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Sample records for allelic frequency distribution

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

    Science.gov (United States)

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

    2015-01-01

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

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

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    Radwan Jacek

    2010-10-01

    Full Text Available Abstract 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.

  3. Difference in PNLIP Allele Frequency Distribution Between High-Marbled and Low-Marbled Cattle

    OpenAIRE

    Tanomura, Hideki; Muramatsu, Youji; Yamamoto, Takuji; Ohta, Takeshi; Kose, Hiroyuki; Yamada, Takahisa

    2011-01-01

    Marbling characterized by the amount and distribution of intramuscular fat is one of the economically important traits of beef cattle. The Pancreatic lipase (Pnlip) gene, involved in the hydrolysis of dietary triglycerides to fatty acids has been previously shown to be regarded as possible candidate for the gene responsible for intramuscular fat content in the rat. It is located within the genomic region of a bovine marbling quantitative trait locus and thus was considered as a positional fun...

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

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2013-06-01

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

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

    OpenAIRE

    Wang, Hong-Dan; Shen, Chun-Mei; Liu, Wen-Juan; Zhang, Yu-Dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-Xia; Zhu, Bo-Feng

    2013-01-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capi...

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

    Institute of Scientific and Technical Information of China (English)

    Hong-dan WANG; Chun-mei SHEN; Wen-juan LIU; Yu-dang ZHANG; Guang YANG; Jiang-wei YAN; Hai-xia QIN

    2013-01-01

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

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

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    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

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

    Science.gov (United States)

    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.

  10. Power of IRT in GWAS: successful QTL mapping of sum score phenotypes depends on interplay between risk allele frequency, variance explained by the risk allele, and test characteristics.

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    van den Berg, Stéphanie M; Service, Susan K

    2012-12-01

    As data from sequencing studies in humans accumulate, rare genetic variants influencing liability to disease and disorders are expected to be identified. Three simulation studies show that characteristics and properties of diagnostic instruments interact with risk allele frequency to affect the power to detect a quantitative trait locus (QTL) based on a test score derived from symptom counts or questionnaire items. Clinical tests, that is, tests that show a positively skewed phenotypic sum score distribution in the general population, are optimal to find rare risk alleles of large effect. Tests that show a negatively skewed sum score distribution are optimal to find rare protective alleles of large effect. For alleles of small effect, tests with normally distributed item parameters give best power for a wide range of allele frequencies. The item-response theory framework can help understand why an existing measurement instrument has more power to detect risk alleles with either low or high frequency, or both kinds.

  11. Estimation of allele frequencies for VNTR loci.

    OpenAIRE

    Devlin, B; Risch, N; Roeder, K

    1991-01-01

    VNTR loci provide valuable information for a number of fields of study involving human genetics, ranging from forensics (DNA fingerprinting and paternity testing) to linkage analysis and population genetics. Alleles of a VNTR locus are simply fragments obtained from a particular portion of the DNA molecule and are defined in terms of their length. The essential element of a VNTR fragment is the repeat, which is a short sequence of basepairs. The core of the fragment is composed of a variable ...

  12. 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

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    Muramatsu Youji

    2011-01-01

    Full Text Available Abstract 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

  13. Frequency-Rank Distributions

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    Brookes, Bertram C.; Griffiths, Jose M.

    1978-01-01

    Frequency, rank, and frequency rank distributions are defined. Extensive discussion on several aspects of frequency rank distributions includes the Poisson process as a means of exploring the stability of ranks; the correlation of frequency rank distributions; and the transfer coefficient, a new measure in frequency rank distribution. (MBR)

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

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    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

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

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    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

  16. Comparative frequency and allelic distribution of ABO and Rh (D blood groups of major tribal communities of southern Bangladesh with general population and their determinants

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    Gourab Dewan

    2015-04-01

    Results: Collectively all tribal had distinct ABO phenotypic frequency (B > A > O > AB which is different from Bengali population (O > B > A > AB. Tripura’s showed a unique pattern of A > B > AB > O. Overall tribal had higher frequency of B and AB group (P  B > A in all study groups except Tripura (A > O > B. Rhesus negative group was very uncommon in study groups. Data among tribal suggest their common origin as well as drift from original population due to possible founder effect among Tripura’s. Despite being malaria endemic zone the protective group O was less (P < 0.0001 among native tribal (23% and high among migrating Bengali (34%.

  17. Estimation of allele frequency and association mapping using next-generation sequencing data

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    Andersen Gitte

    2011-06-01

    Full Text Available Abstract Background Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., X. However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates. Results We evaluate a new maximum likelihood method for estimating allele frequencies in low and medium coverage next-generation sequencing data. The method is based on integrating over uncertainty in the data for each individual rather than first calling genotypes. This method can be applied to directly test for associations in case/control studies. We use simulations to compare the likelihood method to methods based on genotype calling, and show that the likelihood method outperforms the genotype calling methods in terms of: (1 accuracy of allele frequency estimation, (2 accuracy of the estimation of the distribution of allele frequencies across neutrally evolving sites, and (3 statistical power in association mapping studies. Using real re-sequencing data from 200 individuals obtained from an exon-capture experiment, we show that the patterns observed in the simulations are also found in real data. Conclusions Overall, our results suggest that association mapping and estimation of allele frequencies should not be based on genotype calling in low to medium coverage data. Furthermore, if genotype calling methods are used, it is usually better not to filter genotypes based on the call confidence score.

  18. Allele frequency of CODIS 13 in Indonesian population.

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    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

  19. Allele frequency of CODIS 13 in Indonesian population.

    Science.gov (United States)

    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.

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

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    Senthilkumar Pitchalu Kasthurinaidu

    Full Text Available 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.

  1. Allele Frequencies of 10 Autosomal STR Loci from Chakma and Tripura Tribal Populations in Bangladesh

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    Ahmad Ferdous

    2010-01-01

    Full Text Available Allele frequencies of ten autosomal STR loci, D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01, and FGA were investigated in Chakma and Tripura tribal populations of Bangladesh. In both the populations, all loci were in Hardy-Weinberg equilibrium except for FGA locus in Chakma and D21S11 in Tripura. All the loci were highly polymorphic in Chakma population with an observed heterozygosity (Ho of >0.7 and moderately polymorphic in Tripura population (Ho>0.6. However, both the population showed least polymorphism at TH01 locus (Ho<0.6. A comparison between Chakma and Tripura population data revealed statistically significant differences in allele frequency distribution for most of the loci. A similar comparison with the mainstream Bengali population using previously published data from this lab also showed significant difference in allele frequency with these two tribal populations.

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

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    Pairaya Rujirojindakul

    2015-01-01

    Full Text Available 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.

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

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    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

  4. ApoE allele frequencies in Italian sporadic and familial Alzheimer's disease.

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    Sorbi, S; Nacmias, B; Forleo, P; Latorraca, S; Gobbini, I; Bracco, L; Piacentini, S; Amaducci, L

    1994-08-15

    Recent studies have provided evidence of association of apolipoprotein E (ApoE) epsilon 4 allele and late onset familial and sporadic Alzheimer's disease (AD). Epidemiological studies have established allelic variation at the ApoE locus. We have analyzed the ApoE gene polymorphism in a sample of 446 Italian subjects. Our data confirm a significant association between epsilon 4 allele and sporadic AD. The frequency of epsilon 4 allele in early onset familial AD patients was comparable to control values suggesting that epsilon 4 allele does not represent a risk factor for early onset familial AD (EOFAD). Moreover, we found a not previously reported association between ApoE epsilon 2 allele and sporadic AD and EOFAD. PMID:7824157

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

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    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

  6. 中国东北地区汉族癫痫患者HLA-B*1502等位基因分布频率%Distributed frequency of the allele HLA-B * 1502 in Han ethnic epilepsy patients living in northeastern region of China

    Institute of Scientific and Technical Information of China (English)

    何晓静; 汝继玲; 肇丽梅

    2013-01-01

    目的 研究中国东北地区汉族癫痫患者HLA-B * 1502等位基因分布的频率.方法 用聚合酶链反应DNA序列分析法,对125例中国东北地区汉族癫痫患者DNA标本进行HLA-B基因分型.结果 125例DNA标本中,共检测出34种不同的HLA-B等位基因.其中,2例患者携带HLA-B*1502等位基因.HLA-B*1502等位基因在中国东北地区癫痫患者中的分布频率为1.6%.其他分布频率较高的等位基因分别为HLA-B*4001、B*4601、B*4801、B*1302和B*4002.结论 东北地区癫痫患者中HLA-B*1502等位基因分布频率(1.6%)与其在北京地区健康汉族人群中的分布频率近似(1.5%);但远低于其在中国中部、西部及南部地区的分布频率.%Objective To study the distributed frequency of the allele of HLA - B * 1502 in Han ethnic epilepsy patients living in northeastern region of China. Methods The polymerase chain reaction sequence -based typing method was used to detect the genotype of HLA - B * 1502 of all 125 epilepsy patients. Results Among all 125 epilepsy patients, there are 34 different types of alleles and only 2 patients with positive HLA - B * 1502. The distributed frequency of the allele of HLA - B * 1502 in Han ethnic epilepsy patients living in northeastern region of China is 1.6%. The other main alleles with high distributed frequencies are HLA - B * 4001, B * 4601, B * 4801, B * 1302and B * 4002, respectively. Conclusion The distributed frequency of HLA - B * 1502 of Han ethnic epilepsy patients living in northeastern region of China is very similar to that in Beijing, which is far lower than that in central, western and southern regions of China.

  7. Geographical distribution of GmTfl1 alleles in Chinese soybean varieties

    Institute of Scientific and Technical Information of China (English)

    Guifeng; Liu; Lin; Zhao; Benjamin; J.Averitt; Ying; Liu; Bo; Zhang; Ruzhen; Chang; Yansong; Ma; Xiaoyan; Luan; Rongxia; Guan; Lijuan; Qiu

    2015-01-01

    Stem growth habit is an important agronomic trait in soybean and is subject to artificial selection. This study aimed to provide a theory for genotypic selection of stem growth habit for breeding purposes by analyzing the alleles of Gm Tfl1 gene in Chinese soybean varieties and establishing a database of Gm Tfl1 variation. Using knowledge of insertion and deletion(Indel) in the non-coding region and four single-nucleotide polymorphisms(SNPs) in the coding sequences of the Gm Tfl1 gene, four CAPS and one Indel markers were developed and used to test 1120 Chinese soybean varieties. We found that the dominant Gm Tfl1 allele was prevalent in accessions from the Northern ecoregion, whereas the recessive allele, Gmtfl1, was more common in the Southern ecoregion, and the proportions of Gm Tfl1 and recessive alleles were respectively 40.1% and 59.9% in the Huang-Huai ecoregion. The proportion of Gm Tfl1 decreased and that of Gmtfl1 increased, gradually from north to south. Allele Gm Tfl1-a was present in higher proportions in the Huang-Huai spring, Huang-Huai summer, and Northern spring sub-ecoregions than that in the other sub-ecoregions. Gm Tfl1-b was common in the Northeast spring, Northern spring and Southern summer sub-ecoregions. Gmtfl1-ta was found mainly in the Huang-Huai spring,Huang-Huai summer and Southern spring sub-ecoregions. The Gmtfl1-ab allele was distributed in all six soybean sub-ecoregions. The Gmtfl1-bb allele was distributed mainly in the Huang-Huai spring and summer and Southern spring and summer sub-ecoregions,but the Gmtfl1-tb allele was detected only in the Huang-Huai summer sub-ecoregion. The distributions of Gm Tfl1 and Gmtfl1 have shown no large changes in nearly 60 years of breeding, but the frequency of the recessive genotype Gmtfl1 has shown a rising trend in the last 20 years. This study provides a theoretical foundation for breeding new soybean varieties for different ecoregions.

  8. The NQO1 allelic frequency in hindu population of central India varies from that of other Asian populations

    Directory of Open Access Journals (Sweden)

    Parihar Sher

    2010-01-01

    Full Text Available Context: The enzymes encoded by the polymorphic genes NAD (P H: quinone oxidoreductase 1 (NQO1 play an important role in the activation and inactivation of xenobiotics. This enzyme has been associated with xenobiotic related diseases, such as cancer, therapeutic failure and abnormal effects of drugs. Aim: The aim of the present study was to determine the allelic and genotypic frequencies of NQO Hinf I polymorphisms in a Hindu population of Central India. Settings and Design: Polymorphisms of NQO1 were determined in 311 unrelated Hindu individuals. Materials and Methods: Polymerase chain reaction- Restriction Fragment Length Polymorphism (PCR-RFLP analysis in peripheral blood DNA for NQO1 Hinf I polymorphism was used in 311 unrelated Hindu individuals. Statistical Analysis: Allele frequencies were calculated by direct counting. Hardy Weinberg Equilibrium was evaluated using a Chi-square goodness of fit test. Results: The observed allelic frequency was 81% for C (wild and 19% for T (mutant in the total sample. Conclusions: The allelic frequency of "C" was higher than in other Asians (57%, but similar to Caucasians (81%. The genotype distributions for Hinf I polymorphisms were in Hardy-Weinberg equilibrium.

  9. Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

    NARCIS (Netherlands)

    Oddou-Muratorio, S.; Vendramin, G.G.; Buiteveld, J.; Fady, B.

    2009-01-01

    Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite marker

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

    Science.gov (United States)

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

    OpenAIRE

    Greenberg, D A; Kaback, M M

    1982-01-01

    There appear to be several alleles of the hexosaminidase A (HEX A) gene that lead to different clinical syndromes. In addition to the infantile-onset Tay-Sachs disease (TSD), there is a juvenile-onset and an adult-onset form, which are also characterized by low HEX A levels. There are also apparently healthy adults with low HEX A activity. Based primarily on data from population screening for TSD carrier status, we estimate the allele frequency of the combined variant alleles for which data a...

  12. HLA Class II Allele and Haplotype Frequencies in Iranian Patients with Leukemia

    Directory of Open Access Journals (Sweden)

    Farideh Khosravi

    2007-09-01

    Full Text Available Previous studies demonstrated significant differences in a number of HLA allele frequencies in leukemia patients and normal subjects. In this study, we have analyzed HLA class II alleles and haplotypes in 110 leukemia patients (60 acute myelogenous leukemia "AML", 50 chronic myelogenous leukemia"CML" and 180 unrelated normal subjects. Blood samples were collected from all of the patients and control subjects. DNA was extracted by salting out method and HLA typing was performed using PCR-SSP method. Significant positive association with AML was obtained for HLA-DRB1*11allele (35% vs. 24.7%, P=0.033. Two alleles including HLA-DRB4 and -DQB1*0303 were significantly less frequent in AML patients than in controls. HLA-DQB1*0303 allele was never observed in CML patients compared with allele frequency in controls (4.2%. According to haplotype analysis, HLA-DRB1*0101/DQA1*0104/-DQB1*0501 frequencies were significantly higher and -DRB1*16/-DQA1*01021/-DQB1*0501 frequencies were significantly lower in CML patients than in controls .In conclusion it is suggested that HLA-DRB1*16 allele and HLA-DRB1*15/-DQA1*0103/-DQB1*06011 and -DRB1*16/-DQA1*01021/-DQB1*0501 haplotypes predispose individuals to AML and HLA-DRB4 allele predispose to CML. Future studies are needed to confirm these results and establish the role of these associations in AML and CML.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Deise C Friedrich

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

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

    Science.gov (United States)

    Sánchez-Molina, I; Calvet, R

    2000-01-01

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

  16. Low frequency of the scrapile resistance-associated allele and presence of lysine-171 allele of the prion protein gene in Italian Biellese ovine breed

    NARCIS (Netherlands)

    Acutis, P.L.; Sbaiz, L.; Verburg, F.J.; Riina, M.V.; Ru, G.; Moda, G.; Caramelli, M.; Bossers, A.

    2004-01-01

    Frequencies of polymorphisms at codons 136, 154 and 171 of the prion protein (PrP) gene were studied in 1207 pure-bred and cross-bred Italian Biellese rams, a small ovine breed of about 65 000 head in Italy. Aside from the five most common alleles (VRQ, ARQ, ARR, AHQ and ARH), the rare ARK allele wa

  17. Genome Wide Allele Frequency Fingerprints (GWAFFs) of populations via genotyping by sequencing

    DEFF Research Database (Denmark)

    Byrne, Stephen; Czaban, Adrian; Studer, Bruno;

    2013-01-01

    is an outbreeding species, and breeding programs are based upon selection on populations. We tested two restriction enzymes for their efficiency in complexity reduction of the perennial ryegrass genome. The resulting profiles have been termed Genome Wide Allele Frequency Fingerprints (GWAFFs), and we have shown how......-wide scale would be very powerful, examples include the breeding of outbreeding species, varietal protection in outbreeding species, monitoring changes in population allele frequencies. This motivated us to test the potential to use GBS to evaluate allele frequencies within populations. Perennial ryegrass...... these fingerprints can be used to distinguish between plant populations. Even at current costs and throughput, using sequencing to directly evaluate populations on a genome-wide scale is viable. GWAFFs should find many applications, from varietal development in outbreeding species right through to playing a role...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Sachse, C.; Brockmoeller, J.; Bauer, S.; Roots, I. [Humboldt Univ., Berlin (Germany)

    1997-02-01

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

  1. A Theoretical Framework for Association Studies in F2 Family Pools Using Allele Frequencies from Genotyping-By-Sequencing

    DEFF Research Database (Denmark)

    Janss, Luc L; Ashraf, Bilal H; Greve-Pedersen, Morten;

    a sequencing approach to obtain Single Nucleotide Polymorphisms (SNPs) frequencies is considered here. In this work we develop the theoretical framework to perform association studies using allele frequencies from such F2 family pools. We show that expected allele frequencies in the F2 families will have...

  2. Microsatellite D21D210 (GT-12) allele frequencies in sporadic Alzheimer's disease

    International Nuclear Information System (INIS)

    Four disease-causing mutations have so far been described in the amyloid precursor protein gene on chromosome 21 in familial early-onset Alzheimer's disease. Linkage analysis with a fourteen-allele microsatellite at D21S210 named GT-12 has proven useful in the elucidation of amyloid presursor protein gene involvement in Alzheimer's disease families, as it is closely linked to the gene. Most cases of Alzheimer's disease are thought to be sporadic and not familial. However, evidence from earlier studies suggests an important genetic contribution also in sporadic cases, where gene-environment interaction may contribute to the disease. We have determined frequencies of the GT-12 alleles in 78 Swedish and 49 British sporadic Alzheimer's disease cases and 104 healthy elderly control subjects, to investigate if the disease associates with a particular genotype in GT-12. However, no differences in allele frequencies were observed between any of the groups. (au) (26 refs.)

  3. Allelic structure and distribution of 103 STR loci in a Southern Tunisian population

    Indian Academy of Sciences (India)

    Abdellatif Maalej; Ahmed Rebai; Adnen Ayadi; Jomaa Jouida; Hafedh Makni; Hammadi Ayadi

    2004-04-01

    Genotypes of 103 short tandem repeat (STR) markers distributed at an average of 40 cM intervals throughout the genome were determined for 40 individuals from the village of BirEl Hfai (BEH). This village of approximately 31.000 individuals is localized in the south-west of Tunisia. The allele frequency distributions in BEH were compared with those obtained for individuals in the CEPH (Centre d’Etude du Polymorphisme Humain) data using a Kolmogorov–Smirnov two-sample test. Fourteen out of the 103 markers (13.2%) showed significant differences ($P\\lt 0.05$) in distribution between the two populations. Population heterogeneity in BEH was indicated by an excess of observed homozygosity deviations from Hardy–Weinberg equilibrium at 3 loci ($P\\lt 0.0005$). No evidence for genotypic disequilibrium was found for any of the marker pairs. This demonstrated that in spite of a high inbreeding level in the population, few markers showed evidence for a different pattern of allelic distribution compared to CEPH.

  4. Frequency of CCR5Δ32 allele in healthy Bosniak population.

    Directory of Open Access Journals (Sweden)

    Grażyna Adler

    2014-08-01

    Full Text Available 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 lower 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 Hercegovina 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 subjects from Bosnia and Herzegovina (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. 

  5. Allele frequencies of the third component of complement (C3) in MS patients.

    OpenAIRE

    Bulman, D E; Armstrong, H; Ebers, G C

    1991-01-01

    No difference was found in the allele frequency of C3 (third component of complement) in 129 multiple sclerosis (MS) patients compared with both 69 controls or with similar reported controls from the published literature. An association cannot be confirmed between C3 and MS.

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

    Science.gov (United States)

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

    2012-05-01

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

  7. SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Korneliussen, Thorfinn Sand; Albrechtsen, Anders;

    2012-01-01

    calculated using a dynamic programming algorithm and numerically optimized using analytical derivatives. We then use a bayesian method for estimating the sample allele frequency in a single site, and show how the method can be used for genotype calling and SNP calling. We also show how the method can be...

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

    Science.gov (United States)

    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.

  9. Phenotypic and allelic distribution of the ABO and Rhesus (D) blood groups in the Cameroonian population.

    Science.gov (United States)

    Ndoula, S T; Noubiap, J J N; Nansseu, J R N; Wonkam, A

    2014-06-01

    Data on blood group phenotypes are important for blood transfusion programs, for disease association and population genetics studies. This study aimed at reporting the phenotypic and allelic distribution of ABO and Rhesus (Rh) groups in various ethnolinguistic groups in the Cameroonians. We obtained ABO and Rhesus blood groups and self-identified ethnicity from 14,546 Cameroonian students. Ethnicity was classified in seven major ethnolinguistic groups: Afro-Asiatic, Nilo-Saharan, Niger-Kordofanian/West Atlantic, Niger-Kordofanian/Adamawa-Ubangui, Niger-Kordofanian/Benue-Congo/Bantu/Grassfield, Niger-Kordofanian/Benue-Congo/Bantu/Mbam and Niger-Kordofanian/Benue-Congo/Bantu/Equatorial. ABO allelic frequencies were determined using the Bernstein method. Differences in phenotypic distribution of blood groups were assessed using the chi-square test; a P value blood groups O, A, B and AB were 48.62%, 25.07%, 21.86% and 4.45%, respectively. Rhesus-positive was 96.32%. The allelic frequencies of O, A and B genes were 0.6978, 0.1605 and 0.1416, respectively. Phenotypic frequencies of the blood groups in the general study population and in the different ethnolinguistic groups were in agreement with Hardy-Weinberg equilibrium expectations (P > 0.05). The frequencies of O, A, and B blood phenotypes were significantly lower, respectively, in the Nilo-Saharan group (P = 0.009), the Niger-Kordofanian/Benue-Congo/Bantu groups (P = 0.021) and the Niger-Kordofanian/West-Atlantic group. AB blood group was most frequent in the Niger-Kordofanian/Adamawa-Ubangui group (P = 0.024). Our study provides the first data on ethnic distribution of ABO and Rhesus blood groups in the Cameroonian population and suggests that its general profile is similar to those of several sub-Saharan African populations. We found some significant differences in phenotypic distribution amongst major ethnolinguistic groups. These data may be important for blood donor recruitment policy and blood transfusion

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

    Science.gov (United States)

    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

  11. Distribution of a pseudodeficiency allele among Tay-Sachs carriers

    Energy Technology Data Exchange (ETDEWEB)

    Tomczak, J.; Grebner, E.E. (Thomas Jefferson Univ., Philadelphia, PA (United States)); Boogen, C. (Univ. of Essen Medical School (Germany))

    1993-08-01

    Recently Triggs-Raine et al. (1992) identified a new mutation in the gene coding for the [alpha]-subunit of [beta]-hexosaminidase A (hex A), the enzyme whose deficiency causes Tay-Sachs disease. This mutation, a C[sub 739]-to-T transition in exon 7, results in an altered enzyme that is active (albeit at reduced levels) in cells but that has essentially no activity in serum. This so-called pseudodeficient allele was first detected in compound heterozygotes who also carried a Tay-Sachs disease allele and therefore had no detectable hex A in their serum but who were in good health. Carriers of this apparently benign mutation are generally indistinguishable from carriers of a lethal mutation by means of routine enzyme-based screening tests, because the product of the pseudodeficient allele is not detectable in serum and has decreased activity in cells. This suggests that some individuals who have been classified as Tay-Sachs carriers are actually carriers of the pseudodeficient allele and are not at risk to have a child affected with Tay-Sachs disease. The pseudodeficient allele may also be responsible for some inconclusive diagnoses, where leukocyte values fall below the normal range but are still above the carrier range. The fact that there are now two mutant alleles (the psuedodeficient and the adult) that are indistinguishable from the lethal infantile mutations by means of enzyme assay yet that are phenotypically very different and that together may account for as much as 12% of enzyme-defined carriers on the basis of the data here suggests that DNA analysis should be part of a comprehensive screening program. It will be particularly useful to identify the mutations in couples at risk, before they undergo prenatal diagnosis. DNA analysis will also resolve some inconclusive diagnoses.

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

    Science.gov (United States)

    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.

  13. The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data.

    Science.gov (United States)

    Kofler, Robert; Nolte, Viola; Schlötterer, Christian

    2016-01-01

    Sequencing pools of individuals (Pool-Seq) is a cost-effective method to determine genome-wide allele frequency estimates. Given the importance of meta-analyses combining data sets, we determined the influence of different genomic library preparation protocols on the consistency of allele frequency estimates. We found that typically no more than 1% of the variation in allele frequency estimates could be attributed to differences in library preparation. Also read length had only a minor effect on the consistency of allele frequency estimates. By far, the most pronounced influence could be attributed to sequence coverage. Increasing the coverage from 30- to 50-fold improved the consistency of allele frequency estimates by at least 27%. We conclude that Pool-Seq data can be easily combined across different library preparation methods, but sufficient sequence coverage is key to reliable results.

  14. Extremely high frequency of autoimmune-predisposing alleles in medieval specimens

    Institute of Scientific and Technical Information of China (English)

    WITAS H.W.; J(E)DRYCHOWSKA-DA(N)SKA K.; ZAWICKI P.

    2007-01-01

    The precise etiology and reasons for the increase in incidence of autoimmune disorders still remain unclear, and although both genetic and environmental factors have been proven to shape individual predisposition, it is not known which of the factors, if not both, is responsible for the boom observed during the last decades. In order to establish whether a higher frequency of autoimmune-predisposing alleles may explain this increase we took advantage of ancient DNA methodology to establish the genetic predisposition, conferred by cytotoxic T lymphocyte associated antigen-4 (CTLA4) +49A/G and human leukocyte antigens (HLA)DQB157, in population inhabiting Poland in the Middle Ages. After successful typing of 42 individuals from a 12th~14th's century archeological burial site, we found that frequencies of the predisposing alleles in the medieval population were higher than they are at present, suggesting thus that the recently observed incidence increase results most probably from factors of other than genetic nature.

  15. Allele frequencies of 14 STR loci in the population of Malta.

    Science.gov (United States)

    Cassar, M; Farrugia, C; Vidal, C

    2008-05-01

    Allele frequencies of 14 STR loci (D13S317, D16S539, D2S1338, vWA, TPOX, D18S51, D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, TH01 and D3S1358) observed in the population of Malta are being reported. Polymerase chain reaction (PCR) amplification using the AmpFl STR Identifiler kit was performed in a random sample of 157 subjects (314 chromosomes). Markers D2S1338, D18S51 and FGA had the highest power of discrimination (PD) values while TPOX was the least informative marker. Allele frequencies observed in the Maltese population were also compared with those of other populations from the Mediterranean region, Europe and Africa. Our data is useful for anthropological and other comparative studies of populations and is powerful for forensic and paternity testing in the Maltese islands.

  16. Distribution of apolipoprotein E alleles in coras and huicholes from Nayarit and Nahuas and Mestizos from Veracruz, Mexico.

    Science.gov (United States)

    Cruz-Fuentes, Carlos S; González-Sobrino, Blanca Zoila; Gómez-Sanchez, Ariadna; Martínez Rueda, Hortencia; Chávez-Eakle, Rosa Aurora; Serrano Sánchez, Carlos

    2005-12-01

    We report allele frequencies for the most common polymorphism of the APOE gene in Mexican individuals from two regions not previously described: Coras and Huicholes from Nayarit, and Nahuas and mestizos from Veracruz. We also report APOE allele frequencies for inhabitants of Mexico City. These descriptive data underscore the allelic heterogeneity for this particular locus in Mexico.

  17. Ethnic differences in allelic distribution of IFN-g in South African women but no link with cervical cancer

    Directory of Open Access Journals (Sweden)

    Williamson Anna-Lise

    2003-01-01

    Full Text Available Abstract Background The failure of specific types of human papillomaviruses (HPV to raise effective immune responses may be important in the pathogenesis of cervical cancer, the second most common cancer in South African women. Polymorphisms of a number of cytokine genes have been implicated in inducing susceptibility or resistance to cancers caused by infectious agents owing to their role in determining host immune response. Polymorphisms of IL-10 and IFN-γ genes are believed to influence the expression and/or secretion levels of their respective cytokines. Methods and Results In this study, women with histologically proven cancer of the cervix (n = 458 and hospital-based controls (n = 587 were investigated for bi-allelic -1082 (A/G polymorphisms of IL-10 and the bi-allelic +874(A/T polymorphisms of IFN-γ. In addition, the distributions of the allelic frequencies were stratified in both the African and mixed race population groups of South Africa. We found striking differences in the allele distribution of IFN-γ (X2 = 0.02 among the two ethnic groups. A significant increase in the allele distribution of the IFN-γ AA genotype was found in the African group compared to the mixed population group (OR, 0.5; 95% CI, 0.2–1.0. For IL-10 there were no significant allelic differences between the two South African ethnic groups. Furthermore, when the ethnic groups were combined the IL-10 allelic frequencies in the combined South African data were similar to those observed in an Oriental population from Southern China and in an Italian population. However, the allele frequencies of the IFN-γ genotype among the two South African ethnic groups were different when compared to an Italian Caucasoid group. While crude analysis of these data showed both statistically significantly increased and diminished risks of cervical cancer among high producers of INF-γ and low producers of IL-10 respectively, these associations were no longer significant when the

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

    Science.gov (United States)

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

    2014-11-01

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

  19. HLA class II allele and haplotype frequencies in Ethiopian Amhara and Oromo populations.

    Science.gov (United States)

    Fort, M; de Stefano, G F; Cambon-Thomsen, A; Giraldo-Alvarez, P; Dugoujon, J M; Ohayon, E; Scano, G; Abbal, M

    1998-04-01

    HLA class II alleles were identified in 181 healthy unrelated Ethiopian children of both sexes and in 350 European controls from the South of France. The Ethiopian individuals belonged to the two major ethnic groups of the country: Oromo (N=83) and Amhara (N=98). In both panels, genetic polymorphism of HLA class II alleles was analysed for the first time by molecular typing of DRB1, DQA1 and DQB1 loci. Allelic and phenotypic frequencies were compared with those of European controls and other African populations. Construction of HLA class II three-locus haplotypes was also performed. The study revealed some differences between the two groups. Characteristic features of Central and North African populations appeared on the Ethiopian HLA genotypes. Surprisingly, DRB1*11 presented one of the lowest gene frequencies in both Ethiopian ethnic groups in contrast to Europeans and West Africans. Furthermore, this decrease was more marked than those observed using serological techniques in other geographically close East African countries. Oromo and Amhara only showed minor differences in spite of their different origins and histories. One significant difference consisted of a lower DRB1*01 gene frequency in Oromo as reported in most West African people. Some new or rare haplotypes were also observed in the Oromo group. Our results underline the distinctive features of the Ethiopian populations among the few HLA genotyping data available for East African groups and emphasise the major interest of such investigations in this region of Africa.

  20. 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

    OpenAIRE

    Muramatsu Youji; Kose Hiroyuki; Ohta Takeshi; Fujita Tatsuo; Satoh Youichi; Watanabe Naoto; Yamamoto Takuji; Yamada Takahisa

    2011-01-01

    Abstract 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 conside...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  3. Genotype and allele frequencies of heme oxygenase-1 promoter region in a Greek cohort

    Institute of Scientific and Technical Information of China (English)

    Eleni P. Katana; Lemonia G. Skoura; Zacharias G Scouras; Michail A. Daniilidis

    2011-01-01

    Background Heme oxygenase-1 (HO-1) is an enzyme,which catabolizes heme into carbon monoxide,biliverdin and free iron.The induction of this enzyme is an important cytoprotective mechanism,which occurs as an adaptive and beneficial response to a wide variety of oxidant stimuli.HO-1 inducibility is mainly modulated by a (GT)n polymorphism in the promoter region,and has been shown that short (S) repeats are associated with greater up-regulation of HO-1,compared with long (L) repeats.Methods In the present study,250 healthy Greek individuals have been screened in order to estimate the frequencies of (GT)n alleles in the HO-1 gene.Results Nineteen different alleles,ranging from 17 to 39 repeats,with (GT)23 and (GT)30 being the most common ones,were identified.Conclusion The possible role of this polymorphism in disease states is discussed.

  4. Studies on African pygmies. V. Red cell acid phosphatase polymorphism in Babinga pygmies: high frequency of ACPR allele.

    Science.gov (United States)

    Santachiara-Benerecetti, A S; Ranzani, G N; Antonini, G

    1977-11-01

    A group of Babinga Pygmies from the Central African Republic have been analyzed for the acid phosphatase polymorphism with special reference to the ACPR allele. The frequency of this allele (17%) is one of the highest observed in Africa and is comparable only with those reported for the Khoikhoi and the San.

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

    Science.gov (United States)

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    Sala, A; Penacino, G; Corach, D

    1998-10-01

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

  8. HLA allele distribution distinguishes sporadic inclusion body myositis from hereditary inclusion body myopathies.

    Science.gov (United States)

    Koffman, B M; Sivakumar, K; Simonis, T; Stroncek, D; Dalakas, M C

    1998-04-15

    We studied the HLA class II associations in patients with sporadic inclusion body myositis (s-IBM) and hereditary inclusion body myopathies (h-IBM) and attempted to distinguish these myopathies on the basis of HLA allele assignments. Forty-five patients, 30 with s-IBM and 15 with h-IBM, underwent HLA class II allele-specific typing using polymerase chain reaction sequence-specific primers for 71 alleles contained in the DRbeta1, DRbeta3-5, and DQbeta1 loci. In s-IBM, we found a high (up to 77%) frequency of DRbeta1*0301, DRbeta3*0101 (or DRbeta3*0202) and DQbeta1*0201 alleles. No significant association with alleles in the DR and DQ haplotypes was found among the 15 h-IBM patients. The strong association of prominent alleles with s-IBM, but not h-IBM, suggests that s-IBM is a distinct disorder with an immunogenetic background that differs from h-IBM.

  9. Further data on the microsatellite locus D12S67 in worldwide populations: an unusual distribution of D12S67 alleles in Native Americans.

    Science.gov (United States)

    Mitchell, R J; Federle, L; Sofro, A S; Papiha, S S; Briceno, I; Bernal, J E

    2000-08-01

    We report the frequencies of alleles at the microsatellite locus D12S67 in 2 widely separated ethnic groups of the world: 2 populations from Sulawesi, an island in the Indonesian archipelago, and 5 Native American tribes of Colombia, South America. The allele frequencies in the Minihasans and Torajans of Sulawesi are similar to each other (but the modal class allele is different) and in general agreement with those reported in mainland Asian groups, but different from both Europeans and Chinese Han of Taiwan. The 5 Native American tribes (Arsario, Kogui, Ijka, Wayuu, and Coreguaje) display different allele frequencies from those seen in Sulawesi populations, in other groups from Europe and mainland Asia, and in Chinese Han of Taiwan. Native Americans exhibit a bimodal distribution of alleles, unlike other groups, with significant differences among the tribes. The Arsario and Kogui have no admixture with Europeans or Africans and are the most distinctive, while the Wayuu have the most admixture and show most similarity to other groups. The data suggest that nonadmixed Native Americans may be quite distinctive with respect to this marker. The most common allele varies across the 5 tribes, from 249 base pairs to 261 base pairs. All samples exhibit Hardy-Weinberg genotype proportions; heterozygosities are lowest in the 2 nonadmixed Native American tribes. Examination of all the available data indicates that some east Asian and southeast Asian groups are characterized by a high frequency of smaller sized D12S67 alleles, while other populations have a greater proportion of the larger sized alleles. The cumulative, though still highly restricted, population data on locus D12S67 demonstrate that it may be of considerable value in anthropological genetic studies of ethnic groups. Data are required on Native Americans outside Colombia before this marker can be used in admixture studies of this group. PMID:11048795

  10. Geographic differences in allele frequencies of susceptibility SNPs for cardiovascular disease

    Directory of Open Access Journals (Sweden)

    Kullo Iftikhar J

    2011-04-01

    Full Text Available Abstract Background We hypothesized that the frequencies of risk alleles of SNPs mediating susceptibility to cardiovascular diseases differ among populations of varying geographic origin and that population-specific selection has operated on some of these variants. Methods From the database of genome-wide association studies (GWAS, we selected 36 cardiovascular phenotypes including coronary heart disease, hypertension, and stroke, as well as related quantitative traits (eg, body mass index and plasma lipid levels. We identified 292 SNPs in 270 genes associated with a disease or trait at P -8. As part of the Human Genome-Diversity Project (HGDP, 158 (54.1% of these SNPs have been genotyped in 938 individuals belonging to 52 populations from seven geographic areas. A measure of population differentiation, FST, was calculated to quantify differences in risk allele frequencies (RAFs among populations and geographic areas. Results Large differences in RAFs were noted in populations of Africa, East Asia, America and Oceania, when compared with other geographic regions. The mean global FST (0.1042 for 158 SNPs among the populations was not significantly higher than the mean global FST of 158 autosomal SNPs randomly sampled from the HGDP database. Significantly higher global FST (P FST of 2036 putatively neutral SNPs. For four of these SNPs, additional evidence of selection was noted based on the integrated Haplotype Score. Conclusion Large differences in RAFs for a set of common SNPs that influence risk of cardiovascular disease were noted between the major world populations. Pairwise comparisons revealed RAF differences for at least eight SNPs that might be due to population-specific selection or demographic factors. These findings are relevant to a better understanding of geographic variation in the prevalence of cardiovascular disease.

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

    Science.gov (United States)

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

    2014-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Pablo Abdon da Costa Francez

    2011-01-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

    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

  15. Evolutionary dynamics of sporophytic self-incompatibility alleles in plants

    DEFF Research Database (Denmark)

    Schierup, M H; Vekemans, X; Christiansen, F B

    1997-01-01

    The stationary frequency distribution and allelic dynamics in finite populations are analyzed through stochastic simulations in three models of single-locus, multi-allelic sporophytic self-incompatibility. The models differ in the dominance relationships among alleles. In one model, alleles act c...

  16. Frequency of the MDR1 mutant allele associated with multidrug sensitivity in dogs from Brazil

    Directory of Open Access Journals (Sweden)

    Monobe MM

    2015-04-01

    Full Text Available Marina M Monobe,1 João P Araujo Junior,2 Kari V Lunsford,3 Rodrigo C Silva,4 Camilo Bulla41Department of Veterinary Clinics, School of Veterinary Medicine and Animal Science, 2Department of Microbiology and Immunology, Biosciences Institute, Sao Paulo State University (UNESP, Botucatu, Brazil; 3Department of Clinical Sciences and Animal Health Center, 4Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi, MS, USAAbstract: To date, a 4-bp deletion in the MDR1 gene has been detected in more than ten dog breeds, as well as in mixed breed dogs, in several countries, however information regarding this mutation in dogs from Brazil is lacking. For this reason, 103 Collies, 77 Border Collies, 76 Shetland Sheepdogs, 20 Old English Sheepdogs, 55 German Shepherds, 16 Australian Shepherds, and 53 Whippets from Brazil were screened for the presence of the mutation. The heterozygous mutated genotype, MDR1 (+/−, frequency found for Collies, Australian Shepherd, and Shetland Sheepdog was 50.5% (95% CI =41.1%–59.9%, 31.3% (95% CI =8.6%–53.2%, and 15.8% (95% CI =7.7%–23.9%, respectively. Homozygous mutated genotype, MDR1 (−/−, was detected only in Collies 35.9%. The MDR1 allele mutant frequency found for Collies, Australian Shepherd, and Shetland Sheepdog was 61.2% (95% CI =54.8%–67.5%, 15.6% (95% CI =3.1%–28.2%, and 7.9% (95% CI =3.7%–12.1%, respectively. Additionally, even free of the mutant allele, the maximum mutant prevalence (MMP in that population, with 95% CI, was 3.8%, 5.2%, 5.4%, and 13.8% for Border Collies, German Shepherds, Whippets, and Old English Sheepdogs, respectively. In this way, this information is important, not only for MDR1 genotype-based breeding programs and international exchange of breeding animals of predisposed breeds, but also for modification of drug therapy for breeds at risk.Keywords: P-glycoprotein, MDR1 mutation, ivermectin, dog, drug

  17. Association studies using family pools of outcrossing crops based on allele-frequency estimates from DNA sequencing

    DEFF Research Database (Denmark)

    Ashraf, Bilal; Jensen, Just; Asp, Torben;

    2014-01-01

    (resulting in higher LD with causative mutations) and lower sequencing depth. Therefore, association studies using genotyping by sequencing are optimal and use low sequencing depth per sample. The developed framework for association studies using allele frequencies from sequencing can be modified for other...

  18. "HLA Class II Allele and Haplotype Frequencies in Iranian Patients with Acute Myelogenous Leukemia and Control Group "

    Directory of Open Access Journals (Sweden)

    Abdolfattah Sarafnejad

    2006-09-01

    Full Text Available Previous studies have demonstrated some significant differences in HLA allele frequencies in leukemic patients and normal subjects. We have analyzed HLA class II alleles and haplotypes in 60 Iranian patients with acute myelogenous leukemia (AML and 180 unrelated normal subjects. Blood samples were collected after obtaining informed consents. From the patients and control DNA extraction and HLA typing were performed using PCR-SSP method. Significant positive association with the disease was found for HLA-DRB1*11 allele (35% vs. 24.7%, p=0.033. Two alleles including HLA-DRB4 and –DQB1*0303 were found to be significantly decreased in patients compared to controls. Regarding haplotype analysis, no significant association was found between case and control groups. It is suggested that HLA-DRB1*11 allele plays as a presumptive predisposing factor while the HLA-DRB4 and –DQB1*0303 alleles are suggested as protective genetic factors against acute myelogenous leukemia. Larger studies are needed to confirm and establish the role of these associations with acute myelogenous leukemia.

  19. Inference of population splits and mixtures from genome-wide allele frequency data.

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    Joseph K Pickrell

    Full Text Available 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.

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

    Science.gov (United States)

    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 40% had a median overall survival (OS) of 124 days versus an OS that was not reached in patients with 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

  1. Reducing Bias of Allele Frequency Estimates by Modeling SNP Genotype Data with Informative Missingness

    Directory of Open Access Journals (Sweden)

    Wan-Yu eLin

    2012-06-01

    Full Text Available The presence of missing single-nucleotide polymorphism (SNP genotypes is common in genetic data. For studies with low-density SNPs, the most commonly used approach to deal with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is appropriate only when the missingness is random. However, a given assay often has a different capability in genotyping heterozygotes and homozygotes, causing the phenomenon of ‘differential dropout’ in the sense that the missing rates of heterozygotes and homozygotes are different. In practice, differential dropout among genotypes exists in even carefully designed studies, such as the data from the HapMap project and the Wellcome Trust Case Control Consortium. In this study, we propose a statistical method to model the differential dropout among different genotypes. Compared with the naïve method, our method provides more accurate allele frequency estimates when the differential dropout is present. To demonstrate its practical use, we further apply our method to the HapMap data and a scleroderma data set.

  2. HLA-DRB, DQA and DQB allele frequencies in Iranian patients with chronic hepatitis B by PCR-SSP

    OpenAIRE

    Baniaghil S; Sarafnejad A; Amirzargar A; Khosravi F; Ansaripour B; Moradi B; Dorkhosh S; Nikbin B

    2007-01-01

    Background: The outcome of acute hepatitis B infection may be influenced by host genetic factors like human leukocyte antigen (HLA). To investigate the association between the HLA-DRB, DQA1 and DQB1 alleles and chronic hepatitis B infection, 50 patients with chronic hepatitis B (based on 6 months positive of HBsAg and HBc antibody and HBeAg and antibody by serological test), were selected from Turkman population in north east of Iran .Allele frequency in patients were compared with a 65 aged ...

  3. Frequency distribution of coliforms in water distribution systems.

    OpenAIRE

    Christian, R R; Pipes, W O

    1983-01-01

    Nine small water distribution systems were sampled intensively to determine the patterns of dispersion of coliforms. The frequency distributions of confirmed coliform counts were compatible with either the negative-binomial or the lognormal distribution. They were not compatible with either the Poisson or Poisson-plus-added zeroes distribution. The implications of the use of the lognormal distributional model were further evaluated because of its previous use in water quality studies. The geo...

  4. Allelic distributions of CYP2D6 gene copy number variation in the Eastern Han Chinese population

    Institute of Scientific and Technical Information of China (English)

    Hai-hui SHENG; Yun-lan DU; Jian SUN; Hua-sheng XIAO; Ai-ping ZENG; Wen-xiang ZHU; Ren-fang ZHU; Hong-mei LI; Zhi-dong ZHU; Ying QIN; Wei JIN; Yan LIU

    2007-01-01

    Aim: The human cytochrome P450 2D6 (CYP2D6) gene copy number variation, involving CYP2D6 gene deletion (CYP2D6*5) and duplication or multiduplication (CYP2D6*×N), can result in reduced or increased metabolism of many clinically used drugs. The identification of CYP2D6*5 and CYP2D6*×N and the investigation of their allelic distributions in ethnic populations can be important in deter-mining the right drug and dosage for each patient. Methods: The CYP2D6*5 andCYP2D6 genes, and CYP2D6 gene duplication were identified by 2 modified long PCR, respectively. To determine duplicated alleles, a novel long PCR was developed to amplify the entire duplicated CYP2D6 gene which was used as template for subsequent PCR amplification. A total of 363 unrelated Eastern Han Chinese individuals were analyzed for CYP2D6 gene copy number variation. Results: The frequency of CYP2D6*5 and CYP2D6*×N were 4.82% (n=35) and 0.69% (n=5) in the Eastern Han Chinese population, respectively. Of the 5 duplicated alleles, 3were CYP2D6*1×N and 2 were CYP2D6*10×N. One individual was a carrier of both CYP2D6*5 and CYP2D6*1×N. Taken together, the CYP2D6 gene rear-rangements were present in 10.74% of subjects. Conclusion: Allelic distributions of the CYP2D6 gene copy number variation differ among Chinese from different regions, indicating ethnic variety in Chinese. Long PCR are convenient, cost effective, specific and semiquantitative for the detection of the CYP2D6 gene copy number variation, and amplification of the entire duplicated CYP2D6 gene is necessary for the accurate identification of duplicated alleles.

  5. HLA-DRB, DQA and DQB allele frequencies in Iranian patients with chronic hepatitis B by PCR-SSP

    Directory of Open Access Journals (Sweden)

    Baniaghil S

    2007-05-01

    Full Text Available Background: The outcome of acute hepatitis B infection may be influenced by host genetic factors like human leukocyte antigen (HLA. To investigate the association between the HLA-DRB, DQA1 and DQB1 alleles and chronic hepatitis B infection, 50 patients with chronic hepatitis B (based on 6 months positive of HBsAg and HBc antibody and HBeAg and antibody by serological test, were selected from Turkman population in north east of Iran .Allele frequency in patients were compared with a 65 aged and sex match control group from healthy blood donor of that ethnic population. Methods: HLA DRB, DQA1 and DQB1 alleles were determined using polymerase chain reaction based on sequence specific primer (PCR-SSP method. Allele frequencies in patients and control subjects were compared by Epi-info statistical soft-wear. Results: There was a significant increase and positive association in HLA-DRB1*0301, DQA1*0501 and DQB1*0604 allele frequency in patients group while the frequency of HLA-DRB1*1301, 1501 and DQB1*0401 and DQA1*0401, 0102 were lower in patients than control group and shows negative association. Conclusion: In Iranian Torkman population, HLA DRB1*0301, DQA1*0501 and DQB1*0604 have an important role in susceptibility to chronic hepatitis B infection and HLA DRB1*1301, 1501, DQB1*0401 are associated with protection to chronic hepatitis B infection. Larger case control studies may be helpful to confirm our investigation.

  6. Triglyceride associated polymorphisms of the APOA5 gene have very different allele frequencies in Pune, India compared to Europeans

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    Chandak Giriraj R

    2006-10-01

    Full Text Available Abstract Background The APOA5 gene variants, -1131T>C and S19W, are associated with altered triglyceride concentrations in studies of subjects of Caucasian and East Asian descent. There are few studies of these variants in South Asians. We investigated whether the two APOA5 variants also show similar association with various lipid parameters in Indian population as in the UK white subjects. Methods We genotyped 557 Indian adults from Pune, India, and 237 UK white adults for -1131T>C and S19W variants in the APOA5 gene, compared their allelic and genotype frequency and determined their association with fasting serum triglycerides, total cholesterol, HDL and LDL cholesterol levels using univariate general linear analysis. APOC3 SstI polymorphism was also analyzed in 175 Pune Indian subjects for analysis of linkage disequilibrium with the APOA5 variants. Results The APOA5 -1131C allele was more prevalent in Indians from Pune (Pune Indians compared to UK white subjects (allele frequency 20% vs. 4%, p = 0.00001, whereas the 19W allele was less prevalent (3% vs. 6% p = 0.0015. Patterns of linkage disequilibrium between the two variants were similar between the two populations and confirmed that they occur on two different haplotypes. In Pune Indians, the presence of -1131C allele and the 19W allele was associated with a 19% and 15% increase respectively in triglyceride concentrations although only -1131C was significant (p = 0.0003. This effect size was similar to that seen in the UK white subjects. Analysis of the APOC3 SstI polymorphism in 175 Pune Indian subjects showed that this variant is not in appreciable linkage disequilibrium with the APOA5 -1131T>C variant (r2 = 0.07. Conclusion This is the first study to look at the role of APOA5 in Asian Indian subjects that reside in India. The -1131C allele is more prevalent and the 19W allele is less prevalent in Pune Indians compared to UK Caucasians. We confirm that the APOA5 variants are associated

  7. Distribution of HLA alleles in Portugal and Cabo Verde. Relationships with the slave trade route.

    Science.gov (United States)

    Spínola, H; Brehm, A; Williams, F; Jesus, J; Middleton, D

    2002-07-01

    HLA-A, -B, and -DR frequencies were analysed in populations from Portugal and the Madeira and Cabo Verde Archipelagos, aiming to characterize their genetic composition. Portuguese settlers colonized both Archipelagos in the 15th and 16th centuries. Madeira received many sub-Saharan slaves to work in the sugar plantations, and Cabo Verde served as a pivotal market in the Atlantic slave trade and was populated by individuals coming from the Senegambia region of the West African coast. The population of Madeira shows the highest genetic diversity and the presence of alleles and haplotypes usually linked to sub-Saharan populations, the haplotypes accounting for 3.5% of the total. Cabo Verde presents typical markers acknowledged to be of European or Ibero-Mediterranean origin, thus revealing the admixture of European settlers with Sub-Saharan slaves. Altogether the number of European haplotypes reaches 15% of the total. The Portuguese population shows a perceivable and significant heterogeneity both in allele and haplotype frequencies, unveiling a differential input of peoples from different origins. A PCA of the populations studied, plus other relevant ones, clearly shows gene heterogeneity in mainland Portugal as well as the differences and relationships between these populations and Madeira and Cabo Verde. PMID:12418969

  8. Frequency of the apolipoprotein E epsilon 4 allele in a case-control study of early onset Parkinson's disease.

    OpenAIRE

    Whitehead, A S; Bertrandy, S.; Finnan, F; Butler, A; G. D. Smith(Edinburgh University); Ben-Shlomo, Y.

    1996-01-01

    OBJECTIVES: It has been suggested that Parkinson's disease and Alzheimer's disease may share a common or at least overlapping aetiology. The prevalence of dementia among cases of Parkinson's disease is known to be greater than expected in the general population. The frequency of the apolipoprotein epsilon 4 allele in a large case-control study of early onset Parkinson's disease has been examined. METHODS: 215 patients and 212 population based controls were recruited from the Republic of Irela...

  9. High resolution human leukocyte antigen class I allele frequencies and HIV-1 infection associations in Chinese Han and Uyghur cohorts.

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    Yanhou Liu

    Full Text Available 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

  10. Flood Frequency Analysis Using the Gumbel Distribution

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    Never Mujere

    2011-07-01

    Full Text Available This paper presents results of a study carried in Zimbabwe aimed at analysing the frequency of Nyanyadzi River floods using the Gumbel distribution. Extreme floods over recent years had washed away fields, destroyed infrastructure and killed animals. It was hypothesised that Nyanyadzi flood flows obey the Gumbel distribution. The scale and shape parameters of the distribution were estimated using method of moments. Maximum instantaneous flow data covering 30 water years (1969-1999 for station E119 on Nyanyadzi River were collected from the Zimbabwe National Water Authority (ZINWA. A Chisquare χ2 test revealed no significant (p =1.000 differences between recorded and predicted flood flows. Due to goodness of fit of the Gumbel distribution, it was assumed to be appropriate for modelling frequency of Nyanyadzi River floods. The magnitudes of the 100 and 200-year floods were estimated to be 276 and 310 m3/s respectively.

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

    Science.gov (United States)

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

    2002-11-01

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

  12. Identification of Allele Frequency of Factor XI Deficiency (FXID in Holstein Cows Reared in Thrace Region of Turkey

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    Kozet AVANUS

    2016-08-01

    Full Text Available Factor XI (FXI is a protein that plays a key role in plasma coagulation. Factor XI Deficiency (FXID is an autosomal recessive disease caused by an insertion into exon 12 of FXI gene. The aim of this study is to determine the allele frequency of Factor XI Deficiency (FXID in Holstein cows reared in Thrace region of Turkey. Blood samples of 287 Holstein cows were used for DNA isolation. Amplification of FXI gene was followed by the evaluation of PCR products with visualization on 2% agarose gel electrophoresis. FXID mutant allele was not observed in any of the samples used in this study. In conclusion, none of the Holstein cows were neither affected nor carriers for FXID among all analysed Holstein cows reared in Thrace region of Turkey.

  13. Allelic frequency of the MCP-1 promoter -2518 polymorphism in the Turkish population and in Turkish patients with juvenile rheumatoid arthritis.

    Science.gov (United States)

    Ozyürek, A Ruhi; Gürses, Dolunay; Ulger, Zülal; Levent, Ertürk; Bakiler, A Rahmi; Berdeli, Afig

    2007-04-01

    Although genetic and environmental factors contribute to the pathogenesis of juvenile rheumathoid arthritis (JRA), the etiology and pathogenesis remain controversial. The objective of this study was to investigate genotypic and allelic frequencies of monocyte chemoattractant protein-1 (MCP-1) gene -2518 (G/A) polymorphism in the healthy Turkish population and patients with JRA. Genomic DNA was collected from 66 JRA patients and 150 healthy individuals. To evaluate the association of the -2518 (G/A) MCP-1 gene polymorphism with the outcome of JRA, we analyzed the types of JRA and the score on the childhood health assessment questionnaire (C-HAQ score). In the healthy Turkish population, the frequencies of A and G alleles were 71 and 29%, respectively. No significant difference was observed between the JRA patients and healthy subjects in the distribution allelic and genotypic frequencies of the -2518 (G/A) MCP-1 gene polymorphism (p>0.05). However, the AG genotype was found to be higher and the AA genotype was found to be lower in the patients with systemic type JRA compared to those with the other types of JRA (p=0.019). When the JRA patients were evaluated according to the C-HAQ score, we found that the -2518 (G/A) MCP-1 gene polymorphism did not relate the prognosis (p>0.05). AG genotype was found to be higher in the systemic type of JRA. The results indicate that MCP-1 gene polymorphism might slightly associate with patients with systemic JRA. Further studies are needed to elucidate the role of this polymorphism in the pathogenesis of JRA in various populations because this polymorphism has a functional significance and an ethnic difference.

  14. Analysis of HLA-A, HLA-B, HLA-DRB1 allelic, genotypic, and haplotypic frequencies in colombian population

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    Yamín Rocío Arias-Murillo

    2011-01-01

    Full Text Available Introduction: The high polymorphism of the HLA system allows its typification to be used as valuable tool in establishing association to various illnesses, immune and genetic profiles; it also provides a guide to identifying compatibility among donors and receptors of organs transplants. Objective: To establish HLA-A, HLA-B, and HLA.DRB1 allele, genotype and haplotype frequencies among patients treated at Clinica Colsanitas SA. Methods: 561 patients coming from different regions in Colombia, who were attended in 8 centers of the clinical laboratory of the Clinica Colsanitas in different cities of the country from January 2004 to August 2008, were included in this study. All were HLA-A,-B, and -DRB1 typified via SSP PCR. Allele, genotype and haplotype frequencies were estimated with STATA Software Version 9.0 and the GENEPOP genetic analysis package. Results: 19, 28, and 15 different alleles were identified for loci HLA-A,-B and -DRB1, respectively. Alleles found most frequently were A*24 (26.2%, A*02 (26%, B*35(22.7%, and DRB1*04 (24%. The most frequent genotypes were A*02,24 (14.2%, B*07,35 (5.5%, DRB1*01,04, and DRB1*04,04 (6.9%; while most the frequent haplotypes were HLA A*24, B*35 (9.2%, A*24, DRB1*04 (8.1%; B*35, DRB1*04 (7.8%, A*2 DRB1*04 (7.4%. Conclusion: The results obtained provide a useful reference framework for the population studied, allowing compatibility probability calculations to be performed for organ transplants.

  15. Analysis of HLA-A, HLA-B, HLA-DRB1 allelic, genotypic, and haplotypic frequencies in colombian population

    Directory of Open Access Journals (Sweden)

    Yazmin Rocío Árias-Murillo

    2010-12-01

    Full Text Available Introduction: The high polymorphism of the HLA system allows its typification to be used as valuable tool in establishing association to various illnesses, immune and genetic profiles; it also provides a guide to identifying compatibility among donors and receptors of organs transplants.Objective: To establish HLA-A, HLA-B, and HLA.DRB1 allele, genotype and haplotype frequencies among patients treated at Clinica Colsanitas SA.Methods: 561 patients coming from different regions in Colombia, who were attended in 8 centers of the clinical laboratory of the Clinica Colsanitas in different cities of the country from January 2004 to August 2008, were included in this study. All were HLA-A,-B, and -DRB1 typified via SSP PCR. Allele, genotype and haplotype frequencies were estimated with STATA Software Version 9.0 and the GENEPOP genetic analysis package.Results: 19, 28, and 15 different alleles were identified for loci HLA-A,-B and -DRB1, respectively. Alleles found most frequently were A*24 (26.2%, A*02 (26%, B*35(22.7%, and DRB1*04 (24%. The most frequent genotypes were A*02,24 (14.2%, B*07,35 (5.5%, DRB1*01,04, and DRB1*04,04 (6.9%; while most the frequent haplotypes were HLA A*24, B*35 (9.2%, A*24, DRB1*04 (8.1%; B*35, DRB1*04 (7.8%, A*2 DRB1*04 (7.4%.Conclusion: The results obtained provide a useful reference framework for the population studied, allowing compatibility probability calculations to be performed for organ transplants.

  16. ACTN3 allele frequency in humans covaries with global latitudinal gradient.

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    Scott M Friedlander

    Full Text Available 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.

  17. HLA Class II Profile and Distribution of HLA-DRB1 and HLA-DQB1 Alleles and Haplotypes among Lebanese and Bahraini Arabs

    Science.gov (United States)

    Almawi, Wassim Y.; Busson, Marc; Tamim, Hala; Al-Harbi, Einas M.; Finan, Ramzi R.; Wakim-Ghorayeb, Saria F.; Motala, Ayesha A.

    2004-01-01

    The gene frequencies of HLA class II alleles were studied in 95 healthy Lebanese Arab and 72 healthy Bahraini Arab subjects. Our aim was to establish the genetic relationship between Bahraini and Lebanese Arabs in terms of HLA class II gene and haplotype frequencies and to compare these results with frequencies for other countries with populations of Caucasian and non-Caucasian descent. Subjects were unrelated and of both sexes, and HLA-DRB1 and -DQB1 genotyping was done by the PCR sequence-specific primer technique. Comparative analysis of the HLA-DR and -DQ alleles revealed differences in the allelic distribution among Bahraini and Lebanese subjects. Analysis of the 25 HLA-DRB1 alleles that have been investigated showed that the DRB1*040101 and DRB1*110101 alleles were more frequent among Lebanese, whereas DRB1*030101 and DRB1*160101 alleles were more frequent among Bahrainis. Similarly, of the seven HLA-DQB1 alleles analyzed, the presence of DQB1*0201 was more frequent among Bahrainis, whereas DQB1*030101 was more frequent among Lebanese. The DRB1*160101-DQB1*050101 (0.1318 versus 0.0379%) and DRB1*030101-DQB1*0201 (0.1202 versus 0.0321%) haplotypes were more frequent among Bahrainis, while the DRB1*110101-DQB1*030101 (0.3142 versus 0.1198%) and DRB1*040101-DQB1*0302 (0.1416 versus 0.0278%) haplotypes were more frequent in Lebanese subjects. Furthermore, a high prevalence of the DRB1*040101-DRB1*110101-DQB1*0302-DQB1*030101 (12.63 versus 1.35%, P = 0.015) and the homozygous DRB1*110101-DRB1*110101-DQB1*030101-DQB1*030101 (7.37 versus 0.00%, P = 0.046) genotypes was seen among Lebanese, and DRB1*070101-DRB1*160101-DQB1*0201-DQB1*050101 (6.76 versus 0.00%, P = 0.034) was seen more frequently among Bahraini subjects. Our results underline significant differences between these two populations in HLA class II distribution, provide basic information for further studies of major histocompatibility complex heterogeneity among Arabic-speaking countries, and serve as a

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

    Science.gov (United States)

    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.

