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Sample records for allele frequency distribution

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

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

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

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

    PubMed

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

    2015-04-30

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

  3. Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus

    PubMed Central

    Chakraborty, Ranajit; Fuerst, Paul A.; Nei, Masatoshi

    1980-01-01

    With the aim of understanding the mechanism of maintenance of protein polymorphism, we have studied the properties of allele frequency distribution and the number of alleles per locus, using gene-frequency data from a wide range of organisms (mammals, birds, reptiles, amphibians, Drosophila and non-Drosophila invertebrates) in which 20 or more loci with at least 100 genes were sampled. The observed distribution of allele frequencies was U-shaped in all of the 138 populations (mostly species or subspecies) examined and generally agreed with the theoretical distribution expected under the mutation-drift hypothesis, though there was a significant excess of rare alleles (gene frequency, 0 ∼ 0.05) in about a quarter of the populations. The agreement between the mutation-drift theory and observed data was quite satisfactory for the numbers of polymorphic (gene frequency, 0.05 ∼ 0.95) and monomorphic (0.95 ∼ 1.0) alleles.—The observed pattern of allele-frequency distribution was incompatible with the prediction from the overdominance hypothesis. The observed correlations of the numbers of rare alleles, polymorphic alleles and monomorphic alleles with heterozygosity were of the order of magnitude that was expected under the mutation-drift hypothesis. Our results did not support the view that intracistronic recombination is an important source of genetic variation. The total number of alleles per locus was positively correlated with molecular weight in most of the species examined, and the magnitude of the correlation was consistent with the theoretical prediction from mutation-drift hypothesis. The correlation between molecular weight and the number of alleles was generally higher than the correlation between molecular weight and heterozygosity, as expected. PMID:17249018

  4. VNTR allele frequency distributions under the stepwise mutation model: A computer simulation approach

    SciTech Connect

    Shriver, M.D.; Jin, L.; Chakraborty, R.; Boerwinkle, E. )

    1993-07-01

    Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size, and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). The authors estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. The authors then compared simulation expectations with actual data reported in the literature. They used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, it is hypothesized that these three classes of loci are subject to different mutational forces.

  5. Global distribution of allele frequencies at the human dopamine D4 receptor locus

    SciTech Connect

    Chang, F.M.; Kidd, J.R.; Livak, K.J.

    1994-09-01

    The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopaminergic system has been implicated in this neuropsychiatric disorder. Several research groups have reported an association between allelic variants at DRD4 and schizophrenia, while others have been unable to replicate that finding. Knowledge of the appropriate gene frequencies in the underlying populations may resolve these inconsistencies. We have determined the frequencies of 8 different alleles of the 48 bp imperfect tandem repeat of exon 3 at the DRD4 locus in samples from 33 populations around the world. The frequencies vary considerably in the different populations with the most common allele ranging from 16% to 95%. Frequencies and Fst values will be presented for the 3 most common alleles (4-, 7-, and 2- repeat) by continental groupings, but the individual populations vary significantly around the averages. The populations averaged 4.3 alleles (range 2 to 7).

  6. Allele frequency distributions of D1S80 in the Polish population.

    PubMed

    Ciesielka, M; Kozioł, P; Krajka, A

    1996-08-15

    The polymorphism of the D1S80 locus has been analyzed in a population sample of 208 unrelated individuals in the Southeast Poland and 103 mother/child pairs. PCR amplified alleles were separated by a vertical discontinuous polyacrylamide gel electrophoresis system. Nineteen different alleles and 52 phenotypes could be distinguished. The alleles 18 (f = 0.267) and 24 (f = 0.300) were most common in Poland. D1S80 genotype frequencies of Poland population do not deviate from Hardy-Weinberg equilibrium. All mother/child pairs shared at least one D1S80 allele.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2003-01-01

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

  10. Human acetylator polymorphism: estimate of allele frequency in Libya and details of global distribution.

    PubMed Central

    Karim, A K; Elfellah, M S; Evans, D A

    1981-01-01

    Acetylator phenotyping by means of a sulphadimidine tests revealed 65% of Libyan Arabs to be slow acetylators. Hence the frequency of the allele controlling slow acetylation (As) is estimated as q = 0.81 +/- 0.05. This estimate is similar to those previously recorded in European and adjacent Middle Eastern populations. PMID:7328611

  11. A method for estimating the intensity of overdominant selection from the distribution of allele frequencies.

    PubMed Central

    Slatkin, M; Muirhead, C A

    2000-01-01

    A method is proposed for estimating the intensity of overdominant selection scaled by the effective population size, S = 2Ns, from allele frequencies. The method is based on the assumption that, with strong overdominant selection, allele frequencies are nearly at their deterministic equilibrium values and that, to a first approximation, deviations depend only on S. Simulations verify that reasonably accurate estimates of S can be obtained for realistic sample sizes. The method is applied to data from several loci in the major histocompatibility complex (Mhc) in numerous human populations. For alleles distinguished by both serological typing and the sequence of the peptide-binding region, our estimates of S are comparable to those obtained by analysis of DNA sequences in showing that selection is strongest on HLA-B and weaker on HLA-A, HLA-DRB1, and HLA-DQA1. The intensity of selection on HLA-B varied considerably among populations. Two populations, Native American and Inuit, showed an excess rather than a deficiency in homozygosity. Comparable estimates of S were obtained for alleles at Mhc class II loci distinguished by serological reactions (serotyping) and by differences in the amino acid sequences of the peptide-binding region (molecular typing). A comparison of two types of data for DQA1 and DRB1 showed that serotyping led to generally lower estimates of S. PMID:11102400

  12. Allele frequency distribution of 10 MiniSTRs in the Pashtun population of Pakistan.

    PubMed

    Shafique, Muhammad; Shahzad, Muhammad Saqib; Perveen, Uzma; Parveen, Rukhsana; Ali, Azam; Hussain, Manzoor; Rehman, Ziaur; Shahid, Ahmad Ali; Husnain, Tayyab

    2015-05-01

    Two hundred individual samples of Pashtun population from Khyber Pakhtunkhwa province of Pakistan were randomly evaluated through 10 MiniSTR loci (CSF1PO, D7S820, TPOX, D18S51, D2S1338, D13S317, FGA, D5S818, D21S11, and D16S539). The PCR product size was reduced in the range of 65 to 280 bp. A total of 112 alleles were observed containing allelic frequency ranging from 0.0025 to 0.4325. Statistical values for forensic and parentage analysis were calculated including combined power of discrimination (PD), combined power of exclusion (PE), and cumulative probability of matching (PM) and equaled to 0.99999999999768, 0.99984944, and 2.33 × 10(-12), respectively. These MiniSTRs show a high degree of polymorphism information content and discriminatory power which would be helpful to resolve forensic cases and establish DNA database for major population groups of Pakistan. In contrast to different populations, significant differences were also observed on these loci. PMID:25821203

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

    PubMed

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

    2014-04-01

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

  14. Allele frequency distribution of CYP2C9 2 and CYP2C9 3 polymorphisms in six Mexican populations.

    PubMed

    Castelán-Martínez, Osvaldo D; Hoyo-Vadillo, Carlos; Sandoval-García, Emmanuel; Sandoval-Ramírez, Lucila; González-Ibarra, Miriam; Solano-Solano, Gloria; Gómez-Díaz, Rita A; Parra, Esteban J; Cruz, Miguel; Valladares-Salgado, Adán

    2013-07-10

    Allele frequency differences of functional CYP2C9 polymorphisms are responsible for some of the variation in drug response observed in human populations. The most relevant CYP2C9 functional variants are CYP2C9*2 (rs1799853) and CYP2C9 3 (rs1057910). These polymorphisms show variation in allele frequencies among different population groups. The present study aimed to analyze these polymorphisms in 947 Mexican-Mestizo from Mexico City and 483 individuals from five indigenous Mexican populations: Nahua, Teenek, Tarahumara, Purepecha and Huichol. The CYP2C9*2 allele frequencies in the Mestizo, Nahua and Teenek populations were 0.051, 0.007 and 0.005, respectively. As for CYP2C9 3, the allelic frequencies in the Mestizo, Nahua and Teenek populations were 0.04, 0.005 and 0.005, respectively. The CYP2C9 2 and CYP2C9 3 alleles were not observed in the Tarahumara, Purepecha and Huichol populations. These findings are in agreement with previous studies reporting very low allele frequencies for these polymorphisms in American Indigenous populations.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

    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.

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

    SciTech Connect

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

    1993-03-01

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

  19. RHD allele distribution in Africans of Mali

    PubMed Central

    Wagner, Franz F; Moulds, Joann M; Tounkara, Anatole; Kouriba, Bourema; Flegel, Willy A

    2003-01-01

    Background Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking. Results We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa) by evaluating 116 haplotypes. Only 69% could be attributed to standard RHD (55%) or the RHD deletion (14%). The aberrant RHD allele DAU-0 was predicted for 19%, RHDΨ for 7% and Ccdes for 4% of all haplotypes. DAU-3 and the new RHD allele RHD(L207F), dubbed DMA, were found in one haplotype each. A PCR-RFLP for the detection of the hybrid Rhesus box diagnostic for the RHD deletion in Europeans was false positive in 9 individuals, including all carriers of RHDΨ . Including two silent mutations and the RHD deletion, a total of 9 alleles could be differentiated. Conclusion Besides standard RHD and the RHD deletion, DAU-0, RHDΨ and Ccdes are major alleles in Mali. Our survey proved that the most frequent alleles of West Africans have been recognized allowing to devise reliable genotyping and phenotyping strategies. PMID:14505497

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

    PubMed

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

    1991-06-01

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

  1. ALFRED: an allele frequency resource for research and teaching

    PubMed Central

    Rajeevan, Haseena; Soundararajan, Usha; Kidd, Judith R.; Pakstis, Andrew J.; Kidd, Kenneth K.

    2012-01-01

    ALFRED (http://alfred.med.yale.edu) is a free, web accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. Currently, ALFRED has allele frequency tables on over 663 400 polymorphic sites; 170 of them have frequency tables for more than 100 different population samples. In ALFRED, a population may have multiple samples with each ‘sample’ consisting of many individuals on which an allele frequency is based. There are 3566 population samples from 710 different populations with allele frequency tables on at least one polymorphism. Fifty of those population samples have allele frequency data for over 650 000 polymorphisms. Records also have active links to relevant resources (dbSNP, PharmGKB, OMIM, Ethnologue, etc.). The flexible search options and data display and download capabilities available through the web interface allow easy access to the large quantity of high-quality data in ALFRED. PMID:22039151

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

    Kent, Stephen; Kashima, Yoshihisa

    2015-01-01

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

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

    PubMed

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

    2014-04-22

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

  6. 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.

    PubMed

    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.

  7. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of "standardized allele frequencies" that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools-a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

  8. Robust Identification of Local Adaptation from Allele Frequencies

    PubMed Central

    Günther, Torsten; Coop, Graham

    2013-01-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

    2011-01-01

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

  12. Frequency-Rank Distributions

    ERIC Educational Resources Information Center

    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)

  13. Models of Frequency-Dependent Selection with Mutation from Parental Alleles

    PubMed Central

    Trotter, Meredith V.; Spencer, Hamish G.

    2013-01-01

    Frequency-dependent selection (FDS) remains a common heuristic explanation for the maintenance of genetic variation in natural populations. The pairwise-interaction model (PIM) is a well-studied general model of frequency-dependent selection, which assumes that a genotype’s fitness is a function of within-population intergenotypic interactions. Previous theoretical work indicated that this type of model is able to sustain large numbers of alleles at a single locus when it incorporates recurrent mutation. These studies, however, have ignored the impact of the distribution of fitness effects of new mutations on the dynamics and end results of polymorphism construction. We suggest that a natural way to model mutation would be to assume mutant fitness is related to the fitness of the parental allele, i.e., the existing allele from which the mutant arose. Here we examine the numbers and distributions of fitnesses and alleles produced by construction under the PIM with mutation from parental alleles and the impacts on such measures due to different methods of generating mutant fitnesses. We find that, in comparison with previous results, generating mutants from existing alleles lowers the average number of alleles likely to be observed in a system subject to FDS, but produces polymorphisms that are highly stable and have realistic allele-frequency distributions. PMID:23852384

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

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2010-12-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-01

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

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

    PubMed

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

    2013-01-01

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

  18. Worldwide allele frequencies of the human apolipoprotein E gene: climate, local adaptations, and evolutionary history.

