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Sample records for allele frequencies observed

  1. 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

  2. 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.

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

    PubMed

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

    2015-01-01

    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

  4. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  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. 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

  18. 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

  19. 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

  20. 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

  1. 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)

  2. 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

  3. 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).

  4. 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

  5. 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

  6. 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

  7. 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...

  8. 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

  9. 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 ...

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

    PubMed Central

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

    2016-01-01

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

  11. 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

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

    PubMed Central

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

    1985-01-01

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

  13. 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

  14. 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

  15. 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

  16. 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

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

    PubMed Central

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

    2012-01-01

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

  18. 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

  19. 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

  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. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

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

    PubMed

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

    2014-04-01

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

  11. 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

  12. 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

  13. 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

  14. 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...

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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.

  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. 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

  9. 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

  10. 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

  11. Initial frequency of alleles for resistance to Bacillus thuringiensis toxins in field populations of Heliothis virescens

    PubMed Central

    Gould, F.; Anderson, A.; Jones, A.; Sumerford, D.; Heckel, D. G.; Lopez, J.; Micinski, S.; Leonard, R.; Laster, M.

    1997-01-01

    The risk of rapid pest adaptation to an insecticide is highly dependent on the initial frequency of resistance alleles in field populations. Because we have lacked empirical estimates of these frequencies, population–genetic models of resistance evolution have relied on a wide range of theoretical estimates. The recent commercialization of genetically engineered cotton that constitutively produces an insecticidal protein derived from the biocontrol agent, Bacillus thuringiensis (Bt) has raised concern that we lack data needed to quantify the risk of insect pests such as Heliothis virescens rapidly adapting to this ecologically valuable class of toxins. By individually mating over 2,000 male H. virescens moths collected in four states to females of a Bt toxin-resistant laboratory strain, and screening F1 and F2 offspring for tolerance of the toxic protein, we were able to directly estimate the field frequency of alleles for resistance as 1.5 × 10−3. This high initial frequency underscores the need for caution in deploying transgenic cotton to control insect pests. Our single-pair mating technique greatly increases the efficiency of detecting recessive resistance alleles. Because alleles that decrease target site sensitivity to Bt toxins and other insecticides are often recessive, this technique could be useful in estimating resistance allele frequencies in other insects exposed to transgenic insecticidal crops or conventional insecticides. PMID:11038613

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

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

    PubMed Central

    Field, Wesley; Hershberg, Ruth

    2015-01-01

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

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

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

    PubMed

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

    2016-02-13

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

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

    PubMed Central

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

    2016-01-01

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

  15. 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

  16. 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

  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. 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

  19. 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

  20. 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

  1. 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

  2. Variant Alleles, Triallelic Patterns, and Point Mutations Observed in Nuclear Short Tandem Repeat Typing of Populations in Bosnia and Serbia

    PubMed Central

    Huel, René L. M.; Bašić, Lara; Madacki-Todorović, Kamelija; Smajlović, Lejla; Eminović, Izet; Berbić, Irfan; Miloš, Ana; Parsons, Thomas J.

    2007-01-01

    Aim To present a compendium of off-ladder alleles and other genotyping irregularities relating to rare/unexpected population genetic variation, observed in a large short tandem repeat (STR) database from Bosnia and Serbia. Methods DNA was extracted from blood stain cards relating to reference samples from a population of 32 800 individuals from Bosnia and Serbia, and typed using Promega’s PowerPlex®16 STR kit. Results There were 31 distinct off-ladder alleles were observed in 10 of the 15 STR loci amplified from the PowerPlex®16 STR kit. Of these 31 alleles, 3 have not been previously reported. Furthermore, 16 instances of triallelic patterns were observed in 9 of the 15 loci. Primer binding site mismatches that affected amplification were observed in two loci, D5S818 and D8S1179. Conclusion Instances of deviations from manufacturer’s allelic ladders should be expected and caution taken to properly designate the correct alleles in large DNA databases. Particular care should be taken in kinship matching or paternity cases as incorrect designation of any of these deviations from allelic ladders could lead to false exclusions. PMID:17696304

  3. 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

  4. 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

  5. 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

  6. 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

  7. Low Frequency Interstellar Scattering and Pulsar Observations

    NASA Technical Reports Server (NTRS)

    Cordes, James M.

    1992-01-01

    Radio astronomy at frequencies from 2 to 30 MHz challenges time tested methods for extracting usable information from observations. One fundamental reason for this is that propagation effects due to the magnetoionic ionosphere, interplanetary medium, and interstellar matter (ISM) increase strongly with wavelength. The problems associated with interstellar scattering off of small scale irregularities in the electron density are addressed. What is known about interstellar scattering is summarized on the basis of high frequency observations, including scintillation and temporal broadening of pulsars and angular broadening of various galactic and extragalactic radio sources. Then those high frequency phenomena are addressed that are important or detectable at low frequencies. The radio sky becomes much simpler at low frequencies, most pulsars will not be seen as time varying sources, intensity variations will be quenched or will occur on time scales much longer than a human lifetime, and many sources will be angularly broadened and/or absorbed into the noise. Angular broadening measurements will help delineate the galactic distribution and power spectrum of small scale electron density irregularities.

  8. 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

  9. 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

  10. 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

  11. Genetic comparison of lake sturgeon populations: Differentiation based on allelic frequencies at seven microsatellite loci

    USGS Publications Warehouse

    McQuown, E.; Krueger, C.C.; Kincaid, H.L.; Gall, G.A.E.; May, B.

    2003-01-01

    The lake sturgeon (Acipenser fulvescens) has recently become a high priority for restoration management because of the near extinction of the species from many areas of North America. The identification of the level of population differentiation that naturally exists among lake sturgeon populations will be useful in the development of management plans to conserve and restore diversity, and in the choice of donor populations to use for re-introduction. Genetic variation among and within 210 lake sturgeon collected from seven locations (St. Lawrence River, Des Prairies River (tributary to the St. Lawrence River), Mattagami River (Hudson Bay drainage), Menominee River (Lake Michigan drainage), Wolf River (Lake Michigan drainage), Niagara River, and Lake Erie) was examined based on allelic variation at seven microsatellite loci (four disomic and three putative tetrasomic). High levels of variability were detected at these loci. Analyses revealed an average of 8.6 alleles per locus (range 5 to 12 alleles per locus) and heterozygosity values at the four disomic loci ranging from 0.46 to 0.66. Multivariate factor analysis of Nei's genetic distance values produced three distinct population groups that were organized by geography: 1) Mattagami (northern Quebec), 2) Menominee/ Wolf (Lake Michigan - Wisconsin), and 3) St. Lawrence/ Des Prairies/ Niagara/ Erie (lower Great Lakes). Differences based on G-tests summed over all loci occurred between all possible paired comparisons of the collections (P < 0.01). These analyses indicated that lake sturgeon populations are differentiated within the Great Lakes basin. Managers of this species will need to identify individual populations in their jurisdictions and provide separate consideration for their conservation and rehabilitation.

  12. [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

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

    PubMed

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

    2016-10-01

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

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

    PubMed Central

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

    2013-01-01

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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

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

    PubMed

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

    1999-12-01

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

  3. High-Frequency Observations of Blazars

    NASA Technical Reports Server (NTRS)

    Marscher, A. P.; Marchenko-Jorstad, S. G.; Mattox, J. R.; Wehrle, A. E.; Aller, M. F.

    2000-01-01

    We report on the results of high-frequency VLBA observations of 42 gamma-ray bright blazars monitored at 22 and 43 GHz between 1993.9 and 1997.6. In 1997 the observations included polarization-sensitive imaging. The cores of gamma-ray blazars are only weakly polarized, with EVPAs (electric-vector position angles) usually within 40 deg of the local direction of the jet. The EVPAs of the jet components are usually within 20 deg of the local jet direction. The apparent speeds of the gamma-ray bright blazars are considerably faster than in the general population of bright compact radio sources. Two X-ray flares (observed with RXTE) of the quasar PKS 1510-089 appear to be related to radio flares, but with the radio leading the X-ray variations by about 2 weeks. This can be explained either by synchrotron self-Compton emission in a component whose variations are limited by light travel time or by the Mirror Compton model.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Frequency requirements for active earth observation sensors

    NASA Technical Reports Server (NTRS)

    1977-01-01

    The foundation and rationale for the selection of microwave frequencies for active remote sensing usage and for subsequent use in determination of sharing criteria and allocation strategies for the WARC-79 are presented.

  14. 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

  15. 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

  16. 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

  17. 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

  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. Polarimetric Observations at Low Radio Frequencies

    NASA Astrophysics Data System (ADS)

    Farnes, J. S.

    2012-06-01

    Magnetic fields play a fundamental role in the evolution of astrophysical systems. These fields can be studied through wide-field spectropolarimetry, which allows for faint polarised signals to be detected at relatively low radio frequencies. An interferometric polarisation mode has recently become available at the Giant Metrewave Radio Telescope (GMRT). A detailed analysis of the GMRT's instrumental response is presented. The findings are used to create a polarisation pipeline, which in combination with rotation measure (RM) Synthesis is used for the detection of extended linearly polarised emission at 610 MHz. A number of compact sources are detected and their Faraday depth and polarisation fraction are reported. New holography observations of the GMRT's primary beam are presented. Instantaneous off-axis polarisation is substantial and scales with the Stokes I beam. The developed beam models are used to reduce direction-dependent instrumental polarisation, and the Stokes I beam is shown to deviate from circular symmetry. A new technique for electric vector polarisation angle calibration is developed that removes the need for known sources on the sky, eliminates ionospheric effects, and avoids a flaw in current methods which could erroneously yield multiple Faraday components for sources that are well-parameterised by a single RM. A sample of nine galaxies from two Southern Compact Groups are then presented, with constraints being placed on the polarised fraction, RM, spectral index, star formation rate, companion sources, and hydrodynamical state. One galaxy has a displaced peak of radio emission that is extended beyond the disk in comparison to the near-IR disk - suggesting the radio disturbance may be a consequence of ram pressure stripping. Linear polarisation is detected from the core of NGC 7552 at 610 MHz, while another three galaxies ESO 0353-G036, NGC 7590, and NGC 7599 are found to be unpolarised. An analysis of additional extended sources allows for an

  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. Pomology observations, morphometric analysis, ultrastructural study and allelic profiles of "olivastra Seggianese" endocarps from ancient olive trees (Olea europaea L.).

    PubMed

    Milanesi, Claudio; Sorbi, Andrea; Paolucci, Elisa; Antonucci, Francesca; Menesatti, Paolo; Costa, Corrado; Pallottino, Federico; Vignani, Rita; Cimato, Antonio; Ciacci, Andrea; Cresti, Mauro

    2011-01-01

    Preliminary studies of historical sources and remote sensing were used to identify ancient olive trees near archaeological sites and heritage buildings in the Orcia Valley (Siena, Italy). Distinctive characters were assessed by traditional pomological observation. Trees with similar characters were selected on the basis of the features of endocarps, the only structure that survives aerobic deterioration and conserves useful botanical information for centuries. Non-invasive morphometric analysis of endocarp size and shape established morphological variations in individuals of different populations. Plastid organization in the endocarp and location of DNA in the endocarp tegument were detected by morphological and ultrastructural observations using light and electron microscopy. Cytoplasmic markers with high polymorphism were used to test similarity of endocarp and leaf DNA within individuals and to confirm low variability and minimal divergence between individuals. The ancient trees studied showed the same allelic profiles and therefore belonged to a distinct cultivar. The traditional pomological descriptions of the trees, leaves and fruits, morphometric analysis of size, and shape elliptic Fourier analysis of endocarp outline, ultrastructural observations and allelic profiles of endocarp tegument delineated the general species-specific qualities of the cultivar "olivastra Seggianese" of the Orcia Valley. PMID:21262485

  3. 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.

  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. 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...

  7. 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

  8. 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

  9. 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

  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. 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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2003-05-01

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

  14. 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

  15. 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

  16. 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

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

    PubMed Central

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

    2016-01-01

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

  18. 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. 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

  20. Real-Time PCR Genotyping Assay for GM2 Gangliosidosis Variant 0 in Toy Poodles and the Mutant Allele Frequency in Japan

    PubMed Central

    RAHMAN, Mohammad Mahbubur; YABUKI, Akira; KOHYAMA, Moeko; MITANI, Sawane; MIZUKAMI, Keijiro; UDDIN, Mohammad Mejbah; CHANG, Hye-Sook; KUSHIDA, Kazuya; KISHIMOTO, Miori; YAMABE, Remi; YAMATO, Osamu

    2013-01-01

    ABSTRACT GM2 gangliosidosis variant 0 (Sandhoff disease, SD) is a fatal, progressive neurodegenerative lysosomal storage disease caused by mutations of the HEXB gene. In canine SD, a pathogenic mutation (c.283delG) of the canine HEXB gene has been identified in toy poodles. In the present study, a TaqMan probe-based real-time PCR genotyping assay was developed and evaluated for rapid and large-scale genotyping and screening for this mutation. Furthermore, a genotyping survey was carried out in a population of toy poodles in Japan to determine the current mutant allele frequency. The real-time PCR assay clearly showed all genotypes of canine SD. The assay was suitable for large-scale survey as well as diagnosis, because of its high throughput and rapidity. The genotyping survey demonstrated a carrier frequency of 0.2%, suggesting that the current mutant allele frequency is low in Japan. However, there may be population stratification in different places, because of the founder effect by some carriers. Therefore, this new assay will be useful for the prevention and control of SD in toy poodles. PMID:24161966

  1. 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

  2. Observed emotion frequency versus intensity as predictors of socioemotional maladjustment.

    PubMed

    Hernández, Maciel M; Eisenberg, Nancy; Valiente, Carlos; Spinrad, Tracy L; VanSchyndel, Sarah K; Diaz, Anjolii; Berger, Rebecca H; Silva, Kassondra M; Southworth, Jody; Piña, Armando A

    2015-12-01

    The purpose of this study was to assess whether observed emotional frequency (the proportion of instances an emotion was observed) and intensity (the strength of an emotion when it was observed) uniquely predicted kindergartners' (N = 301) internalizing and externalizing problems. Analyses were tested in a structural equation modeling (SEM) framework with data from multireporters (reports of problem behaviors from teachers and parents) and naturalistic observations of emotion in the fall semester. For observed positive emotion, both frequency and intensity negatively predicted parent- or teacher-reported internalizing symptoms. Anger frequency positively predicted parent- and teacher-reported externalizing symptoms, whereas anger intensity positively predicted parent- and teacher-reported externalizing and parent-reported internalizing symptoms. The findings support the importance of examining both aspects of emotion when predicting maladjustment. PMID:26214568

  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. 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

  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. Latitudinal variation of chorus frequency observed in the topside ionosphere

    NASA Astrophysics Data System (ADS)

    Ondoh, T.; Nakamura, Y.; Watanabe, S.; Murakami, T.

    1982-07-01

    Latitudinal variations of chorus band frequency have been obtained from frequency-time VLF spectrograms of relatively long ISIS passes received at Syowa station, Antarctica, in 1977 and 1978. The upper and lower limit frequencies of the dayside chorus decrease with L value, and their latitudinal variations roughly agree with a latitudinal variation of one half of the equatorial gyrofrequency. This result is consistent with the dayside magnetospheric chorus model in which the chorus generated near the equatorial magnetosphere propagates along the field lines in the ducted mode or inwards from the original field line in the nonducted model. Nightside choruses were observed in geomagnetically disturbed periods; thus the generation mechanism for the nightside chorus seems to be different from that of the dayside chorus. A new case was found in which the chorus band frequencies at latitudes beyond the plasmapause are higher than those at latitudes inside the plasmapause.

  8. Observation of frequency doubling in tantalum doped silica fibres

    NASA Technical Reports Server (NTRS)

    Driscoll, T. J.; Lawandy, N. M.; Killian, A.; Rienhart, L.; Morse, T. F.

    1991-01-01

    Second harmonic conversion efficients of 3 x 0,0001 in tantalum-doped silica fibers prepared by the seeding technique are reported. A series of experiments were conducted to characterize the frequency doubling in this fiber and to compare the results to the behavior observed in germanosilicate and rare earth-doped aluminosilicate fibers.

  9. The Behavior Observation Scale for Autism (BOS): Frequency Analyses.

    ERIC Educational Resources Information Center

    Freeman, B. J.; And Others

    Frequency data are reported from a research project aimed at developing the Behavior Observation Scale (BOS), an objective assessment tool for establishing the diagnosis of autism. The goals of the BOS are to differentiate autistic, normal, and mentally retarded children (ages 30 to 60 months) along objective symptom axes involving 67 behaviors.…

  10. Observations of High Frequency Harmonics of the Ionospheric Alfven Resonator

    NASA Astrophysics Data System (ADS)

    Mann, Ian; Usanova, Maria; Bortnik, Jacob; Milling, David; Kale, Andy; Shao, Leo; Miles, David; Rae, I. Jonathan

    We present observations of high frequency harmonics of the ionospheric Alfven Resonator (IAR). These are seen in the form of spectral resonance structures (SRS) recorded by a ground-based search coil magnetometer sampling at 100 samples/s at the Ministik Lake station at L=4.2 within the expanded CARISMA magnetometer array. Previous observational studies have indicated that such SRS are typically confined to frequencies <~5 Hz with only several SRS harmonics being observed. We report the first observations of clear and discrete SRS, which we believe are harmonics of the IAR, and which extend to around 20 Hz in at least 10-12 clear SRS harmonics. We additionally demonstrate the utility of the Bortnik et al. (2007) auto-detection algorithm, designed for Pc1 wavepackets, for characterising the properties of the IAR. Our results also indicate that the cavity supporting SRS in the IAR at this time must be structured to support and trap much higher frequency IAR harmonics than previously assumed. This impacts the potential importance of the IAR for magnetosphere-ionosphere coupling, especially in relation to the impacts of incident Alfven waves on the ionosphere including Alfvenic aurora. Our observations also highlight the potential value of IAR observations for diagnosing the structure of the topside ionosphere, not least using the observed structure of the SRS. These are the first mid-latitude observations demonstrating that the IAR can extend to frequencies beyond those of the lowest few harmonics of the Schumann resonances - significantly suggesting the possibility that the Schumann resonance modes and the IAR may be coupled. The in-situ structure of the IAR is also examined by combining satellite data with conjugate measurements from the ground, and the impacts of the IAR for magnetosphere-ionosphere-thermosphere coupling examined.

  11. 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

  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

    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

  13. 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

  14. Observations of frequency shift associated with schooling fish

    NASA Astrophysics Data System (ADS)

    Diachok, Orest

    2003-04-01

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

  15. 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

  16. 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

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

    PubMed

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

    1997-04-01

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

  18. Solar observations with a low frequency radio telescope

    NASA Astrophysics Data System (ADS)

    Myserlis, I.; Seiradakis, J.; Dogramatzidis, M.

    2012-01-01

    We have set up a low frequency radio monitoring station for solar bursts at the Observatory of the Aristotle University in Thessaloniki. The station consists of a dual dipole phased array, a radio receiver and a dedicated computer with the necessary software installed. The constructed radio receiver is based on NASA's Radio Jove project. It operates continuously, since July 2010, at 20.1 MHz (close to the long-wavelength ionospheric cut-off of the radio window) with a narrow bandwidth (~5 kHz). The system is properly calibrated, so that the recorded data are expressed in antenna temperature. Despite the high interference level of an urban region like Thessaloniki (strong broadcasting shortwave radio stations, periodic experimental signals, CBs, etc), we have detected several low frequency solar radio bursts and correlated them with solar flares, X-ray events and other low frequency solar observations. The received signal is monitored in ordinary ASCII format and as audio signal, in order to investigate and exclude man-made radio interference. In order to exclude narrow band interference and calculate the spectral indices of the observed events, a second monitoring station, working at 36 MHz, is under construction at the village of Nikiforos near the town of Drama, about 130 km away of Thessaloniki. Finally, we plan to construct a third monitoring station at 58 MHz, in Thessaloniki. This frequency was revealed to be relatively free of interference, after a thorough investigation of the region.

  19. 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

  20. Technologies for Low Frequency Radio Observations of the Cosmic Dawn

    NASA Technical Reports Server (NTRS)

    Jones, Dayton L.

    2014-01-01

    The Jet Propulsion Laboratory (JPL) is developing concepts and technologies for low frequency radio astronomy space missions aimed at observing highly redshifted neutral Hydrogen from the Dark Ages. This is the period of cosmic history between the recombination epoch when the microwave background radiation was produced and the re-ionization of the intergalactic medium by the first generation of stars (Cosmic Dawn). This period, at redshifts greater than about 20, is a critical epoch for the formation and evolution of large-scale structure in the universe. The 21-cm spectral line of Hydrogen provides the most promising method for directly studying the Dark Ages, but the corresponding frequencies at such large redshifts are only tens of MHz and thus require space-based observations to avoid terrestrial RFI and ionospheric absorption and refraction. This paper reports on the status of several low frequency technology development activities at JPL, including deployable bi-conical dipoles for a planned lunar-orbiting mission, and both rover-deployed and inflation-deployed long dipole antennas for use on the lunar surface.

  1. Natural frequency identification of smart washer by using adaptive observer

    NASA Astrophysics Data System (ADS)

    Ito, Hitoshi; Okugawa, Masayuki

    2014-04-01

    Bolted joints are used in many machines/structures and some of them have been loosened during long time use, and unluckily these bolt loosening may cause a great accident of machines/structures system. These bolted joint, especially in important places, are main object of maintenance inspection. Maintenance inspection with human- involvement is desired to be improved owing to time-consuming, labor-intensive and high-cost. By remote and full automation monitoring of the bolt loosening, constantly monitoring of bolted joint is achieved. In order to detect loosening of bolted joints without human-involvement, applying a structural health monitoring technique and smart structures/materials concept is the key objective. In this study, a new method of bolt loosening detection by adopting a smart washer has been proposed, and the basic detection principle was discussed with numerical analysis about frequency equation of the system, was confirmed experimentally. The smart washer used in this study is in cantilever type with piezoelectric material, which adds the washer the self-sensing and actuation function. The principle used to detect the loosening of the bolts is a method of a bolt loosening detection noted that the natural frequency of a smart washer system is decreasing by the change of the bolt tightening axial tension. The feature of this proposed method is achieving to identify the natural frequency at current condition on demand by adopting the self-sensing and actuation function and system identification algorithm for varying the natural frequency depending the bolt tightening axial tension. A novel bolt loosening detection method by adopting adaptive observer is proposed in this paper. The numerical simulations are performed to verify the possibility of the adaptive observer-based loosening detection. Improvement of the detection accuracy for a bolt loosening is confirmed by adopting initial parameter and variable adaptive gain by numerical simulation.

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  4. Observation of upper drift modes in radio frequency produced magnetized plasmas with frequency above ion cyclotron frequency

    NASA Astrophysics Data System (ADS)

    Ghosh, Abhijit; Saha, S. K.; Chowdhury, S.; Janaki, M. S.

    2015-12-01

    In a RF produced magnetized argon plasma expanding into a larger expansion chamber, electrostatic modes propagating azimuthally in the direction of the electron diamagnetic drift and frequency greater than the ion cyclotron frequency are observed. In the radial direction, the mode amplitude peaks at a location where the radial density gradient is maximum. The modes are detected at axial locations up to 16 cm away from the entrance aperture. For fixed values of the neutral pressure and magnetic field, the mode frequency is found to be independent of the location at which it is measured. The modes exhibit drift wave characteristics revealing a radial structure with the azimuthal mode number m = 1 at the lower radial locations (r ˜ 3.0 cm) while the m = 2 mode is located in the outer region. Theoretical modeling using a local dispersion relation based on the fluid equations predicts destabilization of the modes with frequency greater than the ion-cyclotron frequency by electron-neutral collisions and exhibiting other drift wave features.

  5. Observation of upper drift modes in radio frequency produced magnetized plasmas with frequency above ion cyclotron frequency

    SciTech Connect

    Ghosh, Abhijit; Saha, S. K.; Chowdhury, S.; Janaki, M. S.

    2015-12-15

    In a RF produced magnetized argon plasma expanding into a larger expansion chamber, electrostatic modes propagating azimuthally in the direction of the electron diamagnetic drift and frequency greater than the ion cyclotron frequency are observed. In the radial direction, the mode amplitude peaks at a location where the radial density gradient is maximum. The modes are detected at axial locations up to 16 cm away from the entrance aperture. For fixed values of the neutral pressure and magnetic field, the mode frequency is found to be independent of the location at which it is measured. The modes exhibit drift wave characteristics revealing a radial structure with the azimuthal mode number m = 1 at the lower radial locations (r ∼ 3.0 cm) while the m = 2 mode is located in the outer region. Theoretical modeling using a local dispersion relation based on the fluid equations predicts destabilization of the modes with frequency greater than the ion-cyclotron frequency by electron-neutral collisions and exhibiting other drift wave features.

  6. In situ observations of medium frequency auroral radio emissions

    NASA Astrophysics Data System (ADS)

    Broughton, M.; Labelle, J. W.; Pfaff, R. F.; Parrot, M.; Yan, X.; Burchill, J. K.

    2013-12-01

    The auroral ionosphere is a region rich with plasma waves that can be studied both in space and on the ground. These waves may mediate energy exchange between particle populations and provide information about the local plasma properties and boundaries. Auroral medium frequency (MF) burst is an impulsive radio emission observed at ground-level from 1.3-4.5 MHz that is associated with local substorm onset. There have been two recent reports of impulsive, broadband, MF waves at high latitudes. Burchill and Pfaff [2005] reported observations from the FAST satellite of impulsive, broadband, MF and low frequency (LF) radio waves. Using data from the DEMETER satellite, Parrot et al. [2009] surveyed MF waves caused by lightning. This study did show a high-latitude population of MF waves. We investigate whether the waves observed by these two satellites are related to auroral MF burst. Using FAST satellite burst mode electric field data from high-latitude (> 60 degrees magnetic), low-altitude (< 1000 km) intervals of moderate to large geomagnetic activity (Kp > 3) from 1996-2002, we have found forty-four examples of impulsive MF waves, all of which are associated with impulsive LF waves. Although MF burst and the waves observed by FAST have similar spectral signatures, they have different magnetic local time dependencies, which suggests that they may be unrelated. A study of MF waves observed at high latitude by DEMETER is ongoing. In situ observations of MF burst could provide crucial information about this heretofore unexplained natural radio emission.

  7. Access to Strain and Other Low Frequency Geophysical Observations

    NASA Astrophysics Data System (ADS)

    Prescott, W.; Hodgkinson, K.; Neuhauser, D.; Silverman, S.; Stites, N. P.; Zuzlewski, S.

    2001-12-01

    With National Earthquake Hazards Program (NEHRP) funding, the U.S. Geological Survey (USGS ) has supported various fault monitoring efforts. In addition to monitoring at seismic frequency bands, the USGS also has supported strain, creep, water level and other instrumental systems operating at "low frequency". Principal investigators include both USGS and academic scientists. The typical observation interval for these data sets is 10 minutes (0.00167 hz). Raw data from most of these instruments are now available at the Northern California Earthquake Data Center (NCEDC). NCEDC is a joint effort of the University of California, Berkeley and the USGS. Raw low frequency data at NCEDC are stored in the SEED format, a standard format adopted for seismic data. And the raw low frequency data can be accessed with seismic querying tools. In a companion effort, the USGS is improving access to processed versions of these data. The raw low frequency data are processed to remove obvious instrumental offsets and spurious outliers. In the case of dilatometer data, the effects of air pressure variations are also removed from the time series. The resulting processed time series are available as plots (most recent week, most recent month, most recent year, and complete time series) and as downloadable files in either a tabular file or an eXtensible Markup Language (XML) file. XML is a standard format containing markup "tags" to identify the fields. The XML file contains all of the information known about the sensors as well as the observations. For example, in addition to the date, time and value, the XML file may contain investigator name and contact information, latitude, longitude, elevation, instrument manufacturer, serial number, digitizer manufacturer, serial number, orientation, and scale factors. The tabular file is a simple space-delimited file containing just the date, time and observed value fields. The XML file is large, but compresses well. For 10 minutes samples, XML

  8. Observing frequency content time evolution of independent hippocampal signals.

    PubMed

    Tanskanen, Jarno M A; Mikkonen, Jarno E; Hyttinen, Jari A K; Penttonen, Markku

    2006-01-01

    In this paper, we propose a method for observing frequency contents of independent hippocampal signals in time. The method is based on calculating independent component analysis (ICA) on electrophysiological multielectrode field potential measurements (MFPMs) in a running window. We have previously proposed a method for observing independently operating neural populations, i.e., functional populations (FUPOs) from MFPMs and outlined the concept, which is elaborated upon and extended in this paper, in order to facilitate analysis of functioning of the target brain area. In this paper, the proposed method is demonstrated with an example with three concurrent hippocampal measurements from an anesthetized rat brain. The proposed method can be applied in analysis of any recordings of neural networks in which contributions from a number of neural populations (NPs) are simultaneously recorded via a number of measurement points (MPs), as well in vivo as in vitro. PMID:17945994

  9. Low frequency radio observations of coronal magnetic field

    NASA Astrophysics Data System (ADS)

    Ramesh, R.; Kathiravan, C.

    2012-07-01

    Magnetic fields play an important role in the dynamics as well as the formation of the structures in the solar corona. Despite its fundamental importance, only a few direct measurements of the coronal magnetic field are available. The existing direct estimates using optical/infrared and radio emissions are limited to the inner corona, i.e., r < 1.2 R , where R is the radius of the Sun. In the outer corona beyond r > 3 R , Faraday rotation observations are used to derive the magnetic field. But due to lack of observational techniques, measurements in the range 1.2 R < r > 3 R (middle corona) are not available until now. As the photosphere, chromosphere, and corona are coupled by the solar magnetic field, the magnetic field strength at these distances is generally obtained by mathematical extrapolation of the observed line-of-sight component of the photospheric magnetic field assuming a potential or force-free model. The Indian Institute of Astrophysics has recently commissioned a radio polarimeter (based on inteferometer techniques) for dedicated obervations of the polarized radio emission from the solar corona. The frequency range of observation is 120-30 MHz which corresponds to a radial distance range of about 1.2-1.8 R. Estimates of weak magnetic fields in the 'undisturbed' Sun (non-flaring sunspot active regions, coronal streamers, etc.) obtained from observations with the above instrument will be presented.

  10. 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

  11. 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

  12. New observations of the low frequency interplanetary radio emissions

    NASA Technical Reports Server (NTRS)

    Kurth, W. S.; Gurnett, D. A.

    1991-01-01

    Recent Voyager 1 observations reveal reoccurrences of the low frequency interplanetary radio emissions. Three of the new events are weak transient events which rise in frequency from the range of 2-2.5 kHz to about 3 kHz with drift rates of approximately 1.5 kHz/year. The first of the transient events begins in mid-1989 and the more recent pair of events both were first detected in late 1991. In addition, there is an apparent onset of a 2-kHz component of the emission beginning near day 70 of 1991. The new transient emissions are barely detectable on Voyager 1 and are below the threshold of detectability on Voyager 2, which is less sensitive than Voyager 1. The new activity provides new opportunities to test various theories of the triggering, generation, and propagation of the outer heliospheric radio emissions and may signal a response of the source of the radio emissions to the increased solar activity associated with the recent peak in the solar cycle.

  13. Multi-epoch Multi-frequency Observations of Double Pulsar using GMRT at lower radio frequencies

    NASA Astrophysics Data System (ADS)

    Joshi, Bhal Chandra

    The double pulsar system, J0737-3039, (Burgay et al. 2003; Lyne et al. 2004) with two radio pulsars in a tight edge-on mildly eccentric orbit with a significant advance of angle of periastron (orbital period Pb = 2.4 hr, orbital inclination angle i = 87.7 deg, eccentricity 0.09, ω = ˙ 17 deg) continues to display interesting and changing phenomenology. The timing observations and this phenomenology has been very useful to test theories of gravity (Kramer and Stairs 2009). We report on last seven years of monitoring of these pulsars at 325 and 235 MHz using GMRT and compare the variation in the phenomenology of the pulsars as a function of observation epoch with that at higher frequencies.

  14. Electromagnetic waves near the proton cyclotron frequency: Stereo observations

    SciTech Connect

    Jian, L. K.; Wei, H. Y.; Russell, C. T.; Luhmann, J. G.; Klecker, B.; Omidi, N.; Isenberg, P. A.; Goldstein, M. L.; Figueroa-Viñas, A.; Blanco-Cano, X.

    2014-05-10

    Transverse, near-circularly polarized, parallel-propagating electromagnetic waves around the proton cyclotron frequency were found sporadically in the solar wind throughout the inner heliosphere. They could play an important role in heating and accelerating the solar wind. These low-frequency waves (LFWs) are intermittent but often occur in prolonged bursts lasting over 10 minutes, named 'LFW storms'. Through a comprehensive survey of them from Solar Terrestrial Relations Observatory A using dynamic spectral wave analysis, we have identified 241 LFW storms in 2008, present 0.9% of the time. They are left-hand (LH) or right-hand (RH) polarized in the spacecraft frame with similar characteristics, probably due to Doppler shift of the same type of waves or waves of intrinsically different polarities. In rare cases, the opposite polarities are observed closely in time or even simultaneously. Having ruled out interplanetary coronal mass ejections, shocks, energetic particles, comets, planets, and interstellar ions as LFW sources, we discuss the remaining generation scenarios: LH ion cyclotron instability driven by greater perpendicular temperature than parallel temperature or by ring-beam distribution, and RH ion fire hose instability driven by inverse temperature anisotropy or by cool ion beams. The investigation of solar wind conditions is compromised by the bias of the one-dimensional Maxwellian fit used for plasma data calibration. However, the LFW storms are preferentially detected in rarefaction regions following fast winds and when the magnetic field is radial. This preference may be related to the ion cyclotron anisotropy instability in fast wind and the minimum in damping along the radial field.

  15. 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

  16. 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

  17. IRIS Arrays: Observing Wavefields at Multiple Scales and Frequencies

    NASA Astrophysics Data System (ADS)

    Sumy, D. F.; Woodward, R.; Frassetto, A.

    2014-12-01

    The Incorporated Research Institutions for Seismology (IRIS) provides instruments for creating and operating seismic arrays at a wide range of scales. As an example, for over thirty years the IRIS PASSCAL program has provided instruments to individual Principal Investigators to deploy arrays of all shapes and sizes on every continent. These arrays have ranged from just a few sensors to hundreds or even thousands of sensors, covering areas with dimensions of meters to thousands of kilometers. IRIS also operates arrays directly, such as the USArray Transportable Array (TA) as part of the EarthScope program. Since 2004, the TA has rolled across North America, at any given time spanning a swath of approximately 800 km by 2,500 km, and thus far sampling 2% of the Earth's surface. This achievement includes all of the lower-48 U.S., southernmost Canada, and now parts of Alaska. IRIS has also facilitated specialized arrays in polar environments and on the seafloor. In all cases, the data from these arrays are freely available to the scientific community. As the community of scientists who use IRIS facilities and data look to the future they have identified a clear need for new array capabilities. In particular, as part of its Wavefields Initiative, IRIS is exploring new technologies that can enable large, dense array deployments to record unaliased wavefields at a wide range of frequencies. Large-scale arrays might utilize multiple sensor technologies to best achieve observing objectives and optimize equipment and logistical costs. Improvements in packaging and power systems can provide equipment with reduced size, weight, and power that will reduce logistical constraints for large experiments, and can make a critical difference for deployments in harsh environments or other situations where rapid deployment is required. We will review the range of existing IRIS array capabilities with an overview of previous and current deployments and examples of data and results. We

  18. 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...

  19. Recommended Rest Frequencies for Observed Interstellar Molecular Microwave Transitions - 2002 Revision

    National Institute of Standards and Technology Data Gateway

    SRD 116 NIST Recommended Rest Frequencies for Observed Interstellar Molecular Microwave Transitions - 2002 Revision (Web, free access)   Critically evaluated transition frequencies for the molecular transitions detected in interstellar and circumstellar clouds are presented.

  20. 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

  1. Dual frequency observations of solar microwave bursts using the VLA

    NASA Technical Reports Server (NTRS)

    Shevgaonkar, R. K.; Kundu, M. R.

    1985-01-01

    Simultaneous VLA observations of microwave bursts at 6 and 2 cm in a solar active region are presented and discussed. Using the full-day synthesis, I and V maps of the active region are produced. The radiation mechanisms at these wavelengths are discussed and the upper and lower bounds on the magnetic field of the active region are derived. The magnetic fields in the microwave burst source are estimated from the brightness temperature and the degree of circular polarization. It is concluded that the 6 cm radiation originates from the bulk heated plasma, whereas the 2 cm radiation is due to the nonthermal particles generated in the energy-release process. The delay between the peaks of emission at the two wavelengths is interpreted using a dc electric field model of flares. Depending on the strength of the electric field and the density in the flaring region, delays in either sense can be observed.

  2. Low-frequency radio observations of poor clusters of galaxies

    NASA Astrophysics Data System (ADS)

    Hanisch, R. J.; White, R. A.

    1981-06-01

    Observations have been made at the Clark Lake Radio Observatory of 16 poor clusters of galaxies at 34.3 MHz. Four of the poor clusters were detected at flux densities greater than 20 Jy. The spectra of the four detected clusters are all rather steep. Two of the detected clusters, AWM 4 and AWM 5, are also known to be X-ray sources. The possibility that the X-ray-emitting gas is heated by Coulomb interactions with the relativistic electrons responsible for the radio emission is investigated, and it is found that the observed X-ray luminosities can be accounted for if the electron energy spectrum extends to very low energies (gamma approximately 1-10). Collective plasma effects may increase the heating efficiency and eliminate the need to extrapolate the electron energy spectrum to such low values.

  3. Low-frequency radio observations of poor clusters of galaxies

    NASA Technical Reports Server (NTRS)

    Hanisch, R. J.; White, R. A.

    1981-01-01

    Observations have been made at the Clark Lake Radio Observatory of 16 poor clusters of galaxies at 34.3 MHz. Four of the poor clusters were detected at flux densities greater than 20 Jy. The spectra of the four detected clusters are all rather steep. Two of the detected clusters, AWM 4 and AWM 5, are also known to be X-ray sources. The possibility that the X-ray-emitting gas is heated by Coulomb interactions with the relativistic electrons responsible for the radio emission is investigated, and it is found that the observed X-ray luminosities can be accounted for if the electron energy spectrum extends to very low energies (gamma approximately 1-10). Collective plasma effects may increase the heating efficiency and eliminate the need to extrapolate the electron energy spectrum to such low values.

  4. A resonance phenomenon observed in a swept frequency experiment on a mother-daughter ionospheric rocket

    NASA Technical Reports Server (NTRS)

    Folkestad, K.; Troim, J.

    1974-01-01

    The report presents observations obtained in a swept frequency experiment conducted in a mother-daughter rocket flight at auroral latitudes. The discussion is essentially restricted to the possible interpretation of the experimental signal structures noted at and in the vicinity of a resonance frequency where signal components apparently are generated by nonlinear mechanisms. Various resonance frequencies have been considered in attempts to identify this multichannel response frequency. It is concluded that of all the possibilities invoked, the best consistency is provided by identifying the frequency concerned with the cone resonance frequency demonstrated experimentally in the case of a laboratory plasma by Fisher and Gould (1971).