  19. The immunogenetics of multiple sclerosis. The frequency of HLA-alleles class 1 and 2 is lower in Southern Brazil than in the European population

    Directory of Open Access Journals (Sweden)

    Lineu Cesar Werneck

    2016-08-01

    Full Text Available ABSTRACT Objective To study the HLA of class 1and 2 in a multiple sclerosis (MS population to verify the susceptibility for the disease in the Southern Brazil. Methods We analyzed patients with MS and controls, by direct sequencing of the genes related to HLA DRB1, DQB1, DPB1, A, B and C alleles with high resolution techniques. Results We found a lower frequency of all HLA alleles class 1 and 2 in MS and controls comparing to the European population. Several alleles had statistical correlation, but after Bonferroni correction, the only allele with significance was the HLA-DQB1*02:03, which has a positive association with MS. Conclusions Our data have different frequency of HLA-alleles than the previous published papers in the Southeast Brazil and European population, possible due to several ethnic backgrounds.

  20. Allele frequency changes due to hitch-hiking in genomic selection programs

    DEFF Research Database (Denmark)

    Liu, Huiming; Sørensen, Anders Christian; Meuwissen, Theo H E;

    2014-01-01

    on phenotype BLUP EBV, but this did not always apply when inbreeding was measured by runs of homozygosity. Compared to genomic BLUP, selection on EBV from Bayesian Lasso led to less genetic drift, reduced the loss of favourable alleles and more effectively controlled the rate of both pedigree and genomic......, rather than just by genetic drift. The hitch-hiking effect is a key factor in the difference between pedigree inbreeding and genomic inbreeding, especially under genomic selection. When implementing long-term genomic selection, strategies for genomic control of inbreeding are essential, due......Background Genomic selection makes it possible to reduce pedigree-based inbreeding over best linear unbiased prediction (BLUP) by increasing emphasis on own rather than family information. However, pedigree inbreeding might not accurately reflect the loss of genetic variation and the true level...

  1. ALLELE DISTRIBUTION OF D12S304, D12S313, D12S1583, D12S1640 AND D12S1708 IN CHINESE HAN POPULATION

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Objective To analyze the genetic polymorphism of 5 STR loci (D12S304, D12S313, D12S1583, D12S1640 and D12S1708) on chromosome 12 in Chinese Han population. Methods EDTA-anticoagulated blood specimens were collected from unrelated individuals of Chinese Han population in Shaanxi province. DNA samples were extracted with the Wizard Genomic DNA purification Kit and were amplified by polymerase chain reaction (PCR) technique. The PCR products were analyzed by ABI 3100 Genetic Analyzer. Results All 5 loci were in Hardy-Weinberg equilibrium. Allele and genotype frequencies, heterozygosity, power of discrimination, polymorphism information content, probability of paternity exclusion and matching probability of each locus were calculated in Excel 2002. Conclusion They are complex loci with lots of evenly distributed alleles and high heterozygosity in Chinese Han population. Thus they are informative polymorphic loci and valuable DNA marker which represents a superior alternative to many established STRs.

  2. Origins, distribution and expression of the Duarte-2 (D2) allele of galactose-1-phosphate uridylyltransferase

    OpenAIRE

    Carney, Amanda E.; Rebecca D Sanders; Garza, Kerry R.; McGaha, Lee Anne; Bean, Lora J. H.; Coffee, Bradford W.; Thomas, James W; Cutler, David J.; Kurtkaya, Natalie L.; Fridovich-Keil, Judith L.

    2009-01-01

    Duarte galactosemia is a mild to asymptomatic condition that results from partial impairment of galactose-1-phosphate uridylyltransferase (GALT). Patients with Duarte galactosemia demonstrate reduced GALT activity and carry one profoundly impaired GALT allele (G) along with a second, partially impaired GALT allele (Duarte-2, D2). Molecular studies reveal at least five sequence changes on D2 alleles: a p.N314D missense substitution, three intronic base changes and a 4 bp deletion in the 5′ pro...

  3. The allelic distribution of -308 Tumor Necrosis Factor-alpha gene polymorphism in South African women with cervical cancer and control women

    Directory of Open Access Journals (Sweden)

    Williamson Anna-Lise

    2006-01-01

    Full Text Available Abstract Background Cervical cancer is due to infection with specific high-risk types of human papillomavirus (HPV. Although the incidence of genital HPV infection in various population groups is high, most of these regress without intervention. Investigating genetic host factors and cellular immune responses, particularly cytokines, could help to understand the association between genital HPV infection and carcinogenesis. The tumor necrosis factor alpha (TNF-α cytokine plays an important role in all stages of cervical cancer and has the ability to induce the regression of human tumors. Therefore the aim of the study was to investigate the allelic distribution of -308 TNF-α gene polymorphism in South African women with cervical cancer compared to control women. Methods Included in our study were women with histologically proven cancer of the cervix (n = 244 and hospital-based controls (n = 228. All patients and controls were from mixed race and black population groups in South Africa. The detection of a bi-allelic -308 (A/G polymorphism in the promoter region of TNF-α was investigated using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR technique. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups. Results In this study we observed no association between the distribution of -308 TNF-α polymorphism and the risk of developing cervical cancer even after combining the data from the two ethnic populations (X2 = 2.26. In addition, using the chi-squared test we found no significant association between the known risk factors for cervical cancer and the allele distribution of -308 TNF-α. However, the frequency of the rare high-producing allele -308A of TNF-α was significantly lower in the South African population when compared to Caucasians and Chinese population groups. Conclusion We demonstrated no association between -308 TNF

  4. The allelic distribution of -308 Tumor Necrosis Factor-alpha gene polymorphism in South African women with cervical cancer and control women

    International Nuclear Information System (INIS)

    Cervical cancer is due to infection with specific high-risk types of human papillomavirus (HPV). Although the incidence of genital HPV infection in various population groups is high, most of these regress without intervention. Investigating genetic host factors and cellular immune responses, particularly cytokines, could help to understand the association between genital HPV infection and carcinogenesis. The tumor necrosis factor alpha (TNF-α) cytokine plays an important role in all stages of cervical cancer and has the ability to induce the regression of human tumors. Therefore the aim of the study was to investigate the allelic distribution of -308 TNF-α gene polymorphism in South African women with cervical cancer compared to control women. Included in our study were women with histologically proven cancer of the cervix (n = 244) and hospital-based controls (n = 228). All patients and controls were from mixed race and black population groups in South Africa. The detection of a bi-allelic -308 (A/G) polymorphism in the promoter region of TNF-α was investigated using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) technique. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups. In this study we observed no association between the distribution of -308 TNF-α polymorphism and the risk of developing cervical cancer even after combining the data from the two ethnic populations (X2 = 2.26). In addition, using the chi-squared test we found no significant association between the known risk factors for cervical cancer and the allele distribution of -308 TNF-α. However, the frequency of the rare high-producing allele -308A of TNF-α was significantly lower in the South African population when compared to Caucasians and Chinese population groups. We demonstrated no association between -308 TNF-α polymorphism and the risk of cervical cancer among two

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Angelica B.W. Boldt

    2009-01-01

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

  8. Frequency of the CCRdelta32 allele in Brazilians: a study in colorectal cancer and in HTLV-I infection

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    Rinaldo W. Pereira

    2000-09-01

    Full Text Available The identification of a 32-bp deletion in the cc-chemokine receptor-5 gene (CCR5delta32 allele that renders homozygous individuals highly resistant to HIV infection has prompted worldwide investigations of the frequency of the CCR5delta32 allele in regional populations. It is important to ascertain if CCR5delta32 is a factor to be considered in the overall epidemiology of HIV in individual populations. With this in mind we determined the CCR5delta32 allele frequency in a large sample (907 individuals of the southeastern Brazilian urban population, stratified as follows: 322 healthy unrelated individuals, 354 unselected colorectal cancer patients, and 229 blood donors. The three groups displayed essentially identical allelic frequencies of CCR5delta32 and pairwise comparisons did not show significant differences. Thus, our results can be pooled to provide a reliable estimate of the CCR5delta32 allele frequency in the southeastern Brazil of 0.053 ± 0.005. The blood donors comprised 50 HTLV-I serologically negative individuals, 115 non-symptomatic individuals HTLV-I positive by ELISA but with indeterminate Western blot results, 49 healthy blood donors HTLV-I positive both at ELISA and Western blot and 15 patients with clinical spinal cord disease (HAM. A suggestive trend was observed, with the CCR5delta32 frequencies decreasing progressively in these four categories. However, when we applied Fischer's exact test no significant differences emerged. We believe that further studies in larger cohorts should be performed to ascertain whether the CCR5delta32 allele influences the chance of becoming infected or developing clinical symptoms of HTLV-I infection.A observação de que indivíduos homozigotos para uma deleção de 32 pares de base no gene que codifica para o receptor 5 de cc-quimiocinas apresentam um menor risco de contrair a infecção por HIV-1 levou à investigação da freqüência deste polimorfismo em várias populações mundiais.

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

    Directory of Open Access Journals (Sweden)

    Mullen Michael P

    2012-01-01

    Full Text Available Abstract 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 ® 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-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving

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

    Science.gov (United States)

    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

  11. Plasmodium falciparum msp1, msp2 and glurp allele frequency and diversity in sub-Saharan Africa

    Directory of Open Access Journals (Sweden)

    Snounou Georges

    2011-04-01

    Full Text Available Abstract Background The efficacy of anti-malarial drugs is assessed over a period of 28-63 days (depending on the drugs' residence time following initiation of treatment in order to capture late failures. However, prolonged follow-up increases the likelihood of new infections depending on transmission intensity. Therefore, molecular genotyping of highly polymorphic regions of Plasmodium falciparum msp1, msp2 and glurp loci is usually carried out to distinguish recrudescence (true failures from new infections. This tool has now been adopted as an integral part of anti-malarial efficacy studies and clinical trials. However, there are concerns over its utility and reliability because conclusions drawn from molecular typing depend on the genetic profile of the respective parasite populations, but this profile is not systematically documented in most endemic areas. This study presents the genetic diversity of P. falciparum msp1, msp2 and glurp markers in selected sub-Saharan Africa countries with varying levels of endemicity namely Malawi, Tanzania, Uganda, Burkina Faso and São Tomé. Methods A total 780 baseline (Day 0 blood samples from children less than seven years, recruited in a randomized controlled clinical trials done between 1996 and 2000 were genotyped. DNA was extracted; allelic frequency and diversity were investigated by PCR followed by capillary electrophoresis for msp2 and fragment sizing by a digitalized gel imager for msp1 and glurp. Results and Conclusion Plasmodium falciparum msp1, msp2 and glurp markers were highly polymorphic with low allele frequencies. A total of 17 msp1 genotypes [eight MAD20-, one RO33- and eight K1-types]; 116 msp2 genotypes [83 3D7 and 33 FC27- types] and 14 glurp genotypes were recorded. All five sites recorded very high expected heterozygosity (HE values (0.68 - 0.99. HE was highest in msp2 locus (HE = 0.99, and lowest for msp1 (HE = 0.68 (P msp1, msp2 and glurp in malaria clinical trials in sub

  12. The distribution of Tap2 alleles among laboratory rat RT1 haplotypes.

    Science.gov (United States)

    Joly, E; Deverson, E V; Coadwell, J W; Günther, E; Howard, J C; Butcher, G W

    1994-01-01

    We are reporting the cDNA sequences of Tap2 from two cima and two cimb rat strains. Comparison of the cDNA sequences shows that these alleles fall into two groups, which we refer to as Tap2-A and Tap2-B. We found that alleles from the Tap2-B group are more closely related to the mouse homologue than are Tap2-A alleles, and among the 48 nucleotides which differ between the Tap2-A and Tap2-B cDNAs, three affect restriction sites. We defined pairs of oligonucleotides which allow amplification of the regions bearing these restriction sites from genomic DNA or cDNA, and this technique has been successful for the genotyping of all of the 56 laboratory strains of Rattus norvegicus tested and for five cell lines tested so far. All 14 known RT1 standard haplotypes were tested, and 7 found to belong to the Tap2-B group, and 7 to Tap2-A. We also found that intron sizes among the alleles of the Tap2-B group fall into two subgroups, providing further insight into the phylogeny of these various haplotypes.

  13. The distribution of Tap2 alleles among laboratory rat RT1 haplotypes.

    Science.gov (United States)

    Joly, E; Deverson, E V; Coadwell, J W; Günther, E; Howard, J C; Butcher, G W

    1994-01-01

    We are reporting the cDNA sequences of Tap2 from two cima and two cimb rat strains. Comparison of the cDNA sequences shows that these alleles fall into two groups, which we refer to as Tap2-A and Tap2-B. We found that alleles from the Tap2-B group are more closely related to the mouse homologue than are Tap2-A alleles, and among the 48 nucleotides which differ between the Tap2-A and Tap2-B cDNAs, three affect restriction sites. We defined pairs of oligonucleotides which allow amplification of the regions bearing these restriction sites from genomic DNA or cDNA, and this technique has been successful for the genotyping of all of the 56 laboratory strains of Rattus norvegicus tested and for five cell lines tested so far. All 14 known RT1 standard haplotypes were tested, and 7 found to belong to the Tap2-B group, and 7 to Tap2-A. We also found that intron sizes among the alleles of the Tap2-B group fall into two subgroups, providing further insight into the phylogeny of these various haplotypes. PMID:8206525

  14. Zipfian Frequency Distributions Facilitate Word Segmentation in Context

    Science.gov (United States)

    Kurumada, Chigusa; Meylan, Stephan C.; Frank, Michael C.

    2013-01-01

    Word frequencies in natural language follow a highly skewed Zipfian distribution, but the consequences of this distribution for language acquisition are only beginning to be understood. Typically, learning experiments that are meant to simulate language acquisition use uniform word frequency distributions. We examine the effects of Zipfian…

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

    Science.gov (United States)

    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, PVikings 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2016-04-01

    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

  18. Helicobacter pylori outer membrane protein Q allele distribution is associated with distinct pathologies in Pakistan.

    Science.gov (United States)

    Yakoob, Javed; Abbas, Zaigham; Khan, Rustam; Salim, Saima Azhar; Awan, Safia; Abrar, Ambar; Jafri, Wasim

    2016-01-01

    Helicobacter pylori (H. pylori) strains expressing outer membrane protein Q (HopQ) promote adherence to the gastric epithelial cell. We characterized HopQ alleles in relation to H. pylori-related disease, histology and virulence markers. Gastric biopsies were obtained at esophagogastroduodenoscopy from patients with upper gastrointestinal symptoms. H. pylori culture, histology and polymerase chain reaction (PCR) for HopQ types, cagA, cagA-promoter and vacA alleles were performed. DNA extracted was used for PCR. Sequencing of PCR products of HopQ types 1 and 2 was followed by BLAST query. We examined 241 H. pylori isolates. HopQ type 1 was positive in 70 (29%) isolates, type 2 in 60 (25%) isolates, while both type 1 and type 2 in 111 (46%) H. pylori isolates, respectively. Nonulcer dyspepsia (NUD) was associated with HopQ type 2 in 48 (41%) isolates, while gastric carcinoma (GC) in 37 (53%) (P<0.001) with type 1 isolates. Gastric ulcers (GU) were 39 (46%) (P<0.001) in H. pylori infection with multiple HopQ alleles compared to 6 (23%) in HopQ type 1. Multivariate analysis demonstrated that multiple HopQ alleles were associated with GU OR 2.9 (1.07-7.8) (P=0.03). HopQ type 1 was associated with cagA 58 (84%) (P<0.001) and cagA-promoter 58 (83%) (P<0.001) compared to 14 (23%) and 17 (28%) respectively, in type 2. VacAs1a was associated with HopQ type 1 in 59 (84%) isolates compared to HopQ type 2 in 35 (58%) (P=0.002) isolates. VacAm1 was associated with HopQ type 1 in 53 (76%) isolates compared to HopQ type 2 in 32 (53%) (P=0.004) isolates. H. pylori infection with multiple HopQ alleles was predominant. H. pylori infection with single HopQ type 1 was associated with GC in the presence of other H. pylori virulence markers.

  19. Frequencies of 23 functionally significant variant alleles related with metabolism of antineoplastic drugs in the Chilean population: comparison with Caucasian and Asian populations

    Directory of Open Access Journals (Sweden)

    Angela Margarita Roco

    2012-11-01

    Full Text Available 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 compare 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 allele frequency (0.12 and GSTT1null (0.11 and GSTM1null (0.36 genotype frequencies 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 considered

  20. Allele distributions at hybrid incompatibility loci facilitate the potential for gene flow between cultivated and weedy rice in the US.

    Directory of Open Access Journals (Sweden)

    Stephanie M Craig

    Full Text Available The accumulation of independent mutations over time in two populations often leads to reproductive isolation. Reproductive isolation between diverging populations may be reinforced by barriers that occur either pre- or postzygotically. Hybrid sterility is the most common form of postzygotic isolation in plants. Four postzygotic sterility loci, comprising three hybrid sterility systems (Sa, s5, DPL, have been recently identified in Oryza sativa. These loci explain, in part, the limited hybridization that occurs between the domesticated cultivated rice varieties, O. sativa spp. japonica and O. sativa spp. indica. In the United States, cultivated fields of japonica rice are often invaded by conspecific weeds that have been shown to be of indica origin. Crop-weed hybrids have been identified in crop fields, but at low frequencies. Here we examined the possible role of these hybrid incompatibility loci in the interaction between cultivated and weedy rice. We identified a novel allele at Sa that seemingly prevents loss of fertility in hybrids. Additionally, we found wide-compatibility type alleles at strikingly high frequencies at the Sa and s5 loci in weed groups, and a general lack of incompatible alleles between crops and weeds at the DPL loci. Our results suggest that weedy individuals, particularly those of the SH and BRH groups, should be able to freely hybridize with the local japonica crop, and that prezygotic factors, such as differences in flowering time, have been more important in limiting weed-crop gene flow in the past. As the selective landscape for weedy rice changes due to increased use of herbicide resistant strains of cultivated rice, the genetic barriers that hinder indica-japonica hybridization cannot be counted on to limit the flow of favorable crop genes into weeds.

  1. Increased frequency of co-existing JAK2 exon-12 or MPL exon-10 mutations in patients with low JAK2(V617F) allelic burden.

    Science.gov (United States)

    Nussenzveig, Roberto H; Pham, Ha T; Perkins, Sherrie L; Prchal, Josef T; Agarwal, Archana M; Salama, Mohamed E

    2016-01-01

    The frequency of co-existing JAK2(V617F)/MPL and JAK2(V617F)/JAK2 exon-12 mutations has not been previously investigated in MPNs. Poor survival was reported in primary myelofibrosis with low JAK2(V617F) allelic burden. However, mutational status of JAK2 exon-12 or MPL were not reported in these patients. This study developed a cost-effective multiplex high resolution melt assay that screens for mutations in JAK2 gene exons-12 and -14 ((V617F)) and MPL gene exon-10. Co-existing mutations with JAK2(V617F) were detected in 2.9% (6/208; two JAK2 exon-12 and four MPL exon-10) patient specimens with known JAK2(V617F) (allelic-burden range: 0.1-96.8%). Co-existing mutations were detected in specimens with < 12% JAK2(V617F) allelic burden. Current WHO guidelines do not recommend further testing once JAK2(V617F) mutation is detected in MPNs. The findings, however, indicate that quantification of JAK2(V617F) allele burden may be clinically relevant in MPNs and in those with low allelic burden additional testing for JAK2 exon-12 and MPL exon-10 mutation should be pursued.

  2. Evaluation of the iPLEX® ADME PGx Pro Panel and allele frequencies of pharmacogenetic markers in Danes

    DEFF Research Database (Denmark)

    Jensen, Line; Børsting, Claus; Dalhoff, Kim;

    2016-01-01

    OBJECTIVES: The iPlex® ADME PGx Pro Panel was developed to investigate 191 polymorphisms including single nucleotide polymorphisms (SNPs), insertion-deletions (INDELS), and copy number variations (CNV) relevant for absorption, distribution, metabolism, and excretion (ADME) of drugs. The purpose of...... Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). RESULTS: The typing quality of 161 SNP assays was categorized as well performing or acceptable, whereas 22 SNP assays were categorized as either questionable or unacceptable. The frequencies of the genotypes observed in the Danish...... population were compared to those of the European reference population from the 1000 Genome Project. Three SNPs (rs737865, rs35167514, and rs34305973) showed statistically significantly differences between the frequencies of the 1000 Genomes Europeans and the Danes. The CNV assays could only be used as a...

  3. Power laws for heavy-tailed distributions: modeling allele and haplotype diversity for the national marrow donor program.

    Directory of Open Access Journals (Sweden)

    Noa Slater

    2015-04-01

    Full Text Available Measures of allele and haplotype diversity, which are fundamental properties in population genetics, often follow heavy tailed distributions. These measures are of particular interest in the field of hematopoietic stem cell transplant (HSCT. Donor/Recipient suitability for HSCT is determined by Human Leukocyte Antigen (HLA similarity. Match predictions rely upon a precise description of HLA diversity, yet classical estimates are inaccurate given the heavy-tailed nature of the distribution. This directly affects HSCT matching and diversity measures in broader fields such as species richness. We, therefore, have developed a power-law based estimator to measure allele and haplotype diversity that accommodates heavy tails using the concepts of regular variation and occupancy distributions. Application of our estimator to 6.59 million donors in the Be The Match Registry revealed that haplotypes follow a heavy tail distribution across all ethnicities: for example, 44.65% of the European American haplotypes are represented by only 1 individual. Indeed, our discovery rate of all U.S. European American haplotypes is estimated at 23.45% based upon sampling 3.97% of the population, leaving a large number of unobserved haplotypes. Population coverage, however, is much higher at 99.4% given that 90% of European Americans carry one of the 4.5% most frequent haplotypes. Alleles were found to be less diverse suggesting the current registry represents most alleles in the population. Thus, for HSCT registries, haplotype discovery will remain high with continued recruitment to a very deep level of sampling, but population coverage will not. Finally, we compared the convergence of our power-law versus classical diversity estimators such as Capture recapture, Chao, ACE and Jackknife methods. When fit to the haplotype data, our estimator displayed favorable properties in terms of convergence (with respect to sampling depth and accuracy (with respect to diversity

  4. Magnitude-frequency distribution of volcanic explosion earthquakes

    Science.gov (United States)

    Nishimura, Takeshi; Iguchi, Masato; Hendrasto, Mohammad; Aoyama, Hiroshi; Yamada, Taishi; Ripepe, Maurizio; Genco, Riccardo

    2016-07-01

    Magnitude-frequency distributions of volcanic explosion earthquakes that are associated with occurrences of vulcanian and strombolian eruptions, or gas burst activity, are examined at six active volcanoes. The magnitude-frequency distribution at Suwanosejima volcano, Japan, shows a power-law distribution, which implies self-similarity in the system, as is often observed in statistical characteristics of tectonic and volcanic earthquakes. On the other hand, the magnitude-frequency distributions at five other volcanoes, Sakurajima and Tokachi-dake in Japan, Semeru and Lokon in Indonesia, and Stromboli in Italy, are well explained by exponential distributions. The statistical features are considered to reflect source size, as characterized by a volcanic conduit or chamber. Earthquake generation processes associated with vulcanian, strombolian and gas burst events are different from those of eruptions ejecting large amounts of pyroclasts, since the magnitude-frequency distribution of the volcanic explosivity index is generally explained by the power law.

  5. 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

    OpenAIRE

    Watanabe, Naoto; Satoh, Youichi; Fujita, Tatsuo; Ohta, Takeshi; Kose, Hiroyuki; Muramatsu, Youji; Yamamoto, Takuji; Yamada, Takahisa

    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 p...

  6. 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).

    Science.gov (United States)

    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

  7. 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.

    Science.gov (United States)

    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

  8. P67L: a cystic fibrosis allele with mild effects found at high frequency in the Scottish population.

    OpenAIRE

    Gilfillan, A.; Warner, J P; Kirk, J M; Marshall, T.; Greening, A; Ho, L. P.; Hargreave, T; Stack, B; McIntyre, D.; Davidson, R.; Dean, J C; Middleton, W; Brock, D J

    1998-01-01

    Only three mutant cystic fibrosis (CF) alleles have to date been established as conferring a dominant mild effect on affected subjects who are compound heterozygotes. We now add a fourth, P67L, which occurs on about 1.4% of Scottish CF chromosomes. Among 13 patients (12 unrelated) with this allele, the average age at diagnosis was 22.5 +/- 11.3 years. None of the cases had consistently raised sweat chloride concentrations, the average value being 57 +/- 9 mmol/l; 77% of the patients were panc...

  9. The frequency characteristics of medium voltage distribution system impedances

    Directory of Open Access Journals (Sweden)

    Liviu Emil Petrean

    2009-10-01

    Full Text Available In this paper we present the frequency characteristics of impedances involved in the electrical equivalent circuit of a large medium voltage distribution system. These impedances influence harmonics distortions propagation occurring due to the nonsinusoidal loads. We analyse the case of a 10 kV large urban distribution system which supplies industrial, commercial and residential customers. The influence of various parameters of the distribution network on the frequency characteristics are presented, in order to assess the interaction of harmonic distortion and distribution system network.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  12. Polymorphisms of the coagulation factor Ⅶ gene and its plasma levels in relation to acute cerebral infarction differences in allelic frequencies between Chinese Han and European populations

    Institute of Scientific and Technical Information of China (English)

    康文英; 王鸿利; 熊立凡; 王学锋; 储海燕; 璩斌; 刘湘帆; 尹俊; 段宝华; 王振义

    2004-01-01

    Background Coagulation factor Ⅶ (F Ⅶ) levels in plasma are usually related to ischemic heart disease (IHD) and cerebral infarction shares many of the risk factors related to IHD. Is there any relationship between factor Ⅶ and cerebral infarction? We investigated the relationship between F Ⅶ and acute cerebral infarction and reported genotype frequencies and allelic frequencies of FⅦ gene polymorphisms in the Chinese Han population.Methods We recruited 62 patients with acute cerebral infarction confirmed by magnetic resonance imaging (MRI) from Ruijin Hospital, and 149 age-matched patients clinically free of vascular disease to act as controls. All of them were unrelated, and were from the Chinese Han population. FⅦ coagulant activity (FⅦc) was determined using an clotting assay, activated FⅦ (FⅦa) and FⅦ Ag were assayed using enzyme immunoassay kits. The FⅦ gene polymorphisms to be detected included-401G/T, -402G/A, 5'F7A1/A2, IVS7 and R353Q. 5'F7 and IVS7 were revealed by means of a PCR and direct agarose gel electrophoresis. The rest were examined by a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results The results showed that FⅦc, FⅦAg and FⅦa were higher in the acute cerebral infarction group than in the control group (P<0.01, P<0.05, P<0.05, respectively). There were no significant differences in the genotype frequencies of FⅦ gene polymorphisms between the two groups. The allelic frequencies in the Chinese Han population were as follows: -401G/T (96.64/3.36), -402G/A (52.01/47.99), 5'F7A1/A2(96.64/3.36), IVS7 H5/H6/H7/H8 (0.34/52.35/46.98/0.34) and R353Q (95.64/4.36). There were significant differences (P<0.01, P<0.001, P<0.001, P<0.001, P<0.001, respectively) in these allelic frequencies between the Chinese Han and European populations.Conclusions The results indicate that increased plasma FⅦ levels may contribute to thrombosis in cerebral infarction. And there was no significant difference

  13. Frequency distribution of DNA repair genes ERCC1 and ERCC2 polymorphisms in South Indian healthy population.

    Science.gov (United States)

    Rao, Katiboina Srinivasa; SureshKumar, Srinivasamurthy; Umamaheswaran, Gurusamy; Paul, Abialbon; Dubashi, Biswajit; Gunaseelan, Karunanithi; Dkhar, Steven Aibor

    2014-09-01

    DNA repair genes are crucial in maintaining the integrity of the whole genome. Single nucleotide polymorphisms (SNPs) in DNA repair genes have been attributed to the development of various cancers. SNPs of DNA repair genes (ERCC1 and ERCC2) have been implicated in the causation of various cancers as well as inter-individual variability in the therapeutic outcomes of platinum based therapy. Thus establishing the frequency of these functional SNPs in the healthy population is of significance. The present study was aimed to establish the allele and genotype frequencies of ERCC1 (19007C>T, rs11615; 8092C>A, rs3212986) and ERCC2 (Asp312Asn, rs1799793) genes in South Indian healthy population and to compare the data from HapMap populations. The study population consisted of 128 healthy South Indian unrelated individuals of either sex aged between 18 and 60 years. Standard phenol-chloroform method was used to extract DNA from peripheral leukocytes. The genotype of DNA repair gene polymorphisms was determined by quantitative real-time polymerase chain reaction using TaqMan genotyping assay. The observed frequency of the studied polymorphisms followed Hardy-Weinberg equilibrium (p>0.05). The frequencies of the minor alleles of the SNPs rs11615 (T), rs3212986 (A) and rs1799793 (A) were 43.8%, 29.3% and 35.6%, respectively. Gender-based analysis showed no significant difference in the frequency pattern. The observed allele and genotype frequencies showed significant ethnic difference between South Indians and other HapMap populations. This is the first study to provide the normative frequency data of allele and genotype distribution of three SNPs of ERCC1 and ERCC2 in South Indian healthy population. It might be useful in future genotype-phenotype association studies, especially for predicting the efficacy and adverse events of platinum based drugs. PMID:25155628

  14. Comparison of allele frequency for HLA-DR and HLA-DQ between patients with ECC and caries-free children

    Directory of Open Access Journals (Sweden)

    Bagherian A

    2008-03-01

    Full Text Available Background: Early childhood caries (ECC is one of the most common diseases of childhood. The etiology of ECC is multifactorial and both genetic and environmental factors play important roles in the pathogenesis of the disease. Genetic variations in the hosts may contribute to changes in the risk for dental caries. Genetic factors such as human leukocyte antigen (HLA have recently been suggested as a predisposing factor. Aim: The aim of this study was to look for an association between HLA-DRB1 and HLA-DQB1 with ECC for developing new strategies for the diagnosis as well as the prevention of the disease. Design: In this study, we extracted the genomic DNAs from whole blood samples of 44 patients with ECC and 35 caries-free children by the salting-out method. We amplified the genomic DNA by PCR-SSP and then HLA-typing was performed for all alleles. Results: The results revealed a significant increase in the frequency of HLA-DRB1FNx0104 in the patient group (P = 0.019. The odds ratio for this allele was detected to be 10. The frequency of HLA-DQB1 alleles was not significantly different between the two groups. Conclusion: The above results suggest that HLA-DRB1FNx0104 is associated with the susceptibility to ECC. Thus HLA-DRB1FNx0104 detection as a molecular marker for early diagnosis of ECC may be recommended.

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Nathália Delvaux

    2015-08-01

    Full Text Available 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.

  17. Recurrent frequency-size distribution of characteristic events

    Directory of Open Access Journals (Sweden)

    S. G. Abaimov

    2009-04-01

    Full Text Available Statistical frequency-size (frequency-magnitude properties of earthquake occurrence play an important role in seismic hazard assessments. The behavior of earthquakes is represented by two different statistics: interoccurrent behavior in a region and recurrent behavior at a given point on a fault (or at a given fault. The interoccurrent frequency-size behavior has been investigated by many authors and generally obeys the power-law Gutenberg-Richter distribution to a good approximation. It is expected that the recurrent frequency-size behavior should obey different statistics. However, this problem has received little attention because historic earthquake sequences do not contain enough events to reconstruct the necessary statistics. To overcome this lack of data, this paper investigates the recurrent frequency-size behavior for several problems. First, the sequences of creep events on a creeping section of the San Andreas fault are investigated. The applicability of the Brownian passage-time, lognormal, and Weibull distributions to the recurrent frequency-size statistics of slip events is tested and the Weibull distribution is found to be the best-fit distribution. To verify this result the behaviors of numerical slider-block and sand-pile models are investigated and the Weibull distribution is confirmed as the applicable distribution for these models as well. Exponents β of the best-fit Weibull distributions for the observed creep event sequences and for the slider-block model are found to have similar values ranging from 1.6 to 2.2 with the corresponding aperiodicities CV of the applied distribution ranging from 0.47 to 0.64. We also note similarities between recurrent time-interval statistics and recurrent frequency-size statistics.

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

    Science.gov (United States)

    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

  19. Visualization of EEG using time-frequency distributions.

    Science.gov (United States)

    Stiber, B Z; Sato, S

    1997-12-01

    The EEG is a time-varying or nonstationary signal. Frequency and amplitude are two of its significant characteristics, and are valuable clues to different states of brain activity. Detection of these temporal features is important in understanding EEGs. Commonly, spectrograms and AR models are used for EEG analysis. However, their accuracy is limited by their inherent assumption of stationarity and their trade-off between time and frequency resolution. We investigate EEG signal processing using existing compound kernel time-frequency distributions (TFDs). By providing a joint distribution of signal intensity at any frequency along time, TFDs preserve details of the temporal structure of the EEG waveform, and can extract its time-varying frequency and amplitude features. We expect that this will have significant implications for EEG analysis and medical diagnosis.

  20. Estimating length frequency distributions of large reef fish underwater

    Science.gov (United States)

    Bell, J. D.; Craik, G. J. S.; Pollard, D. A.; Russell, B. C.

    1985-04-01

    We describe the training of divers to recognise and remove bias in estimating lengths of fish underwater. Divers were asked to allocate objects, from a population ( N=50) with a known length frequency distribution, to ten 100 mm size classes. Observed and expected distributions were then compared and the divers informed of their errors. Training continued until divers consistently produced length frequency distributions that were not significantly different from the expected distribution (α=0.8) by the one sample Kolmogorov-Smirnov (K-S) test. Divers were trained in five trials, but after six months they had lost all their ability and had to be retrained. Three trained divers observing the “same” population of the large reef fish Plectropomus leopardus (Serranidae) produced length frequency distributions that were not significantly different ( P>0.1) on 67% of occasions. Data collected by divers can be used to detect small but real differences in length frequency distributions of populations when analysed using the two sample K-S test. We suggest a means of determining within site variation in length frequency relative to between site variation.

  1. A new allele conferring resistance to Lysinibacillus sphaericus is detected in low frequency in Culex quinquefasciatus field populations

    OpenAIRE

    Menezes, Heverly Suzany Gouveia; Chalegre, Karlos Diogo de Melo; Romão, Tatiany Patrícia; de Oliveira, Cláudia Maria Fontes; de-Melo-Neto, Osvaldo Pompílio; Silva-Filha, Maria Helena Neves Lobo

    2016-01-01

    Background The Cqm1 α-glucosidase of Culex quinquefasciatus larvae acts as the midgut receptor for the binary toxin of the biolarvicide Lysinibacillus sphaericus. Mutations within the cqm1 gene can code for aberrant polypeptides that can no longer be properly expressed or bind to the toxin, leading to insect resistance. The cqm1 REC and cqm1 REC-2 alleles were identified in a laboratory selected colony and both displayed mutations that lead to equivalent phenotypes of refractoriness to L. sph...

  2. Low Frequencies of CCR5-△32 and CCR5-m303, but High Frequencies of CCR2-641 and SDF1-3'A Alleles in Indigenous Ethnic Groups in Mainland China

    Institute of Scientific and Technical Information of China (English)

    WANG Fusheng (王福生); WANG zhe(王哲); Feng Tiejian (冯铁建); HOU Jing(侯静); LI Guanghani(李光汉); CAO Yunzhen(曹韵贞); JIN Lei(金磊); HONG Weiguo(洪卫国); LIU Mingxu (刘明旭); ZHOU YueSu (周越塑); ZHANG Bing (张冰); SHI Ming (施明); WANG JiMing(王吉明); LEI Zhouyun (雷周云)

    2002-01-01

    Objective:The aim in this study was to identify the allelicfrequencies of the chemokine (SDF1-3'A) and chemokinereceptor (CCR5A32, CCR5m303 and CCR2-64I) genesresistant to HIV-1 infection and/or disease progression inindigenous Chinese populations.Methods: By using QIAamp DNA Blood Mini Kit, thegenomic DNA samples were purified from whole peripheralblood of healthy individuals (n=2067) from Han, Uygur,Mongolian and Tibetan ethnic groups, as well as Han patientsincluding HIV-1 carriers (n=330), patients with other sexuallytransmitted diseases (STDs, n=259) and intravenous drugusers (IVDUs, n=125). The allelic polymorphisms wereidentified by means of PCR or PCR-RFLP analyses. Thesequences of randomly selected amplified PCR products werefurther confirmed by direct DNA sequencing.Results: The mutant frequencies were identified to be0%~3.48% for CCR5A32, 0% for CCR5m303,19.15%~28.79% for CCR2-64 and 19.10%~28.73% for SDF1-3'A alleles, respectively, in Chinese healthy individuals fromfour ethnic groups. Our findings indicated the allelicfrequencies vary among the different ethnic groups.Furthermore, the HIV-1 carriers, STD cases and IVDUs (all ofHan ethnicity) were found to have the allelic frequencies of0%~0.19% (CCR5A32), 0% (CCR5m303), 19.31%~20.45%(CCR2-64) and 25.61%~26.83% (SDF1-3'A) with minorvariations in their frequencies between the patients andhealthy Han groups. There was no CCR5-m303 mutationfound in any subject in this study.Conclusion: The examined subjects of four Chinese ethnicorigins showed lower frequencies of CCR5A32 andCCR5m303 alleles, but higher frequencies of mutant CCR2-64I and SDF1-3'A alleles compared to those identified innorthern-European and American Caucasians. Thesignificance of the different frequencies and polymorphisms of the above alleles in Chinese populations needs to be furtherexamined in HIV-1/AIDS diseases.

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

    Directory of Open Access Journals (Sweden)

    Guoping Li

    Full Text Available 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.

  4. Topographical Distributions of Allelic Loss in Individual Non-Small-Cell Lung Cancers

    OpenAIRE

    Yatabe, Yasushi; Konishi, Hiroyuki; Mitsudomi, Tetsuya; Nakamura, Shigeo; Takahashi, Takashi

    2000-01-01

    Non-small-cell carcinomas of the lung, especially adenocarcinomas, are characterized by a high degree of morphological heterogeneity. As carcinogenesis has been suggested to be a multistep process involving sequential accumulation of multiple genetic alterations, morphological heterogeneity may represent a cross-sectional view of genetic alterations within individual tumors. We therefore examined the topographical distribution of loss of heterozygosity (LOH) events within 10 non-small-cell lu...

  5. Distribution of photoperiod-insensitive allele Ppd-A1a and its effect on heading time in Japanese wheat cultivars.

    Science.gov (United States)

    Seki, Masako; Chono, Makiko; Nishimura, Tsutomu; Sato, Mikako; Yoshimura, Yasuhiro; Matsunaka, Hitoshi; Fujita, Masaya; Oda, Shunsuke; Kubo, Katashi; Kiribuchi-Otobe, Chikako; Kojima, Hisayo; Nishida, Hidetaka; Kato, Kenji

    2013-09-01

    The Ppd-A1 genotype of 240 Japanese wheat cultivars and 40 foreign cultivars was determined using a PCR-based method. Among Japanese cultivars, only 12 cultivars, all of which were Hokkaido winter wheat, carried the Ppd-A1a allele, while this allele was not found in Hokkaido spring wheat cultivars or Tohoku-Kyushu cultivars. Cultivars with a photoperiod-insensitive allele headed 6.9-9.8 days earlier in Kanto and 2.5 days earlier in Hokkaido than photoperiod-sensitive cultivars. The lower effect of photoperiod-insensitive alleles observed in Hokkaido could be due to the longer day-length at the spike formation stage compared with that in Kanto. Pedigree analysis showed that 'Purple Straw' and 'Tohoku 118' were donors of Ppd-A1a and Ppd-D1a in Hokkaido wheat cultivars, respectively. Wheat cultivars recently developed in Hokkaido carry photoperiod-insensitive alleles at a high frequency. For efficient utilization of Ppd-1 alleles in the Hokkaido wheat-breeding program, the effect of Ppd-1 on growth pattern and grain yield should be investigated. Ppd-A1a may be useful as a unique gene source for fine tuning the heading time in the Tohoku-Kyushu region since the effect of Ppd-A1a on photoperiod insensitivity appears to differ from the effect of Ppd-B1a and Ppd-D1a.

  6. Distribution of HLA-C alleles in Shandong Han population of China%HLA-C等位基因在中国山东汉族人群中的分布

    Institute of Scientific and Technical Information of China (English)

    朱传福; 张毅; 宋永红; 刘艳; 聂向民; 乔文本; 庄云龙

    2013-01-01

    Objective To analyze the distribution of HLA-C alleles in Shandong Han population of China.Methods One hundred and fifty unrelated potential donors,self-claimed as Han population from Shandong province,were selected from China Marrow Donor Program.Genotypes of HLA-C with the donors were identified by PCR-SBT.The frequencies of allele were calculated with direct counting method and the differences with other populations were analyzed with SPSS16.0 x2 software.Results A total of 25 alleles of HLA-C were observed and the most common alleles were C * 06:02 and C * 07:02 with the frequency of more than 10.00%.Moreover,there were 16 kinds of alleles with the frequency of more than 1.00% accounting for 95.33% of the total alleles.The distribution of HLA-C alleles in Shandong Han population was similar to that in northern Han population,but had some differences with that in southern Han population.In addition,the distribution of HLA-C alleles in Shandong Han population significantly differed from that of German/African American.Conclusion This study on the distribution of HLA-C alleles in Shandong Han population provides valuable references for further studies on the genetics of HLA,cross-match for organ transplantation and other genetic-associated diseases in this population.%目的 分析人类白细胞抗原(human leukocyte antigen,HLA)C等位基因在山东汉人群中的多态性分布.方法 对150名山东汉族无血缘关系的中华骨髓库志愿捐献者,采用聚合酶链反应-测序分型(polymerase chain reaction-sequence based typing,PCR-SBT)方法进行HLA-C基因分型,计数法计算各等位基因频率并采用x2比较与其他人群的差异.结果 观察到HLA-C等位基因25个,最常见等位基因为C*06∶02和C*07∶02,基因频率均超过10.00%,有16个等位基因频率>1.00%,累计基因频率为95.33%.山东汉族人群HLA-C等位基因分布与中国北方汉族最为接近,与南方汉族有一定差异,与德国人和非

  7. HLA-Cw Allele Frequency in Definite Meniere’s Disease Compared to Probable Meniere’s Disease and Healthy Controls in an Iranian Sample

    Directory of Open Access Journals (Sweden)

    Sasan Dabiri

    2016-05-01

    Full Text Available 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.

  8. Incoherent Optical Frequency Domain Reflectometry for Distributed Thermal Sensing

    OpenAIRE

    Karamehmedovic, Emir; Jeppesen, Palle; Peucheret, Christophe; Bjarklev, Anders Overgaard

    2006-01-01

    This thesis reports the main results from an investigation of a fibre-optic distributed temperature sensor based on spontaneous Raman scattering. The technique used for spatial resolving is the incoherent optical frequency domain reflectometry, where a pump laser is sine modulated with a stepwise increasing frequency, after which the inverse Fourier transform is applied to the signal from the backscattered light. This technique is compared with the more conventional optical time domain reflec...

  9. Influences on flood frequency distributions in Irish river catchments

    Directory of Open Access Journals (Sweden)

    S. Ahilan

    2011-04-01

    Full Text Available This study explores influences which result in shifts of flood frequency distributions in Irish rivers. Generalised Extreme Value (GEV type I distributions are recommended in Ireland for estimating flood quantiles. This paper presents the findings of an investigation that identified the GEV statistical distributions that best fit the annual maximum (AM data series extracted from 172 gauging stations of 126 rivers in Ireland. Of these 126 rivers, 25 have multiple gauging stations. Analysis of this data was undertaken to explore hydraulic and hydro-geological factors that influence flood frequency distributions and whether shifts in distributions occur in the down-river direction. The methodology involved determining the shape parameter of GEV distributions that were fitted to AM data at each site and to statistically test this shape parameter to determine whether a type I, type II or type III distribution was valid. The classification of these distributions was further supported by moment and L-moment diagrams and probability plots. Results indicated that of the 143 stations with flow records exceeding 25 yr, data for 92 was best represented by GEV type I distributions and that for another 12 and 39 stations followed type II and type III distributions respectively. The spatial, hydraulic and hydro-geological influences on flood frequency distributions were assessed by incorporating results on an Arc-GIS platform with individual layers showing karst features, flood attenuation polygons and lakes. This data reveals that type I distributions are spatially well represented throughout the country. The majority of type III distributions appear in four distinct clusters in well defined geographical areas where attenuation influences from floodplains and lakes appear to be influential. The majority of type II distributions appear to be in a single cluster in a region in the west of the country that is characterised by a karst landscape. The

  10. k-Casein, b-lactoglobulin and growth hormone allele frequencies and genetic distances in Nelore, Gyr, Guzerá, Caracu, Charolais, Canchim and Santa Gertrudis cattle

    Directory of Open Access Journals (Sweden)

    Paola Augusta Kemenes

    1999-12-01

    Full Text Available The genotypes for k-casein (k-CN, b-lactoglobulin (b-LG and growth hormone (GH were determined by polymerase chain reaction (PCR and restriction enzyme digestion in seven breeds of cattle (Nelore, Gyr, Guzerá, Caracu, Charolais, Canchim and Santa Gertrudis. k-Casein had two alleles with the A allele occurring at a higher frequency in Bos indicus breeds (0.93, 0.92 and 0.91% for Gyr, Guzerá and Nelore, respectively. The b-lactoglobulin locus had two alleles in all of the breeds. European breeds had a higher frequency of the b-LG A allele than Zebu breeds. The GH locus had two alleles (L and V in Bos taurus and was monomorphic (L allele only in all of the Bos indicus breeds evaluated. The highest frequency for the V allele was observed in Charolais cattle. The markers used revealed a considerable similarity among breeds, with two main groups being discernible. One group consisted of Zebu and Santa Gertrudis breeds and the other consisted of European and Canchim breeds.Os genótipos de k-caseína (k-CN, b-lactoglobulina (b-LG e hormônio de crescimento foram determinados por reação em cadeia de polimerase (PCR e digestão com enzima de restrição em sete raças de bovinos (Nelore, Gir, Guzerá, Caracu, Charolesa, Canchim and Santa Gertrudis. A k-caseína apresentou dois alelos e as freqüências mais elevadas para o alelo A foram observadas em Bos indicus (0,93, 0,92 e 0,91% para as raças Gir, Guzerá e Nelore, respectivamente. A b-lactoglobulina apresentou dois alelos em todas as raças estudadas, sendo a freqüência do alelo A mais elevada nas raças européias. O loco de hormônio de crescimento apresentou dois alelos em Bos taurus e foi monomórfico (alelo L em todas as raças zebuínas. A maior freqüência para o alelo V foi observado na raça Charolesa. Os marcadores investigados revelaram alta similaridade entre as raças, com a formação de dois grupos principais: um composto de raças zebuínas e a raça Santa Gertrudis e outro

  11. Photogrammetry and altimetry: Part C: frequency distributions of lunar slopes

    Science.gov (United States)

    Wu, Sherman S.C.; Moore, H.J.

    1972-01-01

    The metric and panoramic cameras aboard the Apollo 16 spacecraft provided photographs on which photogrammetric techniques may be used to obtain precise measurements of horizontal distances and elevations. These measurements of horizontal distances and elevations. These measurements may in turn be used to obtain slope-frequency distributions of lunar surfaces at various slope lengths and for various types of terrain and geologic map units (ref. 30-4). Bistatic radar and photoclinometric methods have also been used to obtain slope-frequency distributions of lunar surfaces. The problem arises as to how well these varied methods correlate with one another (ref. 30-5).

  12. Power Quality Analysis Using Bilinear Time-Frequency Distributions

    Directory of Open Access Journals (Sweden)

    Sha'ameri AhmadZuri

    2010-01-01

    Full Text Available Abstract Bilinear time-frequency distributions (TFDs are powerful techniques that offer good time and frequency resolution of time-frequency representation (TFR. It is very appropriate to analyze power quality signals which consist of nonstationary and multi-frequency components. However, the TFDs suffer from interference because of cross-terms. Many TFDs have been implemented, and there is no fixed window or kernel that can remove the cross-terms for all types of signals. In this paper, the bilinear TFDs are implemented to analyze power quality signals such as smooth-windowed Wigner-Ville distribution (SWWVD, Choi-Williams distribution (CWD, B-distribution (BD, and modified B-distribution (MBD. The power quality signals focused are swell, sag, interruption, harmonic, interharmonic, and transient based on IEEE Std, 1159-1995. A set of performance measures is defined and used to compare the TFRs. It shows that SWWVD presents the best performance and is selected for power quality signal analysis. Thus, an adaptive optimal kernel SWWVD is designed to determine the separable kernel automatically from the input signal.

  13. The frequency-independent control method for distributed generation systems

    OpenAIRE

    Naderi, Siamak; Pouresmaeil, Edris; Wenzhong Gao, David

    2012-01-01

    In this paper a novel frequency-independent control method suitable for distributed generation (DG) is presented. This strategy is derived based on the abc/αβ transformation and abc/dq transformation of the ac system variables. The active and reactive currents injected by the DG are controlled in the synchronously rotating orthogonal dq reference frame. The transformed variables are used in control of the voltage source inverter that connects DG to distribution network. Due to importance of d...

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Hao Sun

    Full Text Available 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.

  17. Similarity of Symbol Frequency Distributions with Heavy Tails

    Science.gov (United States)

    Gerlach, Martin; Font-Clos, Francesc; Altmann, Eduardo G.

    2016-04-01

    Quantifying the similarity between symbolic sequences is a traditional problem in information theory which requires comparing the frequencies of symbols in different sequences. In numerous modern applications, ranging from DNA over music to texts, the distribution of symbol frequencies is characterized by heavy-tailed distributions (e.g., Zipf's law). The large number of low-frequency symbols in these distributions poses major difficulties to the estimation of the similarity between sequences; e.g., they hinder an accurate finite-size estimation of entropies. Here, we show analytically how the systematic (bias) and statistical (fluctuations) errors in these estimations depend on the sample size N and on the exponent γ of the heavy-tailed distribution. Our results are valid for the Shannon entropy (α =1 ), its corresponding similarity measures (e.g., the Jensen-Shanon divergence), and also for measures based on the generalized entropy of order α . For small α 's, including α =1 , the errors decay slower than the 1 /N decay observed in short-tailed distributions. For α larger than a critical value α*=1 +1 /γ ≤2 , the 1 /N decay is recovered. We show the practical significance of our results by quantifying the evolution of the English language over the last two centuries using a complete α spectrum of measures. We find that frequent words change more slowly than less frequent words and that α =2 provides the most robust measure to quantify language change.

  18. Influences on flood frequency distributions in Irish river catchments

    Directory of Open Access Journals (Sweden)

    S. Ahilan

    2012-04-01

    Full Text Available This study explores influences on flood frequency distributions in Irish rivers. A Generalised Extreme Value (GEV type I distribution is recommended in Ireland for estimating flood quantiles in a single site flood frequency analysis. This paper presents the findings of an investigation that identified the GEV statistical distributions that best fit the annual maximum (AM data series extracted from 172 gauging stations of 126 rivers in Ireland. Analysis of these data was undertaken to explore hydraulic and hydro-geological factors that influence flood frequency distributions. A hierarchical approach of increasing statistical power that used probability plots, moment and L-moment diagrams, the Hosking goodness of fit algorithm and a modified Anderson-Darling (A-D statistical test was followed to determine whether a type I, type II or type III distribution was valid. Results of the Hosking et al. method indicated that of the 143 stations with flow records exceeding 25 yr, data for 95 (67% was best represented by GEV type I distributions and a further 9 (6% and 39 (27% stations followed type II and type III distributions respectively. Type I, type II and type III distributions were determined for 83 (58%, 16 (11% and 34 (24% stations respectively using the modified A-D method (data from 10 stations was not represented by GEV family distributions. The influence of karst terrain on these flood frequency distributions was assessed by incorporating results on an Arc-GIS platform showing karst features and using Monte Carlo simulations to assess the significance of the number and clustering of the observed distributions. Floodplain effects were identified by using two-sample t-tests to identify statistical correlations between the distributions and catchment properties that are indicative of strong floodplain activity. The data reveals that type I distributions are spatially well represented throughout the country. While also well represented throughout

  19. HLA Class II Profile and Distribution of HLA-DRB1 and HLA-DQB1 Alleles and Haplotypes among Lebanese and Bahraini Arabs

    OpenAIRE

    Wassim Y Almawi; Busson, Marc; Tamim, Hala; Al-Harbi, Einas M.; Finan, Ramzi R.; Wakim-Ghorayeb, Saria F.; Motala, Ayesha A.

    2004-01-01

    The gene frequencies of HLA class II alleles were studied in 95 healthy Lebanese Arab and 72 healthy Bahraini Arab subjects. Our aim was to establish the genetic relationship between Bahraini and Lebanese Arabs in terms of HLA class II gene and haplotype frequencies and to compare these results with frequencies for other countries with populations of Caucasian and non-Caucasian descent. Subjects were unrelated and of both sexes, and HLA-DRB1 and -DQB1 genotyping was done by the PCR sequence-s...

  20. Distributed coupling and multi-frequency microwave accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Tantawi, Sami G.; Li, Zenghai; Borchard, Philipp

    2016-07-05

    A microwave circuit for a linear accelerator has multiple metallic cell sections, a pair of distribution waveguide manifolds, and a sequence of feed arms connecting the manifolds to the cell sections. The distribution waveguide manifolds are connected to the cell sections so that alternating pairs of cell sections are connected to opposite distribution waveguide manifolds. The distribution waveguide manifolds have concave modifications of their walls opposite the feed arms, and the feed arms have portions of two distinct widths. In some embodiments, the distribution waveguide manifolds are connected to the cell sections by two different types of junctions adapted to allow two frequency operation. The microwave circuit may be manufactured by making two quasi-identical parts, and joining the two parts to form the microwave circuit, thereby allowing for many manufacturing techniques including electron beam welding, and thereby allowing the use of un-annealled copper alloys, and hence greater tolerance to high gradient operation.

  1. Frequency and distribution of Notch mutations in tumor cell lines

    International Nuclear Information System (INIS)

    Deregulated Notch signaling is linked to a variety of tumors and it is therefore important to learn more about the frequency and distribution of Notch mutations in a tumor context. In this report, we use data from the recently developed Cancer Cell Line Encyclopedia to assess the frequency and distribution of Notch mutations in a large panel of cancer cell lines in silico. Our results show that the mutation frequency of Notch receptor and ligand genes is at par with that for established oncogenes and higher than for a set of house-keeping genes. Mutations were found across all four Notch receptor genes, but with notable differences between protein domains, mutations were for example more prevalent in the regions encoding the LNR and PEST domains in the Notch intracellular domain. Furthermore, an in silico estimation of functional impact showed that deleterious mutations cluster to the ligand-binding and the intracellular domains of NOTCH1. For most cell line groups, the mutation frequency of Notch genes is higher than in associated primary tumors. Our results shed new light on the spectrum of Notch mutations after in vitro culturing of tumor cells. The higher mutation frequency in tumor cell lines indicates that Notch mutations are associated with a growth advantage in vitro, and thus may be considered to be driver mutations in a tumor cell line context. The online version of this article (doi:10.1186/s12885-015-1278-x) contains supplementary material, which is available to authorized users

  2. Allelic frequencies of the HLA-B17 antigen group: comparative analysis by serology, IEF and PCR-SSOP typing.

    Science.gov (United States)

    Levine, J E; Yang, S Y

    1995-11-01

    Current typing technology for class I HLA antigens uses serological and/or isoelectric focusing gel electrophoresis. DNA typing for the HLA class I antigens can accurately identify the class I genotype of individuals and cell lines. Here, we report correlation of DNA typing results with serological and IEF results for the B17 group. The B17 antigens are relatively common, being carried by almost 9% of Caucasians and 28% of blacks. In this study, five 10th International Histocompatibility Workshop cell lines carrying B17 and 106 individuals in 61 families carrying B17 were DNA typed for B17 using B17-allele-specific amplification and sequence specific oligonucleotide probe hybridization pattern analysis. 38 (55.07%) out of 69 unrelated haplotypes had B*5701, 23 (33.33%) had B*5801, 6 (8.70%) had B*5702, and 2 (2.90%) had B*5802. DNA typing results correlated well with serological and isoelectric focusing results. In general, there was high degree of agreement between all three methods, although heterozygosity for B17 poses a particular problem for serological and IEF methodology. Both B*5701 and B*5801 have the same electrophoretic mobility on IEF gel, corresponding to B17.2, B*5702 corresponds to B17.1, while B*5802 corresponds to B17.3.

  3. Predicting Baseball Home Run Records Using Exponential Frequency Distributions

    CERN Document Server

    Kelley, D J; Phillips, J A

    2006-01-01

    A new model, which uses the frequency of individuals' annual home run totals, is employed to predict future home run totals and records in Major League Baseball. Complete home run frequency data from 1903--2005 is analyzed, resulting in annual exponential distributions whose changes can be a used as a measure of progression in the sport and serve as a basis against which record-setting performances can be compared. We show that there is an 80% chance that Barry Bonds' current 73 home run record will be broken in the next 10 years, despite the longevity of previous records held by baseball legends Babe Ruth and Roger Marris.

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

    Science.gov (United States)

    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

  5. On the similarity of symbol frequency distributions with heavy tails

    CERN Document Server

    Gerlach, Martin; Altmann, Eduardo G

    2015-01-01

    Quantifying the similarity between symbolic sequences is a traditional problem in Information Theory which requires comparing the frequencies of symbols in different sequences. In numerous modern applications, ranging from DNA over music to texts, the distribution of symbol frequencies is characterized by heavy-tailed distributions (e.g., Zipf's law). The large number of low-frequency symbols in these distributions poses major difficulties to the estimation of the similarity between sequences, e.g., they hinder an accurate finite-size estimation of entropies. Here we show how the accuracy of estimations depend on the sample size~$N$, not only for the Shannon entropy $(\\alpha=1)$ and its corresponding similarity measures (e.g., the Jensen-Shanon divergence) but also for measures based on the generalized entropy of order $\\alpha$. For small $\\alpha$'s, including $\\alpha=1$, the bias and fluctuations in the estimations decay slower than the $1/N$ decay observed in short-tailed distributions. For $\\alpha$ larger ...

  6. Convergence of the frequency-size distribution of global earthquakes

    Science.gov (United States)

    Bell, Andrew F.; Naylor, Mark; Main, Ian G.

    2013-06-01

    The Gutenberg-Richter (GR) frequency-magnitude relation is a fundamental empirical law of seismology, but its form remains uncertain for rare extreme events. Here, we show that the temporal evolution of model likelihoods and parameters for the frequency-magnitude distribution of the global Harvard Centroid Moment Tensor catalog is inconsistent with an unbounded GR relation, despite if being the preferred model at the current time. During the recent spate of 12 great earthquakes in the last 8 years, record-breaking events result in profound steps in favor of the unbounded GR relation. However, between such events the preferred model gradually converges to the tapered GR relation, and the form of the convergence cannot be explained by random sampling of an unbounded GR distribution. The convergence properties are consistent with a global catalog composed of superposed randomly-sampled regional catalogs, each with different upper bounds, many of which have not yet sampled their largest event.

  7. Chirplet Based Nonnegative Time-Frequency Distribution for FMmlet Transform

    Institute of Scientific and Technical Information of China (English)

    ZOUHongxing; WANGDianjun; DAIQionghai; LIYanda

    2005-01-01

    This paper proposes a method of devising a nonnegative Time-frequency distribution (TFD) for displaying the decomposition results of FMmlet transform. Underlying this method are the facts that the chirplet is a special case of FMmlet and that the Wigner-ville distribution (WVD) of Gaussian chirplet is nonnegative. The true essence of the method is to migrate the values of WVDs of Gaussian chirplets to the positions of Instantaneous frequencies (IFs) of the best matched FMmlet atoms for different signal components. The relative merits and usefulness of the resulting TFD are twofold: First, it is nonnegative; second, its localization is identical to that of WVD. Therefore, the resulting TFD is more flexible and advantageous for delineating the time-varying spectral contents of a nonstationary signal.

  8. Distributed Frequency Control in Power Grids Under Limited Communication

    OpenAIRE

    Parandehgheibi, Marzieh; Turitsyn, Konstantin; Modiano, Eytan

    2016-01-01

    In this paper, we analyze the impact of communication failures on the performance of optimal distributed frequency control. We consider a consensus-based control scheme, and show that it does not converge to the optimal solution when the communication network is disconnected. We propose a new control scheme that uses the dynamics of power grid to replicate the information not received from the communication network, and prove that it achieves the optimal solution under any single communicatio...

