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Sample records for allele frequency ranged

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  4. 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).

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2016-03-01

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

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

    SciTech Connect

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

    1993-03-01

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

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

    PubMed Central

    Ackermann, Marit; Beyer, Andreas

    2012-01-01

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

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

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

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

  10. High throughput automated allele frequency estimation by pyrosequencing.

    PubMed

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

    2008-01-01

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

  11. High Throughput Automated Allele Frequency Estimation by Pyrosequencing

    PubMed Central

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

    2008-01-01

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

  12. 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

  13. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

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

    2009-04-01

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

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

    ERIC Educational Resources Information Center

    Nussbaum, Francis, Jr.

    1988-01-01

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

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

    PubMed

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

    1995-07-01

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

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

    PubMed

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

    2007-03-01

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

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

    PubMed Central

    2010-01-01

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

  18. 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

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

    PubMed Central

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

    2010-01-01

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

  20. 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

  1. 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...

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

    PubMed

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

    2008-11-01

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

  3. Transponder System for High-Frequency Ranging

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  4. Frequency skewed optical pulses for range detection

    NASA Astrophysics Data System (ADS)

    Ozharar, Sarper; Gee, Sangyoun; Quinlan, Franklyn; Delfyett, Peter J., Jr.

    2007-04-01

    Frequency skewed optical pulses are generated via both a composite cavity structure in a fiberized semiconductor optical amplifier ring laser and a frequency skew loop outside the laser cavity. The composite cavity technique is similar to rational harmonic mode-locking, however it is based on cavity detuning rather than frequency detuning. These frequency skewed pulses are ideal for range detection applications since their interference results in a range dependent RF signal. The intracavity frequency skewed pulse train showed superior performance in both stability and signal quality.

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

    PubMed

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

    2016-06-01

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

  6. 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 ...

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2002-06-01

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

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

    PubMed

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

    2014-10-01

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

  12. 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

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

    PubMed

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

    2003-01-01

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

  14. 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

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

    PubMed

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

    2008-09-01

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

  16. Frequency of CCR5Δ32 allele in healthy Bosniak population

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

    2010-01-01

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

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

    PubMed

    Gao, Yulin; Wu, Kongming; Gould, Fred

    2009-08-01

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

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

    PubMed

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

    2014-12-01

    As researchers collect spatiotemporal population and genetic data in tandem, models that connect demography and dispersal to genetics are increasingly relevant. The dominant spatiotemporal model of invasion genetics is the stepping-stone model which represents a gradual range expansion in which individuals jump to uncolonized locations one step at a time. However, many range expansions occur quickly as individuals disperse far from currently colonized regions. For these types of expansion, stepping-stone models are inappropriate. To more accurately reflect wider dispersal in many organisms, we created kernel-based models of invasion genetics based on integrodifference equations. Classic theory relating to integrodifference equations suggests that the speed of range expansions is a function of population growth and dispersal. In our simulations, populations that expanded at the same speed but with spread rates driven by dispersal retained more heterozygosity along axes of expansion than range expansions with rates of spread that were driven primarily by population growth. To investigate surfing we introduced mutant alleles in wave fronts of simulated range expansions. In our models based on random mating, surfing alleles remained at relatively low frequencies and surfed less often compared to previous results based on stepping-stone simulations with asexual reproduction. PMID:25201435

  2. Active laser ranging with frequency transfer using frequency comb

    NASA Astrophysics Data System (ADS)

    Zhang, Hongyuan; Wei, Haoyun; Yang, Honglei; Li, Yan

    2016-05-01

    A comb-based active laser ranging scheme is proposed for enhanced distance resolution and a common time standard for the entire system. Three frequency combs with different repetition rates are used as light sources at the two ends where the distance is measured. Pulse positions are determined through asynchronous optical sampling and type II second harmonic generation. Results show that the system achieves a maximum residual of 379.6 nm and a standard deviation of 92.9 nm with 2000 averages over 23.6 m. Moreover, as for the frequency transfer, an atom clock and an adjustable signal generator, synchronized to the atom clock, are used as time standards for the two ends to appraise the frequency deviation introduced by the proposed system. The system achieves a residual fractional deviation of 1.3 × 10-16 for 1 s, allowing precise frequency transfer between the two clocks at the two ends.

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

    PubMed

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

    2002-01-23

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    Rujirojindakul, Pairaya; Chongsuvivatwong, Virasakdi; Limprasert, Pornprot

    2015-01-01

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

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

    PubMed

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

    2014-06-01

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

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

    PubMed

    Cowell, Robert

    2016-07-01

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

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection...

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

    PubMed Central

    2013-01-01

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

  18. 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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2009-01-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed Central

    Der, Ricky; Plotkin, Joshua B.

    2014-01-01

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

  3. 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

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

    PubMed Central

    Waples, R. S.

    1989-01-01

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

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

    PubMed

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

    2015-10-21

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

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

    PubMed

    Verhulst, Brad; Neale, Michael C

    2016-09-01

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

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

    PubMed Central

    Ramasamy, Thirumurugan; Ayyavoo, Jayachitra

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  9. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Racimo, Fernando

    2016-02-01

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

  12. 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.

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

    SciTech Connect

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

    2015-07-22

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2015-06-01

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

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

    PubMed

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

    2012-08-01

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

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

    PubMed

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

    2016-07-01

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

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

    PubMed

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

    2014-03-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2006-06-01

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

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

    PubMed Central

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

    2014-01-01

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

  3. 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

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

    PubMed

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

    2012-01-01

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

  5. 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

  6. 33 CFR 86.01 - Frequencies and range of audibility.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... INLAND NAVIGATION RULES ANNEX III: TECHNICAL DETAILS OF SOUND SIGNAL APPLIANCES Whistles § 86.01 Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525..., which may include the fundamental and/or one or more higher frequencies, which lie within the...

  7. 33 CFR 86.01 - Frequencies and range of audibility.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... INLAND NAVIGATION RULES ANNEX III: TECHNICAL DETAILS OF SOUND SIGNAL APPLIANCES Whistles § 86.01 Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525..., which may include the fundamental and/or one or more higher frequencies, which lie within the...

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... INLAND NAVIGATION RULES ANNEX III: TECHNICAL DETAILS OF SOUND SIGNAL APPLIANCES Whistles § 86.01 Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525..., which may include the fundamental and/or one or more higher frequencies, which lie within the...

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

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... INLAND NAVIGATION RULES ANNEX III: TECHNICAL DETAILS OF SOUND SIGNAL APPLIANCES Whistles § 86.01 Frequencies and range of audibility. The fundamental frequency of the signal shall lie within the range 70-525..., which may include the fundamental and/or one or more higher frequencies, which lie within the...

  10. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  11. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  12. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  13. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  14. 47 CFR 15.202 - Certified operating frequency range.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

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

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Frequency range of radiated measurements. 15.33 Section 15.33 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES General § 15.33 Frequency range of radiated measurements. (a) For an intentional radiator, the spectrum shall be investigated from the lowest...

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  18. A note on the change in gene frequency of a selected allele in partial full-sib mating populations

    SciTech Connect

    Caballero, A.

    1996-02-01

    The change in gene frequency of a selected allele in partial full-sib mating populations was analyzed. The implications of these papers is important in terms of the fixation probability of genes because, for the same equilibrium inbreeding coefficient, fixation rates of mutant genes would be larger for partial full-sib mating than for partial selfing. 4 refs.

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2010-05-11

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

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

    2003-01-01

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

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

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2009-12-01

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

  6. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  7. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  8. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

  9. 47 CFR 18.309 - Frequency range of measurements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Frequency range of measurements. 18.309 Section 18.309 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL INDUSTRIAL, SCIENTIFIC, AND MEDICAL EQUIPMENT Technical Standards § 18.309 Frequency range of measurements. (a) For field...

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

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Frequencies and range of audibility. 86.01 Section 86.01 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INLAND NAVIGATION RULES ANNEX III: TECHNICAL DETAILS OF SOUND SIGNAL APPLIANCES Whistles § 86.01 Frequencies and range of audibility. The...

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

    PubMed

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

    2015-07-01

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

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

    PubMed

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

    2016-02-13

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

  13. 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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  17. 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

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

    PubMed

    Titze, Ingo; Riede, Tobias; Mau, Ted

    2016-06-01

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

  19. Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species

    PubMed Central

    Titze, Ingo; Riede, Tobias; Mau, Ted

    2016-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  2. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  3. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  4. 47 CFR 15.33 - Frequency range of radiated measurements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

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

    PubMed

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

    2012-01-01

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

  6. 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

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

    PubMed

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

    2007-12-01

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

  8. a Pre-Emphasis Technique to Broaden the Usable Frequency Range in Swept-Frequency Systems

    NASA Astrophysics Data System (ADS)

    Gammell, Paul M.; Maruvada, Subha; Liu, Yunbo; Harris, Gerald R.

    2010-02-01

    The usable frequency range of an ultrasonic swept-frequency system can be compromised because of transducer bandwidth limitations or sample frequency response and corresponding signal-to-noise (S/N) considerations. By adding a variable gain amplifier together with an arbitrary waveform generator that is synchronized with the frequency sweep, the dynamic range of the receiver can be accommodated over a wider frequency range. This pre-emphasis approach has been demonstrated for two applications: substitution calibration of hydrophones and attenuation measurements.

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

    PubMed

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

    2016-04-01

    Marker-assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits. PMID:26249527

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

    PubMed

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

    2016-07-01

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

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

    PubMed

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

    2014-04-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

    2012-01-01

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

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

    PubMed

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

    2015-05-01

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

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

    PubMed

    Sánchez-Molina, I; Calvet, R

    2000-01-01

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

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

    PubMed

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

    1997-08-01

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

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

    PubMed

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

    2013-07-01

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

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

    PubMed

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

    2006-07-01

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

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

    PubMed Central

    2013-01-01

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

  20. Experimental limits on gravitational waves in the MHz frequency range

    NASA Astrophysics Data System (ADS)

    Lanza, Robert Kingman, Jr.

    This thesis presents the results of a search for gravitational waves in the 1-11MHz frequency range using dual power-recycled Michelson laser interferometers at Fermi National Accelerator Laboratory. An unprecedented level of sensitivity to gravitational waves in this frequency range has been achieved by cross-correlating the output fluctuations of two identical and co-located 40m long interferometers. This technique produces sensitivities better than two orders of magnitude below the quantum shot-noise limit, within integration times of less than 1 hour. 95% confidence level upper limits are placed on the strain amplitude of MHz frequency gravitational waves at the 10-21 Hz-1/2 level, constituting the best direct limits to date at these frequencies. For gravitational wave power distributed over this frequency range, a broadband upper limit of 2.4x10 -21Hz-1/2 at 95% confidence level is also obtained. This thesis covers the detector technology, the commissioning and calibration of the instrument, the statistical data analysis, and the gravitational wave limit results. Particular attention is paid to the end-to-end calibration of the instrument's sensitivity to differential arm length motion, and so to gravitational wave strain. A detailed statistical analysis of the data is presented as well.

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

    PubMed

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

    2006-06-01

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

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

    PubMed

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

    2013-01-01

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

  3. Improving range resolution with a frequency-hopping technique

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  4. Ring current instabilities in the magnetohydrodynamic frequency range

    NASA Technical Reports Server (NTRS)

    Hasegawa, A.; Chen, L.

    1992-01-01

    This report summarizes recent theoretical developments in ring current plasma instabilities in the magnetohydrodynamic (MHD) frequency range but with the effect of finite Larmor radius, and discusses its relevance to satellite-based observations. Possible instabilities are the bounce resonant instabilities caused by a humped energy distribution, the drift mirror instability caused by an anisotropic pressure and the drift wave type instability caused by a combination of drift-bounce resonance and reduced Alfven frequency due to a high beta loading of the flux tube. Here, beta is proportional to plasma/magnetic pressures. Mechanisms leading to turbulence are also discussed.

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

    PubMed

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

    2016-10-01

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

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

    SciTech Connect

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

    2013-04-15

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

  7. A broadband multifocal metalens in the terahertz frequency range

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2005-06-01

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

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

    PubMed Central

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

    1999-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  12. Long range downwind propagation of low-frequency sound

    NASA Technical Reports Server (NTRS)

    Willshire, W. L., Jr.

    1985-01-01

    The propagation of low-frequency noise outdoors was studied using as the source a large (80-m diameter) 4-megawatt horizontal axis wind turbine. Acoustic measurements were made with low-frequency microphone systems placed on the ground at five downwind sites ranging from 300 m to 10,000 m (6.3 mile) away from the wind turbine. The wind turbine fundamental was 1 Hz and the wind speed was generally 12 - 15 m/s at the hub height (80 m). The harmonic levels, when plotted versus propagation distance, exhibit a 3 dB per doubling of distance divergence. Two plausible explanations identified for this cylindrical spreading behavior were propagation of the low frequency wind turbine noise via a surface wave and downwind refraction. Surface was amplitude predictions were found to be more than 20 dB smaller than the measured levels. Ray-tracing results were used to qualitatively explain measured trends. A normal mode approach was identified as a candidate method for low-frequency acoustic refraction prediction.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  14. Heating by waves in the ion cyclotron frequency range

    SciTech Connect

    Koch, R.

    1996-03-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2010-10-01

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

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

    PubMed

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

    2004-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  19. 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

  20. Large-orbit gyrotron operation in the terahertz frequency range.

    PubMed

    Bratman, V L; Kalynov, Yu K; Manuilov, V N

    2009-06-19

    Coherent terahertz high-harmonic radiation has been obtained in a gyrotron with an axis-encircling electron beam. An electron-optical system with a cusp gun and a following drift section of adiabatic magnetic compression with an area factor of 3000 provides the formation of an 80-keV/0.7-A beam of gyrating electrons in a wide range of voltages and magnetic fields. Stable single-mode generation with a power of 0.3-1.8 kW in microsecond pulses is detected at four frequencies in the range 0.55-1.00 THz at resonant magnetic fields 10.5-14 T. PMID:19659020

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

    DOEpatents

    Kerner, Thomas M.

    2001-01-01

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

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

    PubMed

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

    2008-12-01

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

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

    PubMed

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

    2009-07-01

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

  4. Transport induced by ion cyclotron range of frequencies waves

    SciTech Connect

    Zhang, Debing Xu, Yingfeng; Wang, Shaojie

    2014-11-15

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

  5. The technology of the ion cyclotron range of frequencies

    SciTech Connect

    Hoffman, D.J.; Barber, G.C.

    1988-01-01

    Plasma heating in the ion cyclotron range of frequencies (ICRF) is the least expensive means of accomplishing auxiliary heating in fusion experiments. RF systems comprise two major elements: the transmitter and the antenna. The state of the art for the transmitter is already at the megawatt level. The technology of the antenna is strongly coupled to the plasma character. Typically, these antennas are designed to operate at a high power density (1.2 kW/cm/sup 2/) with an efficiency of 96%. ICRF technology and options have improved over the past few years, owing to development and experiments; however, the optimal combination of options can be defined only when results from confinement experiments and test facilities are in hand. 19 refs., 5 figs., 1 tab.

  6. High precision spectroscopy and imaging in THz frequency range

    NASA Astrophysics Data System (ADS)

    Vaks, Vladimir L.

    2014-03-01

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

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

    PubMed Central

    Kono, Yoshiaki; Kohn, Joshua R.

    2015-01-01

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

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

    PubMed Central

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

    2004-01-01

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

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

    PubMed

    Lucotte, Gérard

    2002-05-01

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

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

    PubMed

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

    1991-06-01

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

  11. 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. Fractional frequency instability in the 10{sup -14} range with a thermal beam optical frequency reference

    SciTech Connect

    McFerran, John J.; Luiten, Andre N.

    2010-02-15

    We demonstrate a means of increasing the signal-to-noise ratio in a Ramsey-Borde interferometer with spatially separated oscillatory fields on a thermal atomic beam. The {sup 1}S{sub 0}{r_reversible}{sup 3}P{sub 1} intercombination line in neutral {sup 40}Ca is used as a frequency discriminator, with an extended cavity diode laser at 423 nm probing the ground state population after a Ramsey-Borde sequence of 657 nm light-field interactions with the atoms. Evaluation of the instability of the Ca frequency reference is carried out by comparison with (i) a hydrogen-maser and (ii) a cryogenic sapphire oscillator. In the latter case the Ca reference exhibits a square-root {Lambda} variance of 9.2x10{sup -14} at 1 s and 2.0x10{sup -14} at 64 s. This is an order-of-magnitude improvement for optical beam frequency references, to our knowledge. The shot noise of the readout fluorescence produces a limiting square-root {Lambda} variance of 7x10{sup -14}/{radical}({tau}), highlighting the potential for improvement. This work demonstrates the feasibility of a portable frequency reference in the optical domain with 10{sup -14} range frequency instability.

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

    PubMed

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

    2015-11-01

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

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

    PubMed

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

    2014-06-01

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

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

    PubMed Central

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

    2003-01-01

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

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

    PubMed

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

    2012-01-01

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

  17. 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

  18. 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

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

    PubMed

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

    2016-03-01

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

  20. A new AC susceptibility instrument for detecting frequency dependence over a wide range of frequencies

    NASA Astrophysics Data System (ADS)

    Kodama, K.

    2008-12-01

    A unique equipment was developed for measuring low-field AC susceptibility over a frequency spectrum ranging from 10 Hz to 4 kHz. The coil system consists of a primary coil for applying an excitation field, and a set of pickup coils linked in series and wound oppositely for compensation. The number of turns for the primary coil is 6,000 and that for the pickup coils is 4,400, using 0.1 mm thick copper wire, wound around a quartz-glass tube of 36 mm in diameter, allowing to measure conventional 10cc samples. The excitation field is produced by a commercial function generator with two independent outputs, capable of generating sinusoidal current with frequencies of 0 to 10 MHz. A mutual inductor coil is connected in series, to which the wave generator supplies, through the second output, a small current that can be adjusted in phase and magnitude to compensate the out-of-balance of the pickup coils. The resulting signal output voltage is fed to a digital rock-in amplifier. The AC frequency spans practically from 10 Hz to 4 kHz due to the limitation of the lock-in amplifier, but can be swept over the entire range with a constant amplitude of the applied field, which is changeable from 0.4 to 1.0 Oe. The outputs from the lock-in amplifier, in both magnitude and phase, are transferred to a PC to obtain the frequency dependence spectrum of both real and imaginary parts of AC susceptibility. The system calibration was made using a paramagnetic Gd2O3 powder as well as several natural samples that have ever been used for inter-laboratory calibrations.

  1. 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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    Arango, Eliana; Carmona-Fonseca, Jaime

    2013-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2016-09-01

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

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

    SciTech Connect

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

    1993-01-01

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

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

    PubMed

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

    1997-04-01

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

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

    PubMed

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

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2003-05-01

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

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

    PubMed

    Sulcebe, Genc; Shyti, Erkena

    2016-08-01

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

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

    PubMed

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

    2011-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  16. Research of polymer fibers for the terahertz frequency range

    NASA Astrophysics Data System (ADS)

    Wang, Dong

    2011-08-01

    Terahertz radiation, with wavelengths from 30 to 3000 microns, has big potential for applications such as biomedical sensing, noninvasive imaging and spectroscopy. Current researches on photonic crystal fibers as THz waveguide has been widely presented, but the sorts of waveguide usually need special fabrication technique and always be difficult to get perfect structure. We report on a new type of polymer photonic crystal fibers for low-loss guidance of THz radiation with general fabrication technique. The use of the cyclic olefin copolymer (COC) Topas, results in THz fibers with relatively low loss and low material dispersion in the THz range. We manufactured a class of THz waveguides with different structures. Then we use a THz time-domain spectroscopy system (THz- TDS) to characterize the Material loss and index of refractive of the waveguides.

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

    PubMed

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

    2013-09-01

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

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

    PubMed

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

    2015-04-01

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

  19. 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

  20. 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

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

    SciTech Connect

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

    2009-07-20

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

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

    PubMed

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

    2016-03-01

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

  3. 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

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

    PubMed Central

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

    2012-01-01

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

  5. Range and Velocity Estimation of Moving Targets Using Multiple Stepped-frequency Pulse Trains

    PubMed Central

    Li, Gang; Meng, Huadong; Xia, Xiang-Gen; Peng, Ying-Ning

    2008-01-01

    Range and velocity estimation of moving targets using conventional stepped-frequency pulse radar may suffer from the range-Doppler coupling and the phase wrapping. To overcome these problems, this paper presents a new radar waveform named multiple stepped-frequency pulse trains and proposes a new algorithm. It is shown that by using multiple stepped-frequency pulse trains and the robust phase unwrapping theorem (RPUT), both of the range-Doppler coupling and the phase wrapping can be robustly resolved, and accordingly, the range and the velocity of a moving target can be accurately estimated.

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

    PubMed

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

    2011-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Sugimoto, Tsuneyoshi; Abe, Touma

    2011-07-01

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

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

    PubMed Central

    Zeisset, Inga; Beebee, Trevor J. C.

    2014-01-01

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

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

    PubMed

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

    1999-12-01

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

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

    PubMed Central

    2012-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

    Kent, Stephen; Kashima, Yoshihisa

    2015-01-01

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

  13. Estimation of ground range on the sweep frequency backscatter leading edge

    NASA Astrophysics Data System (ADS)

    Su, Fanfan; Zhao, Zhengyu; Deng, Feng; Li, Shipeng

    2011-04-01

    The high frequency management system with backscatter radar supplies the real time ionosphere channel conditions to high frequency users, which leads to the demand for the ground range between the radar location and the scatters on the distant ground. The ionosphere electron density profile is usually inversed to obtain the ground range. An inversion algorithm, with which the ground range on the leading edge of the backscatter ionograms can be obtained without electron density, is presented in this paper. The ray path geometry of the backscatter sounding and the change in the group path on the leading edge with operating frequency are used to derive the ground range. Synthesized backscatter ionogram and experimental backscatter ionograms are processed to validate the algorithm. The results indicate that the algorithm is usable for high frequency management system.

  14. 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

  15. Thrombolysis using multi-frequency high intensity focused ultrasound at MHz range: an in vitro study

    NASA Astrophysics Data System (ADS)

    Suo, Dingjie; Guo, Sijia; Lin, Weili; Jiang, Xiaoning; Jing, Yun

    2015-09-01

    High intensity focused ultrasound (HIFU) based thrombolysis has emerged as a promising drug-free treatment approach for ischemic stroke. The large amount of acoustic power required by this approach, however, poses a critical challenge to the future clinical translation. In this study, multi-frequency acoustic waves at MHz range (near 1.5 MHz) were introduced as HIFU excitations to reduce the required power for treatment as well as the treatment time. In vitro bovine blood clots weighing around 150 mg were treated by single-frequency and multi-frequency HIFU. The pulse length was 2 ms for all experiments except the ones where the duty cycle was changed. It was found that dual-frequency thrombolysis efficiency was statistically better than single-frequency under the same acoustic power and excitation condition. When varying the acoustic power but fixing the duty cycle at 5%, it was found that dual-frequency ultrasound can save almost 30% power in order to achieve the same thrombolysis efficiency. In the experiment where the duty cycle was increased from 0.5% to 10%, it was shown that dual-frequency ultrasound can achieve the same thrombolysis efficiency with only half of the duty cycle of single-frequency. Dual-frequency ultrasound could also accelerate the thrombolysis by a factor of 2-4 as demonstrated in this study. No significant differences were found between dual-frequencies with different frequency differences (0.025, 0.05, and 0.1 MHz) and between dual-frequency and triple-frequency. The measured cavitation doses of dual-frequency and triple-frequency excitations were at about the same level but both were significantly higher than that of single-frequency.

  16. 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

  17. 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

  18. Switched capacitor charge pump reduces hysteresis of piezoelectric actuators over a large frequency range.

    PubMed

    Huang, Liang; Ma, Yu Ting; Feng, Zhi Hua; Kong, Fan Rang

    2010-09-01

    Piezoelectric actuators exhibit large hysteresis between the applied voltage and their displacement. A switched capacitor charge pump is proposed to reduce hysteresis and linearize the movement of piezoelectric actuators. By pumping the same amount of charges into the piezoelectric actuator quantitatively, the actuator will be forced to change its length with constant step. Compared with traditional voltage and charge driving, experimental results demonstrated that the piezoelectric stack driven by the charge pump had less hysteresis over a large frequency range, especially at ultralow frequencies. A hysteresis of less than 2.01% was achieved over a frequency range of 0.01-20 Hz using the charge pump driver. PMID:20886997

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

    PubMed Central

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

    2010-01-01

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

  20. A novel technique of image quality objective measurement by wavelet analysis throughout the spatial frequency range

    NASA Astrophysics Data System (ADS)

    Luo, Gaoyong

    2005-01-01

    An essential determinant of the value of surrogate digital images is their quality. Image quality measurement has become crucial for most image processing applications. Over the past years , there have been many attempts to develop models or metrics for image quality that incorporate elements of human visual sensitivity. However, there is no current standard and objective definition of spectral image quality. This paper proposes a reliable automatic method for objective image quality measurement by wavelet analysis throughout the spatial frequency range. This is done by a detailed analysis of an image for a wide range of spatial frequency content, using a combination of modulation transfer function (MTF), brightness, contrast, saturation, sharpness and noise, as a more revealing metric for quality evaluation. A fast lifting wavelet algorithm is developed for computationally efficient spatial frequency analysis, where fine image detail corresponding to high spatial frequencies and image sharpness in regard to lower and mid -range spatial frequencies can be examined and compared accordingly. The wavelet frequency deconstruction is actually to extract the feature of edges in sub-band images. The technique provides a means to relate the quality of an image to the interpretation and quantification throughout the frequency range, in which the noise level is estimated in assisting with quality analysis. The experimental results of using this method for image quality measurement exhibit good correlation to subjective visual quality assessments.

