochlear resonance frequency (CRF) and CF2s emitted by stationary bats and bats actively Doppler-shift compensating on a pendulum. Each of three experimental factors shifted the CRF in a reversible manner. Changes in body temperature produced an average CRF shift of 39 +/- 18 Hz/degrees C. The CRF increased with flight by 150 +/- 100 Hz and returned to baseline values within 10 min after flight. Contralateral sound exposure produced smaller (100 +/- 20 Hz), rapid shifts in the CRF, suggesting that a mechanism different from the temperature- and flight-related shifts was involved. Changes in the CRF induced by temperature and flight were accompanied by shifts in the emitted CF2 of stationary and moving bats. Coupled with a companion study of associated shifts in neural tuning, the concomitant changes in CRF and CF2 provide evidence of cochlear tuning lability in the mustached bat.

  4. Experimental study and prediction of frequency shift of piezoelectric ceramic packages

    NASA Astrophysics Data System (ADS)

    Zhang, Weiping; Roh, Young Sook; Asiz, A.; Xi, Yunping

    2000-05-01

    Frequency shift, due to quartz crystal resonator aging, has been identified as one of the most important quality control problems of quartz crystal products. The problem becomes more significant due to the device miniaturization and high precision standards for telecommunication applications. Since aging induced frequency shift occurs during a long time frame, it is necessary to predict the long-term behavior of the devices based on the short-term data obtained under an accelerated environment. On the other hand, frequency shift is associated with quite large random variation, and thus, a proper probabilistic theory should be used for analyzing test data and for developing a reliable prediction model. Accelerated testing was performed for various types of crystal resonators under elevated temperatures. The frequency shifts of the devices were measured at different testing periods. Markov chain model was used to characterize the frequency shift of the devices. The obtained short-term test results were used for calibrating the probabilistic transition matrix of Markov chain model. The model can then be used for predicting the long-term frequency shift. The time-temperature superposition principle in viscoelasticity was adopted to address the shift in time under different temperatures.

  5. Soliton self-frequency shift in tellurite microstructured fiber

    NASA Astrophysics Data System (ADS)

    Yan, Xin; Qin, Guanshi; Liao, Meisong; Suzuki, Takenobu; Ohishi, Yasutake

    2011-03-01

    We report broad near-infrared soliton source generation in a TeO2-Bi2O3-ZnO-Na2O tellurite microstructured optical fiber pumped by a 1557 nm femtosecond fiber laser. A continuous soliton wavelength shift from 1582 nm to 1851 nm was realized through a tellurite microstructured optical fiber as short as 6.5 cm. Experimental results are in good agreement with the numerical simulations using a generalized nonlinear Schrödinger equation. In addition, an analytical description of the Raman response function of tellurite glass is provided, and a Raman contribution factor of 0.51 is obtained from the actual Raman gain spectrum.

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

    PubMed Central

    Laval, Guillaume; SanCristobal, Magali; Chevalet, Claude

    2003-01-01

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

  7. Hyperfine contribution to spin-exchange frequency shifts in the hydrogen maser

    SciTech Connect

    Verhaar, B.J.; Koelman, J.M.V.A.; Stoof, H.T.C.; Luiten, O.J.; Crampton, S.B.

    1987-05-01

    We have rigorously included hyperfine interactions during electron-spin-exchange collisions between ground-state hydrogen atoms and find additional frequency shifts which are significant for low-temperature atomic hydrogen maser oscillators.

  8. 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.

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

    PubMed

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

    2007-10-01

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

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

    PubMed

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

    1994-01-01

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

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

    DOEpatents

    Nekoogar, Faranak [San Ramon, CA; Dowla, Farid U [Castro Valley, CA

    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.

  12. Bidirectional Shifting Effects of the Sound Intensity on the Best Frequency in the Rat Auditory Cortex

    PubMed Central

    Tao, Can; Zhang, Guangwei; Zhou, Chang; Wang, Lijuan; Yan, Sumei; Zhou, Yi; Xiong, Ying

    2017-01-01

    Frequency and intensity are two independent attributes of sound stimuli. Psychoacoustic studies have found that the sound intensity can affect the perception of frequency; however, the underlying neuronal mechanism remains largely unknown. To investigate if and how the sound level affects the frequency coding for auditory cortical neurons, we recorded the activities of neuronal ensembles and single neurons, as well as the synaptic input evoked by pure tones of different frequency and intensity combinations, in layer 4 of the rat primary auditory cortex. We found that the best frequency (BF) shifted bidirectionally with the increases in intensity. Specifically, the BF of neurons with a low characteristic frequency (CF) shifted lower, whereas the BF of neurons with a higher CF shifted higher. Meanwhile, we found that these shifts in the BF can lead to the expansion of high- and low-frequency areas in the tonotopic map, increasing the evenness of the BF distribution at high intensities. Our results revealed that the frequency tuning can bidirectionally shift with an increase in the sound intensity at both the cellular and population level. This finding is consistent with the perceptual illusions observed in humans and could provide a potential mechanism for this psychoacoustic effect. PMID:28290533

  13. Measuring the shift of a femtosecond laser frequency comb by the interference method

    SciTech Connect

    Basnak, Dmitriy V; Bikmukhametov, K A; Dmitriev, Aleksandr K; Dychkov, Aleksandr S; Kuznetsov, Sergei A; Lugovoy, A A; Mitsziti, P

    2012-01-31

    We have demonstrated the possibility of measuring the femtosecond laser frequency comb shift by the position of a Fabry - Perot interferometer's transmission bands with a statistical error of 10{sup -2} and a systematic shift of 10{sup -1}. (control of laser radiation parameters)

  14. Dependence of the brillouin frequency shift on strain and temperature in a photonic crystal fiber.

    PubMed

    Zou, Lufan; Bao, Xiaoyi; Afshar V, Shahraam; Chen, Liang

    2004-07-01

    The dependence of the Brillouin frequency shift on strain in a photonic crystal fiber (PCF) was measured at a wavelength of 1320 nm for the first time to the authors' knowledge. Together with measurements of the dependence of the Brillouin frequency shift on temperature in the PCF, we demonstrate the feasibility of the highly precise simultaneous measurement of temperature and strain by use of the PCF in a distributed Brillouin sensing system with a spatial resolution of 15 cm.

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

    PubMed

    Wen, Biyang; Li, Ke

    2016-08-17

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

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

    NASA Astrophysics Data System (ADS)

    Wen, Biyang; Li, Ke

    2016-08-01

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

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

    PubMed Central

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

    2009-01-01

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

  19. 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.

  20. 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

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

    PubMed

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

    2013-12-01

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

  2. Circular High-Q Resonating Isotropic Strain Sensors with Large Shift of Resonance Frequency under Stress

    PubMed Central

    Melik, Rohat; Unal, Emre; Perkgoz, Nihan Kosku; Puttlitz, Christian; Demir, Hilmi Volkan

    2009-01-01

    We present circular architecture bioimplant strain sensors that facilitate a strong resonance frequency shift with mechanical deformation. The clinical application area of these sensors is for in vivo assessment of bone fractures. Using a rectangular geometry, we obtain a resonance shift of 330 MHz for a single device and 170 MHz for its triplet configuration (with three side-by-side resonators on chip) under an applied load of 3,920 N. Using the same device parameters with a circular isotropic architecture, we achieve a resonance frequency shift of 500 MHz for the single device and 260 MHz for its triplet configuration, demonstrating substantially increased sensitivity. PMID:22303132

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

    PubMed Central

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

    2016-01-01

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

  4. 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.

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

    PubMed

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

    2012-09-07

    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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

    Camparo, James

    2005-07-01

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

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

    PubMed

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

    2014-08-01

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

  10. Hyperfine frequency shift and Zeeman relaxation in alkali-metal-vapor cells with antirelaxation alkene coating

    NASA Astrophysics Data System (ADS)

    Corsini, Eric P.; Karaulanov, Todor; Balabas, Mikhail; Budker, Dmitry

    2013-02-01

    An alkene-based antirelaxation coating for alkali-metal vapor cells exhibiting Zeeman relaxation times up to 77 s was recently identified by Balabas The long relaxation times, two orders of magnitude longer than in paraffin- (alkane-) coated cells, motivate revisiting the question of what the mechanism is underlying wall-collision-induced relaxation and renew interest in applications of alkali-metal vapor cells to secondary frequency standards. We measure the width and frequency shift of the ground-state hyperfine mF=0→mF'=0 transition (clock resonance) in vapor cells with 85Rb and 87Rb atoms, with an alkene antirelaxation coating. We find that the frequency shift is slightly larger than for paraffin-coated cells and that the Zeeman linewidth scales linearly with the hyperfine frequency shift.

  11. 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.

  12. Investigation of the Frequency Shift of a SAD Circuit Loop and the Internal Micro-Cantilever in a Gas Sensor

    PubMed Central

    Guan, Liu; Zhao, Jiahao; Yu, Shijie; Li, Peng; You, Zheng

    2010-01-01

    Micro-cantilever sensors for mass detection using resonance frequency have attracted considerable attention over the last decade in the field of gas sensing. For such a sensing system, an oscillator circuit loop is conventionally used to actuate the micro-cantilever, and trace the frequency shifts. In this paper, gas experiments are introduced to investigate the mechanical resonance frequency shifts of the micro-cantilever within the circuit loop(mechanical resonance frequency, MRF) and resonating frequency shifts of the electric signal in the oscillator circuit (system working frequency, SWF). A silicon beam with a piezoelectric zinc oxide layer is employed in the experiment, and a Self-Actuating-Detecting (SAD) circuit loop is built to drive the micro-cantilever and to follow the frequency shifts. The differences between the two resonating frequencies and their shifts are discussed and analyzed, and a coefficient α related to the two frequency shifts is confirmed. PMID:22163588

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

    Duru, Kimberley C; Thomas, Bolaji N

    2014-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  17. 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.

  18. Accurate Evaluation of Microwave-Leakage-Induced Frequency Shifts in Fountain Clocks

    NASA Astrophysics Data System (ADS)

    Fang, Fang; Liu, Kun; Chen, Wei-Liang; Liu, Nian-Feng; Suo, Rui; Li, Tian-Chun

    2014-10-01

    We report theoretical calculations of the transition probability errors introduced by microwave leakage in Cs fountain clocks, which will shift the clock frequency. The results show that the transition probability errors are affected by the Ramsey pulse amplitude, the relative phase between the Ramsey field and the leakage field, and the asymmetry of the leakage fields for the upward and downward passages. This effect is quite different for the leakage fields presenting below the Ramsey cavity and above the Ramsey cavity. The leakage-field-induced frequency shifts of the NIM5 fountain clock in different cases are measured. The results are consistent with the theoretical calculations, and give an accurate evaluation of the leakage-field-induced frequency shifts, as distinguished from other microwave-power-related effects for the first time.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2007-05-24

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

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

    PubMed

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

    2013-02-01

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

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

    PubMed

    Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro

    2010-04-01

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

  3. Qualitative analysis of collective mode frequency shifts in L-alanine using terahertz spectroscopy.

    PubMed

    Taulbee, Anita R; Heuser, Justin A; Spendel, Wolfgang U; Pacey, Gilbert E

    2009-04-01

    We have observed collective mode frequency shifts in deuterium-substituted L-alanine, three of which have previously only been calculated. Terahertz (THz) absorbance spectra were acquired at room temperature in the spectral range of 66-90 cm(-1), or 2.0-2.7 THz, for L-alanine (L-Ala) and four L-Ala compounds in which hydrogen atoms (atomic mass = 1 amu) were substituted with deuterium atoms (atomic mass = 2 amu): L-Ala-2-d, L-Ala-3,3,3-d(3), L-Ala-2,3,3,3-d(4), and L-Ala-d(7). The absorbance maxima of two L-Ala collective modes in this spectral range were recorded for multiple spectral measurements of each compound, and the magnitude of each collective mode frequency shift due to increased mass of these specific atoms was evaluated for statistical significance. Calculations were performed which predict the THz absorbance frequencies based on the estimated reduced mass of the modes. The shifts in absorbance maxima were correlated with the location(s) of the substituted deuterium atom(s) in the L-alanine molecule, and the atoms contributing to the absorbing delocalized mode in the crystal structure were deduced using statistics described herein. The statistical analyses presented also indicate that the precision of the method allows reproducible frequency shifts as small as 1 cm(-1) or 0.03 THz to be observed and that these shifts are not random error in the measurement.

  4. 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.

  5. Frequency shifting at fiber-optical event horizons: The effect of Raman deceleration

    SciTech Connect

    Robertson, S.; Leonhardt, U.

    2010-06-15

    Pulses in fibers establish analogs of the event horizon [Philbin et al., Science 319, 1367 (2008)]. At a group-velocity horizon, the frequency of a probe wave is shifted. We present a theoretical model of this frequency shifting, taking into account the deceleration of the pulse caused by the Raman effect. The theory shows that the probe-wave spectrum is sensitive to details of the probe-pulse interaction. Our results indicate an additional loss mechanism in the experiment [Philbin et al., Science 319, 1367 (2008)] that has not been accounted for. Our analysis is also valid for more general cases of the interaction of dispersive waves with decelerated solitons.

  6. New method for lens thickness measurement by the frequency-shifted confocal feedback

    NASA Astrophysics Data System (ADS)

    Tan, Yidong; Zhu, Kaiyi; Zhang, Shulian

    2016-12-01

    We describe a new method for lens thickness and air gap measurement based on the frequency-shifted confocal feedback. The light intensity fluctuation is eliminated by the heterodyne modulation and the detection sensitivity is improved prominently by the frequency-shifted feedback effect. The measurement results for different materials and kinds of lenses are presented in the paper, including K9 plain glasses, fused silica plain glass, and K9 biconvex lens. The uncertainty of the axial positioning is better than 0.0005 mm and the accuracy reaches micron range. It is promising to be applied in the multi-layer interface positioning and measurement area.

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

    SciTech Connect

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

    2016-01-15

    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{sup −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.

  8. 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.

  9. 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

  10. Microwave leakage-induced frequency shifts in the primary frequency standards NIST-F1 and IEN-CSF1.

    PubMed

    Shirley, Jon H; Levi, Filippo; Heavner, Thomas P; Calonico, Davide; Yu, Dai-Hyuk; Jefferts, Steve R

    2006-12-01

    In atomic fountain primary frequency standards, the atoms ideally are subjected to microwave fields resonant with the ground-state, hyperfine splitting only during the two pulses of Ramsey's separated oscillatory field measurement scheme. As a practical matter, however, stray microwave fields can be present that shift the frequency of the central Ramsey fringe and, therefore, adversely affect the accuracy of the standard. We investigate these uncontrolled stray fields here and show that the frequency errors can be measured, and indeed even the location within the standard determined by the behavior of the measured frequency with respect to microwave power in the Ramsey cavity. Experimental results that agree with the theory are presented as well.

