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Sample records for allele frequency spectrum

  1. 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

  2. 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

  3. The Frequency Spectrum Radio.

    ERIC Educational Resources Information Center

    Howkins, John, Ed.

    1979-01-01

    This journal issue focuses on the frequency spectrum used in radio communication and on the World Administrative Radio Conference, sponsored by the International Telecommunication Union, held in Geneva, Switzerland, in the fall of 1979. Articles describe the World Administrative Radio Conference as the most important radio communication conference…

  4. 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

  5. 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

  6. 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

  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. Frequency Allocation; The Radio Spectrum.

    ERIC Educational Resources Information Center

    Federal Communications Commission, Washington, DC.

    The Federal Communications Commission (FCC) assigns segments of the radio spectrum to categories of users, and specific frequencies within each segment to individual users. Since demand for channel space exceeds supply, the process is complex. The radio spectrum can be compared to a long ruler: the portion from 10-540 kiloHertz has been set aside…

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

    SciTech Connect

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

    1993-03-01

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

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

    PubMed Central

    Ackermann, Marit; Beyer, Andreas

    2012-01-01

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

  11. 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

  12. 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

  13. 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

  14. 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

  15. Fast spatial ancestry via flexible allele frequency surfaces

    PubMed Central

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

    2014-01-01

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

  16. 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

  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. Allele-specific tumor spectrum in pten knockin mice.

    PubMed

    Wang, Hui; Karikomi, Matt; Naidu, Shan; Rajmohan, Ravi; Caserta, Enrico; Chen, Hui-Zi; Rawahneh, Maysoon; Moffitt, Julie; Stephens, Julie A; Fernandez, Soledad A; Weinstein, Michael; Wang, Danxin; Sadee, Wolfgang; La Perle, Krista; Stromberg, Paul; Rosol, Thomas J; Eng, Charis; Ostrowski, Michael C; Leone, Gustavo

    2010-03-16

    Germline mutations in the tumor suppressor gene PTEN (phosphatase and tensin homology deleted on chromosome 10) cause Cowden and Bannayan-Riley-Ruvalcaba (BRR) syndromes, two dominantly inherited disorders characterized by mental retardation, multiple hamartomas, and variable cancer risk. Here, we modeled three sentinel mutant alleles of PTEN identified in patients with Cowden syndrome and show that the nonsense Pten(4-5) and missense Pten(C124R) and Pten(G129E) alleles lacking lipid phosphatase activity cause similar developmental abnormalities but distinct tumor spectra with varying severity and age of onset. Allele-specific differences may be accounted for by loss of function for Pten(4-5), hypomorphic function for Pten(C124R), and gain of function for Pten(G129E). These data demonstrate that the variable tumor phenotypes observed in patients with Cowden and BRR syndromes can be attributed to specific mutations in PTEN that alter protein function through distinct mechanisms. PMID:20194734

  19. 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)

  20. The frequency spectrum of the Casimir effect

    SciTech Connect

    Lang, Andrew S.I.D.

    2005-10-01

    The frequency spectrum of the Casimir effect between parallel plates is studied. Calculations are performed for both the massless scalar field and the electromagnetic field cases, first using a spectral weight function, and then via the Fourier transform of the renormalized expectation of the Casimir energy-momentum operator. The Casimir force is calculated using the spectrum for two plates which are perfectly transparent in a frequency band. The result of this calculation suggests a way to detect the frequency spectrum of the Casimir effect.

  1. 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

  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. Universality of the frequency spectrum of laminates

    NASA Astrophysics Data System (ADS)

    Shmuel, Gal; Band, Ram

    2016-07-01

    We show that the frequency spectrum of two-component elastic laminates admits a universal structure, independent of the geometry of the periodic-cell and the specific physical properties. The compactness of the structure enables us to rigorously derive the maximal width, the expected width, and the density of the band-gaps - ranges of frequencies at which waves cannot propagate. In particular, we find that the density of these band-gaps is a universal property of classes of laminates. Rules for tailoring laminates according to desired spectrum properties thereby follow. We show that the frequency spectrum of various finitely deformed laminates are also endowed with the same compact structure. Finally, we explain how our results generalize for laminates with an arbitrary number of components, based on the form of their dispersion relation.

  5. Frequency spectrum analyzer with phase-lock

    DOEpatents

    Boland, Thomas J.

    1984-01-01

    A frequency-spectrum analyzer with phase-lock for analyzing the frequency and amplitude of an input signal is comprised of a voltage controlled oscillator (VCO) which is driven by a ramp generator, and a phase error detector circuit. The phase error detector circuit measures the difference in phase between the VCO and the input signal, and drives the VCO locking it in phase momentarily with the input signal. The input signal and the output of the VCO are fed into a correlator which transfers the input signal to a frequency domain, while providing an accurate absolute amplitude measurement of each frequency component of the input signal.

  6. 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...

  7. Mining the LIPG allelic spectrum reveals the contribution of rare and common regulatory variants to HDL cholesterol.

    PubMed

    Khetarpal, Sumeet A; Edmondson, Andrew C; Raghavan, Avanthi; Neeli, Hemanth; Jin, Weijun; Badellino, Karen O; Demissie, Serkalem; Manning, Alisa K; DerOhannessian, Stephanie L; Wolfe, Megan L; Cupples, L Adrienne; Li, Mingyao; Kathiresan, Sekar; Rader, Daniel J

    2011-12-01

    Genome-wide association studies (GWAS) have successfully identified loci associated with quantitative traits, such as blood lipids. Deep resequencing studies are being utilized to catalogue the allelic spectrum at GWAS loci. The goal of these studies is to identify causative variants and missing heritability, including heritability due to low frequency and rare alleles with large phenotypic impact. Whereas rare variant efforts have primarily focused on nonsynonymous coding variants, we hypothesized that noncoding variants in these loci are also functionally important. Using the HDL-C gene LIPG as an example, we explored the effect of regulatory variants identified through resequencing of subjects at HDL-C extremes on gene expression, protein levels, and phenotype. Resequencing a portion of the LIPG promoter and 5' UTR in human subjects with extreme HDL-C, we identified several rare variants in individuals from both extremes. Luciferase reporter assays were used to measure the effect of these rare variants on LIPG expression. Variants conferring opposing effects on gene expression were enriched in opposite extremes of the phenotypic distribution. Minor alleles of a common regulatory haplotype and noncoding GWAS SNPs were associated with reduced plasma levels of the LIPG gene product endothelial lipase (EL), consistent with its role in HDL-C catabolism. Additionally, we found that a common nonfunctional coding variant associated with HDL-C (rs2000813) is in linkage disequilibrium with a 5' UTR variant (rs34474737) that decreases LIPG promoter activity. We attribute the gene regulatory role of rs34474737 to the observed association of the coding variant with plasma EL levels and HDL-C. Taken together, the findings show that both rare and common noncoding regulatory variants are important contributors to the allelic spectrum in complex trait loci. PMID:22174694

  8. Mining the LIPG Allelic Spectrum Reveals the Contribution of Rare and Common Regulatory Variants to HDL Cholesterol

    PubMed Central

    Raghavan, Avanthi; Neeli, Hemanth; Jin, Weijun; Badellino, Karen O.; Demissie, Serkalem; Manning, Alisa K.; DerOhannessian, Stephanie L.; Wolfe, Megan L.; Cupples, L. Adrienne; Li, Mingyao; Kathiresan, Sekar; Rader, Daniel J.

    2011-01-01

    Genome-wide association studies (GWAS) have successfully identified loci associated with quantitative traits, such as blood lipids. Deep resequencing studies are being utilized to catalogue the allelic spectrum at GWAS loci. The goal of these studies is to identify causative variants and missing heritability, including heritability due to low frequency and rare alleles with large phenotypic impact. Whereas rare variant efforts have primarily focused on nonsynonymous coding variants, we hypothesized that noncoding variants in these loci are also functionally important. Using the HDL-C gene LIPG as an example, we explored the effect of regulatory variants identified through resequencing of subjects at HDL-C extremes on gene expression, protein levels, and phenotype. Resequencing a portion of the LIPG promoter and 5′ UTR in human subjects with extreme HDL-C, we identified several rare variants in individuals from both extremes. Luciferase reporter assays were used to measure the effect of these rare variants on LIPG expression. Variants conferring opposing effects on gene expression were enriched in opposite extremes of the phenotypic distribution. Minor alleles of a common regulatory haplotype and noncoding GWAS SNPs were associated with reduced plasma levels of the LIPG gene product endothelial lipase (EL), consistent with its role in HDL-C catabolism. Additionally, we found that a common nonfunctional coding variant associated with HDL-C (rs2000813) is in linkage disequilibrium with a 5′ UTR variant (rs34474737) that decreases LIPG promoter activity. We attribute the gene regulatory role of rs34474737 to the observed association of the coding variant with plasma EL levels and HDL-C. Taken together, the findings show that both rare and common noncoding regulatory variants are important contributors to the allelic spectrum in complex trait loci. PMID:22174694

  9. Method and apparatus for frequency spectrum analysis

    NASA Technical Reports Server (NTRS)

    Cole, Steven W. (Inventor)

    1992-01-01

    A method for frequency spectrum analysis of an unknown signal in real-time is discussed. The method is based upon integration of 1-bit samples of signal voltage amplitude corresponding to sine or cosine phases of a controlled center frequency clock which is changed after each integration interval to sweep the frequency range of interest in steps. Integration of samples during each interval is carried out over a number of cycles of the center frequency clock spanning a number of cycles of an input signal to be analyzed. The invention may be used to detect the frequency of at least two signals simultaneously. By using a reference signal of known frequency and voltage amplitude (added to the two signals for parallel processing in the same way, but in a different channel with a sampling at the known frequency and phases of the reference signal), the absolute voltage amplitude of the other two signals may be determined by squaring the sine and cosine integrals of each channel and summing the squares to obtain relative power measurements in all three channels and, from the known voltage amplitude of the reference signal, obtaining an absolute voltage measurement for the other two signals by multiplying the known voltage of the reference signal with the ratio of the relative power of each of the other two signals to the relative power of the reference signal.

  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. 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 ...

  12. 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

  13. 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

  14. 47 CFR 2.1057 - Frequency spectrum to be investigated.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Frequency spectrum to be investigated. 2.1057... Frequency spectrum to be investigated. (a) In all of the measurements set forth in §§ 2.1051 and 2.1053, the spectrum shall be investigated from the lowest radio frequency signal generated in the equipment,...

  15. 47 CFR 2.1057 - Frequency spectrum to be investigated.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Frequency spectrum to be investigated. 2.1057... Frequency spectrum to be investigated. (a) In all of the measurements set forth in §§ 2.1051 and 2.1053, the spectrum shall be investigated from the lowest radio frequency signal generated in the equipment,...

  16. 47 CFR 2.1057 - Frequency spectrum to be investigated.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Frequency spectrum to be investigated. 2.1057... Frequency spectrum to be investigated. (a) In all of the measurements set forth in §§ 2.1051 and 2.1053, the spectrum shall be investigated from the lowest radio frequency signal generated in the equipment,...

  17. 47 CFR 2.1057 - Frequency spectrum to be investigated.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Frequency spectrum to be investigated. 2.1057... Frequency spectrum to be investigated. (a) In all of the measurements set forth in §§ 2.1051 and 2.1053, the spectrum shall be investigated from the lowest radio frequency signal generated in the equipment,...

  18. 47 CFR 2.1057 - Frequency spectrum to be investigated.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Frequency spectrum to be investigated. 2.1057... Frequency spectrum to be investigated. (a) In all of the measurements set forth in §§ 2.1051 and 2.1053, the spectrum shall be investigated from the lowest radio frequency signal generated in the equipment,...

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

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

    PubMed

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

    2016-01-01

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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. Terahertz spectrum analyzer based on frequency and power measurement.

    PubMed

    Yee, Dae-Su; Jang, Yudong; Kim, Youngchan; Seo, Dae-Cheol

    2010-08-01

    We demonstrate a terahertz (THz) spectrum analyzer based on frequency and power measurement. A power spectrum of a continuous THz wave is measured through optical heterodyne detection using an electromagnetic THz frequency comb and a bolometer and power measurement using a bolometer with a calibrated responsivity. The THz spectrum analyzer has a frequency precision of 1x10(-11), a frequency resolution of 1Hz, a frequency band up to 1.7THz, and an optical noise equivalent power of approximately 1 pW/Hz(1/2). PMID:20680048

  16. 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

  17. 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

  18. 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

  19. 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...

  20. The communications spectrum: Frequency allocations and auctions

    NASA Astrophysics Data System (ADS)

    Pritchard, Wilbur

    1997-01-01

    Demands on the communications spectrum have increased sharply because of the growth in radio communication services, the large bandwidths now required, and the rapid increases in world population. The problem will be exacerbated by the requirements of high definition television and the enormous amounts of information that will be transmitted by radio. The electromagnetic spectrum is a finite natural resource of great value used for emergency communications and military operations as well as for commercial purposes. Both government and the marketplace have proper roles in the allocation of its resources. There are no viable alternatives to international organizations such as the International Telecommunication Union or to agencies such as the Federal Communications Commission for the regulation of radio communication and the assignment of spectrum to essential public services. Although government auctions of spectrum are justifiable where there is no way to distinguish among commercial entities seeking to use the same bands for similar services, the practice is inherently inequitable and discourages development of new uses for the spectrum by removing investment protection. Recommended alternatives to auctions are: (1) lotteries, which keep assets and proceeds in the economy; and (2) ongoing charges for current as well as new users of the spectrum.

  1. 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

  2. Frequency Spectrum for Integration of Unmanned Aircraft

    NASA Technical Reports Server (NTRS)

    Kerczewski, Robert J.; Wilson, Jeffrey D.; Bishop, William D.

    2013-01-01

    The goal of enabling the integration of unmanned aircraft systems (UAS) into the National Airspace System (NAS) in terms of UAS achieving routine access to the NAS has been established as a national goal in the United States. Among a number of technical barriers that must be overcome to meet this goal is the absence of standard, certifiable communications links supplying the control and non-payload communications (CNPC) function, essentially providing the link over which a pilot on the ground can control the unmanned aircraft (UA). The International Civil Aviation Organization (ICAO) has determined that the CNPC link must operate over protected aviation spectrum. Therefore protected aviation spectrum must be allocated for this function, approved through the processes of the International Telecommunications Union Radiocommunication Sector (ITU-R). Work has progressed in the definition of spectrum requirements for CNPC, and a portion of these requirements has been satisfied through new allocations approved at the ITU-R 2012 World Radiocommunication Conference (WRC-12). Additional work is ongoing or planned to satisfy the remaining spectrum requirements and define the specifications for the usage of CNPC spectrum allocations and develop supporting standards. This paper provides an overview of the status of RF spectrum for UAS CNPC. Issues that have been identified and ongoing analysis and research that will be necessary to fulfill spectrum requirements for UAS CNPC will be discussed. The results of this work will provide for the safe integration of UA into the NAS in both the LOS (Line of Sight) and BLOS (Beyond Line of Sight) realms.

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

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

    PubMed Central

    Ramasamy, Thirumurugan; Ayyavoo, Jayachitra

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  15. 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.

  16. 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

  17. 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

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

    PubMed Central

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

    2016-01-01

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

  19. Device for frequency modulation of a laser output spectrum

    DOEpatents

    Beene, James R.; Bemis, Jr., Curtis E.

    1986-01-01

    A device is provided for fast frequency modulating the output spectrum of multimode lasers and single frequency lasers that are not actively stabilized. A piezoelectric transducer attached to a laser cavity mirror is driven in an unconventional manner to excite resonance vibration of the transducer to rapidly, cyclicly change the laser cavity length. The result is a cyclic sweeping of the output wavelength sufficient to fill the gaps in the laser output frequency spectrum. When such a laser is used to excite atoms or molecules, complete absorption line coverage is made possible.

  20. Device for frequency modulation of a laser output spectrum

    DOEpatents

    Beene, J.R.; Bemis, C.E. Jr.

    1984-07-17

    A device is provided for fast frequency modulating the output spectrum of multimode lasers and single frequency lasers that are not actively stabilized. A piezoelectric transducer attached to a laser cavity mirror is driven in an unconventional manner to excite resonance vibration of the tranducer to rapidly, cyclicly change the laser cavity length. The result is a cyclic sweeping of the output wavelength sufficient to fill the gaps in the laser output frequency spectrum. When a laser is used to excite atoms or molecules, complete absorption line coverage is made possible.

  1. [EMD Time-Frequency Analysis of Raman Spectrum and NIR].

    PubMed

    Zhao, Xiao-yu; Fang, Yi-ming; Tan, Feng; Tong, Liang; Zhai, Zhe

    2016-02-01

    This paper analyzes the Raman spectrum and Near Infrared Spectrum (NIR) with time-frequency method. The empirical mode decomposition spectrum becomes intrinsic mode functions, which the proportion calculation reveals the Raman spectral energy is uniform distributed in each component, while the NIR's low order intrinsic mode functions only undertakes fewer primary spectroscopic effective information. Both the real spectrum and numerical experiments show that the empirical mode decomposition (EMD) regard Raman spectrum as the amplitude-modulated signal, which possessed with high frequency adsorption property; and EMD regards NIR as the frequency-modulated signal, which could be preferably realized high frequency narrow-band demodulation during first-order intrinsic mode functions. The first-order intrinsic mode functions Hilbert transform reveals that during the period of empirical mode decomposes Raman spectrum, modal aliasing happened. Through further analysis of corn leaf's NIR in time-frequency domain, after EMD, the first and second orders components of low energy are cut off, and reconstruct spectral signal by using the remaining intrinsic mode functions, the root-mean-square error is 1.001 1, and the correlation coefficient is 0.981 3, both of these two indexes indicated higher accuracy in re-construction; the decomposition trend term indicates the absorbency is ascending along with the decreasing to wave length in the near-infrared light wave band; and the Hilbert transform of characteristic modal component displays, 657 cm⁻¹ is the specific frequency by the corn leaf stress spectrum, which could be regarded as characteristic frequency for identification. PMID:27209743

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

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

    PubMed

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

    2014-03-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2011-01-01

    The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (FST coefficients) to the present database ranged from FST = 0.0016 between Macapá and Belém to FST = 0.0036 between Macapá and the Iberian Peninsula. PMID:21637540

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

    PubMed

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

    2006-06-01

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

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

    PubMed Central

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

    2014-01-01

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

  14. Compressive sensing of frequency-hopping spread spectrum signals

    NASA Astrophysics Data System (ADS)

    Liu, Feng; Kim, Yookyung; Goodman, Nathan A.; Ashok, Amit; Bilgin, Ali

    2012-06-01

    In this paper, compressive sensing strategies for interception of Frequency-Hopping Spread Spectrum (FHSS) signals are introduced. Rapid switching of the carrier among many frequency channels using a pseudorandom sequence (unknown to the eavesdropper) makes FHSS signals dicult to intercept. The conventional approach to intercept FHSS signals necessitates capturing of all frequency channels and, thus, requires the Analog-to-Digital Converters (ADCs) to sample at very high rates. Using the fact that the FHSS signals have sparse instanta- neous spectra, we propose compressive sensing strategies for their interception. The proposed techniques are validated using Gaussian Frequency-Shift Keying (GFSK) modulated FHSS signals as dened by the Bluetooth specication.

  15. 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

  16. 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

  17. 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.

  18. Signal Description By Means Of A Local Frequency Spectrum

    NASA Astrophysics Data System (ADS)

    Bastiaans, Martin J.

    1984-02-01

    Abstract. The description of a signal by means of a local frequency spec-trum resembles such things as the score in music, the phase space in mechanics, and the ray concept in geometrical optics. Two types of local frequency spectra are presented: the Wigner distribution function and the sliding-window spectrum, the latter having the form of a cross-ambiguity function. The Wigner distribution function in particular can provide a link between Fourier optics and geometrical optics; many properties of the Wigner distribution function, and the way in which it prop-agates through linear systems, can be interpreted in geometric-optical terms. The Wigner distribution function is linearly related to other signal representations like Woodward's ambiguity function, Rihaczek's complex energy density function, and Mark's physical spectrum. An advantage of the Wigner distribution function and its related signal representations is that they can be applied not only to deterministic signals but to stochastic signals as well, leading to such things as Walther's generalized radiance and Sudarshan's Wolf tensor. On the other hand, the sliding-window spectrum has the advantage that a sampling theorem can be formulated for it: the sliding-window spectrum is completely determined by its values at the points of a certain space-frequency lattice, which is exactly the lattice suggested by Gabor in 1946. The sliding-window spectrum thus leads naturally to Gabor's expansion of a signal into a discrete set of properly shifted and modulated versions of an elementary signal, which is again another space-frequency signal representation, and which is related to the degrees of freedom of the signal.

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

    PubMed Central

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

    2010-01-01

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

  20. 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

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

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

    2003-01-01

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

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

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  5. The very low frequency power spectrum of Centaurus X-3

    NASA Technical Reports Server (NTRS)

    Gruber, D. E.

    1988-01-01

    The long-term variability of Cen X-3 on time scales ranging from days to years has been examined by combining data obtained by the HEAO 1 A-4 instrument with data from Vela 5B. A simple interpretation of the data is made in terms of the standard alpha-disk model of accretion disk structure and dynamics. Assuming that the low-frequency variance represents the inherent variability of the mass transfer from the companion, the decline in power at higher frequencies results from the leveling of radial structure in the accretion disk through viscous mixing. The shape of the observed power spectrum is shown to be in excellent agreement with a calculation based on a simplified form of this model. The observed low-frequency power spectrum of Cen X-3 is consistent with a disk in which viscous mixing occurs about as rapidly as possible and on the largest scale possible.

  6. General Triallelic Frequency Spectrum Under Demographic Models with Variable Population Size

    PubMed Central

    Jenkins, Paul A.; Mueller, Jonas W.; Song, Yun S.

    2014-01-01

    It is becoming routine to obtain data sets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study summary statistics that offer enough compression to be tractable, while preserving a great deal of information. One well-studied summary is the site frequency spectrum—the empirical distribution, across segregating sites, of the sample frequency of the derived allele. However, most previous theoretical work has assumed that each site has experienced at most one mutation event in its genealogical history, which becomes less tenable for very large sample sizes. In this work we obtain, in closed form, the predicted frequency spectrum of a site that has experienced at most two mutation events, under very general assumptions about the distribution of branch lengths in the underlying coalescent tree. Among other applications, we obtain the frequency spectrum of a triallelic site in a model of historically varying population size. We demonstrate the utility of our formulas in two settings: First, we show that triallelic sites are more sensitive to the parameters of a population that has experienced historical growth, suggesting that they will have use if they can be incorporated into demographic inference. Second, we investigate a recently proposed alternative mechanism of mutation in which the two derived alleles of a triallelic site are created simultaneously within a single individual, and we develop a test to determine whether it is responsible for the excess of triallelic sites in the human genome. PMID:24214345

  7. 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

  8. Influences of Fundamental Frequency, Formant Frequencies, Aperiodicity, and Spectrum Level on the Perception of Voice Gender

    ERIC Educational Resources Information Center

    Skuk, Verena G.; Schweinberger, Stefan R.

    2014-01-01

    Purpose: To determine the relative importance of acoustic parameters (fundamental frequency [F0], formant frequencies [FFs], aperiodicity, and spectrum level [SL]) on voice gender perception, the authors used a novel parameter-morphing approach that, unlike spectral envelope shifting, allows the application of nonuniform scale factors to transform…

  9. Measurements of the frequency spectrum of transition radiation

    NASA Technical Reports Server (NTRS)

    Cherry, M. L.; Mueller, D.

    1977-01-01

    We report a measurement of the frequency spectrum of X-ray transition radiation. X rays were generated by electrons of 5 and 9 GeV in radiators of multiple polypropylene foils, and detected in the range 4 to 30 keV with a calibrated single-crystal Bragg spectrometer. The experimental results closely reproduce the features of the theoretically predicted spectrum. In particular, the pronounced interference pattern of multifoil radiators and the expected hardening of the radiation with increasing foil thickness are clearly observed. The overall intensity of the radiation is somewhat lower than predicted by calculations.

  10. Compressive detection of frequency-hopping spread spectrum signals

    NASA Astrophysics Data System (ADS)

    Liu, Feng; Marcellin, Michael W.; Goodman, Nathan A.; Bilgin, Ali

    2013-05-01

    In this paper, compressive detection strategies for FHSS signals are introduced. Rapid switching of the carrier frequency among many channels using a pseudorandom sequence makes detection of FHSS signals challenging. The conventional approach to detect these signals is to rapidly scan small segments of the spectrum sequentially. However, such a scanner has the inherent risk of never overlapping with the transmitted signal depending on factors such as rate of hopping and scanning. In this paper, we propose compressive detection strategies that sample the full spectrum in a compressive manner. Theory and simulations are presented to illustrate the benefits of the proposed framework.

  11. 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

  12. Lagrangian Frequency Spectrum as a Diagnostic for Magnetohydrodynamic Turbulence Dynamics

    SciTech Connect

    Busse, Angela; Mueller, Wolf-Christian; Gogoberidze, Grigol

    2010-12-03

    For the phenomenological description of magnetohydrodynamic turbulence competing models exist, e.g., Boldyrev [Phys. Rev. Lett. 96, 115002 (2006)] and Gogoberidze [Phys. Plasmas 14, 022304 (2007)], which predict the same Eulerian inertial-range scaling of the turbulent energy spectrum although they employ fundamentally different basic interaction mechanisms. A relation is found that links the Lagrangian frequency spectrum with the autocorrelation time scale of the turbulent fluctuations {tau}{sub ac} and the associated cascade time scale {tau}{sub cas}. Thus, the Lagrangian energy spectrum can serve to identify weak ({tau}{sub ac}<<{tau}{sub cas}) and strong ({tau}{sub ac{approx}{tau}cas}) interaction mechanisms providing insight into the turbulent energy cascade. The new approach is illustrated by results from direct numerical simulations of two- and three-dimensional incompressible MHD turbulence.

  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. 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

  15. 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

  16. Frequency Correction for MIRO Chirp Transformation Spectroscopy Spectrum

    NASA Technical Reports Server (NTRS)

    Lee, Seungwon

    2012-01-01

    This software processes the flyby spectra of the Chirp Transform Spectrometer (CTS) of the Microwave Instrument for Rosetta Orbiter (MIRO). The tool corrects the effect of Doppler shift and local-oscillator (LO) frequency shift during the flyby mode of MIRO operations. The frequency correction for CTS flyby spectra is performed and is integrated with multiple spectra into a high signal-to-noise averaged spectrum at the rest-frame RF frequency. This innovation also generates the 8 molecular line spectra by dividing continuous 4,096-channel CTS spectra. The 8 line spectra can then be readily used for scientific investigations. A spectral line that is at its rest frequency in the frame of the Earth or an asteroid will be observed with a time-varying Doppler shift as seen by MIRO. The frequency shift is toward the higher RF frequencies on approach, and toward lower RF frequencies on departure. The magnitude of the shift depends on the flyby velocity. The result of time-varying Doppler shift is that of an observed spectral line will be seen to move from channel to channel in the CTS spectrometer. The direction (higher or lower frequency) in the spectrometer depends on the spectral line frequency under consideration. In order to analyze the flyby spectra, two steps are required. First, individual spectra must be corrected for the Doppler shift so that individual spectra can be superimposed at the same rest frequency for integration purposes. Second, a correction needs to be applied to the CTS spectra to account for the LO frequency shifts that are applied to asteroid mode.

  17. Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing.

    PubMed

    Lalonde, Emilie; Albrecht, Steffen; Ha, Kevin C H; Jacob, Karine; Bolduc, Nathalie; Polychronakos, Constantin; Dechelotte, Pierre; Majewski, Jacek; Jabado, Nada

    2010-08-01

    Protein coding genes constitute approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., "whole exome") have the potential to contribute our understanding of human diseases. We used a method for whole-exome sequencing coupling Agilent whole-exome capture to the Illumina DNA-sequencing platform, and investigated two unrelated fetuses from nonconsanguineous families with Fowler Syndrome (FS), a stereotyped phenotype lethal disease. We report novel germline mutations in feline leukemia virus subgroup C cellular-receptor-family member 2, FLVCR2, which has recently been shown to cause FS. Using this technology, we identified three types of genetic abnormalities: point-mutations, insertions-deletions, and intronic splice-site changes (first pathogenic report using this technology), in the fetuses who both were compound heterozygotes for the disease. Although revealing a high level of allelic heterogeneity and mutational spectrum in FS, this study further illustrates the successful application of whole-exome sequencing to uncover genetic defects in rare Mendelian disorders. Of importance, we show that we can identify genes underlying rare, monogenic and recessive diseases using a limited number of patients (n=2), in the absence of shared genetic heritage and in the presence of allelic heterogeneity. PMID:20518025

  18. 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

  19. Genetically Determined Amerindian Ancestry Correlates with Increased Frequency of Risk Alleles for Systemic Lupus Erythematosus

    PubMed Central

    Sanchez, E; Webb, R; Rasmussen, A.; Kelly, J.A; Riba, L.; Kaufman, K.M.; Garcia-de la Torre, I.; Moctezuma, J.F.; Maradiaga-Ceceña, M.A.; Cardiel, M.; Acevedo, E.; Cucho-Venegas, M.; Garcia, M.A.; Gamron, S.; Pons-Estel, B.A.; Vasconcelos, C.; Martin, J.; Tusié-Luna, T.; Harley, J.B.; Richardson, B.; Sawalha, A.H.; Alarcón-Riquelme, M.E.

    2011-01-01

    Objectives To analyze if genetically determined Amerindian ancestry predicts the increased presence of risk alleles of known susceptibility genes for systemic lupus erythematosus. Methods Single nucleotide polymorphisms within 16 confirmed genetic susceptibility loci for SLE were genotyped in a set of 804 Mestizo lupus patients and 667 Mestizo normal healthy controls. In addition, 347 admixture informative markers were genotyped. Individual ancestry proportions were determined using STRUCTURE. Association analysis was performed using PLINK, and correlation of the presence of risk alleles with ancestry was done using linear regression. Results A meta-analysis of the genetic association of the 16 SNPs across populations showed that TNFSF4, STAT4, PDCD1, ITGAM, and IRF5 were associated with lupus in a Hispanic-Mestizo cohort enriched for European and Amerindian ancestry. In addition, two SNPs within the MHC region, previously associated in a genome-wide association study in Europeans, were also associated in Mestizos. Using linear regression we predict an average increase of 2.34 risk alleles when comparing a lupus patient with 100% Amerindian ancestry to an SLE patient with 0% American Indian Ancestry (p<0.0001). SLE patients with 43% more Amerindian ancestry are predicted to carry one additional risk allele. Conclusion Amerindian ancestry increased the number of risk alleles for lupus. PMID:20848568

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-01-01

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

  2. Frequency of the CCR5-delta32 allele in Brazilian populations: A systematic literature review and meta-analysis.

    PubMed

    Silva-Carvalho, Wlisses Henrique Veloso; de Moura, Ronald Rodrigues; Coelho, Antonio Victor Campos; Crovella, Sergio; Guimarães, Rafael Lima

    2016-09-01

    The CCR5 is a chemokine receptor widely expressed by several immune cells that are engaged in inflammatory responses. Some populations have individuals exhibiting a 32bp deletion in the CCR5 gene (CCR5-delta32) that produces a truncated non-functional protein not expressed on the cell surface. This polymorphism, known to be associated with susceptibility to infectious and inflammatory diseases, such as osteomyelitis, pre-eclampsia, systemic lupus erythematous, juvenile idiopathic arthritis, rheumatoid arthritis and HIV/AIDS, is more commonly found in European populations with average frequency of 10%. However, it is also possible to observe a significant frequency in other world populations, such as the Brazilian one. We performed a systematic review and meta-analysis of CCR5-delta32 genetic association studies in Brazilian populations throughout the country to estimate the frequency of this polymorphism. We also compared CCR5-delta32 frequencies across Brazilian regions. The systematic literature reviewed studies involving delta32 allele in Brazilian populations published from 1995 to 2015. Among the reviewed literature, 25 studies including 30 Brazilian populations distributed between the North, Northeast, South and Southeast regions were included in our meta-analysis. We observed an overall allelic frequency of 4% (95%-CI, 0.03-0.05), that was considered moderate and, notably, higher than some European populations, such as Cyprus (2.8%), Italy (3%) and Greece (2.4%). Regarding the regional frequency comparisons between North-Northeast (N-NE) and South-Southeast (S-SE) regions, we observed an allelic frequency of 3% (95%-CI, 0.02-0.04) and 4% (95%-CI, 0.03-0.05), respectively. The populations from S-SE regions had a slightly higher CCR5-delta32 frequency than N-NE regions (OR=1.41, p=0.002). Although there are several studies about the CCR5-delta32 polymorphism and its effect on the immune response of some infectious diseases, this report is the first meta

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

    PubMed

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

    2007-12-01

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

  4. 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

  5. Interpretation of the water surface vibrational sum-frequency spectrum

    NASA Astrophysics Data System (ADS)

    Pieniazek, P. A.; Tainter, C. J.; Skinner, J. L.

    2011-07-01

    We propose a novel interpretation of the water liquid-vapor interface vibrational sum-frequency (VSF) spectrum in terms of hydrogen-bonding classes. Unlike an absorption spectrum, the VSF signal can be considered as a sum of signed contributions from different hydrogen-bonded species in the sample. We show that the recently observed positive feature at low frequency, in the imaginary part of the signal, is a result of cancellation between the positive contributions from four-hydrogen-bonded molecules and negative contributions from those molecules with one or two broken hydrogen bonds. Spectral densities for each of these subgroups span the entire relevant spectral range. Three-body interactions within our newly developed E3B water simulation model prove to be critical in describing the proper balance between different hydrogen-bonded species, as (two-body) SPC/E, TIP4P, and TIP4P/2005 models fail to reproduce the positive feature. The results clarify the molecular origin of the VSF signal, and highlight the importance of many-body interactions for water in heterogeneous situations.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Coding for frequency hopped spread spectrum satellite communications

    NASA Astrophysics Data System (ADS)

    Wang, Q.; Li, G.; Blake, I. F.; Bhargava, V. K.; Chen, Q.

    1992-04-01

    The performance of fast frequency hopped spread spectrum systems with M-ary frequency shift keying and error correction coding under jamming conditions are analyzed. Ratio threshold diversity combining is used. The decoding scheme is error erasure decoding with metrics generated by the diversity combiner. The bit error probability of the system is computed and improvements offered by error correction coding are shown. The performance of several error correction codes is compared under different channel conditions. The notion of an arbitrarily varying channel (AVC) is discussed, including capacities of AVC's and a discrete memoryless channel, and two Gaussian AVC models are described. Coded performance of a slow frequency hopped differential phase shift keying (DPSK) system in presence of both additive white Gaussian noise and tone jamming is studied. The error correlation due to DPSK demodulation and the effect of tone jamming are considered in evaluating the block and decoded error probabilities. The effect of interleaving on system performance is addressed. A nearly optimum code rate for a length 255 Reed-Solomon code is derived for systems employing interleaving. Finally, a parallel approach to the design of universal receivers for unknown and time-varying channels is applied to DPSK systems in the presence of noise and tone interference.

  13. 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

  14. 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

  15. 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.

  16. [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

  17. Application of frequency spectrum analysis in measuring multi-vibrations by using POTDR

    NASA Astrophysics Data System (ADS)

    Wang, Xiangchuan; Zhang, Xuping; Wang, Feng; Chen, Mengmeng; Li, Cunlei

    2011-11-01

    The technology of Polarization Optical Time Domain Reflectometer (POTDR) can be used to obtain the external events' information by measuring the change of state of polarization (SOP) of the Rayleigh backscattering in fiber. When the fiber is disturbed at two different positions simultaneously, we analyze the frequency spectrums of the change of Rayleigh backscattering light which are obtained by POTDR theoretically for ideal fiber, and by numerical simulation for single mode fibers. We find that the frequency spectrums between the first and second events contain the first vibration's frequency and its frequency multiplication. The frequency components of the spectrums after the second event are the linear combination of the first and the second events' frequencies. So we can obtain the location and the frequency information of the two events by analyzing the frequency spectrums. In addition, the frequency distribution in the frequency spectrums from different positions are different because of the different initial SOPs at different positions. So all the actual frequency information can not be obtained from only one frequency spectrum. We add up the frequency spectrums from the positions within a beat length to obtain the perturbation's frequency and the method can reduce the misdiagnosis rate because the sum of the frequency spectrums contains all the initial SOP within a beat length.

  18. Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster.

    PubMed

    Keightley, Peter D; Campos, José L; Booker, Tom R; Charlesworth, Brian

    2016-06-01

    Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high-copy-number elements of the SFS is difficult, however, because of misassignment of alleles as derived vs. ancestral. This is a known problem with parsimony using outgroup species. Here we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups that attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites in protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites in a population of Drosophila melanogaster from phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations and estimate that ∼50% of amino acid substitutions are positively selected but that <0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes ≈ 12. PMID:27098912

  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. The site-frequency spectrum associated with Ξ-coalescents.

    PubMed

    Blath, Jochen; Cronjäger, Mathias Christensen; Eldon, Bjarki; Hammer, Matthias

    2016-08-01

    We give recursions for the expected site-frequency spectrum associated with so-called Xi-coalescents, that is exchangeable coalescents which admit simultaneous multiple mergers of ancestral lineages. Xi-coalescents arise, for example, in association with population models of skewed offspring distributions with diploidy, recurrent advantageous mutations, or strong bottlenecks. In contrast, the simpler Lambda-coalescents admit multiple mergers of lineages, but at most one such merger each time. Xi-coalescents, as well as Lambda-coalescents, can predict an excess of singletons, compared to the Kingman coalescent. We compare estimates of coalescent parameters when Xi-coalescents are applied to data generated by Lambda-coalescents, and vice versa. In general, Xi-coalescents predict fewer singletons than corresponding Lambda-coalescents, but a higher count of mutations of size larger than singletons. We fit examples of Xi-coalescents to unfolded site-frequency spectra obtained for autosomal loci of the diploid Atlantic cod, and obtain different coalescent parameter estimates than obtained with corresponding Lambda-coalescents. Our results provide new inference tools, and suggest that for autosomal population genetic data from diploid or polyploid highly fecund populations who may have skewed offspring distributions, one should not apply Lambda-coalescents, but Xi-coalescents. PMID:27112097

  1. Exponential frequency spectrum and Lorentzian pulses in magnetized plasmas

    SciTech Connect

    Pace, D. C.; Shi, M.; Maggs, J. E.; Morales, G. J.; Carter, T. A.