  1. A novel technique of image quality objective measurement by wavelet analysis throughout the spatial frequency range

    NASA Astrophysics Data System (ADS)

    Luo, Gaoyong

    2004-10-01

    An essential determinant of the value of surrogate digital images is their quality. Image quality measurement has become crucial for most image processing applications. Over the past years , there have been many attempts to develop models or metrics for image quality that incorporate elements of human visual sensitivity. However, there is no current standard and objective definition of spectral image quality. This paper proposes a reliable automatic method for objective image quality measurement by wavelet analysis throughout the spatial frequency range. This is done by a detailed analysis of an image for a wide range of spatial frequency content, using a combination of modulation transfer function (MTF), brightness, contrast, saturation, sharpness and noise, as a more revealing metric for quality evaluation. A fast lifting wavelet algorithm is developed for computationally efficient spatial frequency analysis, where fine image detail corresponding to high spatial frequencies and image sharpness in regard to lower and mid -range spatial frequencies can be examined and compared accordingly. The wavelet frequency deconstruction is actually to extract the feature of edges in sub-band images. The technique provides a means to relate the quality of an image to the interpretation and quantification throughout the frequency range, in which the noise level is estimated in assisting with quality analysis. The experimental results of using this method for image quality measurement exhibit good correlation to subjective visual quality assessments.

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

    NASA Technical Reports Server (NTRS)

    Jain, A. (Inventor)

    1982-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  4. Impedance-based structural health monitoring using neural networks for autonomous frequency range selection

    NASA Astrophysics Data System (ADS)

    Min, Jiyoung; Park, Seunghee; Yun, Chung-Bang

    2010-12-01

    The impedance-based structural health monitoring (SHM) method has come to the forefront in the SHM community due to its practical potential for real applications. In the impedance-based SHM method, the selection of optimal frequency ranges plays an important role in improving the sensitivity of damage detection, since an improper frequency range can lead to erroneous damage detection results and provide false positive damage alarms. To tackle this issue, this paper proposes an innovative technique for autonomous selection of damage-sensitive frequency ranges using artificial neural networks (ANNs). First, the impedance signals are obtained in a wide frequency band, and the signals are split into multiple sub-ranges of this wide band. Then, the predefined damage index is evaluated for each sub-range by comparing impedance signals between the intact and the concurrent cases. Here, the cross correlation coefficients (CCs) are used as the predefined damage index. The ANN is constructed and trained using all CC values at multiple frequency ranges as multi-inputs and the real damage severity as the single output for various preselected damage scenarios, so that subsequent damage estimations may be carried out by selecting the governing frequency ranges autonomously. The performance of the proposed approach has been examined via a series of experimental studies to detect loose bolts and cracks induced on real steel bridge and building structures. It is found that the proposed approach autonomously determines the damage-sensitive frequency ranges and can be used for effective evaluation of damage severity in a wide variety of damage cases in real structures.

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

    PubMed Central

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

    2014-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Technical Reports Server (NTRS)

    Jain, A. (Inventor)

    1979-01-01

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

  8. Application of range imaging lidar for measurement of mechanical vibration and frequency mode distribution

    NASA Astrophysics Data System (ADS)

    Zhang, Hua A.; Zhu, Yonghao; He, Yun

    1993-05-01

    This article reports the application of laser range imaging radar in the measurement of mechanical vibration frequency and the mode distribution, and the periodic motion of the mechanical parts such as a piston rod. The principle of the laser range imaging radar is based on the phase shift of the reflected amplitude modulated laser beam. The mechanical vibration frequency up to 20 KHZ and the minimal retrieved amplitude (or the motion displacement) of 0.5 mm have been achieved with the laser modulating frequency of 40 MHZ. With appropriate modulating frequency, this laser range system can measure the mechanical vibration amplitude, or the moving displacement, from 10-1 mm up to 102 mm, or even higher to the order of meters, which will be useful to measure the vibration and the periodic motion of machines and their parts for field test.

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

    SciTech Connect

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

    2012-01-15

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

  10. Single channel speech separation in modulation frequency domain based on a novel pitch range estimation method

    NASA Astrophysics Data System (ADS)

    Mahmoodzadeh, Azar; Abutalebi, Hamid Reza; Soltanian-Zadeh, Hamid; Sheikhzadeh, Hamid

    2012-12-01

    Computational Auditory Scene Analysis (CASA) has been the focus in recent literature for speech separation from monaural mixtures. The performance of current CASA systems on voiced speech separation strictly depends on the robustness of the algorithm used for pitch frequency estimation. We propose a new system that estimates pitch (frequency) range of a target utterance and separates voiced portions of target speech. The algorithm, first, estimates the pitch range of target speech in each frame of data in the modulation frequency domain, and then, uses the estimated pitch range for segregating the target speech. The method of pitch range estimation is based on an onset and offset algorithm. Speech separation is performed by filtering the mixture signal with a mask extracted from the modulation spectrogram. A systematic evaluation shows that the proposed system extracts the majority of target speech signal with minimal interference and outperforms previous systems in both pitch extraction and voiced speech separation.

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

    SciTech Connect

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

    2003-06-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

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

    SciTech Connect

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

    2015-03-15

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

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

    PubMed

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

    2015-04-01

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

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

    PubMed

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

    2016-05-01

    We present a prototype of a laser frequency auto-locking and re-locking control system designed for laser frequency stabilization in inter-satellite laser ranging system. The controller has been implemented on field programmable gate arrays and programmed with LabVIEW software. The controller allows initial frequency calibrating and lock-in of a free-running laser to a Fabry-Pérot cavity. Since it allows automatic recovery from unlocked conditions, benefit derives to automated in-orbit operations. Program design and experimental results are demonstrated. PMID:27250480

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

    PubMed

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

    2015-06-01

    The operation of a highly sensitive atomic magnetometer using elliptically polarized resonant light is demonstrated. It is based on measurement of zero magnetic field resonance in degenerate two level systems using polarimetric detection. The transmitted light through the polarimeter is used for laser frequency stabilization, whereas reflected light is used for magnetic field measurement. Thus, the experimental geometry allows autonomous frequency stabilization of the laser frequency leading to compact operation of the overall device and has a preliminary sensitivity of <10 pT/Hz(1/2) @ 1 Hz. Additionally, the dynamic range of the device is improved by feedback controlling the bias magnetic field without compromising on its sensitivity. PMID:26133825

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

    SciTech Connect

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

    2015-06-15

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

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

    SciTech Connect

    Dowla, F

    2007-03-14

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

  20. TOPICAL REVIEW: Strategies for increasing the operating frequency range of vibration energy harvesters: a review

    NASA Astrophysics Data System (ADS)

    Zhu, Dibin; Tudor, Michael J.; Beeby, Stephen P.

    2010-02-01

    This review presents possible strategies to increase the operational frequency range of vibration-based micro-generators. Most vibration-based micro-generators are spring-mass-damper systems which generate maximum power when the resonant frequency of the generator matches the frequency of the ambient vibration. Any difference between these two frequencies can result in a significant decrease in generated power. This is a fundamental limitation of resonant vibration generators which restricts their capability in real applications. Possible solutions include the periodic tuning of the resonant frequency of the generator so that it matches the frequency of the ambient vibration at all times or widening the bandwidth of the generator. Periodic tuning can be achieved using mechanical or electrical methods. Bandwidth widening can be achieved using a generator array, a mechanical stopper, nonlinear (e.g. magnetic) springs or bi-stable structures. Tuning methods can be classified into intermittent tuning (power is consumed periodically to tune the device) and continuous tuning (the tuning mechanism is continuously powered). This review presents a comprehensive review of the principles and operating strategies for increasing the operating frequency range of vibration-based micro-generators presented in the literature to date. The advantages and disadvantages of each strategy are evaluated and conclusions are drawn regarding the relevant merits of each approach.

  1. Bendable, low-loss Topas fibers for the terahertz frequency range.

    PubMed

    Nielsen, Kristian; Rasmussen, Henrik K; Adam, Aurèle J L; Planken, Paul C; Bang, Ole; Jepsen, Peter Uhd

    2009-05-11

    We report on a new class of polymer photonic crystal fibers for low-loss guidance of THz radiation. The use of the cyclic olefin copolymer Topas, in combination with advanced fabrication technology, results in bendable THz fibers with unprecedented low loss and low material dispersion in the THz regime.We demonstrate experimentally how the dispersion may be engineered by fabricating both high- and low-dispersion fibers with zero-dispersion frequency in the regime 0.5-0.6 THz. Near-field, frequency-resolved characterization with high spatial resolution of the amplitude and phase of the modal structure proves that the fiber is single-moded over a wide frequency range, and we see the onset of higher-order modes at high frequencies as well as indication of microporous guiding at low frequencies and high porosity of the fiber. Transmission spectroscopy demonstrates low-loss propagation (< 0.1 dB/cm loss at 0.6 THz) over a wide frequency range. PMID:19434192

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

    NASA Astrophysics Data System (ADS)

    Cheong, Chin Wen; Pei, Tan Pei

    2015-10-01

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

  3. The effects of tones on speaking frequency and intensity ranges in Mandarin and Min dialects

    NASA Astrophysics Data System (ADS)

    Chen, Sheng H.

    2005-05-01

    The differences of speaking frequency and intensity in different tonal dialects has not been widely investigated. The purposes of this study were (1) to compare the speaking frequency and speaking intensity ranges of Mandarin and Min and (2) to compare the speaking frequency and intensity ranges of Mandarin and Min to those of American English. The subjects were 80 normal Taiwanese adults divided into two dialect groups, Mandarin and Min. The speaking F0, the highest speaking F0, the lowest speaking F0, the maximum range of speaking F0, and the intensity counterpart were obtained from reading in their native dialects. Statistical analysis revealed that Min speakers had a significantly greater maximum range of speaking intensity and a smaller lowest speaking intensity than Mandarin speakers, which indicated tonal effects by speakers of the Min dialect. Moreover, Mandarin and Min speakers had a greater maximum range of speaking F0 and maximum range of speaking intensity than American English speakers. The data may provide an assessment tool for Mandarin speakers and Min speakers. .

  4. Coherent terahertz-wave generation and detection over a wide frequency range using DAST crystals

    NASA Astrophysics Data System (ADS)

    Minamide, Hiroaki; Ito, Hiromasa

    2009-02-01

    Terahertz-frequency (THz) waves have shown potential for a wide range of applications. We have developed tunable THz-wave sources using nonlinear optical crystals, which have several advantages, including frequency agility, wide tunability, high output, and high coherency. We found that the organic nonlinear crystal of 4-dimethylamino-N-methyl-4-stilbazolium-tosylate (DAST) had particular potential for ultra-wide THz-wave generation from sub-THz to mid-infrared frequencies. Using DAST, we manufactured a coherent, tunable source (1-40 THz) with frequency agility. Moreover, we demonstrated THz-wave detection through up-conversion using DAST or MgO:LiNbO3 nonlinear optical crystals, which provided a fast response, high sensitivity, and room-temperature operation.

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

    PubMed

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

    2010-10-01

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

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

    NASA Technical Reports Server (NTRS)

    1994-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Loizos, G.; Niarchos, D.

    2014-07-01

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

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

    PubMed

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

    2009-04-01

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

  10. Universal MOSFET gate impedance model for 200 MHz-20 GHz frequency range

    NASA Astrophysics Data System (ADS)

    Bandi, Sri Priya R.; Washburn, Clyde; Mukund, P. R.; Kolnik, Jan; Paradis, Ken; Howard, Steve; Burleson, Jeff

    2006-07-01

    The scaling of CMOS technology to 100 nm and below and the endless pursuit of higher operating frequencies drives the need to accurately model effects such as gate leakage and the deterioration of transport characteristics that dominate at those feature sizes and frequencies. Current modeling techniques are frequency limited and require different models for different frequency ranges in order to achieve accuracy goals. In the foundry world, high frequency models are typically empirical in nature and significantly lag their low frequency counterparts in terms of availability. This tends to slow the adoption of new foundry technologies for high performance applications such as extremely high data rate serializer/deserializer (SERDES) transceiver cores. However, design cycle time and time to market while transitioning between technology nodes can be reduced by incorporating a re-usable, industry-standard model. This work proposes such a model for device gate impedance that is simulator-friendly, compact, frequency-independent, and relatively portable across technology nodes. This semi-empirical gate impedance model is based on depletion in the poly-silicon gate electrode. The model performs accurately over 200 MHz-20 GHz at different bias conditions and widths and has been verified by measured data in three technology nodes. The model and model parameter behavior are consistent across technology nodes thereby enabling re-usability and portability.

  11. Cochlear implant melody recognition as a function of melody frequency range, harmonicity, and number of electrodes

    PubMed Central

    Singh, Sonya; Kong, Ying-Yee; Zeng, Fan-Gang

    2009-01-01

    Objective The primary goal of the present study was to determine how cochlear implant melody recognition was affected by the frequency range of the melodies, the harmonicity of these melodies, and the number of activated electrodes. The secondary goal was to investigate whether melody recognition and speech recognition were differentially affected by the limitations imposed by cochlear implant processing. Design Four experiments were conducted. In the first experiment, eleven cochlear implant users used their clinical processors to recognize melodies of complex harmonic tones with their fundamental frequencies being in the low (104-262 Hz), middle (207-523 Hz), and high (414-1046 Hz) ranges. In the second experiment, melody recognition with pure tones was compared to melody recognition with complex harmonic tones in 4 subjects. In the third experiment, melody recognition was measured as a function of the number of electrodes in 5 subjects. In the fourth experiment, vowel and consonant recognition were measured as a function of the number of electrodes in the same 5 subjects who participated in the third experiment. Results Frequency range significantly affected cochlear implant melody recognition with higher frequency ranges producing better performance. Pure tones produced significantly better performance than complex harmonic tones. Increasing the number of activated electrodes did not affect performance with low- and middle-frequency melodies, but produced better performance with high-frequency melodies. Large individual variability was observed for melody recognition but its source seemed to be different from the source of the large variability observed in speech recognition. Conclusion Contemporary cochlear implants do not adequately encode either temporal pitch or place pitch cues. Melody recognition and speech recognition require different signal processing strategies in future cochlear implants. PMID:19194298

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-01-01

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

  14. 24 mm depth range discretely swept optical frequency domain imaging in dentistry

    NASA Astrophysics Data System (ADS)

    Kakuma, Hideo; Choi, DongHak; Furukawa, Hiroyuki; Hiro-Oka, Hideaki; Ohbayashi, Kohji

    2009-02-01

    A large depth range is needed if optical coherence tomography (OCT) is to be used to observe multiple teeth simultaneously. A discretely swept optical frequency domain imaging system with a 24-mm depth range was made by using a superstructure-grating distributed Bragg reflector (SSG-DBR) laser as the light source and setting the frequencystep interval to be 3.13 GHz (λ ~ 0.026 nm). The swept wavelength range was 40 nm centered at 1580 nm, the resolution was 29 μm, and the A-scan rate was 1.3 kHz. Application of the OCT system to a dental phantom was demonstrated.

  15. On the slope of the equilibrium range in the frequency spectrum of wind waves

    NASA Astrophysics Data System (ADS)

    Liu, Paul C.

    1989-04-01

    An effort to empirically assess the slope of the equilibrium range in a wind wave frequency spectrum with a large number of data recorded in the Great Lakes did not serve to clarify the uncertainty between a -4 or a -5 frequency exponent representation. The uncertainty is further compounded by indications that the slope is not necessarily unique, but tends to vary with wave momentum. For sufficiently well developed wind waves the exponent appears to cluster between -3 and -4. For practical applications the f-4 equilibrium range is perhaps an effective approximation. What the correct slope is for the equilibrium range, or even whether or not a unique slope exists, remains elusive and has yet to be satisfactorily substantiated.

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

    NASA Astrophysics Data System (ADS)

    Rozanov, Konstantin N.; Koledintseva, Marina Y.

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  18. An optimal frequency range for assessing the pressure reactivity index in patients with traumatic brain injury.

    PubMed

    Howells, Tim; Johnson, Ulf; McKelvey, Tomas; Enblad, Per

    2015-02-01

    The objective of this study was to identify the optimal frequency range for computing the pressure reactivity index (PRx). PRx is a clinical method for assessing cerebral pressure autoregulation based on the correlation of spontaneous variations of arterial blood pressure (ABP) and intracranial pressure (ICP). Our hypothesis was that optimizing the methodology for computing PRx in this way could produce a more stable, reliable and clinically useful index of autoregulation status. The patients studied were a series of 131 traumatic brain injury patients. Pressure reactivity indices were computed in various frequency bands during the first 4 days following injury using bandpass filtering of the input ABP and ICP signals. Patient outcome was assessed using the extended Glasgow Outcome Scale (GOSe). The optimization criterion was the strength of the correlation with GOSe of the mean index value over the first 4 days following injury. Stability of the indices was measured as the mean absolute deviation of the minute by minute index value from 30-min moving averages. The optimal index frequency range for prediction of outcome was identified as 0.018-0.067 Hz (oscillations with periods from 55 to 15 s). The index based on this frequency range correlated with GOSe with ρ=-0.46 compared to -0.41 for standard PRx, and reduced the 30-min variation by 23%. PMID:24664812

  19. Optimal random frequency range in transcranial pulsed current stimulation indexed by quantitative electroencephalography.

    PubMed

    Morales-Quezada, Leon; Castillo-Saavedra, Laura; Cosmo, Camila; Doruk, Deniz; Sharaf, Ibrahim; Malavera, Alejandra; Fregni, Felipe

    2015-09-01

    Given the recent results provided by previous investigations on transcranial pulsed current stimulation (tPCS) demonstrating its modulatory effects on cortical connectivity; we aimed to explore the application of different random pulsed frequencies. The utility of tPCS as a neuromodulatory technique for cognition performance will come as additional frequency ranges are tested with the purpose to find optimal operational parameters for tPCS. This study was designed to analyze the effects of tPCS using the following random frequencies; 1-5, 6-10, and 11-15 Hz compared with sham on quantitative electroencephalographic changes in the spectral power and interhemispheric coherence of each electroencephalographic frequency band. This was a parallel, randomized, double-blinded, sham-controlled trial. Forty healthy individuals older than 18 years were eligible to participate. The main outcomes were differences in the spectral power analysis and interhemispheric coherence as measured by quantitative electroencephalography. Participants were randomly allocated to four groups of random frequency stimulation and received a single session of stimulation for 20 min with a current intensity of 2 mA delivered by bilateral periauricular electrode clips. We found that a random pulsed frequency between 6-10 Hz significantly increased the power and coherence in frontal and central areas for the alpha band compared with sham stimulation, while 11-15 Hz tPCS decreased the power for the alpha and theta bandwidth. Our findings corroborate the hypothesis that a random frequency ranging into the boundaries of 6-10 Hz induces changes in the naturally occurring alpha oscillatory activity, providing additional data for further studies with tPCS. PMID:26154494

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

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  2. Spectral Decay Characteristics in High Frequency Range of Observed Records from Crustal Large Earthquakes (Part 2)

    NASA Astrophysics Data System (ADS)

    Tsurugi, M.; Kagawa, T.; Irikura, K.

    2012-12-01

    Spectral decay characteristics in high frequency range of observed records from crustal large earthquakes occurred in Japan is examined. It is very important to make spectral decay characteristics clear in high frequency range for strong ground motion prediction in engineering purpose. The authors examined spectral decay characteristics in high frequency range of observed records among three events, the 2003 Miyagi-Ken Hokubu earthquake (Mw 6.1), the 2005 Fukuoka-Ken Seiho-oki earthquake (Mw 6.6), and the 2008 Iwate-Miyagi Nairiku earthquake (Mw 6.9) in previous study [Tsurugi et al.(2010)]. Target earthquakes in this study are two events shown below. *EQ No.1 Origin time: 2011/04/11 17:16, Location of hypocenter: East of Fukushima pref., Mj: 7.0, Mw: 6.6, Fault type: Normal fault *EQ No.2 Origin time: 2011/03/15 22:31, Location of hypocenter: East of Shizuoka pref., Mj: 6.4, Mw: 5.9, Fault type: Strike slip fault The borehole data of each event are used in the analysis. The Butterworth type high-cut filter with cut-off frequency, fmax and its power coefficient of high-frequency decay, s [Boore(1983)], are assumed to express the high-cut frequency characteristics of ground motions. The four parameters such as seismic moment, corner frequency, cut-off frequency and its power coefficient of high-frequency decay are estimated by comparing observed spectra at rock sites with theoretical spectra. The theoretical spectra are calculated based on the omega squared source characteristics convolved with propagation-path effects and high-cut filter shapes. In result, the fmax's of the records from the earthquakes are estimated 8.0Hz for EQ No.1 and 8.5Hz for EQ No.2. These values are almost same with those of other large crustal earthquakes occurred in Japan. The power coefficient, s, are estimated 0.78 for EQ No.1 and 1.65 for EQ No.2. The value for EQ No.2 is notably larger than those of other large crustal earthquakes. It is seems that the value of the power coefficient, s

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

    PubMed

    Graham, Calbert

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Levin, Jacob E.

    1997-05-01

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

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

    SciTech Connect

    Viscor, Ivo; Halamek, Josef; Villa, Marco

    2005-11-15

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

  6. A substructured Trefftz method for updating joint models in the medium-frequency range

    NASA Astrophysics Data System (ADS)

    Dorival, O.; Rouch, P.; Allix, O.

    2008-08-01

    The response of a structure to medium-frequency vibrations is highly dependent on several phenomena. One of these, the behavior of joints between substructures, is essential because it controls the distribution of the power injected into the structure and governs most of the dissipative effects. This paper introduces a new method for the identification of joint parameters from experimental vibration data, inspired by previous works on finite element model updating using the error in the constitutive relation. Since such numerical techniques are not suitable for the medium-frequency range, in which the finite element mesh must be refined, our work uses the numerical framework of the variational theory of complex rays, which is a Trefftz approach entirely dedicated to the calculation of medium-frequency vibrations at very low cost. The main scope of this paper is the presentation of the formulation and its validation against actual and numerically-simulated experimental results.

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Harding, A. K.; Tademaru, E.

    1980-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

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

    PubMed

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

    2016-01-01

    Aiming at the more complex frequency translation, the longer response time and the limited measurement precision in the traditional phase processing, a high-resolution phase processing method by group quantization higher than 100 fs level is proposed in radio frequency measurement range. First, the phase quantization is used as a step value to quantize every phase difference in a group by using the fixed phase relationships between different frequencies signals. The group quantization is formed by the results of the quantized phase difference. In the light of frequency drift mainly caused by phase noise of measurement device, a regular phase shift of the group quantization is produced, which results in the phase coincidence of two comparing signals which obtain high-resolution measurement. Second, in order to achieve the best coincidences pulse, a subtle delay is initiatively used to reduce the width of the coincidences fuzzy area according to the transmission characteristics of the coincidences in the specific medium. Third, a series of feature coincidences pulses of fuzzy area can be captured by logic gate to achieve the best phase coincidences information for the improvement of the measurement precision. The method provides a novel way to precise time and frequency measurement. PMID:27388587

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed Central

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

    2016-01-01

    Aiming at the more complex frequency translation, the longer response time and the limited measurement precision in the traditional phase processing, a high-resolution phase processing method by group quantization higher than 100 fs level is proposed in radio frequency measurement range. First, the phase quantization is used as a step value to quantize every phase difference in a group by using the fixed phase relationships between different frequencies signals. The group quantization is formed by the results of the quantized phase difference. In the light of frequency drift mainly caused by phase noise of measurement device, a regular phase shift of the group quantization is produced, which results in the phase coincidence of two comparing signals which obtain high-resolution measurement. Second, in order to achieve the best coincidences pulse, a subtle delay is initiatively used to reduce the width of the coincidences fuzzy area according to the transmission characteristics of the coincidences in the specific medium. Third, a series of feature coincidences pulses of fuzzy area can be captured by logic gate to achieve the best phase coincidences information for the improvement of the measurement precision. The method provides a novel way to precise time and frequency measurement. PMID:27388587

  14. PROPERTIES OF PHANTOM TISSUE-LIKE POLYMETHYLPENTENE IN THE FREQUENCY RANGE 20–70 MHZ

    PubMed Central

    Madsen, Ernest L; Deaner, Meagan E; Mehi, James

    2011-01-01

    Quantitative ultrasound (QUS) has been employed to characterize soft tissues at ordinary abdominal ultrasound frequencies (2–15 MHz) and is beginning application at high frequencies (20–70 MHz). For example, backscatter and attenuation coefficients can be estimated in vivo using a reference phantom. At high frequencies it is crucial that reverberations do not compromise the measurements. Such reverberations can occur between the phantom's scanning window and transducer components as well as within the scanning window between its surfaces. Transducers are designed to minimize reverberations between the transducer and soft tissue. Thus, the acoustic impedance of a phantom scanning window should be tissue-like; polymethylpentene (TPX) is commonly used because of its tissue-like acoustic impedance. For QUS it is also crucial to correct for the transmission coefficient of the scanning window. Computation of the latter requires knowledge of the ultrasonic properties, viz, density, speed and attenuation coefficients. This work reports values for the ultrasonic properties of two versions of TPX over the high frequency range. One form (TPX film) is used as a scanning window on high frequency phantoms, and at 40 MHz and 22°C was found to have an attenuation coefficient of 120 dB/cm and a propagation speed of 2093 m/s. PMID:21723451

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

    PubMed

    Yager, D D

    1996-04-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  17. Polarization-Entangled Photon Pairs From Periodically-Poled Crystalline Waveguides Over a Range of Frequencies

    PubMed Central

    Heberle, Dylan A; Levine, Zachary H

    2013-01-01

    We propose a method to extend the frequency range of polarization entanglement in periodically poled rubidium-doped potassium titanyl phosphate (Rb:KTP) waveguides. Our calculations predict that output wavelengths from 1130 nm to 1257 nm may be achieved using Rb:KTP by the appropriate selection of a direction of propagation for the waveguide. The fidelity using a poling period of 1 mm is approximately 0.98. PMID:26401438

  18. Long range aircraft detection using high-frequency surface-wave radar

    NASA Astrophysics Data System (ADS)

    Leong, Hank

    1994-12-01

    Experimental data from a high-frequency surface-wave radar (HFSWR) operating at 1.95 MHz at Cape Bonavista, Newfoundland are analyzed to assess the capability of the radar to detect aircraft over an ocean surface. The results of the analysis show that the HFSWR could easily detect and track a low-flying CP-140 Aurora aircraft at ranges between 11 and 56 km. The radar's coverage area coincides with a trans-Atlantic international flight route, and the radar was also able to detect and track some commercial aircraft in range as far as 280 km.