    PubMed

    Eisenberg, Dan T A; Kuzawa, Christopher W; Hayes, M Geoffrey

    2010-09-01

    The epsilon4 allele of the apolipoprotein E (APOE) gene is associated with increased cholesterol levels and heart disease. Population allele frequencies of APOE have previously been shown to vary, with epsilon4 frequencies generally increasing with latitude. We hypothesize that this trend resulted from natural selection protecting against low-cholesterol levels. In high-latitude cold environments and low-latitude hot environments, metabolic rate is elevated, which could require higher cholesterol levels. To explore this hypothesis, we compiled APOE allele frequencies, latitude, temperature, and elevation from populations around the world. epsilon4 allele frequencies show a curvilinear relationship with absolute latitude, with lowest frequencies found in the mid-latitudes where temperatures generally require less expenditure on cooling/thermogenesis. Controlling for population structure in a subset of populations did not appreciably change this pattern of association, consistent with selection pressures that vary by latitude shaping epsilon4 allele frequencies. Temperature records also predict APOE frequency in a curvilinear fashion, with lowest epsilon4 frequencies at moderate temperatures. The model fit between historical temperatures and epsilon4 is less than between latitude and epsilon4, but strengthened after correcting for estimated temperature differences during the Paleolithic. Contrary to our hypothesis, we find that elevation did not improve predictive power, and an integrated measure of the cholesterol effect of multiple APOE alleles was less related to latitude than was epsilon4 alone. Our results lend mixed support for a link between past temperature and human APOE allele distribution and point to the need to develop better models of past climate in future analyses.

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

    PubMed

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

    2000-10-01

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

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

    PubMed

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

    2000-10-01

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

  1. The Joint Allele-Frequency Spectrum in Closely Related Species

    PubMed Central

    Chen, Hua; Green, Richard E.; Pääbo, Svante; Slatkin, Montgomery

    2007-01-01

    We develop the theory for computing the joint frequency spectra of alleles in two closely related species. We allow for arbitrary population growth in both species after they had a common ancestor. We focus on the case in which a single chromosome is sequenced from one of the species. We use classical diffusion theory to show that, if the ancestral species was at equilibrium under mutation and drift and a chromosome from one of the descendant species carries the derived allele, the frequency spectrum in the other species is uniform, independently of the demographic history of both species. We also predict the expected densities of segregating and fixed sites when the chromosome from the other species carries the ancestral allele. We compare the predictions of our model with the site-frequency spectra of SNPs in the four HapMap populations of humans when the nucleotide present in the Neanderthal DNA sequence is ancestral or derived, using the chimp genome as the outgroup. PMID:17603120

  2. Distribution of HLA-B alleles in Mexican Amerindian populations.

    PubMed

    Vargas-Alarcón, Gilberto; Hernández-Pacheco, Guadalupe; Zuñiga, Joaquín; Rodríguez-Pérez, José Manuel; Pérez-Hernández, Nonanzit; Rangel, Carlos; Villarreal-Garza, Cynthia; Martínez-Laso, Jorge; Granados, Julio; Arnaiz-Villena, Antonio

    2003-02-01

    In the present study we analyzed by PCR-SSO technique the HLA-B gene frequencies in 281 healthy individuals from four Mexican Amerindian populations (66 Mayos, 90 Mazatecans, 72 Nahuas and 53 Teenek). The most frequent alleles in all studied populations were HLA-B35, HLA-B39, and HLA-B40; however, some differences were observed between populations. The HLA-B35 allele was the most frequent in three of the four populations studied (Mayos, Nahuas and Teenek), whereas in Mazatecans the most frequent allele was HLA-B39. HLA-B40 presented frequencies higher than 10% in all groups. On the other hand, only Mayos presented an HLA-B51 gene frequency higher than 10%. When comparisons were made, important differences between groups were observed. The Teenek group presented an increased frequency of HLA-B35 when compared to Mazatecans and the HLA-B52 allele was increased in Nahuas and Teenek when compared to Mayos. An increased frequency of HLA-B39 was observed in Mazatecans when compared to Nahuas, Mayos and Teenek. Also, an increased frequency of HLA-B51 was observed in Mayos when compared to Mazatecans and Nahuas. These data corroborate the restricted polymorphism of HLA-B alleles and the high frequency of HLA-B35, HLA-B39 and HLA-B40 alleles in autochthonous American populations. In spite of the restriction in this polymorphism, differences in frequencies of HLA-B alleles could be helpful in distinguishing each of these populations.

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2014-03-01

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

  5. Genotype and allele frequency of CYP2C19*17 in a healthy Iranian population

    PubMed Central

    Payan, Maryam; Tajik, Nader; Rouini, Mohammad Reza; Ghahremani, Mohammad Hossein

    2015-01-01

    Background: Cytochrome P450 2C19 (CYP2C19) is important in metabolism of wide range of drugs. CYP2C19*17 is a novel variant allele which increases gene transcription and therefore results in ultra-rapid metabolizer phenotype (URM). Distribution of this variant allele has not been well studied worldwide. The aim of present study was to investigate allele and genotype frequencies of CYP2C19*17 in a healthy Iranian population and compare them with other ethnic groups. Methods: One hundred eighty healthy unrelated Iranian volunteer took part in this study and were genotyped for CYP2C19 *2, *3, *17 (-3402) by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and CYP2C19*17 (-806) by a nested-PCR assays. The distribution of CYP2C19*17 polymorphism in Iranian population was then compared with other ethnic groups. Results: The CYP2C19*17 allele frequency was 21.6% in Iranian population. Among studied subjects 5.5% were homozygous for CYP2C19*17 and phenotyped as ultra-rapid metabolizers; 28.8% were genotyped as CYP2C19*1*17 (extensive metabolizers) and 3.3% as CYP2C19*2*17 (intermediate metabolizers). Conclusion: The CYP2C19*17 genetic distribution in Iranian population is similar to Middle East or European countries. The high frequency of CYP2C19*17 in Iranian population highlights the importance of this new variant allele in metabolism of CYP2C19 substrates. Thus, future association studies are required to reveal clinical consequence of this genetic polymorphism in carrier individuals. PMID:26793660

  6. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

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

    2009-04-01

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

  7. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

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

    2009-04-01

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

  8. Non-Equilibrium Allele Frequency Spectra Via Spectral Methods

    PubMed Central

    Hey, Jody; Chen, Kevin

    2011-01-01

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

  9. Intracellular Population Genetics: Evidence for Random Drift of Mitochondrial Allele Frequencies in SACCHAROMYCES CEREVISIAE and SCHIZOSACCHAROMYCES POMBE

    PubMed Central

    Thrailkill, Kathryn M.; Birky, C. William; Lückemann, Gudrun; Wolf, Klaus

    1980-01-01

    We report evidence for random drift of mitochondrial allele frequencies in zygote clones of Saccharomyces cerevisiae and Schizosaccharomyces pombe. Monofactorial and bifactorial crosses were done, using strains resistant or sensitive to erythromycin (alleles ER, ES), oligomycin (OR, OS), or diuron (DR, DS). The frequencies of resistant and sensitive cells (and thus the frequencies of the resistant and sensitive alleles) were determined for each of a number of clones of diploid cells arising from individual zygotes. Allele frequencies were extremely variable among these zygote clones; some clones were "uniparental," with mitochondrial alleles from only one parent present. These observations suggest random drift of the allele frequencies in the population of mitochondrial genes within an individual zygote and its diploid progeny. Drift would cease when all the cells in a clone become homoplasmic, due to segregation of the mitochondrial genomes during vegetative cell divisions. To test this, we delayed cell division (and hence segregation) for varying times by starving zygotes in order to give drift more time to operate. As predicted, delaying cell division resulted in an increase in the variance of allele frequencies among the zygote clones and an increase in the proportion of uniparental zygote clones. The changes in form of the allele frequency distributions resembled those seen during random drift in finite Mendelian populations. In bifactorial crosses, genotypes as well as individual alleles were fixed or lost in some zygote clones. However, the mean recombination frequency for a large number of clones did not increase when cell division was delayed. Several possible molecular mechanisms for intracellular random drift are discussed. PMID:7009322

  10. Distribution of HLA-DQA1 alleles in Arab and Pakistani individuals from Dubai, United Arab Emirates.

    PubMed

    Tahir, M A; al Khayat, A Q; al Shamali, F; Budowle, B; Novick, G E

    1997-03-14

    PCR-based typing of the HLA-DQA1 locus, using allele specific oligonucleotide (ASO) probes and reverse dot blot methodology was used to determine allelic distributions and construct a database for Arab and Pakistani individuals living in Dubai. Genotype and allelic frequencies were calculated, and the data were tested for departures from Hardy-Weinberg (HWE) equilibrium. The most frequent HLA-DQA1 alleles among Dubaian Arabs are DQA1 4 and 1.2. Among Pakistanis, the most frequent allele is also DQA1 4. No significant deviations from HWE were detected.

  11. Radio frequency distribution assembly

    NASA Astrophysics Data System (ADS)

    Culley, K. M.

    The Naval Research Laboratory (NRL) Radio Frequency Distribution Assembly (RFDA) is an interface between the Sperry four-channel, fast-switching synthesizer and the EF-111 jamming system antenna ports. The RFDS is a sophisticated, high-speed RF interface designed to convert the banded outputs of the four-channel synthesizer (16 ports) to 36 ports which represent six ordinal directions of arrival (DOA) for the EF-111 jamming system. The RFDS will distribute the RF signals while providing controlled RF amplitudes to simulate the antenna patterns of the EF-111 Electronic Warfare (EW) system. The simulation of the arrival angles which appear between the ordinal directions is performed by controlling the amplitude of the RF signal from the DOA channels. The RFDA is capable of operating over the frequency range of 500MHz to 18GHz, and can rapidly switch between varying frequencies and attenuation levels.

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

    PubMed Central

    2013-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

    Ramasamy, Thirumurugan; Ayyavoo, Jayachitra

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  16. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations.

    PubMed

    Gonzalez-Galarza, Faviel F; Christmas, Stephen; Middleton, Derek; Jones, Andrew R

    2011-01-01

    The allele frequency net database (http://www.allelefrequencies.net) is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. The extensive variability observed in genes and alleles related to the immune system response and its significance in transplantation, disease association studies and diversity in populations led to the development of this electronic resource. At present, the system contains data from 1133 populations in 608,813 individuals on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms. The project was designed to create a central source for the storage of frequency data and provide individuals with a set of bioinformatics tools to analyze the occurrence of these variants in worldwide populations. The resource has been used in a wide variety of contexts, including clinical applications (histocompatibility, immunology, epidemiology and pharmacogenetics) and population genetics. Demographic information, frequency data and searching tools can be freely accessed through the website.

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

    ERIC Educational Resources Information Center

    Nussbaum, Francis, Jr.

    1988-01-01

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

  18. Inference in two dimensions: allele frequencies versus lengths of shared sequence blocks.

    PubMed

    Barton, N H; Etheridge, A M; Kelleher, J; Véber, A

    2013-08-01

    We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ(2), based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FST) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a 'local scale', κ; the rate of gene flow, σ(2), cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ(2). With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ(2).

  19. Allelic distribution of CCR5 and CCR2 genes in an Italian population sample.

    PubMed

    Romano-Spica, V; Ianni, A; Arzani, D; Cattarini, L; Majore, S; Dean, M

    2000-01-20

    Genetic polymorphisms of CCR5 and CCR2 human chemokine receptors have been associated with resistance during HIV-1 infection and disease progression. The protective effect of mutant alleles at these loci has important implications in AIDS pathogenesis. Chemokine receptors have a role in viral entry into target cells as well as in immune response modulation. In the present report, we studied the frequency of CCR5delta32 and CCR264I allelic variants among a representative sample of the Italian population. Observed allelic frequencies were 0.0454 and 0.0655, respectively. In both cases, genotype distribution was in equilibrium as predicted by the Hardy-Weinberg equation. Taken as a whole, about 21% of the population sample was found to be heterozygous for one or another of those two mutated alleles. Distribution of CCR5delta32 and CCR264I allelic variants within a population can be considered as a measure of genetic susceptibility to HIV infection and disease progression. PMID:10659048

  20. Frequencies of Null Alleles at Enzyme Loci in Natural Populations of Ponderosa and Red Pine

    PubMed Central

    Allendorf, Fred W.; Knudsen, Kathy L.; Blake, George M.