    2008-12-15

    Two different experiments involving pressure gradients across the confinement magnetic field in a large plasma column are found to exhibit a broadband turbulence that displays an exponential frequency spectrum for frequencies below the ion cyclotron frequency. The exponential feature has been traced to the presence of solitary pulses having a Lorentzian temporal signature. These pulses arise from nonlinear interactions of drift-Alfven waves driven by the pressure gradients. In both experiments the width of the pulses is narrowly distributed resulting in exponential spectra with a single characteristic time scale. The temporal width of the pulses is measured to be a fraction of a period of the drift-Alfven waves. The experiments are performed in the Large Plasma Device (LAPD-U) [W. Gekelman et al., Rev. Sci. Instrum. 62, 2875 (1991)] operated by the Basic Plasma Science Facility at the University of California, Los Angeles. One experiment involves a controlled, pure electron temperature gradient associated with a microscopic (6 mm gradient length) hot electron temperature filament created by the injection a small electron beam embedded in the center of a large, cold magnetized plasma. The other experiment is a macroscopic (3.5 cm gradient length) limiter-edge experiment in which a density gradient is established by inserting a metallic plate at the edge of the nominal plasma column of the LAPD-U. The temperature filament experiment permits a detailed study of the transition from coherent to turbulent behavior and the concomitant change from classical to anomalous transport. In the limiter experiment the turbulence sampled is always fully developed. The similarity of the results in the two experiments strongly suggests a universal feature of pressure-gradient driven turbulence in magnetized plasmas that results in nondiffusive cross-field transport. This may explain previous observations in helical confinement devices, research tokamaks, and arc plasmas.

  2. 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

  3. 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

  4. 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

  5. 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

  6. QEEG characteristics and spectrum weighted frequency for children diagnosed as autistic spectrum disorder

    PubMed Central

    2010-01-01

    Background Autistic spectrum disorders are a group of neurological and developmental disorders associated with social, communication, sensory, behavioral and cognitive impairments, as well as restricted, repetitive patterns of behavior, activities, or interests. The aim of this study was a) to analyze QEEG findings of autistic patients and to compare the results with data base; and b) to introduce the calculation of spectrum weighted frequency (brain rate) as an indicator of general mental arousal in these patients. Results Results for Q-EEG shows generally increased delta-theta activity in frontal region of the brain. Changes in QEEG pattern appeared to be in a non-linear correlation with maturational processes. Brain rate measured in CZ shows slow brain activity (5. 86) which is significantly lower than normal and corresponds to low general mental arousal. Recent research has shown that autistic disorders have as their basis disturbances of neural connectivity. Neurofeedback seems capable of remediating such disturbances when these data are considered as part of treatment planning. Conclusions Prognosis of this pervasive disorder depends on the intellectual abilities: the better intellectual functioning, the possibilities for life adaptation are higher QEEG shows generally increased delta-theta activity in frontal region of the brain which is related to poor cognitive abilities. Brain rate measured in CZ shows slow brain activity related to under arousal. Pharmacotherapy combined with behavior therapy, social support and especially neurofeedback technique promise slight improvements PMID:20920283

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. Coding for frequency hopped spread spectrum satellite communications

    NASA Astrophysics Data System (ADS)

    Bhargava, Vijay K.; Wang, Qiang; Blake, Ian F.; Li, Gang; Gulliver, T. Aaron; Dravnieks, Olaf

    1990-04-01

    Work aimed at improving the jamming resistance of satellite communications is reviewed. The performance of Reed-Solomon (RS) error correcting codes with slow frequency hopped (SFH) differential phase shift keying (DPSK) signalling is analyzed and evaluated under worst case partial band noise and worst case multitone jamming. A representative set of performance curves is shown. Recommendation on the choice of RS code parameters is given. Two in-hop jamming cancellation schemes for SFH/DPSK systems are proposed. One scheme is based on balanced coding; the other one uses notch filter to cancel jamming tone. The performance of both schemes is illustrated. It is shown that both schemes can work well under certain conditions. Basic principles and techniques for designing interleavers are presented. Block, convolution, and the more recent helical interleavers are considered. The trade-off between diversity and coding for spread spectrum systems, where a low code rate is anticipated, is discussed. An error correction scheme is presented for an M-ary symmetric channel (MSC) characterized by a large error probability (Pe). The value of Pe can be near, but smaller than 1-1/M, for which the channel capacity is zero. Such a large Pe may occur, for example, in a jamming environment. Monte-Carlo simulation results are presented. For the binary symmetric channel (BSC), it is shown that the overall code rate is larger than 0.6 R sub 0, where R sub 0 is the cutoff rate of the channel. For BSC and a large diversity order (m), a method is presented for BER (bit error rate) approximation on the central limit theorem.

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

    PubMed Central

    Faure, Eric

    2008-01-01

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

  16. 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

  17. 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.

  18. Analysis of a discrete spectrum analyzer for the detection of radio frequency interference

    NASA Technical Reports Server (NTRS)

    Levitt, B. K.

    1977-01-01

    As the radio frequency spectrum becomes increasingly overcrowded, interference with mission-critical DSN operations is rising at an alarming rate. To alleviate this problem the DSN is developing a wideband surveillance system for on-site detection and identification of potential sources of radio frequency interference (RFI), which will complement the existing frequency coordination activities. The RFI monitoring system is based on a wideband, multi-look discrete spectrum analyzer operating on fast Fourier transform principles. An extensive general statistical analysis is presented of such spectrum analyzers and derives threshold detection performance formulas for signals of interest. These results are then applied to the design of the RFI spectrum analyzer under development.

  19. 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

  20. High frequency formulation for the acoustic power spectrum due to cascade-turbulence interaction.

    PubMed

    Cheong, Cheolung; Joseph, Phillip; Lee, Soogab

    2006-01-01

    This paper investigates the noise radiated by a cascade of flat-plate airfoils interacting with homogeneous, isotropic turbulence. An analytic formulation for the spectrum of acoustic power of a two-dimensional flat-plate is derived. The main finding of this paper is that the acoustic power spectrum from the cascade of flat airfoils may be split into two distinct frequency regions of low frequency and high frequency, separated by a critical frequency. Below this frequency, cascade effects due to the interaction between neighboring airfoils are shown to be important. At frequencies above the critical frequency, cascade effects are shown to be relatively weak. In this frequency range, acoustic power is shown to be approximately proportional to the number of blades. Based on this finding at high frequencies, an approximate expression is derived for the power spectrum that is valid above the critical frequency and which is in excellent agreement with the exact expression for the broadband power spectrum. The formulation is used to perform a parametric study on the effects on the power spectrum of the blade number, stagger angle, gap-chord ratio, and Mach number. The theory is also shown to provide a close fit to the measured spectrum of rotor-stator interaction. PMID:16454269

  1. Frequency management engineering principles spectrum measurements (reference order 6050.23)

    NASA Astrophysics Data System (ADS)

    Fretz, J. D.

    1982-08-01

    Federal Aviation Administration personnel are frequently involved in the resolution of interference complaints. The skillful use of measurement equipment can be essential to the successful resolution of such complaints. This report provides a summary of the spectrum measurement techniques applicable to Federal Aviation Administration facilities using the radio frequency spectrum. It is oriented toward electromagnetic compatibility measurements made by frequency management engineers but is of interest to anyone involved in radio frequency measurements.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Significant Association of HLA-B Alleles and Genotypes in Thai Children with Autism Spectrum Disorders: A Case-Control Study

    PubMed Central

    Puangpetch, Apichaya; Suwannarat, Pongwut; Chamnanphol, Montri; Koomdee, Napatrupron; Ngamsamut, Nattawat; Limsila, Penkhae; Sukasem, Chonlaphat

    2015-01-01

    Autism is a severe neurodevelopmental disorder. Many susceptible causative genes have been identified. Most of the previous reports showed the relationship between the Human Leukocyte Antigen (HLA) gene and etiology of autism. In order to identify HLA-B alleles associated with autism in Thai population, we compared the frequency of HLA-B allele in 364 autistic subjects with 952 normal subjects by using a two-stage sequence-specific oligonucleotide probe system (PCR-SSOP) method based on flow-cytometry technology. HLA-B⁎13:02 (P = 0.019, OR = 2.229), HLA-B⁎38:02 (P = 0.049, OR = 1.628), HLA-B⁎44:03 (P = 0.016, OR = 1.645), and HLA-B⁎56:01 (P = 1.78 × 10−4, OR = 4.927) alleles were significantly increased in autistic subjects compared with normal subjects. Moreover, we found that the HLA-B⁎18:02 (P = 0.016, OR = 0.375) and HLA-B⁎46:12 (P = 0.008, OR = 0.147) alleles were negatively associated with autism when compared to normal controls. Both alleles might have a protective role in disease development. In addition, four HLA-B genotypes of autistic patients had statistically significant relationship with control groups, consisting of HLA-B⁎3905/⁎5801 (P = 0.032, OR = 24.697), HLA-B⁎2704/⁎5801 (P = 0.022, OR = 6.872), HLA-B⁎3501/⁎4403 (P = 0.021, OR = 30.269), and HLA-B⁎1801/⁎4402 (P = 0.017, OR = 13.757). This is the first report on HLA-B associated with Thai autism and may serve as a marker for genetic susceptibility to autism in Thai population. PMID:26819491

  7. 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

  8. 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

  9. 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

  10. An automatic method to determine cutoff frequency based on image power spectrum

    SciTech Connect

    Beis, J.S.; Celler, A.; Barney, J.S.

    1995-12-01

    The authors present an algorithm for automatically choosing filter cutoff frequency (F{sub c}) using the power spectrum of the projections. The method is based on the assumption that the expectation of the image power spectrum is the sum of the expectation of the blurred object power spectrum (dominant at low frequencies) plus a constant value due to Poisson noise. By considering the discrete components of the noise-dominated high-frequency spectrum as a Gaussian distribution N({mu},{sigma}), the Student t-test determines F{sub c} as the highest frequency for which the image frequency components are unlikely to be drawn from N ({mu},{sigma}). The method is general and can be applied to any filter. In this work, the authors tested the approach using the Metz restoration filter on simulated, phantom, and patient data with good results. Quantitative performance of the technique was evaluated by plotting recovery coefficient (RC) versus NMSE of reconstructed images.

  11. Structure-aware Bayesian compressive sensing for frequency-hopping spectrum estimation

    NASA Astrophysics Data System (ADS)

    Liu, Shengheng; Zhang, Yimin D.; Shan, Tao; Qin, Si; Amin, Moeness G.

    2016-05-01

    Frequency-hopping (FH) is one of the commonly used spread spectrum techniques that finds wide applications in communications and radar systems due to its capability of low probability of intercept, reduced interference, and desirable ambiguity property. In this paper, we consider the blind estimation of the instantaneous FH spectrum without the knowledge of hopping patterns. The FH signals are analyzed in the joint time-frequency domain, where FH signals manifest themselves as sparse entries, thus inviting compressive sensing and sparse reconstruction techniques for FH spectrum estimation. In particular, the signals' piecewise-constant frequency characteristics are exploited in the reconstruction of sparse quadratic time-frequency representations. The Bayesian compressive sensing methods are applied to provide high-resolution frequency estimation. The FH spectrum characteristics are used in the design of signal-dependent kernel within the framework of structure-aware sparse reconstruction.

  12. 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

  13. Frequency Spectrum for New Aviation Data Links: Initial Study Results

    NASA Technical Reports Server (NTRS)

    Matolak, David W.; Branstetter, James R.

    2004-01-01

    We describe results from an initial study to assess the suitability of various spectral bands for supporting the deployment of new aviation data links (ADL). The study focused on systems and spectral bands that can deliver VHF data link (VDL)-or-higher data rates in a two-way communication setting, including air-ground, ground-air, and air-air modes of operation. In the first part of our paper, we briefly discuss the current situation regarding communications, navigation, and surveillance (CNS) links and existing spectrum, and the well-known need for new aviation data links. We next provide an overview of related systems, and discuss key factors involved in the use of spectrum in various bands for any future integrated CNS data link, addressing primarily the lower few layers of the communications protocol stack. Desired attributes of a new ADL system are discussed, and the beneficial aspects of a particular transmission technique spread spectrum are summarized. We also provide a short list of several example potential spectral regions, and note that while none of the existing systems will likely meet the full range of desired features of a new ADL, several systems and spectral regions offer promise in terms of one or more characteristics. A detailed discussion and evaluation of these spectral regions is proposed as future work. We include a few brief examples to illustrate initial technical results regarding spread spectrum overlay, also a subject for future work.

  14. 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

  15. Packet error probabilities in frequency-hopped spread spectrum packet radio networks. Markov frequency hopping patterns considered

    NASA Astrophysics Data System (ADS)

    Georgiopoulos, M.; Kazakos, P.

    1987-09-01

    We compute the packet error probability induced in a frequency-hopped spread spectrum packet radio network, which utilizes first order Markov frequency hopping patterns. The frequency spectrum is divided into q frequency bins and the packets are divided into M bytes each. Every user in the network sends each of the M bytes of his packet at a frequency bin, which is different from the frequency bin used by the previous byte, but equally likely to be any one of the remaining q-1 frequency bins (Markov frequency hopping patterns). Furthermore, different users in the network utilize statistically independent frequency hopping patterns. Provided that, K users have simultaneously transmitted their packets on the channel, and a receiver has locked on to one of these K packets, we present a method for the computation of P sub e (K) (i.e. the probability that this packet is incorrectly decoded). Furthermore, we present numerical results (i.e. P sub e (K) versus K) for various values of the multiple access interference K, when Reed Solomon (RS) codes are used for the encoding of packets. Finally, some useful comparisons, with the packet error probability induced, if we assume that the byte errors are independent, are made; based on these comparisons, we can easily evaluate the performance of our spread spectrum system.

  16. Achieving spectrum conservation for the minimum-span and minimum-order frequency assignment problems

    NASA Technical Reports Server (NTRS)

    Heyward, Ann O.

    1992-01-01

    Effective and efficient solutions of frequency assignment problems assumes increasing importance as the radiofrequency spectrum experiences ever increasing utilization by diverse communications services, requiring that the most efficient use of this resource be achieved. The research presented explores a general approach to the frequency assignment problem, in which such problems are categorized by the appropriate spectrum conserving objective function, and are each treated as an N-job, M-machine scheduling problem appropriate for the objective. Results obtained and presented illustrate that such an approach presents an effective means of achieving spectrum conserving frequency assignments for communications systems in a variety of environments.

  17. A New Proof of the Expected Frequency Spectrum under the Standard Neutral Model

    PubMed Central

    Hudson, Richard R.

    2015-01-01

    The sample frequency spectrum is an informative and frequently employed approach for summarizing DNA variation data. Under the standard neutral model the expectation of the sample frequency spectrum has been derived by at least two distinct approaches. One relies on using results from diffusion approximations to the Wright-Fisher Model. The other is based on Pólya urn models that correspond to the standard coalescent model. A new proof of the expected frequency spectrum is presented here. It is a proof by induction and does not require diffusion results and does not require the somewhat complex sums and combinatorics of the derivations based on urn models. PMID:26197064

  18. A New Proof of the Expected Frequency Spectrum under the Standard Neutral Model.

    PubMed

    Hudson, Richard R

    2015-01-01

    The sample frequency spectrum is an informative and frequently employed approach for summarizing DNA variation data. Under the standard neutral model the expectation of the sample frequency spectrum has been derived by at least two distinct approaches. One relies on using results from diffusion approximations to the Wright-Fisher Model. The other is based on Pólya urn models that correspond to the standard coalescent model. A new proof of the expected frequency spectrum is presented here. It is a proof by induction and does not require diffusion results and does not require the somewhat complex sums and combinatorics of the derivations based on urn models. PMID:26197064

  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 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

  20. 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

  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

    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

  2. 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

  3. Frequency Spectrum of Exact Solutions of the Two-Dimensional Hydrodynamic Equations

    NASA Astrophysics Data System (ADS)

    Abrashkin, A. A.; Yakubovich, E. I.

    2016-05-01

    We show that the discrete frequency spectrum of a plane hydrodynamic flow of ideal incompressible liquid with localized trajectories of the liquid particles can contain only one, two, or an infinite number of harmonics.

  4. 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

  5. Time Correlations and the Frequency Spectrum of Sound Radiated by Turbulent Flows

    NASA Technical Reports Server (NTRS)

    Rubinstein, Robert; Zhou, Ye

    1997-01-01

    Theories of turbulent time correlations are applied to compute frequency spectra of sound radiated by isotropic turbulence and by turbulent shear flows. The hypothesis that Eulerian time correlations are dominated by the sweeping action of the most energetic scales implies that the frequency spectrum of the sound radiated by isotropic turbulence scales as omega(exp 4) for low frequencies and as omega(exp -3/4) for high frequencies. The sweeping hypothesis is applied to an approximate theory of jet noise. The high frequency noise again scales as omega(exp -3/4), but the low frequency spectrum scales as omega(exp 2). In comparison, a classical theory of jet noise based on dimensional analysis gives omega(exp -2) and omega(exp 2) scaling for these frequency ranges. It is shown that the omega(exp -2) scaling is obtained by simplifying the description of turbulent time correlations. An approximate theory of the effect of shear on turbulent time correlations is developed and applied to the frequency spectrum of sound radiated by shear turbulence. The predicted steepening of the shear dominated spectrum appears to be consistent with jet noise measurements.

  6. 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

  7. Communication: Vibrational sum-frequency spectrum of the air-water interface, revisited.

    PubMed

    Ni, Yicun; Skinner, J L

    2016-07-21

    Before 2015, heterodyne-detected sum-frequency-generation experiments on the air-water interface showed the presence of a positive feature at low frequency in the imaginary part of the susceptibility. However, three very recent experiments indicate that this positive feature is in fact absent. Armed with a better understanding, developed by others, of how to calculate sum-frequency spectra, we recalculate the spectrum and find good agreement with these new experiments. In addition, we provide a revised interpretation of the spectrum. PMID:27448864

  8. Communication: Vibrational sum-frequency spectrum of the air-water interface, revisited

    NASA Astrophysics Data System (ADS)

    Ni, Yicun; Skinner, J. L.

    2016-07-01

    Before 2015, heterodyne-detected sum-frequency-generation experiments on the air-water interface showed the presence of a positive feature at low frequency in the imaginary part of the susceptibility. However, three very recent experiments indicate that this positive feature is in fact absent. Armed with a better understanding, developed by others, of how to calculate sum-frequency spectra, we recalculate the spectrum and find good agreement with these new experiments. In addition, we provide a revised interpretation of the spectrum.

  9. 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

  10. 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

  11. 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

  12. Numerical investigation of frequency spectrum in the Hasegawa-Wakatani model

    NASA Astrophysics Data System (ADS)

    Kim, Juhyung; Terry, P. W.

    2013-10-01

    The wavenumber-frequency spectrum of the two-dimensional Hasegawa-Wakatani model is investigated in the hydrodynamic, intermediate, and adiabatic regimes. A nonlinear frequency and a line width related to energy transfer properties provide a measure of the average frequency and spectral broadening, respectively. In the adiabatic regime, narrow spectra, typical of wave turbulence, are observed with a nonlinear frequency shift in the electron drift direction. In the hydrodynamic regime, broad spectra with almost zero nonlinear frequencies are observed. Nonlinear frequency shifts are shown to be related to nonlinear energy transfer by vorticity advection through the high frequency region of the spectrum. In the intermediate regime, the nonlinear frequency shift for density fluctuations is observed to be weaker than that of electrostatic potential fluctuations. The weaker frequency shift of the density fluctuations is due to nonlinear density advection, which favors energy transfer in the low frequency range. Both the nonlinear frequency and the spectral width increase with poloidal wavenumber ky. In addition, in the adiabatic regime where the nonlinear interactions manifest themselves in the nonlinear frequency shift, the cross-phase between the density and potential fluctuations is observed to match a linear relation, but only if the linear response of the linearly stable eigenmode branch is included. Implications of these numerical observations are discussed.

  13. Numerical investigation of frequency spectrum in the Hasegawa-Wakatani model

    SciTech Connect

    Kim, Juhyung; Terry, P. W.

    2013-10-15

    The wavenumber-frequency spectrum of the two-dimensional Hasegawa-Wakatani model is investigated in the hydrodynamic, intermediate, and adiabatic regimes. A nonlinear frequency and a line width related to energy transfer properties provide a measure of the average frequency and spectral broadening, respectively. In the adiabatic regime, narrow spectra, typical of wave turbulence, are observed with a nonlinear frequency shift in the electron drift direction. In the hydrodynamic regime, broad spectra with almost zero nonlinear frequencies are observed. Nonlinear frequency shifts are shown to be related to nonlinear energy transfer by vorticity advection through the high frequency region of the spectrum. In the intermediate regime, the nonlinear frequency shift for density fluctuations is observed to be weaker than that of electrostatic potential fluctuations. The weaker frequency shift of the density fluctuations is due to nonlinear density advection, which favors energy transfer in the low frequency range. Both the nonlinear frequency and the spectral width increase with poloidal wavenumber k{sub y}. In addition, in the adiabatic regime where the nonlinear interactions manifest themselves in the nonlinear frequency shift, the cross-phase between the density and potential fluctuations is observed to match a linear relation, but only if the linear response of the linearly stable eigenmode branch is included. Implications of these numerical observations are discussed.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  16. The spectrum of BRCA1 and BRCA2 alleles in Latin America and the Caribbean: a clinical perspective.

    PubMed

    Dutil, Julie; Golubeva, Volha A; Pacheco-Torres, Alba L; Diaz-Zabala, Hector J; Matta, Jaime L; Monteiro, Alvaro N

    2015-12-01

    Hereditary cancer predisposition gene testing allows the identification of individuals at high risk of cancer that may benefit from increased surveillance, chemoprevention, and prophylactic surgery. In order to implement clinical genetic strategies adapted to each population's needs and intrinsic genetic characteristic, this review aims to present the current status of knowledge about the spectrum of BRCA pathogenic variants in Latin American populations. We have conducted a comprehensive review of 33 studies published between 1994 and 2015 reporting the prevalence and/or spectrum of BRCA1 (OMIM 113705) and BRCA2 (OMIM 600185) variants. The combined sample size for these studies consisted of 4835 individuals from 13 countries in Latin America and the Caribbean, as well as in Hispanics in the United States. A total of 167 unique pathogenic variants have been reported in the existing literature. In unselected breast cancer cases, the prevalence ranged from 1.2 to 27.1%. Some countries presented a few recurrent pathogenic variants, while others were characterized by diverse, non-recurrent variants. The proportion of BRCA pathogenic variants shared between Hispanics in the United States and Latin American populations was estimated at 10.4%. Within Latin America and the Caribbean, 8.2% of the BRCA variants reported were present in more than one country. Countries with high prevalence of BRCA pathogenic variants may benefit from more aggressive testing strategies, while testing of recurrent variant panels might present a cost-effective solution for improving genetic testing in some, but not all, countries. PMID:26564481

  17. 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

  18. 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

  19. 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

  20. Spectrum of vibrational frequencies of crystalline tungsten at temperatures of 293 and 2400 K

    NASA Astrophysics Data System (ADS)

    Semenov, V. A.; Dubovsky, O. A.; Orlov, A. V.; Savostin, D. V.; Sudarev, V. V.

    2014-01-01

    The slow neutron inelastic scattering spectra for a refractory ( T melt = 3680 K) Group VI transition metal of the Periodic Table, namely, tungsten, were measured for the first time in the range from room temperature to 2400 K. Measurements of the neutron scattering spectra of tungsten were performed on a DIN-2PI time-of-flight spectrometer installed at the IBR-2 reactor (Dubna, Russia). The sample was heated in a TS3000 K high-temperature thermostat. The spectrum of vibrational frequencies of the crystal lattice of tungsten at temperatures of 293 and 2400 K was determined from the measured neutron scattering spectra by the iterative method. A softening of the frequency spectrum of tungsten was observed with increasing temperature. This was explained by the increasing role of vibrational anharmonicity effects at high temperatures. The experimental results were compared with model calculations of the frequency spectrum of tungsten.

  1. Dynamics of the frequency spectrum of fluctuations of the interplanetary magnetic field and cosmic rays

    NASA Astrophysics Data System (ADS)

    Bezrodnykh, I. P.; Kuzmin, V. A.; Kozlov, V. I.; Morozova, E. I.; Shafer, Iu. G.

    1982-12-01

    Prognoz-6 data on the dynamics of the fluctuation spectrum of low-energy cosmic-rays tends to support the hypothesis that the modulation of the cosmic-ray fluctuation spectrum has an interplanetary origin. The results indicate that an analogous dynamics is observed in the fluctuation spectrum of the interplanetary magnetic field (IMF), the dynamics in the frequency spectra of cosmic rays and the IMF occurring simultaneously. This suggests that the dynamics of the fluctuation spectrum of cosmic rays is conditioned by the dynamics of the IMF irregularity spectrum. The results also indicate the presence of two bursts of fluctuations of galactic cosmic rays and the IMF in the event of June 9-10, 1968, when the passage of a shock front was noted.

  2. 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

  3. 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

  4. Fractal frequency spectrum in laser resonators and three-dimensional geometric topology of optical coherent waves

    NASA Astrophysics Data System (ADS)

    Tung, J. C.; Tuan, P. H.; Liang, H. C.; Huang, K. F.; Chen, Y. F.

    2016-08-01

    We theoretically verify that the symmetry breaking in spherical resonators can result in a fractal frequency spectrum that is full of numerous new accidental degeneracies to cluster around the unperturbed degenerate cavity. We further experimentally discover that the fractal frequency spectrum excellently reflects the intimate connection between the emission power and the degenerate mode numbers. It is observed that the wave distributions of lasing modes at the accidental degeneracies are strongly concentrated on three-dimensional (3D) geometric topology. Considering the overlapping effect, the wave representation of the coherent states is analytically derived to manifest the observed 3D geometric surfaces.

  5. ION HEATING BY A SPECTRUM OF OBLIQUELY PROPAGATING LOW-FREQUENCY ALFVEN WAVES

    SciTech Connect

    Lu Quanming; Chen Liu

    2009-10-10

    Ion stochastic heating by a monochromatic Alfven wave, which propagates obliquely to the background magnetic field, has been studied by Chen et al. It is shown that ions can be resonantly heated at frequencies a fraction of the ion cyclotron frequency when the wave amplitude is sufficiently large. In this paper, the monochromatic wave is extended to a spectrum of left-hand polarized Alfven waves. When the amplitude of the waves is small, the components of the ion velocity have several distinct frequencies, and their motions are quasi-periodic. However, when the amplitude of the waves is sufficiently large, the components of the ion velocity have a spectrum of continuous frequencies near the ion cyclotron frequency due to the nonlinear coupling between the Alfven waves and the ion gyromotion, and the ion motions are stochastic. Compared with the case of a monochromatic Alfven wave, the threshold of the ion stochastic heating by a spectrum of Alfven waves is much lower. Even when their frequencies are only several percent of the ion cyclotron frequency, the ions can also be stochastically heated. The relevance of this heating mechanism to solar corona is also discussed.

  6. 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

  7. 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

  8. Frequency spectrum might act as communication code between retina and visual cortex I

    PubMed Central

    Yang, Xu; Gong, Bo; Lu, Jian-Wei

    2015-01-01

    AIM To explore changes and possible communication relationship of local potential signals recorded simultaneously from retina and visual cortex I (V1). METHODS Fourteen C57BL/6J mice were measured with pattern electroretinogram (PERG) and pattern visually evoked potential (PVEP) and fast Fourier transform has been used to analyze the frequency components of those signals. RESULTS The amplitude of PERG and PVEP was measured at about 36.7 µV and 112.5 µV respectively and the dominant frequency of PERG and PVEP, however, stay unchanged and both signals do not have second, or otherwise, harmonic generation. CONCLUSION The results suggested that retina encodes visual information in the way of frequency spectrum and then transfers it to primary visual cortex. The primary visual cortex accepts and deciphers the input visual information coded from retina. Frequency spectrum may act as communication code between retina and V1. PMID:26682156

  9. The allelic spectrum of Charcot–Marie–Tooth disease in over 17,000 individuals with neuropathy

    PubMed Central

    DiVincenzo, Christina; Elzinga, Christopher D; Medeiros, Adam C; Karbassi, Izabela; Jones, Jeremiah R; Evans, Matthew C; Braastad, Corey D; Bishop, Crystal M; Jaremko, Malgorzata; Wang, Zhenyuan; Liaquat, Khalida; Hoffman, Carol A; York, Michelle D; Batish, Sat D; Lupski, James R; Higgins, Joseph J

    2014-01-01

    We report the frequency, positive rate, and type of mutations in 14 genes (PMP22, GJB1, MPZ, MFN2, SH3TC2, GDAP1, NEFL, LITAF, GARS, HSPB1, FIG4, EGR2, PRX, and RAB7A) associated with Charcot–Marie–Tooth disease (CMT) in a cohort of 17,880 individuals referred to a commercial genetic testing laboratory. Deidentified results from sequencing assays and multiplex ligation-dependent probe amplification (MLPA) were analyzed including 100,102 Sanger sequencing, 2338 next-generation sequencing (NGS), and 21,990 MLPA assays. Genetic abnormalities were identified in 18.5% (n = 3312) of all individuals. Testing by Sanger and MLPA (n = 3216) showed that duplications (dup) (56.7%) or deletions (del) (21.9%) in the PMP22 gene accounted for the majority of positive findings followed by mutations in the GJB1 (6.7%), MPZ (5.3%), and MFN2 (4.3%) genes. GJB1 del and mutations in the remaining genes explained 5.3% of the abnormalities. Pathogenic mutations were distributed as follows: missense (70.6%), nonsense (14.3%), frameshift (8.7%), splicing (3.3%), in-frame deletions/insertions (1.8%), initiator methionine mutations (0.8%), and nonstop changes (0.5%). Mutation frequencies, positive rates, and the types of mutations were similar between tests performed by either Sanger (n = 17,377) or NGS (n = 503). Among patients with a positive genetic finding in a CMT-related gene, 94.9% were positive in one of four genes (PMP22, GJB1, MPZ, or MFN2). PMID:25614874

  10. Automated Classification of Vowel Category and Speaker Type in the High-Frequency Spectrum

    PubMed Central

    Donai, Jeremy J.; Motiian, Saeid; Doretto, Gianfranco

    2016-01-01

    The high-frequency region of vowel signals (above the third formant or F3) has received little research attention. Recent evidence, however, has documented the perceptual utility of high-frequency information in the speech signal above the traditional frequency bandwidth known to contain important cues for speech and speaker recognition. The purpose of this study was to determine if high-pass filtered vowels could be separated by vowel category and speaker type in a supervised learning framework. Mel frequency cepstral coefficients (MFCCs) were extracted from productions of six vowel categories produced by two male, two female, and two child speakers. Results revealed that the filtered vowels were well separated by vowel category and speaker type using MFCCs from the high-frequency spectrum. This demonstrates the presence of useful information for automated classification from the high-frequency region and is the first study to report findings of this nature in a supervised learning framework.

  11. Automated Classification of Vowel Category and Speaker Type in the High-Frequency Spectrum.

    PubMed

    Donai, Jeremy J; Motiian, Saeid; Doretto, Gianfranco

    2016-04-20

    The high-frequency region of vowel signals (above the third formant or F3) has received little research attention. Recent evidence, however, has documented the perceptual utility of high-frequency information in the speech signal above the traditional frequency bandwidth known to contain important cues for speech and speaker recognition. The purpose of this study was to determine if high-pass filtered vowels could be separated by vowel category and speaker type in a supervised learning framework. Mel frequency cepstral coefficients (MFCCs) were extracted from productions of six vowel categories produced by two male, two female, and two child speakers. Results revealed that the filtered vowels were well separated by vowel category and speaker type using MFCCs from the high-frequency spectrum. This demonstrates the presence of useful information for automated classification from the high-frequency region and is the first study to report findings of this nature in a supervised learning framework. PMID:27588160

  12. 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

  13. 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

  14. 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

  15. Impaired Timing and Frequency Discrimination in High-Functioning Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Bhatara, Anjali; Babikian, Talin; Laugeson, Elizabeth; Tachdjian, Raffi; Sininger, Yvonne S.

    2013-01-01

    Individuals with autism spectrum disorders (ASD) frequently demonstrate preserved or enhanced frequency perception but impaired timing perception. The present study investigated the processing of spectral and temporal information in 12 adolescents with ASD and 15 age-matched controls. Participants completed two psychoacoustic tasks: one determined…

  16. Dynamic jamming effects on code synchronization of frequency-hop spread-spectrum

    NASA Astrophysics Data System (ADS)

    van Grouw, M. G.; Wickert, M. A.

    1989-06-01

    A general scheme for the code synchronization of Frequency-Hop Spread-Spectrum (FHSS) is presented. Synchronization performance is observed in the presence of channel dynamics and is characterized by mean synchronization time and mean time to loss of lock. A fixed-threshold multiple-dwell synchronization scheme is shown to adequately mitigate the effects of random hop jamming.

  17. The frequency spectrum of C sub n sup 2 from MST radar data

    NASA Technical Reports Server (NTRS)

    Nastrom, G. D.

    1986-01-01

    In a recent study (Nastrom et al., 1986), the variability of the refractivity turbulence structure constant, C sub n(2), was examined using observations from the stratosphere troposphere/mesosphere stratosphere troposphere (ST/MST) radar at Poker Flat, Alaska, and Platteville, Colorado. Variations of C2 with height, season, and weather conditions were examined. Also, the autocorrelation function and the frequency distribution of C sub n(2) were studied, and it was shown that C sub n(2), follows a log-normal frequency distribution. One of the more tentative results given in that paper is a first look at the spectrum of log C sub n(2), as a function of frequency at Poker Flat. This spectrum appears to obey a power law relation with frequency, P(F) approx. F(k), with k near -5/3 at periods between about 4 hours and 6 days, and with k near -1 at shorter periods. Power law behavior of a spectrum often helps us to infer the underlying dynamics which give rise to this spectrum, and it is thus of some concern to establish further confidence in the spectral shape. The purpose here is to address these questions.

  18. The width of the frequency spectrum of Pc1 geomagnetic pulsations in quiet and disturbed conditions

    NASA Astrophysics Data System (ADS)

    Feygin, F. Z.; Khabazin, Yu. G.; Kleimenova, N. G.; Malysheva, L. M.; Raita, T.

    2015-03-01

    The relation of the frequency spectrum width of Pc1 geomagnetic pulsations with magnetospheric parameters was theoretically studied. An analytical expression was obtained and numerical calculations were conducted. The formula for the increment (γ) was shown to include an important magnetospheric parameter, the ratio ( V A/ U ‖) of the Alfven velocity to the average velocity of energetic protons along the field line, which significantly affects the frequency spectrum width. The calculations show that the normalized width of the Pc1 frequency spectrum ( x 0 = ωout/Ω i = V A/ U ‖) decreases with decreasing ( V A/ U ‖). With increasing anisotropy of energetic protons A = T ⊥/ T ‖ - 1, the normalized width of Pc1 frequency spectrum is also decreased for a fixed value of the parameter ( V A/ U ‖). These conclusions have been confirmed by analysis of spectrograms conducted in 2005-2010 of ground-based observations of Pc1 on the Scandinavian network of induction magnetometers. Analysis of these data showed that Pc1 pulsations were observed in a narrow frequency band of around 0.2-0.4 Hz, with a central frequency of oscillations in the series f ˜ 0.5-0.7 Hz, in more than 90% of cases in magnetically quiet conditions ( Kp < 2). This corresponds to their generation beyond the plasmasphere. In more disturbed conditions ( Kp ˜ 2-3), the central frequency of Pc1 oscillations was almost twice greater (˜ 1.0-1.2 Hz) and the spectral width was ˜ 0.5-0.7 Hz, which makes it possible to suggest that they can be generated within the plasmasphere.

  19. Joint Scheduling and Spectrum Allocation in Wireless Networks with Frequency-Agile Radios

    NASA Astrophysics Data System (ADS)

    Uddin, Mohammad Faisal; Nurujjaman, Mohammad; Assi, Chadi

    We study the benefits of optimal spectrum allocation in a wireless network with frequency agile radios and we present a cross-layer problem formulation for the joint routing and link scheduling under non-uniform spectrum allocation. We present a primal-dual decomposition to provide an exact solution for this complex optimization problem. Given the difficulty associated with such design, we propose a heuristic approach based on simulated annealing to solve the dual sub-problem of the decomposed model. Numerical results revealed that up to 44% improvement in network performance is obtained when variable-width spectrum band allocation is used, as opposed to the best fixed-width spectrum band allocation for larger networks. Numerical results also confirm that the primal-dual decomposition method using simulated annealing to solve the dual sub-problem, substantially reduces the computation time and achieves near optimal solutions.

  20. Electrochemical impedance spectrum frequency optimization of bitter taste cell-based sensors.

    PubMed

    Hui, Guo-Hua; Ji, Peng; Mi, Shan-Shan; Deng, Shao-Ping

    2013-09-15

    Electrochemical impedance spectrum frequency optimization to bitter taste receptor cell-based sensors is discussed in this paper. The bitter taste receptor cells (the enteroendocrine STC-1 cells and the ICR mouse isolated taste bud cells) are cultured on carbon screen printed electrodes and used as sensing elements. The HEK-293 cells and dead isolated ICR mouse taste bud cells, without bitter taste receptor expression, are used in negative control experiments. The electrochemical impedance spectrum data is recorded and processed by bistable stochastic resonance for signal-to-noise ratio analysis. The bitter taste receptor cell-based sensor selectively responds to bitter tastants. The tastants species and concentrations can be decided by signal-to-noise ratio parameters. The signal-to-noise ratio eigen peak changes with the shift of electrochemical impedance spectrum frequencies. ICR mouse isolated taste bud cell-based sensor presents bitter tastants perception abilities. 9kHz is the optimal frequency for STC-1 cell-based sensor measurement. For isolated ICR mouse taste bud cells, 1.2kHz is the optimal frequency. Negative control experiments results indicate that cells with no taste receptor expression have no discriminating ability for tastant even if they are modulated by different frequencies. The taste cell-based sensor is of great practical value. PMID:23578970

  1. Frequency spectrum of tantalum at temperatures of 293-2300 K

    NASA Astrophysics Data System (ADS)

    Semenov, V. A.; Kozlov, Zh. A.; Krachun, L.; Mateescu, G.; Morozov, V. M.; Oprea, A. I.; Oprea, K.; Puchkov, A. V.