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

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

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

    PubMed

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

    2014-08-01

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

  1. Associations of HLA-A, HLA-B and HLA-C Alleles Frequency with Prevalence of Herpes Simplex Virus Infections and Diseases Across Global Populations: Implication for the Development of an Universal CD8+ T-Cell Epitope-Based Vaccine

    PubMed 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

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

    NASA Technical Reports Server (NTRS)

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

    2014-01-01

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

  3. Reference hearing thresholds in an extended frequency range as a function of age.

    PubMed

    Jilek, Milan; Šuta, Daniel; Syka, Josef

    2014-10-01

    The ISO 7029 (2000) standard defines normative hearing thresholds H (dB hearing level) as a function of age Y (years), given by H = α(Y - 18)(2), up to 8 kHz. The purpose of this study was to determine reference thresholds above 8 kHz. Hearing thresholds were examined using pure-tone audiometry over the extended frequency range 0.125-16 kHz, and the acquired values were used to specify the optimal approximation of the dependence of hearing thresholds on age. A sample of 411 otologically normal men and women 16-70 years of age was measured in both ears using a high-frequency audiometer and Sennheiser HDA 200 headphones. The coefficients of quadratic, linear, polynomial and power-law approximations were calculated using the least-squares fitting procedure. The approximation combining the square function H = α(Y - 18)(2) with a power-law function H = β(Y - 18)(1.5), both gender-independent, was found to be the most appropriate. Coefficient α was determined at frequencies of 9 kHz (α = 0.021), 10 kHz (α = 0.024), 11.2 kHz (α = 0.029), and coefficient β at frequencies of 12.5 kHz (β = 0.24), 14 kHz (β = 0.32), 16 kHz (β = 0.36). The results could be used to determine age-dependent normal hearing thresholds in an extended frequency range and to normalize hearing thresholds when comparing participants differing in age. PMID:25324083

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

    PubMed Central

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

    2015-01-01

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

  5. Allele surfing promotes microbial adaptation from standing variation.

    PubMed

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

    2016-08-01

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

  6. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  10. Fast particles-wave interaction in the Alfven frequency range on the Joint European Torus tokamak

    SciTech Connect

    Fasoli, A.; Borba, D.; Association EURATOM Breizman, B.; Gormezano, C.; Heeter, R. F.; Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543 ; Juan, A.; Mantsinen, M.; Sharapov, S.; Testa, D.

    2000-05-01

    Wave-particle interaction phenomena in the Alfven Eigenmode (AE) frequency range are investigated at the Joint European Torus [P. H. Rebut and B. E. Keen, Fusion Technol. 11, 13 (1987)] using active and passive diagnostic methods. Fast particles are generated by neutral beam injection, ion cyclotron resonance heating, and fusion reactions. External antennas are used to excite stable AEs and measure fast particle drive and damping separately. Comparisons with numerical calculations lead to an identification of the different damping mechanisms. The use of the active AE diagnostic system to generate control signals based on the proximity to marginal stability limits for AE and low-frequency magnetohydrodynamic (MHD) modes is explored. Signatures of the different nonlinear regimes of fast particle driven AE instabilities predicted by theory are found in the measured spectra. The diagnostic use of AE measurements to get information both on the plasma bulk and the fast particle distribution is assessed. (c) 2000 American Institute of Physics.

  11. High-frequency acoustic tracking of odontocetes at the Southern California Offshore Range (SCORE)

    NASA Astrophysics Data System (ADS)

    Hursky, Paul; Abawi, Ahmad T.; Porter, Michael B.; Hildebrand, John A.; Wiggins, Sean M.; Soldevilla, Melissa; Sauter, Allan W.

    2005-09-01

    The SCORE site, located near San Clemente Island, is known to be abundant in marine mammals, and is the site of frequent naval operations, making it an ideal site to study what impact man-made activities may have upon these creatures. In August 2004, an experiment was performed to collect both visual and acoustic observations of odontocetes at the SCORE site. Odontocete vocalizations consist of clicks and whistles. The clicks are very wideband (often 100 kHz), so times of arrival can be measured with extremely high resolution, which makes clicks attractive waveforms for multipath ranging and depth estimation. Although the whistles are narrowband, their fundamental frequency often ranges over tens of kilohertz, so these too can be processed as if they were wideband. We will present results of processing excerpts from several weeks of data recorded on a high-frequency horizontal line array deployed from the FLIP research vessel. Bearing tracks of individuals and groups from a number of different species will be correlated and compared with visual observations. In addition, we will discuss the possibilities for range and depth estimates derived from the multipath arrivals observed in the clicks and whistles.

  12. Analysis of electromagnetic fluctuations of lower hybrid frequency range in MRX

    NASA Astrophysics Data System (ADS)

    Yamada, M.; Ji, H.; Kulsrud, R. M.

    2002-05-01

    In MRX (Magnetic Reconnection Experiment), the detailed magnetic field structure and the plasma profiles of the neutral sheet have been measured and evidences for the physics beyond MHD have been obtained[1]. As the electron-ion collision frequency is reduced, the reconnection rate is observed to be significantly enhanced over the classical value. Both electrostatic and magnetic turbulence of lower hybrid frequency range has been observed in the low collisionality regime. The amplitude of magnetic fluctuation is the largest at the center of neutral sheet while the electropotential fluctuations peak at the edge of the sheath. To describe the physics of this region, much thought has been given to the `` generalized" Ohm's law where electrons and ions are separately treated to satisfy the equations of motion in the neutral sheet plasma. In this `` E-MHD" region electrons but not ions are considered to be magnetized and the lower hybrid drift wave can be connected continuously to an obliquely propagating Whistler wave[2]. In this paper we examine the entire spectrum of waves from the electron cyclotron frequency down to the ion cyclotron frequency. The electric potential fluctuations of lower hybrid frequency were measured [3] and identified as electrostatic lower hybrid drift waves [E-LHDW]. In the present study the properties of elecromagnetic waves are investigated theoretically and compared with the recent experimental data from the MRX neutral sheet plasmas[4]. Also we will discuss physical mechanisms of the enhanced resistivity induced by the electromagnetic waves including magnetic lower hybrid waves [M-LHDW] and Whistler waves. This work is supported by DoE, NASA and NSF. 1. M. Yamada et al., Phys. Plasmas, vol.7, 1781, (2000) 2. R.L. Stenzel and J.M. Urrutia, Phys. Plasmasv.7, 4450, (2000) 3. T. Carter et al., Phys. Rev. Letts. v88, 15001 (2002) 4. H. Ji et al., This meeting (2002)

  13. Radio frequency (RF) time-of-flight ranging for wireless sensor networks

    NASA Astrophysics Data System (ADS)

    Thorbjornsen, B.; White, N. M.; Brown, A. D.; Reeve, J. S.

    2010-03-01

    Position information of nodes within wireless sensor networks (WSNs) is often a requirement in order to make use of the data recorded by the sensors themselves. On deployment the nodes normally have no prior knowledge of their position and thus a locationing mechanism is required to determine their positions. In this paper, we describe a method to determine the point-to-point range between sensor nodes as part of the locationing process. A two-way time-of-flight (TOF) ranging scheme is presented using narrow-band RF. The frequency difference between the transceivers involved with the point-to-point measurement is used to obtain a sub-clock TOF phase offset measurement in order to achieve high resolution TOF measurements. The ranging algorithm has been developed and prototyped on a TI CC2430 development kit with no additional hardware being required. Performance results have been obtained for the line-of-sight (LOS), non-line-of-sight (NLOS) and indoor conditions. Accuracy is typically better than 7.0 m RMS for the LOS condition over 250.0 m and 15.8 m RMS for the NLOS condition over 120.0 m using a 100 sample average. Indoor accuracy is measured to 1.7 m RMS using a 1000 sample average over 8.0 m. Ranging error is linear and does not increase with the increased transmitter-receiver distance. Our TOA ranging scheme demonstrates a novel system where resolution and accuracy are time dependent in comparison with alternative frequency-dependent methods using narrow-band RF.

  14. Doppler imaging with dual-detection full-range frequency domain optical coherence tomography

    PubMed Central

    Meemon, Panomsak; Lee, Kye-Sung; Rolland, Jannick P.

    2010-01-01

    Most of full-range techniques for Frequency Domain Optical Coherence Tomography (FD-OCT) reported to date utilize the phase relation between consecutive axial lines to reconstruct a complex interference signal and hence may exhibit degradation in either mirror image suppression performance or detectable velocity dynamic range or both when monitoring a moving sample such as flow activity. We have previously reported a technique of mirror image removal by simultaneous detection of the quadrature components of a complex spectral interference called a Dual-Detection Frequency Domain OCT (DD-FD-OCT) [Opt. Lett. 35, 1058-1060 (2010)]. The technique enables full range imaging without any loss of acquisition speed and is intrinsically less sensitive to phase errors generated by involuntary movements of the subject. In this paper, we demonstrate the application of the DD-FD-OCT to a phase-resolved Doppler imaging without degradation in either mirror image suppression performance or detectable velocity dynamic range that were observed in other full-range Doppler methods. In order to accommodate for Doppler imaging, we have developed a fiber-based DD-FD-OCT that more efficiently utilizes the source power compared with the previous free-space DD-FD-OCT. In addition, the velocity sensitivity of the phase-resolved DD-FD-OCT was investigated, and the relation between the measured Doppler phase shift and set flow velocity of a flow phantom was verified. Finally, we demonstrate the Doppler imaging using the DD-FD-OCT in a biological sample. PMID:21258488

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

    SciTech Connect

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

    1994-12-01

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

  16. Measurements of the complex permittivity of loss ceramics at microwave frequencies and over large temperature ranges

    SciTech Connect

    Meng, B.; Booske, J.; Cooper, R.; Klein, B.

    1995-12-31

    A system has been developed for measuring the complex permittivities of low loss ceramic materials at frequencies from 2 GHz to 20 GHz and over a temperature range 20-1000{degrees}C. The measurement technique involves a, modified version of tile conventional cavity perturbation method. This extended cavity perturbation technique is presented. Details of the design and fabrication of the circular cylindrical cavity and the input and output coupling transmission lines are discussed. Data are presented for an illustrative measurement of the complex microwave dielectric properties of NaCl single crystals between 20-400{degrees}C. The experimental results are in excellent agreement with theoretical models.

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

    SciTech Connect

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

    1994-06-01

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

  18. Active modulation of refractive index by stress in the terahertz frequency range: erratum.

    PubMed

    Song, Wei; Wang, Zhiyong

    2016-03-20

    A previous paper [Appl. Opt.52, 6364 (2013)APOPAI0003-693510.1364/AO.52.006364] presented experimental work on the stress-optical effect in the terahertz frequency range. Although the theoretical model of experimental measurement is correct, there are two errors in the original version. As a result, the presented experimentally measured value of the refractive index-stress coefficient A of polytetrafluoroethylene (PTFE) is erroneous. This erratum points out the errors in the original paper and reports the correct values. PMID:27140555

  19. Missing data outside the detector range. II. Application to time-frequency entanglement

    NASA Astrophysics Data System (ADS)

    Ray, Megan R.; van Enk, S. J.

    2013-12-01

    In a previous paper, we pointed out the problem of missing data outside the detector range for continuous-variable entanglement verification and quantum key distribution, and we provided a straightforward solution based on entropic separability criteria (as those work better than variance-based criteria). We apply that solution here to the verification of time-frequency entanglement of photon pairs, particularly to the quantum key distribution scheme proposed by Nunn [Opt. ExpressOPEXFF1094-408710.1364/OE.21.015959 21, 15959 (2013)]. We find that the scheme does lead to verifiable entanglement, but that transmission noise quickly destroys the ability to verify the entanglement.

  20. Electrodynamic properties of lead Zirconate-Titanate thin films in the terahertz frequency range

    NASA Astrophysics Data System (ADS)

    Komandin, G. A.; Porodinkov, O. E.; Iskhakova, L. D.; Spektor, I. E.; Volkov, A. A.; Vorotilov, K. A.; Seregin, D. S.; Sigov, A. S.

    2014-11-01

    The transmission/reflection spectra of bilayer structures consisting of thin amorphous and polycrystalline Pb(Zr0.52Ti0.48)O3 ferroelectric films deposited on dielectric substrates of magnesium oxide MgO and sapphire α-Al2O3 were measured in the frequency range of 5-4000 cm-1. Based on these spectra and using the dispersion analysis method, the spectra of complex dielectric permittivity ɛ*(ν) and dynamic conductivity σ'(ν) of the films were simulated, the electrodynamic parameters of the films were determined, and the dielectric dispersion responsible for the formation of static permittivity was found.

  1. Tunable femtosecond laser in the visible range with an intracavity frequency-doubled optical parametric oscillator

    NASA Astrophysics Data System (ADS)

    Zhu, Jiang-Feng; Xu, Liang; Lin, Qing-Feng; Zhong, Xin; Han, Hai-Nian; Wei, Zhi-Yi

    2013-05-01

    We demonstrated experimentally a synchronously pumped intracavity frequency-doubled femtosecond optical parametric oscillator (OPO) using a periodically-poled lithium niobate (PPLN) as the nonlinear material in combination with a lithium triborate (LBO) as the doubling crystal. A Kerr-lens-mode-locked (KLM) Ti:sapphire oscillator at the wavelength of 790 nm was used as the pump source, which was capable of generating pulses with a duration as short as 117 fs. A tunable femtosecond laser covering the 624-672 nm range was realized by conveniently adjusting the OPO cavity length. A maximum average output power of 260 mW in the visible range was obtained at the pump power of 2.2 W, with a typical pulse duration of 205 fs assuming a sech2 pulse profile.

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

    PubMed Central

    2011-01-01

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

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  4. Propagation and dynamics of microwaves in the ECRH frequency range for the FRC

    NASA Astrophysics Data System (ADS)

    Ceccherini, Francesco; Galeotti, Laura; Brambilla, Marco; Barnes, Daniel C.; Yang, Xiaokang; TAE Team

    2014-10-01

    A previously developed FLR code for ICRH studies has been recently upgraded to include the frequency range of interest for ECRH applications. This full wave code is able to use very fine meshes (grid spacing down to 10-3 cm on a single cpu) so that even wavelengths very short with respect to the wall radius can be resolved well. The first wave propagation scheme we have addressed - and in part used for benchmark purposes also - is given by a source placed at a few cm from the first wall with a current oscillating in the longitudinal direction and an ordinary wave propagating in the radial direction. Such a wave propagates through the plasma until the required conditions for O-X-B mode conversion are encountered. The mode-converted electrostatic wave generated at the upper hybrid frequency behaves according to the expected dispersion relation and it is studied in terms of the launched frequency. Initial results indicate that in an elongated FRC configuration under study, the possibility to satisfy all conditions required to have electron absorption in the region beyond the SOL through the O-X-B conversion process strongly depends on the plasma radial profile. Details on this scheme and different examples will be presented.

  5. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the...

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

    PubMed

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

    2002-06-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

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

  8. Antiferromagnetic resonance and dielectric properties of rare-earth ferroborates in the submillimeter frequency range

    SciTech Connect

    Kuz'menko, A. M.; Mukhin, A. A. Ivanov, V. Yu.; Kadomtseva, A. M.; Lebedev, S. P.; Bezmaternykh, L. N.

    2011-07-15

    The magnetoresonance and dielectric properties of a number of crystals of a new family of multiferroics, namely, rare-earth ferroborates RFe{sub 3}(BO{sub 3}){sub 4} (R = Y, Eu, Pr, Tb, Tb{sub 0.25}Er{sub 0.75}), are studied in the sub-millimeter frequency range ({nu} = 3-20 cm{sup -1}). Ferroborates with R = Y, Tb, and Eu exhibit permittivity jumps at temperatures of 375, 198, and 58 K, respectively, which are caused by the R32 {yields} P3{sub 1}21 phase transition. Antiferromagnetic resonance (AFMR) modes in the subsystem of Fe{sup 3+} ions are detected in the range of anti-ferromagnetic ordering (T < T{sub N} = 30-40 K) in all ferroborates that have either an easy-plane (Y, Eu) or easy-axis (Pr, Tb, Tb{sub 0.25}Er{sub 0.75}) magnetic structure. The AFMR frequencies are found to depend strongly on the magnetic anisotropy of a rare-earth ion and its exchange interaction with the Fe subsystem, which determine the type of magnetic structure and the sign and magnitude of an effective anisotropy constant. The basic parameters of the magnetic interactions in these ferroborates are found, and the magnetoelectric contribution to AFMR is analyzed.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2013-11-01

    A wide-frequency and high-resolution frequency measurement method based on the quantized phase step law is presented in this paper. Utilizing a variation law of the phase differences, the direct different frequency phase processing, and the phase group synchronization phenomenon, combining an A/D converter and the adaptive phase shifting principle, a counter gate is established in the phase coincidences at one-group intervals, which eliminates the ±1 counter error in the traditional frequency measurement method. More importantly, the direct phase comparison, the measurement, and the control between any periodic signals have been realized without frequency normalization in this method. Experimental results show that sub-picosecond resolution can be easily obtained in the frequency measurement, the frequency standard comparison, and the phase-locked control based on the phase quantization processing technique. The method may be widely used in navigation positioning, space techniques, communication, radar, astronomy, atomic frequency standards, and other high-tech fields. PMID:24158281

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

    PubMed

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

    1995-04-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    PubMed Central

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kumar, Dilip

    2014-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    SciTech Connect

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

    2014-05-19

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

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

    SciTech Connect

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

    2014-12-15

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

  18. Virtual Acoustic Testing of Spacecraft Over a Broad Frequency Range Using FEM, BEM and Sea

    NASA Astrophysics Data System (ADS)

    Vansant, K.; Borello, G.; De Langhe, K.; Courjal, A.

    2012-07-01

    During launch, a spacecraft is exposed to high levels of structural and acoustical loading. Acceptance tests are carried out before actual launch mimicking these loading conditions to validate that vibration, force and stress levels, which could damage the payload and lead to mission failure, remain below the design envelopes. The acceptance tests themselves, carried out on the actual payload, imply a risk of overtesting. Simulation models make it possible to carry out these tests in the virtual world. They can be used to derive specifications for the desired shaker, loudspeaker or horn excitation signals and to upfront quantify the risk of overtesting. Simulation also allows to uncover and rectify flaws or sensitivities in the spacecraft design rather quickly and at a low cost. This paper will discuss several simulation models (FEM, BEM and SEA) which can be used to mimic an acoustic acceptance test for different frequency ranges of interest.

  19. 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...

  20. Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene Is Associated with Changes in Flowering Time across a Range of Populations1[W

    PubMed Central

    Skøt, Leif; Sanderson, Ruth; Thomas, Ann; Skøt, Kirsten; Thorogood, Danny; Latypova, Galina; Asp, Torben; Armstead, Ian

    2011-01-01

    The Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT) gene and its orthologs in other plant species (e.g. rice [Oryza sativa] OsFTL2/Hd3a) have an established role in the photoperiodic induction of flowering response. The genomic and phenotypic variations associated with the perennial ryegrass (Lolium perenne) ortholog of FT, designated LpFT3, was assessed in a diverse collection of nine European germplasm populations, which together constituted an association panel of 864 plants. Sequencing and genotyping of a series of amplicons derived from the nine populations, containing the complete exon and intron sequences as well as 5′ and 3′ noncoding sequences of LpFT3, identified a total of seven haplotypes. Genotyping assays designed to detect the genomic variation showed that three haplotypes were present in approximately equal proportions and represented 84% of the total, with a fourth representing a further 11%. Of the three major haplotypes, two were predicted to code for identical protein products and the third contained two amino acid substitutions. Association analysis using either a mixed model with a relationship matrix to correct for population structure and relatedness or structured association with further correction using genomic control indicated significant associations between LpFT3 and variation in flowering time. These associations were corroborated in a validation population segregating for the same major alleles. The most “diagnostic” region of genomic variation was situated 5′ of the coding sequence. Analysis of this region identified that the interhaplotype variation was closely associated with sequence motifs that were apparently conserved in the 5′ region of orthologs of LpFT3 from other plant species. These may represent cis-regulatory elements involved in influencing the expression of this gene. PMID:21115808

  1. Study of the dielectric properties of water in the frequency range 75-120 GHz

    NASA Astrophysics Data System (ADS)

    Furashov, N. I.; Dudin, V. E.; Sverdlov, B. A.

    2006-06-01

    We study experimentally the frequency dependences of the refractive index n and the absorption coefficient k of distilled, sea, and river water. The measurements were performed using a quasioptical device with a backward-wave oscillator as the radiation source and OAP-7 optical-acoustic receivers at a water temperature of 27°C in the cell. The quantities n and k were determined from the measured transmission and reflection coefficients of the cell with water by means of joint numerical solution of the equations for these quantities. For distilled water in the frequency range f = 75-120 GHz, we obtained n = 6.142-3.926 · 10-2f[GHz] + 1.307 · 10-4(f[GHz])2 and k = 3.607-2.101 · 10-2 f[GHz] + 5.252 · 10-5(f[GHz])2. On the whole, these data are in good agreement with the measurement results obtained by other authors at several frequencies of the indicated range and coincide with the calculation data based on the models by Meissner and Wentz and by Liebe et al. within the limits of the rms determination errors 0.05 and 0.02 for the parameters n and k, respectively. The values of n and k for different seawater samples and river water containing insoluble admixtures coincide with the values of these quantities for distilled water within the limits of the experimental measurement errors 3-5% and 1-2%, respectively. The dependences n(f) and k(f) obtained experimentally for seawater are compared with those calculated on the basis of the developed models. Measurements of the transmission spectrum of a cell with double distilled water were performed for low power density of radiation (less than µW/cm2) to reproduce the effect of water resonant transparency reported many times in the literature. Our measurements did not reveal any resonant features in the spectral behavior of the refractive index n and the absorption coefficient k of water and gave the same result as for a power density exceeding the threshold of appearance of this effect.

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

    DOEpatents

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

    1999-02-02

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

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

    DOEpatents

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

    1999-02-02

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

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

    PubMed

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

    2016-07-01

    Fundamental properties of warm dense matter are described by the dielectric function, which gives access to the frequency-dependent electrical conductivity; absorption, emission, and scattering of radiation; charged particles stopping; and further macroscopic properties. Different approaches to the dielectric function and the related dynamical collision frequency are compared in a wide frequency range. The high-frequency limit describing inverse bremsstrahlung and the low-frequency limit of the dc conductivity are considered. Sum rules and Kramers-Kronig relation are checked for the generalized linear response theory and the standard approach following kinetic theory. The results are discussed in application to aluminum, xenon, and argon plasmas. PMID:27575226

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  6. Speckle reduction in OCT using massively-parallel detection and frequency-domain ranging

    PubMed Central

    Desjardins, A. E.; Vakoc, B. J.; Tearney, G. J.; Bouma, B. E.

    2009-01-01

    Speckle noise significantly limits the information content provided by coherent optical imaging methods such as optical coherence tomography and its recent derivative, optical frequency-domain imaging (OFDI). In this paper, we demonstrate a novel OFDI system that simultaneously acquires hundreds of angularly resolved images, which can be compounded to reduce speckle noise. The system comprises an InGaAs line-scan camera and an interferometer, configured so that the elements of the detector array simultaneously capture light spanning a backscattering angular range of 32 degrees. On successive read-outs of the array, the wavelength of the laser source was stepped through a range of 130 nm centered at 1295 nm to concurrently generate 400 angle-resolved OFDI images. A theory of angle-resolved OFDI and the design equations of the system are presented. Incoherent averaging of the angle-resolved data is shown to yield substantial speckle reduction (as high as an 8 dB SNR improvement) in images of a tissue phantom and esophageal tissue ex vivo. PMID:19516630

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

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

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

    PubMed

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

    1997-06-01

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

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2015-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

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

    PubMed Central

    Revil, A

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

  16. Development and Operation of the Lower Hybrid Range of Frequency System on JT-60U

    SciTech Connect

    Seki, M.; Ikeda, Y.; Maebara, S.; Moriyama, S.; Naito, O.; Anno, K.; Hiranai, S.; Shimono, M.; Shinozaki, S.; Terakado, M.; Yokokura, K.; Yamamoto, T.; Fujii, T.

    2002-09-15

    Development and operation of a lower hybrid range of frequency (LHRF) system for JT-60U are presented. The LHRF system was constructed in 1986 to study current drive and plasma heating at high injection power. Its main specifications are the total output power 24 MW with 24 high power klystrons, the frequency 1.74 to 2.23 GHz, and the injection power {approx}10 MW with three conventional antennas. To improve the antenna capabilities such as the current drive efficiency, N{sub //peak} controllability and the power injection properties, a 3-divided multi-junction type (CD1' launcher) and a 12-divided multi-junction type (CD2 launcher) are developed. The CD2 launcher can also reduce the number of the transmission lines to one fourth of the original system. The injection power {approx}7 MW is attained, and then the highest current drive efficiency 3.5 x 10{sup 19} m{sup -2}AW{sup -1} and the highest non-inductive driven current 3.6 MA are achieved. The high power klystron capable of the cathode-heater operation times more than 3000 hours is improved. The outgassing rate is estimated with the CD2 launcher as 1-10 x 10{sup -6} Pam{sup 3}/sm{sup 2}, which is sufficiently small not to need the vacuum pumping system for the launcher. Heat load onto the launcher due to the ripple enhanced banana drift loss is first observed in NBI or ICRF heating. From investigation on antenna-plasma coupling, the gas puffing improves distant coupling.

  17. The 110-GHz Electron Cyclotron Range of Frequency System on JT-60U: Design and Operation

    SciTech Connect

    Ikeda, Y.; Kasugai, A.; Moriyama, S.; Kajiwara, K.; Seki, M.; Tsuneoka, M.; Takahashi, K.; Anno, K.; Hamamatsu, K.; Hiranai, S.; Ikeda, Yu.; Imai, T.; Sakamoto, K.; Shimono, M.; Shinozaki, S.; Terakado, M.; Yamamoto, T.; Yokokura, K.; Fujii, T.