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

    PubMed

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

    2014-02-01

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

  6. In situ high-frequency observations of mycorrhizas.

    PubMed

    Allen, Michael F; Kitajima, Kuni

    2013-10-01

    Understanding the temporal variation of soil and root dynamics is a major step towards determining net carbon in ecosystems. We describe the installation and structure of an in situ soil observatory and sensing network consisting of an automated minirhizotron with associated soil and atmospheric sensors. Ectomycorrhizal hyphae were digitized daily during 2011 in a Mediterranean climate, high-elevation coniferous forest. Hyphal length was high, but stable during winter in moist and cold soil. As soil began to warm and dry, simultaneous mortality and production indicating turnover followed precipitation events. Mortality continued through the dry season, although some hyphae persisted through the extremes. With autumn monsoons, rapid hyphal re-growth occurred following each event. Relative hyphal length is dependent upon soil temperature and moisture. Soil respiration is related to the daily change in hyphal production, but not hyphal mortality. Continuous sensor and observation systems can provide more accurate assessments of soil carbon dynamics. PMID:23772913

  7. 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

  8. Coordinated observations using the world largest low-frequency radio telescopes and space misiions

    NASA Astrophysics Data System (ADS)

    Konovalenko, A. A.; Zarka, Ph.; Kolyadin, V. L.; Zakharenko, V. V.; Stepkin, S. V.; Panchenko, M.; Lecacheux, A.; Rucker, H. O.; Fischer, G.; Ulyanov, O. M.; Melnik, V. N.; Litvinenko, G. V.; Sidorchuk, M. A.; Bubnov, I. N.; Vasilyeva, Ya. Yu.; Bojko, A. I.; Shaposhnikov, V.; Mann, G.; Kalinichenko, N. N.; Falkovich, I. S.; Koval, A. A.; Mylostna, K.; Pylaev, O. S.; Shepelev, V. A.; Reznik, A. P.

    2013-09-01

    The positive possibilities of astrophysical objects studies(including the Solar system investigations) using coordinated observations with the largest existing and coming low frequency radio telescopes are shown. The observations of the Sun, Jupiter, Saturn, ant others with UTR-2, URAN, NDA radio telescopes, and WIND, Cassini and STEREO space missions at frequencies lower than 40 MHz have been carried out.

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

    PubMed

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

    2016-04-01

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

  10. 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

  11. Estimating allelic diversity generated by excision of different transposon types.

    PubMed

    Nordborg, M; Walbot, V

    1995-05-01

    Methods are presented for calculating the number and type of different DNA sequences generated by base excision and insertion events at a given site in a known DNA sequence. We calculate, for example, that excision of the Mu1 transposon from the bz1::Mu1 allele of maize should generate more than 500,000 unique alleles given the extent of base deletion (up to 34 bases removed) and base insertion (0-5 bases) observed thus far in sequenced excision alleles. Analysis of this universe of potential alleles can, for example, be used to predict the frequency of creation of stop codons or repair-generated duplications. In general, knowledge of the distribution of alleles can be used to evaluate models of both excision and repair by determining whether particular events occur more frequently than expected. Such quantitative analysis complements the qualitative description provided by the DNA sequence of individual events. Similar methods can be used to evaluate the outcome of other cases of DNA breakage and repair such as programmed V(D)J recombination in immunoglobin genes. PMID:24172918

  12. Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes

    PubMed Central

    2014-01-01

    criterion of superimposing between the FIS expected under clonality and the observed FIS, is effective when amplification difficulties occur in low to moderate frequencies (20-30%). PMID:25027508

  13. Theory and Observations of High Frequency Alfven Eigenmodes in Low Aspect Ratio Plasma

    SciTech Connect

    N.N. Gorelenkov; E. Fredrickson; E. Belova; C.Z. Cheng; D. Gates; S. Kaye; R. White

    2003-06-27

    New observations of sub-cyclotron frequency instability in low aspect ratio plasma in National Spherical Torus Experiments (NSTX) are reported. The frequencies of observed instabilities correlate with the characteristic Alfven velocity of the plasma. A theory of localized Compressional Alfven Eigenmodes (CAE) and Global shear Alfven Eigenmodes (GAE) in low aspect ratio plasma is presented to explain the observed high frequency instabilities. CAE's/GAE's are driven by the velocity space gradient of energetic super-Alfvenic beam ions via Doppler shifted cyclotron resonances. One of the main damping mechanisms of GAE's, the continuum damping, is treated perturbatively within the framework of ideal MHD. Properties of these cyclotron instabilities ions are presented.

  14. Low-frequency Observations of the Moon with the Murchison Widefield Array

    NASA Astrophysics Data System (ADS)

    McKinley, B.; Briggs, F.; Kaplan, D. L.; Greenhill, L. J.; Bernardi, G.; Bowman, J. D.; de Oliveira-Costa, A.; Tingay, S. J.; Gaensler, B. M.; Oberoi, D.; Johnston-Hollitt, M.; Arcus, W.; Barnes, D.; Bunton, J. D.; Cappallo, R. J.; Corey, B. E.; Deshpande, A.; deSouza, L.; Emrich, D.; Goeke, R.; Hazelton, B. J.; Herne, D.; Hewitt, J. N.; Kasper, J. C.; Kincaid, B. B.; Koenig, R.; Kratzenberg, E.; Lonsdale, C. J.; Lynch, M. J.; McWhirter, S. R.; Mitchell, D. A.; Morales, M. F.; Morgan, E.; Ord, S. M.; Pathikulangara, J.; Prabu, T.; Remillard, R. A.; Rogers, A. E. E.; Roshi, A.; Salah, J. E.; Sault, R. J.; Udaya Shankar, N.; Srivani, K. S.; Stevens, J.; Subrahmanyan, R.; Wayth, R. B.; Waterson, M.; Webster, R. L.; Whitney, A. R.; Williams, A.; Williams, C. L.; Wyithe, J. S. B.

    2013-01-01

    A new generation of low-frequency radio telescopes is seeking to observe the redshifted 21 cm signal from the epoch of reionization (EoR), requiring innovative methods of calibration and imaging to overcome the difficulties of wide-field low-frequency radio interferometry. Precise calibration will be required to separate the expected small EoR signal from the strong foreground emission at the frequencies of interest between 80 and 300 MHz. The Moon may be useful as a calibration source for detection of the EoR signature, as it should have a smooth and predictable thermal spectrum across the frequency band of interest. Initial observations of the Moon with the Murchison Widefield Array 32 tile prototype show that the Moon does exhibit a similar trend to that expected for a cool thermally emitting body in the observed frequency range, but that the spectrum is corrupted by reflected radio emission from Earth. In particular, there is an abrupt increase in the observed flux density of the Moon within the internationally recognized frequency modulated (FM) radio band. The observations have implications for future low-frequency surveys and EoR detection experiments that will need to take this reflected emission from the Moon into account. The results also allow us to estimate the equivalent isotropic power emitted by the Earth in the FM band and to determine how bright the Earth might appear at meter wavelengths to an observer beyond our own solar system.

  15. LOW-FREQUENCY OBSERVATIONS OF THE MOON WITH THE MURCHISON WIDEFIELD ARRAY

    SciTech Connect

    McKinley, B.; Briggs, F.; Kaplan, D. L.; Greenhill, L. J.; Bernardi, G.; De Oliveira-Costa, A.; Bowman, J. D.; Tingay, S. J.; Gaensler, B. M.; Oberoi, D.; Johnston-Hollitt, M.; Arcus, W.; Emrich, D.; Barnes, D.; Bunton, J. D.; Cappallo, R. J.; Corey, B. E.; Deshpande, A.; DeSouza, L.; Goeke, R.; and others

    2013-01-01

    A new generation of low-frequency radio telescopes is seeking to observe the redshifted 21 cm signal from the epoch of reionization (EoR), requiring innovative methods of calibration and imaging to overcome the difficulties of wide-field low-frequency radio interferometry. Precise calibration will be required to separate the expected small EoR signal from the strong foreground emission at the frequencies of interest between 80 and 300 MHz. The Moon may be useful as a calibration source for detection of the EoR signature, as it should have a smooth and predictable thermal spectrum across the frequency band of interest. Initial observations of the Moon with the Murchison Widefield Array 32 tile prototype show that the Moon does exhibit a similar trend to that expected for a cool thermally emitting body in the observed frequency range, but that the spectrum is corrupted by reflected radio emission from Earth. In particular, there is an abrupt increase in the observed flux density of the Moon within the internationally recognized frequency modulated (FM) radio band. The observations have implications for future low-frequency surveys and EoR detection experiments that will need to take this reflected emission from the Moon into account. The results also allow us to estimate the equivalent isotropic power emitted by the Earth in the FM band and to determine how bright the Earth might appear at meter wavelengths to an observer beyond our own solar system.

  16. Increase in NRAS mutant allele percentage during metastatic melanoma progression.

    PubMed

    Funck-Brentano, Elisa; Hélias-Rodzewicz, Zofia; Longvert, Christine; Mokhtari, Karima; Saiag, Philippe; Emile, Jean-François

    2016-06-01

    One-fifth of cutaneous melanomas have dominant gain-of-function mutations of the NRAS oncogene. We report the first two cases of increasing NRAS mutant allele frequency in melanoma metastases and show that the chromosomal mechanism of this homozygosity is an increased polysomy of chromosome 1. We observed an increase in NRAS mutant allele percentage (NRAS-MA%) in the metastatic melanoma progression from 2 patients with melanomas harbouring a NRAS mutation (p.Q61K in case 1 and p.Q61R in case 2). In case 1, we observed a NRAS-MA% increase from 18% within the first metastatic node to 81%, 92% and 85% respectively in the three subsequent metastases: lymph node, brain and subcutaneous metastases biopsied 1, 6 and 17 months, respectively, after the initial lymph node biopsy. In case 2, we observed an increase in NRAS-MA% from 40% within the primary melanoma to 63% within the metastatic lymph node. FISH analysis showed the same results in both cases: a frequent polysomy of chromosome 1 in metastasis samples with NRAS mutant allele percentage >60%, while most cells were disomic in the samples with well-balanced heterozygous mutations. The percentage of NRAS mutant allele may increase during metastatic progression and may be associated with chromosomal instability. Further studies are needed to evaluate the prognostic impact of the NRAS homozygous status and/or polyploidy in metastatic cutaneous melanomas. PMID:26990546

  17. Observational Evidence for Variations of the Acoustic Cutoff Frequency with Height in the Solar Atmosphere

    NASA Astrophysics Data System (ADS)

    Wiśniewska, A.; Musielak, Z. E.; Staiger, J.; Roth, M.

    2016-03-01

    Direct evidence for the existence of an acoustic cutoff frequency in the solar atmosphere is given by observations performed by using the HELioseismological Large Regions Interferometric DEvice operating on the Vacuum Tower Telescope located on Tenerife. The observational results demonstrate variations of the cutoff with atmospheric heights. The observed variations of the cutoff are compared to theoretical predictions made by using five acoustic cutoff frequencies that have been commonly used in helioseismology and asteroseismology. The comparison shows that none of the theoretical predictions is fully consistent with the observational data. The implication of this finding is far reaching as it urgently requires either major revisions of the existing methods of finding acoustic cutoff frequencies or developing new methods that would much better account for the physical picture underlying the concept of cutoff frequencies in inhomogeneous media.

  18. Multi-constrained fault estimation observer design with finite frequency specifications for continuous-time systems

    NASA Astrophysics Data System (ADS)

    Zhang, Ke; Jiang, Bin; Shi, Peng; Xu, Jinfa

    2014-08-01

    The design of a multi-constrained full-order fault estimation observer (FFEO) with finite frequency specifications is studied for continuous-time systems. By constructing an augmented system, a multi-constrained FFEO in finite frequency domain is proposed to achieve fault estimation. Meanwhile, the presented FFEO can avoid the overdesign problem generated by the entire frequency domain by the generalised Kalman-Yakubovich-Popov lemma. Furthermore, by introducing slack variables, improved results on FFEO design in different frequency domains are obtained such that different Lyapunov matrices can be separately designed for each constraint. Simulation results are presented to demonstrate the effectiveness and potentials of the proposed techniques.

  19. Morphology of human sweat ducts observed by optical coherence tomography and their frequency of resonance in the terahertz frequency region

    NASA Astrophysics Data System (ADS)

    Tripathi, Saroj R.; Miyata, Eisuke; Ishai, Paul Ben; Kawase, Kodo

    2015-03-01

    It is crucial to understand the various biological effects induced by terahertz (THz) electromagnetic waves with the rapid development of electronic and photonic devices operating in the THz frequency region. The presence of sweat glands plays an important role in THz wave interactions with human skin. We investigated the morphological features of sweat ducts using optical coherence tomography (OCT) to further understand such phenomena. We observed remarkable features of the ducts, such as their clear helical structure. The intersubject and intrasubject variations in the diameter of sweat ducts were considerably smaller than the variations in other structural parameters, such as length and number of turns. Based on the sweat duct dimensions and THz dielectric properties of skin measured using terahertz time-domain spectroscopy (THz-TDS), we calculated the resonating frequency of the sweat duct under the assumption of it functioning as a helical antenna. Here, we show that the resonance frequency in the axial mode of operation lies in the THz wave region with a centre frequency of 0.44 +/- 0.07 THz. We expect that these findings will further our understanding of the various health consequences of the interaction of THz waves with human beings.

  20. Morphology of human sweat ducts observed by optical coherence tomography and their frequency of resonance in the terahertz frequency region

    PubMed Central

    Tripathi, Saroj R.; Miyata, Eisuke; Ishai, Paul Ben; Kawase, Kodo

    2015-01-01

    It is crucial to understand the various biological effects induced by terahertz (THz) electromagnetic waves with the rapid development of electronic and photonic devices operating in the THz frequency region. The presence of sweat glands plays an important role in THz wave interactions with human skin. We investigated the morphological features of sweat ducts using optical coherence tomography (OCT) to further understand such phenomena. We observed remarkable features of the ducts, such as their clear helical structure. The intersubject and intrasubject variations in the diameter of sweat ducts were considerably smaller than the variations in other structural parameters, such as length and number of turns. Based on the sweat duct dimensions and THz dielectric properties of skin measured using terahertz time-domain spectroscopy (THz-TDS), we calculated the resonating frequency of the sweat duct under the assumption of it functioning as a helical antenna. Here, we show that the resonance frequency in the axial mode of operation lies in the THz wave region with a centre frequency of 0.44 ± 0.07 THz. We expect that these findings will further our understanding of the various health consequences of the interaction of THz waves with human beings. PMID:25766116

  1. High-frequency fishbones at JET: theoretical interpretation of experimental observations

    NASA Astrophysics Data System (ADS)

    Zonca, F.; Chen, L.; Botrugno, A.; Buratti, P.; Cardinali, A.; Cesario, R.; Ridolfini, V. Pericoli; JET-EFDA contributors

    2009-08-01

    The existence of fishbone fluctuations at frequencies comparable to those of geodesic acoustic modes (GAM) and beta induced Alfvén eigenmodes (BAE) has been demonstrated theoretically in a recent work (Zonca et al 2007 Nucl. Fusion 47 1588). Here, we show that observation of fishbones at unexpectedly high frequencies in JET (Nabais et al 2005 Phys. Plasmas 12 102509) is well interpreted as experimental evidence of high (GAM/BAE range) frequency fishbones and discuss the insights concerning both supra-thermal particles as well as thermal plasma properties that can be obtained from experimental observations.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed Central

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

    2015-01-01

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

  5. 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.

  6. 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.

  7. Theoretical interpretation of frequency sweeping observations in the Mega-Amp Spherical Tokamak

    NASA Astrophysics Data System (ADS)

    Vann, R. G. L.; Dendy, R. O.; Gryaznevich, M. P.

    2005-03-01

    Frequency sweeping (chirping) of high frequency magnetohydrodynamic modes is widely observed in tokamak plasmas. In this paper observations of chirping in neutral-beam-heated plasmas in the Mega-Amp Spherical Tokamak (MAST) [A. Sykes, R. J. Akers, L. C. Appel et al., Nucl. Fusion 41, 1423 (2001)] are considered, and it is shown that these may be interpreted using the Berk-Breizman augmentation of the Vlasov-Maxwell equations. This model includes an energetic particle source: it leads not only to a single chirp but also to a series of bursting events. This repetitious behavior is characteristic of the chirping seen in experiments such as MAST. The similarity between features in velocity space and features in frequency space reinforces the theory that hole-clump pair formation is responsible for the observed frequency sweeping.

  8. Uncommon HLA alleles identified by hemizygous ultra-high Sanger sequencing: haplotype associations and reconsideration of their assignment in the Common and Well-Documented catalogue.

    PubMed

    Voorter, Christina E M; Groeneweg, Mathijs; Groeneveld, Lisette; Tilanus, Marcel G J

    2016-02-01

    Although the number of HLA alleles still increases, many of them have been reported being uncommon. This is partly due to lack of full length gene sequencing, especially for those alleles belonging to an allele ambiguity in which the first discovered allele has been assigned as the most frequent one. As members of the working group on Common and Well Documented (CWD) alleles and since we implemented full length group-specific sequencing as standard method routinely, we have investigated the presence of presumably rare alleles in our collection of HLA typing data. We identified 50 alleles, that were not previously encountered as Common or Well Documented. Sixteen of them should be added to the CWD catalogue, since we encountered them in 5 or more unrelated individuals. Another 11 could be added, based upon our results and the data present in the IMGT database and the rare allele section of the allele frequencies database. Furthermore, tight associations were observed between several different alleles even at the level of synonymous and non-coding sequences. In addition, in several cases the uncommon allele was found to be more frequent than its common counterpart. PMID:26610902

  9. Effects of anisotropy on the frequency spectrum of gravity waves observed by MST radar

    NASA Technical Reports Server (NTRS)

    Liu, C. H.

    1986-01-01

    In the investigation of gravity waves using mesosphere-stratosphere-troposphere radar data, model gravity-wave spectra have been used. In these model spectra, one usually assumes azimuthal symmetry. The effect of spectral anisotropy on the observed spectrum is studied here. It is shown that for a general Garrett-Munk-type spectrum, the anisotropy does not affect the frequency spectrum observed by the vertically beamed radar. For the oblique beam, however, the observed frequency spectrum is changed. A general gravity wave spectrum including azimuthal anisotropy is considered.

  10. Observations of dust acoustic waves driven at high frequencies: Finite dust temperature effects and wave interference

    SciTech Connect

    Thomas, Edward Jr.; Fisher, Ross; Merlino, Robert L.

    2007-12-15

    An experiment has been performed to study the behavior of dust acoustic waves driven at high frequencies (f>100 Hz), extending the range of previous work. In this study, two previously unreported phenomena are observed--interference effects between naturally excited dust acoustic waves and driven dust acoustic waves, and the observation of finite dust temperature effects on the dispersion relation.

  11. Allelic imbalance within the E-cadherin gene is an infrequent event in prostate carcinogenesis.

    PubMed

    Murant, S J; Rolley, N; Phillips, S M; Stower, M; Maitland, N J

    2000-01-01

    By exploiting two single nucleotide polymorphisms (SNPs) located within the E-cadherin gene, at 16q22, we have determined the frequency of allelic imbalance at this proposed tumor suppressor locus in a series of human prostatic carcinoma DNA samples. Whereas results with seven highly polymorphic microsatellite markers flanking the E-cadherin locus confirmed the existence of three separate loci on chromosome 16, at which allelic imbalance increased with increasing loss of tumor cell differentiation, no allelic imbalance within the E-cadherin gene was detected either by single-strand conformational polymorphism analysis or by direct sequencing. We conclude that the loss of E-cadherin function observed in prostate cancer is not a result of allelic deletion. Genes Chromosomes Cancer 27:104-109, 2000. PMID:10564592

  12. Observations of the frequency tuning effect in the 14 GHz CAPRICE ion source.

    PubMed

    Celona, L; Ciavola, G; Consoli, F; Gammino, S; Maimone, F; Mascali, D; Spädtke, P; Tinschert, K; Lang, R; Mäder, J; Robbach, J; Barbarino, S; Catalano, R S

    2008-02-01

    A set of measurements with the CAPRICE ion source at the GSI test bench has been carried out to investigate its behavior in terms of intensity and shape of the extracted beam when the microwaves generating the plasma sweep in a narrow range of frequency (+/-40 MHz) around the klystron center frequency (14.5 GHz). Remarkable variations have been observed depending on the source and the beamline operating parameters, confirming that a frequency dependent electromagnetic distribution is preserved even in the presence of plasma inside the source. Moreover, these observations confirm that the frequency tuning is a powerful method to optimize the electron cyclotron resonance ion source performances. A description of the experimental setup and of the obtained results is given in the following. PMID:18315291

  13. Observations of a low-frequency cutoff in magnetospheric radio noise received on Imp 6

    NASA Technical Reports Server (NTRS)

    Vesecky, J. F.; Frankel, M. S.

    1975-01-01

    The quasi-continuous component of the magnetospheric noise observed by Imp 6, lying between 30 and 110 kHz, often exhibits a low-frequency cutoff when the spacecraft is in the interplanetary medium or the magnetosheath. A hypothesis is considered in which this low-frequency cutoff, f-co, is caused by overdense plasma situated somewhere along the noise-source-to-satellite path. The plasma is assumed to have a plasma frequency approximately equal to f-co, thus cutting off propagation below f-co.

  14. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

    PubMed

    Hodgson, Jason A; Pickrell, Joseph K; Pearson, Laurel N; Quillen, Ellen E; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D; Perry, George H

    2014-08-22

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa. PMID:24990677

  15. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

    PubMed Central

    Hodgson, Jason A.; Pickrell, Joseph K.; Pearson, Laurel N.; Quillen, Ellen E.; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D.; Perry, George H.

    2014-01-01

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa. PMID:24990677

  16. Low-cost precise measurement of oscillator frequency instability based on GNSS carrier observation

    NASA Astrophysics Data System (ADS)

    Kou, Yanhong; Jiao, Yue; Xu, Dongyang; Zhang, Meng; Liu, Ya; Li, Xiaohui

    2013-03-01

    Global navigation satellite systems (GNSS) receivers can be used in time and frequency metrology by exploiting stable GNSS time scales. This paper proposes a low-cost method for precise measurement of oscillator frequency instability using a single-frequency software GNSS receiver. The only required hardware is a common radio frequency (RF) data collection device driven by the oscillator under test (OUT). The receiver solves the oscillator frequency error in high time resolution using the carrier Doppler observation and the broadcast ephemeris from one of the available satellites employing the onboard reference atomic frequency standard that is more stable than the OUT. Considering the non-stable and non-Gaussian properties of the frequency error measurement, an unbiased finite impulse response (FIR) filter is employed to obtain robust estimation and filter out measurement noise. The effects of different filter orders and convolution lengths are further discussed. The frequency error of an oven controlled oscillator (OCXO) is measured using live Beidou-2/Compass signals. The results are compared with the synchronous measurement using a specialized phase comparator with the standard coordinated universal time (UTC) signal from the master clock H226 in the national time service center (NTSC) of China as its reference. The Allan deviation (ADEV) estimates using the two methods have a 99.9% correlation coefficient and a 0.6% mean relative difference over 1-1000 s intervals. The experiment demonstrates the effectiveness and high precision of the software receiver method.

  17. J16021+3326: NEW MULTI-FREQUENCY OBSERVATIONS OF A COMPLEX SOURCE

    SciTech Connect

    Tremblay, S. E.; Taylor, G. B.; Richards, J. L.; Readhead, A. C. S.; Helmboldt, J. F.; Romani, R. W.; Healey, S. E.

    2010-03-20

    We present multi-frequency Very Long Baseline Array observations of J16021+3326. These observations, along with variability data obtained from the Owens Valley Radio Observatory candidate gamma-ray blazar monitoring program, clearly indicate that this source is a blazar. The peculiar characteristic of this blazar, which daunted previous classification attempts, is that we appear to be observing down a precessing jet, the mean orientation of which is aligned with us almost exactly.

  18. Regular frequency patterns in the classical δ Scuti star HD 144277 observed by the MOST satellite

    NASA Astrophysics Data System (ADS)

    Zwintz, K.; Lenz, P.; Breger, M.; Pamyatnykh, A. A.; Zdravkov, T.; Kuschnig, R.; Matthews, J. M.; Guenther, D. B.; Moffat, A. F. J.; Rowe, J. F.; Rucinski, S. M.; Sasselov, D.; Weiss, W. W.

    2011-09-01

    Context. We present high-precision time-series photometry of the classical δ Scuti star HD 144277 obtained with the MOST (Microvariability and Oscillations of STars) satellite in two consecutive years. The observed regular frequency patterns are investigated asteroseismologically. Aims: HD 144277 is a hot A-type star that is located on the blue border of the classical instability strip. While we mostly observe low radial order modes in classical δ Scuti stars, HD 144277 presents a different case. Its high observed frequencies, i.e., between 59.9 d-1 (693.9 μHz) and 71.1 d-1 (822.8 μHz), suggest higher radial orders. We examine the progression of the regular frequency spacings from the low radial order to the asymptotic frequency region. Methods: Frequency analysis was performed using Period04 and SigSpec. The results from the MOST observing runs in 2009 and 2010 were compared to each other. The resulting frequencies were submitted to asteroseismic analysis. Results: HD 144277 was discovered to be a δ Scuti star using the time-series photometry observed by the MOST satellite. Twelve independent pulsation frequencies lying in four distinct groups were identified. Two additional frequencies were found to be combination frequencies. The typical spacing of 3.6 d-1 corresponds to the spacing between subsequent radial and dipole modes, therefore the spacing between radial modes is twice this value, 7.2 d-1. Based on the assumption of slow rotation, we find evidence that the two radial modes are the sixth and seventh overtones, and the frequency with the highest amplitude can be identified as a dipole mode. Conclusions: The models required to fit the observed instability range need slightly less metallicity and a moderate enhancement of the helium abundance compared to the standard chemical composition. Our asteroseismic models suggest that HD 144277 is a δ Scuti star close to the ZAMS with a mass of 1.66 M⊙. Based on data from the MOST satellite, a Canadian Space

  19. Frequency band enlargement of the penetrator seismometer and its application to moonquake observation

    NASA Astrophysics Data System (ADS)

    Yamada, Ryuhei; Nébut, Tanguy; Shiraishi, Hiroaki; Lognonné, Philippe; Kobayashi, Naoki; Tanaka, Satoshi

    2015-07-01

    Seismic data obtained over a broad frequency range are very useful in investigation of the internal structures of the Earth and other planetary bodies. However, planetary seismic data acquired through the NASA Apollo and Viking programs were obtained only over a very limited frequency range. To obtain effective seismic data over a broader frequency range on planetary surfaces, broadband seismometers suitable for planetary seismology must be developed. In this study, we have designed a new broadband seismometer based on a short-period seismometer whose resonant frequency is 1 Hz for future geophysical missions. The seismometer is of an electromagnetic type, light weight, small size and has good shock-durability, making it suitable for being loaded onto a penetrator, which is a small, hard-landing probe developed in the LUNAR-A Project, a previous canceled mission. We modified the short-period seismometer so as to have a flat frequency response above about 0.1 Hz and the detection limit could be lowered to cover frequencies below the frequency. This enlargement of the frequency band will allow us to investigate moonquakes for lower frequency components in which waveforms are less distorted because strong scattering due to fractured structures near the lunar surface is likely to be suppressed. The modification was achieved simply by connecting a feedback circuit to the seismometer, without making any mechanical changes to the short-period sensor. We have confirmed that the broadband seismometer exhibits the frequency response as designed and allows us to observe long-period components of small ground motions. Methods to improve the performance of the broadband seismometer from the current design are also discussed. These developments should promise to increase the opportunity for application of this small and tough seismometer in various planetary seismological missions.

  20. Co-selection and replacement of resistance alleles to Lysinibacillus sphaericus in a Culex quinquefasciatus colony.

    PubMed

    Chalegre, Karlos Diogo de Melo; Tavares, Daniella A; Romão, Tatiany P; de Menezes, Heverly Suzany G; Nascimento, Nathaly A; de Oliveira, Cláudia Maria F; de-Melo-Neto, Osvaldo P; Silva-Filha, Maria Helena N L

    2015-09-01

    The Cqm1 α-glucosidase, expressed within the midgut of Culex quinquefasciatus mosquito larvae, is the receptor for the Binary toxin (Bin) from the entomopathogen Lysinibacillus sphaericus. Mutations of the Cqm1 α-glucosidase gene cause high resistance levels to this bacterium in both field and laboratory populations, and a previously described allele, cqm1REC, was found to be associated with a laboratory-resistant colony (R2362). This study described the identification of a novel resistance allele, cqm1REC-2, that was co-selected with cqm1REC within the R2362 colony. The two alleles display distinct mutations but both generate premature stop codons that prevent the expression of midgut-bound Cqm1 proteins. Using a PCR-based assay to monitor the frequency of each allele during long-term maintenance of the resistant colony, cqm1REC was found to predominate early on but later was replaced by cqm1REC-2 as the most abundant resistance allele. Homozygous larvae for each allele were then generated that displayed similar high-resistance phenotypes with equivalent low levels of transcript and lack of protein expression for both cqm1REC and cqm1REC-2. In progeny from a cross of homozygous individuals for each allele at a 1 : 1 ratio, analyzed for ten subsequent generations, cqm1REC showed a higher frequency than cqm1REC-2. The replacement of cqm1REC by cqm1REC -2 observed in the R2362 colony, kept for 210 generations, indicates changes in fitness related to traits that are unknown but linked to these two alleles, and constitutes a unique example of evolution of resistance within a controlled laboratory environment. PMID:26131741

  1. Observation of Modes at Frequencies Near the Second Alfvin Gap in TFTR

    SciTech Connect

    Fredrickson. E.; Van Dam, J.W.; Budny, R.V.; Darrow, D.; Fu, G.Y.; Hosea, J.; Phillips, C.K.; Wilson, J.R.

    1999-04-01

    Modes has been observed in the frequency range of the second Alfvenic gap in H-minority ICRF heated plasmas in TFTR. This observation is surprising in that the second gap is generally considered to be small in circular cross section plasmas. The mode is inferred to be a core mode, i.e., localized in some sense within the q=1 surface. This follows from the observation that the time dependence of the mode frequency is consistent with the changes in the central density, with the appearance of the mode in the latter part of the sawtooth period when the central fast ion beta has peaked up, and with the direction of propagation, the last of these being explained by a hollow first ion beta profile, which is only present in the core region. The modes are generally not observed during on-axis H-minority heating, but commonly observed during off-axis heating on the high field side (with the resonant layer outside the q=1 surface). A model has been proposed that the beta of the fast ions opens the second gap, allowing instability. For TFTR parameters, the model predicts a gap width of approximately 10 kHz, which is 2.5% of the second gap frequency. If the backwards mode propagation is due to a hollow fast ion profile (as indicated in the TRANSP calculations), then instability due to wave-particle resonance at the magnetic curvature precessional frequency can occur only if the precessional frequency is reversed--which can indeed be the case for off-axis heating on the high field side. Thus, trapped fast ion pressure effects seem to explain several of the observed features of these second gap fluctuations.

  2. Multi-frequency solar observations at Metsähovi Radio Observatory and KAIRA

    NASA Astrophysics Data System (ADS)

    Kallunki, J.; Uunila, M.; McKay-Bukowski, D.

    2015-08-01

    We describe solar observations carried out for the first time jointly with Kilpisjärvi Atmospheric Imaging Receiver Array (KAIRA) and Aalto University Metsähovi Radio Observatory (MRO). KAIRA is new radio antenna array observing the decimeter and meter wavelength range. It is located near Kilpisjärvi, Finland, and operated by the Sodankylä Geophysical Observatory, University of Oulu. We investigate the feasibility of KAIRA for solar observations, and the additional benefits of carrying out multi-instrument solar observations with KAIRA and the MRO facilities, which are already used for regular solar observations. The data measured with three instruments at MRO, and with KAIRA during time period 2014 April-October were analyzed. One solar radio event, measured on 2014 April 18, was studied in detail. Seven solar flares were recorded with at least two of the three instruments at MRO, and with KAIRA during the chosen time period. KAIRA is a great versatile asset as a new Finnish instrument that can also be used for solar observations. Collaboration observations with MRO instruments and KAIRA enable detailed multi-frequency solar flare analysis. Flare pulsations, flare statistics and radio spectra of single flares can be investigated due to the broad frequency range observations. The Northern locations of both MRO and KAIRA make as long as 15-hour unique solar observations possible during summer time.

  3. The associations of HLA-A, -B, DRB1 alleles and haplotypes in Turkish lymphoma patients.

    PubMed

    Uçar, Fahri; Sönmez, Mehmet; Ermantaş, Nilay; Özbaş, Hasan Mücahit; Cansız, Abide; Balcı, Mustafa; Yılmazz, Mustafa

    2016-07-25

    A significant association between lymphomas and HLA alleles has been shown in previous studies. However, the frequency of HLA alleles and haplotypes has not been studied in Turkish lymphoma patients. We studied HLA-A, -B, -DRB1 alleles and haplotypes in 80 adult lymphomas and 360 unrelated normal subjects by PCR-SSOP method using Luminex technology. The allele frequencies of HLA-A*29, B*07, and DRB1*11 were higher in patients with Hodgkin's lymphoma (HL) compared with the controls [OR; 5.65 (95%CI; 2.16-14.81), P=0.001], [OR; 3.00 (95%CI; 1.50-5.99), P=0.003)], and [OR; 1.80 (95%CI; 1.08-3.01), P=0.002); respectively]. In patients with non-Hodgkin's lymphoma (NHL) HLA-B*51 and DRB1*04 allele frequencies were higher than controls [OR; 2.25 (95%CI; 1.27-4.00), P=0.007] and [OR; 2.14 (95%CI; 1.20-3.78), P=0.01]. The most frequently observed haplotypes were A*02 B*35 DRB1*11 (7.50% vs. 1.89%) in HL patients, A*02 B*51 DRB1*11 (5.00% vs. 1.96%) in NHL patients, and A*02 B*35 DRB1*13 (2.19%) in the controls. We detected four haplotypes specific to NHL, five haplotypes to HL patients. Seven haplotypes were unique to controls. Our findings suggest that in HL patients, HLA-A*29, B*07, and DRB1*11 alleles, and in NHL patients, HLA-B*51 and DRB1*04 alleles might be presumptive predisposing factors. PMID:27063556

  4. 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.

  5. Impact of LISA's Low Frequency Sensitivity on Observations of Massive Black Hole Mergers

    NASA Technical Reports Server (NTRS)

    Baker, J.; Centrella, J.

    2005-01-01

    LISA will be able to detect gravitational waves from inspiralling massive black hole (MBH) binaries out to redshifts z > 10. If the binary masses and luminosity distances can be extracted from the Laser Interferometer Space Antenna (LISA) data stream, this information can be used to reveal the merger history of MBH binaries and their host galaxies in the evolving universe. Since this parameter extraction generally requires that LISA observe the inspiral for a significant fraction of its yearly orbit, carrying out this program requires adequate sensitivity at low frequencies, f < 10(exp -4) Hz. Using several candidate low frequency sensitivities, we examine LISA's potential for characterizing MBH binary coalescences at redshifts z > 1.

  6. Observation of solar radio bursts using swept-frequency radiospectrograph in 20-40 MHz Band

    NASA Astrophysics Data System (ADS)

    Aoyama, Takashi; Oya, Hiroshi

    A new station for the observation of solar decametric radio bursts has been developed at Miyagi Vocational Training College in Tsukidate, Miyagi, Japan. Using the swept frequency radiospectrograph covering a frequency range from 20 MHz to 40 MHz within 200 msec, with bandwidth of 30 KHz, the radio outbursts from the sun have been currently monitored with colored dynamic spectrum display. After July 1982, successful observations provide the data which include all types of solar radio bursts such as type I, II, III, IV and V in the decametric wavelength range. In addition to these typical radio bursts, rising tone bursts with fast drift rate followed by strong type III bursts and a series of bursts repeating rising and falling tone bursts with slow drift rate have been observed.

  7. Torsion-bar antenna for low-frequency gravitational-wave observations.

    PubMed

    Ando, Masaki; Ishidoshiro, Koji; Yamamoto, Kazuhiro; Yagi, Kent; Kokuyama, Wataru; Tsubono, Kimio; Takamori, Akiteru

    2010-10-15

    We propose a novel type of gravitational-wave antenna, formed by two bar-shaped test masses and laser-interferometric sensors to monitor their differential angular fluctuations. This antenna has a fundamental sensitivity to low-frequency signals below 1 Hz, even with a ground-based configuration. In addition, it is possible to expand the observation band to a lower limit determined by the observation time, by using modulation and up-conversion of gravitational-wave signals by rotation of the antenna. The potential sensitivity of this antenna is superior to those of current detectors in a 1 mHz-10 Hz frequency band and is sufficient for observations of gravitational waves radiated from in-spiral and merger events of intermediate-mass black holes. PMID:21230958

  8. 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

  9. Improving Ambiguity Resolution for Medium Baselines Using Combined GPS and BDS Dual/Triple-Frequency Observations.

    PubMed

    Gao, Wang; Gao, Chengfa; Pan, Shuguo; Wang, Denghui; Deng, Jiadong

    2015-01-01

    The regional constellation of the BeiDou navigation satellite system (BDS) has been providing continuous positioning, navigation and timing services since 27 December 2012, covering China and the surrounding area. Real-time kinematic (RTK) positioning with combined BDS and GPS observations is feasible. Besides, all satellites of BDS can transmit triple-frequency signals. Using the advantages of multi-pseudorange and carrier observations from multi-systems and multi-frequencies is expected to be of much benefit for ambiguity resolution (AR). We propose an integrated AR strategy for medium baselines by using the combined GPS and BDS dual/triple-frequency observations. In the method, firstly the extra-wide-lane (EWL) ambiguities of triple-frequency system, i.e., BDS, are determined first. Then the dual-frequency WL ambiguities of BDS and GPS were resolved with the geometry-based model by using the BDS ambiguity-fixed EWL observations. After that, basic (i.e., L1/L2 or B1/B2) ambiguities of BDS and GPS are estimated together with the so-called ionosphere-constrained model, where the ambiguity-fixed WL observations are added to enhance the model strength. During both of the WL and basic AR, a partial ambiguity fixing (PAF) strategy is adopted to weaken the negative influence of new-rising or low-elevation satellites. Experiments were conducted and presented, in which the GPS/BDS dual/triple-frequency data were collected in Nanjing and Zhengzhou of China, with the baseline distance varying from about 28.6 to 51.9 km. The results indicate that, compared to the single triple-frequency BDS system, the combined system can significantly enhance the AR model strength, and thus improve AR performance for medium baselines with a 75.7% reduction of initialization time on average. Besides, more accurate and stable positioning results can also be derived by using the combined GPS/BDS system. PMID:26528977

  10. Improving Ambiguity Resolution for Medium Baselines Using Combined GPS and BDS Dual/Triple-Frequency Observations

    PubMed Central

    Gao, Wang; Gao, Chengfa; Pan, Shuguo; Wang, Denghui; Deng, Jiadong

    2015-01-01

    The regional constellation of the BeiDou navigation satellite system (BDS) has been providing continuous positioning, navigation and timing services since 27 December 2012, covering China and the surrounding area. Real-time kinematic (RTK) positioning with combined BDS and GPS observations is feasible. Besides, all satellites of BDS can transmit triple-frequency signals. Using the advantages of multi-pseudorange and carrier observations from multi-systems and multi-frequencies is expected to be of much benefit for ambiguity resolution (AR). We propose an integrated AR strategy for medium baselines by using the combined GPS and BDS dual/triple-frequency observations. In the method, firstly the extra-wide-lane (EWL) ambiguities of triple-frequency system, i.e., BDS, are determined first. Then the dual-frequency WL ambiguities of BDS and GPS were resolved with the geometry-based model by using the BDS ambiguity-fixed EWL observations. After that, basic (i.e., L1/L2 or B1/B2) ambiguities of BDS and GPS are estimated together with the so-called ionosphere-constrained model, where the ambiguity-fixed WL observations are added to enhance the model strength. During both of the WL and basic AR, a partial ambiguity fixing (PAF) strategy is adopted to weaken the negative influence of new-rising or low-elevation satellites. Experiments were conducted and presented, in which the GPS/BDS dual/triple-frequency data were collected in Nanjing and Zhengzhou of China, with the baseline distance varying from about 28.6 to 51.9 km. The results indicate that, compared to the single triple-frequency BDS system, the combined system can significantly enhance the AR model strength, and thus improve AR performance for medium baselines with a 75.7% reduction of initialization time on average. Besides, more accurate and stable positioning results can also be derived by using the combined GPS/BDS system. PMID:26528977

  11. 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

  12. Experimental observation of standing wave effect in low-pressure very-high-frequency capacitive discharges

    SciTech Connect

    Liu, Yong-Xin; Gao, Fei; Liu, Jia; Wang, You-Nian

    2014-07-28

    Radial uniformity measurements of plasma density were carried out by using a floating double probe in a cylindrical (21 cm in electrode diameter) capacitive discharge reactor driven over a wide range of frequencies (27–220 MHz). At low rf power, a multiple-node structure of standing wave effect was observed at 130 MHz. The secondary density peak caused by the standing wave effect became pronounced and shifts toward the axis as the driving frequency further to increase, indicative of a much more shortened standing-wave wavelength. With increasing rf power, the secondary density peak shift toward the radial edge, namely, the standing-wave wavelength was increased, in good qualitative agreement with the previous theory and simulation results. At higher pressures and high frequencies, the rf power was primarily deposited at the periphery of the electrode, due to the fact that the waves were strongly damped as they propagated from the discharge edge into the center.