  9. Separating More Sources Than Sensors Using Time-Frequency Distributions

    Directory of Open Access Journals (Sweden)

    Belouchrani Adel

    2005-01-01

    Full Text Available We examine the problem of blind separation of nonstationary sources in the underdetermined case, where there are more sources than sensors. Since time-frequency (TF signal processing provides effective tools for dealing with nonstationary signals, we propose a new separation method that is based on time-frequency distributions (TFDs. The underlying assumption is that the original sources are disjoint in the time-frequency (TF domain. The successful method recovers the sources by performing the following four main procedures. First, the spatial time-frequency distribution (STFD matrices are computed from the observed mixtures. Next, the auto-source TF points are separated from cross-source TF points thanks to the special structure of these mixture STFD matrices. Then, the vectors that correspond to the selected auto-source points are clustered into different classes according to the spatial directions which differ among different sources; each class, now containing the auto-source points of only one source, gives an estimation of the TFD of this source. Finally, the source waveforms are recovered from their TFD estimates using TF synthesis. Simulated experiments indicate the success of the proposed algorithm in different scenarios. We also contribute with two other modified versions of the algorithm to better deal with auto-source point selection.

  10. High-resolution time-frequency distributions for fall detection

    Science.gov (United States)

    Amin, Moeness G.; Zhang, Yimin D.; Boashash, Boualem

    2015-05-01

    In this paper, we examine the role of high-resolution time-frequency distributions (TFDs) of radar micro-Doppler signatures for fall detection. The work supports the recent and rising interest in using emerging radar technology for elderly care and assisted living. Spectrograms have been the de facto joint-variable signal representation, depicting the signal power in both time and frequency. Although there have been major advances in designing quadratic TFDs which are superior to spectrograms in terms of detailing the local signal behavior, the contributions of these distributions in the area of human motion classifications and their offerings in enhanced feature extractions have not yet been properly evaluated. The main purpose of this paper is to show the effect of using high-resolution TFD kernels, in lieu of spectrogram, on fall detection. We focus on the extended modified B-distribution (EMBD) and exploit the level of details it provides as compared with the coarse and smoothed time-frequency signatures offered by spectrograms.

  11. Distribution of alpha-2-HS-glycoprotein (AHSG) phenotypes in Cabo Verde (west Africa): description of a new allele, AHSG*32.

    Science.gov (United States)

    Caeiro, J L; Parra, E J; Yuasa, I; Teixeira, C; Llano, C

    1994-04-01

    The genetic polymorphism of alpha-2-HS-glycoprotein (AHSG) was studied in the population of Cabo Verde (West Africa), using isoelectric focusing in polyacrylamide gels followed by immunofixation-silver stain. AHSG frequencies are reported for the first time in a subsaharan African population. In addition to the common variants, AHSG 1 and AHSG 2, five AHSG variants were observed, including a new variant, tentatively designated AHSG 32. The allele frequencies were, AHSG*1: 0.7289, AHSG*2: 0.2111, AHSG*10: 0.0276, AHSG*3: 0.0162, AHSG*11: 0.0081, AHSG*22: 0.0065, AHSG*32:0.0016. PMID:7619771

  12. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.

    Science.gov (United States)

    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

  13. Generalized Exponential Distribution in Flood Frequency Analysis for Polish Rivers

    Science.gov (United States)

    Markiewicz, Iwona; Strupczewski, Witold G.; Bogdanowicz, Ewa; Kochanek, Krzysztof

    2015-01-01

    Many distributions have been used in flood frequency analysis (FFA) for fitting the flood extremes data. However, as shown in the paper, the scatter of Polish data plotted on the moment ratio diagram shows that there is still room for a new model. In the paper, we study the usefulness of the generalized exponential (GE) distribution in flood frequency analysis for Polish Rivers. We investigate the fit of GE distribution to the Polish data of the maximum flows in comparison with the inverse Gaussian (IG) distribution, which in our previous studies showed the best fitting among several models commonly used in FFA. Since the use of a discrimination procedure without the knowledge of its performance for the considered probability density functions may lead to erroneous conclusions, we compare the probability of correct selection for the GE and IG distributions along with the analysis of the asymptotic model error in respect to the upper quantile values. As an application, both GE and IG distributions are alternatively assumed for describing the annual peak flows for several gauging stations of Polish Rivers. To find the best fitting model, four discrimination procedures are used. In turn, they are based on the maximized logarithm of the likelihood function (K procedure), on the density function of the scale transformation maximal invariant (QK procedure), on the Kolmogorov-Smirnov statistics (KS procedure) and the fourth procedure based on the differences between the ML estimate of 1% quantile and its value assessed by the method of moments and linear moments, in sequence (R procedure). Due to the uncertainty of choosing the best model, the method of aggregation is applied to estimate of the maximum flow quantiles. PMID:26657239

  14. Generalized Exponential Distribution in Flood Frequency Analysis for Polish Rivers.

    Science.gov (United States)

    Markiewicz, Iwona; Strupczewski, Witold G; Bogdanowicz, Ewa; Kochanek, Krzysztof

    2015-01-01

    Many distributions have been used in flood frequency analysis (FFA) for fitting the flood extremes data. However, as shown in the paper, the scatter of Polish data plotted on the moment ratio diagram shows that there is still room for a new model. In the paper, we study the usefulness of the generalized exponential (GE) distribution in flood frequency analysis for Polish Rivers. We investigate the fit of GE distribution to the Polish data of the maximum flows in comparison with the inverse Gaussian (IG) distribution, which in our previous studies showed the best fitting among several models commonly used in FFA. Since the use of a discrimination procedure without the knowledge of its performance for the considered probability density functions may lead to erroneous conclusions, we compare the probability of correct selection for the GE and IG distributions along with the analysis of the asymptotic model error in respect to the upper quantile values. As an application, both GE and IG distributions are alternatively assumed for describing the annual peak flows for several gauging stations of Polish Rivers. To find the best fitting model, four discrimination procedures are used. In turn, they are based on the maximized logarithm of the likelihood function (K procedure), on the density function of the scale transformation maximal invariant (QK procedure), on the Kolmogorov-Smirnov statistics (KS procedure) and the fourth procedure based on the differences between the ML estimate of 1% quantile and its value assessed by the method of moments and linear moments, in sequence (R procedure). Due to the uncertainty of choosing the best model, the method of aggregation is applied to estimate of the maximum flow quantiles. PMID:26657239

  15. Frequency distributions: from the sun to the earth

    Directory of Open Access Journals (Sweden)

    N. B. Crosby

    2011-11-01

    Full Text Available The space environment is forever changing on all spatial and temporal scales. Energy releases are observed in numerous dynamic phenomena (e.g. solar flares, coronal mass ejections, solar energetic particle events where measurements provide signatures of the dynamics. Parameters (e.g. peak count rate, total energy released, etc. describing these phenomena are found to have frequency size distributions that follow power-law behavior. Natural phenomena on Earth, such as earthquakes and landslides, display similar power-law behavior. This suggests an underlying universality in nature and poses the question of whether the distribution of energy is the same for all these phenomena. Frequency distributions provide constraints for models that aim to simulate the physics and statistics observed in the individual phenomenon. The concept of self-organized criticality (SOC, also known as the "avalanche concept", was introduced by Bak et al. (1987, 1988, to characterize the behavior of dissipative systems that contain a large number of elements interacting over a short range. The systems evolve to a critical state in which a minor event starts a chain reaction that can affect any number of elements in the system. It is found that frequency distributions of the output parameters from the chain reaction taken over a period of time can be represented by power-laws. During the last decades SOC has been debated from all angles. New SOC models, as well as non-SOC models have been proposed to explain the power-law behavior that is observed. Furthermore, since Bak's pioneering work in 1987, people have searched for signatures of SOC everywhere. This paper will review how SOC behavior has become one way of interpreting the power-law behavior observed in natural occurring phenomenon in the Sun down to the Earth.

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

    Directory of Open Access Journals (Sweden)

    Akala HM

    2014-11-01

    Full Text Available Hoseah M Akala, Angela O Achieng, Fredrick L Eyase, Dennis W Juma, Luiser Ingasia, Agnes C Cheruiyot, Charles Okello, Duke Omariba, Eunice A Owiti, Catherine Muriuki, Redemptah Yeda, Ben Andagalu, Jacob D Johnson, Edwin Kamau Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya 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

  17. Distributed dynamic strain measurement using optical frequency-domain reflectometry.

    Science.gov (United States)

    Zhou, Da-Peng; Chen, Liang; Bao, Xiaoyi

    2016-08-20

    Distributed dynamic strain measurement based on optical frequency-domain reflectometry is proposed. The technique makes use of the wide scanning range of a tunable laser source in a short sweeping time, and subdivides the overall spectrum into narrower frequency windows. The advantage of subdividing the laser spectral range is to improve the measurement uncertainty induced by the laser wavelength difference between repeated scans. The noise-limited dynamic strain resolution is investigated experimentally, indicating that a minimum detectable strain is less than 200 nε for a spatial resolution of 20 cm. By measuring the subdivided spectral shifts in the time sequence along the sensing fiber, the dynamic strain can be properly quantified over a 30 m measurement range for a highest sampling rate of up to 50 Hz. PMID:27556996

  18. [Discovery of a novel A2 allel in ABO blood group system and investigation of its distribution in Han population of Chinese Fujian province].

    Science.gov (United States)

    Zhang, Ai; Chi, Quan; Ren, Ben-Chun

    2012-10-01

    This study was aimed to investigate the distribution of A2 subgroup in Han Population of Chinese Fujian province and its molecular mechanisms. One individual with serologic ABO blood grouping discrepancy was identified with commercially available monoclonal and polyclonal antibodies and lectin: anti-A, anti-B, anti-AB, anti-A1, and anti-H reagents according to the routine laboratory methods. DNA sequences of exon 6, 7 and intron 6 of ABO gene were analyzed by polymerase chain reaction using genomic DNA and direct DNA sequencing or sequencing after gene cloning. Red cells of 3 176 A or AB unrelated individuals were tested with anti-A1. The results showed that this individual was identified as A2 subgroup by serological technology, sequencing analysis indicated the A2 subgroup with novel A variant allele, the novel A allele being different from the allele A101 by 467C > T and 607G > A missense mutation in exon 7, no A2 subgroup was identified from the 3 176 individuals by using standard serological technology. It is concluded that a novel A allele responsible for A2 subgroup composing of 467C > T and 607G > A has been firstly confirmed, and the A2 subgroup is very rare in Chinese Fujian Han population.

  19. The frequency-independent control method for distributed generation systems

    DEFF Research Database (Denmark)

    Naderi, Siamak; Pouresmaeil, Edris; Gao, Wenzhong David

    2012-01-01

    -effective and simple control strategies is obligatory. The new control method of this paper does not need a Phase Locked Loop (PLL) in control circuit and has fast dynamic response in providing active and reactive power to nonlinear load. From extensive simulation results, high performance of this control strategy......In this paper a novel frequency-independent control method suitable for distributed generation (DG) is presented. This strategy is derived based on the . abc/. αβ transformation and . abc/. dq transformation of the ac system variables. The active and reactive currents injected by the DG...

  20. STATISTICAL FEATURE OF PITCH FREQUENCY DISTRIBUTIONS FOR ROBUST SPEAKER IDENTIFICATION

    Institute of Scientific and Technical Information of China (English)

    Zhang Linghua; Zheng Baoyu; Yang Zhen

    2005-01-01

    This letter proposes an effective and robust speech feature extraction method based on statistical analysis of Pitch Frequency Distributions (PFD) for speaker identification. Compared with the conventional cepstrum, PFD is relatively insensitive to Additive White Gaussian Noise (AWGN), but it does not show good performance for speaker identification, even if under clean environments. To compensate this shortcoming, PFD and conventional cepstrum are combined to make the ultimate decision, instead of simply taking one kind of features into account.Experimental results indicate that the hybrid approach can give outstanding improvement for text-independent speaker identification under noisy environments corrupted by AWGN.

  1. Single Frequency Network Based Distributed Passive Radar Technology

    Directory of Open Access Journals (Sweden)

    Wan Xian-rong

    2015-01-01

    Full Text Available The research and application of passive radar are heading from single transmitter-receiver pair to multiple transmitter-receiver pairs. As an important class of the illuminators of opportunity, most of modern digital broadcasting and television systems work on Single Frequency Network (SFN, which intrinsically determines that the passive radar based on such illuminators must be distributed and networked. In consideration of the remarkable working and processing mode of passive radar under SFN configuration, this paper proposes the concept of SFN-based Distributed Passive Radar (SDPR. The main characteristics and key problems of SDPR are first described. Then several potential solutions are discussed for part of the key technologies. The feasibility of SDPR is demonstrated by preliminary experimental results. Finally, the concept of four network convergence that includes the broadcast based passive radar network is conceived, and its application prospects are discussed.

  2. ANALYTICAL MODEL FOR MARS CRATER-SIZE FREQUENCY DISTRIBUTION

    Directory of Open Access Journals (Sweden)

    W. Bruckman

    2009-01-01

    Full Text Available We present a theoretical and analytical curve that reproduces essential features of the frequency distributions vs. diameter of the 42,000 impact craters contained in Barlow's Mars Catalog. The model is derived using reasonable simple assumptions that allow us to relate the present craters population with the craters population at each particular epoch. The model takes into consideration the reduction of the number of craters as a function of time caused by their erosion and obliteration, and this provides a simple and natural explanation for the presence of di erent slopes in the empirical log-log plot of number of craters (N vs. diameter (D. A mean life for martians craters as a function of diameter is deduced, and it is shown that this result is consistent with the corresponding determination of craters mean life based on Earth data. Arguments are given to suggest that this consistency follows from the fact that a crater mean life is proportional to its volumen. It also follows that in the absence of erosions and obliterations, when craters are preserved, we would have N / 1=D4:3, which is a striking conclusion, since the exponent 4:3 is larger than previously thought. Such an exponent implies a similar slope in the extrapolated impactors size-frequency distribution.

  3. Identification of Electrooculography Signals Frequency Energy Distribution Using Wavelet Algorithm

    Directory of Open Access Journals (Sweden)

    W. M. Bukhari

    2011-01-01

    Full Text Available Problem statement: The time frequency analysis of non-stationary signals has been the considerable research effort in recent years. Wavelet transform is one of the favored tool for the analyzing the biomedical signals. Approach: We describe the identification of Electro-Oculograph (EOG signals of eye movement potentials by using wavelet algorithm which gives a lot of information than FFT. The capability of wavelet transform was to distribute the signal energy with the change of time in different frequency bands. This will showed the characteristic of the signals since energy was an important physical variable in signal analysis. The EOG signals were captured using electrodes placed on the forehead around the eyes to record the eye movements. The wavelet features used to determine the characteristic of eye movement waveform. This technique adopted because it was a non-invasive, inexpensive and accurate. The new technology enhancement has allowed the EOG signals captured using the Neuronal EEG-9200. The recorded data was composed of an eye movement toward four directions, i.e., downward, upward, leftward and rightward. The proposed analysis for each eyes signal is analyzed by using Wavelet Transform (WT with energy algorithm and by comparing the energy distribution with the change of time and frequency of each signal. Results: A wavelet Scalogram was plotted to display the different percentages of energy for each wavelet coefficient towards different movement. Conclusion: From the result, it is proved that the different EOG signals exhibit differences in signals energy with their corresponding scale such as leftward with scale 6 (8- 16Hz, rightward with scale 8 (2-4Hz, downward with scale 9 (1-2Hz and upward with level 7 (4-8Hz. Statistically, the results in this study indicate that there are 93% (averages significance differences in the extracted features of wavelet Scalogram analysis.

  4. ALLELE DISTRIBUTION OF FIVE X-CHROMOSOME SHORT TANDEM REPEAT LOCI IN EWENKE POPULATION OF NORTH CHINA

    Institute of Scientific and Technical Information of China (English)

    Shan-zhi Gu; Teng Chen; Qing-bo Liu; Bing Yu; Sheng-bin Li

    2005-01-01

    Objective To study the allele genetic polymorphism of five short tandem repeat (STR) loci on X-chromosome in Ewenke population of north China and to provide basic data for forensic identification.Methods Genomic DNA was extracted from EDTA-whole blood of Ewenke population by Chelex-100. The DNA samples were amplified by PCR and were analyzed by polyacrylamide gel electrophoresis and silver staining. The sequence length variations of DXS6799, DXS8378, DXS101, HPRTB, and DXS6789 loci on X-chromosome in 98unrelated Ewenke individuals were investigated.Results All five loci analyzed showed high polymorphism and genetic stability. The data of the five X-chromosome STR loci in Ewenke ethnic group of China was in accordance with Hardy-Weinberg equilibrium by Chi-square test.Conclusion Allele polymorphism of five X-chromosome STR loci can be used as a genetic marker for forensic identification and population genetic research.

  5. Orthogonal Frequency-Division Multiplexed Quantum Key Distribution

    Science.gov (United States)

    Bahrani, Sima; Razavi, Mohsen; Salehi, Jawad A.

    2015-12-01

    We propose orthogonal frequency division multiplexing (OFDM), as a spectrally efficient multiplexing technique, for quantum key distribution (QKD) at the core of trustednode quantum networks. Two main schemes are proposed and analyzed in detail, considering system imperfections, specifically, time misalignment issues. It turns out that while multiple service providers can share the network infrastructure using the proposed multiplexing techniques, no gain in the total secret key generation rate is obtained if one uses conventional all-optical passive OFDM decoders. To achieve a linear increase in the key rate with the number of channels, an alternative active setup for OFDM decoding is proposed, which employs an optical switch in addition to conventional passive circuits. We show that by using our proposed decoder the bandwidth utilization is considerably improved as compared to conventional wavelength division multiplexing techniques.

  6. Daily tornado frequency distributions in the United States

    International Nuclear Information System (INIS)

    The authors examine daily tornado counts in the United States over the period 1994–2012 and find strong evidence for a power-law relationship in the distribution frequency. The scaling exponent is estimated at 1.64 (0.019 s.e.) giving a per tornado-day probability of 0.014% (return period of 71 years) that a tornado day produces 145 tornadoes as was observed on 27 April 2011. They also find that the total number of tornadoes by damage category on days with at least one violent tornado follows an exponential rule. On average, the daily number of tornadoes in the next lowest damage category is approximately twice the number in the current category. These findings are important and timely for tornado hazard models and for seasonal and sub-seasonal forecasts of tornado activity. (paper)

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

    Science.gov (United States)

    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

  8. Directional spatial frequency analysis of lipid distribution in atherosclerotic plaque

    Science.gov (United States)

    Korn, Clyde; Reese, Eric; Shi, Lingyan; Alfano, Robert; Russell, Stewart

    2016-04-01

    Atherosclerosis is characterized by the growth of fibrous plaques due to the retention of cholesterol and lipids within the artery wall, which can lead to vessel occlusion and cardiac events. One way to evaluate arterial disease is to quantify the amount of lipid present in these plaques, since a higher disease burden is characterized by a higher concentration of lipid. Although therapeutic stimulation of reverse cholesterol transport to reduce cholesterol deposits in plaque has not produced significant results, this may be due to current image analysis methods which use averaging techniques to calculate the total amount of lipid in the plaque without regard to spatial distribution, thereby discarding information that may have significance in marking response to therapy. Here we use Directional Fourier Spatial Frequency (DFSF) analysis to generate a characteristic spatial frequency spectrum for atherosclerotic plaques from C57 Black 6 mice both treated and untreated with a cholesterol scavenging nanoparticle. We then use the Cauchy product of these spectra to classify the images with a support vector machine (SVM). Our results indicate that treated plaque can be distinguished from untreated plaque using this method, where no difference is seen using the spatial averaging method. This work has the potential to increase the effectiveness of current in-vivo methods of plaque detection that also use averaging methods, such as laser speckle imaging and Raman spectroscopy.

  9. LPI Radar Waveform Recognition Based on Time-Frequency Distribution

    Directory of Open Access Journals (Sweden)

    Ming Zhang

    2016-10-01

    Full Text Available In this paper, an automatic radar waveform recognition system in a high noise environment is proposed. Signal waveform recognition techniques are widely applied in the field of cognitive radio, spectrum management and radar applications, etc. We devise a system to classify the modulating signals widely used in low probability of intercept (LPI radar detection systems. The radar signals are divided into eight types of classifications, including linear frequency modulation (LFM, BPSK (Barker code modulation, Costas codes and polyphase codes (comprising Frank, P1, P2, P3 and P4. The classifier is Elman neural network (ENN, and it is a supervised classification based on features extracted from the system. Through the techniques of image filtering, image opening operation, skeleton extraction, principal component analysis (PCA, image binarization algorithm and Pseudo–Zernike moments, etc., the features are extracted from the Choi–Williams time-frequency distribution (CWD image of the received data. In order to reduce the redundant features and simplify calculation, the features selection algorithm based on mutual information between classes and features vectors are applied. The superiority of the proposed classification system is demonstrated by the simulations and analysis. Simulation results show that the overall ratio of successful recognition (RSR is 94.7% at signal-to-noise ratio (SNR of −2 dB.

  10. Duality Revisited: Construction of Fractional Frequency Distributions Based on Two Dual Lotka Laws.

    Science.gov (United States)

    Egghe, L.; Rao, I. K. Ravichandra

    2002-01-01

    Discussion of fractional frequency distributions of authors with a certain (fractional) number of papers focuses on the use of Lotka laws to model theoretical fractional frequency distributions with one parameter. Shows that irregular fractional frequency distributions are a consequence of Lotka's law, not breakdowns of the law. (Author/LRW)

  11. High genetic diversity and distribution of Bubu-DQA alleles in swamp buffaloes (Bubalus bubalis carabanesis): identification of new Bubu-DQA loci and haplotypes.

    Science.gov (United States)

    Mishra, S K; Niranjan, S K; Banerjee, B; Dubey, P K; Gonge, D S; Mishra, B P; Kataria, R S

    2016-07-01

    In this study, genetic diversity analysis of MHC class II-DQA locus helped in identification of 25 new Bubu-DQA nucleotide sequences in swamp buffaloes (Bubalus bubalis carabanesis, Bubu). Phylogenetic analysis revealed the distribution of the buffalo DQA sequences in two major clusters of DQA1 and DQA2 genes, sharing common lineages with corresponding cattle alleles, possibly due to trans-species evolution. However, a highly divergent sequence, Bubu-DQA*2501, homologous to cattle (BoLA) DQA3 allele, was identified, indicating the existence of an additional locus; putative DQA3 in buffalo. PCR-RFLP analysis revealed extensive duplication of DQA locus in swamp buffaloes, sharing DQA1, DQA2, and DQA3 alleles in different combinations in duplicated haplotypes. Higher dN than dS values and Wu-Kabat variability at peptide-binding regions in Bubu-DQA indicated high polymorphism with balancing selection. Levels of genetic diversity within DQA sequences and duplication in a small population of swamp buffalo indicate the genetic richness of the species, important for fitness. PMID:27177904

  12. A WIDE DISTRIBUTION OF A NEW VRN-B1c ALLELE OF WHEAT TRITICUM AESTIVUM L. IN RUSSIA, UKRAINE AND ADJACENT REGIONS: A LINK WITH THE HEADING TIME AND ADAPTIVE POTENTIAL

    Directory of Open Access Journals (Sweden)

    Shcherban A.

    2012-08-01

    Full Text Available The adaptation of common wheat (T. aestivum L. to diverse environmental conditions is greatly under the control of genes involved in determination of vernalization response (Vrn-1 genes. It was found that the variation in common wheat heading time is affected not only by combination of Vrn-1 homoeoalleles but also by multiple alleles at a separate Vrn-1 locus. Previously, we described the Vrn-B1c allele from T.aestivum cv. 'Saratovskaya 29' and found significant differences in the structure of the first (1st intron of this allele when compared to another highly abundant Vrn-B1a allele, specifically, the deletion of 0.8 kb coupled with the duplication of 0.4 kb. We suggested that the changes in the intron 1 of Vrn-B1c allele caused earlier ear emergence in the near-isogenic line and cultivars, carrying this allele. In this study we investigate the distribution of the Vrn-B1c allele in a wide set of spring wheat cultivars from Russia, Ukraine and adjacent regions. The analysis revealed that 40% of Russian and 53% of Ukranian spring wheat cultivars contain the Vrn-B1c allele. The high distribution of the Vrn-B1c allele can be explained by a frequent using of 'Saratovskaya 29' in the breeding process inside the studied area. From the other hand, the predominance of the Vrn-B1c allele among cultivars cultivated in West Siberia and Kazakhstan may be due to the selective advantage of this allele for the region where there is a high risk of early fall frosts.

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

    Science.gov (United States)

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

    2015-02-01

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

  14. 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

    Science.gov (United States)

    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

  15. On the frequency-magnitude distribution of converging boundaries

    Science.gov (United States)

    Marzocchi, W.; Laura, S.; Heuret, A.; Funiciello, F.

    2011-12-01

    The occurrence of the last mega-thrust earthquake in Japan has clearly remarked the high risk posed to society by such events in terms of social and economic losses even at large spatial scale. The primary component for a balanced and objective mitigation of the impact of these earthquakes is the correct forecast of where such kind of events may occur in the future. To date, there is a wide range of opinions about where mega-thrust earthquakes can occur. Here, we aim at presenting some detailed statistical analysis of a database of worldwide interplate earthquakes occurring at current subduction zones. The database has been recently published in the framework of the EURYI Project 'Convergent margins and seismogenesis: defining the risk of great earthquakes by using statistical data and modelling', and it provides a unique opportunity to explore in detail the seismogenic process in subducting lithosphere. In particular, the statistical analysis of this database allows us to explore many interesting scientific issues such as the existence of different frequency-magnitude distributions across the trenches, the quantitative characterization of subduction zones that are able to produce more likely mega-thrust earthquakes, the prominent features that characterize converging boundaries with different seismic activity and so on. Besides the scientific importance, such issues may lead to improve our mega-thrust earthquake forecasting capability.

  16. Multiscale Point Correspondence Using Feature Distribution and Frequency Domain Alignment

    Directory of Open Access Journals (Sweden)

    Zeng-Shun Zhao

    2012-01-01

    Full Text Available In this paper, a hybrid scheme is proposed to find the reliable point-correspondences between two images, which combines the distribution of invariant spatial feature description and frequency domain alignment based on two-stage coarse to fine refinement strategy. Firstly, the source and the target images are both down-sampled by the image pyramid algorithm in a hierarchical multi-scale way. The Fourier-Mellin transform is applied to obtain the transformation parameters at the coarse level between the image pairs; then, the parameters can serve as the initial coarse guess, to guide the following feature matching step at the original scale, where the correspondences are restricted in a search window determined by the deformation between the reference image and the current image; Finally, a novel matching strategy is developed to reject the false matches by validating geometrical relationships between candidate matching points. By doing so, the alignment parameters are refined, which is more accurate and more flexible than a robust fitting technique. This in return can provide a more accurate result for feature correspondence. Experiments on real and synthetic image-pairs show that our approach provides satisfactory feature matching performance.

  17. The size-frequency distribution of elliptical impact craters

    Science.gov (United States)

    Collins, G. S.; Elbeshausen, D.; Davison, T. M.; Robbins, S. J.; Hynek, B. M.

    2011-10-01

    Impact craters are elliptical in planform if the impactor's trajectory is below a threshold angle of incidence. Laboratory experiments and 3D numerical simulations demonstrate that this threshold angle decreases as the ratio of crater size to impactor size increases. According to impact cratering scaling laws, this implies that elliptical craters occur at steeper impact angles as crater size or target strength increases. Using a standard size-frequency distribution for asteroids impacting the terrestrial planets we estimate the fraction of elliptical craters as a function of crater size on the Moon, Mars, Earth, Venus and Mercury. In general, the expected fraction of elliptical craters is ~ 2-4% for craters between 5 and 100-km in diameter, consistent with the observed population of elliptical craters on Mars. At larger crater sizes both our model and observations suggest a dramatic increase in the fraction of elliptical craters with increasing crater diameter. The observed fraction of elliptical craters larger than 100-km diameter is significantly greater than our model predictions, which may suggest that there is an additional source of large elliptical craters other than oblique impact.

  18. Distribution of photoperiod-insensitive alleles Ppd-B1a and Ppd-D1a and their effect on heading time in Japanese wheat cultivars.

    Science.gov (United States)

    Seki, Masako; Chono, Makiko; Matsunaka, Hitoshi; Fujita, Masaya; Oda, Shunsuke; Kubo, Katashi; Kiribuchi-Otobe, Chikako; Kojima, Hisayo; Nishida, Hidetaka; Kato, Kenji

    2011-12-01

    The genotypes of photoperiod response genes Ppd-B1 and Ppd-D1 in Japanese wheat cultivars were determined by a PCR-based method, and heading times were compared among genotypes. Most of the Japanese wheat cultivars, except those from the Hokkaido region, carried the photoperiod-insensitive allele Ppd-D1a, and heading was accelerated 10.3 days compared with the Ppd-D1b genotype. Early cultivars with Ppd-D1a may have been selected to avoid damage from preharvest rain. In the Hokkaido region, Ppd-D1a frequency was lower and heading date was late regardless of Ppd-D1 genotype, suggesting another genetic mechanism for late heading in Hokkaido cultivars. In this study, only 11 cultivars proved to carry Ppd-B1a, and all of them carried another photoperiod-insensitive allele, Ppd-D1a. The Ppd-B1a/Ppd-D1a genotype headed 6.7 days earlier than the Ppd-B1b/Ppd-D1a genotype, indicating a significant effect of Ppd-B1a in the genetic background with Ppd-D1a. Early-maturity breeding in Japan is believed to be accelerated by the introduction of the Ppd-B1a allele into medium-heading cultivars carrying Ppd-D1a. Pedigree analysis showed that Ppd-B1a in three extra-early commercial cultivars was inherited from 'Shiroboro 21' by early-heading Chugoku lines bred at the Chugoku Agriculture Experimental Station.

  19. Association between the CCR5 32-bp deletion allele and late onset of schizophrenia

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Timm, Sally; Wang, August G;

    2006-01-01

    OBJECTIVE: The 32-bp deletion allele in chemokine receptor CCR5 has been associated with several immune-mediated diseases and might be implicated in schizophrenia as well. METHOD: The authors genotyped DNA samples from 268 schizophrenia patients and 323 healthy subjects. Age at first admission......-onset schizophrenia) and healthy subjects differed significantly. This was reflected in an increased frequency of the deletion allele in the patient subgroup. Patients with ages at first admission below and above 40 years significantly differed in distribution of genotypes and alleles, with an overrepresentation...... of the deletion allele in the latter subgroup of patients. CONCLUSIONS: These findings suggest that the CCR5 32-bp deletion allele is a susceptibility factor for schizophrenia with late onset. Alternatively, the CCR5 32-bp deletion allele may act as a modifier by delaying the onset of schizophrenia without...

  20. HLA-A, HLA-B, HLA-DRB1 allele and haplotype frequencies in 6384 umbilical cord blood units and transplantation matching and engraftment statistics in the Zhejiang cord blood bank of China.

    Science.gov (United States)

    Wang, F; He, J; Chen, S; Qin, F; Dai, B; Zhang, W; Zhu, F M; Lv, H J

    2014-02-01

    Umbilical cord blood (UCB) is a widely accepted source of progenitor cells, and now, many cord blood banks were established. Here, we analysed the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies, HLA matching possibilities for searching potential donors and outcome of UCB transplantations in Zhejiang cord blood bank of China. A total of 6384 UCB units were characterized for 17 HLA-A, 30 HLA-B and 13 HLA-DRB1 alleles at the first field resolution level. Additionally, B*14, B*15 and B*40 were typed to the second field level. A total of 1372 distinct A-B-DRB1 haplotypes were identified. The frequencies of 7 haplotypes were more than 1%, and 439 haplotypes were blood bank of Zhejiang province. These data can help to select potential UCB donors for transplantation and used to assess the scale of new cord blood banking endeavours.

  1. Study on resonance frequency distribution of high-overtone bulk acoustic resonators

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hui; WANG Zuoqing; ZHANG Shuyi

    2005-01-01

    Based on the method of characterizing piezo-films by the resonance frequency distributions, the factors influencing the resonance frequency distribution of a High-overtone Bulk Acoustic Resonator (HBAR) consisting of a piezoelectric thin film with twoelectrodes and a substrate are studied. Some HBARs are simulated. The results manifest that changing the acoustic impedance ratio of the substrate to piezo-film the distribution of the space of the parallel resonance frequency and the effective electromechanical coupling factor are changed. When the fundamental mode of the piezo-film is at high frequency, changing the acoustic impedance ratio of the electrode to piezo-film and the thickness of the electrodes make the resonance frequency distribution of HBARs change. These results manifest that the HBARs can be resonant at specified frequencies by means of adjusting the factors affecting the resonance frequency distribution.

  2. Helicobacter pylori vacA s1a and s1b alleles from clinical isolates from different regions of Chile show a distinct geographic distribution

    Institute of Scientific and Technical Information of China (English)

    MI Díaz; A Kirberg; E Hebel; J Fierro; R Bravo; F Siegel; G Leon; G Klapp; A Venegas; A Valdivia; P Martínez; JL Palacios; P Harris; J Novales; E Garrido; D Valderrama; C Shilling

    2005-01-01

    AIM: To establish the most common vacA alleles in Helicobacter pylori(H pylori) strains isolated from Chilean patients and its relationship with gastritis and gastroduodenal ulcers.METHODS: Two hundred and forty five H pylori clinical isolates were obtained from 79 biopsies from Chilean infected patients suffering from gastrointestinal diseases. An average of 2-3 strains per patient was isolated and the vacA genotype was analyzed by PCR and 3% agarose electrophoresis. Some genotypes were checked by DNA sequencing.RESULTS: The most prevalent vacA genotype inChilean patients was s1b m1 (76%), followed by s1a m1 (21%). In contrast, the s2 m2 genotype was scarcely represented (3%).The s1b m1 genotype was found most frequently linked to gastropathies (P<0.05) rather than ulcers. Ulcers were found more commonly in male and older patients. Curiously, patients living in cities located North and far South of Santiago, the capital and largest Chilean city, carried almost exclusively strains with the s1b m1 genotype. In contrast, patients from Santiago and cities located South of Santiago carried strains with either one or both s1a m1 and s1b m1 genotypes.Regarding the s2 m2 genotype, comparison with GenBank sequences revealed that Chilean s2 sequence was identical to those of Australian, American, and Colombian strains but quite different from those of Alaska and India.CONCLUSION: Differences in geographic distribution of the s and m vaccA alleles in Chile and a relationship of s1b m1 genotype with gastritis were found. Sequence data in part support a hispanic origin for the vacA genotype.Asymmetric distribution of genotypes s1b m1 and s2 m2recedes H Pyloristrain distribution in Spain and Portugal.

  3. HLA-A and HLA-B allele frequencies in a mestizo population from Guadalajara, Mexico, determined by sequence-based typing.

    Science.gov (United States)

    Leal, C A; Mendoza-Carrera, F; Rivas, F; Rodriguez-Reynoso, S; Portilla-de Buen, E

    2005-12-01

    HLA-A and HLA-B genes were typed by DNA sequencing in a mestizo population from Guadalajara, Jalisco, Mexico. Thirty-seven HLA-A and 51 HLA-B alleles were observed in 103 samples. The common typical Amerindian alleles (>5%) and haplotypes (>or=2.0%) found were A*02010101, *24020101, *310102, B*350101, and *4002, and A*310102-B*4002, A*240201-B*350101, and the typical European alleles were A*010101, *29010101, B*1402, B*180101, and A*020101-B*1402, A*020101-B*510101, and A*3002-B*180101. This reflects the blending of the two main parental populations of mestizos: Amerindian and Iberian. Mexicans were found to be relatively closer to the Portuguese than to Spaniards. This proximity may indicate a larger Portuguese influence in Mexicans than previously considered. Present data contribute to the understanding of the genetic structure in Mexico.

  4. Alleles Distribution Survey and Analysis of Gene Locus in CODIS Database of Han Population in Northwest of Hubei Province%鄂西北周边汉族人群CODIS数据库基因座等位基因的分布频率调查和分析

    Institute of Scientific and Technical Information of China (English)

    王晓勋; 李瑞明; 陈敏; 贺娇; 尹霞; 胡巧林; 梅俊; 吴惠超

    2014-01-01

    目的:本实验收集鄂西北周边汉族人群做亲权鉴定人的标本,确认无血缘关系的个体作为该地区随机抽样人群,检测其CODIS数据库中所有13个等位基因座中各等位基因的分布频率.方法:应用Chelex提取DNA,AmpFISTR Identifiler试剂盒扩增,毛细管电泳分型.对每个等位基因座等位基因分布进行统计计算,检测每个等位基因座哈德温伯格平衡(Hard-Wenborger平衡).结果:在被检测的387位无关个体中13个CODIS等位基因座共检出148个等位基因型以及13个等位基因座中等位基因的分布频率.结论:为本地区等位基因数据库的建立提供第一手的等位基因频率和相关统计学资料.应用适合本地人群的等位基因频率可以提高亲权鉴定和个体识别中累积父权指数的可靠性.%Objective To collect the samples of Han poplulation around northwest of Hubei province for paternity testing,the unrelated individuals were selected as a random sample of a northwest population in Hubei province,then to analyze the allele frequency of 13 allelic loci in CODIS database.Methods The Chelex-extracting DNA method,AmpFISTR Identifilerbased method for gene amplification,and DNA typing by capillary electrophoresis were used to detect these samples,respectively.The allele frequency were calculated in every allelic loci of these samples,and the Hard-Weinberg equilibrium of them were also analyzed.Results The 148 allelotype and 13 distribution frequencies of allelic loci were detected from 13 CODIS allelic loci of 387 unrelated individuals.Conclusion This research has established the valuable first-hand database on the allele frequency and related statistical data in the region,which could provide beneficial help for improving the reliability of paternity identification and cumulative paternity index in the local population.

  5. Dynamic Response to Pedestrian Loads with Statistical Frequency Distribution

    DEFF Research Database (Denmark)

    Krenk, Steen

    2012-01-01

    by the harmonic components. Measurements indicate that the footfall frequency of a group of pedestrians has a coefficient of variation of the order 0.05–0.1. This is considerably larger than the response bandwidth of a typical lightly damped structure, and at resonance this has a significant influence...

  6. Distribution of HIV-1 resistance-conferring polymorphic alleles SDF-1-3′A, CCR2-64I and CCR5-32 in diverse populations of Andhra Pradesh, South India

    Indian Academy of Sciences (India)

    G. V. Ramana; A. Vasanthi; M. Khaja; B. Su; V. Govindaiah; L. Jin; L. Singh; R. Chakraborty

    2001-12-01

    Polymorphic allelic variants of chemokine receptors CCR2 and CCR5, as well as of stromal-derived factor-1 SDF-1, the ligand for the chemokine receptor CXCR4, are known to have protective effects against HIV-1 infection and to be involved with delay in disease progression. We have studied the DNA polymorphisms at the loci that encode these proteins in 525 healthy individuals without any history of HIV-1 infection from 11 diverse populations of Andhra Pradesh, South India. The two protective alleles SDF-1-3′A and CCR2-64I at the SDF-1 and CCR2 loci, respectively, are present in all populations studied, although their frequencies differ considerably across populations (from 17% to 35% for the SDF-1-3′A allele, and from 3% to 17% for CCR2-64I). In contrast the CCR5-32 allele is observed only in three populations (Yamani, Pathan and Kamma), all in low frequencies (i.e. 1% to 3%). The mean number of mutant alleles (for the three loci together) carried by each individual varies from 0.475 (in Vizag Brahmins) to 0.959 (in Bohra Muslims). The estimated relative hazard values for the populations, computed from the three-locus genotype data, are comparable to those from Africa and Southeast Asia, where AIDS is known to be widespread.

  7. Fast and memory-efficient algorithms for computing quadratic time–frequency distributions

    OpenAIRE

    O'Toole, J.M.; Boashash, B.

    2013-01-01

    This paper presents algorithms that compute DTFDs with minimal computation and memory loads. (Additional details can be found in the comprehensive book on Time-Frequency Signal Analysis and Processing (see http://www.elsevier.com/locate/isbn/0080443354). In addition, the most recent upgrade of the original software package that calculates Time-Frequency Distributions and Instantaneous Frequency estimators can be downloaded from the web site: www.time-frequency.net. This was the first...

  8. Frequency and distribution studies of asymmetrical versus symmetrical chromosome aberrations

    International Nuclear Information System (INIS)

    Two aspects of the relationship between Asymmetrical (A) and Symmetrical (S) radiation-induced chromosomal aberrations are considered in this paper. (1) Are A and S truly alternative modes of lesion interaction. Relative frequencies for chromatid-type and chromosome-type are examined, and new lymphocyte data using banding is used to look at this, and also for parallelism in chromosome participation of the two forms for various aberration categories. All the tests applied suggest that A and S are alternative interaction modes. (2) The long-term survival characteristics of A and S are discussed, and the differences in expected frequencies of derived S per surviving cell from chromosome-type and chromatid-types are stressed. Since many in vivo tissues have varying mixtures of potential chromatid and chromosome aberration-bearing target cells, ultimate cell survival and derived S frequencies may differ between tissues for the same absorbed dose. An Appendix gives Relative Corrected Lengths (RCL) for chromosomes of the human karyotype which should be used when testing the various exchange aberration categories for random chromosome participation. (orig.)

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

    Science.gov (United States)

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

    2010-10-01

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

  10. Frequency-wavenumber processing for infrasound distributed arrays.

    Science.gov (United States)

    Costley, R Daniel; Frazier, W Garth; Dillion, Kevin; Picucci, Jennifer R; Williams, Jay E; McKenna, Mihan H

    2013-10-01

    The work described herein discusses the application of a frequency-wavenumber signal processing technique to signals from rectangular infrasound arrays for detection and estimation of the direction of travel of infrasound. Arrays of 100 sensors were arranged in square configurations with sensor spacing of 2 m. Wind noise data were collected at one site. Synthetic infrasound signals were superposed on top of the wind noise to determine the accuracy and sensitivity of the technique with respect to signal-to-noise ratio. The technique was then applied to an impulsive event recorded at a different site. Preliminary results demonstrated the feasibility of this approach. PMID:24116535

  11. Radar signal analysis of ballistic missile with micro-motion based on time-frequency distribution

    Science.gov (United States)

    Wang, Jianming; Liu, Lihua; Yu, Hua

    2015-12-01

    The micro-motion of ballistic missile targets induces micro-Doppler modulation on the radar return signal, which is a unique feature for the warhead discrimination during flight. In order to extract the micro-Doppler feature of ballistic missile targets, time-frequency analysis is employed to process the micro-Doppler modulated time-varying radar signal. The images of time-frequency distribution (TFD) reveal the micro-Doppler modulation characteristic very well. However, there are many existing time-frequency analysis methods to generate the time-frequency distribution images, including the short-time Fourier transform (STFT), Wigner distribution (WD) and Cohen class distribution, etc. Under the background of ballistic missile defence, the paper aims at working out an effective time-frequency analysis method for ballistic missile warhead discrimination from the decoys.

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

    Science.gov (United States)

    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

  13. 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.

    Science.gov (United States)

    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 grade (P 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 quality. PMID:24398843

  14. Lack of polymorphism at MC1R wild-type allele and evidence of domestic allele introgression across European wild boar populations

    DEFF Research Database (Denmark)

    Canu, Antonio; Vilaça, Sibelle T.; Iacolina, Laura;

    2016-01-01

    , two loci which have been under strong artificial selection during domestication. These loci influence coat colour and number of vertebrae, respectively. A total of 145 wild boars were sampled throughout Europe, to evaluate frequency and spatial distribution of domestic alleles and patterns...

  15. Distributed multi-frequency image reconstruction for radio-interferometry

    CERN Document Server

    Deguignet, Jérémy; Mary, David; Ferrari, Chiara

    2016-01-01

    The advent of enhanced technologies in radio interferometry and the perspective of the SKA telescope bring new challenges in image reconstruction. One of these challenges is the spatio-spectral reconstruction of large (Terabytes) data cubes with high fidelity. This contribution proposes an alternative implementation of one such 3D prototype algorithm, MUFFIN (MUlti-Frequency image reconstruction For radio INterferometry), which combines spatial and spectral analysis priors. Using a recently proposed primal dual algorithm, this new version of MUFFIN allows a parallel implementation where computationally intensive steps are split by spectral channels. This parallelization allows to implement computationally demanding translation invariant wavelet transforms (IUWT), as opposed to the union of bases used previously. This alternative implementation is important as it opens the possibility of comparing these efficient dictionaries, and others, in spatio-spectral reconstruction. Numerical results show that the IUWT-...

  16. Incoherent Optical Frequency Domain Reflectometry for Distributed Thermal Sensing

    DEFF Research Database (Denmark)

    Karamehmedovic, Emir

    2006-01-01

    increasing frequency, after which the inverse Fourier transform is applied to the signal from the backscattered light. This technique is compared with the more conventional optical time domain reflectometry, where a short pulse is sent through the fibre, and the location of the scattering section...... developed and implemented in Matlab. The computer model is calibrated and tested, and describes the entire system with high precision. Noise analysis and digital processing of the detected signal are discussed as well. An equation describing the standard deviation of the measured temperature is derived...... resolution of order 1m is strived to be achieved. These demands are attempted to be reached by employing a low-loss telecom-grade transmission single-mode fibre or an alternative fibre as the sensing fibre, and a pump laser operating in the low loss region of silica. An analysis of the optical module...

  17. Randomized algorithms for tracking distributed count, frequencies, and ranks

    DEFF Research Database (Denmark)

    Zengfeng, Huang; Ke, Yi; Zhang, Qin

    2012-01-01

    We show that randomization can lead to significant improvements for a few fundamental problems in distributed tracking. Our basis is the count-tracking problem, where there are k players, each holding a counter ni that gets incremented over time, and the goal is to track an ∑-approximation...... of their sum n=∑ini continuously at all times, using minimum communication. While the deterministic communication complexity of the problem is θ(k/ε • log N), where N is the final value of n when the tracking finishes, we show that with randomization, the communication cost can be reduced to θ(√k/ε • log N...

  18. Randomized Algorithms for Tracking Distributed Count, Frequencies, and Ranks

    DEFF Research Database (Denmark)

    Huang, Zengfeng; Yi, Ke; Zhang, Qin

    2011-01-01

    We show that randomization can lead to significant improvements for a few fundamental problems in distributed tracking. Our basis is the {\\em count-tracking} problem, where there are $k$ players, each holding a counter $n_i$ that gets incremented over time, and the goal is to track an $\\eps......$-approximation of their sum $n=\\sum_i n_i$ continuously at all times, using minimum communication. While the deterministic communication complexity of the problem is $\\Theta(k/\\eps \\cdot \\log N)$, where $N$ is the final value of $n$ when the tracking finishes, we show that with randomization, the communication cost can...

  19. Damage Detection Based on Cross-Term Extraction from Bilinear Time-Frequency Distributions

    Directory of Open Access Journals (Sweden)

    Ma Yuchao

    2014-01-01

    Full Text Available Abundant damage information is implicated in the bilinear time-frequency distribution of structural dynamic signals, which could provide effective support for structural damage identification. Signal time-frequency analysis methods are reviewed, and the characters of linear time-frequency distribution and bilinear time-frequency distribution typically represented by the Wigner-Ville distribution are compared. The existence of the cross-term and its application in structural damage detection are demonstrated. A method of extracting the dominant term is proposed, which combines the short-time Fourier spectrum and Wigner-Ville distribution; then two-dimensional time-frequency transformation matrix is constructed and the complete cross-term is extracted finally. The distribution character of which could be applied to the structural damage identification. Through theoretical analysis, model experiment and numerical simulation of the girder structure, the change rate of cross-term amplitude is validated to identify the damage location and degree. The effectiveness of the cross-term of bilinear time-frequency distribution for damage detection is confirmed and the analytical method of damage identification used in structural engineering is available.

  20. Transient voltage distribution in stator winding of electrical machine fed from a frequency converter

    OpenAIRE

    Oyegoke, Bolarin S.

    2000-01-01

    Standard induction motors are exposed to steep-fronted, non-sinusoidal voltages when fed from frequency converters. These wave patterns can be destructive to the insulation. The aim of the present work is to develop methods of predicting the magnitude and distribution of fast voltage within the stator winding of an electric machine fed from a frequency converter. Three methods of predicting the magnitude and distribution of fast voltages within form windings commonly used in medium and hi...

  1. Investigation of Dual Radio-Frequency Driven Sheaths and Ion Energy Distributions Bombarding an Insulating Substrate

    Institute of Scientific and Technical Information of China (English)

    WANG Li-Hong; DAI Zhong-Ling; WANG Yu-Nian

    2006-01-01

    @@ Dual radio-frequency (rf) sources at widely different frequencies are often simultaneously used to separately optimize the plasma parameters and ion energy distributions (IEDs) incident onto a substrate. Characteristics of collisionless dual rf biased-sheaths and IEDs impinging on an insulating substrate are studied with a self consistent one-dimensional fluid model.

  2. Secondary Frequency and Voltage Control of Islanded Microgrids via Distributed Averaging

    DEFF Research Database (Denmark)

    W. Simpson-Porco, John; Shafiee, Qobad; Dorfler, Florian;

    2015-01-01

    actions. The frequency controller rapidly regulates the microgrid frequency to its nominal value while maintaining active power sharing among the distributed generators. Tuning of the voltage controller provides a simple and intuitive trade-off between the conflicting goals of voltage regulation...

  3. Daris, a low-frequency distributed aperture array for radio astronomy in space

    NARCIS (Netherlands)

    Boonstra, A.J.; Saks, N.; Bentum, M.J.; Klooster, van 't K.; Falcke, H.

    2010-01-01

    DARIS (Distributed Aperture Array for Radio Astronomy in Space) is a radio astronomy space mission concept aimed at observing the low-frequency radio sky in the range 1-10 MHz. Because of the Earth's ionospheric disturbances and opaqueness, this frequency range can only be observed from space. The a

  4. Velocity Distribution of Effective Atoms in a Small Optically Pumped Cesium Beam Frequency Standard

    Institute of Scientific and Technical Information of China (English)

    CHEN Jingbiao; WANG Fengzhi; YANG Donghai; WANG YiQiu

    2001-01-01

    In this paper, the velocity distribution of effective atoms in a small optically pumped cesium beam frequency standard has been achieved from the Fourier transforms of the experimentally recorded Ramsey patterns. The result fits well with the theoretical calculation. The second order Doppler shift correction of the small cesium atomic clock is obtained from the velocity distribution of effective atoms.

  5. The frequency-area distribution of volcanic units on Venus: Implications for planetary resurfacing

    OpenAIRE

    Romeo Briones, Ignacio; Turcotte, Donald L.

    2009-01-01

    The areas of volcanic units on Venus have been measured on the 1:5000000 geological maps published by NASA/USGS. These data were used to obtain a frequency-area distribution. The cumulative frequency-area distribution of 1544 specific occurrence of units cover six orders of magnitude from the largest unit (30 106 km2) to the smallest (20 km2). The probability distribution function has been calculated. The medium and large volcanic units correlate well with a power-law (fractal) r...

  6. Sub-nanosecond machine timing and frequency distribution via serial data links

    CERN Document Server

    Rohlev, A; Serrano, J; Cattin, M; Settler, M

    2008-01-01

    FERMI@ELETTRA is a 4th generation light source under construction at Sincrotrone Trieste. It will be operated as a seeded FEL driven by a warm S-band Linac which places very stringent specifications on control of the amplitude and phase of the RF stations. The local clock generation and distribution system at each station will not be based on the phase reference distribution but rather on a separate frequency reference distribution which has significantly less stringent phase stability requirements. This frequency reference will be embedded in the serial data link to each station and has the further advantage of being able to broadcast synchronous machine timing signals with sub-nanosecond temporal accuracy. The phase and amplitude of the phase reference line is measured for each pulse and used to calibrate the other measurements. This paper describes the architecture used to distribute the frequency reference along with the precision machine timing and clocking signals.

  7. Quantitatively differentiating microstructures of tissues by frequency distributions of Mueller matrix images

    Science.gov (United States)

    He, Chao; He, Honghui; Li, Xianpeng; Chang, Jintao; Wang, Ye; Liu, Shaoxiong; Zeng, Nan; He, Yonghong; Ma, Hui

    2015-10-01

    We present a new way to extract characteristic features of the Mueller matrix images based on their frequency distributions and the central moments. We take the backscattering Mueller matrices of tissues with distinctive microstructures, and then analyze the frequency distribution histograms (FDHs) of all the matrix elements. For anisotropic skeletal muscle and isotropic liver tissues, we find that the shapes of the FDHs and their central moment parameters, i.e., variance, skewness, and kurtosis, are not sensitive to the sample orientation. Comparisons among different tissues further indicate that the frequency distributions of Mueller matrix elements and their corresponding central moments can be used as indicators for the characteristic microstructural features of tissues. A preliminary application to human cervical cancerous tissues shows that the distribution curves and central moment parameters may have the potential to give quantitative criteria for cancerous tissues detections.

  8. Coastal waters monitoring data: frequency distributions of the principal water quality variables

    OpenAIRE

    Di Lorenzo, Bianca; Maria Grazia FINOIA; Marina AMORI; Russo, Simone; Giovanardi, Franco

    2006-01-01

    Examining the results of the Italian national programme of marine coastal monitoring, the old problem has arisen about the choice of the most appropriate procedures and methods to validate data and screen preliminary data. Therefore, statistical distributions of water quality parameters have been taken into consideration, in order to assign appropriate frequency distributions to all the routinely measured variables. Each sample distribution has been analysed and defined by a probability densi...

  9. Allelic variations in Glu-1 and Glu-3 loci of historical and modern Iranian bread wheat (Triticum aestivum L.) cultivars

    Indian Academy of Sciences (India)

    Ali Izadi-Darbandi; Bahman Yazdi-Samadi; Ali-Akbar Su-Boushehri; Mohsen Mohammadi

    2010-08-01

    Proline and glutamine-rich wheat seed endosperm proteins are collectively referred to as prolamins. They are comprised of HMW-GSs, LMW-GSs and gliadins. HMW-GSs are major determinants of gluten elasticity and LMW-GSs considerably affect dough extensibility and maximum dough resistance. The inheritance of glutenin subunits follows Mendelian genetics with multiple alleles in each locus. Identification of the banding patterns of glutenin subunits could be used as an estimate for screening high quality wheat germplasm. Here, by means of a two-step 1D-SDS-PAGE procedure, we identified the allelic variations in high and low-molecular-weight glutenin subunits in 65 hexaploid wheat (Triticum aestivum L.) cultivars representing a historical trend in the cultivars introduced or released in Iran from the years 1940 to 1990. Distinct alleles 17 and 19 were detected for Glu-1 and Glu-3 loci, respectively. The allelic frequencies at the Glu-1 loci demonstrated unimodal distributions. At Glu-A1, Glu-B1 and Glu-D1, we found that the most frequent alleles were the null, 7 + 8, 2 + 12 alleles, respectively, in Iranian wheat cultivars. In contrast, Glu-3 loci showed bimodal or trimodal distributions. At Glu-A3, the most frequent alleles were c and e. At Glu-B3 the most frequent alleles were a, b and c. At Glu-D3 locus, the alleles b and a, were the most and the second most frequent alleles in Iranian wheat cultivars. This led to a significantly higher Nei coefficient of genetic variations in Glu-3 loci (0.756) as compared to Glu-1 loci (0.547). At Glu-3 loci, we observed relatively high quality alleles in Glu-A3 and Glu-D3 loci and low quality alleles at Glu-B3 locus.

  10. Distribution of Voltage-Gated Sodium Channel (Nav) Alleles among the Aedes aegypti Populations In Central Java Province and Its Association with Resistance to Pyrethroid Insecticides.

    Science.gov (United States)

    Sayono, Sayono; Hidayati, Anggie Puspa Nur; Fahri, Sukmal; Sumanto, Didik; Dharmana, Edi; Hadisaputro, Suharyo; Asih, Puji Budi Setia; Syafruddin, Din

    2016-01-01

    The emergence of insecticide resistant Aedes aegypti mosquitoes has hampered dengue control efforts. WHO susceptibility tests, using several pyrethroid compounds, were conducted on Ae. aegypti larvae that were collected and raised to adulthood from Semarang, Surakarta, Kudus and Jepara in Java. The AaNaV gene fragment encompassing kdr polymorphic sites from both susceptible and resistant mosquitoes was amplified, and polymorphisms were associated with the resistant phenotype. The insecticide susceptibility tests demonstrated Ae, aegypti resistance to the pyrethroids, with mortality rates ranging from 1.6%-15.2%. Three non-synonymous polymorphisms (S989P, V1016G and F1534C) and one synonymous polymorphism (codon 982) were detected in the AaNaV gene. Eight AaNaV alleles were observed in specimens from Central Java. Allele 3 (SGF) and allele 7 (PGF) represent the most common alleles found and demonstrated strong associations with resistance to pyrethroids (OR = 2.75, CI: 0.97-7.8 and OR = 7.37, CI: 2.4-22.5, respectively). This is the first report of 8 Ae. aegypti AaNaV alleles, and it indicates the development of resistance in Ae. aegypti in response to pyrethroid insecticide-based selective pressure. These findings strongly suggest the need for an appropriate integrated use of insecticides in the region. The 989P, 1016G and 1534C polymorphisms in the AaNaV gene are potentially valuable molecular markers for pyrethroid insecticide resistance monitoring.

  11. Distribution of Voltage-Gated Sodium Channel (Nav Alleles among the Aedes aegypti Populations In Central Java Province and Its Association with Resistance to Pyrethroid Insecticides.

    Directory of Open Access Journals (Sweden)

    Sayono Sayono

    Full Text Available The emergence of insecticide resistant Aedes aegypti mosquitoes has hampered dengue control efforts. WHO susceptibility tests, using several pyrethroid compounds, were conducted on Ae. aegypti larvae that were collected and raised to adulthood from Semarang, Surakarta, Kudus and Jepara in Java. The AaNaV gene fragment encompassing kdr polymorphic sites from both susceptible and resistant mosquitoes was amplified, and polymorphisms were associated with the resistant phenotype. The insecticide susceptibility tests demonstrated Ae, aegypti resistance to the pyrethroids, with mortality rates ranging from 1.6%-15.2%. Three non-synonymous polymorphisms (S989P, V1016G and F1534C and one synonymous polymorphism (codon 982 were detected in the AaNaV gene. Eight AaNaV alleles were observed in specimens from Central Java. Allele 3 (SGF and allele 7 (PGF represent the most common alleles found and demonstrated strong associations with resistance to pyrethroids (OR = 2.75, CI: 0.97-7.8 and OR = 7.37, CI: 2.4-22.5, respectively. This is the first report of 8 Ae. aegypti AaNaV alleles, and it indicates the development of resistance in Ae. aegypti in response to pyrethroid insecticide-based selective pressure. These findings strongly suggest the need for an appropriate integrated use of insecticides in the region. The 989P, 1016G and 1534C polymorphisms in the AaNaV gene are potentially valuable molecular markers for pyrethroid insecticide resistance monitoring.

  12. Estimating the flood frequency distribution at seasonal and annual time scales

    Directory of Open Access Journals (Sweden)

    E. Baratti

    2012-12-01

    Full Text Available We propose an original approach to infer the flood frequency distribution at seasonal and annual time scale. Our purpose is to estimate the peak flow that is expected for an assigned return period T, independently of the season in which it occurs (i.e. annual flood frequency regime, as well as in different selected sub-yearly periods (i.e. seasonal flood frequency regime. While a huge literature exists on annual flood frequency analysis, few studies have focused on the estimation of seasonal flood frequencies despite the relevance of the issue, for instance when scheduling along the months of the year the construction phases of river engineering works directly interacting with the active river bed, like for instance dams. An approximate method for joint frequency analysis is presented here that guarantees consistency between fitted annual and seasonal distributions, i.e. the annual cumulative distribution is the product of the seasonal cumulative distribution functions, under the assumption of independence among floods in different seasons. In our method the parameters of the seasonal frequency distributions are fitted by maximising an objective function that accounts for the likelihoods of both seasonal and annual peaks. In contrast to previous studies, our procedure is conceived to allow the users to introduce subjective weights to the components of the objective function in order to emphasize the fitting of specific seasons or of the annual peak flow distribution. An application to the time series of the Blue Nile daily flows at the Sudan–Ethiopia border is presented.

  13. Estimating the flood frequency distribution at seasonal and annual time scale

    Directory of Open Access Journals (Sweden)

    E. Baratti

    2012-06-01

    Full Text Available We propose an original approach to infer the flood frequency distribution at seasonal and annual time scale. Our purpose is to estimate the peak flow that is expected for an assigned return period T, independently of the season in which it occurs (i.e. annual flood frequency regime, as well as in different selected sub-yearly periods (i.e. seasonal flood frequency regime. While a huge literature exists on annual flood frequency analysis, few studies have focused on the estimation of seasonal flood frequencies despite the relevance of the issue, for instance when scheduling along the months of the year the construction phases of river engineering works directly interacting with the active river bed, like for instance dams. An approximate method for joint frequency analysis is presented here that guarantees consistency between fitted annual and seasonal distributions, i.e. the annual cumulative distribution is the product of the seasonal cumulative distribution functions, under the assumption of independence among floods in different seasons. In our method the parameters of the seasonal frequency distributions are fitted by maximising an objective function that accounts for the likelihoods of both seasonal and annual peaks. Differently from previous studies, our procedure is conceived to allow the users to introduce subjective weights to the components of the objective function in order to emphasize the fitting of specific seasons or of the annual peak flow distribution. An application to the time series of the Blue Nile daily flows at Sudan-Ethiopia border is presented.

  14. Bonus-Malus System with the Claim Frequency Distribution is Geometric and the Severity Distribution is Truncated Weibull

    Science.gov (United States)

    Santi, D. N.; Purnaba, I. G. P.; Mangku, I. W.