    2002-09-15

    The electron cyclotron range of frequency (ECRF) system was designed and operated on the JT-60U to locally heat and control plasmas. The frequency of 110 GHz was adopted to inject the fundamental O-mode from the low field side with an oblique injection angle. The system is composed of four 1 MW-level gyrotrons, four transmission lines, and two antennae. The gyrotron is featured by a collector potential depression (CPD) and a gaussian beam output through a diamond window. The CPD enables JAERI to drive the gyrotron under the condition of the main DC voltage of 60 kV without a thyristor regulation. The gaussian mode from the gyrotron is effectively transformed to HE{sub 11} mode in the 31.75 mm diameter corrugated waveguide. About 75% of the output power of the gyrotrons can be injected into plasmas through the waveguides about 60 m in length. There are two antennae to control the deposition position of the EC wave during a plasma discharge. One is connected with three RF lines to steer the EC beams in the poloidal direction. The other is to control the EC beam in the toroidal and poloidal directions by two steerable mirrors.On the operation in 2000, the power of 1.5 to 1.6 MW for 3 s was successfully injected into plasmas using three gyrotrons. Local profile control was demonstrated by using the antennae. This capability was devoted to improve the plasma performance such as high T{sub e} production more than 15 keV and suppression of the MHD activities. In 2001, the fourth gyrotron, whose structure was improved for long pulse operation, has been installed for a total injection power of {approx}3 MW.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  19. Higher-frequency extension of the gauging ranges of vector receivers in the nonuniform field of measuring chambers

    NASA Astrophysics Data System (ADS)

    Gordienko, V. A.; Goncharenko, B. I.; Zadorozhnyi, S. S.; Starkova, M. V.

    2012-09-01

    The paper discusses the frequency-dependent error of gauging acoustic receivers in the field of a standing wave and the fundamental possibility of extending the operating range of gauging of hydrophones toward high frequencies and finite-size vector receivers (acoustic pressure gradient receivers) in a vertical liquid column, oscillating in a small-volume cylindrical chamber.

  20. Three dimensional ray tracing Jovian magnetosphere in the low frequency range

    NASA Technical Reports Server (NTRS)

    Menietti, J. D.

    1982-01-01

    Ray tracing of the Jovian magnetosphere in the low frequency range (1+40 MHz) has resulted in a new understanding of the source mechanism for Io dependent decametric radiation (DAM). Our three dimensional ray tracing computer code has provided model DAM arcs at 10 deg. intervals of Io longitude source positions for the full 360 deg of Jovian system III longitude. In addition, particularly interesting arcs were singled out for detailed study and modelling. Dependent decametric radiation arcs are categorized according to curvature--the higher curvature arcs are apparently due to wave stimulation at a nonconstant wave normal angle, psi. The psi(f) relationship has a signature that is common to most of the higher curvature arcs. The low curvature arcs, on the other hand, are adequately modelled with a constant wave normal angle of close to 90 deg. These results imply that for higher curvature arcs observed for from Jupiter (to diminish spacecraft motion effects) the electrons providing the gyroemission are relativistically beamed.

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

    SciTech Connect

    Hantao Ji; Russell Kulsrud; William Fox; Masaaki Yamada

    2005-06-10

    By employing a local two-fluid theory, we investigate an obliquely propagating electromagnetic instability in the lower hybrid frequency range driven by cross-field current or relative drifts between electrons and ions. The theory self-consistently takes into account local cross-field current and accompanying pressure gradients. It is found that the instability is caused by reactive coupling between the backward propagating whistler (fast) waves in the moving electron frame, and the forward propagating sound (slow) waves in the ion frame when the relative drifts are large. The unstable waves we consider propagate obliquely to the unperturbed magnetic field and have mixed polarization with significant electromagnetic components. A physical picture of the instability emerges in the limit of large wave number characteristic of the local approximation. The primary positive feedback mechanism is based on reinforcement of initial electron density perturbations by compression of electron fluid via induced Lorentz force. The resultant waves are qualitatively consistent with the measured electromagnetic fluctuations in reconnecting current sheet in a laboratory plasma.

  2. Observations of the radio noise background in the frequency range 150-180 kHz

    NASA Astrophysics Data System (ADS)

    Knowles, S. H.; Kelly, F. J.; Waltman, W. B.; Odenwald, S.

    1985-05-01

    Observations were made of the radio noise background in the frequency range 150-180 kHz to provide reference data for the design of the ground wave emergency network system. These observations were undertaken at Nanjemoy, Maryland, during early summer 1983 and included 41 days of data recording. The noise environment was found to be dominated by impulsive thunderstorm noise. A typical nighttime mean noise power spectral density was 1×10-15 W m-2 Hz-1 (noise factor of 107 dB above kT0), while a typical daytime level was at least 14 dB quieter. However, the daytime level was at times significantly higher, especially during the presence of a local thunderstorm front. During local thunderstorm activity, impulses with peak power spectral density of 1×10-14 W m-2 Hz-1 were observed frequently, while the most energetic pulse detected during our monitoring period had a peak power spectral density of 6.8×10-14 W m-2 Hz-1 (Fa = 125 dB). Sample amplitude probability distributions and time probability distributions are presented for day/quiet, night, and thunderstorm conditions. Agreement with the mean noise level predictions of CCIR report 322 is satisfactory within the accuracy limits of the CCIR data.

  3. Ion cyclotron range of frequencies heating and current drive in deuterium-tritium plasmas

    NASA Astrophysics Data System (ADS)

    Phillips, C. K.; Bell, M. G.; Bell, R.; Bretz, N.; Budny, R. V.; Darrow, D. S.; Grek, B.; Hammett, G.; Hosea, J. C.; Hsuan, H.; Ignat, D.; Majeski, R.; Mazzucato, E.; Nazikian, R.; Park, H.; Rogers, J. H.; Schilling, G.; Stevens, J. E.; Synakowski, E.; Taylor, G.; Wilson, J. R.; Zarnstorff, M. C.; Zweben, S. J.; Bush, C. E.; Goldfinger, R.; Jaeger, E. F.; Murakami, M.; Rasmussen, D.; Bettenhausen, M.; Lam, N. T.; Scharer, J.; Sund, R.; Sauter, O.

    1995-06-01

    The first experiments utilizing high-power radio waves in the ion cyclotron range of frequencies to heat deuterium-tritium (D-T) plasmas have been completed on the Tokamak Fusion Test Reactor [Fusion Technol. 21, 13 (1992)]. Results from the initial series of experiments have demonstrated efficient core second harmonic tritium (2ΩT) heating in parameter regimes approaching those anticipated for the International Thermonuclear Experimental Reactor [D. E. Post, Plasma Physics and Controlled Nuclear Fusion Research, Proceedings of the 13th International Conference, Washington, DC, 1990 (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 239]. Observations are consistent with modeling predictions for these plasmas. Efficient electron heating via mode conversion of fast waves to ion Bernstein waves has been observed in D-T, deuterium-deuterium (D-D), and deuterium-helium-4 (D-4He) plasmas with high concentrations of minority helium-3 (3He) (n3He/ne≳10%). Mode conversion current drive in D-T plasmas was simulated with experiments conducted in D-3He-4He plasmas. Results show a directed propagation of the mode converted ion Bernstein waves, in correlation with the antenna phasing.

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

    PubMed

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

    2014-02-01

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

  5. Ion cyclotron range of frequencies heating of plasma with small impurity production

    DOEpatents

    Ohkawa, Tihiro

    1987-01-01

    Plasma including plasma ions is magnetically confined by a magnetic field. The plasma has a defined outer surface and is intersected by resonance surfaces of respective common ion cyclotron frequency of a predetermined species of plasma ions moving in the magnetic field. A radio frequency source provides radio frequency power at a radio frequency corresponding to the ion cyclotron frequency of the predetermined species of plasma ions moving in the field at a respective said resonance surface. RF launchers coupled to the radio frequency source radiate radio frequency energy at the resonance frequency onto the respective resonance surface within the plasma from a plurality of locations located outside the plasma at such respective distances from the intersections of the respective resonance surface and the defined outer surface and at such relative phases that the resulting interference pattern provides substantially null net radio frequency energy over regions near and including substantial portions of the intersections relative to the radio frequency energy provided thereby at other portions of the respective resonance surface within the plasma.

  6. Two efficient methods for measuring hydrophone frequency response in the 100 kHz to 2 MHz range

    NASA Astrophysics Data System (ADS)

    Harris, G. R.; Maruvada, S.; Gammell, P. M.

    2004-01-01

    As new medical applications of ultrasound emerge with operating frequencies in the hundreds of kilohertz to low megahertz region, it becomes more important to have convenient calibration methods for hydrophones in this frequency range. Furthermore, short diagnostic ultrasound pulses affected by finite amplitude distortion require that the hydrophone frequency response be known well below the center frequency. National standards laboratories can provide accurate calibration data at these frequencies, but the two methods now employed, laser interferometry and three-transducer reciprocity, are both single-frequency techniques, and they can be time-consuming procedures. Therefore, two efficient methods for generating a wideband acoustic pressure spectrum have been implemented to cover this frequency range. In one method a high-voltage pulse generator was used to excite a thick piezoelectric ceramic disk, producing a plane-wave acoustic pressure transient <1 µs in duration with peak amplitude of about 40 kPa. In the other technique, time delay spectrometry (TDS), a purpose-built 1-3 piezoelectric composite source transducer weakly focused at 20 cm was swept over the 0-2 MHz range. Its transmitting voltage response at 1 MHz was 11 kPa/V. The broadband pulse technique has the advantage of being simpler to implement, but TDS has a much greater signal-to-noise ratio because of the frequency-swept narrowband filter employed.

  7. Linearization of the Frequency Sweep of a Frequency-Modulated Continuous-Wave Semiconductor Laser Radar and the Resulting Ranging Performance

    NASA Astrophysics Data System (ADS)

    Karlsson, Christer J.; Olsson, Fredrik Å. A.

    1999-05-01

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

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

    PubMed

    Karlsson, C J; Olsson, F A

    1999-05-20

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

  9. Milliwatt-level frequency combs in the 8-14 μm range via difference frequency generation from an Er:fiber oscillator.

    PubMed

    Gambetta, Alessio; Coluccelli, Nicola; Cassinerio, Marco; Gatti, Davide; Laporta, Paolo; Galzerano, Gianluca; Marangoni, Marco

    2013-04-01

    We report on the generation of mid-infrared (mid-IR) pulses with a maximum average optical power of 4 mW and wide tunability in the 8-14 μm range via difference frequency generation (DFG) in GaSe from an Er:fiber laser oscillator. The DFG process is seeded with self-frequency shifted Raman solitons that are shown to be phase coherent within the whole tuning range, from 1.76 to 1.93 μm. Interference measurements between adjacent pulses at the idler wavelengths attest coherence transfer to the mid-IR. PMID:23546275

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

    PubMed

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

    2016-09-01

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

  11. Masking of short stimuli by noises with spiked spectra: II. Time summation and frequency selectivity of hearing in a narrow frequency range

    NASA Astrophysics Data System (ADS)

    Rimskaya-Korsakova, L. K.; Lalayants, M. R.; Supin, A. Ya.; Tavartkiladze, G. A.

    2011-03-01

    The thresholds of masking of short high-frequency pulses with either different durations (1.25-25 ms) and similar central frequency or different central frequencies (3.6-4.4 kHz) but similar durations were measured to reveal manifestations of the properties of peripheral encoding in auditory perception. Noises with a spiked amplitude spectrum structure were used as maskers. The central frequency and the frequency band of a masker were 4 and 1 kHz, respectively. The central frequencies of a stimulus and a masker being equal, the noise the central frequency of which coincided with the frequency corresponding to a dip of an indented spectrum was called an off(rip)-frequency masker. Owing to the off(rip)-masker, stimuli-induced masking thresholds were formed taking into account excitation in a narrow region of a basila membrane and auditory nerve fibers with characteristic frequencies from a narrow range. High-frequency pulses with an envelope in the form of the Gaussian function and sinusoidal filling were used as stimuli. At masker levels of 30 dB above the auditory threshold, frequencies of off(rip)-masker spectra spikes of 500-2000 Hz, and a central stimulus frequency of 4 kHz, the thresholds of tonal stimuli (25 ms in duration) masking in two out of three probationers were higher than the thresholds of masking of compact stimuli (1.25 ms in duration). In the third probationer, on the contrary, the thresholds of tonal stimuli masking were lower than the thresholds of compact stimuli masking. At masker levels of 50 dB, individual threshold differences disappeared. The obtained results were interpreted in the context of implementation of different methods of auditory encoding of the intensity. The methods were based on either the average frequency of auditory nerve pulsations or the number of fibers participating in the response. The interpretation was also carried out in the context of revealing manifestations of nonlinear properties of basila membrane displacements

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

    NASA Astrophysics Data System (ADS)

    Trollinger, Valerie L.

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

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

    PubMed

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

    2016-04-01

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

  14. The Influence of Fundamental Frequency and Sound Pressure Level Range on Breathing Patterns in Female Classical Singing

    ERIC Educational Resources Information Center

    Collyer, Sally; Thorpe, C. William; Callaghan, Jean; Davis, Pamela J.

    2008-01-01

    Purpose: This study investigated the influence of fundamental frequency (F0) and sound pressure level (SPL) range on respiratory behavior in classical singing. Method: Five trained female singers performed an 8-s messa di voce (a crescendo and decrescendo on one F0) across their musical F0 range. Lung volume (LV) change was estimated, and…

  15. Detecting range expansions from genetic data

    PubMed Central

    Peter, Benjamin M; Slatkin, Montgomery

    2014-01-01

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

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

    SciTech Connect

    Merezhkin, V. G.

    2009-06-15

    There are two close empirical scalings, namely, the T-11 and neo-Alcator ones, that provide correct estimates for the energy confinement time in tokamaks in ohmic heating regimes in the linear part of the dependence {tau}{sub E}(n-bar{sub e}) in the range of low values of n-bar{sub e} and <{nu}{sub e}{sup *}> {<=} 1. The similar character of electron energy confinement in this range, which expands with increasing magnetic field B{sub 0}, has stimulated the search for dimensionless parameters and simple physical models that would explain the experimentally observed dependences {chi}{sub e} {approx} 1/n{sub e} and {tau}{sub Ee} {approx} n-bar{sub e}. In 1987, T. Okhawa showed that the experimental data were satisfactorily described by the formula {chi}{sub eperpendicular} = (c{sup 2}/{omega}{sub pe}{sup 2}){nu}{sub e}/qR, in deriving of which the random spatial leap along the radius r on the electron trajectory was assumed to be the same as that in the coefficient of the poloidal field diffusion, while the repetition rate of these leaps was assumed to be {nu}{sub e}/qR. In 2004, J. Callen took into account the decrease in the fraction of transient electrons with increasing toroidal ratio {epsilon} = r/R and corrected the coefficient c{sup 2}/{omega}{sub pe}{sup 2} in Okhawa equation by the factor {sigma}{sub ||} {sup Sp}/{sigma}{sub ||}{sup neo}. If one takes into account this correction and assumes that the frequency of the stochastic process is equal to the reciprocal of the half-period of rotation of a trapped electron along its banana trajectory, then the resulting expression for {chi}{sub eperpendicular} will coincide with the T-11 scaling: {chi}{sub e}{sup an} {infinity} {epsilon}{sup 1.75}(T{sub e}/A{sub i}){sup 0.5}/(n{sub e}qR) at Ai = 1. If the same stochastic process also involves ions, it may result in the opening of the orbit of a trapped ion at the distance {approx}(c/{omega}{sub pe})(m{sub i}/m{sub e}){sup 1/4}. In this case, the calculated coefficient

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

    PubMed

    Cleary, R; Braddick, O J

    1990-01-01

    When an array of random dots is displaced, the ability to report the direction of apparent motion is subject to an upper spatial limit (dmax). Using spatially low-pass filtered random dot kinematograms we show that dmax is dependent on the upper cut-off frequency of the stimulus (Fh). The extent of this dependence is critically dependent on the size of the stimulus. Our results suggest a process whereby low spatial frequency motion information is masked by the presence of high spatial frequencies in the same region of the field, analogous to phenomena occurring in the perception of static form (e.g. the Abraham Lincoln effect). The effects of stimulus size on dmax, found for broad-band stimuli by ourselves and others, result from a loss of high frequency sensitivity at increased retinal eccentricities; this loss reduces the masking effect of high frequencies, as stimulus size increases. PMID:2309465

  18. Relationships between range access as monitored by radio frequency identification technology, fearfulness, and plumage damage in free-range laying hens.

    PubMed

    Hartcher, K M; Hickey, K A; Hemsworth, P H; Cronin, G M; Wilkinson, S J; Singh, M

    2016-05-01

    Severe feather-pecking (SFP), a particularly injurious behaviour in laying hens (Gallus gallus domesticus), is thought to be negatively correlated with range use in free-range systems. In turn, range use is thought to be inversely associated with fearfulness, where fearful birds may be less likely to venture outside. However, very few experiments have investigated the proposed association between range use and fearfulness. This experiment investigated associations between range use (time spent outside), fearfulness, plumage damage, and BW. Two pens of 50 ISA Brown laying hens (n=100) were fitted with radio frequency identification (RFID) transponders (contained within silicone leg rings) at 26 weeks of age. Data were then collected over 13 days. A total of 95% of birds accessed the outdoor run more than once per day. Birds spent an average duration of 6.1 h outside each day over 11 visits per bird per day (51.5 min per visit). The top 15 and bottom 15 range users (n=30), as determined by the total time spent on the range over 13 days, were selected for study. These birds were tonic immobility (TI) tested at the end of the trial and were feather-scored and weighed after TI testing. Birds with longer TI durations spent less time outside (P=0.01). Plumage damage was not associated with range use (P=0.68). The small group sizes used in this experiment may have been conducive to the high numbers of birds utilising the outdoor range area. The RFID technology collected a large amount of data on range access in the tagged birds, and provides a potential means for quantitatively assessing range access in laying hens. The present findings indicate a negative association between fearfulness and range use. However, the proposed negative association between plumage damage and range use was not supported. The relationships between range use, fearfulness, and SFP warrant further research. PMID:26593871

  19. Rapid estimation of frequency response functions by close-range photogrammetry

    NASA Technical Reports Server (NTRS)

    Tripp, J. S.

    1985-01-01

    The accuracy of a rapid method which estimates the frequency response function from stereoscopic dynamic data is computed. It is shown that reversal of the order of the operations of coordinate transformation and Fourier transformation, which provides a significant increase in computational speed, introduces error. A portion of the error, proportional to the perturbation components normal to the camera focal planes, cannot be eliminated. The remaining error may be eliminated by proper scaling of frequency data prior to coordinate transformation. Methods are developed for least squares estimation of the full 3x3 frequency response matrix for a three dimensional structure.

  20. Effects of the gaseous and liquid water content of the atmosphere on range delay and Doppler frequency

    NASA Technical Reports Server (NTRS)

    Flock, W. L.

    1981-01-01

    When high precision is required for range measurement on Earth space paths, it is necessary to correct as accurately as possible for excess range delays due to the dry air, water vapor, and liquid water content of the atmosphere. Calculations based on representative values of atmospheric parameters are useful for illustrating the order of magnitude of the expected delays. Range delay, time delay, and phase delay are simply and directly related. Doppler frequency variations or noise are proportional to the time rate of change of excess range delay. Tropospheric effects were examined as part of an overall consideration of the capability of precision two way ranging and Doppler systems.

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

    PubMed

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

    2007-01-01

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

  2. A self-analyzing double-loop digital controller in laser frequency stabilization for inter-satellite laser ranging.

    PubMed

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

    2015-04-01

    We present a digital controller specially designed for laser frequency stabilization in the application of inter-satellite laser ranging. The prototype of controller is developed using field programmable gate arrays programmed with National Instruments LabVIEW software. The controller is flexible, self-analyzing, and easily optimized with build-in system analysis. Application and performance of the controller to a laser frequency stabilization system designed for spaceborne scientific missions are demonstrated. PMID:25933873

  3. The influence of interlayer exchange coupling in giant-magnetoresistive devices on spin diode effect in wide frequency range

    SciTech Connect

    Ziętek, Sławomir Skowroński, Witold; Wiśniowski, Piotr; Czapkiewicz, Maciej; Stobiecki, Tomasz; Ogrodnik, Piotr; Barnaś, Józef

    2015-09-21

    Spin diode effect in a giant magnetoresistive strip is measured in a broad frequency range, including resonance and off-resonance frequencies. The off-resonance dc signal is relatively strong and also significantly dependent on the exchange coupling between magnetic films through the spacer layer. The measured dc signal is described theoretically by taking into account magnetic dynamics induced by Oersted field created by an ac current flowing through the system.

  4. Oscillating two stream instability of electromagnetic pump in the ion cyclotron range of frequency in a plasma

    SciTech Connect

    Ahmad, Nafis; Tripathi, V. K.; Rafat, M.; Husain, Mudassir M.

    2009-06-15

    An analytical formalism of oscillating two stream instability of a large amplitude electromagnetic wave in the ion cyclotron range of frequency in a plasma is developed. The instability produces electrostatic ion cyclotron sidebands and a driven low frequency mode. The nonlinear coupling arises primarily due to the motion of ions and is strong when the pump frequency is close to ion cyclotron frequency and the oscillatory ion velocity is a significant fraction of acoustic speed. For propagation perpendicular to the ambient magnetic field, the X-mode pump wave produces flute type perturbation with maximum growth rate at some specific wavelengths, which are three to four times larger than the ion Larmor radius. For propagation at oblique angles to ambient magnetic field, the ion cyclotron O-mode, the growth rate increases with the wave number of the low frequency mode.

  5. High Dynamic Range Observations of Solar Coronal Transients at Low Radio Frequencies with a Spectro-correlator

    NASA Astrophysics Data System (ADS)

    Hariharan, K.; Ramesh, R.; Kathiravan, C.; Abhilash, H. N.; Rajalingam, M.

    2016-02-01

    A new antenna system with a digital spectro-correlator that provides high temporal, spectral, and amplitude resolutions has been commissioned at the Gauribidanur Observatory near Bangalore in India. Presently, it is used for observations of the solar coronal transients in the scarcely explored frequency range ≈30-15 MHz. The details of the antenna system, the associated receiver setup, and the initial observational results are reported. Some of the observed transients exhibited quasi-periodicity in their time profiles at discrete frequencies. Estimates of the associated magnetic field strength (B) indicate that B ≈ 0.06-1 G at a typical frequency such as 19.5 MHz.

  6. Wide-frequency range, dynamic matching network and power system for the “Shoelace” radio frequency antenna on the Alcator C-Mod tokamak

    SciTech Connect

    Golfinopoulos, Theodore LaBombard, Brian; Burke, William; Parker, Ronald R.; Parkin, William; Woskov, Paul

    2014-04-15

    A wide-frequency range (50–300 kHz) power system has been implemented for use with a new RF antenna – the “Shoelace” antenna – built to drive coherent plasma fluctuations in the edge of the Alcator C-Mod tokamak. A custom, dynamically tunable matching network allows two commercial 1 kW, 50-Ω RF amplifiers to drive the low-impedance, inductive load presented by the antenna. This is accomplished by a discretely variable L-match network, with 81 independently selected steps available for each of the series and parallel legs of the matching configuration. A compact programmable logic device provides a control system that measures the frequency with better than 1 kHz accuracy and transitions to the correct tuning state in less than 1 ms. At least 85% of source power is dissipated in the antenna across the operational frequency range, with a minimum frequency slew rate of 1 MHz/s; the best performance is achieved in the narrower band from 80 to 150 kHz which is of interest in typical experiments. The RF frequency can be run with open-loop control, following a pre-programmed analog waveform, or phase-locked to track a plasma fluctuation diagnostic signal in real time with programmable phase delay; the amplitude control is always open-loop. The control waveforms and phase delay are programmed remotely. These tools have enabled first-of-a-kind measurements of the tokamak edge plasma system response in the frequency range and at the wave number at which coherent fluctuations regulate heat and particle transport through the plasma boundary.

  7. Wide-frequency range, dynamic matching network and power system for the "Shoelace" radio frequency antenna on the Alcator C-Mod tokamak.

    PubMed

    Golfinopoulos, Theodore; LaBombard, Brian; Burke, William; Parker, Ronald R; Parkin, William; Woskov, Paul

    2014-04-01

    A wide-frequency range (50-300 kHz) power system has been implemented for use with a new RF antenna - the "Shoelace" antenna - built to drive coherent plasma fluctuations in the edge of the Alcator C-Mod tokamak. A custom, dynamically tunable matching network allows two commercial 1 kW, 50-Ω RF amplifiers to drive the low-impedance, inductive load presented by the antenna. This is accomplished by a discretely variable L-match network, with 81 independently selected steps available for each of the series and parallel legs of the matching configuration. A compact programmable logic device provides a control system that measures the frequency with better than 1 kHz accuracy and transitions to the correct tuning state in less than 1 ms. At least 85% of source power is dissipated in the antenna across the operational frequency range, with a minimum frequency slew rate of 1 MHz/s; the best performance is achieved in the narrower band from 80 to 150 kHz which is of interest in typical experiments. The RF frequency can be run with open-loop control, following a pre-programmed analog waveform, or phase-locked to track a plasma fluctuation diagnostic signal in real time with programmable phase delay; the amplitude control is always open-loop. The control waveforms and phase delay are programmed remotely. These tools have enabled first-of-a-kind measurements of the tokamak edge plasma system response in the frequency range and at the wave number at which coherent fluctuations regulate heat and particle transport through the plasma boundary. PMID:24784610

  8. Wide-frequency range, dynamic matching network and power system for the "Shoelace" radio frequency antenna on the Alcator C-Mod tokamak

    NASA Astrophysics Data System (ADS)

    Golfinopoulos, Theodore; LaBombard, Brian; Burke, William; Parker, Ronald R.; Parkin, William; Woskov, Paul

    2014-04-01

    A wide-frequency range (50-300 kHz) power system has been implemented for use with a new RF antenna - the "Shoelace" antenna - built to drive coherent plasma fluctuations in the edge of the Alcator C-Mod tokamak. A custom, dynamically tunable matching network allows two commercial 1 kW, 50-Ω RF amplifiers to drive the low-impedance, inductive load presented by the antenna. This is accomplished by a discretely variable L-match network, with 81 independently selected steps available for each of the series and parallel legs of the matching configuration. A compact programmable logic device provides a control system that measures the frequency with better than 1 kHz accuracy and transitions to the correct tuning state in less than 1 ms. At least 85% of source power is dissipated in the antenna across the operational frequency range, with a minimum frequency slew rate of 1 MHz/s; the best performance is achieved in the narrower band from 80 to 150 kHz which is of interest in typical experiments. The RF frequency can be run with open-loop control, following a pre-programmed analog waveform, or phase-locked to track a plasma fluctuation diagnostic signal in real time with programmable phase delay; the amplitude control is always open-loop. The control waveforms and phase delay are programmed remotely. These tools have enabled first-of-a-kind measurements of the tokamak edge plasma system response in the frequency range and at the wave number at which coherent fluctuations regulate heat and particle transport through the plasma boundary.