  13. Frequency driven inversion of tunnel magnetoimpedance and observation of positive tunnel magnetocapacitance in magnetic tunnel junctions

    NASA Astrophysics Data System (ADS)

    Parui, Subir; Ribeiro, Mário; Atxabal, Ainhoa; Bedoya-Pinto, Amilcar; Sun, Xiangnan; Llopis, Roger; Casanova, Fèlix; Hueso, Luis E.

    2016-08-01

    The relevance for modern computation of non-volatile high-frequency memories makes ac-transport measurements of magnetic tunnel junctions (MTJs) crucial for exploring this regime. Here, we demonstrate a frequency-mediated effect in which the tunnel magnetoimpedance reverses its sign in a classical Co/Al2O3/NiFe MTJ, whereas we only observe a gradual decrease in the tunnel magnetophase. Such effects are explained by the capacitive coupling of a parallel resistor and capacitor in the equivalent circuit model of the MTJ. Furthermore, we report a positive tunnel magnetocapacitance effect, suggesting the presence of a spin-capacitance at the two ferromagnet/tunnel-barrier interfaces. Our results are important for understanding spin transport phenomena at the high frequency regime in which the spin-polarized charge accumulation due to spin-dependent penetration depth at the two interfaces plays a crucial role.

  14. Allelic associations of two polymorphic microsatellites in intron 40 of the human von Willebrand factor gene

    SciTech Connect

    Pena, S.D.J.; De Souza, K.T. ); De Andrade, M.; Chakraborty, R. )

    1994-01-18

    At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of individuals revealed 36 different haplotypes in a sample of 338 chromosomes examined. Allele frequencies between generations and gender at each locus were not significantly different, and the genotype frequencies were consistent with their Hardy-Weinberg expectations. Linkage disequilibrium between loci is highly significant with positive allele size association; that is, large alleles at the loci tend to occur together, and so do the same alleles. Variability at each locus appeared to have arisen in a stepwise fashion, suggesting replication slippage as a possible mechanism of production of new alleles. However, the authors observed an increased number of haplotypes, in contrast with the predictions of a stepwise production of variation in the entire region, suggesting some form of cooperative changes between loci that could be due to either gene conversion, or a common control mechanism of production of new variation at these repeat polymorphism sites. The high degree of polymorphism (gene diversity values of 72% and 78% at vWF1 and vWF2, respectively, and of 93% at the haplotype level) makes these markers informative for paternity testing, genetic counseling, and individual-identification purposes.

  15. Association of the apolipoprotein E {epsilon}4 allele with clinical subtypes of autopsy-confirmed Alzheimer`s Disease

    SciTech Connect

    Zubenko, G.S.; Stiffler, S.; Kopp, U.

    1994-09-15

    Consistent with previous reports, we observed a significant association of the APOE {epsilon}4 allele with Alzheimer`s Disease (AD) in a series of 91 autopsy-confirmed cases. The {epsilon}4 allele frequency was higher in cases with a family history of AD-like dementia (0.54 {+-} 0.07), although the {epsilon}4 allele frequency in the AD cases with a negative family history (0.38 {+-} 0.05) remained significantly greater than that for the non-AD control group (0.13 {+-} 0.03). A similar increase in {epsilon}4 allele frequency (0.54 {+-} 0.07) was observed in the AD cases with amyloid angiopathy, compared to those who did not have amyloid angiopathy (0.35 {+-} 0.04). Contrary to previous reports, no effect of the dosage of the {epsilon}4 allele was found on the age of onset of dementia among the AD cases and, contrary to reports suggesting an association of {epsilon}4 and atherosclerosis, the {epsilon}4 allele frequency was similar in cases with or without concurrent brain infarcts. Modest but consistent correlations were observed between the dosage of {epsilon}4 alleles and the cortical density of senile plaques, but not neurofibrillary tangles. The last finding suggests that the pathogenic events mediated by the {epsilon}4 allele may be more directly involved in the formation of senile plaques, the identifying lesions in AD, than neurofibrillary tangles. A robust association of both the presence of an {epsilon}4 allele and a family history of AD-like dementia with concurrent amyloid angiopathy occurred within our sample of AD cases. This association arose from an interaction of the {epsilon}4 allele with a separate familial factor for which a family history of dementia served as a surrogate. These results suggest that amyloid angiopathy may be a common or central feature of a form of familial AD that is associated with the transmission of the APOE {epsilon}4 allele. 22 refs., 2 figs., 5 tabs.

  16. Comparison between observations and models of the Mozambique Channel transport: Seasonal cycle and eddy frequencies

    NASA Astrophysics Data System (ADS)

    van der Werf, P. M.; van Leeuwen, P. J.; Ridderinkhof, H.; de Ruijter, W. P. M.

    2010-02-01

    A time series of the observed transport through an array of moorings across the Mozambique Channel is compared with that of six model runs with ocean general circulation models. In the observations, the seasonal cycle cannot be distinguished from red noise, while this cycle is dominant in the transport of the numerical models. It is found, however, that the seasonal cycles of the observations and numerical models are similar in strength and phase. These cycles have an amplitude of 5 Sv and a maximum in September, and can be explained by the yearly variation of the wind forcing. The seasonal cycle in the models is dominant because the spectral density at other frequencies is underrepresented. Main deviations from the observations are found at depths shallower than 1500 m and in the 5/y-6/y frequency range. Nevertheless, the structure of eddies in the models is close to the observed eddy structure. The discrepancy is found to be related to the formation mechanism and the formation position of the eddies. In the observations, eddies are frequently formed from an overshooting current near the mooring section, as proposed by Ridderinkhof and de Ruijter (2003) and Harlander et al. (2009). This causes an alternation of events at the mooring section, varying between a strong southward current, and the formation and passing of an eddy. This results in a large variation of transport in the frequency range of 5/y-6/y. In the models, the eddies are formed further north and propagate through the section. No alternation similar to the observations is observed, resulting in a more constant transport.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  18. Balloon observations of ultra-low-frequency waves in the electric field above the South Pole

    SciTech Connect

    Liao, B.; Benbrrook, J.R.; Bering E.A. III; Byrne, G.J.; Theall, J.R. )

    1988-01-01

    The physics of ultra-low-frequency waves in the magnetosphere, near the cusp and in the polar cap, is important because this region is one where ultra-low-frequency wave energy from the magnetopause can most easily enter the magnetosphere. During the 1985-1986 South Pole balloon campaign, eight stratospheric balloon payloads were launched from Amundsen-Scott Station, South Geographic Pole, Antarctica, to record data on ultra-low-frequency waves. The payloads were instrumented with three-axis double-probe electric field detectors and X-ray scintillation counters. This paper concentrates on the third flight of this series, which was launched at 2205 universal time on 21 December 1985. Good data were received from the payload until the transmitter failed at 0342 universal time on 22 December. During most of the four hours that the balloon was afloat, an intense ultra-low-frequency wave event was in progress. The electric-field data from this period have been examined in detail and compared with magnetic field data, obtained with ground-based fluxgate and induction magnetometers to determine the characteristics of the waves. After float was reached, the electric-field data in figure 1 show large-amplitude, quasi-periodic fluctuations suggesting the presence of intense ultra-low-frequency wave activity. In conclusion, the electric-field signature observed from flight 3 appears to have been essentially an electrostatic event or possibly a short-wavelength hydromagnetic wave with a varying and interesting polarization character. The authors are continuing the analysis of the data to determine the source of the observed ultra-low-frequency waves.

  19. Ground Radar Polarimetric Observations of High-Frequency Earth-Space Communication Links

    NASA Technical Reports Server (NTRS)

    Bolen, Steve; Chandrasekar, V.; Benjamin, Andrew

    2002-01-01

    Strategic roadmaps for NASA's Human Exploration and Development of Space (REDS) enterprise support near-term high-frequency communication systems that provide moderate to high data rates with dependable service. Near-earth and human planetary exploration will baseline Ka-Band, but may ultimately require the use of even higher frequencies. Increased commercial demand on low-frequency earth-space bands has also led to increased interest in the use of higher frequencies in regions like K u - and K,- band. Data is taken from the Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR), which operates at 13.8 GHz, and the true radar reflectivity profile is determined along the PR beam via low-frequency ground based polarimetric observations. The specific differential phase (Kdp) is measured along the beam and a theoretical model is used to determine the expected specific attenuation (k). This technique, called the k-Kdp method, uses a Fuzzy-Logic model to determine the hydrometeor type along the PR beam from which the appropriate k-Kdp relationship is used to determine k and, ultimately, the total path-integrated attenuation (PIA) on PR measurements. Measurements from PR and the NCAR S-POL radar were made during the TEFLUN-B experiment that took place near Melbourne, FL in 1998, and the TRMM-LBA campaign near Ji-Parana, Brazil in 1999.

  20. The Lockman Hole project: LOFAR observations and spectral index properties of low-frequency radio sources

    NASA Astrophysics Data System (ADS)

    Mahony, E. K.; Morganti, R.; Prandoni, I.; van Bemmel, I. M.; Shimwell, T. W.; Brienza, M.; Best, P. N.; Brüggen, M.; Rivera, G. Calistro; de Gasperin, F.; Hardcastle, M. J.; Harwood, J. J.; Heald, G.; Jarvis, M. J.; Mandal, S.; Miley, G. K.; Retana-Montenegro, E.; Röttgering, H. J. A.; Sabater, J.; Tasse, C.; van Velzen, S.; van Weeren, R. J.; Williams, W. L.; White, G. J.

    2016-09-01

    The Lockman Hole is a well-studied extragalactic field with extensive multi-band ancillary data covering a wide range in frequency, essential for characterising the physical and evolutionary properties of the various source populations detected in deep radio fields (mainly star-forming galaxies and AGNs). In this paper we present new 150-MHz observations carried out with the LOw Frequency ARray (LOFAR), allowing us to explore a new spectral window for the faint radio source population. This 150-MHz image covers an area of 34.7 square degrees with a resolution of 18.6×14.7 arcsec and reaches an rms of 160 μJy beam-1 at the centre of the field. As expected for a low-frequency selected sample, the vast majority of sources exhibit steep spectra, with a median spectral index of α _{150}^{1400}=-0.78± 0.015. The median spectral index becomes slightly flatter (increasing from α _{150}^{1400}=-0.84 to α _{150}^{1400}=-0.75) with decreasing flux density down to S150 ˜10 mJy before flattening out and remaining constant below this flux level. For a bright subset of the 150-MHz selected sample we can trace the spectral properties down to lower frequencies using 60-MHz LOFAR observations, finding tentative evidence for sources to become flatter in spectrum between 60 and 150 MHz. Using the deep, multi-frequency data available in the Lockman Hole, we identify a sample of 100 Ultra-steep spectrum (USS) sources and 13 peaked spectrum sources. We estimate that up to 21 per cent of these could have z > 4 and are candidate high-z radio galaxies, but further follow-up observations are required to confirm the physical nature of these objects.

  1. A Study of High Frequency Water Quality Observations in the Little Bear River Utah, USA (Invited)

    NASA Astrophysics Data System (ADS)

    Horsburgh, J. S.; Spackman Jones, A.; Stevens, D. K.; Tarboton, D. G.; Mesner, N. O.

    2010-12-01

    Process-based understanding of short and longer-term behavior of catchments is important to our ability to predict hydrologic system response. The time scale of many processes is on the order of minutes to hours, not weeks to months, and understanding the linkages between catchment hydrology and hydrochemistry requires measurements on a time scale consistent with these processes. We present a study of continuous, high frequency water quality observations within the Little Bear River Utah, USA, with the overarching goals of improving understanding of the hydrologic and hydrochemical response of the watershed, the timing, duration, and sources of water quality constituent fluxes, and development of the observing infrastructure and cyberinfrastructure needed to better quantify these fluxes. We installed high frequency water quality and discharge monitoring instrumentation at seven locations within the Little Bear River, along with 4 continuous weather and soil moisture monitoring stations. We developed and implemented the cyberinfrastructure required to manage the data from sensor to publication using components of the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System. We describe our sensor network design, cyberinfrastructure, and data collection procedures and provide results from our analyses that demonstrate how the scope and resolution of high frequency sensor data enable identification of trends and analysis of hydrologic and hydrochemical behavior that could not be observed by more traditional water quality monitoring. Using continuous, high frequency data from multiple sites, we demonstrate the dynamic hydrologic and hydrochemical response in the Little Bear as well as the importance of sampling frequency in the estimation of water quality constituent fluxes. We also examine the importance of early spring snowmelt in contributing to annual loads of total phosphorus and total suspended solids and

  2. Simulation of airborne radar observations of precipitating systems at various frequency bands

    NASA Astrophysics Data System (ADS)

    Louf, Valentin; Pujol, Olivier; Riedi, Jérôme

    2013-05-01

    The choice of the microwave frequency is of considerable importance for precipitating system observations by airborne radar. Currently, these radars operate at X-band (f = 10 GHz), although other frequency bands, may be used jointly or not. Since the measured reflectivity Zm is f-depending, different physical information about precipitating systems could be obtained. Herein, a comparison of reflectivity fields at different frequency bands is presented. A realistic and flexible model of precipitating systems is presented and simulations of airborne radar observations are performed. Simulated reflectivity fields are degraded as/increases because of Mie effects and microwave attenuation. At S, C and X-bands, attenuation is weak and Mie effects slightly increase the backscattered signal such that they can compensate attenuation at X and Ku bands. The Ka and W-bands suffer from a strong attenuation and significant Mie effects which seriously alter Zm-fields. For a squall line, the closer convective tower hides the farther ones, which is problematic for a pilot to estimate hazard at long distance. In addition, because hail is the main meteorological hazard for civil aviation, hail-rain discrimination is discussed and clarified for convective systems. It appears that S, C, and X-bands are the best ones, but the significant size of antenna used is prohibitive. Higher frequencies are more difficult to use on civil aviation due to high ambiguities and a too strongly attenuated microwave signal.

  3. Measurement of acoustic glitches in solar-type stars from oscillation frequencies observed by Kepler

    SciTech Connect

    Mazumdar, A.; Monteiro, M. J. P. F. G.; Cunha, M. S.; Ballot, J.; Antia, H. M.; Basu, S.; Houdek, G.; Silva Aguirre, V.; Christensen-Dalsgaard, J.; Metcalfe, T. S.; Mathur, S.; García, R. A.; Verner, G. A.; Chaplin, W. J.; Sanderfer, D. T.; Seader, S. E.; Smith, J. C.

    2014-02-10

    For the very best and brightest asteroseismic solar-type targets observed by Kepler, the frequency precision is sufficient to determine the acoustic depths of the surface convective layer and the helium ionization zone. Such sharp features inside the acoustic cavity of the star, which we call acoustic glitches, create small oscillatory deviations from the uniform spacing of frequencies in a sequence of oscillation modes with the same spherical harmonic degree. We use these oscillatory signals to determine the acoustic locations of such features in 19 solar-type stars observed by the Kepler mission. Four independent groups of researchers utilized the oscillation frequencies themselves, the second differences of the frequencies and the ratio of the small and large separation to locate the base of the convection zone and the second helium ionization zone. Despite the significantly different methods of analysis, good agreement was found between the results of these four groups, barring a few cases. These results also agree reasonably well with the locations of these layers in representative models of the stars. These results firmly establish the presence of the oscillatory signals in the asteroseismic data and the viability of several techniques to determine the location of acoustic glitches inside stars.

  4. Combined Radiometer-Radar Microphysical Profile Estimations with Emphasis on High Frequency Brightness Temperature Observations

    NASA Technical Reports Server (NTRS)

    Jackson, Gail Skofronick; Wang, James R.; Heymsfield, Gerald M.; Hood, Robbie; Manning, Will; Meneghini, Robert; Weinman, James A.; Hildebrand, Peter (Technical Monitor)

    2001-01-01

    Information about the vertical microphysical cloud structure is useful in many modeling and predictive practices. Radiometers and radars are used to observe hydrometeor properties. This paper describes an iterative retrieval algorithm that combines the use of airborne active and wideband (10 to 340 GHz) passive observations to estimate the vertical content and particle size distributions of liquid and frozen hydrometeors. The physically-based retrieval algorithm relies on the high frequencies (greater than 89 GHz) to provide details on the frozen hydrometeors. Neglecting the high frequencies yielded acceptable estimates of the liquid profiles, but the ice profiles were poorly retrieved. Airborne radar and radiometer observations from the third Convection and Moisture EXperiment (CAMEX-3) were used in the retrieval algorithm as constraints. Nadir profiles were estimated for a minute each of flight time (approximately 12.5 km along track) from an anvil, convection, and quasi- stratiform rain. The complex structure of the frozen hydrometeors required the most iterations for convergence for the anvil cloud type. The wideband observations were found to more than double the estimated frozen hydrometeor content as compared to retrievals using only 90-GHz and below. The convective and quasi-stratiform quickly reached convergence (minimized difference between observations and calculations using the estimated profiles). A qualitative validation using coincident in situ CAMEX-3 observations shows that the retrieved particle size distributions are well corroborated with independent measurements.

  5. Multi-frequency observation of Galactic micro-quasar Cygnus X-3 during flare

    NASA Astrophysics Data System (ADS)

    Patra, D.; Pal, S.; Ishwara-Chandra, C. H.; Rao, A. P.

    We studied the multi-frequency radio observations of the Galactic micro-quasar Cygnus X-3 using the Giant Metrewave Radio Telescope at 244, 325, 614 and 1280 MHz and Very Large Array at 8.43, 22.5 and 43.3 GHz during various flaring activities between 2006 to 2009. We have calculated the two point spectral index from the simultaneous observations at 244 and 614 MHz. These spectral index varies from positive (optically thick) and negative (optically thin) values which is consistent with the synchrotron self absorption model. We calculated some physical parameters such as the size of emitting region, turn over frequency and corresponding peak flux using the synchrotron self absorption model. The size of the emitting region are different at different time of the flare.

  6. Simultaneous ground-satellite observations of Pi 2 magnetic pulsations and their high frequency enhancement

    NASA Technical Reports Server (NTRS)

    Arthur, C. W.; Mcpherron, R. L.

    1980-01-01

    Pi 2 magnetic pulsations are a frequent occurrence at the earth's surface and have been shown to be clearly correlated with substorm expansion onset. These pulsations are also observed in space at synchronous orbit at the same time as they are seen on the ground at the satellite conjugate point. This brief report describes three days in 1969 on which Pi 2 magnetic pulsations were simultaneously observed at the synchronous satellite ATS 1 and at Tungsten, N.W.T., Canada, near the foot of the ATS 1 magnetic field line. These Pi 2 bursts all exhibit the characteristic waveform and frequency, as well as an 0.3 Hz enhancement, at both locations. This high frequency enhancement appears to be an integral part of Pi 2 bursts both on the surface and at synchronous orbit and should be considered in the development of models of generation mechanisms.

  7. Satellite observations of type 3 solar radio bursts at low frequencies

    NASA Technical Reports Server (NTRS)

    Fainberg, J.; Stone, R. G.

    1973-01-01

    Type III solar radio bursts were observed from 10 MHz to 10 KHz by satellite experiments above the terrestrial plasmasphere. Solar radio emission in this frequency range results from excitation of the interplanetary plasma by energetic particles propagating outward along open field lines over distances from 5 solar radii to at least 1 AU from the sun. This review summarizes the morphology, characteristics and analysis of individual as well as storms of bursts. Burst rise times are interpreted in terms of exciter length and dispersion while decay times refer to the radiation damping process. The combination of radio observations at the lower frequencies and in-situ measurements on nonrelativistic electrons at 1 AU provide data on the energy range and efficiency of the wave-particle interactions responsible for the radio emission.

  8. Low Frequency Loss in Regional Scale Flux Observations from a Tall Tower

    NASA Astrophysics Data System (ADS)

    Bosveld, F. C.; Schalkwijk, J.; Siebesma, A. P.

    2010-09-01

    Direct measurements of surface fluxes are nowadays often performed with the eddy-correlation technique. The method is well established for observations in the lowest few meters of the atmosphere which gives flux estimates with a footprint of typically 100 m. Models and satellite products often give results on the kilometer scale or larger and benefit for their evaluation from flux estimates with larger horizontal scales. Until now only a limited number of techniques are available for direct flux observation at larger scale, e.g. airborne eddy correlation, tall tower based observations and scintillometers. Elevated observations "see" a larger footprint. We focus on tall tower flux observations. Specific problems arise when estimating surface fluxes from these elevated observations related to storage below the observation level and advection. A third concern and the focus of this presentation is the increase of length scale of the transporting turbulent eddies when going to higher levels in the atmospheric boundary layer and the related issue of low frequency loss. With the Cabauw 200 m meteorological tower in the Netherlands a unique platform is available to perform tall tower flux observations. The tower has been equipped with eddy correlation systems at 5, 60, 100 and 180 m height which measures fluxes of momentum, temperature, humidity and CO2. In addition wind speed, temperature, humidity and CO2 concentration are measured at a number of intermediate levels. This set of instruments has been augmented with an extra large aperture scintillometer which operates at the 60 m level over the 10 km path between a TV-tower and the Cabauw meteorological tower. Typically turbulence flux data is calculated on a 10 to 30 minute time basis. For atmospheric surface layer observation well established similarity relations exist to estimate low-frequency flux contributions. Low frequency contributions above the surface layer are less well established. We have analysed a large

  9. Low-frequency waves within isolated magnetic clouds and complex structures: STEREO observations

    NASA Astrophysics Data System (ADS)

    Siu-Tapia, A.; Blanco-Cano, X.; Kajdic, P.; Aguilar-Rodriguez, E.; Russell, C. T.; Jian, L. K.; Luhmann, J. G.

    2015-04-01

    Complex Structures (CSs) formed by the interaction of magnetic cloud (MC)-like structures with other transients (e.g., another MC, a stream interaction region, or a fast stream of solar wind) were frequently observed in the interplanetary space by STEREO spacecraft during the solar minimum 23 and the rising phase of the solar cycle 24. Here we report the presence of low-frequency waves (LFWs) inside some isolated MCs (IMCs) and inside the CSs observed by STEREO during such period (2007-2011). It is important to study in detail the properties of waves in space plasmas since particle distribution functions can be modified by wave-particle interactions. We compare wave characteristics within IMCs with those waves observed inside CSs. Both left-handed (LH) and right-handed (RH), near-circularly polarized, transverse and almost parallel-propagating LFWs (around the proton cyclotron frequency) were sporadically observed inside both IMCs and CSs. In contrast, compressive mirror-mode waves (MMs) were observed only within CSs. We studied local plasma conditions inside the IMCs and CSs to gain insight about wave origin: most of the MMs within CSs were observed in regions with enhanced plasma beta (β>1) the majority of the LH waves were found in low beta plasmas (β<1), and the RH waves were predominantly observed at moderate betas (0.4<β≤2). These observations are in agreement with linear kinetic theory predictions for the growth of the mirror, the LH ion cyclotron, and the RH ion firehose instability, respectively. It is possible that the waves were generated locally inside the IMCs and CSs via temperature anisotropies. The plasma beta enhancements that were frequently observed inside the CSs may be the result of compressions and heating taking place inside the interacting structures.

  10. Observation of modes at frequencies near the second Alfven gap in TFTR

    SciTech Connect

    Fredrickson, E.; Van Dam, J.W.; Budny, R.V.; Darrow, D.; Fu, G.Y.; Hosea, J.; Phillips, C.K.; Wilson, J.R.

    2000-04-26

    Modes have been observed near the frequency of the second Alfven gap during off-axis H-minority heating experiments in the circular cross-section Tokamak Fusion Test Reactor. The observation of these modes is surprising in that the second gap, which is generally opened with ellipticity, is expected to be small, of order (r/R){sup 2}. A model is proposed in which the second gap is opened by the fast ion beta, which is shown to be able to introduce mode coupling, much as toroidal effects introduce mode coupling for Toroidal Alfven Eigenmodes (TAE). The modes are seen with and without accompanying TAE mode activity.

  11. 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

  12. Distribution of HLA-DRB1 and HLA-DQB1 alleles in Lak population of Iran.

    PubMed

    Varzi, Ali Mohammad; Shahsavar, Farhad; Tarrahi, Mohammad Javad

    2016-07-01

    Human leukocyte antigen (HLA) genes are the most polymorphic loci in the human genome and encode the highly polymorphic molecules critically involved in immune responses. Anthropological studies based on highly polymorphic HLA genes provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine the HLA-DRB1 and HLA-DQB1 allele frequencies in 100 unrelated Lak individuals from Lorestan province of Iran. Finally, we compared the results with those previously described in four other Iranian populations. Commercial HLA-Type kits were used for determination of the HLA-DRB1 and HLA-DQB1 allele frequencies. Differences between populations in the distribution of HLA-DRB1 and HLA-DQB1 alleles were estimated by χ2 test with Yate's correction and Fisher's exact test. The most frequent HLA-DRB1 alleles were (*)1103=4 (23%), (*)1502 (9.5%), (*)0701 (9%), (*)0301 (8.5%), (*)1101 (7.5%) and (*)1501 (6%) while HLA-DQB1(*)0301 (40%), (*)0201 (15%), (*)0502 (10.5%), (*)0303 (10%), (*)0602=3 (9.5%), and (*)0501 (7.5%) were the most frequent alleles in Lak population. HLA-DRB1(*)0409, (*)0804, (*)1102, (*)1112, (*)1405, and HLA-DQB1(*)0503, (*)0604 were the least observed frequencies in Lak population. Our results based on HLA-DRB1 and HLA-DQB1 allele frequencies showed that the Lak population possesses the previously reported general features of the Lur and Kurd populations but still with unique, decreased or increased frequencies of several alleles. In other words, the Lak population is close to Lurs Khorramabadi and Kurd but far from Lurs Kohkiloyeh/Boyerahmad and Bakhtiari. PMID:27189628

  13. Significant reduction in arc frequency biased solar cells: Observations, diagnostics, and mitigation technique(s)

    NASA Technical Reports Server (NTRS)

    Upschulte, B. L.; Weyl, G. M.; Marinelli, W. J.; Aifer, E.; Hastings, D.; Snyder, D.

    1991-01-01

    A variety of experiments were performed which identify key factors contributing to the arcing of negatively biased high voltage solar cells. These efforts have led to reduction of greater than a factor of 100 in the arc frequency of a single cell following proper remediation procedures. Experiments naturally lead to and focussed on the adhesive/encapsulant that is used to bond the protective cover slip to the solar cell. An image-intensified charge coupled device (CCD) camera system recorded UV emission from arc events which occurred exclusively along the interfacial edge between the cover slip and the solar cell. Microscopic inspection of this interfacial region showed a bead of encapsulant along this entire edge. Elimination of this encapsulant bead reduced the arc frequency by two orders of magnitude. Water contamination was also identified as a key contributor which enhances arcing of the encapsulant bead along the solar cell edge. Spectrally resolved measurements of the observable UV light shows a feature assignable to OH(A-X) electronic emission, which is common for water contaminated discharges. Experiments in which the solar cell temperature was raised to 85 C showed a reduced arcing frequency, suggesting desorption of H2O. Exposing the solar cell to water vapor was shown to increase the arcing frequency. Clean dry gases such as O2, N2, and Ar show no enhancement of the arcing rate. Elimination of the exposed encapsulant eliminates any measurable sensitivity to H2O vapor.

  14. The highest frequency detection of a radio relic: 16 GHz AMI observations of the `Sausage' cluster

    NASA Astrophysics Data System (ADS)

    Stroe, Andra; Rumsey, Clare; Harwood, Jeremy J.; van Weeren, Reinout J.; Röttgering, Huub J. A.; Saunders, Richard D. E.; Sobral, David; Perrott, Yvette C.; Schammel, Michel P.

    2014-06-01

    We observed the cluster CIZA J2242.8+5301 with the Arcminute Microkelvin Imager at 16 GHz and present the first high radio-frequency detection of diffuse, non-thermal cluster emission. This cluster hosts a variety of bright, extended, steep-spectrum synchrotron-emitting radio sources, associated with the intracluster medium, called radio relics. Most notably, the northern, Mpc-wide, narrow relic provides strong evidence for diffusive shock acceleration in clusters. We detect a puzzling, flat-spectrum, diffuse extension of the southern relic, which is not visible in the lower radio-frequency maps. The northern radio relic is unequivocally detected and measures an integrated flux of 1.2 ± 0.3 mJy. While the low-frequency (<2 GHz) spectrum of the northern relic is well represented by a power law, it clearly steepens towards 16 GHz. This result is inconsistent with diffusive shock acceleration predictions of ageing plasma behind a uniform shock front. The steepening could be caused by an inhomogeneous medium with temperature/density gradients or by lower acceleration efficiencies of high energy electrons. Further modelling is necessary to explain the observed spectrum.

  15. Airborne Remote Observations of L-Band Radio Frequency Interference and Implications for Satellite Missions

    NASA Technical Reports Server (NTRS)

    Laymon, Charles; Srinivasan, Karthik; Limaye, Ashutosh

    2011-01-01

    Passive remote sensing of the Earth s surface and atmosphere from space has significant importance in operational and research environmental studies, in particular for the scientific understanding, monitoring and prediction of climate change and its impacts. Passive remote sensing requires the measurement of naturally occurring radiations, usually of very low power levels, which contain essential information on the physical process under investigation. As such, these sensed radio frequency bands are a unique natural resource enabling space borne passive sensing of the atmosphere and the Earth s surface that deserves adequate allocation to the Earth Exploration Satellite Service and absolute protection from interference. Unfortunately, radio frequency interference (RFI) is an increasing problem for Earth remote sensing, particularly for passive observations of natural emissions. Because these natural signals tend to be very weak, even low levels of interference received by a passive sensor may degrade the fidelity of scientific data. The characteristics of RFI (low-level interference and radar-pulse noise) are not well known because there has been no systematic surveillance, spectrum inventory or mapping of RFI. While conducting a flight experiment over central Tennessee in May 2010, RFI, a concern for any instrument operating in the passive L band frequency, was observed across 16 subbands between 1402-1427 MHz. Such a survey provides rare characterization data from which to further develop mitigation technologies as well as to identify bandwidths to avoid in future sensor formulation.

  16. Observations of Low Frequency Solar Radio Bursts from the Rosse Solar-Terrestrial Observatory

    NASA Astrophysics Data System (ADS)

    Zucca, P.; Carley, E. P.; McCauley, J.; Gallagher, P. T.; Monstein, C.; McAteer, R. T. J.

    2012-10-01

    The Rosse Solar-Terrestrial Observatory (RSTO; http://www.rosseobservatory.ie) was established at Birr Castle, Co. Offaly, Ireland (53°05'38.9″, 7°55'12.7″) in 2010 to study solar radio bursts and the response of the Earth's ionosphere and geomagnetic field. To date, three Compound Astronomical Low-cost Low-frequency Instrument for Spectroscopy in Transportable Observatory (CALLISTO) spectrometers have been installed, with the capability of observing in the frequency range of 10 - 870 MHz. The receivers are fed simultaneously by biconical and log-periodic antennas. Nominally, frequency spectra in the range of 10 - 400 MHz are obtained with four sweeps per second over 600 channels. Here, we describe the RSTO solar radio spectrometer set-up, and present dynamic spectra of samples of type II, III and IV radio bursts. In particular, we describe the fine-scale structure observed in type II bursts, including band splitting and rapidly varying herringbone features.

  17. Paternal-specific S-allele transmission in sweet cherry (Prunus avium L.): the potential for sexual selection.

    PubMed

    Hedhly, A; Wünsch, A; Kartal, Ö; Herrero, M; Hormaza, J I

    2016-03-01

    Homomorphic self-incompatibility is a well-studied example of a physiological process that is thought to increase population diversity and reduce the expression of inbreeding depression. Whereas theoretical models predict the presence of a large number of S-haplotypes with equal frequencies at equilibrium, unequal allele frequencies have been repeatedly reported and attributed to sampling effects, population structure, demographic perturbation, sheltered deleterious mutations or selection pressure on linked genes. However, it is unclear to what extent unequal segregations are the results of gametophytic or sexual selection. Although these two forces are difficult to disentangle, testing S-alleles in the offspring of controlled crosses provides an opportunity to separate these two phenomena. In this work, segregation and transmission of S-alleles have been characterized in progenies of mixed donors and fully compatible pollinations under field conditions in Prunus avium. Seed set patterns and pollen performance have also been characterized. The results reveal paternal-specific distorted transmission of S-alleles in most of the crosses. Interestingly, S-allele segregation within any given paternal or maternal S-locus was random. Observations on pollen germination, pollen tube growth rate, pollen tube cohort size, seed set dynamics and transmission patterns strongly suggest post-pollination, prezygotic sexual selection, with male-male competition as the most likely mechanism. According to these results, post-pollination sexual selection takes precedence over frequency-dependent selection in explaining unequal S-haplotype frequencies. PMID:26559165

  18. Experimental observation of further frequency upshift from dc to ac radiation converter with perpendicular dc magnetic field

    PubMed

    Higashiguchi; Yugami; Gao; Niiyama; Sasaki; Takahashi; Ito; Nishida

    2000-11-20

    A frequency upshift of a short microwave pulse is generated by the interaction between a relativistic underdense ionization front and a periodic electrostatic field with a perpendicular dc magnetic field. When the dc magnetic field is applied, further frequency upshift of 3 GHz is observed with respect to an unmagnetized case which has typically a GHz range. The radiation frequency depends on both the plasma density and the strength of the dc magnetic field, i.e., the plasma frequency and the cyclotron frequency. The frequency of the emitted radiation is in reasonable agreement with the theoretical values. PMID:11082591

  19. A fault detection observer design for LPV systems in finite frequency domain

    NASA Astrophysics Data System (ADS)

    Chen, Jianliang; Cao, Yong-Yan; Zhang, Weidong

    2015-03-01

    This paper addresses the fault detection observer design problem for linear parameter-varying systems. Two finite frequency performance indexes are introduced to measure the fault sensitivity and the disturbance robustness. First, the H- index fault sensitivity condition in finite frequency domain is obtained by generalised Kalman-Yakubovich-Popov lemma and new linearisation techniques. Then, with the aid of Kalman-Yakubovich-Popov lemma and projection lemma, the stability and robustness conditions are derived. It turns out that the non-convexity problem which is caused by dealing with the above three conditions can be translated into a bilinear matrix inequality optimisation problem by increasing the dimensions of slack variable matrix. An iterative linear matrix inequality algorithm is proposed to get the solution. The effectiveness of the filter is shown via three numerical examples.

  20. High-frequency observations of δ2H and δ18O in storm rainfall

    NASA Astrophysics Data System (ADS)

    Stoecker, F.; Klaus, J.; Pangle, L. A.; Garland, C.; McDonnell, J. J.

    2012-12-01

    Stable isotopes ratios of hydrogen (2H/1H) and oxygen (18O/16O) are indispensable tools for investigation of the hydrologic cycle. Recent technological advances with laser spectroscopy now enable high-frequency measurement of key water cycle components. While the controls on rainfall isotope composition have been known generally for some time, our understanding of the effect of inter- and intra-storm processes on fine scale rainfall isotope composition is poorly understood. Here we present a new approach to observe inter- and intra-storm isotope variability in precipitation in high-frequency. We investigate the temporal development of δ2H and δ18O within and between discrete rainstorm. δ2H and δ18O in precipitation was measured from November 2011 to February 2012 in Corvallis, OR using a flow-cell combined with a Liquid Water Isotope Analyzer (LWIA-24d, Los Gatos Research, Inc.). The average sample frequency was 15 samples per hour, resulting in more than 3100 samples during the observation period. 27 separate rainstorms were identified in the dataset based on minimum inter-event time, minimum precipitation depth, and minimum number of isotope measurements. Event meteoric water lines were developed for each event. We observed short-term isotopic patterns (e.g., V-shaped trends), high-rate changes (5.3‰/h) and large absolute changes in isotopic composition (20‰) on intra-event scale. V-shaped trends appeared to be related to individual storm fronts detected by air temperature, cloud heights (NEXRAD radar echo tops) and cloud trajectories (Hybrid Single Particle Lagrangian Integrated Trajectory Model (HYSPLIT)). Despite this, we could detect no linear correlation between event-based isotopic variables (slope, δ2H-intercept, δ2H, δ18O) and the event meteoric water line. Furthermore, the composite event meteoric water line (i.e. the local meteoric water line) showed a wider spread for heavy isotopes than for light isotopes, caused presumably by different

  1. Statistics of Natural Populations. II. Estimating an Allele Probability in Families Descended from Cryptic Mothers

    PubMed Central

    Arnold, Jonathan; Morrison, Melvin L.

    1985-01-01

    In population studies, adults are frequently difficult or inconvenient to identify for genotype, but a family profile of genotypes can be obtained from an unidentified female crossed with a single unidentified male. The problem is to estimate an allele frequency in the cryptic parental gene pool from the observed family profiles. For example, a worker may wish to estimate inversion frequencies in Drosophila; inversion karyotypes are cryptic in adults but visible in salivary gland squashes from larvae. A simple mixture model, which assumes the Hardy-Weinberg law, Mendelian laws and a single randomly chosen mate per female, provides the vehicle for studying three competing estimators of an allele frequency. A simple, heuristically appealing estimator called the Dobzhansky estimator is compared with the maximum likelihood estimator and a close relative called the grouped profiles estimator. The Dobzhansky estimator is computationally simple, consistent and highly efficient and is recommended in practice over its competitors. PMID:17246258

  2. Vibration Mode Observation of Piezoelectric Disk-type Resonator by High Frequency Laser Doppler Vibrometer

    NASA Astrophysics Data System (ADS)

    Matsumura, Takeshi; Esashi, Masayoshi; Harada, Hiroshi; Tanaka, Shuji

    For future mobile phones based on cognitive radio technology, a compact multi-band RF front-end architecture is strongly required and an integrated multi-band RF filter bank is a key component in it. Contour-mode resonators are receiving increased attention for a multi-band filter solution, because its resonant frequency is mainly determined by its size and shape, which are defined by lithography. However, spurious responses including flexural vibration are also excited due to its thin structure. To improve resonator performance and suppress spurious modes, visual observation with a laser probe system is very effective. In this paper, we have prototyped a mechanically-coupled disk-array filter, which consists of a Si disk and 2 disk-type resonators of higher-order wine-glass mode, and observed its vibration modes using a high-frequency laser-Doppler vibrometer (UHF-120, Polytec, Inc.). As a result, it was confirmed that higher order wine-glass mode vibration included a compound displacement, and that its out-of-plane vibration amplitude was much smaller than other flexural spurious modes. The observed vibration modes were compared with FEM (Finite Element Method) simulation results. In addition, it was also confirmed that the fabrication error, e.g. miss-alignment, induced asymmetric vibration.