    2016-01-01

    Bonus-Malus system is said to be optimal if it is financially balanced for insurance companies and fair for policyholders. Previous research about Bonus-Malus system concern with the determination of the risk premium which applied to all of the severity that guaranteed by the insurance company. In fact, not all of the severity that proposed by policyholder may be covered by insurance company. When the insurance company sets a maximum bound of the severity incurred, so it is necessary to modify the model of the severity distribution into the severity bound distribution. In this paper, optimal Bonus-Malus system is compound of claim frequency component has geometric distribution and severity component has truncated Weibull distribution is discussed. The number of claims considered to follow a Poisson distribution, and the expected number λ is exponentially distributed, so the number of claims has a geometric distribution. The severity with a given parameter θ is considered to have a truncated exponential distribution is modelled using the Levy distribution, so the severity have a truncated Weibull distribution.

  15. NEW TECHNOLOGY FOR FAULT DIAGNOSIS BASED ON WAVELET DENOISING AND MODIFIED EXPONENTIAL TIME-FREQUENCY DISTRIBUTION

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Fast wavelet multi-resolution analysis (wavelet MRk)provides a effective tool for analyzing and canceling disturbing components in original signal. Because of its exponential frequency axis, this method isn't suitable for extracting harmonic components. The modified exponential time-frequency distribution(MED)overcomes the problems of Wigner distribution(WD), can suppress cross-terms and cancel noise further more. MED provides high resolution in both time and frequency domains, so it can make out weak period impulse components from signal with mighty harmonic components. According to the "time" behavior, together with "frequency" behavior in one figure, the essential structure of a signal is revealed clearly. According to the analysis of algorithm and fault diagnosis example, the joint of wavelet MRA and MED is a powerful tool for fault diagnosis.

  16. Inferring the flood frequency distribution for an ungauged basin using a spatially distributed rainfall-runoff model

    Directory of Open Access Journals (Sweden)

    G. Moretti

    2008-08-01

    Full Text Available The estimation of the peak river flow for ungauged river sections is a topical issue in applied hydrology. Spatially distributed rainfall-runoff models can be a useful tool to this end, since they are potentially able to simulate the river flow at any location of the watershed drainage network. However, it is not fully clear to what extent these models can provide reliable simulations over a wide range of spatial scales. This issue is investigated here by applying a spatially distributed, continuous simulation rainfall-runoff model to infer the flood frequency distribution of the Riarbero River. This is an ungauged mountain creek located in northern Italy, whose drainage area is 17 km2. The hydrological model is first calibrated by using a 1-year record of hourly meteorological data and river flows observed at the outlet of the 1294 km2 wide Secchia River basin, of which the Riarbero is a tributary. The model is then validated by performing a 100-year long simulation of synthetic river flow data, which allowed us to compare the simulated and observed flood frequency distributions at the Secchia River outlet and the internal cross river section of Cavola Bridge, where the basin area is 337 km2. Finally, another simulation of hourly river flows was performed by referring to the outlet of the Riarbero River, therefore allowing us to estimate the related flood frequency distribution. The results were validated by using estimates of peak river flow obtained by applying hydrological similarity principles and a regional method. The results show that the flood flow estimated through the application of the distributed model is consistent with the estimate provided by the regional procedure as well as the behaviors of the river banks. Conversely, the method based on hydrological similarity delivers an estimate that seems to be not as reliable. The analysis highlights interesting perspectives for the application of

  17. Application of Choi—Williams Reduced Interference Time Frequency Distribution to Machinery Diagnostics

    Directory of Open Access Journals (Sweden)

    Howard A. Gaberson

    1995-01-01

    Full Text Available This article discusses time frequency analysis of machinery diagnostic vibration signals. The short time Fourier transform, the Wigner, and the Choi–Williams distributions are explained and illustrated with test cases. Examples of Choi—Williams analyses of machinery vibration signals are presented. The analyses detect discontinuities in the signals and their timing, amplitude and frequency modulation, and the presence of different components in a vibration signal.

  18. Genetic heterogeneity within electrophoretic "alleles" of xanthine dehydrogenase in Drosophila pseudoobscura.

    Science.gov (United States)

    Singh, R S; Lewontin, R C; Felton, A A

    1976-11-01

    An experimental plan for an exhaustive determination of genic variation at structural gene loci is presented. In the initial steps of this program, 146 isochromosomal lines from 12 geographic populations of D. pseudoobscura were examined for allelic variation of xanthine dehydrogenase by the serial use of 4 different electrophoretic conditions and a head stability test. The 5 criteria revealed a total of 37 allelic classes out of the 146 genomes examined where only 6 had been previously revealed by the usual method of gel electrophoresis. This immense increase in genic variation also showed previously unsuspected population differences between the main part of the species distribution and the isolated population of Bogotá population. The average heterozygosity at the Xdh locus is at least 72% in natural populations. This result, together with the very large number of alleles segregating and the pattern of allelic frequencies, has implications for theories of genetic polymorphism which are discussed.

  19. Effect on Stratum Gradient Frequency Distribution of Landslides in the Three Gorges Area of Northeast Chongqing

    Institute of Scientific and Technical Information of China (English)

    FAN Xiaoyi; QIAO Jianping

    2006-01-01

    The landslide data were calculated in the Three Gorges Area of northeast Chongqing. The results showed that landslide frequency distributions of gradients accorded with the Weibull probability density distribution function. The landslide hazard ratios of gradients were acquired by Weibull accumulation probability distribution function in the different geological units. There was discord between landslide hazard ratio of different geological units and variance of landslide gradient. But they were approximate homology in the strata of Jurassic. The results indicate that the Weibull distribution can quantitatively evaluate the landslide hazard ratios of gradients of the different strata in the Three Gorges Area.

  20. Distributed feedback terahertz frequency quantum cascade lasers with dual periodicity gratings

    CERN Document Server

    Castellano, F; Li, L H; Pitanti, A; Tredicucci, A; Linfield, E H; Davies, A G; Vitiello, M S

    2016-01-01

    We have developed terahertz frequency quantum cascade lasers that exploit a double-periodicity distributed feedback grating to control the emission frequency and the output beam direction independently. The spatial refractive index modulation of the gratings necessary to provide optical feedback at a fixed frequency and, simultaneously, a far-field emission pattern centered at controlled angles, was designed through use of an appropriate wavevector scattering model. Single mode THz emission at angles tuned by design between 0{\\deg} and 50{\\deg} was realized, leading to an original phase-matching approach, lithographically independent, for highly collimated THz QCLs.

  1. [Features of the distribution of alleles of the HLA-DRB1 04 and HLA-DQB1 03 genes among healthy people of European origin in Western Siberia].

    Science.gov (United States)

    Sartakova, M L; Konenkov, V I; Kimura, A

    1993-04-01

    The allelic HLA-DRB1 04 and HLA-DQB1 03 polymorphism in caucasians living among the West Siberia Mongoloid aborigenes was studied. As a result of our studies, it was shown that the HLA-DRB1 0403/07 predominates and HLA-DRB1 0404/08 is absent in the Russian population of West Siberia, in contrast to those among Caucasians living in West Europe and North America. The frequencies of HLA-DQB1 03 alleles are similar to those observed among the all Caucasians. Gametic association HLA-DR4 - HLA-DQw was found for the first time in Caucasians of West Siberia. PMID:8354474

  2. Finite Time Control for Fractional Order Nonlinear Hydroturbine Governing System via Frequency Distributed Model

    Directory of Open Access Journals (Sweden)

    Bin Wang

    2016-01-01

    Full Text Available This paper studies the application of frequency distributed model for finite time control of a fractional order nonlinear hydroturbine governing system (HGS. Firstly, the mathematical model of HGS with external random disturbances is introduced. Secondly, a novel terminal sliding surface is proposed and its stability to origin is proved based on the frequency distributed model and Lyapunov stability theory. Furthermore, based on finite time stability and sliding mode control theory, a robust control law to ensure the occurrence of the sliding motion in a finite time is designed for stabilization of the fractional order HGS. Finally, simulation results show the effectiveness and robustness of the proposed scheme.

  3. Interference structure of shallow water reverberation in time-frequency distribution

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The striations of the reverberation spectrum in the time-frequency distribution were observed in a shallow water acoustic experiment in 2002. A model following the coherent reverberation model developed in 2002 is presented to explain the observed striations. To examine the consistency between the measured data and numerical predictions, we have used a method based on Radon transform for determining the slope of the striations to the measured reverberation data and numerical predictions. The results indicate that the previously developed coherent reverberation model can predict the interference structure of the reverberation intensity in the time-frequency distribution.

  4. Universal spectrum for DNA base CG frequency distribution in Takifugu rubripes (Puffer fish) genome

    CERN Document Server

    Selvam, A M

    2007-01-01

    The frequency distribution of DNA bases A, C, G, T exhibit fractal fluctuations, namely a zigzag pattern of an increase followed by a decrease of all orders of magnitude along the length of the DNA molecule. Selfsimilar fractal fluctuations are ubiquitous to space-time fluctuations of dynamical systems in nature. The power spectra of fractal fluctuations exhibit inverse power law form signifying long-range space-time correlations such that there is two-way communication between local (small-scale) and global (large-scale) perturbations. In this paper it is shown that DNA base CG frequency distribution in Takifugu rubripes (Puffer fish) Genome Release 4 exhibit universal inverse power law form of the statistical normal distribution consistent with a general systems theory model prediction of quantumlike chaos governing fractal space-time distributions. The model predictions are (i) quasicrystalline Penrose tiling pattern for the nested coiled structure thereby achieving maximum packing efficiency for the DNA m...

  5. On the frequency distribution of neutral particles from low-energy strong interactions

    CERN Document Server

    Colecchia, Federico

    2016-01-01

    The rejection of the contamination, or background, from low-energy strong interactions at hadron collider experiments is a topic that has received significant attention in the field of particle physics. This article builds on a particle-level view of collision events, in line with recently-proposed subtraction methods. While conventional techniques in the field usually concentrate on probability distributions, our study is, to our knowledge, the first attempt at estimating the frequency distribution of background particles across the kinematic space inside individual collision events. In fact, while the probability distribution can generally be estimated given a model of low-energy strong interactions, the corresponding frequency distribution inside a single event typically deviates from the average and cannot be predicted a priori. We present preliminary results in this direction, and establish a connection between our technique and the particle weighting methods that have been the subject of recent investig...

  6. Robustness of time frequency distribution based features for automated neonatal EEG seizure detection.

    Science.gov (United States)

    Nagaraj, S B; Stevenson, N J; Marnane, W P; Boylan, G B; Lightbody, G

    2014-01-01

    In this paper we examined the robustness of a feature-set based on time-frequency distributions (TFDs) for neonatal EEG seizure detection. This feature-set was originally proposed in literature for neonatal seizure detection using a support vector machine (SVM). We tested the performance of this feature-set with a smoothed Wigner-Ville distribution and modified B distribution as the underlying TFDs. The seizure detection system using time-frequency signal and image processing features from the TFD of the EEG signal using modified B distribution was able to achieve a median receiver operator characteristic area of 0.96 (IQR 0.91-0.98) tested on a large clinical dataset of 826 h of EEG data from 18 full-term newborns with 1389 seizures. The mean AUC was 0.93. PMID:25570580

  7. Size-frequency distribution of boulders ≥7 m on comet 67P/Churyumov-Gerasimenko

    Science.gov (United States)

    Pajola, Maurizio; Vincent, Jean-Baptiste; Güttler, Carsten; Lee, Jui-Chi; Bertini, Ivano; Massironi, Matteo; Simioni, Emanuele; Marzari, Francesco; Giacomini, Lorenza; Lucchetti, Alice; Barbieri, Cesare; Cremonese, Gabriele; Naletto, Giampiero; Pommerol, Antoine; El-Maarry, Mohamed R.; Besse, Sébastien; Küppers, Michael; La Forgia, Fiorangela; Lazzarin, Monica; Thomas, Nicholas; Auger, Anne-Thérèse; Sierks, Holger; Lamy, Philippe; Rodrigo, Rafael; Koschny, Detlef; Rickman, Hans; Keller, Horst U.; Agarwal, Jessica; A'Hearn, Michael F.; Barucci, Maria A.; Bertaux, Jean-Loup; Da Deppo, Vania; Davidsson, Björn; De Cecco, Mariolino; Debei, Stefano; Ferri, Francesca; Fornasier, Sonia; Fulle, Marco; Groussin, Olivier; Gutierrez, Pedro J.; Hviid, Stubbe F.; Ip, Wing-Huen; Jorda, Laurent; Knollenberg, Jörg; Kramm, J.-Rainer; Kürt, Ekkehard; Lara, Luisa M.; Lin, Zhong-Yi; Lopez Moreno, Jose J.; Magrin, Sara; Marchi, Simone; Michalik, Harald; Moissl, Richard; Mottola, Stefano; Oklay, Nilda; Preusker, Frank; Scholten, Frank; Tubiana, Cecilia

    2015-11-01

    Aims: We derive for the first time the size-frequency distribution of boulders on a comet, 67P/Churyumov-Gerasimenko (67P), computed from the images taken by the Rosetta/OSIRIS imaging system. We highlight the possible physical processes that lead to these boulder size distributions. Methods: We used images acquired by the OSIRIS Narrow Angle Camera, NAC, on 5 and 6 August 2014. The scale of these images (2.44-2.03 m/px) is such that boulders ≥7 m can be identified and manually extracted from the datasets with the software ArcGIS. We derived both global and localized size-frequency distributions. The three-pixel sampling detection, coupled with the favorable shadowing of the surface (observation phase angle ranging from 48° to 53°), enables unequivocally detecting boulders scattered all over the illuminated side of 67P. Results: We identify 3546 boulders larger than 7 m on the imaged surface (36.4 km2), with a global number density of nearly 100/km2 and a cumulative size-frequency distribution represented by a power-law with index of -3.6 +0.2/-0.3. The two lobes of 67P appear to have slightly different distributions, with an index of -3.5 +0.2/-0.3 for the main lobe (body) and -4.0 +0.3/-0.2 for the small lobe (head). The steeper distribution of the small lobe might be due to a more pervasive fracturing. The difference of the distribution for the connecting region (neck) is much more significant, with an index value of -2.2 +0.2/-0.2. We propose that the boulder field located in the neck area is the result of blocks falling from the contiguous Hathor cliff. The lower slope of the size-frequency distribution we see today in the neck area might be due to the concurrent processes acting on the smallest boulders, such as i) disintegration or fragmentation and vanishing through sublimation; ii) uplifting by gas drag and consequent redistribution; and iii) burial beneath a debris blanket. We also derived the cumulative size-frequency distribution per km2 of

  8. Distribution of Voltage-Gated Sodium Channel (Nav) Alleles among the Aedes aegypti Populations In Central Java Province and Its Association with Resistance to Pyrethroid Insecticides

    Science.gov (United States)

    Sayono, Sayono; Hidayati, Anggie Puspa Nur; Fahri, Sukmal; Sumanto, Didik; Dharmana, Edi; Hadisaputro, Suharyo; Asih, Puji Budi Setia; Syafruddin, Din

    2016-01-01

    The emergence of insecticide resistant Aedes aegypti mosquitoes has hampered dengue control efforts. WHO susceptibility tests, using several pyrethroid compounds, were conducted on Ae. aegypti larvae that were collected and raised to adulthood from Semarang, Surakarta, Kudus and Jepara in Java. The AaNaV gene fragment encompassing kdr polymorphic sites from both susceptible and resistant mosquitoes was amplified, and polymorphisms were associated with the resistant phenotype. The insecticide susceptibility tests demonstrated Ae, aegypti resistance to the pyrethroids, with mortality rates ranging from 1.6%–15.2%. Three non-synonymous polymorphisms (S989P, V1016G and F1534C) and one synonymous polymorphism (codon 982) were detected in the AaNaV gene. Eight AaNaV alleles were observed in specimens from Central Java. Allele 3 (SGF) and allele 7 (PGF) represent the most common alleles found and demonstrated strong associations with resistance to pyrethroids (OR = 2.75, CI: 0.97–7.8 and OR = 7.37, CI: 2.4–22.5, respectively). This is the first report of 8 Ae. aegypti AaNaV alleles, and it indicates the development of resistance in Ae. aegypti in response to pyrethroid insecticide-based selective pressure. These findings strongly suggest the need for an appropriate integrated use of insecticides in the region. The 989P, 1016G and 1534C polymorphisms in the AaNaV gene are potentially valuable molecular markers for pyrethroid insecticide resistance monitoring. PMID:26939002

  9. On the existence of hysteresis in the Kuramoto model with bimodal frequency distributions

    OpenAIRE

    Montbrió, Ernest; Pazó, Diego

    2009-01-01

    We investigate the transition to synchronization in the Kuramoto model with bimodal distributions of the natural frequencies. Previous studies have concluded that the model exhibits a hysteretic phase transition if the bimodal distribution is close to a unimodal one, due to the shallowness the central dip. Here we show that proximity to the unimodal-bimodal border does not necessarily imply hysteresis when the width, but not the depth, of the central dip tends to zero. We draw this conclusio...

  10. Existence of hysteresis in the Kuramoto model with bimodal frequency distributions

    OpenAIRE

    Pazó, Diego; Montbrió, Ernest

    2009-01-01

    We investigate the transition to synchronization in the Kuramoto model with bimodal distributions of the natural frequencies. Previous studies have concluded that the model exhibits a hysteretic phase transition if the bimodal distribution is close to a unimodal one, due to the shallowness the central dip. Here we show that proximity to the unimodal-bimodal border does not necessarily imply hysteresis when the width, but not the depth, of the central dip tends to zero. We draw this conclusion...

  11. Nonexistence of cross-term free time-frequency distribution with concentration of Wigner-Ville distribution

    Institute of Scientific and Technical Information of China (English)

    邹红星; 卢旭光; 戴琼海; 李衍达

    2002-01-01

    Wigner-Ville distribution (WVD) is recognized as being a powerful tool and a nucleus in time-frequency representation (TFR) which gives an excellent time-frequency concentration, and more importantly, has many desirable properties. A major shortcoming of WVD is the inherent cross-term (CT) interference. Although solutions to this problem from the bulk of contributions to the literature concerning TFR are currently available, none has been able to completely eliminate the CT's in WVD. It is therefore a common belief that if there exists an auxiliary time-frequency distribution (TFD) which has the same auto-terms (AT's) as that in WVD, but has CT's with the opposite sign, then, by adding the auxiliary TFD to WVD, an ideal TFD, which preserves the concentration of WVD while annihilating the CT's, is readily obtained. However, we prove that the auxiliary TFD does not exist. Moreover, it is found that in general, CT free joint distributions with their concentrations close to that of WVD do not exist either.

  12. Frequency of three Hex A mutant alleles among Jewish and non-Jewish carriers identified in a Tay-Sachs screening program.

    OpenAIRE

    Paw, B H; Tieu, P T; Kaback, M M; Lim, J; Neufeld, E F

    1990-01-01

    Mutations in the HEX A gene, encoding the alpha-subunit of beta-hexosaminidase A (Hex A), are the cause of Tay-Sachs disease as well as of juvenile, chronic, and adult GM2 gangliosidoses. We have examined the distribution of three mutations--a 4-nucleotide insertion in exon 11, a G----C transversion at a 5' splice site in intron 12, and a 269Gly----Ser amino acid substitution in exon 7--among individuals enzymatically diagnosed as carriers of Hex A deficiency. Mutation analysis included polym...

  13. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: A cohort allelic sums test (CAST)

    International Nuclear Information System (INIS)

    A method is described to discover if a gene carries one or more allelic mutations that confer risk for any specified common disease. The method does not depend upon genetic linkage of risk-conferring mutations to high frequency genetic markers such as single nucleotide polymorphisms. Instead, the sums of allelic mutation frequencies in case and control cohorts are determined and a statistical test is applied to discover if the difference in these sums is greater than would be expected by chance. A statistical model is presented that defines the ability of such tests to detect significant gene-disease relationships as a function of case and control cohort sizes and key confounding variables: zygosity and genicity, environmental risk factors, errors in diagnosis, limits to mutant detection, linkage of neutral and risk-conferring mutations, ethnic diversity in the general population and the expectation that among all exonic mutants in the human genome greater than 90% will be neutral with regard to any effect on disease risk. Means to test the null hypothesis for, and determine the statistical power of, each test are provided. For this 'cohort allelic sums test' or 'CAST', the statistical model and test are provided as an Excel (TM) program, CASTAT (C) at http://epidemiology.mit.edu. Based on genetics, technology and statistics, a strategy of enumerating the mutant alleles carried in the exons and splice sites of the estimated ∼25,000 human genes in case cohort samples of 10,000 persons for each of 100 common diseases is proposed and evaluated: A wide range of possible conditions of multi-allelic or mono-allelic and monogenic, multigenic or polygenic (including epistatic) risk are found to be detectable using the statistical criteria of 1 or 10 ''false positive'' gene associations per 25,000 gene-disease pair-wise trials and a statistical power of >0.8. Using estimates of the distribution of both neutral and gene-inactivating nondeleterious mutations in humans and

  14. Short alleles revealed by PCR demonstrate no heterozygote deficiency at minisatellite loci D1S7, D7S21, and D12S11

    Energy Technology Data Exchange (ETDEWEB)

    Alonso, S.; Castro, A.; Fernandez-Fernandez, I.; Pancorbo, M.M. de [Universidad del Pais Vasco, Vizcaya (Spain)

    1997-02-01

    Short VNTR alleles that go undetected after conventional Southern blot hybridization may constitute an alternative explanation for the heterozygosity deficiency observed at some minisatellite loci. To examine this hypothesis, we have employed a screening procedure based on PCR amplification of those individuals classified as homozygotes in our databases for the loci D1S7, D7S21, and D12S11. The results obtained indicate that the frequency of these short alleles is related to the heterozygosity deficiency observed. For the most polymorphic locus, D1S7, {approximately}60% of those individuals previously classified as homozygotes were in fact heterozygotes for a short allele. After the inclusion of these new alleles, the agreement between observed and expected heterozygosity, along with other statistical tests employed, provide additional evidence for lack of population substructuring. Comparisons of allele frequency distributions reveal greater differences between racial groups than between closely related populations. 45 refs., 3 figs., 6 tabs.

  15. ESTIMATION OF CARRIER FREQUENCY OFFSETS FOR MIMO SYSTEMS WITH DISTRIBUTED TRANSMIT ANTENNAS

    Institute of Scientific and Technical Information of China (English)

    Deng Kai; Tang Youxi; Lei Xia; Li Shaoqian

    2007-01-01

    The problem of estimating the carrier frequency offsets in Multiple-Input Multiple-Output (MIMO) systems with distributed transmit antennas is addressed. It is supposed that the transmit antennas are distributed while the receive antennas are still centralized, and the general case where both the time delays and the frequency offsets are possibly different for each transmit antenna is considered. The channel is supposed to be frequency flat, and the macroscopic fading is also taken into consideration. A carrier frequency offset estimator based on Maximum Likelihood (ML) is proposed,which can separately estimate the frequency offset for each transmit antenna and exploit the spatial diversity. The Cramer-Rao Bound (CRB) for synchronous MIMO (i.e., the time delays for each transmit antenna are all equal) is also derived. Simulation results are given to illustrate the performance of the estimator and compare it with the CRB. It is shown that the estimator can provide satisfactory frequency offset estimates and its performance is close to the CRB for the Signal-to-Noise Ratio (SNR) below 20dB.

  16. Topology Optimization of Distributed Mass Dampers for Low-frequency Vibration Suppression

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard; Lazarov, Boyan Stefanov

    2007-01-01

    In this paper the method of topology optimization is used to find optimized parameter distributions for a multiple mass damper system with the purpose of minimizing the low-frequency steady-state response of a carrier structure. An effective density model that describes the steady-state effect...

  17. Dairy cow defecation and urination frequency and spatial distribution in relation to time-limited grazing

    NARCIS (Netherlands)

    Oudshoorn, F.W.; Kristensen, T.; Sharak Nadimi, I.

    2008-01-01

    The objective of this paper was to investigate the effect of limited grazing time on urination and defecation frequency, spatial distribution of excrement in the paddock, and the resulting nitrogen balance at animal and field level. During a 6-week period in early summer, 60 Holstein Frisian dairy c

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

    Energy Technology Data Exchange (ETDEWEB)

    Slatkin, M.; Rannala, B. [Univ of California, Berkeley, CA (United States)

    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.

  19. Altered Crossover Distribution and Frequency in Spermatocytes of Infertile Men with Azoospermia.

    Science.gov (United States)

    Ren, He; Ferguson, Kyle; Kirkpatrick, Gordon; Vinning, Tanya; Chow, Victor; Ma, Sai

    2016-01-01

    During meiosis, homologous chromosomes pair to facilitate the exchange of DNA at crossover sites along the chromosomes. The frequency and distribution of crossover formation are tightly regulated to ensure the proper progression of meiosis. Using immunofluorescence techniques, our group and others have studied the meiotic proteins in spermatocytes of infertile men, showing that this population displays a reduced frequency of crossovers compared to fertile men. An insufficient number of crossovers is thought to promote chromosome missegregation, in which case the faulty cell may face meiotic arrest or contribute to the production of aneuploid sperm. Increasing evidence in model organisms has suggested that the distribution of crossovers may also be important for proper chromosome segregation. In normal males, crossovers are shown to be rare near centromeres and telomeres, while frequent in subtelomeric regions. Our study aims to characterize the crossover distribution in infertile men with non-obstructive (NOA) and obstructive azoospermia (OA) along chromosomes 13, 18 and 21. Eight of the 16 NOA men and five of the 21 OA men in our study displayed reduced crossover frequency compared to control fertile men. Seven NOA men and nine OA men showed altered crossover distributions on at least one of the chromosome arms studied compared to controls. We found that although both NOA and OA men displayed altered crossover distributions, NOA men may be at a higher risk of suffering both altered crossover frequencies and distributions compared to OA men. Our data also suggests that infertile men display an increase in crossover formation in regions where they are normally inhibited, specifically near centromeres and telomeres. Finally, we demonstrated a decrease in crossovers near subtelomeres, as well as increased average crossover distance to telomeres in infertile men. As telomere-guided mechanisms are speculated to play a role in crossover formation in subtelomeres, future

  20. Frequency-coded quantum key distribution using amplitude-phase modulation

    Science.gov (United States)

    Morozov, Oleg G.; Gabdulkhakov, Il'daris M.; Morozov, Gennady A.; Zagrieva, Aida R.; Sarvarova, Lutsia M.

    2016-03-01

    Design principals of universal microwave photonics system for quantum key distribution with frequency coding are concerned. Its concept is based on the possibility of creating the multi-functional units to implement the most commonly used technologies of frequency coding: amplitude, phase and combined amplitude-phase modulation and re-modulation of optical carrier. The characteristics of advanced systems based on classical approaches and prospects of their development using a combination of amplitude modulation and phase commutation are discussed. These are the valuations how to build advanced systems with frequency coding quantum key distribution, including at their symmetric and asymmetric constructions, using of the mechanisms of the photon polarization states passive detection, based on the filters for wavelength division multiplexing of modulated optical carrier side components.

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

    Science.gov (United States)

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

    1993-05-01

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

  2. Algorithms for Blind Components Separation and Extraction from the Time-Frequency Distribution of Their Mixture

    Directory of Open Access Journals (Sweden)

    B. Barkat

    2004-10-01

    Full Text Available We propose novel algorithms to select and extract separately all the components, using the time-frequency distribution (TFD, of a given multicomponent frequency-modulated (FM signal. These algorithms do not use any a priori information about the various components. However, their performances highly depend on the cross-terms suppression ability and high time-frequency resolution of the considered TFD. To illustrate the usefulness of the proposed algorithms, we applied them for the estimation of the instantaneous frequency coefficients of a multicomponent signal and the results are compared with those of the higher-order ambiguity function (HAF algorithm. Monte Carlo simulation results show the superiority of the proposed algorithms over the HAF.

  3. Radiative equilibrium in Monte Carlo radiative transfer using frequency distribution adjustment

    CERN Document Server

    Baes, M; Davies, J I; Whitworth, A P; Sabatini, S; Roberts, S; Linder, S M; Evans, R; Baes, Maarten; Stamatellos, Dimitris; Davies, Jonathan I.; Whitworth, Anthony P.; Sabatini, Sabina; Roberts, Sarah; Linder, Suzanne M.; Evans, Rhodri

    2005-01-01

    The Monte Carlo method is a powerful tool for performing radiative equilibrium calculations, even in complex geometries. The main drawback of the standard Monte Carlo radiative equilibrium methods is that they require iteration, which makes them numerically very demanding. Bjorkman & Wood recently proposed a frequency distribution adjustment scheme, which allows radiative equilibrium Monte Carlo calculations to be performed without iteration, by choosing the frequency of each re-emitted photon such that it corrects for the incorrect spectrum of the previously re-emitted photons. Although the method appears to yield correct results, we argue that its theoretical basis is not completely transparent, and that it is not completely clear whether this technique is an exact rigorous method, or whether it is just a good and convenient approximation. We critically study the general problem of how an already sampled distribution can be adjusted to a new distribution by adding data points sampled from an adjustment ...

  4. Orthogonal frequency division multiplexed quantum key distribution in the presence of Raman noise

    Science.gov (United States)

    Bahrani, Sima; Razavi, Mohsen; Salehi, Jawad A.

    2016-04-01

    In this paper, we investigate the performance of orthogonal frequency division multiplexed quantum key distribution (OFDM-QKD) in an integrated quantum-classical wavelength-division-multiplexing system. The presence of an intense classical signal alongside the quantum one generates Raman background noise. Noise reduction techniques should, then, be carried out at the receiver to suppress this crosstalk noise. In this work, we show that OFDM-QKD enables efficient filtering, in time and frequency domains, making it an attractive solution for the high-rate links at the core of quantum-classical networks.

  5. High-Frequency Waves in a Random Distribution of Metallic Nanoparticles in an External Magnetic Field

    Science.gov (United States)

    Moradi, Afshin

    2016-09-01

    Propagation of magnetoplasma waves at an angle to a static magnetic field is studied for a random distribution of spherical metallic nanoparticles. A general analytical expression for dispersion relation of the system is derived and useful expressions are obtained in the limiting cases. It is found that the interaction between longitudinal and transverse modes leads to coupled modes in the vicinity of the frequency √ {f + ξ } {ω _p}, where ξ is the ratio of the volume occupied by all the nanoparticles to the entire volume, ωp the plasma frequency of electrons inside a nanoparticle, and f a geometrical factor of order unity (1/3 for spherical nanoparticles).

  6. Few-mode fiber based distributed curvature sensor through quasi-single-mode Brillouin frequency shift.

    Science.gov (United States)

    Wu, Hao; Wang, Ruoxu; Liu, Deming; Fu, Songnian; Zhao, Can; Wei, Huifeng; Tong, Weijun; Shum, Perry Ping; Tang, Ming

    2016-04-01

    We proposed and demonstrated a few-mode fiber (FMF) based optical-fiber sensor for distributed curvature measurement through quasi-single-mode Brillouin frequency shift (BFS). By central-alignment splicing FMF and single-mode fiber (SMF) with a fusion taper, a SMF-components-compatible distributed curvature sensor based on FMF is realized using the conventional Brillouin optical time-domain analysis system. The distributed BFS change induced by bending in FMF has been theoretically and experimentally investigated. The precise BFS response to the curvature along the fiber link has been calibrated. A proof-of-concept experiment is implemented to validate its effectiveness in distributed curvature measurement. PMID:27192275

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

    Science.gov (United States)

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

    1985-01-01

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

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

    International Nuclear Information System (INIS)

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

  9. 976 nm single-frequency distributed Bragg reflector fiber laser.

    Science.gov (United States)

    Zhu, Xiushan; Shi, Wei; Zong, Jie; Nguyen, Dan; Norwood, Robert A; Chavez-Pirson, Arturo; Peyghambarian, N

    2012-10-15

    A single-frequency distributed Bragg reflector (DBR) fiber laser at 976 nm was developed with a 2 cm long highly ytterbium-doped phosphate fiber and a pair of silica fiber Bragg gratings. More than 100 mW of linearly polarized output was achieved from the all-fiber DBR laser with a linewidth less than 3 kHz. The outstanding features of this single-frequency laser also include ultralow relative intensity noise and high wavelength stability. This fiber laser is an excellent seeder for high-power 976 nm narrow-linewidth laser amplifiers that can be used for efficient coherent blue-light generation through frequency doubling. PMID:23073399

  10. Mode locking at terahertz frequencies using a distributed Bragg reflector laser with a sampled grating.

    Science.gov (United States)

    Hou, Lianping; Haji, Mohsin; Marsh, John H

    2013-04-01

    We present a highly reproducible method of producing terahertz (THz) optical pulses using a class of mode-locked AlGaInAs/InP laser operating in the 1.55 μm wavelength range. The device uses a sample grating distributed Bragg reflector to provide strong frequency selectivity at the mode-locked frequency while the distributed reflectors relax the fabrication tolerances and ensure the cavity can self adjust to being an integral number of mode-locked periods in length. The measured devices provide nearly transform-limited pulse trains at 640 GHz or 1.28 THz with a high degree of controllability and operate with consistent performance over a wide range of drive conditions. Being low cost and compact sources of THz radiation, these lasers will open up many applications, including systems for high-speed optical communication and THz imaging. PMID:23546261

  11. The Distribution and Frequency of the Terms "Pride" and "Prejudice" in Jane Austen's Pride and Prejudice

    Directory of Open Access Journals (Sweden)

    Tanja Dromnes

    2009-03-01

    Full Text Available In this article we examine the title terms of Jane Austen's Pride and Prejudice (1813 with particular attention to their distribution and frequency in the text. Our method is to connect the statistical material gathered on frequency and distribution to a narratological analysis of the terms, with special emphasis on whether they occur within the focalization of the external narrator, or that of character-focalizers. In order to approach this task, we have availed ourselves of the narratological theories of Mieke Bal. We conclude that there is a differentiation among types of focalization in the novel that enhances the thematic structure of match-making. Although Jane Austen wrote and published her major works two centuries ago, they continue to fascinate literary scholars and general readers alike.

  12. The Size-Frequency Distribution of the Zodiacal Cloud Evidence from the Solar System Dust Bands

    CERN Document Server

    Grogan, K; Durda, D D

    2000-01-01

    Recent observations of the size-frequency distribution of zodiacal cloud particles obtained from the cratering record on the LDEF satellite (Love and Brownlee 1993) reveal a significant large particle population (100 micron diameter or greater) near 1 AU. Our previous modeling of the Solar System dust bands (Grogan et al 1997), features of the zodiacal cloud associated with the comminution of Hirayama family asteroids, has been limited by the fact that only small particles (25 micron diameter or smaller) have been considered. This was due to the prohibitively large amount of computing power required to numerically analyze the dynamics of larger particles. The recent availability of cheap, fast processors has finally made this work possible. Models of the dust bands are created, built from individual dust particle orbits, taking into account a size-frequency distribution of the material and the dynamical history of the constituent particles. These models are able to match both the shapes and amplitudes of the ...

  13. Time-Frequency Distribution of Music based on Sparse Wavelet Packet Representations

    DEFF Research Database (Denmark)

    Endelt, Line Ørtoft

    We introduce a new method for generating time-frequency distributions, which is particularly useful for the analysis of music signals. The method presented here is based on $\\ell1$ sparse representations of music signals in a redundant wavelet packet dictionary. The representations are found usin......, by masking the energy from less structured music instruments. We present four examples for visualizing structured content, including vocal and single instrument....

  14. Dynamics of fully coupled rotators with unimodal and bimodal frequency distribution

    OpenAIRE

    Olmi, Simona; Torcini, Alessandro

    2015-01-01

    We analyze the synchronization transition of a globally coupled network of N phase oscillators with inertia (rotators) whose natural frequencies are unimodally or bimodally distributed. In the unimodal case, the system exhibits a discontinuous hysteretic transition from an incoherent to a partially synchronized (PS) state. For sufficiently large inertia, the system reveals the coexistence of a PS state and of a standing wave (SW) solution. In the bimodal case, the hysteretic synchronization t...

  15. On the distribution of high-frequency stock market traded volume: a dynamical scenario

    OpenAIRE

    Silvio M. Duarte Queiros

    2005-01-01

    This manuscript reports a stochastic dynamical scenario whose associated stationary probability density function is exactly a previously proposed one to adjust high-frequency traded volume distributions. This dynamical conjecture, physically connected to superstatiscs, which is intimately related with the current nonextensive statistical mechanics framework, is based on the idea of local fluctuations in the mean traded volume associated to financial markets agents herding behaviour. The corro...

  16. Inferential procedures in stable distributions for class frequency data on incomes

    OpenAIRE

    Dijk, Herman; Kloek, Teun

    1980-01-01

    textabstractThis paper discusses inferential procedures for the family of stable distributions, when the data are tabulated in the form of interval frequencies. The estimation criteria used are minimum chi-square and multinomial maximum likelihood. In evaluating the theoretical probabilities corresponding to the intervals, use is made of the inversion theorem for characteristic functions. Chi-square tail probabilities for independent samples are pooled by means of theKolmogorov statistic. As ...

  17. Chirplet Wigner-Ville distribution for time-frequency representation and its application

    Science.gov (United States)

    Chen, G.; Chen, J.; Dong, G. M.

    2013-12-01

    This paper presents a Chirplet Wigner-Ville Distribution (CWVD) that is free for cross-term that usually occurs in Wigner-Ville distribution (WVD). By transforming the signal with frequency rotating operators, several mono-frequency signals without intermittent are obtained, WVD is applied to the rotated signals that is cross-term free, then some frequency shift operators corresponding to the rotating operator are utilized to relocate the signal‧s instantaneous frequencies (IFs). The operators‧ parameters come from the estimation of the IFs which are approached with a polynomial functions or spline functions. What is more, by analysis of error, the main factors for the performance of the novel method have been discovered and an effective signal extending method based on the IFs estimation has been developed to improve the energy concentration of WVD. The excellent performance of the novel method was manifested by applying it to estimate the IFs of some numerical signals and the echolocation signal emitted by the Large Brown Bat.

  18. 春化、光周期和矮秆基因在不同国家小麦品种中的分布及其效应%Distribution of Allelic Variation for Vernalization, Photoperiod, and Dwarfing Genes and Their Effects on Growth Period and Plant Height among Cultivars from Major Wheat Producing Countries

    Institute of Scientific and Technical Information of China (English)

    杨芳萍; 李式昭; 何中虎; 夏先春; 张勇; 张晓科; 刘建军; 唐建卫; 杨学明; 张俊儒; 刘茜

    2012-01-01

    To efficiently use exotic resources in Chinese wheat breeding programs, we investigated the heading date, maturity date, and plant height of 100 representative cultivars collected from 14 countries at eight locations in China, and detected the allelic variations of vernalization loci VRN-1 and VRN-B3, photoperiod gene Ppd-Dla, and dwarfing genes Rht-Bib and Rht-Dib by means of molecular markers. The frequencies of vernalization loci were 8.0% for Vrn-Ala, 21.0% for Vrn-BI, 21.0% for Vrn-DI and 64.0% for vrn-AI+vm-BI+ vrn-Dl, except for the absence of dominant allele Vrn-B3 in all tested materials. Dominant vernalization alleles Vrn-Ala, Vm-BI, and Vm-DI were mainly observed in cultivars from Chinese spring wheat region, Italy, India, Canada, Mexico, and Australia; whereas, cultivars carrying all recessive alleles at the four vernalization loci and vm-AI+ vrn-DI+Vm-BI+vm-B3 genotype were mostly found in cultivars from Chinese winter wheat region, United States (US) winter wheat region, Russia winter wheat region, United Kingdom (UK), France, Germany, Romania, Turkey, and Hungary. All cultivars headed normally when sown in autumn. Cultivars with dominant alleles showed earlier heading date than those with recessive alleles, and genotypes with two or more dominant alleles showed additive effects. Some European and US cultivars with recessive genes at the four vernalization loci could not mature in Yangling and Chengdu. Under spring-sown condition, the cultivars with dominant vernalization alleles showed high heading frequency; in contrast, most cultivars with recessive alleles failed to head. Gene Ppd-Dla was distributed mainly in cultivars from China, France, Romania, Russia, Mexico, Australia, and India with the total frequency of 68%. Most cultivars with Ppd-Dlb were from high latitude regions, such as UK, Germany, Hungary, and Canada. The Ppd-Dla genotypes appeared to head earlier than the Ppd-Dlb genotypes. Daylight condition had no effect on maturity of most Ppd

  19. Frequency and distribution analysis of chromosomal translocations induced by x-ray in human lymphocytes

    International Nuclear Information System (INIS)

    The characteristic of ionizing radiation suggests that induced chromosomal damage in the form of translocations would appear to be randomly distributed. However, the outcome of tests performed in vitro and in vivo (irradiated individuals) are contradictories. The most translocation-related chromosomes, as far as some studies reveal on one hand, appear to be less involved in accordance with others. These data, together with those related to molecular mechanisms involved in translocations production suggest that in G0 -irradiated cells, the frequency and distribution of this kind of chromosomal rearrangement, does not take place at random. They seem to be affected by in-nucleus chromosome distribution, by each chromosome's DNA length and functional features, by the efficiency of DNA repair mechanisms, and by inter individual differences. The objective of this study was to establish the frequency pattern of each human chromosome involved in radio-induced translocations, as well as to analyze the importance the chromosome length, the activity of DNA polymerase- dependant repair mechanisms, and inter individual differences within the scope of such distribution. To achieve the goals, peripheral blood lymphocytes from healthy donors were irradiated in presence and absence of 2'-3' dideoxithimidine (ddThd), a Β - DNA polymerase inhibitor, which takes part in the base repair mechanism (B E R). The results showed that: The presence of ddThd during the irradiation increase the basal frequency of radioinduced translocations in 60 %. This result suggests that ddThd repair synthesis inhibition can be in itself a valid methodology for radiation-induced bases damage assessment, damage which if not BER-repaired may result in translocation-leading double strand breaks. A statistically significant correlation between translocation frequency and chromosome length, in terms of percentage of genome, has been noticed both in (basal) irradiation and in irradiation with ddThd inhibitor

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

    Directory of Open Access Journals (Sweden)

    Carol A Soderlund

    Full Text Available 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

  1. Proposal of a function for modelling the hourly frequency distributions of photosynthetically active radiation

    Science.gov (United States)

    Tovar-Pescador, J.; Pozo-Vazquez, D.; Batlles, J.; López, G.; Muñoz-Vicente, D.

    2004-10-01

    Solar irradiance is a key factor in the physiological processes of living beings. To obtain simple correlations for the estimation of the performance of biological systems, which transform the solar energy by photosynthesis, and to generate synthetic data, it is necessary to know the frequency distributions of photosynthetically active radiation (PAR). In this work we carried out an analysis of the properties of hourly values of PAR data, using 9 years of data collected in southern Spain. In particularly, its dependence on the optical mass, for all type of skies including cloudy skies, is studied. Results shows that, for a given value of the optical mass, the PAR density distributions are not symmetrical and have a certain degree of bimodality. The increment in the optical mass value has two effects on the PAR distributions, the first one is a shift toward lower values of the maximum and the second one is a decrease in the range of PAR values. Finally, a model of the frequency distribution of PAR values, based on a new kind of functions related to the Boltzmann’s statistic, is proposed. The parameters of these functions depend just on the optical mass. Results show a very good agreement between the data and the model proposed.

  2. 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.

    Science.gov (United States)

    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

  3. Coastal waters monitoring data: frequency distributions of the principal water quality variables

    Directory of Open Access Journals (Sweden)

    Bianca DI LORENZO

    2006-08-01

    Full Text Available Examining the results of the Italian national programme of marine coastal monitoring, the old problem has arisen about the choice of the most appropriate procedures and methods to validate data and screen preliminary data. Therefore, statistical distributions of water quality parameters have been taken into consideration, in order to assign appropriate frequency distributions to all the routinely measured variables. Each sample distribution has been analysed and defined by a probability density function (p.d.f., by means of a powerful method of data analysis (Johnson 1949 that allows for the computation of statistical parameters of a wide variety of non-normal distributions. The resulting Johnson distributions are then classified depending on four fundamental categories of frequency distributions: normal, log-normal, bounded and unbounded. Theoretical aspects of the method are explained and discussed in an adequate way, so as to allow for practical applications. The shape and nature of these curves require further consideration, in order to understand the behaviour of water quality variables and to make comparison among different coastal zones. To this end, two coastal systems were considered in this work: the Emilia-Romagna coastal area of the NW Adriatic Sea and the Tuscany littoral of the Northern Tyrrhenian Sea. There are notable advantages to the adopted approach. First it offers the possibility to overcome severe constraints requested by the normality assumption, and avoids the troublesome search for the most appropriate transformation function (i.e. for ensuring normality. Second, it avoids searching for other kinds of theoretical distributions that are appropriate for the data. In our approach, the density functions are opportunely integrated, in such a way that, for whatever value assumed by a given variable, the corresponding expected percentage point value under the respective frequency curve, can be calculated, and vice versa. We

  4. Allelic variation in a willow warbler genomic region is associated with climate clines.

    Directory of Open Access Journals (Sweden)

    Keith W Larson

    Full Text Available Local adaptation is an important process contributing to population differentiation which can occur in continuous or isolated populations connected by various amounts of gene flow. The willow warbler (Phylloscopus trochilus is one of the most common songbirds in Fennoscandia. It has a continuous breeding distribution where it is found in all forested habitats from sea level to the tree line and therefore constitutes an ideal species for the study of locally adapted genes associated with environmental gradients. Previous studies in this species identified a genetic marker (AFLP-WW1 that showed a steep north-south cline in central Sweden with one allele associated with coastal lowland habitats and the other with mountainous habitats. It was further demonstrated that this marker is embedded in a highly differentiated chromosome region that spans several megabases. In the present study, we sampled 2,355 individuals at 128 sites across all of Fennoscandia to study the geographic and climatic variables associated with the allele frequency distributions of WW1. Our results demonstrate that 1 allele frequency patterns significantly differ between mountain and lowland populations, 2 these allele differences coincide with extreme temperature conditions and the short growing season in the mountains, and milder conditions in coastal areas, and 3 the northern-allele or "altitude variant" of WW1 occurs in willow warblers that occupy mountainous habitat regardless of subspecies. Finally these results suggest that climate may exert selection on the genomic region associated with these alleles and would allow us to develop testable predictions for the distribution of the genetic marker based on climate change scenarios.

  5. A Dynamic Assignment of Extrinsic Information Distribution by a Frequency Means for Iterative Turbo Decoder

    Institute of Scientific and Technical Information of China (English)

    YANGFengfan

    2003-01-01

    In this paper, a new strategy for iterative turbo decoding is proposed, where a Generalized Gaussian distribution (GGD) is applied to model the statistical distributions of the extrinsic information generated by the component decoders. An Euclidean distance criterion is also introduced to choose a most likely candidate of the extrinsic information distribution before the each constituent decoding by a novel frequency means. The simulation results show that performance of an iterative decoder with this new technique surpasses the conventional Gaussian solution for the extrinsic information under the same channel conditions. Meanwhile, the evolution process of the extrinsic information density function can be tracked from iteration to iteration in the sense of the proposed criterion.

  6. Transverse Inhomogeneous Carrier-Envelope Phase Distribution of Idler Generated through Difference-Frequency-Generation

    International Nuclear Information System (INIS)

    The transverse inhomogeneous carrier-envelope phase (CEP) distribution of idler generated through difference-frequency-generation (DFG) in quadratic nonlinear crystals is theoretically studied. In practical CEP stabilized DFG setups, the pump and the signal are usually Gaussian beams with non-uniform intensity distribution. Since the idler CEP is dependent on gain, this non-uniform intensity distribution leads to inhomogeneous gain across the aperture of the idler beam, resulting in a varying transverse idler CEP. Simulation results show that in practical settings, in the high-gain regime, transverse inhomogeneous CEP can be much smaller compared with π/2. However, when gain on the propagation axis reaches saturation, CEP difference can well exceed π/2. (fundamental areas of phenomenology (including applications))

  7. Distributed Secondary Voltage and Frequency Control for Islanded Microgrids with Uncertain Communication Links

    DEFF Research Database (Denmark)

    Lu, Xiaoqing; Yu, Xinghuo; Lai, Jingang;

    2016-01-01

    This paper presents a robust distributed secondary control (DSC) scheme for inverter-based microgrids (MGs) in a distribution sparse network with uncertain communication links. By using the iterative learning mechanics, two discrete-time DSC controllers are designed, which enable all distributed...... energy resources (DERs) in a MG to achieve the voltage/frequency restoration and active power sharing accuracy, respectively. In special, the secondary control inputs are merely updated at the end of each round of iteration, and thus each DER only needs to share information with its neighbors...... intermittently in a low-bandwidth communication manner. This way, the communication costs are greatly reduced, and some sufficient conditions on the system stability and robustness to the uncertainties are also derived by using the tools of Lyapunov stability theory, algebraic graph theory, and matrix inequality...

  8. Allelic diversity and haplotype frequencies of HLA-A,B,DRB1 loci in Tibet population of China%中国西藏藏族人群HLA-A/B/DRB1座位基因遗传多态性和单体型分析

    Institute of Scientific and Technical Information of China (English)

    刘孟黎; 齐珺; 沈春梅; 刘晟; 王小芳

    2011-01-01

    Objective To investigate the human leukocyte antigen(HLA)-A, B, DRB1 alleles and haplotype frequencies and the distribution characteristics in Tibet population of China. Methods HLA genotype data of 343 unrelated Tibetans were identified by PCR-SSO Luminex. HLA-A, B, DRB1 allele and haplotype frequencies were calculated by computer software named Arleguin which was based on Expectation-Maximization(EM) algorithms. Results 13,24 and 13 specificities of HLA alleles were identified on the HLA-A, B, and DRB1 loci, respectively. The most frequent alleles were A *02 (30.47%) ,A * 24 (29. 74% ), and A * 11 ( 12. 83% ) at the HLA-A locus, B* 51 ( 19. 68% ), B* 15 (62) ( 13. 41% ), and B* 40(61) (12. 54%) at the HLA-B locus and DRB1 *04(24.49% ) ,DRB1*08(17.49%) ,and DRB1 * 11(14.87% ) at HLA-DRB1 locus. There were significant differences in the most frequent allelic distribution of HLA-A, B, DRB1 between Tibetan and Ningxia Hui, Mongol and Han ethnics ( P = 0. 0000). A total of 247 kinds of HLA-A-B-DR haplotypes ( with a theoretical frequency of 32. 89% ), 113 kinds of HLA-A-B haplotypes,82 kinds of A-DR and 126 kinds for B-DR haplotypes were obtained,with a theoretical frequency of 60. 43% ,72. 57% and 64. 62%, respectively. HLA-A11-B15 (HF = 0. 15%,RLD = 100% ) ,A31-B75 ( HF = 0. 15%, RLD = 100% ) ,A3-B63 ( HF = 0. 15%, RLD = 100% ), B18-DR4 ( HF =0. 29%, RLD = 100% ), B15-DR4 ( HF = 0. 15%, RLD = 100% ) and B75-DR15 ( HF = 0. 15%, RLD = 100% ) showed significant positive linkage disequilibrium. Conclusion HLA-A, B, and DRB1 gene and haplotype frequencies and linkage disequilibrium data of Tibeten ethnic population, different from Ningxia Hui, Mongol and Han ethnics, present their own characteristics.%目的 分析西藏藏族HLA-A/B/DRB1座位基因遗传多态性和单体型特征.方法 采用PCR-SSO Luminex流式磁珠分型方法对343名西藏藏族无关个体作HLA-A/B/DRBI座位基因分型.应用直接计数法

  9. Evidence of increasing L1014F kdr mutation frequency in Anopheles gambiae s.l. pyrethroid resistant following a nationwide distribution of LLINs by the Beninese National Malaria Control Programme

    Institute of Scientific and Technical Information of China (English)

    Nazaire Azoun; Rock Akpon; Martin Akogbto

    2014-01-01

    Objective:To determine the susceptibility status to pyrethroid in Anopheles gambiae s.l. (An. gambiae), the distribution of kdr“Leu-Phe”mutation in malaria vectors in Benin and to compare the current frequency of kdr“Leu-Phe”mutation to the previous frequency after long-lasting insecticide treated nets implementation. Methods: Larvae and pupae of An. gambiae s.l. mosquitoes were collected from the breeding sites in Littoral, Zou, Borgou and Alibori provinces. CDC susceptibility tests were conducted on unfed females mosquitoes aged 2-5 d old. An. gambiae mosquitoes were identified to species using PCR techniques. Molecular assays were also carried out to identify kdr mutations in individual mosquitoes. Results: The results showed that An. gambiae Malanville and Suru-lere populations were resistant to deltamethrin. Regarding An. gambiae Parakou and Bohicon populations, they were resistant to permethrin. PCR revealed 100%of mosquitoes tested were An. gambiae s.s. The L1014F kdr mutation was found in An. gambiae s.s. Malanville and Parakou at various allelic frequencies. The increase of kdr allelic frequency was positively correlated with CDC bioassays data. Conclusions: Pyrethroid resistance is widespread in malaria vector in Benin and kdr mutation is the main resistance mechanism involved. More attention may be paid for the future success of malaria control programmes based on LLINs with pyrethroids in the country.

  10. Blind Separation of Nonstationary Sources Based on Spatial Time-Frequency Distributions

    Directory of Open Access Journals (Sweden)

    Zhang Yimin

    2006-01-01

    Full Text Available Blind source separation (BSS based on spatial time-frequency distributions (STFDs provides improved performance over blind source separation methods based on second-order statistics, when dealing with signals that are localized in the time-frequency (t-f domain. In this paper, we propose the use of STFD matrices for both whitening and recovery of the mixing matrix, which are two stages commonly required in many BSS methods, to provide robust BSS performance to noise. In addition, a simple method is proposed to select the auto- and cross-term regions of time-frequency distribution (TFD. To further improve the BSS performance, t-f grouping techniques are introduced to reduce the number of signals under consideration, and to allow the receiver array to separate more sources than the number of array sensors, provided that the sources have disjoint t-f signatures. With the use of one or more techniques proposed in this paper, improved performance of blind separation of nonstationary signals can be achieved.

  11. Using frequency maps to explore the distribution function of the Milky Way stellar halo

    Directory of Open Access Journals (Sweden)

    Valluri M.

    2012-02-01

    Full Text Available Resolved surveys of the Milky Way's stellar halo can obtain all 6 phase space coordinates of tens of thousands of individual stars, making it possible to compute their 3-dimensional orbits. When frequency mapping is applied to such orbits they also represent the underlying phase space distribution function since the orbits that the are drawn from 3. A frequency maps clearly separates out the major types of orbits that constitute the DF and their relative abundances. The structure of the frequency maps, especially the locations of resonant orbits, reflects the formation history and shape of the dark matter potential and its orientation relative to the disk. The application of frequency analysis to cosmological hydrodynamic simulations of disk galaxies shows that the orbital families occupied by halo stars and dark matter particles are very similar, implying that stellar halo orbits can be used to constrain the DF of the dark matter halo, possibly impacting the interpretation of results from direct dark matter detection experiments. An application of these methods to a sample of ~ 16,000 Milky Way halo and thick disk stars from the SDSS-SEGUE survey yields a frequency map with strong evidence for resonant trapping of halo stars by the Milky Way disk, in a manner predicted by controlled simulations in which the disk grows adiabatically. The application of frequency analysis methods to current and future phase space data for Milky Way halo stars will provide new insights into the formation history of the different components of the Galaxy and the DF of the halo.

  12. ELSTAB-Fiber-Optic Time and Frequency Distribution Technology: A General Characterization and Fundamental Limits.

    Science.gov (United States)

    Krehlik, Przemyslaw; Sliwczynski, Lukasz; Buczek, Lukasz; Kolodziej, Jacek; Lipinski, Marcin

    2016-07-01

    In this paper, we present an overview of the electronically stabilized (thus named ELSTAB) fiber-optic time and frequency (T&F) distribution system based on our idea of using variable electronic delay lines as compensating elements. Various extensions of the basic system, allowing building a long-haul, multiuser network are described. The fundamental limitations of the method arising from fiber chromatic dispersion and system dynamics are discussed. We briefly characterize the main hardware challenge of the system, which is the design of a pair of low-noise, precisely matched delay lines. Finally, we present experimental results with T&F distribution over up to 615 km of fiber, where we demonstrate frequency stability in the range of 1-7 ×10(-17) for 10(5) s averaging and time calibration with accuracy well below 50 ps. Also, practical implementation of the ELSTAB in the Polish T&F distribution network is shown. PMID:26599816

  13. An efficient causative event-based approach for deriving the annual flood frequency distribution

    Science.gov (United States)

    Li, Jing; Thyer, Mark; Lambert, Martin; Kuczera, George; Metcalfe, Andrew

    2014-03-01

    In ungauged catchments or catchments without sufficient streamflow data, derived flood frequency methods are often applied to provide the basis for flood risk assessment. The most commonly used event-based methods, such as design storm and joint probability approaches are able to give fast estimation, but can also lead to prediction bias and uncertainties due to the limitations of inherent assumptions and difficulties in obtaining input information (rainfall and catchment wetness) related to events that cause extreme floods. An alternative method is a long continuous simulation which produces more accurate predictions, but at the cost of massive computational time. In this study a hybrid method was developed to make the best use of both event-based and continuous approaches. The method uses a short continuous simulation to provide inputs for a rainfall-runoff model running in an event-based fashion. The total probability theorem is then combined with the peak over threshold method to estimate annual flood distribution. A synthetic case study demonstrates the efficacy of this procedure compared with existing methods of estimating annual flood distribution. The main advantage of the hybrid method is that it provides estimates of the flood frequency distribution with an accuracy similar to the continuous simulation approach, but with dramatically reduced computation time. This paper presents the method at the proof-of-concept stage of development and future work is required to extend the method to more realistic catchments.

  14. Rock size-frequency distribution analysis at the Chang'E-3 landing site

    Science.gov (United States)

    Di, Kaichang; Xu, Bin; Peng, Man; Yue, Zongyu; Liu, Zhaoqin; Wan, Wenhui; Li, Lichun; Zhou, Jianliang

    2016-01-01

    This paper presents a comprehensive analysis of the rock size-frequency distribution at the Chang'E-3 landing site. Using 84 Navcam stereo images acquired at 7 waypoints by the Yutu rover and an interactive stereo image processing system, a total of 582 rocks larger than 0.05 m in diameter were identified and measured. The statistical results of the size-frequency distribution show that the cumulative fractional area covered by rocks versus their diameter follows a simple exponential function and has a convex-up shape on log-log graphs with the slope increasing with diameter. The cumulative number of rocks versus diameter derived by numerically integrating the cumulative fractional area also shows a good fit with the data. A diameter-height relationship was also determined from height and diameter ratios. The observed rock statistics were also compared with those from other lunar missions, including the Surveyor, Apollo, and Lunokhod missions; results suggest that the rock distribution at the Chang'E-3 landing site is similar to that found by Surveyor III.

  15. Allelic Diversity of MSP1 Gene in Plasmodium falciparum from Rural and Urban Areas of Gabon.

    Science.gov (United States)

    Mawili-Mboumba, Denise Patricia; Mbondoukwe, Noé; Adande, Elvire; Bouyou-Akotet, Marielle Karine

    2015-08-01

    The present study determined and compared the genetic diversity of Plasmodium falciparum strains infecting children living in 2 areas from Gabon with different malaria endemicity. Blood samples were collected from febrile children from 2008 to 2009 in 2 health centres from rural (Oyem) and urban (Owendo) areas. Genetic diversity was determined in P. falciparum isolates by analyzing the merozoite surface protein-1 (msp1) gene polymorphism using nested-PCR. Overall, 168 children with mild falciparum malaria were included. K1, Ro33, and Mad20 alleles were found in 110 (65.5%), 94 (55.9%), and 35 (20.8%) isolates, respectively, without difference according to the site (P>0.05). Allelic families' frequencies were comparable between children less than 5 years old from the 2 sites; while among the older children the proportions of Ro33 and Mad20 alleles were 1.7 to 2.0 fold higher at Oyem. Thirty-three different alleles were detected, 16 (48.5%) were common to both sites, and 10 out of the 17 specific alleles were found at Oyem. Furthermore, multiple infection carriers were frequent at Oyem (57.7% vs 42.2% at Owendo; P=0.04) where the complexity of infection was of 1.88 (±0.95) higher compared to that found at Owendo (1.55±0.75). Extended genetic diversity of P. falciparum strains infecting Gabonese symptomatic children and high multiplicity of infections were observed in rural area. Alleles common to the 2 sites were frequent; the site-specific alleles predominated in the rural area. Such distribution of the alleles should be taken into accounts when designing MSP1 or MSP2 malaria vaccine.

  16. Dynamics of two populations of phase oscillators with different frequency distributions

    CERN Document Server

    Terada, Yu

    2014-01-01

    A large variety of rhythms have been observed in nature. These rhythms can be often regarded to interact with each other, such as electroencephalogram (EEG) in the brain. To investigate the dynamical properties of such systems, in this paper, we consider two populations of phase oscillators with different frequency distributions, particularly under the condition that the average frequency of fast oscillators is almost equal to the integral multiple of that of slow oscillators. What is the most important point is that we have to use the specific type of the coupling function derived from the phase reduction theory. Under some additional assumption, moreover, we can reduce the system consisting of two populations of coupled phase oscillators to a low-dimensional system in the continuum limit. As a result, we find chimera states in which clustering and incoherent states coexist. We also confirm that the behaviors of the derived low-dimensional model fairly agree with that of the original one.