  9. Measurements of ICRF (ion cyclotron range of frequencies) loading with a ridged waveguide coupler on PLT

    SciTech Connect

    Greene, G.J.; Wilson, J.R.; Colestock, P.L.; Fortgang, C.M.; Hosea, J.C.; Hwang, D.Q.; Nagy, A.

    1987-11-01

    An ICRF ridged waveguide coupler has been installed on PLT for measurements of plasma loading. The coupler was partially filled with TiO/sub 2/ dielectric in order to sufficiently lower the cutoff frequency and utilized a tapered ridge for improved matching. Vacuum field measurements indicated a single propagating mode in the coupler and emphasized the importance of considering the fringing fields at the mouth of the waveguide. Low power experiments were carried out at 72.6 and 95.0 MHz without any external impedance matching network. Plasma loading increased rapidly as the face of the coupler approached the plasma, and, at fixed position, increased with line-averaged plasma density. At the lower frequency, the reflection coefficient exhibited a minimum (<8%) at a particular coupler position. At both frequencies, measurements indicated efficient power coupling to the plasma. Magnetic probe signals showed evidence of dense eigenmodes suggesting excitation of the fast wave. 24 refs., 13 figs.

  10. Isoelectric focusing of superoxide dismutase: report of the unique SOD A*2 allele in a US white population.

    PubMed

    DeCroo, S; Kamboh, M I; Leppert, M; Ferrell, R E

    1988-01-01

    An isoelectric focusing procedure in an ultranarrow pH range (5.0-5.5) polyacrylamide gel is described for the determination of superoxide dismutase (SOD) phenotypes. The occurrence of the rare SOD A*2 allele in the Caucasian population of Utah is also reported at a polymorphic frequency (0.011). The presence of the SOD A 2 unique allele in the Mormons of Utah is compatible with their historical affinity with Scandinavians. PMID:3350528

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  12. High-Precise Spectrometry of the Terahertz Frequency Range: The Methods, Approaches and Applications

    NASA Astrophysics Data System (ADS)

    Vaks, Vladimir

    2012-01-01

    In the paper we present a high precise THz technique (frequency synthesizers and spectrometer) and its applications for noninvasive medical diagnostics and security systems. The cornerstone of the presented devices is multipliers and mixers based on quantum superlattice structures. The multipliers based on superlattice structures are shown to be more effective than Schottky diodes and provide THz radiation up to 8.1 THz.

  13. New space research frequency band proposals in the 20- to 40.5-GHz range

    NASA Technical Reports Server (NTRS)

    Bishop, D. F.

    1991-01-01

    Future space research communications systems may require spectra above 20 GHz. Frequency bands above 20 GHz are identified that are suitable for space research. The selection of the proper bands depends on consideration of interference with other radio services, adequate bandwidths, link performance, and technical requirements for practical implementation.

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

    NASA Technical Reports Server (NTRS)

    Menietti, J. D.

    1984-01-01

    Ray tracing studies of Jovian low frequency emissions were studied. A comprehensive three-dimensional ray tracing computer code for examination of model Jovian decametric (DAM) emission was developed. The improvements to the computer code are outlined and described. The results of the ray tracings of Jovian emissions will be presented in summary form.

  15. Extended parametric gain range in photonic crystal fibers with strongly frequency-dependent field distributions.

    PubMed

    Petersen, Sidsel R; Alkeskjold, Thomas T; Olausson, Christina B; Lægsgaard, Jesper

    2014-08-15

    The parametric gain range of a degenerate four-wave mixing process is determined in the undepleted pump regime. The gain range is considered with and without taking the mode field distributions of the four-wave mixing components into account. It is found that the mode field distributions have to be included to evaluate the parametric gain correctly in dispersion-tailored speciality fibers and that mode profile engineering can provide a way to increase the parametric gain range. PMID:25121901

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

    SciTech Connect

    Aoki, Makoto; Hiromoto, Norihisa

    2015-10-15

    We describe a 4-K-cryocooled dual-band terahertz (THz) photoconductive detector system with background-limited performance. The detector system comprises two THz photoconductive detectors covering a response in a wide frequency range from 1.5 to 4 THz, low noise amplifiers, optical low-pass filters to eliminate input radiation of higher frequencies, and a mechanical 4 K Gifford-McMahon refrigerator that provides practical and convenient operation without a liquid He container. The electrical and optical performances of the THz detector system were evaluated at a detector temperature of 4 K under 300 K background radiation. We proved that the detector system can achieve background-limited noise-equivalent-power on the order of 10{sup −14} W/Hz{sup 1/2} in the frequency range from 1.5 to 4 THz even if the vibration noise of the mechanical refrigerator is present.

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

    NASA Astrophysics Data System (ADS)

    Aoki, Makoto; Hiromoto, Norihisa

    2015-10-01

    We describe a 4-K-cryocooled dual-band terahertz (THz) photoconductive detector system with background-limited performance. The detector system comprises two THz photoconductive detectors covering a response in a wide frequency range from 1.5 to 4 THz, low noise amplifiers, optical low-pass filters to eliminate input radiation of higher frequencies, and a mechanical 4 K Gifford-McMahon refrigerator that provides practical and convenient operation without a liquid He container. The electrical and optical performances of the THz detector system were evaluated at a detector temperature of 4 K under 300 K background radiation. We proved that the detector system can achieve background-limited noise-equivalent-power on the order of 10-14 W/Hz1/2 in the frequency range from 1.5 to 4 THz even if the vibration noise of the mechanical refrigerator is present.

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

    PubMed

    Aoki, Makoto; Hiromoto, Norihisa

    2015-10-01

    We describe a 4-K-cryocooled dual-band terahertz (THz) photoconductive detector system with background-limited performance. The detector system comprises two THz photoconductive detectors covering a response in a wide frequency range from 1.5 to 4 THz, low noise amplifiers, optical low-pass filters to eliminate input radiation of higher frequencies, and a mechanical 4 K Gifford-McMahon refrigerator that provides practical and convenient operation without a liquid He container. The electrical and optical performances of the THz detector system were evaluated at a detector temperature of 4 K under 300 K background radiation. We proved that the detector system can achieve background-limited noise-equivalent-power on the order of 10(-14) W/Hz(1/2) in the frequency range from 1.5 to 4 THz even if the vibration noise of the mechanical refrigerator is present. PMID:26520978

  19. Investigation of the optical properties of normal fibroblasts and fibroblasts cultured with cancer cells in terahertz frequency range

    NASA Astrophysics Data System (ADS)

    Strepitov, E. A.; Liakhov, E. P.; Balbekin, N. S.; Khodzitsky, M. K.; Smolyanskaya, O. A.; Trulyov, A. S.; Serebryakova, M. K.

    2015-07-01

    The optical properties of normal fibroblasts and fibroblasts cultured with cancer cells were studied in the frequency range of 0.2 - 1.0 THz. The results show the possibility to distinguish healthy cells from corrupted ones using their optical parameters.

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

    SciTech Connect

    Biddle, A. P.

    1980-06-01

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

  1. Comment on "Mode Conversion of Waves In The Ion-Cyclotron Frequency Range in Magnetospheric Plasmas"

    SciTech Connect

    Kim, Eun; Johnson, J. R.

    2014-02-01

    Recently, Kazakov and Fulop [1] studied mode conversion (MC) at the ion-ion hybrid (IIH) resonance in planetary magnetospheric plasmas by simplifying the dispersion relation of the fast wave (FW) modes to describe a cutoff-resonance (CR) pair near the IIH resonance, which can be reduced to a Budden problem. They suggested that when the IIH resonance frequency (ωS) approaches the crossover frequency (ωcr), and the parallel wavenumber (k∥) is close to the critical wavenumber k* ∥(ωS = ωcr), MC can be efficient for arbitrary heavy ion density ratios. In this Comment, we argue that (a) the FW dispersion relation cannot be simplified to the CR pair especially near ωcr because in many parameter regimes there is a cutoff-resonance-cutoff (CRC) triplet that completely changes the wave absorption; and (b) the maximum MC efficiency does not always occur near k∥ ≈ k*∥∥.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  3. 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.

  4. 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.

  5. Evaluation of range-separated hybrid density functionals for the prediction of vibrational frequencies, infrared intensities, and Raman activities†

    PubMed Central

    Jiménez-Hoyos, Carlos A.; Janesko, Benjamin G.

    2016-01-01

    We present an assessment of different density functionals, with emphasis on range-separated hybrids, for the prediction of fundamental and harmonic vibrational frequencies, infrared intensities, and Raman activities. Additionally, we discuss the basis set convergence of vibrational properties of H2O with long-range corrected hybrids. Our results show that B3LYP is the best functional for predicting vibrational frequencies (both fundamental and harmonic); the screened-PBE hybrid (HSE) density functional works best for infrared intensities, and the long-range corrected PBE (LC-ωPBE), M06-HF, and M06-L density functionals are almost as good as MP2 for predicting Raman activities. We show the predicted Raman spectrum of adenine as an example of a medium-size molecule where a DFT/Sadlej pVTZ calculation is affordable and compare our results against the experimental spectrum. PMID:18989473

  6. Optical heterodyning with a frequency difference of 1 THz in the 850-nm range.

    PubMed

    Acef, O; Nez, F; Rovera, G D

    1994-09-01

    We report our recent progress on detection of large frequency difference (up to 1.028 THz, Deltalambda = 2.5 nm) between two laser diodes at 852 nm, using a Schottky diode as harmonic mixer/detector. Using the 11th harmonic of a klystron operating at 93.5 GHz or the 991-GHz line of an optically pumped HCOOH far-infrared laser, we were able to observe a signal-to-noise ratio of 2 dB in a 1-MHz-resolution bandwidth. PMID:19855492

  7. Dielectric properties of aluminum silver alloy thin films in optical frequency range

    SciTech Connect

    Yang Guang; Sun Jingbo; Zhou Ji

    2011-06-15

    The dielectric properties of direct current (dc) magnetron sputtering aluminum silver alloy films in optical frequency have been quantitatively studied by variable angle spectroscopic ellipsometry. The structure and surface topography of the alloy films were characterized using scanning probe microscopy and x-ray diffraction. The Drude-Lorentz model was used to simulate the dielectric function of Al-Ag alloy films. Meanwhile, the effective medium theory has been utilized for the treatment of surface roughness. We found that the interband transition around 1.5 eV can be shifted through a variable annealing temperature and a changeable silver percentage of Al-Ag alloys.

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

    PubMed Central

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Guillory, Joffray; Šmíd, Radek; García-Márquez, Jorge; Truong, Daniel; Alexandre, Christophe; Wallerand, Jean-Pierre

    2016-07-01

    We have developed an optical Absolute Distance Meter (ADM) based on the measurement of the phase accumulated by a Radio Frequency wave during its propagation in the air by a laser beam. In this article, the ADM principle will be described and the main results will be presented. In particular, we will emphasize how the choice of an appropriate photodetector can significantly improve the telemeter performances by minimizing the amplitude to phase conversion. Our prototype, tested in the field, has proven its efficiency with a resolution better than 15 μm for a measurement time of 10 ms and distances up to 1.2 km.

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

    PubMed

    Guillory, Joffray; Šmíd, Radek; García-Márquez, Jorge; Truong, Daniel; Alexandre, Christophe; Wallerand, Jean-Pierre

    2016-07-01

    We have developed an optical Absolute Distance Meter (ADM) based on the measurement of the phase accumulated by a Radio Frequency wave during its propagation in the air by a laser beam. In this article, the ADM principle will be described and the main results will be presented. In particular, we will emphasize how the choice of an appropriate photodetector can significantly improve the telemeter performances by minimizing the amplitude to phase conversion. Our prototype, tested in the field, has proven its efficiency with a resolution better than 15 μm for a measurement time of 10 ms and distances up to 1.2 km. PMID:27475593

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Technical Reports Server (NTRS)

    Wong, Hung K.; Smith, Charles W.

    1994-01-01

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

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

    SciTech Connect

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

    2013-12-31

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

  14. Study of transmission line attenuation in broad band millimeter wave frequency range

    NASA Astrophysics Data System (ADS)

    Pandya, Hitesh Kumar B.; Austin, M. E.; Ellis, R. F.

    2013-10-01

    Broad band millimeter wave transmission lines are used in fusion plasma diagnostics such as electron cyclotron emission (ECE), electron cyclotron absorption, reflectometry and interferometry systems. In particular, the ECE diagnostic for ITER will require efficient transmission over an ultra wide band, 100 to 1000 GHz. A circular corrugated waveguide transmission line is a prospective candidate to transmit such wide band with low attenuation. To evaluate this system, experiments of transmission line attenuation were performed and compared with theoretical loss calculations. A millimeter wave Michelson interferometer and a liquid nitrogen black body source are used to perform all the experiments. Atmospheric water vapor lines and continuum absorption within this band are reported. Ohmic attenuation in corrugated waveguide is very low; however, there is Bragg scattering and higher order mode conversion that can cause significant attenuation in this transmission line. The attenuation due to miter bends, gaps, joints, and curvature are estimated. The measured attenuation of 15 m length with seven miter bends and eighteen joints is 1 dB at low frequency (300 GHz) and 10 dB at high frequency (900 GHz), respectively.

  15. A new ionosphere-free ambiguity resolution method for long-range baseline with GNSS triple-frequency signals

    NASA Astrophysics Data System (ADS)

    Xu, Ying; Ji, Shengyue; Chen, Wu; Weng, Duojie

    2015-10-01

    New GNSS systems (i.e. GPS modernization, BeiDou, and Galileo) will provide multiple navigation signals for reliable navigation services. The triple or even multiple frequency signals are expected to bring great benefits to the ambiguity resolution (AR) over long-range baselines, which is always regarded as a huge challenge. Another issue in the long baseline AR is the unmodeled ionospheric delay, which is one of the major errors in ranging signals. A new triple-frequency, ionosphere-free technique for ambiguity resolution of long-range baseline is developed in this study. In this technique, the optimal observation combinations are chosen considering the effect of ionospheric delay. At the same time, using this technique, the double difference (DD) ionospheric delay is nullified in the ambiguity search process. The performance of the new technique is examined using the simulated GPS triple frequency data as well as the real BDS observation. Results show that the ambiguity can be fixed within 10 min for GPS and BDS long-range baselines with this new technique.

  16. Frequency and Fitness Consequences of Bacteriophage Φ6 Host Range Mutations

    PubMed Central

    Ford, Brian E.; Sun, Bruce; Carpino, James; Chapler, Elizabeth S.; Ching, Jane; Choi, Yoon; Jhun, Kevin; Kim, Jung D.; Lallos, Gregory G.; Morgenstern, Rachelle; Singh, Shalini; Theja, Sai; Dennehy, John J.

    2014-01-01

    Viruses readily mutate and gain the ability to infect novel hosts, but few data are available regarding the number of possible host range-expanding mutations allowing infection of any given novel host, and the fitness consequences of these mutations on original and novel hosts. To gain insight into the process of host range expansion, we isolated and sequenced 69 independent mutants of the dsRNA bacteriophage Φ6 able to infect the novel host, Pseudomonas pseudoalcaligenes. In total, we found at least 17 unique suites of mutations among these 69 mutants. We assayed fitness for 13 of 17 mutant genotypes on P. pseudoalcaligenes and the standard laboratory host, P. phaseolicola. Mutants exhibited significantly lower fitnesses on P. pseudoalcaligenes compared to P. phaseolicola. Furthermore, 12 of the 13 assayed mutants showed reduced fitness on P. phaseolicola compared to wildtype Φ6, confirming the prevalence of antagonistic pleiotropy during host range expansion. Further experiments revealed that the mechanistic basis of these fitness differences was likely variation in host attachment ability. In addition, using computational protein modeling, we show that host-range expanding mutations occurred in hotspots on the surface of the phage's host attachment protein opposite a putative hydrophobic anchoring domain. PMID:25409341

  17. Ion cyclotron range of frequencies heating and flow generation in deuterium{endash}tritium plasmas

    SciTech Connect

    Wilson, J.R.; Bell, R.E.; Bernabei, S.; Hill, K.; Hosea, J.C.; LeBlanc, B.; Majeski, R.; Nazikian, R.; Ono, M.; Phillips, C.K.; Schilling, G.; von Goeler, S.; Bush, C.E.; Hanson, G.R.

    1998-05-01

    Recent radio-frequency heating experiments on the Tokamak Fusion Test Reactor (TFTR) [Hawryluk {ital et al.}, Plasma Phys. Controlled Fusion {bold 33}, 1509 (1991)] have focused on developing tools for both pressure and current profile control in deuterium{endash}tritium (DT) plasmas. A new antenna was added to investigate pressure profile control utilizing direct ion Bernstein wave (IBW) heating. This was the first time direct IBW heating was explored on TFTR. Plasma heating and driven poloidal flows are observed. Previously heating and current drive via mode-converted IBW waves had been demonstrated in non-DT plasmas but efforts in DT plasmas had been unsuccessful. This lack of success had been ascribed to the presence of a small {sup 7}Li minority ion population. In the most recent experiments {sup 6}Li was used exclusively for machine conditioning and mode-conversion heating consistent with theory is now observed in DT plasmas. {copyright} {ital 1998 American Institute of Physics.}

  18. High power heating in the ion cyclotron range of frequencies in the Wisconsin Tokapole II

    SciTech Connect

    Biddle, A. P.; Sprott, J. C.

    1980-09-01

    Fast wave heating at the second, third, and fourth harmonics of the ion cyclotron resonance, and slow wave heating at the fundamental in a single ion species hydrogen plasma, are found to be in good agreement with warm plasma theory at rf power levels less than or equal to 130 kW. Ion heating is negligible off an eigenmode. Ion body temperatures are more than doubled to 75 eV from the 35 eV ohmically heated case with tails comprising 8% of the plasma at 320 eV. No deleterious effects except a non-disruptive 10% shortening of the discharge length caused by impurity influx are noted. A passive mode tracking technique allows approx. = 40% increase in power deposition in a passing eigenmode over that of a fixed frequency rf source. Ion temperatures are limited by charge exchange due to the < 50 eV central temperature and the small 13 cm radius current channel.

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

    PubMed

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

    2015-04-01

    A novel signal processing technique using sinusoidal optical frequency modulation of an inexpensive continuous-wave laser diode source is proposed that allows highly linear interferometric phase measurements in a simple, self-referencing setup. Here, the use of a smooth window function is key to suppress unwanted signal components in the demodulation process. Signals from several interferometers with unequal optical path differences can be multiplexed, and, in contrast to prior work, the optical path differences are continuously variable, greatly increasing the practicality of the scheme. In this paper, the theory of the technique is presented, an experimental implementation using three multiplexed interferometers is demonstrated, and detailed investigations quantifying issues such as linearity and robustness against instrument drift are performed. PMID:25968772

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

    SciTech Connect

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

    2014-01-15

    Using a surface piezoresistor diffusion method and front-side only micromachining process, a planar piezoresistive vibration sensor was successfully developed with a simple structure, lower processing cost and fewer packaging difficulties. The vibration sensor had a large sector proof mass attached to a narrow flexure. Optimization of the boron diffusion piezoresistor placed on the edge of the narrow flexure greatly improved the sensitivity. Planar vibration sensors were fabricated and measured in order to analyze the effects of the sensor dimensions on performance, including the values of flexure width and the included angle of the sector. Sensitivities of fabricated planar sensors of 0.09–0.46 mV/V/g were measured up to a test frequency of 60 Hz. The sensor functioned at low voltages (<3 V) and currents (<1 mA) with a high sensitivity and low drift. At low background noise levels, the sensor had performance comparable to a commercial device.

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

    PubMed

    Dumenko, V N

    1995-01-01

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

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

    PubMed

    Dushanova, Juliana; Philipova, Dolja; Nikolova, Gloria

    2010-06-15

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

  3. Low-frequency source for very long-range underwater communication.

    PubMed

    Mosca, Frédéric; Matte, Guillaume; Shimura, Takuya

    2013-01-01

    Very long-range underwater acoustic communication (UAC) is crucial for long cruising (>1000 km) autonomous underwater vehicles (AUVs). Very long-range UAC source for AUV must exhibit high electro-acoustic efficiency (>60%) and compactness. This paper describes the Janus-Hammer Bell (JHB) transducer that has been designed for this purpose and meets those requirements. The transducer works on the 450-550 Hz bandwidth and reaches source level above 200 dB (ref. 1 μPa at 1 m) with 1 kW excitation and full immersion capability. JHB source has been used for communication experiments by the Japanese institute for marine technology (Japan Agency for Marine-Earth Science and Technology) achieving a baud rate of 100 bits/s at 1000 km. PMID:23298019

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed Central

    Sato, Katsufumi; Watanuki, Yutaka; Takahashi, Akinori; Miller, Patrick J.O; Tanaka, Hideji; Kawabe, Ryo; Ponganis, Paul J; Handrich, Yves; Akamatsu, Tomonari; Watanabe, Yuuki; Mitani, Yoko; Costa, Daniel P; Bost, Charles-André; Aoki, Kagari; Amano, Masao; Trathan, Phil; Shapiro, Ari; Naito, Yasuhiko

    2006-01-01

    It is obvious, at least qualitatively, that small animals move their locomotory apparatus faster than large animals: small insects move their wings invisibly fast, while large birds flap their wings slowly. However, quantitative observations have been difficult to obtain from free-ranging swimming animals. We surveyed the swimming behaviour of animals ranging from 0.5 kg seabirds to 30 000 kg sperm whales using animal-borne accelerometers. Dominant stroke cycle frequencies of swimming specialist seabirds and marine mammals were proportional to mass−0.29 (R2=0.99, n=17 groups), while propulsive swimming speeds of 1–2 m s−1 were independent of body size. This scaling relationship, obtained from breath-hold divers expected to swim optimally to conserve oxygen, does not agree with recent theoretical predictions for optimal swimming. Seabirds that use their wings for both swimming and flying stroked at a lower frequency than other swimming specialists of the same size, suggesting a morphological trade-off with wing size and stroke frequency representing a compromise. In contrast, foot-propelled diving birds such as shags had similar stroke frequencies as other swimming specialists. These results suggest that muscle characteristics may constrain swimming during cruising travel, with convergence among diving specialists in the proportions and contraction rates of propulsive muscles. PMID:17476766

  6. Predicted and measured EMI shielding effectiveness of a metallic mesh coating on a sapphire window over a broad frequency range

    NASA Astrophysics Data System (ADS)

    Jacoby, Keith T.; Pieratt, Matthew W.; Halman, Jennifer I.; Ramsey, Keith A.

    2009-05-01

    Metallic mesh thin film coatings have been used for many years to provide electromagnetic interference (EMI) shielding on infrared windows and domes. The level of EMI shielding effectiveness (SE) of metallic mesh coatings when used in a high frequency application is understood and characterized. Conversely, the level of SE of these metallic mesh coatings when used in a low frequency application has been called into question. In a recent study, we applied an appropriately designed metallic mesh coating to a sapphire window, mounted that window in a fixture, and tested the SE of the window assembly over a frequency range that envelopes the various military platforms covered in MIL-STD-461 (10 kHz to 18 GHz) for a radiated emissions test. The test plan was devised in such a way as to independently assess the individual contributions of the aperture, the mounting, and the metallic mesh coating to the total shielding. The results of our testing will be described in this paper. Additionally, the test results will be compared to the predicted SE for both the aperture and the metallic mesh coated window in order to validate the predictive model. Finally, an assessment of the appropriateness of the use of metallic mesh coatings for EMI shielding in a low and/or broad range frequency application will be made.

  7. A MEMS Interface IC With Low-Power and Wide-Range Frequency-to-Voltage Converter for Biomedical Applications.

    PubMed

    Arefin, Md Shamsul; Redouté, Jean-Michel; Yuce, Mehmet Rasit

    2016-04-01

    This paper presents an interface circuit for capacitive and inductive MEMS biosensors using an oscillator and a charge pump based frequency-to-voltage converter. Frequency modulation using a differential crossed coupled oscillator is adopted to sense capacitive and inductive changes. The frequency-to-voltage converter is designed with a negative feedback system and external controlling parameters to adjust the sensitivity, dynamic range, and nominal point for the measurement. The sensitivity of the frequency-to-voltage converter is from 13.28 to 35.96 mV/MHz depending on external voltage and charging current. The sensitivity ranges of the capacitive and inductive interface circuit are 17.08 to 54.4 mV/pF and 32.11 to 82.88 mV/mH, respectively. A capacitive MEMS based pH sensor is also connected with the interface circuit to measure the high acidic gastric acid throughout the digestive tract. The sensitivity for pH from 1 to 3 is 191.4 mV/pH with 550 μV(pp) noise. The readout circuit is designed and fabricated using the UMC 0.18 μm CMOS technology. It occupies an area of 0.18 mm (2) and consumes 11.8 mW. PMID:26954843

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

    NASA Astrophysics Data System (ADS)

    Bergeault, Eric

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

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

    NASA Astrophysics Data System (ADS)

    Wu, Jingbo; Mayorov, Alexander S.; Wood, Christopher D.; Mistry, Divyang; Li, Lianhe; Muchenje, Wilson; Rosamond, Mark C.; Chen, Li; Linfield, Edmund H.; Davies, A. Giles; Cunningham, John E.