  3. IS THE OBSERVED HIGH-FREQUENCY RADIO LUMINOSITY DISTRIBUTION OF QSOs BIMODAL?

    SciTech Connect

    Mahony, Elizabeth K.; Sadler, Elaine M.; Croom, Scott M.; Murphy, Tara; Ekers, Ronald D.; Feain, Ilana J.

    2012-07-20

    The distribution of QSO radio luminosities has long been debated in the literature. Some argue that it is a bimodal distribution, implying that there are two separate QSO populations (normally referred to as 'radio-loud' and 'radio-quiet'), while others claim it forms a more continuous distribution characteristic of a single population. We use deep observations at 20 GHz to investigate whether the distribution is bimodal at high radio frequencies. Carrying out this study at high radio frequencies has an advantage over previous studies as the radio emission comes predominantly from the core of the active galactic nucleus, and hence probes the most recent activity. Studies carried out at lower frequencies are dominated by the large-scale lobes where the emission is built up over longer timescales (10{sup 7}-10{sup 8} yr), thereby confusing the sample. Our sample comprises 874 X-ray-selected QSOs that were observed as part of the 6dF Galaxy Survey. Of these, 40% were detected down to a 3{sigma} detection limit of 0.2-0.5 mJy. No evidence of bimodality is seen in either the 20 GHz luminosity distribution or in the distribution of the R{sub 20} parameter: the ratio of the radio to optical luminosities traditionally used to classify objects as being either radio-loud or radio-quiet. Previous results have claimed that at low radio luminosities, star formation processes can dominate the radio emission observed in QSOs. We attempt to investigate these claims by stacking the undetected sources at 20 GHz and discuss the limitations in carrying out this analysis. However, if the radio emission was solely due to star formation processes, we calculate that this corresponds to star formation rates ranging from {approx}10 M{sub Sun} yr{sup -1} to {approx}2300 M{sub Sun} yr{sup -1}.

  4. Selective observation of starch in a water plant using optical sum-frequency microscopy

    NASA Astrophysics Data System (ADS)

    Miyauchi, Yoshihiro; Sano, Haruyuki; Mirzutani, Goro

    2006-07-01

    The photosynthesis, transfer, and storage of starch are the most important biogenic processes occurring in plants. In order to observe the colorless and transparent starch granules in a plant, a chemical pretreatment such as staining of the starch is currently required, which seriously damages the tissue cells in the plant. We demonstrate that nondestructive chemical analysis of starch granules in a plant can be performed by using optical second-harmonic and sum-frequency microscopy. These techniques for in vivo analysis will provide extremely useful information about saccharides in a plant and can be extended to the analysis of many other materials, from living tissue to semiconductors.

  5. The effects of pulsed, high frequency radio waves on rat liver (ultrastructural and biomedical observations)

    SciTech Connect

    Pop, L.; Muresan, M.; Comorosan, S.; Paslaru, L. )

    1989-01-01

    The effects of a high frequency electromagnetic field, generated by a Diapulse instrument (Diapulse Corporation of America) on rat liver has been investigated. Ultrastructural aspects are described and quantitative determinations of mitochondrial enzymes MAO, CyT-Ox, MDH, SDH and ATP-ase recorded. The standard therapeutic parameters generally used with the Diapulse instrument in medicine were found to induce a stimulation effect at the investigated level, without apparent degenerative modifications. A concordance between the qualitative ultrastructural data and quantitative subcellular enzymic determinations has been observed.

  6. Experimental Observation and Computational Analysis of Striations in Electronegative Capacitively Coupled Radio-Frequency Plasmas

    NASA Astrophysics Data System (ADS)

    Liu, Yong-Xin; Schüngel, Edmund; Korolov, Ihor; Donkó, Zoltán; Wang, You-Nian; Schulze, Julian

    2016-06-01

    Self-organized spatial structures in the light emission from the ion-ion capacitive rf plasma of a strongly electronegative gas (CF4 ) are observed experimentally for the first time. Their formation is analyzed and understood based on particle-based kinetic simulations. These "striations" are found to be generated by the resonance between the driving radio frequency and the eigenfrequency of the ion-ion plasma (derived from an analytical model) that establishes a modulation of the electric field, the ion densities, as well as the energy gain and loss processes of electrons in the plasma. The growth of the instability is followed by the numerical simulations.

  7. Low Frequency Waves Through the Gulf of California: Observations and Models

    NASA Astrophysics Data System (ADS)

    Flores-Morales, A. L.; Pares-Sierra, A.

    2007-05-01

    Long time series of sea surface temperature and surface height along the Mexican Pacific coast show that propagating coastal Kelvin waves, some cases propagate to the interior of the Gulf of California, while in some other cases they completely skip the gulf and the waves propagate through the gulf mouth to the western side of the peninsula de Baja California and to the north. Using satellite observations to identified events and a combination of numerical (ROMS) and analytical model, we investigate this phenomena focusing on discerning the set of conditions (mainly intensity and frequency of the waves) that determine which of these two main outcomes develops. Preliminary results are presented.

  8. Comparison between Modern Violin Bridge and Baroque Violin Bridge by Photoelastic Observation and Frequency Analysis

    NASA Astrophysics Data System (ADS)

    Matsutani, Akihiro

    2004-05-01

    A comparison between the modern bridge and the baroque bridge of the violin by photoelastic observation was carried out. The relationship between the stress part and the hole is symmetric in the modern and baroque bridges. The measured spectral envelopes of baroque bridges are similar to those of modern bridges in D- or G-strings, and have peaks at a frequency higher than those of modern bridges in E-string. The visualization method as used in this study may provide hints for the design of violin bridges.

  9. Frequency Calibration of Molecular Line Observing System of the TM65m Radio Telescope

    NASA Astrophysics Data System (ADS)

    Li, J.; Wu, Y. J.; Qiao, H. H.; Wang, J. Z.; Zuo, X. T.

    2015-11-01

    In order to carry out molecular line observations with the TM65m radio telescope, we carry out the frequency calibration and test observations of DIBAS (Digital Backend System), which is the spectrometer of the telescope. First, we test the performance of DIBAS with PCAL signals. We find that the spectral resolution is equal to the channel width, and the inaccuracy of spectral resolution is much lower than the channel width. Second, we observed hhco\\ lines toward two sources. The centroid velocity of calibrated data is consistent with GBT (Robert C. Byrd Green Bank Telescope) observations. At last, we observed 1665 MHz OH maser lines toward W3(OH) for one hour. The line shapes keep stable, and the RMS (Root Mean Squares) noise levels are consistent with theoretical values. We also observed 6.7 GHz methanol masers toward W3(OH) for several scans with a separation of about one hour. The line shapes of each scans are well consistent with each other.

  10. Veritas Observations of Relativistic Outflows in - and Intermediate-Frequency BL Lac Objects

    NASA Astrophysics Data System (ADS)

    Prokoph, Heike

    2014-03-01

    The majority of blazars detected at very high energies (VHE; E > 100 GeV) are high-frequency-peaked BL Lac objects (HBLs). Low- and intermediate-frequency-peaked BL Lacs (LBLs/IBLs with synchrotron-peak frequencies in the infrared and optical regime) are generally more powerful, more luminous, and have a richer jet environment than HBLs. However, only a handful of these IBL and LBLs have been detected by ground-based gamma-ray telescopes, typically during high-flux states. The VERITAS array has been monitoring five known VHE LBLs/IBLs since 2009: 3C 66A, W Comae, PKS 1424+240, S5 0716+714 and BL Lacertae, with typical exposures of 5-10 hours per year. The results of these long-term observations are presented, including a bright, subhour-scale VHE flare of BL Lacertae in June 2011, the first low-state detections of 3C 66A and W Comae, and the detection and characterization of the IBL B2 1215+30.

  11. Experimental observation on a frequency spectrum of a plate mode of a predominantly leaky nature

    PubMed

    Durinck; Thys; Rembert; Izbicki

    1999-06-01

    The problem of normal propagation modes of a plate submerged in a fluid is usually treated by considering continuous leaky Lamb waves or by considering transient waves. Angular plate resonances are associated with modes obtained by the first approach, whereas frequency plate resonances are associated with modes obtained using the second method. The dispersion curves for these two kinds of mode are almost identical, except for certain modes at large phase speed. In an experiment one is never dealing with one of these extreme situations because the applied signal is never infinitely long and the beam used to insonify the plate is never infinitely wide. In this paper we report on the manifestation in the transmission frequency spectrum, of a plate mode of a predominantly leaky nature. The extra mode, which has never been reported on, is observed between the cutoff frequencies of the symmetrical transient modes S1 and S2 of a submerged aluminium plate. The modes are identified by means of an Argand diagram. PMID:10499808

  12. Multi-frequency observation of high mass X-ray binary Cygnus X-3 during flares

    NASA Astrophysics Data System (ADS)

    Pal, Sabyasachi; Patra, Dusmanta; Ishwara-Chandra, C. H.; Rao, A. P.

    2016-07-01

    We studied the multi-frequency properties of the Galactic high mass X-ray binary Cygnus X-3 during various flaring activities using The Rossi X-ray Timing Explorer (RXTE), the Giant Metrewave Radio Telescope (GMRT), Jansky Very Large Array (JVLA) etc. The flare of 2006 May-June was one of the largest flare in the history of the source which is thoroughly discussed. We also observed few large flares of this source between 2007 and 2009. We commented on correlation and lag between X-ray and radio emissions during flares. We construct the radio spectrum of the source in the rising and fading phase of flares using GMRT, JVLA and published results using RATAN. We clearly see that the turn-over frequency is shifting towards lower frequencies as the flares evolve gradually. The two point spectral index between 614 MHz and 235 MHz varies from positive (optically thick) and negative (optically thin) values which is consistent with the synchrotron self absorption model. We calculated some physical parameters of the source such as the size of emitting region using the synchrotron self absorption model. The size of the emitting region expands with the flare. We estimate the velocity of the expansion of the blob in the non-relativistic range from the expansion of the size of emitting region.

  13. 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

  14. An Innovative Dual Frequency PPP Model for Combined GPS/Galileo Observations

    NASA Astrophysics Data System (ADS)

    Afifi, Akram; El-Rabbany, Ahmed

    2015-03-01

    This paper develops a new dual-frequency precise point positioning model, which combines GPS and Galileo observables. The addition of Galileo satellite system offers more visible satellites to the user, which is expected to enhance the satellite geometry and the overall PPP solution in comparison with GPS-only PPP solution. However, combining GPS and Galileo observables introduces additional biases, which require rigorous modelling, including the GPS to Galileo time offset, and Galileo satellite hardware delay. In this research, a GPS/Galileo ionosphere-free linear combination PPP model is developed. The additional biases of the GPS/Galileo combination are lumped and accounted for through the introduction of a new unknown parameter, inter-systems bias, in the PPP mathematical model. It is shown that a subdecimeter positioning accuracy level and 25% reduction in the solution convergence time can be achieved with the developed GPS/Galileo PPP model.

  15. LOW-FREQUENCY RADIO OBSERVATIONS OF PICOFLARE CATEGORY ENERGY RELEASES IN THE SOLAR ATMOSPHERE

    SciTech Connect

    Ramesh, R.; Sasikumar Raja, K.; Kathiravan, C.; Satya Narayanan, A.

    2013-01-10

    We report low-frequency (80 MHz) radio observations of circularly polarized non-thermal type I radio bursts ({sup n}oise storms{sup )} in the solar corona whose estimated energy is {approx}10{sup 21} erg. These are the weakest energy release events reported to date in the solar atmosphere. The plot of the distribution of the number of bursts (dN) versus their corresponding peak flux density in the range S to S+dS shows a power-law behavior, i.e., dN {proportional_to} S {sup {gamma}} dS. The power-law index {gamma} is in the range -2.2 to -2.7 for the events reported in the present work. The present results provide independent observational evidence for the existence of picoflare category energy releases in the solar atmosphere which are yet to be explored.

  16. Observation of modes at frequencies near the second Alfven gap in TFTR

    SciTech Connect

    Fredrickson, E.; Van Dam, J. W.; Budny, R. V.; Darrow, D.; Fu, G. Y.; Hosea, J.; Phillips, C. K.; Wilson, J. R.

    1999-09-20

    Modes have been observed near the frequency of the second Alfven gap during off-axis H-minority heating experiments on TFTR. The observation of these modes is surprising in that the second gap, which is generally opened with ellipticity, is expected to be small, of order (r/R){sup 2}, since TFTR plasmas are circular in cross-section. A model is proposed in which the second gap is opened by the fast ion beta, which is shown to be able to introduce mode coupling, much as toroidal effects introduce mode coupling for Toroidal Alfven Eigenmodes (TAE). The modes are seen with and without accompanying TAE mode activity. (c) 1999 American Institute of Physics.

  17. Comparison of flood frequency estimates from synthetic and observed data on small drainage areas in Mississippi

    USGS Publications Warehouse

    Colson, B.E.

    1986-01-01

    In 1964 the U.S. Geological Survey in Mississippi expanded the small stream gaging network for collection of rainfall and runoff data to 92 stations. To expedite availability of flood frequency information a rainfall-runoff model using available long-term rainfall data was calibrated to synthesize flood peaks. Results obtained from observed annual peak flow data for 51 sites having 16 yr to 30 yr of annual peaks are compared with the synthetic results. Graphical comparison of the 2, 5, 10, 25, 50, and 100-year flood discharges indicate good agreement. The root mean square error ranges from 27% to 38% and the synthetic record bias from -9% to -18% in comparison with the observed record. The reduced variance in the synthetic results is attributed to use of only four long-term rainfall records and model limitations. The root mean square error and bias is within the accuracy considered to be satisfactory. (Author 's abstract)

  18. Observed frequency-independent torque in flagellar bacterial motors optimizes space exploration.

    PubMed

    Di Salvo, Mario E; Condat, C A

    2012-12-01

    A surprising feature of many bacterial motors is the apparently conserved form of their torque-frequency relation. Experiments indicate that the torque provided by the bacterial rotary motor is approximately constant over a large range of angular speeds. This is observed in both monotrichous and peritrichous bacteria, independently of whether they are propelled by a proton flux or by a Na(+) ion flux. If the relation between angular speed ω and swimming speed is linear, a ω-independent torque implies that the power spent in active motion is proportional to the instantaneous bacterial speed. Using realistic values of the relevant parameters, we show that a constant torque maximizes the volume of the region explored by a bacterium in a resource-depleted medium. Given that nutrients in the ocean are often concentrated in separate, ephemeral patches, we propose that the observed constancy of the torque may be a trait evolved to maximize bacterial survival in the ocean. PMID:23367976

  19. Dual-frequency and dual-polarization VLBI observations of the stellar system Algol

    NASA Technical Reports Server (NTRS)

    Lestrade, Jean-Francois; Mutel, Robert L.; Preston, Robert A.; Phillips, Robert B.

    1988-01-01

    Results of multiepoch VLBI observations of the stellar system Algol are presented, including dual-polarization and dual-frequency measurements at 2.3 and 8.4 GHz. The brightness temperature of the radio source is generally between 3 x 10 to the 8th K and 5 x 10 to the 9th K and is consistent with gyrosynchrotron emission from energetic electrons with mean energy less than 1 MeV in an active coronal region. Two exceptional events were observed: a high-brightness, broad-band outburst occurring simultaneously at 2.3 and 8.4 GHz, and a short-duration, highly polarized and high-brightness temperature outburst at 1.66 GHz. A simple physical model which includes all three types of emission is suggested.

  20. Observing the Moon at Microwave Frequencies Using a Large-Diameter Deep Space Network Antenna

    NASA Astrophysics Data System (ADS)

    Morabito, David D.; Imbriale, William; Keihm, Stephen

    2008-03-01

    The Moon radiates energy at infrared and microwave wavelengths, in addition to reflecting sunlight at optical wavelengths. As a result, an antenna pointed at or near the Moon will result in an increase in system operating noise temperature, which needs to be accounted for in RF telecommunications, radio science or radiometric link calculations. The NASA Deep Space Network (DSN) may use its large-diameter antennas in future lunar robotic or human missions, and thus it is important to understand the nature of this temperature incre ase as a function of observing frequency, lunar phase, and angular position of the antenna beam on the lunar disk. This paper reports on a comprehensive lunar noise temperature measurement campaign and associated theoretical treatment for a 34-m diameter Deep Space Network antenna observing an extended source such as the Moon. A set of measurements over a wide range of lunar phase angles was acquired at DSS-13, a 34-m diameter beam waveguide antenna (BWG) located at Goldstone, California at 2.3 GHz (S-band), 8.4 GHz (X-band) and 32 GHz (Ka-band). For validation purposes, independent predictions of noise temperature increase were derived using a physical optics characterization of the 34-m diameter antenna gain patterns and Apollo model-based brightness temperature maps of the Moon as input. The model-based predictions of noise temperature increase were compared with the measurements at all three frequencies. In addition, a methodology is presented that relates noise temperature increase due to the Moon to disk-centered or disk-averaged brightness temperature of the Moon at the microwave frequencies of interest. Comparisons were made between the measurements and models in the domain of lunar disk-centered and disk-averaged brightness temperatures. It is anticipated that the measurements and associated theoretical development will be useful in developing telecommunications strategies for future high-rate Ka-band communications where large

  1. High spatial resolution radar observations of ultralow frequency waves in the southern polar cap

    NASA Astrophysics Data System (ADS)

    Bland, Emma C.; McDonald, Andrew J.

    2016-05-01

    We present an analysis of ultralow frequency (ULF) waves detected in the southern polar cap using the Super Dual Auroral Radar Network (SuperDARN). These waves manifest as quasi-sinusoidal oscillations in the Doppler velocity, which arise due to the oscillating ULF wave electric field in the F region ionosphere. The event reported in this study occurred during the southern polar winter under quiet geomagnetic conditions. The 1.1-1.3 mHz oscillations were observed throughout the polar cap by the McMurdo, Dome C East, and South Pole Station SuperDARN radars and also by the Dome Concordia and Scott Base magnetometers at corrected geomagnetic latitudes of ˜89°S and ˜80°S, respectively. In contrast to large-scale toroidal field line resonances observed at auroral latitudes, we find that the magnetic perturbation vector of the polar cap oscillations did not undergo a 90° rotation upon transmission from the ionosphere to the ground and was instead rotated by about 30°. The polar cap oscillations were also accompanied by simultaneous field line resonance (FLR) activity in the dayside auroral zone, in the field of view of the Zhongshan SuperDARN radar. This FLR occurred at the same frequency and exhibited a similar azimuthal phase velocity to the polar cap oscillations, indicating that they may have been driven by the same source mechanism.

  2. Field observation of low-to-mid-frequency acoustic propagation characteristics of an estuarine salt wedge.

    PubMed

    Reeder, D Benjamin

    2016-01-01

    The estuarine environment often hosts a salt wedge, the stratification of which is a function of the tide's range and speed of advance, river discharge volumetric flow rate, and river mouth morphology. Competing effects of temperature and salinity on sound speed in this stratified environment control the degree of acoustic refraction occurring along an acoustic path. A field experiment was carried out in the Columbia River Estuary to test the hypothesis: the estuarine salt wedge is acoustically observable in terms of low-to-mid-frequency acoustic propagation. Linear frequency-modulated acoustic signals in the 500-2000 Hz band were transmitted during the advance and retreat of the salt wedge during May 27-29, 2013. Results demonstrate that the salt wedge front is the dominant physical mechanism controlling acoustic propagation in this environment: received signal energy is relatively stable before and after the passage of the salt wedge front when the acoustic path consists of a single medium (either entirely fresh water or entirely salt water), and suffers a 10-15 dB loss and increased variability during salt wedge front passage. Physical parameters and acoustic propagation modeling corroborate and inform the acoustic observations. PMID:26827001

  3. Sea level measurements using multi-frequency GPS and GLONASS observations

    NASA Astrophysics Data System (ADS)

    Löfgren, Johan S.; Haas, Rüdiger

    2014-12-01

    Global Positioning System (GPS) tide gauges have been realized in different configurations, e.g., with one zenith-looking antenna, using the multipath interference pattern for signal-to-noise ratio (SNR) analysis, or with one zenith- and one nadir-looking antenna, analyzing the difference in phase delay, to estimate the sea level height. In this study, for the first time, we use a true Global Navigation Satellite System (GNSS) tide gauge, installed at the Onsala Space Observatory. This GNSS tide gauge is recording both GPS and Globalnaya Navigatsionnaya Sputnikovaya Sistema (GLONASS) signals and makes it possible to use both the one- and two-antenna analysis approach. Both the SNR analysis and the phase delay analysis were evaluated using dual-frequency GPS and GLONASS signals, i.e., frequencies in the L-band, during a 1-month-long campaign. The GNSS-derived sea level results were compared to independent sea level observations from a co-located pressure tide gauge and show a high correlation for both systems and frequency bands, with correlation coefficients of 0.86 to 0.97. The phase delay results show a better agreement with the tide gauge sea level than the SNR results, with root-mean-square differences of 3.5 cm (GPS L1 and L2) and 3.3/3.2 cm (GLONASS L1/L2 bands) compared to 4.0/9.0 cm (GPS L1/L2) and 4.7/8.9 cm (GLONASS L1/L2 bands). GPS and GLONASS show similar performance in the comparison, and the results prove that for the phase delay analysis, it is possible to use both frequencies, whereas for the SNR analysis, the L2 band should be avoided if other signals are available. Note that standard geodetic receivers using code-based tracking, i.e., tracking the un-encrypted C/A-code on L1 and using the manufacturers' proprietary tracking method for L2, were used. Signals with the new C/A-code on L2, the so-called L2 C , were not tracked. Using wind speed as an indicator for sea surface roughness, we find that the SNR analysis performs better in rough sea

  4. Near-field Observations of Very-low-frequency Earthquakes on the San Andreas Fault

    NASA Astrophysics Data System (ADS)

    Peña-Castro, A. F.; Harrington, R. M.; Cochran, E. S.

    2015-12-01

    Fault rupture at varying time scales has been detected in multiple subduction zones, e.g., in slow-slip events (SSEs), very-low-frequency earthquakes (VLFEs), and low-frequency earthquakes (LFEs) or tectonic tremor. However, only LFEs or tremor have been identified and studied in detail along strike-slip faults, like the San Andreas Fault (SAF). Here, we present evidence for VLFEs on the SAF near Parkfield, California. Using data from permanent broadband stations and a temporary deployment of 13 broadband stations installed in 2010-2011 near Cholame, California, we detect 5 VLFEs, with 1 VLFE occurring unambiguosly when there is visible tremor activity. We check that the signals we detect are local by confirming that they appear only on stations within a 70 km radius, and removing time periods when teleseismic events occur, as identified in the global Centroid Moment Tensor (CMT) and the Northern California Seismic Network (NCSN) catalogs. VLFEs have to-date been observed to only occur simultaneously in time and space with tremor activity, but our detections suggests that VLFEs can occur independent of tremor along strike-slip faults. This may indicate that the slipping patches that produce slow earthquakes in transform faults have different mechanical properties than the patches in subducting plates, althought it does not rule out that VLFEs are only observed with tremor in subduction zones simply due to detection methods. An approximate estimation of the apparent velocity, based on a grid-search location using variance reduction, suggests that the observed phase velocity of the VLFEs is ~ 3km/s, corresponding to surface waves. We perform a focal mechanism inversion with a grid search to find a more precise location, depth and orientation of the VLFEs. These results provide new insight into the behavior of the SAF and more generally contribute to an improved understanding of transform fault systems.

  5. 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

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

    PubMed 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

  7. 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.

  8. Evidence of low frequency waves penetration in the ionosphere observed by Chibis-M satellite

    NASA Astrophysics Data System (ADS)

    Pronenko, Vira; Dudkin, Fedir; Korepanov, Valery

    2016-07-01

    Chibis-M microsatellite (MS) was launched using ISS infrastructure to the 500 km circular orbit with inclination 52° and successfully operated during the years 2012-2014. One of the main tasks of this experiment was the study of how powerful natural and technogenic processes are reflected in the ionosphere. For this study, the magnetic wave complex (MWC) was used which measured one electrical component and three components of the magnetic vector in the frequency range 0.1 Hz-40 kHz. Due to the proximity of the magnetic sensors and the satellite control system, their high sensitivity (up to 0.02 pT/sqrt(Hz)) was not used in full because the level of magnetic noise was about 10 pT/sqrt(Hz) in the low-frequency range. Nevertheless, owing to the symmetric fixation of the electric probes relative to the satellite body, the electrical sensor provided high accuracy measurements (about 0.8-0.04 (µV/m)/sqrt(Hz)) in the frequency range of 0.1-40 000 Hz, despite the very small measurement base of 0.42 m. This allowed us to collect valuable information which revealed a number of interesting physical effects, especially in ultralow frequency (ULF) range. In ULF range the ionospheric emissions with a central frequency of 50 (60) Hz - power line emissions (PLE) and the Schumann resonance harmonics (SR) were detected, though, according to the present model of the ionosphere, they have not penetrate there. A detailed study of the obtained data revealed the features of PLE and SR. The spatial distribution of PLE and their connection with the power lines location on the ground were analyzed. It was found that the intensity of PLE depends on the load characteristics of the power line and usually has a minimum in the morning. The cases of an extra long distance of PLE propagation in the Earth's ionosphere over oceans in the equatorial region have been also observed. Further, it was detected that PLE has been recorded both in the shaded and sunlit parts of the orbits and their

  9. Observations on the Reliability of Rubidium Frequency Standards on Block 2/2A GPS Satellites

    NASA Technical Reports Server (NTRS)

    Dieter, Gary L.

    1996-01-01

    Currently, the block 2/2A Global Positioning System (GPS) satellites are equipped with two rubidium frequency standards. These frequency standards were originally intended to serve as the back-ups to two cesium frequency standards. As the constellation ages, the master Control Station is forced to initialize and increasing number or rubidium frequency standards. Unfortunately the operational use of these frequency standards has not lived up to initial expectations. Although the performance of these rubidium frequency standards has met and even exceeded GPS requirements, their reliability has not. The number of unscheduled outage times and the short operational lifetimes of the rubidium frequency standards compare poorly to the track record of the cesium frequency standards. Only a small number of rubidium frequency standards have actually been made operational. Of these, a large percentage have exhibited poor reliability. If this trend continues, it is unlikely that the rubidium frequency standards will help contribute to the navigation payload meeting program specification.

  10. MESSENGER Magnetic Field Observations of Upstream Ultra-Low Frequency Waves at Mercury

    NASA Technical Reports Server (NTRS)

    Le, G.; Chi, P. J.; Boardsen, S.; Blanco-Cano, X.; Anderosn, B. J.; Korth, H.

    2012-01-01

    The region upstream from a planetary bow shock is a natural plasma laboratory containing a variety of wave particle phenomena. The study of foreshocks other than the Earth's is important for extending our understanding of collisionless shocks and foreshock physics since the bow shock strength varies with heliocentric distance from the Sun, and the sizes of the bow shocks are different at different planets. The Mercury's bow shock is unique in our solar system as it is produced by low Mach number solar wind blowing over a small magnetized body with a predominately radial interplanetary magnetic field. Previous observations of Mercury upstream ultra-low frequency (ULF) waves came exclusively from two Mercury flybys of Mariner 10. The MESSENGER orbiter data enable us to study of upstream waves in the Mercury's foreshock in depth. This paper reports an overview of upstream ULF waves in the Mercury's foreshock using high-time resolution magnetic field data, 20 samples per second, from the MESSENGER spacecraft. The most common foreshock waves have frequencies near 2 Hz, with properties similar to the I-Hz waves in the Earth's foreshock. They are present in both the flyby data and in every orbit of the orbital data we have surveyed. The most common wave phenomenon in the Earth's foreshock is the large-amplitude 30-s waves, but similar waves at Mercury have frequencies at near 0.1 Hz and occur only sporadically with short durations (a few wave cycles). Superposed on the "30-s" waves, there are spectral peaks at near 0.6 Hz, not reported previously in Mariner 10 data. We will discuss wave properties and their occurrence characteristics in this paper.

  11. HLA alleles and haplotypes among the Lakota Sioux: report of the ASHI minority workshops, part III.

    PubMed

    Leffell, Mary S; Fallin, M Daniele; Hildebrand, William H; Cavett, Joshua W; Iglehart, Brian A; Zachary, Andrea A

    2004-01-01

    Human leukocyte antigen (HLA) class I and II alleles were defined for 302 Lakota Sioux American Indians as part of the American Society for Histocompatibility and Immunogenetics coordinated studies on minority populations. The study group was comprised of adult volunteers from the Cheyenne River and Ogala Sioux tribes residing, respectively, on the Cheyenne River and Pine Ridge Reservations in South Dakota. Of the participants, 263 (87%) claimed full American Indian ancestry through both maternal and paternal grandparents. The study group included 25 nuclear families that were informative for genotyping. HLA phenotypes from 202 adults with no other known first-degree relative included in the study were used for calculation of allele and haplotype frequencies by maximum likelihood estimation. HLA-A, -B, and -Cw alleles were found to be in Hardy Weinberg equilibrium. Deviation from equilibrium was observed for DRB1 alleles (p=0.01), but could be attributed to the sample size and the occurrence of some genotypes with low expected frequencies. Polymorphism among the Sioux was limited with four to seven alleles comprising >80% of those observed at each locus. Several alleles were found at high frequency (0.05-0.30) among the Sioux that are also prevalent in other Native Americans and Alaska Natives, including: A*2402, *3101, and *0206; B*3501,*3901, *5101, and *2705; Cw*0702, *0404, and *03041; DRB1*0407, *0404, *1402, and *16021; and DQB1*0301, *0302, and *0402. DRB1*0811, which has been only previously described in Navajo and Tlingit Indians, was found to occur at a frequency of 0.119 among the Sioux. Two new alleles were defined among the Sioux: Cw*0204 and DRB1*040703, which were found in two and four individuals, respectively. In the haplotype analyses, significant linkage disequilibrium (p<0.00001) was seen in all pairwise comparisons of loci and numerous two and three locus haplotypes were found to have strong, positive linkage disequilibrium values. The two most

  12. 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

  13. Stellar radial velocities using a laser frequency comb: Application and observations in the near infrared

    NASA Astrophysics Data System (ADS)

    Osterman, Steve

    2011-04-01

    The laser frequency comb presents the potential for a revolutionary increase in radial velocity precision by providing a calibration reference of unprecedented quality in terms of wavelength knowledge, repeatability, number, density, and regularity of lines. However, implementation has proven challenging, particularly in the near infrared. Nevertheless, with the right combination of comb and instrument, promising first steps have been taken, allowing for the derivation of stellar radial velocities in a wavelength range which is well suited to the observation of M dwarfs. These stars, with low mass and low luminosity, are the most prevalent class of stars within 10 parsecs and can be expected to yield a higher reflex velocity for a terrestrial mass planet in the liquid water habitable zone than would be the case with a more massive star such as our own. We present the design and both laboratory and on-sky performance of an H-band laser frequency comb used in conjunction with the Penn State Pathfinder testbed spectrograph and discuss lessons learned and plans for follow on testing with both the Pathfinder and the CSHELL instruments.

  14. Developments of frequency comb microwave reflectometer for the interchange mode observations in LHD plasma

    NASA Astrophysics Data System (ADS)

    Soga, R.; Tokuzawa, T.; Watanabe, K. Y.; Tanaka, K.; Yamada, I.; Inagaki, S.; Kasuya, N.

    2016-02-01

    We have upgraded the multi-channel microwave reflectometer system which uses a frequency comb as a source and measure the distribution of the density fluctuation caused by magneto-hydro dynamics instability. The previous multi-channel system was composed of the Ka-band, and the U-band system has been developed. Currently, the U-band system has eight frequency channels, which are 43.0, 45.0, 47.0, 49.0, 51.0, 53.0, 55.0, and 57.0 GHz, in U-band. Before the installation to the Large Helical Device (LHD), several tests for understanding the system characteristics, which are the phase responsibility, the linearity of output signal, and others, have been carried out. The in situ calibration in LHD has been done for the cross reference. In the neutral beam injected plasma experiments, we can observe the density fluctuation of the interchange mode and obtain the radial distribution of fluctuation amplitude.

  15. Electromagnetic waves with frequencies near the local proton gyrofrequency: ISEE-3 1 AU observations

    NASA Technical Reports Server (NTRS)

    Tsurutani, Bruce T.; Arballo, John K.; Mok, John; Smith, Edward J.; Mason, Glenn M.; Tan, Lun C.

    1994-01-01

    Low Frequency (LF) electromagnetic waves with periods near the local proton gyrofrequency have been detected in interplanetary space by the magnetometer onboard International-Sun-Earth-Explorer-3 (ISEE-3). Transverse peak-to-peak amplitudes as large as delta vector B/absolute value of B approximately 0.4 have been noted with compressional components (Delta absolute value of B/absolute value of B) typically less than or = 0.1. Generally, the waves have even smaller amplitudes, or are not detectable within the solar wind turbulence. The waves are elliptically/linearly polarized and are often, but not always, found to propagate nearly along vector B(sub zero). Both right- and left-hand polarizations in the spacecraft-frame have been detected. The waves are observed during all orientations of the interplanetary magnetic field, with the Parker spiral orientation being the most common case. Because the waves are detected at and near the local proton cyclotron frequency, the generation mechanism must almost certainly be solar wind pickup of freshly created hydrogen ions. Possible sources for the hydrogen are the Earth's atmosphere, coronal mass ejections from the Sun, comets and interstellar neutral atoms. At this time it is not obvious which potential source is the correct one. Statistical tests employing over one year of ISEE-3 data will be done in the near future to eliminate/confirm some of these possibilities.

  16. Observations of high-frequency harmonic tremor in Fogo, Cape Verde Islands

    NASA Astrophysics Data System (ADS)

    Heleno, Sandra I. N.; Faria, Bruno V. E.; Bandomo, Zuleyka; Fonseca, João F. B. D.

    2006-11-01

    We report observations of high-frequency (HF) volcanic tremor, with spectral peaks in the band 5-20 Hz, recorded in Fogo Island, Cape Verde archipelago. Several occurrences are characterized by regularly spaced spectral peaks, but the fundamental frequency is missing. The signal is strong enough to be weakly detected on the southern islands of the archipelago, at distances of 20, 80 and 120 km from Fogo. This widespread detection of the HF tremor suggests that the propagation of the energy is made as T-waves propagating in the ocean sound channel. After correcting for site effects, the spatial pattern of amplitudes in Fogo and Brava Islands clearly indicates an offshore source. Active seamounts recently discovered in the vicinity of Fogo and Brava Islands [Hansteen, T.H., Grevemeyer, I., Hanel, K., Kraus, G., Schneider, J., Masson, D.G., Le Bas, T., Faria, B., 2006. Seamounts at the Cape Verde Islands: the geosphere-hydrosphere-biosphere connection, Seamount Biogeosciences Network, Workshop volume, La Jolla, March 24-25, 2006, 27-29.] are proposed to be the source of the HF tremor.

  17. Spectral analysis of temperature and Brunt-Vaisala frequency fluctuations observed by radiosondes

    NASA Technical Reports Server (NTRS)

    Tsuda, T.; Vanzandt, T. E.; Kato, S.; Fukao, S.; Sato, T.

    1989-01-01

    Recent studies have revealed that vertical wave number spectra of wind velocity and temperture fluctuations in the troposphere and the lower stratosphere are fairly well explained by a saturated gravity wave spectrum. But N(2) (N:Brunt-Vaisala (BV) frequency) spectra seem to be better for testing the scaling of the vertical wave number spectra in layers with different stratifications, beause its energy density is proportional only to the background value of N(2), while that for temperature depends on both the BV frequency and the potential temperature. From temperature profiles observed in June to August 1987 over the MU Observatory, Japan, by using a radiosonde with 30 m height resolution, N(2) spectra are determined in the 2 to 8.5 km (troposphere) and 18.5 to 25 km (lower stratosphere) ranges. Although individual spectra show fairly large day-by-day variability, the slope of the median of 34 spectra agrees reasonably with the theoretical value of -1 in the wave number range of 6 x 10(-4) similar to 3 x 10(-3) (c/m). The ratio of the spectral energy between these two height regions is about equal to the ratio of N(2), consistent with the prediction of saturated gravity wave theory.

  18. 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.

  19. Multiyear high-frequency physical and environmental observations at the Guadiana Estuary

    NASA Astrophysics Data System (ADS)

    Garel, E.; Ferreira, Ó.

    2015-07-01

    High-frequency data collected continuously over a multiyear time frame are required for investigating the various agents that drive ecological and hydrodynamic processes in estuaries. Here, we present water quality and current in-situ observations from a fixed monitoring station operating from 2008 to 2014 in the lower Guadiana Estuary, southern Portugal (37°11.30' N, 7°24.67' W). The data were recorded by: a multi-parametric probe providing hourly records of temperature, chlorophyll, dissolved oxygen, turbidity, and pH at a water depth of ~ 1 m; and, a bottom-mounted acoustic Doppler current profiler measuring the pressure, near-bottom temperature, and flow velocity through the water column every 15 min. The time-series, in particular the probe one, present substantial data gaps arising from equipment failure and maintenance, which are ineluctable with this type of observations in harsh environments. However, prolonged (months-long) periods of observations during contrasted external forcing conditions are available. The raw data are reported together with quality flags indicating the status (valid/non-valid) of each record. Hourly river discharge data from two hydrographic stations located near the estuary head are also provided to support data analysis and interpretation. The dataset is publicly available at PANGAEA (doi:10.1594/PANGAEA.845750) in machine-readable format.

  20. Multi-year high-frequency physical and environmental observations at the Guadiana Estuary

    NASA Astrophysics Data System (ADS)

    Garel, E.; Ferreira, Ó.

    2015-11-01

    High-frequency data collected continuously over a multi-year time frame are required for investigating the various agents that drive ecological and hydrodynamic processes in estuaries. Here, we present water quality and current in situ observations from a fixed monitoring station operating from 2008 to 2014 in the lower Guadiana Estuary, southern Portugal (37°11.30' N, 7°24.67' W). The data were recorded by a multi-parametric probe providing hourly records (temperature, salinity, chlorophyll, dissolved oxygen, turbidity, and pH) at a water depth of ~ 1 m, and by a bottom-mounted acoustic Doppler current profiler measuring the pressure, near-bottom temperature, and flow velocity through the water column every 15 min. The time series data, in particular the probe ones, present substantial gaps arising from equipment failure and maintenance, which are ineluctable with this type of observation in harsh environments. However, prolonged (months-long) periods of multi-parametric observations during contrasted external forcing conditions are available. The raw data are reported together with flags indicating the quality status of each record. River discharge data from two hydrographic stations located near the estuary head are also provided to support data analysis and interpretation. The data set is publicly available in machine-readable format at PANGAEA (doi:10.1594/PANGAEA.845750).

  1. 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.

  2. MAVEN observation of an obliquely propagating low-frequency wave upstream of Mars

    NASA Astrophysics Data System (ADS)

    Ruhunusiri, Suranga; Halekas, J. S.; Connerney, J. E. P.; Espley, J. R.; McFadden, J. P.; Mazelle, C.; Brain, D.; Collinson, G.; Harada, Y.; Larson, D. E.; Mitchell, D. L.; Livi, R.; Jakosky, B. M.

    2016-03-01

    We report Mars Atmosphere and Volatile EvolutioN mission observations of a large amplitude low-frequency plasma wave that propagated oblique to the ambient magnetic field upstream of Mars along with a non-solar-wind plasma component that had a flow velocity perpendicular to the magnetic field. We consider nine possibilities for this wave that include various combinations of its propagation direction, polarization in the solar wind frame, and ion source responsible for its generation. Using the observed wave parameters and the measured plasma parameters as constraints, we uniquely identify the wave by systematically discarding these possibilities. We determine that the wave is a right-hand polarized wave that propagated upstream in the solar wind frame. We find two possibilities for the ion source that can be responsible for this wave generation. They are either newly born pickup protons or reflected solar wind protons from the bow shock. We determine that the observed non-solar-wind component is not responsible for the wave generation, and it is likely that the non-solar-wind component was merely perturbed by the passage of the wave.