  17. Dynamics of two populations of phase oscillators with different frequency distributions

    Science.gov (United States)

    Terada, Yu; Aoyagi, Toshio

    2016-07-01

    A large variety of rhythms are observed in nature. Rhythms such as electroencephalogram signals in the brain can often be regarded as interacting. In this study, we investigate the dynamical properties of rhythmic systems in two populations of phase oscillators with different frequency distributions. We assume that the average frequency ratio between two populations closely approximates some small integer. Most importantly, we adopt a specific coupling function derived from phase reduction theory. Under some additional assumptions, the system of two populations of coupled phase oscillators reduces to a low-dimensional system in the continuum limit. Consequently, we find chimera states in which clustering and incoherent states coexist. Finally, we confirm consistent behaviors of the derived low-dimensional model and the original model.

  18. Distributed vibration sensing with time-resolved optical frequency-domain reflectometry.

    Science.gov (United States)

    Zhou, Da-Peng; Qin, Zengguang; Li, Wenhai; Chen, Liang; Bao, Xiaoyi

    2012-06-01

    The distributed vibration or dynamic strain information can be obtained using time-resolved optical frequency-domain reflectometry. Time-domain information is resolved by measuring Rayleigh backscatter spectrum in different wavelength ranges which fall in successive time sequence due to the linear wavelength sweep of the tunable laser source with a constant sweeping rate. The local Rayleigh backscatter spectrum shift of the vibrated state with respect to that of the non-vibrated state in time sequence can be used to determine dynamic strain information at a specific position along the fiber length. Standard single-mode fibers can be used as sensing head, while the measurable frequency range of 0-32 Hz with the spatial resolution of 10 cm can be achieved up to the total length of 17 m. PMID:22714342

  19. Single-frequency thulium-doped distributed-feedback fibre laser

    DEFF Research Database (Denmark)

    Agger, Søren; Povlsen, Jørn Hedegaard; Varming, Poul

    2004-01-01

    We have successfully demonstrated a single-frequency distributed-feedback (DFB) thulium-doped silica fiber laser emitting at a wavelength of 1735 nm. The laser cavity is less than 5 cm long and is formed by intracore UV-written Bragg gratings with a phase shift. The laser is pumped at 790 nm from...... a Ti:sapphire laser and has a threshold pump power of 59 mW. The laser has a maximum output power of 1 mW in a singlefrequency, single-polarization radiation mode and is tunable over a few nanometers. To the best of the authors’ knowledge, this is the first report of a single-frequency DFB fiber laser...... that uses thulium as the amplifying medium. The lasing wavelength is the longest demonstrated with DFB fiber lasers and yet is among the shortest obtained for thulium-doped silica fiber lasers....

  20. The frequency distribution of vitamin D Receptor fok I gene polymorphism among Ugandan pulmonary TB patients

    Science.gov (United States)

    Acen, Ester L.; Worodria, William; Mulamba, Peter; Kambugu, Andrew; Erume, Joseph

    2016-01-01

    Background: Mycobacterium tuberculosis (TB) is still a major problem globally and especially in Africa. Vitamin D deficiency has been linked to TB in the past and studies have found vitamin D deficiency to be common among Ugandan TB patients. The functional activity of vitamin D is dependent on the genotype of the vitamin D receptor (VDR) polymorphic genes. Recent findings have indicated that VDR polymorphisms may cause increased resistance or susceptibility to TB. The vitamin D ligand and its receptor play a pivotal role in innate immunity by eliciting antimicrobial activity, which is important in prevention of TB. The fok I vitamin D receptor gene has extensively been examined in TB patients but findings so far have been inconclusive. Objectives: This study sought to investigate the frequency distribution of the VDR fok I gene polymorphisms in pulmonary TB patients and controls. Methods: A pilot case control study of 41 newly diagnosed TB patients and 41 healthy workers was set up. Vitamin D receptor fok I gene was genotyped. Results: The frequency distribution of fok I genotype in Ugandan TB patients was 87.8% homozygous-dominant (FF), 7.3% (Ff) heterozygous and 4.8% (ff) homozygous recessive. For normal healthy subjects the frequencies were (FF) 92.6%, (Ff) 2.4% and (ff) 4.8%. No significant difference was observed in the FF and ff genotypes among TB patients and controls. The Ff heterozygous genotype distribution appeared more in TB patients than in controls. A significant difference was observed in the fok I genotype among gender p value 0.02. No significant difference was observed in ethnicity, p value 0.30. Conclusions: The heterozygous Ff fok I genotype may be associated with TB in the Ugandan population.

  1. Colony size-frequency distribution of pocilloporid juvenile corals along a natural environmental gradient in the Red Sea

    KAUST Repository

    Lozano-Cortes, Diego

    2015-10-29

    Coral colony size-frequency distributions can be used to assess population responses to local environmental conditions and disturbances. In this study, we surveyed juvenile pocilloporids, herbivorous fish densities, and algal cover in the central and southern Saudi Arabian Red Sea. We sampled nine reefs with different disturbance histories along a north–south natural gradient of physicochemical conditions (higher salinity and wider temperature fluctuations in the north, and higher turbidity and productivity in the south). Since coral populations with negatively skewed size-frequency distributions have been associated with unfavorable environmental conditions, we expected to find more negative distributions in the southern Red Sea, where corals are potentially experiencing suboptimal conditions. Although juvenile coral and parrotfish densities differed significantly between the two regions, mean colony size and size-frequency distributions did not. Results suggest that pocilloporid colony size-frequency distribution may not be an accurate indicator of differences in biological or oceanographic conditions in the Red Sea.

  2. Temperature distribution in an ohmic-heated electrical contact at high signal frequencies

    Science.gov (United States)

    Timsit, Roland S.; Luttgen, Andrea

    2016-03-01

    In classical contact theory, the temperature T of contact spots in an electrical interface passing a DC current is determined by the voltage drop V across the contact, i.e., the V-T relation. This paper reports on evaluations of the temperature distribution in a single circular contact spot in a copper-copper contact heated by an AC current. The steady-state maximum temperature was computed numerically for an AC electrical current of fixed amplitude and a frequency ranging from 100 Hz to 100 MHz. The computed temperature was compared with the predictions of the V-T relation.

  3. All-Optical Frequency Modulated High Pressure MEMS Sensor for Remote and Distributed Sensing

    DEFF Research Database (Denmark)

    Reck, Kasper; Thomsen, Erik Vilain; Hansen, Ole

    2011-01-01

    We present the design, fabrication and characterization of a new all-optical frequency modulated pressure sensor. Using the tangential strain in a circular membrane, a waveguide with an integrated nanoscale Bragg grating is strained longitudinally proportional to the applied pressure causing...... a shift in the Bragg wavelength. The simple and robust design combined with the small chip area of 1 × 1.8 mm2 makes the sensor ideally suited for remote and distributed sensing in harsh environments and where miniaturized sensors are required. The sensor is designed for high pressure applications up...

  4. Performance of low-cost commercial fiber-optic transceivers for reference frequency distribution

    Science.gov (United States)

    Dragonette, Richard; Suter, Joseph J.

    1993-01-01

    Precision time and frequency reference signals were effectively disseminated using high-quality intricate fiber-optic distribution systems. The quality of signals distributed by such systems is excellent, but the cost of these systems makes them unavailable to many potential users. A study of signal quality maintained using inexpensive commercial transmitter/receiver pairs is undertaken. Seven different transmitter/receiver pairs obtained from four different manufacturers were thoroughly tested using a 5 MHz sinusoid derived from a precision, temperature controlled, crystal-controlled oscillator. The electrical signal output from each fiber-optic receiver was tested for spectral purity, single-sideband phase noise, and AM noise, and the results are tabulated and discussed without identification of the manufacturer or the equipment model number.

  5. Universal spectrum for DNA base C+G frequency distribution in Human chromosomes 1 to 24

    CERN Document Server

    Selvam, A M

    2007-01-01

    Power spectra of human DNA base C+G frequency distribution in all available contiguous sections exhibit the universal inverse power law form of the statistical normal distribution for the 24 chromosomes. Inverse power law form for power spectra of space-time fluctuations is generic to dynamical systems in nature and indicate long-range space-time correlations. A recently developed general systems theory predicts the observed non-local connections as intrinsic to quantumlike chaos governing space-time fluctuations of dynamical systems. The model predicts the following. (1) The quasiperiodic Penrose tiling pattern for the nested coiled structure of the DNA molecule in the chromosome resulting in maximum packing efficiency. (2) The DNA molecule functions as a unified whole fuzzy logic network with ordered two-way signal transmission between the coding and non-coding regions. Recent studies indicate influence of non-coding regions on functions of coding regions in the DNA molecule.

  6. Low Frequency Oscillations of the Heat Distribution in the Global Upper Ocean Layers

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The heat distributions in the upper layers of the ocean have been studied and some important low frequency oscillations (LFOs) are already found and quantified by using various characteristic factors. In this paper, the 'heat center' of a sea area is defined with a simple method. Then the temperature data set of the upper layer of the global ocean (from surface down to 400 m, 1955 - 2003) is analyzed to detect the possible LFOs. Not only some zonal LFOs, which were reported early, but also some strong LFOs of the vertical and meridional heat distribution, which might imply some physical sense, are detected. It should be noted that the similar vertical oscillation pattern can be found in the Pacific Ocean, Atlantic Ocean and Indian Ocean. Results from some preliminary studies show that the vertical LFO might be caused by the solar irradiance anomalies. This study may help reveal some unknown dynamical processes in the global oceans and may also benefit other related studies.

  7. Exact results for the Kuramoto model with a bimodal frequency distribution

    DEFF Research Database (Denmark)

    Martens, Erik Andreas; Barreto, E.; Strogatz, S. H.;

    2009-01-01

    We analyze a large system of globally coupled phase oscillators whose natural frequencies are bimodally distributed. The dynamics of this system has been the subject of long-standing interest. In 1984 Kuramoto proposed several conjectures about its behavior; ten years later, Crawford obtained...... the first analytical results by means of a local center manifold calculation. Nevertheless, many questions have remained open, especially about the possibility of global bifurcations. Here we derive the system’s stability diagram for the special case where the bimodal distribution consists of two equally......, where all the oscillators are desynchronized; partial synchrony, where a macro- scopic group of phase-locked oscillators coexists with a sea of desynchronized ones; and a standing wave state, where two counter-rotating groups of phase-locked oscillators emerge. Analytical results are presented...

  8. Size-frequency distribution of boulders ≥10 m on comet 103P/Hartley 2

    Science.gov (United States)

    Pajola, Maurizio; Lucchetti, Alice; Bertini, Ivano; Marzari, Francesco; A'Hearn, Michael F.; La Forgia, Fiorangela; Lazzarin, Monica; Naletto, Giampiero; Barbieri, Cesare

    2016-01-01

    Aims: We derive the size-frequency distribution of boulders on comet 103P/Hartley 2, which are computed from the images taken by the Deep Impact/HRI-V imaging system. We indicate the possible physical processes that lead to these boulder size distributions. Methods: We used images acquired by the High Resolution Imager-Visible CCD camera on 4 November 2010. Boulders ≥10 m were identified and manually extracted from the datasets with the software ArcGIS. We derived the global size-frequency distribution of the illuminated side of the comet (~50%) and identified the power-law indexes characterizing the two lobes of 103P. The three-pixel sampling detection, together with the shadowing of the surface, enables unequivocally detection of boulders scattered all over the illuminated surface. Results: We identify 332 boulders ≥10 m on the imaged surface of the comet, with a global number density of nearly 140/km2 and a cumulative size-frequency distribution represented by a power law with index of -2.7 ± 0.2. The two lobes of 103P show similar indexes, i.e., -2.7 ± 0.2 for the bigger lobe (called L1) and -2.6+ 0.2/-0.5 for the smaller lobe (called L2). The similar power-law indexes and similar maximum boulder sizes derived for the two lobes both point toward a similar fracturing/disintegration phenomena of the boulders as well as similar lifting processes that may occur in L1 and L2. The difference in the number of boulders per km2 between L1 and L2 suggests that the more diffuse H2O sublimation on L1 produce twice the boulders per km2 with respect to those produced on L2 (primary activity CO2 driven). The 103P comet has a lower global power-law index (-2.7 vs. -3.6) with respect to 67P. The global differences between the two comets' activities, coupled with a completely different surface geomorphology, make 103P hardly comparable to 67P. A shape distribution analysis of boulders ≥30 m performed on 103P suggests that the cometary boulders show more elongated shapes

  9. Association of HLA-B Alleles With Human Immunodeficiency Virus Type 1 Infection in the Yi Ethnic Group in Sichuan Province

    Institute of Scientific and Technical Information of China (English)

    MING-YAN XU; YI-MING SHAO; KUN-XUE HONG; XIAO-LING DENG; JUN LI; HONG PENG; YU-HUA RUAN; GUAN-MING QIN; HUI XING; XIAO-HU XU

    2004-01-01

    Objective To determine the distribution of HLA-B alleles in the Chinese Yi ethnic group and its association with HIV infection. Methods One hundred and six unrelated healthy HIV negative and 73 HIV positive Chinese Yi ethnic individuals were typed by PCR-SSP. Results The frequency of alleles B*07, B*35, and B*46 were increased in HIV-1-positive subjects, whereas the alleles B*55, B*44 and B*78 were absent in the HIV-infected persons studied. The B*46 allele was present in a significantly higher gene frequency among HIV-1-positive individuals (P=0.02, OR=3.32, 95% CI=1.13-9.78) compared with control subjects. Conclusion HLA-B*46 may be associated with its susceptibility to HIV-1 infections.

  10. Advanced multi-frequency radar: Design, preliminary measurements and particle size distribution retrieval

    Science.gov (United States)

    Majurec, Ninoslav

    lower output power of klystron amplifiers (comparing to magnetrons) is compensated by use of pulse compression (linear FM). The problem of range sidelobes (pulse compression artifacts) has been solved by using appropriate windowing functions in the receiver. Satisfactory sidelobe suppression level of 45 dB has been demonstrated in the lab. The currently best achievable range resolution of the AMFR system is 30 m (corresponds to 5 MHz receiver BW, set by the sampling rate of the Analog-to-Digital card). During the design stage, various polarization schemes have been investigated. The polarization scheme analysis showed the switching polarization scheme to be the best suited for the AMFR system. The AMFR subsystems were partially finished in the winter of 2005. Some preliminary tests were conducted in January 2006. Antenna platform was fabricated in summer 2006. The final assembly took place in the fall of 2006. Early results are presented in the dissertation. These results were helpful in revealing of certain problems in the radar system (i.e. immediate processing computer synchronization) that needed to be addressed during system development. Stratiform rain event occurred on December 18 2006 has been analyzed in detail. A number of commonly used theoretical particle size distributions is presented. Furthermore, it is shown that a fully calibrated multi-frequency radar system has capability of separating scattering and attenuation effects. This was accomplished by fitting the theoretical models into the measured data. An alternative method of estimating rain rate that relies on the dual wavelength ratios is also presented. Although not as powerful as theoretical model fitting, it has its merits for off-zenith observations. During January 2007, AMFR system participated in the C3VP experiment (Canadian CloudSat/CALIPSO Validation Project) in south Ontario, Canada. Some of the data obtained during C3VP experiment has been analyzed and presented. Analysis of these two

  11. The frequency and distribution of canine leishmaniosis diagnosed by veterinary practitioners in Europe.

    Science.gov (United States)

    Mattin, M J; Solano-Gallego, L; Dhollander, S; Afonso, A; Brodbelt, D C

    2014-06-01

    This study aimed to evaluate the frequency and spatial distribution of canine leishmaniosis (CanL) in France, Greece, Italy, Portugal and Spain. An online questionnaire investigated the location and frequency of CanL cases diagnosed by veterinary practitioners. Further data from the practice management systems of veterinary clinics in France were provided by a financial benchmarking company in relation to all treatment and test invoice data from participating practices. The geographical and temporal web interest in leishmaniosis was explored using Google Trends. Veterinary practitioners from France, Greece, Italy, Portugal and Spain completed 1231 questionnaires. The percentage of practice-attending dogs with a veterinary diagnosis of CanL ranged from 0.71% in France to 7.80% in Greece. However, due to regional differences in response rates, particularly in France, the mean regional estimates may better reflect the disease burden. Benchmarking data relating to approximately 180,000 dogs estimated that 0.05% of dogs attending veterinary clinics were treated for CanL or euthanased with suspected CanL in France. The regional frequency of Google web queries for leishmaniosis generally reflected the spatial patterns of disease identified from the other data sources. In conclusion, CanL was a relatively common diagnosis in veterinary clinics in many regions of the countries studied. Knowledge of CanL in endemic areas can direct the use of preventative measures and help estimate the likelihood of infection in dogs visiting or inhabiting these countries. PMID:24767097

  12. Weak-coherent-state-based time-frequency quantum key distribution

    Science.gov (United States)

    Zhang, Yequn; Djordjevic, Ivan B.; Neifeld, Mark A.

    2015-11-01

    We study large-alphabet quantum key distribution (QKD) based on the use of weak-coherent states and the time-frequency uncertainty relation. The large alphabet is achieved by dividing time and spectrum into M bins resulting in a frame similar to traditional pulse-position modulation (in time domain). However, the non-uniform occurrence of a photon prepared in a time/frequency bin creates the space for eavesdropping. By analysis, we show that a new intercept-resend attack strategy exists, which is stronger than that has been reported in the literature and hence the secret key rate of time-frequency QKD (TF-QKD) can be more tightly bounded. We then analyse the secret key rates of TF-QKD under various practical issues, such as channel loss, background noise, jitter and atmospheric turbulence in order to better understand the applicability of TF-QKD. Further, we discuss the information reconciliation for TF-QKD. Specifically, we investigate the layered coding scheme for TF-QKD based on quasi-cyclic low-density parity-check codes against jitter and atmospheric turbulence. By simulation, we demonstrate that information reconciliation can be efficiently achieved.

  13. 男性冲动攻击行为的15个短串联重复序列基因位点等位基因频率的病例对照研究%Case-control study of allele frequencies of 15 short tandem repeat loci in males with impulsive violent behavior

    Institute of Scientific and Technical Information of China (English)

    杨春; 巴华杰; 高志勤; 赵汉清; 余海鹰; 过伟

    2013-01-01

    背景:遗传多态性短串联重复序列(short tandem repeats, STRs)分析是用于检测基因型和表型之间关联的公认方法,但它以前没有在冲动攻击行为的遗传学研究中使用。  目的:在有冲动攻击行为史的男性和无冲动攻击行为史的男性对照组之间,比较15个STR基因位点(D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818和FGA)不同多态性的发生率。  方法:应用AmpFlSTR®Identifiler™试剂盒比较407个有冲动性攻击行为的案例和415个对照的15个STR基因位点等位基因的分布。  结果:有冲动攻击行为史的男性以下等位基因的平均频率显著低于对照组:TH01的等位基因10(OR=0.29,95%CI=0.16-0.52, p  结论:据我们所知,本项行为遗传学研究首次清楚表明了特定的遗传标记与非精神病罪犯的冲动暴力行为之间的密切关系。进一步的前瞻性工作将需要确定已辨识出的等位基因是否可以被认为是冲动攻击行为的危险因素以及导致这种关系的基本机制。%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

  14. An efficient hybrid causative event-based approach for deriving the annual flood frequency distribution

    Science.gov (United States)

    Thyer, Mark; Li, Jing; Lambert, Martin; Kuczera, George; Metcalfe, Andrew

    2015-04-01

    Flood extremes are driven by highly variable and complex climatic and hydrological processes. Derived flood frequency methods are often used to predict the flood frequency distribution (FFD) because they can provide predictions in ungauged catchments and evaluate the impact of land-use or climate change. This study presents recent work on development of a new derived flood frequency method called the hybrid causative events (HCE) approach. The advantage of the HCE approach is that it combines the accuracy of the continuous simulation approach with the computational efficiency of the event-based approaches. Derived flood frequency methods, can be divided into two classes. Event-based approaches provide fast estimation, but can also lead to prediction bias due to limitations of inherent assumptions required for obtaining input information (rainfall and catchment wetness) for events that cause large floods. Continuous simulation produces more accurate predictions, however, at the cost of massive computational time. The HCE method uses a short continuous simulation to provide inputs for a rainfall-runoff model running in an event-based fashion. A proof-of-concept pilot study that the HCE produces estimates of the flood frequency distribution with similar accuracy as the continuous simulation, but with dramatically reduced computation time. Recent work incorporated seasonality into the HCE approach and evaluated with a more realistic set of eight sites from a wide range of climate zones, typical of Australia, using a virtual catchment approach. The seasonal hybrid-CE provided accurate predictions of the FFD for all sites. Comparison with the existing non-seasonal hybrid-CE showed that for some sites the non-seasonal hybrid-CE significantly over-predicted the FFD. Analysis of the underlying cause of whether a site had a high, low or no need to use seasonality found it was based on a combination of reasons, that were difficult to predict apriori. Hence it is recommended

  15. NODC Standard Product: International ocean atlas Volume 4 - Atlas of temperature / salinity frequency distributions (2 disc set) (NODC Accession 0101473)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This Atlas presents more than 80,000 plots of the empirical frequency distributions of temperature and salinity for each 5-degree square area of the North Atlantic...

  16. Impact of protection settings of the distributed generation frequency under 1MW in the national electric system

    International Nuclear Information System (INIS)

    A literature review is conducted to understand the distributed generation, the reason for the introduction into modern power systems and other distributed generation technologies based on renewable energies that have been installed around the country. The frequency protections of distributed generation equipment under 1MW are studied according to international standards like IEEE-1547 and specifications of equipment manufacturers. The influence of the recommended international standards settings are investigated for systems of distributed generation, the performance in frequency that have presented under some frequency perturbation, as well as the influence that can have on the national and regional electrical system, with different amounts of technologies included in the national system. The recommended settings are evaluated through simulations in PSSE program in the context of the behavior of the frequency in the national electric system

  17. Spatially distributed patterns of oscillatory coupling between high-frequency amplitudes and low-frequency phases in human iEEG

    NARCIS (Netherlands)

    Maris, Eric; van Vugt, Marieke; Kahana, Michael

    2011-01-01

    Spatially distributed coherent oscillations provide temporal windows of excitability that allow for interactions between distinct neuronal groups. It has been hypothesized that this mechanism for neuronal communication is realized by bursts of high-frequency oscillations that are phase-coupled to a

  18. Random Genetic Drift and Gamete Frequency

    OpenAIRE

    Mano, Shuhei

    2005-01-01

    An analytic expression of conditional expectation of transient gamete frequency, given that one of the two loci remains polymorphic, is obtained in terms of the diffusion process by calculating the moments of the distribution. Using this expression, a model where linkage disequilibrium is introduced by a single mutation is considered. The conditional expectation of the gamete frequency given that the locus with the mutant allele remains polymorphic is presented. The behavior is significantly ...

  19. Magnitude-frequency distribution of submarine landslides in the Gioia Basin (southern Tyrrhenian Sea)

    Science.gov (United States)

    Casas, D.; Chiocci, F.; Casalbore, D.; Ercilla, G.; de Urbina, J. Ortiz

    2016-07-01

    Regional inventories and magnitude-frequency relationships provide critical information about landslides and represent a first step in landslide hazard assessment. Despite this, the availability of accurate inventories in the marine environment remains poor because of the commonly low accessibility of high-resolution data at regional scales. Evaluating high-resolution bathymetric data spanning the time interval 2007-2011 for the Gioa Basin of the southern Tyrrhenian Sea yielded a landslide inventory of 428 events affecting an area of >85 km2 and mobilizing approximately 1.4 km3 of sediment. This is the first time that this area is studied in such detail, justifying comparison with other areas both onland and offshore. Statistical analyses revealed that the cumulative distribution of the dataset is characterized by two right-skewed probability distributions with a heavy tail. Moreover, evidence of a rollover for smaller landslide volumes is consistent with similar trends reported in other settings worldwide. This may reflect an observational limitation and the site-specific geologic factors that influence landslide occurrence. The robust validation of both power-law and log-normal probability distributions enables the quantification of a range of probabilities for new extreme events far from the background landslide sizes defined in the area. This is a useful tool at regional scales, especially in geologically active areas where submarine landslides can occur frequently, such as the Gioia Basin.

  20. Monetizing Leakage Risk of Geologic CO2 Storage using Wellbore Permeability Frequency Distributions

    Science.gov (United States)

    Bielicki, Jeffrey; Fitts, Jeffrey; Peters, Catherine; Wilson, Elizabeth

    2013-04-01

    Carbon dioxide (CO2) may be captured from large point sources (e.g., coal-fired power plants, oil refineries, cement manufacturers) and injected into deep sedimentary basins for storage, or sequestration, from the atmosphere. This technology—CO2 Capture and Storage (CCS)—may be a significant component of the portfolio of technologies deployed to mitigate climate change. But injected CO2, or the brine it displaces, may leak from the storage reservoir through a variety of natural and manmade pathways, including existing wells and wellbores. Such leakage will incur costs to a variety of stakeholders, which may affect the desirability of potential CO2 injection locations as well as the feasibility of the CCS approach writ large. Consequently, analyzing and monetizing leakage risk is necessary to develop CCS as a viable technological option to mitigate climate change. Risk is the product of the probability of an outcome and the impact of that outcome. Assessment of leakage risk from geologic CO2 storage reservoirs requires an analysis of the probabilities and magnitudes of leakage, identification of the outcomes that may result from leakage, and an assessment of the expected economic costs of those outcomes. One critical uncertainty regarding the rate and magnitude of leakage is determined by the leakiness of the well leakage pathway. This leakiness is characterized by a leakage permeability for the pathway, and recent work has sought to determine frequency distributions for the leakage permeabilities of wells and wellbores. We conduct a probabilistic analysis of leakage and monetized leakage risk for CO2 injection locations in the Michigan Sedimentary Basin (USA) using empirically derived frequency distributions for wellbore leakage permeabilities. To conduct this probabilistic risk analysis, we apply the RISCS (Risk Interference of Subsurface CO2 Storage) model (Bielicki et al, 2013a, 2012b) to injection into the Mt. Simon Sandstone. RISCS monetizes leakage risk

  1. Plug-in hybrid electric vehicles as a source of distributed frequency regulation

    Science.gov (United States)

    Mullen, Sara Kathryn

    The movement to transform the North American power grid into a smart grid may be accomplished by expanding integrated sensing, communications, and control technologies to include every part of the grid to the point of end-use. Plug-in hybrid electric vehicles (PHEV) provide an opportunity for small-scale distributed storage while they are plugged-in. With large numbers of PHEV and the communications and sensing associated with the smart grid, PHEV could provide ancillary services for the grid. Frequency regulation is an ideal service for PHEV because the duration of supply is short (order of minutes) and it is the highest priced ancillary service on the market offering greater financial returns for vehicle owners. Using Simulink a power system simulator modeling the IEEE 14 Bus System was combined with a model of PHEV charging and the controllers which facilitate vehicle-to-grid (V2G) regulation supply. The system includes a V2G controller for each vehicle which makes regulation supply decisions based on battery state, user preferences, and the recommended level of supply. A PHEV coordinator controller located higher in the system has access to reliable frequency measurements and can determine a suitable local automatic generation control (AGC) raise/lower signal for participating vehicles. A first step implementation of the V2G supply system where battery charging is modulated to provide regulation was developed. The system was simulated following a step change in loading using three scenarios: (1) Central generating units provide frequency regulation, (2) PHEV contribute to primary regulation analogous to generator speed governor control, and (3) PHEV contribute to primary and secondary regulation using an additional integral term in the PHEV control signal. In both cases the additional regulation provided by PHEV reduced the area control error (ACE) compared to the base case. Unique contributions resulting from this work include: (1) Studied PHEV energy systems

  2. Peripheral T-cell lymphoma: Frequency and distribution in a tertiary referral center in South India

    Directory of Open Access Journals (Sweden)

    Deepak K Burad

    2012-01-01

    Full Text Available Background and Aim: Peripheral T/NK-cell lymphomas are uncommon types of non-Hodgkin′s lymphoma (NHL with a higher frequency in Far East countries as compared to the West. This study was undertaken to ascertain the frequency and distribution pattern of peripheral T-cell lymphomas (PTCLs diagnosed in a tertiary care center in South India. Materials and Methods: This retrospective study was carried out in Department of General Pathology, Christian Medical College, Vellore. The time period was for 2 years from 1 st January 2008 till 31st December 2009. All PTCLs were reviewed and classified according to the World Health Organization (WHO 2008 classification. Results: Of a total of 1032 cases of NHL, 180 cases were PTCL, which accounted for 17.4% cases of all the NHLs. Of these, PTCL, not otherwise specified (PTCL, NOS was the most common subtype (48 cases, 26.1%, followed by anaplastic large cell lymphoma (41 cases, 22.8%, mycosis fungoides (21 cases, 11.7%, angioimmunoblastic T-cell lymphoma (16 cases, 8.9%, subcutaneous panniculitis like T-cell lymphoma (15 cases, 8.4%, extranodal NK/T-cell lymphoma, nasal type (12 cases, 6.7%, and hepatosplenic T-cell lymphoma (10 cases, 5.6%. The most common primary site of presentation was nodal accounting for 42% followed by cutaneous (34%, upper aerodigestive sites (8.9%, spleen (6.7%, and gastrointestinal tract (GIT; 3.3%. Conclusions: This is the largest single study on PTCLs in India and we document that its frequency is higher than that reported in Western literature and previous Indian studies and almost similar to that reported in some Far East studies. The frequency of mycosis fungoides, subcutaneous panniculitis like T-cell lymphoma, and hepatosplenic T-cell lymphoma was higher than that reported in the World literature and previous Indian studies. The frequency of extranodal NK/T-cell lymphoma and angioimmunoblastic T-cell lymphoma was much lower than that reported in the Far East literature.

  3. Frequency and distribution of leakages in steam generators of gas-cooled reactors

    International Nuclear Information System (INIS)

    In gas cooled reactors with graphitic primary circuit structures - such as HTR, AGR or Magnox - the water ingress is an event of great safety concern. Water or steam entering the primary circuit react with the hot graphite and carbon-oxide and hydrogen are produced. As the most important initiating event a leak in a steam generator must be taken into account. From the safety point of view as well as for availability reasons it is necessary to construct reliable boilers. Thus the occurrence of a boiler leak should be a rare event. In the context of a probabilistic safety study for an HTR-Project much effort was invested to get information about the frequency and the size distribution of tube failures in steam generators of gas cooled reactors. The main data base was the boiler tube failure statistics of United Kingdom gas cooled reactors. The data were selected and applied to a modern HTR steam generator design. A review of the data showed that the failure frequency is not connected with the load level (pressures, temperatures) or with the geometric size of the heating surface of the boiler. Design, construction, fabrication, examination and operation conditions have the greatest influence an the failure frequency but they are practically not to be quantified. The typical leak develops from smallest size. By erosion effects of the entering water or steam it is enlarged to perhaps some mm2, then usually it is detected by moisture monitors. Sudden tube breaks were not reported in the investigated period. As a rule boiler leaks in gas cooled reactors are much more, rare then leaks in steam generators of light water reactors and fossil fired boilers. (author)

  4. Implications of the shape of design hyetograph in the derived flood frequency distribution

    Science.gov (United States)

    Sordo-Ward, A.; Bianucci, P.; Garrote, L.

    2012-04-01

    Hydrometeorological methods for rainfall-runoff transformation are frequently used when the hydrological design of hydraulic infrastructures is considered. These methods imply to determinate the design storm which is usually characterised by the return period of its total depth of precipitation. In the other hand, the shape of the hyetograph, i.e. the temporal pattern of the storm, has a relevant implication in the resulting hydrograph. In this work we analysed the influence that the within-storm rainfall intensity distribution has on the derived flood frequency (DFF) law. This was addressed by comparing the DFF's obtained from two different ensembles of hyetographs with the same total depth frequency distribution and constant total duration. One ensemble of hyetograph (BA) was determined using the alternating blocks method which is usually assumed to provide more adverse hydrological load. The second ensemble (MC) was obtained using a stochastic storm generator developed in a Monte Carlo framework. The ratios between corresponding maximum flows were calculated for selected return periods (RP) as a measure of the difference between both DFF's. The variation of this quotient was analysed regarding the return period and basin configuration. We considered three different discretization scales for the 1241-km2 Manzanares River basin with outlet near Rivas-Vaciamadrid, in the Region of Madrid (Spain). The three levels correspond to high resolution (HR, basin divided into 62 sub-catchments), medium resolution (MR, 33 sub-catchments), and low resolution (LR, 14 sub-catchments). For the case studied, and for the three configuration considered, the DFF obtained from the alternating blocks hyetograph was not such adverse as it was expected to be. The flow peak ratio kept practically constant across the RP range. While the BA-quantiles for each subbasin's DFF were higher than MC-quantiles in a 10% to 40%; the peak flow ratios at the catchment outlet took values close to one

  5. Separating cognitive processes with principal components analysis of EEG time-frequency distributions

    Science.gov (United States)

    Bernat, Edward M.; Nelson, Lindsay D.; Holroyd, Clay B.; Gehring, William J.; Patrick, Christopher J.

    2008-08-01

    Measurement of EEG event-related potential (ERP) data has been most commonly undertaken in the time-domain, which can be complicated to interpret when separable activity overlaps in time. When the overlapping activity has distinct frequency characteristics, however, time-frequency (TF) signal processing techniques can be useful. The current report utilized ERP data from a cognitive task producing typical feedback-related negativity (FRN) and P300 ERP components which overlap in time. TF transforms were computed using the binomial reduced interference distribution (RID), and the resulting TF activity was then characterized using principal components analysis (PCA). Consistent with previous work, results indicate that the FRN was more related to theta activity (3-7 Hz) and P300 more to delta activity (below 3 Hz). At the same time, both time-domain measures were shown to be mixtures of TF theta and delta activity, highlighting the difficulties with overlapping activity. The TF theta and delta measures, on the other hand, were largely independent from each other, but also independently indexed the feedback stimulus parameters investigated. Results support the view that TF decomposition can greatly improve separation of overlapping EEG/ERP activity relevant to cognitive models of performance monitoring.

  6. Effect of low frequency MHD instability on fast ion distribution in NSTX

    Science.gov (United States)

    Hao, G.; Liu, D.; Heidbrink, W. W.; Podesta, M.; Fredrickson, E. D.; Bortolon, A.; White, R.; Darrow, D.; Fu, G. Y.; Wang, Z. R.; Kramer, G. J.; Liu, Y. Q.; Tritz, K.

    2015-11-01

    In NSTX spherical tokamak plasmas, the onset of low-frequency MHD modes cause a rapid ~ 25% reduction in the fast-ion D-alpha (FIDA) signal. These, 5-20 kHz instabilities are commonly observed in the early phase of neutral beam heated plasmas that often have reversed magnetic shear in the plasma core. The collapse of the core fast ion density is measured by the vertical FIDA diagnostic. Although the profile flattens, changes in spectral shape are modest, suggesting that much of the distribution function is affected. Meanwhile, a modest increase of fast-ion losses is indicated by the measurements from neutron and fast-ion loss detectors. Moreover, this mode is always accompanied by Compressional Alfven Eigenmode (CAE). This suggests that low-f MHD instabilities can cause the redistribution of fast ions in both real and velocity space. Preliminary simulation results from the MARS-F code suggest that the low-f instability is a coupled infernal-peeling mode. The dependence of the mode's onset on the equilibrium parameters and its effect on the fast ion distribution will be computed, and compared with experimental measurements. Work supported by U.S. DOE DE-AC0209CH11466, DE-FG02-06ER54867, and DE-FG03-02ER54681.

  7. Ion energy distribution functions behind the sheaths of magnetized and non-magnetized radio frequency discharges

    International Nuclear Information System (INIS)

    The effect of a magnetic field on the characteristics of capacitively coupled radio frequency discharges is investigated and found to be substantial. A one-dimensional particle-in-cell simulation shows that geometrically symmetric discharges can be asymmetrized by applying a spatially inhomogeneous magnetic field. This effect is similar to the recently discovered electrical asymmetry effect. Both effects act independently, they can work in the same direction or compensate each other. Also the ion energy distribution functions at the electrodes are strongly affected by the magnetic field, although only indirectly. The field influences not the dynamics of the sheath itself but rather its operating conditions, i.e. the ion flux through it and voltage drop across it. To support this interpretation, the particle-in-cell results are compared with the outcome of the recently proposed ensemble-in-spacetime algorithm. Although that scheme resolves only the sheath and neglects magnetization, it is able to reproduce the ion energy distribution functions with very good accuracy, regardless of whether the discharge is magnetized or not. (paper)

  8. Allelic variants of the genes of apolipoproteins B and CII in patients with coronary heart disease and in healthy individuals from the Moscow population

    Energy Technology Data Exchange (ETDEWEB)

    Pogoda, T.V.; Kolosova, T.V.; Lyudvikova, E.K. [Institute of Molecular Genetics, Moscow (Russian Federation)] [and others

    1995-07-01

    Allelic frequencies of a microsatellite of the apolipoprotein CII gene (APOCII) and a minisatellite of the apolipoprotein B gene (APOB) were studied by using polymerase chain reaction (PCR). The study was conducted on a random sample of male Moscow inhabitants and a sample of patients with coronary heart disease (CHD) from the same population. Fourteen variants of the APOB minisatellite (the 82% heterozygosity level) and 13 alleles of the APOCII microsatellite (the 85% heterozygosity level) were found. CHD patients significantly differed from the control group in the distributions of alleles in these loci: APOB 32, APOB 46, APOB 48, and APOB 50 as well as APOCII 17 and APOCII 29 were found more frequently. A relationship was found between the distributions of APOB and APOCII in the CHD patients. The CHD patients with alleles APOCII 21 and APOCII 30 very often had the allele APOB 32; and patients with the genotype APOB 34, 36 had the allele APOCII 29 even more often than affected individuals in general. Individuals of the control group with the allele APOCII30 exhibited hypertriglyceridemia without increased levels of total cholesterol and apolipoprotein B in plasma. 14 refs., 3 figs., 6 tabs.

  9. Functional shape of the earthquake frequency-magnitude distribution and completeness magnitude

    Science.gov (United States)

    Mignan, A.

    2012-08-01

    We investigated the functional shape of the earthquake frequency-magnitude distribution (FMD) to identify its dependence on the completeness magnitude Mc. The FMD takes the form N(m) ∝ exp(-βm)q(m) where N(m) is the event number, m the magnitude, exp(-βm) the Gutenberg-Richter law and q(m) a detection function. q(m) is commonly defined as the cumulative Normal distribution to describe the gradual curvature of bulk FMDs. Recent results however suggest that this gradual curvature is due to Mc heterogeneities, meaning that the functional shape of the elemental FMD has yet to be described. We propose a detection function of the form q(m) = exp(κ(m - Mc)) for m FMD of angular shape. The two FMD models are compared in earthquake catalogs from Southern California and Nevada and in synthetic catalogs. We show that the angular FMD model better describes the elemental FMD and that the sum of elemental angular FMDs leads to the gradually curved bulk FMD. We propose an FMD shape ontology consisting of 5 categories depending on the Mc spatial distribution, from Mc constant to Mc highly heterogeneous: (I) Angular FMD, (II) Intermediary FMD, (III) Intermediary FMD with multiple maxima, (IV) Gradually curved FMD and (V) Gradually curved FMD with multiple maxima. We also demonstrate that the gradually curved FMD model overestimates Mc. This study provides new insights into earthquake detectability properties by using seismicity as a proxy and the means to accurately estimate Mc in any given volume.

  10. Tuning and optimization of the field distribution for 4-rod Radio Frequency Quadrupole linacs

    International Nuclear Information System (INIS)

    In this thesis, the tuning process of the 4-rod Radio Frequency Quadrupole has been analyzed and a theory for the prediction of the tuning plate's influence on the longitudinal voltage distribution was developed together with RF design options for the optimization of the fringe fields. The basic principles of the RFQ's particle dynamics and resonant behavior are introduced in the theory part of this thesis. All studies that are presented are based on the work on four RFQs of recent linac projects. These RFQs are described in one chapter. Here, the projects are introduced together with details about the RFQ parameters and performance. In the meantime two of these RFQs are in full operation at NSCL at MSU and FNAL. One is operating in the test phase of the MedAustron Cancer Therapy Center and the fourth one for LANL is about to be built. The longitudinal voltage distribution has been studied in detail with a focus on the influence of the RF design with tuning elements and parameters like the electrodes overlap or the distance between stems. The theory for simulation methods for the field flatness that were developed as part of this thesis, as well as its simulation with CST MWS have been analyzed and compared to measurements. The lumped circuit model has proven to predict results with an accuracy that can be used in the tuning process of 4-rod RFQs. Together with results from the tuning studies, the studies on the fringe fields of the 4-rod structure lead to a proposal for a 4-rod RFQ model with an improved field distribution in the transverse and longitudinal electric field.

  11. Allele coding in genomic evaluation

    DEFF Research Database (Denmark)

    Standen, Ismo; Christensen, Ole Fredslund

    2011-01-01

    coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being the best. \\paragraph*{Conclusions:} Different allele coding methods lead to the same inference in the marker-based and equivalent models when a fixed...... effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous...... genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call...

  12. Heterogenous Distribution of MTHFR Gene Variants among Mestizos and Diverse Amerindian Groups from Mexico

    Science.gov (United States)

    Contreras-Cubas, Cecilia; Sánchez-Hernández, Beatríz E.; García-Ortiz, Humberto; Martínez-Hernández, Angélica; Barajas-Olmos, Francisco; Cid, Miguel; Mendoza-Caamal, Elvia C.; Centeno-Cruz, Federico; Ortiz-Cruz, Gabriela; Jiménez-López, José Concepción; Córdova, Emilio J.; Salas-Bautista, Eva Gabriela; Saldaña-Alvarez, Yolanda; Fernández-López, Juan Carlos; Mutchinick, Osvaldo M.

    2016-01-01

    Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in folate metabolism. Folate deficiency has been related to several conditions, including neural tube defects (NTDs) and cardiovascular diseases. Hence, MTHFR genetic variants have been studied worldwide, particularly the C677T and A1298C. We genotyped the C677T and A1298C MTHFR polymorphisms in Mexican Amerindians (MAs), from the largest sample included in a genetic study (n = 2026, from 62 ethnic groups), and in a geographically-matched Mexican Mestizo population (MEZ, n = 638). The 677T allele was most frequent in Mexican individuals, particularly in MAs. The frequency of this allele in both MAs and MEZs was clearly enriched in the South region of the country, followed by the Central East and South East regions. In contrast, the frequency of the 1298C risk allele in Mexicans was one of the lowest in the world. Both in MAs and MEZs the variants 677T and 1298C displayed opposite allele frequency gradients from southern to northern Mexico. Our findings suggest that in Mestizos the 677T allele was derived from Amerindians while the 1298C allele was a European contribution. Some subgroups showed an allele frequency distribution that highlighted their genetic diversity. Notably, the distribution of the frequency of the 677T allele was consistent with that of the high incidence of NTDs reported in MEZ. PMID:27649570

  13. Frequency assessment of spatially distributed generations of flood scenarios: an application on Italian territory

    Science.gov (United States)

    Lomazzi, M.; Roth, G.; Rudari, R.; Taramasso, A. C.; Ghizzoni, T.; Benedetti, R.; Espa, G.; Terpessi, C.

    2009-12-01

    The flooding risk impact on society cannot be understated: it influences land use and territorial planning and development at both physical and regulatory levels. To cope with it, a variety of actions can be put in place, involving multidisciplinary competences. Mitigation measures goes from the improvement of monitoring systems to the development of hydraulic structures, throughout land use restrictions, civil protection and insurance plans. All of those options present social and economic impacts, either positive or negative, whose proper estimate should rely on the assumption of appropriate - present and future - scenarios, i.e. quantitative event descriptions in terms of i) the flood hazard, with its probability of occurrence, extension, intensity, and duration, ii) the exposed values and iii) their vulnerability. At present, initial attention has been devoted to the design of flood scenarios, or ensembles of them, and to the evaluation of their frequency of occurrence. In the present work, a model for spatially distributed flood scenarios generation and frequency assessment is proposed and applied to the Italian territory. The study area has been divided into homogeneous regions according to their hydrologic, orographic and meteoclimatic characteristics. A statistical model for flood scenarios simulation has been implemented throughout a conditional approach based on MCMC simulations by using i) a historical flood events catalogue; ii) a homogeneous regions correlation matrix; and iii) an auxiliary variables data set. In this framework, the role of the information stored in the historical flood events catalogue "Aree Vulnerate Italiane" (AVI, http://avi.gndci.cnr.it/), produced by the Italian National Research Council, is of crucial importance.

  14. Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape.

    Science.gov (United States)

    Georghiou, S B; Seifert, M; Catanzaro, D; Garfein, R S; Valafar, F; Crudu, V; Rodrigues, C; Victor, T C; Catanzaro, A; Rodwell, T C

    2016-07-01

    Molecular diagnostic assays, with their ability to rapidly detect resistance-associated mutations in bacterial genes, are promising technologies to control the spread of drug-resistant tuberculosis (DR-TB). Sequencing assays provide detailed information for specific gene regions and can help diagnostic assay developers prioritize mutations for inclusion in their assays. We performed pyrosequencing of seven Mycobacterium tuberculosis gene regions (katG, inhA, ahpC, rpoB, gyrA, rrs, and eis) for 1,128 clinical specimens from India, Moldova, and South Africa. We determined the frequencies of each mutation among drug-resistant and -susceptible specimens based on phenotypic drug susceptibility testing results and examined mutation distributions by country. The most common mutation among isoniazid-resistant (INH(r)) specimens was the katG 315ACC mutation (87%). However, in the Eastern Cape, INH(r) specimens had a lower frequency of katG mutations (44%) and higher frequencies of inhA (47%) and ahpC (10%) promoter mutations. The most common mutation among rifampin-resistant (RIF(r)) specimens was the rpoB 531TTG mutation (80%). The mutation was common in RIF(r) specimens in Mumbai (83%) and Moldova (84%) but not the Eastern Cape (17%), where the 516GTC mutation appeared more frequently (57%). The most common mutation among fluoroquinolone-resistant specimens was the gyrA 94GGC mutation (44%). The rrs 1401G mutation was found in 84%, 84%, and 50% of amikacin-resistant, capreomycin-resistant, and kanamycin (KAN)-resistant (KAN(r)) specimens, respectively. The eis promoter mutation -12T was found in 26% of KAN(r) and 4% of KAN-susceptible (KAN(s)) specimens. Inclusion of the ahpC and eis promoter gene regions was critical for optimal test sensitivity for the detection of INH resistance in the Eastern Cape and KAN resistance in Moldova. (This study has been registered at ClinicalTrials.gov under registration number NCT02170441.).

  15. Frequency and Distribution of Microsatellites in the Genome of Filamentous Fungus, Neurospora crassa

    Institute of Scientific and Technical Information of China (English)

    LI Cheng-yun; LI Jin-bin; ZHOU Xiao-gang; ZHANG Shao-song; XU Ming-hui

    2005-01-01

    A total of 38.0 Mb of publicly available DNA sequence in Neurospora crassa was researched for mono- to hexanucleotide simple sequence repeats (SSR or microsatellite) to determine the type, size and frequency. A total of 14 788 SSRs were observed in the whole genomic DNA sequence, about one every 2.57 kb, with the criteria of SSR length >15 bp and 80%matches. The most abundant microsatellite was trinucleotide repeat, the number was 4 729, followed by hexanucleotide and mononucleotide repeats, the numbers were 2 940 and 2 489 respectively, and the least abundance was dinucleotide repeat, only 691 were found. Among the 10 082 ORFs, 4 094 SSRs were harbored in 2 373 ORF (no intron) of the organism.One thousand and fifty six ORFs harbored only one SSR. Similar with other organisms, tri- and hexanucleotide repeats were predominant in ORFs, 54.1 and 48.8% oftri- and hexanucleotide repeats were distributed in ORF region. The density of these two motifs was overpresented in coding regions, because ORF region and coding region constitutes only 46 and 38.3% of genomic sequence, respectively. Upstream and downstream 300 bp of regulatory regions were high density regions of SSRs, particularly density of pentanucleotide SSR in upstream region was as high as five times of average density in genomic DNA, density of di- and tetranucleotide SSR was also more than two times of average density. The density of penta-, tetra-, di- and mononucleotide SSRs was relatively higher than average density. There were 47 SSRs in mitochondria 64 840 bp DNA sequence, their distribution is similar with genomic DNA sequence. These results suggested that SSRs were clustered in regulatory regions of genomic DNA.

  16. Impact of Channel-like Erosion Patterns on the Frequency-Magnitude Distribution of Earthquakes

    Science.gov (United States)

    Rohmer, J.; Aochi, H.

    2015-12-01

    Reactive flow at depth (either related to underground activities like enhancement of hydrocarbon recovery, CO2 storage or to natural flow like in hydrothermal zones) can alter fractures' topography, which might in turn change their seismic responses. Depending on the flow and reaction rates, instability of the dissolution front can lead to a wormhole-like pronounced erosion pattern (Szymczak & Ladd, JGR, 2009). In a fractal structure of rupture process (Ide & Aochi, JGR, 2005), we question how the perturbation related to well-spaced long channels alters rupture propagation initiated on a weak plane and eventually the statistical feature of rupture appearance in Frequency-Magnitude Distribution FMD (Rohmer & Aochi, GJI, 2015). Contrary to intuition, a spatially uniform dissolution is not the most remarkable case, since it affects all the events proportionally to their sizes leading to a downwards translation of FMD: the slope of FMD (b-value) remains unchanged. An in-depth parametric study was carried out by considering different pattern characteristics: spacing S varying from 0 to 100 and length L from 50 to 800 and fixing the width w=1. The figure shows that there is a region of optimum channels' characteristics for which the b-value of the Gutenberg Richter law is significantly modified with p-value ~10% (corresponding to area with red-coloured boundaries) given spacing to length ratio of the order of ~1/40: large magnitude events are more significantly affected leading to an imbalanced distribution in the magnitude bins of the FMD. The larger the spacing, the lower the channel's influence. The decrease of the b-value between intact and altered fractures can reach values down to -0.08. Besides, a spatial analysis shows that the local seismicity anomaly concentrates in a limited zone around the channels: this opens perspective for detecting these eroded regions through high-resolution imaging surveys.

  17. High-frequency oscillations in distributed neural networks reveal the dynamics of human decision making

    Directory of Open Access Journals (Sweden)

    Adrian G Guggisberg

    2008-03-01

    Full Text Available We examine the relative timing of numerous brain regions involved in human decisions that are based on external criteria, learned information, personal preferences, or unconstrained internal considerations. Using magnetoencephalography (MEG and advanced signal analysis techniques, we were able to non-invasively reconstruct oscillations of distributed neural networks in the high-gamma frequency band (60–150 Hz. The time course of the observed neural activity suggested that two-alternative forced choice tasks are processed in four overlapping stages: processing of sensory input, option evaluation, intention formation, and action execution. Visual areas are activated fi rst, and show recurring activations throughout the entire decision process. The temporo-occipital junction and the intraparietal sulcus are active during evaluation of external values of the options, 250–500 ms after stimulus presentation. Simultaneously, personal preference is mediated by cortical midline structures. Subsequently, the posterior parietal and superior occipital cortices appear to encode intention, with different subregions being responsible for different types of choice. The cerebellum and inferior parietal cortex are recruited for internal generation of decisions and actions, when all options have the same value. Action execution was accompanied by activation peaks in the contralateral motor cortex. These results suggest that high-gamma oscillations as recorded by MEG allow a reliable reconstruction of decision processes with excellent spatiotemporal resolution.

  18. Quantifying the spatiotemporal distribution of Ultralow Frequency waves in global simulations

    Science.gov (United States)

    Komar, C. M.; Glocer, A.; Hartinger, M.; Fok, M. C. H.; Murphy, K. R.

    2015-12-01

    It is well known that relativistic electrons in the outer radiation belt are highly dynamic and respond to impulsive interplanetary structures interacting with Earth's magnetic field. Two known mechanisms that contribute to the observed dynamics of these electron populations are: Ultralow Frequency (ULF) waves and magnetopause shadowing. The former causes the electrons to change their radial location in order to conserve the quantity associated with the electrons' azimuthal drift around Earth; the latter describes the process by which these electrons leave Earth's inner magnetosphere and are lost to interplanetary space. The present work couples the bounce-averaged kinetic Comprehensive Inner Magnetosphere-Ionosphere (CIMI) model to simulate the ring current and radiation belt populations with the Block Adaptive Tree Solar wind Roe-type Upwind Scheme (BATS-R-US) global magnetospheric MHD and ionospheric potential models in order to quantify the radial, azimuthal, and temporal distribution of ULF waves generated by the interaction between impulsive solar wind structures and Earth's magnetic field. Changes to and losses of relativistic (1-5 MeV) electron populations resulting from the aforementioned mechanisms are investigated.

  19. Seasonal Variation and Frequency Distribution of Ectoparasites in Crossbreed Cattle in Southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Maria do Socorro Ferraz da Costa

    2014-01-01

    Full Text Available The aims of this study were to evaluate the seasonal variation and frequency distribution of Rhipicephalus (Boophilus microplus, Haematobia irritans, and Dermatobia hominis on crossbred heifers under field conditions in the northeast of Minas Gerais state, southeastern Brazil. From November 2007 to September 2009 (23 months, 40 heifers aged 16.6±2.4 months were divided into groups A (1/4 Holstein × 3/4 Gir and B (1/2 Holstein × 1/2 Gir and had the monthly infestation estimated along with the climatic conditions. The mean maximum and minimum temperatures were 28.5 and 19°C, respectively. The ectoparasites were present on animals in all months of the year. The levels of ticks on the animals were low (3.0±0.2 ticks/animal, with the highest density in midwinter. The temperature was the climatic factor that most influenced the tick levels. The population of H. irritans (13.9±0.3 flies/animal and D. hominis (1.5±0.2 larvae/animal on heifers was more influenced by rainfall and exhibited two population peaks during the year. 1/2 Holstein heifers harbored significantly more H. irritans and D. hominis than 1/4 Holstein heifers. The results are discussed considering the most appropriate periods to apply ectoparasiticides and the genetic make-up of the animals.

  20. Blind Identification of Distributed Antenna Systems with Multiple Carrier Frequency Offsets

    CERN Document Server

    Yu, Yuanning; Poor, H Vincent

    2007-01-01

    In spatially distributed multiuser antenna systems, the received signal contains multiple carrier-frequency offsets (CFOs) arising from mismatch between the oscillators of transmitters and receivers. This results in a time-varying rotation of the data constellation, which needs to be compensated at the receiver before symbol recovery. In this paper, a new approach for blind CFO estimation and symbol recovery is proposed. The received base-band signal is over-sampled, and its polyphase components are used to formulate a virtual Multiple-Input Multiple-Output (MIMO) problem. By applying blind MIMO system estimation techniques, the system response can be estimated and decoupled versions of the user symbols can be recovered, each one of which contains a distinct CFO. By applying a decision feedback Phase Lock Loop (PLL), the CFO can be mitigated and the transmitted symbols can be recovered. The estimated MIMO system response provides information about the CFOs that can be used to initialize the PLL, speed up its ...

  1. Earthquake frequency-magnitude distribution and fractal dimension in mainland Southeast Asia

    Science.gov (United States)

    Pailoplee, Santi; Choowong, Montri

    2014-12-01

    The 2004 Sumatra and 2011 Tohoku earthquakes highlighted the need for a more accurate understanding of earthquake characteristics in both regions. In this study, both the a and b values of the frequency-magnitude distribution (FMD) and the fractal dimension ( D C ) were investigated simultaneously from 13 seismic source zones recognized in mainland Southeast Asia (MLSEA). By using the completeness earthquake dataset, the calculated values of b and D C were found to imply variations in seismotectonic stress. The relationships of D C -b and D C -( a/ b) were investigated to categorize the level of earthquake hazards of individual seismic source zones, where the calibration curves illustrate a negative correlation between the D C and b values ( D c = 2.80 - 1.22 b) and a positive correlation between the D C and a/ b ratios ( D c = 0.27( a/ b) - 0.01) with similar regression coefficients ( R 2 = 0.65 to 0.68) for both regressions. According to the obtained relationships, the Hsenwi-Nanting and Red River fault zones revealed low-stress accumulations. Conversely, the Sumatra-Andaman interplate and intraslab, the Andaman Basin, and the Sumatra fault zone were defined as high-tectonic stress regions that may pose risks of generating large earthquakes in the future.

  2. Influence of electrode material on measured ion kinetic-energy distributions in radio-frequency discharges

    International Nuclear Information System (INIS)

    The measurement of ion kinetic energies is important for understanding processes that occur in discharges, e.g., the influence of ions on the etching of semiconductor materials in plasma reactors. Direct measurements of ion kinetic energies striking surfaces exposed to the discharge requires sampling through an orifice in a surface. Difficulties with ion sampling through a small aperture, manifested by errors or distortions in measured ion kinetic-energy distributions (IEDs) have been encountered in previous investigations of both dc and radio-frequency (rf) discharges. The errors are usually most significant at relatively low ion energies. Previous measurements in our laboratory of IEDs for ions sampled through a 0.1-mm hole in a grounded, aluminum electrode for rf discharges in argon showed evidence of reduced detection efficiency (discrimination) for low energy ions (<10 eV), and apparent shifts in the measured ion energies for plasmas generated in other gases. It has been suggested that surface charging at or near the sampling orifice can cause both discrimination and energy shifts. The existence of an insulating, or partially insulating, layer of aluminum oxide on the surface of an electrode allows the possibility of surface-charge accumulation. In the present work, IEDs were measured at both aluminum and 304 stainless-steel grounded electrodes with 0.1 mm sampling orifices in rf plasmas generated in argon and oxygen

  3. Langmuir probe and electron energy distribution function measurements of radio frequency ion source

    International Nuclear Information System (INIS)

    In this work a single langmuir probe is used to investigate the low pressure radio-frequency (RF) discharge in argon. The current-voltage characteristic of the probe is used to provide the fundamental plasma parameters, including the electron temperature (Te), electron density (ne), floating potential (vf) and plasma potential (vp).The data are collected at plasma source pressure varying from 1 to 80 mtorr and the discharge powers in the range of 25-250 w. The measurements give an electron density and temperature of ne=1.8 x 1010 to 9.2 x 1011 cm-3 and Te=1.75 to 4.5 eV, respectively. The electron energy distribution function (EEDF) and some elementary processes involved in the RF gas discharge is deduced. The influence of the RF power and plasma cell pressure on ne,Te and vp of the plasma has been examined. The evaluation of the EEDF and its behavior with the pressure in the plasma source is also revealed.

  4. Crater size-frequency distribution measurements and age of the Compton-Belkovich Volcanic Complex

    Science.gov (United States)

    Shirley, K. A.; Zanetti, M.; Jolliff, B.; van der Bogert, C. H.; Hiesinger, H.

    2016-07-01

    The Compton-Belkovich Volcanic Complex (CBVC) is a 25 × 35 km feature on the lunar farside marked by elevated topography, high albedo, high thorium concentration, and high silica content. Morphologies indicate that the complex is volcanic in origin and compositions indicate that it represents rare silicic volcanism on the Moon. Constraining the timing of silicic volcanism at the complex is necessary to better understand the development of evolved magmas and when they were active on the lunar surface. We employ image analysis and crater size-frequency distribution (CSFD) measurements on several locations within the complex and at surrounding impact craters, Hayn (87 km diameter), and Compton (160 km diameter), to determine relative and absolute model ages of regional events. Using CSFD measurements, we establish a chronology dating regional resurfacing events and the earliest possible onset of CBVC volcanism at ∼3.8 Ga, the formation of Compton Crater at 3.6 Ga, likely resurfacing by volcanism at the CBVC at ∼3.5 Ga, and the formation of Hayn Crater at ∼1 Ga. For the CBVC, we find the most consistent results are obtained using craters larger than 300 m in diameter; the small crater population is affected by their approach to an equilibrium condition and by the physical properties of regolith at the CBVC.

  5. 北京汉族和约鲁巴人群ROR2基因单核苷酸多态性的比较研究%Comparison of minor allele frequencies and haplotype frequencies for single nucleotide polymorphisms in ROR2 gene using HapMap data for Chinese Hans in Beijing and Yoruban in Ibadan in Nigeria

    Institute of Scientific and Technical Information of China (English)

    王红; 赵凯平

    2011-01-01

    Objective:To provide basis for single nucleotide polymorphisms (SNPs) determination and analysis for R0R2 genes related etiologic studies in Chinese Hans in Beijing (CHB) and Yoruban in Iba-dan in Nigeria ( YRI) populations. Methods: SNPs in R0R2 gene were analyzed and compared for minor allele frequencies (MAFs) , haplotype frequencies, linkage disequilibrium patterns, and tag SNPs using CHB and YRI data from HapMap by Haploview 4. 2 program. SNPs were screened for eligibility using quality control criteria of genotyping call rate >80% , Hardy-Weinberg equilibrium test P >0.01, gender difference P>0. 05 and MAF >0. 01. Tag SNPs were determined under the criteria for r2≥0. 8 and logarithm of the odds radio ≥3 in pairwise eligible SNPs and compared between the CHB and YRI samples. Common Tag SNPs for CHB and YRI were reported by Haploview program directly or identified a-mong SNPs which were higly related to Haploview program directly reported tag SNPs by SPSS 13. 0. Results: Among the 404 and 403 SNPs genotyped in ROR2 genes in the CHB and YRI samples released by HapMap project, there were five SNPs located at exon 6 or 9 where changes of alleles for rs 1076112 and rs 10820900 caused missense mutation. Among the 394 SNPs genotyped in both the populations, a total number of 101 (25. 6% ) SNPs were monotonic among which 66 (65. 3% ) SNPs were common in both CHB and YRI. The rs 1135150 and rs2230577 which were monotonic in YRI and eligible in CHB located at exon 9. Nine ungenotyped SNPs in CHB were all eligible in YRI, and 6 out of 10 ungenotyped SNPs in YRI were eligible in CHB. The proportion of common SNPs (214) were 81.4% and 73. 3% in eligible CHB (263) and YRI (292) SNPs where 177 (82. 7% ) had the same minor alleles and 30 SNPs also had MAF difference ratios<20% that represented 11.4% and 10.3% of the total number of eligible SNPs in CHB and YRI respectively. Among the 18 and 26 haplotype blocks formed in 214 common eligible SNPs, two independent

  6. Space-frequency analysis with parallel computing in a phase-sensitive optical time-domain reflectometer distributed sensor.