    1982-01-01

    Pinus ponderosa and P. resinosa population samples have mean frequencies of enzymatically inactive alleles of 0.0031 and 0.0028 at 29 and 27 enzyme loci, respectively. Such alleles are rare and are apparently maintained by selection-mutation balance. Ponderosa pine have much higher amounts of allozymic and polygenic phenotypic variation than red pine, yet both species have similar frequencies of null alleles. Thus, null alleles apparently do not contribute to polygenic variation, as has been suggested. The concordance between allozymic and polygenic variation adds support to the view that allozyme studies may be valuable in predicting the relative amount of polygenic variation in populations. PMID:17246067

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

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

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

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

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

    In population genetic studies, the allele frequency spectrum (AFS) efficiently summarizes genome-wide polymorphism data and shapes a variety of allele frequency-based summary statistics. While existing theory typically features equilibrium conditions, emerging methodology requires an analytical understanding of the build-up of the allele frequencies over time. In this work, we use the framework of Poisson random fields to derive new representations of the non-equilibrium AFS for the case of a Wright-Fisher population model with selection. In our approach, the AFS is a scaling-limit of the expectation of a Poisson stochastic integral and the representation of the non-equilibrium AFS arises in terms of a fixation time probability distribution. The known duality between the Wright-Fisher diffusion process and a birth and death process generalizing Kingman's coalescent yields an additional representation. The results carry over to the setting of a random sample drawn from the population and provide the non-equilibrium behavior of sample statistics. Our findings are consistent with and extend a previous approach where the non-equilibrium AFS solves a partial differential forward equation with a non-traditional boundary condition. Moreover, we provide a bridge to previous coalescent-based work, and hence tie several frameworks together. Since frequency-based summary statistics are widely used in population genetics, for example, to identify candidate loci of adaptive evolution, to infer the demographic history of a population, or to improve our understanding of the underlying mechanics of speciation events, the presented results are potentially useful for a broad range of topics. PMID:27378747

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

    PubMed

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

    2008-05-01

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

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

    PubMed

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

    2015-10-21

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

  5. Analysis of simple tandem repeat (STR) marker allele distributions in a Balinese population

    SciTech Connect

    Morell, R.; Ashler, J.H.; Friedman, T.B.

    1994-09-01

    Genotypes for 53 simple tandem repeat (STR) markers distributed at greater than 39 cM intervals throughout the genome were determined for 46 individuals from the village of Bengkala, Bali. This village dates to at least the thirteenth century, has approximately 2,200 individuals and has an oral and written tradition suggesting genetic bottlenecks. The allele frequency distributions in Bengkala were compared with distributions obtained by typing individuals in the CEPH data base using a Kolmogorov-Smirnov two sample test. Twenty-eight of the 53 markers showed differences (p<0.05) in distribution between the two populations. Allele frequencies of tetranucleotide STRs were much more similar between the two populations than were those of dinucleotide STRs (p < 0.0043). This may be due to the higher mutation rate of tetranucleotide STRs, combining with selection on repeat lengths, to produce a {open_quotes}stable{close_quotes} allele distribution. Population heterogeneity in Bengkala was indicated by an excess of observed homozygosity, deviations from Hardy-Weinberg equilibrium at seven loci, and significant genotypic disequilibrium between physically unlinked loci. These analyses serve as a resource to map a gene causing non-syndromal autosomal recessive deafness in Bengkala, and to corroborate the anthropological study of the history and social structure of the village.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2014-10-01

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

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

    PubMed

    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

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

    PubMed

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

    2009-12-01

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

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

    PubMed

    Verhulst, Brad; Neale, Michael C

    2016-09-01

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

  11. Geographic distributions of Idh-1 alleles in a cricket are linked to differential enzyme kinetic performance across thermal environments

    PubMed Central

    Huestis, Diana L; Oppert, Brenda; Marshall, Jeremy L

    2009-01-01

    Background Geographic clines within species are often interpreted as evidence of adaptation to varying environmental conditions. However, clines can also result from genetic drift, and these competing hypotheses must therefore be tested empirically. The striped ground cricket, Allonemobius socius, is widely-distributed in the eastern United States, and clines have been documented in both life-history traits and genetic alleles. One clinally-distributed locus, isocitrate dehydrogenase (Idh-1), has been shown previously to exhibit significant correlations between allele frequencies and environmental conditions (temperature and rainfall). Further, an empirical study revealed a significant genotype-by-environmental interaction (GxE) between Idh-1 genotype and temperature which affected fitness. Here, we use enzyme kinetics to further explore GxE between Idh-1 genotype and temperature, and test the predictions of kinetic activity expected under drift or selection. Results We found significant GxE between temperature and three enzyme kinetic parameters, providing further evidence that the natural distributions of Idh-1 allele frequencies in A. socius are maintained by natural selection. Differences in enzyme kinetic activity across temperatures also mirror many of the geographic patterns observed in allele frequencies. Conclusion This study further supports the hypothesis that the natural distribution of Idh-1 alleles in A. socius is driven by natural selection on differential enzymatic performance. This example is one of several which clearly document a functional basis for both the maintenance of common alleles and observed clines in allele frequencies, and provides further evidence for the non-neutrality of some allozyme alleles. PMID:19460149

  12. HLA-DRB1 allele distribution and its relation to rheumatoid arthritis in eastern Black Sea Turkish population.

    PubMed

    Uçar, Fahri; Karkucak, Murat; Alemdaroğlu, Emel; Capkin, Erhan; Yücel, Burcu; Sönmez, Mehmet; Tosun, Mehmet; Karaca, Adem

    2012-04-01

    Rheumatoid arthritis (RA [MIM 180300]) is a complex, polygenic inflammatory autoimmune disease, resulting from interactions between genetic and environmental factors. Some of the RA-associated HLA-DRB1 alleles have shared epitope, but their distribution varies among different racial/ethnic groups. This study was aimed at investigating the distribution of HLA-DRB1 alleles in patients with RA in eastern Black Sea region of Turkey. DNA samples of 320 patients with RA and 360 healthy controls were studied for the determination of HLA-DRB1 allele distribution using PCR-SSP method. The allele frequencies of HLA-DRB1*01, *04, and *09 were higher in patients with RA compared with the controls (P < 0.005, P < 0.0001, and P < 0.01, respectively). On the other hand, in patients with RA, HLA-DRB1*13 allele was lower than the controls (P < 0.001). Of the HLA-DRB1*04 subgroups, *0401 (40.83% vs. 18.75%, P < 0.001) was the most frequent allele in patients with RA, while DRB1*0402 (30.00% vs. 12.50%, P < 0.005) allele in the controls. HLA-DRB1 allele frequencies in the patients with RA and the controls showed Hardy-Weinberg rule compliance. Results of this study indicate that HLA-DRB1*01, *04, and *09 alleles were associated with RA, and HLA-DRB1*13 was protective allele against RA. Among the subgroups of HLA-DRB1*04, *0401 was detected to be RA associated, while *0402 was being protective. These results have some differences compared with previous reports originating from other regions of Turkey. PMID:21246357

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  16. Comparative allele distribution at 16 STR loci between the Andean and coastal population from Peru.

    PubMed

    Talledo, Michael; Gavilan, Martín; Choque, Cecilia; Aiquipa, Lina; Arévalo, Jorge; Montoya, Ysabel

    2010-07-01

    In the present study, we analysed the allelic distribution of 16 autosomal short tandem repeats (STRs) performed on unrelated individuals from seven different Peruvian cities, three highland Andean cities and four coastal ones. The loci investigated were F13A01, FESFPS, vWA, CSF1PO, TPOX, TH01, D16S539, D7S820, D13S317, D5S818, D19S253, F13B, D21S11, LPL and D8S1179 y D3S1358. The allele frequency, statistical parameters, Hardy-Weinberg equilibrium and population pair comparison across all loci were determinate. The combined matching probability for the 16 loci was 5.41136 x 10(-15) and the combined probability of exclusion (PE) was 0.999998307. The results showed new local databases for the evaluation of Andean and coastal Peruvian populations in human identity testing.

  17. Influence of admixture components on CYP2C9*2 allele frequency in eight indigenous populations from Northwest Mexico.

    PubMed

    Sosa-Macías, M; Lazalde-Ramos, B P; Galaviz-Hernández, C; Rangel-Villalobos, H; Salazar-Flores, J; Martínez-Sevilla, V M; Martínez-Fierro, M L; Dorado, P; Wong, M L; Licinio, J; LLerena, A

    2013-12-01

    We previously documented the lowest frequency of CYP2C9*2 in Mexican indigenous Tepehuanos followed by Mestizos and Mexican-Americans populations, suggesting a negative correlation between the CYP2C9*2 frequency and the degree of Asian ancestry in indigenous Americans. We determined the influence of ethnic admixture components on the CYP2C9 allele distribution in 505 Amerindian from eight indigenous populations through genotyping CYP2C9*2, *3 and *6 alleles by real-time PCR and molecular evaluation of ancestry. The frequencies for CYP2C9*2 were 0.026 in Seris and 0.057 in Mayos, being higher than in Asians (P<0.001). CYP2C9*3 was found in Tarahumaras (0.104), Mayos (0.091), Tepehuanos (0.075), Guarijíos (0.067), Huicholes (0.033) and Coras (0.037), with East Asians having lower frequencies than the former three groups (P<0.001). CYP2C9*6 was not found. The frequency of CYP2C9*2 was lower in Amerindians than in European populations, and higher than their Asian ancestors. The presence of this allele in ethnic groups in Mexico can be explained by European admixture.

  18. Analysis and frequency of bovine lymphocyte antigen DRB3.2 alleles in Jersey cows.

    PubMed

    Gilliespie, B E; Jayarao, B M; Dowlen, H H; Oliver, S P

    1999-09-01

    Jersey cows (n = 172) were genotyped for the bovine lymphocyte antigen (BoLA)-DRB3.2 allele by polymerase chain reaction and restriction fragment length polymorphism analysis. Bovine DNA was isolated from aliquots of whole blood. A two-step polymerase chain reaction followed by digestion with restriction endonucleases RsaI, BstyI, and HaeIII was conducted on the DNA from Jersey cattle. Twenty-four BoLA-DRB3.2 alleles were identified with frequencies ranging from 0.3 to 22.9%. Thirteen allele types were similar to those reported previously; and 11 were new allele types that have not been reported previously. Allele types reported previously include: BoLA-DRB3.2*2, *8, *10, *15, *17, *20, *21, *22, *23, *25, *28, *36, and *37. Their frequencies were 0.3, 11.3, 22.9, 13.6, 5.5, 3.7, 10.7, 3.5, 0.9, 0.3, 4.7, 9.3, and 0.9%, respectively. Of the new allele types detected, *ibe occurred at the highest frequency (6.1%) in Jersey cows from this herd. The six most frequently isolated alleles (BoLA-DRB3.2*8, *10, *15, *21, *36, and *ibe) accounted for 73.9% of the alleles in the population of this herd. Results of this study demonstrate that the BoLA-DRB3.2 locus is highly polymorphic in Jersey cattle.

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

    PubMed

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

    2016-05-01

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

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

    PubMed Central

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

    2016-01-01

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

  1. Genetic variability and distribution of mating type alleles in field populations of Leptosphaeria maculans from France.

    PubMed

    Gout, Lilian; Eckert, Maria; Rouxel, Thierry; Balesdent, Marie-Hélène

    2006-01-01

    Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used. PMID:16391041

  2. [RHD 1227A allele frequency among Rh negative population and random population].

    PubMed

    Wu, Jun-Jie; Hong, Xiao-Zhen; Xu, Xian-Guo; Ma, Kai-Rong; Zhu, Fa-Ming; Yan, Li-Xing

    2006-12-01

    To investigate the frequency of RHD 1227A allele in Rh negative population and random population, an AS-PCR (allele specific-polymerase chain reaction) method was employed to detect RHD 1227A allele. RHD gene copy was determined by D zygosity test and RHD exon 9 nucleotide sequence analysis. The results showed that among 143 Rh negative donors, forty-one RHD 1227A allele carriers were detected, and 8 (19.51%) out of which were RhCCdee, 32 (78.05%) were RhCcdee, and 1 (2.44%) was RhCcdEe. Thirty-five Rh negative RHD 1227A carriers had RHD gene deletion, and the remaining carriers were RHD 1227A homozygous. Seven (1.43%) individuals were detected with RHD 1227A allele among 489 random donors. They were all G/A heterozygous at RHD 1227 site. Serological test indicated that they were normal Rh positive phenotype. It is concluded that the frequency of RHD 1227A allele is 16.43% among Rh negative population and 0.72% among the random population.

  3. HLA-A, HLA-B, and HLA-DRB1 allele distribution in a large Armenian population sample.

    PubMed

    Matevosyan, L; Chattopadhyay, S; Madelian, V; Avagyan, S; Nazaretyan, M; Hyussian, A; Vardapetyan, E; Arutunyan, R; Jordan, F

    2011-07-01

    Human leukocyte antigen (HLA)-A, HLA-B, and HLA-DRB1 gene frequencies were investigated in 4279 unrelated Armenian bone marrow donors. HLA alleles were defined by using PCR amplification with sequence specific primers (PCR-SSP) high- and low-resolution kits. The aim of this study was to examine the HLA diversity at the high-resolution level in a large Armenian population sample, and to compare HLA allele group distribution in Armenian subpopulations. The most frequently observed alleles in the HLA class I were HLA-A*0201, A*0101, A*2402, A*0301, HLA-B*5101, HLA-B*3501, and B*4901. Among DRB1 alleles, high frequencies of DRB1*1104 and DRB1*1501 were observed, followed by DRB1*1101 and DRB1*1401. The most common three-locus haplotype found in the Armenian population was A*33-B*14-DRB1*01, followed by A*03-B*35-DRB1*01. Our results show a similar distribution of alleles in Armenian subpopulations from different countries, and from different regions of the Republics of Armenia and Karabagh. The low level of genetic distances between subpopulations indicates a high level of population homogeneity, and the genetic distances between Armenians and other populations show Armenians as a distinct ethnic group relative to others, reflecting the fact that Armenians have been an 'isolated population' throughout centuries. This study is the first comprehensive investigation of HLA-allele group distribution in a subset of Armenian populations, and the first to provide HLA-allele and haplotype frequencies at a high-resolution level. It is a valuable reference for organ transplantation and for future studies of HLA-associated diseases in Armenian populations.