  11. 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

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

    PubMed

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

    2005-08-01

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

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

    PubMed

    González, César A; Rubinsky, Boris

    2006-06-01

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

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

    PubMed

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

    2012-01-01

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

  15. Tracing part-per-billion line shifts with direct-frequency-comb Vernier spectroscopy

    NASA Astrophysics Data System (ADS)

    Siciliani de Cumis, M.; Eramo, R.; Coluccelli, N.; Cassinerio, M.; Galzerano, G.; Laporta, P.; De Natale, P.; Cancio Pastor, P.

    2015-01-01

    Accurate frequency measurements of molecular transitions around 2 μ m are performed by using a direct-frequency-comb spectroscopy approach that combines an Er+ frequency-comb oscillator at 1.5 μ m , a Tm-Ho fiber amplifier, and a Fabry-Perot-filter, high-resolution dispersive spectrometer optical multiplex-detection system. This apparatus has unique performances in terms of a wide dynamic range to integrate the intensity per comb mode, which allows one to measure molecular absorption profiles with high precision. Spectroscopic information about transition frequencies and linewidths is very accurately determined. Relative frequency uncertainties of the order of a few parts in 10-9 are achieved for rovibrational transitions of the CO2 molecule around 5100 cm-1. Moreover, tiny frequency shifts due to molecular collisions and interacting laser power using direct comb spectroscopy are investigated in a systematic way.

  16. 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.

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

    PubMed

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

    2013-08-07

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

  18. Frequency Hopping, Multiple Frequency-Shift Keying, Coding, and Optimal Partial-Band Jamming.

    DTIC Science & Technology

    1982-08-01

    the data modulation of most frequency-hopping systems. 4S Haykin, Communication Systems, John Wiley & Sons, Inc., New York (1978). 5 R. F. Pawula , On...Systems, 4, Academic Press, Inc., New York (1975). (4) S. Haykin, Commaunicationi Systems, John Wiley & Sons, Inc., New York (1978). (5) R. F. Pawula

  19. 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.

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

    PubMed

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

    2007-08-01

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

  1. Motional frequency shifts of trapped ions in the Lamb-Dicke regime

    SciTech Connect

    Lizuain, I.; Muga, J. G.; Eschner, J.

    2007-09-15

    First order Doppler effects are usually ignored in laser driven trapped ions when the recoil frequency is much smaller than the trapping frequency (Lamb-Dicke regime). This means that the central, carrier excitation band is supposed to be unaffected by vibronic transitions in which the vibrational number changes. While this is strictly true in the Lamb-Dicke limit (infinitely tight confinement), the vibronic transitions do play a role in the Lamb-Dicke regime. In this paper we quantify the asymptotic behavior of their effect with respect to the Lamb-Dicke parameter. In particular, we give analytical expressions for the frequency shift, 'pulling' or 'pushing', produced in the carrier absorption band by the vibronic transitions both for Rabi and Ramsey schemes. This shift is shown to be independent of the initial vibrational state.

  2. 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.

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

    PubMed Central

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

    2013-01-01

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

  4. Transient Raman response and soliton self-frequency shift in tellurite microstructured fiber

    NASA Astrophysics Data System (ADS)

    Yan, Xin; Qin, Guanshi; Liao, Meisong; Suzuki, Takenobu; Ohishi, Yasutake

    2010-12-01

    We report on the Raman response function and the soliton self-frequency shift in a tellurite microstructured fiber pumped at 1557 nm. The Raman response function in a tellurite fiber quantifies a contribution of the Raman fraction to the nonlinear optical response. Continuous soliton wavelength shift from 1582 to 1851 nm is observed in a tellurite microstructured optical fiber with the length of 6.5 cm. The experimental results strongly correlated with the numerical simulations based on a generalized nonlinear Schrödinger equation.

  5. Self-density frequency shift measurements of Raman N 2 Q-branch transitions

    NASA Astrophysics Data System (ADS)

    Lavorel, B.; Chaux, R.; Saint-Loup, R.; Berger, H.

    1987-04-01

    We report stimulated Raman investigations of N 2 Q-branch transitions in view to measure the self-density frequency shift. These measurements performed at 295 K over the density range 0.02-0.8 Amagat lead to a mean shift value equal to -5.5×10 -3 cm -1/Amagat. Moreover, our data extrapolated at zero density allowed new refinements of the N 2 molecular constants: v0=2329.91165 (17) cm -1, B1- B0=-0.0173714 (22) cm -1 and D1- D0=(7.6±5.0)×10 -9 cm -1.

  6. Interplay of Density Gradients and Nonlinear Frequency Shifts in Stimulated Raman Scattering

    NASA Astrophysics Data System (ADS)

    Strozzi, D. J.; Williams, E. A.; Langdon, A. B.; Bers, A.; Ram, A. K.; Shoucri, M. M.

    2004-11-01

    In an inhomogeneous medium, parametric instabilities are only resonant over a finite region of space. A WKB analysis that accounts only for the wavenumber mismatch d(k_0-k_1-k_2)/dx, for a linear inhomogeneity and sufficiently large system, shows the convective gain is independent of the system size, and the relative directions of wave propagation and density gradient. (M. N. Rosenbluth, Phys. Rev. Lett. 29, 565 (1972)). In Raman scattering, the resonant frequency of the electron plasma wave (EPW) depends on its amplitude (G. J. Morales and T. M. O'Neil, Phys. Rev. Lett. 28, 417 (1972)). The EPW amplitude and therefore its frequency shift vary in space. We study how the inhomogeneity due to a density gradient and the spatially-varying frequency shift interact. The detunings due to wavenumber mismatch and frequency shift may counteract or enhance each other. We study these effects and their consequences for SRS saturation in inhomogeneous media with kinetic simulations using the 1-D, Eulerian Vlasov code ELVIS (D. J. Strozzi et al., Comp. Phys. Comm., accepted).

  7. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    1999-01-01

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

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

    PubMed Central

    Kiesler, Kevin M.; Vallone, Peter M.

    2013-01-01

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

  11. 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

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

    PubMed Central

    Patıroğlu, Türkan; Akar, H. Haluk

    2016-01-01

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

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

    PubMed

    Patıroğlu, Türkan; Akar, H Haluk

    2016-12-01

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

  14. MHz few-body frequency shift detected in a cold {sup 85}Rb Rydberg gas

    SciTech Connect

    Han Jianing

    2011-11-15

    We have observed a density-dependent frequency shift of more than 4 MHz in a cold {sup 85}Rb Rydberg gas trapped in a magneto-optical trap. A one-dimensional linearly aligned four-body model is proposed to explain the experimental data, and the calculation matches the experimental data. The calculation also shows that if the energy detuning between the two coupled states, the nsnsns(n+1)s and nsnsnpnp states in this case, is small, the lowest level of the nsnsnpnp manifold has the maximum mixing probability, causing a frequency shift instead of line broadening. The results reported may be used for few-body blockade, Rydberg single-atom imaging, studying few-body to many-body transitions and interactions, and few-body ionization as well as quantum metrology.

  15. 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.

  16. Photonic analog-to-digital converter using soliton self-frequency shift and interleaving spectral filters.

    PubMed

    Xu, Chris; Liu, Xiang

    2003-06-15

    We propose a novel ultrafast photonic analog-to-digital converter that uses the soliton self-frequency shift in an optical fiber as an optical power-to-frequency conversion mechanism and a set of interleaving spectral filters as the optical comparators. Our method does all the signal processing in the optical domain and requires binary receivers in only the electronic domain. In contrast to the usual exponential scaling, the simultaneous binary search architecture that we propose results in a flash analog-to-digital converter with remarkable linear scaling between the number of comparators and the number of bits resolved.

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

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2013-04-01

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

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

    PubMed Central

    Reppert, Mike; Tokmakoff, Andrei

    2013-01-01

    The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm−1 for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm−1. These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra. PMID:23574217

  19. Nonlinear frequency shift in Raman backscattering and its implications for plasma diagnostics

    NASA Astrophysics Data System (ADS)

    Kaganovich, D.; Hafizi, B.; Palastro, J. P.; Ting, A.; Helle, M. H.; Chen, Y.-H.; Jones, T. G.; Gordon, D. F.

    2016-12-01

    Raman backscattered radiation of intense laser pulses in plasmas is investigated for a wide range of intensities relevant to laser wakefield acceleration. The weakly nonlinear dispersion relation for Raman backscattering predicts an intensity and density dependent frequency shift that is opposite to that suggested by a simple relativistic consideration. This observation has been benchmarked against experimental results, providing a novel diagnostic for laser-plasma interactions.

  20. Synthesis of virtual Brillouin frequency shift profiles in BOTDA sensors using optical source dithering

    NASA Astrophysics Data System (ADS)

    Urricelqui, Javier; Sagues, Mikel; Loayssa, Alayn

    2014-05-01

    We demonstrate a novel concept for Brillouin optical time domain analysis sensors that is based on synthesizing a virtual Brillouin frequency shift profile along the sensing fiber. The technique is based on modulating the wavelength of the optical source with a periodic waveform that is synchronized to the pump pulse. Application of this new tool to the compensation of non-local effects and Brillouin-induced noise in distributed sensors is experimentally demonstrated.

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

    PubMed

    Wang, Gao; Liu, Shao-Cong; Wen, Qiang; Zhao, Hui; Zhao, Yu

    2013-04-01

    In order to obtain the distribution of the temperature in the range of the granary precisely and stably, we designed a temperature measurement system of the fiber Bragg grating. Through the fiber-optic network the system can detect granary temperature in a wide range, and there is a linear relationship between the measured temperature by fiber Bragg grating and the center wavelength, so according to the function of spectrum linear frequency shift it obtained precise temperature in the granary. The working wavelengths of each grating in the system are separated from each other. After reflected by 3 dB coupler, the wavelength detection and demodulation system was used to measure the linear frequency shift of the plurality grating, and the system can get temperature data of everywhere in the granary. The experimental obtained the temperature information by equipments, such as LPT-101 light source, optical fiber with FBG encapsulated, magnification processing circuit, simulation granary, etc. With Origin software the diagram of the relationship between the frequency shift of the measured temperature and wavelength was drawn, and compared with the traditional measuring method of the K-type thermocouple measurement data. Experimental results show that the measured temperature of the fiber Bragg grating is closer to standard temperature, and the anti-jamming ability can meet the requirements of the granary large range temperature monitoring.

  2. Measurement of a hyperfine-induced spin-exchange frequency shift in atomic hydrogen

    SciTech Connect

    Walsworth, R.L.; Silvera, I.F. ); Mattison, E.M.; Vessot, R.F.C. )

    1992-09-01

    We have measured a hyperfine-induced spin-exchange frequency shift in the atomic-hydrogen ground-state hyperfine transition. A recent quantum-mechanical treatment of low-energy hydrogen-hydrogen scattering by Koelman {ital et} {ital al}. (Phys. Rev. A 38, 3535 (1988)) predicts such frequency shifts to become large at low temperature, and to affect the performance of atomic clocks such as the cryogenic hydrogen maser. The experiment reported here was performed with a hydrogen maser operating near room temperature, where the reported hyperfine effects are predicted to be small, but measurable. Using an adiabatic fast passage (AFP) technique to vary the incoming atomic population in the masing states from approximately 100% (AFP on) to 50% (AFP off), we determined the change in the dimensionless hyperfine-induced frequency-shift parameter {Omega} to be {Omega}{sub on}{minus}{Omega}{sub off}=5.38 (1.06){times}10{sup {minus}4}. The theoretical prediction at this temperature is {Omega}{sub on}{minus}{Omega}{sub off}={minus}0.76{times}10{sup {minus}4} to {minus}1.12{times}10{sup {minus}4}, for the range of masing-state populations used in the present experiment. We review the relevant theory, report our experimental method and results, and discuss possible reasons for the discrepancy between experiment and theory.

  3. 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

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

    PubMed

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

    2012-09-01

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

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

    PubMed Central

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

    2009-01-01

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

  6. Estimation of the blood Doppler frequency shift by a time-varying parametric approach.

    PubMed

    Girault, J M; Kouamé, D; Ouahabi, A; Patat, F

    2000-03-01

    Doppler ultrasound is widely used in medical applications to extract the blood Doppler flow velocity in the arteries via spectral analysis. The spectral analysis of non-stationary signals and particularly Doppler signals requires adequate tools that should present both good time and frequency resolutions. It is well-known that the most commonly used time-windowed Fourier transform, which provides a time-frequency representation, is limited by the intrinsic trade-off between time and frequency resolutions. Parametric methods have then been introduced as an alternative to overcome this resolution problem. However, the performance of those methods deteriorates when high non-stationarities are present in the Doppler signal. For the purpose of accurately estimating the Doppler frequency shift, even when the temporal flow velocity is rapid (high non-stationarity), we propose to combine the use of the time-varying autoregressive (AR) method and the (dominant) pole frequency. This proposed method performs well in the context where non-stationarities are very high. A comparative evaluation has been made between classical (FFT based) and AR (both block and recursive) algorithms. Among recursive algorithms we test an adaptive recursive method as well as a time-varying recursive method. Finally, the superiority of the time-varying parametric approach in terms of frequency tracking and delay in the frequency estimate is illustrated for both simulated and in vivo Doppler signals.

  7. 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

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

    PubMed

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

    2000-10-01

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

  9. 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

  10. Simultaneously measured signals in scanning probe microscopy with a needle sensor: Frequency shift and tunneling current

    NASA Astrophysics Data System (ADS)

    Morawski, Ireneusz; Voigtländer, Bert

    2010-03-01

    We present combined noncontact scanning force microscopy and tunneling current images of a platinum(111) surface obtained by means of a 1 MHz quartz needle sensor. The low-frequency circuit of the tunneling current was combined with a high-frequency signal of the quartz resonator enabling full electrical operation of the sensor. The frequency shift and the tunneling current were detected simultaneously, while the feedback control loop of the topography signal was fed using one of them. In both cases, the free signal that was not connected to the feedback loop reveals proportional-integral controller errorlike behavior, which is governed by the time derivative of the topography signal. A procedure is proposed for determining the mechanical oscillation amplitude by utilizing the tunneling current also including the average tip-sample work function.

  11. 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.

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

    SciTech Connect

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

    2015-06-20

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

  13. Frequency shifts of resonant modes of the Sun due to near-surface convective scattering

    NASA Astrophysics Data System (ADS)

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

    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 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Williams, R C; McAuley, J E

    1992-01-01

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

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

    PubMed Central

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

    2017-01-01

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

  17. Mixed quantum-classical molecular dynamics analysis of the molecular-level mechanisms of vibrational frequency shifts.