    Science.gov (United States)

    Hui, Xiaonan; Ye, Taihang; Zheng, Shilie; Zhou, Jinhai; Chi, Hao; Jin, Xiaofeng; Zhang, Xianmin

    2014-10-01

    For a phase-sensitive optical time-domain reflectometer (ϕ-OTDR) distributed sensor system, space-frequency analysis can reduce the false alarm by analyzing the frequency distribution compared with the traditional difference value method. We propose a graphics processing unit (GPU)-based parallel computing method to perform multichannel fast Fourier transform (FFT) and realize the real-time space-frequency analysis. The experiment results show that the time taken by the multichannel FFT decreased considerably based on this GPU parallel computing. The method can be completed with a sensing fiber up to 16 km long and an entry-level GPU. Meanwhile, the GPU can reduce the computing load of the central processing unit from 70% down to less than 20%. We carried out an experiment on a two-point space-frequency analysis, and the results clearly and simultaneously show the vibration point locations and frequency components. The sensor system outputs the real-time space-frequency spectra continuously with a spatial resolution of 16.3 m and frequency resolution of 2.25 Hz.

  7. Real-Time Analysis of an Active Distribution Network - Coordinated Frequency Control for Islanding Operation

    DEFF Research Database (Denmark)

    Cha, Seung-Tae

    of the BESS as a primary frequency regulator during island-ing transition. The effectiveness of proposed primary frequency control strategy is illus-trated by using two test cases (i.e. IEEE 9-bus and Bornholm). In both cases, the fre-quency regulation performance is highly improved without degrading...

  8. Life History, Diet, Abundance and Distribution, and Length-Frequencies of Selected Invertebrates in Florida Bay, Everglades National Park, Florida

    OpenAIRE

    Powell, Allyn B.; LaCroix, Michael W.; Cheshire, Robin T.; Thayer, Gordon W.

    2006-01-01

    This report presents information on the life history, diet, abundance and distribution, and length-frequency distributions of five invertebrates in Florida Bay, Everglades National Park. Collections were made with an otter trawl in basins on a bi-monthly basis. Non-parametric statistics were used to test spatial and temporal differences in the abundance of invertebrates when numbers were appropriate (i. e., $25). Invertebrate species are presented in four sections. The sections on Life H...

  9. Correlation between carboxylesterase alleles and insecticide resistance in Culex pipiens complex from China

    Directory of Open Access Journals (Sweden)

    Liu Yangyang

    2011-12-01

    Full Text Available Abstract Background In China, large amounts of chemical insecticides are applied in fields or indoors every year, directly or indirectly bringing selection pressure on vector mosquitoes. Culex pipiens complex has evolved to be resistant to all types of chemical insecticides, especially organophosphates, through carboxylesterases. Six resistant carboxylesterase alleles (Ester were recorded previously and sometimes co-existed in one field population, representing a complex situation for the evolution of Ester genes. Results In order to explore the evolutionary scenario, we analyzed the data from an historical record in 2003 and a recent investigation on five Culex pipiens pallens populations sampled from north China in 2010. Insecticide bioassays showed that these five populations had high resistance to pyrethroids, medium resistance to organophosphates, and low resistance to carbamates. Six types of Ester alleles, EsterB1, Ester2, Ester8, Ester9, EsterB10, and Ester11 were identified, and the overall pattern of their frequencies in geographic distribution was consistent with the report seven years prior to this study. Statistical correlation analysis indicated that Ester8 and Ester9 positively correlated with resistance to four insecticides, and EsterB10 to one insecticide. The occurrences of these three alleles were positively correlated, while the occurrence of EsterB1 was negatively correlated with Ester8, indicating an allelic competition. Conclusion Our analysis suggests that one insecticide can select multiple Ester alleles and one Ester allele can work on multiple insecticides. The evolutionary scenario of carboxylesterases under insecticide selection is possibly "one to many".

  10. Determination of impact crater size-frequency distributions in GIS environments

    Science.gov (United States)

    Kneissl, Thomas; van Gasselt, Stephan; Neukum, Gerhard

    2010-05-01

    Analysis of crater size-frequency distributions (CSFD) of impact craters on planetary surfaces is a well-established method to derive absolute ages on the basis of remotelysensed image data. Although modelling approaches and the derivation of absolute ages from a given CSFD have been described in considerable depth since the late 1960s, there is no standardized methodology and guideline for measuring impact-crater diameters and area sizes that are both needed in order to determine absolute ages in a correct way. Distortions of distances (i.e., diameters) and areas within different map projections are considerable error sources within this measurement phase. In order to address that problem and to minimize such errors, a software extension for ESRI's ArcMap (ArcGIS) has been developed where CSFDs on planetary surfaces can be measured independently of image and data frame map projections and which can be theoretically transferred to every GI system capable of working with different map projections. Using this new approach each digitized impact crater is internally projected to a stereographic map projection with the crater's central-point set as the projection center. In this projection the circle is defined without any distortion of its shape (i.e., conformality). Using a sinusoidal map projection with a center longitude set to the crater's centralpoint, the diameter of the impact crater is measured along this central meridian which is true-scale and does not show any distortion. The crater is re-projected to the map projection of the current data frame and stored as vector geometry with attributes (shapefile). Output of this workflow comprises correct impact-crater diameters and area sizes in sinusoidal map projections and can be used for further processing, e.g., absolute age determinations. For GIS-based measurements we strongly recommend our procedure to be the standardised methodology to determine CSFD on planetary surfaces in order to minimize map distortion

  11. Frequency distributions of Escherichia coli in the confectionery products offered in retail market in Isfahan

    Directory of Open Access Journals (Sweden)

    Rasoul Rezaei

    2016-06-01

    Full Text Available Introduction: Raw ingredients used in confectionary carry high risk of infection with Escherichia coli. Since confectionaries are offered in the market in quite varied forms and types and there is a great difference in the sanitary status of the confectionaries, this study aimed at evaluation of E.coli   frequency distribution in different types of confectionery products in Isfahan market. In addition, the effect of moisture content, products category and the sanitary level of the confectionaries as well as product types (Industrially or traditionally produced on the contamination level were studied. Materials and methods: A total of 200 samples were randomly collected from confectioneries in Isfahan city through simple random sampling method. Preparation and dilution procedures were conducted under sterile conditions. Samples were cultured on EMB agar medium. Later, some of the positive isolates were randomly selected and confirmed by TSI and IMVIC test. Data analysis was performed using descriptive indices. Also, one way ANOVA and LSD test or independent t test were applied to determine the statistically significant difference between the mean E.coli cell numbers in the categorized groups of sweets. Results: It was found that 19% of the total tested samples were contaminated with E.coli strains. The mean, median and maximum of contamination were (35±.5, (0 and (3.4 CFU/gr, respectively. Moisture content, products category and being traditionally or industrially produced have significant effects on the level of contamination; while, the sanitary status of the traditional confectionaries as graded in this study has no impact on the average E.coli cell count. Discussion and conclusion: Regarding the microbial quality, at least about 25% of the sweets in the market do not meet the national standards of confectionary products. Implementation of strict hygiene regulation in the traditional confectionaries is in need to provide the public with

  12. Determination of High-Frequency Current Distribution Using EMTP-Based Transmission Line Models with Resulting Radiated Electromagnetic Fields

    Energy Technology Data Exchange (ETDEWEB)

    Mork, B; Nelson, R; Kirkendall, B; Stenvig, N

    2009-11-30

    Application of BPL technologies to existing overhead high-voltage power lines would benefit greatly from improved simulation tools capable of predicting performance - such as the electromagnetic fields radiated from such lines. Existing EMTP-based frequency-dependent line models are attractive since their parameters are derived from physical design dimensions which are easily obtained. However, to calculate the radiated electromagnetic fields, detailed current distributions need to be determined. This paper presents a method of using EMTP line models to determine the current distribution on the lines, as well as a technique for using these current distributions to determine the radiated electromagnetic fields.

  13. A New Function for Modelling Diameter Frequency Distribution in the Tropical Rain Forest of Xishuangbanna, Southwest of China

    Institute of Scientific and Technical Information of China (English)

    Lu Yuanchang; Lei Xiangdong; Jiang Lei

    2003-01-01

    Permanent plots in the montane tropical rain forests in Xishuangbanna, southwest China, were established, and different empirical models, based on observation data of these plots in 1992, were built to model diameter frequency distributions. The focus of this study is on predicting accuracy of stem number in the larger diameter classes, which is much more important than that of the smaller trees, from the view of forest management, and must be adequately considered in the modelling and estimate. There exist 3 traditional ways of modelling the diameter frequency distribution: the negative exponential function model, limiting line function model, and Weibull distribution model. In this study, a new model, named as the logarithmic J-shape function, together with the others, was experimented and was found as a more suitable model for modelling works in the tropical forests.

  14. A Frequency-List of Sentence Structures: Distribution of Kernel Sentences

    Science.gov (United States)

    Geens, Dirk

    1974-01-01

    A corpus of 10,000 sentences extracted from British theatrical texts was used to construct a frequency list of kernel sentence structures. Thirty-one charts illustrate the analyzed results. The procedures used and an interpretation of the frequencies are given. Such lists might aid foreign language teachers in course organization. Available from…

  15. Collective properties of injection-induced earthquake sequences: 2. Spatiotemporal evolution and magnitude frequency distributions

    Science.gov (United States)

    Dempsey, David; Suckale, Jenny; Huang, Yihe

    2016-05-01

    Probabilistic seismic hazard assessment for induced seismicity depends on reliable estimates of the locations, rate, and magnitude frequency properties of earthquake sequences. The purpose of this paper is to investigate how variations in these properties emerge from interactions between an evolving fluid pressure distribution and the mechanics of rupture on heterogeneous faults. We use an earthquake sequence model, developed in the first part of this two-part series, that computes pore pressure evolution, hypocenter locations, and rupture lengths for earthquakes triggered on 1-D faults with spatially correlated shear stress. We first consider characteristic features that emerge from a range of generic injection scenarios and then focus on the 2010-2011 sequence of earthquakes linked to wastewater disposal into two wells near the towns of Guy and Greenbrier, Arkansas. Simulations indicate that one reason for an increase of the Gutenberg-Richter b value for induced earthquakes is the different rates of reduction of static and residual strength as fluid pressure rises. This promotes fault rupture at lower stress than equivalent tectonic events. Further, b value is shown to decrease with time (the induced seismicity analog of b value reduction toward the end of the seismic cycle) and to be higher on faults with lower initial shear stress. This suggests that faults in the same stress field that have different orientations, and therefore different levels of resolved shear stress, should exhibit seismicity with different b-values. A deficit of large-magnitude events is noted when injection occurs directly onto a fault and this is shown to depend on the geometry of the pressure plume. Finally, we develop models of the Guy-Greenbrier sequence that captures approximately the onset, rise and fall, and southwest migration of seismicity on the Guy-Greenbrier fault. Constrained by the migration rate, we estimate the permeability of a 10 m thick critically stressed basement

  16. Distributed Generation Integration in the Electric Grid: Energy Storage System for Frequency Control

    Directory of Open Access Journals (Sweden)

    Maurizio Delfanti

    2014-01-01

    Full Text Available During the last few years generation from renewable energy sources (RESs has grown considerably in European electrical networks. Transmission system operators are greatly concerned about the impact of RESs on the operational security and efficiency of their networks and more in general of the ENTSO-E interconnected system. Grid codes are to be revised in order to harmonise the rules regarding the connection of RES power plants. A main issue concerns frequency control: frequency is greatly affected by RESs intermittency and its deviations must be limited as much as possible in order to guarantee a suitable level of power quality. To improve frequency stability, in the future, Grid codes could extend frequency control requirements also to RES units, whereas today they are applied only to conventional power plants. Energy storage systems can be a possible solution to increase the flexibility and performance of RES power plants: they allow generators to modulate their power injections without wasting renewable energy. In this paper, the authors studied the suitability of extending frequency control to RES units integrating them with energy storage systems. In particular, the paper focuses on the impact of frequency control on the storage lifetime by analysing the power charge/discharge in response to real frequency oscillations.

  17. The Impact Crater Size-Frequency Distribution on Pluto Follows a Truncated Pareto Distribution: Results from a First Data Set Based on the Recent New Horizons' Flyby

    CERN Document Server

    Zaninetti, L

    2015-01-01

    Recently it could be shown ( that the impact crater size-frequency distribution of Pluto (based on an analysis of first images obtained by the recent New Horizons flyby) follows a power law alpha = 2.4926 in the interval of diameter (D) values ranging from 3.75 km to the largest determined value of 37.77 km. A reanalysis of this data set revealed that the whole crater SFD (i.e., with values in the interval of 1.2-37.7 km) can be described by a truncated Pareto distribution.

  18. HLA-A and HLA-B alleles associated in psoriasis patients from Mumbai, Western India

    Directory of Open Access Journals (Sweden)

    Shankarkumar Umapathy

    2011-01-01

    Full Text Available Background: Psoriasis, a common autoimmune disorder characterized by T cell-mediated keratinocyte hyperproliferation, is known to be associated with the presence of certain specific Human Leukocyte Antigen (HLA alleles. Aim: To evaluate distribution of HLA-A and HLA-B alleles and hence identify the susceptible allele of psoriasis from patients in Western India. Materials and Methods: The study design included 84 psoriasis patients and 291 normal individuals as controls from same geographical region. HLA-A and HLA-B typing was done using Serology typing. Standard statistical analysis was followed to identify the odds ratio (OR, allele frequencies, and significant P value using Graphpad software. Results: The study revealed significant increase in frequencies of HLA-A2 (OR-3.976, P<0.0001, B8 (OR-5.647, P<0.0001, B17 (OR-5.452, P<0.0001, and B44 (OR-50.460, P<0.0001, when compared with controls. Furthermore, the frequencies of HLA-A28 (OR-0.074, P=0.0024, B5 (OR-0.059, P<0.0001, B12 (OR-0.051, P=0.0002, and B15 (OR-0.237, P=0.0230 were significantly decreased in psoriasis patients. Conclusion: This study shows the strong association of HLA-A2, B8, and B17 antigens with psoriasis conferring susceptibility to psoriasis patients from Western India, while the antigens HLA-A28, B5, and B12 show strong negative association with the disease.

  19. Time variation in amplitude-frequency distribution of deep non-volcanic tremors in the Bungo Channel region, southwest Japan

    Science.gov (United States)

    Hanakawa, Y.; Suda, N.

    2009-12-01

    Magnitude-frequency distribution of earthquakes follows the Gutenberg-Richter law. The slope of this law, b value, represents the relative occurrence of large and small earthquakes. Since magnitude is defined as corrected logarithmic amplitude, amplitude-frequency distribution of earthquakes is linear on log-log graph. On the other hand, that of non-volcanic tremors is linear on semi-log graph, indicating that it follows the exponential distribution, not the power-law distribution [Hiramatsu et al., 2008]. Thus the slope of amplitude-frequency distribution for tremors is equivalent to b value for earthquakes. In this study, we investigated time variation in the slope of amplitude-frequency distribution from analyses of tremor activities in the Bungo Channel region, where long-term slow slip events occurred in 1997 and 2003. We analyzed vertical-component records from Hi-net and the seismic networks of Japan Meteorological Agency and universities for the five-year period between 2004 and 2008. We also used records from the temporal seismic station in Hiburi Island installed by us in the period after Sept. 2004. In the Bungo Channel region, tremor activity occurs with a recurrence interval of approximately two months. We observed a total of 35 activities including small ones in the analysis period. To detect tremors and determine their hypocenters, we used the same software as Automatic Tremor Monitoring System (ATMOS) [Suda et al., in press]. We obtained frequency distribution of reduced displacements (RDs) for each tremor activity. RD is RMS amplitude of ground displacement corrected with hypocentral distance [Aki and Koyanagi, 1981], and it is proportional to seismic moment rate. The observed slopes of RD-frequency distribution for active swarms were approximately constant in the period between 2004 and 2006, but they declined in 2007. At the end of 2008, the slopes decreased bellow half the values between 2004 and 2006. As well as b value, the slope represents

  20. Practical implementation and evaluation of a quantum-key-distribution scheme based on the time-frequency uncertainty

    Science.gov (United States)

    Leifgen, Matthias; Elschner, Robert; Perlot, Nicolas; Weinert, Carl; Schubert, Colja; Benson, Oliver

    2015-10-01

    We implement a quantum-key-distribution protocol which works in analogy to the BB84 protocol with two discrete states each in frequency and time. Its security relies on the frequency-time uncertainty. We show how the protocol is realized with commercial telecom components and discuss technical constraints of existing equipment. In order to evaluate the performance and the security of the protocol against specific attacks we explore quantitatively a large set of parameters. Based on these studies we suggest how further enhancement of security can be obtained with existing technology.

  1. Distributed Raman optical amplification in phase coherent transfer of optical frequencies

    CERN Document Server

    Clivati, Cecilia; Calonico, Davide; Faralli, Stefano; Levi, Filippo; Mura, Alberto; Poli, Nicola

    2012-01-01

    We describe the application of Raman Optical-fiber Amplification (ROA) for the phase coherent transfer of optical frequencies in an optical fiber link. ROA uses the transmission fiber itself as a gain medium for bi-directional coherent amplification. In a test setup we evaluated the ROA in terms of on-off gain, signal-to-noise ratio, and phase noise added to the carrier. We transferred a laser frequency in a 200 km optical fiber link with an additional 16 dB fixed attenuator (equivalent to 275 km of fiber on a single span), and evaluated both co-propagating and counter-propagating amplification pump schemes, demonstrating nonlinear effects limiting the co-propagating pump configuration. The frequency at the remote end has a fractional frequency instability of 3e-19 over 1000 s with the optical fiber link noise compensation.

  2. On the Binning and Associated Uncertainty of Crater Diameter Size-Frequency Distributions

    Science.gov (United States)

    Weaver, B. P.; Robbins, S. J.; Plesko, C. S.; Riggs, J. D.

    2015-05-01

    The tabulation and graphical display of crater size-frequency data (crater diameters) is a critical part of analyzing crater populations, but despite a landmark 1979 paper, standardization remains elusive. We will discuss recommendations.

  3. Controller design for flexible, distributed parameter mechanical arms via combined state space and frequency domain techniques

    Science.gov (United States)

    Book, W. J.; Majett, M.

    1982-01-01

    The potential benefits of the ability to control more flexible mechanical arms are discussed. A justification is made in terms of speed of movement. A new controller design procedure is then developed to provide this capability. It uses both a frequency domain representation and a state variable representation of the arm model. The frequency domain model is used to update the modal state variable model to insure decoupled states. The technique is applied to a simple example with encouraging results.

  4. The role of human demographic history in determining the distribution and frequency of transferase-deficient galactosaemia mutations.

    LENUS (Irish Health Repository)

    Flanagan, J M

    2010-02-01

    Classical or transferase-deficient galactosaemia is an inherited metabolic disorder caused by mutation in the human Galactose-1-phosphate uridyl transferase (GALT) gene. Of some 170 causative mutations reported, fewer than 10% are observed in more than one geographic region or ethnic group. To better understand the population history of the common GALT mutations, we have established a haplotyping system for the GALT locus incorporating eight single nucleotide polymorphisms and three short tandem repeat markers. We analysed haplotypes associated with the three most frequent GALT gene mutations, Q188R, K285N and Duarte-2 (D2), and estimated their age. Haplotype diversity, in conjunction with measures of genetic diversity and of linkage disequilibrium, indicated that Q188R and K285N are European mutations. The Q188R mutation arose in central Europe within the last 20 000 years, with its observed east-west cline of increasing relative allele frequency possibly being due to population expansion during the re-colonization of Europe by Homo sapiens in the Mesolithic age. K285N was found to be a younger mutation that originated in Eastern Europe and is probably more geographically restricted as it arose after all major European population expansions. The D2 variant was found to be an ancient mutation that originated before the expansion of Homo sapiens out of Africa.

  5. A Study of GluK1 Kainate Receptor Polymorphisms in Down Syndrome Reveals Allelic Non-Disjunction at 1173(C/T

    Directory of Open Access Journals (Sweden)

    Debarati Ghosh

    2009-01-01

    Full Text Available Mechanisms underlying Down syndrome (DS-related mental retardation (MR remain poorly understood. In trisomic offspring, non-disjunction may result in the reduction to homozygosity of a susceptibility allele inherited from a heterozygous parent. Accordingly, we sought evidence for allelic non-disjunction in the GluK1 gene that encodes the critical kainite-binding glutamate receptor subunit-5, maps to chromosome 21q22.1 in the DS critical region and is expressed in brain regions responsible for learning and memory. Three polymorphisms of GluK1 [522(A/C rs363538; 1173(C/T rs363430 and 2705(T/C rs363504] were genotyped in 86 DS patient families by means of PCR-coupled RFLP assays and evaluated with respect to allele frequency, heterozygosity, linkage disequilibrium, stage and parental origin of allelic non-disjunction. We report that the distribution of allele frequencies is in Hardy-Weinberg equilibrium. Moderate heterozygosity (0.339 and a major allele frequency of 0.78 render the 1173(C/T marker informative. Pair-wise comparisons reveal that 522(A/C-1173(C/T [χ2 = 31.2, df = 1, p = 0.0001; D’ = 0.42] and 1173(C/T-2705(T/C [χ2 = 18.3, df = 1, p = 0.0001; D’ = 0.34] are in significant linkage disequilibrium of weak magnitude. The estimated ratio of meiosis-I to meiosis-II errors arising from allelic non-disjunction of 1173(C/T is 4:1 in maternal cases and 2:1 in paternal cases. Studies including additional markers and patient samples are warranted to further substantiate present findings.

  6. A simple marriage model for the power-law behaviour in the frequency distributions of family names

    Science.gov (United States)

    Wu, Hao-Yun; Chou, Chung-I.; Tseng, Jie-Jun

    2011-01-01

    In many countries, the frequency distributions of family names are found to decay as a power law with an exponent ranging from 1.0 to 2.2. In this work, we propose a simple marriage model which can reproduce this power-law behaviour. Our model, based on the evolution of families, consists of the growth of big families and the formation of new families. Preliminary results from the model show that the name distributions are in good agreement with empirical data from Taiwan and Norway.

  7. Intensity-modulated linear-frequency-modulated continuous-wave lidar for distributed media: fundamentals of technique

    OpenAIRE

    Batet Torrell, Óscar; Dios Otín, Víctor Federico; Comerón Tejero, Adolfo; Agishev, Ravil R.

    2010-01-01

    We analyze the intensity-modulation frequency-modulated continuous-wave (FMCW) technique for lidar remote sensing in the context of its application to distributed media. The goal of the technique is the reproduction of the sounded-medium profile along the emission path. A conceptual analysis is carried out to show the problems the basic version of the method presents for this application. The principal point is the appearance of a bandpass filtering effect, which seems to hinder its use in...

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

    Science.gov (United States)

    Parolín, Maria L; Carnese, Francisco R

    2009-04-01

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

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

    Science.gov (United States)

    Parolín, Maria L; Carnese, Francisco R

    2009-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Maria L. Parolín

    2009-01-01

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

  11. Frequency analysis for planned islanding operation in the Danish distribution system - Bornholm

    DEFF Research Database (Denmark)

    Chen, Yu; Xu, Zhao; Østergaard, Jacob

    2008-01-01

    The power system in the Danish island Bornholm is a distribution system with a high penetration of wind generation, which is representative for expected future power systems. During the period from 11th to 14th September 2007, the Distribution System Operator (DSO) Ostkraft in Bornholm conducted ...

  12. Altered Frequency Distribution in the Electroencephalogram is Correlated to the Analgesic Effect of Remifentanil

    DEFF Research Database (Denmark)

    Graversen, Carina; Malver, Lasse P; Kurita, Geana P;

    2015-01-01

    Opioids alter resting state brain oscillations by multiple and complex factors, which are still to be elucidated. To increase our knowledge, multi-channel electroencephalography (EEG) was subjected to multivariate pattern analysis (MVPA), to identify the most descriptive frequency bands and scalp...... individual changes in heat pain in the delta (p = 0.045), theta (p = 0.038) and alpha (p = 0.039) bands and to bone pain in the alpha band (p = 0.0092). Hence, MVPA of multi-channel EEG was able to identify frequency bands and corresponding channels most sensitive to altered brain activity during...... locations altered by remifentanil in healthy volunteers. Sixty-two channels of resting EEG followed by independent measures of pain scores to heat and bone pain were recorded in 21 healthy males before and during remifentanil infusion in a placebo-controlled, double-blind crossover study. EEG frequency...

  13. Apolipoprotein E Alleles, Dyslipidemia,and Coronary Heart Disease

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective To describe the association between apolipoprotein E alleles, dyslipidemia, and coronary heart disease (CHD). Methods Using polymerase chain reaction (PCR) the restriction fragment length polymorphism (RFLP), we studied the apolipoprotein E genotypes in 142 patients with coronary artery disease (CAD) and 131 age-matched healthy subjects, as well as the association between apolipoprotein, plasma lipids, and CHD. Results Compared with the E3 allele, the E4 allele was associated with elevated total cholesterol (TC) values (average increase about 0.32-0.58 mmol/L), low-density lipoprotein cholesterol (LDL-C) values, and apolipoprotein B (APOB). The E2 allele has opposite effects (average decrease about 0.34-0.61 mmol/L at TC). Both in cases and controls, the allelic frequency of E3/3 was highest, reaching 67.8% of whole volume, hemozygote of apo E3 was moderate, and homozygote E4/4 was low, E2/2 and E4/2 were rare. The frequencies of E3/4 and E4/4 were significantly higher in patients with CAD compared with controls (P<0.001).Conclusion Apolipoprotein E alleles are important genetic markers for dyslipidemia and CHD.The carrier of E4 gene was the risk factor of CHD.

  14. Distributed Raman optical amplification in phase coherent transfer of optical frequencies

    OpenAIRE

    Clivati, Cecilia; Bolognini, Gabriele; Calonico, Davide; Faralli, Stefano; Levi, Filippo; Mura, Alberto; Poli, Nicola

    2012-01-01

    We describe the application of Raman Optical-fiber Amplification (ROA) for the phase coherent transfer of optical frequencies in an optical fiber link. ROA uses the transmission fiber itself as a gain medium for bi-directional coherent amplification. In a test setup we evaluated the ROA in terms of on-off gain, signal-to-noise ratio, and phase noise added to the carrier. We transferred a laser frequency in a 200 km optical fiber link with an additional 16 dB fixed attenuator (equivalent to 27...

  15. Root system topology and diameter distribution of species from habitats differing in inundation frequency

    NARCIS (Netherlands)

    Bouma, T.J.; Nielsen, K.F.; Van Hal, J.; Koutstaal, B.P.

    2001-01-01

    1. We compared the root systems of seven halophytic species that occur at different elevations on a salt marsh, in order to (i) test the hypothesis that variations in root system architecture reflect adaptation to inundation frequency or nitrogen limitation, and (ii) verify the theoretically predict

  16. A low-frequency distributed aperture array for radio astronomy in space

    OpenAIRE

    Boonstra, A.J.; Saks, N.; Falcke, H.; Klein-Wolt, M.; Bentum, M.J.; Rajan, R.T.; Wijnholds, S. J.; Arts, M.; Klooster, van 't, K.; Beliën, F.

    2010-01-01

    The frequency band below 30 MHz is one of the last unexplored bands in radio astronomy. This band is well suited for studying the early cosmos at high hydrogen redshifts, the so-called dark ages, extragalactic surveys, (extra) solar planetary bursts, and high energy particle physics. In addition, space research such as space weather tomography, are also areas of scientific interest.

  17. A low-frequency distributed aperture array for radio astronomy in space

    NARCIS (Netherlands)

    Boonstra, A.J.; Saks, N.; Falcke, H.; Klein-Wolt, M.; Bentum, M.J.; Rajan, R.T.; Wijnholds, S.J.; Arts, M.; Klooster, van 't K.; Beliën, F.

    2010-01-01

    The frequency band below 30 MHz is one of the last unexplored bands in radio astronomy. This band is well suited for studying the early cosmos at high hydrogen redshifts, the so-called dark ages, extragalactic surveys, (extra) solar planetary bursts, and high energy particle physics. In addition, sp

  18. DARIS : a low-frequency distributed aperture array for radio astronomy in space

    NARCIS (Netherlands)

    Boonstra, A.J.; Saks, N.; Falcke, H.; Klein-Wolt, M.; Bentum, M.J.; Rajan, R.T.; Wijnholds, M.; Arts, M.; Klooster, van 't K.; Beliën, F.

    2010-01-01

    The frequency band below 30 MHz is one of the last unexplored bands in radio astronomy. This band is well suited for studying the early cosmos at high hydrogen redshifts, the so-called dark ages, extragalactic surveys, (extra) solar planetary bursts, and high energy particle physics. In addition, sp

  19. Improving Frequency Stability Based on Distributed Control of Multiple Load Aggregators

    DEFF Research Database (Denmark)

    Hu, Jianqiang; Cao, Jinde; Guerrero, Josep M.;

    2016-01-01

    loads, to provide frequency regulation services. Specifically, a leader-following communication protocol is considered for the load aggregators in which there is a centralized pinner (leader) and multiple load aggregators (followers). The regulation objective is generated from the pinner and only shared...

  20. The molecular determination of HLA-Cw alleles in the Mandenka (West Africa) reveals a close genetic relationship between Africans and Europeans.

    Science.gov (United States)

    Sanchez-Mazas, A; Steiner, Q G; Grundschober, C; Tiercy, J M

    2000-10-01

    HLA-Cw alleles were determined by high-resolution polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) oligotyping in a sample of 165 Mandenka, a population from Eastern Senegal previously analysed for A/B and DRB/DQB polymorphisms. A total of 18 Cw alleles were identified, with Cw*0401/5 and 1601 accounting for a combined frequency of 36%. A comparison of Cw allele frequencies among several populations of different origins, Mandenka, Swiss, English, Ashkenazi Jews from the UK and Japanese, reveals a high genetic heterogeneity among them, but also a much closer relationship between Mandenka, Europeans and Ashkenazi than between any of these populations and Japanese. Cw*0501, Cw*0701 and Cw*1601, among others, appear to be restricted to the European and African populations. Many B-Cw haplotypes exhibit a significant linkage disequilibrium in the Mandenka, among which B*3501-Cw*0401 and B*7801-Cw*1601, formed by the most frequent B and Cw alleles, and B*5201-Cw*1601, B*5702-Cw*18 and B*4410-Cw*0401, not yet observed in other populations. B*3501-Cw*0401 is found with similar frequencies in Europeans. The results possibly support a close historical relationship between Africans and Europeans as compared to East Asiatics. However, the HLA-Cw frequency distributions are characterised by an excess of heterozygotes, indicating that balancing selection may have played a role in the evolution of this polymorphism.

  1. Signal processing method based on group delay calculation for distributed Bragg wavelength shift in optical frequency domain reflectometry.

    Science.gov (United States)

    Wada, Daichi; Igawa, Hirotaka; Murayama, Hideaki; Kasai, Tokio

    2014-03-24

    A signal processing method based on group delay calculations is introduced for distributed measurements of long-length fiber Bragg gratings (FBGs) based on optical frequency domain reflectometry (OFDR). Bragg wavelength shifts in interfered signals of OFDR are regarded as group delay. By calculating group delay, the distribution of Bragg wavelength shifts is obtained with high computational efficiency. We introduce weighted averaging process for noise reduction. This method required only 3.5% of signal processing time which was necessary for conventional equivalent signal processing based on short-time Fourier transform. The method also showed high sensitivity to experimental signals where non-uniform strain distributions existed in a long-length FBG.

  2. Relation between the shape of high frequency heating coil and the temperature distribution in specimen during thermal fatigue test

    International Nuclear Information System (INIS)

    The high frequency heating apparatus used for thermal fatigue tests, the relation between the shape of heating coils, and the temperature distribution of specimens was experimentally examined for SUS 304 stainless steel. Relations between heating coil dimensions and heating rate, the most ideal coil shape for various specimen types, and the effects of temperature range and specimen shape on temperature distribution are described. Results show that the heating rate increases with decreasing distance from specimen surface to heating coil and with increasing coil tube diameter. For the general cylindrical and hour glass type specimens, the most ideal coil shapes are a separate type and a parallel type coil, respectively, as judged from the point of temperature distribution. (U.S.)

  3. Distributed Control of Inverter-Based Lossy Microgrids for Power Sharing and Frequency Regulation Under Voltage Constraints

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Chin-Yao; Zhang, Wei

    2016-01-19

    This paper presents a new distributed control framework to coordinate inverter-interfaced distributed energy resources (DERs) in island microgrids. We show that under bounded load uncertainties, the proposed control method can steer the microgrid to a desired steady state with synchronized inverter frequency across the network and proportional sharing of both active and reactive powers among the inverters. We also show that such convergence can be achieved while respecting constraints on voltage magnitude and branch angle differences. The controller is robust under various contingency scenarios, including loss of communication links and failures of DERs. The proposed controller is applicable to lossy mesh microgrids with heterogeneous R/X distribution lines and reasonable parameter variations. Simulations based on various microgrid operation scenarios are also provided to show the effectiveness of the proposed control method.

  4. Conformists and Contrarians in a Kuramoto Model with Uniformly Distributed Natural Frequencies

    Institute of Scientific and Technical Information of China (English)

    YUAN Di; YANG Jun-Zhong

    2013-01-01

    A generalization of the Kuramoto model in which oscillators are coupled to the mean field with random signs is investigated in this work.We focus on a situation in which the natural frequencies of oscillators follow a uniform probability density.By numerically simulating the model,we find that the model supports a modulated travelling wave state except for already reported π state and travelling wave state in the one with natural frequencies following Lorenztian probability density or a delta function.The dependence of the observed dynamics on the parameters of the model is explored and we find that the onset of synchronization in the model displays a non-monotonic dependence on both positive and negative coupling strength.

  5. Spatial variations in the frequency-magnitude distribution of earthquakes in the southwestern Okinawa Trough

    OpenAIRE

    Lin, Jing-yi; Sibuet, Jean-claude; Lee, Chao-Shing; Hsu, Shu-kun; Klingelhoefer, Frauke

    2007-01-01

    The relations between the frequency of occurrence and the magnitude of earthquakes are established in the southern Okinawa Trough for 2823 relocated earthquakes recorded during a passive ocean bottom seismometer experiment. Three high b-values areas are identified: (1) for an area offshore of the Ilan Plain, south of the andesitic Kueishantao Island from a depth of 50 km to the surface, thereby confirming the subduction component of the island andesites; (2) for a body lying along the 123.3 d...

  6. Multiple-view time-frequency distribution based on the empirical mode decomposition

    OpenAIRE

    Stevenson, Nathan J.; Mesbah, Mostefa; Boashash, Boualem

    2010-01-01

    This paper proposes a composite TFD based on a multiple-view Approach where the IMFs of an EMD are used to construct a series of views in the ambiguity domain by highlighting concentrations of energy in the ambiguity domain and overcoming interferences in TFDs. (Additional details can be found in the comprehensive book on Time-Frequency Signal Analysis and Processing (see http://www.elsevier.com/locate/isbn/0080443354). In addition, the most recent upgrade of the original so...

  7. Allele frequencies of 5 short tandem repeat loci of Kashin-Beck disease patients on chromosome 12%大骨节病患者12号染色体5个短串联重复序列位点基因频率分析

    Institute of Scientific and Technical Information of China (English)

    平智广; 刘莉; 郭雄

    2008-01-01

    Objective To analyze the allele frequencies of 5 short tandem repeat(STR)loci(D12S313,D12S304,D12S1640,D12S1708 and D12S1583)on chromosome 12 among Kashin-Beck disease(KBD)patients and the control population living in the area suffered from KBD.Methods Fifty KBD patient8 and 50 non-KBD patients were chosen in endemic afea of Shaanxi Province,5 STR loci on chromosome 12 were genotyped by the technology of polymerase chain reacfion(PCR)and capillary electmphoresis.The pelymorphisms of STR in these popIllations were analyzed.The allele and genotype frequencies of each STR in the corresponding groups were caleulated and compared. Results In KBD group,the 5 STR loci had 8,6,7,5 and 11 types ofalleles and 17,11,15,8 and 28 genotypes, respectively;while in the control group,the number of aUele types of 5 STR loci were 6,8,6,4 and 10,the number of genotype of those loci were 13,21,14,8 and 23,respectively The allele frequence of D12S304 locus was statiBtically significant between KBD patients and controls(P<0.05),especially for the 319 bp allele(P<0.006 25). Conclusion There is an association between D12S304 locus and KBD.The 319 bp allele might play the key role.%目的 分析大骨节病(Kashin-Beck disease,KBD)病区患者与非患者在12号染色体上5个短串联重复序列(short tandem repeat,STR)位点的多态性并比较其差异.方法 在陕西省KBD病区选择KBD患者(病例组)和非KBD患者(对照组)各50人,采集静脉血,利用PCR扩增和毛细管电泳技术,对12号染色体上5个STR位点(D12S313、D12S304、D12S1640、D12S1708和D12S1583)进行分型,分析各位点在上述人群中的多态性,计算5个位点在相应人群中等位基因与基因型频率,对各位点的等位基冈及基因型频率进行比较.结果 上述5种位点,病例组分别检出8,6、7、5和11种等位基因以及17、11、15、8和28种基因型;在对照组中检出6、8、6、4和10种等位基因以及13、21、14、8和23种基因型;在D12S304位点,病

  8. Analysis of the HLA-A,-B allele polymorphism in 5844 umbilical cord blood samples taken from Han population of Shandong province

    Institute of Scientific and Technical Information of China (English)

    YUN PENG DAI; WEN YING YAN; BAI JUN SHEN; LI JUN CHEN; FEI GAO; HONG MEI WANG

    2006-01-01

    To investigate the HLA-A, -B allele polymorphism in Han population of Shandong province and to explore the possibility to find out the HLA-A,-B-matched cord blood donors for stem cell transplantation to be used in other area in China, 5844 umbilical cord blood samples were taken from Han population donors of Shandong province, and assayed with PCR-sequence-oligonucleotide (PCR-SSO) assay. In Shandong Han donors, 20 alleles at HLA-A locus and 46 alleles at HLA-B locus could be detected as revealed in the present study. Among the 20 alleles at HLA-A locus, the most prevalent five alleles included A * 02(0. 3041), A * 11 (0. 1443), A * 24(0. 1434), A * 30(0. 0975) and A * 33(0.0859), while, the alleles with lower gene frequencies included A * 34(0. 0006), A * 25 (0.0005), A * 66(0.0005), A * 74(0.0004) and A * (0.0001). Of the 46 HLA-B alleles detected, the most prevalent five alleles were B * 13(0. 1348), B * 51(0.0713), B * 62(0.0712), B * 61 (0.0676) and B * 60(0.0642); while alleles with lower gene frequencies included B * 77(0.0001),B * 76(0.0002), B * 47(0.0003), B * 42(0.0003) and B * 72(0.0004). In comparison with those of the other Han population in China, the HLA-A, -B gene frequencies in the umbilical cord blood of Shandong province possess unique distribution features among the investigated populations from various regions of the same race origin, and the differences in various regions of the same race were less than those among the different race. It is evident that the HLA-A,-B alleles of the umbilical cord blood taken in Shangdong province show high degree of polymorphism, and it might be part of those of Northern Han population in China. So, it is reasonable for patients of Northern Chinese to receive HLA class Ⅰ -match transplant of cord blood stem cells for tissue and organ transplantation from Shangdong umbilical cord blood bank.

  9. Radarclinometry: Bootstrapping the radar reflectance function from the image pixel-signal frequency distribution and an altimetry profile

    Science.gov (United States)

    Wildey, R.L.

    1988-01-01

    A method is derived for determining the dependence of radar backscatter on incidence angle that is applicable to the region corresponding to a particular radar image. The method is based on enforcing mathematical consistency between the frequency distribution of the image's pixel signals (histogram of DN values with suitable normalizations) and a one-dimensional frequency distribution of slope component, as might be obtained from a radar or laser altimetry profile in or near the area imaged. In order to achieve a unique solution, the auxiliary assumption is made that the two-dimensional frequency distribution of slope is isotropic. The backscatter is not derived in absolute units. The method is developed in such a way as to separate the reflectance function from the pixel-signal transfer characteristic. However, these two sources of variation are distinguishable only on the basis of a weak dependence on the azimuthal component of slope; therefore such an approach can be expected to be ill-conditioned unless the revision of the transfer characteristic is limited to the determination of an additive instrumental background level. The altimetry profile does not have to be registered in the image, and the statistical nature of the approach minimizes pixel noise effects and the effects of a disparity between the resolutions of the image and the altimetry profile, except in the wings of the distribution where low-number statistics preclude accuracy anyway. The problem of dealing with unknown slope components perpendicular to the profiling traverse, which besets the one-to-one comparison between individual slope components and pixel-signal values, disappears in the present approach. In order to test the resulting algorithm, an artificial radar image was generated from the digitized topographic map of the Lake Champlain West quadrangle in the Adirondack Mountains, U.S.A., using an arbitrarily selected reflectance function. From the same map, a one-dimensional frequency

  10. The Impact Crater Size-Frequency Distribution on Pluto Follows a Truncated Pareto Distribution: Results from a First Data Set Based on the Recent New Horizons' Flyby

    Directory of Open Access Journals (Sweden)

    Zaninetti L.

    2016-01-01

    Full Text Available Recently it could be shown (Scholkmann, Prog. in Phys. , 2016, v. 12(1, 26-29 that the impact crater size-frequency distribution of Pluto (based on an analysis of first images obtained by the recent New Horizons’ flyby follows a power law (α =2.4926±0.3309 in the interval of diameter ( D values ranging from 3.75±1.14 km to the largest deter- mined value of 37.77 km. A reanalysis of this data set revealed that the whole crater SFD (i.e., with values in the interval of 1.2–37.7 km can be described by a truncated Pareto distribution.

  11. Voltage and frequency control in the Islanded portion of the CIGRE Low Voltage distribution network

    DEFF Research Database (Denmark)

    Mustafa, Ghullam; Bak, Claus Leth; Buriro, Ehsan Ali

    2016-01-01

    Islanding is a condition where a portion of the power network comprising of the loads and Distributed Generation units is isolated from the rest of the power grid and forms a Micro Grid. In this condition, it becomes essential for the islanded MG to operate in a stable and controlled manner by pr...

  12. THE CHARACTERISTICS OF THUNDERSTORM FREQUENCY VARIATION AND THEIR POSSIBLE RELATION WITH THE ADJUSTMENT OF CROP DISTRIBUTION IN THE LEIZHOU PENINSULA

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yu; NIU Sheng-jie

    2009-01-01

    In order to research possible influences of the adjustment of plant distribution on the development frequency of thunderstorms over the Leizhou Peninsula,mathematic statistic methods, including correlation analyses,11 kinds of fitting models and all-variable regression methods,were used for analyses and research. The results show that the average trend of the number of annual thunderstorm days is descending obviously,and there are thunderstorms in all seasons,in which warm post-midday thunderstorms have taken up the most part,and high frequency is found from May to September,and the starting and ending dates of thunderstorms have a great annual discrepancy. The vegetation structure has been improved along with the reduction of rice fields and the area increment of sugarcane and fruits planting,which results in the decrease of the number of thunderstorm days; the change in the characteristics of winter spare fields,which is caused by the planting of vegetables,limits the formation of thunderstorms in early winter and late spring. Meanwhile,the area adjustment of peanut planting has little influence on the variation of thunderstorm days. The adjustment of principal crop distribution,such as rice, sugarcane,fruits and vegetables,may have obvious influence on the formation of thunderstorms,and sugarcane has the largest effect,followed in turn by rice,vegetables and fruits,and the adjustment of crop distribution has little influence on the starting and ending dates of thunderstorms.

  13. The diversity of bovine MHC class II DRB3 and DQA1 alleles in different herds of Japanese Black and Holstein cattle in Japan.

    Science.gov (United States)

    Miyasaka, Taku; Takeshima, Shin-nosuke; Matsumoto, Yuki; Kobayashi, Naohiko; Matsuhashi, Tamako; Miyazaki, Yoshiyuki; Tanabe, Yoshihiro; Ishibashi, Kazuki; Sentsui, Hiroshi; Aida, Yoko

    2011-02-01

    In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for bovine diseases and immunological traits. In this study, we sequenced alleles of the BoLA class II loci, BoLA-DRB3 and BoLA-DQA1, from 650 Japanese cattle from six herds [three herds (507 animals) of Japanese Black cattle and three herds (143 animals) of Holstein cattle] using polymerase chain reaction-sequence-based typing (PCR-SBT) methods. We identified 26 previously reported distinct DRB3 alleles in the two populations: 22 in Japanese Black and 17 in Holstein. The number of DRB3 alleles detected in each herd ranged from 9 to 20. Next, we identified 15 previously reported distinct DQA1 alleles: 13 in Japanese Black and 10 in Holstein. The number of alleles in each herd ranged from 6 to 10. Thus, allelic divergence is significantly greater for DRB3 than for DQA1. A population tree on the basis of the frequencies of the DRB3 and DQA1 alleles showed that, although the genetic distance differed significantly between the two cattle breeds, it was closely related within the three herds of each breed. In addition, Wu-Kabat variability analysis indicated that the DRB3 gene was more polymorphic than the DQA1 gene in both breeds and in all herds, and that the majority of the hypervariable positions within both loci corresponded to pocket-forming residues. The DRB3 and DQA1 heterozygosity for both breeds within each herd were calculated based on the Hardy-Weinberg equilibrium. Only one Japanese Black herd showed a significant difference between the expected and observed heterozygosity at both loci. This is the first report presenting a detailed study of the allelic distribution of BoLA-DRB3 and -DQA1 genes in Japanese Black and Holstein cattle from different farms in Japan. These results may help to develop improved livestock breeding strategies in the future. PMID:20965236

  14. Matrix factorization to time-frequency distribution for structural health monitoring

    Science.gov (United States)

    Chang, Chia-Ming; Huang, Shieh-Kung

    2016-04-01

    Structural health monitoring enables structural information to be acquired through sensing technology, and is of need to early detect problems and damages in structures. Health monitoring strategies are often realized through a combination of qualitative sensing systems and high-performance structural integrity assessment methods. Structural deviations can be then effectively identified by interpreting the raw sensor measurements using signal processing techniques. The objective of this study is to develop a new structural health monitoring method that applies a matrix factorization algorithm to a time-frequency representation of multi-channel signals measured from a structure. This method processes vibrational input and/or output responses of structures to improve raw data quality, to estimate structural responses, to derive signal features, and to detect structural variations. For example, the proposed method can reduce the signal noise by utilizing first few principle vectors to reconstruct the measured signals. For frequency-domain responses, this method can smooth the phase to obtain a better input-output relationship of a structure. Additionally, the method removes abnormal signals in time series, allowing better understanding of structural behavior. Due to communication loss, this method is able to recover lost data from other channel measurements in a structure. Moreover, the proposed method transforms the signal components into a specific domain and then yield meaningful characteristics. All these features are numerically verified using experimental data, and the proposed method permits more detailed investigation of structural behavior.

  15. Distributed demand side management via smart appliances contributing to frequency control

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-chen

    2015-01-01

    Nowadays renewable energy has become a trend for energy production but its variable nature has made balancing of demand and supply of the power grid difficult. Dynamic demand management using smart appliances is proposed to serve as a way that part of the regulation burden of balancing demand and supply is shifted to the demand side. However, if all appliances respond to the same frequency deviation, they may start to synchronize, causing large power overshoots and instability of the power grid. Therefore, the idea of implementing randomness into the frequency control of the appliances is proposed and this is what we call a stochastic approach. Simulators are built from scratch to model both scenarios. The effect of synchronization is analyzed and the parameters that can affect the synchronization are investigated. It has been found that the larger the contribution from the smart appliances to the power grid, the easier and faster the synchronization takes place. The stochastic approach solves the problem of synchronization and averages out the large power overshoot. However, the overall performance of stochastic operations is unacceptable due to the randomness in the operation though the mean and variance are as expected. More advanced feedback policies and schemes may be designed to achieve a better performance.

  16. Low-frequency vibration energy harvester using a spherical permanent magnet with controlled mass distribution

    Science.gov (United States)

    Choi, Yunhee; Ju, Suna; Chae, Song Hee; Jun, Sangbeom; Ji, Chang-Hyeon

    2015-06-01

    This paper presents a vibration energy harvester using a springless spherical permanent magnet with a non-uniform mass distribution as a proof mass. The magnet has been designed to have the center of mass below the geometrical center, which generates a roly-poly-like motion in response to external vibrations and maintains the upright position. Utilizing this roly-poly-like magnet, proof-of-concept electromagnetic energy harvesters have been fabricated, tested and analyzed. An analytical model which explains the motion of the magnet assembly and resulting output voltage has been developed by finite element analysis of the magnetic field distribution and motion analysis of the magnet assembly. With the fabricated device, a maximum open-circuit voltage of 48.85 mVrms and an output power of 9.03 μW have been obtained in response to a 20 Hz sinusoidal vibration at 3 g acceleration.

  17. Magnitude-frequency characteristics and preparatory factors for spatial debris-slide distribution in the northern Faroe Islands

    DEFF Research Database (Denmark)

    Dahl, Mads-Peter Jakob; Jensen, Niels H.; Veihe, Anita;

    2013-01-01

    the magnitude and frequency of their debris-slide origins as well as identifying which preparatory factors are responsible for the spatial debris-slide distribution in the landscape. For that purpose a debris-slide inventory was generated from aerial photo interpretation (API), fieldwork and anecdotal sources...... expressed as topographic scar area can be predicted from the power-law function: Y = 936.26X(-1277), r(2) = 0.98 while a physical explanation is preferred for the roll-over pattern of smaller slope failures. The DFA is able to correctly classify app. 70% of the modeled terrain units into their pre...

  18. Frequency dependence of the Hall-potential distribution in quantum Hall systems: Roles of edge channels and current contacts

    OpenAIRE

    Shima, Kousuke; Akera, Hiroshi

    2014-01-01

    The spatial dependence of the Hall potential induced in a two-dimensional electron system (2DES) by AC source-drain voltage is studied theoretically in the incoherent linear transport in the strong-magnetic-field regime. The local capacitance approximation is employed in which the potential at each point of the 2DES is proportional to the induced charge at the same point It is shown that the frequency dependence of the induced charge distribution is described by three time constants, tau(e) f...

  19. Intensity-modulated linear-frequency-modulated continuous-wave lidar for distributed media: fundamentals of technique.

    Science.gov (United States)

    Batet, Oscar; Dios, Federico; Comeron, Adolfo; Agishev, Ravil

    2010-06-10

    We analyze the intensity-modulation frequency-modulated continuous-wave (FMCW) technique for lidar remote sensing in the context of its application to distributed media. The goal of the technique is the reproduction of the sounded-medium profile along the emission path. A conceptual analysis is carried out to show the problems the basic version of the method presents for this application. The principal point is the appearance of a bandpass filtering effect, which seems to hinder its use in this context. A modified version of the technique is proposed to overcome this problem. A number of computer simulations confirm the ability of the modified FMCW technique to sound distributed media. PMID:20539357

  20. Adaptive Time-Frequency Distribution Based on Time-Varying Autoregressive and Its Application to Machine Fault Diagnosis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The time-varying autoregressive (TVAR) modeling of a non-stationary signal is studied. In the proposed method, time-varying parametric identification of a non-stationary signal can be translated into a linear time-invariant problem by introducing a set of basic functions. Then, the parameters are estimated by using a recursive least square algorithm with a forgetting factor and an adaptive time-frequency distribution is achieved. The simulation results show that the proposed approach is superior to the short-time Fourier transform and Wigner distribution. And finally, the proposed method is applied to the fault diagnosis of a bearing, and the experiment result shows that the proposed method is effective in feature extraction.

  1. Inferring Protective CD8+ T-Cell Epitopes for NS5 Protein of Four Serotypes of Dengue Virus Chinese Isolates Based on HLA-A, -B and -C Allelic Distribution: Implications for Epitope-Based Universal Vaccine Design.

    Directory of Open Access Journals (Sweden)

    Jiandong Shi

    Full Text Available Dengue is one of the most globally serious vector-borne infectious diseases in tropical and subtropical areas for which there are currently no effective vaccines. The most highly conserved flavivirus protein, NS5, is an indispensable target of CD8+ T-cells, making it an ideal vaccine design target. Using the Immune Epitope Database (IEDB, CD8+ T-cell epitopes of the dengue virus (DENV NS5 protein were predicted by genotypic frequency of the HLA-A,-B, and-C alleles in Chinese population. Antigenicity scores of all predicted epitopes were analyzed using VaxiJen v2.0. The IEDB analysis revealed that 116 antigenic epitopes for HLA-A (21,-B (53, and-C (42 had high affinity for HLA molecules. Of them, 14 had 90.97-99.35% conversancy among the four serotypes. Moreover, five candidate epitopes, including 200NS5210 (94.84%, A*11:01, 515NS5525 (98.71%, A*24:02, 225NS5232 (99.35%, A*33:03, 516NS5523 (98.71%, A*33:03, and 284NS5291 (98.06%, A*33:03, were presented by HLA-A. Four candidate epitopes, including 234NS5241 (96.77%, B*13:01, 92NS599 (98.06%, B*15:01, B*15:02, and B*46:01, 262NS5269 (92.90%, B*38:02, and 538NS5547 (90.97%, B*51:01, were presented by HLA-B. Another 9 candidate epitopes, including 514NS5522 (98.71%, C*01:02, 514NS5524 (98.71%, C*01:02 and C*14:02, 92NS599 (98.06%, C*03:02 and C*15:02, 362NS5369 (44.84%, C*03:04 and C*08:01, 225NS5232 (99.35%, C*04:01, 234NS5241(96.77%, C*04:01, 361NS5369 (94.84%, C*04:01, 515NS5522 (98.71%, C*14:02, 515NS5524 (98.71%, C*14:02, were presented by HLA-C. Further data showed that the four-epitope combination of 92NS599 (B*15:01, B*15:02, B*46:01, C*03:02 and C*15:02, 200NS5210 (A*11:01, 362NS5369 (C*03:04, C*08:01, and 514NS5524 (C*01:02, C*14:02 could vaccinate >90% of individuals in China. Further in vivo study of our inferred novel epitopes will be needed for a T-cell epitope-based universal vaccine development that may prevent all four China-endemic DENV serotypes.

  2. Non-extensive statistical physics applied to heat flow and the earthquake frequency-magnitude distribution in Greece

    Science.gov (United States)

    Papadakis, Giorgos; Vallianatos, Filippos; Sammonds, Peter

    2016-08-01

    This study investigates seismicity in Greece and its relation to heat flow, based on the science of complex systems. Greece is characterised by a complex tectonic setting, which is represented mainly by active subduction, lithospheric extension and volcanism. The non-extensive statistical physics formalism is a generalisation of Boltzmann-Gibbs statistical physics and has been successfully used for the analysis of a variety of complex systems, where fractality and long-range interactions are important. Consequently, in this study, the frequency-magnitude distribution analysis was performed in a non-extensive statistical physics context, and the non-extensive parameter, qM, which is related to the frequency-magnitude distribution, was used as an index of the physical state of the studied area. Examination of the spatial distribution of qM revealed its relation to the spatial distribution of seismicity during the period 1976-2009. For focal depths ≤40 km, we observe that strong earthquakes coincide with high qM values. In addition, heat flow anomalies in Greece are known to be strongly related to crustal thickness; a thin crust and significant heat flow anomalies characterise the central Aegean region. Moreover, the data studied indicate that high heat flow is consistent with the absence of strong events and consequently with low qM values (high b-values) in the central Aegean region and around the volcanic arc. However, the eastern part of the volcanic arc exhibits strong earthquakes and high qM values whereas low qM values are found along the North Aegean Trough and southwest of Crete, despite the fact that strong events are present during the period 1976-2009 in both areas.

  3. Association between HLA class I and class II alleles and the outcome of West Nile virus infection: an exploratory study.

    Directory of Open Access Journals (Sweden)

    Marion C Lanteri

    Full Text Available BACKGROUND: West Nile virus (WNV infection is asymptomatic in most individuals, with a minority developing symptoms ranging from WNV fever to serious neuroinvasive disease. This study investigated the impact of host HLA on the outcome of WNV disease. METHODS: A cohort of 210 non-Hispanic mostly white WNV(+ subjects from Canada and the U.S. were typed for HLA-A, B, C, DP, DQ, and DR. The study subjects were divided into three WNV infection outcome groups: asymptomatic (AS, symptomatic (S, and neuroinvasive disease (ND. Allele frequency distribution was compared pair-wise between the AS, S, and ND groups using χ2 and Fisher's exact tests and P values were corrected for multiple comparisons (Pc. Allele frequencies were compared between the groups and the North American population (NA used as a control group. Logistic regression analysis was used to evaluate the potential synergistic effect of age and HLA allele phenotype on disease outcome. RESULTS: The alleles HLA-A*68, C*08 and DQB*05 were more frequently associated with severe outcomes (ND vs. AS, P(A*68 = 0.013/Pc = 0.26, P(C*08 = 0.0075/Pc = 0.064, and P(DQB1*05 = 0.029/Pc = 0.68, However the apparent DQB1*05 association was driven by age. The alleles HLA-B*40 and C*03 were more frequently associated with asymptomatic outcome (AS vs. S, P(B*40 = 0.021/Pc = 0.58 and AS vs. ND P(C*03 = 0.039/Pc = 0.64 and their frequencies were lower within WNV(+ subjects with neuroinvasive disease than within the North American population (NA vs. S, P(B*40 = 0.029 and NA vs. ND, P(C*03 = 0.032. CONCLUSIONS: Host HLA may be associated with the outcome of WNV disease; HLA-A*68 and C*08 might function as "susceptible" alleles, whereas HLA-B*40 and C*03 might function as "protective" alleles.

  4. CTG repeats distribution and Alu insertion polymorphism at myotonic dystrophy (DM) gene in Amhara and Oromo populations of Ethiopia.

    Science.gov (United States)

    Gennarelli, M; Pavoni, M; Cruciani, F; De Stefano, G; Dallapiccola, B; Novelli, G

    1999-01-01

    Myotonic dystrophy (DM) is a dominantly inherited neuromuscular disease, highly variable and multisystemic, which is caused by the expansion of a CTG repeat located in the 3' untranslated region of the DMPK gene. Normal alleles show a copy number of 5-37 repeats on normal chromosomes, amplified to 50-3000 copies on DM chromosomes. The trinucleotide repeat shows a trimodal allele distribution in the majority of the examined population. The first class includes alleles carrying (CTG)5, the second class, alleles in the range 7-18 repeats, and the third class, alleles (CTG) > or =19. The frequency of this third class is directly related to the prevalence of DM in different populations, suggesting that normal large-sized alleles predispose toward DM. We studied CTG repeat allele distribution and Alu insertion and/or deletion polymorphism at the myotonic dystrophy locus in two major Ethiopian populations, the Amhara and Oromo. CTG allele distribution and haplotype analysis on a total of 224 normal chromosomes showed significant differences between the two ethnic groups. These differences have a bearing on the out-of-Africa hypothesis for the origin of the DM mutation. In addition, (CTG) > or =19 were exclusively detected in the Amhara population, confirming the predisposing role of these alleles compared with the DM expansion-mutation.

  5. Multilocus Inherited Neoplasia Alleles Syndrome

    DEFF Research Database (Denmark)

    Whitworth, James; Skytte, Anne-Bine; Sunde, Lone;

    2016-01-01

    as multilocus inherited neoplasia alleles syndrome [MINAS]) in patients with unusual inherited cancer syndrome phenotypes. To facilitate the clinical management of novel cases of MINAS, we have established a database to collect information on what is likely to be an increasingly recognized cohort...

  6. The distribution of spectral index of magnetic field and ion velocity in Pi2 frequency band in BBFs: THEMIS statistics

    Science.gov (United States)

    Wu, Q.; Du, A. M.; Volwerk, M.; Wang, G. Q.

    2016-09-01

    A statistical study of the THEMIS FGM and ESA data is performed on turbulence of magnetic field and velocity for 218 selected 12 min intervals in BBFs. The spectral index α in the frequency range of 0.005-0.06 Hz are Gaussian distributions. The peaks indexes of total ion velocity Vi and parallel velocity V‖ are 1.95 and 2.07 nearly the spectral index of intermittent low frequency turbulence with large amplitude. However, most probable α of perpendicular velocity V⊥ is about 1.75. It is a little bigger than 5/3 of Kolmogorov (1941). The peak indexes of total magnetic field BT is 1.70 similar to V⊥. Compression magnetic field B‖ are 1.85 which is smaller than 2 and bigger than 5/3 of Kolmogorov (1941). The most probable spectral index of shear B⊥ is about 1.44 which is close to 3/2 of Kraichnan (1965). Max V⊥ have little effect on the power magnitude of VT and V‖ but is positively correlated to spectral index of V⊥. The spectral power of BT, B‖ and B⊥ increase with max perpendicular velocity but spectral indexes of them are negatively correlated to V⊥. The spectral index and the spectral power of magnetic field over the frequency interval 0.005-0.06 Hz is very different from that over 0.08-1 Hz.