    2010-05-01

    The temperature dependence of the frequency spectrum of tantalum in the temperature range from room temperature to 2300 K has been studied for the first time using inelastic slow-neutron scattering. The inelastic slow-neutron scattering spectra have been measured at different temperatures on a DIN-2PI time-of-flight spectrometer installed at the IBR-2 nuclear reactor (Joint Institute for Nuclear Research, Dubna, Russia) with the use of a TS3000K high-temperature thermostat. From the measured spectra, the frequency spectra of the tantalum crystal lattice have been determined at temperatures of 293, 1584, and 2300 K by the iteration method. As the temperature increases, the frequency spectrum, on the whole, is softened and the specific features manifested themselves at room temperature are smoothed. The variations observed have been explained by the increase in the role of the effects of vibration anharmonism at high temperatures.

  2. Prospects and limitations for use of frequency spectrum from 40 to 300 GHz

    NASA Technical Reports Server (NTRS)

    Catoe, C. E.

    1979-01-01

    The existing and future use of the electromagnetic spectrum from 40 to 300 gigahertz is discussed. The activities envisioned for this segment of the electromagnetic spectrum fall generically into two basic categories: communications and remote sensing. The communications services considered for this region are focused on the existing and future frequency allocations that are required for terrestrial radio services, space to ground radio services, space to space radio services, and space to deep space radio services. The remote sensing services considered for this region are divided into two groups of activities: earth viewing and space viewing.

  3. 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

  4. 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)

  5. 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

  6. Inversion to estimate ocean wave directional spectrum from high-frequency radar

    NASA Astrophysics Data System (ADS)

    Hisaki, Yukiharu

    2015-04-01

    An high-frequency (HF) radar observes ocean surface currents and waves by radiating HF radio waves to the sea surface and analyzing the backscattered signals. Ocean wave spectrum is estimated from the first- and the second-order scattering of Doppler spectra by the inversion. The estimation of ocean surface currents is robust, because the surface currents can be derived from the peak Doppler frequency of the first-order scattering in the Doppler spectrum. The method to estimate ocean wave spectra is complicated and the second-order scattering in the Doppler spectrum is fragile, which is affected by the noise in the Doppler spectrum. A new method to estimate ocean wave spectra from HF radar is developed. This method is the extension of Hisaki (1996, 2005, 2006, 2009, 2014). The new method can be applied to both the single radar and dual radar array case, while the previous methods can be applied only the single radar case (Hisaki, 2005, 2006, 2009, 2014) or dual radar case (Hisaki, 1996). Ocean wave spectra are estimated in the regular grid cells, while wave spectra are estimated on the polar grids points with the origin of the radar position in the previous method for single radar case. The governing equations for wave estimation are the integral equations which relate the wave spectrum to the Doppler spectrum, and the energy balance equation under the assumption of stationarity. The regularization constraints in the horizontal space and the wave frequency-direction space are also used for the estimation. The unknowns, which are spectral values, surface wind speeds and directions, are estimated by seeking the minimum of the objective function, which is defined as the sum of weighted squares of the equations. The signal to noise ratio in the Doppler spectrum for wave estimation must be high. We selected the Doppler spectra using the SOM (Self organization map ) analysis method. The method will be demonstrated by comparing with in-situ observed data, in which only

  7. [Super-low-frequency spectrum analysis for buried faults in coalfield].

    PubMed

    Chen, Li; Qin, Qi-Ming; Zhen, Guang-Wei; Wang, Nan; Bai, Yan-Bing; Chen, Chao

    2013-08-01

    Based on the super-low-frequency (SLF) electromagnetic detection technology, the advanced detection for the buried fault in the coalfield is still at the exploratory stage, while the technology has a strong practical significance for production and design of the coal mine. Firstly, in this paper, the SLF electromagnetic detection signals were collected in study area. Spectrum analysis of SLF signal by wavelet transform can remove high-frequency noise. Secondly, the profile of the measuring line across the fault was analyzed and interpreted geologically. Accordingly SLF spectrum characteristics of the buried fault could be researched. Finally, combined with the geological and seismic data, the characteristics and distribution of fault structures can be verified in the mining area. The results show that: the buried fault could be detected quickly and effectively by SLF electromagnetic detection Hence, SLF electromagnetic detection technology is an effective method for buried fault detection. PMID:24159862

  8. Error correction coding for frequency-hopping multiple-access spread spectrum communication systems

    NASA Technical Reports Server (NTRS)

    Healy, T. J.

    1982-01-01

    A communication system which would effect channel coding for frequency-hopped multiple-access is described. It is shown that in theory coding can increase the spectrum utilization efficiency of a system with mutual interference to 100 percent. Various coding strategies are discussed and some initial comparisons are given. Some of the problems associated with implementing the type of system described here are discussed.

  9. The Low-frequency Radio Catalog of Flat-spectrum Sources

    NASA Astrophysics Data System (ADS)

    Massaro, F.; Giroletti, M.; D'Abrusco, R.; Masetti, N.; Paggi, A.; Cowperthwaite, Philip S.; Tosti, G.; Funk, S.

    2014-07-01

    A well known property of the γ-ray sources detected by Cos-B in the 1970s, by the Compton Gamma-Ray Observatory in the 1990s, and recently by the Fermi observations is the presence of radio counterparts, particularly for those associated with extragalactic objects. This observational evidence is the basis of the radio-γ-ray connection established for the class of active galactic nuclei known as blazars. In particular, the main spectral property of the radio counterparts associated with γ-ray blazars is that they show a flat spectrum in the GHz frequency range. Our recent analysis dedicated to search blazar-like candidates as potential counterparts for the unidentified γ-ray sources allowed us to extend the radio-γ-ray connection in the MHz regime. We also showed that blazars below 1 GHz maintain flat radio spectra. Thus, on the basis of these new results, we assembled a low-frequency radio catalog of flat-spectrum sources built by combining the radio observations of the Westerbork Northern Sky Survey and of the Westerbork in the southern hemisphere catalog with those of the NRAO Very Large Array Sky survey (NVSS). This could be used in the future to search for new, unknown blazar-like counterparts of γ-ray sources. First, we found NVSS counterparts of Westerbork Synthesis Radio Telescope radio sources, and then we selected flat-spectrum radio sources according to a new spectral criterion, specifically defined for radio observations performed below 1 GHz. We also described the main properties of the catalog listing 28,358 radio sources and their logN-logS distributions. Finally, a comparison with the Green Bank 6 cm radio source catalog was performed to investigate the spectral shape of the low-frequency flat-spectrum radio sources at higher frequencies.

  10. Frequency allocations for passive use of the radio spectrum to make scientific studies

    NASA Technical Reports Server (NTRS)

    Stull, M. A.; Alexander, G.

    1976-01-01

    The paper examines the legal implications of frequency allocations for passive use of the radio spectrum, which refer to receive-only radio services. Such receive-only services refer to the reception of radio signals generated by nonhuman agencies as in radio astronomy or in the search for extraterrestrial intelligence. Juridical interpretations of the public interest and of necessity are applied to these passive services.

  11. THE LOW-FREQUENCY RADIO CATALOG OF FLAT-SPECTRUM SOURCES

    SciTech Connect

    Massaro, F.; Giroletti, M.; D'Abrusco, R.; Paggi, A.; Cowperthwaite, Philip S.; Masetti, N.; Tosti, G.; Funk, S.

    2014-07-01

    A well known property of the γ-ray sources detected by Cos-B in the 1970s, by the Compton Gamma-Ray Observatory in the 1990s, and recently by the Fermi observations is the presence of radio counterparts, particularly for those associated with extragalactic objects. This observational evidence is the basis of the radio-γ-ray connection established for the class of active galactic nuclei known as blazars. In particular, the main spectral property of the radio counterparts associated with γ-ray blazars is that they show a flat spectrum in the GHz frequency range. Our recent analysis dedicated to search blazar-like candidates as potential counterparts for the unidentified γ-ray sources allowed us to extend the radio-γ-ray connection in the MHz regime. We also showed that blazars below 1 GHz maintain flat radio spectra. Thus, on the basis of these new results, we assembled a low-frequency radio catalog of flat-spectrum sources built by combining the radio observations of the Westerbork Northern Sky Survey and of the Westerbork in the southern hemisphere catalog with those of the NRAO Very Large Array Sky survey (NVSS). This could be used in the future to search for new, unknown blazar-like counterparts of γ-ray sources. First, we found NVSS counterparts of Westerbork Synthesis Radio Telescope radio sources, and then we selected flat-spectrum radio sources according to a new spectral criterion, specifically defined for radio observations performed below 1 GHz. We also described the main properties of the catalog listing 28,358 radio sources and their logN-logS distributions. Finally, a comparison with the Green Bank 6 cm radio source catalog was performed to investigate the spectral shape of the low-frequency flat-spectrum radio sources at higher frequencies.

  12. 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

  13. Frequency notching effects on GPR imagery while operating in crowded spectrum scenarios

    NASA Astrophysics Data System (ADS)

    Phelan, Brian R.; Ressler, Marc A.; Ranney, Kenneth I.; Smith, Gregory D.; Sherbondy, Kelly D.; Narayanan, Ram M.

    2016-05-01

    Over the past decade, the radio frequency (RF) spectrum in which radar, telecommunication, navigational, and other systems operate has become increasingly crowded. The Army Research Laboratory has developed a Stepped-Frequency Radar (SFR) which can avoid areas of the RF spectrum in which systems are already operating. This allows for mitigation of RF interference (RFI) on the radar, as well as reduction in the interference from the radar that might affect other systems. This paper addresses the impact of frequency notching on GPR imagery, and methods of mitigating negative effects. The SFR operates over 300-2000 MHz, with a minimum frequency step size of 1 MHz. The radar transmits and receives in pulsed intervals, allowing for receiver blanking of close-in targets. The SFR is vehicle mounted and utilizes two dualpolarized transmit (Tx) horn antennas on either side of the receiver (Rx) antenna aperture, which consists of 16 Vivaldi notch antennas (which can be rotated to either H or V polarization). The radar is capable of completing a sweep over its entire operating band in <250 μsec. Furthermore, the radar is capable of coherently averaging directly on the field programmable gate array (FPGA) in which it digitizes the Rx channels, albeit at the cost of increased data collection time.

  14. A measurement of the low frequency spectrum of the cosmic microwave background radiation

    SciTech Connect

    Levin, S.M.

    1987-04-01

    As part of a larger effort to measure the spectrum of the Cosmic Background Radiation (CBR) at low frequencies, the intensity of the CBR has been measured at a frequency of 1.410 GHz. The measurement was made by comparing the power received from the sky with the power received from a specially designed cooled calibration target with known properties. Sources of radiation other than the CBR were then identified and subtracted to calculate the antenna temperature of the CBR at 1.410 GHz. The instrument used to measure the CBR was a total-power microwave radiometer with a 25 MHz bandwidth centered at 1.410 GHz. The radiometer had a noise temperature of 80 K, and sufficient data were taken that radiometer noise did not contribute significantly to the total measurement error. The sources of error were predominantly systematic in nature, and the largest error was due to uncertainty in the reflection characteristics of the cold-load calibrator. Identification and subtraction of signals from the Galaxy (0.7 K) and the Earth's atmosphere (0.8 K) were also significant parts of the data reduction and error analysis. The brightness temperature of the Cosmic Background Radiation at 1.410 GHz is 222. +- 0.55 Kelvin. The spectrum of the CBR, as determined by this measurement and other published results, is consistent with a blackbody spectrum of temperature 2.741 +- 0.016. Constraints on the amount by which the CBR spectrum deviates from Planck spectrum are used to place limits on energy releases early in the history of the universe. 55 refs., 25 figs., 8 tabs.

  15. 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

  16. 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

  17. 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

  18. 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

  19. Performance evaluation of frequency-hopped spread spectrum multi-hop networks

    NASA Astrophysics Data System (ADS)

    Gluck, J. W.; Geraniotis, Evaggelos A.

    1988-11-01

    Primary and secondary multiple-access interference processes are characterized for multi-hop packet radio networks, in which users are assumed to be Poisson-distributed in the plane and to use frequency hopped spread-spectrum signaling with a receiver-oriented assignment of frequency-hopping patterns. The throughput per node and the average forward progress are then evaluated for frequency-hopped multi-hop networks that employ Random Forward Routing with fixed transmission radius (RFR) and most forward progress routing with fixed transmission radius (MFR). The optimal average number of neighbors and transmission radius are derived for these cases when Reed-Solomon forward-error-control coding with minimum distance decoding or binary convolutional coding with Viterbi decoding is employed.

  20. 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

  1. Statistical properties of the site-frequency spectrum associated with lambda-coalescents.

    PubMed

    Birkner, Matthias; Blath, Jochen; Eldon, Bjarki

    2013-11-01

    Statistical properties of the site-frequency spectrum associated with Λ-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent parameters introduced by certain Λ-coalescents for data sets too large for full-likelihood methods is our focus. The recursions for the expected values we obtain can be used to find the parameter values that give the best fit to the observed frequency spectrum. The expected values are also used to approximate the probability a (derived) mutation arises on a branch subtending a given number of leaves (DNA sequences), allowing us to apply a pseudolikelihood inference to estimate coalescence parameters associated with certain subclasses of Λ-coalescents. The properties of the pseudolikelihood approach are investigated on simulated as well as real mtDNA data sets for the high-fecundity Atlantic cod (Gadus morhua). Our results for two subclasses of Λ-coalescents show that one can distinguish these subclasses from the Kingman coalescent, as well as between the Λ-subclasses, even for a moderate (maybe a few hundred) sample size. PMID:24026094

  2. Visible-frequency metasurfaces for broadband anomalous reflection and high-efficiency spectrum splitting (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Li, Zhongyang; Palacios, Edgar; Bütün, Serkan; Aydin, Koray

    2015-09-01

    Metasurfaces offer new degrees of freedom in moulding the optical wavefronts by introducing abrupt and drastic changes in the amplitude, phase and/or polarization of electromagnetic radiation at the wavelength scale. By carefully arranging multiple subwavelength anisotropic or gradient optical resonators, metasurfaces have been shown to enable anomalous transmission, anomalous reflection, optical holograms and spin-orbit interaction. However, experimental realization of high-performance metasurfaces that can operate at visible frequency range has been a significant challenge due to high optical losses of plasmonic materials and difficulties in fabricating several subwavelength plasmonic resonators with high uniformity. Here, we propose a highly-efficient yet a simple metasurface design comprising of a single, anisotropic trapezoid-shape antenna in its unit cell. We demonstrate broadband (450 - 850 nm) anomalous reflection and spectrum splitting at visible and near-IR frequencies with 85% conversion efficiency. Average power ratio of anomalous reflection to the strongest diffraction mode was calculated to be on the order of 1000 and measured to be on the order of 10. The anomalous reflected photons have been visualized using a CCD camera, and broadband spectrum splitting performance has been confirmed experimentally using a free space, angle-resolved reflection measurement setup. Metasurface design proposed in this study is a clear departure from conventional metasurfaces utilizing multiple, anisotropic and/or gradient optical resonators, and could enable high-efficiency, broadband metasurfaces for achieving flat high SNR optical spectrometers, polarization beam splitters, directional emitters and spectrum splitting surfaces for photovoltaics.

  3. Broadband radio-frequency spectrum analysis in spectral-hole-burning media.

    PubMed

    Colice, Max; Schlottau, Friso; Wagner, Kelvin H

    2006-09-01

    We demonstrate a 20 GHz spectrum analyzer with 1 MHz resolution and >40 dB dynamic range using spectral-hole-burning (SHB) crystals, which are cryogenically cooled crystal hosts lightly doped with rare-earth ions. We modulate a rf signal onto an optical carrier using an electro-optic intensity modulator to produce a signal beam modulated with upper and lower rf sidebands. Illuminating SHB crystals with modulated beams excites only those ions resonant with corresponding modulation frequencies, leaving holes in the crystal's absorption profile that mimic the modulation power spectrum and persist for up to 10 ms. We determine the spectral hole locations by probing the crystal with a chirped laser and detecting the transmitted intensity. The transmitted intensity is a blurred-out copy of the power spectrum of the original illumination as mapped into a time-varying signal. Scaling the time series associated with the transmitted intensity by the instantaneous chirp rate yields the modulated beam's rf power spectrum. The homogeneous linewidth of the rare-earth ions, which can be <100 kHz at cryogenic temperatures, limits the fundamental spectral resolution, while the medium's inhomogeneous linewidth, which can be >20 GHz, determines the spectral bandwidth. PMID:16912776

  4. 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

  5. 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

  6. 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

  7. The complete frequency spectrum of physiological tremor can be recreated by broadband mechanical or electrical drive.

    PubMed

    Vernooij, Carlijn Andrea; Lakie, Martin; Reynolds, Raymond Francis

    2015-01-15

    Two frequency peaks of variable preponderance have been reported for human physiological finger tremor. The high-frequency peak (20-25 Hz, seen only in postural tremor) is generally attributed to mechanical resonance, whereas the lower frequency peak (8-12 Hz, seen in both postural and kinetic tremor) is usually attributed to synchronous central or reflexive neural drive. In this study, we determine whether mechanical resonance could generate both peaks. In relaxed subjects, an artificial finger tremor was evoked by random mechanical perturbations of the middle finger or random electrical muscular stimulation of the finger extensor muscle. The high and the low frequencies observed in physiological tremor could both be created by either type of artificial input at appropriate input intensity. Resonance, inferred from cross-spectral gain and phase, occurred at both frequencies. To determine any neural contribution, we compared truly passive subjects with those who exhibited some electromyographic (EMG) activity in the finger extensor; artificially created tremor spectra were almost identical between groups. We also applied electrical stimuli to two clinically deafferented subjects lacking stretch reflexes. They exhibited the same artificial tremor spectrum as control subjects. These results suggest that both typical physiological finger tremor frequencies can be reproduced by random artificial input; neither requires synchronized neural input. We therefore suggest that mechanical resonance could generate both dominant frequency peaks characteristic of physiological finger tremor. The inverse relationship between the input intensity and the resulting tremor frequency can be explained by a movement-dependent reduction in muscle stiffness, a conjecture we support using a simple computational model. PMID:25376782

  8. Spectrum of Finite Frequency Pump Kinetic Alfvén Wave in the Solar Wind

    NASA Astrophysics Data System (ADS)

    Modi, K. V.; Sharma, R. P.; Gaur, Nidhi

    2016-01-01

    The nonlinear interaction between the kinetic Alfvén wave (KAW) and the slow magnetosonic wave is studied. The dynamical equation for the slow magnetosonic wave, in the presence of a ponderomotive force due to finite frequency KAW (ω0<ω_{ci}, where ω0 is the frequency of the KAW and ω_{ci} is the ion gyro frequency) is developed and then numerically solved for the solar wind parameters around 1 AU. Three different propagation angles of the slow magnetosonic wave (θ = 70°, 75°, and 85°) are considered. Our results reveal that due to the nonlinear interplay between the waves, the nature of the formation of localised structures becomes complex and depends on the different propagation angles of the slow magnetosonic wave. The power spectrum of a KAW shows the Kolmogorov scaling in larger scales but exhibits steepening in smaller scales. The scaling index of the power spectrum of the KAW depends on the propagation angles of the slow magnetosonic wave. Therefore, the heating of plasma particles in the solar wind may show such dependence. The present results are consistent with the observation of the Cluster spacecraft for the solar wind around 1 AU.

  9. Microstructure Imaging Using Frequency Spectrum Spatially Resolved Acoustic Spectroscopy F-Sras

    NASA Astrophysics Data System (ADS)

    Sharples, S. D.; Li, W.; Clark, M.; Somekh, M. G.

    2010-02-01

    Material microstructure can have a profound effect on the mechanical properties of a component, such as strength and resistance to creep and fatigue. SRAS—spatially resolved acoustic spectroscopy—is a laser ultrasonic technique which can image microstructure using highly localized surface acoustic wave (SAW) velocity as a contrast mechanism, as this is sensitive to crystallographic orientation. The technique is noncontact, nondestructive, rapid, can be used on large components, and is highly tolerant of acoustic aberrations. Previously, the SRAS technique has been demonstrated using a fixed frequency excitation laser and a variable grating period (к-vector) to determine the most efficiently generated SAWs, and hence the velocity. Here, we demonstrate an implementation which uses a fixed grating period with a broadband laser excitation source. The velocity is determined by analyzing the measured frequency spectrum. Experimental results using this "frequency spectrum SRAS" (f-SRAS) method are presented. Images of microstructure on an industrially relevant material are compared to those obtained using the previous SRAS method ("k-SRAS"), excellent agreement is observed. Moreover, f-SRAS is much simpler and potentially much more rapid than k-SRAS as the velocity can be determined at each sample point in one single laser shot, rather than scanning the grating period.

  10. 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

  11. High resolution interrogation system for fiber Bragg grating (FBG) sensor application using radio frequency spectrum analyser

    NASA Astrophysics Data System (ADS)

    Muhammad, F. D.; Zulkifli, M. Z.; Harun, S. W.; Ahmad, H.

    2013-05-01

    In this paper, we propose a fiber Bragg grating (FBG) interrogation system for high resolution sensor application based on radio frequency (RF) generation technique by beating a single longitudinal mode (SLM) fiber ring laser with an external tunable laser source (TLS). The external TLS provides a constant wavelength (CW), functioning as the reference signal for the frequency beating technique. The TLS used has a constant output power and wavelength over time. The sensor signal is provided by the reflected wavelength of a typical fiber Bragg grating (FBG) in the SLM fiber ring laser, which consists of a 1 m long highly doped Erbium doped fiber as the gain medium. The key to ensure the SLM laser oscillation is the role of graphene as saturable absorber which is opposed to the commonly used unpumped erbiumdoped fiber and this consequently contributes to the simple and short cavity design of our proposed system. The signal from the SLM fiber ring laser, which is generated by the FBG in response to external changes, such as temperature, strain, air humidity and air movement, is heterodyned with the CW signal from the TLS at a 6 GHz photodetector using a 3-dB fused coupler to generate the frequency beating. This proposed system is experimentally demonstrated as a temperature sensor and the results shows that the frequency response of the system towards the changes in temperature is about 1.3 GHz/°C, taking into account the resolution bandwidth of 3 MHz of the radio frequency spectrum analyzer (RFSA).

  12. An adaptive approach to computing the spectrum and mean frequency of Doppler signals.

    PubMed

    Herment, A; Giovannelli, J F

    1995-01-01

    Modern ultrasound Doppler systems are facing the problem of processing increasingly shorter data sets. Spectral analysis of the strongly nonstationary Doppler signal needs to shorten the analysis window while maintaining a low variance and high resolution spectrum. Color flow imaging requires estimation of the Doppler mean frequency from even shorter Doppler data sets to obtain both a high frame rate and high spatial resolution. We reconsider these two estimation problems in light of adaptive methods. A regularized parametric method for spectral analysis as well as an adapted mean frequency estimator are developed. The choice of the adaptive criterion is then addressed and adaptive spectral and mean frequency estimators are developed to minimize the mean square error on estimation in the presence of noise. Two suboptimal spectral and mean-frequency estimators are then derived for real-time applications. Finally, their performance is compared to that of both the FFT based periodogram and the AR parametric spectral analysis for the spectral estimator, and, to both the correlation angle and the Kristoffersen's [8] estimators for the mean frequency estimator using Doppler data recorded in vitro. PMID:7638930

  13. Frequency spectrum and scale dependence of a propulsive self-excited vortex generator

    NASA Astrophysics Data System (ADS)

    Whittlesey, Robert; Dabiri, John

    2012-11-01

    We describe the development and characterization of a passive device that creates a train of vortex rings from a steady incoming flow. The device consists of a collapsible tube enclosed in an air-tight chamber which undergoes self-excited oscillations under specific conditions of flow rate and transmural pressure. An experimental parameter study was conducted in order to determine the oscillation frequency spectrum of the device, and its dependence on the nozzle diameter. For certain combinations of flow rate and transmural pressure, the frequency of self-excited oscillations, and hence vortex formation, is independent of device size over an order of magnitude range of device volume. These results have a particular interest for the development of vehicles utilizing vortex-enhanced propulsion (Ruiz et al., JFM, 2011). Continued work in this area has focused on the implementation of this device to a self-propelled submarine. Support is greatly appreciated from ONR Awards N000140810918 and N000141010137.

  14. Effect of motion frequency spectrum on subjective comfort response. [modeling passenger reactions to commercial aircraft flights

    NASA Technical Reports Server (NTRS)

    Jacobson, I. D.; Schoultz, M. B.; Blake, J. C.

    1973-01-01

    In order to model passenger reaction to present and future aircraft environments, it is necessary to obtain data in several ways. First, of course, is the gathering of environmental and passenger reaction data on commercial aircraft flights. In addition, detailed analyses of particular aspects of human reaction to the environment are best studied in a controllable experimental situation. Thus the use of simulators, both flight and ground based, is suggested. It is shown that there is a reasonably high probability that the low frequency end of the spectrum will not be necessary for simulation purposes. That is, the fidelity of any simulation which omits the very low frequency content will not yield results which differ significantly from the real environment. In addition, there does not appear to be significant differences between the responses obtained in the airborne simulator environment versus those obtained on commercial flights.

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

    NASA Astrophysics Data System (ADS)

    Liu, Paul C.

    1989-04-01

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

  16. 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

  17. Recombination and the frequency spectrum in Drosophila melanogaster and Drosophila simulans.

    PubMed

    Przeworski, M; Wall, J D; Andolfatto, P

    2001-03-01

    Most "tests of neutrality" assess whether particular data sets depart from the predictions of a standard neutral model with no recombination. For Drosophila, where nuclear polymorphism data routinely show evidence of genetic exchange, the assumption of no recombination is often unrealistic. In addition, while conservative, this assumption is made at the cost of a great loss in power. Perhaps as a result, tests of the frequency spectrum based on zero recombination suggest an adequate fit of Drosophila polymorphism data to the predictions of the standard neutral model. Here, we analyze the frequency spectrum of a large number of loci in Drosophila melanogaster and D. simulans using two summary statistics. We use an estimate of the population recombination rate based on a laboratory estimate of the rate of crossing over per physical length and an estimate of the species' effective population size. In contrast to previous studies, we find that roughly half of the loci depart from the predictions of the standard neutral model. The extent of the departure depends on the exact recombination rate, but the global pattern that emerges is robust. Interestingly, these departures from neutral expectations are not unidirectional. The large variance in outcomes may be due to a complex demographic history and inconsistent sampling, or to the pervasive action of natural selection. PMID:11230530

  18. Visible-frequency metasurfaces for broadband anomalous reflection and high-efficiency spectrum splitting.

    PubMed

    Li, Zhongyang; Palacios, Edgar; Butun, Serkan; Aydin, Koray

    2015-03-11

    Ultrathin metasurfaces have recently emerged as promising materials that have huge potential to enable novel, flat optical components, and surface-confined, miniature photonic devices. Metasurfaces offer new degrees of freedom in molding the optical wavefronts by introducing abrupt and drastic changes in the amplitude, phase, and/or polarization of electromagnetic radiation at the wavelength scale. By carefully arranging multiple subwavelength anisotropic or gradient optical resonators, metasurfaces have been shown to enable anomalous transmission, anomalous reflection, optical holograms, and spin-orbit interaction. However, experimental realization of high-performance metasurfaces that can operate at visible frequency range has been a significant challenge due to high optical losses of plasmonic materials and difficulties in fabricating several plasmonic resonators of subwavelength size with high uniformity. Here, we propose a highly efficient yet a simple metasurface design comprising of a single, anisotropic silver antenna in its unit cell. We demonstrate broadband (450-850 nm) anomalous reflection and spectrum splitting at visible and near-IR frequencies with high conversion efficiency. Average power ratio of anomalous reflection to the strongest diffraction mode was calculated to be on the order of 10(3) and measured to be on the order of 10. The anomalous reflected photons have been visualized using a charge-coupled device camera, and broadband spectrum splitting performance has been confirmed experimentally using a free space, angle-resolved reflection measurement setup. Metasurface design proposed in this study is a clear departure from conventional metasurfaces utilizing multiple, anisotropic and/or gradient optical resonators and could enable high-efficiency, broadband metasurfaces for achieving flat high signal-to-noise ratio optical spectrometers, polarization beam splitters, directional emitters, and spectrum splitting surfaces for photovoltaics. PMID

  19. Developmental Changes in the Fundamental Frequency (f0) of Infants' Cries: A Study of Children with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Esposito, Gianluca; Venuti, Paola

    2010-01-01

    Episodes of crying with higher fundamental frequency (f0) are perceived as more aversive and distressful than lower frequency cries. Besides, previous studies have speculated that in children with Autism Spectrum Disorder (ASD) higher f0 may account for evoking mental states of uneasiness in the caregiver. Moreover no evidence on developmental…

  20. 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

  1. Estimation of the turbulent boundary layer pressure wavenumber-frequency spectrum using a fixed probe pair

    NASA Technical Reports Server (NTRS)

    Mathur, Gopal P.; Cannon, Mark R.

    1990-01-01

    The turbulent boundary layer (TBL) pressure fluctuations represent a dominant source of aircraft interior noise during cruise. The wavenumber-frequency characteristics of the TBL pressure field become important when determining its coupling with the aircraft structure and the resulting sound radiation into the interior of the aircraft. A technique is presented to estimate the TBL pressure wavenumber-frequency spectrum using a fixed probe pair consisting of two microphones. Flight test data from the McDonnel Douglas Ultra High Bypass Demonstrator aircraft were used to estimate the TBL pressure wavenumber-frequency spectra. These data were compared with selected wall pressure prediction models based on the existing wind tunnel data. The estimated in-flight spectral levels for the Demonstrator aircraft were in good agreement with the TBL wall pressure prediction models in the medium wavenumber range. The estimated TBL wavenumber spectral levels were found to be on the higher side in the low wavenumber region when compared with the predicted levels.

  2. 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

  3. 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

  4. Jamming effects on code synchronization of burst-mode frequency-hop spread-spectrum

    NASA Astrophysics Data System (ADS)

    van Grouw, Mike G.; Wicker, Mark A.

    The authors characterize the performance of a multiple-dwell FHSS (frequency-hopping spread-spectrum) code synchronization scheme in the presence of channel dynamics. Random hop jamming is assumed. The coarse acquisition system uses both passive and active correlation to implement a serial search of the code-uncertainty region. The in-lock monitoring is accomplished using a two-dwell active correlator with a relatively long integration time. Both burst- and continuous-mode communications links are considered. Appropriate performance parameters are developed, and design considerations are discussed. Performance curves are given for the various cases considered. Although a fixed-threshold multiple-dwell synchronization scheme adequately mitigates the effects of dynamic jamming in a continuous-mode communications link, it is shown to be inadequate for a burst-mode communications link.

  5. Tunable ultranarrow spectrum selective absorption in a graphene monolayer at terahertz frequency

    NASA Astrophysics Data System (ADS)

    Wu, Jun

    2016-06-01

    Complete absorption in a graphene monolayer at terahertz frequency through the critical coupling effect is investigated. It is achieved by sandwiching the graphene monolayer between a dielectric grating and a Bragg grating. The designed graphene absorber exhibits near-unity absorption at resonance but with an ultranarrow spectrum and antenna-like response, which is attributed to the combined effects of guided mode resonance with dielectric grating and the photonic band gap with Bragg grating. In addition to numerical simulation, the electric field distributions are also illustrated to provide a physical understanding of the perfect absorption effect. Furthermore, the absorption performance can be tuned by only changing the Fermi level of graphene, which is beneficial for real application. It is believed that this study may be useful for designing next-generation graphene-based optoelectronic devices.

  6. Proposal Drafted for Allocating Space-to-Space Frequencies in the GPS Spectrum Bands

    NASA Technical Reports Server (NTRS)

    Spence, Rodney L.

    2000-01-01

    Radionavigation Satellite Service (RNSS) systems such as the U.S. Global Positioning System (GPS) and the Russian Global Navigation Satellite System (GLONASS) are primarily being used today in the space-to-Earth direction (i.e., from GPS satellite to Earth user) for a broad range of applications such as geological surveying; aircraft, automobile, and maritime navigation; hiking and mountain climbing; and precision farming and mining. However, these navigation systems are being used increasingly in space. Beginning with the launch of the TOPEX/Poseidon remote-sensing mission in 1992, over 90 GPS receivers have flown onboard spacecraft for such applications as real-time spacecraft navigation, three-axis attitude control, precise time synchronization, precision orbit determination, and atmospheric profiling. In addition to use onboard many science spacecraft, GPS has been used or is planned to be used onboard the shuttles, the International Space Station, the International Space Station Emergency Crew Return Vehicle, and many commercial satellite systems such as Orbcomm, Globalstar, and Teledesic. From a frequency spectrum standpoint, however, one important difference between the space and terrestrial uses of GPS is that it is being used in space with no interference protection. This is because there is no frequency allocation for the space-to-space use of GPS (i.e., from GPS satellite to user spacecraft) in the International Telecommunications Union (ITU) regulatory table of frequency allocations. If another space-based or groundbased radio system interferes with a spaceborne GPS user, the spaceborne user presently has no recourse other than to accept the interference. Consequently, for the past year and a half, the NASA Glenn Research Center at Lewis Field and other Government agencies have been working within ITU toward obtaining a GPS space-to-space allocation at the next World Radio Conference in the year 2000 (WRC 2000). Numerous interference studies have been

  7. Frequency and spectrum of Wolcott–Rallison syndrome in Saudi Arabia: a systematic review

    PubMed Central

    Habeb, Abdelhadi M.

    2013-01-01

    Background Wolcott–Rallison syndrome (WRS) is caused by recessive EIF2AK3 gene mutations and characterized by permanent neonatal diabetes (PNDM), skeletal dysplasia, and recurrent hepatitis. The frequency of this rare syndrome is largely unknown. Objectives To define the frequency and spectrum of WRS in the Kingdom of Saudi Arabia (KSA) based on published data. Methods The Medline database was searched for published articles on WRS. The number of reported cases from KSA was compared to the total number of WRS cases reported worldwide. The genotype and phenotype of WRS patients from KSA were reviewed. Results Ten articles describing 23 WRS patients from 12 Saudi families from 1995 to 2012 were identified. This figure accounts for 27.7% (23/83) of the patients and 22.2% (12/54) of the families with WRS reported worldwide until January 2013. All Saudi patients with WRS presented with PNDM, and they represent 59% of all PNDM cases from WRS. At reporting, 73% of patients experienced recurrent hepatitis, 56.5% had skeletal abnormalities, and 39.1% of them were dead. There was a variation in the phenotype even between affected siblings. Genetic diagnosis was confirmed in all 12 families with no correlation between the genotype and phenotype. Eight of the nine EIF2AK3 mutations were only reported in these families, and one was shared with a patient from Qatar, a neighboring Arab state. Conclusions No study on the frequency of WRS has been published. However, the available data indicate that KSA has the largest collection of patients with WRS worldwide, and nine of the identifiable EIF2AK3 mutations appear to be confined to Arabs. Establishing a national or international registry for WRS would provide more reliable data on this rare condition. PMID:23759358

  8. Low-frequency velocity correlation spectrum of fluid in a porous media by modulated gradient spin echo.

    PubMed

    Stepisnik, J; Callaghan, P T

    2001-01-01

    In addition to the fast correlation for local stochastic motion, the molecular velocity correlation function in a fluid enclosed within the pore boundaries features a slow long time-tail decay. Here we present its study by the NMR modulated gradient spin-echo method (MGSE) [1] on a system of water trapped in the space between the closely packed polystyrene beads. With MGSE pulse sequence, a repetitive train of RF pulses with interspersed gradient pulses periodically modulates the spin phase. It gives the spin echo attenuation proportional to a value of the molecular velocity correlation spectrum at the modulation frequency. Covering the frequency range between Hz and MHz, it is a complement to the quasi-elastic neutron scattering, and so a suitable technique for the investigation of low frequency molecular dynamics in fluids. In our experiment, it enables to extract the low frequency correlation spectrum of water molecules confined in porous media. The function exhibits a negative long time-tail characteristic (a low frequency decay of the spectrum), which can be interpreted as a molecular back scattering on boundaries. The results can be well fitted with the spectrum calculated from the solution of the Langevin equation for restricted diffusion (which exhibits an exponential decay) [2] as well as with the spectrum obtained when simulating the hydrodynamics of molecular motion constrained by capillary walls (which gives an algebraic decay) [3]. Despite much work on theories and simulation, which predict slow negative long time tail of molecular velocity correlation dynamics in confined fluids, the obtained velocity correlation spectrum is the first experimental evidence to confirm these effects. The obtained dependence of spin echo attenuation on time, gradient strength and modulation frequency is also the first experimental verification of the recently developed approach to the spin echo in porous media, that uses the spin phase average with the cumulant expansion

  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. Joint envelope and frequency order spectrum analysis based on iterative generalized demodulation for planetary gearbox fault diagnosis under nonstationary conditions

    NASA Astrophysics Data System (ADS)

    Feng, Zhipeng; Chen, Xiaowang; Liang, Ming

    2016-08-01

    Planetary gearbox vibration signals under nonstationary conditions are characterized by time-varying nature and complex multi-components, making it very difficult to extract features for fault diagnosis. Order spectrum analysis is one of the effective approaches for nonstationary signal analysis of rotating machinery. The main idea of order analysis is to map the time-varying frequency components into constant ones. Inspired by this idea, we propose a new order spectrum analysis method to exploit the unique property of iterative generalized demodulation in converting arbitrary instantaneous frequency trajectories of multi-component signals into constant frequency lines on the time-frequency plane. This new method is completely algorithm-based and tachometer/encoder-free, thus easy to implement. It does not involve equi-angular resampling commonly required by most order tracking methods and is hence free from the decimation and/or interpolation error. The proposed order analysis method can eliminate the time-variation effect of frequency and thus can effectively reveal the harmonic order constituents of nonstationary multi-component signals. However, the planetary gearbox vibration signals also lead to complex sideband orders. As such, we further propose to analyze the order spectrum of amplitude envelope. This will eliminate the complex sideband orders in the order spectrum of original signals, leading to a substantially simplified and more reliable gear characteristic frequency identification process. Nevertheless, the gear and/or planet carrier rotating frequency orders, which are irrelevant to gear fault, may still exist. To avoid possible misleading results due to such frequency orders, we also propose to analyze the order spectrum of instantaneous frequency. Theoretically, the peaks present in frequency order spectrum directly correspond to the gear characteristic frequency orders, which can be used to extract gear fault signature more explicitly. The proposed

  11. High-Resolution Time-Frequency Spectrum-Based Lung Function Test from a Smartphone Microphone.

    PubMed

    Thap, Tharoeun; Chung, Heewon; Jeong, Changwon; Hwang, Ki-Eun; Kim, Hak-Ryul; Yoon, Kwon-Ha; Lee, Jinseok

    2016-01-01

    In this paper, a smartphone-based lung function test, developed to estimate lung function parameters using a high-resolution time-frequency spectrum from a smartphone built-in microphone is presented. A method of estimation of the forced expiratory volume in 1 s divided by forced vital capacity (FEV₁/FVC) based on the variable frequency complex demodulation method (VFCDM) is first proposed. We evaluated our proposed method on 26 subjects, including 13 healthy subjects and 13 chronic obstructive pulmonary disease (COPD) patients, by comparing with the parameters clinically obtained from pulmonary function tests (PFTs). For the healthy subjects, we found that an absolute error (AE) and a root mean squared error (RMSE) of the FEV₁/FVC ratio were 4.49% ± 3.38% and 5.54%, respectively. For the COPD patients, we found that AE and RMSE from COPD patients were 10.30% ± 10.59% and 14.48%, respectively. For both groups, we compared the results using the continuous wavelet transform (CWT) and short-time Fourier transform (STFT), and found that VFCDM was superior to CWT and STFT. Further, to estimate other parameters, including forced vital capacity (FVC), forced expiratory volume in 1 s (FEV₁), and peak expiratory flow (PEF), regression analysis was conducted to establish a linear transformation. However, the parameters FVC, FEV1, and PEF had correlation factor r values of 0.323, 0.275, and -0.257, respectively, while FEV₁/FVC had an r value of 0.814. The results obtained suggest that only the FEV1/FVC ratio can be accurately estimated from a smartphone built-in microphone. The other parameters, including FVC, FEV1, and PEF, were subjective and dependent on the subject's familiarization with the test and performance of forced exhalation toward the microphone. PMID:27548164

  12. 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

  13. Two-photon spectrum of 87Rb using optical frequency comb

    NASA Astrophysics Data System (ADS)

    Wang, Li-Rong; Zhang, Yi-Chi; Xiang, Shao-Shan; Cao, Shu-Kai; Xiao, Lian-Tuan; Jia, Suo-Tang

    2015-06-01

    The high precision two-photon excitation measurements for 5S1/2 (Fg = 2) to 5D5/2 (Fe = 4 to 1) of 87Rb are performed by using an optical frequency comb. The two counter-propagating femtosecond pulses (5S1/2 → 5P3/2 at 780 nm, and 5P3/2 → 5D5/2 at 776 nm) act on 87Rb vapor, and the Doppler broadened background signal is effectively eliminated. The temperature and power dependences of the two-photon spectrum are studied in this paper. Project supported by the National Basic Research Program of China (Grant No. 2012CB921603), the Program for Changjiang Scholars and Innovative Research Team in University (Grant No. IRT13076), the National Natural Science Foundation of China (Grant Nos. 61378049 and 10934004), the International Science and Technology Cooperation Program of China (Grant No. 2011DFA12490), and the Natural Science Foundation of Shanxi Province, China (Grant No. 2011011004).