    2015-10-01

    Terahertz frequency time-domain spectroscopy employing free-space radiation has frequently been used to probe the elementary excitations of low-dimensional systems. The diffraction limit, however, prevents its use for the in-plane study of individual laterally-defined nanostructures. Here, we demonstrate a planar terahertz frequency plasmonic circuit in which photoconductive material is monolithically integrated with a two-dimensional electron system. Plasmons with a broad spectral range (up to ~ 400 GHz) are excited by injecting picosecond-duration pulses, generated and detected by a photoconductive semiconductor, into a high mobility two-dimensional electron system. Using voltage modulation of a Schottky gate overlying the two-dimensional electron system, we form a tuneable plasmonic cavity, and observe electrostatic manipulation of the plasmon resonances. Our technique offers a direct route to access the picosecond dynamics of confined electron transport in a broad range of lateral nanostructures.

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

    PubMed

    Wu, Jingbo; Mayorov, Alexander S; Wood, Christopher D; Mistry, Divyang; Li, Lianhe; Muchenje, Wilson; Rosamond, Mark C; Chen, Li; Linfield, Edmund H; Davies, A Giles; Cunningham, John E

    2015-01-01

    Terahertz frequency time-domain spectroscopy employing free-space radiation has frequently been used to probe the elementary excitations of low-dimensional systems. The diffraction limit, however, prevents its use for the in-plane study of individual laterally-defined nanostructures. Here, we demonstrate a planar terahertz frequency plasmonic circuit in which photoconductive material is monolithically integrated with a two-dimensional electron system. Plasmons with a broad spectral range (up to ~ 400 GHz) are excited by injecting picosecond-duration pulses, generated and detected by a photoconductive semiconductor, into a high mobility two-dimensional electron system. Using voltage modulation of a Schottky gate overlying the two-dimensional electron system, we form a tuneable plasmonic cavity, and observe electrostatic manipulation of the plasmon resonances. Our technique offers a direct route to access the picosecond dynamics of confined electron transport in a broad range of lateral nanostructures. PMID:26487263

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

    PubMed Central

    Wu, Jingbo; Mayorov, Alexander S.; Wood, Christopher D.; Mistry, Divyang; Li, Lianhe; Muchenje, Wilson; Rosamond, Mark C.; Chen, Li; Linfield, Edmund H.; Davies, A. Giles; Cunningham, John E.

    2015-01-01

    Terahertz frequency time-domain spectroscopy employing free-space radiation has frequently been used to probe the elementary excitations of low-dimensional systems. The diffraction limit, however, prevents its use for the in-plane study of individual laterally-defined nanostructures. Here, we demonstrate a planar terahertz frequency plasmonic circuit in which photoconductive material is monolithically integrated with a two-dimensional electron system. Plasmons with a broad spectral range (up to ~ 400 GHz) are excited by injecting picosecond-duration pulses, generated and detected by a photoconductive semiconductor, into a high mobility two-dimensional electron system. Using voltage modulation of a Schottky gate overlying the two-dimensional electron system, we form a tuneable plasmonic cavity, and observe electrostatic manipulation of the plasmon resonances. Our technique offers a direct route to access the picosecond dynamics of confined electron transport in a broad range of lateral nanostructures. PMID:26487263

  12. The mechanism of modulation of geoacoustic emission intensity by weak electromagnetic fields in the audio-frequency range

    NASA Astrophysics Data System (ADS)

    Gavrilov, V. A.

    2016-07-01

    We propose a physical mechanism explaining the mechanism of modulation of the geoacoustic emission intensity by an external electromagnetic field in the audio-frequency range, which was previously revealed as a result of borehole measurements at the Petropavlovsk-Kamchatskii geodynamic testing area. It was established that electric double layers (EDL) at the interface between solid and liquid phases in a fluidsaturated geological medium play a key role in the mechanism proposed.

  13. High-Power Electron Landau-Heating Experiments in the Lower Hybrid Frequency Range in a Tokamak Plasma

    NASA Astrophysics Data System (ADS)

    Porkolab, M.; Lloyd, B.; Takase, Y.; Bonoli, P.; Fiore, C.; Gandy, R.; Granetz, R.; Griffin, D.; Gwinn, D.; Lipschultz, B.; Marmar, E.; McCool, S.; Pachtman, A.; Pappas, D.; Parker, R.; Pribyl, P.; Rice, J.; Terry, J.; Texter, S.; Watterson, R.; Wolfe, S.

    1984-09-01

    The effectiveness of plasma heating by electron Landau interaction in the lower hybrid range of frequencies in tokamak plasmas is demonstrated. Upon injection of 850 kW of rf power at a density of n―e~=1.4×1014 cm-3, an electron temperature increase of 1.0 keV and an ion temperature increase of 0.8 keV was achieved. These results are compared with transport and ray-tracing code predictions.

  14. An experimental investigation of thermoacoustic lasers operating in audible frequency range

    NASA Astrophysics Data System (ADS)

    Kolhe, Sanket Anil

    Thermoacoustic lasers convert heat from a high-temperature heat source into acoustic power while rejecting waste heat to a low temperature sink. The working fluids involved can be air or noble gases which are nontoxic and environmentally benign. Simple in construction due to absence of moving parts, thermoacoustic lasers can be employed to achieve generation of electricity at individual homes, water-heating for domestic purposes, and to facilitate space heating and cooling. The possibility of utilizing waste heat or solar energy to run thermoacoustic devices makes them technically promising and economically viable to generate large quantities of acoustic energy. The research presented in this thesis deals with the effects of geometric parameters (stack position, stack length, tube length) associated with a thermoacoustic laser on the output sound wave. The effects of varying input power on acoustic output were also studied. Based on the experiments, optimum operating conditions were identified and qualitative and/or quantitative explanations were provided to justify our observations. It was observed that the maximum sound pressure level was generated for the laser with the stack positioned at a distance of quarter lengths of a resonator from the closed end. Higher sound pressure levels were recorded for the laser with longer stack lengths and longer resonator lengths. Efforts were also made to develop high-frequency thermoacoustic lasers.

  15. Occupational exposures to high frequency electromagnetic fields in the intermediate range ( >300 Hz-10 MHz).

    PubMed

    Floderus, Birgitta; Stenlund, Carin; Carlgren, Frank

    2002-12-01

    The aim of this study was to identify work situations with electromagnetic fields of 300 Hz-10 MHz and to characterize the occupational exposure. Work place investigations included descriptions of the work environment and physical measurements. We estimated electric (E) and magnetic (H) fields by spot measurements in air, by logged exposure data, and when possible, we recorded induced currents in limbs. The instruments used were Wandel and Golterman EFA-3, NARDA 8718, Holaday HI-3702. The exposure sources comprised five induction furnaces, seven induction heaters, one surface treatment equipment, four units of electronic article surveillance (EAS), and medical devices for surgery and muscle stimulation. The induction furnaces operated at 480 Hz-7 kHz, and the maximum values of logged data varied between 512-2,093 V/m (E field) and 10.5-87.3 A/m (H field). The induction heaters (3.8 kHz-1.25 MHz) also showed high maximum exposure values of both E and H fields. Three EAS units, an electromagnetic plate at a library, a luggage control unit, and an antitheft gate, showed E fields reaching 658-1,069 V/m. The H fields were comparatively lower, except for the antitheft gate (5 and 7.5 kHz) showing a maximum value of 27.2 A/m (recorded during repair). Induced currents of 5-13 mA were measured for the medical devices. The study improves the basis for an exposure assessment for epidemiological studies of long term effects of exposures to high frequency electromagnetic fields. PMID:12395411

  16. Low-frequency predictability of the Dynamical Extended-Range Forecast Experiment

    NASA Technical Reports Server (NTRS)

    Nogues-Peagle, Julia; Rodgers, Dennis A.; Mo, Kingtse C.

    1992-01-01

    The objective of the study was to analyze data from the Dynamical Extended-Range Forecast Experiment conducted from January 1986 to March 1987, and to evaluate differences between analysis and forecasts with emphasis on the tropical 30-50-day oscillation. The diagnostic toll used is the projection of analysis and forecast data onto the normal modes of a primitive equation model. Examination of zonal-wind anomalies in the tropics shows that the forecast model predicts propagation of intraseasonal variations more accurately for slow propagation rates. The forecast amplitude is generally weaker than the analyzed amplitude. Analyzed kinetic energy and error fields exhibit similar horizontal scales for internal and external modes. External Rossby-mode components maximize in the extratropics while Rossby internal modes exhibit patterns that extend over the entire globe.

  17. A Constant Energy-Per-Cycle Ring Oscillator Over a Wide Frequency Range for Wireless Sensor Nodes

    PubMed Central

    Lee, Inhee; Sylvester, Dennis; Blaauw, David

    2016-01-01

    This paper presents an energy-efficient oscillator for wireless sensor nodes (WSNs). It avoids short-circuit current by minimizing the time spent in the input voltage range from Vthn to [Vdd − |Vthp|]. A current-feeding scheme with gate voltage control enables the oscillator to operate over a wide frequency range. A test chip is fabricated in a 0.18 μm CMOS process. The measurements show that the proposed oscillator achieves a constant energy-per-cycle (EpC) of 0.8 pJ/cycle over the 21–60 MHz frequency range and is more efficient than a conventional current-starved ring oscillator (CSRO) below 300 kHz at 1.8 V supply voltage. As an application example, the proposed oscillator is implemented in a switched-capacitor DC–DC converter. The converter is 11%–56% more efficient for load power values ranging from 583 pW to 2.9 nW than a converter using a conventional CSRO. PMID:27546899

  18. Excitation of the surface flute waves in electron cyclotron frequency range by internal rotating electron beam in a coaxial waveguide

    NASA Astrophysics Data System (ADS)

    Blednov, O.; Girka, I.; Girka, V.; Pavlenko, I.; Sydora, R.

    2014-12-01

    The initial stage of interaction between a gyrating beam of electrons, which move along Larmor orbits in a narrow gap between a cylindrical plasma layer and an internal screen of a metal coaxial waveguide and electromagnetic eigen waves, is studied theoretically. These waves are extraordinary polarized ones; they propagate along the azimuthal angle across an axial external steady magnetic field in the electron cyclotron frequency range. The numerical analysis shows that the excitation process is stable enough in respect to changing plasma waveguide parameters. The wider the plasma layer, the broader the range of plasma waveguide parameters within which effective wave excitation takes place. The main influence on the excitation of these modes is performed by the applied axial magnetic field, namely: its increase leads to an increase of growth rate and a broadening of the range of the waveguide parameters within which wave excitation is effective.

  19. A reconfigurable multi-mode multi-band transmitter with integrated frequency synthesizer for short-range wireless communication

    NASA Astrophysics Data System (ADS)

    Nan, Qi; Fan, Chen; Lingwei, Zhang; Xiaoman, Wang; Baoyong, Chi

    2013-09-01

    A reconfigurable multi-mode direct-conversion transmitter (TX) with integrated frequency synthesizer (FS) is presented. The TX as well as the FS is designed with a flexible architecture and frequency plan, which helps to support all the 433/868/915 MHz ISM band signals, with the reconfigurable bandwidth from 250 kHz to 2 MHz. In order to save power and chip area, only one 1.8 GHz VCO is adopted to cover the whole frequency range. All the operation modes can be regulated in real time by configuring the integrated register-bank through an SPI interface. Implemented in 180 nm CMOS, the FS achieves a frequency coverage of 320-460 MHz and 620-920 MHz. The lowest phase noise can be -107 dBc/Hz at a 100 kHz offset and -126 dBc/Hz at a 1 MHz offset. The transmitter features a + 10.2 dBm peak output power with a +9.5 dBm 1-dB-compression point and 250 kHz/500 kHz/1 MHz/2 MHz reconfigurable signal bandwidth.

  20. Temperature and frequency characteristics of low-loss MnZn ferrite in a wide temperature range

    NASA Astrophysics Data System (ADS)

    Sun, Ke; Lan, Zhongwen; Yu, Zhong; Xu, Zhiyong; Jiang, Xiaona; Wang, Zihui; Liu, Zhi; Luo, Ming

    2011-05-01

    A low-loss Mn0.7Zn0.24Fe2.06O4 ferrite has been prepared by a solid-state reaction method. The MnZn ferrite has a high initial permeability, μi (3097), a high saturation induction, Bs (526 mT), a high Curie temperature, Tc (220 °C), and a low core loss, PL (≤ 415 kW/m3) in a wide temperature (25-120 °C) and frequency (10-100 kHz) range. As the temperature increases, an initial decrease followed by a subsequent increase of hysteresis loss, Ph, and eddy current loss, Pe is observed. Both Ph and Pe increase with increasing frequency. When f ≥ 300 kHz, a residual loss, Pr, appears. Pe increases with increasing temperature and frequency. The temperature and frequency dependence of Ph can be explained by irreversible domain wall movements, Pe by the skin effect, and Pr by domain wall resonance, respectively.

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

    PubMed

    Lee, Ming-Chun; Marx, Christopher J

    2013-03-01

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

  2. Development of calibration techniques for ultrasonic hydrophone probes in the frequency range from 1 to 100 MHz

    PubMed Central

    Umchid, S.; Gopinath, R.; Srinivasan, K.; Lewin, P. A.; Daryoush, A. S.; Bansal, L.; El-Sherif, M.

    2009-01-01

    The primary objective of this work was to develop and optimize the calibration techniques for ultrasonic hydrophone probes used in acoustic field measurements up to 100 MHz. A dependable, 100 MHz calibration method was necessary to examine the behavior of a sub-millimeter spatial resolution fiber optic (FO) sensor and assess the need for such a sensor as an alternative tool for high frequency characterization of ultrasound fields. Also, it was of interest to investigate the feasibility of using FO probes in high intensity fields such as those employed in HIFU (High Intensity Focused Ultrasound) applications. In addition to the development and validation of a novel, 100 MHz calibration technique the innovative elements of this research include implementation and testing of a prototype FO sensor with an active diameter of about 10 μm that exhibits uniform sensitivity over the considered frequency range and does not require any spatial averaging corrections up to about 75 MHz. The results of the calibration measurements are presented and it is shown that the optimized calibration technique allows the sensitivity of the hydrophone probes to be determined as a virtually continuous function of frequency and is also well suited to verify the uniformity of the FO sensor frequency response. As anticipated, the overall uncertainty of the calibration was dependent on frequency and determined to be about ±12% (±1 dB) up to 40 MHz, ±20% (±1.5 dB) from 40 to 60 MHz and ±25% (±2 dB) from 60 to 100 MHz. The outcome of this research indicates that once fully developed and calibrated, the combined acousto-optic system will constitute a universal reference tool in the wide, 100 MHz bandwidth. PMID:19110289

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

    NASA Astrophysics Data System (ADS)

    Ege, Kerem; Boutillon, Xavier; Rébillat, Marc

    2013-03-01

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

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

    NASA Technical Reports Server (NTRS)

    Stutzman, Warren L.

    1989-01-01

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

  5. Numerical simulation of the electromagnetic fields excited by loop antennas in plasma in the whistler frequency range

    SciTech Connect

    Koldanov, V. A.; Korobkov, S. V.; Gushchin, M. E.; Kostrov, A. V.

    2011-08-15

    The electromagnetic fields excited by circular loop antennas in a magnetized plasma in the whistler frequency range are simulated by the finite-difference time-domain method. The spatial structure of quasi-monochromatic fields excited in the near- and far-field zones by an antenna with a harmonic current, as well as the dynamics of the electromagnetic field excited by an antenna with a current in the form of a single video pulse, is studied. Simulations performed for a uniform plasma and uniform ambient magnetic field agree well with the results of theoretical analysis and model laboratory experiments performed on large-scale plasma devices.

  6. Negative permittivity and permeability spectra of Cu/yttrium iron garnet hybrid granular composite materials in the microwave frequency range

    SciTech Connect

    Tsutaoka, Takanori Fukuyama, Koki; Kinoshita, Hideaki; Kasagi, Teruhiro; Yamamoto, Shinichiro; Hatakeyama, Kenichi

    2013-12-23

    The relative complex permittivity and permeability spectra of the coagulated copper and yttrium iron garnet (Cu/YIG) hybrid granular composite materials have been studied in the microwave range. The insulator to metal transition was observed at the percolation threshold of Cu particle content (φ{sub Cu} = 16.0 vol. %) in the electrical conductivity. In the percolation threshold, the low frequency plasmonic state caused by the metallic Cu particle networks was observed. The percolated Cu/YIG granular composites show simultaneous negative permittivity and permeability spectra under external magnetic fields.

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

    PubMed

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

    2009-04-01

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

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

    SciTech Connect

    Bonetti, Stefano Chen, Zhao; Kukreja, Roopali; Spoddig, Detlef; Schöppner, Christian; Meckenstock, Ralf; Ollefs, Katharina; Ney, Andreas; Pinto, Jude; Houanche, Richard; Frisch, Josef; Stöhr, Joachim; Dürr, Hermann A.; Ohldag, Hendrik

    2015-09-15

    We present a scanning transmission x-ray microscopy setup combined with a novel microwave synchronization scheme for studying high frequency magnetization dynamics at synchrotron light sources. The sensitivity necessary to detect small changes in the magnetization on short time scales and nanometer spatial dimensions is achieved by combining the excitation mechanism with single photon counting electronics that is locked to the synchrotron operation frequency. Our instrument is capable of creating direct images of dynamical phenomena in the 5-10 GHz range, with high spatial resolution. When used together with circularly polarized x-rays, the above capabilities can be combined to study magnetic phenomena at microwave frequencies, such as ferromagnetic resonance (FMR) and spin waves. We demonstrate the capabilities of our technique by presenting phase resolved images of a ∼6 GHz nanoscale spin wave generated by a spin torque oscillator, as well as the uniform ferromagnetic precession with ∼0.1° amplitude at ∼9 GHz in a micrometer-sized cobalt strip.

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

    NASA Astrophysics Data System (ADS)

    Bonetti, Stefano; Kukreja, Roopali; Chen, Zhao; Spoddig, Detlef; Ollefs, Katharina; Schöppner, Christian; Meckenstock, Ralf; Ney, Andreas; Pinto, Jude; Houanche, Richard; Frisch, Josef; Stöhr, Joachim; Dürr, Hermann A.; Ohldag, Hendrik

    2015-09-01

    We present a scanning transmission x-ray microscopy setup combined with a novel microwave synchronization scheme for studying high frequency magnetization dynamics at synchrotron light sources. The sensitivity necessary to detect small changes in the magnetization on short time scales and nanometer spatial dimensions is achieved by combining the excitation mechanism with single photon counting electronics that is locked to the synchrotron operation frequency. Our instrument is capable of creating direct images of dynamical phenomena in the 5-10 GHz range, with high spatial resolution. When used together with circularly polarized x-rays, the above capabilities can be combined to study magnetic phenomena at microwave frequencies, such as ferromagnetic resonance (FMR) and spin waves. We demonstrate the capabilities of our technique by presenting phase resolved images of a ˜6 GHz nanoscale spin wave generated by a spin torque oscillator, as well as the uniform ferromagnetic precession with ˜0.1° amplitude at ˜9 GHz in a micrometer-sized cobalt strip.

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

    PubMed

    Bonetti, Stefano; Kukreja, Roopali; Chen, Zhao; Spoddig, Detlef; Ollefs, Katharina; Schöppner, Christian; Meckenstock, Ralf; Ney, Andreas; Pinto, Jude; Houanche, Richard; Frisch, Josef; Stöhr, Joachim; Dürr, Hermann A; Ohldag, Hendrik

    2015-09-01

    We present a scanning transmission x-ray microscopy setup combined with a novel microwave synchronization scheme for studying high frequency magnetization dynamics at synchrotron light sources. The sensitivity necessary to detect small changes in the magnetization on short time scales and nanometer spatial dimensions is achieved by combining the excitation mechanism with single photon counting electronics that is locked to the synchrotron operation frequency. Our instrument is capable of creating direct images of dynamical phenomena in the 5-10 GHz range, with high spatial resolution. When used together with circularly polarized x-rays, the above capabilities can be combined to study magnetic phenomena at microwave frequencies, such as ferromagnetic resonance (FMR) and spin waves. We demonstrate the capabilities of our technique by presenting phase resolved images of a ∼6 GHz nanoscale spin wave generated by a spin torque oscillator, as well as the uniform ferromagnetic precession with ∼0.1° amplitude at ∼9 GHz in a micrometer-sized cobalt strip. PMID:26429444

  11. 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...

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

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

    SciTech Connect

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

    1996-08-01

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

  14. Intermediate frequency band digitized high dynamic range radiometer system for plasma diagnostics and real-time Tokamak control

    SciTech Connect

    Bongers, W. A.; Beveren, V. van; Westerhof, E.; Goede, A. P. H.; Krijger, B.; Berg, M. A. van den; Graswinckel, M. F.; Schueller, F. C.; Thoen, D. J.; Nuij, P. J. W. M.; Baar, M. R. de; Donne, A. J. H.; Hennen, B. A.; Kantor, M.

    2011-06-15

    An intermediate frequency (IF) band digitizing radiometer system in the 100-200 GHz frequency range has been developed for Tokamak diagnostics and control, and other fields of research which require a high flexibility in frequency resolution combined with a large bandwidth and the retrieval of the full wave information of the mm-wave signals under investigation. The system is based on directly digitizing the IF band after down conversion. The enabling technology consists of a fast multi-giga sample analog to digital converter that has recently become available. Field programmable gate arrays (FPGA) are implemented to accomplish versatile real-time data analysis. A prototype system has been developed and tested and its performance has been compared with conventional electron cyclotron emission (ECE) spectrometer systems. On the TEXTOR Tokamak a proof of principle shows that ECE, together with high power injected and scattered radiation, becomes amenable to measurement by this device. In particular, its capability to measure the phase of coherent signals in the spectrum offers important advantages in diagnostics and control. One case developed in detail employs the FPGA in real-time fast Fourier transform (FFT) and additional signal processing. The major benefit of such a FFT-based system is the real-time trade-off that can be made between frequency and time resolution. For ECE diagnostics this corresponds to a flexible spatial resolution in the plasma, with potential application in smart sensing of plasma instabilities such as the neoclassical tearing mode (NTM) and sawtooth instabilities. The flexible resolution would allow for the measurement of the full mode content of plasma instabilities contained within the system bandwidth.

  15. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection

    PubMed Central

    Sams, Aaron J.; Hawks, John; Keinan, Alon

    2015-01-01

    The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles. PMID:25467111

  16. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection.

    PubMed

    Sams, Aaron J; Hawks, John; Keinan, Alon

    2015-02-01

    The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles. PMID:25467111

  17. 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

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

    SciTech Connect

    Durodié, F. Dumortier, P.; Vrancken, M.; Messiaen, A.; Huygen, S.; Louche, F.; Van Schoor, M.; Vervier, M.; Winkler, K.

    2014-06-15

    ITER's Ion Cyclotron Range of Frequencies (ICRF) system [Lamalle et al., Fusion Eng. Des. 88, 517–520 (2013)] comprises two antenna launchers designed by CYCLE (a consortium of European associations listed in the author affiliations above) on behalf of ITER Organisation (IO), each inserted as a Port Plug (PP) into one of ITER's Vacuum Vessel (VV) ports. Each launcher is an array of 4 toroidal by 6 poloidal RF current straps specified to couple up to 20 MW in total to the plasma in the frequency range of 40 to 55 MHz but limited to a maximum system voltage of 45 kV and limits on RF electric fields depending on their location and direction with respect to, respectively, the torus vacuum and the toroidal magnetic field. A crucial aspect of coupling ICRF power to plasmas is the knowledge of the plasma density profiles in the Scrape-Off Layer (SOL) and the location of the RF current straps with respect to the SOL. The launcher layout and details were optimized and its performance estimated for a worst case SOL provided by the IO. The paper summarizes the estimated performance obtained within the operational parameter space specified by IO. Aspects of the RF grounding of the whole antenna PP to the VV port and the effect of the voids between the PP and the Blanket Shielding Modules (BSM) surrounding the antenna front are discussed. These blanket modules, whose dimensions are of the order of the ICRF wavelengths, together with the clearance gaps between them will constitute a corrugated structure which will interact with the electromagnetic waves launched by ICRF antennas. The conditions in which the grooves constituted by the clearance gaps between the blanket modules can become resonant are studied. Simple analytical models and numerical simulations show that mushroom type structures (with larger gaps at the back than at the front) can bring down the resonance frequencies, which could lead to large voltages in the gaps between the blanket modules and perturb the

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    ITER's Ion Cyclotron Range of Frequencies (ICRF) system [Lamalle et al., Fusion Eng. Des. 88, 517-520 (2013)] comprises two antenna launchers designed by CYCLE (a consortium of European associations listed in the author affiliations above) on behalf of ITER Organisation (IO), each inserted as a Port Plug (PP) into one of ITER's Vacuum Vessel (VV) ports. Each launcher is an array of 4 toroidal by 6 poloidal RF current straps specified to couple up to 20 MW in total to the plasma in the frequency range of 40 to 55 MHz but limited to a maximum system voltage of 45 kV and limits on RF electric fields depending on their location and direction with respect to, respectively, the torus vacuum and the toroidal magnetic field. A crucial aspect of coupling ICRF power to plasmas is the knowledge of the plasma density profiles in the Scrape-Off Layer (SOL) and the location of the RF current straps with respect to the SOL. The launcher layout and details were optimized and its performance estimated for a worst case SOL provided by the IO. The paper summarizes the estimated performance obtained within the operational parameter space specified by IO. Aspects of the RF grounding of the whole antenna PP to the VV port and the effect of the voids between the PP and the Blanket Shielding Modules (BSM) surrounding the antenna front are discussed. These blanket modules, whose dimensions are of the order of the ICRF wavelengths, together with the clearance gaps between them will constitute a corrugated structure which will interact with the electromagnetic waves launched by ICRF antennas. The conditions in which the grooves constituted by the clearance gaps between the blanket modules can become resonant are studied. Simple analytical models and numerical simulations show that mushroom type structures (with larger gaps at the back than at the front) can bring down the resonance frequencies, which could lead to large voltages in the gaps between the blanket modules and perturb the RF

  20. Differential effects of the APOE e4 allele on different domains of cognitive ability across the life-course.

    PubMed

    Marioni, Riccardo E; Campbell, Archie; Scotland, Generation; Hayward, Caroline; Porteous, David J; Deary, Ian J

    2016-06-01

    The association between APOE genotype and cognitive function suggests a positive role for the e2 allele and a negative role for the e4 allele. Both alleles have relatively low frequencies in the general population; hence, meta-analyses have been based on many small, heterogeneous studies. Here, we report the APOE-cognition associations in the largest single analysis to date. APOE status and cognitive ability were measured in 18 337 participants from the Generation Scotland study between 2006 and 2011. The age range was 18-94 years with a mean of 47 (SD 15). Four cognitive domains were assessed: verbal declarative memory (paragraph recall), processing speed (digit symbol substitution), verbal fluency (phonemic verbal fluency), and vocabulary (Mill Hill synonyms). Linear regression was used to assess the associations between APOE genetic status and cognition. Possession of the e4 allele was associated with lower scores on the measures of memory and processing speed in subjects aged >60. Across all age ranges, the e4 allele was linked to better verbal fluency scores. In younger subjects (≤60 years) the e4 allele was linked to higher vocabulary scores. There were no associations between the e2 allele and cognitive ability. As seen in previous meta-analyses, the APOE e4 allele is linked to poorer cognitive performance in the domains of memory and processing speed. By contrast, positive associations were seen between the e4 allele and measures of verbal fluency and vocabulary. All associations were relatively small and, in many cases, nominally significant despite the very large sample size. PMID:26395552

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    SciTech Connect

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

    1987-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Idehara, Toshitaka; Sabchevski, Svilen Petrov

    2012-07-01

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

  4. A wide-frequency range AC magnetometer to measure the specific absorption rate in nanoparticles for magnetic hyperthermia

    NASA Astrophysics Data System (ADS)

    Garaio, E.; Collantes, J. M.; Garcia, J. A.; Plazaola, F.; Mornet, S.; Couillaud, F.; Sandre, O.