    PubMed

    Morales, Christine M; Thompson, Ward H

    2007-06-28

    A detailed analysis of the origins of vibrational frequency shifts of diatomic molecules (I2 and ICl) in a rare gas (Xe) liquid is presented. Specifically, vibrationally adiabatic mixed quantum-classical molecular dynamics simulations are used to obtain the instantaneous frequency shifts and correlate the shifts to solvent configurations. With this approach, important mechanistic questions are addressed, including the following: How many solvent atoms determine the frequency shift? What solvent atom configurations lead to blue shifts, and which lead to red shifts? What is the effect of solute asymmetry? The mechanistic analysis can be generally applied and should be useful in understanding what information is provided by infrared and Raman spectra about the environment of the probed vibrational mode.

  18. An evaluation of the frequency shift caused by collisions with background gas in the primary frequency standard NPL-CsF2.

    PubMed

    Szymaniec, Krzysztof; Lea, Stephen; Liu, Kun

    2014-01-01

    Collisions between cold cesium atoms and background gas atoms at ambient temperature reduce the cold atom signal in a fountain clock and at the same time produce a shift in the measured clock frequency. We evaluate the shift in the NPL-CsF2 cesium fountain primary frequency standard based on measurements of the fractional loss of cold atoms from the atomic cloud during the interrogation time combined with a model by Gibble that quantifies the relationship between the loss and the frequency shift.

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2014-03-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Detection of damaged supports under railway track based on frequency shift

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    In railway transportation systems, the tracks are usually fastened on sleepers which are supported by the ballast. A lot of research has been conducted to guarantee the safety of railway track because of its importance, and more concern is expressed about monitoring of track itself such as railway level and alignment. The ballast and fasteners which provide strong support to the railway track are important as well whereas the detection of loose or missing fasteners and damaged ballast mainly relies on visual inspection. Although it is reliable when the fastener is missing and the damaged ballast is on the surface, it provides less help if the fastener is only loose and the damaged ballast is under the sleepers, which are however frequently observed in practice. This paper proposes an approach based on frequency shift to identify the damaged supports including the loose or missing fasteners and damaged ballast. In this study, the rail-sleeper-ballast system is modeled as an Euler beam evenly supported by a series of springs, the stiffness of which are reduced when the fastener is loose or missing and the ballast under the sleepers is damaged. An auxiliary mass is utilized herein and when it is mounted on the beam, the natural frequencies of the whole system will change with respect to the location of the auxiliary mass. The auxiliary mass induced frequency shift is analyzed and it is found the natural frequencies change periodically when the supports are undamaged, whereas the periodicity will be broken due to damaged supports. In fact, the natural frequencies drop clearly when the auxiliary mass moves over the damaged support. A special damage index only using the information of the damaged states is proposed and both numerical and experimental examples are carried out to validate the proposed method.

  6. Narrow-linewidth chirped frequency comb from a frequency-shifted feedback Ti:sapphire laser seeded by a phase-modulated single-frequency fiber laser.

    PubMed

    Brandl, Matthias F; Mücke, Oliver D

    2010-12-15

    Frequency-shifted feedback (FSF) lasers have emerged as powerful tools for precision distance metrology. At the output of a Michelson interferometer, the detected rf spectra of the FSF laser light contain a length-dependent heterodyne beat signal whose linewidth ultimately limits the achievable accuracy of length measurements. Here, we demonstrate a narrow-linewidth chirped frequency comb from an FSF Ti:sapphire ring laser seeded by a phase-modulated, ultra-low-phase-noise, single-frequency fiber laser. We experimentally investigate the influence of the seed laser linewidth on the resulting width and shape of the length-dependent rf beat signal. An ultranarrow heterodyne beat linewidth of <20 Hz is observed.

  7. Correlation of the bond-length change and vibrational frequency shift in model hydrogen-bonded complexes of pyrrole

    NASA Astrophysics Data System (ADS)

    McDowell, Sean A. C.

    2017-04-01

    An MP2 computational study of model hydrogen-bonded pyrrole⋯YZ (YZ = NH3, NCH, BF, CO, N2, OC, FB) complexes was undertaken in order to examine the variation of the Nsbnd H bond length change and its associated vibrational frequency shift. The chemical hardness of Y, as well as the YZ dipole moment, were found to be important parameters in modifying the bond length change/frequency shift. The basis set effect on the computed properties was also assessed. A perturbative model, which accurately reproduced the ab initio Nsbnd H bond length changes and frequency shifts, was useful in rationalizing the observed trends.

  8. Spatial-carrier phase-shifting digital holography utilizing spatial frequency analysis for the correction of the phase-shift error.

    PubMed

    Tahara, Tatsuki; Shimozato, Yuki; Awatsuji, Yasuhiro; Nishio, Kenzo; Ura, Shogo; Matoba, Osamu; Kubota, Toshihiro

    2012-01-15

    We propose a single-shot digital holography in which the complex amplitude distribution is obtained by spatial-carrier phase-shifting (SCPS) interferometry and the correction of the inherent phase-shift error occurred in this interferometry. The 0th order diffraction wave and the conjugate image are removed by phase-shifting interferometry and Fourier transform technique, respectively. The inherent error is corrected in the spatial frequency domain. The proposed technique does not require an iteration process to remove the unwanted images and has an advantage in the field of view in comparison to a conventional SCPS technique.

  9. Gravitational light deflection, time delay and frequency shift in Einstein-Aether theory

    NASA Astrophysics Data System (ADS)

    Tang, Kai; Huang, Tian-Yi; Tang, Zheng-Hong

    2010-01-01

    Einstein-Aether gravity theory has been proven successful in passing experiments of different scales. Especially its Eddington parameters β and γ have the same numerical values as those in general relativity. Recently Xie and Huang (2008) have advanced this theory to a second post-Newtonian approximation for an N-body model and obtained an explicit metric when the bodies are point-like masses. This research considers light propagation in the above gravitational field, and explores the light deflection, time delay, frequency shift etc. The results will provide for future experiments in testing gravity theories.

  10. Light Aberration, Deflection and Frequency Shift in Einstein-aether Gravity Theory

    NASA Astrophysics Data System (ADS)

    Tang, Kai

    2009-05-01

    Einstein-Aether gravity theory has been proven successful in passing experiments of different scales. Especially its Eddington parameters γand βhave the same numerical values as those in general relativity. Recently Xie and Huang (2008) have advanced this theory to a second post-Newtonian approximation for an N-body model and obtained a explicit metric when the bodies are point-like masses. This research considers light propagation in the above gravitational field, explore the light aberration, deflection, time delay, frequency shift etc. The results will provide for future experiments in testing gravity theories.

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

    PubMed

    Rai, V; Yadav, U; Kumar, P

    2012-06-15

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

  12. 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.

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

    PubMed

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

    2012-12-01

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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

    2010-04-13

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

  16. Extinction-ratio-independent electrical method for measuring chirp parameters of Mach-Zehnder modulators using frequency-shifted heterodyne.

    PubMed

    Zhang, Shangjian; Wang, Heng; Zou, Xinhai; Zhang, Yali; Lu, Rongguo; Liu, Yong

    2015-06-15

    An extinction-ratio-independent electrical method is proposed for measuring chirp parameters of Mach-Zehnder electric-optic intensity modulators based on frequency-shifted optical heterodyne. The method utilizes the electrical spectrum analysis of the heterodyne products between the intensity modulated optical signal and the frequency-shifted optical carrier, and achieves the intrinsic chirp parameters measurement at microwave region with high-frequency resolution and wide-frequency range for the Mach-Zehnder modulator with a finite extinction ratio. Moreover, the proposed method avoids calibrating the responsivity fluctuation of the photodiode in spite of the involved photodetection. Chirp parameters as a function of modulation frequency are experimentally measured and compared to those with the conventional optical spectrum analysis method. Our method enables an extinction-ratio-independent and calibration-free electrical measurement of Mach-Zehnder intensity modulators by using the high-resolution frequency-shifted heterodyne technique.

  17. Effect of level on the discrimination of harmonic and frequency-shifted complex tones at high frequencies.

    PubMed

    Moore, Brian C J; Sek, Aleksander

    2011-05-01

    Moore and Sęk [J. Acoust. Soc. Am. 125, 3186-3193 (2009)] measured discrimination of a harmonic complex tone and a tone in which all harmonics were shifted upwards by the same amount in Hertz. Both tones were passed through a fixed bandpass filter and a background noise was used to mask combination tones. Performance was well above chance when the fundamental frequency was 800 Hz, and all audible components were above 8000 Hz. Moore and Sęk argued that this suggested the use of temporal fine structure information at high frequencies. However, the task may have been performed using excitation-pattern cues. To test this idea, performance on a similar task was measured as a function of level. The auditory filters broaden with increasing level, so performance based on excitation-pattern cues would be expected to worsen as level increases. The results did not show such an effect, suggesting that the task was not performed using excitation-pattern cues.

  18. 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.

  19. 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.

  20. Doppler Frequency-Shift Compensated Photorefractive Interferometer for Ultrasound Detection on Objects in Motion

    NASA Astrophysics Data System (ADS)

    Campagne, B.; Blouin, A.; Néron, C.; Monchalin, J.-P.

    2003-03-01

    Two-wave mixing based interferometry has been demonstrated to be a powerful technique for non-contact, broadband and speckle insensitive measurements of the small surface displacements produced by ultrasonic waves propagating in an object. When the object is in rapid motion along the line-of-sight of the probing laser or when the laser beam is rapidly scanned on a wavy surface, the two-wave mixing photorefractive interferometer loses sensitivity to the point it could become useless. To circumvent the Doppler frequency-shift produced by this relative motion, we propose a dynamic compensation scheme. We report a particularly simple scheme to implement this concept by monitoring the low-frequency output signal of a balanced two-wave mixing demodulator whose output is proportional to the frequency difference between the pump and signal beams, and feeding this signal back to the acousto-optic shifter. With this new concept, the two-wave mixing interferometer can operate on objects in rapid motion while maintaining its sensitivity to low frequency ultrasound.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Multi-spatial-frequency and phase-shifting profilometry using a liquid crystal phase modulator.

    PubMed

    Joo, Kyung-Il; Park, Chang-Sub; Park, Min-Kyu; Park, Kyung-Woo; Park, Ji-Sub; Seo, Youngmin; Hahn, Joonku; Kim, Hak-Rin

    2012-05-10

    Optical profilometry is widely applied for measuring the morphology of objects by projecting predetermined patterns on them. In this technique, the compact size is one of the interesting issues for practical applications. The generation of pattern by the interference of coherent light sources has a potential to reduce the dimension of the illumination part. Moreover, this method can make fine patterns without projection optics, and the illumination part is free of restriction from the numerical aperture of the projection optics. In this paper, a phase-shifting profilometry is implemented by using a single liquid crystal (LC) cell. The LC phase modulator is designed to generate the interference patterns with several different spatial frequencies by changing selection of the spacing between the micro-pinholes. We manufactured the LC phase modulator and calibrated it by measuring the phase modulation amount depending on an applied voltage. Our optical profilometry using the single LC cell can generate multi-spatial frequency patterns as well as four steps of the phase-shifted patterns. This method can be implemented compactly, and the reconstructed depth profile is obtained without a phase-unwrapping algorithm.

  6. 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.

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

    PubMed Central

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

    2016-01-01

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

  8. 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.

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

    PubMed

    Swoboda, P; Hohn, B; Gal, S

    1993-02-01

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

  10. High-Accuracy Measurement of the Blackbody Radiation Frequency Shift of the Ground-State Hyperfine Transition in Cs133

    NASA Astrophysics Data System (ADS)

    Jefferts, S. R.; Heavner, T. P.; Parker, T. E.; Shirley, J. H.; Donley, E. A.; Ashby, N.; Levi, F.; Calonico, D.; Costanzo, G. A.

    2014-02-01

    We report a high-accuracy direct measurement of the blackbody radiation shift of the Cs133 ground-state hyperfine transition. This frequency shift is one of the largest systematic frequency biases encountered in realizing the current definition of the International System of Units (SI) second. Uncertainty in the blackbody radiation frequency shift correction has led to its being the focus of intense theoretical effort by a variety of research groups. Our experimental measurement of the shift used three primary frequency standards operating at different temperatures. We achieved an uncertainty a factor of five smaller than the previous best direct measurement. These results tend to validate the claimed accuracy of the recently calculated values.

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

    PubMed

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

    2009-05-01

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

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

    PubMed

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

    1996-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2002-10-01

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

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

    PubMed

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

    2015-03-31

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

  17. 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

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

    PubMed

    Jónás, Dávid; Ducrocq, Vincent; Croiseau, Pascal

    2017-04-01

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

  19. Frequency shift, damping, and tunneling current coupling with quartz tuning forks in noncontact atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Nony, Laurent; Bocquet, Franck; Para, Franck; Loppacher, Christian

    2016-09-01

    A combined experimental and theoretical approach to the coupling between frequency-shift (Δ f ) , damping, and tunneling current (It) in combined noncontact atomic force microscopy/scanning tunneling microscopy using quartz tuning forks (QTF)-based probes is reported. When brought into oscillating tunneling conditions, the tip located at the QTF prong's end radiates an electromagnetic field which couples to the QTF prong motion via its piezoelectric tensor and loads its electrodes by induction. Our approach explains how those It-related effects ultimately modify the Δ f and the damping measurements. This paradigm to the origin of the coupling between It and the nc-AFM regular signals relies on both the intrinsic piezoelectric nature of the quartz constituting the QTF and its electrodes design.

  20. Theoretical analyses of resonant frequency shift in anomalous dispersion enhanced resonant optical gyroscopes

    NASA Astrophysics Data System (ADS)

    Lin, Jian; Liu, Jiaming; Zhang, Hao; Li, Wenxiu; Zhao, Lu; Jin, Junjie; Huang, Anping; Zhang, Xiaofu; Xiao, Zhisong

    2016-12-01

    Rigorous expressions of resonant frequency shift (RFS) in anomalous dispersion enhanced resonant optical gyroscopes (ADEROGs) are deduced without making approximation, which provides a precise theoretical guidance to achieve ultra-sensitive ADEROGs. A refractive index related modification factor is introduced when considering special theory of relativity (STR). We demonstrate that the RFS will not be ”infinitely large” by using critical anomalous dispersion (CAD) and negative modification does not exist, which make the mechanism of anomalous dispersion enhancement clear and coherent. Although step change of RFS will happen when the anomalous dispersion condition varies, the amplification of RFS is limited by attainable variation of refractive index in practice. Moreover, it is shown that the properties of anomalous dispersion will influence not only the amplification of RFS, but also the detection range of ADEROGs.

  1. 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.