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

    PubMed

    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 <0.05 being considered as statistically significant. The frequencies of the antigens of 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

  5. Frequency of CCR5Δ32 allele in healthy Bosniak population.

    PubMed

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

    2014-08-28

    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.

  6. Frequency of CCR5Δ32 allele in healthy Bosniak population

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2012-05-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-09-01

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

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

    SciTech Connect

    Tomczak, J.; Grebner, E.E. ); Boogen, C. )

    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.

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

    PubMed

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

    2002-01-23

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

  14. Distribution of FMR-1 and associated microsatellite alleles in a normal Chinese population

    SciTech Connect

    Zhong, N.; Houck, G.E. Jr.; Li, S.; Dobkin, C.; Brown, W.T.; Xixian Liu; Shen Gou

    1994-07-15

    The CGG repeat size distribution of the fragile X mental retardation gene (FMR-1) was studied in a population of normal Chinese X chromosomes along with that of two proximal microsatellite polymorphic markers: FRAXAC1 and DXS548. The most common CGG repeat allele was 29 (47.2%) with 30 being second most common (26%). This distribution was different from that seen in Caucasian controls, where the most common allele was 30 repeats. Other differences with Caucasian controls included a secondary model peak at 36 repeats and the absence of peaks at 20 or 23 repeats. There were only two FRAXAC1 and five DXS548 alleles found in the Chinese sample. A striking linkage disequilibrium of FMR-1 alleles with FRAXAC1 alleles was observed, in that 90% of the 29 CGG repeat alleles but only 41% of the 30 CGG repeat alleles had the FRAXAC1 152 bp allele (18 AC repeats). This disequilibrium suggests that slippage between the closely spaced normal CGG repeat alleles, 29 and 30, and between 152 and 154 FRAXAC1 alleles is very rare. This study lays the groundwork for an understanding of founder chromosome effects in comparing Asian and Caucasian populations. 29 refs., 5 tabs.

  15. Increased TNFA*2, but not TNFB*1, allele frequency in Spanish atopic patients.

    PubMed

    Castro, J; Tellería, J J; Linares, P; Blanco-Quirós, A

    2000-01-01

    Tumor necrosis factor (TNF) is a potent proinflammatory cytokine involved in asthma and atopy. Increased TNF-alpha levels have been found in airway biopsies and bronchoalveolar lavage fluids from asthmatic patients. Constitutional variations in the TNF-alpha secretion levels in vitro are associated with molecular polymorphisms located within and around the TNF loci. Our study objective was to investigate the association between atopy and two described di-allelic polymorphisms in the TNF locus: a G to A transition at position -308 in the 5'-promoter region of the TNFA gene (TNFA*1 and TNFA*2 alleles) and an Ncol restriction fragment length polymorphism (RFLP) in the first intron of the TNFB gene (TNFB*1 and TNFB*2 alleles). The genetic study was performed in 65 unrelated atopic patients and 60 healthy controls. The regions of interest were amplified from genomic DNA using specific primers and polymerase chain reaction. SSP-PCR analysis for TNFA -308 polymorphism genotyping and endonuclease digestion analysis for the TNFB Ncol RFLP were used. The frequency of the TNFA*2 allele was significantly higher in atopic subjects compared to the control group (38.5% vs. 10.5%; chi2 = 32.06; p <0.0001). The TNFA*2 allele is associated with a higher risk for the development of atopy (risk ratio = 9.44; EF = 0.65; chi2 = 30.06 p <0.0005). On the other hand, no significant association between the TNFB alleles and atopy was found. In conclusion, the TNFA*2 allele could be also a genetic risk marker for the predisposition to atopy in our population, as has been reported in other studies. Either the TNFA gene itself or a linked gene on chromosome region 6p21, which has yet to be identified, is a candidate gene for susceptibility to atopy. PMID:10923589

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    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.

  18. Serum lipid levels and M/L55 allele distribution of HDL paraoxonase gene in Saami and Finnish men.

    PubMed

    Malin, R; Lehtinen, S; Luoma, P; Näyhä, S; Hassi, J; Koivula, T; Lehtimäki, T

    2001-01-01

    Paraoxonase (PON) is an antioxidative enzyme, which eliminates lipid peroxides. The mutation in codon 55 of PON1 gene causes a change of methionine (M-allele) to leucine (L-allele) and influences PON activity. The Saami are a population living in the northern part of Fennoscandia. In previous studies their death rate from coronary artery disease (CAD) was found to be low. We compared PON M/L55 allele frequencies of 68 Saami and 68 Finnish men and related the PON genotypes to plasma lipid levels and to the levels of autoantibodies against oxidized LDL. The M/L55 genotypes were determined by PCR and restriction enzyme digestion. ELISA was used to measure antibodies against oxidized LDL. The L- and M-allele frequencies were 64% and 36% in Saami population and 64% and 36% in Finnish men, respectively (p = NS, Fisher's exact test). There were also no significant differences in plasma lipid levels or in antibody levels against oxidized LDL between PON genotypes or between Saami and Finnish men. Our results indicate that the PON M/L55 genotype is not associated with plasma lipid levels or the levels of autoantibodies against oxidized LDL in these populations. The Saami men have the same PON M/L55 allele distribution as the Finnish men and the PON genotype might thus not be one factor protecting Saami against CAD.

  19. Distribution of repeat unit differences between alleles at tandem repeat microsatellite loci

    SciTech Connect

    Jin, L. |; Zhong, Y.; Chakraborty, R.

    1994-09-01

    PCR-based assays of tandemly repeated microsatellite loci detect genetic variation from which alleles may be scored by their repeat unit lengths. Comparison of allele sizes from such data yields a probability distribution (P{sub k}) of repeat unit differences (k) between alleles segregating in a population. We show that this distribution (P{sub k}; k = 0, 1,2,...) provides insight regarding the mechanism of production of new alleles at such loci and the demographic history of populations, far better than that obtained from other summary measures (e.g., heterozygosity, number of alleles, and the range of allele sizes). The distributions of P{sub k} under multi-step stepwise models of mutation are analytically derived, which show that when a population is at equilibrium under the mutation-drift balance, the distribution of repeat unit differences between alleles is positively skewed with a mode larger than zero. However, when the heterozygosity at a locus is low (say, less than 40%), P{sub k} is a monotonically decreasing function of k. Applications of this theory to data on repeat unit sizes at over 1,240 microsatellite loci from the Caucasians, categorized by the average heterozygosity of loci, indicate that at most microsatellite loci new alleles are produced by stepwise mutations, and this is consistent with the replication slippage mechanism of mutations. The repeat size changes of mutants are probably within one or two units of alleles from which the mutants arise. Distributions of P{sub k} at microsatellite loci located within genes show evidence of allele size constraints. No significant evidence of recent expansion of population sizes in the Caucasians is detected by the distribution of P{sub k}.

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

    PubMed

    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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

    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.

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

    PubMed

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

    2014-11-01

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

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

    PubMed

    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.

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

    PubMed Central

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

    2016-01-01

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

  7. HLA-A, -B and -DR allele and haplotype frequencies in Malays.

    PubMed

    Dhaliwal, J S; Shahnaz, M; Too, C L; Azrena, A; Maiselamah, L; Lee, Y Y; Irda, Y A; Salawati, M

    2007-03-01

    One thousand four hundreds and forty-five Malays registered with the Malaysian Marrow Donor Registry were typed for HLA-A, HLA-B and HLA-DR. Fifteen HLA-A, twenty nine HLA-B and fourteen HLA-DR alleles were detected. The most common HLA-A alleles and their frequencies were HLA-A24 (0.35), HLA-A11 (0.21) and HLA-A2 (0.15). The most common HLA-B alleles were HLA-B15 (0.26), HLA-B35 (0.11) and HLA-B18 (0.10) while the most common HLA-DR alleles were HLA-DR15 (0.28), HLA-DR12 (0.27) and HLA-DR7 (0.10). A24-B15-DR12 (0.047), A24-B15-DR15 (0.03) and the A24-B35-DR12 (0.03) were the most frequent haplotypes. This data may be useful in determining the probability of finding a matched donor and for estimating the incidence of HLA associated diseases.

  8. PCR/oligonucleotide probe typing of HLA class II alleles in a Filipino population reveals an unusual distribution of HLA haplotypes

    SciTech Connect

    Bugawan, T.L.; Chang, J.D.; Erlich, H.A. ); Klitz, W. )

    1994-02-01

    The authors have analyzed the distribution of HLA class II alleles and haplotypes in a Filipino population by PCR amplification of the DRB1, DQB1, and DPB1 second-exon sequences from buccal swabs obtained from 124 family members and 53 unrelated individuals. The amplified DNA was typed by using nonradioactive sequence-specific oligonucleotide probes. Twenty-two different DRB1 alleles, including the novel Filipino *1105, and 46 different DRB1/DQB1 haplotypes, including the unusual DRB1*0405-DQB1*0503, were identified. An unusually high frequency (f = .383) of DPB1*0101, a rare allele in other Asian populations, was also observed. In addition, an unusual distribution of DRB1 alleles and haplotypes was seen in this population, with DR2 (f = .415) and DRB1*1502-DQB1*0502 (f = .233) present at high frequencies. This distribution of DRB1 alleles differs from the typical HLA population distribution, in which the allele frequencies are more evenly balanced. The distribution of HLA class II alleles and haplotypes in this Filipino population is different from that of other Asian and Pacific groups: of those populations studied to date, the Indonesian population is the most similar. DRB1*1502-DQB1*0502 was in strong linkage disequilibrium (D[prime] = .41) with DPB 1*0101 (f = .126, for the extended haplotype), which is consistent with selection for this DR, DQ, DP haplotype being responsible for the high frequency of these three class II alleles in this populations. 30 refs., 2 figs., 6 tabs.

  9. Phylogenetic relationship analysis of Iranians and other world populations using allele frequencies at 12 polymorphic markers.

    PubMed

    Fazeli, Zahra; Vallian, Sadeq

    2012-12-01

    The estimation of genetic distance between populations could improve our viewpoint about human migration and its genetic origin. In this study, we used allele frequency data of 12 polymorphic markers on 250 individuals (500 alleles) from the Iranian population to estimate genetic distance between the Iranians and other world populations. The phylogenetic trees for three different sets of allele frequency data were constructed. Our results revealed the genetic similarity between the Iranians and European populations. The lowest genetic distance was observed between the Iranians and some populations reside in Russia. Furthermore, the high genetic distance was observed between the Iranians and East Asian populations. The data suggested that the Iranians might have relatively close evolutionary history with Europeans, but historically independent from East Asian populations. The evaluation of genetic distance between Indians populations and Iranians was also performed. The Indian groups showed low genetic distance with others, but high genetic distance with the Iranians. This study could provide a new insight into the evolutionary history of the Iranian population.