  14. Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents?

    PubMed Central

    Eldon, Bjarki; Birkner, Matthias; Blath, Jochen; Freund, Fabian

    2015-01-01

    The ability of the site-frequency spectrum (SFS) to reflect the particularities of gene genealogies exhibiting multiple mergers of ancestral lines as opposed to those obtained in the presence of population growth is our focus. An excess of singletons is a well-known characteristic of both population growth and multiple mergers. Other aspects of the SFS, in particular, the weight of the right tail, are, however, affected in specific ways by the two model classes. Using an approximate likelihood method and minimum-distance statistics, our estimates of statistical power indicate that exponential and algebraic growth can indeed be distinguished from multiple-merger coalescents, even for moderate sample sizes, if the number of segregating sites is high enough. A normalized version of the SFS (nSFS) is also used as a summary statistic in an approximate Bayesian computation (ABC) approach. The results give further positive evidence as to the general eligibility of the SFS to distinguish between the different histories. PMID:25575536

  15. Frequency and Clinical Correlates of Sleep-Related Problems Among Anxious Youth with Autism Spectrum Disorders.

    PubMed

    Nadeau, Joshua M; Arnold, Elysse B; Keene, Amanda C; Collier, Amanda B; Lewin, Adam B; Murphy, Tanya K; Storch, Eric A

    2015-08-01

    Sleep-related problems (SRPs) are common and problematic among anxious youth but have not been investigated in anxious youth with autism spectrum disorder (ASD). Participants were 102 youth (ages 7-16 years) with ASD and comorbid anxiety. Youth and their primary caregiver were administered the Pediatric Anxiety Rating Scale. Parents completed the Multidimensional Anxiety Scale for Children-Parent (MASC-P) Report, Social Responsiveness Scale, and the Child Behavior Checklist (CBCL). A measure of SRPs was created from items from the CBCL and MASC-P. Results suggest SRPs were relatively common among youth with ASD and comorbid anxiety. The number of SRPs endorsed directly associated with parent ratings of social deficits, internalizing and externalizing symptoms, and anxiety symptoms, as well as with clinician-rated anxiety symptoms. Parent-rated internalizing symptoms predicted frequency of SRPs over and above social deficits, externalizing symptoms, and parent- and clinician-rated anxiety symptoms. A subset of 40 participants who completed family-based cognitive-behavioral therapy (CBT) experienced reduced SRPs following treatment. Implications, study limitations, and recommendations for future research are discussed. PMID:25239284

  16. Optical frequency comb generation with a flat-top spectrum from a mode-locked Yb fiber laser

    NASA Astrophysics Data System (ADS)

    Jang, Gwang Hoon; Yoon, Tai Hyun

    2012-02-01

    We present an ultrabroadband supercontinuum (SC) frequency comb generation covering the optical spectrum more than 1.2 octave from 570 nm to 1350 nm with a near flat-top power spectrum by using a mode-locked Yb fiber laser at 1030 nm as a master oscillator (MO). The repetition rate of the MO that has a spectral-width of 28 nm is 152 MHz and is phase-locked to a reference frequency synthesizer. A power amplifier is used to boost up the output power up to 1.3 W and the positively chirped amplified pulses are compressed by using a transmission grating pair. We used a commercially-available 10-cm long photonic crystal fiber that has two zero-dispersion wavelengths at 800 nm and 1093 nm, respectively, to generate an ultrabroadband SC frequency comb. Optical spectrum depending on the frequency chirp and pulse-width of the amplified pulses are analyzed to find an optimum coupling power as well as an optimum chirp parameter. We found that a dimensionless chirp parameter of 8.6 and a pulse-width of 517 fs for a chirped Gaussian pulse resulted in the optimum spectrum width of 1.2 octave.

  17. Probability-Based Pattern Recognition and Statistical Framework for Randomization: Modeling Tandem Mass Spectrum/Peptide Sequence False Match Frequencies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Estimating and controlling the frequency of false matches between a peptide tandem mass spectrum and candidate peptide sequences is an issue pervading proteomics research. To solve this problem, we designed an unsupervised pattern recognition algorithm for detecting patterns with various lengths fr...

  18. Time variation in the low-frequency spectrum of Vela-like pulsar B1800-21

    NASA Astrophysics Data System (ADS)

    Basu, Rahul; Rożko, Karolina; Lewandowski, Wojciech; Kijak, Jarosław; Dembska, Marta

    2016-05-01

    We report the flux measurement of the Vela-like pulsar B1800-21 at the low radio frequency regime over multiple epochs spanning several years. The spectrum shows a turnover around the GHz frequency range and represents a typical example of gigahertz-peaked spectrum (GPS) pulsar. Our observations revealed that the pulsar spectrum show a significant evolution during the observing period with the low-frequency part of the spectrum becoming steeper, with a higher turnover frequency, for a period of several years before reverting back to the initial shape during the latest measurements. The spectral change over times spanning several years requires dense structures, with free electron densities around 1000-20 000 cm-3 and physical dimensions ˜220 au, in the interstellar medium (ISM) traversing across the pulsar line of sight. We look into the possible sites of such structures in the ISM and likely mechanisms particularly the thermal free-free absorption as possible explanations for the change.

  19. Frequency-domain method for measuring spectral properties in multiple-scattering media: methemoglobin absorption spectrum in a tissuelike phantom

    NASA Astrophysics Data System (ADS)

    Fishkin, Joshua B.; So, Peter T. C.; Cerussi, Albert E.; Gratton, Enrico; Fantini, Sergio; Franceschini, Maria Angela

    1995-03-01

    We have measured the optical absorption and scattering coefficient spectra of a multiple-scattering medium (i.e., a biological tissue-simulating phantom comprising a lipid colloid) containing methemoglobin by using frequency-domain techniques. The methemoglobin absorption spectrum determined in the multiple-scattering medium is in excellent agreement with a corrected methemoglobin absorption spectrum obtained from a steady-state spectrophotometer measurement of the optical density of a minimally scattering medium. The determination of the corrected methemoglobin absorption spectrum takes into account the scattering from impurities in the methemoglobin solution containing no lipid colloid. Frequency-domain techniques allow for the separation of the absorbing from the scattering properties of multiple-scattering media, and these techniques thus provide an absolute

  20. High-frequency excess in the radio continuum spectrum of the type-1 Seyfert galaxy NGC 985

    NASA Astrophysics Data System (ADS)

    Doi, Akihiro; Inoue, Yoshiyuki

    2016-08-01

    The Seyfert galaxy NGC 985 is known to show a high-frequency excess in its radio continuum spectrum at a milli-Jansky level on the basis of previous observations at 1.4-15 GHz; a steep spectrum at low frequencies (a spectral index, α = -1.10 ± 0.03) changes at ˜10 GHz into an inverted spectrum at higher frequencies (α = +0.86 ± 0.09). We conduct new observations at 15-43 GHz using the Very Large Array and at 100 GHz using the Nobeyama Millimeter Array. As a result, the high-frequency excess has been confirmed as continuing at even higher radio frequencies, up to 43 GHz. The non-detection at 100 GHz was not so strong a constraint, and therefore the spectral behavior above 43 GHz remains unclear. The astrometric position of the high-frequency excess component coincides with the optical position of the Seyfert nucleus and the low-frequency radio position to an accuracy of 0{^''.}1, corresponding to ˜80 pc; the radio source size is constrained to be <0{^''.}02, corresponding to <16 pc. We discuss the physical origin of the observed high-frequency excess component. Dust emission at the Rayleigh-Jeans regime, free-free emission from X-ray radiating high-temperature plasma, free-free emission from the ensemble of broad-line region clouds, or thermal synchrotron from hot accretion flow cannot be responsible for the observed radio flux. Compact jets under synchrotron self-absorption may be unlikely in terms of observed time scales. Alternatively, we cannot rule out the hypotheses of synchrotron jets free-free absorbed by a circumnuclear photo-ionized region, and self-absorbed nonthermal synchrotron from disk corona, as the origin of the high-frequency excess component.

  1. High-frequency excess in the radio continuum spectrum of the type-1 Seyfert galaxy NGC 985

    NASA Astrophysics Data System (ADS)

    Doi, Akihiro; Inoue, Yoshiyuki

    2016-06-01

    The Seyfert galaxy NGC 985 is known to show a high-frequency excess in its radio continuum spectrum at a milli-Jansky level on the basis of previous observations at 1.4-15 GHz; a steep spectrum at low frequencies (a spectral index, α = -1.10 ± 0.03) changes at ˜10 GHz into an inverted spectrum at higher frequencies (α = +0.86 ± 0.09). We conduct new observations at 15-43 GHz using the Very Large Array and at 100 GHz using the Nobeyama Millimeter Array. As a result, the high-frequency excess has been confirmed as continuing at even higher radio frequencies, up to 43 GHz. The non-detection at 100 GHz was not so strong a constraint, and therefore the spectral behavior above 43 GHz remains unclear. The astrometric position of the high-frequency excess component coincides with the optical position of the Seyfert nucleus and the low-frequency radio position to an accuracy of 0{^''.}1, corresponding to ˜80 pc; the radio source size is constrained to be <0{^''.}02, corresponding to <16 pc. We discuss the physical origin of the observed high-frequency excess component. Dust emission at the Rayleigh-Jeans regime, free-free emission from X-ray radiating high-temperature plasma, free-free emission from the ensemble of broad-line region clouds, or thermal synchrotron from hot accretion flow cannot be responsible for the observed radio flux. Compact jets under synchrotron self-absorption may be unlikely in terms of observed time scales. Alternatively, we cannot rule out the hypotheses of synchrotron jets free-free absorbed by a circumnuclear photo-ionized region, and self-absorbed nonthermal synchrotron from disk corona, as the origin of the high-frequency excess component.

  2. What can be found in scalp EEG spectrum beyond common frequency bands. EEG–fMRI study

    NASA Astrophysics Data System (ADS)

    Marecek, R.; Lamos, M.; Mikl, M.; Barton, M.; Fajkus, J.; I, Rektor; Brazdil, M.

    2016-08-01

    Objective. The scalp EEG spectrum is a frequently used marker of neural activity. Commonly, the preprocessing of EEG utilizes constraints, e.g. dealing with a predefined subset of electrodes or a predefined frequency band of interest. Such treatment of the EEG spectrum neglects the fact that particular neural processes may be reflected in several frequency bands and/or several electrodes concurrently, and can overlook the complexity of the structure of the EEG spectrum. Approach. We showed that the EEG spectrum structure can be described by parallel factor analysis (PARAFAC), a method which blindly uncovers the spatial–temporal–spectral patterns of EEG. We used an algorithm based on variational Bayesian statistics to reveal nine patterns from the EEG of 38 healthy subjects, acquired during a semantic decision task. The patterns reflected neural activity synchronized across theta, alpha, beta and gamma bands and spread over many electrodes, as well as various EEG artifacts. Main results. Specifically, one of the patterns showed significant correlation with the stimuli timing. The correlation was higher when compared to commonly used models of neural activity (power fluctuations in distinct frequency band averaged across a subset of electrodes) and we found significantly correlated hemodynamic fluctuations in simultaneously acquired fMRI data in regions known to be involved in speech processing. Further, we show that the pattern also occurs in EEG data which were acquired outside the MR machine. Two other patterns reflected brain rhythms linked to the attentional and basal ganglia large scale networks. The other patterns were related to various EEG artifacts. Significance. These results show that PARAFAC blindly identifies neural activity in the EEG spectrum and that it naturally handles the correlations among frequency bands and electrodes. We conclude that PARAFAC seems to be a powerful tool for analysis of the EEG spectrum and might bring novel insight to the

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

    PubMed Central

    2011-01-01

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

  4. MATERNAL ALCOHOL CONSUMPTION PRODUCING FETAL ALCOHOL SPECTRUM DISORDERS (FASD): QUANTITY, FREQUENCY, AND TIMING OF DRINKING

    PubMed Central

    May, Philip A.; Blankenship, Jason; Marais, Anna-Susan; Gossage, J. Phillip; Kalberg, Wendy O.; Joubert, Belinda; Cloete, Marise; Barnard, Ronel; De Vries, Marlene; Hasken, Julie; Robinson, Luther K.; Adnams, Colleen M.; Buckley, David; Manning, Melanie; Parry, Charles; Hoyme, H. Eugene; Tabachnick, Barbara; Seedat, Soraya

    2013-01-01

    Background Concise, accurate measures of maternal prenatal alcohol use are needed to better understand fetal alcohol spectrum disorders (FASD). Methods Measures of drinking by mothers of children with specific FASD diagnoses and mothers of randomly-selected controls are compared and also correlated with physical and cognitive/behavioral outcomes. Results Measures of maternal alcohol use can differentiate maternal drinking associated with FASD from that of controls and some from mothers of alcohol-exposed normals. Six variables that combine quantity and frequency concepts distinguish mothers of FASD children from normal controls. Alcohol use variables, when applied to each trimester and three months prior to pregnancy, provide insight on critical timing of exposure as well. Measures of drinking, especially bingeing, correlate significantly with increased child dysmorphology and negative cognitive/behavioral outcomes in children, especially low non-verbal IQ, poor attention, and behavioral problems. Logistic regression links (p<.001) first trimester drinking (vs. no drinking) with FASD, elevating FASD likelihood 12 times; first and second trimester drinking increases FASD outcomes 61 times; and drinking in all trimesters 65 times. Conversely, a similar regression (p=.008) indicates that drinking only in the first trimester makes the birth of a child with an FASD 5 times less likely than drinking in all trimesters. Conclusions There is significant variation in alcohol consumption both within and between diagnostic groupings of mothers bearing children diagnosed within the FASD continuum. Drinking measures are empirically identified and correlated with specific child outcomes. Alcohol use, especially heavy use, should be avoided throughout pregnancy. PMID:23932841

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. Spectrum and frequency of GJB2, GJB6 and SLC26A4 gene mutations among nonsyndromic hearing loss patients in eastern part of India.

    PubMed

    Adhikary, Bidisha; Ghosh, Sudakshina; Paul, Silpita; Bankura, Biswabandhu; Pattanayak, Arup Kumar; Biswas, Subhradev; Maity, Biswanath; Das, Madhusudan

    2015-12-01

    Genetically caused nonsyndromic hearing loss is highly heterogeneous. Inspite of this large heterogeneity, mutations in the genes GJB2, GJB6 and SLC26A4 are major contributors. The mutation spectrum of these genes varies among different ethnic groups. Only a handful of studies focused on the altered genetic signature of these genes in different demographic regions of India but never focused on the eastern part of the country. Our study for the first time aimed to characterize the mutation profile of these genes in hearing loss patients of West Bengal state, India. Mutations in GJB2, GJB6 and SLC26A4 genes were screened by bidirectional sequencing from 215 congenital nonsyndromic hearing loss patients. Radiological diagnosis was performed in patients with SLC26A4 mutations by temporal bone CT scan. The study revealed that 4.65% and 6.97% patients had monoallelic and biallelic GJB2 mutations respectively. Six mutations were identified, p.W24X being the most frequent one accounting for 71.05% of the mutated alleles. Mutations in GJB6 including the previously identified deletion mutation (GJB6-D13S1830) were not identified in our study. Further, no patients harbored biallelic mutations in the SLC26A4 gene or the common inner ear malformation Enlarged Vestibular Aqueduct (EVA). The mutation profile of GJB2 in our study is distinct from other parts of India, suggesting that the mutation spectrum of this gene varies with ethnicity and geographical origin. The absence of GJB6 mutations and low frequency of SLC26A4 mutations suggest that additional genetic factors may also contribute to this disease. PMID:26188157

  7. Spectrum and Frequency of the GJB2 Gene Pathogenic Variants in a Large Cohort of Patients with Hearing Impairment Living in a Subarctic Region of Russia (the Sakha Republic)

    PubMed Central

    Posukh, Olga L.; Teryutin, Fedor M.; Solovyev, Aisen V.; Klarov, Leonid A.; Romanov, Georgii P.; Gotovtsev, Nyurgun N.; Kozhevnikov, Andrey A.; Kirillina, Elena V.; Sidorova, Oksana G.; Vasilyevа, Lena M.; Fedotova, Elvira E.; Morozov, Igor V.; Bondar, Alexander A.; Solovyevа, Natalya A.; Kononova, Sardana K.; Rafailov, Adyum M.; Sazonov, Nikolay N.; Alekseev, Anatoliy N.; Tomsky, Mikhail I.; Dzhemileva, Lilya U.; Khusnutdinova, Elza K.; Fedorova, Sardana A.

    2016-01-01

    Pathogenic variants in the GJB2 gene, encoding connexin 26, are known to be a major cause of hearing impairment (HI). More than 300 allelic variants have been identified in the GJB2 gene. Spectrum and allelic frequencies of the GJB2 gene vary significantly among different ethnic groups worldwide. Until now, the spectrum and frequency of the pathogenic variants in exon 1, exon 2 and the flanking intronic regions of the GJB2 gene have not been described thoroughly in the Sakha Republic (Yakutia), which is located in a subarctic region in Russia. The complete sequencing of the non-coding and coding regions of the GJB2 gene was performed in 393 patients with HI (Yakuts—296, Russians—51, mixed and other ethnicities—46) and in 187 normal hearing individuals of Yakut (n = 107) and Russian (n = 80) populations. In the total sample (n = 580), we revealed 12 allelic variants of the GJB2 gene, 8 of which were recessive pathogenic variants. Ten genotypes with biallelic recessive pathogenic variants in the GJB2 gene (in a homozygous or a compound heterozygous state) were found in 192 out of 393 patients (48.85%). We found that the most frequent GJB2 pathogenic variant in the Yakut patients was c.-23+1G>A (51.82%) and that the second most frequent was c.109G>A (2.37%), followed by c.35delG (1.64%). Pathogenic variants с.35delG (22.34%), c.-23+1G>A (5.31%), and c.313_326del14 (2.12%) were found to be the most frequent among the Russian patients. The carrier frequencies of the c.-23+1G>A and с.109G>A pathogenic variants in the Yakut control group were 10.20% and 2.80%, respectively. The carrier frequencies of с.35delG and c.101T>C were identical (2.5%) in the Russian control group. We found that the contribution of the GJB2 gene pathogenic variants in HI in the population of the Sakha Republic (48.85%) was the highest among all of the previously studied regions of Asia. We suggest that extensive accumulation of the c.-23+1G>A pathogenic variant in the indigenous Yakut

  8. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. Investigation of the Moessbauer Spectrum Quality as a Dependence on the Frequency of the Velocity Signal

    SciTech Connect

    Pechousek, J.

    2010-07-13

    This paper is focused on a quality characterizing the Moessbauer spectra measured for various frequencies of the velocity signal. Standard electromechanical double-loudspeaker drive and digital PID velocity controller were used for calibration spectra measurement in the frequency interval from 4 up to 100 Hz. Several parameters were evaluated for recommendation of the suitable velocity signal frequency.

  11. Spectra of the HB 21 supernova remnant: Evidence of spectrum flattening at the low frequencies

    NASA Astrophysics Data System (ADS)

    Borka, D.; Borka Jovanovic, V.; Uroševic, D.

    2012-04-01

    We use observations of the continuum radio emission at 1420, 820, 408, 34.5 and 22 MHz to estimate the mean brightness temperatures of the HB 21 supernova remnant (SNR) at five frequencies. We also present mean spectral index of HB1. The spectra of HB 21 are estimated from mean temperatures versus frequency plots for 1420, 820, 408, 34.5 and 22 MHz. We also present T-T plots of three frequency pairs: between 1420-34.5, 1420-22, 34.5-22 MHz. We notice flatter spectral indices at frequencies below 408 MHz. Probably this is due to the absorption by thermal plasma at low frequencies.

  12. Sharpening coarse-to-fine stereo vision by perceptual learning: asymmetric transfer across the spatial frequency spectrum.

    PubMed

    Li, Roger W; Tran, Truyet T; Craven, Ashley P; Leung, Tsz-Wing; Chat, Sandy W; Levi, Dennis M

    2016-01-01

    Neurons in the early visual cortex are finely tuned to different low-level visual features, forming a multi-channel system analysing the visual image formed on the retina in a parallel manner. However, little is known about the potential 'cross-talk' among these channels. Here, we systematically investigated whether stereoacuity, over a large range of target spatial frequencies, can be enhanced by perceptual learning. Using narrow-band visual stimuli, we found that practice with coarse (low spatial frequency) targets substantially improves performance, and that the improvement spreads from coarse to fine (high spatial frequency) three-dimensional perception, generalizing broadly across untrained spatial frequencies and orientations. Notably, we observed an asymmetric transfer of learning across the spatial frequency spectrum. The bandwidth of transfer was broader when training was at a high spatial frequency than at a low spatial frequency. Stereoacuity training is most beneficial when trained with fine targets. This broad transfer of stereoacuity learning contrasts with the highly specific learning reported for other basic visual functions. We also revealed strategies to boost learning outcomes 'beyond-the-plateau'. Our investigations contribute to understanding the functional properties of the network subserving stereovision. The ability to generalize may provide a key principle for restoring impaired binocular vision in clinical situations. PMID:26909178

  13. Sharpening coarse-to-fine stereo vision by perceptual learning: asymmetric transfer across the spatial frequency spectrum

    PubMed Central

    Tran, Truyet T.; Craven, Ashley P.; Leung, Tsz-Wing; Chat, Sandy W.; Levi, Dennis M.

    2016-01-01

    Neurons in the early visual cortex are finely tuned to different low-level visual features, forming a multi-channel system analysing the visual image formed on the retina in a parallel manner. However, little is known about the potential ‘cross-talk’ among these channels. Here, we systematically investigated whether stereoacuity, over a large range of target spatial frequencies, can be enhanced by perceptual learning. Using narrow-band visual stimuli, we found that practice with coarse (low spatial frequency) targets substantially improves performance, and that the improvement spreads from coarse to fine (high spatial frequency) three-dimensional perception, generalizing broadly across untrained spatial frequencies and orientations. Notably, we observed an asymmetric transfer of learning across the spatial frequency spectrum. The bandwidth of transfer was broader when training was at a high spatial frequency than at a low spatial frequency. Stereoacuity training is most beneficial when trained with fine targets. This broad transfer of stereoacuity learning contrasts with the highly specific learning reported for other basic visual functions. We also revealed strategies to boost learning outcomes ‘beyond-the-plateau’. Our investigations contribute to understanding the functional properties of the network subserving stereovision. The ability to generalize may provide a key principle for restoring impaired binocular vision in clinical situations. PMID:26909178

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

    PubMed Central

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

    2013-01-01

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

  15. Application of ground vibration frequency spectrum analysis as a tool for optimizing the blast design in large open pit mines

    SciTech Connect

    Rao, K.R.

    1994-12-31

    This paper explains the methodology for assessing the efficiency of rockmass fragmentation by explosive blasting, from ground vibration frequency spectrum analysis of the blast event. Explosives are used in the mining, quarrying and construction industries for fragmenting rockmass to a suitable size. When an explosive charge is detonated, in addition to fragmenting the rockmass, it will also generate ground vibration and air vibrations. Efficiency of a blast depend upon percentage of blast energy wasted in generating ground vibrations and air vibrations. This in turn will depend upon rockmass characteristics, amount of explosive energy used per delay and spatial distribution of explosive in the rockmass. Ground vibrations and air vibrations, arising out of explosive detonation in a rockmass, could be captured by micro-computer based engineering seismograph and sound level meter. Typical frequency range indicative of efficient rockmass fragmentation for a particular rockmass can be identified from ground vibration frequency spectra analysis of the blast event on a personal computer applying Fast Fourier transforms (FFT). The typical frequency range indicative of efficient rockmass fragmentation depends upon rockmass impedance and can be estimated from rockmass characteristics and monitoring few trial blasts. Blast event efficiency is estimated by comparing the typical frequency range with the dominant frequency range of the blast event record. A large number of blast events monitored and analyzed by the author in different rockmass formations and correlation of the results with observations made while fragmented material is lifted and loaded into trucks indicated that ground vibration frequency spectrum analysis could be used as a reliable and cost effective tool for assessing the blasting efficiency and optimizing blast design in large open-pit mines.

  16. 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

  17. 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

  18. On the frequency and amplitude spectrum and the fluctuations at the output of a communication receiver.

    PubMed

    Planat, M; Eckert, C

    2000-01-01

    A mixer cascaded with a low-pass filter is the basic piece of any communication receiver. The frequency and amplitude fluctuations of beat signals recorded at the output of the mixer plus filter set-up are investigated experimentally and explained on the basis of number theory in relation to the Riemann problem concerning the distribution of prime numbers. The frequency of the beat signal is obtained from a diophantine approximation of the frequency ratio of the input oscillators. The amplitude is defined globally from the position of resolved fractions with respect to an equally spaced graduation. Time series analysis methods show that frequency fluctuations present a transition from white frequency noise to 1/f frequency noise close to resonance; the latter is compatible with an underlying fractal attractor. The same transition is observed in the case of time series computed from continued fraction expansions. PMID:18238658

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

    NASA Astrophysics Data System (ADS)

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

    2002-09-01

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

  20. Spectrum of hot water in the 2000-4750 cm -1 frequency range

    NASA Astrophysics Data System (ADS)

    Zobov, Nikolai F.; Shirin, Sergei V.; Polyansky, Oleg L.; Barber, Robert J.; Tennyson, Jonathan; Coheur, Pierre-François; Bernath, Peter F.; Carleer, Michel; Colin, Reginald

    2006-05-01

    An emission spectrum recorded in an oxyacetylene torch [P.-F. Coheur, P.F. Bernath, M. Carleer, R. Colin, O.L. Polyansky, N.F. Zobov, S.V. Shirin, R.J. Barber, J. Tennyson, J. Chem. Phys. 122 (2005) 074307] is analyzed for the region covering stretching fundamentals and associated hot bands of water. Many lines could be assigned on the basis of previously determined energy levels. New assignments made with a new variational linelist allow a further 800 energy levels covering 15 vibrational states and rotations up to J = 32 to be assigned. A simultaneous re-analysis of previously reported sunspot absorption spectra leads to the assignment of 581 further lines in the L-band spectrum and 67 in the N-band spectrum.

  1. Time-frequency analysis of transient evoked-otoacoustic emissions in individuals with auditory neuropathy spectrum disorder.

    PubMed

    Narne, Vijaya Kumar; Prabhu, P Prashanth; Chatni, Suma

    2014-07-01

    The aim of the study was to describe and quantify the cochlear active mechanisms in individuals with Auditory Neuropathy Spectrum Disorders (ANSD). Transient Evoked Otoacoustic Emissions (TEOAEs) were recorded in 15 individuals with ANSD and 22 individuals with normal hearing. TEOAEs were analyzed by Wavelet transform method to describe and quantify the characteristics of TEOAEs in narrow-band frequency regions. It was noted that the amplitude of TEOAEs was higher and latency slightly shorter in individuals with ANSD compared to normal hearing individuals at low and mid frequencies. The increased amplitude and reduced latencies of TEOAEs in ANSD group could be attributed to the efferent system damage, especially at low and mid frequencies seen in individuals with ANSD. Thus, wavelet analysis of TEOAEs proves to be another important tool to understand the patho-physiology in individuals with ANSD. PMID:24768764

  2. Low-Frequency Measurments of the Cosmic Background RadiationSpectrum

    SciTech Connect

    Smoot, G.F.; De Amici, G.; Friedman, S.D.; Witebsky, C.; Sironi,G.; Bonelli, G.; Mandolesi, N.; Cortiglioni, S.; Morigi, G.; Partridge,R.B.; Danese, L.; De Zotti, G.

    1984-11-01

    The long-wavelength spectrum of the cosmic background radiation has been measured at five wavelengths (0.33, 0.9, 3.0, 6.3, and 12.0 cm). These measurements represent a continuation of the work reported by Smoot et al. (1983). The combine results have a weighted average of 2.73 {+-} 0.05 K and are consistent with past measurements. They limit the possible Compton distortion of the Cosmic Background Radiation spectrum to less than 8%.

  3. Doubly Stochastic Earthquake Source Model: "Omega-Square" Spectrum and Low High-Frequency Directivity Revealed by Numerical Experiments

    NASA Astrophysics Data System (ADS)

    Gusev, A. A.

    2014-10-01

    Since its formulation in 1967-1970, the classical ω -2 model of earthquake source spectrum awaits a consistent theoretical foundation. To obtain one, stochastic elements are incorporated both into the final structure of the fault and into the mode of rupture propagation. The main components of the proposed "doubly stochastic" model are: (1) the Andrews's concept, that local stress drop over a fault is a random self-similar field; (2) the concept of rupture with running slip pulse, after Heaton; (3) the hypothesis that a rupture front is a tortuous, multiply connected ("lacy") fractal polyline that occupies a strip of finite width close to the slip-pulse width; and (4) the assumption that the propagation distance of fault-guided, mostly Rayleigh waves from a failing spot on a fault is determined by the slip-pulse width. Waveforms produced by this model are determined based on the fault asperity failure model after Das and Kostrov. Properties of the model are studied by numerical experiments. At high frequency, simulated source spectra behave as ω -2, and acceleration spectra are flat. Their level, at a given seismic moment and rms stress drop, is inversely related to the relative width of the slip pulse. When this width is relatively low, a well-defined second corner frequency (lower cutoff of acceleration spectrum) is seen. The model shows clear dependence of propagation-related directivity on frequency. Between the first and the second corner frequency, amplitude spectra are strongly enhanced for the forward direction; whereas, above the second corner frequency, directivity is significantly reduced. Still, it is not inhibited totally, suggesting incomplete incoherence of the simulated radiator at high frequencies.

  4. Characterization of the eigenmode frequency spectrum influenced by the polarization states and light field distribution in a nonplanar ring resonator.

    PubMed

    Li, Dong; Bi, Chao; Zhao, Jianlin

    2016-04-20

    We present the evolution of the eigenmode frequency spectrum in a nonplanar ring resonator based on the Jones matrix and the Fresnel-Kirchhoff diffraction integral. Taking the modes TEM(q+1)01 and TEMq10 with different polarization states as examples, we numerically derive the frequency difference between them versus the folding angles of the resonator by considering the polarization and the light field distribution of the eigenmodes synchronously. It can be found that the extreme values of frequency difference between TEM(q+1)01 and TEMq10 are particularly affected by the polarization states of the eigenmode, and the locations of these consecutive extreme values correspond to the total image rotation angle with values of the integer multiple of 90°. Moreover, the influence of the resonator structure on the frequency difference of eigenmodes with the identical polarization state is also analyzed. The results prove that the frequency difference between the fundamental mode and higher order modes declines with the increase of the spherical mirrors' radius of curvature but increases with the augmentation of the resonator's total length. These interesting findings are important for the mode selection in high-accuracy ring laser gyroscopes with nonplanar structure by modulating the polarization states and the light field distribution of the eigenmodes to control the frequency difference between them. PMID:27140100

  5. Vocal Patterns in Infants with Autism Spectrum Disorder: Canonical Babbling Status and Vocalization Frequency

    ERIC Educational Resources Information Center

    Patten, Elena; Belardi, Katie; Baranek, Grace T.; Watson, Linda R.; Labban, Jeffrey D.; Oller, D. Kimbrough

    2014-01-01

    Canonical babbling is a critical milestone for speech development and is usually well in place by 10 months. The possibility that infants with autism spectrum disorder (ASD) show late onset of canonical babbling has so far eluded evaluation. Rate of vocalization or "volubility" has also been suggested as possibly aberrant in infants with…

  6. 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

  7. A new method of charged particle identification based on frequency spectrum analysis

    NASA Astrophysics Data System (ADS)

    Jin-Tao, Zhu; Guo-Fu, Liu; Jun, Yang; Xiao-Liang, Luo; Lei, Zhang; Li-Feng, Ji

    2016-03-01

    A new frequency domain method for charged particle identification, called Frequency Ratio Analysis (FRA), is proposed by analyzing the frequency spectra of proton pulses and alpha pulses acquired from a totally depleted Si detector. Identification performance of the FRA method is evaluated and compared with two time domain methods, the current pulse amplitude method and the second moment method. The results show that the FRA method is not only feasible and effective but also superior to the two time domain methods, as it achieves an obvious increase in value of the figure-of-merit (FOM). Supported by National Natural Science Foundation of China (11175254, 11375264)

  8. Calculation of the frequency spectrum of an electron beam in a klystron with premodulation

    NASA Astrophysics Data System (ADS)

    Alekseev, Iu. K.; Kostienko, A. I.

    1982-12-01

    The combined modulation of the electron beam in a klystron with a triode gun is considered. Amplitude modulation of current density (static control) is followed by modulation of electron velocities (dynamic control). The spectral characteristics of the convection current at the input of the energy-extraction device are calculated for large ratios of the dynamic and static control frequencies. Calculations point to the possibility of using low-frequency preliminary amplitude modulation to enhance the electronic efficiency of pulsed klystrons, operating both in the amplification and frequency-multiplication modes.

  9. Optical NRZ-to-RZ format conversion based on frequency chirp linearization and spectrum slicing

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Huo, Li; Chen, Xin; Jiang, Xiangyu; Lou, Caiyun

    2015-12-01

    A flexible optical NRZ-to-RZ format converter based on a time lens followed by optical filtering is proposed and demonstrated experimentally. After frequency chirp linearization, 9-tone ultra-flat optical frequency comb of 25-GHz frequency spacing within 1 dB power variation is obtained. By changing the shape of the following optical band-pass filter, 3.4-ps Nyquist-shaped RZ signal and 3.7-ps Gaussian-shaped RZ signal are both achieved. The sensitivity improvements at a bit error rate of 10-9 are 3.3 dB and 1.7 dB, respectively.

  10. Device for recording the 20 Hz - 200 KHz sound frequency spectrum using teletransmission

    NASA Technical Reports Server (NTRS)

    Baciu, I.

    1974-01-01

    The device described consists of two distinct parts: (1) The sound pickup system consisting of the wide-frequency band condenser microphone which contains in the same assembly the frequency-modulated oscillator and the output stage. Being transistorized and small, this system can be easily moved, so that sounds can be picked up even in places that are difficult to reach with larger devices. (2) The receiving and recording part is separate and can be at a great distance from the sound pickup system. This part contains a 72 MHz input stage, a frequency changer that gives an intermediate frequency of 30 MHz and a multichannel analyzer coupled to an oscilloscope and a recorder.