  2. 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.

  3. Theoretical analyses of resonant frequency shift in anomalous dispersion enhanced resonant optical gyroscopes

    PubMed Central

    Lin, Jian; Liu, Jiaming; Zhang, Hao; Li, Wenxiu; Zhao, Lu; Jin, Junjie; Huang, Anping; Zhang, Xiaofu; Xiao, Zhisong

    2016-01-01

    Rigorous expressions of resonant frequency shift (RFS) in anomalous dispersion enhanced resonant optical gyroscopes (ADEROGs) are deduced without making approximation, which provides a precise theoretical guidance to achieve ultra-sensitive ADEROGs. A refractive index related modification factor is introduced when considering special theory of relativity (STR). We demonstrate that the RFS will not be ”infinitely large” by using critical anomalous dispersion (CAD) and negative modification does not exist, which make the mechanism of anomalous dispersion enhancement clear and coherent. Although step change of RFS will happen when the anomalous dispersion condition varies, the amplification of RFS is limited by attainable variation of refractive index in practice. Moreover, it is shown that the properties of anomalous dispersion will influence not only the amplification of RFS, but also the detection range of ADEROGs. PMID:27941897

  4. Theoretical analyses of resonant frequency shift in anomalous dispersion enhanced resonant optical gyroscopes.

    PubMed

    Lin, Jian; Liu, Jiaming; Zhang, Hao; Li, Wenxiu; Zhao, Lu; Jin, Junjie; Huang, Anping; Zhang, Xiaofu; Xiao, Zhisong

    2016-12-12

    Rigorous expressions of resonant frequency shift (RFS) in anomalous dispersion enhanced resonant optical gyroscopes (ADEROGs) are deduced without making approximation, which provides a precise theoretical guidance to achieve ultra-sensitive ADEROGs. A refractive index related modification factor is introduced when considering special theory of relativity (STR). We demonstrate that the RFS will not be "infinitely large" by using critical anomalous dispersion (CAD) and negative modification does not exist, which make the mechanism of anomalous dispersion enhancement clear and coherent. Although step change of RFS will happen when the anomalous dispersion condition varies, the amplification of RFS is limited by attainable variation of refractive index in practice. Moreover, it is shown that the properties of anomalous dispersion will influence not only the amplification of RFS, but also the detection range of ADEROGs.

  5. A Frequency-Shift Method to Measure Shear-Wave Attenuation in Soft Tissues.

    PubMed

    Bernard, Simon; Kazemirad, Siavash; Cloutier, Guy

    2017-03-01

    In vivo quantification of shear-wave attenuation in soft tissues may help to better understand human tissue rheology and lead to new diagnostic strategies. Attenuation is difficult to measure in acoustic radiation force elastography because the shear-wave amplitude decreases due to a combination of diffraction and viscous attenuation. Diffraction correction requires assuming a cylindrical wavefront and an isotropic propagation medium, which may not be the case in some applications. In this paper, the frequency-shift method, used in ultrasound imaging and seismology, was adapted for shear-wave attenuation measurement in elastography. This method is not sensitive to diffraction effects. For a linear frequency dependence of the attenuation, a closed-form relation was obtained between the decrease in the peak frequency of the gamma-distributed wave amplitude spectrum and the attenuation coefficient of the propagation medium. The proposed method was tested against a plane-wave reference method in homogeneous agar-gelatin phantoms with 0%, 10%, and 20% oil concentrations, and hence different attenuations of 0.117, 0.202, and 0.292 [Formula: see text]/Hz, respectively. Applicability to biological tissues was demonstrated with two ex vivo porcine liver samples (0.79 and 1.35 [Formula: see text]/Hz) and an in vivo human muscle, measured along (0.43 [Formula: see text]/Hz) and across (1.77 [Formula: see text]/Hz) the tissue fibers. In all cases, the data supported the assumptions of a gamma-distributed spectrum for the source and linear frequency attenuation for the tissue. This method provides tissue attenuation, which is relevant diagnostic information to model viscosity, in addition to shear-wave velocity used to assess elasticity. Data processing is simple and could be performed automatically in real time for clinical applications.

  6. 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.

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

    PubMed

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

    2014-01-01

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

  8. 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

  9. 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

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

    PubMed

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

    2015-07-30

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

  11. 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

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

    SciTech Connect

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

    1994-09-01

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

  13. Estimate of ionicity of zeolite NaA using the frequency shift values of physisorbed molecular hydrogen

    NASA Astrophysics Data System (ADS)

    Larin, Alexander V.

    1996-08-01

    An estimate of the ionicity of the zeolite NaA is given. It is based on the fitting of the frequency shift value of the fundamental vibrational transition in physisorbed molecular hydrogen. The interaction energy U is calculated by ion-molecule pairwise addition with the ions of the zeolite. Frequency shift values are calculated as a displacement of vibrational levels of the fundamental transition due to the interaction of hydrogen with the zeolite.The level positions are calculated by integration of the Schrodinger vibrational equation. The contributions to the total frequency shift value of a hindered rotation and of a centre of mass vibration are estimated. The influence of the zeolite parameters on the resulting ionicity is discussed.

  14. 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.

  15. 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.

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

    PubMed

    Todd, N B; Todd, L M

    1976-01-01

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

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

    PubMed

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

    2015-07-03

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

  18. 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.

  19. Spectroscopic studies of the solute—solvent interaction in dye-doped polymers: frequency-dependent pressure shifts

    NASA Astrophysics Data System (ADS)

    Reul, S.; Richter, W.; Haarer, D.

    1991-05-01

    The method of hole burning spectroscopy is an excellent means to investigate small shifts and broadenings of quasi-homogeneous optical lines of dye molecules embedded in an amorphous matrix, caused by slight changes in the microscopic matrix environment after applying hydrostatic pressure. We have investigated the pressure-induced line shifts of free-base phthalocyanine in the polymer matrices polyethylene and polystyrene. The experimental data confirm the theoretical prediction of Laird and Skinner pertaining to the frequency dependence of the pressure-induced shifts and the corresponding broadening effects of spectral holes.

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

    PubMed

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

    2015-01-01

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

  1. 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

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

    PubMed

    Galán, Roberto F

    2009-09-01

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

  3. First Observation of a (1,0) Mode Frequency Shift of an Electron Plasma at Antiproton Beam Injection

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Galán, Roberto F.

    2009-09-01

    We provide an analytical expression for the mean frequency shift in phase oscillators as a function of the standard deviation, σ and the autocorrelation time, τ of small random perturbations. We show that the frequency shift is negative and proportional to σ2 . Its absolute value increases monotonically with τ , approaching an asymptote determined by the L2 -norm of the phase-response curve. We validate our theoretical predictions with computer simulations and discuss their implications for the design of electronic oscillators and for the encoding of information in biological neural networks.

  5. 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.

  6. Modified reverse tapering method to prevent frequency shift of the radiation in the planar undulator

    NASA Astrophysics Data System (ADS)

    Shim, Chi Hyun; Ko, In Soo; Parc, Yong Woon

    2017-03-01

    This paper presents a modified reverse tapering method to generate a polarized soft x ray in x-ray free-electron lasers (XFELs) with a higher photon power and a shorter undulator length than the simple linear reverse tapering method. In the proposed method, a few untapered planar undulators are added before the simple linear reverse tapering section of the undulator line. This simple modification prevents the frequency shift of the radiation that occurs when the simple linear reverse tapering method is applied to planar undulators. In the proposed method, the total length of planar undulators decreased in spite of the additional untapered undulators. When the modified reverse tapering method is used with four untapered planar undulators, the total length of the planar undulators is 64.6 m. On the other hand, the required length of the planar undulators is 94.6 m when the simple linear reverse tapering method is used. The proposed method gives us a way to generate a soft x-ray pulse (1.24 keV) with a high degree of polarization (>0.99 ) and radiation power (>30 GW ) at the new undulator line with a 10-GeV electron beam in the Pohang Accelerator Laboratory X-ray Free-Electron Laser. This method can be applied in the existing XFELs in the world without any change in the undulator lines.

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    PubMed Central

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

    2002-01-01

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

  11. 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.

  12. Precision measurement of the 1{ital S} ground-state Lamb shift in atomic hydrogen and deuterium by frequency comparison

    SciTech Connect

    Weitz, M.; Huber, A.; Schmidt-Kaler, F.; Leibfried, D.; Vassen, W.; Zimmermann, C.; Pachucki, K.; Haensch, T.W.; Julien, L.; Biraben, F.

    1995-10-01

    We have measured the hydrogen and deuterium 1{ital S} Lamb shift by direct optical frequency comparison of the 1{ital S}-2{ital S} and 2{ital S}-4{ital S}/4{ital D} two-photon transitions. Our result of 8172.874(60) MHz for the 1{ital S} Lamb shift in hydrogen is in agreement with the theoretical value of 8172.802(40) MHz. For the 1{ital S} Lamb shift in deuterium, we obtain a value of 8183.807(78) MHz, from which we derive a deuteron matter radium of 1.945(28) fm. The precision of our value for the 1{ital S} Lamb shift has surpassed that of radio frequency measurements of the 2{ital S}-2{ital P} Lamb shift. By comparison with a recent absolute measurement of the hydrogen 1{ital S}-2{ital S} transition frequency, we deduce a value for the Rydberg constant {ital R}{sub {infinity}}=109 737.315 684 9(30) cm{sup {minus}1}.

  13. Image reconstruction algorithm for recovering high-frequency information in parallel phase-shifting digital holography [Invited].

    PubMed

    Xia, Peng; Shimozato, Yuki; Tahara, Tatsuki; Kakue, Takashi; Awatsuji, Yasuhiro; Nishio, Kenzo; Ura, Shogo; Kubota, Toshihiro; Matoba, Osamu

    2013-01-01

    We propose an image reconstruction algorithm for recovering high-frequency information in parallel phase-shifting digital holography. The proposed algorithm applies three kinds of interpolations and generates three different kinds of object waves. A Fourier transform is applied to each object wave, and the spatial-frequency domain is divided into 3×3 segments for each Fourier-transformed object wave. After that the segment in which interpolation error is the least among the segments having the same address of the segment in the spatial-frequency domain is extracted. The extracted segments are combined to generate an information-enhanced spatial-frequency spectrum of the object wave, and after that the formed spatial-frequency spectrum is inversely Fourier transformed. Then the high-frequency information of the reconstructed image is recovered. The effectiveness of the proposed algorithm was verified by a numerical simulation and an experiment.

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

    PubMed

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

    1997-12-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Schreiber, Eric; Peichl, Markus; Jirousek, Matthias

    2013-10-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-09-01

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

  19. Solvent dependent frequency shift and Raman noncoincidence effect of Sdbnd O stretching mode of Dimethyl sulfoxide in liquid binary mixtures

    NASA Astrophysics Data System (ADS)

    Upadhyay, Ganesh; Devi, Th. Gomti; Singh, Ranjan K.; Singh, A.; Alapati, P. R.

    2013-05-01

    The isotropic and anisotropic Raman peak frequencies of Sdbnd O stretching mode of Dimethyl sulfoxide (DMSO) have been discussed in different chemical and isotopic solvent molecules using different mechanisms. The shifting of peak frequency in further dilution of DMSO with solvent molecule is observed for all solvents. Transition dipole - transition dipole interaction and hydrogen bonding may play a major role in shifting of peak frequencies. The non-coincidence effect (NCE) of DMSO was determined for all the solvents and compared with four theoretical models such as McHale's model, Mirone's modification of McHale's model, Logan's model and Onsager-Fröhlich dielectric continuum model respectively. Most of the theoretical models are largely consistent with our experimental data.

  20. M-ary frequency shift keying with differential phase detector in satellite mobile channel with narrowband receiver filter

    NASA Astrophysics Data System (ADS)

    Korn, I.; Namet, M.

    1990-02-01

    An expression is derived for the error probability of M-ary frequency-shift keying with differential phase detector and narrow-band receiver filter in the satellite mobile (Rician) channel, which includes as special cases the Gaussian and land mobile (Rayleigh) channels. The error probability is computed as a function of various system parameters for M = 2, 4, and 8 symbols and the third-order Butterworth receiver filter. The error probability increases with Doppler frequency and with the shift of the channel from Gaussian through Rician to Rayleigh. The optimum normalized bandwidth per bit is in the vicinity of one, and the optimum modulation index for binary symbols is about 0.6. The threshold for quaternary symbols can be optimized to about 0.9 of the modulation index. For Rician and Rayleigh channels with nonzero Doppler frequency, there is an error floor; therefore, diversity or coding may be required to achieve a desired error probability.

  1. The effect of classical and quantum dynamics on vibrational frequency shifts of H2 in clathrate hydrates.

    PubMed

    Plattner, Nuria; Meuwly, Markus

    2014-01-14

    Vibrational frequency shifts of H2 in clathrate hydrates are important to understand the properties and elucidate details of the clathrate structure. Experimental spectra of H2 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 H2 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 H2 vibrations in the different clathrate cage types agree favorably with experiment. Also, the simulations demonstrate that H2 in the 5(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(12) cage quantum effects lead to frequency increases and double occupation is unlikely. This is different for the 5(12)6(4) cages for which higher occupation numbers than one H2 per cage are likely.

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

    SciTech Connect

    Plattner, Nuria; Meuwly, Markus

    2014-01-14

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

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

    PubMed

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

    2015-11-01

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

  4. 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.

  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

    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.

  6. 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

  7. 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.

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

    PubMed

    Gorlov, Ivan P; Gorlova, Olga Y; Amos, Christopher I

    2015-07-01

    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.

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

    PubMed

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

    2013-03-05

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

  11. A dual-frequency online PMP method with phase-shifting parallel to moving direction of measured object

    NASA Astrophysics Data System (ADS)

    Peng, Kuang; Cao, Yiping; Wu, Yingchun; Chen, Cheng; Wan, Yingying

    2017-01-01

    A dual-frequency online phase measurement profilometry (PMP) method with phase-shifting parallel to moving direction of measured object is proposed in this paper. The high-frequency fringe is used for the better modulation patterns in pixel matching and it is not modified by the measured object's surface. Based on the relative positive between the moving measured object and digital light processing (DLP), the high-frequency fringe in each dual-frequency deformed pattern after pixel matching is the same. As a result, the phase can be calculated directly by the improved Stoilov algorithm without filtering out the low-frequency component containing the measured object's height information. As there is no filtering process in phase calculation, the valid information loss can be avoided so that the accuracy of the proposed method can be guaranteed. Simulations and experiments prove the method's feasibility and precision.

  12. 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

  13. 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

  14. 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

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

    PubMed

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

    1995-05-20

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

  16. Solvent-induced infrared frequency shifts in aromatic nitriles are quantitatively described by the vibrational Stark effect.