  3. Picosecond laser-induced breakdown at 5321 and 5347 A - Observation of frequency-dependent behavior

    NASA Technical Reports Server (NTRS)

    Smith, W. L.; Bechtel, J. H.; Bloembergen, N.

    1977-01-01

    A study is presented of picosecond laser-induced breakdown at 3547 and 5321 A of several materials. The thresholds obtained for breakdown at 5321 A are compared to previous results obtained at 1.064 microns using the same laser system. This comparison illustrates the transition of bulk laser-induced breakdown as it becomes increasingly frequency dependent. UV picosecond pulses are obtained by mixing 5321 A and 1.064 micron pulses in a KH2PO4 crystal. Upper and lower bounds on the 3547 A breakdown threshold are defined, although some effects of walk-off distortion and self-focusing are observed. The results are discussed with reference to models for the intrinsic processes involved in the breakdown, i.e., avalanche and multiphoton ionization.

  4. Core damage frequency observations and insights of LWRs based on the IPEs

    SciTech Connect

    Dingman, S.E.; Camp, A.L.; Drouin, M.T.

    1995-04-01

    Seventy-eight plants are expected to submit Individual Plant Examinations (IPEs) for severe accident vulnerabilities to the US Nuclear Regulatory Commission (NRC). The majority of the plants have elected to perform full Level 1 probabilistic risk assessments (PRAs) to meet the intent of the IPEs. Because of this, it is possible to compare the results from the IPE submittals to determine general observations and {open_quotes}lessons learned{close_quotes} from the IPEs. The IPE Insights Program is performing this evaluation, and preliminary results are presented in this paper. The core damage frequency and core damage sequences are identified and compared for pressurized water reactors and boiling water reactors. Examination of the results indicates that variations among plant results are due to a combination of actual plant design/operational features and analysis approaches. The findings are consistent with previous NRC studies, such as WASH-1400 and NUREG-1150.

  5. Core damage frequency observations and insights of LWRs based on the IPEs

    SciTech Connect

    Dingman, S.E.; Camp, A.L.; Drouin, M.T.; Kolaczkowski, A.; Darby, J.; LaChance, J.L.; Yakle, J.

    1995-01-01

    Seventy-eight plants are expected to submit Individual Plant Examinations (IPEs) for severe accident vulnerabilities to the U.S. Nuclear Regulatory Commission (NRC). The majority of the plants have elected to perform full Level 1 probabilistic risk assessments (PRAs) to meet the intent of the IPES. Because of this, it is possible to compare the results from the IPE submittals to determine general observations and {open_quotes}lessons learned{close_quotes} from the IPES. The IPE Insights Program is performing this evaluation, and preliminary results are presented in this paper. The core damage frequency and core damage sequences are identified and compared for pressurized water reactors and boiling water reactors. Examination of the results indicates that variations among plant results are due to a combination of actual plant design/operational features and analysis approaches. The findings are consistent with previous NRC studies, such as WASH-1400 and NUREG-1 150.

  6. The Burden of JAK2V617F Mutated Allele in Turkish Patients With Myeloproliferative Neoplasms

    PubMed Central

    Yonal-Hindilerden, Ipek; Daglar-Aday, Aynur; Akadam-Teker, Basak; Yilmaz, Ceylan; Nalcaci, Meliha; Yavuz, Akif Selim; Sargin, Deniz

    2015-01-01

    Background Studies regarding the impact of JAK2V617F allele burden on phenotypic properties and clinical course in Philadelphia-negative myeloproliferative neoplasms (Ph-negative MPNs) have reported variable results. We aimed to analyze the association of mutated JAK2V617F allele burden with laboratory characteristics and clinical phenotype in Turkish patients (107 essential thrombocythemia (ET) and 77 primary myelofibrosis (PMF)). Methods Peripheral blood samples of 184 patients with Ph-negative MPNs were analyzed for JAK2V617F allele status and burden. JAK2 MutaScreen assay (Ipsogen, Luminy Biotech, Marseille, France) was used to detect the JAK2V617F status and quantitative JAK2V617F allele burdens in genomic DNA using TaqMan allelic discrimination. Results Frequency of JAK2V617F-positive patients with high mutation load (allele burden > 50%) was higher in PMF compared to ET (23.4% and 4.7%, respectively; P = 0.001). We found significant association between ET patients with high JAK2V617F allele burden and lower hemoglobin (Hgb) and hematocrit (Hct), higher LDH levels and more prevalent massive splenomegaly (P = 0.001, P = 0.001, P = 0.012 and P = 0.015, respectively). ET patients with high mutation load displayed higher prevalence of bleeding compared to low mutation load and wild-type mutational status (P = 0.003). Rate of DVT was significantly higher in ET patients with mutant allele burden in upper half compared to lower half and wild-type (P = 0.029). We observed significant association between PMF patients with high JAK2V617F allele burden and higher Hgb, Hct levels and leukocyte counts (P = 0.003, P = 0.021 and P = 0.001, respectively). Conclusions Our study demonstrated JAK2V617F allele burden correlates with clinical features in ET and PMF. We conclude quantification of JAK2V617F mutation contributes to the workup of Ph-negative MPNs. PMID:25584101

  7. Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern.

    PubMed

    Trask, Amanda E; Bignal, Eric M; McCracken, Davy I; Monaghan, Pat; Piertney, Stuart B; Reid, Jane M

    2016-07-01

    Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However

  8. Observation of multi-scale oscillation of laminar lifted flames with low-frequency AC electric fields

    SciTech Connect

    Ryu, S.K.; Kim, Y.K.; Kim, M.K.; Won, S.H.; Chung, S.H.

    2010-01-15

    The oscillation behavior of laminar lifted flames under the influence of low-frequency AC has been investigated experimentally in coflow jets. Various oscillation modes were existed depending on jet velocity and the voltage and frequency of AC, especially when the AC frequency was typically smaller than 30 Hz. Three different oscillation modes were observed: (1) large-scale oscillation with the oscillation frequency of about 0.1 Hz, which was independent of the applied AC frequency, (2) small-scale oscillation synchronized to the applied AC frequency, and (3) doubly-periodic oscillation with small-scale oscillation embedded in large-scale oscillation. As the AC frequency decreased from 30 Hz, the oscillation modes were in the order of the large-scale oscillation, doubly-periodic oscillation, and small-scale oscillation. The onset of the oscillation for the AC frequency smaller than 30 Hz was in close agreement with the delay time scale for the ionic wind effect to occur, that is, the collision response time. Frequency-doubling behavior for the small-scale oscillation has also been observed. Possible mechanisms for the large-scale oscillation and the frequency-doubling behavior have been discussed, although the detailed understanding of the underlying mechanisms will be a future study. (author)

  9. Observation of the Mating Behavior of Honey Bee (Apis mellifera L.) Queens Using Radio-Frequency Identification (RFID): Factors Influencing the Duration and Frequency of Nuptial Flights

    PubMed Central

    Heidinger, Ina Monika Margret; Meixner, Marina Doris; Berg, Stefan; Büchler, Ralph

    2014-01-01

    We used radio-frequency identification (RFID) to record the duration and frequency of nuptial flights of honey bee queens (Apis mellifera carnica) at two mainland mating apiaries. We investigated the effect of a number of factors on flight duration and frequency: mating apiary, number of drone colonies, queen’s age and temperature. We found significant differences between the two locations concerning the number of flights on the first three days. We also observed an effect of the ambient temperature, with queens flying less often but longer at high temperatures compared to lower temperatures. Increasing the number of drone colonies from 33 to 80 colonies had no effect on the duration or on the frequency of nuptial flights. Since our results agree well with the results of previous studies, we suggest RFID as an appropriate tool to investigate the mating behavior of honey bee queens. PMID:26462822

  10. Observation of the Mating Behavior of Honey Bee (Apis mellifera L.) Queens Using Radio-Frequency Identification (RFID): Factors Influencing the Duration and Frequency of Nuptial Flights.

    PubMed

    Heidinger, Ina Monika Margret; Meixner, Marina Doris; Berg, Stefan; Büchler, Ralph

    2014-01-01

    We used radio-frequency identification (RFID) to record the duration and frequency of nuptial flights of honey bee queens (Apis mellifera carnica) at two mainland mating apiaries. We investigated the effect of a number of factors on flight duration and frequency: mating apiary, number of drone colonies, queen's age and temperature. We found significant differences between the two locations concerning the number of flights on the first three days. We also observed an effect of the ambient temperature, with queens flying less often but longer at high temperatures compared to lower temperatures. Increasing the number of drone colonies from 33 to 80 colonies had no effect on the duration or on the frequency of nuptial flights. Since our results agree well with the results of previous studies, we suggest RFID as an appropriate tool to investigate the mating behavior of honey bee queens. PMID:26462822

  11. CCN frequency distributions and aerosol chemical composition from long-term observations at European ACTRIS supersites

    NASA Astrophysics Data System (ADS)

    Decesari, Stefano; Rinaldi, Matteo; Schmale, Julia Yvonne; Gysel, Martin; Fröhlich, Roman; Poulain, Laurent; Henning, Silvia; Stratmann, Frank; Facchini, Maria Cristina

    2016-04-01

    Cloud droplet number concentration is regulated by the availability of aerosol acting as cloud condensation nuclei (CCN). Predicting the air concentrations of CCN involves knowledge of all physical and chemical processes that contribute to shape the particle size distribution and determine aerosol hygroscopicity. The relevance of specific atmospheric processes (e.g., nucleation, coagulation, condensation of secondary organic and inorganic aerosol, etc.) is time- and site-dependent, therefore the availability of long-term, time-resolved aerosol observations at locations representative of diverse environments is strategic for the validation of state-of-the-art chemical transport models suited to predict CCN concentrations. We focused on long-term (year-long) datasets of CCN and of aerosol composition data including black carbon, and inorganic as well as organic compounds from the Aerosol Chemical Speciation Monitor (ACSM) at selected ACTRIS supersites (http://www.actris.eu/). We discuss here the joint frequency distribution of CCN levels and of aerosol chemical components concentrations for two stations: an alpine site (Jungfraujoch, CH) and a central European rural site (Melpitz, DE). The CCN frequency distributions at Jungfraujoch are broad and generally correlated with the distributions of the concentrations of aerosol chemical components (e.g., high CCN concentrations are most frequently found for high organic matter or black carbon concentrations, and vice versa), which can be explained as an effect of the strong seasonality in the aerosol characteristics at the mountain site. The CCN frequency distributions in Melpitz show a much weaker overlap with the distributions of BC concentrations or other chemical compounds. However, especially at high CCN concentration levels, a statistical correlation with organic matter (OM) concentration can be observed. For instance, the number of CCN (with particle diameter between 20 and 250 nm) at a supersaturation of 0.7% is

  12. Catalog of low frequency oscillations of the earth's magnetic field as observed at ATS-1 during January 1968

    NASA Technical Reports Server (NTRS)

    Cummings, W. D.; Lyons, D.

    1974-01-01

    A catalog of ATS-1 observed magnetic field oscillations is presented. The catalog holds only those events with a duration of at least ten minutes and with a frequency that remains roughly constant. Events are distinguished on the basis of the frequency of oscillations. A comparison was made between ATS-1 data and other ground and satellite magnetometer data.

  13. Global Survey and Statistics of Radio-Frequency Interference in AMSR-E Land Observations

    NASA Technical Reports Server (NTRS)

    Njoku, Eni G.; Ashcroft, Peter; Chan, Tsz K.; Li, Li

    2005-01-01

    Radio-frequency interference (RFI) is an increasingly serious problem for passive and active microwave sensing of the Earth. To satisfy their measurement objectives, many spaceborne passive sensors must operate in unprotected bands, and future sensors may also need to operate in unprotected bands. Data from these sensors are likely to be increasingly contaminated by RFI as the spectrum becomes more crowded. In a previous paper we reported on a preliminary investigation of RFI observed over the United States in the 6.9-GHz channels of the Advanced Microwave Scanning Radiometer (AMSR-E) on the Earth Observing System Aqua satellite. Here, we extend the analysis to an investigation of RFI in the 6.9- and 10.7-GHz AMSR-E channels over the global land domain and for a one-year observation period. The spatial and temporal characteristics of the RFI are examined by the use of spectral indices. The observed RFI at 6.9 GHz is most densely concentrated in the United States, Japan, and the Middle East, and is sparser in Europe, while at 10.7 GHz the RFI is concentrated mostly in England, Italy, and Japan. Classification of RFI using means and standard deviations of the spectral indices is effective in identifying strong RFI. In many cases, however, it is difficult, using these indices, to distinguish weak RFI from natural geophysical variability. Geophysical retrievals using RFI-filtered data may therefore contain residual errors due to weak RFI. More robust radiometer designs and continued efforts to protect spectrum allocations will be needed in future to ensure the viability of spaceborne passive microwave sensing.

  14. Solar Observations at THz Frequencies on Board of a Trans-Antartic Stratospheric Balloon Flight

    NASA Astrophysics Data System (ADS)

    Kaufmann, Pierre; Abrantes, André; Bortolucci, Emilio; Caspi, Amir; Fernandes, Luis Olavo T.; Kropotov, Grigory; Kudaka, Amauri; Laurent, Glenn Thomas; Machado, Nelson; Marcon, Rogério; Marun, Adolfo; Nicolaev, Valery; Hidalgo Ramirez, Ray Fernando; Raulin, Jean-Pierre; Saint-Hilaire, Pascal; Shih, Albert; Silva, Claudemir; Timofeevsky, Alexander

    2016-05-01

    Sub-THz and 30 THz solar burst observations revealed a new spectral component, with fluxes increasing towards THz frequencies, simultaneously with the well known component peaking at microwaves, bringing challenging constraints for interpretation. The THz flare spectra can be completed with measurements made from space. A new system of two photometers was built to observe the Sun at 3 and 7 THz named SOLAR-T. An innovative optical setup allows observations of the full solar disk and detect small burst with sub-second time resolution. The photometers use two Golay cell detectors at the foci of 7.6 cm Cassegrain telescopes. The incoming radiation undergoes low-pass filters made of rough surface primary mirrors and membranes, 3 and 7 THz band-pass filters, and choppers. The system has been integrated to redundant data acquisition system and Iridium short-burst data services telemetry for monitoring during the flight. SOLAR-T has been flown coupled to U.C. Berkeley solar hard X-ray and gamma-ray imaging spectro-polarimeter GRIPS experiment launched on a NASA CSBF stratospheric balloon from U.S. McMurdo base on January 19, 2016, on a trans-Antarctic flight. The mission ended on January 30. The SOLAR-T on-board computers were recovered from the payload that landed in the Argentina Mountain Range, nearly 2100 km from McMurdo. The SOLAR-T performance was successfully attained, with full space qualification instrumentation. Preliminary results provide the solar disk THz brightness temperatures and indicate a 7 THz burst enhancement time coincident to a sub-THz burst observed by SST during the 28 January GOES C9.6 class soft X-ray burst, the largest occurred during the flight.

  15. Runoff-generated debris flows: Observations and modeling of surge initiation, magnitude, and frequency

    NASA Astrophysics Data System (ADS)

    Kean, Jason W.; McCoy, Scott W.; Tucker, Gregory E.; Staley, Dennis M.; Coe, Jeffrey A.

    2013-12-01

    during intense rainstorms plays a major role in generating debris flows in many alpine areas and burned steeplands. Yet compared to debris flow initiation from shallow landslides, the mechanics by which runoff generates a debris flow are less understood. To better understand debris flow initiation by surface water runoff, we monitored flow stage and rainfall associated with debris flows in the headwaters of two small catchments: a bedrock-dominated alpine basin in central Colorado (0.06 km2) and a recently burned area in southern California (0.01 km2). We also obtained video footage of debris flow initiation and flow dynamics from three cameras at the Colorado site. Stage observations at both sites display distinct patterns in debris flow surge characteristics relative to rainfall intensity (I). We observe small, quasiperiodic surges at low I; large, quasiperiodic surges at intermediate I; and a single large surge followed by small-amplitude fluctuations about a more steady high flow at high I. Video observations of surge formation lead us to the hypothesis that these flow patterns are controlled by upstream variations in channel slope, in which low-gradient sections act as "sediment capacitors," temporarily storing incoming bed load transported by water flow and periodically releasing the accumulated sediment as a debris flow surge. To explore this hypothesis, we develop a simple one-dimensional morphodynamic model of a sediment capacitor that consists of a system of coupled equations for water flow, bed load transport, slope stability, and mass flow. This model reproduces the essential patterns in surge magnitude and frequency with rainfall intensity observed at the two field sites and provides a new framework for predicting the runoff threshold for debris flow initiation in a burned or alpine setting.

  16. Runoff-generated debris flows: observations and modeling of surge initiation, magnitude, and frequency

    USGS Publications Warehouse

    Kean, Jason W.; McCoy, Scott W.; Tucker, Gregory E.; Staley, Dennis M.; Coe, Jeffrey A.

    2013-01-01

    Runoff during intense rainstorms plays a major role in generating debris flows in many alpine areas and burned steeplands. Yet compared to debris flow initiation from shallow landslides, the mechanics by which runoff generates a debris flow are less understood. To better understand debris flow initiation by surface water runoff, we monitored flow stage and rainfall associated with debris flows in the headwaters of two small catchments: a bedrock-dominated alpine basin in central Colorado (0.06 km2) and a recently burned area in southern California (0.01 km2). We also obtained video footage of debris flow initiation and flow dynamics from three cameras at the Colorado site. Stage observations at both sites display distinct patterns in debris flow surge characteristics relative to rainfall intensity (I). We observe small, quasiperiodic surges at low I; large, quasiperiodic surges at intermediate I; and a single large surge followed by small-amplitude fluctuations about a more steady high flow at high I. Video observations of surge formation lead us to the hypothesis that these flow patterns are controlled by upstream variations in channel slope, in which low-gradient sections act as “sediment capacitors,” temporarily storing incoming bed load transported by water flow and periodically releasing the accumulated sediment as a debris flow surge. To explore this hypothesis, we develop a simple one-dimensional morphodynamic model of a sediment capacitor that consists of a system of coupled equations for water flow, bed load transport, slope stability, and mass flow. This model reproduces the essential patterns in surge magnitude and frequency with rainfall intensity observed at the two field sites and provides a new framework for predicting the runoff threshold for debris flow initiation in a burned or alpine setting.

  17. Mesospheric potassium layer observation by a frequency-tunable resonance scattering lidar system

    NASA Astrophysics Data System (ADS)

    Ejiri, Mitsumu K.; Nakamura, Takuji; Kawahara, Takuya D.; Abo, Makoto; Nishiyama, Takanori; Tsuda, Takuo T.

    J/pulse at approximately 25 Hz (i.e., ~3-4 W) and the backscattered signal is received with a 83 cm (or 35 cm) diameter telescope. Three-frequency wind/temperature measurement method [She and Yu, 1994] is applied to measurement of K density and temperature profiles and the wavelengths of laser pulse are calibrated by an assumption that 1-hour mean of measured vertical wind speed is zero m/s. In this talk, current status of the system developments and the observation results of K density and temperature in the mid-latitude will be presented.

  18. FIRST SPECTROSCOPIC IMAGING OBSERVATIONS OF THE SUN AT LOW RADIO FREQUENCIES WITH THE MURCHISON WIDEFIELD ARRAY PROTOTYPE

    SciTech Connect

    Oberoi, Divya; Matthews, Lynn D.; Lonsdale, Colin J.; Benkevitch, Leonid; Cairns, Iver H.; Lobzin, Vasili; Emrich, David; Wayth, Randall B.; Arcus, Wayne; Morgan, Edward H.; Williams, Christopher; Prabu, T.; Vedantham, Harish; Williams, Andrew; White, Stephen M.; Allen, G.; Barnes, David; Bernardi, Gianni; Bowman, Judd D.; Briggs, Frank H.

    2011-02-20

    We present the first spectroscopic images of solar radio transients from the prototype for the Murchison Widefield Array, observed on 2010 March 27. Our observations span the instantaneous frequency band 170.9- 201.6 MHz. Though our observing period is characterized as a period of 'low' to 'medium' activity, one broadband emission feature and numerous short-lived, narrowband, non-thermal emission features are evident. Our data represent a significant advance in low radio frequency solar imaging, enabling us to follow the spatial, spectral, and temporal evolution of events simultaneously and in unprecedented detail. The rich variety of features seen here reaffirms the coronal diagnostic capability of low radio frequency emission and provides an early glimpse of the nature of radio observations that will become available as the next generation of low-frequency radio interferometers come online over the next few years.

  19. Combining Saturnian Craters and Kuiper Belt Observations to Build an Outer Solar System Impactor Size-Frequency Distribution

    NASA Astrophysics Data System (ADS)

    Minton, D. A.; Richardson, J. E.; Thomas, P.; Kirchoff, M.; Schwamb, M. E.

    2012-05-01

    Using Cassini mission imagery of the icy satellites of Saturn, numerical simulations, and telescopic observation data we produce a model size frequency distribution for outer solar system impactors spanning tens of meters to thousands of kilometers.

  20. Combining Saturnian Craters and Kuiper Belt Observations to Build an Outer Solar System Impactor Size-Frequency Distribution

    NASA Astrophysics Data System (ADS)

    Minton, D. A.; Richardson, J. E.; Thomas, P.; Kirchoff, M.; Schwamb, M. E.

    2012-03-01

    Using Cassini mission imagery of the icy satellites of Saturn, numerical simulations, and telescopic observation data we produce a model size frequency distribution for outer solar system impactors spanning tens of meters to thousands of kilometers.

  1. High frequency water quality and flow observations of a hypereutrophic Coastal Plain millpond

    NASA Astrophysics Data System (ADS)

    Andres, S.; Ullman, W. J.; Voynova, Y. G.

    2014-12-01

    Eutrophication due to runoff of N and P occurs in many impoundments in agricultural areas around the world with deleterious impacts on fisheries, drinking water, and recreational resources. Coursey Pond, a hypereutrophic, shallow, Coastal Plain mill pond located on the Murderkill River in central Delaware has seasonal algal blooms between May and October. High frequency automated water quality, meteorlogical, and flow observations initiated in June 2014 as part of the NEWRNet project provide insights into the relationships between hydrologic events, changes in water quality, and primary productivity. During blooms the pond becomes stratified, allowing for dissolved oxygen (DO) levels at the surface to exceed 150% saturation, while DO within 2 m of the surface to falls below 50% saturation. During fair weather turbidity and dissolved organic carbon (DOC) also gradually rise. Turbidity, DOC, and DO quickly decrease in response to storms and increased flow, indicating that storms are important regulators of water column stratification. Decreases in primary productivity due to decreased sunlight, dilution by addition of rain and runoff, and mixing in response to storm winds and flows abruptly end blooms, although they often return within a few days of storm events. Analysis of hourly meterological data will help determine the importance of solar insolation, winds, and rainfall intensity to the timing, rate, and magnitude of these water quality changes. Groundwater is the primary source of water to the streams that feed the pond and delivers nitrogen as nitrate. Historical grab sample nitrate concentration data from summer months (<1 mg/L) in comparison to winter months (4-8 mg/L) indicate that primary productivity consumes nearly all available nitrate during algal blooms, and perhaps improving water quality in downstream areas. There is no clear relationship between storms, flow and nitrate in the short period of high frequency observations, when nitrate concentrations

  2. Gamma Ray and Very Low Frequency Radio Observations from a Balloon-Borne Platform

    NASA Astrophysics Data System (ADS)

    Quinn, C.; Sheldon, A.; Cully, C. M.; Davalos, A.; Osakwe, C.; Galts, D.; Delfin, J.; Duffin, C.; Mansell, J.; Russel, M.; Bootsma, M.; Williams, R.; Patrick, M.; Mazzino, M. L.; Knudsen, D. J.

    2015-12-01

    The University of Calgary's Student Organization for Aerospace Research (SOAR) built an instrument to participate in the High Altitude Student Platform (HASP) initiative organized by Louisiana State University and supported by the NASA Balloon Program Office (BPO) and the Louisiana Space Consortium (LaSPACE). The HASP platform will be launched in early September 2015 from Fort Sumner, New Mexico and will reach heights of 36 kilometers with a flight duration of 15 to 20 hours. The instrument, Atmospheric Phenomenon Observer Gamma/VLF Emissions Experiment (APOGEE), measures Terrestrial Gamma-Ray Flashes (TGF) and sferics from lightning strikes with the use of Geiger tubes and a VLF detector. TGFs, which are quick bursts of high energy radiation that can occur alongside lightning, are believed to be the result of Relativistic Runaway Electron Avalanche (RREA). RREA occurs when a large number of relativistic electrons overcome atmospheric frictional forces and accelerate to relativistic velocities which excite secondary electrons that collide with the atmosphere causing bremsstrahlung radiation. Lightning strikes also produce sferics within the Extremely Low Frequency (ELF) and Very Low Frequency (VLF) bands which can be detected and used to locate the strikes. The goal of APOGEE is to further investigate the link between TGFs and RREA. These phenomena are very difficult to measure together as Bremsstrahlung radiation is easily detected from space but ionospheric reflection facilitates surface detection of sferics. A high altitude balloon provides a unique opportunity to study both phenomena using one instrument because both phenomena can easily be detected from its altitude. APOGEE has been designed and built by undergraduate students at the University of Calgary with faculty assistance and funding, and is equipped with three devices for data collection: a camera to have visual conformation of events, a series of Geiger Tubes to obtain directional gamma readings, and

  3. High frequency variations of Earth Rotation Parameters from GPS and GLONASS observations.

    PubMed

    Wei, Erhu; Jin, Shuanggen; Wan, Lihua; Liu, Wenjie; Yang, Yali; Hu, Zhenghong

    2015-01-01

    The Earth's rotation undergoes changes with the influence of geophysical factors, such as Earth's surface fluid mass redistribution of the atmosphere, ocean and hydrology. However, variations of Earth Rotation Parameters (ERP) are still not well understood, particularly the short-period variations (e.g., diurnal and semi-diurnal variations) and their causes. In this paper, the hourly time series of Earth Rotation Parameters are estimated using Global Positioning System (GPS), Global Navigation Satellite System (GLONASS), and combining GPS and GLONASS data collected from nearly 80 sites from 1 November 2012 to 10 April 2014. These new observations with combining different satellite systems can help to decorrelate orbit biases and ERP, which improve estimation of ERP. The high frequency variations of ERP are analyzed using a de-trending method. The maximum of total diurnal and semidiurnal variations are within one milli-arcseconds (mas) in Polar Motion (PM) and 0.5 milli-seconds (ms) in UT1-UTC. The semidiurnal and diurnal variations are mainly related to the ocean tides. Furthermore, the impacts of satellite orbit and time interval used to determinate ERP on the amplitudes of tidal terms are analyzed. We obtain some small terms that are not described in the ocean tide model of the IERS Conventions 2010, which may be caused by the strategies and models we used or the signal noises as well as artifacts. In addition, there are also small differences on the amplitudes between our results and IERS convention. This might be a result of other geophysical excitations, such as the high-frequency variations in atmospheric angular momentum (AAM) and hydrological angular momentum (HAM), which needs more detailed analysis with more geophysical data in the future. PMID:25635416

  4. High Frequency Variations of Earth Rotation Parameters from GPS and GLONASS Observations

    PubMed Central

    Wei, Erhu; Jin, Shuanggen; Wan, Lihua; Liu, Wenjie; Yang, Yali; Hu, Zhenghong

    2015-01-01

    The Earth's rotation undergoes changes with the influence of geophysical factors, such as Earth's surface fluid mass redistribution of the atmosphere, ocean and hydrology. However, variations of Earth Rotation Parameters (ERP) are still not well understood, particularly the short-period variations (e.g., diurnal and semi-diurnal variations) and their causes. In this paper, the hourly time series of Earth Rotation Parameters are estimated using Global Positioning System (GPS), Global Navigation Satellite System (GLONASS), and combining GPS and GLONASS data collected from nearly 80 sites from 1 November 2012 to 10 April 2014. These new observations with combining different satellite systems can help to decorrelate orbit biases and ERP, which improve estimation of ERP. The high frequency variations of ERP are analyzed using a de-trending method. The maximum of total diurnal and semidiurnal variations are within one milli-arcseconds (mas) in Polar Motion (PM) and 0.5 milli-seconds (ms) in UT1-UTC. The semidiurnal and diurnal variations are mainly related to the ocean tides. Furthermore, the impacts of satellite orbit and time interval used to determinate ERP on the amplitudes of tidal terms are analyzed. We obtain some small terms that are not described in the ocean tide model of the IERS Conventions 2010, which may be caused by the strategies and models we used or the signal noises as well as artifacts. In addition, there are also small differences on the amplitudes between our results and IERS convention. This might be a result of other geophysical excitations, such as the high-frequency variations in atmospheric angular momentum (AAM) and hydrological angular momentum (HAM), which needs more detailed analysis with more geophysical data in the future. PMID:25635416

  5. Preliminary Analysis of Observations on the Ultra-Low Frequency Electric Field in the Beijing Region

    NASA Astrophysics Data System (ADS)

    Zhuang, Jiancang; Vere-Jones, David; Guan, Huaping; Ogata, Yosihiko; Ma, Li

    2005-06-01

    This paper presents a preliminary analysis of observations on ultra-low frequency ground electric signals from stations operated by the China Seismological Bureau over the last 20 years. A brief description of the instrumentation, operating procedures and data processing procedures is given. The data analyzed consists of estimates of the total strengths (cumulated amplitudes) of the electric signals during 24-hour periods. The thresholds are set low enough so that on most days a zero observation is returned. Non-zero observations are related to electric and magnetic storms, occasional man-made electrical effects, and, apparently, some pre-, co-, or postseismic signals. The main purpose of the analysis is to investigate the extent that the electric signals can be considered as preseismic in character. For this purpose the electric signals from each of five stations are jointly analyzed with the catalogue of local earthquakes within circular regions around the selected stations. A version of Ogata’s Lin-Lin algorithm is used to estimate and test the existence of a pre-seismic signal. This model allows the effect of the electric signals to be tested, even after allowing for the effects of earthquake clustering. It is found that, although the largest single effect influencing earthquake occurrence is the clustering tendency, there remains a significant preseismic component from the electrical signals. Additional tests show that the apparent effect is not postseismic in character, and persists even under variations of the model and the time periods used in the analysis. Samples of the data are presented and the full data sets have been made available on local websites.

  6. Estimation of rockfall frequency from simulated trajectories and observed tree impacts

    NASA Astrophysics Data System (ADS)

    Monnet, Jean-Matthieu; Bourrier, Franck; Lopez Saez, Jérôme; Corona, Christophe

    2014-05-01

    While significant progress has been achieved regarding the modeling of rockfall propagation, including the interaction with forest cover, the estimation of the spatial distribution of rockfall frequency in release areas remains a challenging task. Indeed, the very low number of observed events makes any statistical modeling difficult, so that estimations are generally based on expert knowledge regarding the rock structure of start zone and a few recorded events. Meanwhile, recent dendrochronological studies have shown that trees, as silent witnesses of numerous events, bring information about the spatial distribution of rockfall trajectories. This data can be compared to simulated trajectories in order to reconstruct the most probable start zones. This study presents a methodological framework for the resolution of this problem and a real-case example. Consider a forest patch f located below a cliff with Ns potential rockfall start points. The expected value of the number of impacts in this forest patch during lapse T can be calculated as (1) : δΣNs Impacts(f) = T × (pstart(i)× ppropagation(i,f)) i=1 (1) with pstart(i) the probability of rockfall for the start point i, ppropagation(i,f) the probability that a rockfall from start point i impacts at least one tree in the forest patch f . The matrix formulation for the whole forest divided in Nf forest patches is (2): Impact1×Nf = T × P start1×Nf ×P propagationNs×Nf (2) Ppropagation can be estimated with numerical simulations, by taking into account the current state of the forest stand if trees are measured and georeferenced, and if the volume of rockfall is known. Impact can be also be observed on the field. Under the assumption that the forest stand and the start frequencies do not change during lapse T , the equation system (2) can be solved for the Nf coefficients of Pstart. This framework was tested on a rockfall area located in Valdrôme, France, where more than 1000 trees were measured and geolocated

  7. 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

  8. 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

  9. 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

  10. Observation of ion-cyclotron-frequency mode-conversion flow drive in tokamak plasmas.

    PubMed

    Lin, Y; Rice, J E; Wukitch, S J; Greenwald, M J; Hubbard, A E; Ince-Cushman, A; Lin, L; Porkolab, M; Reinke, M L; Tsujii, N

    2008-12-01

    Strong toroidal flow (Vphi) and poloidal flow (Vtheta) have been observed in D-3He plasmas with ion cyclotron range of frequencies (ICRF) mode-conversion (MC) heating on the Alcator C-Mod tokamak. The toroidal flow scales with the rf power Prf (up to 30 km/s per MW), and is significantly larger than that in ICRF minority heated plasmas at the same rf power or stored energy. The central Vphi responds to Prf faster than the outer regions, and the Vphi(r) profile is broadly peaked for r/a < or =0.5. Localized (0.3 < or = r/a < or =0.5) Vtheta appears when Prf > or =1.5 MW and increases with power (up to 0.7 km/s per MW). The experimental evidence together with numerical wave modeling suggests a local flow drive source due to the interaction between the MC ion cyclotron wave and 3He ions. PMID:19113561

  11. The widest frequency radio relic spectra: observations from 150 MHz to 30 GHz

    NASA Astrophysics Data System (ADS)

    Stroe, Andra; Shimwell, Timothy; Rumsey, Clare; van Weeren, Reinout; Kierdorf, Maja; Donnert, Julius; Jones, Thomas W.; Röttgering, Huub J. A.; Hoeft, Matthias; Rodríguez-Gonzálvez, Carmen; Harwood, Jeremy J.; Saunders, Richard D. E.

    2016-01-01

    Radio relics are patches of diffuse synchrotron radio emission that trace shock waves. Relics are thought to form when intracluster medium electrons are accelerated by cluster merger-induced shock waves through the diffusive shock acceleration mechanism. In this paper, we present observations spanning 150 MHz to 30 GHz of the `Sausage' and `Toothbrush' relics from the Giant Metrewave and Westerbork telescopes, the Karl G. Jansky Very Large Array, the Effelsberg telescope, the Arcminute Microkelvin Imager and Combined Array for Research in Millimeter-wave Astronomy. We detect both relics at 30 GHz, where the previous highest frequency detection was at 16 GHz. The integrated radio spectra of both sources clearly steepen above 2 GHz, at the ≳6σ significance level, supporting the spectral steepening previously found in the `Sausage' and the Abell 2256 relic. Our results challenge the widely adopted simple formation mechanism of radio relics and suggest more complicated models have to be developed that, for example, involve re-acceleration of aged seed electrons.

  12. The birth of a quasiparticle in silicon observed in time-frequency space.

    PubMed

    Hase, Muneaki; Kitajima, Masahiro; Constantinescu, Anca Monia; Petek, Hrvoje

    2003-11-01

    The concept of quasiparticles in solid-state physics is an extremely powerful tool for describing complex many-body phenomena in terms of single-particle excitations. Introducing a simple particle, such as an electron, hole or phonon, deforms a many-body system through its interactions with other particles. In this way, the added particle is 'dressed' or 'renormalized' by a self-energy cloud that describes the response of the many-body system, so forming a new entity--the quasiparticle. Using ultrafast laser techniques, it is possible to impulsively generate bare particles and observe their subsequent dressing by the many-body interactions (that is, quasiparticle formation) on the time and energy scales governed by the Heisenberg uncertainty principle. Here we describe the coherent response of silicon to excitation with a 10-femtosecond (10(-14) s) laser pulse. The optical pulse interacts with the sample by way of the complex second-order nonlinear susceptibility to generate a force on the lattice driving coherent phonon excitation. Transforming the transient reflectivity signal into frequency-time space reveals interference effects leading to the coherent phonon generation and subsequent dressing of the phonon by electron-hole pair excitations. PMID:14603313

  13. DENSITY OF WARM IONIZED GAS NEAR THE GALACTIC CENTER: LOW RADIO FREQUENCY OBSERVATIONS

    SciTech Connect

    Roy, Subhashis

    2013-08-10

    We have observed the Galactic center (GC) region at 0.154 and 0.255 GHz with the Giant Metrewave Radio Telescope. A total of 62 compact likely extragalactic (EG) sources are detected. Their scattering sizes decrease linearly with increasing angular distance from the GC up to about 1 Degree-Sign . The apparent scattering sizes of the sources are more than an order of magnitude less than predicted earlier by the NE2001 model of Galactic electron distribution within 359. Degree-Sign 5 < l < 0. Degree-Sign 5 and -0. Degree-Sign 5 < b < 0. Degree-Sign 5 (Hyperstrong Scattering Region) of the Galaxy. High free-free optical depths ({tau}) are observed toward most of the extended non-thermal sources within 0. Degree-Sign 6 from the GC. Significant variation of {tau} indicates that the absorbing medium is patchy at an angular scale of {approx}10' and n{sub e} is {approx}10 cm{sup -3}, which matches the NE2001 model. This model predicts the EG sources to be resolved out from 1.4 GHz interferometric surveys. However, out of 10 EG sources expected in the region, 8 likely EG are present in the 1.4 GHz catalog. Ionized interfaces of dense molecular clouds to the ambient medium are most likely responsible for strong scattering and low radio frequency absorption. However, dense GC clouds traced by CS J = 1-0 emission are found to have a narrow distribution of {approx}0. Degree-Sign 2 across the Galactic plane. Angular distribution of most EG sources seen through the so-called Hyperstrong Scattering Region are random in b, and typically {approx}7 out of 10 sources will not be seen through the dense molecular clouds, which explains why most of them are not scatter broadened at 1.4 GHz.

  14. Tetrasomic Segregation for Multiple Alleles in Alfalfa

    PubMed Central

    Quiros, Carlos F.

    1982-01-01

    Evidence of tetrasomic inheritance in alfalfa, Medicago sativa L. and M. falcata L., for multiple codominant alleles at three isozymic loci is reported in this study. The locus Prx-1 governing anodal peroxidase and the loci Lap-1 and Lap-2 governing anodal leucine-aminopeptidase were studied by starch gel electrophoresis in seedling root tissue or seeds. The progenies from several di-, tri- or tetra-allelic plants belong to the species M. sativa and M. falcata and their hybrids were studied for the segregation of the three genes. In all cases, tetrasomic inheritance of chromosomal-type segregation was observed. In another progeny resulting from the crossing of two plants involving four different alleles at locus Lap-2, tetrasomic segregation with the possible occurrence of double reduction was observed. This study presents direct evidence of autotetraploidy and the existence of tetra-allelic loci in alfalfa. It also supports the concept that the species M. sativa and M. falcata are genetically close enough to be considered biotypes of a common species. PMID:17246077

  15. Biased Allelic Expression in Human Primary Fibroblast Single Cells

    PubMed Central

    Borel, Christelle; Ferreira, Pedro G.; Santoni, Federico; Delaneau, Olivier; Fort, Alexandre; Popadin, Konstantin Y.; Garieri, Marco; Falconnet, Emilie; Ribaux, Pascale; Guipponi, Michel; Padioleau, Ismael; Carninci, Piero; Dermitzakis, Emmanouil T.; Antonarakis, Stylianos E.

    2015-01-01

    The study of gene expression in mammalian single cells via genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblasts over 133,633 unique heterozygous single-nucleotide variants (hetSNVs). We observed that at the snapshot of analyses, each cell contained mostly transcripts from one allele from the majority of genes; indeed, 76.4% of the hetSNVs displayed stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibited a haplotype-consistent allelic ratio; in contrast, distant sites located in two different genes were independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in the majority of the single cells at a given time point were rare and enriched with highly expressed genes. The relative abundance of each allele in a cell was controlled by some regulatory mechanisms given that we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability. PMID:25557783

  16. Very low frequency radio events with a reduced intensity observed by the low-altitude DEMETER spacecraft

    NASA Astrophysics Data System (ADS)

    Záhlava, J.; Němec, F.; Santolík, O.; Kolmašová, I.; Parrot, M.; Rodger, C. J.