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

    PubMed

    Cowell, Robert

    2016-07-01

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

  11. Mamu-DQA1 allele and genotype frequencies in a randomly sampled breeding colony of rhesus macaques (Macaca mulatta).

    PubMed

    Rolfs, B K; Lorenz, J G; Wu, C C; Lerche, N W; Smith, D G

    2001-04-01

    We studied the allelic and genotypic distribution of the major histocompatibility class-II locus DQA1 observed in a random sample of Indian rhesus macaques (Macaca mulatta) from a major breeding facility in the United States. The DNA was isolated from whole blood samples collected between 1991 and 1994 from 65 Indian rhesus monkeys. Polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP), which involves use of specific amplification of DQA1 exon 2 and subsequent restriction digestion of the 242-base pair fragment, was used to genotype the animals for the 20 known macaque (Mamu)-DQA1 alleles. Frequencies for four alleles (DQA1*240x, *2502, *2503 and *0102) differed significantly from those reported in a smaller sample of rhesus macaques from the German Primate Center. The modest genetic survey of Mamu-DQA1 genotypes presented here will be particularly useful in designing epidemiologic studies that investigate associations between immunogenetic background and disease susceptibility in macaque models of human disease.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed Central

    Faure, Eric

    2008-01-01

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

  14. The distribution of MICA alleles in an Austrian population: evidence for increasing polymorphism.

    PubMed

    Wenda, Sabine; Faé, Ingrid; Sanchez-Mazas, Alicia; Nunes, José M; Mayr, Wolfgang R; Fischer, Gottfried F

    2013-10-01

    The Major Histocompatibility Complex Class I Chain-Related Gene A (MICA) is located 46.4 Kb centromeric to HLA-B locus on chromosome 6; 84 alleles have been described so far. To assess the distribution of MICA alleles in an Austrian population, 322 unrelated Austrian blood donors have been typed for MICA by direct sequencing of amplified exons 2-5; sequencing of exon 6 and separating alleles by haplotype specific primers or by cloning was performed to resolve ambiguities. HLA-B was typed at low level resolution and linkage disequilibrium was determined. We observed 20 already known and four novel MICA alleles. MICA*008:01/04 was the most frequent allele (42%), followed by MICA*002:01 (11%) and MICA*009:01 (9%), three alleles (MICA*029, *067 and *068) were observed only once. No deviation from the Hardy Weinberg equilibrium was observed. Linkage disequilibrium between MICA and HLA-B alleles was observed, most extensively between MICA*008:01/04 and HLA-B*07. Our population data are in agreement with other European populations. The fact that four novel alleles have been observed indicates that the polymorphism of MICA is larger than currently estimated.

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

    PubMed

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

    2009-01-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

    Sala, A; Penacino, G; Corach, D

    1998-10-01

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

  18. Frequency of CYP2C9 alleles in Koreans and their effects on losartan pharmacokinetics

    PubMed Central

    Bae, Jung-woo; Choi, Chang-ik; Kim, Mi-jeong; Oh, Da-hee; Keum, Seul-ki; Park, Jung-in; Kim, Bo-hye; Bang, Hye-kyoung; Oh, Sung-gon; Kang, Byung-sung; Park, Hyun-joo; Kim, Hae-deun; Ha, Ji-hey; Shin, Hee-jung; Kim, Young-hoon; Na, Han-sung; Chung, Myeon-woo; Jang, Choon-gon; Lee, Seok-yong

    2011-01-01

    Aim: CYP2C9 enzyme metabolizes numerous clinically important drugs. The aim of this study is to investigate the frequencies of CYP2C9 genotypes and the effects of selected alleles on losartan pharmacokinetics in a large sample of the Korean population. Methods: The CYP2C9 gene was genotyped in 1796 healthy Korean subjects. CYP2C9 alleles (CYP2C9*1, *2, *3 and *13 alleles) were measured using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay and direct sequencing assay. The enzymatic activity of each CYP2C9 genotype was evaluated using losartan as the substrate. Results: The frequencies of CYP2C9*1, *3 and *13 allele were 0.952 (95% confidence interval 0.945–0.959), 0.044 (95% CI 0.037–0.051) and 0.005 (95% CI 0.003–0.007), respectively. The frequencies of the CYP2C9*1/*1, *1/*3, *1/*13 and *3/*3 genotypes were 0.904 (95% CI 0.890–0.918), 0.085 (95% CI 0.072–0.098), 0.009 (95% CI 0.005–0.013) and 0.001 (95% CI 0.000–0.002), respectively. In the pharmacokinetics studies, the AUC0–∞ of losartan in CYP2C9*3/*3 subjects was 1.42-fold larger than that in CYP2C9*1/*1 subjects, and the AUC0–∞ of E-3174, a more active metabolite of losartan, in CYP2C9*3/*3 subjects was only 12% of that in CYP2C9*1/*1 subjects. Conclusion: The results confirmed the frequencies of CYP2C9 genotypes in a large cohort of Koreans, and detected the CYP2C9*3/*3 genotype. CYP2C9*3/*3 subjects metabolized much less losartan into E-3174 than CYP2C9*1/*1 subjects. PMID:21841812

  19. Initial frequency of alleles conferring resistance to Bacillus thuringiensis poplar in a field population of Chrysomela tremulae.

    PubMed Central

    Génissel, Anne; Augustin, Sylvie; Courtin, Claudine; Pilate, Gilles; Lorme, Philippe; Bourguet, Denis

    2003-01-01

    Globally, the estimated total area planted with transgenic plants producing Bacillus thuringiensis (Bt) toxins was 12 million hectares in 2001. The risk of target pests becoming resistant to these toxins has led to the implementation of resistance-management strategies. The efficiency and sustainability of these strategies, including the high-dose plus refuge strategy currently recommended for North American maize, depend on the initial frequency of resistance alleles. In this study, we estimated the initial frequencies of alleles conferring resistance to transgenic Bt poplars producing Cry3A in a natural population of the poplar pest Chrysomela tremulae (Coleoptera: Chrysomelidae). We used the F(2) screen method developed for detecting resistance alleles in natural pest populations. At least three parents of the 270 lines tested were heterozygous for a major Bt resistance allele. We estimated mean resistance-allele frequency for the period 1999-2001 at 0.0037 (95% confidence interval = 0.00045-0.0080) with a detection probability of 90%. These results demonstrate that (i) the F(2) screen method can be used to detect major alleles conferring resistance to Bt-producing plants in insects and (ii) the initial frequency of alleles conferring resistance to Bt toxin can be close to the highest theoretical values that are expected prior to the use of Bt plants if considering fitness costs and typical mutation rates. PMID:12737656

  20. D9S1120, a simple STR with a common Native American-specific allele: forensic optimization, locus characterization and allele frequency studies.

    PubMed

    Phillips, C; Rodriguez, A; Mosquera-Miguel, A; Fondevila, M; Porras-Hurtado, L; Rondon, F; Salas, A; Carracedo, A; Lareu, M V

    2008-12-01

    The simple tetrameric STR D9S1120 exhibits a common population-specific allele of 9 repeats (9RA) reported to have an average frequency of 0.36 in Native Americans from both North and South of the continent. Apart from the presence of 9RA in two northeast Siberian populations, D9S1120 shows variability exclusive to, and universal in all American populations studied to date. This STR therefore provides an informative forensic marker applicable in countries with significant proportions of Native American populations or ancestry. We have re-designed PCR primers that reduce the amplified product sizes reported in NCBI UniSTS by more than a third and have characterized the repeat structure of D9S1120. The 9RA allele shares the same repeat structure as the majority of other D9S1120 alleles and so originates from a slippage-diminution mutation rather than an independent deletion. We confirm the previously reported allele frequencies from a range of populations indicating a global heterozygosity range for D9S1120 of 66-75% and estimate the proportion of Native American-diagnostic genotypes to average 53%, underlining the potential usefulness of this STR in both forensic identification and in population genetics studies of the Americas.

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

    PubMed

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

    2007-03-01

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

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

    PubMed

    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.

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

    PubMed

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

    2012-06-01

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

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

    PubMed

    Racimo, Fernando

    2016-02-01

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

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

    PubMed Central

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

    2016-01-01

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

  6. Apolipoprotein A-IV-2 allele: association of its worldwide distribution with adult persistence of lactase and speculation on its function and origin.

    PubMed

    Weinberg, R B

    1999-11-01

    Apolipoprotein A-IV (apo A-IV) is a 46-Kd plasma glycoprotein that may play a major role in intestinal lipid absorption. A genetic polymorphism in the apo A-IV gene, apo A-IV-2, encodes a His-->Gln substitution at codon 360 that alters the biological function of this apolipoprotein. As the worldwide distribution of the apo A-IV-2 allele appeared similar to the frequency of a genetic polymorphism that determines the persistence of lactase into adulthood, we examined the relationship between the apo A-IV-2 and lactase persistence polymorphisms by compiling the prevalence of adult lactase persistence in all populations in which the frequency of the apo A-IV-2 allele has been determined. Across 29 groups, there was an extremely strong correlation (4 = 0.937, P < 0.000001) between apo A-IV-2 allele frequency and the prevalence of adult lactase persistence. Apo A-IV-2 allele frequency was highest in Iceland, an ancient Viking colony, and decreased across Europe in a north-to-south and west-to-east gradient, generally following hypothetical isoclines for the lactase persistence gene. There were no correlations between the population frequencies of the apo E2, E3, or E4 alleles and either the prevalence of lactase persistence or the frequency of the apo A-IV-2 allele. In light of the effects of the apo A-IV-2 polymorphism on lipid metabolism, we speculate that the apo A-IV-2 allele may have originated in ancient Scandinavia, spread by conferring a nutritional advantage in the setting of a lifelong high milkfat intake, and was later carried southwards by the Viking incursions into Europe.

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

    PubMed

    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

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

    PubMed Central

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

    1997-01-01

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

  9. CYP2D6 allele distribution in Macedonians, Albanians and Romanies in the Republic of Macedonia

    PubMed Central

    Kuzmanovska, M; Dimishkovska, M; Maleva Kostovska, I; Noveski, P; Sukarova Stefanovska, E

    2015-01-01

    Abstract Cytochrome P450 2D6 (CYP2D6) is an enzyme of great importance for the metabolism of clinically used drugs. More than 100 variants of the CYP2D6 gene have been identified so far. The aim of this study was to investigate the allele distribution of CYP2D6 gene variants in 100 individuals of each of the Macedonian, Albanian and Romany population, by genotyping using long range polymerase chain reaction (PCR) and a multiplex single base extension method. The most frequent variants and almost equally distributed in the three groups were the fully functional alleles *1 and *2. The most common non functional allele in all groups was *4 that was found in 22.5% of the Albanians. The most common allele with decreased activity was *41 which was found in 23.0% of the Romany ethnic group, in 11.0% of the Macedonians and in 10.5% of the Albanians. Seven percent of the Albanians, 6.0% of the Romani and 4.0% of the Macedonians were poor metabolizers, while 5.0% of the Macedonians, 1.0% of Albanians and 1.0% of the Romanies were ultrarapid metabolizers. We concluded that the CYP2D6 gene locus is highly heterogeneous in these groups and that the prevalence of the CYP2D6 allele variants and genotypes in the Republic of Macedonia is in accordance with that of other European populations.

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

    PubMed

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

    2014-10-01

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

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

    PubMed Central

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

    2014-01-01

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

  12. Allele and haplotype frequencies for HLA-DQ in Iranian celiac disease patients

    PubMed Central

    Rostami-Nejad, Mohammad; Romanos, Jihane; Rostami, Kamran; Ganji, Azita; Ehsani-Ardakani, Mohammad Javad; Bakhshipour, Ali-Reza; Zojaji, Homayoun; Mohebbi, Seyed Reza; Zali, Mohammad-Reza; Wijmenga, Cisca

    2014-01-01

    AIM: To assess the distribution of human leukocyte antigen (HLA)-DQ2 and -DQ8 in Iranian celiac disease (CD) patients and compare them to healthy Iranian controls. METHODS: To predict the HLA-DQA1 and -DQB1 genes, we used six previously reported HLA-tagging single nucleotide polymorphism to determine HLA genotypes in 59 Iranian patients with ‘biopsy-confirmed’ CD and in 151 healthy Iranian individuals. To test the transferability of the method, 50 cases and controls were also typed using a commercial kit that identifies individual carriers of DQ2, DQ7 and DQ8 alleles. RESULTS: In this pilot study 97% of CD cases (n = 57) and 58% of controls (n = 87) were carriers of HLA-DQ2 and/or HLA-DQ8 heterodimers, either in the homozygous or heterozygous state. The HLA-DQ pattern of these 57 CD patients: heterozygous DQ2.2 (n = 14) and homozygous DQ2.2 (n = 1), heterozygous DQ2.5 (n = 33) and homozygous DQ2.5 (n = 8), heterozygous DQ8 (n = 13) and homozygous DQ8 (n = 2). Two CD patients were negative for both DQ2 and DQ8 (3%). CONCLUSION: The prevalence of DQ8 in our CD population was higher than that reported in other populations (25.4%). As reported in other populations, our results underline the primary importance of HLA-DQ alleles in the Iranian population’s susceptibility to CD. PMID:24876751

  13. Haemoglobin polymorphism in atlantic cod (Gadus morhua): Allele frequency variation between yearclasses in a Norwegian fjord stock

    NASA Astrophysics Data System (ADS)

    Mork, J.; Sundnes, G.

    1985-03-01

    A total of 262 specimens (0-, and 1-group) of Atlantic cod (Gadus morhua) representing 4 different yearclasses were caught in Trondheimsfjorden, Norway, during 1977 1984. They were genotyped by agar gel electrophoresis for the polymorphic haemoglobin locus HbI (Sick, 1961). The analyses revealed a highly significant (P=0.0003) heterogeneity of HbI allele frequencies between yearclasses. The difference in the frequency of the HbI-1 allele between the first (1977) and the last (1983) yearclass amounted to 0.18 (±0.07). The results appear to support recent reports on considerable selection effects at HbI, and stress the unreliability of allele frequencies at this locus for use in studies of the genetic population structure of cod.