    PubMed

    Levinson, Nicholas M; Fried, Stephen D; Boxer, Steven G

    2012-09-06

    The physical properties of solvents strongly affect the spectra of dissolved solutes, and this phenomenon can be exploited to gain insight into the solvent-solute interaction. The large solvatochromic shifts observed for many dye molecules in polar solvents are due to variations in the solvent reaction field, and these shifts are widely used to estimate the change in the dye's dipole moment upon photoexcitation, which is typically on the order of ∼1-10 D. In contrast, the change in dipole moment for vibrational transitions is approximately 2 orders of magnitude smaller. Nonetheless, vibrational chromophores display significant solvatochromism, and the relative contributions of specific chemical interactions and electrostatic interactions are debated, complicating the interpretation of vibrational frequency shifts in complex systems such as proteins. Here we present a series of substituted benzonitriles that display widely varying degrees of vibrational solvatochromism. In most cases, this variation can be quantitatively described by the experimentally determined Stark tuning rate, coupled with a simple Onsager-like model of solvation, reinforcing the view that vibrational frequency shifts are largely caused by electrostatic interactions. In addition, we discuss specific cases where continuum solvation models fail to predict solvatochromic shifts, revealing the necessity for more advanced theoretical models that capture local aspects of solute-solvent interactions.

  17. A high accuracy ultrasonic distance measurement system using binary frequency shift-keyed signal and phase detection

    NASA Astrophysics Data System (ADS)

    Huang, S. S.; Huang, C. F.; Huang, K. N.; Young, M. S.

    2002-10-01

    A highly accurate binary frequency shift-keyed (BFSK) ultrasonic distance measurement system (UDMS) for use in isothermal air is described. This article presents an efficient algorithm which combines both the time-of-flight (TOF) method and the phase-shift method. The proposed method can obtain larger range measurement than the phase-shift method and also get higher accuracy compared with the TOF method. A single-chip microcomputer-based BFSK signal generator and phase detector was designed to record and compute the TOF, two phase shifts, and the resulting distance, which were then sent to either an LCD to display or a PC to calibrate. Experiments were done in air using BFSK with the frequencies of 40 and 41 kHz. Distance resolution of 0.05% of the wavelength corresponding to the frequency of 40 kHz was obtained. The range accuracy was found to be within ±0.05 mm at a range of over 6000 mm. The main advantages of this UDMS system are high resolution, low cost, narrow bandwidth requirement, and ease of implementation.

  18. Slope measurement of a phase object using a polarizing phase-shifting high-frequency Ronchi grating interferometer.

    PubMed

    Toto-Arellano, Noel-Ivan; Martínez-García, Amalia; Rodríguez-Zurita, Gustavo; Rayas-Álvarez, Juan Antonio; Montes-Perez, Areli

    2010-11-20

    An interferometric method to measure the slope of phase objects is presented. The analysis was performed by implementing a polarizing phase-shifting cyclic shear interferometer coupled to a 4-f Fourier imaging system with crossed high-frequency Ronchi gratings. This system can obtain nine interference patterns with adjustable phase shifts and variable lateral shear. In order to extract the slope of a phase object, it is only analyzed using four patterns obtained in a single shot, and applying the classical method of phase extraction.

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  3. 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.

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

    PubMed

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

    1996-08-01

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

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

    PubMed

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

    2013-10-01

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

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

    PubMed

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

    2014-08-01

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

  7. 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.

  8. 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.

  9. Laser Doppler velocity measurement without directional ambiguity by using frequency shifted incident beams

    NASA Technical Reports Server (NTRS)

    Mazumder, M. K.

    1970-01-01

    Laser Doppler heterodyning system for velocity measurements without directional ambiguity, employing incident beams of different frequencies through rotating diffraction grating or Bragg cell application

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  12. 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.

  13. 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

  14. 3D absolute shape measurement of live rabbit hearts with a superfast two-frequency phase-shifting technique

    PubMed Central

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

    2013-01-01

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

  15. 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

  16. 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.

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

    PubMed Central

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

    2016-01-01

    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

  18. Determination of pressure from measured Raman frequency shifts of anhydrite and its application in fluid inclusions and HDAC experiments

    NASA Astrophysics Data System (ADS)

    Yuan, Xueyin; Mayanovic, Robert A.; Zheng, Haifei

    2016-12-01

    A new geobarometry was derived from the quantified relationships among Raman vibrational frequencies of anhydrite, pressure and temperature, as determined from in-situ micro-Raman spectroscopy of natural anhydrite crystals measured at p-T conditions up to 560 °C and 1400 MPa by using a hydrothermal diamond anvil cell (HDAC). With this geobarometry, the pressure in HDAC experiments and in anhydrite-bearing fluid inclusions can be determined directly from the ν1, 1016, ν3, 1128 and ν3, 1160 Raman frequency shifts of anhydrite at high p-T conditions relative to their values measured at ambient conditions. The pressure can be determined to an accuracy of better than 30 MPa based on the attainable accuracy of ±0.1 cm-1 for the fitted ν1 Raman peak positions, provided the measured spectra are calibrated using the emission peak of an external fluorescent light source. The feasibility and reliability of this geobarometry were verified by rebuilding the p-T history of two fluid inclusions from the ν1 frequency shifts of anhydrite daughter minerals from room to high temperatures, and by measuring the phase-transition pressures of calcite-CaCO3(II)-CaCO3(III) sequence at ambient temperature in a HDAC experiment using anhydrite as a Raman pressure sensor.

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

    PubMed Central

    2009-01-01

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

  20. 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.

  1. 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}.

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

    PubMed

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

    2004-01-01

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

  3. 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.

  4. Solvent-induced frequency shifts: configuration interaction singles combined with the effective fragment potential method.

    PubMed

    Arora, Pooja; Slipchenko, Lyudmila V; Webb, Simon P; DeFusco, Albert; Gordon, Mark S

    2010-07-01

    The simplest variational method for treating electronic excited states, configuration interaction with single excitations (CIS), has been interfaced with the effective fragment potential (EFP) method to provide an effective and computationally efficient approach for studying the qualitative effects of solvents on the electronic spectra of molecules. Three different approaches for interfacing a non-self-consistent field (SCF) excited-state quantum mechanics (QM) method and the EFP method are discussed. The most sophisticated and complex approach (termed fully self consistent) calculates the excited-state electron density with fully self-consistent accounting for the polarization (induction) energy of effective fragments. The simplest approach (method 1) includes a strategy that indirectly adds the EFP perturbation to the CIS wave function and energy via modified Hartree-Fock molecular orbitals, so that there is no direct EFP interaction with the excited-state density. An intermediate approach (method 2) accomplishes the latter in a noniterative perturbative manner. Theoretical descriptions of the three approaches are presented, and test results of solvent-induced shifts using methods 1 and 2 are compared with fully ab initio values. These comparisons illustrate that, at least for the test cases examined here, modification of the ground-state Hartree-Fock orbitals is the largest and most important factor in the calculated solvent-induced shifts. Method 1 is then employed to study the aqueous solvation of coumarin 151 and compared with experimental measurements.

  5. Method for the calculation of the vibrational frequency shift of physisorbed molecules. Application to H2 adsorbed in NaA zeolite

    NASA Astrophysics Data System (ADS)

    Larin, A. V.; Cohen De Lara, E.

    1994-11-01

    The vibrational frequency shift of physisorbed diatomic molecules is related to the interaction with the adsorbent expressed in terms of the internuclear distance ρ. It is calculated by the Schrödinger equation, the perturbation theory, and a simplified method. We show that it is sufficient to calculate the interaction potential for the values of ρ in the ground and first vibrational states in order to get a precision of 10% on the frequency shift. The comparison between the theoretical and experimental frequency shift of H2 adsorbed in NaA zeolite is used to adjust the interaction potential, especially in terms of the ionicity of the crystal.

  6. Hydrogen maser wall shift experiments and determination of the unperturbed hyperfine frequency of the ground state of the hydrogen atom

    SciTech Connect

    Cheng, Y.M.; Hua, Y.L.; Chen, C.B.; Gao, J.H.; Shen, W.

    1980-12-01

    Experiments on hydrogen maser wall shift are described in detail. Values of K(40 C) -293 + or - 17 mHz.cm and a(40 C) (-17 + or 2) x 10 to the -3rd per deg C were obtained. The unperturbed hyperfine frequency of the ground state of the hydrogen atom was obtained by comparing five hydrogen masers to Loran C signals for one month. The average value with respect to TAI is 1,420,405,751.768 + or - 0.002 Hz.

  7. Anomalous Resonance Frequency Shift of a Microelectromechanical Oscillator in Superfluid ^3 He-B

    NASA Astrophysics Data System (ADS)

    Zheng, P.; Jiang, W. G.; Barquist, C. S.; Lee, Y.; Chan, H. B.

    2017-02-01

    A superfluid ^3 He film with a thickness of 1.25 μm was studied using a microelectromechanical oscillator at various pressures of 9.2, 18.2, 25.2, and 28.6 bars. The oscillator was driven in the linear damping regime where the damping coefficient is independent of the velocity of the oscillator. The resonance frequency shows weak temperature and pressure dependences in the low temperature limit. An inertia coefficient of ≈ 0.1 was obtained in the ballistic regime. When the temperature rose from the lowest temperature, the resonance frequency of the resonator exhibited an unusual behavior, a rapid increase beyond the intrinsic value as temperature increases, for 9.2 and 18.2 bars.

  8. Generation of ultrahigh and tunable repetition rates in CW injection-seeded frequency-shifted feedback lasers.

    PubMed

    Guillet de Chatellus, H; Jacquin, O; Hugon, O; Glastre, W; Lacot, E; Marklof, J

    2013-07-01

    We show both theoretically and experimentally that frequency-shifted feedback (FSF) lasers seeded with a single frequency laser can generate Fourier transform-limited pulses with a repetition rate tunable and limited by the spectral bandwidth of the laser. We demonstrate experimentally in a FSF laser with a 150 GHz spectral bandwidth, the generation of 6 ps-duration pulses at repetition rates tunable over more than two orders of magnitude between 0.24 and 37 GHz, by steps of 80 MHz. A simple linear analytical model i.e. ignoring both dynamic and non-linear effects, is sufficient to account for the experimental results. This possibility opens new perspectives for various applications where lasers with ultra-high repetition rates are required, from THz generation to ultrafast data processing systems.

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

    PubMed

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

    2015-02-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2010-08-01

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

  12. Modelling the matrix shift on the vibrational frequency of ThO by DFT-D3 calculations

    NASA Astrophysics Data System (ADS)

    Kovács, Attila; Rode, Joanna E.

    2017-03-01

    Benchmark calculations with a goal to find dispersion-corrected DFT-D3 methods suitable for a reliable estimation of matrix shifts on the vibrational frequency were carried out on the ThO molecule in three rare gas (Rg = Ne, Ar, and Kr) matrices. The matrices were modelled by the explicit approach, in which a single and a double shell of Rg atoms around ThO was considered. The selection of exchange-correlation functionals was based on test calculations on triatomic ThO⋯ Rg models. The B3LYP, PBE0, CAM-B3LYP, and LC-ω PBE functionals were found to be the best suited for the estimation of matrix shifts. The single shell of Rg's around ThO accounted for a major part of the shifts; the addition of a second Rg shell resulted only in a minor improvement. Continuum solvation models considerably overestimated the effect of Rg matrices both when the whole matrix was treated by the model and when the first shell was treated explicitly and the rest with a continuum solvation model.

  13. Spectral line decomposition and frequency shifts in Al Heα group emission from laser-produced plasma

    NASA Astrophysics Data System (ADS)

    Renner, O.; Adámek, P.; Angelo, P.; Dalimier, E.; Förster, E.; Krousky, E.; Rosmej, F. B.; Schott, R.

    2006-05-01

    Precise spectroscopic observations of K-shell emission from highly stripped Al ions immersed in dense, constrained-flow laser-produced plasma is reported. By using a vertical dispersion Johann spectrometer, the time-integrated spectra of the Al Heα group were measured with a high spectral and spatial resolution. The complex spectral profiles modified by the satellite formation, line broadening and frequency shifts were decomposed into individual pseudo-Voigt components by using a code GASPED based on a problem-dependent genetic algorithm. The method uses eight operators tailored to the problem of spectral decomposition and variable-size genomes to fit the data with a varying number of spectral lines. The spectra fitting was based on anticipatory theoretical knowledge of the satellite structure simulated by the multilevel collisional-radiative code MARIA and on an assumption of the aggregate plasma-induced shift of the parent lines and their satellites. The analysis of the spectral profiles revealed systematic red shifts of the resonance and the intercombination lines. Their magnitude is commensurate with predictions of the atomic data and spectral line shape codes combined with the 1D hydrodynamic modeling of the plasma conditions and independent electron density measurements. The results obtained corroborate the feasibility of an accurate decomposition of the spectral profiles encompassing optically thick and thin lines overlapped by a strong satellite emission.

  14. Pilot Signal Generation Scheme Using Frequency-Dependent Cyclic Shift ZC Sequence for Inter-Cell Interference Mitigation

    NASA Astrophysics Data System (ADS)

    Imamura, Daichi; Ogawa, Yoshihiko; Iwai, Takashi; Takata, Tomohumi; Hiramatsu, Katsuhiko; Miya, Kazuyuki; Homma, Koichi

    In this paper, we study and propose an inter-cell co-channel interference (CCI) mitigation method for pilot signals using cyclic shift Zadoff-Chu (CS-ZC) sequences for SC-FDMA-based uplink without tight scheduler coordination among cells. Firstly, we investigate the issue of severe detection performance degradation created by the lack of orthogonality among the pilot signals without alignment of the allocated frequency resource positions among cells when using the conventional CS-ZC sequences generation scheme. Secondly, we identify the primary factor causing the issue. Thirdly, we propose a frequency-dependent CS-ZC sequence generation scheme by allocating the same spectrum elements of the ZC sequence to the overlapped subcarriers among cells to mitigate the inter-cell CCI of the pilot signals without alignment of the frequency resource positions among cells. Finally, we confirm the validity of the proposal using uplink data BLER evaluation under a multipath fading condition by computer simulation compared to the conventional method, and show that the proposal achieves around 0.9dB and 0.6dB better performance at 10% BLER than the conventional method for 1 RB and 2 RBs frequency offsets in 3 RBs transmission bandwidth, respectively.

  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.

  16. 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.

  17. 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.

  18. 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,

  19. 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.

  20. 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.

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

    PubMed

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

    1997-12-01

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

  3. Dissipation and resonance frequency shift of a resonator magnetically coupled to a semiclassical spin

    PubMed Central

    de Voogd, J. M.; Wagenaar, J. J. T.; Oosterkamp, T. H.