    2015-11-01

    We present results of a systematic study of unusual very low frequency (VLF) radio events with a reduced intensity observed in the frequency-time spectrograms measured by the low-orbiting Detection of Electro-Magnetic Emissions Transmitted from Earthquake Regions (DEMETER) spacecraft. They occur exclusively on the nightside. During these events, the intensity of fractional hop whistlers at specific frequencies is significantly reduced. These frequencies are usually above about 3.4 kHz (second Earth-ionosphere waveguide cutoff frequency), but about 20% of events extend down to about 1.7 kHz (first Earth-ionosphere waveguide cutoff frequency). The frequencies of a reduced intensity vary smoothly with time. We have inspected 6.5 years of DEMETER data, and we identified in total 1601 such events. We present a simple model of the event formation based on the wave propagation in the Earth-ionosphere waveguide. We apply the model to two selected events, and we demonstrate that the model is able to reproduce both the minimum frequencies of the events and their approximate frequency-time shapes. The overall geographic distribution of the events is shifted by about 3000 km westward and slightly southward with respect to the areas with high long-term average lightning activity. We demonstrate that this shift is related to the specific DEMETER orbit, and we suggest its qualitative explanation by the east-west asymmetry of the wave propagation in the Earth-ionosphere waveguide.

  17. Accuracy of Single Frequency GPS Observations Processing In Near Real-time With Use of Code Predicted Products

    NASA Astrophysics Data System (ADS)

    Wielgosz, P. A.

    In this year, the system of active geodetic GPS permanent stations is going to be estab- lished in Poland. This system should provide GPS observations for a wide spectrum of users, especially it will be a great opportunity for surveyors. Many of surveyors still use cheaper, single frequency receivers. This paper focuses on processing of single frequency GPS observations only. During processing of such observations the iono- sphere plays an important role, so we concentrated on the influence of the ionosphere on the positional coordinates. Twenty consecutive days of GPS data from 2001 year were processed to analyze the accuracy of a derived three-dimensional relative vec- tor position between GPS stations. Observations from two Polish EPN/IGS stations: BOGO and JOZE were used. In addition to, a new test station - IGIK was created. In this paper, the results of single frequency GPS observations processing in near real- time are presented. Baselines of 15, 27 and 42 kilometers and sessions of 1, 2, 3, 4, and 6 hours long were processed. While processing we used CODE (Centre for Orbit De- termination in Europe, Bern, Switzerland) predicted products: orbits and ionosphere info. These products are available in real-time and enable near real-time processing. Software Bernese v. 4.2 for Linux and BPE (Bernese Processing Engine) mode were used. These results are shown with a reference to dual frequency weekly solution (the best solution). Obtained GPS positional time and GPS baseline length dependency accuracy is presented for single frequency GPS observations.

  18. Different Alleles of a Gene Encoding Leucoanthocyanidin Reductase (PaLAR3) Influence Resistance against the Fungus Heterobasidion parviporum in Picea abies.

    PubMed

    Nemesio-Gorriz, Miguel; Hammerbacher, Almuth; Ihrmark, Katarina; Källman, Thomas; Olson, Åke; Lascoux, Martin; Stenlid, Jan; Gershenzon, Jonathan; Elfstrand, Malin

    2016-08-01

    Despite the fact that fungal diseases are a growing menace for conifers in modern silviculture, only a very limited number of molecular markers for pathogen resistance have been validated in conifer species. A previous genetic study indicated that the resistance of Norway spruce (Picea abies) to Heterobasidion annosum s.l., a pathogenic basidiomycete species complex, is linked to a quantitative trait loci that associates with differences in fungal growth in sapwood (FGS) that includes a gene, PaLAR3, which encodes a leucoanthocyanidin reductase. In this study, gene sequences showed the presence of two PaLAR3 allelic lineages in P. abies. Higher resistance was associated with the novel allele, which was found in low frequency in the four P. abies populations that we studied. Norway spruce plants carrying at least one copy of the novel allele showed a significant reduction in FGS after inoculation with Heterobasidion parviporum compared to their half-siblings carrying no copies, indicating dominance of this allele. The amount of (+) catechin, the enzymatic product of PaLAR3, was significantly higher in bark of trees homozygous for the novel allele. Although we observed that the in vitro activities of the enzymes encoded by the two alleles were similar, we could show that allele-specific transcript levels were significantly higher for the novel allele, indicating that regulation of gene expression is responsible for the observed effects in resistance, possibly caused by differences in cis-acting elements that we observe in the promoter region of the two alleles. PMID:27317690

  19. Multiple-Station Observation of Frequency Dependence and Polarization Characteristics of ELF/VLF waves generated via Ionospheric Modification

    NASA Astrophysics Data System (ADS)

    Maxworth, A. S.; Golkowski, M.; Cohen, M.; Moore, R. C.

    2014-12-01

    Generation of Extremely Low Frequency (ELF) and Very Low Frequency (VLF) signals through ionospheric modification has been practiced for many years. Heating the lower ionosphere with high power HF waves allows for modulation of natural current systems. Our experiments were carried out at the High Frequency Active Auroral Research Program (HAARP) facility in Alaska, USA. In this experiment, the ionosphere was heated with a vertical amplitude modulating signal and the modulation frequency was changed sequentially within an array of 40 frequencies followed by a frequency ramp. The observed magnetic field amplitude and polarization of the generated ELF/VLF signals were analyzed for multiple sites and as a function of modulation frequency. Our three observation sites: Chistochina, Paxson and Paradise are located within 36km (azimuth 47.7°), 50.2km (azimuth -20°) and 99km (azimuth 80.3°) respectively. We show that the peak amplitudes observed as a function of frequency result from vertical resonance in the Earth-ionosphere waveguide and can be used to diagnose the D-region profile. Polarization analysis showed that out of the three sites Paxson shows the highest circularity in the magnetic field polarization, compared to Chistochina and Paradise which show highly linear polarizations. The experimental results were compared with a theoretical simulation model results and it was clear that in both cases, the modulated Hall current dominates the observed signals at Chistochina and Paradise sites and at Paxson there is an equal contribution from Hall and Pedersen currents. The Chistochina site shows the highest magnetic field amplitudes in both experimental and simulation environments. Depending upon the experimental and simulation observations at the three sites, a radiation pattern for the HAARP ionospheric heater can be mapped

  20. Shallow very-low-frequency earthquakes around Japan: Recent studies and observation

    NASA Astrophysics Data System (ADS)

    Ito, Y.; Obara, K.; Asano, Y.; Fujimoto, H.; Hino, R.; Ashi, J.; Tsuji, T.

    2008-12-01

    Very-low-frequency (VLF) earthquakes have been observed in three regions around Japan. (1) Deep VLF earthquakes have occurred in the down-dip part of the Nankai subduction zone [Ito et al., 2007]. (2) Shallow VLF earthquakes have occurred within the accretionary prism in the up-dip portion of the Nankai subduction zone [Obara and Ito, 2005; Ito and Obara, 2006]. The stress drops of these shallow VLF events were very low, in the range 0.1--10kPa; this corresponds to 0.1--1% of the range for ordinary earthquakes [Ito and Obara, 2006]. Ito and Obara [2006] suggested that the largest shallow VLF earthquake (MW 4.0) occurred on a circular fault of radius ~5--10 km. They proposed that the shallow VLF events were related to numerous reverse fault systems located in areas of high fluid pressure within the accretionary prism. (3) Shallow VLF earthquakes have occurred in the region off Tokachi, northern Japan, along the Japan Trench [Asano et al., 2008], where the Pacific Plate subducts beneath the Japanese land area. The occurrence of these shallow VLF earthquakes suggests that VLF events can occur on the plate boundary at depths shallower than that of the main seismogenic zone [Asano et al., EPS, 2008]. The megasplay faults in the Nankai subduction zone are observed to generate a reverse-polarity reflection on seismic reflection profiles [Park et al.,2002]; this may indicate the existence of an elevated fluid process in the fault zones [Shipley et al., 1994]. Hydrodynamics phenomena responsible for the seismic signals detected by ocean bottom seismometers were first reported by Brown et al. (2005) using osmotically-driven fluid flow meters (CAT meters); these meters were used to detect temporal changes in the rate of cold seepage of a shallow subduction system in the regions of the Costa Rica subduction zone. The Pacific plate is subducting beneath Tohoku, northeastern Japan, at the Japan Trench. An aseismic slip has been observed to occur as a post- seismic slip following

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

    PubMed

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

    2010-03-15

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

  2. The Miniature Radio Frequency Instruments (Mini-RF) Global Observations of Earth's Moon

    NASA Technical Reports Server (NTRS)

    Cahill, Joshua T. S.; Thomson, B. J.; Patterson, G. Wesley; Bussey, D. Benjamin J.; Neish, Catherine D.; Lopez, Norberto R.; Turner, F. Scott; Aldridge, T.; McAdam, M.; Meyer, H. M.; Raney, R. K.; Carter, L. M.; Spudis, P. D.; Hiesinger, H.; Pasckert, J. H.

    2014-01-01

    Radar provides a unique means to analyze the surface and subsurface physical properties of geologic deposits, including their wavelength-scale roughness, the relative depth of the deposits, and some limited compositional information. The NASA Lunar Reconnaissance Orbiter's (LRO) Miniature Radio Frequency (Mini-RF) instrument has enabled these analyses on the Moon at a global scale. Mini-RF has accumulated 67% coverage of the lunar surface in S-band (12.6 cm) radar with a resolution of 30 m/pixel. Here we present new Mini-RF global orthorectified uncontrolled S-band maps of the Moon and use them for analysis of lunar surface physical properties. Reported here are readily apparent global- and regional-scale differences in lunar surface physical properties that suggest three distinct terranes, namely: a (1) Nearside Radar Dark Region; (2) Orientale basin and continuous ejecta; and the (3) Highlands Radar Bright Region. Integrating these observations with new data from LRO's Diviner Radiometer rock abundance maps, as well Clementine and Lunar Prospector derived compositional values show multiple distinct lunar surface terranes and sub-terranes based upon both physical and compositional surface properties. Previous geochemical investigations of the Moon suggested its crust is best divided into three to four basic crustal provinces or terranes (Feldspathic Highlands Terrane (-An and -Outer), Procellarum KREEP Terrane, and South Pole Aitken Terrane) that are distinct from one another. However, integration of these geochemical data sets with new geophysical data sets allows us to refine these terranes. The result shows a more complex view of these same crustal provinces and provides valuable scientific and hazard perspectives for future targeted human and robotic exploration.

  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. Eddy-driven low-frequency variability: physics and observability through altimetry

    NASA Astrophysics Data System (ADS)

    Penduff, Thierry; Sérazin, Guillaume; Arbic, Brian; Mueller, Malte; Richman, James G.; Shriver, Jay F.; Morten, Andrew J.; Scott, Robert B.

    2015-04-01

    Model studies have revealed the propensity of the eddying ocean circulation to generate strong low-frequency variability (LFV) intrinsically, i.e. without low-frequency atmospheric variability. In the present study, gridded satellite altimeter products, idealized quasi-geostrophic (QG) turbulent simulations, and realistic high-resolution global ocean simulations are used to study the spontaneous tendency of mesoscale (relatively high frequency and high wavenumber) kinetic energy to non-linearly cascade towards larger time and space scales. The QG model reveals that large-scale variability, arising from the well-known spatial inverse cascade, is associated with low frequencies. Low-frequency, low-wavenumber energy is maintained primarily by nonlinearities in the QG model, with forcing (by large-scale shear) and friction playing secondary roles. In realistic simulations, nonlinearities also generally drive kinetic energy to low frequencies and low wavenumbers. In some, but not all, regions of the gridded altimeter product, surface kinetic energy is also found to cascade toward low frequencies. Exercises conducted with the realistic model suggest that the spatial and temporal filtering inherent in the construction of gridded satellite altimeter maps may contribute to the discrepancies seen in some regions between the direction of frequency cascade in models versus gridded altimeter maps. Finally, the range of frequencies that are highly energized and engaged these cascades appears much greater than the range of highly energized and engaged wavenumbers. Global eddying simulations, performed in the context of the CHAOCEAN project in collaboration with the CAREER project, provide estimates of the range of timescales that these oceanic nonlinearities are likely to feed without external variability.

  5. Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population.

    PubMed

    Nakaoka, Hirofumi; Mitsunaga, Shigeki; Hosomichi, Kazuyoshi; Shyh-Yuh, Liou; Sawamoto, Taiji; Fujiwara, Tsutomu; Tsutsui, Naohisa; Suematsu, Koji; Shinagawa, Akira; Inoko, Hidetoshi; Inoue, Ituro

    2013-01-01

    The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago. PMID:23577161

  6. Detection of Ancestry Informative HLA Alleles Confirms the Admixed Origins of Japanese Population

    PubMed Central

    Nakaoka, Hirofumi; Mitsunaga, Shigeki; Hosomichi, Kazuyoshi; Shyh-Yuh, Liou; Sawamoto, Taiji; Fujiwara, Tsutomu; Tsutsui, Naohisa; Suematsu, Koji; Shinagawa, Akira; Inoko, Hidetoshi; Inoue, Ituro

    2013-01-01

    The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago. PMID:23577161

  7. Melt Distribution in the Ethiopian Rift System: Constraints From Seismic Observations and Finite-Frequency Modelling

    NASA Astrophysics Data System (ADS)

    Angus, D.; Hammond, J. O.; Kendall, J.; Wookey, J.

    2008-12-01

    As part of the Ethiopian Afar Geoscientific Lithospheric Experiment (EAGLE) 79 seismic stations were deployed, for up to 18 months, in the Main Ethiopian Rift (MER). Many indicators of melt were observed leading to the idea that magma was driving the rifting process in this region. Some of the best evidence for melt came from observations of anisotropy in studies of surface waves and shear-wave splitting. The shear- wave splitting shows fast directions which change abruptly from being rift parallel on the rift flanks to magmatic-segment parallel in the rift valley. This was interpreted in terms of melt-induced anisotropy. The abrupt change in splitting parameters over small lateral distances suggests that the source of anisotropy is shallow. To further constrain the location of the anisotropy and study the ability of shear-wave splitting to identify sharp lateral changes in anisotropy, we model finite-frequency waveforms for a suite of model representations of the rift zone. This allows us to determine the lateral and vertical extent of the melt-induced anisotropy. The results show how a simple model with two regimes of anisotropy can explain the variability across the rift, in both delay time and shear-wave polarization, over short length scales of the order 20- 40 km. Our models have enabled us to constrain the anisotropic characteristics beneath the MER. Our best model has a 9% anisotropy on the western rift margin, with fast directions of 30°, a 100 km wide rift zone with fast direction of 20° inside the rift zone and with 9% anisotropy close to the western margin, 7% elsewhere, and 7% anisotropy on the eastern margin with fast directions of 30°. In all regions of the model we constrain anisotropy to begin at a depth of 90 km. The depth of anisotropy co-incides with the proposed depth of melt initiation beneath the region, based on geochemistry. Also the elevated splitting beneath the western margin supports evidence of low velocities and highly conductive

  8. Real time observation of low frequency heme protein vibrations using femtosecond coherence spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhu, L.; Li, P.; Huang, M.; Sage, J. T.; Champion, P. M.

    1994-01-01

    Femtosecond laser pulses, resonant with the Soret bands of myoglobin (Mb) and cytochrome c, are used to probe coherent low frequency nuclear motion of the heme group. The time domain analysis is in good agreement with frequencies obtained independently using spontaneous resonance Raman spectroscopy. The deoxyMb data reveal a strong oscillation near 300 fs (~ 100 cm-1) and a persistent feature also appears near 50 cm-1. This is near the frequency expected for heme doming motion, which has been associated with the ligand binding reaction coordinate of Mb.

  9. 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

  10. Enhanced frequency spectra of winds at the mesoscale based on radar profiler observations

    NASA Technical Reports Server (NTRS)

    Nastrom, G. D.; Gage, K. S.

    1990-01-01

    Frequency spectra of horizontal winds in the troposphere and stratosphere, over a range of periods and frequencies, have been studied by means of two radar profilers, located at Plattenville, Colorado, and Poker Flat, Alaska, to determine if the spectra deviations from a consistent power law behavior can be verified in a statistical sense. At Plattenville, the spectrum of both zonal and meridional winds in the troposphere is found to obey a low-frequency regime at periods longer than a few hours and a high-frequency regime at periods less than 1/2 hour. The energy levels in the high-frequency regime are enhanced over those obtained by extrapolation of the low-frequency regime by a factor of 4. At Poker Flat, a similar pattern is found in the stratosphere, and the magnitude of the enhancement factor is 1.7. It is suggested that the enhanced amplitudes reflect the effects of upward-propagating gravity waves launched by the flow over a rough terrain, and that they influence the dynamics of the large-scale circulation to a great extent.

  11. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck

    PubMed Central

    Balick, Daniel J.; Do, Ron; Cassa, Christopher A.; Reich, David; Sunyaev, Shamil R.

    2015-01-01

    Population bottlenecks followed by re-expansions have been common throughout history of many populations. The response of alleles under selection to such demographic perturbations has been a subject of great interest in population genetics. On the basis of theoretical analysis and computer simulations, we suggest that this response qualitatively depends on dominance. The number of dominant or additive deleterious alleles per haploid genome is expected to be slightly increased following the bottleneck and re-expansion. In contrast, the number of completely or partially recessive alleles should be sharply reduced. Changes of population size expose differences between recessive and additive selection, potentially providing insight into the prevalence of dominance in natural populations. Specifically, we use a simple statistic, BR≡∑xipop1/∑xjpop2, where x i represents the derived allele frequency, to compare the number of mutations in different populations, and detail its functional dependence on the strength of selection and the intensity of the population bottleneck. We also provide empirical evidence showing that gene sets associated with autosomal recessive disease in humans may have a B R indicative of recessive selection. Together, these theoretical predictions and empirical observations show that complex demographic history may facilitate rather than impede inference of parameters of natural selection. PMID:26317225

  12. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck.

    PubMed

    Balick, Daniel J; Do, Ron; Cassa, Christopher A; Reich, David; Sunyaev, Shamil R

    2015-08-01

    Population bottlenecks followed by re-expansions have been common throughout history of many populations. The response of alleles under selection to such demographic perturbations has been a subject of great interest in population genetics. On the basis of theoretical analysis and computer simulations, we suggest that this response qualitatively depends on dominance. The number of dominant or additive deleterious alleles per haploid genome is expected to be slightly increased following the bottleneck and re-expansion. In contrast, the number of completely or partially recessive alleles should be sharply reduced. Changes of population size expose differences between recessive and additive selection, potentially providing insight into the prevalence of dominance in natural populations. Specifically, we use a simple statistic, [Formula: see text], where xi represents the derived allele frequency, to compare the number of mutations in different populations, and detail its functional dependence on the strength of selection and the intensity of the population bottleneck. We also provide empirical evidence showing that gene sets associated with autosomal recessive disease in humans may have a BR indicative of recessive selection. Together, these theoretical predictions and empirical observations show that complex demographic history may facilitate rather than impede inference of parameters of natural selection. PMID:26317225

  13. 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

  14. Distribution of CGG repeats and FRAXAC1/DXS548 alleles in South American populations.

    PubMed

    Mingroni-Netto, Regina Célia; Angeli, Claudia B; Auricchio, Maria Teresa B M; Leal-Mesquita, Emygdia R; Ribeiro-dos-Santos, Andrea K C; Ferrari, Iris; Hutz, Mara H; Salzano, Francisco M; Hill, Kim; Hurtado, A Magdalena; Vianna-Morgante, Angela M

    2002-08-15

    In order to assess the molecular variability related to fragile X (FMR1 locus), we investigated the distribution of CGG repeats and DXS548/FRAXAC1 haplotypes in normal South American populations of different ethnic backgrounds. Special attention was given to Amerindian Wai-Wai (Northern Brazil) and Ache (Paraguay), as well as to Brazilian isolated communities of African ancestry, the remnants of quilombos. Comparison of samples from quilombos, Amerindians, and the ethnically mixed, but mainly European-derived population of São Paulo revealed that the 30-copy allele of the fragile X gene is the most frequent in all groups. A second peak at 20 repeats was present in the population of São Paulo only, confirming this as a European peculiarity. The distribution of DXS548 and FRAXAC1 alleles led to a high expected heterozygosity in African Brazilians, followed by that observed in the population of São Paulo. Amerindians showed the lowest diversity in CGG repeats and DXS548/FRAXAC1 haplotypes. Some rare alleles, for example, the 148-bp (FRAXAC1) or 200-bp (DXS548) variants, which seem to be almost absent in Europe, occurred in higher frequencies among African Brazilians. This suggests a general trend for higher genetic diversity among Africans; these rarer alleles could be African in origin and would have been lost or possibly were not present in the groups that gave rise to the Europeans. PMID:12210320

  15. Association between AgI-CA alleles and severity of autosomal recessive proximal spina lmuscular atrophy

    SciTech Connect

    DiDonato, C.J.; Carpten, J.D.; Fuerst, P.; Ingraham, S.E.; Mendell, J.R.; Burghes, A.H.M.; Morgan, K.; Prescott, G.; Simard, L.R.; McPherson, J.D.

    1994-12-01

    The gene for autosomal recessive proximal spinal muscular atrophy (SMA) has been mapped to an 850-kb interval on 5q11.2-q13.3, between the centromeric D5S823 and telomeric D5S557 markers. We report a new complex marker, Ag1-CA, that lies in this interval, whose primers produce one, two, or rarely three amplification-fragment-length variants (AFLVs) per allele. Class I chromosomes are those which amplify a single AFLV allele, and class II chromosomes are those which amplify an allele with two or three AFLVs. Ag1-CA shows highly significant allelic association with type I SMA in both the French Canadian (Hopital Sainte-Justine (HSJ)) and American (Ohio State University (OSU)) populations (P < .0001). Significant association between the Ag1-CA genotype and disease severity was also observed. Type I patients were predominantly homozygous for class I chromosomes (P = .0003 OSU; P = 0.0012 HSJ), whereas the majority of type II patients were heterozygous for class I and II chromosomes (P = .0014 OSU; P = .001 HSJ). There was no significant difference in Ag1-CA genotype frequencies between type III patients (P = .5 OSU; P = .25 HSJ) and the paired normal chromosomes from both carrier parents. Our results indicate that Ag1-CA is the most closely linked marker to SMA and defines the critical candidate-gene region. Finally, we have proposed a model that should be taken into consideration when screening candidates SMA genes.

  16. Observation of millimeter-wave oscillations from resonant tunneling diodes and some theoretical considerations of ultimate frequency limits

    NASA Technical Reports Server (NTRS)

    Sollner, T. C. L. G.; Brown, E. R.; Goodhue, W. D.; Le, H. Q.

    1987-01-01

    Recent observations of oscillation frequencies up to 56 GHz in resonant tunneling structures are discussed in relation to calculations by several authors of the ultimate frequency limits of these devices. It is found that calculations relying on the Wentzel-Kramers-Brillouin (WKB) approximation give limits well below the observed oscillation frequencies. Two other techniques for calculating the upper frequency limit were found to give more reasonable results. One method employs the solution of the time-dependent Schroedinger equation obtained by Kundrotas and Dargys (1986); the other uses the energy width of the transmission function for electrons through the double-barrier structure. This last technique is believed to be the most accurate since it is based on general results for the lifetime of any resonant state. It gives frequency limits on the order of 1 THz for two recently fabricated structures. It appears that the primary limitation of the oscillation frequency for double-barrier resonant-tunneling diodes is imposed by intrinsic device circuit parameters and by the transit time of the depletion layer rather than by time delays encountered in the double-barrier region.

  17. THE LOW-FREQUENCY CHARACTERISTICS OF PSR J0437–4715 OBSERVED WITH THE MURCHISON WIDE-FIELD ARRAY

    SciTech Connect

    Bhat, N. D. R.; Ord, S. M.; Tremblay, S. E.; Tingay, S. J.; Oronsaye, S.; Emrich, D.; Deshpande, A. A.; Van Straten, W.; Briggs, F.; Bernardi, G.; Bowman, J. D.; Cappallo, R. J.; Corey, B. E.; Goeke, R.; Hewitt, J. N.; Greenhill, L. J.; Kasper, J. C.; Hazelton, B. J.; Johnston-Hollitt, M.; Kaplan, D. L.; and others

    2014-08-20

    We report on the detection of the millisecond pulsar PSR J0437–4715 with the Murchison Wide-field Array (MWA) at a frequency of 192 MHz. Our observations show rapid modulations of pulse intensity in time and frequency that arise from diffractive scintillation effects in the interstellar medium (ISM), as well as prominent drifts of intensity maxima in the time-frequency plane that arise from refractive effects. Our analysis suggests that the scattering screen is located at a distance of ∼80-120 pc from the Sun, in disagreement with a recent claim that the screen is closer (∼10 pc). Comparisons with higher frequency data from Parkes reveal a dramatic evolution of the pulse profile with frequency, with the outer conal emission becoming comparable in strength to that from the core and inner conal regions. As well as demonstrating the high time resolution science capabilities currently possible with the MWA, our observations underscore the potential to conduct low-frequency investigations of timing-array millisecond pulsars, which may lead to increased sensitivity in the detection of nanoHertz gravitational waves via the accurate characterization of ISM effects.

  18. 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)

  19. High Angular Resolution Radio Observations of a Coronal Mass Ejection Source Region at Low Frequencies during a Solar Eclipse

    NASA Astrophysics Data System (ADS)

    Ramesh, R.; Kathiravan, C.; Barve, Indrajit V.; Rajalingam, M.

    2012-01-01

    We carried out radio observations of the solar corona in the frequency range 109-50 MHz during the annular eclipse of 2010 January 15 from the Gauribidanur Observatory, located about 100 km north of Bangalore in India. The radio emission in the above frequency range originates typically in the radial distance range ≈1.2-1.5 R ⊙ in the "undisturbed" solar atmosphere. Our analysis indicates that (1) the angular size of the smallest observable radio source (associated with a coronal mass ejection in the present case) is ≈1' ± 0farcm3, (2) the source size does not vary with radial distance, (3) the peak brightness temperature of the source corresponding to the above size at a typical frequency like 77 MHz is ≈3 × 109 K, and (4) the coronal magnetic field near the source region is ≈70 mG.

  20. Kvn Source-Frequency Phase-Referencing Observation of 3c 66A and 3c 66B

    NASA Astrophysics Data System (ADS)

    Zhao, Guang-Yao; Jung, Taehyun; Dodson, Richard; Rioja, Maria; Sohn, Bong Won

    2015-09-01

    In this proceedings, preliminary results of the KVN Source-Frequency Phase-Referencing (SFPR) observation of 3C 66A and 3C 66B are presented. The motivation of this work is to measure the core-shift of these 2 sources and study the temporal evolution of the jet opacity. Two more sources were observed as secondary reference calibrators and each source was observed at 22, 43, and 86 GHz simultaneously. Our preliminary results show that after using the observations at the lower frequency to calibrate those at the higher frequency of the same source, the residual visibility phases for each source at the higher frequencies became more aligned, and the coherence time became much longer; also, the residual phases for different sources, within 10 degrees angular separations, follow similar trends. After reference to the nearby calibrator, the SFPRed maps were obtained as well as the astrometric measurements, i.e. the combined coreshift. The measurements were found to be affected by structural blending effects because of the large beamsize of KVN, but this can be corrected with higher resolution maps (e.g. KAVA maps). *%K Astrometry, radio continuum: galaxies, galaxies: active, galaxy: individual(3C 66A, 3C 66B), techniques: interferometric *%O 3C 66A, 3C 66B

  1. Resonances observed on mother-daughter rocket flights in the ionosphere. [signal frequency enhancement in auroral zones

    NASA Technical Reports Server (NTRS)

    Folkestad, K.; Troeim, J.

    1973-01-01

    Resonance phenomena have been observed in swept frequency experiments carried out on two mother-daughter Nike-Tomahawk rocket flights at auroral latitudes. The experimental method is briefly described and characteristic samples of the results are presented. A possible interpretation of some main resonances is offered, involving cold plasma cone resonances.

  2. Optimized trigger for ultra-high-energy cosmic-ray and neutrino observations with the low frequency radio array

    NASA Astrophysics Data System (ADS)

    Singh, K.; Mevius, M.; Scholten, O.; Anderson, J. M.; van Ardenne, A.; Arts, M.; Avruch, M.; Asgekar, A.; Bell, M.; Bennema, P.; Bentum, M.; Bernadi, G.; Best, P.; Boonstra, A.-J.; Bregman, J.; van de Brink, R.; Broekema, C.; Brouw, W.; Brueggen, M.; Buitink, S.; Butcher, H.; van Cappellen, W.; Ciardi, B.; Coolen, A.; Damstra, S.; Dettmar, R.; van Diepen, G.; Dijkstra, K.; Donker, P.; Doorduin, A.; Drost, M.; van Duin, A.; Eisloeffel, J.; Falcke, H.; Garrett, M.; Gerbers, M.; Grießmeier, J.-M.; Grit, T.; Gruppen, P.; Gunst, A.; van Haarlem, M.; Hoeft, M.; Holties, H.; Hörandel, J.; Horneffer, L. A.; Huijgen, A.; James, C.; de Jong, A.; Kant, D.; Kooistra, E.; Koopman, Y.; Koopmans, L.; Kuper, G.; Lambropoulos, P.; van Leeuwen, J.; Loose, M.; Maat, P.; Mallary, C.; McFadden, R.; Meulman, H.; Mol, J.-D.; Morawietz, J.; Mulder, E.; Munk, H.; Nieuwenhuis, L.; Nijboer, R.; Norden, M. J.; Noordam, J.; Overeem, R.; Paas, H.; Pandey, V. N.; Pandey-Pommier, M.; Pizzo, R.; Polatidis, A.; Reich, W.; de Reijer, J.; Renting, A.; Riemers, P.; Roettgering, H.; Romein, J.; Roosjen, J.; Ruiter, M.; Schoenmakers, A.; Schoonderbeek, G.; Sluman, J.; Smirnov, O.; Stappers, B.; Steinmetz, M.; Stiepel, H.; Stuurwold, K.; Tagger, M.; Tang, Y.; Ter Veen, S.; Vermeulen, R.; de Vos, M.; Vogt, C.; van der Wal, E.; Weggemans, H.; Wijnholds, S.; Wise, M.; Wucknitz, O.; Yattawatta, S.; van Zwieten, J.

    2012-02-01

    When an ultra-high energy neutrino or cosmic-ray strikes the Lunar surface a radio-frequency pulse is emitted. We plan to use the LOFAR radio telescope to detect these pulses. In this work we propose an efficient trigger implementation for LOFAR optimized for the observation of short radio pulses.

  3. Electromagnetic Waves with Frequencies Near the Local Proton Gryofrequency: ISEF-3 1 AU Observations

    NASA Technical Reports Server (NTRS)

    Tsurutani, B.

    1993-01-01

    Low Frequency electromagnetic waves with periods near the local proton gyrofrequency have been detected near 1 AU by the magnetometer onboard ISEE-3. For these 1 AU waves two physical processes are possible: solar wind pickup of nuetral (interstellar?) particles and generation by relativistic electron beams propagating from the Sun.

  4. Magnetic Force Nanoprobe for Direct Observation of Audio Frequency Tonotopy of Hair Cells.

    PubMed

    Kim, Ji-Wook; Lee, Jae-Hyun; Ma, Ji-Hyun; Chung, Eunna; Choi, Hongsuh; Bok, Jinwoong; Cheon, Jinwoo

    2016-06-01

    Sound perception via mechano-sensation is a remarkably sensitive and fast transmission process, converting sound as a mechanical input to neural signals in a living organism. Although knowledge of auditory hair cell functions has advanced over the past decades, challenges remain in understanding their biomechanics, partly because of their biophysical complexity and the lack of appropriate probing tools. Most current studies of hair cells have been conducted in a relatively low-frequency range (<1000 Hz); therefore, fast kinetic study of hair cells has been difficult, even though mammalians have sound perception of 20 kHz or higher. Here, we demonstrate that the magnetic force nanoprobe (MFN) has superb spatiotemporal capabilities to mechanically stimulate spatially-targeted individual hair cells with a temporal resolution of up to 9 μs, which is equivalent to approximately 50 kHz; therefore, it is possible to investigate avian hair cell biomechanics at different tonotopic regions of the cochlea covering a full hearing frequency range of 50 to 5000 Hz. We found that the variation of the stimulation frequency and amplitude of hair bundles creates distinct mechanical responsive features along the tonotopic axis, where the kinetics of the hair bundle recovery motion exhibits unique frequency-dependent characteristics: basal, middle, and apical hair bundles can effectively respond at their respective ranges of frequency. We revealed that such recovery kinetics possesses two different time constants that are closely related to the passive and active motilities of hair cells. The use of MFN is critical for the kinetics study of free-standing hair cells in a spatiotemporally distinct tonotopic organization. PMID:27215487

  5. Low-radio-frequency eclipses of the redback pulsar J2215+5135 observed in the image plane with LOFAR

    PubMed Central

    Broderick, J. W.; Fender, R. P.; Breton, R. P.; Stewart, A. J.; Rowlinson, A.; Swinbank, J. D.; Hessels, J. W. T.; Staley, T. D.; van der Horst, A. J.; Bell, M. E.; Carbone, D.; Cendes, Y.; Corbel, S.; Eislöffel, J.; Falcke, H.; Grießmeier, J.-M.; Hassall, T. E.; Jonker, P.; Kramer, M.; Kuniyoshi, M.; Law, C. J.; Markoff, S.; Molenaar, G. J.; Pietka, M.; Scheers, L. H. A.; Serylak, M.; Stappers, B. W.; ter Veen, S.; van Leeuwen, J.; Wijers, R. A. M. J.; Wijnands, R.; Wise, M. W.; Zarka, P.

    2016-01-01

    The eclipses of certain types of binary millisecond pulsars (i.e. ‘black widows’ and ‘redbacks’) are often studied using high-time-resolution, ‘beamformed’ radio observations. However, they may also be detected in images generated from interferometric data. As part of a larger imaging project to characterize the variable and transient sky at radio frequencies <200 MHz, we have blindly detected the redback system PSR J2215+5135 as a variable source of interest with the Low-Frequency Array (LOFAR). Using observations with cadences of two weeks – six months, we find preliminary evidence that the eclipse duration is frequency dependent (∝ν−0.4), such that the pulsar is eclipsed for longer at lower frequencies, in broad agreement with beamformed studies of other similar sources. Furthermore, the detection of the eclipses in imaging data suggests an eclipsing medium that absorbs the pulsed emission, rather than scattering it. Our study is also a demonstration of the prospects of finding pulsars in wide-field imaging surveys with the current generation of low-frequency radio telescopes. PMID:27279782

  6. Low-radio-frequency eclipses of the redback pulsar J2215+5135 observed in the image plane with LOFAR

    NASA Astrophysics Data System (ADS)

    Broderick, J. W.; Fender, R. P.; Breton, R. P.; Stewart, A. J.; Rowlinson, A.; Swinbank, J. D.; Hessels, J. W. T.; Staley, T. D.; van der Horst, A. J.; Bell, M. E.; Carbone, D.; Cendes, Y.; Corbel, S.; Eislöffel, J.; Falcke, H.; Grießmeier, J.-M.; Hassall, T. E.; Jonker, P.; Kramer, M.; Kuniyoshi, M.; Law, C. J.; Markoff, S.; Molenaar, G. J.; Pietka, M.; Scheers, L. H. A.; Serylak, M.; Stappers, B. W.; ter Veen, S.; van Leeuwen, J.; Wijers, R. A. M. J.; Wijnands, R.; Wise, M. W.; Zarka, P.

    2016-07-01

    The eclipses of certain types of binary millisecond pulsars (i.e. `black widows' and `redbacks') are often studied using high-time-resolution, `beamformed' radio observations. However, they may also be detected in images generated from interferometric data. As part of a larger imaging project to characterize the variable and transient sky at radio frequencies <200 MHz, we have blindly detected the redback system PSR J2215+5135 as a variable source of interest with the Low-Frequency Array (LOFAR). Using observations with cadences of two weeks - six months, we find preliminary evidence that the eclipse duration is frequency dependent (∝ν-0.4), such that the pulsar is eclipsed for longer at lower frequencies, in broad agreement with beamformed studies of other similar sources. Furthermore, the detection of the eclipses in imaging data suggests an eclipsing medium that absorbs the pulsed emission, rather than scattering it. Our study is also a demonstration of the prospects of finding pulsars in wide-field imaging surveys with the current generation of low-frequency radio telescopes.

  7. Low-radio-frequency eclipses of the redback pulsar J2215+5135 observed in the image plane with LOFAR

    NASA Astrophysics Data System (ADS)

    Broderick, J. W.; Fender, R. P.; Breton, R. P.; Stewart, A. J.; Rowlinson, A.; Swinbank, J. D.; Hessels, J. W. T.; Staley, T. D.; van der Horst, A. J.; Bell, M. E.; Carbone, D.; Cendes, Y.; Corbel, S.; Eislöffel, J.; Falcke, H.; Grießmeier, J.-M.; Hassall, T. E.; Jonker, P.; Kramer, M.; Kuniyoshi, M.; Law, C. J.; Markoff, S.; Molenaar, G. J.; Pietka, M.; Scheers, L. H. A.; Serylak, M.; Stappers, B. W.; ter Veen, S.; van Leeuwen, J.; Wijers, R. A. M. J.; Wijnands, R.; Wise, M. W.; Zarka, P.

    2016-04-01

    The eclipses of certain types of binary millisecond pulsars (i.e. `black widows' and `redbacks') are often studied using high-time-resolution, `beamformed' radio observations. However, they may also be detected in images generated from interferometric data. As part of a larger imaging project to characterize the variable and transient sky at radio frequencies <200 MHz, we have blindly detected the redback system PSR J2215+5135 as a variable source of interest with the Low-Frequency Array (LOFAR). Using observations with cadences of 2 weeks - 6 months, we find preliminary evidence that the eclipse duration is frequency dependent (∝ν-0.4), such that the pulsar is eclipsed for longer at lower frequencies, in broad agreement with beamformed studies of other similar sources. Furthermore, the detection of the eclipses in imaging data suggests an eclipsing medium that absorbs the pulsed emission, rather than scattering it. Our study is also a demonstration of the prospects of finding pulsars in wide-field imaging surveys with the current generation of low-frequency radio telescopes.

  8. Immunoglobulin light chain allelic inclusion in systemic lupus erythematosus.

    PubMed

    Fraser, Louise D; Zhao, Yuan; Lutalo, Pamela M K; D'Cruz, David P; Cason, John; Silva, Joselli S; Dunn-Walters, Deborah K; Nayar, Saba; Cope, Andrew P; Spencer, Jo

    2015-08-01

    The principles of allelic exclusion state that each B cell expresses a single light and heavy chain pair. Here, we show that B cells with both kappa and lambda light chains (Igκ and Igλ) are enriched in some patients with the systemic autoimmune disease systemic lupus erythematosus (SLE), but not in the systemic autoimmune disease control granulomatosis with polyangiitis. Detection of dual Igκ and Igλ expression by flow cytometry could not be abolished by acid washing or by DNAse treatment to remove any bound polyclonal antibody or complexes, and was retained after two days in culture. Both surface and intracytoplasmic dual light chain expression was evident by flow cytometry and confocal microscopy. We observed reduced frequency of rearrangements of the kappa-deleting element (KDE) in SLE and an inverse correlation between the frequency of KDE rearrangement and the frequency of dual light chain expressing B cells. We propose that dual expression of Igκ and Igλ by a single B cell may occur in some patients with SLE when this may be a consequence of reduced activity of the KDE. PMID:26036683

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

    PubMed

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

    1999-01-01

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

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

    PubMed Central

    Amos, Christopher I.