  11. Detection of sinusoidal amplitude modulation in logarithmic frequency sweeps across wide regions of the spectrum

    PubMed Central

    Hsieh, I-Hui; Saberi, Kourosh

    2010-01-01

    Many natural sounds such as speech contain concurrent amplitude and frequency modulation (AM and FM), with the FM components often in the form of directional frequency sweeps or glides. Most studies of modulation coding, however, have employed one modulation type in stationary carriers, and in cases where mixed-modulation sounds have been used, the FM component has typically been confined to an extremely narrow range within a critical band. The current study examined the ability to detect AM signals carried by broad logarithmic frequency sweeps using a 2-alternative forced-choice adaptive psychophysical design. AM detection thresholds were measured as a function of signal modulation rate and carrier sweep frequency region. Thresholds for detection of AM in a sweep carrier ranged from -8 dB for an AM rate of 8 Hz to -30 dB at 128 Hz. Compared to thresholds obtained for stationary carriers (pure tones and filtered Gaussian noise), detection of AM carried by frequency sweeps substantially declined at low (12 dB at 8 Hz) but not high modulation rates. Several trends in the data, including sweep- versus stationary-carrier threshold patterns and effects of frequency region were predicted from a modulation filterbank model with an envelope-correlation decision statistic. PMID:20144700

  12. 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

  13. Low Frequency Measurement of the Spectrum of the Cosmic Background Radiation

    DOE R&D Accomplishments Database

    Smoot, G. F.; De Amici, G.; Friedman, S. D.; Witebsky, C.; Mandolesi, N.; Partridge, R. B.; Sironi, G.; Danese, L.; De Zotti, G.

    1983-06-01

    We have made measurements of the cosmic background radiation spectrum at 5 wavelengths (0.33, 0.9, 3, 6.3, and 12 cm) using radiometers with wavelength-scaled corrugated horn antennas having very low sidelobes. A single large-mouth (0.7 m diameter) liquid-helium-cooled absolute reference load was used for all five radiometers. The results of the observations are consistent with previous measurements and represent a significant improvement in accuracy.

  14. 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

  15. Frequency-domain synthesis of the fatigue load spectrum for the NPS 100-kW wind turbine

    SciTech Connect

    Sutherland, H.J. ); Osgood, R.M. )

    1992-08-28

    The LIFE2 code is a fatigue/fracture mechanics code that is specialized to the analysis of wind turbine components. This code permits the analysis of both time series and frequency domain data. Two frequency-domain stress spectra techniques contained in this code are used to analyze the measured frequency loads spectra from the Northern Power Systems 100-kW turbine. In the first, the cycle content is determined using the entire stress spectrum, an FFT and a rainflow counter. In the second technique, the cycle content is determined using time series data for the deterministic (azimuth average) loads and frequency spectra data for the non-deterministic (random) loads. Results of the two techniques are compared to cycle counts obtained directly from time series data. These results provide the wind turbine designer with two techniques for determining the cycle-counts from frequency data and illustrate the accuracy that the designer can expect from various cycle-counting techniques. Moreover, these results illustrate the importance of relatively long time series data on the determination of the high-stress tail in the distribution of the stress cycles.

  16. Effects of weekly low-frequency rTMS on autonomic measures in children with autism spectrum disorder

    PubMed Central

    Casanova, Manuel Fernando; Hensley, Marie K.; Sokhadze, Estate M.; El-Baz, Ayman S.; Wang, Yao; Li, Xiaoli; Sears, Lonnie

    2014-01-01

    The term autism spectrum disorder (ASD) describes a range of conditions characterized by impairments in social interactions, communication, and by restricted and repetitive behaviors. Autism spectrum disorder may also present with symptoms suggestive of autonomic nervous system (ANS) dysfunction. The objective of this study was to determine the effect of 18 sessions of low frequency (LF) repetitive transcranial magnetic stimulation (rTMS) on autonomic function in children with ASD by recording electrocardiogram (ECG) and electrodermal activity (EDA) pre- post- and during each rTMS session. The autonomic measures of interest in this study were R-R cardiointervals in EKG (R-R), time and frequency domain measures of heart rate variability (HRV) and skin conductance level (SCL). Heart rate variability measures such as R-R intervals, standard deviation of cardiac intervals, pNN50 (percentage of cardiointervals >50 ms different from preceding interval), power of high frequency (HF) and LF components of HRV spectrum, LF/HF ratio, were then derived from the recorded EKG. We expected that the course of 18 weekly inhibitory LF rTMS applied to the dorsolateral prefrontal cortex (DLPFC) would enhance autonomic balance by facilitating frontal inhibition of limbic activity thus resulting in decreased overall heart rate (HR), increased HRV (in a form of increased HF power), decreased LF power (resulting in decreased LF/HF ratio), and decreased SCL. Behavioral evaluations post-18 TMS showed decreased irritability, hyperactivity, stereotype behavior and compulsive behavior ratings while autonomic measures indicated a significant increase in cardiac interval variability and a decrease of tonic SCL. The results suggest that 18 sessions of LF rTMS in ASD results in increased cardiac vagal control and reduced sympathetic arousal. PMID:25374530

  17. Orthostatic Tremor: A Spectrum of Fast and Slow Frequencies or Distinct Entities?

    PubMed Central

    Rigby, Heather B.; Rigby, Matthew H.; Caviness, John N.

    2015-01-01

    Background Orthostatic tremor (OT) is defined by the presence of a high-frequency (13–18 Hz) tremor of the legs upon standing associated with a feeling of unsteadiness. However, some patients have discharge frequencies of <13 Hz, so-called “slow OT”. The aim of this study was to characterize patients with unsteadiness upon standing found to have <13 Hz tremor discharges on neurophysiologic testing. Methods A retrospective review was performed on all subjects with a diagnosis of OT who were referred to the Mayo Clinic, Scottsdale, AZ, between 1999 and 2013 for confirmation using neurophysiology. Results Fourteen of 28 subjects (50%) had OT discharges of <13 Hz, of whom eight had frequencies of <10 Hz and six had frequencies of 10–13 Hz. Lower frequency discharges tended to have a broader spectral peak, greater variability in discharge duration, and lower inter-muscular coherence. Subjects with <13 Hz OT had shorter mean disease duration at time of neurophysiology testing (2.00 years in <10 Hz group, 7.96 years 10–13 Hz group, and 11.43 years >13 Hz; p = 0.002). The proportion of subjects who experienced gait unsteadiness (85.7% vs. 66.6% vs. 21.4%; p = 0.016), falls (37.5% vs. 50% vs. 0%; p = 0.010), and had abnormal gait on examination (71.4% vs. 66.0% vs. 14.3%; p = 0.017) was greater in those with low and intermediate frequencies. Discussion Slow tremor electromyography frequencies (<13 Hz) may characterize a substantial proportion of patients labeled as OT. These subjects may have greater gait involvement and higher likelihood of falls leading to earlier presentation to subspecialty care. PMID:26317042

  18. Multiple optical code-label processing using multi-wavelength frequency comb generator and multi-port optical spectrum synthesizer.

    PubMed

    Moritsuka, Fumi; Wada, Naoya; Sakamoto, Takahide; Kawanishi, Tetsuya; Komai, Yuki; Anzai, Shimako; Izutsu, Masayuki; Kodate, Kashiko

    2007-06-11

    In optical packet switching (OPS) and optical code division multiple access (OCDMA) systems, label generation and processing are key technologies. Recently, several label processors have been proposed and demonstrated. However, in order to recognize N different labels, N separate devices are required. Here, we propose and experimentally demonstrate a large-scale, multiple optical code (OC)-label generation and processing technology based on multi-port, a fully tunable optical spectrum synthesizer (OSS) and a multi-wavelength electro-optic frequency comb generator. The OSS can generate 80 different OC-labels simultaneously and can perform 80-parallel matched filtering. We also demonstrated its application to OCDMA. PMID:19547075

  19. Spatial frequency spectrum of the x-ray scatter distribution in CBCT projections

    SciTech Connect

    Bootsma, G. J.; Verhaegen, F.; Jaffray, D. A.

    2013-11-15

    Purpose: X-ray scatter is a source of significant image quality loss in cone-beam computed tomography (CBCT). The use of Monte Carlo (MC) simulations separating primary and scattered photons has allowed the structure and nature of the scatter distribution in CBCT to become better elucidated. This work seeks to quantify the structure and determine a suitable basis function for the scatter distribution by examining its spectral components using Fourier analysis.Methods: The scatter distribution projection data were simulated using a CBCT MC model based on the EGSnrc code. CBCT projection data, with separated primary and scatter signal, were generated for a 30.6 cm diameter water cylinder [single angle projection with varying axis-to-detector distance (ADD) and bowtie filters] and two anthropomorphic phantoms (head and pelvis, 360 projections sampled every 1°, with and without a compensator). The Fourier transform of the resulting scatter distributions was computed and analyzed both qualitatively and quantitatively. A novel metric called the scatter frequency width (SFW) is introduced to determine the scatter distribution's frequency content. The frequency content results are used to determine a set basis functions, consisting of low-frequency sine and cosine functions, to fit and denoise the scatter distribution generated from MC simulations using a reduced number of photons and projections. The signal recovery is implemented using Fourier filtering (low-pass Butterworth filter) and interpolation. Estimates of the scatter distribution are used to correct and reconstruct simulated projections.Results: The spatial and angular frequencies are contained within a maximum frequency of 0.1 cm{sup −1} and 7/(2π) rad{sup −1} for the imaging scenarios examined, with these values varying depending on the object and imaging setup (e.g., ADD and compensator). These data indicate spatial and angular sampling every 5 cm and π/7 rad (∼25°) can be used to properly capture

  20. Wide bandwidth instantaneous radio frequency spectrum analyzer based on nitrogen vacancy centers in diamond

    NASA Astrophysics Data System (ADS)

    Chipaux, M.; Toraille, L.; Larat, C.; Morvan, L.; Pezzagna, S.; Meijer, J.; Debuisschert, T.

    2015-12-01

    We propose an original analog method to perform instantaneous and quantitative spectral analysis of microwave signals. An ensemble of nitrogen-vacancy (NV) centers held in a diamond plate is pumped by a 532 nm laser. Its photoluminescence is imaged through an optical microscope and monitored by a digital camera. An incoming microwave signal is converted into a microwave field in the area of the NV centers by a loop shaped antenna. The resonances induced by the magnetic component of that field are detected through a decrease of the NV centers photoluminescence. A magnetic field gradient induces a Zeeman shift of the resonances and transforms the frequency information into spatial information, which allows for the simultaneous analysis of the microwave signal in the entire frequency bandwidth of the device. The time dependent spectral analysis of an amplitude modulated microwave signal is demonstrated over a bandwidth of 600 MHz , associated to a frequency resolution of 7 MHz , and a refresh rate of 4 ms . With such integration time, a field of a few hundreds of μ W can be detected. Since the optical properties of NV centers can be maintained even in high magnetic field, we estimate that an optimized device could allow frequency analysis in a range of 30 GHz , only limited by the amplitude of the magnetic field gradient. In addition, an increase of the NV centers quantity could lead both to an increase of the microwave sensitivity and to a decrease of the minimum refresh rate down to a few μ s .

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

    PubMed

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

    2007-01-01

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

  2. Spread-spectrum technique for passive multiplexing of reflective frequency-out fiber optic sensors exhibiting identical characteristics

    NASA Astrophysics Data System (ADS)

    Uttamchandani, Deepak G.; Rao, Yun-Jiang; Culshaw, Brian

    1993-03-01

    A spread spectrum multiplexing (SSM) system for an array of reflective, frequency-out fiber optic sensors of identical characteristics has been developed. This system allows accessing of a large number of sensors with high sampling frequency of up to a few MHz and simultaneously permits a considerable improvement of the system optical power budget over single pulse time-division multiplexing methods. An experimental SSM system has been assembled and tested and the experiments have successfully demonstrated the passive multiplexing of eight reflective frequency-out fiber optic sensors with a vibration frequency of 17.36 kHz. Crosstalk of approximately -22 dB has been observed, which is in agreement with theoretical results expected from consideration of the code length of the pseudorandom bit sequence used and the sensor number in the network. Additionally, a novel digital PRBS exhibiting zero auto-correlation at non-zero delays has been modelled and experimentally tested, yielding promising results for sensor multiplexing.

  3. Frequency and spectrum of mutations at codons 12 and 13 of the C-K-ras gene in human tumors

    SciTech Connect

    Capella, G.; Cronauer-Mitra, S.; Peinado, M.A.; Perucho, M. )

    1991-06-01

    The frequency of point mutations at codons 12 and 13 of the c-K-ras gene has been determined in a panel of more than 400 human tumors. Mutant c-K-ras genes were detected in about 75% of adenocarcinomas of the pancreas; 40% of adenomas and carcinomas of the colon and rectum; 30% of carcinomas of the bile duct; 25% of carcinomas of the lung, and in lower frequency in other carcinomas, including liver, stomach, and kidney. No mutations were found in carcinomas of the breast, prostate, esophagus, and gall bladder, among others. Comparative analysis of the spectrum of mutations show that while G to A transitions were the most frequent mutations in pancreatic and colo-rectal tumors, G to T transversions were more prevalent in lung carcinomas. The aspartic acid mutation at codon 13 (GGC {r arrow} GAC) was relatively frequent in colo-rectal tumors but rare in pancreatic and lung carcinomas. The differences in the mutation spectrum of the c-K-ras gene in cancers of the gastrointestinal and respiratory tracts are suggestive of differential exposure to genotoxic agents.

  4. [Changes in the EEG frequency spectrum in various phases of mental stress].

    PubMed

    Mecklinger, A; Bösel, R

    1989-01-01

    To obtain evidence about the relationship between spontaneous EEG activity and mental activity, an experiment was designed and executed with EEG recordings during a concept-learning task. We varied task performance (self-paced vs. machine-paced) and distinguished different stages of information processing during task performance. Using factor analysis calculated on all spectral coefficients, we found two orthogonal variables in the clinical alpha band. Alpha 2 power (10.5-12 Hz) seems to reflect the overall processing demands imposed on the individuals. Furthermore, there are different EEG frequency patterns during perceptual-central- compared with response-related processing as well as during processing of positive vs. negative feedback. The results suggest using (1) conservative procedures in hypothesis testing and (2) procedures to reduce between subject variability (a posteriori defined frequency variables, relative power values, scaling of reaction values) in further studies relating EEG activity to mental activity during task performance. PMID:2588701

  5. Frequency spectrum analysis on the force contribution in a micronewton electromagnetic thruster

    NASA Astrophysics Data System (ADS)

    Charrier, Dimitri

    An electromagnetic thruster based on a coil-disc system showed micrometer displacements on a translation pendulum. Discrepancies were shown between experimental results and numerical calculations. The aim of this study is to reduce discrepancies between experimental results and the model prediction. To do so, an improved model is proposed where the coil circuit is seen as i) a RL circuit and ii) a RLC circuit, where R, L and C are respectively the coil resistance, inductance and stray capacitance. The analysis revealed that i) the RL circuit has a working device onset frequency above 170 kHz ii) in the RLC case, the stray capacitance C of the coil must be much below the order of pF for having working coil-disc device frequencies. This work was financially supported by the French CPER (Région Poitou-Charentes).

  6. Perturbative approach in the frequency domain for the intensity correlation spectrum in electromagnetically induced transparency

    NASA Astrophysics Data System (ADS)

    Florez, H. M.; González, C.; Martinelli, M.

    2016-07-01

    Correlation spectroscopy has been proposed as a spectroscopic technique for measuring the coherence between the ground states in electromagnetically induced transparency (EIT). While in the time domain the steep dispersion in the EIT condition accounts for the robustness of the correlation linewidth against power broadening, such physical insight was not directly established in the frequency domain. We propose a perturbative approach to describe the correlation spectroscopy of two noisy lasers coupled to a Λ transition in cold atoms, leading to EIT. Such approach leads to an analytical expression that maps the intensity correlation directly in terms of the absorption and dispersion of the light fields. Low and high perturbative regimes are investigated and demonstrate that, for coherent light sources, the first-order term in perturbation expansion represents a sufficient description for the correlation. Sideband resonances are also observed, showing the richness of the frequency domain approach.

  7. Frequency and spectrum of hemoglobinopathy mutations in a Uruguayan pediatric population

    PubMed Central

    Luz, Julio Da; Ávila, Amalia; Icasuriaga, Sandra; Gongóra, María; Castillo, Luis; Serrón, Alejandra; Kimura, Elza Miyuki; Costa, Fernando Ferreira; Sans, Mónica; Sonati, Maria de Fátima

    2013-01-01

    Hemoglobinopathies are the most common recessive diseases worldwide but their prevalence in Uruguay has not been investigated. In this study, 397 unrelated outpatient children from the Pereira Rosell Hospital Center (CHPR), as well as 31 selected patients with microcytic anemia and 28 β-thalassemia carriers were analyzed for hemoglobinopathies by using biochemical and molecular biology methods. Parametric and non-parametric methods were used to compare the hematological indices between groups of genotypes. Of the 397 patients in the first group, approximately 1% (0.76% HbS and 0.25% β-thalassemia) had a mutation in the HBB gene and 3.3% had β-thalassemia. These mutations had a heterogeneous distribution that varied according to individual ancestry. HbS was found exclusively in individuals with declared African ancestry and had a carrier frequency of 2.2%. The frequency of α-thalassemia carriers in outpatients of European and African ancestry was 1.2% and 6.5%, respectively. In contrast, the frequency of α-thalassemia carriers in patients with microcytic anemia was 25.8%, significantly higher (p < 0.01) than that observed in the sample as a whole and in Afro-descendants and Euro-descendants. Significant differences were observed in the hematological parameters between individuals with thalassemia genotypes and those with a normal genotype. These results indicate that hemoglobinopathies are a relevant health problem in Uruguay. PMID:24130436

  8. Frequency and Spectrum of Genomic Integration of Recombinant Adeno-Associated Virus Serotype 8 Vector in Neonatal Mouse Liver▿

    PubMed Central

    Inagaki, Katsuya; Piao, Chuncheng; Kotchey, Nicole M.; Wu, Xiaolin; Nakai, Hiroyuki

    2008-01-01

    Neonatal injection of recombinant adeno-associated virus serotype 8 (rAAV8) vectors results in widespread transduction in multiple organs and therefore holds promise in neonatal gene therapy. On the other hand, insertional mutagenesis causing liver cancer has been implicated in rAAV-mediated neonatal gene transfer. Here, to better understand rAAV integration in neonatal livers, we investigated the frequency and spectrum of genomic integration of rAAV8 vectors in the liver following intraperitoneal injection of 2.0 × 1011 vector genomes at birth. This dose was sufficient to transduce a majority of hepatocytes in the neonatal period. In the first approach, we injected mice with a β-galactosidase-expressing vector at birth and quantified rAAV integration events by taking advantage of liver regeneration in a chronic hepatitis animal model and following partial hepatectomy. In the second approach, we performed a new, quantitative rAAV vector genome rescue assay by which we identified rAAV integration sites and quantified integrations. As a result, we find that at least ∼0.05% of hepatocytes contained rAAV integration, while the average copy number of integrated double-stranded vector genome per cell in the liver was ∼0.2, suggesting concatemer integration. Twenty-three of 34 integrations (68%) occurred in genes, but none of them were near the mir-341 locus, the common rAAV integration site found in mouse hepatocellular carcinoma. Thus, rAAV8 vector integration occurs preferentially in genes at a frequency of 1 in approximately 103 hepatocytes when a majority of hepatocytes are once transduced in the neonatal period. Further studies are warranted to elucidate the relationship between vector dose and integration frequency or spectrum. PMID:18614641

  9. Response of Historical Buildings on Induced Signal with Exactly Defined Frequency Spectrum

    NASA Astrophysics Data System (ADS)

    Strunc, J.; Broz, M.

    2009-04-01

    Buildings are important historical signs of all periods. Every age had its architectural aspect. Nowadays we have to change many old town centres in sense of modern style of living but not destroying any national memories. Our team had taken part at many engineering processes using vibration or impact methods during building new facilities nearby historically important houses and palaces. We would like to present techniques for computing transfer function between the sites - place of the application of building technology, mainly using a heavy industry - and near building. For building subterraneous places are used special vibrators for with frequencies several tens Herz (eg. 30 Hz). This sinusoidal signal can be used for finding a transfer function. Such information offers other possibilities - especially we can assume critical, resonant, frequency of building(s). This method suppose of using several (at least two) sensors with common time basis. One sensor is place next to the source of vibration(s) and the other are at the basement(s) of examined building. Application of such approach can be also used in civil engineering for measuring carrying-capacity concrete piles. Detail description of both mentioned processes and computations will be presented.

  10. Frequency spectrum of transepithelial potential difference reveals transport-related oscillations.

    PubMed

    Montalbetti, Nicolás; Fischbarg, Jorge

    2009-09-16

    How epithelia transport fluid is a fundamental issue that is unresolved. Explanations offered include molecular engines, local transcellular osmosis, local paracellular osmosis, and paracellular fluid transport. On the basis of experimental and theoretical work done on corneal endothelium, a fluid transporting epithelium, we suggest electroosmotic coupling at the level of the intercellular junctions driven by the transendothelial electrical potential difference as an explanation of paracellular fluid transport. We collect frequency spectra of that potential difference in real-time. For what we believe is the first time for any epithelium, we report that, unexpectedly, the potential difference displays oscillations at many characteristic frequencies. We also show that on both stimulating cell activity and inhibiting ion transport mechanisms, there are corresponding changes in the oscillations amplitudes that mirror changes known previously in rates of fluid transport. We believe these findings provide a novel tool to study the kinetics of electrogenic elements such as channels and transporters, which from this evidence would give rise to current oscillations with characteristic periods going from 150 ms to 8 s. PMID:19751657

  11. Frequency spectrum method-based stress analysis for oil pipelines in earthquake disaster areas.

    PubMed

    Wu, Xiaonan; Lu, Hongfang; Huang, Kun; Wu, Shijuan; Qiao, Weibiao

    2015-01-01

    When a long distance oil pipeline crosses an earthquake disaster area, inertial force and strong ground motion can cause the pipeline stress to exceed the failure limit, resulting in bending and deformation failure. To date, researchers have performed limited safety analyses of oil pipelines in earthquake disaster areas that include stress analysis. Therefore, using the spectrum method and theory of one-dimensional beam units, CAESAR II is used to perform a dynamic earthquake analysis for an oil pipeline in the XX earthquake disaster area. This software is used to determine if the displacement and stress of the pipeline meet the standards when subjected to a strong earthquake. After performing the numerical analysis, the primary seismic action axial, longitudinal and horizontal displacement directions and the critical section of the pipeline can be located. Feasible project enhancement suggestions based on the analysis results are proposed. The designer is able to utilize this stress analysis method to perform an ultimate design for an oil pipeline in earthquake disaster areas; therefore, improving the safe operation of the pipeline. PMID:25692790

  12. Spectrum and Anisotropy of Turbulence from Multi-frequency Measurement of Synchrotron Polarization

    NASA Astrophysics Data System (ADS)

    Lazarian, A.; Pogosyan, D.

    2016-02-01

    We consider turbulent synchrotron-emitting media that also exhibit Faraday rotation and provide a statistical description of synchrotron polarization fluctuations. In particular, we consider these fluctuations as a function of the spatial separation of the direction of the measurements and as a function of wavelength for the same line of sight. On the basis of our general analytical approach, we introduce several measures that can be used to obtain the spectral slopes and correlation scales of both the underlying magnetic turbulence responsible for emission and the spectrum of the Faraday rotation fluctuations. We show the synergetic nature of these measures and discuss how the study can be performed using sparsely sampled interferometric data. We also discuss how additional characteristics of turbulence can be obtained, including the turbulence anisotropy and the three-dimensional direction of the mean magnetic field. In addition, we consider the cases when the synchrotron emission and Faraday rotation regions are spatially separated. Appealing to our earlier study, we explain that our new results are applicable to a wide range of spectral indexes of relativistic electrons responsible for synchrotron emission. We expect wide application of our techniques, both with existing synchrotron data sets and with big forthcoming data sets from LOFAR and SKA.

  13. Frequency Spectrum Method-Based Stress Analysis for Oil Pipelines in Earthquake Disaster Areas

    PubMed Central

    Wu, Xiaonan; Lu, Hongfang; Huang, Kun; Wu, Shijuan; Qiao, Weibiao

    2015-01-01

    When a long distance oil pipeline crosses an earthquake disaster area, inertial force and strong ground motion can cause the pipeline stress to exceed the failure limit, resulting in bending and deformation failure. To date, researchers have performed limited safety analyses of oil pipelines in earthquake disaster areas that include stress analysis. Therefore, using the spectrum method and theory of one-dimensional beam units, CAESAR II is used to perform a dynamic earthquake analysis for an oil pipeline in the XX earthquake disaster area. This software is used to determine if the displacement and stress of the pipeline meet the standards when subjected to a strong earthquake. After performing the numerical analysis, the primary seismic action axial, longitudinal and horizontal displacement directions and the critical section of the pipeline can be located. Feasible project enhancement suggestions based on the analysis results are proposed. The designer is able to utilize this stress analysis method to perform an ultimate design for an oil pipeline in earthquake disaster areas; therefore, improving the safe operation of the pipeline. PMID:25692790

  14. Robust frequency diversity based algorithm for clutter noise reduction of ultrasonic signals using multiple sub-spectrum phase coherence

    SciTech Connect

    Gongzhang, R.; Xiao, B.; Lardner, T.; Gachagan, A.; Li, M.

    2014-02-18

    This paper presents a robust frequency diversity based algorithm for clutter reduction in ultrasonic A-scan waveforms. The performance of conventional spectral-temporal techniques like Split Spectrum Processing (SSP) is highly dependent on the parameter selection, especially when the signal to noise ratio (SNR) is low. Although spatial beamforming offers noise reduction with less sensitivity to parameter variation, phased array techniques are not always available. The proposed algorithm first selects an ascending series of frequency bands. A signal is reconstructed for each selected band in which a defect is present when all frequency components are in uniform sign. Combining all reconstructed signals through averaging gives a probability profile of potential defect position. To facilitate data collection and validate the proposed algorithm, Full Matrix Capture is applied on the austenitic steel and high nickel alloy (HNA) samples with 5MHz transducer arrays. When processing A-scan signals with unrefined parameters, the proposed algorithm enhances SNR by 20dB for both samples and consequently, defects are more visible in B-scan images created from the large amount of A-scan traces. Importantly, the proposed algorithm is considered robust, while SSP is shown to fail on the austenitic steel data and achieves less SNR enhancement on the HNA data.

  15. Crater shape and size-frequency distribution in determining the topographic power spectrum of a cratered surface

    NASA Astrophysics Data System (ADS)

    Rosenburg, M. A.; Aharonson, O.; Smith, D. E.; Zuber, M. T.; Zhang, X.

    2010-12-01

    The statistical properties of a heavily cratered planetary surface reflect several factors that govern its formation and subsequent modification: the size-frequency distribution of impactors, the corresponding distribution of crater sizes, crater morphology, and downslope movement of material on steep slopes. We develop and apply a new cratered terrain-generating model to study the relative contributions of the crater size-frequency distribution and crater shape to the power spectral density of a surface that accumulates impacts. By monitoring surviving rim fragments through time, we derive the relationship between the size-frequency distribution of observable craters and its production function, whose slope we vary. This permits us to explore the criteria for equilibrium. Further, we examine the effects of changes in crater morphology with size—the transition from simple to complex crater shapes, as well as the appearance of complex features such as central peaks, peak rings, and wall terraces—on the slope of the power spectrum, utilizing the new global topography dataset provided by the Lunar Orbiter Laser Altimeter (LOLA) to characterize the power spectra of several lunar craters. Finally, we compare our findings on the dependencies of the power spectral slope to the observed roughness properties at several length scales of lunar terrains in various stages of saturation, from young maria to ancient highlands.

  16. Possibility of quantitative estimation of blood cell forms by the spatial-frequency spectrum analysis

    NASA Astrophysics Data System (ADS)

    Spiridonov, Igor N.; Safonova, Larisa P.; Samorodov, Andrey V.

    2000-05-01

    At present in hematology there are no quantitative estimates of such important for the cell classification parameters: cell form and nuclear form. Due to the absence of the correlation between morphological parameters and parameters measured by hemoanalyzers, both flow cytometers and computer recognition systems, do not provide the completeness of the clinical blood analysis. Analysis of the spatial-frequency spectra of blood samples (smears and liquid probes) permit the estimate the forms quantitatively. On the results of theoretical and experimental researches carried out an algorithm of the form quantitative estimation by means of SFS parameters has been created. The criteria of the quality of these estimates have been proposed. A test bench based on the coherent optical and digital processors. The received results could be applied for the automated classification of ether normal or pathological blood cells in the standard blood smears.

  17. Investigating the frequency spectrum of mechanical quality factor for piezoelectric materials based on phenomenological model

    NASA Astrophysics Data System (ADS)

    Shi, Weijia; Zhao, Hui; Ma, Jie; Yao, Yu; Uchino, Kenji

    2015-10-01

    Heat generation due to losses restricts piezoelectric materials from maintaining a high power density, which will further limit the miniaturization of piezoelectric devices. As an evaluation index of the loss level, the mechanical quality factor shows an opposite tendency with losses. The mechanical quality factor should therefore be evaluated. By new methods to determine the mechanical quality factor, the highest mechanical quality factor has been discovered within the working bandwidth other than the resonance and antiresonance frequencies, which is almost double the value at the resonance. In this study, the prime determinant of the maximum value has been experimentally investigated on the basis of the phenomenological model of the admittance phase. The investigation experimentally infers that the change in the tendency of the phase leads to the appearance of the maximum value. Thus, the new phenomenon is experimentally explained for the first time.

  18. Measurements of ocean surface spectrum from an aircraft using the two-frequency microwave resonance technique

    NASA Technical Reports Server (NTRS)

    Johnson, J. W.; Weissman, D. E.; Jones, W. L.

    1982-01-01

    The present investigation is concerned with the results of a two-frequency (Delta k) microwave radar experiment conducted from an aircraft and aimed primarily at the development of remote sensing techniques to measure ocean surface wave spectral characteristics. The experiment was conducted as part of the Maritime Remote Sensing (MARSEN) project in the North Sea during the autumn of 1979. The objective was to demonstrate the feasibility of and study the performance of the Delta k technique from a higher altitude platform, at shallower incidence angles, and at higher Doppler velocities than earlier stationary platform experiments allowed. A quantitative engineering evaluation of the results of two comprehensive flights is provided, and the qualitative significance of the results is discussed from a geophysical point of view in terms of the existing theory.

  19. Optimum rate Reed-Solomon codes for frequency-hopped spread-spectrum multiple-access communication systems

    NASA Astrophysics Data System (ADS)

    Kim, Sang W.; Stark, Wayne

    1989-02-01

    The authors consider a multiple-access frequency-hopped spread-spectrum communication system with Reed-Solomon codes. The performance measures of interest are an achieveable region and the channel throughput. The achieveable rate region is the set of all pairs of code rate and number of users for which communication is possible with error probability below a fixed value. The throughput measures the expected number of successful codeword transmissions per unit bandwidth. Two models of interference are considered. For these two models, the authors determine the optimal number of users for a given bandwidth and the optimal rate Reed-Solomon code that maximize the throughput. They also determine the achieveable region for these models.

  20. Robust rate-adaptive hybrid ARQ scheme for frequency-hopped spread-spectrum multiple-access communication systems

    NASA Astrophysics Data System (ADS)

    Bigloo, Amir M. Y.; Gulliver, T. Aaron; Wang, Q.; Bhargava, Vijay K.

    1994-06-01

    This paper considers the application of rate-adaptive coding (RAC) to a spread spectrum multiple access (SSMA) communication system. Specifically, RAC using a variable rate Reed-Solomon (RS) code with a single decoder is applied to frequency-hopped SSMA. We show that this combination can accommodate a larger number of users compared to that with conventional fixed-rate coding. This increase is a result of a reduction in the channel interference from other users. The penalty for this improvement in most cases is a slight increase in the delay (composed of propagation and decoding delay). The throughput and the undetected error probability for a Q-ary symmetric channel are analyzed, and performance results are presented.

  1. 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.

  2. 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.

  3. Tapering the sky response for angular power spectrum estimation from low-frequency radio-interferometric data

    PubMed Central

    Choudhuri, Samir; Bharadwaj, Somnath; Roy, Nirupam; Ghosh, Abhik; Ali, Sk. Saiyad

    2016-01-01

    It is important to correctly subtract point sources from radio-interferometric data in order to measure the power spectrum of diffuse radiation like the Galactic synchrotron or the Epoch of Reionization 21-cm signal. It is computationally very expensive and challenging to image a very large area and accurately subtract all the point sources from the image. The problem is particularly severe at the sidelobes and the outer parts of the main lobe where the antenna response is highly frequency dependent and the calibration also differs from that of the phase centre. Here, we show that it is possible to overcome this problem by tapering the sky response. Using simulated 150 MHz observations, we demonstrate that it is possible to suppress the contribution due to point sources from the outer parts by using the Tapered Gridded Estimator to measure the angular power spectrum Cℓ of the sky signal. We also show from the simulation that this method can self-consistently compute the noise bias and accurately subtract it to provide an unbiased estimation of Cℓ. PMID:27274703

  4. The probability of multiple correct packet receptions in a multireceiver frequency-hopped spread-spectrum system

    NASA Astrophysics Data System (ADS)

    Geraniotis, Evaggelos

    1991-09-01

    In this report we develop exact expressions and approximations for the probability of exactly l correct packet receptions in a group of m receivers, given that k packets are transmitted simultaneously from users employing frequency-hopping spread-spectrum (FH/SS) and Reed-Solomon (RS) coding. This quantity is essential for the design and performance evaluation of multiple-access protocols in spread-spectrum packet radio networks. The evaluations are carried out for MFSK modulation with noncoherent demodulation and various types of RS minimum-distance decoding with erasures and/or errors decoding. Packet synchronous FH/SSMA systems that are hop-synchronous or hop-asynchronous are considered. The exact expressions developed have computational complexity that grows exponentially with m, thus making their evaluation for large m prohibitive. In light of such difficulties, two approximations are considered: one based on Gaussian multivariate distributions with linear computational requirements in m and k, and another based on the assumption of independent receiver operation (IROA), which has minimum computational complexity. Extensive comparisons of the approximations with the exact results establish their validity over different ranges of the system parameters.

  5. Tapering the sky response for angular power spectrum estimation from low-frequency radio-interferometric data

    NASA Astrophysics Data System (ADS)

    Choudhuri, Samir; Bharadwaj, Somnath; Roy, Nirupam; Ghosh, Abhik; Ali, Sk. Saiyad

    2016-06-01

    It is important to correctly subtract point sources from radio-interferometric data in order to measure the power spectrum of diffuse radiation like the Galactic synchrotron or the Epoch of Reionization 21-cm signal. It is computationally very expensive and challenging to image a very large area and accurately subtract all the point sources from the image. The problem is particularly severe at the sidelobes and the outer parts of the main lobe where the antenna response is highly frequency dependent and the calibration also differs from that of the phase centre. Here, we show that it is possible to overcome this problem by tapering the sky response. Using simulated 150 MHz observations, we demonstrate that it is possible to suppress the contribution due to point sources from the outer parts by using the Tapered Gridded Estimator to measure the angular power spectrum Cℓ of the sky signal. We also show from the simulation that this method can self-consistently compute the noise bias and accurately subtract it to provide an unbiased estimation of Cℓ.

  6. [Spectrum of species and infection frequency of endoparasites in bitches and their puppies in south Germany].

    PubMed

    Gothe, R; Reichler, I

    1990-02-01

    Toxocara canis, Toxascaris leonina, hookworms, Trichuris vulpis, Strongyloides, Hammondia heydorni, Sarcocystis spp., Isospora canis and Isospora ohioensis and/or Isospora burrowsi of at least 9 species were detected in 100 randomly selected dog families in Southern Germany. Examinations carried out 5 to 9 times at weekly intervals revealed a monoinfection in 37 litters, infection with two parasite species in 28 litters, with three species in 10 litters and with four species in 6 litters. During the investigation period, 29 of the examined litters did not excrete helminth eggs, and, of these, 19 also did not excrete oocysts/sporocysts. In order of decreasing frequency among the dog families, the excretion extent of the litters and their mothers was as follows: Toxocara canis 67% and 45%, Isospora ohioensis/burrowsi 36% and 24%, Sarcocystis spp. 12% and 19%, Isospora canis 16% and 8%, Hammondia heydorni 7% and 6%, hookworms 6% and 7% and Toxascaris leonina 3% and 8%, respectively. Trichuris vulpis and Strongyloides eggs were only detected in 6 and 3 of the bitches, respectively. PMID:2326798

  7. Dissecting the Molecular Structure of the Air/Water Interface from Quantum Simulations of the Sum-Frequency Generation Spectrum.