    2017-01-01

    We calculate the change of the properties of a resonator, when coupled to a semiclassical spin by means of the magnetic field. Starting with the Lagrangian of the complete system, we provide an analytical expression for the linear response function for the motion in the case of a mechanical resonator and the current for the case of an electromagnetic resonator, thereby considering the influence of the resonator on the spin and vice versa. This analysis shows that the resonance frequency and effective dissipation factor can change significantly due to the relaxation times of the spin. We first derive this for a system consisting of a spin and mechanical resonator and thereafter apply the same calculations to an electromagnetic resonator. Moreover, the applicability of the method is generalized to a resonator coupled to two-level systems and more, providing a key to understand some of the problems of two-level systems in quantum devices. PMID:28186145

  4. Dissipation and resonance frequency shift of a resonator magnetically coupled to a semiclassical spin

    NASA Astrophysics Data System (ADS)

    de Voogd, J. M.; Wagenaar, J. J. T.; Oosterkamp, T. H.

    2017-02-01

    We calculate the change of the properties of a resonator, when coupled to a semiclassical spin by means of the magnetic field. Starting with the Lagrangian of the complete system, we provide an analytical expression for the linear response function for the motion in the case of a mechanical resonator and the current for the case of an electromagnetic resonator, thereby considering the influence of the resonator on the spin and vice versa. This analysis shows that the resonance frequency and effective dissipation factor can change significantly due to the relaxation times of the spin. We first derive this for a system consisting of a spin and mechanical resonator and thereafter apply the same calculations to an electromagnetic resonator. Moreover, the applicability of the method is generalized to a resonator coupled to two-level systems and more, providing a key to understand some of the problems of two-level systems in quantum devices.

  5. Stabilized soliton self-frequency shift and 0.1- PHz sideband generation in a photonic-crystal fiber with an air-hole-modified core.

    PubMed

    Liu, Bo-Wen; Hu, Ming-Lie; Fang, Xiao-Hui; Li, Yan-Feng; Chai, Lu; Wang, Ching-Yue; Tong, Weijun; Luo, Jie; Voronin, Aleksandr A; Zheltikov, Aleksei M

    2008-09-15

    Fiber dispersion and nonlinearity management strategy based on a modification of a photonic-crystal fiber (PCF) core with an air hole is shown to facilitate optimization of PCF components for a stable soliton frequency shift and subpetahertz sideband generation through four-wave mixing. Spectral recoil of an optical soliton by a red-shifted dispersive wave, generated through a soliton instability induced by high-order fiber dispersion, is shown to stabilize the soliton self-frequency shift in a highly nonlinear PCF with an air-hole-modified core relative to pump power variations. A fiber with a 2.3-microm-diameter core modified with a 0.9-microm-diameter air hole is used to demonstrate a robust soliton self-frequency shift of unamplified 50-fs Ti: sapphire laser pulses to a central wavelength of about 960 nm, which remains insensitive to variations in the pump pulse energy within the range from 60 to at least 100 pJ. In this regime of frequency shifting, intense high- and low-frequency branches of dispersive wave radiation are simultaneously observed in the spectrum of PCF output. An air-hole-modified-core PCF with appropriate dispersion and nonlinearity parameters is shown to provide efficient four-wave mixing, giving rise to Stokes and anti-Stokes sidebands whose frequency shift relative to the pump wavelength falls within the subpetahertz range, thus offering an attractive source for nonlinear Raman microspectroscopy.

  6. 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.

  7. 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.

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

    PubMed

    Spitsyn, V A; Afanas'eva, I S

    2001-12-01

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

  9. 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.

  10. 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.

  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.

    PubMed

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

    2016-06-05

    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. Synthesis of Brillouin frequency shift profiles to compensate non-local effects and Brillouin induced noise in BOTDA sensors.

    PubMed

    Urricelqui, Javier; Sagues, Mikel; Loayssa, Alayn

    2014-07-28

    We present a novel technique for Brillouin optical time domain analysis (BOTDA) sensors that simultaneously compensates non-local effects and reduces Brillouin noise. The technique relies on the wavelength modulation of the optical source to modify the Brillouin interaction between probe and pump waves during their propagation. The resulting Brillouin distribution mimics the wavelength modulation, creating a virtual Brillouin frequency shift profile along the sensing fiber. The fundamentals of the technique are first described theoretically and using numerical simulations. Then, proof-of-concept experiments demonstrate the capabilities of the system to reduce large variations of the pump power resulting from the interaction with high probe powers and to decrease the Brillouin induced noise enhancing the signal to noise ratio (SNR) of the system. Furthermore, we show, for the first time to our knowledge, measurements of the Brillouin distribution using an injected optical power higher than the Brillouin threshold of the fiber.

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

    PubMed

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

    2005-12-30

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

  15. Self-frequency-shifted solitons in a polarization-maintaining, very-large-mode area, Er-doped fiber amplifier.

    PubMed

    Nicholson, J W; Desantolo, A; Kaenders, W; Zach, A

    2016-10-03

    We demonstrate soliton self-frequency-shifted, femtosecond-pulse amplification in a newly-developed, polarization-maintaining, Er-doped, very-large-mode-area fiber amplifier. The PM-VLMA Er fiber had a core diameter of 50 μm, an effective area of ~1050 μm2, and Er absorption of 50 dB/m. The measured birefringence beat length of the PM-VLMA Er fiber was 14.1 mm. The soliton wavelength could be shifted by more than 90 nm. The soliton generation process resulted in remarkably clean, 86 fs pulses with 21 nJ energy at 1650 nm and 244 kW peak power from an all-fiber, fusion spliced system without bulk-optics for pulse compression. The polarization extinction ratio of the soliton was greater than 40 dB, and the M2 was 1.1. The fully polarization-maintaining fiber laser system provides robust and stable soliton generation. Peak-to-peak variation in the soliton wavelength, measured over the course of an hour was only 0.03% and pulse energy variation was only 0.5%.

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

    PubMed Central

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

    2013-01-01

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

  17. 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...

  18. Sensing Escherichia coli O157:H7 via frequency shift through a self-assembled monolayer based QCM immunosensor*

    PubMed Central

    Wang, Li-jiang; Wu, Chun-sheng; Hu, Zhao-ying; Zhang, Yuan-fan; Li, Rong; Wang, Ping

    2008-01-01

    By means of the specific immuno-recognition and ultra-sensitive mass detection, a quartz crystal microbalance (QCM) biosensor for Escherichia coli O157:H7 detection was developed in this work. As a suitable surfactant, 16-mercaptohexadecanoic acid (MHDA) was introduced onto the Au surface of QCM, and then self-assembled with N-hydroxysuccinimide (NHS) raster as a reactive intermediate to provide an active interface for the specific antibody immobilization. The binding of target bacteria with the immobilized antibodies decreased the sensor’s resonant frequency, and the frequency shift was correlated to the bacterial concentration. The stepwise assembly of the immunosensor was characterized by means of the electrochemical techniques. Using the immersion-dry-immersion procedure, this QCM biosensor could detect 2.0×102 colony forming units (CFU)/ml E. coli O157:H7. In order to reduce the fabrication time, a polyelectrolyte layer-by-layer self-assembly (LBL-SA) method was adopted for fast construction. Finally, the reproducibility of this biosensor was discussed. PMID:18257134

  19. Frequency shifts of vibrational and rotational states of dilute H2, D2, and HD impurities in solid Ar under pressure

    NASA Astrophysics Data System (ADS)

    Silvi, B.; Chandrasekharan, V.; Chergui, M.; Etters, R. D.

    1986-02-01

    The frequency shifts of the vibrational and rotational transitions of H2, D2, and HD molecules trapped in solid Ar are calculated at zero temperature and at pressures 0<=P<=373 kbar. It is found that the pure vibrational and rotational-vibrational transition frequencies are strongly red-shifted in the solid at P=0, compared to gas-phase values, and the agreement with Raman scattering measurements is generally good. The calculated pure rotational transitions also show a small red shift at P=0 in the solid and are in generally good agreement with the measurements of Jodl and Bier, but less so with those of Prochaska and Andrews, who, except for D2(Ar), measure small blue shifts. The calculated local-mode frequencies of the impurity molecules in the solid at P=0 are also in good agreement with experiment, especially when thermal corrections are considered. With increasing pressure all transition frequencies and the local-mode frequencies are strongly blue-shifted with respect to P=0 solid values.

  20. Analytical solutions of the first three frequency shifts of AFM non-uniform probe subjected to the Lennard-Jones force.

    PubMed

    Lin, Shueei-Muh; Liauh, Chihng-Tsung; Wang, Wen-Rong; Ho, Shing-Huei

    2006-04-01

    The role of higher cantilever modes is important to obtain some material contrast. The analysis of AFM subjected to a short-range force can improve greatly the studies of surface topography and interaction energies and interaction forces, especially for chemical and biological materials. When the tip-sample distance is in the order of inter-atomic spacing, the short-range tip-sample force is usually simulated by the Lennard-Jones model. In this study, the analytical method to determine the frequency shift of AFM subjected to the Lennard-Jones force is proposed. The closed-form solution of the partial differential equation with a nonlinear boundary condition is derived and then the corresponding frequency shifts of higher modes can be determined easily. Moreover, the conventional perturbation method is usually used to determine the frequency shift, but only for the first mode. This is because the original continuous beam system is transformed into a discrete lumped-masses model. Although the above disadvantages exist, the lumped-masses model is simple and intuitive. Using the principle of dynamic strain energy, the conventional perturbation method is revised successfully to determine the frequency shifts of higher modes. The assessment of the generalized perturbation method and the proposed method is made. Finally, the effects of several parameters on the first three frequency shifts are investigated.

  1. Frequency of the HLA-B*1502 allele contributing to carbamazepine-induced hypersensitivity reactions in a cohort of Malaysian epilepsy patients.

    PubMed

    Then, Sue-Mian; Rani, Zam Zureena Mohd; Raymond, Azman Ali; Ratnaningrum, Safrina; Jamal, Rahman

    2011-09-01

    We describe the association of the HLA-B*1502 allele in 27 epilepsy patients (19 Malays, 8 Chinese) treated with carbamazepine (CBZ) at the UKM Medical Center (UKMMC), 6 with CBZ-Steven Johnson Syndrome (CBZ-SJS), 11 with CBZ-induced rash, 2 with suspected phenytoin-induced rash and 8 negative controls. Our study showed that 10 (6 Malay, 4 Chinese) patients were positive for HLA-B*1502. Out of the 10 patients, six were confirmed to have CBZ-SJS (p = 0.0006), while four patients developed a skin rash. However there were 6 Malay patients and 1 Chinese patient that developed a skin rash after CBZ administration who were not positive for the allele, indicating that there might be more that one allele associated with CBZ-induced hypersensitivity. Another 2 patients were suspected of having phenytoin-induced rash, instead of CBZ, and these patients did not have HLA-B*1502. In conclusion, this study confirmed the association of HLA-B*1502 with CBZ-SJS among Malaysian epilepsy patients, however there might be other genes that could be responsible for the CBZ-induced rash.

  2. Static and dynamic polarizability and the Stark and blackbody-radiation frequency shifts of the molecular hydrogen ions H2+, HD+, and D2+

    NASA Astrophysics Data System (ADS)

    Schiller, S.; Bakalov, D.; Bekbaev, A. K.; Korobov, V. I.

    2014-05-01

    We calculate the dc Stark effect for three molecular hydrogen ions in the nonrelativistic approximation. The effect is calculated both in dependence on the rovibrational state and in dependence on the hyperfine state. We discuss special cases and approximations. We also calculate the ac polarizabilities for several rovibrational levels and therefrom evaluate accurately the blackbody radiation shift, including the effects of excited electronic states. The results enable the detailed evaluation of certain systematic shifts of the transitions frequencies for the purpose of ultrahigh-precision optical, microwave, or radio-frequency spectroscopy in ion traps.

  3. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

    PubMed Central

    Chesler, Elissa J.; Gatti, Daniel M.; Morgan, Andrew P.; Strobel, Marge; Trepanier, Laura; Oberbeck, Denesa; McWeeney, Shannon; Hitzemann, Robert; Ferris, Martin; McMullan, Rachel; Clayshultle, Amelia; Bell, Timothy A.; Manuel de Villena, Fernando Pardo; Churchill, Gary A.

    2016-01-01

    Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility. PMID:27694113

  4. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection.

    PubMed

    Chesler, Elissa J; Gatti, Daniel M; Morgan, Andrew P; Strobel, Marge; Trepanier, Laura; Oberbeck, Denesa; McWeeney, Shannon; Hitzemann, Robert; Ferris, Martin; McMullan, Rachel; Clayshultle, Amelia; Bell, Timothy A; Manuel de Villena, Fernando Pardo; Churchill, Gary A

    2016-12-07

    Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility.

  5. High frequency and allele-specific differences of BRCA1 founder mutations in breast cancer and ovarian cancer patients from Belarus.

    PubMed

    Bogdanova, N V; Antonenkova, N N; Rogov, Y I; Karstens, J H; Hillemanns, P; Dörk, T

    2010-10-01

    Breast cancer and ovarian cancer are common malignancies in Belarus accounting for about 3500 and 800 new cases per year, respectively. For breast cancer, the rates and age of onset appear to vary significantly in regions differentially affected by the Chernobyl accident. We assessed the frequency and distribution of three BRCA1 founder mutations 5382insC, 4153delA and Cys61Gly in two hospital-based series of 1945 unselected breast cancer patients and of 201 unselected ovarian cancer patients from Belarus as well as in 1019 healthy control females from the same population. Any of these mutations were identified in 4.4% of the breast cancer patients, 26.4% of the ovarian cancer patients and 0.5% of the controls. In the breast cancer patients, BRCA1 mutations were strongly associated with earlier age at diagnosis, with oestrogen receptor (ER) negative tumours and with a first-degree family history of breast cancer, although only 35% of the identified BRCA1 mutation carriers had such a family history. There were no marked differences in the regional distribution of BRCA1 mutations, so that the significant differences in age at diagnosis and family history of breast cancer patients from areas afflicted by the Chernobyl accident could not be explained by BRCA1. We next observed a higher impact and a shifted mutational spectrum of BRCA1 in the series of Byelorussian ovarian cancer patients where the three founder mutations accounted for 26.4% (53/201). While the Cys61Gly mutation appeared underrepresented in ovarian cancer as compared with breast cancer cases from the same population (p = 0.01), the 4153delA mutation made a higher contribution to ovarian cancer than to breast cancer (p < 0.01). BRCA1 mutations were significantly enriched among ovarian cancer cases with a first-degree family history of breast or ovarian cancer, whereas the median age at ovarian cancer diagnosis was not different between mutation carriers and non-carriers. Taken together, these results

  6. 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

  7. Increasing long term response by selecting for favorable minor alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2015-09-01

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

  9. The influence of human leukocyte antigen class I alleles and their population frequencies on human immunodeficiency virus type 1 control among African Americans.