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

    PubMed

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

    2011-01-01

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

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

    PubMed Central

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

    2011-01-01

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

  16. The effects of selection and genetic drift on the genomic distribution of sexually antagonistic alleles.

    PubMed

    Mullon, Charles; Pomiankowski, Andrew; Reuter, Max

    2012-12-01

    Sexual antagonism (SA) occurs when an allele that is beneficial to one sex, is detrimental to the other. This conflict can result in balancing, directional, or disruptive selection acting on SA alleles. A body of theory predicts the conditions under which sexually antagonistic mutants will invade and be maintained in stable polymorphism under balancing selection. There remains, however, considerable debate over the distribution of SA genetic variation across autosomes and sex chromosomes, with contradictory evidence coming from data and theory. In this article, we investigate how the interplay between selection and genetic drift will affect the genomic distribution of sexually antagonistic alleles. The effective population sizes can differ between the autosomes and the sex chromosomes due to a number of ecological factors and, consequently, the distribution of SA genetic variation in genomes. In general, we predict the interplay of SA selection and genetic drift should lead to the accumulation of SA alleles on the X in male heterogametic (XY) species and, on the autosomes in female heterogametic (ZW) species, especially when sexual competition is strong among males.

  17. Confidence intervals for population allele frequencies: the general case of sampling from a finite diploid population of any size.

    PubMed

    Fung, Tak; Keenan, Kevin

    2014-01-01

    The estimation of population allele frequencies using sample data forms a central component of studies in population genetics. These estimates can be used to test hypotheses on the evolutionary processes governing changes in genetic variation among populations. However, existing studies frequently do not account for sampling uncertainty in these estimates, thus compromising their utility. Incorporation of this uncertainty has been hindered by the lack of a method for constructing confidence intervals containing the population allele frequencies, for the general case of sampling from a finite diploid population of any size. In this study, we address this important knowledge gap by presenting a rigorous mathematical method to construct such confidence intervals. For a range of scenarios, the method is used to demonstrate that for a particular allele, in order to obtain accurate estimates within 0.05 of the population allele frequency with high probability (> or = 95%), a sample size of > 30 is often required. This analysis is augmented by an application of the method to empirical sample allele frequency data for two populations of the checkerspot butterfly (Melitaea cinxia L.), occupying meadows in Finland. For each population, the method is used to derive > or = 98.3% confidence intervals for the population frequencies of three alleles. These intervals are then used to construct two joint > or = 95% confidence regions, one for the set of three frequencies for each population. These regions are then used to derive a > or = 95%% confidence interval for Jost's D, a measure of genetic differentiation between the two populations. Overall, the results demonstrate the practical utility of the method with respect to informing sampling design and accounting for sampling uncertainty in studies of population genetics, important for scientific hypothesis-testing and also for risk-based natural resource management. PMID:24465792

  18. High frequency power distribution system

    NASA Technical Reports Server (NTRS)

    Patel, Mikund R.

    1986-01-01

    The objective of this project was to provide the technology of high frequency, high power transmission lines to the 100 kW power range at 20 kHz frequency. In addition to the necessary design studies, a 150 m long, 600 V, 60 A transmission line was built, tested and delivered for full vacuum tests. The configuration analysis on five alternative configurations resulted in the final selection of the three parallel Litz straps configuration, which gave a virtually concentric design in the electromagnetic sense. Low inductance, low EMI and flexibility in handling are the key features of this configuration. The final design was made after a parametric study to minimize the losses, weight and inductance. The construction of the cable was completed with no major difficulties. The R,L,C parameters measured on the cable agreed well with the calculated values. The corona tests on insulation samples showed a safety factor of 3.

  19. Variation in Meiotic Recombination Frequencies Between Allelic Transgenes Inserted at Different Sites in the Drosophila melanogaster Genome

    PubMed Central

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

    2013-01-01

    Meiotic crossovers are distributed nonrandomly across the genome. Classic studies in Drosophila suggest that the position of a gene along a chromosome arm can affect the outcome of the recombination process, with proximity to the centromere being associated with lower crossing over. To examine this phenomenon molecularly, we developed an assay that measures meiotic crossovers and noncrossover gene conversions between allelic transgenes inserted into different genomic positions. To facilitate collecting a large number of virgin females, we developed a useful genetic system that kills males and undesired classes of females. We found that the recombination frequency at a site in the middle of the X chromosome, where crossovers are normally frequent, was similar to the frequency at the centromere-proximal end of the euchromatin, where crossovers are normally infrequent. In contrast, we recovered no recombinants—crossovers or noncrossovers—at a site on chromosome 4 and at a site toward the distal end of the X chromosome. These results suggest that local sequence or chromatin features have a stronger impact on recombination rates in this transgene assay than position along the chromosome arm. PMID:23797104

  20. Gene frequencies of ABO and Rh (D) blood group alleles in a healthy infant population in Ibadan, Nigeria.

    PubMed

    Omotade, O O; Adeyemo, A A; Kayode, C M; Falade, S L; Ikpeme, S

    1999-01-01

    The ABO and Rhesus blood group systems remain the most important blood group systems clinically. In order to provide gene frequency values for the ABO and Rh (D) alleles in a healthy infant population in south west Nigeria, 4748 healthy infants were typed for ABO and Rh (D) blood groups over a five year period (1988-1992). Overall, 2575 (54.2%) were blood group O, 1023 (21.6%) were blood group A, 1017 (21.4%) were blood group B and 133 (2.8%) were blood group AB. The distribution of the ABO blood groups did not differ significantly from those expected under the Hardy Weinberg equilibrium (Goodness-of-fit X2 = 6.09, df = 3, p = 0.1075). The proportions of the infants belonging to the various ABO blood groups did not vary significantly over the period of the study (X2 = 14.53, df = 12, p = 0.268). Overall gene frequencies for the O, A and B genes were 0.7398, 0.1305 and 0.1298 respectively. For the Rh (D) gene, 4520 (95.2%) were Rh-positive while 228 (4.8%) were Rh-negative. However, the proportions of Rh (D) negative infants varied significantly over the period of the study, with a particular year (1991) having nearly twice the usual frequency of Rh-negative individuals (X2 = 31.17, df =, p < 0.001). The frequency of the Rh (D) gene was 0.7809. These figures are reported in the hope that they may find some use as reference for studies of ABO blood groups in health and disease, especially since they were obtained in an infant population in which it is expected that selection pressures should not have started to act to any significant extent.

  1. Distribution of the lactase persistence-associated variant alleles -13910* T and -13915* G among the people of Oman and Yemen.

    PubMed

    Al-Abri, Abdul Rahim; Al-Rawas, Omar; Al-Yahyaee, Saeed; Al-Habori, Molham; Al-Zubairi, Adel Sharaf; Bayoumi, Riad

    2012-06-01

    The high prevalence of lactase persistence (LP) among the people of Saudi Arabia is associated with the -13915(*)G variant allele upstream of the lactase gene (LCT). We, therefore, examined the frequency of the commonly known LP associated SNPs among randomly collected samples from Omani and Yemeni adult populations and obtained further data on the distribution of the two most common LP-associated variants, -13910(*)T and -13915T(*)G, in the Arabian Peninsula. The DNA fragment containing all the reported LP- associated SNPs was amplified and genotyped. The frequency of the -13915(*)G allele was highest among Dhofari Arabs of southern Oman (0.72) followed by Yemeni Arabs (0.54) and Arabs of northern Oman (0.14). It was not detected in Omanis of Asian origin. The frequency of the -13910(*)T allele was extremely low in Arabs of northern and southern Oman (0.00-0.01) and Yemenis (0.002). However, it had a frequency of 0.160 among Omanis of Asian origin. Results show that the highest frequency of the LCT -13915(*)G variant allele appears to be in the south of the Arabian Peninsula with clinal decrease within the Peninsula and further out in surrounding countries. PMID:23256641

  2. Distribution of the lactase persistence-associated variant alleles -13910* T and -13915* G among the people of Oman and Yemen.

    PubMed

    Al-Abri, Abdul Rahim; Al-Rawas, Omar; Al-Yahyaee, Saeed; Al-Habori, Molham; Al-Zubairi, Adel Sharaf; Bayoumi, Riad

    2012-06-01

    The high prevalence of lactase persistence (LP) among the people of Saudi Arabia is associated with the -13915(*)G variant allele upstream of the lactase gene (LCT). We, therefore, examined the frequency of the commonly known LP associated SNPs among randomly collected samples from Omani and Yemeni adult populations and obtained further data on the distribution of the two most common LP-associated variants, -13910(*)T and -13915T(*)G, in the Arabian Peninsula. The DNA fragment containing all the reported LP- associated SNPs was amplified and genotyped. The frequency of the -13915(*)G allele was highest among Dhofari Arabs of southern Oman (0.72) followed by Yemeni Arabs (0.54) and Arabs of northern Oman (0.14). It was not detected in Omanis of Asian origin. The frequency of the -13910(*)T allele was extremely low in Arabs of northern and southern Oman (0.00-0.01) and Yemenis (0.002). However, it had a frequency of 0.160 among Omanis of Asian origin. Results show that the highest frequency of the LCT -13915(*)G variant allele appears to be in the south of the Arabian Peninsula with clinal decrease within the Peninsula and further out in surrounding countries.

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

    SciTech Connect

    Caballero, A.

    1996-02-01

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

  4. Determination of the allelic frequencies of an L-myc and a p53 polymorphism in human lung cancer.

    PubMed

    Weston, A; Ling-Cawley, H M; Caporaso, N E; Bowman, E D; Hoover, R N; Trump, B F; Harris, C C

    1994-04-01

    The L-myc and p53 genes have been implicated in lung cancer. Both of these genes have restriction fragment length polymorphisms (RFLPs) that could account for differential expression or activity of variant forms. An EcoRI restriction site in the L-myc gene was previously reported to be a predictor of poor prognosis in Japanese lung cancer patients. There are several RFLPs in the p53 gene. In exon 4 there is a polymorphism that codes for either an arginine or proline residue at codon 72. We previously reported the frequency of DNA-RFLPs at these gene loci revealed by EcoRI and AccII respectively. Here we report results from a study comparing lung cancer cases (n = 31) with chronic obstructive pulmonary disease controls (n = 49). No association was found between these RFLPs and disease status. Previous observations that the frequencies of these RFLPs varied by race were confirmed. The p53 arginine allele was found to be more common in Caucasians (0.71) than African-Americans (0.50). The EcoRI restriction site present allele in L-myc was more frequent in African-Americans (0.71) than Caucasians (0.49). Thus, the allelic frequency for L-myc was similar in African-Americans to that reported for Japanese, and the allelic frequency for p53 was similar in Caucasians to that reported for Japanese.

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

    PubMed

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

    2015-01-01

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

  6. First report on HLA-DPA1 gene allelic distribution in the general Lebanese population

    PubMed Central

    Haddad, Joseph; Shammaa, Dina; Abbas, Fatmeh; Mahfouz, Rami A.R.

    2016-01-01

    Aims HLA-DPA1 is an important marker in bone marrow and organ transplantation and a highly emerging screening parameter in histocompatibility laboratories. Being highly polymorphic, it has another significant value in detecting population origins and migrations. This is the first study to assess DPA1 allele frequencies in an Arab population. Methods The HLA DPA1 alleles were identified using the One-Lambda assays on a Luminex reverse SSO DNA typing system. Our study included 101 individuals coming from different Lebanese geographical areas representing the different communities and religious sects of the country. Results We compared the results of this study to 16 different populations and found very interesting similarities and differences between Lebanese people and individuals of European ancestry. Conclusion This study is the first to describe the different allelic frequencies of HLA-DPA1 in the Lebanese population and will serve as a template that can be later used for disease association studies both at the level of the country and internationally. PMID:27014585

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

    PubMed Central

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

    2015-01-01

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

  8. Reducing bias of allele frequency estimates by modeling SNP genotype data with informative missingness.

    PubMed

    Lin, Wan-Yu; Liu, Nianjun

    2012-01-01

    The presence of missing single-nucleotide polymorphism (SNP) genotypes is common in genetic studies. For studies with low-density SNPs, the most commonly used approach to dealing with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is valid 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. Under the assumption of Hardy-Weinberg equilibrium and no genotyping error, we here 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. PMID:22719749

  9. Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies.