    PubMed

    Medders, Gregory R; Paesani, Francesco

    2016-03-23

    The molecular characterization of the air/water interface is a key step in understanding fundamental multiphase phenomena ranging from heterogeneous chemical processes in the atmosphere to the hydration of biomolecules. The apparent simplicity of the air/water interface, however, masks an underlying complexity associated with the dynamic nature of the water hydrogen-bond network that has so far hindered an unambiguous characterization of its microscopic properties. Here, we demonstrate that the application of quantum many-body molecular dynamics, which enables spectroscopically accurate simulations of water from the gas to the condensed phase, leads to a definitive molecular-level picture of the interface region. For the first time, excellent agreement is obtained between the simulated vibrational sum-frequency generation spectrum and the most recent state-of-the-art measurements, without requiring any empirical frequency shift or ad hoc scaling of the spectral intensity. A systematic dissection of the spectral features demonstrates that a rigorous representation of nuclear quantum effects as well as of many-body energy and electrostatic contributions is necessary for a quantitative reproduction of the experimental data. The unprecedented accuracy of the simulations presented here indicates that quantum many-body molecular dynamics can enable predictive studies of aqueous interfaces, which by complementing analogous experimental measurements will provide unique molecular insights into multiphase and heterogeneous processes of relevance in chemistry, biology, materials science, and environmental research. PMID:26943730

  8. Allelic background of LEPRE1 mutations that cause recessive forms of osteogenesis imperfecta in different populations

    PubMed Central

    Pepin, Melanie G; Schwarze, Ulrike; Singh, Virendra; Romana, Marc; Jones-LeCointe, Altheia; Byers, Peter H

    2013-01-01

    Biallelic mutations in LEPRE1 result in recessively inherited forms of osteogenesis imperfecta (OI) that are often lethal in the perinatal period. A mutation (c.1080+1G>T, IVS5+1G>T) in African Americans has a carrier frequency of about 1/240. The mutant allele originated in West Africa in tribes of Ghana and Nigeria where the carrier frequencies are 2% and 5%. By examining 200 samples from an African-derived population in Tobago and reviewing hospital neonatal death records, we determined that the carrier frequency of c.1080+1G>T was about one in 200 and did not contribute to the neonatal deaths recorded over a 3-year period of time in Trinidad. In the course of sequence analysis, we found surprisingly high LEPRE1 allelic diversity in the Tobago DNA samples in which there were 11 alleles distinguished by a single basepair variant in or near exon 5. All the alleles found in the Tobago population that were within the sequence analysis region were found in the African American population in the Exome Variant Project. This diversity appeared to reflect the geographic origin of the original population in Tobago. In 44 individuals with biallelic LEPRE1 mutations identified by clinical diagnostic testing, we found the sequence alterations occurred on seven of the 11 variant alleles. All but one of the mutations identified resulted in mRNA or protein instability for the majority of the transcripts from the altered allele. These findings suggest that the milder end of the clinical spectrum could be due to as yet unidentified missense mutations in LEPRE1. PMID:24498616

  9. High-Frequency Observation of Water Spectrum and Its Application in Monitoring of Dynamic Variation of Suspended Materials in the Hangzhou Bay.

    PubMed

    Dai, Qian; Pan, De-lu; He, Xian-qiang; Zhu, Qian-kun; Gong, Fang; Huang, Hai-qing

    2015-11-01

    In situ measurement of water spectrum is the basis of the validation of the ocean color remote sensing. The traditional method to obtain the water spectrum is based on the shipboard measurement at limited stations, which is difficult to meet the requirement of validation of ocean color remote sensing in the highly dynamic coastal waters. To overcome this shortage, continuously observing systems of water spectrum have been developed in the world. However, so far, there are still few high-frequency observation systems of the water spectrum in coastal waters, especially in the highly turbid and high-dynamic waters. Here, we established a high-frequency water-spectrum observing system based on tower in the Hangzhou Bay. The system measures the water spectrum at a step of 3 minutes, which can fully match the satellite observation. In this paper, we primarily developed a data processing method for the tower-based high-frequency water spectrum data, to realize automatic judgment of clear sky, sun glint, platform shadow, and weak illumination, etc. , and verified the processing results. The results show that the normalized water-leaving radiance spectra obtained through tower observation have relatively high consistency with the shipboard measurement results, with correlation coefficient of more than 0. 99, and average relative error of 9.96%. In addition, the long-term observation capability of the tower-based high-frequency water-spectrum observing system was evaluated, and the results show that although the system has run for one year, the normalized water-leaving radiance obtained by this system have good consistency with the synchronously measurement by Portable spectrometer ASD in respect of spectral shape and value, with correlation coefficient of more than 0.90 and average relative error of 6.48%. Moreover, the water spectra from high-frequency observation by the system can be used to effectively monitor the rapid dynamic variation in concentration of suspended

  10. Inferring the age of a fixed beneficial allele.

    PubMed

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

    2016-01-01

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

  11. Distinguishing defect induced intermediate frequency modes from combination modes in the Raman spectrum of single walled carbon nanotubes

    SciTech Connect

    Singh, Dilip K.; Iyer, Parameswar K.; Giri, P. K.

    2012-03-15

    Understanding of the origin of some of the intermediate frequency modes (IFMs) in the Raman spectrum of carbon nanotubes has remained controversial in the literature. In this work, through controlled introduction and elimination of defects in carbon nanotubes, we attempt to isolate the IFMs due to structural defects from that of the combination modes in single walled carbon nanotubes (SWCNTs). Our investigations on pristine and defect engineered SWCNTs using ion-irradiation, thermal annealing, and laser processing show systematic changes in the IFMs in the range 400-1200 cm{sup -1} and its manipulation with the processing parameters. In particular, we found that the intensity of IFM at 929 cm{sup -1} scale up with the increasing defect concentration, while that at 668 cm{sup -1} follows opposite behavior. New IFM peaks were observed upon the creation of a controlled amount of structural defects through 30 keV N{sup +} ion irradiation. Elimination of defects through vacuum annealing results into reduction of intensity of some IFMs identified as defect related, while the intensity of characteristic combination modes correspondingly increases. Our results show that the IFMs observed at 709, 805, 868, 926, and 1189 cm{sup -1} are due to structural defects in the SWCNTs, while those in the range 400-550 cm{sup -1} and at 669 cm{sup -1} are due to the combination modes. Our x-ray photoelectron spectroscopy analysis on ion irradiated SWCNTs supports the Raman results.

  12. Genetic instability of the lozenge locus in Drosophila melanogaster: Characterization of the lz{sup 75V} allele

    SciTech Connect

    Voloshina, M.A.; Golubovskii, M.D.

    1995-12-01

    Genetic properties of lz{sup 75V}, an unstable allele of the lozenge locus, are described. The lz{sup 75V} allele appeared in progeny of a male from a Far East natural population of Drosophila melanogaster. Mutation of this allele produces a broad spectrum of mutant derivatives with phenotypes varying from normal to extreme. The arising alleles can be stable or unstable. Some lz{sup 75V} derivatives continuously preserve their spontaneous mutability in laboratory conditions, whereas other alleles of the same family show progressive stabilization at the intralocus or intrachromosome level. Instability of the lz{sup 75V}-bearing X chromosome is locus-specific: only the lozenge gene mutates with high frequency, while visible mutations at other loci rarely occur. As shown previously, the lz{sup 75V} allele appears to be caused by a P-element insertion. The appearance of spontaneous instability is discussed with regard to the general problem of transposition regulation in mobile elements. Different systems of hybrid dysgenesis, and, in particular, P elements are assumed to play an important role in induction of unstable mutations in nature. 24 refs., 5 tabs.

  13. Dual-Frequency Observations of 140 Compact, Flat-Spectrum Active Galactic Nuclei for Scintillation-Induced Variability

    NASA Technical Reports Server (NTRS)

    Koay, J. Y.; Macquart, J.- P.; Rickett, B. J.; Bignall, H. E.; Lovell, J. E. J.; Reynolds, C.; Jauncey, D. L.; Pursimo, T.; Kedziora-Chudczer, L.; Ojha, R.

    2012-01-01

    The 4.9 GHz Micro-Arcsecond Scintillation-Induced Variability (MASIV) Survey detected a drop in Interstellar Scintillation (ISS) for sources at red shifts z > or approx. 2, indicating an apparent increase in angular diameter or a decrease in flux density of the most compact components of these sources, relative to their extended emission. This can result from intrinsic source size effects or scatter broadening in the Intergalactic Medium (IGM) , in excess of the expected (1+z)1/2 angular diameter scaling of brightness temperature limited sources resulting from cosmological expansion. We report here 4.9 GHz and 8.4 GHz observations and data analysis for a sample of 140 compact, fiat-spectrum sources which may allow us to determine the origin of this angular diameter-redshift relation by exploiting their different wavelength dependences. In addition to using ISS as a cosmological probe, the observations provide additional insight into source morphologies and the characteristics of ISS. As in the MASIV Survey, the variability of the sources is found to be significantly correlated with line-of-sight H(alpha) intensities, confirming its link with ISS. For 25 sources, time delays of about 0.15 to 3 days are observed between the scintillation patterns at both frequencies, interpreted as being caused by a shift in core positions when probed at different optical depths. Significant correlation is found between ISS amplitudes and source spectral index; in particular, a large drop in ISS amplitudes is observed at alpha < -0.4 confirming that steep spectrum sources scintillate less. We detect a weakened redshift dependence of ISS at 8.4 GHz over that at 4.9 GHz, with the mean variance at 4-day timescales reduced by a factor of 1.8 in the z > 2 sources relative to the z < 2 sources, as opposed to the factor of 3 decrease observed at 4.9 GHz. This suggests scatter broadening in the IGM, but the interpretation is complicated by subtle selection effects that will be explored

  14. DUAL-FREQUENCY OBSERVATIONS OF 140 COMPACT, FLAT-SPECTRUM ACTIVE GALACTIC NUCLEI FOR SCINTILLATION-INDUCED VARIABILITY

    SciTech Connect

    Koay, J. Y.; Macquart, J.-P.; Bignall, H. E.; Reynolds, C.; Rickett, B. J.; Lovell, J. E. J.; Jauncey, D. L.; Pursimo, T.; Kedziora-Chudczer, L.; Ojha, R.

    2011-10-15

    The 4.9 GHz Micro-Arcsecond Scintillation-Induced Variability (MASIV) Survey detected a drop in interstellar scintillation (ISS) for sources at redshifts z {approx}> 2, indicating an apparent increase in angular diameter or a decrease in flux density of the most compact components of these sources relative to their extended emission. This can result from intrinsic source size effects or scatter broadening in the intergalactic medium (IGM) in excess of the expected (1 + z){sup 1/2} angular diameter scaling of brightness temperature limited sources resulting from cosmological expansion. We report here 4.9 GHz and 8.4 GHz observations and data analysis for a sample of 140 compact, flat-spectrum sources which may allow us to determine the origin of this angular diameter-redshift relation by exploiting their different wavelength dependences. In addition to using ISS as a cosmological probe, the observations provide additional insight into source morphologies and the characteristics of ISS. As in the MASIV Survey, the variability of the sources is found to be significantly correlated with line-of-sight H{alpha} intensities, confirming its link with ISS. For 25 sources, time delays of about 0.15-3 days are observed between the scintillation patterns at both frequencies, interpreted as being caused by a shift in core positions when probed at different optical depths. Significant correlation is found between ISS amplitudes and source spectral index; in particular, a large drop in ISS amplitudes is observed at {alpha} < -0.4 confirming that steep spectrum sources scintillate less. We detect a weakened redshift dependence of ISS at 8.4 GHz over that at 4.9 GHz, with the mean variance at four-day timescales reduced by a factor of 1.8 in the z > 2 sources relative to the z < 2 sources, as opposed to the factor of three decrease observed at 4.9 GHz. This suggests scatter broadening in the IGM, but the interpretation is complicated by subtle selection effects that will be

  15. 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

  16. Comparative analysis of the apo(a) gene, apo(a) glycoprotein, and plasma concentrations of Lp(a) in three ethnic groups. Evidence for no common "null" allele at the apo(a) locus.

    PubMed Central

    Gaw, A; Boerwinkle, E; Cohen, J C; Hobbs, H H

    1994-01-01

    Distributions of plasma lipoprotein(a) (Lp[a]) concentrations exhibit marked interracial differences. Apolipoprotein(a) (apo[a]), the unique constituent of Lp(a), is highly polymorphic in length due to allelic variations in the number of kringle 4(K-4)-encoding sequences. Plasma Lp(a) concentrations are inversely related to the number of K-4 repeats in the apo(a) alleles. To determine the contribution of this length variation to the interracial variation in plasma Lp(a) levels, we compared apo(a) allele size, glycoprotein size, and plasma Lp(a) concentrations in Caucasians, Chinese, and African Americans. Caucasians and African Americans had very different distributions of plasma Lp(a) concentrations yet there was no significant difference in the overall frequency distributions of their apo(a) alleles. Over the entire size spectrum of apo(a) alleles, the plasma Lp(a) levels were higher in African Americans than in Caucasians. Conversely, Caucasians and Chinese had similar plasma Lp(a) concentrations but significantly different apo(a) allele size distributions. Therefore, interracial differences in the plasma concentrations of Lp(a) are not due to differences in the frequency distributions of apo(a) alleles. We also examined the relationship between apo(a) allele size and the presence of detectable plasma apo(a) protein in plasma. Apo(a) alleles associated with no detectable plasma protein were not of uniformly large size, as had been expected, but were distributed over the entire size spectrum. From this analysis, we conclude that there is no common "null" allele at the apo(a) locus. Images PMID:8200989

  17. Low-Frequency Repetitive Transcranial Magnetic Stimulation (rTMS) Modulates Evoked-Gamma Frequency Oscillations in Autism Spectrum Disorder (ASD)

    PubMed Central

    Baruth, Joshua M.; Casanova, Manuel F.; El-Baz, Ayman; Horrell, Tim; Mathai, Grace; Sears, Lonnie; Sokhadze, Estate

    2010-01-01

    Introduction It has been reported that individuals with Autism Spectrum Disorder (ASD) have abnormal reactions to the sensory environment and visuo-perceptual abnormalities. Electrophysiological research has provided evidence that gamma band activity (30-80 Hz) is a physiological indicator of the co-activation of cortical cells engaged in processing visual stimuli and integrating different features of a stimulus. A number of studies have found augmented and indiscriminative gamma band power at early stages of visual processing in ASD; this may be related to decreased inhibitory processing and an increase in the ratio of cortical excitation to inhibition. Low frequency or ‘slow’ (≤1HZ) repetitive transcranial magnetic stimulation (rTMS) has been shown to increase inhibition of stimulated cortex by the activation of inhibitory circuits. Methods We wanted to test the hypothesis of gamma band abnormalities at early stages of visual processing in ASD by investigating relative evoked (i.e. ~ 100 ms) gamma power in 25 subjects with ASD and 20 age-matched controls using Kanizsa illusory figures. Additionally, we wanted to assess the effects of 12 sessions of bilateral ‘slow’ rTMS to the dorsolateral prefrontal cortex (DLPFC) on evoked gamma activity using a randomized controlled design. Results In individuals with ASD evoked gamma activity was not discriminative of stimulus type, whereas in controls early gamma power differences between target and non-target stimuli were highly significant. Following rTMS individuals with ASD showed significant improvement in discriminatory gamma activity between relevant and irrelevant visual stimuli. We also found significant improvement in the responses on behavioral questionnaires (i.e., irritability, repetitive behavior) as a result of rTMS. Conclusion We proposed that ‘slow’ rTMS may have increased cortical inhibitory tone which improved discriminatory gamma activity at early stages of visual processing. rTMS has the

  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. A new step towards understanding Embedded Figures Test performance in the autism spectrum: the radial frequency search task.

    PubMed

    Almeida, Renita A; Dickinson, J Edwin; Maybery, Murray T; Badcock, Johanna C; Badcock, David R

    2010-01-01

    The Embedded Figure Test (EFT) requires locating a simple shape embedded within a background of overlapping target-irrelevant scene elements. Observers with autism, or those with high levels of autistic-like traits, typically outperform matched comparison groups on the EFT. This research investigated the critical visual properties which give rise to this improved performance. The EFT is a search task and so here a radial frequency (RF) search task was created to directly explore efficacy of visual search and also the influence of element overlap on performance. In all conditions, the task was to detect whether the target RF3 (a triangular shape chosen for its visual properties) was present among a number of distracter RF4 (a square shape) patterns. The conditions employed were: 'singles', where all the patterns were spatially discrete, 'pairs', where two overlapping elements formed each cluster, and 'quads', comprising four overlapping elements per cluster. Compared to students scoring low on the Autism Spectrum Quotient (AQ; n=27), those scoring high on the AQ (n=23) were faster on the EFT and also significantly less influenced by increasing set size of the stimulus array in all RF search task conditions. However, the group difference in RF search performance was unaffected by the amount of stimulus overlap. Thus a simple search task is sufficient to detect a performance advantage associated with higher levels of autistic traits and has the advantages of a solid footing in visual theory and being readily repeatable for the purpose of assessing performance variability and change with interventions. PMID:19786040

  20. 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

  1. Estimation of Scatterer Diameter by Normalized Power Spectrum of High-Frequency Ultrasonic RF Echo for Assessment of Red Blood Cell Aggregation

    NASA Astrophysics Data System (ADS)

    Fukushima, Taku; Hasegawa, Hideyuki; Kanai, Hiroshi

    2011-07-01

    Red blood cell (RBC) aggregation, as one of the determinants of blood viscosity, plays an important role in blood rheology, including the condition of blood. RBC aggregation is induced by the adhesion of RBCs when the electrostatic repulsion between RBCs weakens owing to increases in protein and saturated fatty acid levels in blood, excessive RBC aggregation leads to various circulatory diseases. This study was conducted to establish a noninvasive quantitative method for assessment of RBC aggregation. The power spectrum of ultrasonic RF echoes from nonaggregating RBCs, which shows the frequency property of scattering, exhibits Rayleigh behavior. On the other hand, ultrasonic RF echoes from aggregating RBCs contain the components of reflection, which have no frequency dependence. By dividing the measured power spectrum of echoes from RBCs in the lumen by that of echoes from a posterior wall of the vein in the dorsum manus, the attenuation property of the propagating medium and the frequency responses of transmitting and receiving transducers are removed from the former spectrum. RBC aggregation was assessed by the diameter of a scatterer, which was estimated by minimizing the square difference between the measured normalized power spectrum and the theoretical power spectrum. In this study, spherical scatterers with diameters of 5, 11, 15, and 30 µm were measured in basic experiments. The estimated scatterer diameters were close to the actual diameters. Furthermore, the transient change of the scatterer diameters were measured in an in vivo experiment with respect to a 24-year-old healthy male during the avascularization using a cuff. The estimated diameters (12-22 µm) of RBCs during avascularization were larger than the diameters (4-8 µm) at rest and after recirculation. These results show the possibility of the use of the proposed method for noninvasive assessment of RBC aggregation.

  2. Rotationally resolved à 2Πg←X˜2Πu electronic spectrum of triacetylene cation by frequency modulation absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Sinclair, Wayne E.; Pfluger, David; Linnartz, Harold; Maier, John P.

    1999-01-01

    The spectrum of the à 2Πg←X˜2Πu 000 band system of the triacetylene cation and isotopic derivatives DC6H+ and C6D2+ have been studied at Doppler-limited resolution using frequency modulation absorption spectroscopy. The ions were generated in a liquid-nitrogen-cooled hollow cathode discharge incorporated in a White cell. A discharge modulation in combination with the frequency modulation technique was used to enhance the detection sensitivity. Analyses of the rotational structure yield accurate rotational and spin-orbit interaction constants of triacetylene cation in the two electronic states and information on its geometry.

  3. ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Influence of a Single Frequency Electromagnetic Wave on Energy Spectrum of Nonpolariton System in a Kerr Nonlinear Blackbody

    NASA Astrophysics Data System (ADS)

    Zeng, Qi-Jun; Cheng, Ze

    2010-06-01

    In a Kerr nonlinear blackbody, bare photons with opposite wave vectors and helicities are bound into pairs and unpaired photons are transformed into a different kind of quasiparticle, the nonpolariton. The present paper investigates the influence of a single frequency electromagnetic wave on the energy spectrum of the nonpolariton system. We find that the wave can lead to an energy shift of nonpolaritons. Moreover, we calculate the first-order energy shift on certain conditions.

  4. Discovery of a low-frequency broad quasi-periodic oscillation peak in the power density spectrum of Cygnus X-1 with Granat/SIGMA

    NASA Astrophysics Data System (ADS)

    Vikhlinin, A.; Churazov, E.; Gilfanov, M.; Sunyaev, R.; Dyachkov, A.; Khavenson, N.; Kremnev, R.; Sukhanov, K.; Ballet, J.; Laurent, P.; Salotti, L.; Claret, A.; Olive, J. F.; Denis, M.; Mandrou, P.; Roques, J. P.

    1994-03-01

    A transient broad (delta(f)/f = 0.8 approximately 1) very low frequency (approximately 0.04-0.07 Hz) and strong (fractional rms variations are at the level of approximately 10-15% of total source intensity) quasi-periodic oscillations (QPO) feature was discovered by the SIGMA telescope onboard the Granat observatory in the power density spectra of Cygnus X-1; the source was during all the observations carried out in 1990-1992 in its standard (low or hard) spectral state (Sunyaev & Truemper 1979) with average 40-150 keV flux, corresponding appproximately to the 'nominal' gamma2 level of the source (Ling et al. 1979). The power density spectra, obtained in the 4 x 10-4-10 Hz frequency range, typically exhibit strong very low frequency noise below a few millihertz increasing toward lower frequencies, a nearly flat region from a few millihertz up to a break frequency fbr = 0.04 approximately 0.1 Hz and a power-law spectrum as f-1 above the break frequency. The QPO feature, when observed, was centered below or near the break frequency fbr.

  5. Universal form of the carrier frequency of scalar and vector paraxial X waves with orbital angular momentum and arbitrary frequency spectrum

    NASA Astrophysics Data System (ADS)

    Ornigotti, Marco; Conti, Claudio; Szameit, Alexander

    2015-10-01

    We report on the dependence of the carrier frequency of a nondiffracting optical pulse on the amount of orbital angular momentum it carries. We provide a unified universal form of such a dependence for the cases of both scalar and vector pulses with arbitrary frequency spectra. For the case of paraxial optical pulses we consider two different examples, namely, pulses with exponentially decaying spectra and Gaussian spectra.

  6. 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

  7. Visual Search Performance in the Autism Spectrum II: The Radial Frequency Search Task with Additional Segmentation Cues

    ERIC Educational Resources Information Center

    Almeida, Renita A.; Dickinson, J. Edwin; Maybery, Murray T.; Badcock, Johanna C.; Badcock, David R.

    2010-01-01

    The Embedded Figures Test (EFT) requires detecting a shape within a complex background and individuals with autism or high Autism-spectrum Quotient (AQ) scores are faster and more accurate on this task than controls. This research aimed to uncover the visual processes producing this difference. Previously we developed a search task using radial…

  8. An Electromagnetic Spectrum for Millennial Students: Teaching Light, Color, Energy, and Frequency Using the Electronic Devices of Our Time

    ERIC Educational Resources Information Center

    Murphy, Maureen Kendrick

    2010-01-01

    In this article, a comparison of student learning outcomes is made in sophomore-level physical science classes using a "traditional" pedagogical approach versus a "modern" approach. Specifically, when students were taught the electromagnetic spectrum using diagrams and examples that incorporate technological advances and electronic devices of our…

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

    PubMed

    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

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

    PubMed 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

  11. 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.

  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. The onset of shear modes in the high frequency spectrum of simple disordered systems: Current knowledge and perspectives

    DOE PAGESBeta

    Cunsolo, Alessandro; Suvorov, Alexey; Cai, Yong Q.

    2015-10-20

    In this study, nearly two decades of thorough Inelastic X Ray Scattering (IXS) studies of transverse-like excitation in the spectrum simple amorphous materials are reviewed. A particular attention is given to the case of liquid water and other prototypical samples, through a discussion of both solved and still open issues. Finally, the perspectives opened up by the development of next generation IXS instruments with unprecedented contrast and resolution bandwidth are briefly illustrated.

  14. Frequency-comb referenced spectroscopy of v4- and v5-excited hot bands in the 1.5 μm spectrum of C2H2

    NASA Astrophysics Data System (ADS)

    Twagirayezu, Sylvestre; Cich, Matthew J.; Sears, Trevor J.; McRaven, Christopher P.; Hall, Gregory E.

    2015-10-01

    Doppler-free transition frequencies for v4- and v5-excited hot bands have been measured in the v1 + v3 band region of the spectrum of acetylene using saturation dip spectroscopy with an extended cavity diode laser referenced to a frequency comb. The frequency accuracy of the measured transitions, as judged from line shape model fits and comparison to known frequencies in the v1 + v3 band itself, is between 3 and 22 kHz. This is some three orders of magnitude improvement on the accuracy and precision of previous line position estimates that were derived from the analysis of high-resolution Fourier transform infrared absorption spectra. Comparison to transition frequencies computed from constants derived from published Fourier transform infrared spectra shows that some upper rotational energy levels suffer specific perturbations causing energy level shifts of up to several hundred MHz. These perturbations are due to energy levels of the same rotational quantum number derived from nearby vibrational levels that become degenerate at specific energies. Future identification of the perturbing levels will provide accurate relative energies of excited vibrational levels of acetylene in the 7100-7600 cm-1 energy region.

  15. Inverse problem in ionospheric science: prediction of solar soft-X-ray spectrum from very low frequency radiosonde results

    NASA Astrophysics Data System (ADS)

    Palit, S.; Ray, S.; Chakrabarti, S. K.

    2016-05-01

    X-rays and gamma-rays from astronomical sources such as solar flares are mostly absorbed by the Earth's atmosphere. Resulting electron-ion production rate as a function of height depends on the intensity and wavelength of the injected spectrum and therefore the effects vary from one source to another. In other words, the ion density vs. altitude profile has the imprint of the incident photon spectrum. In this paper, we investigate whether we can invert the problem uniquely by deconvolution of the VLF amplitude signal to obtain the details of the injected spectrum. We find that it is possible to do this up to a certain accuracy. This leads us to the possibility of uninterrupted observation of X-ray photon spectra of solar flares that are often hindered by the restricted observation window of space satellites to avoid charge particle damages. Such continuous means of observation are essential in deriving information on time evolution of physical processes related to electron acceleration and interaction with plasma in solar atmosphere. Our method is useful to carry out a similar exercise to infer the spectra of more energetic events such as the Gamma Ray Bursts (GRBs), Soft Gamma-ray Repeaters (SGRs) etc., by probing even the lower part of the Earth's atmosphere. We thus show that to certain extent, the Earth's atmosphere could be used as a gigantic detector of relatively strong astronomical events.

  16. Prediction soft-X-ray spectrum of solar flares from Very Low Frequency observations: an inverse problem in ionospheric science

    NASA Astrophysics Data System (ADS)

    Palit, Sourav; Chakrabarti, Sandip Kumar; Ray, Suman

    2016-07-01

    Earth's lower ionosphere and upper atmosphere absorb X-rays and gamma-rays from astronomical sources such as solar flares, Short Gamma ray Repeaters (SGRs) or Gamma Ray Bursts (GRBs). The electron-ion production rates due to the ionization of such energetic photons at different heights depend on the intensity and wavelength of the injected spectrum and hence vary from one source to another. Obviously the ion density vs. altitude profile has the imprint of the incident photon spectrum. In this paper, we examine the possibility of inverting the electron density-height profiles uniquely by deconvolution of the VLF amplitude signal to obtain information on the injected spectrum. We have been able to reproduce the soft-X-ray part of the injected spectra from two different classes of solar flares with satisfactory accuracy. With the possibilities of probing even lower parts of the atmosphere, the method presented here is useful to carry out a similar exercise to infer the higher energy part of solar flare spectra and spectra of more energetic events such as the GRBs, SGRs etc. We show that to a certain accuracy, the Earth's atmosphere may be used as a gigantic detector of relatively strong ionizing extra-terrestrial events.

  17. Harnessing the Single Ion: Precision Measurements across the Optical Spectrum using a Trapped Strontium Ion Optical Frequency Standard

    NASA Astrophysics Data System (ADS)

    Madej, Alan

    2001-04-01

    Slightly over 25 years have passed since H. Dehmelt first proposed the concept of a frequency standard based on a single, trapped ion; at rest and probed by a highly stable laser. In the intervening years, dramatic advances have been made in the laser cooling and manipulation of atoms and ions, Hz level stabilization of lasers, and recently, in the direct measurement of optical frequencies to Cs atomic time standards. Today, the dream of such an ultimate, nearly unperturbed frequency standard has reached its first practical realizations. We describe our work using a single trapped and laser cooled ion of strontium that is probed on the ultra-narrow 445 THz (674 nm), 5s ^2S_1/2 - 4d ^2D_5/2 electric quadrupole transition of 0.4 Hz natural width. Through direct Cs atomic clock based measurements performed in 1998, the ^88Sr^+ system was measured to an accuracy of 200 Hz (5 X 10-13) and became the first internationally recognized single ion optical frequency standard. Under current experimental conditions, the magnitudes of the systematic shifts in the line center are estimated to be less than 1 part in 10^15. The Sr^+ ion system has been used in our laboratory in the measurement of an accurate laser system at 1.5 μm which was stabilized on a narrow two-photon transition in Rb at 778 nm. Recently, the single Sr^+ reference has been applied to the measurement of the 474 THz (633 nm) I_2/HeNe laser which is currently the most widely employed optical frequency standard and forms the basis for world-wide precision length metrology. Moreover, a single ion based measurement of the JILA/NIST, I_2/HeNe system has verified the accuracy of optical frequency measurement using mode-locked femtosecond lasers to a level of 700 Hz. The recent breakthrough in absolute frequency determination provided by femtosecond laser frequency combs has indeed provided a straightforward technology to relate disparate optical frequencies with each other and to Rf atomic clocks. Work will be

  18. A spectral-timing analysis of the kHz QPOs in 4U 1636-53: the frequency-energy resolved RMS spectrum

    NASA Astrophysics Data System (ADS)

    Ribeiro, Evandro M.; Mendez, Mariano; Zhang, Guo-Bao; De Avellar, Márcio G. B.

    2016-07-01

    Our understanding of quasi-periodic oscillations (QPO) has been further advanced in the last few years by the use of combined spectral and timing techniques, and it is now clear that QPO properties are closely related to the spectral state of the source in which they appear. In this work we used all the available RXTE observations of the neutron-star low-mass X-ray binary 4U~1636-53 to study the properties of the kilohertz QPO as a function of energy and frequency. By following the frequency evolution of the kHz QPOs we created frequency-resolved fractional RMS spectra. We also studied the connection between the frequency of the kHz QPOs and the parameters of the model that fits the X-ray energy spectrum. We show the dependence of the QPO properties in a multi-parameter space, and we discuss the implication of our results to the mechanism that produces the QPOs. Our results provide input to the next generation of spectral-timing models, which will help us understand the variability and the environment around the neutron star in these systems.

  19. A Revised Method of Presenting Wavenumber-Frequency Power Spectrum Diagrams That Reveals the Asymmetric Nature of Tropical Large-scale Waves

    NASA Technical Reports Server (NTRS)

    Chao, Winston C.; Yang, Bo; Fu, Xiouhua

    2007-01-01

    The popular method of presenting wavenumber-frequency power spectrum diagrams for studying tropical large-scale waves in the literature is shown to give an incomplete presentation of these waves. The so-called "convectively-coupled Kelvin (mixed Rossby-gravity) waves" are presented as existing only in the symmetric (antisymmetric) component of the diagrams. This is obviously not consistent with the published composite/regression studies of "convectively-coupled Kelvin waves," which illustrate the asymmetric nature of these waves. The cause of this inconsistency is revealed in this note and a revised method of presenting the power spectrum diagrams is proposed. When this revised method is used, "convectively-coupled Kelvin waves" do show anti-symmetric components, and "convectively-coupled mixed Rossby-gravity waves (also known as Yanai waves)" do show a hint of symmetric components. These results bolster a published proposal that these waves be called "chimeric Kelvin waves," "chimeric mixed Rossby-gravity waves," etc. This revised method of presenting power spectrum diagrams offers a more rigorous means of comparing the General Circulation Models (GCM) output with observations by calling attention to the capability of GCMs in correctly simulating the asymmetric characteristics of the equatorial waves.

  20. 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

  1. 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

  2. Do car-mounted mobile measurements used for radio-frequency spectrum regulation have an application for exposure assessments in epidemiological studies?

    PubMed

    Bolte, John F B; Maslanyj, Myron; Addison, Darren; Mee, Terry; Kamer, Jos; Colussi, Loek

    2016-01-01

    Knowing the spatial and temporal trends in environmental exposure to radiofrequency electromagnetic fields is important in studies investigating whether there are associated health effects on humans and ecological effects on plants and animals. The main objective of this study is to assess whether the RFeye car-mounted mobile measurement system used for radio frequency spectrum monitoring in The Netherlands and the United Kingdom could be of value in assessing exposure over large areas as an alternative to measuring exposure with personal exposure meters or using complex modelling techniques. We evaluated the responses of various body-worn personal exposure meters in comparison with the mobile measurement system for spectrum monitoring. The comparison was restricted to downlink mobile communication in the GSM900 and GSM1800 frequency bands. Repeated measurements were performed in three areas in Cambridge, United Kingdom and in three areas in Amersfoort, The Netherlands. We found that exposure assessments through the car-mounted measurements are at least of similar quality to exposure modelling and better than the body worn exposimeter data due to the absence of the shielding effect. The main conclusion is that the mobile measurements provide an efficient and low cost alternative particularly in mapping large areas. PMID:26540087

  3. Evaluation of the Fourier Frequency Spectrum Peaks of Milk Electrical Conductivity Signals as Indexes to Monitor the Dairy Goats' Health Status by On-Line Sensors.

    PubMed

    Zaninelli, Mauro; Agazzi, Alessandro; Costa, Annamaria; Tangorra, Francesco Maria; Rossi, Luciana; Savoini, Giovanni

    2015-01-01

    The aim of this study is a further characterization of the electrical conductivity (EC) signal of goat milk, acquired on-line by EC sensors, to identify new indexes representative of the EC variations that can be observed during milking, when considering not healthy (NH) glands. Two foremilk gland samples from 42 Saanen goats, were collected for three consecutive weeks and for three different lactation stages (LS: 0-60 Days In Milking (DIM); 61-120 DIM; 121-180 DIM), for a total amount of 1512 samples. Bacteriological analyses and somatic cells counts (SCC) were used to define the health status of the glands. With negative bacteriological analyses and SCC < 1,000,000 cells/mL, glands were classified as healthy. When bacteriological analyses were positive or showed a SCC > 1,000,000 cells/mL, glands were classified as NH. For each milk EC signal, acquired on-line and for each gland considered, the Fourier frequency spectrum of the signal was calculated and three representative frequency peaks were identified. To evaluate data acquired a MIXED procedure was used considering the HS, LS and LS × HS as explanatory variables in the statistical model.Results showed that the studied frequency peaks had a significant relationship with the gland's health status. Results also explained how the milk EC signals' pattern change in case of NH glands. In fact, it is characterized by slower fluctuations (due to the lower frequencies of the peaks) and by an irregular trend (due to the higher amplitudes of all the main frequency peaks). Therefore, these frequency peaks could be used as new indexes to improve the performances of algorithms based on multivariate models which evaluate the health status of dairy goats through the use of gland milk EC sensors. PMID:26307993

  4. Evaluation of the Fourier Frequency Spectrum Peaks of Milk Electrical Conductivity Signals as Indexes to Monitor the Dairy Goats’ Health Status by On-Line Sensors

    PubMed Central

    Zaninelli, Mauro; Agazzi, Alessandro; Costa, Annamaria; Tangorra, Francesco Maria; Rossi, Luciana; Savoini, Giovanni

    2015-01-01

    The aim of this study is a further characterization of the electrical conductivity (EC) signal of goat milk, acquired on-line by EC sensors, to identify new indexes representative of the EC variations that can be observed during milking, when considering not healthy (NH) glands. Two foremilk gland samples from 42 Saanen goats, were collected for three consecutive weeks and for three different lactation stages (LS: 0–60 Days In Milking (DIM); 61–120 DIM; 121–180 DIM), for a total amount of 1512 samples. Bacteriological analyses and somatic cells counts (SCC) were used to define the health status of the glands. With negative bacteriological analyses and SCC < 1,000,000 cells/mL, glands were classified as healthy. When bacteriological analyses were positive or showed a SCC > 1,000,000 cells/mL, glands were classified as NH. For each milk EC signal, acquired on-line and for each gland considered, the Fourier frequency spectrum of the signal was calculated and three representative frequency peaks were identified. To evaluate data acquired a MIXED procedure was used considering the HS, LS and LS × HS as explanatory variables in the statistical model.Results showed that the studied frequency peaks had a significant relationship with the gland’s health status. Results also explained how the milk EC signals’ pattern change in case of NH glands. In fact, it is characterized by slower fluctuations (due to the lower frequencies of the peaks) and by an irregular trend (due to the higher amplitudes of all the main frequency peaks). Therefore, these frequency peaks could be used as new indexes to improve the performances of algorithms based on multivariate models which evaluate the health status of dairy goats through the use of gland milk EC sensors. PMID:26307993

  5. Extensive sequence variation in rice blast resistance gene Pi54 makes it broad spectrum in nature

    PubMed Central

    Thakur, Shallu; Singh, Pankaj K.; Das, Alok; Rathour, R.; Variar, M.; Prashanthi, S. K.; Singh, A. K.; Singh, U. D.; Chand, Duni; Singh, N. K.; Sharma, Tilak R.

    2015-01-01

    Rice blast resistant gene, Pi54 cloned from rice line, Tetep, is effective against diverse isolates of Magnaporthe oryzae. In this study, we prospected the allelic variants of the dominant blast resistance gene from a set of 92 rice lines to determine the nucleotide diversity, pattern of its molecular evolution, phylogenetic relationships and evolutionary dynamics, and to develop allele specific markers. High quality sequences were generated for homologs of Pi54 gene. Using comparative sequence analysis, InDels of variable sizes in all the alleles were observed. Profiling of the selected sites of SNP (Single Nucleotide Polymorphism) and amino acids (N sites ≥ 10) exhibited constant frequency distribution of mutational and substitutional sites between the resistance and susceptible rice lines, respectively. A total of 50 new haplotypes based on the nucleotide polymorphism was also identified. A unique haplotype (H_3) was found to be linked to all the resistant alleles isolated from indica rice lines. Unique leucine zipper and tyrosine sulfation sites were identified in the predicted Pi54 proteins. Selection signals were observed in entire coding sequence of resistance alleles, as compared to LRR domains for susceptible alleles. This is a maiden report of extensive variability of Pi54 alleles in different landraces and cultivated varieties, possibly, attributing broad-spectrum resistance to Magnaporthe oryzae. The sequence variation in two consensus region: 163 and 144 bp were used for the development of allele specific DNA markers. Validated markers can be used for the selection and identification of better allele(s) and their introgression in commercial rice cultivars employing marker assisted selection. PMID:26052332

  6. Cosmic Electromagnetic Radiation: The sky shine covers an enormous spectrum of frequencies, revealing a cosmic picture in some detail.