    PubMed

    Lazaryan, Aleksandr; Song, Wei; Lobashevsky, Elena; Tang, Jianming; Shrestha, Sadeep; Zhang, Kui; McNicholl, Janet M; Gardner, Lytt I; Wilson, Craig M; Klein, Robert S; Rompalo, Anne; Mayer, Kenneth; Sobel, Jack; Kaslow, Richard A

    2011-04-01

    Populations of African ancestry continue to account for a disproportionate burden of the human immunodeficiency virus type 1 (HIV-1) epidemic in the United States. We investigated the effects of human leukocyte antigen (HLA) class I markers in association with virologic and immunologic control of HIV-1 infection among 338 HIV-1 subtype B-infected African Americans in 2 cohorts: Reaching for Excellence in Adolescent Care and Health (REACH) and HIV Epidemiology Research Study (HERS). One-year treatment-free interval measurements of HIV-1 RNA viral loads and CD4(+) T cells were examined both separately and combined to represent 3 categories of HIV-1 disease control (76 controllers, 169 intermediates, and 93 noncontrollers). Certain previously or newly implicated HLA class I alleles (A*32, A*36, A*74, B*14, B*1510, B*3501, B*45, B*53, B*57, Cw*04, Cw*08, Cw*12, and Cw*18) were associated with 1 or more of the endpoints in univariate analyses. After multivariable adjustments for other genetic and nongenetic risk factors of HIV-1 progression, the subset of alleles more strongly or consistently associated with HIV-1 disease control included A*32, A*74, B*14, B*45, B*53, B*57, and Cw*08. Carriage of infrequent HLA-B but not HLA-A alleles was associated with more favorable disease outcomes. Certain HLA class I associations with control of HIV-1 infection cross the boundaries of race and viral subtype, whereas others appear confined within one or the other of those boundaries.

  10. (H2O)2(g): Monomer/dimer vibrational frequency shifts in Bopp-Jancsó-Heinzinger- and Matsuoka-Clementi-Yoshimine-Lie-type flexible potentials

    NASA Astrophysics Data System (ADS)

    Slanina, Zdeněk

    1991-01-01

    Harmonic vibrational analysis of the water dimer is reported for four BJH- and four MCYL-type flexible water-water potentials. The calculated monomer/dimer frequency shifts correspond reasonably well to the available observed terms, the BJH-type flexible potentials (with the gas-phase intramolecular potential) yielding a slightly better agreement.

  11. Hybrid Hard and Soft Decision Decoding of Reed-Solomon Codes for M-ary Frequency-Shift Keying

    DTIC Science & Technology

    2010-06-01

    efficient modulation schemes such as M-ary phase-shift keying. Since JTIDS /Link-16 uses quasi-orthogonal, cyclic code-shift keying (CCSK), in this...keying. Since JTIDS /Link-16 uses quasi-orthogonal, cyclic code-shift keying (CCSK), in this thesis, soft decision decoding of RS encoded symbols is...87 VII. APPLICATION OF HYBRID HD SD RS DECODING IN ALE AND JTIDS /LINK-16

  12. 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

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

    PubMed

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

    2016-09-01

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

  14. High-Frequency (1)H NMR Chemical Shifts of Sn(II) and Pb(II) Hydrides Induced by Relativistic Effects: Quest for Pb(II) Hydrides.

    PubMed

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-10-17

    The role of relativistic effects on (1)H NMR chemical shifts of Sn(II) and Pb(II) hydrides is investigated by using fully relativistic DFT calculations. The stability of possible Pb(II) hydride isomers is studied together with their (1)H NMR chemical shifts, which are predicted in the high-frequency region, up to 90 ppm. These (1)H signals are dictated by sizable relativistic contributions due to spin-orbit coupling at the heavy atom and can be as large as 80 ppm for a hydrogen atom bound to Pb(II). Such high-frequency (1)H NMR chemical shifts of Pb(II) hydride resonances cannot be detected in the (1)H NMR spectra with standard experimental setup. Extended (1)H NMR spectral ranges are thus suggested for studies of Pb(II) compounds. Modulation of spin-orbit relativistic contribution to (1)H NMR chemical shift is found to be important also in the experimentally known Sn(II) hydrides. Because the (1)H NMR chemical shifts were found to be rather sensitive to the changes in the coordination sphere of the central metal in both Sn(II) and Pb(II) hydrides, their application for structural investigation is suggested.

  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. High frequency of SLC22A12 variants causing renal hypouricemia 1 in the Czech and Slovak Roma population; simple and rapid detection method by allele-specific polymerase chain reaction.

    PubMed

    Gabrikova, Dana; Bernasovska, Jarmila; Sokolova, Jitka; Stiburkova, Blanka

    2015-10-01

    Renal hypouricemia is a rare heterogeneous inherited disorder characterized by impaired tubular uric acid transport with severe complications, such as acute kidney injury. Type 1 and 2 are caused by loss-of-function mutations in the SLC22A12 and SLC2A9 gene, respectively. A cohort of 881 randomly chosen ethnic Roma from two regions in Eastern Slovakia and two regions in the Czech Republic participated. Genomic DNA was isolated from buccal swabs and/or from blood samples. The c.1245_1253del and c.1400C>T genotypes were determined using polymerase chain reaction with allele-specific primers in a multiplex arrangement and/or direct sequencing of exon 7 and 9. Allele frequencies and genotypes were tested for Hardy-Weinberg equilibrium using the Chi-square test. 25 subjects were heterozygous and three were homozygous for the c.1245_1253del, while 92 subjects were heterozygous and two were homozygous for the c.1400C>T. Moreover, two participants were compound heterozygotes. Frequencies of the c.1245_1253del and c.1400C>T variants were 1.87 and 5.56 %, respectively. Our finding confirms an uneven geographical and ethnic distribution of SLC22A12 mutant variants. We found that the c.1245_1253del and c.1400C>T variants were present in the Czech and Slovak Roma population at unexpectedly high frequencies. Renal hypouricemia should be kept in mind during differential diagnostic on Roma patients with low serum uric acid concentrations.

  17. A novel allelic variant of the human TSG-6 gene encoding an amino acid difference in the CUB module. Chromosomal localization, frequency analysis, modeling, and expression.

    PubMed

    Nentwich, Hilke A; Mustafa, Zehra; Rugg, Marilyn S; Marsden, Brian D; Cordell, Martin R; Mahoney, David J; Jenkins, Suzanne C; Dowling, Barbara; Fries, Erik; Milner, Caroline M; Loughlin, John; Day, Anthony J

    2002-05-03

    Tumor necrosis factor-stimulated gene-6 (TSG-6) encodes a 35-kDa protein, which is comprised of contiguous Link and CUB modules. TSG-6 protein has been detected in the articular joints of osteoarthritis (OA) patients, with little or no constitutive expression in normal adult tissues. It interacts with components of cartilage matrix (e.g. hyaluronan and aggrecan) and thus may be involved in extracellular remodeling during joint disease. In addition, TSG-6 has been found to have anti-inflammatory properties in models of acute and chronic inflammation. Here we have mapped the human TSG-6 gene to 2q23.3, a region of chromosome 2 linked with OA. A single nucleotide polymorphism was identified that involves a non-synonymous G --> A transition at nucleotide 431 of the TSG-6 coding sequence, resulting in an Arg to Gln alteration in the CUB module (at residue 144 in the preprotein). Molecular modeling of the CUB domain indicated that this amino acid change might lead to functional differences. Typing of 400 OA cases and 400 controls revealed that the A(431) variant identified here is the major TSG-6 allele in Caucasians (with over 75% being A(431) homozygotes) but that this polymorphism is not a marker for OA susceptibility in the patients we have studied. Expression of the Arg(144) and Gln(144) allotypes in Drosophila Schneider 2 cells, and functional characterization, showed that there were no significant differences in the ability of these full-length proteins to bind hyaluronan or form a stable complex with inter-alpha-inhibitor.

  18. Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape.

    PubMed

    Delourme, R; Bousset, L; Ermel, M; Duffé, P; Besnard, A L; Marquer, B; Fudal, I; Linglin, J; Chadœuf, J; Brun, H

    2014-10-01

    Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for durability of major resistance genes. This was demonstrated in the Leptosphaeria maculans/Brassica napus pathosystem in a 5year recurrent selection field experiment on lines harboring the qualitative resistance gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of the virulent isolate population. In this study we continued this recurrent selection experiment in the same way to examine whether the pathogen population could adapt and render the major gene ineffective in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an effective approach for controlling the pathogen epidemics over time. This combination did not prevent isolates virulent against the major gene from amplifying in the long term but the quantitative resistance significantly delayed for 5years the loss of effectiveness of the qualitative resistance and disease severity was maintained at a low level on the genotype with both types of resistance after the fungus population had adapted to the major gene. We also showed that diversity of AvrLm6 virulence alleles was comparable in isolates recovered after the recurrent selection on lines carrying either the major gene alone or in combination with quantitative resistance: a single repeat-induced point mutation and deletion events were observed in both situations. Breeding varieties which combine qualitative and quantitative resistance can effectively contribute to disease control by increasing the potential for durability of major resistance genes.

  19. 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.

  20. Genetic parameters and allele frequencies of five new European Standard Set STR loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in the population of Romania

    PubMed Central

    Stanciu, Florin; Vladu, Simona; Cuţăr, Veronica; Cocioabă, Daniela; Iancu, Florentina; Cotolea, Adnana; Stoian, Ionel Marius

    2013-01-01

    Aim To establish allele frequencies and genetic parameters for 5 new European Standard Set short tandem repeat (STR) loci in the population of Romania and to compare them with those in other populations. Methods DNA was isolated using QIAamp 96 DNA Swab BioRobot Kit and Chelex 100 methods. Polymerase chain reaction amplification was done using Investigator ESSplexPlus Kit (D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, and vWA). For DNA typing, Applied Biosystems 3500/3500xL Genetic Analyzer was used. Statistical analysis was done using Powerstats, GDA, and Arlequin software. Results Power of discrimination and polymorphism information content was highest for two new ESS loci, D1S1656 and D12S391. Comparison of allele frequencies for 5 new ESS loci in Romanian population with previously published population data showed significant differences for all compared populations, with the exception of Hungary. Geographically more distant populations, such as Spain, Sweden, United Kingdom, Germany, and Portugal differed more than closer populations. Conclusion New ESS STR loci are very useful for the analysis of forensic samples (persons or traces) due to their characteristics (shortness and high polymorphism). In comparisons with other common STR markers, they have a higher power of discrimination and also higher polymorphism information content, and could be used in any national DNA database. PMID:23771753

  1. The asteroseismic surface effect from a grid of 3D convection simulations - I. Frequency shifts from convective expansion of stellar atmospheres

    NASA Astrophysics Data System (ADS)

    Trampedach, Regner; Aarslev, Magnus J.; Houdek, Günter; Collet, Remo; Christensen-Dalsgaard, Jørgen; Stein, Robert F.; Asplund, Martin

    2017-03-01

    We analyse the effect on adiabatic stellar oscillation frequencies of replacing the near-surface layers in 1D stellar structure models with averaged 3D stellar surface convection simulations. The main difference is an expansion of the atmosphere by 3D convection, expected to explain a major part of the asteroseismic surface effect, a systematic overestimation of p-mode frequencies due to inadequate surface physics. We employ pairs of 1D stellar envelope models and 3D simulations from a previous calibration of the mixing-length parameter, α. That calibration constitutes the hitherto most consistent matching of 1D models to 3D simulations, ensuring that their differences are not spurious, but entirely due to the 3D nature of convection. The resulting frequency shift is identified as the structural part of the surface effect. The important, typically non-adiabatic, modal components of the surface effect are not included in this analysis, but relegated to future papers. Evaluating the structural surface effect at the frequency of maximum mode amplitude, νmax , we find shifts from δν = -0.8 μHz for giants at log g = 2.2 to - 35 μHz for a (Teff = 6901 K, log g = 4.29) dwarf. The fractional effect δν(νmax )/νmax , ranges from -0.1 per cent for a cool dwarf (4185 K, 4.74) to -6 per cent for a warm giant (4962 K, 2.20).

  2. An intuitive picture of the physics underlying optical ranging using frequency shifted feedback lasers seeded by a phase-modulated field

    NASA Astrophysics Data System (ADS)

    Yatsenko, L. P.; Shore, B. W.; Bergmann, K.

    2009-06-01

    Frequency shifted feedback (FSF) lasers have been demonstrated to have interesting and useful features when used for optical ranging. The use of a phase-modulated seed to the FSF laser dramatically improves the signal-to-noise ratio, enabling distance measurements with the accuracy expected of optical interferometry. We present here an intuitively accessible description of the physics that underlies this dramatic enhancement of optical ranging signals. Unlike a free-running FSF laser, each one of the many equidistant frequency components of the seeded FSF laser spectrum (typically >104) has a definite amplitude, and a phase which varies with component number and modulation frequency Ω of the seed radiation. Suitable adjustment of Ω gives all components a common phase; the resulting constructive interference enhances the signal by orders of magnitude.

  3. Isotope shifts and transition frequencies for the S and P states of lithium: Bethe logarithms and second-order relativistic recoil

    NASA Astrophysics Data System (ADS)

    Wang, L. M.; Li, Chun; Yan, Z.-C.; Drake, G. W. F.

    2017-03-01

    Isotope shifts and total transition frequencies are calculated for the 2 2S-3 2S transition of the lithium isotopes 6Li, 7Li, 8Li, 9Li, and the halo nucleus 11Li. The accuracy is improved for previously calculated relativistic and quantum electrodynamic corrections, and in particular a disagreement for the Bethe logarithm is resolved for the ground 2S state. Our previous result is confirmed for the 2 2P state. We use the pseudostate expansion method to perform the sum over virtual intermediate states. Results for the second-order relativistic recoil term of order α2(μ/M ) 2 Ry are shown to make a significant contribution relative to the theoretical uncertainty, but because of accidental cancellations the final result for the isotope shift is nearly unchanged. However, the spin-orbit term makes an unexpectedly large contribution to the splitting isotope shift (SIS) for the 2 1/2 2P -2 3/2 2P fine structure, increasing the theoretical value for the 6Li-7Li isotopes to 0.556 31 (7 )±0.001 MHz. A comparison is made with high-precision measurements and other calculations for the SIS and for the total 2 2S-3 2S transition frequency.

  4. Characterization of the treefrog null allele, 1991

    SciTech Connect

    Guttman, S.I.