    PubMed

    Pagnamenta, Alistair T; Lise, Stefano; Harrison, Victoria; Stewart, Helen; Jayawant, Sandeep; Quaghebeur, Gerardine; Deng, Alexander T; Murphy, Valerie Elizabeth; Sadighi Akha, Elham; Rimmer, Andy; Mathieson, Iain; Knight, Samantha J L; Kini, Usha; Taylor, Jenny C; Keays, David A

    2012-01-01

    The development of next generation sequencing (NGS) has radically transformed the scientific landscape, making it possible to sequence the exome of any given individual in a cost-effective way. The power of this approach has been demonstrated by a number of groups who have identified pathogenic mutations in small pedigrees that have been resistant to traditional genetic mapping. Recently it has become clear that exome sequencing has great potential with respect to sporadic disease and the identification of de novo mutations. This is highlighted by studies reporting whole-exome sequencing of patient-parental trios affected by learning disability, autism and schizophrenia. It is widely anticipated that the introduction of this technique into a clinical setting will revolutionise genetic diagnosis. However, the sensitivity of NGS exome sequencing is currently unclear. Here, we describe the exome sequencing of DNA samples from a patient with double cortex syndrome and her parents, resulting in the detection of a mosaic splicing mutation in LIS1. This variant was found at an allele frequency of just 18%, demonstrating that NGS methods have the capacity to identify pathogenic mosaic mutations present at a low level. PMID:22129557

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

    PubMed

    Pickrell, Joseph K; Pritchard, Jonathan K

    2012-01-01

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

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

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

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

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

    PubMed

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

    2009-01-01

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

  13. Explosive synchronization with asymmetric frequency distribution

    NASA Astrophysics Data System (ADS)

    Zhou, Wenchang; Chen, Lumin; Bi, Hongjie; Hu, Xin; Liu, Zonghua; Guan, Shuguang

    2015-07-01

    In this work, we study the synchronization in a generalized Kuramoto model with frequency-weighted coupling. In particular, we focus on the situations in which the frequency distributions of oscillators are asymmetric. For typical unimodal frequency distributions, such as Lorentzian, Gaussian, triangle, and even special Rayleigh, we find that the synchronization transition in the model generally converts from the first order to the second order as the central frequency shifts toward positive direction. We characterize two interesting coherent states in the system: In the former, two phase-locking clusters are formed, rotating with the same frequency. They correspond to those oscillators with relatively high frequencies while the oscillators with relatively small frequencies are not entrained. In the latter, two phase-locking clusters rotate with different frequencies, leading to the oscillation of the order parameter. We further conduct theoretical analysis to reveal the relation between the asymmetric frequency distribution and the conversion of synchronization type, and justify the coherent states observed in the system.

  14. Identification of internal variation in the pseudoautosomal VNTR DXYS17, with nonrandom distribution of the alleles on the X and the Y chromosomes

    SciTech Connect

    Decorte, R.; Wu, R.; Marynen, P.; Cassiman, J.J.

    1994-03-01

    The PCR technique was used to analyze the DXYS17 locus in the pseudoautosomal region of the X and the Y chromosomes. Analysis on an automated DNA sequencer allowed for sensitive and highly accurate typing of 16 different alleles with a size between 480 and 1,100 bp. Two DXYS17 alleles migrated with the same size on agarose or denaturing polyacrylamide gels but with different mobilities on nondenaturing polyacrylamide gels. Sequence analysis showed that, while an identical number of repeats were present in both alleles, differences in the composition of the units were observed. The origin of these differences was found in the 28- and 33-bp units, which only had a specific repeat pattern at the 5' and 3' ends of the region. The genotype distribution for DXYS17 in a Caucasian population did not deviate from the values expected under Hardy-Weinberg equilibrium. However, the frequency of one allele and one genotype was significantly different between males and females. Segregation analysis showed that this difference was the result of a nonrandom distribution of certain alleles on the sex chromosomes in males. 31 refs., 4 figs., 2 tabs.

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

    PubMed Central

    Whitehead, A S; Bertrandy, S; Finnan, F; Butler, A; Smith, G D; 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 Ireland between 1992 and 1994. Cases had to have disease onset at 55 years or younger and be born after 1925. RESULTS: The frequency of the epsilon 4 allele was almost identical between cases of Parkinson's disease (14.6%) and healthy controls (13.3%). There was no relation between epsilon 4 status and disease onset, disease duration, Hoehn and Yahr score, and disease progression. The frequency of the epsilon 4 allele was not increased among 10 patients with Parkinson's disease with dementia (10.0%) compared with the other patients without dementia (14.8%). There was no association between epsilon 4 allele status and either a history of smoking, family history of dementia, or Parkinson's disease, or being born in a rural area. The odds ratio for the ApoE epsilon 4 allele associated with Parkinson's disease was 1.10 (95% confidence interval (95% CI) 0.68-1.79), adjusting for age group, sex, and residential status. The pooled odds ratio from a meta-analysis of six studies of ApoE epsilon 4 status and Parkinson's disease was 0.94 (95% CI 0.69-1.27). CONCLUSIONS: The results from our study as well as the pooled meta-analysis exclude any important role for ApoE epsilon 4 status in the development of Parkinson's disease. Our results similarly do not support its role either in dementia associated with Parkinson's disease or disease prognosis. PMID:8890771

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

    PubMed

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

    2016-02-13

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

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

    PubMed Central

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

    2016-01-01

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

  18. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes

    PubMed Central

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

    2015-01-01

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. PMID:26560341

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-11-01

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

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

    PubMed

    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.

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

    PubMed Central

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

    2015-01-01

    It has been 12 years since the Allele Frequency Net Database (AFND; http://www.allelefrequencies.net) was first launched, providing the scientific community with an online repository for the storage of immune gene frequencies in different populations across the world. There have been a significant number of improvements from the first version, making AFND a primary resource for many clinical and scientific areas including histocompatibility, immunogenetics, pharmacogenetics and anthropology studies, among many others. The most widely used part of AFND stores population frequency data (alleles, genes or haplotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex class I chain-related genes (MIC) and a number of cytokine gene polymorphisms. AFND now contains >1400 populations from more than 10 million healthy individuals. Here, we report how the main features of AFND have been updated to include a new section on ‘HLA epitope’ frequencies in populations, a new section capturing the results of studies identifying HLA associations with adverse drug reactions (ADRs) and one for the examination of infectious and autoimmune diseases associated with KIR polymorphisms—thus extending AFND to serve a new user base in these growing areas of research. New criteria on data quality have also been included. PMID:25414323

  5. HLA class II profile and distribution of HLA-DRB1 and HLA-DQB1 alleles and haplotypes among Lebanese and Bahraini Arabs.

    PubMed

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

    2004-07-01

    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

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

    PubMed Central

    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

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

    PubMed Central

    2012-01-01

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

  8. Allele and haplotype frequencies of HLA-A, B, C, DRB1 and DQB1 genes in polytransfused patients in ethnically diverse populations from Brazil.

    PubMed

    Rodrigues, C; Macedo, L C; Bruder, A V; Quintero, F d C; de Alencar, J B; Sell, A M; Visentainer, J E L

    2015-10-01

    The red blood transfusion is a practice often used in patients with haematological and oncological diseases. However, the investigation of human leucocyte antigen (HLA) system frequency in these individuals is of great importance because multiple transfusions may lead to HLA alloimmunization. Brazil is a country that was colonized by many other ethnicities, leading to a mixed ethnicity and regionalized population. In view of the importance of HLA typing in these patients, the aim of this study was to investigate the allele and haplotype frequencies from polytransfused patients from three different regions from Brazil. HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 genotyping of 366 patients was performed by PCR-SSO, based on the Luminex technology (One Lambda(®) ), and the anti-HLA class I and class II antibodies were analysed using LabScreen Single Antigen Antibody Detection (One Lambda, Inc.). Allele and haplotype frequencies of polytransfused patients of three regions from Brazil were obtained using the Arlequin program. The most frequent allele frequencies observed were HLA-A*02, A*03, B*15, B*35, B*51, C*07, C*04, C*03, DRB1*13, DRB1*11, DRB1*07, DRB1*03, DRB1*01, DQB1*03, DQB1*02, DQB1*06 and DQB1*05. There were differences between the groups for allele variants HLA-B*57 (between Group 1 and Group 2) and HLA-C*12 (between Group 1 and Group 3). The most frequent haplotypes found in the sample were HLA-A*01B*08DRB1*03, DRBI*07DQB1*02, DRB1*01DQB1*05, DRB1*13DQB1*06 and A*02B*35. HLA class I and II antibodies were detected in 77.9% and 63.9% patients, respectively, while the both alloantibodies were detected in 62 (50.9%) patients. In conclusion, the HLA typing for polytransfused patients in each region has a great importance, as seen in this study; individuals from different regions from Brazil have HLA distribution not completely homogeneous.

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

    USGS Publications Warehouse

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

    2003-01-01

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

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

    PubMed

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

    2007-10-01

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

  11. Allele frequencies of BRAFV600 mutations in primary melanomas and matched metastases and their relevance for BRAF inhibitor therapy in metastatic melanoma

    PubMed Central

    Satzger, Imke; Marks, Lena; Kerick, Martin; Klages, Sven; Berking, Carola; Herbst, Rudolf; Völker, Bernward; Schacht, Vivien; Timmermann, Bernd; Gutzmer, Ralf

    2015-01-01

    Background The detection of BRAFV600 mutations in patients with metastatic melanoma is important because of the availability of BRAF inhibitor therapy. However, the clinical relevance of the frequency of BRAFV600 mutant alleles is unclear. Patients and Methods Allele frequencies of BRAFV600 mutations were analyzed by ultra-deep next-generation sequencing in formalin-fixed, paraffin-embedded melanoma tissue (75 primary melanomas and 88 matched metastases). In a second study, pretreatment specimens from 76 patients who received BRAF inhibitors were retrospectively analyzed, and BRAFV600 allele frequencies were correlated with therapeutic results. Results Thirty-five patients had concordantly BRAF-positive and 36 (48%) patients had concordantly BRAF-negative primary melanomas and matched metastases, and four patients had discordant samples with low allele frequencies (3.4–5.2%). Twenty-six of 35 patients with concordant samples had BRAFV600E mutations, three of whom had additional mutations (V600K in two patients and V600R in one) and nine patients had exclusively non-V600E mutations (V600K in eight patients and V600E -c.1799_1800TG > AA- in one patient). The frequency of mutated BRAFV600 alleles was similar in the primary melanoma and matched metastasis in 27/35 patients, but differed by >3-fold in 8/35 of samples. BRAFV600E allele frequencies in pretreatment tumor specimens were not significantly correlated with treatment outcomes in 76 patients with metastatic melanoma who were treated with BRAF inhibitors. Conclusions BRAFV600 mutation status and allele frequency is consistent in the majority of primary melanomas and matched metastases. A small subgroup of patients has double mutations. BRAFV600 allele frequencies are not correlated with the response to BRAF inhibitors. PMID:26498143

  12. Is the European spatial distribution of the HIV-1-resistant CCR5-Delta32 allele formed by a breakdown of the pathocenosis due to the historical Roman expansion?

    PubMed

    Faure, Eric; Royer-Carenzi, Manuela

    2008-12-01

    We studied the possible effects of the expansion of ancient Mediterranean civilizations during the five centuries before and after Christ on the European distribution of the mutant allele for the chemokine receptor gene CCR5 which has a 32-bp deletion (CCR5-Delta32). There is a strong evidence for the unitary origin of the CCR5-Delta32 mutation, this it is found principally in Europe and Western Asia, with generally a north-south downhill cline frequency. Homozygous carriers of this mutation show a resistance to HIV-1 infection and a slower progression towards AIDS. However, HIV has clearly emerged too recently to have been the selective force on CCR5. Our analyses showed strong negative correlations in Europe between the allele frequency and two historical parameters, i.e. the first colonization dates by the great ancient Mediterranean civilizations, and the distances from the Northern frontiers of the Roman Empire in its greatest expansion. Moreover, other studies have shown that the deletion frequencies in both German Bronze Age and Swedish Neolithic populations were similar to those found in the corresponding modern populations, and this deletion has been found in ancient DNA of around 7000 years ago, suggesting that in the past, the deletion frequency could have been relatively high in European populations. In addition, in West Nile virus pathogenesis, CCR5 plays an antimicrobial role showing that host genetic factors are highly pathogen-specific. Our results added to all these previous data suggest that the actual European allele frequency distribution might not be due to genes spreading, but to a negative selection resulting in the spread of pathogens principally during Roman expansion. Indeed, as gene flows from colonizers to European native populations were extremely low, the mutational changes might be associated with vulnerability to imported infections. To date, the nature of the parasites remains unknown; however, zoonoses could be incriminated.