    PubMed

    Hafner, E M

    1964-09-18

    Within a few decades astronomy has extended the compass of its observations from the visible spectrum downward to radio waves and upward to the highest energies known to science. The major new accomplishments are in the radio and x-ray bands, and in the associated study of cosmic ray electrons. Synchrotron radiation is known to be a mechanism for radio signals; discrete x-ray sources have been found; the intensity and the charge ratio of galactic electrons are under study. Experimental results at energies above the x-ray region are less firm. The sun surely emits gamma rays at energies of about 1 Mev during flare activity, and instruments in deep space have probably recorded the general galactic glow of similar photons. Upper limits for fluxes have been set at 100 Mev and beyond. To some extent the physical processes which give rise to the extraterrestrial radiation are familiar to workers in the terrestrial laboratory. Synchrotron radiation is an example; the bremsstrahlung of electrons, the production of neutral pions in p-p collisions, and the annihilation of electron and nucleon pairs are others. Some proposed mechanisms are, and perhaps always will be, purely speculative in the sense that they are not directly observable in the laboratory. The inverse Compton effect, possibly one of the sources of a metagalactic sky glow of hard photons, is in this class. There is little chance that spontaneous creation of matter, even if it occurs in nature, can be observed on a terrestrial scale. And the extreme physical conditions proposed for neutron stars are beyond our ability to reproduce. Only through interpretation of astronomical data can we test the validity of these ideas. The many pictures of the universe given by the vast electromagnetic spectrum are essential to the synthesis of our concepts. PMID:17802004

  7. High-frequency oscillatory response to illusory contour in typically developing boys and boys with autism spectrum disorders.

    PubMed

    Stroganova, Tatiana A; Orekhova, Elena V; Prokofyev, Andrey O; Tsetlin, Marina M; Gratchev, Vitaliy V; Morozov, Alexey A; Obukhov, Yuriy V

    2012-06-01

    Illusory contour (IC) perception, a fruitful model for studying the automatic contextual integration of local image features, can be used to investigate the putative impairment of such integration in children with autism spectrum disorders (ASD). We used the illusory Kanizsa square to test how the phase-locked (PL) gamma and beta electroencephalogram (EEG) responses of typically developing (TD) children aged 3-7 years and those with ASD were modulated by the presence of IC in the image. The PL beta and gamma activity strongly differentiated between IC and control figures in both groups of children (IC effect). However, the timing, topography, and direction of the IC effect differed in TD and ASD children. Between 40 msec and 120 msec after stimulus onset, both groups demonstrated lower power of gamma oscillations at occipital areas in response to IC than in response to the control figure. In TD children, this relative gamma suppression was followed by relatively higher parieto-occipital gamma and beta responses to IC within 120-270 msec after stimulus onset. This second stage of IC processing was absent in children with ASD. Instead, their response to IC was characterized by protracted (40-270 msec) relative reduction of gamma and beta oscillations at occipital areas. We hypothesize that children with ASD rely more heavily on lower-order processing in the primary visual areas and have atypical later stage related to higher-order processes of contour integration. PMID:21458787

  8. SLC26A2 disease spectrum in Sweden - high frequency of recessive multiple epiphyseal dysplasia (rMED).

    PubMed

    Mäkitie, O; Geiberger, S; Horemuzova, E; Hagenäs, L; Moström, E; Nordenskjöld, M; Grigelioniene, G; Nordgren, A

    2015-03-01

    Diastrophic dysplasia (DTD) is an autosomal recessive skeletal dysplasia caused by SLC26A2 mutations. Clinical features include short stature, joint contractures, spinal deformities, and cleft palate. SLC26A2 mutations also result in other skeletal dysplasias, including the milder recessive multiple epiphyseal dysplasia (rMED). DTD is overrepresented in Finland and we speculated that this may have influenced the prevalence and spectrum of SLC26A2-related skeletal conditions also in Sweden. We reviewed the patient registry at Department of Clinical Genetics, Karolinska University Hospital, Stockholm to identify subjects with SLC26A2 mutations. Seven patients from six families were identified; clinical data were available for six patients. All but one patient had one or two copies of the Finnish SLC26A2 founder mutation IVS1+2T>C. Arg279Trp mutation was present in compound heterozygous form in five patients with phenotypes consistent with rMED. Their heights ranged from -2.6 to -1.4 standard deviation units below normal mean and radiographic features included generalised epiphyseal dysplasia and double-layered patellae. Two rMED patients had hypoplastic C2 and cervical kyphosis, a severe manifestation previously described only in DTD. Our study confirms a high prevalence of rMED in Sweden and expands the phenotypic manifestations of rMED. PMID:24598000

  9. Two-frequency microwave resonance measurements from an aircraft - A quantitative estimate of the directional ocean surface spectrum

    NASA Technical Reports Server (NTRS)

    Johnson, J. W.; Weissman, D. E.

    1984-01-01

    The use of the two-frequency microwave-resonance technique for airborne measurements of ocean surface-wave spectral components is examined in a summary of experiments conducted with a coherent Ku-band radar flown on a P-3 aircraft in the 1979 MARSEN and 1980 ARSLOE projects. The 1D theoretical formulation used in the analysis of the MARSEN data by Johnson et al. (1982) is extended to the 2D case; the experimental conditions are described in detail; and typical data are presented graphically, analyzed, and compared with independent measurements obtained with a surface-contour radar. The 3.5-deg pencil-beam configuration used in ARSLOE is shown to produce spectra with good directional characteristics (strong resonances at angles of incidence 13-48 deg). It is found that the proper inversion of radar data to surface-elevation spectra requires surface-reflectivity-modulation sources in addition to the long-wave orbital velocity.

  10. 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

  11. Inherent-jitter effects in the new rapid acquisition method for frequency-hopped push-to-talk spread spectrum systems: A jitter-fighting scheme

    NASA Astrophysics Data System (ADS)

    Pereira, Jorge M. N.; Albuquerque, Augusto A.

    1988-12-01

    A critical problem in Push-to-Talk Frequency-Hopped Spread-Spectrum systems is its vulnerability to eavesdropping during the necessary preamble, or to possible reproduction by a would-be interferer. A new acquisition method has been envisioned, and is presented, to reduce this weakness, permitting the receiver to work in lower signal-to-noise ratio and to acquire faster than in any known system. The essence of the new method is the use of sliding-window integration non-coherent detectors and a decision rate much higher than the hopping one, and coincident with the window-relocation rate. The inherent-jitter effects in the new method are described, and results presented for an optimal (omniscient) system, after jitter-bypassing. A jitter-fighting scheme is then proposed and its performance and adequacy analyzed.

  12. New insights on frequency combinations and ‘forbidden frequencies’ in the de Haas–van Alphen spectrum of κ-(ET)2Cu(SCN)2

    NASA Astrophysics Data System (ADS)

    Audouard, Alain; Fortin, Jean-Yves; Vignolles, David; Laukhin, Vladimir N.; Kushch, Nataliya D.; Yagubskii, Eduard B.

    2016-07-01

    de Haas–van Alphen oscillations of the organic metal κ-(ET)2Cu(SCN)2 have been measured up to 55 T at liquid helium temperatures. The Fermi surface of this charge transfer salt is a textbook example of a linear chain of orbits coupled by magnetic breakdown. Accordingly, the oscillation spectrum is composed of linear combinations of the frequencies linked to the α and magnetic breakdown-induced β orbits. The field and temperature dependence of all the observed Fourier components, in particular the ‘forbidden frequency’ β -α which cannot correspond to a classical orbit, are quantitatively accounted for by analytical calculations based on a second order development of the free energy, i.e. beyond the first order Lifshitz–Kosevich formula.

  13. Wide allelic heterogeneity with predominance of large IDS gene complex rearrangements in a sample of Mexican patients with Hunter syndrome.

    PubMed

    Alcántara-Ortigoza, M A; García-de Teresa, B; González-Del Angel, A; Berumen, J; Guardado-Estrada, M; Fernández-Hernández, L; Navarrete-Martínez, J I; Maza-Morales, M; Rius-Domínguez, R

    2016-05-01

    Hunter syndrome or mucopolysaccharidosis type II (MPSII) is caused by pathogenic variants in the IDS gene. This is the first study that examines the mutational spectrum in 25 unrelated Mexican MPSII families. The responsible genotype was identified in 96% of the families (24/25) with 10 novel pathogenic variants: c.133G>C, c.1003C>T, c.1025A>C, c.463_464delinsCCGTATAGCTGG, c.754_767del, c.1132_1133del, c.1463del, c.508-1G>C, c.1006+1G>T and c.(-217_103del). Extensive IDS gene deletions were identified in four patients; using DNA microarray analysis two patients showed the loss of the entire AFF2 gene, and epilepsy developed in only one of them. Wide allelic heterogeneity was noted, with large gene alterations (e.g. IDS/IDSP1 gene inversions, partial to extensive IDS deletions, and one chimeric IDS-IDSP1 allele) that occurred at higher frequencies than previously reported (36% vs 18.9-29%). The frequency of carrier mothers (80%) is consistent with previous descriptions (>70%). Carrier assignment allowed molecular prenatal diagnoses. Notably, somatic and germline mosaicism was identified in one family, and two patients presented thrombocytopenic purpura and pancytopenia after idursulfase enzyme replacement treatment. Our findings suggest a wide allelic heterogeneity in Mexican MPSII patients; DNA microarray analysis contributes to further delineation of the resulting phenotype for IDS and neighboring loci deletions. PMID:26762690

  14. Hybrid spread spectrum radio system

    DOEpatents

    Smith, Stephen F [London, TN; Dress, William B [Camas, WA

    2010-02-09

    Systems and methods are described for hybrid spread spectrum radio systems. A method, includes receiving a hybrid spread spectrum signal including: fast frequency hopping demodulating and direct sequence demodulating a direct sequence spread spectrum signal, wherein multiple frequency hops occur within a single data-bit time and each bit is represented by chip transmissions at multiple frequencies.

  15. 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

  16. 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

  17. Initial results from spatially averaged coherency, frequency-wavenumber, and horizontal to vertical spectrum ratio microtremor survey methods for site hazard study at Launceston, Tasmania

    NASA Astrophysics Data System (ADS)

    Claprood, Maxime; Asten, Michael W.

    2009-02-01

    The Tamar rift valley runs through the City of Launceston, Tasmania. Damage has occurred to city buildings due to earthquake activity in Bass Strait. The presence of the ancient valley, the Tamar valley, in-filled with soft sediments that vary rapidly in thickness from 0 to 250m over a few hundreds metres, is thought to induce a 2D resonance pattern, amplifying the surface motions over the valley and in Launceston. Spatially averaged coherency (SPAC), frequency-wavenumber (FK) and horizontal to vertical spectrum ratio (HVSR) microtremor survey methods are combined to identify and characterise site effects over the Tamar valley. Passive seismic array measurements acquired at seven selected sites were analysed with SPAC to estimate shear wave velocity (slowness) depth profiles. SPAC was then combined with HVSR to improve the resolution of these profiles in the sediments to an approximate depth of 125m. Results show that sediments thicknesses vary significantly throughout Launceston. The top layer is composed of as much as 20m of very soft Quaternary alluvial sediments with a velocity from 50m/s to 125m/s. Shear-wave velocities in the deeper Tertiary sediment fill of the Tamar valley, with thicknesses from 0 to 250m vary from 400m/s to 750m/s. Results obtained using SPAC are presented at two selected sites (GUN and KPK) that agree well with dispersion curves interpreted with FK analysis. FK interpretation is, however, limited to a narrower range of frequencies than SPAC and seems to overestimate the shear wave velocity at lower frequencies. Observed HVSR are also compared with the results obtained by SPAC, assuming a layered earth model, and provide additional constraints on the shear wave slowness profiles at these sites. The combined SPAC and HVSR analysis confirms the hypothesis of a layered geology at the GUN site and indicates the presence of a 2D resonance pattern across the Tamar valley at the KPK site.

  18. MAGIC gamma-ray and multi-frequency observations of flat spectrum radio quasar PKS 1510-089 in early 2012

    NASA Astrophysics Data System (ADS)

    Aleksić, J.; Ansoldi, S.; Antonelli, L. A.; Antoranz, P.; Babic, A.; Bangale, P.; Barres de Almeida, U.; Barrio, J. A.; Becerra González, J.; Bednarek, W.; Bernardini, E.; Biland, A.; Blanch, O.; Bonnefoy, S.; Bonnoli, G.; Borracci, F.; Bretz, T.; Carmona, E.; Carosi, A.; Carreto Fidalgo, D.; Colin, P.; Colombo, E.; Contreras, J. L.; Cortina, J.; Covino, S.; Da Vela, P.; Dazzi, F.; De Angelis, A.; De Caneva, G.; De Lotto, B.; Delgado Mendez, C.; Doert, M.; Domínguez, A.; Dominis Prester, D.; Dorner, D.; Doro, M.; Einecke, S.; Eisenacher, D.; Elsaesser, D.; Farina, E.; Ferenc, D.; Fonseca, M. V.; Font, L.; Frantzen, K.; Fruck, C.; García López, R. J.; Garczarczyk, M.; Garrido Terrats, D.; Gaug, M.; Godinović, N.; González Muñoz, A.; Gozzini, S. R.; Hadasch, D.; Hayashida, M.; Herrera, J.; Herrero, A.; Hildebrand, D.; Hose, J.; Hrupec, D.; Idec, W.; Kadenius, V.; Kellermann, H.; Kodani, K.; Konno, Y.; Krause, J.; Kubo, H.; Kushida, J.; La Barbera, A.; Lelas, D.; Lewandowska, N.; Lindfors, E.; Lombardi, S.; López, M.; López-Coto, R.; López-Oramas, A.; Lorenz, E.; Lozano, I.; Makariev, M.; Mallot, K.; Maneva, G.; Mankuzhiyil, N.; Mannheim, K.; Maraschi, L.; Marcote, B.; Mariotti, M.; Martínez, M.; Mazin, D.; Menzel, U.; Meucci, M.; Miranda, J. M.; Mirzoyan, R.; Moralejo, A.; Munar-Adrover, P.; Nakajima, D.; Niedzwiecki, A.; Nilsson, K.; Nishijima, K.; Noda, K.; Nowak, N.; Orito, R.; Overkemping, A.; Paiano, S.; Palatiello, M.; Paneque, D.; Paoletti, R.; Paredes, J. M.; Paredes-Fortuny, X.; Partini, S.; Persic, M.; Prada, F.; Prada Moroni, P. G.; Prandini, E.; Preziuso, S.; Puljak, I.; Reinthal, R.; Rhode, W.; Ribó, M.; Rico, J.; Rodriguez Garcia, J.; Rügamer, S.; Saggion, A.; Saito, T.; Saito, K.; Satalecka, K.; Scalzotto, V.; Scapin, V.; Schultz, C.; Schweizer, T.; Shore, S. N.; Sillanpää, A.; Sitarek, J.; Snidaric, I.; Sobczynska, D.; Spanier, F.; Stamatescu, V.; Stamerra, A.; Steinbring, T.; Storz, J.; Strzys, M.; Sun, S.; Surić, T.; Takalo, L.; Takami, H.; Tavecchio, F.; Temnikov, P.; Terzić, T.; Tescaro, D.; Teshima, M.; Thaele, J.; Tibolla, O.; Torres, D. F.; Toyama, T.; Treves, A.; Uellenbeck, M.; Vogler, P.; Wagner, R. M.; Zandanel, F.; Zanin, R.; MAGIC Collaboration; Lucarelli, F.; Pittori, C.; Vercellone, S.; Verrecchia, F.; AGILE Collaboration; Buson, S.; D'Ammando, F.; Stawarz, L.; Giroletti, M.; Orienti, M.; Fermi-LAT Collaboration; Mundell, C.; Steele, I.; Zarpudin, B.; Raiteri, C. M.; Villata, M.; Sandrinelli, A.; Lähteenmäki, A.; Tammi, J.; Tornikoski, M.; Hovatta, T.; Readhead, A. C. S.; Max-Moerbeck, W.; Richards, J. L.; Jorstad, S.; Marscher, A.; Gurwell, M. A.; Larionov, V. M.; Blinov, D. A.; Konstantinova, T. S.; Kopatskaya, E. N.; Larionova, L. V.; Larionova, E. G.; Morozova, D. A.; Troitsky, I. S.; Mokrushina, A. A.; Pavlova, Yu. V.; Chen, W. P.; Lin, H. C.; Panwar, N.; Agudo, I.; Casadio, C.; Gómez, J. L.; Molina, S. N.; Kurtanidze, O. M.; Nikolashvili, M. G.; Kurtanidze, S. O.; Chigladze, R. A.; Acosta-Pulido, J. A.; Carnerero, M. I.; Manilla-Robles, A.; Ovcharov, E.; Bozhilov, V.; Metodieva, I.; Aller, M. F.; Aller, H. D.; Fuhrman, L.; Angelakis, E.; Nestoras, I.; Krichbaum, T. P.; Zensus, J. A.; Ungerechts, H.; Sievers, A.

    2014-09-01

    Aims: Amongst more than fifty blazars detected in very high energy (VHE, E> 100 GeV) γ rays, only three belong to the subclass of flat spectrum radio quasars (FSRQs). The detection of FSRQs in the VHE range is challenging, mainly because of their soft spectra in the GeV-TeV regime. MAGIC observed PKS 1510-089 (z = 0.36) starting 2012 February 3 until April 3 during a high activity state in the high energy (HE, E> 100 MeV) γ-ray band observed by AGILE and Fermi. MAGIC observations result in the detection of a source with significance of 6.0 standard deviations (σ). We study the multi-frequency behaviour of the source at the epoch of MAGIC observation, collecting quasi-simultaneous data at radio and optical (GASP-WEBT and F-Gamma collaborations, REM, Steward, Perkins, Liverpool, OVRO, and VLBA telescopes), X-ray (Swift satellite), and HE γ-ray frequencies. Methods: We study the VHE γ-ray emission, together with the multi-frequency light curves, 43 GHz radio maps, and spectral energy distribution (SED) of the source. The quasi-simultaneous multi-frequency SED from the millimetre radio band to VHE γ rays is modelled with a one-zone inverse Compton model. We study two different origins of the seed photons for the inverse Compton scattering, namely the infrared torus and a slow sheath surrounding the jet around the Very Long Baseline Array (VLBA) core. Results: We find that the VHE γ-ray emission detected from PKS 1510-089 in 2012 February-April agrees with the previous VHE observations of the source from 2009 March-April. We find no statistically significant variability during the MAGIC observations on daily, weekly, or monthly time scales, while the other two known VHE FSRQs (3C 279 and PKS 1222+216) have shown daily scale to sub-hour variability. The γ-ray SED combining AGILE, Fermi and MAGIC data joins smoothly and shows no hint of a break. The multi-frequency light curves suggest a common origin for the millimetre radio and HE γ-ray emission, and the HE

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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

  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. Going far beyond the near-field diffraction limit via plasmonic cavity lens with high spatial frequency spectrum off-axis illumination.

    PubMed

    Zhao, Zeyu; Luo, Yunfei; Zhang, Wei; Wang, Changtao; Gao, Ping; Wang, Yanqin; Pu, Mingbo; Yao, Na; Zhao, Chengwei; Luo, Xiangang

    2015-01-01

    For near-field imaging optics, minimum resolvable feature size is highly constrained by the near-field diffraction limit associated with the illumination light wavelength and the air distance between the imaging devices and objects. In this study, a plasmonic cavity lens composed of Ag-photoresist-Ag form incorporating high spatial frequency spectrum off-axis illumination (OAI) is proposed to realize deep subwavelength imaging far beyond the near-field diffraction limit. This approach benefits from the resonance effect of the plasmonic cavity lens and the wavevector shifting behavior via OAI, which remarkably enhances the object's subwavelength information and damps negative imaging contribution from the longitudinal electric field component in imaging region. Experimental images of well resolved 60-nm half-pitch patterns under 365-nm ultra-violet light are demonstrated at air distance of 80 nm between the mask patterns and plasmonic cavity lens, approximately four-fold longer than that in the conventional near-field lithography and superlens scheme. The ultimate air distance for the 60-nm half-pitch object could be theoretically extended to 120 nm. Moreover, two-dimensional L-shape patterns and deep subwavelength patterns are illustrated via simulations and experiments. This study promises the significant potential to make plasmonic lithography as a practical, cost-effective, simple and parallel nano-fabrication approach. PMID:26477856

  6. Using Singular Spectrum Analysis to Identify Low-Frequency Components in Climate and Runoff in Two Physiographic Regions of the Colorado River Basin

    NASA Astrophysics Data System (ADS)

    Sedmera, K. A.; Duffy, C. J.

    2001-05-01

    In this research singular spectrum analysis (SSA) is used to study the spatio-temporal patterns in historical records of precipitation (P), temperature (T), and runoff (Q) in the San Juan and the San Pedro river basins. These two sub-basins of the Colorado River are considered to be representative of the Colorado Plateau and Basin and Range physiographic provinces, respectively. SSA is a diagnostic signal-processing tool used in our research to identify important changes in the climate and runoff within a regional watershed, such as the two mentioned. Our goals are to better understand the relative importance of land use and climate change on the runoff from these two landforms (using SSA) and to begin developing a multi-scale dynamical model that reflects the characteristic processes and scales of the regional hydrology and hydrogeology. The main theme of this poster is a general discussion of how the climatic forcing of the San Pedro and San Juan watersheds relate to the regional runoff pattern. In general, the analysis shows that the climate and runoff records for these watersheds are primarily dominated by the annual/seasonal cycle and relatively weak interannual (ENSO) oscillations. The ENSO signal in P and T appears to be stronger at higher elevations than at lower elevations. Runoff results show that these two basins (and even a few sub-basins in the San Juan region) respond differently to these low-frequency inputs. Both basins appear to act as a low-pass filter on the P and T inputs (likely due to surface and groundwater storage effects), causing the low-frequency content to become more dominant downstream. The trends in some of the runoff records are easily attributed to the installation of reservoirs and land use changes (irrigation). Phase-plane plots of the "noise-free" P-T-Q records for each physiographic region are given to compare the low-frequency response within and between basins. These results suggest that there are only a few unique hydrologic

  7. 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.

  8. Battlefield spectrum management

    NASA Astrophysics Data System (ADS)

    Sivakumar, C.

    1997-06-01

    Modern tactical communications systems rely on radios to support network and user connectivity. One of the challenges for network planners and managers is to make best use of scarce and vulnerable frequency spectrum resources to support the communication needs of war fighters. With the wide variety of Iris radio types typically to be deployed in the battlefield (ranging from high frequency to super high frequency), a comprehensive suite of tools is necessary to ensure that frequency interference is kept minimum. Without a sophisticated frequency spectrum management system, the most advanced tactical communications systems could be rendered useless, jeopardizing human life and national security. For these reasons, it is important to develop an Iris wide battlefield spectrum management capability that takes full advantage of current frequency spectrum management research and development (R&D), related tools, and supporting technology for assigning frequencies. This session briefly describes various assignment strategies being adopted in the Iris BFSM for overcoming cosite/collocated/farsite interferences along with the propagation models [from high frequency (HF) to super high frequency (SHF)] used for the assignment of frequencies. Also a brief thread outlining the process for generating frequency allocation/assignment request and analysis of frequency interference is discussed.

  9. The Frequency of Anti-Aquaporin-4 Ig G Antibody in Neuromyelitis Optica and Its Spectrum Disorders at a Single Tertiary Referral Center in Malaysia

    PubMed Central

    Viswanathan, Shanthi; Arip, Masita; Dhaliwal, Jasbir S.; Rose, Norzainie; Muda, Sobri; Puvanarajah, Santhi Datuk; Rafia, Mohammad Hanip; Wing Loong, Mark Cheong

    2014-01-01

    Background. In the past the occurrence of neuromyelitis optica in Malaysia was thought to be uncommon and the frequency of anti-aquaporin-4 Ig G antibody was unknown. Objective. To evaluate the frequency of anti-aquaporin-4 Ig G antibody (Anti-AQP4 antibody) amongst patients with neuromyelitis optica (NMO) and its spectrum disorders (NMOSD) and the differences between the seropositive and seronegative groups. Methods. Retrospectively, 96 patients with NMO/high risk syndromes for NMOSD (HRS-NMOSD) were identified out of 266 patients with idiopathic inflammatory demyelinating disease from a single center hospital based registry. Anti-AQP4 seropositivity was found in 38/48 (79.2%) with NMO, 12/21 (57.1%) with brain involvement at high risk for NMOSD, 12/15 (80%) with transverse myelitis (i.e., 11/15 with relapsing transverse myelitis and one with monophasic transverse myelitis), and 3/7 (42.8%) with relapsing optic neuritis. Sixty-five out of 96 patients, that is, 67.7%, with NMO/HRS for NMOSD were seropositive. Seropositivity was significantly associated with female gender, a higher number of mean relapses, that is, 5.15 ± 4.42 versus 2.10 ± 1.68, longer length of spinal cord lesions, that is, 6.6 ± 4.9 versus 2.9 ± 2.5, vertebral bodies, higher EDSS, 4.5 ± 2.4 versus 2.4 ± 2.6, presence of paroxysmal tonic spasms, and blindness (unilateral/bilateral); P < 0.001. Longitudinally extensive cord lesions (contiguous or linear), presence of lesions in the cervical and thoracic regions, and involvement of the central gray matter or holocord regions on axial scans, were also significantly associated with seropositivity; P < 0.001. Conclusion. NMO and HRS for NMOSD are present in larger numbers than previously thought in Malaysia. More than 2/3rds are seropositive. Seropositive and seronegative NMO/NMOSD have differences that are useful in clinical practice. PMID:25548676

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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-allele homozygous (allelic disparity). The chi-squared and Cochran-Armitage trend tests were used to examine whether there is an association between high levels of disparity in single nucleotide polymorphisms (SNPs) and molecular, clinical and tumour-related parameters. To identify pathways and network functions over-represented within the resulting gene sets, we used Ingenuity Pathway Analysis (IPA). Results To identify loci with a high level of disparity, we selected SNPs 1) with a substantial degree of disparity and 2) with substantial frequency (at least 50% of the samples heterozygous for the respective locus). We report the overall difference in disparity in high-grade tumours compared to low-grade tumours (p-value < 0.001) and significant associations between disparity in multiple single loci and clinical parameters. The most significantly associated network functions within the genes represented in the loci of disparity were identified, including lipid metabolism, small-molecule biochemistry, and nervous system development and function. No evidence for over-representation of directional disparity in a list of stem cell genes was obtained, however genes appeared to be more often altered by deletion than by

  16. Sex differences in the JAK2V617F allele burden in chronic myeloproliferative disorders

    PubMed Central

    Stein, Brady L.; Williams, Donna M.; Wang, Nae-Yuh; Rogers, Ophelia; Isaacs, Mary Ann; Pemmaraju, Naveen; Spivak, Jerry L.; Moliterno, Alison R.

    2010-01-01

    Background The JAK2V617F allele burden is a variable measure, determined by the frequency of mitotic recombination events and the expansion of JAK2V617F clones. Since variability in the JAK2V617F allele burden is partly responsible for the distinct phenotypes seen in the myeloproliferative disorders, the objective of this study was to identify modifiers of the allele burden. Design and Methods Blood samples were obtained between May 2005 and January 2009 from 272 patients with essential thrombocytosis, polycythemia vera, and myelofibrosis. The JAK2V617F allele burden was measured by an allele-specific quantitative polymerase chain reaction using DNA from purified neutrophils. Repeated measures, on average 2 years apart, were available for 104 patients. Results Sex, age at diagnosis, and disease duration all independently influenced the JAK2V617F allele burden. When considering all patients with myeloproliferative disorders, women had significantly lower allele burdens than men (P=0.04). In those patients with repeated measures, the increase in allele burden per year between the first and second evaluations was significantly less in females than in males. Among those who experienced disease evolution, females were 4.5 times more likely to have evolution from essential thrombocytosis to polycythemia vera, but 0.23 times as likely to have evolution from essential thrombocytosis to myelofibrosis. Conclusions Sex is an independent factor accounting for variability in the JAK2V617F allele burden. We speculate that lower allele burdens in females reflect a lower frequency of mitotic recombination events in females than in males, and should be considered when evaluating the relationship of allele burden to disease phenotype and also in evaluating responses to JAK2V617F-inhibitors. Because sex may influence genotype and/or clonal expansion, underpinning the variability in JAK2V617F allele burden, it will be important to explore factors that determine susceptibility to

  17. Invasive Allele Spread under Preemptive Competition

    NASA Astrophysics Data System (ADS)

    Yasi, J. A.; Korniss, G.; Caraco, T.

    We study a discrete spatial model for invasive allele spread in which two alleles compete preemptively, initially only the "residents" (weaker competitors) being present. We find that the spread of the advantageous mutation is well described by homogeneous nucleation; in particular, in large systems the time-dependent global density of the resident allele is well approximated by Avrami's law.

  18. IMPROVED DETERMINATION OF THE 1{sub 0}-0{sub 0} ROTATIONAL FREQUENCY OF NH{sub 3}D{sup +} FROM THE HIGH-RESOLUTION SPECTRUM OF THE {nu}{sub 4} INFRARED BAND

    SciTech Connect

    Domenech, J. L.; Cueto, M.; Herrero, V. J.; Tanarro, I.; Tercero, B.; Cernicharo, J.; Fuente, A.

    2013-07-01

    The high-resolution spectrum of the {nu}{sub 4} band of NH{sub 3}D{sup +} has been measured by difference frequency IR laser spectroscopy in a multipass hollow cathode discharge cell. From the set of molecular constants obtained from the analysis of the spectrum, a value of 262817 {+-} 6 MHz ({+-}3{sigma}) has been derived for the frequency of the 1{sub 0}-0{sub 0} rotational transition. This value supports the assignment to NH{sub 3}D{sup +} of lines at 262816.7 MHz recorded in radio astronomy observations in Orion-IRc2 and the cold prestellar core B1-bS.

  19. Analysis of the inter-alpha-trypsin inhibitor polymorphism in west Africa: description of a new allele, ITI*7.

    PubMed

    Caeiro, J L; Liste, I; Vogt, U; Ribeiro, J C

    1994-01-01

    Inter-alpha-trypsin inhibitor (ITI) phenotypes were classified in the West African population of Cabo Verde by polyacrylamide gel isoelectric focusing, followed by immunofixation and silver staining. Gene frequencies of the alleles ITI*1, ITI*2, ITI*3, and ITI*4 were calculated to be 0.532, 0.153, 0.307 and 0.002, respectively. A new rare allele, ITI*7, was found, providing evidence for further genetic variability of the ITI protein. The ITI*7 allele frequency has been determined to 0.006. The assumption that allele ITI*3 may be used to characterize populations of African origin is supported by our data. PMID:7532128

  20. Persistence of the common Hartnup disease D173N allele in populations of European origin.

    PubMed

    Azmanov, Dimitar N; Rodgers, Helen; Auray-Blais, Christiane; Giguère, Robert; Bailey, Charles; Bröer, Stefan; Rasko, John E J; Cavanaugh, Juleen A

    2007-11-01

    Hartnup disorder is an aminoaciduria that results from mutations in the recently described gene SLC6A19 on chromosome 5p15.33. The disease is inherited in a simple recessive manner and ten different mutations have been described to date. One mutation, the D173N allele, is present in 42% of Hartnup chromosomes from apparently unrelated families from both Australia and North America. We report an investigation of the origins of the D173N allele using a unique combination of variants including SNPs, microsatellites, and a VNTR across 211 Kb spanning the SLC6A19 locus. All individuals who carry the mutant allele share an identical core haplotype suggesting a single common ancestor, indicating that the elevated frequency of the D173N allele is not a result of recurrent mutation. Analyses of these data indicate that the allele is more than 1000 years old. We compare the reasons for survival of this allele with other major alleles in some other common autosomal recessive diseases occurring in European Caucasians. We postulate that survival of this allele may be a consequence of failure of the allele to completely inactivate the transport of neutral amino acids. PMID:17555458

  1. Identification of novel alleles of the rice blast resistance gene Pi54

    NASA Astrophysics Data System (ADS)

    Vasudevan, Kumar; Gruissem, Wilhelm; Bhullar, Navreet K.

    2015-10-01

    Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs.

  2. Identification of novel alleles of the rice blast resistance gene Pi54

    PubMed Central

    Vasudevan, Kumar; Gruissem, Wilhelm; Bhullar, Navreet K.

    2015-01-01

    Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs. PMID:26498172

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

    PubMed

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

    2002-06-01

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

  4. 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

    Background Pathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright’s FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright’s FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex. Methods We have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright’s FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles. Results We show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents. Conclusion Our

  5. Estimating the age of alleles by use of intraallelic variability

    SciTech Connect

    Slatkin, M.; Rannala, B.

    1997-02-01

    A method is presented for estimating the age of an allele by use of its frequency and the extent of variation among different copies. The method uses the joint distribution of the number of copies in a population sample and the coalescence times of the intraallelic gene genealogy conditioned on the number of copies. The linear birth-death process is used to approximate the dynamics of a rare allele in a finite population. A maximum-likelihood estimate of the age of the allele is obtained by Monte Carlo integration over the coalescence times. The method is applied to two alleles at the cystic fibrosis (CFTR) locus, {Delta}F508 and G542X, for which intraallelic variability at three intronic microsatellite loci has been examined. Our results indicate that G542X is somewhat older than {Delta}F508. Although absolute estimates depend on the mutation rates at the microsatellite loci, our results support the hypothesis that {Delta}F508 arose <500 generations ({approx}10,000 years) ago. 32 refs., 4 figs.

  6. 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

  7. The Social Communication Assessment for Toddlers with Autism (SCATA): An Instrument to Measure the Frequency, Form and Function of Communication in Toddlers with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Drew, Auriol; Baird, Gillian; Taylor, Emma; Milne, Elizabeth; Charman, Tony

    2007-01-01

    The Social Communication Assessment for Toddlers with Autism (SCATA) was designed to measure non-verbal communication, including early and atypical communication, in young children with autism spectrum disorder. Each communicative act is scored according to its form, function, role and complexity. The SCATA was used to measure communicative…

  8. Variety Is Not the Spice of Life for People with Autism Spectrum Disorders: Frequency Ratings of Central, Variable and Inappropriate Aspects of Common Real-Life Events

    ERIC Educational Resources Information Center

    Loth, Eva; Happe, Francesca; Gomez, Juan Carlos

    2010-01-01

    This study used a novel rating task to investigate whether high-functioning individuals with autism spectrum disorder (ASD) have difficulties distinguishing essential from variable aspects of familiar events. Participants read stories about everyday events and judged how often central, variable, and inappropriate event-components normally occur in…

  9. Accelerating Spectrum Sharing Technologies

    SciTech Connect

    Juan D. Deaton; Lynda L. Brighton; Rangam Subramanian; Hussein Moradi; Jose Loera

    2013-09-01

    Spectrum sharing potentially holds the promise of solving the emerging spectrum crisis. However, technology innovators face the conundrum of developing spectrum sharing technologies without the ability to experiment and test with real incumbent systems. Interference with operational incumbents can prevent critical services, and the cost of deploying and operating an incumbent system can be prohibitive. Thus, the lack of incumbent systems and frequency authorization for technology incubation and demonstration has stymied spectrum sharing research. To this end, industry, academia, and regulators all require a test facility for validating hypotheses and demonstrating functionality without affecting operational incumbent systems. This article proposes a four-phase program supported by our spectrum accountability architecture. We propose that our comprehensive experimentation and testing approach for technology incubation and demonstration will accelerate the development of spectrum sharing technologies.

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

    PubMed

    Axtner, Jan; Sommer, Simone

    2012-12-01

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

  11. Spectrum of hemoglobinopathies among the primitive tribes: a multicentric study in India.

    PubMed

    Mohanty, Dipika; Mukherjee, Malay B; Colah, Roshan B; Wadia, Mahrukh; Ghosh, Kanjaksha; Chottray, Guru Prasad; Jain, Dipty; Italia, Yazdi; Ashokan, Kumar S; Kaul, Rajni; Shukla, Deepak K; Muthuswamy, Vasantha

    2015-03-01

    We evaluated the spectrum of hemoglobinopathies among the primitive tribal groups from 4 states in India. A total of 15,200 individuals from 14 primitive tribal groups were studied by automated high-performance liquid chromatography. The hemoglobin S (HbS) allele frequency varied from 0.011 to 0.120 and the β-thalassemia allele frequency from 0.005 to 0.024. It is interesting to note that a very high HbS allele frequency was observed among the Dravidian (0.060-0.120) and Indo-European (0.060-0.076) as compared with Austro-Asiatic (0.011-0.022) speaking tribal groups. Although statistical analysis of the data did not show any ethnic differences within the states, regional differences were observed between the states for both HbS and β-thalassemia traits. HbS was found to be the most common hemoglobinopathy followed by β-thalassemia. A health plan for identifying sickle-cell homozygotes in the neonatal period with proper medical intervention is desirable. PMID:23513007

  12. Sporadic inclusion body myositis: HLA-DRB1 allele interactions influence disease risk and clinical phenotype.

    PubMed

    Mastaglia, Frank L; Needham, Merrilee; Scott, Adrian; James, Ian; Zilko, Paul; Day, Timothy; Kiers, Lynette; Corbett, Alastair; Witt, Campbell S; Allcock, Richard; Laing, Nigel; Garlepp, Michael; Christiansen, Frank T

    2009-11-01

    Susceptibility to sIBM is strongly associated with the HLA-DRB1*03 allele and the 8.1 MHC ancestral haplotype (HLA-A1, B8, DRB1*03) but little is known about the effects of allelic interactions at the DRB1 locus or disease-modifying effects of HLA alleles. HLA-A, B and DRB1 genotyping was performed in 80 Australian sIBM cases and the frequencies of different alleles and allele combinations were compared with those in a group of 190 healthy controls. Genotype-phenotype correlations were also investigated. Amongst carriers of the HLA-DRB1*03 allele, DRB1*03/*01 heterozygotes were over-represented in the sIBM group (p<0.003) while. DRB1*03/*04 heterozygotes were under-represented (p<0.008). The mean age-at-onset (AAO) was 6.5 years earlier in DRB1*03/*01 heterozygotes who also had more severe quadriceps muscle weakness than the rest of the cohort. The findings indicate that interactions between the HLA-DRB1*03 allele and other alleles at the DRB1 locus can influence disease susceptibility and the clinical phenotype in sIBM. PMID:19720533

  13. Micro acoustic spectrum analyzer

    DOEpatents

    Schubert, W. Kent; Butler, Michael A.; Adkins, Douglas R.; Anderson, Larry F.