  7. Time-frequency distribution decomposition with applications to recognize the looseness state of the viscoelastic sandwich structure

    Science.gov (United States)

    Yan, Wang; Zhang, Zhousou; Qu, Jinxiu; Sun, Chuang

    2016-07-01

    In general, a vibration signal consists of several frequency modulation (FM) components. Every component contains different information, and can be characterized by its instantaneous amplitude (IA) and instantaneous phase (IP). In engineering applications, conventional time-frequency analysis methods and signal decomposition methods have shown their power in investigating features of the vibration signal. However, they are limited in resolution and it is hard to analyze these FM components individually. To overcome these deficiencies, a novel signal decomposition algorithm, named time-frequency distribution decomposition (TFDD), is proposed in this paper, which reconstructs one FM component of the signal at a time by estimating its IP and IA. The IA and IP are approximated by two polynomial functions respectively. One important advantage of TFDD is that it can directly extract the component we are interested in. Therefore, we can analyze the key component of the signal with little influence from other components. This will help us to characterize the vibration signal more deeply. Furthermore, it is very stable to noise. This is conductive to protecting the information of the vibration signal. The effectiveness of the TFDD is validated by a numerical simulation and the study of the vibration response signal collected from a viscoelastic sandwich structure (VSS). From the value of permutation entropy of the component extracted by TFDD, the looseness state of the VSS is recognized.

  8. Spatial variations in the frequency-magnitude distribution of earthquakes in the southwestern Okinawa Trough

    Science.gov (United States)

    Lin, J.-Y.; Sibuet, J.-C.; Lee, C.-S.; Hsu, S.-K.; Klingelhoefer, F.

    2007-04-01

    The relations between the frequency of occurrence and the magnitude of earthquakes are established in the southern Okinawa Trough for 2823 relocated earthquakes recorded during a passive ocean bottom seismometer experiment. Three high b-values areas are identified: (1) for an area offshore of the Ilan Plain, south of the andesitic Kueishantao Island from a depth of 50 km to the surface, thereby confirming the subduction component of the island andesites; (2) for a body lying along the 123.3°E meridian at depths ranging from 0 to 50 km that may reflect the high temperature inflow rising up from a slab tear; (3) for a third cylindrical body about 15 km in diameter beneath the Cross Backarc Volcanic Trail, at depths ranging from 0 to 15 km. This anomaly might be related to the presence of a magma chamber at the base of the crust already evidenced by tomographic and geochemical results. The high b-values are generally linked to magmatic and geothermal activities, although most of the seismicity is linked to normal faulting processes in the southern Okinawa Trough.

  9. Lewis Investigates Frequency Sharing Between Future NASA Space Systems and Local Multipoint Distribution Systems in the 27-GHz Band

    Science.gov (United States)

    1997-01-01

    At the request of the Federal Communications Commission (FCC), the NASA Lewis Research Center undertook an intensive study to examine the feasibility of frequency sharing between future NASA space services and proposed Local Multipoint Distribution Systems (LMDS) in the 25.25- to 27.5-GHz band. This follows NASA's earlier involvement in the FCC's 1994 Negotiated Rule Making Committee which studied frequency sharing between Ka-band Fixed Satellite Services and LMDS in the 27.5- to 29.5-GHz band. LMDS is a terrestrial, cellular, wireless communication service primarily intended to provide television distribution from hub stations located within relatively small cells to fixed subscriber receivers. Some proposed systems, however, also plan to offer interactive services via subscriber-to-hub transmissions. LMDS providers anticipate that their systems will be a cost-effective alternative to cable television systems, especially in urban areas. LMDS proponents have expressed an interest in using frequencies below 27.5 GHz. NASA, however, plans to operate three types of space systems below 27.5 GHz. The H, I, and J follow-on satellites for the Tracking and Data Relay Satellite System (TDRSS), which are planned for launch beginning in 1999, are designed to receive high-data-rate transmissions (up to 800 Mbps) from low-Earth orbiting "user" spacecraft in the 25.25- to 27.5-GHz band. In this case, the potential interference is the aggregate interference from LMDS transmitters (both hubs and subscribers) into the TDRSS tracking receive beams as they sweep over the Earth's surface while tracking lower altitude user spacecraft.

  10. Spatial distribution of spectral parameters of high latitude geomagnetic disturbances in the Pc5/Pi3 frequency range

    Directory of Open Access Journals (Sweden)

    V. A. Pilipenko

    2010-09-01

    Full Text Available We analyze spectral parameters of the geomagnetic disturbances within the 1–4 mHz (Pc5/Pi3 frequency range for 29 observatories from polar to auroral latitudes. The main object of this study is the broadband (noise background under quiet and moderately disturbed conditions. To obtain a quantitative description of background high-latitude long period ULF activity the log-log dependence of the spectral power on frequency is expanded over Legendre polynomials, and the coefficients of this expansion (spectral moments are used to describe the most common features of these spectra. Not only the spectral power, but also the spectral slope and higher spectral moments, averaged over relatively long time intervals, demonstrate a systematic dependence on corrected geomagnetic (CGM latitude, Φ, and magnetic local time, MLT. The 2-D distributions of the spectral moments in Φ-MLT coordinates are characterized by existence of structures, narrow in latitude and extended in MLT, which can be attributed to the projections of different magnetospheric domains. Spatio-temporal distributions of spectral power of elliptically (P-component and randomly (N-component polarized signal are similar, but not identical. The N-component contribution to the total signal becomes non-negligible in regions with a high local activity, such as the auroral oval and dayside polar cusp. The spectral slope indicates a larger relative contribution of higher frequencies upon the latitude decrease, probably, as a result of the resonant effects in the ULF noise. The higher spectral moments are also controlled mostly by CGM latitude and MLT and are fundamentally different for the polarized and non-polarized components. This study is a step towards the construction of an empirical model of the ULF wave power in Earth's magnetosphere.

  11. The global size-frequency distribution of boulders > 7 m on Comet 67P Churyumov-Gerasimenko

    Science.gov (United States)

    Pajola, Maurizio; Baptiste Vincent, Jean; Lee, Jui-Chi; Ip, Wing-Huen; Lin, Zhong-Yi; Bertini, Ivano; Massironi, Matteo; Simioni, Emanuele; Barbieri, Cesare; Cremonese, Gabriele; Marzari, Francesco; Naletto, Giampiero; Giacomini, Lorenza; Jorda, Laurent; Thomas, Nicholas; Pommerol, Antoine; Kueppers, Michael; Moissl, Richard; Besse, Sebastien; Sierks, Holger

    2015-04-01

    After a ten years journey through the Solar System, the ESA Rosetta spacecraft reached on 6 August 2014 its primary target, the Jupiter family comet 67P/Churyumov-Gerasimenko, hereafter 67P. During the approaching phase, several images of the nucleus of comet 67P, captured by the OSIRIS scientific imaging camera, have been taken to study its structure, activity and the surface morphology. The close distance between spacecraft and comet, and the high resolution of our images, provided a unique opportunity to study features which could not have been detected before on other comets, but yet hold key parameters to derive the physical properties of the surface. We made use of the images acquired by the OSIRIS Narrow Angle Camera, NAC, on 5 and 6 August 2014 in order to study the statistical size-frequency distribution and the morphological properties of both clustered and isolated roundish structures ("boulders") scattered all over the currently illuminated side of the comet (70% of the total surface). Such dataset has been taken at a distance ranging between 131.45 and 109.76 km far from the comet center and the scale of these images (2.44 - 2.03 m/px) is such that boulders ≥ 7 m can be unequivocally identified and extracted. These images are the last ones where the entire comet is 2048 x 2048 pixels full frame and they cover a complete comet rotation (12.4 h), hence providing the possibility to derive a global size-frequency distribution statistics of the presently illuminated surface of 67P. A total amount of 3526 boulders has been identified on the surface of the comet: i) 2218 belonging to the big lobe, body, ii) 1115 boulders are located on the small lobe, head, while iii) 213 boulders belong to the transition region between the two lobes, called the neck. Here, global cumulative size-frequency distributions of boulders per square km are presented, together with specific and localized areas distributions. Moreover we indicate the different formation processes

  12. [Polymorphism of human HLA-DRB1 leukocyte antigen alleles and its association to juvenile rheumatoid arthritis in a sample of Colombian mestizo children].

    Science.gov (United States)

    Garavito, Gloria; Malagón, Clara; Ramírez, Luis A; De La Cruz, Oscar F; Uribe, Oscar; Navarro, Edgar; Iglesias, Antonio; Martínez, Paz; Jaraquemada, Dolores; Egea, Eduardo

    2003-09-01

    Oligotypes of the human leukocyte antigen HLA Class II, DRB1 alleles were characterized at the molecular level in a group of Colombian children suffering juvenile rheumatoid arthritis (JRA). The distribution of these alleles was examined in a group of Colombian mestizo children (genetic admixture of Amerindians, Europeans and Africans) suffering from clinically distinct JRA subsets in order to detect HLA allele frequency differences in patients with different JRA subsets. A group of 65 patients with JRA and 65 controls were characterized for the subtypes of the HLA-DRB1 alleles using polymerase chain reaction with sequence-specific oligonucleotide probes (PCR-SSOP). The oligotyping protocol recommended by the 12th International Histocompatibility Workshop held in St. Malo, Paris, in 1996, was used. Subtype HLA-DRB1*1104 was the allele most strongly associated with susceptibility to JRA (Fisher's p = 0.013, odds ratio (OR) = 16.79, etiologic fraction (EF) = 0.93). HLA-DRB1*1602 was also associated with susceptibility to a lesser degree (Fisher's p = 0.016, OR = 8.98, EF = 0.88). HLA-DRB1 alleles participating in JRA protection were HLA-DRB1*1501 (preventive fraction (PF) = 0.466, p = 0.005) and HLA DRB1*1402 (PF = 0.49, p = 0.009). The relationship between some HLA-DRB1 alleles and clinical features was also compared. The presence of rheumatic factor was associated with the alleles HLA-DRB1*0407 (p = 0.05, OR = 11.2, EF = 0.45) and HLA-DRB1*1302 (p = 0.02, OR = 22.8, EF = 0.63). There was also an association between HLA-DRB1*0701 (p = 0.001, OR = 58, EF = 0.73) with expressing ANA +. We found that in the oligoarticular subset, the allele HLA-DRB1*1104 (p = 0.0034, OR = 41.53, EF = 0.97) was the one expressed most commonly. In the poliarticular group, the alleles most frequently expressed were HLA-DRB1*0404 (Fisher's p = 0.012, OR = 8.75, EF = 0.88). In patients with systemic JRA, the HLA-DRB1*1602 allele (p = 0.005, OR = 21.33, EF = 0.95) was most frequent. These

  13. 基于STR基因频率探究我国32个行政区域汉族亚群的遗传特征%Genetic Characteristics of Han Subpopulations of 32 Administrative Area in China Based on Allele Frequencies of Short Tandem Repeat Loci

    Institute of Scientific and Technical Information of China (English)

    张蒙; 饶健安; 赵艳超; 窦浩宇; 徐眑; 何淼

    2014-01-01

    Exploring the molecular genetics relationships between Han subpopulations in different admin-istrative regions of China are always noticed by academics.Short tandem repeat (STR)has been often used in molecular genetics studies.The cluster analysis,principal component analysis and MCOA analy-sis had been used in this paper,we focused on the nine common STR loci (D8S1179,D21S11, D7S820,D3S1358,D13S317,vWA,D18S51,D5S818,FGA)allele frequency data of Han subpopula-tions from 32 administrative regions in China,in order to initially explore the molecular genetics relation-ships,the spatial distribution characteristics and distribution pattern of the Chinese Han subpopulations. The studies revealed that the Han nationality could be segregated into two groups which are the Southern and the Northern Han by the Yangtze River.In the Northern areas of China,the Han subpopulations from Shandong and Tianjin have large genetic distance with others;In the Southern areas,the genetic relation-ships within the Han subpopulations of Hong Kong,Hainan and Guangxi are much closed and greatly dif-ferent from the others.The Han subpopulation of Xiamen is comparatively closed to Northern Han.Prin-cipal component scatter plot reflects that the spatial distribution pattern of Han subpopulations is wide dis-tribution and gathered tightly in small areas in China.The three main factors contributing to the distribu-tion characteristics of Han subpopulations in China are geographic isolation by the Yangtze River,floods in history and the population migration caused by wars or disasters using MCOA analysis method.%探究我国不同行政区域汉族亚群间的分子遗传学关系一直是广受学术界关注的问题。短串联重复序列(STR)常应用于分子遗传学研究。综合采用了聚类分析、主成分分析和MCOA分析等统计学方法,对我国32个行政区域汉族亚群的9个常见STR基因座(D8S1179、D21S11、D7S820、D3S1358、D13S317、vWA、D18S51、D5S818

  14. Frequency Locking and Monitoring Based on Bi-directional Terahertz Radiation of a 3rd-Order Distributed Feedback Quantum Cascade Laser

    NARCIS (Netherlands)

    Van Marrewijk, N.; Mirzaei, B.; Hayton, D.; Gao, J.R.; Kao, T.Y.; Hu, Q.; Reno, J.L.

    2015-01-01

    We have performed frequency locking of a dual, forward reverse emitting third-order distributed feedback quantum cascade laser (QCL) at 3.5 THz. By using both directions of THz emission in combination with two gas cells and two power detectors, we can for the first time perform frequency stabilizati

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

    Energy Technology Data Exchange (ETDEWEB)

    Poduslo, S.E. [Texas Tech Univ., Lubbock, TX (United States); Schwankhaus, J.D. [Department of Veterans Affairs, Lubbock, TX (United States)

    1994-09-01

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

  16. Sensitivity of Photolysis Frequencies and Key Tropospheric Oxidants in a Global Model to Cloud Vertical Distributions and Optical Properties

    Science.gov (United States)

    Liu, Hongyu; Crawford, James H.; Considine, David B.; Platnick, Steven; Norris, Peter M.; Duncan, Bryan N.; Pierce, Robert B.; Chen, Gao; Yantosca, Robert M.

    2009-01-01

    Clouds affect tropospheric photochemistry through modification of solar radiation that determines photolysis frequencies. As a follow-up study to our recent assessment of the radiative effects of clouds on tropospheric chemistry, this paper presents an analysis of the sensitivity of such effects to cloud vertical distributions and optical properties (cloud optical depths (CODs) and cloud single scattering albedo), in a global 3-D chemical transport model (GEOS-Chem). GEOS-Chem was driven with a series of meteorological archives (GEOS1- STRAT, GEOS-3 and GEOS-4) generated by the NASA Goddard Earth Observing System data assimilation system. Clouds in GEOS1-STRAT and GEOS-3 have more similar vertical distributions (with substantially smaller CODs in GEOS1-STRAT) while those in GEOS-4 are optically much thinner in the tropical upper troposphere. We find that the radiative impact of clouds on global photolysis frequencies and hydroxyl radical (OH) is more sensitive to the vertical distribution of clouds than to the magnitude of column CODs. With random vertical overlap for clouds, the model calculated changes in global mean OH (J(O1D), J(NO2)) due to the radiative effects of clouds in June are about 0.0% (0.4%, 0.9%), 0.8% (1.7%, 3.1%), and 7.3% (4.1%, 6.0%), for GEOS1-STRAT, GEOS-3 and GEOS-4, respectively; the geographic distributions of these quantities show much larger changes, with maximum decrease in OH concentrations of approx.15-35% near the midlatitude surface. The much larger global impact of clouds in GEOS-4 reflects the fact that more solar radiation is able to penetrate through the optically thin upper-tropospheric clouds, increasing backscattering from low-level clouds. Model simulations with each of the three cloud distributions all show that the change in the global burden of ozone due to clouds is less than 5%. Model perturbation experiments with GEOS-3, where the magnitude of 3-D CODs are progressively varied from -100% to 100%, predict only modest

  17. Modeling and distributed gain scheduling strategy for load frequency control in smart grids with communication topology changes.

    Science.gov (United States)

    Liu, Shichao; Liu, Xiaoping P; El Saddik, Abdulmotaleb

    2014-03-01

    In this paper, we investigate the modeling and distributed control problems for the load frequency control (LFC) in a smart grid. In contrast with existing works, we consider more practical and real scenarios, where the communication topology of the smart grid changes because of either link failures or packet losses. These topology changes are modeled as a time-varying communication topology matrix. By using this matrix, a new closed-loop power system model is proposed to integrate the communication topology changes into the dynamics of a physical power system. The globally asymptotical stability of this closed-loop power system is analyzed. A distributed gain scheduling LFC strategy is proposed to compensate for the potential degradation of dynamic performance (mean square errors of state vectors) of the power system under communication topology changes. In comparison to conventional centralized control approaches, the proposed method can improve the robustness of the smart grid to the variation of the communication network as well as to reduce computation load. Simulation results show that the proposed distributed gain scheduling approach is capable to improve the robustness of the smart grid to communication topology changes.

  18. Modeling and distributed gain scheduling strategy for load frequency control in smart grids with communication topology changes.

    Science.gov (United States)

    Liu, Shichao; Liu, Xiaoping P; El Saddik, Abdulmotaleb

    2014-03-01

    In this paper, we investigate the modeling and distributed control problems for the load frequency control (LFC) in a smart grid. In contrast with existing works, we consider more practical and real scenarios, where the communication topology of the smart grid changes because of either link failures or packet losses. These topology changes are modeled as a time-varying communication topology matrix. By using this matrix, a new closed-loop power system model is proposed to integrate the communication topology changes into the dynamics of a physical power system. The globally asymptotical stability of this closed-loop power system is analyzed. A distributed gain scheduling LFC strategy is proposed to compensate for the potential degradation of dynamic performance (mean square errors of state vectors) of the power system under communication topology changes. In comparison to conventional centralized control approaches, the proposed method can improve the robustness of the smart grid to the variation of the communication network as well as to reduce computation load. Simulation results show that the proposed distributed gain scheduling approach is capable to improve the robustness of the smart grid to communication topology changes. PMID:24200162

  19. Gilbert's syndrome: High frequency of the (TA)7 TAA allele in India and its interaction with a novel CAT insertion in promoter of the gene for bilirubin UDP-glucuronosyltransferase 1 gene

    Institute of Scientific and Technical Information of China (English)

    Shabana Farheen; Sanghamitra Sengupta; Amal Santra; Suparna Pal; Gopal Krishna Dhali; Meenakshi Chakravorty; Partha P Majumder; Abhijit Chowdhury

    2006-01-01

    AIM: To identify the variants in UDP-glucuronosyltransferase 1 (UGT1A1) gene in Gilbert's syndrome (GS) and to estimate the association between homozygosity for TA insertion and GS in India, as well as the frequency of TA insertion and its impact among normal controls in India.METHODS: Ninety-five GS cases and 95 normal controls were selected. Liver function and other tests were done. The promoter and all 5 exons of UGT1A1 gene were resequenced. Functional assessment of a novel trinucleotide insertion was done byin silico analysis and by estimating UGT1A1 promoter activity carried out by luciferase reporter assay of appropriate constructs in Hep G2 cell line.RESULTS: Among the GS patients, 80% were homozygous for the TA insertion, which was several-fold higher than reports from other ethnic groups. The mean UCB level was elevated among individuals with only one copy of this insertion, which was not significantly different from those with two copies. Many new DNA variants in UGT1A1 gene were discovered, including a trinucleotide (CAT) insertion in the promoter found in a subset (10%) of GS patients, but not among normal controls. In-silico analysis showed marked changes in the DNA-folding of the promoter and functional analysis showed a 20-fold reduction in transcription efficiency of UGT1A1 gene resulting from this insertion, thereby significantly elevating the UCB level.CONCLUSION: The genetic epidemiology of GS is variable across ethnic groups and the epistatic interactions among UGT1A1 promoter variants modulate bilirubin glucuronidation.

  20. Age of an allele and gene genealogies of nested subsamples for populations admitting large offspring numbers

    OpenAIRE

    Eldon, Bjarki

    2012-01-01

    Coalescent processes, including mutation, are derived from Moran type population models admitting large offspring numbers. Including mutation in the coalescent process allows for quantifying the turnover of alleles by computing the distribution of the number of original alleles still segregating in the population at a given time in the past. The turnover of alleles is considered for specific classes of the Moran model admitting large offspring numbers. Versions of the Kingman coalescent are a...

  1. HLA Class II Alleles Susceptibility Markers of Type 1 Diabetes Fail to Specify Phenotypes of Ketosis-Prone Diabetes in Adult Tunisian Patients

    Directory of Open Access Journals (Sweden)

    Lilia Laadhar

    2011-01-01

    Full Text Available We aimed to characterize the different subgroups of ketosis-prone diabetes (KPD in a sample of Tunisian patients using the Aβ scheme based on the presence or absence of β-cell autoantibodies (A+ or A− and β-cell functional reserve (β+ or β− and we investigated whether HLA class II alleles could contribute to distinct KPD phenotypes. We enrolled 43 adult patients with a first episode of ketosis. For all patients we evaluated clinical parameters, β-cell autoimmunity, β-cell function and HLA class II alleles. Frequency distribution of the 4 subgroups was 23.3% A+β−, 23.3% A−β−, 11.6% A+β+ and 41.9% A−β+. Patients from the group A+β− were significantly younger than those from the group A−β− (P=.002. HLA susceptibility markers were significantly more frequent in patients with autoantibodies (P=.003. These patients also had resistance alleles but they were more frequent in A+β+ than A+β− patients (P=.04. Insulin requirement was not associated to the presence or the absence of HLA susceptibility markers. HLA class II alleles associated with susceptibility to autoimmune diabetes have not allowed us to further define Tunisian KPD groups. However, high prevalence of HLA resistance alleles in our patients may reflect a particular genetic background of Tunisian KPD population.

  2. Age-related prevalence, intensity and frequency distribution of gastrointestinal helminth infection in urban slum children from Kuala Lumpur, Malaysia.

    Science.gov (United States)

    Bundy, D A; Kan, S P; Rose, R

    1988-01-01

    The gastrointestinal helminth infection status of 1574 children living in a slum area of Kuala Lumpur, Malaysia was assessed by quantitative coprology. Almost two-thirds were infected with Trichuris trichiura, 49.6% with Ascaris lumbricoides, and 5.3% with hookworm. Infection prevalence rose rapidly to a stable asymptote at 7 years of age, and the age-intensity profile was convex with maximal values in the 5-10 year age classes. This pattern was the same for males and females, but differed markedly between different ethnic groups. The frequency distributions of A. lumbricoides and T. trichiura were highly overdispersed (k values were 0.21 and 0.27, respectively), and age-dependent over the 0-8 year age classes. This suggests that the force of infection with these nematodes is lower in infants than in older children.

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

    Science.gov (United States)

    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

  4. Semicircular canal dehiscence: Frequency and distribution on temporal bone CT and its relationship with the clinical outcomes

    Energy Technology Data Exchange (ETDEWEB)

    Elmali, Muzaffer, E-mail: muzafel@yahoo.com.tr [Department of Radiology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Polat, Ahmet Veysel, E-mail: veyselp@hotmail.com [Department of Radiology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Kucuk, Harun, E-mail: hardrmd@yahoo.com [Department of Otorhinolaryngology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Atmaca, Sinan, E-mail: sinanatmaca@yahoo.com [Department of Otorhinolaryngology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey); Aksoy, Ahmet, E-mail: toxocara47@hotmail.com [Department of Otorhinolaryngology, Ondokuz Mayis University, Faculty of Medicine, Samsun (Turkey)

    2013-10-01

    Purpose: In this study, we aimed to investigate the frequency of SCD and its distribution and relationship with clinical outcomes on thin-section CT of the temporal bone. Materials and methods: Digital temporal bone CT images of 850 consecutive patients (1700 temporal bone CTs, 5100 SCs) who presented with a range of complaints such as vertigo, deafness, ear pain, fullness, and discharge between January 2008 and December 2011 were re-evaluated. Axial and oblique coronal reconstruction images of the temporal bone were made with a reconstruction thickness of 0.5 mm. Additionally, superior SC was evaluated in two perpendicular planes. Results: Out of 850 patients, 70 had completely normal temporal bone CT. Ninety-three patients had at least one SCD. In the temporal bone-based evaluation, 119 (26 bilateral, 67 unilateral) of 1700 temporal bones (7%) showed dehiscence. The SC-based evaluation revealed 125 SCD (2.5%) in 5100 SCs. The total number and rates of SCD were as follows: superior 103 (82.4%), posterior 13 (10.4%), and lateral nine (7.2%). Twenty of the 93 patients with SCD (21.5%) revealed no other findings on their temporal bone CTs. We determined a significant correlation between vestibular complaints, conductive hearing loss and SCD but there was no correlation between mixed, sensorineural hearing loss and SCD. Conclusion: We determined the frequency of SCD in 11% of patients and 7% of temporal bones. With regards to the distribution, the superior SC showed the highest dehiscence rate (82.4%). We found a significant correlation between vestibular symptoms, conductive hearing loss and SCD.

  5. Determination of plasma frequency, damping constant, and size distribution from the complex dielectric function of noble metal nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Mendoza Herrera, Luis J.; Arboleda, David Muñetón [Centro de Investigaciones Ópticas (CIOp), (CONICET La Plata-CIC) (Argentina); Schinca, Daniel C.; Scaffardi, Lucía B., E-mail: lucias@ciop.unlp.edu.ar [Centro de Investigaciones Ópticas (CIOp), (CONICET La Plata-CIC) (Argentina); Departamento de Ciencias Básicas, Facultad de Ingeniería, UNLP (Argentina)

    2014-12-21

    This paper develops a novel method for simultaneously determining the plasma frequency ω{sub P}   and the damping constant γ{sub free} in the bulk damped oscillator Drude model, based on experimentally measured real and imaginary parts of the metal refractive index in the IR wavelength range, lifting the usual approximation that restricts frequency values to the UV-deep UV region. Our method was applied to gold, silver, and copper, improving the relative uncertainties in the final values for ω{sub p} (0.5%–1.6%) and for γ{sub free} (3%–8%), which are smaller than those reported in the literature. These small uncertainties in ω{sub p} and γ{sub free} determination yield a much better fit of the experimental complex dielectric function. For the case of nanoparticles (Nps), a series expansion of the Drude expression (which includes ω{sub p} and γ{sub free} determined using our method) enables size-dependent dielectric function to be written as the sum of three terms: the experimental bulk dielectric function plus two size corrective terms, one for free electron, and the other for bound-electron contributions. Finally, size distribution of nanometric and subnanometric gold Nps in colloidal suspension was determined through fitting its experimental optical extinction spectrum using Mie theory based on the previously determined dielectric function. Results are compared with size histogram obtained from Transmission Electron Microscopy (TEM)

  6. Multi-frequency monitoring of gamma-ray loud blazars: I. Light curves and spectral energy distributions

    CERN Document Server

    Bach, U; Villata, M; Fuhrmann, L; Buemi, C S; Larionov, V M; Leto, P; Arkharov, A A; Coloma, J M; Di Paola, A; Dolci, M; Efimova, N; Forne, E; Ibrahimov, M A; Hagen-Thorn, V; Konstantinova, T; Kopatskaya, E; Lanteri, L; Kurtanidze, O M; Maccaferri, G; Nikolashvili, M G; Orlati, A; Ros, J A; Tosti, G; Trigilio, C; Umana, G

    2006-01-01

    Context: Being dominated by non-thermal emission from aligned relativistic jets, blazars allow us to elucidate the physics of extragalactic jets, and, ltimately, how the energy is extracted from the central black hole in radio-loud active galactic nuclei. Aims: Crucial information is provided by broad-band spectral energy distributions (SEDs), their trends with luminosity and correlated multi-frequency variability. With this study we plan to obtain a database of contemporaneous radio-to-optical spectra of a sample of blazars, which are and will be observed by current and future high-energy satellites. Methods: Since December 2004 we are performing a monthly multi-frequency radio monitoring of a sample of 35 blazars at the antennas in Medicina and Noto. Contemporaneous near-IR and optical observations for all our observing epochs are organised. Results: Until June 2006 about 4000 radio measurements and 5500 near-IR and optical measurements were obtained. Most of the sources show significant variability in all ...

  7. Identification and characterization of variant alleles at CODIS STR loci.

    Science.gov (United States)

    Allor, Catherine; Einum, David D; Scarpetta, Marco

    2005-09-01

    Short tandem repeat (STR) profiles from 32,671 individuals generated by the ABI Profiler Plus and Cofiler systems were screened for variant alleles not represented within manufacturer-provided allelic ladders. A total of 85 distinct variants were identified at 12 of the 13 CODIS loci, most of which involve a truncated tetranucleotide repeat unit. Twelve novel alleles, identified at D3S1358, FGA, D18S51, D5S818, D7S820 and TPOX, were confirmed by nucleotide sequence analysis and include both insertions and deletions involving the repeat units themselves as well as DNA flanking the repeat regions. Population genetic data were collected for all variants and frequencies range from 0.0003 (many single observations) to 0.0042 (D7S820 '10.3' in North American Hispanics). In total, the variant alleles identified in this study are carried by 1.6% of the estimated 1 million individuals tested annually in the U.S. for the purposes of parentage resolution. A paternity case involving a recombination event of paternal origin is presented and demonstrates how variant alleles can significantly strengthen the genetic evidence in troublesome cases. In such instances, increased costs and turnaround time associated with additional testing may be eliminated.

  8. Spatial Genetic Structure of Two HIV-I-resistant Polymorphisms (CCR2-64Ⅰand SDF1-3'A) Alleles in Population of Shandong Province, China

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Objective To explore the spatial genetic structure of two HIV-I-resistant polymorphisms (CCR2-64Ⅰand SDF1-3'A) alleles in the population of Shandong Province, China. Methods Using the techniques of spatial stratified sampling and spatial statistics, the spatial genetic structure of the locus (CCR2-64Ⅰand SDF1-3'A), which was shown to be important co-receptor for HIV infection, was quantified from the populations of 36 sampled counties of Shandong Province, and a total of 3147 and 3172 samples were taken for testing CCR2-64I and SDF1-3'A respectively from individuals without known history of HIV-I infection and AIDS symptoms. Results There were significantly spatial genetic structures of the two alleles at different spatial distance classes on the scale of populations, but on the scale of individuals, no spatial structure was found in either the whole area of Shandong Province or the area of each sampled county. Although the change of frequencies of the two alleles with geographic locations in Shandong Province both showed gradual increase trends, their changing directions were inverse. The frequency of CCR2-64I allele gradually increased from the southwest to the northeast, while the frequency of SDF1-3'A allele gradually increased from the northeast to the southwest. However the RH to AIDS of combined types of their different genotypes did not represent obvious geographic diversity on the whole area of the Province. Conclusion The frequency of allele usually has some spatial genetic structures or spatial autocorrelation with different spatial distance classes, but the genotypes of individuals have random distribution in the same geographic area. Evaluating spatial distribution of the genetic susceptibility of HIV (AIDS) to CCR2-64I and SDF1-3'A alleles, should focus on the frequencies of combined genotypes of CCR2 and SDF1 based on the two-locus genotypes of each individual rather than the frequencies of CCR2-64I and SDF1-3'A alleles.

  9. Protective effect of the AT137RQ and ARQK176 PrP alleles against classical scrapie in Sarda breed sheep

    Science.gov (United States)

    Vaccari, Gabriele; Scavia, Gaia; Sala, Marcello; Cosseddu, Gianmario; Chiappini, Barbara; Conte, Michela; Esposito, Elena; Lorenzetti, Raniero; Perfetti, Gabriella; Marconi, Paola; Scholl, Francesco; Barbaro, Katia; Bella, Antonino; Nonno, Romolo; Agrimi, Umberto

    2009-01-01

    The susceptibility of sheep to scrapie is under the control of the host’s prion protein (PrP) gene and is also influenced by the strain of the agent. PrP polymorphisms at codons 136 (A/V), 154 (R/H) and 171 (Q/R/H) are the main determinants of susceptibility/resistance of sheep to classical scrapie. They are combined in four main variants of the wild-type ARQ allele: VRQ, AHQ, ARH and ARR. Breeding programmes have been undertaken on this basis in the European Union and the USA to increase the frequency of the resistant ARR allele in sheep populations. Herein, we report the results of a multi-flock study showing the protective effect of polymorphisms other than those at codons 136, 154 and 171 in Sarda breed sheep. All ARQ/ARQ affected sheep (n = 154) and 378 negative ARQ/ARQ controls from four scrapie outbreaks were submitted to sequencing of the PrP gene. The distribution of variations other than those at the standard three codons, between scrapie cases and negative controls, was statistically different in all flocks. In particular, the AT137RQ and ARQK176 alleles showed a clear protective effect. This is the first study demonstrating a protective influence of alleles other than ARR under field conditions. If further investigations in other sheep breeds and with other scrapie sources confirm these findings, the availability of various protective alleles in breeding programmes of sheep for scrapie resistance could be useful in breeds with a low frequency of the ARR allele and would allow maintaining a wider variability of the PrP gene. PMID:19171116

  10. Combined Deterministic and Stochastic Approach to Determine Spatial Distribution of Drought Frequency and Duration in the Great Hungarian Plain

    Science.gov (United States)

    Szabó, J. A.; Kuti, L.; Bakacsi, Zs.; Pásztor, L.; Tahy, Á.

    2009-04-01

    Drought is one of the major weather driven natural hazards, which has most harm impacts on environment, agricultural and hydrological factors than the other hazards. In spite of the fact that Hungary - that country is situated in Central Europe - belongs to the continental climate zone (influenced by Atlantic and Mediterranean streams) and this weather conditions should be favourable for agricultural production, the drought is a serious risk factor in Hungary, especially on the so called "Great Hungarian Plain", which area has been hit by severe drought events. These drought events encouraged the Ministry of Environment and Water of Hungary to embark on a countrywide drought planning programme to coordinate drought planning efforts throughout the country, to ensure that available water is used efficiently and to provide guidance on how drought planning can be accomplished. With regard to this plan, it is indispensable to analyze the regional drought frequency and duration in the target region of the programme as fundamental information for the further works. According to these aims, first we initiated a methodological development for simulating drought in a non-contributing area. As a result of this work, it has been agreed that the most appropriate model structure for our purposes using a spatially distributed physically based Soil-Vegetation-Atmosphere Transfer (SVAT) model embedded into a Markov Chain-Monte Carlo (MCMC) algorithm for estimate multi-year drought frequency and duration. In this framework: - the spatially distributed SVAT component simulates all the fundamental SVAT processes (such as: interception, snow-accumulation and melting, infiltration, water uptake by vegetation and evapotranspiration, vertical and horizontal distribution of soil moisture, etc.) taking the groundwater table as lower, and the hydrometeorological fields as upper boundary conditions into account; - and the MCMC based stochastic component generates time series of daily weather

  11. Invasive Allele Spread under Preemptive Competition

    OpenAIRE

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

    2005-01-01

    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.

  12. Modeling the evolution and distribution of the frequency's second derivative and the braking index of pulsar spin

    International Nuclear Information System (INIS)

    We model the evolution of the spin frequency's second derivative v.. and the braking index n of radio pulsars with simulations within the phenomenological model of their surface magnetic field evolution, which contains a long-term power-law decay modulated by short-term oscillations. For the pulsar PSR B0329+54, a model with three oscillation components can reproduce its v.. variation. We show that the “averaged” n is different from the instantaneous n, and its oscillation magnitude decreases abruptly as the time span increases, due to the “averaging” effect. The simulated timing residuals agree with the main features of the reported data. Our model predicts that the averaged v.. of PSR B0329+54 will start to decrease rapidly with newer data beyond those used in Hobbs et al. We further perform Monte Carlo simulations for the distribution of the reported data in |v..| and |n| versus characteristic age τC diagrams. It is found that the magnetic field oscillation model with decay index α = 0 can reproduce the distributions quite well. Compared with magnetic field decay due to the ambipolar diffusion (α = 0.5) and the Hall cascade (α = 1.0), the model with no long term decay (α = 0) is clearly preferred for old pulsars by the p-values of the two-dimensional Kolmogorov-Smirnov test. (paper)

  13. Updating the geographical distribution and frequency of Aedes albopictus in Brazil with remarks regarding its range in the Americas

    Directory of Open Access Journals (Sweden)

    Roberta Gomes Carvalho/

    2014-09-01

    Full Text Available The geographical distribution of Aedes albopictus in Brazil was updated according to the data recorded across the country over the last eight years. Countrywide house indexes (HI for Ae. albopictus in urban and suburban areas were described for the first time using a sample of Brazilian municipalities. This mosquito is currently present in at least 59% of the Brazilian municipalities and in 24 of the 27 federal units (i.e., 26 states and the Federal District. In 34 Brazilian municipalities, the HI values for Ae. albopictus were higher than those recorded for Ae. aegypti, reaching figures as high as HI = 7.72 in the Southeast Region. Remarks regarding the current range of this mosquito species in the Americas are also presented. Nineteen American countries are currently infested and few mainland American countries have not confirmed the occurrence of Ae. albopictus. The large distribution and high frequency of Ae. albopictus in the Americas may become a critical factor in the spread of arboviruses like chikungunya in the new world.

  14. A Multiplex Allele Specific Polymerase Chain Reaction (MAS-PCR) for the Detection of Factor V Leiden and Prothrombin G20210A

    Science.gov (United States)

    Bagheri, Morteza; Rad, Isa Abdi

    2011-01-01

    ABSTRACT Introduction: In order to determine the frequencies of factor V Leiden and prothrombin G20210A point mutations in the Iranian population with Azeri Turkish origin. Material and methods: 120 unrelated individuals from general population randomly selected and were examined for factor V Leiden and prothrombin G20210A mutations using a multiplex allele specific polymerase chain reaction (MAS-PCR) assay Outcomes: The frequency of prothrombin G20210A mutation was 2.08%, which means 5 chromosomes out of 240 chromosomes had prothrombin G20210A mutation. The distribution of prothrombin 20210 GG, GA, AA genotypes and prothrombin 20210A allele were 37(92.5%), 3(7.5%), 0(0%) and 3(3.75%) in males and 78(97.5%), 2(2.5%), 0(0%) and 2(1.25%) in females, respectively. Factor V Leiden was not found in our tested group (zero chromosomes out of 240 chromosomes). Analysis of the observed frequencies in the studied groups indicates that there is no statistically significant difference between females and males, regarding prothrombin G20210A mutation (p value>0.05). Conclusions: This is the first study in its own kind in this population and implies that the frequency of Factor V Leiden G1691A (R506Q, FV-Leiden) allele is extremely low but the prothrombin G20210A mutation is more frequent in the tested group. PMID:21977183

  15. Demographic history and rare allele sharing among human populations

    Science.gov (United States)

    Gravel, Simon; Henn, Brenna M.; Gutenkunst, Ryan N.; Indap, Amit R.; Marth, Gabor T.; Clark, Andrew G.; Yu, Fuli; Gibbs, Richard A.; Bustamante, Carlos D.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Lander, Eric S.; Altshuler, David L.; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; McKernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Lehrach, Hans; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Egholm, Michael; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Mardis, Elaine R.; Wilson, Richard K.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Durbin, Richard M.; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Gibbs, Richard A.; Wheeler, David; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Li, Ruiqiang; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Li, Guoqing; Wang, Jian; Yang, Huanming; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan-Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Altshuler, David L.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Cibulskis, Kristian; Fennell, Tim J.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Jaffe, David B.; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shefler, Erica; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Clark, Andrew G.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Flicek, Paul; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Stütz, Adrian M.; Humphray, Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Chakravarti, Aravinda; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Hyland, Fiona C. L.; Manning, Jonathan M.; McLaughlin, Stephen F.; Peckham, Heather E.; Sakarya, Onur; Sun, Yongming A.; Tsung, Eric F.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Sudbrak, Ralf; Albrecht, Marcus W.; Amstislavskiy, Vyacheslav S.; Herwig, Ralf; Parkhomchuk, Dimitri V.; Sherry, Stephen T.; Agarwala, Richa; Khouri, Hoda M.; Morgulis, Aleksandr O.; Paschall, Justin E.; Phan, Lon D.; Rotmistrovsky, Kirill E.; Sanders, Robert D.; Shumway, Martin F.; Xiao, Chunlin; McVean, Gil A.; Auton, Adam; Iqbal, Zamin; Lunter, Gerton; Marchini, Jonathan L.; Moutsianas, Loukas; Myers, Simon; Tumian, Afidalina; Desany, Brian; Knight, James; Winer, Roger; Craig, David W.; Beckstrom-Sternberg, Steve M.; Christoforides, Alexis; Kurdoglu, Ahmet A.; Pearson, John V.; Sinari, Shripad A.; Tembe, Waibhav D.; Haussler, David; Hinrichs, Angie S.; Katzman, Sol J.; Kern, Andrew; Kuhn, Robert M.; Przeworski, Molly; Hernandez, Ryan D.; Howie, Bryan; Kelley, Joanna L.; Melton, S. Cord; Abecasis, Gonçalo R.; Li, Yun; Anderson, Paul; Blackwell, Tom; Chen, Wei; Cookson, William O.; Ding, Jun; Kang, Hyun Min; Lathrop, Mark; Liang, Liming; Moffatt, Miriam F.; Scheet, Paul; Sidore, Carlo; Snyder, Matthew; Zhan, Xiaowei; Zöllner, Sebastian; Awadalla, Philip; Casals, Ferran; Idaghdour, Youssef; Keebler, John; Stone, Eric A.; Zilversmit, Martine; Jorde, Lynn; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; Sahinalp, S. Cenk; Sudmant, Peter H.; Mardis, Elaine R.; Chen, Ken; Chinwalla, Asif; Ding, Li; Koboldt, Daniel C.; McLellan, Mike D.; Dooling, David; Weinstock, George; Wallis, John W.; Wendl, Michael C.; Zhang, Qunyuan; Durbin, Richard M.; Albers, Cornelis A.; Ayub, Qasim; Balasubramaniam, Senduran; Barrett, Jeffrey C.; Carter, David M.; Chen, Yuan; Conrad, Donald F.; Danecek, Petr; Dermitzakis, Emmanouil T.; Hu, Min; Huang, Ni; Hurles, Matt E.; Jin, Hanjun; Jostins, Luke; Keane, Thomas M.; Le, Si Quang; Lindsay, Sarah; Long, Quan; MacArthur, Daniel G.; Montgomery, Stephen B.; Parts, Leopold; Stalker, James; Tyler-Smith, Chris; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Balasubramanian, Suganthi; Bjornson, Robert; Du, Jiang; Grubert, Fabian; Habegger, Lukas; Haraksingh, Rajini; Jee, Justin; Khurana, Ekta; Lam, Hugo Y. K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; Li, Yingrui; Luo, Ruibang; Marth, Gabor T.; Garrison, Erik P.; Kural, Deniz; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; McCarroll, Steven A.; Banks, Eric; DePristo, Mark A.; Handsaker, Robert E.; Hartl, Chris; Korn, Joshua M.; Li, Heng; Nemesh, James C.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Degenhardt, Jeremiah; Kaganovich, Mark; Clarke, Laura; Smith, Richard E.; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Humphray, Sean; Cheetham, R. Keira; Eberle, Michael; Kahn, Scott; Murray, Lisa; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Peckham, Heather E.; Sun, Yongming A.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Xiao, Chunlin; Iqbal, Zamin; Desany, Brian; Blackwell, Tom; Snyder, Matthew; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; Chen, Ken; Chinwalla, Asif; Ding, Li; McLellan, Mike D.; Wallis, John W.; Hurles, Matt E.; Conrad, Donald F.; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Du, Jiang; Grubert, Fabian; Haraksingh, Rajini; Jee, Justin; Khurana, Ekta; Lam, Hugo Y. K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; Gibbs, Richard A.; Bainbridge, Matthew; Challis, Danny; Coafra, Cristian; Dinh, Huyen; Kovar, Christie; Lee, Sandy; Muzny, Donna; Nazareth, Lynne; Reid, Jeff; Sabo, Aniko; Yu, Fuli; Yu, Jin; Marth, Gabor T.; Garrison, Erik P.; Indap, Amit; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Ward, Alistair N.; Wu, Jiantao; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Garimella, Kiran V.; Hartl, Chris; Shefler, Erica; Sougnez, Carrie L.; Wilkinson, Jane; Clark, Andrew G.; Gravel, Simon; Grubert, Fabian; Clarke, Laura; Flicek, Paul; Smith, Richard E.; Zheng-Bradley, Xiangqun; Sherry, Stephen T.; Khouri, Hoda M.; Paschall, Justin E.; Shumway, Martin F.; Xiao, Chunlin; McVean, Gil A.; Katzman, Sol J.; Abecasis, Gonçalo R.; Blackwell, Tom; Mardis, Elaine R.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Koboldt, Daniel C.; Durbin, Richard M.; Balasubramaniam, Senduran; Coffey, Allison; Keane, Thomas M.; MacArthur, Daniel G.; Palotie, Aarno; Scott, Carol; Stalker, James; Tyler-Smith, Chris; Gerstein, Mark B.; Balasubramanian, Suganthi; Chakravarti, Aravinda; Knoppers, Bartha M.; Abecasis, Gonçalo R.; Bustamante, Carlos D.; Gharani, Neda; Gibbs, Richard A.; Jorde, Lynn; Kaye, Jane S.; Kent, Alastair; Li, Taosha; McGuire, Amy L.; McVean, Gil A.; Ossorio, Pilar N.; Rotimi, Charles N.; Su, Yeyang; Toji, Lorraine H.; TylerSmith, Chris; Brooks, Lisa D.; Felsenfeld, Adam L.; McEwen, Jean E.; Abdallah, Assya; Juenger, Christopher R.; Clemm, Nicholas C.; Collins, Francis S.; Duncanson, Audrey; Green, Eric D.; Guyer, Mark S.; Peterson, Jane L.; Schafer, Alan J.; Abecasis, Gonçalo R.; Altshuler, David L.; Auton, Adam; Brooks, Lisa D.; Durbin, Richard M.; Gibbs, Richard A.; Hurles, Matt E.; McVean, Gil A.

    2011-01-01

    High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

  16. Maximizing allele detection: Effects of analytical threshold and DNA levels on rates of allele and locus drop-out.

    Science.gov (United States)

    Rakay, Christine A; Bregu, Joli; Grgicak, Catherine M

    2012-12-01

    Interpretation of DNA evidence depends upon the ability of the analyst to accurately compare the DNA profile obtained from an item of evidence and the DNA profile of a standard. This interpretation becomes progressively more difficult as the number of 'drop-out' and 'drop-in' events increase. Analytical thresholds (AT) are typically selected to ensure the false detection of noise is minimized. However, there exists a tradeoff between the erroneous labeling of noise as alleles and the false non-detection of alleles (i.e. drop-out). In this study, the effect ATs had on both types of error was characterized. Various ATs were tested, where three relied upon the analysis of baseline signals obtained from 31 negative samples. The fourth AT was determined by utilizing the relationship between RFU signal and DNA input. The other ATs were the commonly employed 50, 150 and 200 RFU thresholds. Receiver Operating Characteristic (ROC) plots showed that although high ATs completely negated the false labeling of noise, DNA analyzed with ATs derived using analysis of the baseline signal exhibited the lowest rates of drop-out and the lowest total error rates. In another experiment, the effect small changes in ATs had on drop-out was examined. This study showed that as the AT increased from ∼10 to 60 RFU, the number of heterozygous loci exhibiting the loss of one allele increased. Between ATs of 60 and 150 RFU, the frequency of allelic drop-out remained constant at 0.27 (±0.02) and began to decrease when ATs of 150 RFU or greater were utilized. In contrast, the frequency of heterozygous loci exhibiting the loss of both alleles consistently increased with AT. In summary, for samples amplified with less than 0.5ng of DNA, ATs derived from baseline analysis of negatives were shown to decrease the frequency of drop-out by a factor of 100 without significantly increasing rates of erroneous noise detection.

  17. Fixed bin frequency distribution for the VNTR Loci D2S44, D4S139, D5S110, and D8S358 in a population sample from Minas Gerais, Brazil

    Directory of Open Access Journals (Sweden)

    Parreira Kleber Simônio

    2002-01-01

    Full Text Available Fixed bin frequencies for the VNTR loci D2S44, D4S139, D5S110, and D8S358 were determined in a Minas Gerais population sample. The data were generated by RFLP analysis of HaeIII-digested genomic DNA and chemiluminescent detection. The four VNTR loci have met Hardy-Weinberg equilibrium, and there was no association of alleles among VNTR loci. The frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a DNA profile in the general Brazilian population.

  18. End plate marrow changes in the asymptomatic lumbosacral spine: frequency, distribution and correlation with age and degenerative changes

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Christine B. [Department of Radiology, VA Healthcare System, 3350 La Jolla Village Drive, CA 92161, La Jolla (United States); Vande Berg, Bruno C.; Malghem, Jacques [Department of Radiology, Cliniques Universitaires St Luc Universite Catholique de Louvain, 10 av Hippocrate, 1200, Brussels (Belgium); Tavernier, Thierry [Service de Radiologie, Clinique de la Sauvegarde, Av David Ben Gourion, 69009, Lyon (France); Cotten, Anne [Service de Radiologie Osteoarticulaire, Hopital R Salengro, 59037, Lille Cedex (France); Laredo, Jean-Denis [Service de Radiologie Osteo-articulaire, Hopital Lariboisiere, 2 rue Ambroise Pare, 75475, Paris Cedex 10 (France); Vallee, Christian [Service d' imagerie medicale, Hopital Raymond Poincare, 104 Boulevard R.Poincare, 92380, Garches (France)

    2004-07-01

    To investigate the frequency and distribution of end plate marrow signal intensity changes in an asymptomatic population and to correlate these findings with patient age and degenerative findings in the spine. MR imaging studies of the lumbosacral (LS) spine in 59 asymptomatic subjects were retrospectively reviewed by 2 musculoskeletal radiologists to determine the presence and location of fat-like and edema-like marrow signal changes about the end plates of the L1-2 through L5-S1 levels. The presence of degenerative changes in the spine was recorded as was patient age. Descriptive statistics were utilized to determine the frequency and associations of end plate findings and degenerative changes in the spine. Interobserver variability was determined by a kappa score. Binomial probability was used to predict the prevalence of the end plate changes in a similar subject population. The Fisher exact test was performed to determine statistical significance of the relationship of end plate changes with degenerative changes in the spine, superior versus inferior location about the disc and age of the patient population. Focal fat-like signal intensity adjacent to the vertebral end-plate was noted in 15 out of 59 subjects by both readers, and involved 38 and 36 out of 590 end plates by readers 1 and 2, respectively. Focal edema-like signal intensity adjacent to the vertebral end plate was noted in 8 out of 59 subjects by both readers and involved 11 and 10 out of 590 end plates by readers 1 and 2, respectively. Either fat or edema signal intensity occurred most often at the anterior (p<.05) aspects of the mid-lumbar spine and was seen in an older sub-population of the study (p<.05). End plate marrow signal intensity changes are present in the lumbar spine of some asymptomatic subjects with a characteristic location along the spine and in vertebral end plates. (orig.)

  19. [Allelic polymorphism of kappa-casein gene (CSN3) in Russian cattle breeds and its informative value as a genetic marker].

    Science.gov (United States)

    Sulimova, G E; Abani Azari, M; Rostamzadeh, J; Mohammad Abani, M R; Lazebnyĭ, O E

    2007-01-01

    The frequencies of the kappa-casein gene (CSN3) alleles and genotypes have been determined in five Russian cattle breeds (Bestuzhev, Kalmyk, Russian Black Pied, Yaroslavl, and Yakut breeds) by means of PCR-RFLP analysis using two independent restriction nucleases (HinfI and TaqI) and by allele-specific PCR. Typing alleles A and B of CSN3 is of practical importance, because allele B is correlated with commercially valuable parameters of milk productivity (protein content and milk yield) and improves the cheese yielding capacity. The frequencies of the B allele of CSN3 in the breeds studied vary from 0.16 to 0.50; and those of the AB and BB genotypes, from 0.27 to 0.60 and from 0.02 to 0.23, respectively. The Yaroslavl breed had the highest frequencies of CSN3 allele B and genotype BB (0.50 and 0.23, respectively). The frequencies of the B allele and BB genotype in other breeds studied varied from 0.25 to 0.32 and from 0.03 to 0.09, respectively. In none of the breeds studied have the observed and expected heterozygosities been found to differ from each other significantly. However, the observed genotype distributions significantly differ from the expected one in some herds (in most such cases, an excess of heterozygotes is observed). Two herds of the Yaroslavl breed dramatically differ from each other in the heterozygosity level: a deficit (D = -0.14) and an excess (D = 0.20) of heterozygotes have been observed at the Mikhailovskoe and Gorshikha farms, respectively. In general, however, the heterozygosity of the Yaroslavl breed corresponds to the expected level (D = 0.04). Analysis of breeds for homogeneity with the use of Kulback's test has shown that all cattle breeds studied are heterogeneous, the CSN3 diversity within breeds being higher than that among different breeds, which is confirmed by low Fst values (0.0025-0.0431). Thus, a DNA marker based on CSN3 gene polymorphism is extremely important for breeding practice as a marker of milk quality; however, it is

  20. Allele polymorphism and haplotype diversity of MICA/B in Tujia nationality of Zhangjiajie, Hunan Province, China.

    Science.gov (United States)

    Wang, Y J; Zhang, N J; Chen, E; Chen, C J; Bu, Y H; Yu, P

    2016-05-01

    Previous studies indicate the distribution of major histocompatibility complex class I chain-related genes A (MICA) and B (MICB) alleles and haplotypes varies widely between different ethnic populations and geographic areas. It is meaningful to investigate allelic frequencies and establish a genetic database. In this study, we firstly reported the polymorphic variation of MICA/B in 187 healthy, unrelated Tujia individuals in Zhangjiajie region, China. Using polymerase chain reaction-sequence specific priming (PCR-SSP) and sequencing-based typing (PCR-SBT), we identified eight MICA-sequence alleles, four MICA-short tandem repeat variants, and 13 MICB variants, of which MICA(∗)008:04 (29.41%), MICA(∗)A5 (29.68%), MICA(∗)A5.1 (29.68%) and MICB(∗)005:02 (39.57%) were the most frequent. Linkage disequilibrium analysis further revealed MICB(∗)005:02-MICA(∗)019 (13.10%) and MICB(∗)002-MICA(∗)008:04 (9.89%) as the most common two-locus haplotypes. Data comparison by neighbor-joining dendrograms and principal component analysis to verify allelic frequencies in other Chinese and Asia ethnic groups showed that the Zhangjiajie Tujias were genetically closer to the Guangdong Han population, based on MICA loci variability. Our results provide new information about the MICA/B gene polymorphism in Chinese Tujia population, which will form the basis for future studies on the potential role of MICA/B in allogeneic organ transplantation and disease susceptibility in related ethnic groups.

  1. Allele polymorphism and haplotype diversity of MICA/B in Tujia nationality of Zhangjiajie, Hunan Province, China.

    Science.gov (United States)

    Wang, Y J; Zhang, N J; Chen, E; Chen, C J; Bu, Y H; Yu, P

    2016-05-01

    Previous studies indicate the distribution of major histocompatibility complex class I chain-related genes A (MICA) and B (MICB) alleles and haplotypes varies widely between different ethnic populations and geographic areas. It is meaningful to investigate allelic frequencies and establish a genetic database. In this study, we firstly reported the polymorphic variation of MICA/B in 187 healthy, unrelated Tujia individuals in Zhangjiajie region, China. Using polymerase chain reaction-sequence specific priming (PCR-SSP) and sequencing-based typing (PCR-SBT), we identified eight MICA-sequence alleles, four MICA-short tandem repeat variants, and 13 MICB variants, of which MICA(∗)008:04 (29.41%), MICA(∗)A5 (29.68%), MICA(∗)A5.1 (29.68%) and MICB(∗)005:02 (39.57%) were the most frequent. Linkage disequilibrium analysis further revealed MICB(∗)005:02-MICA(∗)019 (13.10%) and MICB(∗)002-MICA(∗)008:04 (9.89%) as the most common two-locus haplotypes. Data comparison by neighbor-joining dendrograms and principal component analysis to verify allelic frequencies in other Chinese and Asia ethnic groups showed that the Zhangjiajie Tujias were genetically closer to the Guangdong Han population, based on MICA loci variability. Our results provide new information about the MICA/B gene polymorphism in Chinese Tujia population, which will form the basis for future studies on the potential role of MICA/B in allogeneic organ transplantation and disease susceptibility in related ethnic groups. PMID:26972750

  2. THE CHARACTERISTICS OF TEMPORAL AND SPATIAL DISTRIBUTION OF TROPICAL CYCLONE FREQUENCIES OVER THE SOUTH CHINA SEA AND ITS AFFECTING OCEANIC FACTORS IN THE PAST 50 YEARS

    Institute of Scientific and Technical Information of China (English)

    LI Chun-hui; LIU Chun-xia; CHENG Zheng-quan

    2007-01-01

    The characteristics of temporal and spatial distribution of tropical cyclone frequencies over the South China Sea areas and its affecting factors in the past 50yrs are analyzed based on typhoon data that provided by CMA and Simple Ocean Data Assimilation (SODA). The results show that the tropical cyclone frequencies from June to October show concentrated geographic distribution, for they mainly distribute over the SCS area from 15 - 20 °N. The characteristics present significant interdecadal changes. The impact of oceanic factors on the tropical cyclone frequencies in the SCS area is mainly realized by La Ni(n)a and La Ni(n)a-like events before 1975 but mainly by El Ni(n)o and El Nifo-like events after 1975.

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

    Science.gov (United States)

    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

  4. 中国北京汉族人群和日本东京人群ROR2基因单核苷酸多态性比较%Comparison of minor allele frequency and haplotype frequencies for single nucleotide polymorphisms in receptor tyrosine kinase-like orphan receptor 2 gene using HapMap data from Han Chinese in Beijing (CHB) and Japanese in Tokyo (JPT)

    Institute of Scientific and Technical Information of China (English)

    王红; 赵凯平

    2011-01-01

    Objective Single nucleotide polymorphisms(SNPs) in receptor tyrosine kinaselike orphan receptor 2 (ROR2) gene were analyzed and compared between Han Chinese in Beijing(CHB) and Japanese in Tokyo(JPT) using the HapMap data,to provide basis for SNP determination.ROR2 gene related etiologic studies were conducted in the above mentioned two populations.Methods Monotonic and un-monotonic SNPs of ROR2 gene were distinguished by Haploviewprogram.Minor allele frequency (MAF),haplotype blocks and haplotype frequencies were analyzed ineligible SNPs and tag SNPs respectively with genotyping call rate >80%,MAF>1%,H-Wequilibrium (P>0.01) and no gender difference (P>0.05).Tag SNPs were determined under thecriteria of r2≥0.8 or logarithm of the odd score (LOD) ≥3 for pairwise eligible SNPs in CHB and JPT.Common tag SNPs for CHB and JPT were directly reported by Haploview program or being identified from those which were higly related to tag SNPs reported by haploview program under SPSS 13.0 software.Results A total of 404 common SNPs were provided for both CHB and JPT samples by HapMap,where 101 common monotonic SNPs between CHB and JPT had the common minor alleles.The common SNPs between CHB and JPT were 257.In the 257 common eligible SNPs,224 (87.2%) had common minor alleles.Among the 18 and 27 haplotype blocks identified in 257common eligible SNPs between CHB and JPT,except for 2 independent haplotype blocks identified only in JPT.Other haplotype blocks between CHB and JPT were overlapped partly or completely.A number of 50 common tag SNPs between CHB and JPT were determined and the proportions in CHB and JPT were 64.9% and 70.4% respectively.Conclusion Analysis of HapMap data provided an opportunity to avoid monotonic SNPs that had been included in ROR2 gene related etiologic studies.SNPs in ROR2 gene had common features in alleles,MAF,haplotype blocks and haplotype frequencies between CHB and JPT populations,which were consistent with the geographic and

  5. Multistation template matching to characterize frequency-magnitude distributions of induced seismicity in the Central and Eastern US

    Science.gov (United States)

    Brudzinski, M. R.; Skoumal, R.; Currie, B.

    2015-12-01

    We analyze the frequency-magnitude distribution (FMD) of recent seismic sequences thought to be induced by wastewater injection and hydraulic fracturing in the Central and Eastern U.S. to investigate their physical origin and improve hazard estimates. Multistation template matching is utilized to increase the number of events analyzed by lowering the magnitude of detection. In cases where local deployments are available, we demonstrate that the FMD obtained through template matching using regional data are comparable to those obtained from traditional detection using the local deployment. Since deployments usually occur after seismicity has already been identified, catalogs constructed with regional data offer the advantage of providing a more complete history of the seismicity. We find two primary groups of FMDs for induced sequences: those that generally follow the Gutenberg-Richter power-law and those that generally do not. All of the induced sequences are typically characterized by swarm-like behavior, but the non-power-law FMDs are also characterized by a clustering of events at low magnitudes and particularly low aftershock productivity for a continental interior. Each of the observations in the non-power law FMD cases is predicted by numerical simulations of a seismogenic zone governed by a viscoelastic damage rheology with low effective viscosity in the fault zone. Such a reduction in effective viscosity is expected if fluid injection increases fluid pressures in the fault zone to the point that the fault zone begins to dilate.

  6. Uncertainty Quantification for a Climatology of the Frequency and Spatial Distribution of North Atlantic Tropical Cyclone Landfalls

    Science.gov (United States)

    Tolwinski-Ward, S. E.; Stransky, S. M.