    2014-11-01

    Measurement of specific absorption rate (SAR) of magnetic nanoparticles is crucial to assert their potential for magnetic hyperthermia. To perform this task, calorimetric methods are widely used. However, those methods are not very accurate and are difficult to standardize. In this paper, we present AC magnetometry results performed with a lab-made magnetometer that is able to obtain dynamic hysteresis-loops in the AC magnetic field frequency range from 50 kHz to 1 MHz and intensities up to 24 kA m-1. In this work, SAR values of maghemite nanoparticles dispersed in water are measured by AC magnetometry. The so-obtained values are compared with the SAR measured by calorimetric methods. Both measurements, by calorimetry and magnetometry, are in good agreement. Therefore, the presented AC magnetometer is a suitable way to obtain SAR values of magnetic nanoparticles.

  5. Wide-range and fast-convergence frequency offset estimator by BER-aiding for optical coherent receivers

    NASA Astrophysics Data System (ADS)

    Li, Zhiyu; Chen, Xue; Zhou, Weiqin; Zhu, Hai; Zhou, Xian; Zhang, Zhiguo

    2009-11-01

    Optical coherent detection with digital signal processing (DSP) attracts more and more interests owing to its high performance. Due to a free-running local oscillator (LO) on the receiver, a frequency offset (FO) to the optical carrier brings phase distortion with which data can not be correctly decided and decoded. All-digital feed-forward FO estimation algorithms for optical (D)QPSK coherent receivers, such as PADE, have advantages of low complexity and stable-running wide range of estimation. However, it only converges under the condition that the initialed FO is near enough to the real FO while possible FO with typical tunable lasers can be very large. In order to solve this problem, we present a novel FO estimation scheme by BER aiding. This scheme has been demonstrated to be accurate and effective to break the restriction of PADE by simulation.

  6. Computational dosimetry in embryos exposed to electromagnetic plane waves over the frequency range of 10 MHz-1.5 GHz.

    PubMed

    Kawai, Hiroki; Nagaoka, Tomoaki; Watanabe, Soichi; Saito, Kazuyuki; Takahashi, Masaharu; Ito, Koichi

    2010-01-01

    This paper presents calculated specific absorption rate (SAR) dosimetry in 4 and 8 week Japanese pregnant-woman models exposed to plane waves over the frequency range of 10 MHz-1.5 GHz. Two types of 2 mm spatial-resolution pregnant-woman models comprised a woman model, which is similar to the average-sized Japanese adult female in height and weight, with a cubic (4 week) embryo or spheroidal (8 week) one. The averaged SAR in the embryos exposed to vertically and horizontally polarized plane waves at four kinds of propagation directions are calculated from 10 MHz to 1.5 GHz. The results indicate that the maximum average SAR in the embryos exposed to plane waves is lower than 0.08 W kg(-1) when the incident power density is at the reference level of ICNIRP guideline for general public environment. PMID:20009180

  7. 750 nm 1.5 W frequency-doubled semiconductor disk laser with a 44 nm tuning range.

    PubMed

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

    2015-10-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1977-01-01

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

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

    SciTech Connect

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

    2014-08-10

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

  10. Shear Properties of Brain Tissue over a Frequency Range Relevant for Automotive Impact Situations: New Experimental Results.

    PubMed

    Nicolle, Stéphane; Lounis, Mourad; Willinger, Rémy

    2004-11-01

    This research aims at improving the definition of the shear linear material properties of brain tissue. A comparison between human and porcine white and gray matter samples was carried out over a new large frequency range associated with both traffic road and non-penetrating ballistic impacts. Oscillatory experiments were performed by using an original custom-designed oscillatory shear testing device. The findings revealed that no significant difference occured between the linear viscoelastic behavior of the porcine and the human brain tissue. On the average, the storage modulus (G') and the loss modulus (G") of the white matter increased respectively from 2.1 +/- 0.9 kPa to 16.8 +/- 2.0 kPa and from 0.4 +/- 0.2 kPa to 18.7 +/- 2.3 kPa between 0.1 and 6300 Hz at 37 degrees C. In addition, the gray and white matter behaviors seemed to be similar at small strains. The reliability of the data and the robustness of the experimental protocol were checked using a standard rheometer (Bohlin C-VOR 150). A good agreement was found between the data obtained in the frequency and time field. As a result, the linear relaxation modulus was determined over an extensive time range (from 10(-5) s to 300 s). In a first approach, the nonlinear behavior of brain tissue was studied using stress relaxation tests. Brain tissue showed significant shear softening for strains above 1% and the time relaxation behavior was independent of the applied strain. On this basis, a visco-hyperelastic model was proposed using the generalized Maxwell model and the Ogden hyperelastic model. These models respectively describe the linear relaxation modulus and the strain dependence of the shear stress. PMID:17230269

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    SciTech Connect

    Ono, Masayuki.

    1993-05-01

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

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

    SciTech Connect

    Ono, Masayuki

    1993-05-01

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

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

    SciTech Connect

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

    2014-07-01

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

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

    USGS Publications Warehouse

    Arthur, Steve M.; Schwartz, Charles C.

    1999-01-01

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

  16. Negative Selection on BRCA1 Susceptibility Alleles Sheds Light on the Population Genetics of Late-Onset Diseases and Aging Theory

    PubMed Central

    Pavard, Samuel; Metcalf, C. Jessica E.

    2007-01-01

    The magnitude of negative selection on alleles involved in age-specific mortality decreases with age. This is the foundation of the evolutionary theory of senescence. Because of this decrease in negative selection with age, and because of the absence of reproduction after menopause, alleles involved in women's late-onset diseases are generally considered evolutionarily neutral. Recently, genetic and epidemiological data on alleles involved in late onset-diseases have become available. It is therefore timely to estimate selection on these alleles. Here, we estimate selection on BRCA1 alleles leading to susceptibility to late-onset breast and ovarian cancer. For this, we integrate estimates of the risk of developing a cancer for BRCA1-carriers into population genetics frameworks, and calculate selection coefficients on BRCA1 alleles for different demographic scenarios varying across the extent of human demography. We then explore the magnitude of negative selection on alleles leading to a diverse range of risk patterns, to capture a variety of late-onset diseases. We show that BRCA1 alleles may have been under significant negative selection during human history. Although the mean age of onset of the disease is long after menopause, variance in age of onset means that there are always enough cases occurring before the end of reproductive life to compromise the selective value of women carrying a susceptibility allele in BRCA1. This seems to be the case for an extended range of risk of onset functions varying both in mean and variance. This finding may explain the distribution of BRCA1 alleles' frequency, and also why alleles for many late-onset diseases, like certain familial forms of cancer, coronary artery diseases and Alzheimer dementia, are typically recent and rare. Finally, we discuss why the two most popular evolutionary theories of aging, mutation accumulation and antagonistic pleiotropy, may underestimate the effect of selection on survival at old ages. PMID

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

    PubMed

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

    2016-05-15

    PbIn6Te10 is a new mid-infrared (IR) nonlinear crystal with a very wide transparency range from 1.7 up to 31 μm. Calculated phase-matching angles show possibility of frequency conversion throughout the transparency range. Sum frequency generation of multiline carbon monoxide (CO) laser and difference frequency generation when mixing CO and carbon dioxide laser radiation were experimentally studied. Laser-induced damage threshold and frequency conversion efficiency under multiline CO laser pumping were measured. PMID:27177010

  18. Effective conductivity and permittivity of unsaturated clayey materials in the frequency range 1 mHz to 1GHz: A unified model and its appications in hydrogeophysics

    NASA Astrophysics Data System (ADS)

    Revil, A.

    2012-12-01

    A model combining low frequency complex conductivity and high frequency permittivity is developed in the frequency range from 1 mHz to 1 GHz. The low frequency conductivity depends on the pore water conductivity and a surface conductivity term that is mostly controlled by the electrical diffuse layer, the outer component of the electrical double layer coating the surface of the clay minerals. The frequency dependence of the effective quadrature conductivity shows three domains. Below a critical frequency fd that depends on the dynamic pore throat size, the quadrature conductivity is frequency dependent. Between fd and a second critical frequency fp, the quadrature conductivity is generally well described by a plateau (there are however few exception to this rule showing a well-characterized peak but still with a relatively weak frequency dependence). The characteristic frequency fd controls the transition between double layer polarization and the effect of the high frequency permittivity of the material. The Maxwell-Wagner polarization is found to be relatively negligible. For a broad range of frequencies below 1 MHz, the effective permittivity exhibits a strong dependence with the cation exchange capacity and the specific surface area. At high frequency, above the critical frequency fd, the effective permittivity reaches a high-frequency asymptotic limit that is controlled by the two Archie's exponent m and n like the low-frequency electrical conductivity. The unified model is compared with various datasets from the literature and is able to explain fairly well a broad number of observations with a very small number of textural and electrochemical parameters. It canbe therefore used to interpret induced polarization, induction-based electromagnetic methods, GPR data, and seismoelectric measurements to characterize the vadose zone.

  19. A More Precise Empirical Formula for Estimating Normalized Fog Attenuation in the Millimeter-Wave Frequency Range 30 ~ 100 GHz

    NASA Astrophysics Data System (ADS)

    Mao, Xia; Liu, Yun-Long; Chen, Li-Jiang; Xue, Yu-Li

    2013-04-01

    At millimeter wavelengths, normalized fog attenuation (NFA) in units of (dB/km)/ (g/m3) is generally calculated by the Rayleigh approximation when working wavelengths are much larger than the average diameter of fog droplets. The calculations of the Rayleigh approximation are much less than those of Mie scattering theory, but still complex and heavy. To solve the above problem and facilitate the engineering applications of the Rayleigh approximation, a new empirical formula is discussed to estimate NFA in the frequency range 30 ~ 100 GHz and the fog common temperature range -8 ~ 20 °C. The simulation results of the new formula are compared with those got by other three empirical formulae: the Altshuler empirical formula, the Liebe empirical formula and the Zhao empirical formula. Maximal absolute value of the relative errors (MAVRE) and Pearson correlation coefficient (PCC) indicate the largest deviation of estimated results and the fitting performance of an empirical formula, respectively. Comparisons show that the MAVRE of the new formula is only 4.482 %, which is much smaller than those of the other three formulae. The mean value of the Pearson correlation coefficients (PCCs) of the proposed formula is 0.999943, larger than those of other methods. Additionally, relative error (RE) curves of the four empirical formulae are given at four certain temperatures -8 °C, 0 °C, 10 °C and 20 °C.

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

    NASA Astrophysics Data System (ADS)

    Ho, Kevin Ming-Jiang

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

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

    PubMed Central

    Yokoyama, Shozo; Nei, Masatoshi

    1979-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    Lock-in amplifier (LIA) has been proposed as a detection technique for optical sensors because it can measure low signal in high noise level. LIA uses synchronous method, so the input signal frequency is locked to a reference frequency that is used to carry out the measurements. Generally, input signal frequency of LIA used in optical sensors is determined by modulation frequency of optical signal. It is important to understand the noise characteristics of the trans-impedance amplifier (TIA) to determine the modulation frequency. The TIA has a frequency range in which noise is minimized by the capacitance of photo diode (PD) and the passive component of TIA feedback network. When the modulation frequency is determined in this range, it is possible to design a robust system to noise. In this paper, we propose a method for the determination of optical signal modulation frequency selection by using the noise characteristics of TIA. Frequency response of noise in TIA is measured by spectrum analyzer and minimum noise region is confirmed. The LIA and TIA circuit have been designed as a hybrid circuit. The optical sensor is modeled by the laser diode (LD) and photo diode (PD) and the modulation frequency was used as the input to the signal generator. The experiments were performed to compare the signal to noise ratio (SNR) of the minimum noise region and the others. The results clearly show that the SNR is enhanced in the minimum noise region of TIA.

  3. Free-Ranging Male Koalas Use Size-Related Variation in Formant Frequencies to Assess Rival Males

    PubMed Central

    Charlton, Benjamin D.; Whisson, Desley A.; Reby, David

    2013-01-01

    Although the use of formant frequencies in nonhuman animal vocal communication systems has received considerable recent interest, only a few studies have examined the importance of these acoustic cues to body size during intra-sexual competition between males. Here we used playback experiments to present free-ranging male koalas with re-synthesised bellow vocalisations in which the formants were shifted to simulate either a large or a small adult male. We found that male looking responses did not differ according to the size variant condition played back. In contrast, male koalas produced longer bellows and spent more time bellowing when they were presented with playbacks simulating larger rivals. In addition, males were significantly slower to respond to this class of playback stimuli than they were to bellows simulating small males. Our results indicate that male koalas invest more effort into their vocal responses when they are presented with bellows that have lower formants indicative of larger rivals, but also show that males are slower to engage in vocal exchanges with larger males that represent more dangerous rivals. By demonstrating that male koalas use formants to assess rivals during the breeding season we have provided evidence that male-male competition constitutes an important selection pressure for broadcasting and attending to size-related formant information in this species. Further empirical studies should investigate the extent to which the use of formants during intra-sexual competition is widespread throughout mammals. PMID:23922967

  4. Study of toroidal flow generation by ion cyclotron range of frequency minority heating in the Alcator C-Mod plasma

    NASA Astrophysics Data System (ADS)

    Murakami, S.; Itoh, K.; Zheng, L. J.; Van Dam, J. W.; Bonoli, P.; Rice, J. E.; Fiore, C. L.; Gao, C.; Fukuyama, A.

    2016-01-01

    The averaged toroidal flow of energetic minority ions during ICRF (ion cyclotron range of frequencies) heating is investigated in the Alcator C-Mod plasma by applying the GNET code, which can solve the drift kinetic equation with complicated orbits of accelerated energetic particles. It is found that a co-directional toroidal flow of the minority ions is generated in the region outside of the resonance location, and that the toroidal velocity reaches more than 40% of the central ion thermal velocity (Vtor ˜ 300 km/s with PICRF ˜ 2 MW). When we shift the resonance location to the outside of |r /a |˜0.5 , the toroidal flow immediately inside of the resonance location is reduced to 0 or changes to the opposite direction, and the toroidal velocity shear is enhanced at r/a ˜ 0.5. A radial diffusion equation for toroidal flow is solved by assuming a torque profile for the minority ion mean flow, and good agreements with experimental radial toroidal flow profiles are obtained. This suggests that the ICRF driven minority ion flow is related to the experimentally observed toroidal rotation during ICRF heating in the Alcator C-Mod plasma.

  5. Plasma waves in the range of the lower hybrid frequency - ISEE 1 and 2 observations at the earth's bow shock

    NASA Technical Reports Server (NTRS)

    Mellott, M. M.; Greenstadt, E. W.

    1988-01-01

    This report presents a characterization of plasma wave noise in the range of the lower hybrid frequency associated with 65 crossings of earth's bow shock observed by the ISEE 1 and 2 satellites. Wave growth generally becomes detectable at the upstream edge of the shock foot, increases at the upstream edge of the shock ramp, peaks within the ramp, and then quickly decays to steady downstream values. The upstream extent of the noise is on the same order as that of specularly reflected gyrating ions. Similar profiles were observed in subcritical and supercritical shocks, and no special behavior was associated with the first critical Mach number. Spectra in the foot and ramp were similar in shape, although the noise was 1 to 2 orders of magnitude more intense in the shock ramps than in the feet. Electric field intensities are positively correlated with solar wind speed and inversely related to electron beta and Mach number. Magnetic components are positively correlated with Mach number and beta. The results are generally consistent with suggestions that the noise consists of lower hybrid waves driven by reflected gyrating ions in the foot, and by additional instabilities, such as the cross-field current, in the shock ramp.

  6. Inferring the age of a fixed beneficial allele.

    PubMed

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

    2016-01-01

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

  7. Photonic approach for microwave frequency measurement with adjustable measurement range and resolution using birefringence effect in highly non-linear fiber.

    PubMed

    Feng, Danqi; Xie, Heng; Qian, Lifen; Bai, Qinhong; Sun, Junqiang

    2015-06-29

    We experimentally demonstrate a novel approach for microwave frequency measurement utilizing birefringence effect in the highly non-linear fiber (HNLF). A detailed theoretical analysis is presented to implement the adjustable measurement range and resolution. By stimulating a complementary polarization-domain interferometer pair in the HNLF, a mathematical expression that relates the microwave frequency and amplitude comparison function is developed. We carry out a proof-to-concept experiment. A frequency measurement range of 2.5-30 GHz with a measurement error within 0.5 GHz is achieved except 16-17.5 GHz. This method is all-optical and requires no high-speed electronic components. PMID:26191769

  8. Population genetics of the vitamin D binding protein (GC) subtypes in the Asian-Pacific area: description of new alleles at the GC locus.

    PubMed

    Kamboh, M I; Ranford, P R; Kirk, R L

    1984-01-01

    Isoelectric focussing (IEF) in thin layer polyacrylamide gels pH range 4-6.5 has been used to analyse the GC phenotypes of 4233 individuals from 28 different population groups in the Asian, Pacific, and Australian area. Because this technique reveals subtypes of the common GC*1 allele, there is almost a two-fold increase in the mean heterozygosity at the GC locus using IEF compared with conventional electrophoresis. The highest frequency (above 50%) of the GC*1S allele was encountered in Indian populations, reflecting genetic affinities with Europeans. By comparison, east and south east Asians are unique offing maximum values of the GC*1F allele (50%). With the exception of a few Pacific populations which show similar frequencies to east Asians, all other groups in the Pacific area, including Australia, have values of GC*1F similar to GC*1S ranging from 27% to 40%. The GC*2 frequency in most populations varies from 20% to 30%. However, some Polynesian groups have values up to 40% and Australian Aborigines less than 10%. Among other alleles, GC*1A1 is found to be widely distributed among Australian Aborigines and Melanesians and occurs sporadically in Polynesians, Micronesians, and in the Lesser Sunda Islands. Four new alleles, GC*1C24, GC*1C35 Aborigine, GC*1A21, and GC*1A22 are described. The gene frequency data at the GC locus has been used to calculate Nei genetic distances between the populations studied. PMID:6541632

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

    SciTech Connect

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

    1995-05-01

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

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

    PubMed

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

    2015-05-01

    Genotyping of polymorphic short tandem repeats (STRs) loci is widely used in forensic DNA analysis. STR loci eventually present tri-allelic pattern as a genotyping irregularity and, in that situation, the doubt about the tri-allele locus frequency calculation can reduce the analysis strength. In the TPOX human STR locus, tri-allelic genotypes have been reported with a widely varied frequency among human populations. We investigate whether there is a single extra allele (the third allele) in the TPOX tri-allelic pattern, what it is, and where it is, aiming to understand its genomic anatomy and to propose the knowledge of this TPOX extra allele from genetic profile, thus preserving the two standard TPOX alleles in forensic analyses. We looked for TPOX tri-allelic subjects in 75,113 Brazilian families. Considering only the parental generation (mother+father) we had 150,226 unrelated subjects evaluated. From this total, we found 88 unrelated subjects with tri-allelic pattern in the TPOX locus (0.06%; 88/150,226). Seventy three of these 88 subjects (73/88; 83%) had the Clayton's original Type 2 tri-allelic pattern (three peaks of even intensity). The remaining 17% (15/88) show a new Type 2 derived category with heterozygote peak imbalance (one double dose peak plus one regular sized peak). In this paper we present detailed data from 66 trios (mother+father+child) with true biological relationships. In 39 of these families (39/66; 59%) the extra TPOX allele was transmitted either from the mother or from the father to the child. Evidences indicated the allele 10 as the extra TPOX allele, and it is on the X chromosome. The present data, which support the previous Lane hypothesis, improve the knowledge about tri-allelic pattern of TPOX CODIS' locus allowing the use of TPOX profile in forensic analyses even when with tri-allelic pattern. This evaluation is now available for different forensic applications. PMID:25549886

  11. Ion-cyclotron range of frequencies in the scrape-off-layer: fine structure radial electric fields

    NASA Astrophysics Data System (ADS)

    Cziegler, I.; Terry, J. L.; Wukitch, S. J.; Garrett, M. L.; Lau, C.; Lin, Y.

    2012-10-01

    Gas-puff-imaging techniques are utilized to detect radial electric field structures in the scrape-off-layer (SOL) of the Alcator C-Mod tokamak via the observation of poloidal motion of advected fluctuations. When the diagnostic's field of view is magnetically connected to the ion-cyclotron range of frequencies (ICRF) active antennas, large (up to 8 km s-1) poloidal velocities are observed in a radial region encompassing both field lines terminating on and those passing in front of the antennas. The radial electric field switches sign indicating a peak in the potential profile corresponding to the transition from piercing to passing field lines. The electric field extends a few centimeters into the SOL and its local magnitude is of order Er ≈ 20-30 kV m-1. The corresponding plasma potentials scale as the square root of RF power; the poloidal structure is peaked when the field lines are connected to the top and bottom of the antenna. This structure is consistent with the presence of potential structures arising as a consequence of sheath rectification of the RF waves. The most striking result, however, is that the radial penetration λ⊥ of the potential structures is an order of magnitude larger than the basic theoretical expectation (λ⊥ ≈ 10δe, where δe is the skin depth). This substantial broadening is expected to have a strong impact on RF impurity physics. A (weak) power dependence observed in the width of the poloidal velocity features is explained as a competition between the RF induced and the background potential gradients.

  12. Face Recognition Is Affected by Similarity in Spatial Frequency Range to a Greater Degree Than Within-Category Object Recognition

    ERIC Educational Resources Information Center

    Collin, Charles A.; Liu, Chang Hong; Troje, Nikolaus F.; McMullen, Patricia A.; Chaudhuri, Avi

    2004-01-01

    Previous studies have suggested that face identification is more sensitive to variations in spatial frequency content than object recognition, but none have compared how sensitive the 2 processes are to variations in spatial frequency overlap (SFO). The authors tested face and object matching accuracy under varying SFO conditions. Their results…

  13. High-power free-electron maser with frequency multiplication operating in a shortwave part of the millimeter wave range

    NASA Astrophysics Data System (ADS)

    Bandurkin, I. V.; Kaminsky, A. K.; Perelstein, E. A.; Peskov, N. Yu.; Savilov, A. V.; Sedykh, S. N.

    2012-08-01

    The possibility of using frequency multiplication in order to obtain high-power short-wavelength radiation from a free-electron maser (FEM) with a Bragg resonator has been studied. Preliminary experiments with an LIU-3000 (JINR) linear induction accelerator demonstrate the operation of a frequency-multiplying FEM at megawatt power in the 6- and 4-mm wave bands on the second and third harmonic, respectively.