    2004-11-23

    A micro acoustic spectrum analyzer for determining the frequency components of a fluctuating sound signal comprises a microphone to pick up the fluctuating sound signal and produce an alternating current electrical signal; at least one microfabricated resonator, each resonator having a different resonant frequency, that vibrate in response to the alternating current electrical signal; and at least one detector to detect the vibration of the microfabricated resonators. The micro acoustic spectrum analyzer can further comprise a mixer to mix a reference signal with the alternating current electrical signal from the microphone to shift the frequency spectrum to a frequency range that is a better matched to the resonant frequencies of the microfabricated resonators. The micro acoustic spectrum analyzer can be designed specifically for portability, size, cost, accuracy, speed, power requirements, and use in a harsh environment. The micro acoustic spectrum analyzer is particularly suited for applications where size, accessibility, and power requirements are limited, such as the monitoring of industrial equipment and processes, detection of security intrusions, or evaluation of military threats.

  14. Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles | Office of Cancer Genomics

    Cancer.gov

    Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic.

  15. The CCR5Δ32 allele is not a major predisposing factor for severe H1N1pdm09 infection

    PubMed Central

    2014-01-01

    Background Host genetic factors are thought to modulated the severity of disease caused by infection with the 2009 H1N1 pandemic influenza virus (H1N1pdm09). The human CCR5 gene encodes a cytokine receptor important for cell-mediated immune response against H1N1pdm09. A 32-bp polymorphic deletion in the coding sequence of CCR5, the so-called CCR5Δ32 allele, segregates in populations of European ancestry with a frequency of 8-15%. A high proportion of CCR5Δ32 heterozygotes was reported in a sample of white Canadian critically-ill H1N1pdm09 infected subjects, suggesting an association with disease severity. Methods We recruited 29 H1N1pdm09 infected subjects from Southern Europe (mostly Italians) with a wide clinical spectrum of disease symptoms; the sample included 7 subjects who developed acute respiratory distress syndrome requiring extracorporeal membrane oxygenation. The CCR5Δ32 variant was genotyped in all subjects. Results The CCR5Δ32 allele was found in one single subject, who developed a very mild form and was not hospitalized. Conclusions The CCR5Δ32 allele was not found to be associated with the risk of H1N1pdm09 infection or with a severe disease course. PMID:25100510

  16. Frequency-comb referenced spectroscopy of v₄₋ and v₅₋excited hot bands in the 1.5 and μm spectrum of C₂H₂

    SciTech Connect

    Twagirayezu, Sylvestre; Cich, Matthew J.; Sears, Trevor J.; McRaven, Christopher P.; Hall, Gregory E.

    2015-07-14

    Doppler-free transition frequencies for v₄₋ and v₅₋excited hot bands have been measured in the v₁ + v₃ band region of the spectrum of acetylene using saturation dip spectroscopy with an extended cavity diode laser referenced to a frequency comb. The frequency accuracy of the measured transitions, as judged from line shape model fits and comparison to known frequencies in the v₁ + v₃ band itself, is between 3 and 22 kHz. This is some three orders of magnitude improvement on the accuracy and precision of previous line position estimates that were derived from the analysis of high-resolution Fourier transform infrared absorption spectra. Comparison to transition frequencies computed from constants derived from published Fourier transform infrared spectra shows that some upper rotational energy levels suffer specific perturbations causing energy level shifts of up to several hundred MHz. These perturbations are due to energy levels of the same rotational quantum number derived from nearby vibrational levels that become degenerate at specific energies. Future identification of the perturbing levels will provide accurate relative energies of excited vibrational levels of acetylene in the 7100–7600 cm⁻¹ energy region.

  17. Frequency-comb referenced spectroscopy of v₄₋ and v₅₋excited hot bands in the 1.5 and μm spectrum of C₂H₂

    DOE PAGESBeta

    Twagirayezu, Sylvestre; Cich, Matthew J.; Sears, Trevor J.; McRaven, Christopher P.; Hall, Gregory E.

    2015-07-14

    Doppler-free transition frequencies for v₄₋ and v₅₋excited hot bands have been measured in the v₁ + v₃ band region of the spectrum of acetylene using saturation dip spectroscopy with an extended cavity diode laser referenced to a frequency comb. The frequency accuracy of the measured transitions, as judged from line shape model fits and comparison to known frequencies in the v₁ + v₃ band itself, is between 3 and 22 kHz. This is some three orders of magnitude improvement on the accuracy and precision of previous line position estimates that were derived from the analysis of high-resolution Fourier transform infraredmore » absorption spectra. Comparison to transition frequencies computed from constants derived from published Fourier transform infrared spectra shows that some upper rotational energy levels suffer specific perturbations causing energy level shifts of up to several hundred MHz. These perturbations are due to energy levels of the same rotational quantum number derived from nearby vibrational levels that become degenerate at specific energies. Future identification of the perturbing levels will provide accurate relative energies of excited vibrational levels of acetylene in the 7100–7600 cm⁻¹ energy region.« less

  18. Frequency noise in frequency swept fiber laser.

    PubMed

    Pedersen, Anders Tegtmeier; Rottwitt, Karsten

    2013-04-01

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

  19. Forced oscillation technique. Reference values for resistance and reactance over a frequency spectrum of 2-26 Hz in healthy children aged 2.3-12.5 years.

    PubMed

    Duiverman, E J; Clément, J; van de Woestijne, K P; Neijens, H J; van den Bergh, A C; Kerrebijn, K F

    1985-01-01

    The forced pseudo-random noise oscillation technique is a method by which total respiratory resistance (Rrs) and reactance (Xrs) can be measured simultaneously at various frequencies by means of complex oscillations, superimposed at the mouth during spontaneous quiet breathing. Reference values were obtained in 255 healthy Caucasian children of Dutch descent aged 2.3-12.5 years. Rrs and Xrs vs frequency (f) curves are mainly determined by the child's sex, age, height and weight. Taking complete Rrs and Xrs-f curves into account, we found that Rrs values were significantly higher in young boys than in young girls. They were equal at about 8 years, but at about 12 years of age Rrs values were again significantly higher in boys than in girls. Frequency dependence of Rrs was found in healthy boys up to about 5 years of age, but not in girls of the same age or in older children. These data suggest differences in airway diameter between boys and girls. At all ages Xrs was significantly lower in boys than in girls. This suggests differences in bronchial patency of peripheral airways, boys being at a disadvantage. It is concluded that multiple frequency oscillometry is a method which is ideal for children from the age of about 3 years. The possibility of measuring Rrs as well as frequency dependence of Rrs and Xrs simultaneously is the major advantage over other oscillation devices. PMID:3995199

  20. How Old Is the Most Recent Ancestor of Two Copies of an Allele?

    PubMed Central

    Patterson, Nick J.

    2005-01-01

    An important clue to the evolutionary history of an allele is the structure of the neighboring region of the genome, which we term the genomic background of the allele. Consider two copies of the allele. How similar we expect their genomic background to be is strongly influenced by the age of their most recent common ancestor (MRCA). We apply diffusion theory, first used by Motoo Kimura as a tool for predicting the changes in allele frequencies over time and developed by him in many articles in this journal, to prove a variety of new results on the age of the MRCA under the simplest demographic assumptions. In particular, we show that the expected age of the MRCA of two copies of an allele with population frequency f is just 2Nf generations, where N is the effective population size. Our results are a first step in running exact coalescent simulations, where we also simulate the history of the population frequency of an allele. PMID:15520271

  1. Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure

    PubMed Central

    Chen, Hua; Slatkin, Montgomery

    2013-01-01

    It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144−0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories. PMID:23797107

  2. Analysis of the rich frequency spectrum of KIC 10670103 revealing the most slowly rotating subdwarf B star in the Kepler field

    NASA Astrophysics Data System (ADS)

    Reed, M. D.; Foster, H.; Telting, J. H.; Østensen, R. H.; Farris, L. H.; Oreiro, R.; Baran, A. S.

    2014-06-01

    We analyse 2.75 yr of Kepler spacecraft observations of the pulsating subdwarf B star KIC 10670103. These 1.4 million measurements have an impressive duty cycle of 93.8 per cent, a frequency resolution of 0.017 μHz, and a 5σ detection limit of 0.1 parts-per-thousand (ppt). We detect 278 periodicities, making KIC 10670103 the richest pulsating subdwarf B star to date. Frequencies range from 23 to 673 μHz (0.4 and 11.8 h), with amplitudes from the detection limit up to 14 ppt. Follow-up spectroscopic data were obtained from which it was determined that KIC 10670103 does not show significant radial velocity variations. Updated atmospheric model fits determined Teff = 21 485 ± 540 K, log g = 5.14 ± 0.05, and log N(He)/N(H) = -2.60 ± 0.04. We identify pulsation modes using asymptotic period spacings and frequency multiplets. The frequency multiplets indicate a spin period of 88 ± 8 d. Of the 278 periodicities detected in KIC 10670103, 163 (59 per cent) have been associated with low-degree (ℓ ≤ 2) pulsation modes, providing tight constraints for model fitting. While the data are exquisite, amplitudes (and some frequencies) are not stable over the course of the observations, requiring tools which are non-standard for compact pulsators such as sliding Fourier transforms and Lorentzian fitting. Using the 163 identified pulsation modes, it is possible to make detailed examinations of the pulsation structure; including where the pulsation power is concentrated in radial order, over what frequency range mode trapping is inefficient, and how power switches between multiplet members.

  3. Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles.

    PubMed

    Hoffert, Jason D; Pisitkun, Trairak; Miller, R Lance

    2012-06-01

    Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially in the last 5-10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and the number of breeding rounds. Therefore, a well planned breeding strategy is critical for keeping costs to a minimum. However, designing a viable breeding strategy can be challenging. With so many different variables this would be an ideal task for a computer program. To facilitate this process, we created a Java-based program called Conditional Allele Mouse Planner (CAMP). CAMP is designed to provide an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. We provide a description of CAMP, how to use it, and offer it freely as an application. PMID:21870117

  4. Hereditary fructose intolerance: frequency and spectrum mutations of the aldolase B gene in a large patients cohort from France--identification of eight new mutations.

    PubMed

    Davit-Spraul, Anne; Costa, Catherine; Zater, Mokhtar; Habes, Dalila; Berthelot, Jacques; Broué, Pierre; Feillet, François; Bernard, Olivier; Labrune, Philippe; Baussan, Christiane

    2008-08-01

    We investigated the molecular basis of hereditary fructose intolerance (HFI) in 160 patients from 92 families by means of a PCR-based mutation screening strategy, consisting of restriction enzyme digestion and direct sequencing. Sixteen different mutations of the aldolase B (ALDOB) gene were identified in HFI patients. As in previous studies, p.A150P (64%), p.A175D (16%) and p.N335K (5%) were the most common mutated alleles, followed by p.R60X, p.A338V, c.360_363delCAAA (p.N120KfsX30), c.324G>A (p.K108K) and c.625-1G>A. Eight novel mutations were also identified in 10 families with HFI: a one-base deletion (c.146delT (p.V49GfsX27)), a small deletion (c.953del42bp), a small insertion (c.689ins TGCTAA (p.K230MfsX136)), one splice site mutation (c.112+1G>A), one nonsense mutation (c.444G>A (p.W148X)), and three missense mutations (c.170G>C (p.R57P), c.839C>A (p.A280P) and c.932T>C (p.L311P)). Our strategy allows to diagnose 75% of HFI patients using restriction enzymatic analysis and to enlarge the diagnosis to 97% of HFI patients when associated with direct sequencing. PMID:18541450

  5. Zellweger Spectrum

    MedlinePlus

    ... the Zellweger spectrum result from defects in the assembly of a cellular structure called the peroxisome, and ... Zellweger spectrum are caused by defects in the assembly of the peroxisome. There are at least 12 ...

  6. Study on the ternary mixed ligand complex of palladium(II)-aminophylline-fluorescein sodium by resonance Rayleigh scattering, second-order scattering and frequency doubling scattering spectrum and its analytical application.

    PubMed

    Chen, Peili; Liu, Shaopu; Liu, Zhongfang; Hu, Xiaoli

    2011-01-01

    The interaction between palladium(II)-aminophylline and fluorescein sodium was investigated by resonance Rayleigh scattering, second-order scattering and frequency doubling scattering spectrum. In pH 4.4 Britton-Robinson (BR) buffer medium, aminophylline (Ami) reacted with palladium(II) to form chelate cation([Pd(Ami)]2+), which further reacted with fluorescein sodium (FS) to form ternary mixed ligand complex [Pd(Ami)(FS)2]. As a result, resonance Rayleigh scattering (RRS), second-order scattering (SOS) and frequency doubling scattering spectrum (FDS) were enhanced. The maximum scattering wavelengths of [Pd(Ami)(FS)2] were located at 300 nm (RRS), 650 nm (SOS) and 304 nm (FDS). The scattering intensities were proportional to the Ami concentration in a certain range and the detection limits were 7.3 ng mL(-1) (RRS), 32.9 ng mL(-1) (SOS) and 79.1 ng mL(-1) (FDS), respectively. Based on it, the new simple, rapid, and sensitive scattering methods have been proposed to determine Ami in urine and serum samples. Moreover, the formation mechanism of [Pd(Ami)(FS)2] and the reasons for enhancement of RRS were fully discussed. PMID:21163688

  7. Frequency of PER, VEB, SHV, TEM and CTX-M Genes in Resistant Strains of Pseudomonas aeruginosa Producing Extended Spectrum β-Lactamases

    PubMed Central

    Bokaeian, Mohmmad; Shahraki Zahedani, Shahram; Soltanian Bajgiran, Morteza; Ansari Moghaddam, Alireza

    2014-01-01

    Background: Pseudomonas aeruginosa is the most common pathogen causing nosocomial infections. Resistance of P. aeruginosa strains to broad-spectrum cephalosporins may be mediated by extended-spectrum β-lactamases (ESBLs). Objectives: We intended to investigate the prevalence of ESBLs and antimicrobial susceptibilities of P. aeruginosa isolated from patients in Zahedan, Iran. Materials and Methods: In this cross-sectional study, during 2012–2013, 116 P. aeruginosa isolates were collected from a teaching hospital in Zahedan, Iran. Susceptibility to eight antimicrobial agents was carried out by disk diffusion method. The ESBL producing strains were detected by combination disk test (CDT). ESBL positive isolates as well as other isolates showing minimum inhibitory concentrations (MICs) ≥ 4 μg/mL for ceftazidime, cefotaxime, ceftriaxone and aztreonam, were screened for the presence of the genes encoding blaTEM, blaSHV, blaPER-1 and blaVEB-1, by polymerase chain reaction (PCR). Results: Ciprofloxacin and piperacillin were the most efficient antipseudomonal agents. The results disclosed that 19 (16.37%) of the isolates were multidrug resistant and 8 (6.89%) were ESBL-positive. Of the 116 isolates, 30 (25.86%) were resistant to at least one of the antibiotics ceftazidime, ceftriaxone, cefotaxime or aztreonam and among these 30 (100%), 4 (13.3%), 2 (6.6%) and 2 (6.6%), amplified blaTEM, blaVEB-1, blaPER-1 and blaSHV, respectively. From the 30 TEM-positive isolates, 22 were ESBL-negative. Sequencing of the ESBL genes verified the accuracy of the PCR products. Conclusions: According to our results, blaTEM-116 was the most frequent isolated ESBL gene among the P. aeruginosa strains isolated from patients. PMID:25789123

  8. Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer

    PubMed Central

    Halabi, Najeeb M.; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G.; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A.; Malek, Joel A.; Rafii, Arash

    2016-01-01

    Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

  9. Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer.

    PubMed

    Halabi, Najeeb M; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A; Malek, Joel A; Rafii, Arash

    2016-01-01

    Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

  10. Tracing pastoralist migrations to southern Africa with lactase persistence alleles.

    PubMed

    Macholdt, Enrico; Lede, Vera; Barbieri, Chiara; Mpoloka, Sununguko W; Chen, Hua; Slatkin, Montgomery; Pakendorf, Brigitte; Stoneking, Mark

    2014-04-14

    Although southern African Khoisan populations are often assumed to have remained largely isolated during prehistory, there is growing evidence for a migration of pastoralists from eastern Africa some 2,000 years ago, prior to the arrival of Bantu-speaking populations in southern Africa. Eastern Africa harbors distinctive lactase persistence (LP) alleles, and therefore LP alleles in southern African populations may be derived from this eastern African pastoralist migration. We sequenced the lactase enhancer region in 457 individuals from 18 Khoisan and seven Bantu-speaking groups from Botswana, Namibia, and Zambia and additionally genotyped four short tandem repeat (STR) loci that flank the lactase enhancer region. We found nine single-nucleotide polymorphisms, of which the most frequent is -14010(∗)C, which was previously found to be associated with LP in Kenya and Tanzania and to exhibit a strong signal of positive selection. This allele occurs in significantly higher frequency in pastoralist groups and in Khoe-speaking groups in our study, supporting the hypothesis of a migration of eastern African pastoralists that was primarily associated with Khoe speakers. Moreover, we find a signal of ongoing positive selection in all three pastoralist groups in our study, as well as (surprisingly) in two foraging groups. PMID:24704073

  11. 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

  12. 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

  13. Pyrosequencing for Accurate Imprinted Allele Expression Analysis

    PubMed Central

    Yang, Bing; Damaschke, Nathan; Yao, Tianyu; McCormick, Johnathon; Wagner, Jennifer; Jarrard, David

    2016-01-01

    Genomic imprinting is an epigenetic mechanism that restricts gene expression to one inherited allele. Improper maintenance of imprinting has been implicated in a number of human diseases and developmental syndromes. Assays are needed that can quantify the contribution of each paternal allele to a gene expression profile. We have developed a rapid, sensitive quantitative assay for the measurement of individual allelic ratios termed Pyrosequencing for Imprinted Expression (PIE). Advantages of PIE over other approaches include shorter experimental time, decreased labor, avoiding the need for restriction endonuclease enzymes at polymorphic sites, and prevent heteroduplex formation which is problematic in quantitative PCR-based methods. We demonstrate the improved sensitivity of PIE including the ability to detect differences in allelic expression down to 1%. The assay is capable of measuring genomic heterozygosity as well as imprinting in a single run. PIE is applied to determine the status of Insulin-like Growth Factor-2 (IGF2) imprinting in human and mouse tissues. PMID:25581900

  14. Rapid spectrum measurement at 3  μm over 100  nm wavelength range using mid-infrared difference frequency generation source.

    PubMed

    Abe, Masashi; Nishida, Yoshiki; Tadanaga, Osamu; Tokura, Akio; Takenouchi, Hirokazu

    2016-04-01

    We demonstrate a broadband rapid scanning light source in the 3-μm region by using difference frequency generation (DFG). The DFG source consists of a module with quasi-phase-matched LiNbO3 ridge waveguides, a 1-μm-band wide swept range laser for the pump source, and a 1.5-μm continuous wave laser for the signal source. The sweep rate and the tuning bandwidth of this source are 20 kHz and 100 nm, respectively. This source enables us to evaluate the temperature dependence of absorbance of methane gas. PMID:27192241

  15. 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

  16. Reintroduction of a Homocysteine Level-Associated Allele into East Asians by Neanderthal Introgression.

    PubMed

    Hu, Ya; Ding, Qiliang; He, Yungang; Xu, Shuhua; Jin, Li

    2015-12-01

    In this study, we present an analysis of Neanderthal introgression at the dipeptidase 1 gene, DPEP1. A Neanderthal origin for the putative introgressive haplotypes was demonstrated using an established three-step approach. This introgression was under positive natural selection, reached a frequency of >50%, and introduced a homocysteine level- and pigmentation-associated allele (rs460879-T) into East Asians. However, the same allele was also found in non-East Asians, but not from Neanderthal introgression. It is likely that rs460879-T was lost in East Asians and was reintroduced subsequently through Neanderthal introgression. Our findings suggest that Neanderthal introgression could reintroduce an important previously existing allele into populations where the allele had been lost. This study sheds new light on understanding the contribution of Neanderthal introgression to the adaptation of non-Africans. PMID:26392408

  17. No Association Between CEL-HYB Hybrid Allele and Chronic Pancreatitis in Asian Populations.

    PubMed

    Zou, Wen-Bin; Boulling, Arnaud; Masamune, Atsushi; Issarapu, Prachand; Masson, Emmanuelle; Wu, Hao; Sun, Xiao-Tian; Hu, Liang-Hao; Zhou, Dai-Zhan; He, Lin; Fichou, Yann; Nakano, Eriko; Hamada, Shin; Kakuta, Yoichi; Kume, Kiyoshi; Isayama, Hiroyuki; Paliwal, Sumit; Mani, K Radha; Bhaskar, Seema; Cooper, David N; Férec, Claude; Shimosegawa, Tooru; Chandak, Giriraj R; Chen, Jian-Min; Li, Zhao-Shen; Liao, Zhuan

    2016-06-01

    A hybrid allele between the carboxyl ester lipase gene (CEL) and its pseudogene, CELP (called CEL-HYB), generated by nonallelic homologous recombination between CEL intron 10 and CELP intron 10', was found to increase susceptibility to chronic pancreatitis in a case-control study of patients of European ancestry. We attempted to replicate this finding in 3 independent cohorts from China, Japan, and India, but failed to detect the CEL-HYB allele in any of these populations. The CEL-HYB allele might therefore be an ethnic-specific risk factor for chronic pancreatitis. An alternative hybrid allele (CEL-HYB2) was identified in all 3 Asian populations (1.7% combined carrier frequency), but was not associated with chronic pancreatitis. PMID:26946345

  18. Comparison of Matching Pursuit Algorithm with Other Signal Processing Techniques for Computation of the Time-Frequency Power Spectrum of Brain Signals.

    PubMed

    Chandran K S, Subhash; Mishra, Ashutosh; Shirhatti, Vinay; Ray, Supratim

    2016-03-23

    Signals recorded from the brain often show rhythmic patterns at different frequencies, which are tightly coupled to the external stimuli as well as the internal state of the subject. In addition, these signals have very transient structures related to spiking or sudden onset of a stimulus, which have durations not exceeding tens of milliseconds. Further, brain signals are highly nonstationary because both behavioral state and external stimuli can change on a short time scale. It is therefore essential to study brain signals using techniques that can represent both rhythmic and transient components of the signal, something not always possible using standard signal processing techniques such as short time fourier transform, multitaper method, wavelet transform, or Hilbert transform. In this review, we describe a multiscale decomposition technique based on an over-complete dictionary called matching pursuit (MP), and show that it is able to capture both a sharp stimulus-onset transient and a sustained gamma rhythm in local field potential recorded from the primary visual cortex. We compare the performance of MP with other techniques and discuss its advantages and limitations. Data and codes for generating all time-frequency power spectra are provided. PMID:27013668

  19. Comparison of Matching Pursuit Algorithm with Other Signal Processing Techniques for Computation of the Time-Frequency Power Spectrum of Brain Signals

    PubMed Central

    Chandran KS, Subhash; Mishra, Ashutosh; Shirhatti, Vinay

    2016-01-01

    Signals recorded from the brain often show rhythmic patterns at different frequencies, which are tightly coupled to the external stimuli as well as the internal state of the subject. In addition, these signals have very transient structures related to spiking or sudden onset of a stimulus, which have durations not exceeding tens of milliseconds. Further, brain signals are highly nonstationary because both behavioral state and external stimuli can change on a short time scale. It is therefore essential to study brain signals using techniques that can represent both rhythmic and transient components of the signal, something not always possible using standard signal processing techniques such as short time fourier transform, multitaper method, wavelet transform, or Hilbert transform. In this review, we describe a multiscale decomposition technique based on an over-complete dictionary called matching pursuit (MP), and show that it is able to capture both a sharp stimulus-onset transient and a sustained gamma rhythm in local field potential recorded from the primary visual cortex. We compare the performance of MP with other techniques and discuss its advantages and limitations. Data and codes for generating all time-frequency power spectra are provided. PMID:27013668

  20. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

    PubMed

    Soderlund, Carol A; Nelson, William M; Goff, Stephen A

    2014-01-01

    Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele

  1. Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression

    PubMed Central

    Soderlund, Carol A.; Nelson, William M.; Goff, Stephen A.

    2014-01-01

    Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele

  2. 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

  3. Complex and multi-allelic copy number variation in human disease

    PubMed Central

    McCarroll, Steven A.

    2015-01-01

    Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels—alleles, allele frequencies, structural features—that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs’ low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV–disease relationships that remain to be discovered. PMID:26163405

  4. The role of culture-gene coevolution in morality judgment: examining the interplay between tightness-looseness and allelic variation of the serotonin transporter gene.

    PubMed

    Mrazek, Alissa J; Chiao, Joan Y; Blizinsky, Katherine D; Lun, Janetta; Gelfand, Michele J

    2013-01-01

    This research provides novel insights into the evolutionary basis of cultural norm development and maintenance. We yield evidence for a unique culture-gene coevolutionary model between ecological threat, allelic frequency of the serotonin transporter polymorphism (5-HTTLPR), cultural tightness-looseness-the strength of norms and tolerance for deviance from norms-and moral justifiability. As hypothesized, the results across 21 nations show that: (a) propensity for ecological threat correlates with short (S) allele frequency in the 5-HTTLPR, (b) allelic frequency in the 5-HTTLPR and vulnerability to ecological threat both correlate with cultural tightness-looseness, (c) susceptibility to ecological threat predicts tightness-looseness via the mediation of S allele carriers, and (d) frequency of S allele carriers predicts justifiability of morally relevant behavior via tightness-looseness. This research highlights the importance of studying the interplay between environmental, genetic, and cultural factors underlying contemporary differences in social behavior and presents an empirical framework for future research. PMID:24404439

  5. 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

  6. MHC class II alleles and haplotypes in patients with pemphigus vulgaris from India.

    PubMed

    Delgado, J C; Yunis, D E; Bozón, M V; Salazar, M; Deulofeut, R; Turbay, D; Mehra, N K; Pasricha, J S; Raval, R S; Patel, H; Shah, B K; Bhol, K; Alper, C A; Ahmed, A R; Yunis, E J

    1996-12-01

    Pemphigus vulgaris (PV) is a blistering disease of the skin and mucous membranes characterized by an autoantibody response against a keratinocyte adhesion molecule, desmoglein 3, causing acantholysis and blister formation. We compared high resolution MHC class II alleles and haplotype frequencies (HLA-DRB, DQA1 and DQB1) in 37 patients with PV to 89 haplotypes of normal relatives from New Delhi and Ahmedabad. We found that PV patients had significantly increased frequencies of DRB1*1404 (P < 0.0001), DQA1*0101 (P = 0.001), and DQB1*0503 (P < 0.0001). These associations were due to the increased frequencies of the haplotype HLA-DRB1*1404, DRB3*0202, DQA1*0101, DQB1*0503 in patients compared to control haplotypes (p < 0.0001). Also, patients from Ahmedabad had a significant increase in HLA-DQB1*0302 (p = 0.03). An identical amino acid sequence (Leu-Leu-Glu-Arg-Arg-Arg-Ala-Glu), in positions 67-74 of the beta domain of DRB alleles is restricted to some DR14 alleles. Therefore, there are three possible explanations for class II allele involvement in autoantibody in PV patients with class II haplotypes marked by HLA-DR14. First, the class II alleles could be markers for an unidentified susceptibility gene in linkage disequilibrium with them. Second, the primary association could be with DQB1*0503 and the association with HLA-DR14 alleles would be the result of linkage disequilibrium. Third, the HLA-DRB1 locus susceptibility could involve a specific amino acid sequence in the third hypervariable region shared by several HLA-DR14 alleles. PMID:9008309

  7. Geographically Distinct and Domain-Specific Sequence Variations in the Alleles of Rice Blast Resistance Gene Pib

    PubMed Central

    Vasudevan, Kumar; Vera Cruz, Casiana M.; Gruissem, Wilhelm; Bhullar, Navreet K.

    2016-01-01

    Rice blast is caused by Magnaporthe oryzae, which is the most destructive fungal pathogen affecting rice growing regions worldwide. The rice blast resistance gene Pib confers broad-spectrum resistance against Southeast Asian M. oryzae races. We investigated the allelic diversity of Pib in rice germplasm originating from 12 major rice growing countries. Twenty-five new Pib alleles were identified that have unique single nucleotide polymorphisms (SNPs), insertions and/or deletions, in addition to the polymorphic nucleotides that are shared between the different alleles. These partially or completely shared polymorphic nucleotides indicate frequent sequence exchange events between the Pib alleles. In some of the new Pib alleles, nucleotide diversity is high in the LRR domain, whereas, in others it is distributed among the NB-ARC and LRR domains. Most of the polymorphic amino acids in LRR and NB-ARC2 domains are predicted as solvent-exposed. Several of the alleles and the unique SNPs are country specific, suggesting a diversifying selection of alleles in various geographical locations in response to the locally prevalent M. oryzae population. Together, the new Pib alleles are an important genetic resource for rice blast resistance breeding programs and provide new information on rice-M. oryzae interactions at the molecular level. PMID:27446145

  8. Spectrum Recombination.

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    1984-01-01

    Describes several methods of executing lecture demonstrations involving the recombination of the spectrum. Groups the techniques into two general classes: bringing selected portions of the spectrum together using lenses or mirrors and blurring the colors by rapid movement or foreshortening. (JM)

  9. Three allele combinations associated with Multiple Sclerosis

    PubMed Central

    Favorova, Olga O; Favorov, Alexander V; Boiko, Alexey N; Andreewski, Timofey V; Sudomoina, Marina A; Alekseenkov, Alexey D; Kulakova, Olga G; Gusev, Eugenyi I; Parmigiani, Giovanni; Ochs, Michael F

    2006-01-01

    Background Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As genotyping methods improve throughput, approaches that can explore multigene interactions appropriately should lead to improved understanding of MS. Methods 286 unrelated patients with definite MS and 362 unrelated healthy controls of Russian descent were genotyped at polymorphic loci (including SNPs, repeat polymorphisms, and an insertion/deletion) of the DRB1, TNF, LT, TGFβ1, CCR5 and CTLA4 genes and TNFa and TNFb microsatellites. Each allele carriership in patients and controls was compared by Fisher's exact test, and disease-associated combinations of alleles in the data set were sought using a Bayesian Markov chain Monte Carlo-based method recently developed by our group. Results We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*04 were also reidentified as MS-associated. Conclusion These results represent an independent validation of MS association with DRB1*15(2) and TNFa9 in Russians and are the first to find the interplay of three loci in conferring susceptibility to MS. They demonstrate the efficacy of our approach for the identification of complex-disease-associated combinations of alleles. PMID:16872485

  10. Cultivation of Staphylococcus epidermidis in the Human Spaceflight Environment Leads to Alterations in the Frequency and Spectrum of Spontaneous Rifampicin-Resistance Mutations in the rpoB Gene.

    PubMed

    Fajardo-Cavazos, Patricia; Nicholson, Wayne L

    2016-01-01

    Bacteria of the genus Staphylococcus are persistent inhabitants of human spaceflight habitats and represent potential opportunistic pathogens. The effect of the human spaceflight environment on the growth and the frequency of mutations to antibiotic resistance in the model organism Staphylococcus epidermidis strain ATCC12228 was investigated. Six cultures of the test organism were cultivated in biological research in canisters-Petri dish fixation units for 122 h on orbit in the International Space Station (ISS) as part of the SpaceX-3 resupply mission. Asynchronous ground controls (GCs) consisted of identical sets of cultures cultivated for 122 h in the ISS Environmental Simulator at Kennedy Space Center. S. epidermidis exhibited significantly lower viable counts but significantly higher frequencies of mutation to rifampicin (Rif) resistance in space vs. GC cultures. The spectrum of mutations in the rpoB gene leading to Rif(R) was altered in S. epidermidis isolates cultivated in the ISS compared to GCs. The results suggest that the human spaceflight environment induces unique physiologic stresses on growing bacterial cells leading to changes in mutagenic potential. PMID:27446039

  11. Cultivation of Staphylococcus epidermidis in the Human Spaceflight Environment Leads to Alterations in the Frequency and Spectrum of Spontaneous Rifampicin-Resistance Mutations in the rpoB Gene

    PubMed Central

    Fajardo-Cavazos, Patricia; Nicholson, Wayne L.

    2016-01-01

    Bacteria of the genus Staphylococcus are persistent inhabitants of human spaceflight habitats and represent potential opportunistic pathogens. The effect of the human spaceflight environment on the growth and the frequency of mutations to antibiotic resistance in the model organism Staphylococcus epidermidis strain ATCC12228 was investigated. Six cultures of the test organism were cultivated in biological research in canisters–Petri dish fixation units for 122 h on orbit in the International Space Station (ISS) as part of the SpaceX-3 resupply mission. Asynchronous ground controls (GCs) consisted of identical sets of cultures cultivated for 122 h in the ISS Environmental Simulator at Kennedy Space Center. S. epidermidis exhibited significantly lower viable counts but significantly higher frequencies of mutation to rifampicin (Rif) resistance in space vs. GC cultures. The spectrum of mutations in the rpoB gene leading to RifR was altered in S. epidermidis isolates cultivated in the ISS compared to GCs. The results suggest that the human spaceflight environment induces unique physiologic stresses on growing bacterial cells leading to changes in mutagenic potential. PMID:27446039

  12. Allelic Associations between 100 DNA Markers and High versus Low IQ.

    ERIC Educational Resources Information Center

    Plomin, Robert; And Others

    1995-01-01

    For DNA markers in or near genes of neurological relevance, allelic frequencies were compared for groups of high- and low-IQ children (total sample of 86). This study adds 40 markers to the 60 already studied. Only one showed a significant association with IQ in original and replication samples. (SLD)

  13. Improving VHF Spectrum Utilization

    NASA Technical Reports Server (NTRS)

    Andro, Monty; Orr, Richard; Foore, Larry; Sheehe, Charles; Freeman, Mark; Nguyen, Thanh; Bretmersky, Steven; Laberge, Chuck; Buchanan, David

    2004-01-01

    Limited VHF communications system capacity and increasing air traffic results in congestion of the aviation VHF spectrum. The voice communications errors and delayed channel access create system congestion and air traffic delays. Regulatory subdivision of bands for specific functions limits flexibility in the frequency usage. The objective of this viewgraph presentation is to identify near/mid/far term technologies to improve the performance and spectrum efficiency of current and emerging VHF communications systems. Select technologies with the highest potential, perform research and development to bring them to implementation stage.

  14. Semiparametric Allelic Tests for Mapping Multiple Phenotypes: Binomial Regression and Mahalanobis Distance.

    PubMed

    Majumdar, Arunabha; Witte, John S; Ghosh, Saurabh

    2015-12-01

    Binary phenotypes commonly arise due to multiple underlying quantitative precursors and genetic variants may impact multiple traits in a pleiotropic manner. Hence, simultaneously analyzing such correlated traits may be more powerful than analyzing individual traits. Various genotype-level methods, e.g., MultiPhen (O'Reilly et al. []), have been developed to identify genetic factors underlying a multivariate phenotype. For univariate phenotypes, the usefulness and applicability of allele-level tests have been investigated. The test of allele frequency difference among cases and controls is commonly used for mapping case-control association. However, allelic methods for multivariate association mapping have not been studied much. In this article, we explore two allelic tests of multivariate association: one using a Binomial regression model based on inverted regression of genotype on phenotype (Binomial regression-based Association of Multivariate Phenotypes [BAMP]), and the other employing the Mahalanobis distance between two sample means of the multivariate phenotype vector for two alleles at a single-nucleotide polymorphism (Distance-based Association of Multivariate Phenotypes [DAMP]). These methods can incorporate both discrete and continuous phenotypes. Some theoretical properties for BAMP are studied. Using simulations, the power of the methods for detecting multivariate association is compared with the genotype-level test MultiPhen's. The allelic tests yield marginally higher power than MultiPhen for multivariate phenotypes. For one/two binary traits under recessive mode of inheritance, allelic tests are found to be substantially more powerful. All three tests are applied to two different real data and the results offer some support for the simulation study. We propose a hybrid approach for testing multivariate association that implements MultiPhen when Hardy-Weinberg Equilibrium (HWE) is violated and BAMP otherwise, because the allelic approaches assume HWE

  15. Semi-parametric Allelic Tests For Mapping Multiple Phenotypes: Binomial Regression And Mahalanobis Distance

    PubMed Central

    Majumdar, Arunabha; Witte, John S.; Ghosh, Saurabh

    2016-01-01

    Binary phenotypes commonly arise due to multiple underlying quantitative precursors. Genetic variants may impact multiple traits in a pleiotropic manner. Hence, simultaneously analyzing such correlated traits may be more powerful than analyzing individual traits. Various genotype-level methods, e.g. MultiPhen [O'Reilly et al., 2012], have been developed to identify genetic factors underlying a multivariate phenotype. For univariate phenotypes, the usefulness and applicability of allele-level tests have been investigated. The test of allele frequency difference among cases and controls is commonly used for mapping case-control association. However, allelic methods for multivariate association mapping have not been studied much. We explore two allelic tests of multivariate association: one using a Binomial regression model based on inverted regression of genotype on phenotype (BAMP), and the other employing the Mahalanobis distance between two sample means of the multivariate phenotype vector for two alleles at a SNP (DAMP). These methods can incorporate both discrete and continuous phenotypes. Some theoretical properties for BAMP are studied. Using simulations, the power of the methods for detecting multivariate association are compared with the genotype-level test MultiPhen. The allelic tests yield marginally higher power than MultiPhen for multivariate phenotypes. For one/two binary traits under recessive mode of inheritance, allelic tests are found substantially more powerful. All three tests are applied to two real data and the results offer some support for the simulation study. Since the allelic approaches assume Hardy-Weinberg Equilibrium (HWE), we propose a hybrid approach for testing multivariate association that implements MultiPhen when HWE is violated and BAMP otherwise. PMID:26493781