    2014-12-01

    We develop a Bayesian hierarchical model for the climatological frequency of Atlantic Basin tropical cyclone (TC) landfalls along the coast of North and Central America. The model is explicitly spatial, with a covariance structure that incorporates the effects of coastline geometry, and is resolved at impacts-relevant, 50-mile coastal increments. The model is based on a negative binomial regression on the phase of the Southern Oscillation, North Atlantic Oscillation, and the Atlantic Multidecadal Oscillation, and also accounts explicitly for the time-dependent uncertainty in the historical data used to fit it. The statistically-inferred climatology is interpreted in terms of current scientific understanding of the mechanisms through which related large-scale climatic variability affects the development and motion of Atlantic tropical cyclones. We also probe the spatial posterior probability distribution to quantify and rank the uncertainty in the climatology of TC landfalls that can be attributed to climatic variability, model parameter uncertainty, uncertainty in the historical landfall positions, a possible undercount bias early in the historical record, and sampling variability from the finite length of the observations. Given more detailed, expert information about uncertainty for each specific storm in the historical dataset, the model could be used to develop a definitive TC landfall climatology. It could also be used in conjunction with spatial information about exposures for risk management applications.

  7. Spatial and Temporal Analysis on the Distribution of Active Radio-Frequency Identification (RFID Tracking Accuracy with the Kriging Method

    Directory of Open Access Journals (Sweden)

    Xin Liu

    2014-10-01

    Full Text Available Radio frequency identification (RFID technology has already been applied in a number of areas to facilitate the tracking process. However, the insufficient tracking accuracy of RFID is one of the problems that impedes its wider application. Previous studies focus on examining the accuracy of discrete points RFID, thereby leaving the tracking accuracy of the areas between the observed points unpredictable. In this study, spatial and temporal analysis is applied to interpolate the continuous distribution of RFID tracking accuracy based on the Kriging method. An implementation trial has been conducted in the loading and docking area in front of a warehouse to validate this approach. The results show that the weak signal area can be easily identified by the approach developed in the study. The optimum distance between two RFID readers and the effect of the sudden removal of readers are also presented by analysing the spatial and temporal variation of RFID tracking accuracy. This study reveals the correlation between the testing time and the stability of RFID tracking accuracy. Experimental results show that the proposed approach can be used to assist the RFID system setup process to increase tracking accuracy.

  8. Modernized method of estimating the parameters of LFM signals based on the time-frequency distribution correction and the use of the Hough transformation

    OpenAIRE

    Cheng, B. L.; Kubrak, A. N.

    2009-01-01

    The method has been modernized for obtaining the parameter estimation of the fine structure of LFM signals (linear-frequency-modulated signals) at small values of the signal-to-noise ratio. The development of this method was based on the analysis of the signal time-frequency distribution (TFD) and the Hough transform. The specific feature of this method is correction of the time-frequency parameters in the TFD image considered and the use of the principle of detecting the straight line by the...

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

    Science.gov (United States)

    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

  10. Quantitative assessment on the orientation and distribution of carbon fibers in a conductive polymer composite using high-frequency ultrasound.

    Science.gov (United States)

    Lin, Yi-Hsun; Huang, Chih-Chung; Wang, Shyh-Hau

    2012-05-01

    uniformly in the deeper regions of the samples. This study validates that the distribution and orientation of CFs in conductive polymer composites could be sensitively and quantitatively assessed by high-frequency ultrasound in conjunction with current analysis methods.

  11. Human leukocyte antigen class II susceptibility conferring alleles among non-insulin dependent diabetes mellitus patients

    International Nuclear Information System (INIS)

    To determine the frequency of Human Leukocyte Antigen (HLA) class II susceptibility conferring alleles among type 2 Diabetes mellitus patients, in comparison with healthy controls. Cross-sectional comparative study. Patients with non-insulin dependent Diabetes mellitus meeting World Health Organization criteria were studied. These were compared with age and gender matched healthy control subjects. For each subject (patients as well as controls), DNA was extracted from ethylene diamine tetra-acetate sample and HLA class II DRB1 typing was carried out at allele group level (DRB1*01-DRB1*16) by sequence specific primers. Human leukocyte antigen DRB1 type was determined by agarose gel electrophoresis and results were recorded. Frequencies were determined as number of an allele divided by total number of alleles per group; p-value was computed using Pearson's chi-square test. Among the 100 patients, there were 63 males and 37 females with 68 controls. A total of 13 different HLA DRB1 alleles were detected, with DRB1*15 being the commonest in both the groups. The allele DRB1*13 had statistically significant higher frequency in patient group as compared to controls (p 0.005). HLA DRB1*13 was found with a significantly increased frequency in non-insulin dependent Diabetes mellitus. (author)

  12. Time–frequency analysis of nonstationary complex magneto-hydro-dynamics in fusion plasma signals using the Choi–Williams distribution

    Energy Technology Data Exchange (ETDEWEB)

    Xu, L.Q.; Hu, L.Q., E-mail: lqhu@ipp.ac.cn; Chen, K.Y.; Li, E.Z.

    2013-11-15

    Highlights: • Choi–Williams distribution yields excellent time–frequency resolution for discrete signal. • CWD method provides clear time–frequency pictures of EAST and HT-7 fast MHD events. • CWD method has advantages to wavelets transform scalogram and the short-time Fourier transform spectrogram. • We discuss about how to choose the windows and free parameter of CWD method. -- Abstract: The Choi–Williams distribution is applied to the time–frequency analysis of signals describing rapid magneto-hydro-dynamic (MHD) modes and events in tokamak plasmas. A comparison is made with Soft X-ray (SXR) signals as well as Mirnov signal that shows the advantages of the Choi–Williams distribution over both continuous wavelets transform scalogram and the short-time Fourier transform spectrogram. Examples of MHD activities in HT-7 and EAST tokamak are shown, namely the onset of coupling tearing modes, high frequency precursors of sawtooth, and low frequency MHD instabilities in edge localized mode (ELM) free in H mode discharge.

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

    Science.gov (United States)

    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

  14. Structure-borne low-frequency noise from multi-span bridges: A prediction method and spatial distribution

    Science.gov (United States)

    Song, X. D.; Wu, D. J.; Li, Q.; Botteldooren, D.

    2016-04-01

    Structure-borne noise from railway bridges at far-field points is an important indicator in environmental noise assessment. However, studies that predict structure-borne noise tend to model only single-span bridges, thus ignoring the sound pressure radiating from adjacent spans. To simulate the noise radiating from multi-span bridges induced by moving vehicles, the vibrations of a multi-span bridge are first obtained from a three-dimensional (3D) vehicle-track-bridge dynamic interaction simulation using the mode superposition method. A procedure based on the 2.5-dimensional (2.5D) boundary element method (BEM) is then presented to promote the efficiency of acoustical computation compared with the 3D BEM. The simulated results obtained from both the single-span and multi-span bridge models are compared with the measured results. The sound predictions calculated from the single-span model are accurate only for a minority of near-field points. In contrast, the sound pressures calculated from the multi-span bridge model match the measured results in both the time and frequency domains for all of the near-field and far-field points. The number of bridge spans required in the noise simulation is then recommended related to the distance between the track center and the field points of interest. The spatial distribution of multi-span structure-borne noise is also studied. The variation in sound pressure levels is insignificant along the length of the bridge, which validates the finding that the sound test section can be selected at an arbitrary plane perpendicular to the multi-span bridge.

  15. Critical periods for foetal mortality in gilts identified by analysing the length distribution of mummified foetuses and frequency of non-fresh stillborn piglets

    NARCIS (Netherlands)

    Lende, van der T.; Rens, van B.T.T.M.

    2003-01-01

    The objective of this study was to investigate the timing of foetal mortality in gilts of a segregating F2 cross of Large White and Meishan pigs on the basis of the length distribution of mummified foetuses and the frequency of non-fresh stillborn piglets in order to establish whether critical perio

  16. Major histocompatibility complex class I chain related (MIC) A gene, TNFa microsatellite alleles and TNFB alleles in juvenile idiopathic arthritis patients from Latvia.

    Science.gov (United States)

    Nikitina Zake, Liene; Cimdina, Ija; Rumba, Ingrida; Dabadghao, Preethi; Sanjeevi, Carani B

    2002-05-01

    In order to analyze involvement of major histocompatibility complex class I chain-related gene A (MICA) and tumor necrosis factor a (TNFa) microsatellite polymorphisms as well as TNFB gene in juvenile idiopathic arthritis (JIA), we studied 128 patients divided into groups according to clinical features [monoarthritis (n = 14), oligoarthritis (n = 58), polyarthritis (n = 50), and systemic (n = 6)], and 114 age- and sex-matched healthy controls from Latvia. DNA samples were amplified with specific primers and used for genotyping of MICA and TNFa microsatellite. Typing for a biallelic NcoI polymerase chain reaction RFLP polymorphism located at the first intron of TNFB gene was done as follows: restriction digests generated fragments of 555bp and 185bp for TNFB*1 allele, and 740bp for TNFB*2 allele. The results were compared between cases and controls. We found significant increase of MICA allele A4 (p = 0.009; odds ratio [OR] = 2.3) and allele TNFa2 (p = 0.0001; OR = 4.4) in patients compared with controls. The frequency of allele TNFa9 was significantly decreased (p = 0.0001; OR = 0.1) in patients with JIA. No significant differences of TNFB allele frequency were found. Our data suggest that MICA and TNFa microsatellite polymorphisms may be used as markers for determination of susceptibility and protection from JIA.

  17. Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles.

    Science.gov (United States)

    Orozco-terWengel, Pablo; Kapun, Martin; Nolte, Viola; Kofler, Robert; Flatt, Thomas; Schlötterer, Christian

    2012-10-01

    The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome-wide false discovery rates heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects.

  18. Correlation of DNA fragment sizes within loci in the presence of non-detectable alleles.

    Science.gov (United States)

    Chakraborty, R; Li, Z

    1995-01-01

    At present most forensic databases of DNA profiling of individuals consist of DNA fragment sizes measured from Southern blot restriction fragment length polymorphism (RFLP) analysis. Statistical studies of these databases have revealed that, when fragment sizes are measured from RFLP analysis, some of the single-band patterns of individuals may actually be due to heterozygosity of alleles in which fragment size resulting from one allele remains undetected. In this work, we evaluate the effect of such allelic non-detectability on correlation of fragment sizes within individuals at a locus, and its impact on the inference of independence of fragment sizes within loci. We show that when non-detectable alleles are present in a population at a locus, positive correlations of fragment sizes are expected, which increase with the proportion of non-detectable alleles at the locus. Therefore, a non-zero positive correlation is not a proof of allelic dependence within individuals. Applications of this theory to the current forensic RFLP databases within the US show that there is virtually no evidence of significant allelic dependence within any of the loci. Therefore, the assumption that DNA fragment sizes within loci are independent is valid, and hence, the population genetic principles of computing DNA profile frequencies by multiplying binned frequencies of fragment sizes are most likely to be appropriate for forensic applications of DNA typing data.

  19. HLA-DRB1 allele polymorphisms in genetic susceptibility to esophageal carcinoma

    Institute of Scientific and Technical Information of China (English)

    Jun Lin; Chang-Sheng Deng; Jie Sun; Xian-Gong Zheng; Xing Huang; Yan Zhou; Ping Xiong; Ya-Ping Wang

    2003-01-01

    AIM: To probe into the genetic susceptibility of HLA-DRB1 alleles to esophageal carcinoma in Han Chinese in Hubei Province.METHODS: HLA-DRB1 allele polymorphisms were typed by polymerase chain reaction with sequence-specific primers (PCR-SSP) in 42 unrelated patients with esophageal cancer and 136 unrelated normal control subjects and the associated HLA-DRB1 allele was measured by nucleotide sequence analysis with PCR.SAS software was used in statistics.RESULTS: Allele frequency (AF) of HLA-DRB1·0901 was significantly higher in esophageal carcinoma patients than that in the normal controls (0.2500 vs0.1397, P=0.028, the odds ratio 2.053, etiologic fraction 0.1282). After analyzed the allele nucleotide sequence of HLA-DRB1·0901 which approachs to the corresponded exon 2 sequence of the allele in genebank. There was no association between patients and controls in the rested HLA-DRB1 alleles.CONCLUSION: HLA-DRB1·0901 allele is more common in the patients with esophageal carcinoma than in the healthy controls, which is positively associated with the patients of Hubei Han Chinese. Individuals carrying HLA-DRB1·0901may be susceptible to esophageal carcinoma.

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

    Science.gov (United States)

    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.

  1. Characterization of CCR5△32、 CCR2b-64I、 CX3CR1-249I280M and SDF1-3'A Allelic Polymorphisms in the Chinese Uygur Population

    Institute of Scientific and Technical Information of China (English)

    LIU Mingxu(刘明旭); WANG Fusheng(王福生); JIN Lei(金磊); HONG Weiguo(洪卫国); LEI Zhouyun(雷周云); ZHANG Bing(张冰); HOU Jing(候静); ZHANG Zhanping(张战平); TANG Chunjun(唐纯军)

    2002-01-01

    Objectives: Allelic polymorphisms of CCR5△32 、CCR2b-64I,CX3CR1-249I280M and SDF1-3'A associatedwith HIV-1 infection and disease progression wereinvestigated in indigenous Uygur populations from theXinjiang Uygur Autonomous Region of China.Methods: The study population comprised 316 healthyUygur subjects with an age range of 1-80 years old, fromwhom whole peripheral blood samples were collected andnone were HIV-1 seropositive. Genomic DNA samples werepurified using a Qiagen Blood Kit. Genotyping of theaforementioned four alleles was performed using PCR orPCR/RFLP assay, and further confirmed by direct DNAsequencing.Results: The allelic frequencies in Chinese Uygurpopulation were as follows: 3.48% for CCR5△32; 19.45% forCCR2b-64I; 13.8% for CX3CR1-249I280M haplotype, and20.41% for SDF1-3'A. Mutant allele distributions amongUygur populations were in accordance with theHardy-Weinberg equilibrium. No statistical difference wasfound between the frequency of the three HIV coreceptors andtheir respective ligand genes.Conclusion: The frequency of SDF1-3'A andCX3CR1-249I280M haplotypes in these Uygur populationswas similar to that of Caucasian people, while the frequency ofthe CCR2b-64I haplotype more closely matched the HanChinese. The frequency of CCR5△32 in Uygur populationswas between Caucasian and Han frequencies, the more closelymatching the frequency in Medi-Asia people. No geneticlinkage between any two of the three HIV coreceptor geneswas found, but obvious genetic linkages existed betweenCX3CR1-249I and CX3CR1-280M,with even higher linkagedegrees than Caucasian people.

  2. Analysis of the eclipsing binaries in the LMC discovered by OGLE: Period distribution and frequency of the short-period binaries

    CERN Document Server

    Mazeh, T; North, P; Mazeh, Tsevi; Tamuz, Omer; North, Pierre

    2006-01-01

    We review the results of our analysis of the OGLE LMC eclipsing binaries (Mazeh, Tamuz & North 2006), using EBAS -- Eclipsing Binary Automated Solver, an automated algorithm to fit lightcurves of eclipsing binaries (Tamuz, Mazeh & North 2006). After being corrected for observational selection effects, the set of detected eclipsing binaries yielded the period distribution and the frequency of all LMC short-period binaries, and not just the eclipsing systems. Somewhat surprisingly, the period distribution is consistent with a flat distribution in log P between 2 and 10 days. The total number of binaries with periods shorter than 10 days in the LMC was estimated to be about 5000. This figure led us to suggest that (0.7 +- 0.4)% of the main-sequence A- and B-type stars are found in binaries with periods shorter than 10 days. This frequency is substantially smaller than the fraction of binaries found by small Galactic radial-velocity surveys of B stars.

  3. Analysis of allele frequencies of HLA-DRB1 * 12 : 01 : 01G and HLA-DRB1 * 14 : 01 : 01G groups%HLA-DRB1*12:01:01G和HLA-DRB1*14:01:01G组内等位基因频率的统计分析

    Institute of Scientific and Technical Information of China (English)

    何俊俊; 章伟; 和艳敏; 王炜; 韩浙东; 陈男英; 朱发明; 吕杭军; 严力行

    2012-01-01

    目的 区分并计算人类白细胞抗原(human leukocyte antigen,HLA) HLA-DRB1* 12:01:01G(HLA-DRB1* 12:01:01/12:06/12:10/12:17)和HLA-DRB1* 14:01:01G(DRB1* 14:01:01/14:54)组内等位基因及其相对频率,并分析其与HLA-DRB3和HLA-DQB1的连锁情况.方法 收集115例HLA-DRB1*12:01:01G组和108例HLA-DRB1*14:01:01G组标本,采用单核苷酸序列分析(polymerase chain reaction-sequence based typing,PCR-SBT)方法检测HLA-DRB1* 12:01:01G组等位基因的第1~3外显子序列和HLA-DRB1* 14:01:01G组的第2、3外显子序列.HLA-DRB3和HLA-DQB1基因分型采用PCR-SBT方法.结果 115例HLA-DRB1* 12:01:01G组标本中,101例(87.8%)为HLA-DRB1* 12:01:01,14例(12.2%)为HLA-DRB1* 12:10,未发现HLA-DRB1* 12:06和HLA-DRB1* 12:17. 108例HLA-DRB1*14:01:01G组标本全部为HLA-DRB1*14:54. HLA-DRB1*12:01:01与HLA-DRB3* 01:01:02和HLA-DQB1* 03:01连锁,HLA-DRB1* 12:10则与HLA-DRB3* 02:02:01和HLA-DQB1* 03:01连锁.HLA-DRB1* 14:54与HLA-DRB3* 02:02:01和HLA-DQB1* 05:02、*05:03连锁.结论 HLA-DRB1* 12:01:01G组中HLA-DRB1* 12:01:01频率最高,而HLA-DRB1* 14:01:01G组则以HLA-DRB1* 14:54频率最高.%Objective To discriminate and analyze the relative frequencies of alleles in HLA-DRB1 * 12:01:01G(HLA-DRB1 * 12:01:01 /12:06/12:10/12:17) and HLA-DRB1 * 14:01:01G (DRB1 * 14:01:01/14:54) groups and assess their associations with HLA-DRB3 and HLA-DQB1 loci.Methods A total of 115 DNA samples previously typed as HLA-DRB1 * 12:01:01G and 108 samples from HLA-DRB1 * 14:01:01G were selected.DNA sequences for exons 1 to 3 of the HLA-DRB1 locus were analyzed for HLA-DRB1 * 12:01:01G,and exons 2 to 3 were analyzed for HLA-DRB1 * 14:01:01G by polymerase chain reaction sequence-based typing (PCR-SBT).Genotyping of HLA-DRB3 and HLA-DQB1 were achieved by PCRSBT.Results Among 115 samples previously typed as HLA-DRB1 * 12:01:01G,101 (87.8%) were confirmed as HLA-DRB1 * 12:01:01 and 14 (12.2%) were HLA-DRB1 * 12:10,but HLA-DRB1 * 12:06 and HLA-DRB1 * 12

  4. Ion energy distributions in a pulsed dual frequency inductively coupled discharge of Ar/CF{sub 4} and effect of duty ratio

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, Anurag; Seo, Jin Seok; Kim, Tae Hyung [Department of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 440-746 (Korea, Republic of); Yeom, Geun Young, E-mail: gyyeom@skku.edu [Department of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 440-746 (Korea, Republic of); SKKU Advanced Institute of Nanotechnology(SAINT), Sungkyunkwan University, Suwon, Gyeonggi-do 440-746 (Korea, Republic of)

    2015-08-15

    Controlling time averaged ion energy distribution (IED) is becoming increasingly important in many plasma material processing applications for plasma etching and deposition. The present study reports the evolution of ion energy distributions with radio frequency (RF) powers in a pulsed dual frequency inductively discharge and also investigates the effect of duty ratio. The discharge has been sustained using two radio frequency, low (P{sub 2 MHz} = 2 MHz) and high (P{sub 13.56 MHz} = 13.56 MHz) at a pressure of 10 mTorr in argon (90%) and CF{sub 4} (10%) environment. The low frequency RF powers have been varied from 100 to 600 W, whereas the high frequency powers from 200 to 1200 W. Typically, IEDs show bimodal structure and energy width (energy separation between the high and low energy peaks) increases with increasing P{sub 13.56 MHz}; however, it shows opposite trends with P{sub 2 MHz}. It has been observed that IEDs bimodal structure tends to mono-modal structure and energy peaks shift towards low energy side as duty ratio increases, keeping pulse power owing to mode transition (capacitive to inductive) constant.

  5. Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of transmission

    Directory of Open Access Journals (Sweden)

    Riazuddin Sheikh

    2008-05-01

    Full Text Available Abstract Background Information regarding hepatitis C virus genotypes and subtypes circulating in Pakistan and various risk factors for their transmission are not known well. The specific objective of this study was to find out the frequency of various HCV genotypes present in well-characterized Pakistani HCV isolates and their possible routes of transmission. Methods A total of 3351 serum samples were tested by type-specific genotyping assay. Out of 3351 HCV RNA positive patients, 2039 were males and 1312 were females. As regard as genotyped samples, 2165 belonged to Punjab region, 823 belonged to N.W.F.P., 239 to Sindh and 124 patients were from Balochistan. Results Out of the total 3351 tested serum samples, type-specific PCR fragments were observed in 3150 (94.00% serum samples. The distribution of genotypes of the typeable samples as determined by this assay, was as follows: 1664 (49.05% genotype 3a; 592 (17.66% genotype 3b; 280 (8.35% genotype 1a; 252 (7.52% genotype 2a; 101 (3.01% genotype 1b; 50 (1.49% with genotype 4; 25 (0.75% with 3c; 27 (0.80% genotype 2b; 6 (0.18% with subtype 5a; 5 (0.15% genotype 1c; 4 (0.12% with subtype 6a; 3 (0.09% genotype 2c; and 161 (4.80% patients were infected with mixed infection. Two hundred and one (5.99% serum samples were found untypeable by the present genotyping system. More than 86% and 72% patients with genotypes 3a and 3b respectively had received multiple injections in past. For genotypes 1a and 1b the route of transmission was major/minor surgery along with unknown reasons. Majority of the cases with type 2a, 2b and indeterminate genotypes were sporadic. Mixed infections were common in thalassaemic patients. Conclusion The most common HCV genotype in Pakistan is type 3a. Regional difference in genotypes was observed only in Balochistan province of Pakistan. More than 70% of the cases were acquired in hospitals through reuse of needles/syringes and major/minor surgery that is very common in this

  6. Distribution of Allelic Variation for Genes of Vernalization and Photoperiod among Wheat Cultivars from 23 Countries%春化和光周期基因等位变异在23个国家小麦品种中的分布

    Institute of Scientific and Technical Information of China (English)

    杨芳萍; 韩利明; 阎俊; 夏先春; 张勇; 曲延英; 王忠伟; 何中虎

    2011-01-01

    Molecular markers for vernalization genes Vrn-A1, Vrn-B1, Vrn-D1 and Vrn-B3 and photoperiod gene Ppd-D1 were used to detect the presence of these genes among 755 cultivars from 23 countries. Days to heading and physiological maturity of these cultivars were also recorded in Anyang, Henan province, China to provide information for their utilization in Chinese wheat breeding program. Frequencies of Vrn-A1, Vrn-B1, Vm-D1, and vrn-A1+vrn-B1+vrn-D1 were 13.0%, 21.1%, 15.6%, and 64.2%, respectively. Dominant allele Vrn-B3 was absent in all tested materials. Dominant vernalization alleles Vm-A1, Vm-B1, and Vrn-D1 were mainly observed in Chinese spring wheat and middle and upper Yangtze Valley winter wheat regions, Italy, India, Japan, Canada, Mexico, Chile, Argentina, and Australia with spring type, while cultivars carryied all recessive alleles at the four vernalization loci. The gene recombination of vrn-A1, vrn-D1, and Vrn-B1 was found in winter wheat regions of northern China, middle and southern US, Germany, France, Norway, Ukraine, Russia, Turkey, Iran, Hungary, Bulgaria, Romania, and Serbia,where the wheat growth habit is winter type. The frequency of Ppd-D1a was 55.2%, and photoperiod sensitive allele Ppd-D1b was mainly observed in cultivars from higher latitude regions of US, Germany, Norway, Hungary, northeastern China, Canada, Chile, and Argentina; while photoperiod insensitive allele Ppd-D1a was observed in the other wheat-growing regions. Most of cultivars with photoperiod insensitive allele Ppd-D1a could complete physiological maturity in Anyang, whereas cultivars from Germany, Norway, Hungary, northwestern US, northeast China, Chile and Argentina could not mature well. In Anyang, flowering time was not speeded up by the presence of dominant vernalization allele Vrn-A1a, cultivars with Vrn-B1 and Vrn-D1 could head normally due to the completion of vernalization requirement during winter season.%为促进国外资源在我国小麦育种中的有效利

  7. Energy storage systems impact on the short-term frequency stability of distributed autonomous microgrids, an analysis using aggregate models

    DEFF Research Database (Denmark)

    Serban, Ioan; Teodorescu, Remus; Marinescu, Corneliu

    2013-01-01

    This study analyses the integration impact of battery energy storage systems (BESSs) on the short-term frequency control in autonomous microgrids (MGs). Short-term frequency stability relates with the primary or speed control level, as defined in the regulations of the classical grids. The focus...... of storing and releasing energy when required by the system. Therefore the need of boosting the MG power reserves by adding energy storage systems is often a requirement. The study highlights the improvement in the MG short-term frequency stability brought by an original BESS control structure enhanced...

  8. Nanostructures for very broadband or multi-frequency transition from wave beams to a subwavelength light distributions

    CERN Document Server

    Luukkonen, O; Simovski, C

    2011-01-01

    In this paper we suggest and theoretically study a tapered plasmonic nanostructure which connects the incident wave beam with a subwavelength spatial region where the field is locally enhanced in a broad frequency range or for different operation frequencies. This spatial region has a frequency stable location near the contour of the tapered structure. This results from a special waveguide mode which can also exist in the tapered structure. We foresee many possible applications for our structure from prospective near-field scanning optical microscopes to interconnects between conventional optical waveguides and prospective optical nanocircuits.

  9. Distribution, Frequency and Variation of Stripe Rust Resistance Loci Yr10, Lr34/Yr18 and Yr36 in Chinese Wheat Cultivars

    Institute of Scientific and Technical Information of China (English)

    Cuiling Yuan; Hui Jiang; Honggang Wang; Kun Li; Heng Tang; Xianbin Li; Daolin Fu

    2012-01-01

    Wheat stripe rust is a devastating disease in many regions of the world.In wheat,49 resistance genes for stripe rust have been officially documented,but only three genes are cloned,including the race-specific resistance Yr10 candidate gene (Yr10CG) and slow-rusting genes Lr34/Yr18 (hereafter designated as Yr18) and Yr36.In this study,we developed gene-specific markers for these genes and used them to screen a collection of 659 wheat accessions,including 485 Chinese cultivars.Thirteen percent and eleven percent of the tested Chinese cultivars were positive for the markers for Yr10CG and Yr18RH (the resistant haplotype of Yr18),respectively,but none were positive for the Yr36 marker.Since there is a limited use of the Yr10 gene in Chinese wheat,the relatively high frequency of wheat varieties with the Yr10CG marker suggests that the identity of the Yr10 gene is unknown.With regards to the Yr18 gene,29% of the tested cultivars that are used in the Middle and Lower Yangtze Valleys' winter wheat zone were positive for Yr18RH markers.A non-functional allele of Yr18RHwas identified in ‘Mingxian 169',a commonly used susceptible check for studying stripe rust.The data presented here will provide useful information for marker-assisted selection for wheat stripe rust resistance.

  10. Influence of the CXCL1 rs4074 A allele on alcohol induced cirrhosis and HCC in patients of European descent.

    Directory of Open Access Journals (Sweden)

    Hans Dieter Nischalke

    Full Text Available BACKGROUND AND AIMS: CXCL1 (CXC chemokine-ligand-1 is a ligand for CXC chemokine receptor 2 expressed on hepatic stellate cells (HSC. Thus, CXCL1 might contribute to HSC activation and fibrogenesis. In the present study, we investigated the influence of the CXCL1 rs4074 polymorphism on the occurrence of alcohol induced liver cirrhosis and hepatocellular carcinoma (HCC. METHODS: The study involved 458 patients with alcoholic cirrhosis (170 with HCC, 115 alcoholics without liver disease and 342 healthy controls. All subjects were genotyped for the CXCL1 rs4074 polymorphism and CXCL1 serum levels of 132 patients were measured. In vitro CXCL1 secretion in TLR-transfected cell lines were studied by ELISA. RESULTS: Distribution of the CXCL1 genotypes (GG/GA/AA was 159/219/80 in patients with alcoholic cirrhosis, 52/44/19 in alcoholic controls and 158/140/44 in healthy controls. Patients with alcohol-induced cirrhosis were significantly more often carriers of the CXCL1 rs4074 A allele (65.3% than alcoholics without liver disease (54.8%, OR=1.55; 95%CI=1.025-2.350; p=0.04 and healthy controls (53.8%, OR=1.62; 95%CI=1.212-2.151; p=0.001. Accordingly, the frequency of the CXCL1 rs4074 A allele was significantly higher in the cirrhotic patients than in the subjects without cirrhosis (41.4% vs. 33.9%, OR=1.38, 95% CI:1.14-1.66, p=0.001. Furthermore cirrhotic carriers of the CXCL1 rs4074 A allele had significantly higher CXCL1 serum levels than carriers of the GG genotype. In contrast to sera from healthy controls, sera from patients with alcoholic cirrhosis induced CXCL1 secretion in TLR2- (p=0.016 and TLR4- (p=0.008 transfected HEK293 cells. This finding indicates that sera from patients with alcoholic cirrhosis contain soluble ligands that can induce CXCL1 production via stimulation of TLRs. CONCLUSION: The enhanced CXCL1 serum levels in carriers of the rs4074 A allele together with their increased frequency in patients with alcohol induced cirrhosis

  11. Distribution of apolipoprotein E gene polymorphism in students and in high-educated elderly from Serbia

    Directory of Open Access Journals (Sweden)

    Maksimović Nela

    2013-01-01

    Full Text Available Apolipoprotein E (ApoE play important role in lipid metabolism and in processes of remodeling and reparation in central nervous system. Three common ApoE isoforms, ApoE2, ApoE3 and ApoE4, show strong genetic determination by ε2, ε3, and ε4 allele. In human genome gene encoding Apolipoprotein E (APOE is located on cromosome 19, and ε2/ε3/ε4 haplotype system is defined by 2 non-synonymous single nucleotide polymorphisms (SNPs in the APOE exon 4. The frequency of the three APOE alleles and corresponding genotypes varies across human populations, with possible clinical implications. At least, variable distribution of ε4 allele may contribute to the regional risk of cardiovascular and Alzheimer’s diseases. Allele-frequency comparisons between younger and older populations suggest an effect of APOE on mortality, but these data are not consistently confirmed. In the present study we have analyzed the distribution of APOE gene polymorphism in a group of University students and retained University professors living in Serbia. After DNA extraction from peripheral blood samples, the APOE genotype was determined by polymerase chain reaction (PCR followed with HhaI restriction digestion. We found no statistically significant difference in alleles and genotypes distribution between younger and elder group of participants. Also, there was no significant difference compared to APOE data previously obtained in YUSAD cohort of healthy school children (15 y of age from different regions of Serbia. In both of our groups, as well as in YUSAD cohort, frequency of APOE ε4 allele was <10%. The observed frequencies are lower than in neighboring countries, but similar with Spanish data and some Asian populations. Our results do not support important role of APOE ε4 in the morbidity and mortality in Serbian population, but gene-environmental-social interactions should be considered. [Projekat Ministarstva nauke Republike Srbije, br. ON175091

  12. A Corpus-Based Lexical Study on Frequency and Distribution of Coxhead's Awl Word Families in Medical Research Articles (RAs)

    Science.gov (United States)

    Chen, Qi; Guang-Chun, Ge

    2007-01-01

    We conducted a lexical study on the word frequency and the text coverage of the 570 word families from Coxhead's Academic Word List (AWL) in medical research articles (RAs) based on a corpus of 50 medical RAs written in English with 190425 running words. By computer analysis, we found that the text coverage of the AWL words accounted for around…

  13. Applications of the Dirichlet distribution to forensic match probabilities.

    Science.gov (United States)

    Lange, K

    1995-01-01

    The Dirichlet distribution provides a convenient conjugate prior for Bayesian analyses involving multinomial proportions. In particular, allele frequency estimation can be carried out with a Dirichlet prior. If data from several distinct populations are available, then the parameters characterizing the Dirichlet prior can be estimated by maximum likelihood and then used for allele frequency estimation in each of the separate populations. This empirical Bayes procedure tends to moderate extreme multinomial estimates based on sample proportions. The Dirichlet distribution can also be employed to model the contributions from different ancestral populations in computing forensic match probabilities. If the ancestral populations are in genetic equilibrium, then the product rule for computing match probabilities is valid conditional on the ancestral contributions to a typical person of the reference population. This fact facilitates computation of match probabilities and tight upper bounds to match probabilities.

  14. Hierarchical structure of genetic distances: Effects of matrix size, spatial distribution and correlation structure among gene frequencies

    Directory of Open Access Journals (Sweden)

    Flávia Melo Rodrigues

    1998-06-01

    Full Text Available Geographic structure of genetic distances among local populations within species, based on allozyme data, has usually been evaluated by estimating genetic distances clustered with hierarchical algorithms, such as the unweighted pair-group method by arithmetic averages (UPGMA. The distortion produced in the clustering process is estimated by the cophenetic correlation coefficient. This hierarchical approach, however, can fail to produce an accurate representation of genetic distances among populations in a low dimensional space, especially when continuous (clinal or reticulate patterns of variation exist. In the present study, we analyzed 50 genetic distance matrices from the literature, for animal taxa ranging from Platyhelminthes to Mammalia, in order to determine in which situations the UPGMA is useful to understand patterns of genetic variation among populations. The cophenetic correlation coefficients, derived from UPGMA based on three types of genetic distance coefficients, were correlated with other parameters of each matrix, including number of populations, loci, alleles, maximum geographic distance among populations, relative magnitude of the first eigenvalue of covariance matrix among alleles and logarithm of body size. Most cophenetic correlations were higher than 0.80, and the highest values appeared for Nei's and Rogers' genetic distances. The relationship between cophenetic correlation coefficients and the other parameters analyzed was defined by an "envelope space", forming triangles in which higher values of cophenetic correlations are found for higher values in the parameters, though low values do not necessarily correspond to high cophenetic correlations. We concluded that UPGMA is useful to describe genetic distances based on large distance matrices (both in terms of elevated number of populations or alleles, when dimensionality of the system is low (matrices with large first eigenvalues or when local populations are separated

  15. Genotype and Allele Frequency of the 27-bp Tandem RepeatPolymorphism in the Endothelial Nitric Oxide SynthaseGene in Chinese Population%中国人eNOS基因VNTR多态性的基因型与等位基因频率

    Institute of Scientific and Technical Information of China (English)

    路萍; 郑晓飞; 吕星; 吴苏华; 邢瑞云; 孙琪云; 韩莉; 蓝红

    2001-01-01

    一氧化氮合酶(nitric oxide synthase,NOS)催化L-精氨酸的氧化反应生成L-瓜氨酸和一氧化氮(nitric oxide,NO).NO可通过cGMP依赖的信号传导途径介导平滑肌细胞舒张,是调节血管张力的重要信使分子.NO尚可抑制血小板凝集,对血栓形成起重要调节作用.目前在哺乳动物中已发现细胞来源、表达方式和活性调节不同的3种NOS同工酶,分别为神经元型NOS(neuronal NOS,nNOS)、诱导型NOS(inducible NOS,iNOS)和内皮细胞型NOS(endothelial NOS,eNOS).人的eNOS基因位于第7号染色体长臂(7q36),全长约21kb,含有26个外显子和25个内含子.eNOS基因存在多个与心脑血管疾病相关的基因多态性位点.其中位于第4内含子的一个以27bp为核心的数目可变性串联重复序列(variable number of tandem repeat,VNTR)多态性位点,已被证实与原发性高血压、心肌梗死和静脉血栓形成有关.目前在我国尚缺乏NOS基因多态性在正常人群中基因型及等位基因频率分布的统计资料.为此,我们从316名健康中国人的基因组DNA检测了eNOS基因第4内含子VNTR多态性的基因型和等位基因,鉴定出重复6次、5次和4次的3种等位基因,以及6/5杂合、5/5纯合、5/4杂合和4/4纯合的4种基因型.同时我们将正常中国人eNOS 基因VNTR 多态性的基因型和等位基因频率与其他种族的相关资料进行了统计对比.结果表明,中国人eNOS基因VNTR的各种基因型和等位基因频率与日本人相似,4/4纯合基因型频率与高加索人差异显著,各种基因型和等位基因频率与非裔美国人均存在显著差异.%Genotype and allele frequency of the polymorphic 27-bp repeat, a variable number of tandem repeats (VNTR) located in intron 4 of the endothelial nitric oxide synthase gene, were analyzed in 316 healthy Chinese individuals. Four genotypes, namely 6/5-repeats heterozygous, 5/5-repeats homozygous,5/4-repeats heterozygous and 4/4-repeats homozygous

  16. ABO血型系统中1种新A2等位基因的发现及在中国福建地区汉族人群中A2亚型调查%Discovery of A Novel A2 Allel in ABO Blood Group System and Investigation of Its Distribution in Han Population of Chinese Fujian Province

    Institute of Scientific and Technical Information of China (English)

    张爱; 池泉; 任本春

    2012-01-01

    This study was aimed to investigate the distribution of A2 subgroup in Han Population of Chinese Fujian province and its molecular mechanisms . One individual with serologic ABO blood grouping discrepancy was identified with commercially available monoclonal and polyclonal antibodies and lectin: anti-A, anti-B, anti-AB, anti-Al, and anti-H reagents according to the routine laboratory methods. DNA sequences of exon 6, 7 and intron 6 of ABO gene were analyzed by polymerase chain reaction using genomic DNA and direct DNA sequencing or sequencing after gene cloning. Red cells of 3 176 A or AB unrelated individuals were tested with anti- Al. The results showed that this individual was identified as A2 subgroup by serological technology, sequencing analysis indicated the A2 subgroup with novel A variant allele , the novel A allele being different from the allele A101 by 467C > T and 607G > A missense mutation in exon 7, no A2 subgroup was identified from the 3 176 individuals by using standard serological technology. It is concluded that a novel A allele responsible for A2 subgroup composing of 467C > T and 607G > A has been firstly confirmed, and the A2 subgroup is very rare in Chinese Fujian Han population.%本研究探讨ABO血型系统中A2亚型在中国福建地区汉族人群中的分布频率及其分子机制.采用血清学方法鉴定1例A2亚型标本,PCR扩增ABO基因第6、7外显子及第6内含子,PCR产物经割胶纯化后直接测序,并对含有突变位点的扩增片段进行单倍体序列分析;用抗-A1单克隆血清筛查福建地区3176例A或AB型汉族无偿献血者.结果表明,该例A2亚型的基因型鉴定为A/ Olv,与A101相比,其第7外显子存在467C>T和607G>A突变,分别导致多肽链P156L和E203K替换;经标准血清学方法检测,3176例随机A或AB型献血者(同时期健康献血者约16527人)未检出A2亚型.结论:首次发现467C>T和607G>A组合的A2等位基因,A2亚型在福建地区汉族人群中罕见.

  17. RANTES In1.1C allele polymorphisms in 13 Chinese ethnic populations

    Institute of Scientific and Technical Information of China (English)

    QIAN Yuan; SUN Hao; CHU Jia-you

    2009-01-01

    Background The In1.1C single nucleotide polymorphism (SNP) allele results in reduced RANTES transcription, which is associated with increased frequency of HIV-1 infection, and rapid progression to AIDS among HIV-1-infected individuals. This study aimed to study the mutant frequency and polymorphism of RANTES in Chinese populations.Methods The genotypes of RANTES In1.1C were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) with the digestion of restriction endonuclease Mbo Ⅱ.Results Of the 617 individuals, 290 (47%) were carriers of the RANTES In1.1C allele, 52 of whom were homozygotes,whereas 238 were heterozygotes. The frequency of the RANTES In1.1C allele in those tested individuals was 0.2840.The frequencies of Inl.lC allele vaded from 0.07-0.27 in most of the populations in South-west China except for the two Lisu populations, while the frequencies of In1.1C spans from 0.35 to 0.45 in North-west China. The prevalence of the allele varied substantially between the South-west groups and North-west groups (X2=7.838, P=0.006).Conclusions The prevalence of the RANTES In1.1C allele varies substantially between the South-west groups and North-west groups. There is no significant difference between the groups with different languages, which suggests that language relationship is not consistent with the genetic relationship. These results have important implications for the design, assessment, and implementation of HIV-1 vaccines.

  18. Beneficial role of D allele in controlling ACE levels: a study among Brahmins of north India

    Indian Academy of Sciences (India)

    SHOBHA KUMARI; NIDHI SHARMA; SUNIL THAKUR; PRAKASH R. MONDAL; KKALLUR N. SARASWATHY

    2016-06-01

    India being a country with vast diversity is expected to have different dietary and life style patterns which in turn may lead topopulation-specific environmental risk factors. Further, the interaction of these risk factors with the genetic makeup of pop-ulation makes it either susceptible or resistant to cardiovascular disease. One such candidate gene is angiotensin convertingenzyme (ACE) for various cardiovascular mechanisms. ACE is the key enzyme of the renin angiotensin aldosterone systempathway which maintains homeostasis blood pressure in the body and any variation in the levels is reported to be associatedwith various complex diseases. The DD genotype is found to increase ACE levels, which is associated with cardiovasculardiseases and decrease in ACE levels are associated with kidney diseases. The aim of this study was to understand the distribu-tion of ACE I/D polymorphism and ACE levels among Brahmins of National Capital Region (NCR) north India, with respectto age and sex ratio distribution. In this study, 136 subjects of which 50 males and 86 females, who were unrelated up to firstcousin, aged 25 to70 years were studied.ACEgene was found to be polymorphic with high frequency of heterozygote (ID)followed by II and DD genotypes. The studied population was found to be in Hardy–Weinberg equilibrium with respect toACE I/D polymorphism (P =0.55). I allele frequency was found to be higher (0.560) than the D allele (0.44). The medianlevel of ACE was found to be 65.96 ng/mL (48.12–86.24) which is towards lower side of the normal range. ACE levels werefound to be increased among individual having either of the homozygotes that is II or DD and higher frequency of heterozy-gote (ID) is indicative of advantage in the population by maintaining lower ACE levels. The limitation of the present study islow sample size, however, the merit is that the subjects belonged to a Mendalian population with a common gene pool

  19. Beneficial role of D allele in controlling ACE levels: a study among Brahmins of north India.

    Science.gov (United States)

    Kumari, Shobha; Sharma, Nidhi; Thakur, Sunil; Mondal, Prakash R; Saraswathy, Kallur N

    2016-06-01

    India being a country with vast diversity is expected to have different dietary and life style patterns which in turn may lead to population-specific environmental risk factors. Further, the interaction of these risk factors with the genetic makeup of population makes it either susceptible or resistant to cardiovascular disease. One such candidate gene is angiotensin converting enzyme (ACE) for various cardiovascular mechanisms. ACE is the key enzyme of the renin angiotensin aldosterone system pathway which maintains homeostasis blood pressure in the body and any variation in the levels is reported to be associated with various complex diseases. The DD genotype is found to increase ACE levels, which is associated with cardiovascular diseases and decrease in ACE levels are associated with kidney diseases. The aim of this study was to understand the distribution of ACE I/D polymorphism and ACE levels among Brahmins of National Capital Region (NCR) north India, with respect to age and sex ratio distribution. In this study, 136 subjects of which 50 males and 86 females, who were unrelated up to first cousin, aged 25 to70 years were studied. ACE gene was found to be polymorphic with high frequency of heterozygote (ID) followed by II and DD genotypes. The studied population was found to be in Hardy-Weinberg equilibrium with respect to ACE I/D polymorphism (P = 0.55). I allele frequency was found to be higher (0.560) than the D allele (0.44). The median level of ACE was found to be 65.96 ng/mL (48.12-86.24) which is towards lower side of the normal range. ACE levels were found to be increased among individual having either of the homozygotes that is II or DD and higher frequency of heterozygote (ID) is indicative of advantage in the population by maintaining lower ACE levels. The limitation of the present study is low sample size, however, the merit is that the subjects belonged to a Mendalian population with a common gene pool. PMID:27350671

  20. Frequency distributions of 90Sr and 137Cs concentrations in an ecosystem of the "Red Forest" area in the Chernobyl exclusion zone.

    Science.gov (United States)

    Gaschak, Sergey P; Makliuk, Yulia A; Maksimenko, Andrey M; Bondarkov, Mikhail D; Chizhevsky, Igor; Caldwell, Eric F; Jannik, G Timothy; Farfán, Eduardo B

    2011-10-01

    In the most highly contaminated region of the Chernobyl Exclusion Zone, the "Red Forest" site, the accumulation of the major dose-affecting radionuclides (90Sr and 137Cs) within the components of an ecological system encompassing 3,000 m(2) was characterized. The sampled components included soils (top 0-10 cm depth), Molina caerulea (blue moor grass), Camponotus vagus (carpenter ants), and Pelobates fuscus (spade-footed toad). In a comparison among the components of this ecosystem, the 90Sr and 137Cs concentrations measured in 40 separate grids exhibited significant differences, while the frequency distribution of the values was close to a logarithmically-normal leptokurtic distribution with a significant right-side skew. While it is important to identify localized areas of high contamination or "hot spots," including these values in the arithmetic mean may overestimate the exposure risk. In component sample sets that exhibited logarithmically normal distribution, the geometric mean more accurately characterizes a site. Ideally, risk assessment is most confidently achieved when the arithmetic and geometric means are most similar, meaning the distribution approaches normal. Through bioaccumulation, the highest concentrations of 90Sr and 137Cs were measured in the blue moor grass and spade-footed toad. These components also possessed distribution parameters that shifted toward a normal distribution. PMID:21878766

  1. FREQUENCY DISTRIBUTIONS OF 90SR AND 137CS CONCENTRATIONS IN AN ECOSYSTEM OF THE 'RED FOREST' AREA IN THE CHERNOBYL EXCLUSION ZONE

    Energy Technology Data Exchange (ETDEWEB)

    Farfan, E.; Jannik, T.; Caldwell, E.

    2011-10-01

    In the most highly contaminated region of the Chernobyl Exclusion Zone: the 'Red Forest' site, the accumulation of the major dose-affecting radionuclides ({sup 90}Sr and {sup 137}Cs) within the components of an ecological system encompassing 3,000 m{sup 2} were characterized. The sampled components included soils (top 0-10 cm depth), Molina caerulea (blue moor grass), Camponotus vagus (carpenter ants) and Pelobates fuscus (spade-footed toad). In a comparison among the components of this ecosystem, the {sup 90}Sr and {sup 137}Cs concentrations measured in 40 separate grids exhibited significant differences, while the frequency distribution of the values were close to a logarithmically normal leptokurtic distribution with a significant right-side skew. While it is important to identify localized areas of high contamination or 'hot spots,' including these values in the arithmetic mean may overestimate the exposure risk. In component sample sets that exhibited logarithmically normal distribution, the geometrical mean more accurately characterizes a site. Ideally, risk assessment is most confidently achieved when the arithmetic and geometrical means are most similar, meaning the distribution approaches normal. Through bioaccumulation, the highest concentrations of {sup 90}Sr and {sup 137}Cs were measured in the blue moor grass and spade-footed toad. These components also possessed distribution parameters that shifted toward a normal distribution.

  2. Frequency distributions of 90Sr and 137Cs concentrations in an ecosystem of the "Red Forest" area in the Chernobyl exclusion zone.

    Science.gov (United States)

    Gaschak, Sergey P; Makliuk, Yulia A; Maksimenko, Andrey M; Bondarkov, Mikhail D; Chizhevsky, Igor; Caldwell, Eric F; Jannik, G Timothy; Farfán, Eduardo B

    2011-10-01

    In the most highly contaminated region of the Chernobyl Exclusion Zone, the "Red Forest" site, the accumulation of the major dose-affecting radionuclides (90Sr and 137Cs) within the components of an ecological system encompassing 3,000 m(2) was characterized. The sampled components included soils (top 0-10 cm depth), Molina caerulea (blue moor grass), Camponotus vagus (carpenter ants), and Pelobates fuscus (spade-footed toad). In a comparison among the components of this ecosystem, the 90Sr and 137Cs concentrations measured in 40 separate grids exhibited significant differences, while the frequency distribution of the values was close to a logarithmically-normal leptokurtic distribution with a significant right-side skew. While it is important to identify localized areas of high contamination or "hot spots," including these values in the arithmetic mean may overestimate the exposure risk. In component sample sets that exhibited logarithmically normal distribution, the geometric mean more accurately characterizes a site. Ideally, risk assessment is most confidently achieved when the arithmetic and geometric means are most similar, meaning the distribution approaches normal. Through bioaccumulation, the highest concentrations of 90Sr and 137Cs were measured in the blue moor grass and spade-footed toad. These components also possessed distribution parameters that shifted toward a normal distribution.

  3. Application of Linear Quadratic Gaussian and Coefficient Diagram Techniques to Distributed Load Frequency Control of Power Systems

    Directory of Open Access Journals (Sweden)

    Tarek Hassan Mohamed

    2015-12-01

    Full Text Available This paper presented both the linear quadratic Gaussian technique (LQG and the coefficient diagram method (CDM as load frequency controllers in a multi-area power system to deal with the problem of variations in system parameters and load demand change. The full states of the system including the area frequency deviation have been estimated using the Kalman filter technique. The efficiency of the proposed control method has been checked using a digital simulation. Simulation results indicated that, with the proposed CDM + LQG technique, the system is robust in the face of parameter uncertainties and load disturbances. A comparison between the proposed technique and other schemes is carried out, confirming the superiority of the proposed CDM + LQG technique.

  4. Dielectric permittivity tensor and low frequency instabilities of a magnetoactive current-driven plasma with nonextensive distribution

    Energy Technology Data Exchange (ETDEWEB)

    Niknam, A. R., E-mail: a-niknam@sbu.ac.ir [Laser and Plasma Research Institute, Shahid Beheshti University, G.C., Tehran (Iran, Islamic Republic of); Rastbood, E.; Khorashadizadeh, S. M. [Physics Department, University of Birjand, Birjand (Iran, Islamic Republic of)

    2015-12-15

    The dielectric permittivity tensor of a magnetoactive current-driven plasma is obtained by employing the kinetic theory based on the Vlasov equation and Lorentz transformation formulas with an emphasize on the q-nonextensive statistics. By deriving the q-generalized dispersion relation of the low frequency modes in this plasma system, the possibility and properties of filamentation and ion acoustic instabilities are then studied. It is shown that the occurrence and the growth rate of these instabilities depend strongly on the nonextensive parameters, external magnetic field strength, and drift velocity. It is observed that the growth rate of ion acoustic instability is affected by the magnetic field strength much more than that of the filamentation instability in the low frequency range. The external magnetic field facilitates the development of the ion-acoustic instability. It is also shown that the filamentation is the dominant instability only for the high value of drift velocity.

  5. Frequency distribution of sickle cell anemia, sickle cell trait and sickle/beta-thalassemia among anemic patients in Saudi Arabia

    OpenAIRE

    Elsayid, Mohieldin; Al-Shehri, Mohammed Jahman; Alkulaibi, Yasser Abdullah; Alanazi, Abdullah; Qureshi, Shoeb

    2015-01-01

    Background: Notwithstanding, the growing incidence of sickle cell hemoglobinopathies (SCH) such as sickle cell anemia (SCA) or sickle cell disease, sickle/beta-thalassemia; the exact prevalence remains obscure in Saudi Arabia. Hence, this study is an attempt to determine the frequency of SCA and sickle cell trait (SCT) among all anemic patients with SCH treated at the King Abdul-Aziz Medical City (KAMC), Riyadh, Saudi Arabia. Furthermore, the hemoglobin (Hb) S and other Hb patterns (Hb AS and...

  6. Effects of topography, soil type and forest age on the frequency and size distribution of canopy gap disturbances in a tropical forest

    Directory of Open Access Journals (Sweden)

    E. Lobo

    2013-04-01

    Full Text Available Treefall gaps are the major source of disturbance in most tropical forests. The frequency and size of these gaps have important implications for forest ecosystem processes as they can influence the functional trait distribution of tree communities, stand-level above-ground biomass and productivity. However, we still know little about the relative importance of environmental drivers of gap disturbance regimes because existing studies vary greatly in criteria used for defining gaps, in the spatial extent of the study area, and the spatial resolution of canopy height measurements. Here we use LiDAR (light detecting and ranging to explore how forest age, topography and soil type affect canopy disturbance patterns across a 1500 ha tropical forest landscape in central Panama. We characterize disturbance based on the frequency distribution of gap sizes (the "gap size distribution", and the area of the forest affected by gaps (the "gap area fraction". We found that slope and forest age had significant effects on the gap size distribution, with a higher frequency of large gaps associated with old-growth forests and more gentle slopes. Slope and forest age had similar effects on the gap area fraction, however gap area fraction was also affected by soil type and by aspect. We conclude that variation in disturbance patterns across the landscape can be linked to factors that act at the fine scale (such as aspect or slope, and factors that show heterogeneity at coarser scales (such as forest age or soil type. Awareness of the role of different environmental factors influencing gap formation can help scale-up the impacts of canopy disturbance on forest communities measured at the plot scale to landscape and regional scales.

  7. Geographic distribution of haplotype diversity at the bovine casein locus.

    OpenAIRE

    Moazami-Goudarzi Katy; Lenstra Johannes A; Ajmone-Marsan Paolo; Williams John L; Zaragoza Pilar; Özbeyaz Ceyhan; Ibeagha-Awemu Eveline M; Jann Oliver C; Erhardt Georg

    2004-01-01

    Abstract The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within ...

  8. Estimating the power law distribution of Earth electrical conductivity from low-frequency, controlled-source electromagnetic data

    Science.gov (United States)

    Beskardes, G. D.; Weiss, C. J.; Everett, M. E.

    2013-12-01

    Electromagnetic methods of geophysical exploration are a reflection of the spatio-temporal variability in ground conductivity, a macroscopic physical property that is a function of lithology, pore-scale surface chemistry, fracture networks, and the presence and distribution of fluids and partial melts. As such, the bulk electrical properties of some representative elementary volume within the subsurface derive from the macroscopic effect of charge buildup and current pathways across a range of length scales within. Quantifying this relationship between multiscale electrical properties and the observed geophysical data is a critical step toward meaningful geologic interpretation. Previously we presented evidence of near-surface electromagnetic data whose small scale fluctuations are both repeatable and fractally distributed -- an observation that supports the notion of a spatially hierarchical Earth. Bounded by the end member cases from homogenized isotropic and anisotropic media, we present numerical modeling results from textured and spatially-correlated, stochastic geologic media, demonstrating that the electromagnetic response is a power law distribution similar to that seen in the earlier observational data, rather than a smooth response polluted with Gaussian noise as is commonly assumed. Furthermore, we show that such power law behavior is dependent on correlation length within the medium and that the power law distribution of Earth conductivity can be estimated from that of the observed electromagnetic data.

  9. Effects of fade distribution on a mobile satellite downlink and uplink performance in a frequency reuse cellular configuration

    Science.gov (United States)

    Boutin, Karl; Lecours, Michel; Pelletier, Marcel; Delisle, Gilles Y.

    1990-01-01

    In a mobile satellite system with a frequency reuse cellular configuration, significant co-channel interference can be experienced due to the antenna sidelobe level. The signal will be subjected not only to its own fading, but also to the effect of the varying degree of fading on co-channel interferer, and this interference will behave differently in the up and in the down link. This paper presents a quantitative evaluation of the combined effects of fades and co-channel interference on a mobile satellite link.

  10. Impact of routine episodic emissions on the expected frequency distribution of emissions from oil and gas production sources.

    Science.gov (United States)

    Smith, N.; Blewitt, D.; Hebert, L. B.

    2015-12-01

    In coordination with oil and gas operators, we developed a high resolution (oil and gas emissions over a year. We include routine emissions from condensate tanks, dehydrators, pneumatic devices, fugitive leaks and liquids unloading. We explore the variability in natural gas emissions from these individual well-pad sources, and find that routine short-term episodic emissions such as tank flashing and liquids unloading result in the appearance of a skewed, or 'fat-tail' distribution of emissions, from an individual well-pad over time. Additionally, we explore the expected variability in emissions from multiple wells with different raw gas composition, gas/liquids production volumes and control equipment. Differences in well-level composition, production volume and control equipment translate into differences in well-level emissions leading to a fat-tail distribution of emissions in the absence of operational upsets. Our results have several implications for recent studies focusing on emissions from oil and gas sources. Time scale of emission estimates are important and have important policy implications. Fat tail distributions may not be entirely driven by avoidable mechanical failures, and are expected to occur under routine operational conditions from short-duration emissions (e.g., tank flashing, liquid unloading). An understanding of the expected distribution of emissions for a particular population of wells is necessary to evaluate whether the observed distribution is more skewed than expected. Temporal variability in well-pad emissions make comparisons to annual average emissions inventories difficult and may complicate the interpretation of long-term ambient fenceline monitoring data. Sophisticated change detection algorithms will be necessary to identify when true operational upsets occur versus routine short-term emissions.

  11. CYP2C9 polymorphism in patients with epilepsy: genotypic frequency analyzes andphenytoin adverse reactions correlation

    Directory of Open Access Journals (Sweden)

    Carlos Alexandre Twardowschy

    2011-04-01

    Full Text Available OBJECTIVE: CYP2C9 is a major enzyme in human drug metabolism and the polymorphism observed in the corresponding gene may affect therapeutic outcome during treatment. The distribution of variant CYP2C9 alleles and prevalence of phenytoin adverse reactions were hereby investigated in a population of patients diagnosed with epilepsy. METHOD: Allele-specific PCR analysis was carried out in order to determine frequencies of the two most common variant alleles, CYP2C9*2 and CYP2C9*3 in genomic DNA isolated from 100 epileptic patients. We also analyzed the frequency of phenytoin adverse reactions among those different genotypes groups. The data was presented as mean±standard deviation. RESULTS: The mean age at enrollment was 39.6±10.3 years (range, 17-72 years and duration of epilepsy was 26.5±11.9 years (range 3-48 years. The mean age at epilepsy onset was 13.1±12.4 years (range, 1 month-62 years. Frequencies of CYP2C9*1 (84%, CYP2C9*2 (9% and CYP2C9*3 (7% were similar to other published reports. Phenytoin adverse reactions were usually mild and occurred in 15% patients, without correlation with the CYP2C9 polymorphism (p=0.34. CONCLUSION: Our findings indicate an overall similar distribution of the CYP2C9 alleles in a population of patients diagnosed with epilepsy in the South of Brazil, compared to other samples. This sample of phenytoin users showed no drug related adverse reactions and CYP2C9 allele type correlation. The role of CYP2C9 polymorphism influence on phenytoin adverse reaction remains to be determined since some literature evidence and our data found negative results.

  12. Multidimensional earthquake frequency distributions consistent with self-organization of complex systems: The interdependence of magnitude, interevent time and interevent distance

    Science.gov (United States)

    Tzanis, A.; Vallianatos, F.

    2012-04-01

    the G-R law predicts, but also to the interevent time and distance by means of well defined power-laws. We also demonstrate that interevent time and distance are not independent of each other, but also interrelated by means of well defined power-laws. We argue that these relationships are universal and valid for both local and regional tectonic grains and seismicity patterns. Eventually, we argue that the four-dimensional hypercube formed by the joint distribution of earthquake frequency, magnitude, interevent time and interevent distance comprises a generalized distribution of the G-R type which epitomizes the temporal and spatial interdependence of earthquake activity, consistent with expectation for a stationary or evolutionary critical system. Finally, we attempt to discuss the emerging generalized frequency distribution in terms of non-extensive statistical physics. Acknowledgments. This work was partly supported by the THALES Program of the Ministry of Education of Greece and the European Union in the framework of the project "Integrated understanding of Seismicity, using innovative methodologies of Fracture Mechanics along with Earthquake and Non-Extensive Statistical Physics - Application to the geodynamic system of the Hellenic Arc - SEISMO FEAR HELLARC".

  13. Comparative analysis of the frequency, distribution and population sizes of yeasts associated with canine seborrheic dermatitis and healthy skin.

    Science.gov (United States)

    Yurayart, Chompoonek; Chindamporn, Ariya; Suradhat, Sanipa; Tummaruk, Padet; Kajiwara, Susumu; Prapasarakul, Nuvee

    2011-03-24

    The purpose of this study was to investigate the diversity of yeast associated with the degree of canine seborrheic dermatitis (SD) by anatomical sites. Fifty-seven samples were divided as 17 healthy skin, 20 with primary seborrheic dermatitis (PSD), and 20 with secondary seborrheic dermatitis (SSD). Yeast isolation and characterization were carried out based on microscopical features and biochemical properties. DNA analysis at the internal transcribed spacer I of 26S rDNA region was utilized for species confirmation. Four species of yeast consisting Malassezia pachydermatis, Malassezia furfur, Candida parapsilosis and Candida tropicalis recovered from examined dogs. M. pachydermatis and C. parapsilosis were isolated from all dogs, but C. tropicalis and M. furfur were recovered from 3 healthy dogs and one diseased dog, respectively. The number of M. pachydermatis and C. parapsilosis in diseased dogs was higher than that of healthy specimens (P<0.01). High frequency and population size of C. parapsilosis were closely associated to PSD, while those of M. pachydermatis were associated with both PSD and SSD (P<0.01). C. parapsilosis were predominant at the perianal area. This study demonstrated the co-colonization of M. pachydermatis and C. parapsilosis in large amounts and frequency associated with stage of disease and anatomical site. PMID:20961712