    2015-01-01

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

  11. Evidence for changes in the magnitude and frequency of observed rainfall vs. snowmelt driven floods in Norway

    NASA Astrophysics Data System (ADS)

    Vormoor, Klaus; Lawrence, Deborah; Schlichting, Lena; Wilson, Donna; Wong, Wai Kwok

    2016-07-01

    There is increasing evidence for recent changes in the intensity and frequency of heavy precipitation and in the number of days with snow cover in many parts of Norway. The question arises as to whether these changes are also discernable with respect to their impacts on the magnitude and frequency of flooding and on the processes producing high flows. In this study, we tested up to 211 catchments for trends in peak flow discharge series by applying the Mann-Kendall test and Poisson regression for three different time periods (1962-2012, 1972-2012, 1982-2012). Field-significance was tested using a bootstrap approach. Over threshold discharge events were classified into rainfall vs. snowmelt dominated floods, based on a simple water balance approach utilizing a nationwide 1 × 1 km2 gridded data set with daily observed rainfall and simulated snowmelt data. Results suggest that trends in flood frequency are more pronounced than trends in flood magnitude and are more spatially consistent with observed changes in the hydrometeorological drivers. Increasing flood frequencies in southern and western Norway are mainly due to positive trends in the frequency of rainfall dominated events, while decreasing flood frequencies in northern Norway are mainly the result of negative trends in the frequency of snowmelt dominated floods. Negative trends in flood magnitude are found more often than positive trends, and the regional patterns of significant trends reflect differences in the flood generating processes (FGPs). The results illustrate the benefit of distinguishing FGPs rather than simply applying seasonal analyses. The results further suggest that rainfall has generally gained an increasing importance for the generation of floods in Norway, while the role of snowmelt has been decreasing and the timing of snowmelt dominated floods has become earlier.

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

    SciTech Connect

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

    1991-10-02

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

  13. First Stellar Radial Velocities with a Laser Frequency Comb: Observations in the NIR H Band

    NASA Astrophysics Data System (ADS)

    Osterman, Steve; Diddams, S.; Quinlan, F.; Ycas, G.; Mahadevan, S.; Ramsey, L.; Bender, C.; Redman, S.; Terrien, R.; Botzer, B.

    2011-01-01

    Advances in high precision radial velocity spectroscopy have been hindered by the lack of suitable wavelength references. This has been especially the case in the infrared where until recently radial velocity precision has been limited to 50-100m/s, hindering investigations such as the search for extrasolar planets orbiting cooler M stars at these wavelengths. To redress deficiency this we have developed a 25GHz laser frequency comb spanning the H band and suitable for use with spectrographs with spectral resolution in the range of 40,000 - 60,000, with RV precision limited by instrument stability and object S/N rather than by the lack of a suitable wavelength standard. We will present CU/NIST frequency comb performance and results obtained using the Pennsylvania State University's Pathfinder Spectrograph on the Hobby Eberly Telescope and will discuss lessons learned.

  14. Low Frequency Radar Sensor Observations of Tropical Forests in the Panama Canal Area

    NASA Technical Reports Server (NTRS)

    Imhoff, M. L.; Lawrence, W.; Condit, R.; Wright, J.; Johnson, P.; Hyer, J.; May, L.; Carson, S.; Smith, David E. (Technical Monitor)

    2000-01-01

    A synthetic aperture radar sensor operating in 5 bands between 80 and 120 MHz was flown over forested areas in the canal zone of the Republic of Panama in an experiment to measure biomass in heavy tropical forests. The sensor is a pulse coherent SAR flown on a small aircraft and oriented straight down. The doppler history is processed to collect data on the ground in rectangular cells of varying size over a range of incidence angles fore and aft of nadir (+45 to - 45 degrees). Sensor data consists of 5 frequency bands with 20 incidence angles per band. Sensor data for over 12+ sites were collected with forest stands having biomass densities ranging from 50 to 300 tons/ha dry above ground biomass. Results are shown exploring the biomass saturation thresholds using these frequencies, the system design is explained, and preliminary attempts at data visualization using this unique sensor design are described.

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

    PubMed

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

    2014-07-11

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

  16. A multifrequency study of giant radio sources - I. Low-frequency Giant Metrewave Radio Telescope observations of selected sources

    NASA Astrophysics Data System (ADS)

    Konar, C.; Jamrozy, M.; Saikia, D. J.; Machalski, J.

    2008-01-01

    We present low-frequency observations with the Giant Metrewave Radio Telescope of a sample of giant radio sources, and high-frequency observations of three of these sources with the Very Large Array. From multifrequency observations of the lobes, we estimate the magnetic field strengths using three different approaches, and show that these differ at most by a factor of ~3. For these large radio sources, the inverse-Compton losses usually dominate over synchrotron losses when estimates of the classical minimum energy magnetic field are used, consistent with earlier studies. However, this is often not true if the magnetic fields are close to the values estimated using the formalism of Beck & Krause. We also examine the spectral indices of the cores and any evidence of recurrent activity in these sources. We probe the environment using the symmetry parameters of these sources and suggest that their environments are often asymmetric on scales of ~1 Mpc, consistent with earlier studies.

  17. Space borne GPM dual-frequency radar simulation from high resolution ground radar observations.

    SciTech Connect

    Rose, C. R.; Chandrasekar, V.

    2004-01-01

    The Global Precipitation Measurement (GPM) mission is dedicated to improving the understanding of the global water cycle by measuring and mapping precipitation throughout the globe. The core GPM satellite will incorporate two separate precipitation radars: one operating at Ku-band (13.6 GHz) and the other at Ka band (35.6 GHz). Each radar beam will be steered such that they both point to the same location in the atmosphere. The main purpose of the dual-frequency radar system is to resolve the DSD in precipitation as well as discriminate between rain and ice. With the two beams collocated on the same precipitation volume, new algorithms are being developed to reliably es timate attenuation and rain rate. Any algorithm is based on models of precipitation. In addition, the GPM system assumes collocated beams and matched resolu tion volumes. Electromagnetic and microphysical models have been developed based on ground-based dual-frequency radar data at S-band to simulate Ku- and Ka-band results for comparison with the new GPM algorithms. This paper evaluates the dual-frequency inversion algorithm with synthesized S-band and known perfect data and presents results. Results show the expected performance of the new dual-precipitation radar algorithms with the potential for guiding algorithm and system improvements.

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

    PubMed

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

    2000-10-01

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

  19. Geostatistical analysis of allele presence patterns among American black bears in eastern North Carolina

    USGS Publications Warehouse

    Thompson, L.M.; Van Manen, F.T.; King, T.L.

    2005-01-01

    Highways are one of the leading causes of wildlife habitat fragmentation and may particularly affect wide-ranging species, such as American black bears (Ursus americanus). We initiated a research project in 2000 to determine potential effects of a 4-lane highway on black bear ecology in Washington County, North Carolina. The research design included a treatment area (highway construction) and a control area and a pre- and post-construction phase. We used data from the pre-construction phase to determine whether we could detect scale dependency or directionality among allele occurrence patterns using geostatistics. Detection of such patterns could provide a powerful tool to measure the effects of landscape fragmentation on gene flow. We sampled DNA from roots of black bear hair at 70 hair-sampling sites on each study area for 7 weeks during fall of 2000. We used microsatellite analysis based on 10 loci to determine unique multi-locus genotypes. We examined all alleles sampled at ???25 sites on each study area and mapped their presence or absence at each hair-sample site. We calculated semivariograms, which measure the strength of statistical correlation as a function of distance, and adjusted them for anisotropy to determine the maximum direction of spatial continuity. We then calculated the mean direction of spatial continuity for all examined alleles. The mean direction of allele frequency variation was 118.3?? (SE = 8.5) on the treatment area and 172.3?? (SE = 6.0) on the control area. Rayleigh's tests showed that these directions differed from random distributions (P = 0.028 and P < 0.001, respectively), indicating consistent directional patterns for the alleles we examined in each area. Despite the small spatial scale of our study (approximately 11,000 ha for each study area), we observed distinct and consistent patterns of allele occurrence, suggesting different directions of gene flow between the study areas. These directions seemed to coincide with the

  20. Schizophrenia susceptibility alleles are enriched for alleles that affect gene expression in adult human brain

    PubMed Central

    Richards, Alexander L; Jones, Lesley; Moskvina, Valentina; Kirov, George; Gejman, Pablo V; Levinson, Douglas F; Sanders, Alan R; Purcell, Shaun; Visscher, Peter M; Craddock, Nick; Owen, Michael J; Holmans, Peter; O’Donovan, Michael C

    2016-01-01

    It is widely thought that alleles that influence susceptibility to common diseases, including schizophrenia, will frequently do so through effects on gene expression. Since only a small proportion of the genetic variance for schizophrenia has been attributed to specific loci, this remains an unproven hypothesis. The International Schizophrenia Consortium (ISC) recently reported a substantial polygenic contribution to that disorder, and that schizophrenia risk alleles are enriched among SNPs selected for marginal evidence for association (p<0.5) from genome wide association studies (GWAS). It follows that if schizophrenia susceptibility alleles are enriched for those that affect gene expression, those marginally associated SNPs which are also eQTLs should carry more true association signals compared with SNPs which are not. To test this, we identified marginally associated (p<0.5) SNPs from two of the largest available schizophrenia GWAS datasets. We assigned eQTL status to those SNPs based upon an eQTL dataset derived from adult human brain. Using the polygenic score method of analysis reported by the ISC, we observed and replicated the observation that higher probability cis-eQTLs predicted schizophrenia better than those with a lower probability for being a cis-eQTL. Our data support the hypothesis that alleles conferring risk of schizophrenia are enriched among those that affect gene expression. Moreover, our data show that notwithstanding the likely developmental origin of schizophrenia, studies of adult brain tissue can in principle allow relevant susceptibility eQTLs to be identified. PMID:21339752

  1. Distribution of CYP2D6 alleles and phenotypes in the Brazilian population.

    PubMed

    Friedrich, Deise C; Genro, Júlia P; Sortica, Vinicius A; Suarez-Kurtz, Guilherme; de Moraes, Maria Elizabete; Pena, Sergio D J; dos Santos, Andrea K Ribeiro; Romano-Silva, Marco A; Hutz, Mara H

    2014-01-01

    The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions. PMID:25329392

  2. Distribution of CYP2D6 Alleles and Phenotypes in the Brazilian Population

    PubMed Central

    Sortica, Vinicius A.; Suarez-Kurtz, Guilherme; de Moraes, Maria Elizabete; Pena, Sergio D. J.; dos Santos, Ândrea K. Ribeiro; Romano-Silva, Marco A.; Hutz, Mara H.

    2014-01-01

    Abstract The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions. PMID:25329392

  3. The Behavior Observation Scale for Autism (BOS): Relationship of Frequency of Behavior to IQ.

    ERIC Educational Resources Information Center

    Freeman, B. J.; And Others

    The Behavior Observation Scale (BOS) was administered to 53 autistic children, 35 mentally retarded children matched for MA, and 33 normal children (all 2 to 5 years old) in an attempt to quantify autistic behavior. Ss were observed 3 days for 3 minutes through a one way mirror in a playroom setting where occurrence of 67 behaviors on the BOS was…

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

    SciTech Connect

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

    1994-09-15

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

  5. Intense low-frequency chorus waves observed by Van Allen Probes: Fine structures and potential effect on radiation belt electrons

    NASA Astrophysics Data System (ADS)

    Gao, Zhonglei; Su, Zhenpeng; Zhu, Hui; Xiao, Fuliang; Zheng, Huinan; Wang, Yuming; Shen, Chao; Wang, Shui

    2016-02-01

    Frequency distribution is a vital factor in determining the contribution of whistler mode chorus to radiation belt electron dynamics. Chorus is usually considered to occur in the frequency range 0.1-0.8fce_eq (with the equatorial electron gyrofrequency fce_eq). We here report an event of intense low-frequency chorus with nearly half of wave power distributed below 0.1fce_eq observed by Van Allen Probe A on 27 August 2014. This emission propagated quasi-parallel to the magnetic field and exhibited hiss-like signatures most of the time. The low-frequency chorus can produce the rapid loss of low-energy (˜0.1 MeV) electrons, different from the normal chorus. For high-energy (≥0.5 MeV) electrons, the low-frequency chorus can yield comparable momentum diffusion to that of the normal chorus but much stronger (up to 2 orders of magnitude) pitch angle diffusion near the loss cone.

  6. Toroidal wave frequency at L=6-10: AMPTE/CCE Observations and Comparison with Theoretical Model

    NASA Technical Reports Server (NTRS)

    Takahashi, Kazue; Denton, Richard E.; Gallaher, Dennis

    2003-01-01

    Magnetospheric standing Alfven waves are guided along the ambient magnetic field and their frequency depends on the mass density of the plasma distributed along the field lines. These properties allow us to use Alfen waves to map time-dependent phenomena between space and ground and to estimate the mass density. In this paper we present a statistical study of the spatial variation of the fundamental frequency f(sub T1) of toroidal-mode standing Alfen waves in the L range from 6 to 10, where L indicates the maximum geocentric distance on the field line. The data used for this analysis are energetic particle flux anisotropy (proxy of transverse electric field) and magnetic field measurements from the Active Magnetospheric Particle Tracer Explorers Charge Composition Explorer (CCE) spacecraft. Using CCE data covering 4 years we obtained approximately 5000 20-min intervals containing a clear signature of toroidal waves. The median f(sub T1), is 6-10 mHz at L=7 and decreases to 4-8 mHz at L = . The frequency tends to be lower at noon than at midnight. The observed frequencies are compared with numerically derived frequencies using an empirical mass density model and a magnetic field model. We found a good agreement for 12-24 MLT but a large discrepancy near MLT= 3. This may indicate that the flux tubes at this local time are more heavily loaded than specified in the Gallagher et al. model.

  7. Evaluation of Long-Term Cloud-Resolving Model Simulations Using Satellite Radiance Observations and Multi-Frequency Satellite Simulators

    NASA Technical Reports Server (NTRS)

    Matsui, Toshihisa; Zeng, Xiping; Tao, Wei-Kuo; Masunaga, Hirohiko; Olson, William S.; Lang, Stephen

    2008-01-01

    This paper proposes a methodology known as the Tropical Rainfall Measuring Mission (TRMM) Triple-Sensor Three-step Evaluation Framework (T3EF) for the systematic evaluation of precipitating cloud types and microphysics in a cloud-resolving model (CRM). T3EF utilizes multi-frequency satellite simulators and novel statistics of multi-frequency radiance and backscattering signals observed from the TRMM satellite. Specifically, T3EF compares CRM and satellite observations in the form of combined probability distributions of precipitation radar (PR) reflectivity, polarization-corrected microwave brightness temperature (Tb), and infrared Tb to evaluate the candidate CRM. T3EF is used to evaluate the Goddard Cumulus Ensemble (GCE) model for cases involving the South China Sea Monsoon Experiment (SCSMEX) and Kwajalein Experiment (KWAJEX). This evaluation reveals that the GCE properly captures the satellite-measured frequencies of different precipitating cloud types in the SCSMEX case but underestimates the frequencies of deep convective and deep stratiform types in the KWAJEX case. Moreover, the GCE tends to simulate excessively large and abundant frozen condensates in deep convective clouds as inferred from the overestimated GCE-simulated radar reflectivities and microwave Tb depressions. Unveiling the detailed errors in the GCE s performance provides the best direction for model improvements.

  8. Nature's starships. I. Observed abundances and relative frequencies of amino acids in meteorites

    SciTech Connect

    Cobb, Alyssa K.; Pudritz, Ralph E. E-mail: pudritz@physics.mcmaster.ca

    2014-03-10

    The class of meteorites called carbonaceous chondrites are examples of material from the solar system which have been relatively unchanged from the time of their initial formation. These meteorites have been classified according to the temperatures and physical conditions of their parent planetesimals. We collate available data on amino acid abundance in these meteorites and plot the concentrations of different amino acids for each meteorite within various meteorite subclasses. We plot average concentrations for various amino acids across meteorites separated by subclass and petrologic type. We see a predominance in the abundance and variety of amino acids in CM2 and CR2 meteorites. The range in temperature corresponding to these subclasses indicates high degrees of aqueous alteration, suggesting aqueous synthesis of amino acids. Within the CM2 and CR2 subclasses, we identify trends in relative frequencies of amino acids to investigate how common amino acids are as a function of their chemical complexity. These two trends (total abundance and relative frequencies) can be used to constrain formation parameters of amino acids within planetesimals. Our organization of the data supports an onion shell model for the temperature structure of planetesimals. The least altered meteorites (type 3) and their amino acids originated near cooler surface regions. The most active amino acid synthesis likely took place at intermediate depths (type 2). The most altered materials (type 1) originated furthest toward parent body cores. This region is likely too hot to either favor amino acid synthesis or for amino acids to be retained after synthesis.

  9. Reconstructing the prior probabilities of allelic phylogenies.

    PubMed Central

    Golding, G Brian

    2002-01-01

    In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually "rare" topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4N(mu) (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions. PMID:12072482

  10. The effect of the lunar cycle on frequency of births: a retrospective observational study in Indian population.

    PubMed

    Bharati, Saswata; Sarkar, Malay; Haldar, Partha Sarathi; Jana, Swapan; Mandal, Subrata

    2012-01-01

    For ancient period moon has been held responsible for many biological activities. That way, lunar cycle, by activity of moon, has been held responsible for increase in number of child birth. In this retrospective, observational study, we examined a total of 9890 full-term spontaneous deliveries as well as non-elective cesarean sections that occurred throughout 12 lunar months (February 7 th , 2008-January 25 th , 2009) in a rural medical college to evaluate the influence of the lunar position on the distribution of deliveries among Indian population. Student's 't' test and ANOVA were used for statistical analysis where each delivery was considered as a single measure. We found no significant differences in the frequency of births during various phase of lunar cycle regardless of route of delivery. Our observations do not support the hypothesis of a relationship between lunar cycle and the frequency of obstetric deliveries. PMID:22910625

  11. Observation of fluctuation-driven particle flux reduction by low-frequency zonal flow in a linear magnetized plasma

    SciTech Connect

    Chen, R.; Xie, J. L. Yu, C. X.; Liu, A. D.; Lan, T.; Li, H.; Liu, W. D.; Zhang, S. B.; Kong, D. F.; Hu, G. H.

    2015-01-15

    Low-frequency zonal flow (ZF) has been observed in a linear magnetic plasma device, exhibiting significant intermittency. Using the conditional analysis method, a time-averaged fluctuation-induced particle flux was observed to consistently decrease as ZF increased in amplitude. A dominant fraction of the flux, which is driven by drift-wave harmonics, is reversely modulated by ZF in the time domain. Spectra of the flux, together with each of the related turbulence properties, are estimated subject to two conditions, i.e., when potential fluctuation series represents a strong ZF intermittency or a very weak ZF component. Comparison of frequency-domain results demonstrates that ZF reduces the cross-field particle transport primarily by suppressing the density fluctuation as well as decorrelating density and potential fluctuations.

  12. Allelic association and extended haplotype analysis of the spinal muscular atrophy (SMA) candidate region in the French Candadian population

    SciTech Connect

    Simard, L.R.; Prescott, G.; Rochette, C. |

    1994-09-01

    SMA is a common lower motor neuron disease characterized by progressive proximal limb and trunk muscle weakness. Despite the wide range in phenotypic severity, all three clinical types of childhood SMAs map to chromosome 5q11.2-5q13.3. The proximal (D5S557) flanking markers span about 1 Mb. We have previously demonstrated significant linkage disequilibrium between D5S125, D5S435, D5S351, JK53CA1/2 and SMA in the French Canadian population. We now present data for three new DNA markers mapping between D5S435 and D5S557 kindly provided to us by Drs. B. Wirth (A31), A. Burghes (Ag1) and A. MacKenzie (CATT-40G1). We identified 10 different A31 Alleles whose frequencies were similar for both normal and SMA chromosomes. Ag1 is a complex multi-allelic marker and specific primers amplified 1 (Class I), 2 or rarely 3 (Class II) alleles per chromosome. We observed significant association between Ag1 and SMA. For example, the 100 bp Ag1 fragment was typed on 20 of 73 SMA chromosomes and 0 of 74 normal chromosomes (p=<10{sup -4}). We also observed significant association between Ag1 Class genotypes and phenotypic severity. Class I chromosomes predominated in Type I SMA (p=.001) while Type II SMA individuals were generally heterozygous Class I/Class II (p=.001). Finally, we provide evidence for allelic association between Type I SMA and CATT-40G1, a tri-allelic sublocus of CATT-1. All of our Type I SMA chromosomes (n=20) carried a null allele compared to 40% of normal chromosomes (p=<10{sup -4}). Extended haplotype analyses indicated that > 19% of French Canadian SMA chromosomes appear to be ancestrally related to two unique haplotypes indicating their utility for linkage disequilibrium mapping.

  13. A Position- and Velocity-Sensorless Control for Synchronous Reluctance Motor with Disturbance Observer Using High Frequency Voltages and Currents

    NASA Astrophysics Data System (ADS)

    Tamaoki, Masakazu; Tomita, Mutuwo; Chen, Zhiqian; Doki, Shinji; Okuma, Shigeru

    Synchronous reluctance motors (SynRMs) are characterized by their sturdiness, and several sensorless control methods of SynRMs have been proposed. In their methods, flux is estimated and the rotor position is estimated from the flux. The induced voltages for flux estimation are small at low speed. In this paper, new position estimation method is proposed using the disturbance observer based on high frequency currents. Simulation results show that the proposed system is very useful.

  14. Observations on the magnitude-frequency distribution of Earth-crossing asteroids

    NASA Technical Reports Server (NTRS)

    Shoemaker, Eugene M.; Shoemaker, Carolyn S.

    1987-01-01

    During the past decade, discovery of Earth-crossing asteroids has continued at the pace of several per year; the total number of known Earth crossers reached 70 as of September, 1986. The sample of discovered Earth crossers has become large enough to provide a fairly strong statistical basis for calculations of mean probabilities of asteroid collision with the Earth, the Moon, and Venus. It is also now large enough to begin to address the more difficult question of the magnitude-frequency distribution and size distribution of the Earth-crossing asteroids. Absolute V magnitude, H, was derived from reported magnitudes for each Earth crosser on the basis of a standard algorithm that utilizes a physically realistic phase function. The derived values of H range from 12.88 for (1627) Ivar to 21.6 for the Palomar-Leiden object 6344, which is the faintest and smallest asteroid discovered.

  15. Frequency domain observations of small motions at concrete/steel interfaces

    SciTech Connect

    Bonner, B.P.

    1996-06-01

    When two rough interfaces in contact are driven in harmonic motion, the frictional resistance to shear causes the response of the driven system to be nonlinear. Displacement along the interface cannot be described by a linear predictor, one analogous to Hooke`s law for elastic response. Laboratory experiments are described here to illustrate that the resulting motion is not random, but produces measurable and characteristic output at harmonics of the driving frequency. Although the geometry of the tests is not practical for evaluating the integrity of steel/concrete interfaces in structures, the results illustrate that the principle should apply to other geometries where shearing forces can be applied to interfaces to determine the quality of bonding.

  16. Observations of low-frequency radio emissions in the earth's magnetosphere

    NASA Technical Reports Server (NTRS)

    Filbert, Paul C.; Kellogg, Paul J.

    1989-01-01

    Electromagnetic radiation in the earth's magnetosphere was investigated for the frequency range between 10 kHz and 80 kHz, using data from the Minnesota Plasma Wave Experiment aboard the IMP 6 spacecraft. Two types of radio emissions were examined, the first being the nonthermal continuum radiation, and the second, much more impulsive, is the radiation which lies between 10 and 60 kHz. The first type of radiation was found to correlate with the enhancements of the magnetic substorm index AE and to follow the onset of the negative bay feature of the AU index by about 20 min. The second radiation was found to correlate with auroral kilometric radiation (AKR) on a time scale of about 1 min; this radiation was found to have a source direction very near that of the coincident AKR.

  17. HLA-DRB1 alleles in four Amerindian populations from Argentina and Paraguay

    PubMed Central

    2009-01-01

    The major histocompatibility complex (MHC) is one of the biological systems of major polymorphisms. The study of HLA class II variability has allowed the identification of several alleles that are characteristic to Amerindian populations, and it is an excellent tool to define the relations and biological affinities among them. In this work, we analyzed the allelic distribution of the HLA-DRB1 class II locus in four Amerindian populations: Mapuche (n = 34) and Tehuelche (n = 23) from the Patagonian region of Argentina, and Wichi SV (n = 24) and Lengua (n = 17) from the Argentinean and Paraguayan Chaco regions, respectively. In all of these groups, relatively high frequencies of Amerindian HLA-DRB1 alleles were observed (DRB1*0403, DRB1*0407, DRB1*0411, DRB1*0417, DRB1*0802, DRB1*0901, DRB1*1402, DRB1*1406 and DRB1*1602). However, we also detected the presence of non-Amerindian variants in Mapuche (35%) and Tehuelche (22%). We compared our data with those obtained in six indigenous groups of the Argentinean Chaco region and in a sample from Buenos Aires City. The genetic distance dendrogram showed a clear-cut division between the Patagonian and Chaco populations, which formed two different clusters. In spite of their linguistic differences, it can be inferred that the biological affinities observed are in concordance with the geographic distributions and interethnic relations established among the groups studied. PMID:21637670

  18. HLA-DRB1 alleles in four Amerindian populations from Argentina and Paraguay.

    PubMed

    Parolín, Maria L; Carnese, Francisco R

    2009-04-01

    The major histocompatibility complex (MHC) is one of the biological systems of major polymorphisms. The study of HLA class II variability has allowed the identification of several alleles that are characteristic to Amerindian populations, and it is an excellent tool to define the relations and biological affinities among them. In this work, we analyzed the allelic distribution of the HLA-DRB1 class II locus in four Amerindian populations: Mapuche (n = 34) and Tehuelche (n = 23) from the Patagonian region of Argentina, and Wichi SV (n = 24) and Lengua (n = 17) from the Argentinean and Paraguayan Chaco regions, respectively. In all of these groups, relatively high frequencies of Amerindian HLA-DRB1 alleles were observed (DRB1*0403, DRB1*0407, DRB1*0411, DRB1*0417, DRB1*0802, DRB1*0901, DRB1*1402, DRB1*1406 and DRB1*1602). However, we also detected the presence of non-Amerindian variants in Mapuche (35%) and Tehuelche (22%). We compared our data with those obtained in six indigenous groups of the Argentinean Chaco region and in a sample from Buenos Aires City. The genetic distance dendrogram showed a clear-cut division between the Patagonian and Chaco populations, which formed two different clusters. In spite of their linguistic differences, it can be inferred that the biological affinities observed are in concordance with the geographic distributions and interethnic relations established among the groups studied. PMID:21637670

  19. Low Frequency Oscillations in Assimilated Global Datasets Using TRMM Rainfall Observations

    NASA Technical Reports Server (NTRS)

    Tao, Li; Yang, Song; Zhang, Zhan; Hou, Arthur; Olson, William S.

    2004-01-01

    Global datasets for the period May-August 1998 from the Goddard Earth Observing System (GEOS) data assimilation system (DAS) with/without assimilated Tropical Rainfall Measuring Mission (TRMM) precipitation are analyzed against European Center for Medium-Range Weather Forecast (ECMWF) output, NOAA observed outgoing longwave radiation (OLR) data, and TRMM measured rainfall. The purpose of this study is to investigate the representation of the Madden-Julian Oscillation (MJO) in GEOS assimilated global datasets, noting the impact of TRMM observed rainfall on the MJO in GEOS data assimilations. A space-time analysis of the OLR data indicates that the observed OLR exhibits a spectral maximum for eastward-propagating wavenumber 1-3 disturbances with periods of 20-60 days in the 0deg-30degN latitude band. The assimilated OLR has a similar feature but with a smaller magnitude. However, OLR spectra from assimilations including TRMM rainfall data show better agreement with observed OLR spectra than spectra from assimilations without TRMM rainfall. Similar results are found for wavenumber 4-6 disturbances. There is a spectral peak for eastward-propagating wavenumber 4-6 disturbances with periods of 20-40 days near the equator, while for westward-moving disturbances, a spectral peak is noted for periods of 30-50 days near 25degN. To isolate the MJO, a 30-50 day band filter is selected for this study. It was found that the eastward-propagating waves from the band-filtered observed OLR between 10degs- 10degN are located in the eastern hemisphere. Similar patterns are evident in surface rainfall and the 850 hPa wind field. Assimilation of TRMM-observed rainfall reveals more distinct MJO features in the analysis than without rainfall assimilation. Similar analyses are also conducted over the Indian summer monsoon and East Asia summer monsoon regions, where the MJO is strongly related to the summer monsoon active-break patterns.

  20. Evolution of HLA class II molecules: Allelic and amino acid site variability across populations.

    PubMed Central

    Salamon, H; Klitz, W; Easteal, S; Gao, X; Erlich, H A; Fernandez-Viña, M; Trachtenberg, E A; McWeeney, S K; Nelson, M P; Thomson, G

    1999-01-01

    Analysis of the highly polymorphic beta1 domains of the HLA class II molecules encoded by the DRB1, DQB1, and DPB1 loci reveals contrasting levels of diversity at the allele and amino acid site levels. Statistics of allele frequency distributions, based on Watterson's homozygosity statistic F, reveal distinct evolutionary patterns for these loci in ethnically diverse samples (26 populations for DQB1 and DRB1 and 14 for DPB1). When examined over all populations, the DQB1 locus allelic variation exhibits striking balanced polymorphism (P < 10(-4)), DRB1 shows some evidence of balancing selection (P < 0.06), and while there is overall very little evidence for selection of DPB1 allele frequencies, there is a trend in the direction of balancing selection (P < 0.08). In contrast, at the amino acid level all three loci show strong evidence of balancing selection at some sites. Averaged over polymorphic amino acid sites, DQB1 and DPB1 show similar deviation from neutrality expectations, and both exhibit more balanced polymorphic amino acid sites than DRB1. Across ethnic groups, polymorphisms at many codons show evidence for balancing selection, yet data consistent with directional selection were observed at other codons. Both antigen-binding pocket- and non-pocket-forming amino acid sites show overall deviation from neutrality for all three loci. Only in the case of DRB1 was there a significant difference between pocket- and non-pocket-forming amino acid sites. Our findings indicate that balancing selection at the MHC occurs at the level of polymorphic amino acid residues, and that in many cases this selection is consistent across populations. PMID:10224269

  1. Ancestry of the Timorese: age-related macular degeneration associated genotype and allele sharing among human populations from throughout the world.

    PubMed

    Morrison, Margaux A; Magalhaes, Tiago R; Ramke, Jacqueline; Smith, Silvia E; Ennis, Sean; Simpson, Claire L; Portas, Laura; Murgia, Federico; Ahn, Jeeyun; Dardenne, Caitlin; Mayne, Katie; Robinson, Rosann; Morgan, Denise J; Brian, Garry; Lee, Lucy; Woo, Se J; Zacharaki, Fani; Tsironi, Evangelia E; Miller, Joan W; Kim, Ivana K; Park, Kyu H; Bailey-Wilson, Joan E; Farrer, Lindsay A; Stambolian, Dwight; DeAngelis, Margaret M

    2015-01-01

    We observed that the third leading cause of blindness in the world, age-related macular degeneration (AMD), occurs at a very low documented frequency in a population-based cohort from Timor-Leste. Thus, we determined a complete catalog of the ancestry of the Timorese by analysis of whole exome chip data and haplogroup analysis of SNP genotypes determined by sequencing the Hypervariable I and II regions of the mitochondrial genome and 17 genotyped YSTR markers obtained from 535 individuals. We genotyped 20 previously reported AMD-associated SNPs in the Timorese to examine their allele frequencies compared to and between previously documented AMD cohorts of varying ethnicities. For those without AMD (average age > 55 years), genotype and allele frequencies were similar for most SNPs with a few exceptions. The major risk allele of HTRA1 rs11200638 (10q26) was at a significantly higher frequency in the Timorese, as well as 3 of the 5 protective CFH (1q32) SNPs (rs800292, rs2284664, and rs12066959). Additionally, the most commonly associated AMD-risk SNP, CFH rs1061170 (Y402H), was also seen at a much lower frequency in the Korean and Timorese populations than in the assessed Caucasian populations (C ~7 vs. ~40%, respectively). The difference in allele frequencies between the Timorese population and the other genotyped populations, along with the haplogroup analysis, also highlight the genetic diversity of the Timorese. Specifically, the most common ancestry groupings were Oceanic (Melanesian and Papuan) and Eastern Asian (specifically Han Chinese). The low prevalence of AMD in the Timorese population (2 of 535 randomly selected participants) may be due to the enrichment of protective alleles in this population at the 1q32 locus. PMID:26217379

  2. Ancestry of the Timorese: age-related macular degeneration associated genotype and allele sharing among human populations from throughout the world

    PubMed Central

    Morrison, Margaux A.; Magalhaes, Tiago R.; Ramke, Jacqueline; Smith, Silvia E.; Ennis, Sean; Simpson, Claire L.; Portas, Laura; Murgia, Federico; Ahn, Jeeyun; Dardenne, Caitlin; Mayne, Katie; Robinson, Rosann; Morgan, Denise J.; Brian, Garry; Lee, Lucy; Woo, Se J.; Zacharaki, Fani; Tsironi, Evangelia E.; Miller, Joan W.; Kim, Ivana K.; Park, Kyu H.; Bailey-Wilson, Joan E.; Farrer, Lindsay A.; Stambolian, Dwight; DeAngelis, Margaret M.

    2015-01-01

    We observed that the third leading cause of blindness in the world, age-related macular degeneration (AMD), occurs at a very low documented frequency in a population-based cohort from Timor-Leste. Thus, we determined a complete catalog of the ancestry of the Timorese by analysis of whole exome chip data and haplogroup analysis of SNP genotypes determined by sequencing the Hypervariable I and II regions of the mitochondrial genome and 17 genotyped YSTR markers obtained from 535 individuals. We genotyped 20 previously reported AMD-associated SNPs in the Timorese to examine their allele frequencies compared to and between previously documented AMD cohorts of varying ethnicities. For those without AMD (average age > 55 years), genotype and allele frequencies were similar for most SNPs with a few exceptions. The major risk allele of HTRA1 rs11200638 (10q26) was at a significantly higher frequency in the Timorese, as well as 3 of the 5 protective CFH (1q32) SNPs (rs800292, rs2284664, and rs12066959). Additionally, the most commonly associated AMD-risk SNP, CFH rs1061170 (Y402H), was also seen at a much lower frequency in the Korean and Timorese populations than in the assessed Caucasian populations (C ~7 vs. ~40%, respectively). The difference in allele frequencies between the Timorese population and the other genotyped populations, along with the haplogroup analysis, also highlight the genetic diversity of the Timorese. Specifically, the most common ancestry groupings were Oceanic (Melanesian and Papuan) and Eastern Asian (specifically Han Chinese). The low prevalence of AMD in the Timorese population (2 of 535 randomly selected participants) may be due to the enrichment of protective alleles in this population at the 1q32 locus. PMID:26217379

  3. The low-frequency continuum as observed in the solar wind from ISEE 3 - Thermal electrostatic noise

    NASA Technical Reports Server (NTRS)

    Hoang, S.; Steinberg, J.-L.; Epstein, G.; Tilloles, P.; Fainberg, J.; Stone, R. G.

    1980-01-01

    The low frequency continuum (LFC) noise between 30 and 200 kHz has been investigated from the ISEE 3 spacecraft in the solar wind by means of a radio astronomy experiment more sensitive than previously available. It is demonstrated that the LFC radiation observed in the solar wind is in the form of longitudinal plasma waves rather than transverse electromagnetic waves. The observed spectral characteristics are found to be a function of antenna length. In addition, both the absence of antenna spin modulation and the fact that these plasma waves do not propagate to large distances imply a local origin for the LFC.

  4. Observations of low-frequency inertia-gravity waves in the lower stratosphere over Arecibo

    NASA Technical Reports Server (NTRS)

    Cornish, C. R.; Larsen, M. F.

    1989-01-01

    Results are presented of a detailed analysis of the horizontal wind data in the subtropical upper troposphere and lower stratosphere, obtained with the 430-MHz radar at Arecibo (Puerto Rico) in May 1982 and April 1983. Both sets of observations displayed a slowly varying anticyclonically rotating persistent structure in the wind field just above the tropopause, of the type that would be expected if the oscillations were associated with quasi-inertial period waves. The quasi-inertial period structure in the Arecibo observations appears to be typical of the results of a number of other studies, indicating that quasi-inertial period waves are a ubiquitous feature in the lower stratosphere, similar to what is observed in the oceans.

  5. Low-frequency radio observations of SN 2011dh and the evolution of its post-shock plasma properties

    NASA Astrophysics Data System (ADS)

    Yadav, Naveen; Ray, Alak; Chakraborti, Sayan

    2016-06-01

    We present late time, low-frequency observations of SN 2011dh made using the Giant Metrewave Radio Telescope (GMRT). Our observations at 325, 610 and 1280 MHz conducted between 93 and 421 d after the explosion supplement the millimeter and centimetre wave observations conducted between 4 and 15 d after explosion using the Combined Array for Research in Millimeter-wave Astronomy (CARMA) and extensive radio observations (1.0-36.5 GHz) conducted between 16 and 93 d after explosion using Jansky Very Large Array (JVLA). We fit a synchrotron self absorption model (SSA) to the 610 and 1280 MHz radio light curves. We use it to determine the radius (Rp) and magnetic field (Bp) at 173 and 323 d after the explosion. A comparison of the peak radio luminosity Lop with the product of the peak frequency νp and time to peak tp shows that the supernova evolves between the epochs of CARMA, JVLA and GMRT observations. It shows a general slowing down of the expansion speed of the radio emitting region on a time-scale of several hundred days during which the shock is propagating through a circumstellar medium set up by a wind with a constant mass-loss parameter, dot{M}/{v}_w. We derive the mass-loss parameter (A⋆) based on 610 and 1280 MHz radio light curves, which are found to be consistent with each other within error limits.

  6. Comparison of signal to noise ratios from spatial and frequency domain formulations of nonprewhitening model observers in digital mammography

    SciTech Connect

    Sisini, Francesco; Zanca, Federica; Marshall, Nicholas W.; Taibi, Angelo; Cardarelli, Paolo; Bosmans, Hilde

    2012-09-15

    Purpose: Image quality indices based upon model observers are promising alternatives to laborious human readings of contrast-detail images. This is especially appealing in digital mammography as limiting values for contrast thresholds determine, according to some international protocols, the acceptability of these systems in the radiological practice. The objective of the present study was to compare the signal to noise ratios (SNR) obtained with two nonprewhitening matched filter model observer approaches, one in the spatial domain and the other in the frequency domain, and with both of them worked out for disks as present in the CDMAM phantom. Methods: The analysis was performed using images acquired with the Siemens Novation and Inspiration digital mammography systems. The spatial domain formulation uses a series of high dose CDMAM images as the signal and a routine exposure of two flood images to calculate the covariance matrix. The frequency domain approach uses the mathematical description of a disk and modulation transfer function (MTF) and noise power spectrum (NPS) calculated from images. Results: For both systems most of the SNR values calculated in the frequency domain were in very good agreement with the SNR values calculated in the spatial domain. Both the formulations in the frequency domain and in the spatial domain show a linear relationship between SNR and the diameter of the CDMAM discs. Conclusions: The results suggest that both formulations of the model observer lead to very similar figures of merit. This is a step forward in the adoption of figures of merit based on NPS and MTF for the acceptance testing of mammography systems.