    1992-04-01

    Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

  5. Characterization of the treefrog null allele

    SciTech Connect

    Guttman, S.I. . Dept. of Zoology)

    1990-12-01

    As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

  6. HLA-A, HLA-B, HLA-DRB1 allele and haplotype frequencies in 6384 umbilical cord blood units and transplantation matching and engraftment statistics in the Zhejiang cord blood bank of China.

    PubMed

    Wang, F; He, J; Chen, S; Qin, F; Dai, B; Zhang, W; Zhu, F M; Lv, H J

    2014-02-01

    Umbilical cord blood (UCB) is a widely accepted source of progenitor cells, and now, many cord blood banks were established. Here, we analysed the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies, HLA matching possibilities for searching potential donors and outcome of UCB transplantations in Zhejiang cord blood bank of China. A total of 6384 UCB units were characterized for 17 HLA-A, 30 HLA-B and 13 HLA-DRB1 alleles at the first field resolution level. Additionally, B*14, B*15 and B*40 were typed to the second field level. A total of 1372 distinct A-B-DRB1 haplotypes were identified. The frequencies of 7 haplotypes were more than 1%, and 439 haplotypes were <0.01%. A*02-B*46-DRB1*09, A*33-B*58-DRB1*03 and A*30-B*13-DRB1*07 were the most common haplotypes, with frequencies of 4.4%, 3.3%, and 2.9%, respectively. Linkage disequilibrium(LD) analysis showed that there were 83 A-B, 106 B-DRB1, 54 A-DRB1 haplotypes with positive LD, in which 51 A-B, 60 B-DRB1, 32 A-DRB1 haplotypes exhibited a significant LD (P < 0.05). In 682 search requests, 12.9%, 40.0% and 42.7% of patients were found to have 6 of 6, 5 of 6 and 4 of 6 HLA-A, HLA-B and HLA-DRB1 matching donors, respectively. A total of 30 UCB units were transplanted to 24 patients (3 patients not evaluated due to early death); 14 of 21 patients (66.7%) engrafted. This study reveals the HLA distribution and its transplantation application in the cord blood bank of Zhejiang province. These data can help to select potential UCB donors for transplantation and used to assess the scale of new cord blood banking endeavours.

  7. Soliton self-frequency shift and third-harmonic generation in a four-hole As₂S₅ microstructured optical fiber.

    PubMed

    Cheng, Tonglei; Usaki, Ryo; Duan, Zhongchao; Gao, Weiqing; Deng, Dinghuan; Liao, Meisong; Kanou, Yasuhire; Matsumoto, Morio; Misumi, Takashi; Suzuki, Takenobu; Ohishi, Yasutake

    2014-02-24

    Soliton self-frequency shift (SSFS) and third-harmonic generation (THG) are observed in a four-hole As2S5 chalcogenide microstructured optical fiber (MOF). The As2S5 MOF is tapered to offer an ideal environment for SSFS. After tapering, the zero-dispersion wavelength (ZDW) shifts from 2.02 to 1.61 μm, and the rate of SSFS can be enhanced by increasing the energy density of the pulse. By varying the average input power from 220 to 340 mW, SSFS of a soliton central wavelength from 2.206 to 2.600 μm in the mid-infrared is observed in the tapered segment, and THG at 632 nm is observed in the untapered segment.

  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. 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

    2016-05-11

    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.

  10. Allele frequencies in the VRN-A1, VRN-B1 and VRN-D1 vernalization response and PPD-B1 and PPD-D1 photoperiod sensitivity genes, and their effects on heading in a diverse set of wheat cultivars (Triticum aestivum L.).

    PubMed

    Kiss, Tibor; Balla, Krisztina; Veisz, Ottó; Láng, László; Bedő, Zoltán; Griffiths, Simon; Isaac, Peter; Karsai, Ildikó

    2014-01-01

    Heading of cereals is determined by complex genetic and environmental factors in which genes responsible for vernalization and photoperiod sensitivity play a decisive role. Our aim was to use diagnostic molecular markers to determine the main allele types in VRN-A1, VRN-B1, VRN-D1, PPD-B1 and PPD-D1 in a worldwide wheat collection of 683 genotypes and to investigate the effect of these alleles on heading in the field. The dominant VRN-A1, VRN-B1 and VRN-D1 alleles were present at a low frequency. The PPD-D1a photoperiod-insensitive allele was carried by 57 % of the cultivars and was most frequent in Asian and European cultivars. The PPD-B1 photoperiod-insensitive allele was carried by 22 % of the genotypes from Asia, America and Europe. Nine versions of the PPD-B1-insensitive allele were identified based on gene copy number and intercopy structure. The allele compositions in PPD-D1, PPD-B1 and VRN-D1 significantly influenced heading and together explained 37.5 % of the phenotypic variance. The role of gene model increased to 39.1 % when PPD-B1 intercopy structure was taken into account instead of overall PPD-B1 type (sensitive vs. insensitive). As a single component, PPD-D1 had the most important role (28.0 % of the phenotypic variance), followed by PPD-B1 (12.3 % for PPD-B1_overall, and 15.1 % for PPD-B1_intercopy) and VRN-D1 (2.2 %). Significant gene interactions were identified between the marker alleles within PPD-B1 and between VRN-D1 and the two PPD1 genes. The earliest heading genotypes were those with the photoperiod-insensitive allele in PPD-D1 and PPD-B1, and with the spring allele for VRN-D1 and the winter alleles for VRN-A1 and VRN-B1. This combination could only be detected in genotypes from Southern Europe and Asia. Late-heading genotypes had the sensitivity alleles for both PPD1 genes, regardless of the allelic composition of the VRN1 genes. There was a 10-day difference in heading between the earliest and latest groups under field conditions.

  11. First pure frequency measurement of an optical transition in helium: Lamb shift on the 2[sup 3][ital S][sub 1] metastable level

    SciTech Connect

    Pavone, F.S.; Marin, F.; De Natale, P.; Inguscio, M. , University of Florence, Largo E. Fermi, 2 I-50125 Firenze ); Biraben, F. )

    1994-07-04

    The 2[sup 3][ital S][sub 1-]3[sup 3][ital P][sub 0][sup 4]He transition at [lambda][sub 0]=389 nm is measured with respect to a previously frequency calibrated [sup 87]Rb two-photon transition at 2[lambda][sub 0]=778 nm. The [sup 4]He absolute frequency is 770 732 839 058 (190) kHz, with an accuracy of 2.4 parts in 10[sup 10]. A Lamb shift value of +4057.61 (79) MHz, with 600 kHz uncertainty arising from the theoretical position of the 3[sup 3][ital P][sub 0] energy level, is extracted for the 2[sup 3][ital S][sub 1] level. This value is more than 2 orders of magnitude more accurate than the current best theoretical predictions.

  12. 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.

  13. 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.

  14. 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

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

    PubMed

    Torii, Hajime

    2016-09-15

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

  16. 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.

  17. Comparison of HLA allelic imputation programs.

    PubMed

    Karnes, Jason H; Shaffer, Christian M; Bastarache, Lisa; Gaudieri, Silvana; Glazer, Andrew M; Steiner, Heidi E; Mosley, Jonathan D; Mallal, Simon; Denny, Joshua C; Phillips, Elizabeth J; Roden, Dan M

    2017-01-01

    Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations.

  18. Comparison of HLA allelic imputation programs

    PubMed Central

    Shaffer, Christian M.; Bastarache, Lisa; Gaudieri, Silvana; Glazer, Andrew M.; Steiner, Heidi E.; Mosley, Jonathan D.; Mallal, Simon; Denny, Joshua C.; Phillips, Elizabeth J.; Roden, Dan M.

    2017-01-01

    Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations. PMID:28207879

  19. 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

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

    PubMed Central

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

    2016-01-01

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

  1. An in-building network based on community access television integration with quadrature phase-shift keying orthogonal frequency-division multiplexing

    NASA Astrophysics Data System (ADS)

    Chen, Chia-Yi; Lin, Ying-Pyng; Lu, Hai-Han; Wu, Po-Yi; Lin, Huang-Chang; Wu, Hsiao-Wen

    2012-07-01

    An in-building network based on cable television (CATV) integration with quadrature phase-shift keying (QPSK) orthogonal frequency-division multiplexing (OFDM) transport over a combination of single-mode fibers (SMF) and perfluorinated graded-index plastic optical fibers (GI-POF) is proposed and experimentally demonstrated. In this system, a 1558.5 nm optical signal is directly transmitted along two fiber spans (20 km SMF + 25 m GI-POF). An optimum guard band is carefully established to ensure that no very substantial signal interference is induced between the CATV and QPSK OFDM bands. Error free transmission with sufficiently low bit error rate values was achieved for 1.25 Gbps/771.5 MHz QPSK OFDM signals; also, acceptable carrier-to-noise ratio, composite second-order, and composite triple-beat performances were obtained for CATV signals. This proposed network is significant because it is economical and convenient to install.

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

    PubMed

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

    2010-02-01

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

  3. Vibrational frequency shifts of diatomic molecules in interaction with a Na + cation by ab initio calculations. Comparison with experiment on H 2 and N 2 adsorbed in NaA zeolite

    NASA Astrophysics Data System (ADS)

    Koubi, Laure; Blain, Monique; de Lara, Evelyne Cohen; Leclerq, Jean-Marie

    1994-01-01

    Ab initio calculations on H 2 and N 2 and on the same molecules in the presence of a Na + cation are presented. The equilibrium configuration and the vibrational frequency shift due to the interaction are calculated. The potential energy surfaces are obtained by local osculatory interpolations and extrapolations. The vibrational frequencies are calculated by the Numerov—Cooley method. The direction of the frequency shift is found to be related to the orientation of the diatomic molecule with respect to the cation. The results are compared with experimental data on induced infrared bands of H 2 and N 2 adsorbed in NaA zeolite.

  4. 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...

  5. 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

  6. Differential patterns of spatial divergence in microsatellite and allozyme alleles: further evidence for locus-specific selection in the acorn barnacle, Semibalanus balanoides?

    PubMed

    Dufresne, F; Bourget, E; Bernatchez, L

    2002-01-01

    We compared patterns of genetic structure at potentially selected (two allozyme loci) and neutral molecular markers (six microsatellite loci) in the acorn barnacle, Semibalanus balanoides from the Gulf of St. Lawrence. Our results confirmed the presence of a geographical shift in alleles MPI and GPI near the Miramichi River. In contrast, no significant patterns of population differentiation among samples located north and south of the river mouth were detected for four of six microsatellite loci. However, analysis of molecular variance (amova) at individual loci revealed that a significant proportion of the total variance in allele frequencies was partitioned among samples located north and south of the river for both the allozyme and the other two microsatellite loci. The two most common alleles at these microsatellites showed frequencies that were highly correlated (r = 0.65-0.74, P < 0.05) with those of the MPI*2 allele, perhaps because of either physical linkage or epistasis. The two allozyme loci were significantly correlated in barnacles located north of the Miramichi River (r = 0.86, P < 0.05). Overall, our results supported the hypothesis that the broad scale pattern of allozyme allelic shifts is maintained by selection. They also indicated that microsatellites may not always behave in a neutral way and must be used cautiously, especially when evidence for genetic structuring relies on only a few assayed loci.

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

    PubMed

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

    2014-05-01

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

  8. 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.

  9. 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

  10. 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.

  11. HLA-B alleles of the Cayapa of Ecuador: new B39 and B15 alleles.

    PubMed

    Garber, T L; Butler, L M; Trachtenberg, E A; Erlich, H A; Rickards, O; De Stefano, G; Watkins, D I

    1995-01-01

    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.

  12. Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

    PubMed

    Remington, David L

    2015-12-01

    Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology.

  13. Microsatellite null alleles and estimation of population differentiation.

    PubMed

    Chapuis, Marie-Pierre; Estoup, Arnaud

    2007-03-01

    Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation. Computer simulations based on the coalescent were used to investigate the evolutionary dynamics of null alleles, their impact on F(ST) and genetic distances, and the efficiency of estimators of null allele frequency. Further, we explored how the existing method for correcting genotype data for null alleles performed in estimating F(ST) and genetic distances, and we compared this method with a new method proposed here (for F(ST) only). Null alleles were likely to be encountered in populations with a large effective size, with an unusually high mutation rate in the flanking regions, and that have diverged from the population from which the cloned allele state was drawn and the primers designed. When populations were significantly differentiated, F(ST) and genetic distances were overestimated in the presence of null alleles. Frequency of null alleles was estimated precisely with the algorithm presented in Dempster et al. (1977). The conventional method for correcting genotype data for null alleles did not provide an accurate estimate of F(ST) and genetic distances. However, the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction. F(ST) estimation from corrected genotype frequencies performed well when restricted to visible allele sizes. Both the proposed method and the traditional correction method have been implemented in a program that is available free of charge at http://www.montpellier.inra.fr/URLB/. We used 2 published microsatellite data sets based on original and redesigned pairs of primers to empirically confirm our simulation results.

  14. 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

  15. Estimating Relatedness in the Presence of Null Alleles.

    PubMed

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

    2016-01-01

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

  16. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots

    PubMed Central

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

    2015-01-01

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

  17. 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.

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

    PubMed

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

    2014-02-10

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

  19. Analysis of elite variety tag SNPs reveals an important allele in upland rice.

    PubMed

    Lyu, Jun; Zhang, Shilai; Dong, Yang; He, Weiming; Zhang, Jing; Deng, Xianneng; Zhang, Yesheng; Li, Xin; Li, Baoye; Huang, Wangqi; Wan, Wenting; Yu, Yang; Li, Qiong; Li, Jun; Liu, Xin; Wang, Bo; Tao, Dayun; Zhang, Gengyun; Wang, Jun; Xu, Xun; Hu, Fengyi; Wang, Wen

    2013-01-01

    Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single-nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cis-epoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically important alleles.

  20. 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.

  1. A 400-mV 2.4-GHz frequency-shift keying transmitter using a capacitor switch across a transformer for a wide tuning range voltage-controlled oscillator

    NASA Astrophysics Data System (ADS)

    Miyahara, Yasunori; Ishikawa, Keisuke; Kuroda, Tadahiro

    2017-04-01

    We use a simple directly modulated closed loop to develop a 2.1-mW, 2.4-GHz frequency-shift keying (FSK) transmitter that operates on 400-mV DC supply. Connecting a capacitor bank switch via a transformer in the voltage control oscillator (VCO) to the frequency-divider circuit expands the frequency tuning range without reducing VCO performance. A prototype was fabricated using the 65-nm standard CMOS process with a chip size of 1.65 × 1.85 mm2. A modulation output signal spectrum of ‑42 dBc at 1.5 MHz with ‑6 dBm at the PA buffer output terminal; moreover, a VCO phase noise