  14. Characterization and performance of a field aligned ion cyclotron range of frequency antenna in Alcator C-Mod

    SciTech Connect

    Wukitch, S. J.; Garrett, M. L.; Ochoukov, R.; Terry, J. L.; Hubbard, A.; Labombard, B.; Lau, C.; Lin, Y.; Lipschultz, B.; Miller, D.; Reinke, M. L.; Whyte, D.; Collaboration: Alcator C-Mod Team

    2013-05-15

    Ion cyclotron range of frequency (ICRF) heating is expected to provide auxiliary heating for ITER and future fusion reactors where high Z metallic plasma facing components (PFCs) are being considered. Impurity contamination linked to ICRF antenna operation remains a major challenge particularly for devices with high Z metallic PFCs. Here, we report on an experimental investigation to test whether a field aligned (FA) antenna can reduce impurity contamination and impurity sources. We compare the modification of the scrape of layer (SOL) plasma potential of the FA antenna to a conventional, toroidally aligned (TA) antenna, in order to explore the underlying physics governing impurity contamination linked to ICRF heating. The FA antenna is a 4-strap ICRF antenna where the current straps and antenna enclosure sides are perpendicular to the total magnetic field while the Faraday screen rods are parallel to the total magnetic field. In principle, alignment with respect to the total magnetic field minimizes integrated E|| (electric field along a magnetic field line) via symmetry. A finite element method RF antenna model coupled to a cold plasma model verifies that the integrated E|| should be reduced for all antenna phases. Monopole phasing in particular is expected to have the lowest integrated E||. Consistent with expectations, we observed that the impurity contamination and impurity source at the FA antenna are reduced compared to the TA antenna. In both L and H-mode discharges, the radiated power is 20%–30% lower for a FA-antenna heated discharge than a discharge heated with the TA-antennas. However, inconsistent with expectations, we observe RF induced plasma potentials (via gas-puff imaging and emissive probes to be nearly identical for FA and TA antennas when operated in dipole phasing). Moreover, the highest levels of RF-induced plasma potentials are observed using monopole phasing with the FA antenna. Thus, while impurity contamination and sources are indeed

  15. Characterization and performance of a field aligned ion cyclotron range of frequency antenna in Alcator C-Moda)

    NASA Astrophysics Data System (ADS)

    Wukitch, S. J.; Garrett, M. L.; Ochoukov, R.; Terry, J. L.; Hubbard, A.; Labombard, B.; Lau, C.; Lin, Y.; Lipschultz, B.; Miller, D.; Reinke, M. L.; Whyte, D.; Alcator C-Mod Team

    2013-05-01

    Ion cyclotron range of frequency (ICRF) heating is expected to provide auxiliary heating for ITER and future fusion reactors where high Z metallic plasma facing components (PFCs) are being considered. Impurity contamination linked to ICRF antenna operation remains a major challenge particularly for devices with high Z metallic PFCs. Here, we report on an experimental investigation to test whether a field aligned (FA) antenna can reduce impurity contamination and impurity sources. We compare the modification of the scrape of layer (SOL) plasma potential of the FA antenna to a conventional, toroidally aligned (TA) antenna, in order to explore the underlying physics governing impurity contamination linked to ICRF heating. The FA antenna is a 4-strap ICRF antenna where the current straps and antenna enclosure sides are perpendicular to the total magnetic field while the Faraday screen rods are parallel to the total magnetic field. In principle, alignment with respect to the total magnetic field minimizes integrated E|| (electric field along a magnetic field line) via symmetry. A finite element method RF antenna model coupled to a cold plasma model verifies that the integrated E|| should be reduced for all antenna phases. Monopole phasing in particular is expected to have the lowest integrated E||. Consistent with expectations, we observed that the impurity contamination and impurity source at the FA antenna are reduced compared to the TA antenna. In both L and H-mode discharges, the radiated power is 20%-30% lower for a FA-antenna heated discharge than a discharge heated with the TA-antennas. However, inconsistent with expectations, we observe RF induced plasma potentials (via gas-puff imaging and emissive probes to be nearly identical for FA and TA antennas when operated in dipole phasing). Moreover, the highest levels of RF-induced plasma potentials are observed using monopole phasing with the FA antenna. Thus, while impurity contamination and sources are indeed

  16. Detection of a strong rfi-threat in the BI NGO frequency range due to the new Chinese satellite navigation system COMPASS at 1207.14 MHz

    NASA Astrophysics Data System (ADS)

    Monstein, Chr.

    2013-06-01

    Currently, a simple in-sensitive but cheap receiving system (which was originally designed for solar observations) is configured to receive frequencies covering BINGO frequency range from 960 MHz up to 1260 MHz. During the day the antenna tracks the sun but in the night the 5m parabolic dish is pointing to the sky to a fixed position at azimuth 180° and elevation 80°.

  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. PMID:26368021

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

    PubMed

    Lessard, Sabin; Lahaie, Philippe

    2009-06-01

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

  19. Development of the arc attachment at HID lamp electrodes in the range from low to RF-frequencies

    NASA Astrophysics Data System (ADS)

    Reinelt, J.; Langenscheidt, O.; Westermeier, M.; Awakowicz, P.; Mentel, J.

    2008-07-01

    At cathodes of high intensity discharges two different modes of arc attachment are observed: a diffuse mode characterized by a low current density and a uniformly distributed high global temperature, and a spot mode with a high current density and a high local but low global surface temperature. For dc and low frequency operation an investigation of these different modes has already been presented. Different modes of arc attachment are shown in the case of RF operation (up to 1 MHz operation frequency) of the Bochum model lamp. Images of the arc attachment demonstrate that with increasing frequencies the occurrence of the spot mode is reduced. But it cannot be excluded that it arises accidentally at high frequencies. It is found that with increasing frequency the differences between the electrode tip temperature in the cathodic and the anodic half period are levelled and that the course of the electrode sheath voltage (ESV(t)) adjusts to the sinusoidal current waveform resulting in an increase in the average power input into the electrodes with proceeding adjustment. Moreover, it indicates a reshaping of the electrode boundary layers.

  20. High-resolution observation of field-aligned irregularities in the ionosphere using multi-frequency range imaging of VHF atmospheric radar

    NASA Astrophysics Data System (ADS)

    Chen, Jenn-Shyong; Furumoto, Jun-ichi; Su, Ching-Lun; Chu, Yen-Hsyang

    Field-aligned irregularity (FAI) in the ionosphere is a topic of interest to atmospheric radar community. In addition to the field-aligned characteristic, quasi-periodic (QP) appearance of FAI echoes has been observed frequently by very-high-frequency (VHF) atmospheric radar. The occurrence range of QP FAI echoes changes with time, and the slope of range versus time can be positive or negative, depending on occurrence time of the echoes. Several mechanisms responsible for the QP FAI echoes have been proposed, e.g., modulation in altitude by a passing atmospheric gravity wave, semidiurnal neutral-wind variation, and so on. Owing to the finite pulse length of radar in observation, the range resolution of measurement is limited within hundreds of meters. In view of this, the range imaging (RIM) using multiple frequencies has been employed to improve the range resolution of measurement. The multi-frequency technique transmits a set of slightly different frequencies sequentially during each radar pulse, and the radar returns at different transmitting frequencies are received, respectively. With adaptive retrieval algorithms for these radar returns, it is capable of resolving the echo structures at meter scale in the range direction. RIM has been employed in the lower atmosphere successfully. In this study, the performance of RIM for FAI was first carried out with the Middle and Upper atmosphere Radar (46 MHz; 34.85(°) N, 136.10(°) N; Japan) and the Chung-Li VHF radar (52 MHz; 24.9(°) N, 121.1(°) E; Taiwan). Some initial results of high-resolution FAI echoes within the range gate will be shown.

  1. Interaction of electromagnetic radiation in the 20–200 GHz frequency range with arrays of carbon nanotubes with ferromagnetic nanoparticles

    PubMed Central

    Atdayev, Agylych; Danilyuk, Alexander L

    2015-01-01

    Summary The interaction of electromagnetic radiation with a magnetic nanocomposite based on carbon nanotubes (CNT) is considered within the model of distributed random nanoparticles with a core–shell morphology. The approach is based on a system composed of a CNT conducting resistive matrix, ferromagnetic inductive nanoparticles and the capacitive interface between the CNT matrix and the nanoparticles, which form resonance resistive–inductive–capacitive circuits. It is shown that the influence of the resonant circuits leads to the emergence of specific resonances, namely peaks and valleys in the frequency dependence of the permeability of the nanocomposite, and in the frequency dependence of the reflection and transmission of electromagnetic radiation. PMID:25977874

  2. Metamaterial near-field sensor for deep-subwavelength thickness measurements and sensitive refractometry in the terahertz frequency range

    SciTech Connect

    Reinhard, Benjamin; Schmitt, Klemens M.; Neu, Jens; Wollrab, Viktoria; Beigang, Rene; Rahm, Marco

    2012-05-28

    We present a metamaterial-based terahertz (THz) sensor for thickness measurements of subwavelength-thin materials and refractometry of liquids and liquid mixtures. The sensor operates in reflection geometry and exploits the frequency shift of a sharp Fano resonance minimum in the presence of dielectric materials. We obtained a minimum thickness resolution of 12.5 nm (1/16 000 times the wavelength of the THz radiation) and a refractive index sensitivity of 0.43 THz per refractive index unit. We support the experimental results by an analytical model that describes the dependence of the resonance frequency on the sample material thickness and the refractive index.

  3. Are ‘Endurance’ Alleles ‘Survival’ Alleles? Insights from the ACTN3 R577X Polymorphism

    PubMed Central

    Fiuza-Luces, Carmen; Ruiz, Jonatan R.; Rodríguez-Romo, Gabriel; Santiago, Catalina; Gómez-Gallego, Félix; Yvert, Thomas; Cano-Nieto, Amalia; Garatachea, Nuria

    2011-01-01

    Exercise phenotypes have played a key role for ensuring survival over human evolution. We speculated that some genetic variants that influence exercise phenotypes could be associated with exceptional survival (i.e. reaching ≥100years of age). Owing to its effects on muscle structure/function, a potential candidate is the Arg(R)577Ter(X) polymorphism (rs1815739) in ACTN3, the structural gene encoding the skeletal muscle protein α-actinin-3. We compared the ACTN3 R577X genotype/allele frequencies between the following groups of ethnically-matched (Spanish) individuals: centenarians (cases, n = 64; 57 female; age range: 100–108 years), young healthy controls (n = 283, 67 females, 216 males; 21±2 years), and humans who are at the two end-points of exercise capacity phenotypes, i.e. muscle endurance (50 male professional road cyclists) and muscle power (63 male jumpers/sprinters). Although there were no differences in genotype/allele frequencies between centenarians (RR:28.8%; RX:47.5%; XX:23.7%), and controls (RR:31.8%; RX:49.8%; XX:18.4%) or endurance athletes (RR:28.0%; RX:46%; XX:26.0%), we observed a significantly higher frequency of the X allele (P = 0.019) and XX genotype (P = 0.011) in centenarians compared with power athletes (RR:47.6%; RX:36.5%;XX:15.9%). Notably, the frequency of the null XX (α-actinin-3 deficient) genotype in centenarians was the highest ever reported in non-athletic Caucasian populations. In conclusion, despite there were no significant differences with the younger, control population, overall the ACTN3 genotype of centenarians resembles that of world-class elite endurance athletes and differs from that of elite power athletes. Our preliminary data would suggest a certain ‘survival’ advantage brought about by α-actinin-3 deficiency and the ‘endurance’/oxidative muscle phenotype that is commonly associated with this condition. PMID:21407828

  4. Particle simulations of mode conversion between slow mode and fast mode in lower hybrid range of frequencies

    NASA Astrophysics Data System (ADS)

    Jia, Guozhang; Xiang, Nong; Wang, Xueyi; Huang, Yueheng; Lin, Yu

    2016-01-01

    The propagation and mode conversion of lower hybrid waves in an inhomogeneous plasma are investigated by using the nonlinear δf algorithm in a two-dimensional particle-in-cell simulation code based on the gyrokinetic electron and fully kinetic ion (GeFi) scheme [Lin et al., Plasma Phys. Controlled Fusion 47, 657 (2005)]. The characteristics of the simulated waves, such as wavelength, frequency, phase, and group velocities, agree well with the linear theoretical analysis. It is shown that a significant reflection component emerges in the conversion process between the slow mode and the fast mode when the scale length of the density variation is comparable to the local wavelength. The dependences of the reflection coefficient on the scale length of the density variation are compared with the results based on the linear full wave model for cold plasmas. It is indicated that the mode conversion for the waves with a frequency of 2.45 GHz (ω ˜ 3ωLH, where ωLH represents the lower hybrid resonance) and within Tokamak relevant amplitudes can be well described in the linear scheme. As the frequency decreases, the modification due to the nonlinear term becomes important. For the low-frequency waves (ω ˜ 1.3ωLH), the generations of the high harmonic modes and sidebands through nonlinear mode-mode coupling provide new power channels and thus could reduce the reflection significantly.

  5. Voltage tuning of the resonance frequency of electroactive polymer membranes over a range of more than 75%

    NASA Astrophysics Data System (ADS)

    Dubois, Philippe; Rosset, Samuel; Niklaus, Muhamed; Shea, Herbert

    2009-05-01

    We report on a novel technique to control the resonance frequency of polymer membranes, without additional external actuators. An electrostatic force is used to apply compressive stress to a dielectric electroactive polymers membrane, consisting of a 25 micron thick, 1 to 4 mm diameter, polydimethylsiloxane (PDMS) film bonded onto patterned silicon or Pyrex wafers. Both sides of the membranes are rendered conductive by low-energy metal ion implantation. Ion implantation is chosen because it stiffens the membrane much less than sputtering a film of similar thickness [1][2]. The initial resonance frequency of the membrane is given by its geometry, the Young's modulus and stress of the composite film. The technique presented here allows tuning the resonance frequency from this initial value down to zero (at the buckling threshold) by adding compressive stress due to a voltage difference applied to the electrodes on both sides of the membrane. We have measured a reduction of the first mode resonance frequency of up to 77% (limited by dielectric breakdown) for ion-implanted membranes [3]. The tuning is repeatable and allows for continuous variation. Excellent agreement was found between our measurements and an analytical model we developed based on the Rayleigh-Ritz theory.

  6. The Y-associated XY275 low allele is not restricted to indigenous African peoples.

    PubMed Central

    Spurdle, A; Ramsay, M; Jenkins, T

    1992-01-01

    The level of linkage disequilibrium between the XY275 MspI polymorphism and the X and Y boundaries was investigated in 21 different southern African populations. A full range of frequencies of the high allele was observed on the 1,013 X chromosomes studied, in keeping with published data. In previous studies fixation of the high allele on the Y chromosome was observed in all but two groups--a Pygmy and a Tsumkwe San population. However, in the present study of 673 Y chromosomes, the low allele was found to be associated with the Y chromosome in several different Bantu-speaking negroid groups, the Khoisan-speaking negroid Dama, the Khoisan, two groups of mixed ancestry, and the South African Asiatic-Indian population. The discovery of the low allele on Y chromosomes of caucasoid individuals suggests that more than one class of Y chromosome gave rise to the present-day non-African population. The data also fail to provide support for the theory that Africa is the site of origin of Homo sapiens, but they equally do not exclude it. Images Figure 2 PMID:1598910

  7. Distribution of HLA class I alleles differs in celiac disease patients according to age of onset.

    PubMed

    Vogelsang, Harald; Panzer, Simon; Mayr, Wolfgang R; Granditsch, Gerhard; Fischer, Gottfried F

    2003-03-01

    Celiac disease (CD) or gluten-sensitive enteropathy is strongly associated with HLA-DQ alleles; more than 95% of patients are DQB1*02. However, the uniform association with HLA-DQ alleles does not explain the clinical heterogeneity, especially the wide range in the age of onset of CD. We asked whether the age of onset of CD is also influenced by class I genes of the human MHC. We performed HLA typing in three groups of patients suffering from CD. The age of onset in the first group (N = 200) was before 15 years of age, in the second group (N = 62) between 15 and 40 years, in the third group (N = 59) after 40 years. We observed a statistically significant increase in the frequencies of HLA-B8 and Cw7 with increasing age of onset. In conclusion, we conclude that distinct alleles from the class I region of the human MHC might lead to late onset of CD. In particular, relatives of CD patients with the disease-prone HLA class I alleles HLA-B8 and Cw7 should be followed up carefully for late onset of CD. PMID:12757179

  8. [Genetic study of the Penta E locus and identification of rare alleles].

    PubMed

    Lai, Li; Shen, Xiaoli; Han, Lili; Chen, Dian; Hu, Jie

    2015-10-01

    OBJECTIVE To study the genetic polymorphisms of Penta E locus in Fujian Han population. METHODS Polymorphisms of the Penta E locus in 851 unrelated individuals were analyzed using polymerase chain reaction-short tandem repeat (PCR-STR). The mutation rate of rare alleles was analyzed in 494 paternity identification cases (in a total of 674 meiosis). RESULTS Twenty-six alleles were identified for the Penta E locus, with their frequencies ranging from 0.0006 to 0.1528. There were 7 rare alleles, among which Penta E-28.4 ([AAAGA]29) was identified for the first time. Genetic parameters of the Penta E locus in Fujian Han population were obtained, including PIC= 0.91, PE= 0.817, PD= 0.986, and mutation rate= 0.0015. CONCLUSION The Penta E locus is highly polymorphic and has a low mutation rate in Fujian Han population. It also has a good prospect in genetics applications. DNA sequencing is a good method for identifying rare alleles. PMID:26418985

  9. Nonlinear frequency up-conversion of femtosecond pulses from an erbium fibre laser to the range of 0.8 - 1 {mu}m in silica fibres

    SciTech Connect

    Anashkina, E A; Andrianov, A V; Kim, A V

    2013-03-31

    We consider different mechanisms of nonlinear frequency up-conversion of femtosecond pulses emitted by an erbium fibre system ({lambda} = 1.5 {mu}m) to the range of 0.8 - 1.2 {mu}m in nonlinear silica fibres. The generation efficiency and the centre frequencies of dispersive waves are found as functions of the parameters of the fibre and the input pulse. Simple analytical estimates are obtained for the spectral distribution of the intensity and the frequency shift of a wave packet in the region of normal dispersion during the emission of a high-order soliton under phase matching conditions. In the geometrical optics approximation the frequency shifts are estimated in the interaction of dispersive waves with solitons in various regimes. (extreme light fields and their applications)

  10. Validity of segmental multiple-frequency bioelectrical impedance analysis to estimate body composition of adults across a range of body mass indexes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objective: Compare estimates of body composition using segmental, multiple frequency bioelectrical impedance analysis (MF-BIA) with dual x-ray absorptiometry (DXA) in healthy adults across a range of body mass index (BMI). Methods: Percent body fat (%BF), fat-mass (FM), and fat-free mass (FFM) asses...

  11. Influence of temporal noise on the skin blood flow measurements performed by cooled thermal imaging camera: limit possibilities within each physiological frequency range

    NASA Astrophysics Data System (ADS)

    Sagaidachnyi, A. A.; Volkov, I. U.; Fomin, A. V.

    2016-04-01

    This paper describes limit possibilities of modern cooled thermal imaging cameras as a tool for estimation of blood flow oscillations at the surface of living body. Skin temperature oscillations, as we assumed, are a consequence of the blood flow oscillations. We considered the temperature sensitivity 0.01-0.02 °C as a typical for the most of modern cooled long wave thermal imaging cameras. Fourier filter used to investigate the temperature signal separately within endothelial, neurogenic, myogenic, respiratory and cardiac frequency ranges. The level of temporal noise has been estimated during measurements of no living body with stabilized temperature ~ 24°C. The level of temperature oscillations has been calculated for the group of healthy subjects within each frequency range. Thus, we were able to determine signal-to-noise ratio within frequency band [0.001, 1] Hz. As a result, we determine that skin temperature oscillations measured by thermal imaging camera with sensitivity 0.02°C have the upper frequency limit ~ 0.2 Hz. In other words, within the respiratory and cardiac frequency ranges of blood flow oscillations the noise level exceeds signal one, and temperature measurements at the skin surface are practically useless. The endothelial, neurogenic and myogenic components of the temperature oscillations contain ~98% of the total spectral power of the signal. We have plot the empirical extrapolated curve of sensitivity of thermal imaging camera vs. frequency of the temperature oscillations. The data analysis shows that measurements of skin temperature oscillations within respiratory and cardiac ranges require the temperature sensitivity at least ~ 0.01°C and 0.001°C, respectively.

  12. Excitation of electrostatic waves in the electron cyclotron frequency range during magnetic reconnection in laboratory overdense plasmas

    SciTech Connect

    Kuwahata, A.; Igami, H.; Kawamori, E.; Kogi, Y.; Inomoto, M.; Ono, Y.

    2014-10-15

    We report the observation of electromagnetic radiation at high harmonics of the electron cyclotron frequency that was considered to be converted from electrostatic waves called electron Bernstein waves (EBWs) during magnetic reconnection in laboratory overdense plasmas. The excitation of EBWs was attributed to the thermalization of electrons accelerated by the reconnection electric field around the X-point. The radiative process discussed here is an acceptable explanation for observed radio waves pulsation associated with major flares.

  13. Large separations or regular technical patterns? Could data sampling mimic the frequency range of pulsating Delta Scuti stars?

    NASA Astrophysics Data System (ADS)

    Paparo, Margit; Benko, Jozsef M.; Hareter, Markus; Guzik, Joyce A.

    2015-08-01

    Asteroseismology allows unique information on the inner structure of stars. The large separation between the consecutive radial orders and the small separation of the modes with different l values are well-known and useful parameters characterizing solar-type oscillations. The large separation was derived only for a few Delta Scuti stars which are pulsating in the non-asymptotic regime. Theoretical investigations do not predict a high level of regularity of the excited modes. We carried out a search for regularity in a sample of Delta Scuti stars observed by CoRoT (91 stars). Usually the Fourier Transform or the histogram of frequency differences were used. The echelle diagrams represent the regularity when it was found. As a preliminary step we isolated set(s) of frequencies with quasi-equal spacing. Surprisingly not only a single pattern but up to six patterns were found in most of the stars. The patterns are regularly shifted with respect to each other. The echelle diagrams helped to reduce the scatter of the spacing. The derived spacing supported the better interpretation of the FT diagrams. There is no doubt of the existence of regular patterns. The interpretation is questionable: do the Delta Scuti stars behave so regularly, or we are faced with a technical pattern that obscures the real frequency pattern of the low amplitude Delta Scuti pulsation?

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

    PubMed Central

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

    1998-01-01

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

  15. Note: Ultra-high frequency ultra-low dc power consumption HEMT amplifier for quantum measurements in millikelvin temperature range.

    PubMed

    Korolev, A M; Shnyrkov, V I; Shulga, V M

    2011-01-01

    We have presented theory and experimentally demonstrated an efficient method for drastically reducing the power consumption of the rf/microwave amplifiers based on HEMT in unsaturated dc regime. Conceptual one-stage 10 dB-gain amplifier showed submicrowatt level of the power consumption (0.95 μW at frequency of 0.5 GHz) when cooled down to 300 mK. Proposed technique has a great potential to design the readout amplifiers for ultra-deep-cooled cryoelectronic quantum devices. PMID:21280864

  16. A robust statistical method to detect null alleles in microsatellite and SNP datasets in both panmictic and inbred populations.

    PubMed

    Girard, Philippe

    2011-01-01

    Null alleles are common technical artifacts in genetic-based analysis. Powerful methods enabling their detection in either panmictic or inbred populations have been proposed. However, none of these methods appears unbiased in both types of mating systems, necessitating a priori knowledge of the inbreeding level of the population under study. To counter this problem, I propose to use the software FDist2 to detect the atypical fixation indices that characterize markers with null alleles. The rational behind this approach and the parameter settings are explained. The power of the method for various sample sizes, degrees of inbreeding and null allele frequencies is evaluated using simulated microsatellite and SNP datasets and then compared to two other null allele detection methods. The results clearly show the robustness of the method proposed here as well as its greater accuracy in both panmictic and inbred populations for both types of marker. By allowing a proper detection of null alleles for a wide range of mating systems and markers, this new method is particularly appealing for numerous genetic studies using co-dominant loci. PMID:21381434

  17. What Is a Recessive Allele?

    ERIC Educational Resources Information Center

    American Biology Teacher, 1991

    1991-01-01

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

  18. Loading and Asymmetry Measurements and Modeling for the National Spherical Torus Experiment Ion Cyclotron Range of Frequencies System

    SciTech Connect

    Swain, D.W.; Carter, M.D.; Wilson, J.R.; Ryan, P.M.; Wilgen, J.B.; Hosea, J.; Rosenberg, A.

    2003-06-15

    The ion cyclotron heating and current drive system on the National Spherical Torus Experiment (NSTX) has delivered over 3 MW reliably for pulse lengths over 100 ms with various phasings of the antennas. A circuit model of the system that includes the 12 coupled antennas and six radio-frequency sources has been developed that gives good agreement with vacuum measurements. When it is used to experimentally determine the S-matrix of the system under different plasma conditions, pronounced asymmetries in the off-diagonal values of the S-matrix are seen. The S-matrix in the presence of plasma has been calculated with the RANT3D code using measured edge density profiles in front of the antenna; these agree remarkably well with the measurements. The asymmetry is caused primarily by the large pitch angle of the magnetic field in front of the antenna, coupled with the gradients in the plasma edge.

  19. Loading and Asymmetry Measurements and Modeling for the National Spherical Torus Experiment Ion Cyclotron Range of Frequencies System

    SciTech Connect

    Swain, David W; Carter, Mark Dwain; Wilson, J. R.; Ryan, Philip Michael; Wilgen, John B; Hosea, J.; Rosenberg, A.

    2003-01-01

    The ion cyclotron heating and current drive system on the National Spherical Torus Experiment (NSTX) has delivered over 3 MW reliably for pulse lengths over 100 ms with various phasings of the antennas. A circuit model of the system that includes the 12 coupled antennas and six radio-frequency sources has been developed that gives good agreement with vacuum measurements. When it is used to experimentally determine the S-matrix of the system under different plasma conditions, pronounced asymmetries in the off-diagonal values of the S-matrix are seen. The S-matrix in the presence of plasma has been calculated with the RANT3D code using measured edge density profiles in front of the antenna; these agree remarkably well with the measurements. The asymmetry is caused primarily by the large pitch angle of the magnetic field in front of the antenna, coupled with the gradients in the plasma edge.

  20. Dielectric properties measurement method in the microwave frequencies range for non-polar/polar liquid mixtures characterization

    NASA Astrophysics Data System (ADS)

    Surducan, E.; Neamtu, C.; Ienciu, M.; Surducan, V.; Limare, A.; Fourel, L.

    2015-12-01

    We present a method based on dielectric properties measurements over a large spectrum of frequencies, in the microwave (MW) domain, in order to characterize a liquid mixture. The liquid mixtures consist of non-polar fluids (silicone oil, diesel fuel) and polar additives, in order to increase the specific MW absorption of the mixture for further MW power processing. We have measured the MW specific absorptions for mixtures of silicone oil with 20% and 30% (w/w) isopropanol. In both cases, the mixtures are sufficiently stable over time to allow further studies of thermal convection dynamics initiated by MW heating. For a mixture of diesel fuel with 10% (w/w) alkyl polyglycoside, the main observation was that its MW specific absorption varies over time after the mechanical mixing process.