  7. Applications of high-frequency resolution, wide-field VLBI: observations of nearby star-forming galaxies & habitable exoplanetary candidates

    NASA Astrophysics Data System (ADS)

    Rampadarath, Hayden

    2014-04-01

    Until recently, the maximum observable field of view of Very Long Baseline Interferometric (VLBI) observations was limited, predominantly, by the ability to process large volumes of data. However, the availability of software correlators and high performance computing have provided the means to overcome these restrictions, giving rise to the technique of wide-field VLBI. This thesis reports on the application of this technique to investigate two different science cases: (1) to explore the use of VLBI for targeted searches for extra-terrestrial intelligence (SETI); (2) to investigate the compact radio source populations, supernovae, and star formation rates and the interstellar media of nearby star-forming galaxies. Radio sources detected with VLBI will display characteristic variations as a function of time and frequency that are dependent on their locations with respect to the observing phase centre. Thus, a planet with a radio emitting civilisation, bright enough to be detected, can be identified and separated from human generated signals through VLBI observations. This idea was tested on a VLBI observation of the planetary system Gliese 581. The dataset was searched for candidate SETI signals, in both time and frequency, with amplitudes greater than five times the baseline sensitivity on all baselines. Candidate signals were selected and through the use of automated, statistical data analysis techniques were ruled out as originating from the Gliese 581 system. The results of this study place an upper limit of 7 MW/Hz on the power output of any isotropic emitter located in the Gliese 581 system, within this frequency range. While the study was unable to identify any signals originating from Gliese 581, the techniques presented are applicable to the next-generation interferometers, such as the long baselines of the Square Kilometre Array.

  8. Tidal currents in the Malta - Sicily Channel from high-frequency radar observations

    NASA Astrophysics Data System (ADS)

    Cosoli, Simone; Drago, Aldo; Ciraolo, Giuseppe; Capodici, Fulvio

    2015-10-01

    Two years of sea surface current measurements acquired since August 2012 by High-Frequency SeaSonde radars over the relatively shallow shelf area dividing the Maltese Islands from Sicily (the Malta - Sicily Channel), are used to characterize the surface tidal currents in the region. Tidal currents are generally weak and concentrated in the semidiurnal and diurnal bands, barely exceeding 3 cm s-1 in the semidiurnal band (M2, S2), and below 6 cm s-1 in the diurnal band (K1, O1). In the middle part of the basin, the M2 currents oscillate along the main Channel axis; on the contrary the S2 oscillations are oriented along the energetic Atlantic Ionian Stream (AIS) flow. Diurnal tides have a more circular pattern, also following the AIS path and with a significant intensification in proximity of the shelf break, thus suggesting a substantial contribution from internal tides in the region. Phase contours suggest the presence of amphidromic points for both the semidiurnal and diurnal constituents, located in the central area of the Channel for S2, O1 and K1, but slightly shifted towards north-west for the M2 component.

  9. The nature of the low-frequency emission of M 51. First observations of a nearby galaxy with LOFAR

    NASA Astrophysics Data System (ADS)

    Mulcahy, D. D.; Horneffer, A.; Beck, R.; Heald, G.; Fletcher, A.; Scaife, A.; Adebahr, B.; Anderson, J. M.; Bonafede, A.; Brüggen, M.; Brunetti, G.; Chyży, K. T.; Conway, J.; Dettmar, R.-J.; Enßlin, T.; Haverkorn, M.; Horellou, C.; Iacobelli, M.; Israel, F. P.; Junklewitz, H.; Jurusik, W.; Köhler, J.; Kuniyoshi, M.; Orrú, E.; Paladino, R.; Pizzo, R.; Reich, W.; Röttgering, H. J. A.

    2014-08-01

    Context. Low-frequency radio continuum observations (<300 MHz) can provide valuable information on the propagation of low-energy cosmic ray electrons (CRE). Nearby spiral galaxies have hardly been studied in this frequency range because of the technical challenges of low-frequency radio interferometry. This is now changing with the start of operations of LOFAR. Aims: We aim to study the propagation of low-energy CRE in the interarm regions and the extended disk of the nearly face-on spiral galaxy Messier 51. We also search for polarisation in M 51 and other extragalactic sources in the field. Methods: The grand-design spiral galaxy M 51 was observed with the LOFAR High Frequency Antennas (HBA) and imaged in total intensity and polarisation. This observation covered the frequencies between 115 MHz and 175 MHz with 244 subbands of 8 channels each, resulting in 1952 channels. This allowed us to use RM synthesis to search for polarisation. Results: We produced an image of total emission of M 51 at the mean frequency of 151 MHz with 20'' resolution and 0.3 mJy rms noise, which is the most sensitive image of a galaxy at frequencies below 300 MHz so far. The integrated spectrum of total radio emission is described well by a power law, while flat spectral indices in the central region indicate thermal absorption. We observe that the disk extends out to 16 kpc and see a break in the radial profile near the optical radius of the disk. The radial scale lengths in the inner and outer disks are greater at 151 MHz, and the break is smoother at 151 MHz than those observed at 1.4 GHz. The arm-interarm contrast is lower at 151 MHz than at 1400 MHz, indicating propagation of CRE from spiral arms into interarm regions. The correlations between the images of radio emission at 151 MHz and 1400 MHz and the FIR emission at 70 μm reveal breaks on scales of 1.4 and 0.7 kpc, respectively. The total (equipartition) magnetic field strength decreases from about 28 μG in the central region to

  10. Electromagnetic ion cyclotron waves observed near the oxygen cyclotron frequency by ISEE 1 and 2

    NASA Technical Reports Server (NTRS)

    Fraser, B. J.; Samson, J. C.; Hu, Y. D.; Mcpherron, R. L.; Russell, C. T.

    1992-01-01

    The first results of observations of ion cyclotron waves by the elliptically orbiting ISEE 1 and 2 pair of spacecraft are reported. The most intense waves (8 nT) were observed in the outer plasmasphere where convection drift velocities were largest and the Alfven velocity was a minimum. Wave polarization is predominantly left-handed with propagation almost parallel to the ambient magnetic field, and the spectral slot and polarization reversal predicted by cold plasma propagation theory are identified in the wave data. Computations of the experimental wave spectra during the passage through the plasmapause show that the spectral slots relate to the local plasma parameters, possibly suggesting an ion cyclotron wave growth source near the spacecraft. A regular wave packet structure seen over the first 30 min of the event is attributed to the modulation of this energy source by the Pc 5 waves seen at the same time.

  11. The 2011 Tohoku tsunami south of Oahu: High-frequency Doppler radio observations and model simulations of currents

    NASA Astrophysics Data System (ADS)

    Benjamin, L. R.; Flament, P.; Cheung, K. F.; Luther, D. S.

    2016-02-01

    A 16 MHz high-frequency Doppler radio (HFDR) deployed on the south shore of Oahu (Hawaii) detected oscillatory radial currents following the arrival of the 2011 Tohoku tsunami. The observations over a two-dimensional area provided an opportunity for intercomparison with the spatial patterns of currents and the resonant modes predicted by a nonhydrostatic model. Over the 50 m deep Penguin Bank, extending west from Molokai, the observed currents are intensified in two areas: 43 min period currents of 0.27 m s-1 lasting 6 h are observed on the south part of the bank, while 27 min period currents of 0.14 m s-1 lasting 2 h are observed on the north. The spatial EOFs suggest that standing full-waves and 3/2 waves formed over the bank. Modeled currents over Penguin Bank are similar to the observations but their north-south asymmetry is less pronounced than observed. Nearshore, observed alongshore currents showed long-period oscillations of 43 min that stretched along the entire coastline, while modeled currents show strong evidence for edge waves. EOF analysis of the nearshore signal suggests that the HFDR and model reveal different processes. The discrepancy might be attributed to the fact that both the Penguin Bank and nearshore observations are limited by HFDR sensitivity to azimuthal sidelobe contamination and decreased angular resolution at high steering angles.

  12. Ultra Low Frequency Waves Observed in the Inner Magnetosphere by Magnetospheric Multiscale

    NASA Astrophysics Data System (ADS)

    Strangeway, Robert J.; Russell, Christopher T.; Burch, James L.; Torbert, Roy B.; Magnes, Werner; Plaschke, Ferdinand; Fischer, David; Leinweber, Hannes K.; Anderson, Brian A.; Bromund, Kenneth R.; Le, Guan; Nakamura, Rumi; Baumjohann, Wolfgang; Slavin, James A.; Kepko, Larry; Argall, Matthew R.; Chi, Peter

    2016-04-01

    Magnetospheric Multiscale (MMS) was launched on March 13, 2015 into a low inclination orbit with apogee around 12 Earth radii in the pre-dawn local time sector. The spacecraft were initially in a string-of-pearls configuration as the orbit precessed through the nightside inner magnetosphere. This spacecraft configuration allowed for unambiguous determination of the azimuthal wave number of the waves, and we typically find them to be westward propagating in the nightside. This is consistent with drift resonance with ions. The MMS spacecraft observed both toroidal and poloidal waves. This initial case study indicates that the poloidal waves were observed near the magnetic equator, with the spacecraft around 8-10 Earth radii. This might be expected for drift resonance with ions in the ~ 10 keV range, corresponding to the plasma sheet rather than the ring current. The toroidal waves, on the other hand, were observed much closer in, and quite far from the equator. They also had a significant component of their phase velocity outward, to higher latitudes. Their azimuthal phase velocity was much larger than the poloidal waves. It is possible that these waves are shear-mode waves that have been mode converted from fast-mode waves, which in turn have been generated by an external source.

  13. Magnetospheric Multiscale Observations of Ultra Low Frequency Waves in the Inner Magnetosphere

    NASA Astrophysics Data System (ADS)

    Strangeway, R. J.; Russell, C. T.; Burch, J. L.; Torbert, R. B.; Magnes, W.; Plaschke, F.; Leinweber, H. K.; Bromund, K. R.; Fischer, D.; Anderson, B. J.; Le, G.; Chutter, M.; Slavin, J. A.; Kepko, L.; Le Contel, O.; Nakamura, R.; Baumjohann, W.; Argall, M. R.; Chi, P. J.

    2015-12-01

    The apogee of the Magnetospheric Multiscale (MMS) spacecraft was in the predawn local time sector early in the MMS commissioning phase. On several orbits in this phase MMS observed large amplitude (10s of nT) Pc5 pulsations, typically around 5 to 7 Earth radii, near dawn. Because MMS was in a string-of-pearls configuration we could determine the phase velocity of the waves along the spacecraft separation vector. Preliminary analysis indicates that this was of the order 30-50 km/s, much larger than the spacecraft velocity. Furthermore, the waves are propagating tailwards. Given a nominal wave period of the order 5 minutes, the wavelength of the waves is around 2 Earth radii, assuming azimuthal propagation. This corresponds to an m-number of about 20. The waves used for this initial study were observed on several successive orbits during the recovery phase of the March 17, 2015 geomagnetic storm. We will present additional analysis of the properties of these ULF waves as observed during the MMS commissioning phase, during which time the spacecraft apogee migrated from dawn to dusk through the nightside.

  14. HIGH ANGULAR RESOLUTION RADIO OBSERVATIONS OF A CORONAL MASS EJECTION SOURCE REGION AT LOW FREQUENCIES DURING A SOLAR ECLIPSE

    SciTech Connect

    Ramesh, R.; Kathiravan, C.; Barve, Indrajit V.; Rajalingam, M. E-mail: kathir@iiap.res.in E-mail: rajalingam@iiap.res.in

    2012-01-10

    We carried out radio observations of the solar corona in the frequency range 109-50 MHz during the annular eclipse of 2010 January 15 from the Gauribidanur Observatory, located about 100 km north of Bangalore in India. The radio emission in the above frequency range originates typically in the radial distance range Almost-Equal-To 1.2-1.5 R{sub Sun} in the 'undisturbed' solar atmosphere. Our analysis indicates that (1) the angular size of the smallest observable radio source (associated with a coronal mass ejection in the present case) is Almost-Equal-To 1' {+-} 0.'3, (2) the source size does not vary with radial distance, (3) the peak brightness temperature of the source corresponding to the above size at a typical frequency like 77 MHz is Almost-Equal-To 3 Multiplication-Sign 10{sup 9} K, and (4) the coronal magnetic field near the source region is Almost-Equal-To 70 mG.

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

    SciTech Connect

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

    1994-09-01

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

  16. Detection of High-Frequency Oscillations and Damping from Multi-slit Spectroscopic Observations of the Corona

    NASA Astrophysics Data System (ADS)

    Samanta, T.; Singh, J.; Sindhuja, G.; Banerjee, D.

    2016-01-01

    During the total solar eclipse of 11 July 2010, multi-slit spectroscopic observations of the solar corona were performed from Easter Island, Chile. To search for high-frequency waves, observations were taken at a high cadence in the green line at 5303 Å that is due to [Fe xiv] and the red line at 6374 Å that is due to [Fe x]. The data were analyzed to study the periodic variations in intensity, Doppler velocity, and line width using wavelet analysis. The data with high spectral and temporal resolution enabled us to study the rapid dynamical changes within coronal structures. We find that at certain locations, each parameter shows significant oscillation with periods ranging from 6 - 25 s. For the first time, we were able to detect damping of high-frequency oscillations with periods of about 10 s. If the observed damped oscillations are due to magnetohydrodynamic waves, then they can contribute significantly to the heating of the corona. From a statistical study we try to characterize the nature of the observed oscillations while considering the distribution of power in different line parameters.

  17. Three-dimensional effects in polarization signatures as observed from precipitating clouds by low frequency ground-based microwave radiometers

    NASA Astrophysics Data System (ADS)

    Battaglia, A.; Simmer, C.; Czekala, H.

    2006-09-01

    Consistent negative polarization differences (i.e. differences between the vertical and the horizontal brightness temperature) are observed when looking at precipitating systems by ground-based radiometers at slant angles. These signatures can be partially explained by one-dimensional radiative transfer computations that include oriented non-spherical raindrops. However some cases are characterized by polarization values that exceed differences expected from one-dimensional radiative transfer. A three-dimensional fully polarized Monte Carlo model has been used to evaluate the impact of the horizontal finiteness of rain shafts with different rain rates at 10, 19, and 30 GHz. The results show that because of the reduced slant optical thickness in finite clouds, the polarization signal can strongly differ from its one-dimensional counterpart. At the higher frequencies and when the radiometer is positioned underneath the cloud, significantly higher negative values for the polarization are found which are also consistent with some observations. When the observation point is located outside of the precipitating cloud, typical polarization patterns (with troughs and peaks) as a function of the observation angle are predicted. An approximate 1-D slant path radiative transfer model is considered as well and results are compared with the full 3-D simulations to investigate whether or not three-dimensional effects can be explained by geometry effects alone. The study has strong relevance for low-frequency passive microwave polarimetric studies.

  18. Three-dimensional effects in polarization signatures as observed from precipitating clouds by low frequency ground-based microwave radiometers

    NASA Astrophysics Data System (ADS)

    Battaglia, A.; Simmer, C.; Czekala, H.

    2006-06-01

    Consistent negative polarization differences (i.e. differences between the vertical and the horizontal brightness temperature) are observed when looking at precipitating systems by ground-based radiometers at slant angles. These signatures can be partially explained by one-dimensional radiative transfer computations that include oriented non-spherical raindrops. However some cases are characterized by polarization values that exceed differences expected from one-dimensional radiative transfer. A three-dimensional fully polarized Monte Carlo model has been used to evaluate the impact of the horizontal finiteness of rain shafts with different rain rates at 10, 19, and 30 GHz. The results show that because of the reduced slant optical thickness in finite clouds, the polarization signal can strongly differ from its one-dimensional counterpart. At the higher frequencies and when the radiometer is positioned underneath the cloud, significantly higher negative values for the polarization are found which are also consistent with some observations. When the observation point is located outside of the precipitating cloud, typical polarization patterns (with troughs and peaks) as a function of the observation angle are predicted. An approximate 1-D slant path radiative transfer model is considered as well and results are compared with the full 3-D simulations to investigate whether or not three-dimensional effects can be explained by geometry effects alone. The study has strong relevance for low-frequency passive microwave polarimetric studies.

  19. Observation of rovibrational dephasing of molecules in parahydrogen crystals by frequency domain spectroscopy

    PubMed

    Katsuki; Momose

    2000-04-10

    Rotation-vibration transitions of methane molecules embedded in parahydrogen crystals were investigated through Fourier transform infrared spectroscopy. Each transition shows extremely sharp peaks with a Lorentzian line shape profile, which indicates the spectra are free from inhomogeneous broadening. The steep temperature dependence of the linewidths observed in the range between 3.7 and 8. 5 K is interpreted to be a result of the pure dephasing relaxation mechanism. A remarkable difference in population relaxation widths between stretching and bending vibrational excited states was also found. PMID:11019071

  20. Analysis of the magnitude and frequency of peak discharge and maximum observed peak discharge in New Mexico

    USGS Publications Warehouse

    Waltemeyer, S.D.

    1996-01-01

    Equations for estimating the magnitude of peak discharges for recurrence intervals of 2, 5, 10, 25, 50, 100, and 500 years were updated for New Mexico. The equations represent flood response for eight distinct physiographic regions of New Mexico. Additionally, a regional equation was developed for basins less than 10 square miles and below 7,500 feet in mean basin elevation. Flood-frequency relations were updated for 201 gaging stations on unregulated streams in New Mexico and the bordering areas of adjacent States. The analysis described in this report used data collected through 1993. A low-discharge threshold was applied to frequency analysis of 140 gaging stations. Inclusion of these low peak flows affects the fitting of the lower tail and the upper tail of the distribution. Peak discharges can be estimated at an ungaged site on a stream that has a gaging station upstream or downstream. These estimates are derived using the drainage-area ratio and the drainage-area exponent from the regional regression equation of the respective region. Flood-frequency estimates for 201 gaged sites were weighted by estimates from the regional regression equation. The observed, predicted, and weighted flood-frequency data were computed for each gaging station. A maximum observed peak discharge as related to drainage area was determined for eight physiographic regions in New Mexico. Peak-discharge data collected at 201 gaging stations were used to develop a maximum peak-discharge relation as an alternative method of estimating the peak discharge of an extreme event.

  1. Observations of a free-energy source for intense electrostatic waves. [in upper atmosphere near upper hybrid resonance frequency

    NASA Technical Reports Server (NTRS)

    Kurth, W. S.; Frank, L. A.; Gurnett, D. A.; Burek, B. G.; Ashour-Abdalla, M.

    1980-01-01

    Significant progress has been made in understanding intense electrostatic waves near the upper hybrid resonance frequency in terms of the theory of multiharmonic cyclotron emission using a classical loss-cone distribution function as a model. Recent observations by Hawkeye 1 and GEOS 1 have verified the existence of loss-cone distributions in association with the intense electrostatic wave events, however, other observations by Hawkeye and ISEE have indicated that loss cones are not always observable during the wave events, and in fact other forms of free energy may also be responsible for the instability. Now, for the first time, a positively sloped feature in the perpendicular distribution function has been uniquely identified with intense electrostatic wave activity. Correspondingly, we suggest that the theory is flexible under substantial modifications of the model distribution function.

  2. Ionospheric electron density irregularities observed by satellite-to-satellite, dual-frequency, low-low Doppler tracking link

    NASA Technical Reports Server (NTRS)

    Estes, R. D.; Grossi, M. D.

    1984-01-01

    A low-low, satellite-to-satellite, dual-frequency, Doppler tracking experiment was performed. The data are analyzed here for irregularities in electron density at the altitude of 212 km. The differential Doppler data with the relative motion term removed are integrated to obtain a representation of the electron density variation along the satellite path. Well-known large-scale features such as the equatorial geomagnetic anomaly and day/night ionization level differences are clearly observed in the integrated data. The larger crest of the morning geomagnetic anomaly is seen to occur in the southern (winter) hemisphere in agreement with previous observations. In addition, a sharp peak in the electron density at the day-to-night transition point is observed in two consecutive revolutions. This effect may be due to the previously postulated atmospheric shock wave generated by supersonic motion of the terminator.

  3. Evidence of Increasing Acoustic Emissivity at High Frequency with Solar Cycle 23 in Sun-as-a-star Observations

    SciTech Connect

    Simoniello, R.; Finsterle, W.

    2009-09-16

    We used long high-quality unresolved (Sun-as-a-star observations) data collected by GOLF and VIRGO instruments on board the ESA/NASA SOHO satellite to investigate the amplitude variation with solar cycle 23 in the high-frequency band (5.7<{nu}<6.3 mHz). We found an enhancement of acoustic emissivity over the ascending phase of about 18{+-}3 in velocity observations and a slight enhancement of 3{+-}2 in intensity. Mode conversion from fast acoustic to fast magneto-acoustic waves could explain the enhancement in velocity observations. These findings open up the possibility to apply the same technique to stellar intensity data, in order to investigate stellar-magnetic activity.

  4. 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

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

    PubMed

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

    1998-08-01

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

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

    PubMed Central

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

    2009-01-01

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

  7. Satellite-borne study of seismic phenomena by low frequency magnetic field observations

    NASA Astrophysics Data System (ADS)

    Schwingenschuh, Konrad; Magnes, Werner; Xuhui, Shen; Wang, Jindong; Pollinger, Andreas; Hagen, Christian; Prattes, Gustav; Eichelberger, Hans-Ulrich; Wolbang, Daniel; Boudjada, Mohammed Y.; Besser, Bruno P.; Rozhnoi, Alexander A.; Zhang, Tielong

    2015-04-01

    A combined scalar-vector magnetic field experiment will be flown on the upcoming CSES mission (China Seismo-Electromagnetic Satellite). Magnetic field data from DC to 30 Hz will be measured with an accuracy of about 10 pT. A fluxgate instrument will provide the 3 magnetic field components and a new type of an optically pumped magnetometer [see Pollinger, 2010] will measure the magnitude of the ambient magnetic field. The satellite will operate in a Sun synchronous polar orbit at an altitude of about 500 km and with an inclination of 97°. We present a model of magnetic field fluctuations in the upper ionosphere based on previous satellite observations and on a model of the lithospheric-atmospheric-ionospheric coupling. Pollinger et al., CDSM-a new scalar magnetometer, EGU General Assembly 2010

  8. Space- and time-resolved observation of extreme laser frequency upshifting during ultrafast-ionization

    SciTech Connect

    Giulietti, A.; Koester, P.; Levato, T.; Pathak, N. C.; André, A.; Dobosz Dufrénoy, S.; Monot, P.; Giulietti, D.; Hosokai, T.; Kotaki, H.; Labate, L.; Gizzi, L. A.; Nuter, R.

    2013-08-15

    A 65-fs, 800-nm, 2-TW laser pulse propagating through a nitrogen gas jet has been experimentally studied by 90° Thomson scattering. Time-integrated spectra of scattered light show unprecedented broadening towards the blue which exceeds 300 nm. Images of the scattering region provide for the first time a space- and time-resolved description of the process leading quite regularly to such a large upshift. The mean shifting rate was as high as δλ/δt ≈ 3 Å/fs, never observed before. Interferometry shows that it occurs after partial laser defocusing. Numerical simulations prove that such an upshift is consistent with a laser-gas late interaction, when laser intensity has decreased well below relativistic values (a{sub 0}≪ 1) and ionization process involves most of the laser pulse. This kind of interaction makes spectral tuning of ultrashort intense laser pulses possible in a large spectral range.

  9. Observation of Ω mode electron heating in dusty argon radio frequency discharges

    SciTech Connect

    Killer, Carsten; Bandelow, Gunnar; Schneider, Ralf; Melzer, André; Matyash, Konstantin

    2013-08-15

    The time-resolved emission of argon atoms in a dusty plasma has been measured with phase-resolved optical emission spectroscopy using an intensified charge-coupled device camera. For that purpose, three-dimensional dust clouds have been confined in a capacitively coupled rf argon discharge with the help of thermophoretic levitation. While electrons are exclusively heated by the expanding sheath (α mode) in the dust-free case, electron heating takes place in the entire plasma bulk when the discharge volume is filled with dust particles. Such a behavior is known as Ω mode, first observed in electronegative plasmas. Furthermore, particle-in-cell simulations have been carried out, which reproduce the trends of the experimental findings. These simulations support previous numerical models showing that the enhanced atomic emission in the plasma can be attributed to a bulk electric field, which is mainly caused by the reduced electrical conductivity due to electron depletion.

  10. Dual-Frequency Interferometric SAR Observations of a Tropical Rain-Forest

    NASA Technical Reports Server (NTRS)

    Rigot, E.

    1996-01-01

    Repeat-pass, interferometric, radar observations of tropical rain-forest collected by the Shuttle Imaging Radar C (SIR-C) in the state of Rondonia, Brazil, reveal signal coherence is destroyed at C-band (5.6-cm) in the forest, whereas L-band (24-cm) radar signals remain strongly coherent over the entire landscape. At L-band, the rms difference in inferred topographic height between the forest and adjacent clearings is 5 m, equivalent to the height noise. Atmospheric delays are large, however, forming kilometer-sized anomalies with a 1.2-cm rms one way. Radar interferometric studies of the humid tropics must therefore be conducted at long radar wavelengths, with kilometric base-lines or with two antennas operating simultaneously.

  11. Dual-Frequency Interferometric SAR Observations of a Tropical Rain-Forest

    NASA Technical Reports Server (NTRS)

    Rignot, E.

    1996-01-01

    Repeat-pass, interferometric, radar observations of tropical rain-forest collected by the Shuttle Imaging Radar C (SIR-C) in the state of Rondonia, Brazil, reveal signal coherence is destroyed at C-band (5.6-cm) in the forest, whereas L-band (24-cm) radar signals remain strongly coherent over the entire landscape. At L-band, the rms difference in inferred topographic height between the forest and adjacent clearings is 5 m, equivalent to the height noise. Atmospheric delays are large, however, forming kilometer-sized anomalies with a 1.2-cm rms one way. Radar interferometric studies of the humid tropics must therefore be conducted at long radar wavelengths, with kilometric baselines or with two antennas operating simultaneously.

  12. Observations and transport theory analysis of low frequency, acoustic mode propagation in the Eastern North Pacific Ocean.

    PubMed

    Chandrayadula, Tarun K; Colosi, John A; Worcester, Peter F; Dzieciuch, Matthew A; Mercer, James A; Andrew, Rex K; Howe, Bruce M

    2013-10-01

    Second order mode statistics as a function of range and source depth are presented from the Long Range Ocean Acoustic Propagation EXperiment (LOAPEX). During LOAPEX, low frequency broadband signals were transmitted from a ship-suspended source to a mode-resolving vertical line array. Over a one-month period, the ship occupied seven stations from 50 km to 3200 km distance from the receiver. At each station broadband transmissions were performed at a near-axial depth of 800 m and an off-axial depth of 350 m. Center frequencies at these two depths were 75 Hz and 68 Hz, respectively. Estimates of observed mean mode energy, cross mode coherence, and temporal coherence are compared with predictions from modal transport theory, utilizing the Garrett-Munk internal wave spectrum. In estimating the acoustic observables, there were challenges including low signal to noise ratio, corrections for source motion, and small sample sizes. The experimental observations agree with theoretical predictions within experimental uncertainty. PMID:24116512

  13. Frequency sweep rates of rising tone electromagnetic ion cyclotron waves: Comparison between nonlinear theory and Cluster observation

    SciTech Connect

    He, Zhaoguo; Zong, Qiugang Wang, Yongfu; Liu, Siqing; Lin, Ruilin; Shi, Liqin

    2014-12-15

    Resonant pitch angle scattering by electromagnetic ion cyclotron (EMIC) waves has been suggested to account for the rapid loss of ring current ions and radiation belt electrons. For the rising tone EMIC wave (classified as triggered EMIC emission), its frequency sweep rate strongly affects the efficiency of pitch-angle scattering. Based on the Cluster observations, we analyze three typical cases of rising tone EMIC waves. Two cases locate at the nightside (22.3 and 22.6 magnetic local time (MLT)) equatorial region and one case locates at the duskside (18MLT) higher magnetic latitude (λ = –9.3°) region. For the three cases, the time-dependent wave amplitude, cold electron density, and cold ion density ratio are derived from satellite data; while the ambient magnetic field, thermal proton perpendicular temperature, and the wave spectral can be directly provided by observation. These parameters are input into the nonlinear wave growth model to simulate the time-frequency evolutions of the rising tones. The simulated results show good agreements with the observations of the rising tones, providing further support for the previous finding that the rising tone EMIC wave is excited through the nonlinear wave growth process.

  14. Phase speed and frequency-dependent damping of longitudinal intensity oscillations in coronal loop structures observed with AIA/SDO

    NASA Astrophysics Data System (ADS)

    Abedini, A.

    2016-04-01

    Longitudinal intensity oscillations along coronal loops that are interpreted as signatures of magneto-acoustic waves are observed frequently in different coronal structures. The aim of this paper is to estimate the physical parameters of the slow waves and the quantitative dependence of these parameters on their frequencies in the solar corona loops that are situated above active regions with the Atmospheric Imaging Assembly (AIA) onboard Solar Dynamic Observatory (SDO). The observed data on 2012-Feb-12, consisting of 300 images with an interval of 24 seconds in the 171 Å and 193 Å passbands is analyzed for evidence of propagating features as slow waves along the loop structures. Signatures of longitudinal intensity oscillations that are damped rapidly as they travel along the loop structures were found, with periods in the range of a few minutes to few tens of minutes. Also, the projected (apparent) phase speeds, projected damping lengths, damping times and damping qualities of filtered intensities centred on the dominant frequencies are measured in the range of Cs ≃38-79 km s^{-1}, Ld≃ 23-68 Mm, τd≃7-21 min and τ_{d/P}≃0.34-0.77, respectively. The theoretical and observational results of this study indicate that the damping times and damping lengths increase with increasing the oscillation periods, and are highly sensitive function of oscillation period, but the projected speeds and the damping qualities are not very sensitive to the oscillation periods. Furthermore, the magnitude values of physical parameters are in good agreement with the prediction of the theoretical dispersion relations of high-frequency MHD waves (>1.1 mHz) in a coronal plasma with electron number density in the range of ne≃107-10^{12} cm^{-3}.

  15. Polymorphic Foraging Behavior Among Caenorhabditis elegans: Frequency- and Density-Dependent Selection

    PubMed Central

    Dennehy, John J.; Livdahl, Todd P.

    2004-01-01

    Strains of Caenorhabditis elegans obtained from their natural soil environment exhibit one of two forms of foraging behavior. Some strains forage solitarily and disperse evenly on a bacterial lawn. Other strains move rapidly until they encounter groups of conspecifics, and then slow their movement and join the group. Strains expressing these behaviors are globally widespread and have been isolated from the same location, suggesting a foraging polymorphism. We hypothesized that density-dependent selection maintains both foraging alleles in populations. Alternatively, both foraging alleles could be retained in populations through frequency-dependent selection. We tested both of these hypotheses by manipulating strain density and frequency, and observing changes in population density over time. Our results indicated that neither density- nor frequency-dependent selection appears to be responsible for the observed polymorphism. The clumping strain consistently out-competed the solitary strain over all treatment levels. We suggest other potential factors that may maintain both alleles in populations. PMID:19262816

  16. Tetra-allelic SNPs: Informative forensic markers compiled from public whole-genome sequence data.

    PubMed

    Phillips, C; Amigo, J; Carracedo, Á; Lareu, M V

    2015-11-01

    Multiple-allele single nucleotide polymorphisms (SNPs) are potentially useful for forensic DNA analysis as they can provide more discrimination power than normal binary SNPs. In addition, the presence in a profile of more than two alleles per marker provides a clearer indication of mixed DNA than assessments of imbalanced signals in the peak pairs of binary SNPs. Using the 1000 Genomes Phase III human variant data release of 2014 as the starting point, this study collated 961 tetra-allelic SNPs that pass minimum sequence quality thresholds and where four separate nucleotide substitution alleles were detected. Although most of these loci had three of the four alleles in combined frequencies of 2% or less, 160 had high heterozygosities with 50 exceeding those of 'ideal' 0.5:0.5 binary SNPs. From this set of most polymorphic tetra-allelic SNPs, we identified markers most informative for forensic purposes and explored these loci in detail. Subsets of the most polymorphic tetra-allelic SNPs will make useful additions to current panels of forensic identification SNPs and ancestry-informative SNPs. The 24 most discriminatory tetra-allelic SNPs were estimated to detect more than two alleles in at least one marker per profile in 99.9% of mixtures of African contributors. In European contributor mixtures 99.4% of profiles would show multiple allele patterns, but this drops to 92.6% of East Asian contributor mixtures due to reduced levels of polymorphism for the 24 SNPs in this population group. PMID:26209763

  17. Seasonal Variation of Frequency of High Current Lightning Discharges Observed by JLDN

    NASA Astrophysics Data System (ADS)

    Saito, Mikihisa; Ishii, Masaru; Fujii, Fumiyuki; Matsui, Michihiro

    Seasonal variations of number of high current lightning discharges exceeding 100kA observed by JLDN (Japanese Lightning Detection Network) were analyzed. The months with averaged altitudes of -10°C level higher than 5.7km are classified as ordinary summer from the viewpoint of lightning activity. Meanwhile, on the coast of the Sea of Japan, more than 90% of negative high current lightning discharges were -GC (Ground to Cloud) strokes in the months when monthly averaged altitudes of -10°C level are lower than 2.7km. These months are classified as the winter lightning season when upward lightning flashes frequently occur. Months other than winter or summer are classified as spring or autumn. In these seasons, the proportions of positive high current lightning discharges are higher than those of negative discharges like winter. Thus, the charge structure in the thunderclouds of spring and autumn may be similar to that in winter, and high current lightning strokes tend to occur. Since this variation of seasons is different in each area of Japan, relation of seasons, areas, and densities of high current lightning discharges were analyzed.

  18. Low Frequency Radio Observations of Bi-directional Electron Beams in the Solar Corona

    NASA Astrophysics Data System (ADS)

    Carley, E.; Reid, H.; Vilmer, N.; Gallagher, P.

    2015-12-01

    The radio signature of a shock travelling through the solar corona is known as a type II solar radio burst. In rare cases, these bursts can exhibit a fine structure known as 'herringbones' which are a direct indicator of particle acceleration occurring at the shock front. However, few studies have been performed on herringbones and the details of the underlying particle acceleration processes are unknown. Here, we use an image processing technique known as the Hough transform to statistically analyse the herringbone fine structure in a radio burst at 20-90MHz observed from the Rosse Solar-Terrestrial Observatory on 2011 September 22. We identify 188 individual bursts which are signatures of bi-directional electron beams continuously accelerated to speeds of 0.16 c. This occurs at a shock acceleration site initially at a constant altitude of 0.6 Rsun in the corona, followed by a shift to 0.5 Rsun. The anti-sunward beams travel a distance of 170 Mm (and possibly further) away from the acceleration site, while those travelling toward the sun come to a stop sooner, reaching a smaller distance of 112 Mm. We show that the stopping distance for the sunward beams may depend on the total number density and the velocity of the beam. Our study concludes that a detailed statistical analysis of herringbone fine structure can provide information on the physical properties of the corona which lead to these relatively rare radio bursts.

  19. Low-frequency observations of drifting, non-thermal continuum radio emission associated with the solar coronal mass ejections

    SciTech Connect

    Ramesh, R.; Kishore, P.; Barve, Indrajit V.; Kathiravan, C.; Mulay, Sargam M.; Wang, T. J.

    2013-11-20

    Low-frequency (80 MHz) imaging and spectral (≈85-20 MHz) observations of moving type IV radio bursts associated with coronal mass ejections (CMEs) from the Sun on three different days are reported. The estimated drift speed of the bursts is in the range ≈150-500 km s{sup –1}. We find that all three bursts are most likely due to second harmonic plasma emission from the enhanced electron density in the associated white-light CMEs. The derived maximum magnetic field strength of the latter is B ≈ 4 G at a radial distance of r ≈ 1.6 R {sub ☉}.

  20. An estimate of the magnetic field strength associated with a solar coronal mass ejection from low frequency radio observations

    SciTech Connect

    Sasikumar Raja, K.; Ramesh, R.; Hariharan, K.; Kathiravan, C.; Wang, T. J.

    2014-11-20

    We report ground based, low frequency heliograph (80 MHz), spectral (85-35 MHz), and polarimeter (80 and 40 MHz) observations of drifting, non-thermal radio continuum associated with the 'halo' coronal mass ejection that occurred in the solar atmosphere on 2013 March 15. The magnetic field strengths (B) near the radio source were estimated to be B ≈ 2.2 ± 0.4 G at 80 MHz and B ≈ 1.4 ± 0.2 G at 40 MHz. The corresponding radial distances (r) are r ≈ 1.9 R {sub ☉} (80 MHz) and r ≈ 2.2 R {sub ☉} (40 MHz).

  1. Simulations and Tests of Prototype Antenna System for Low Frequency Radio Experiment (LORE) Space Payload for Space Weather Observations

    NASA Astrophysics Data System (ADS)

    Pethe, Kaiwalya; Galande, Shridhar; Jamadar, Sachin; Mahajan, S. P.; Patil, R. A.; Joshi, B. C.; Manoharan, P. K.; Roy, Jayashree; Kate, G.

    2016-03-01

    Low frequency Radio Experiment (LORE) is a proposed space payload for space weather observations from space, operating between few kHz to 30 MHz. This paper presents preliminary design and practical implementation of LORE antenna systems, which consist of three mutually orthogonal mono-poles. Detailed computational electromagnetic simulations, carried out to study the performance of the antenna systems, are presented followed up by laboratory tests of the antennas as well as radiation tests with a long range test range, designed for this purpose. These tests form the first phase of the design and implementation of the full LORE prototype later in the year.

  2. Experimental observation of left polarized wave absorption near electron cyclotron resonance frequency in helicon antenna produced plasma

    SciTech Connect

    Barada, Kshitish K.; Chattopadhyay, P. K.; Ghosh, J.; Kumar, Sunil; Saxena, Y. C.

    2013-01-15

    Asymmetry in density peaks on either side of an m = +1 half helical antenna is observed both in terms of peak position and its magnitude with respect to magnetic field variation in a linear helicon plasma device [Barada et al., Rev. Sci. Instrum. 83, 063501 (2012)]. The plasma is produced by powering the m = +1 half helical antenna with a 2.5 kW, 13.56 MHz radio frequency source. During low magnetic field (B < 100 G) operation, plasma density peaks are observed at critical magnetic fields on either side of the antenna. However, the density peaks occurred at different critical magnetic fields on both sides of antenna. Depending upon the direction of the magnetic field, in the m = +1 propagation side, the main density peak has been observed around 30 G of magnetic field. On this side, the density peak around 5 G corresponding to electron cyclotron resonance (ECR) is not very pronounced, whereas in the m = -1 propagation side, very pronounced ECR peak has been observed around 5 G. Another prominent density peak around 12 G has also been observed in m = -1 side. However, no peak has been observed around 30 G on this m = -1 side. This asymmetry in the results on both sides is explained on the basis of polarization reversal of left hand polarized waves to right hand polarized waves and vice versa in a bounded plasma system. The density peaking phenomena are likely to be caused by obliquely propagating helicon waves at the resonance cone boundary.

  3. DRD4 dopamine receptor allelic diversity in various primate species

    SciTech Connect

    Adamson, M.; Higley, D.; O`Brien, S.

    1994-09-01

    The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

  4. Allele-specific disparity in breast cancer

    PubMed Central

    2011-01-01

    Background In a cancer cell the number of copies of a locus may vary due to amplification and deletion and these variations are denoted as copy number alterations (CNAs). We focus on the disparity of CNAs in tumour samples, which were compared to those in blood in order to identify the directional loss of heterozygosity. Methods We propose a numerical algorithm and apply it to data from the Illumina 109K-SNP array on 112 samples from breast cancer patients. B-allele frequency (BAF) and log R ratio (LRR) of Illumina were used to estimate Euclidian distances. For each locus, we compared genotypes in blood and tumour for subset of samples being heterozygous in blood. We identified loci showing preferential disparity from heterozygous toward either the A/B-