  13. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations

    PubMed Central

    Vina, Marcelo A. Fernandez; Hollenbach, Jill A.; Lyke, Kirsten E.; Sztein, Marcelo B.; Maiers, Martin; Klitz, William; Cano, Pedro; Mack, Steven; Single, Richard; Brautbar, Chaim; Israel, Shosahna; Raimondi, Eduardo; Khoriaty, Evelyne; Inati, Adlette; Andreani, Marco; Testi, Manuela; Moraes, Maria Elisa; Thomson, Glenys; Stastny, Peter; Cao, Kai

    2012-01-01

    The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans. PMID:22312049

  14. Allelic Diversity and Geographical Distribution of the Gene Encoding Plasmodium falciparum Merozoite Surface Protein-3 in Thailand

    PubMed Central

    Sawaswong, Vorthon; Simpalipan, Phumin; Siripoon, Napaporn; Harnyuttanakorn, Pongchai; Pattaradilokrat, Sittiporn

    2015-01-01

    Merozoite surface proteins (MSPs) of malaria parasites play critical roles during the erythrocyte invasion and so are potential candidates for malaria vaccine development. However, because MSPs are often under strong immune selection, they can exhibit extensive genetic diversity. The gene encoding the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum displays 2 allelic types, K1 and 3D7. In Thailand, the allelic frequency of the P. falciparum msp-3 gene was evaluated in a single P. falciparum population in Tak at the Thailand and Myanmar border. However, no study has yet looked at the extent of genetic diversity of the msp-3 gene in P. falciparum populations in other localities. Here, we genotyped the msp-3 alleles of 63 P. falciparum samples collected from 5 geographical populations along the borders of Thailand with 3 neighboring countries (Myanmar, Laos, and Cambodia). Our study indicated that the K1 and 3D7 alleles coexisted, but at different proportions in different Thai P. falciparum populations. K1 was more prevalent in populations at the Thailand-Myanmar and Thailand-Cambodia borders, whilst 3D7 was more prevalent at the Thailand-Laos border. Global analysis of the msp-3 allele frequencies revealed that proportions of K1 and 3D7 alleles of msp-3 also varied in different continents, suggesting the divergence of malaria parasite populations. In conclusion, the variation in the msp-3 allelic patterns of P. falciparum in Thailand provides fundamental knowledge for inferring the P. falciparum population structure and for the best design of msp-3 based malaria vaccines. PMID:25925176

  15. Graphical modeling of the joint distribution of alleles at associated loci.

    PubMed

    Thomas, Alun; Camp, Nicola J

    2004-06-01

    Pairwise linkage disequilibrium, haplotype blocks, and recombination hotspots provide only a partial description of the patterns of dependences and independences between the allelic states at proximal loci. On the gross scale, where recombination and spatial relationships dominate, the associations can be reasonably described in these terms. However, on the fine scale of current high-density maps, the mutation process is also important and creates associations between loci that are independent of the physical ordering and that can not be summarized with pairwise measures of association. Graphical modeling provides a standard statistical framework for characterizing precisely these sorts of complex stochastic data. Although graphical models are often used in situations in which assumptions lead naturally to specific models, it is less well known that estimation of graphical models is also a developed field. We show how decomposable graphical models can be fitted to dense genetic data. The objective function is the maximized log likelihood for the model penalized by a multiple of the model's degrees of freedom. We also describe how this can be modified to incorporate prior information of locus position. Simulated annealing is used to find good solutions. Part of the appeal of this approach is that categorical phenotypes can be included in the same analysis and association with polymorphisms can be assessed jointly with the interlocus associations. We illustrate our method with genotypic data from 25 loci in the ELAC2 gene. The results contain third- and fourth-order locus interactions and show that, at this density of markers, linkage disequilibrium is not a simple function of physical distance. Graphical models provide more flexibility to express these features of the joint distribution of alleles than do monotonic functions connecting physical and genetic maps.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-08-01

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

  18. Distribution of the FYBES and RHCE*ce(733C>G) alleles in an Argentinean population: Implications for transfusion medicine

    PubMed Central

    Cotorruelo, Carlos M; Fiori, Silvana V; Borrás, Silvia E García; Racca, Liliana L; Biondi, Claudia S; Racca, Amelia L

    2008-01-01

    Background The understanding of the molecular bases of blood groups makes possible the identification of red cell antigens and antibodies using molecular approaches, especially when haemagglutination is of limited value. The practical application of DNA typing requires the analysis of the polymorphism and allele distribution of the blood group genes under study since genetic variability was observed among different ethnic groups. Urban populations of Argentina are assumed to have a white Caucasian European genetic component. However, historical and biological data account for the influence of other ethnic groups. In this work we analyse FY and RH blood group alleles attributed to Africans and that could have clinical implications in the immune destruction of erythrocytes. Methods We studied 103 white trios (father, mother and child, 309 samples) from the city of Rosario by allele specific PCRs and serological methods. The data obtained were analysed with the appropriate statistical test considering only fathers and mothers (n = 206). Results We found the presence of the FY*BES and RHCE*ce(733C>G) alleles and an elevated frequency (0.0583) for the Dce haplotype. The number of individuals with a concomitant occurrence of both alleles was significantly higher than that expected by chance. We found that 4.68% of the present gene pool is composed by alleles primarily associated with African ancestry and about 10% of the individuals carried at least one RH or FY allele that is predominantly observed among African populations. Thirteen percent of Fy(b-) subjects were FY*A/FY*BES. Conclusion Taken together, the results suggest that admixture events between African slaves and European immigrants at the beginning of the 20th century made the physical characteristics of black Africans to be invisible nowadays. Considering that it was a recent historical event, the FY*BES and RHCE*ce(733C>G) alleles did not have time to become widespread but remain concentrated within families

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

    PubMed Central

    Carney, Amanda E.; Sanders, Rebecca D.; 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′ proximal sequence. The four non-coding sequence changes are unique to D2. The p.N314D substitution, however, is not; it is found together with a silent polymorphism, p.L218(TTA), on functionally normal Duarte-1 alleles (D1, also called Los Angeles or LA alleles). The HapMap database reveals that p.N314D is a common human variant, and cross-species comparisons implicate D314 as the ancestral allele. The p.N314D substitution is also functionally neutral in mammalian cell and yeast expression studies. In contrast, the 4 bp 5′ deletion characteristic of D2 alleles appears to be functionally impaired in reporter gene transfection studies. Here we present allele-specific qRT–PCR evidence that D2 alleles express less mRNA in vivo than their wild-type counterparts; the difference is small but statistically significant. Furthermore, we characterize the prevalence of the 4 bp deletion in GG, NN and DG populations; the deletion appears exclusive to D2 alleles. Combined, these data strongly implicate the 4 bp 5′ deletion as a causal mutation in Duarte galactosemia and suggest that direct tests for this deletion, as proposed here, could enhance or supplant current tests, which define D2 alleles on the basis of the presence and absence of linked coding sequence polymorphisms. PMID:19224951

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

    PubMed

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

    2016-10-01

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

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

    PubMed

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

    1999-12-01

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

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

    PubMed Central

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

    2014-01-01

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

  3. Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers

    PubMed Central

    Hippolyte, I.; Jenny, C.; Gardes, L.; Bakry, F.; Rivallan, R.; Pomies, V.; Cubry, P.; Tomekpe, K.; Risterucci, A. M.; Roux, N.; Rouard, M.; Arnaud, E.; Kolesnikova-Allen, M.; Perrier, X.

    2012-01-01

    Background and Aims The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships. Methods Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed. Key Results and Conclusions We determine the closest diploid progenitors of the triploid ‘Cavendish’ and ‘Gros Michel’ subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. ‘Cavendish’, ‘Plantain’ and ‘Mutika-Lujugira’), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference. PMID:22323428

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  6. Oligonucleotide frequencies in DNA follow a Yule distribution.

    PubMed

    Martindale, C; Konopka, A K

    1996-03-01

    We show that ranked oligonucleotide frequencies in both protein-coding and non-coding regions from several genomes fit poorly to the Zipf distribution, but that the same frequency data give excellent fit to the Yule distribution. The parameters of the Yule distribution for oligonucleotide frequencies in exons are the same (within error limits) as the parameters for introns. This precludes application of Yule or Zipf distribution of ranked oligonucleotide frequencies to annotating new genomic sequences.

  7. POPTREEW: web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities.

    PubMed

    Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro

    2014-06-01

    POPTREE software, including the command line (POPTREE) and the Windows (POPTREE2) versions, is available to perform evolutionary analyses of allele frequency data, computing distance measures for constructing population trees and average heterozygosity (H) (measure of genetic diversity within populations) and G(ST) (measure of genetic differentiation among subdivided populations). We have now developed a web version POPTREEW (http://www.med.kagawa-u.ac.jp/∼genomelb/takezaki/poptreew/) to provide cross-platform access to all POPTREE functions including interactive tree editing. Furthermore, new POPTREE software (POPTREE, POPTREE2, and POPTREEW) computes standardized G(ST) and Jost's D, which may be appropriate for data with high variability, and accepts genotype data in GENEPOP format as an input.

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

    PubMed

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

    2007-05-24

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

  9. High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program.

    PubMed

    Zhou, Xiao-Yang; Zhu, Fa-Ming; Li, Jian-Ping; Mao, Wei; Zhang, De-Mei; Liu, Meng-Li; Hei, Ai-Lian; Dai, Da-Peng; Jiang, Ping; Shan, Xiao-Yan; Zhang, Bo-Wei; Zhu, Chuan-Fu; Shen, Jie; Deng, Zhi-Hui; Wang, Zheng-Lei; Yu, Wei-Jian; Chen, Qiang; Qiao, Yan-Hui; Zhu, Xiang-Ming; Lv, Rong; Li, Guo-Ying; Li, Guo-Liang; Li, Heng-Cong; Zhang, Xu; Pei, Bin; Jiao, Li-Xin; Shen, Gang; Liu, Ying; Feng, Zhi-Hui; Su, Yu-Ping; Xu, Zhao-Xia; Di, Wen-Ying; Jiang, Yao-Qin; Fu, Hong-Lei; Liu, Xiang-Jun; Liu, Xiang; Zhou, Mei-Zhen; Du, Dan; Liu, Qi; Han, Ying; Zhang, Zhi-Xin; Cai, Jian-Ping

    2015-01-01

    Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis

  10. High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program

    PubMed Central

    Zhou, Xiao-Yang; Zhu, Fa-Ming; Li, Jian-Ping; Mao, Wei; Zhang, De-Mei; Liu, Meng-Li; Hei, Ai-Lian; Dai, Da-Peng; Jiang, Ping; Shan, Xiao-Yan; Zhang, Bo-Wei; Zhu, Chuan-Fu; Shen, Jie; Deng, Zhi-Hui; Wang, Zheng-Lei; Yu, Wei-Jian; Chen, Qiang; Qiao, Yan-Hui; Zhu, Xiang-Ming; Lv, Rong; Li, Guo-Ying; Li, Guo-Liang; Li, Heng-Cong; Zhang, Xu; Pei, Bin; Jiao, Li-Xin; Shen, Gang; Liu, Ying; Feng, Zhi-Hui; Su, Yu-Ping; Xu, Zhao-Xia; Di, Wen-Ying; Jiang, Yao-Qin; Fu, Hong-Lei; Liu, Xiang-Jun; Liu, Xiang; Zhou, Mei-Zhen; Du, Dan; Liu, Qi; Han, Ying; Zhang, Zhi-Xin; Cai, Jian-Ping

    2015-01-01

    Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis

  11. Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies.

    PubMed

    Papadopoulos, Petros; Viennas, Emmanouil; Gkantouna, Vassiliki; Pavlidis, Cristiana; Bartsakoulia, Marina; Ioannou, Zafeiria-Marina; Ratbi, Ilham; Sefiani, Abdelaziz; Tsaknakis, John; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P

    2014-01-01

    FINDbase (http://www.findbase.org) aims to document frequencies of clinically relevant genomic variations, namely causative mutations and pharmacogenomic markers, worldwide. Each database record includes the population, ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related databases and the genetic variation together with its frequency in that population. Here, we report, in addition to the regular data content updates, significant developments in FINDbase, related to data visualization and querying, data submission, interrelation with other resources and a new module for genetic disease summaries. In particular, (i) we have developed new data visualization tools that facilitate data querying and comparison among different populations, (ii) we have generated a new FINDbase module, built around Microsoft's PivotViewer (http://www.getpivot.com) software, based on Microsoft Silverlight technology (http://www.silverlight.net), that includes 259 genetic disease summaries from five populations, systematically collected from the literature representing the documented genetic makeup of these populations and (iii) the implementation of a generic data submission tool for every module currently available in FINDbase.

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

    PubMed

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

    2008-12-01

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

  13. Lower frequency of sister chromatid exchanges and altered frequency of HLA B-region alleles among individuals with sporadic dysplastic nevi.

    PubMed

    Illeni, M T; Rovini, D; Di Lernia, M; Cascinelli, N; Ghidoni, A

    1997-01-01

    Sister chromatid exchanges (SCE) were analyzed in peripheral blood lymphocytes of 24 individuals, following diagnosis, and prior to surgical removal, of a sporadic dysplastic nevus (DN). Lower SCE values and variability were found in 23 sporadic DN individuals compared with controls (2.52 +/- 0.12 and 3.76 +/- 0.22 SCE/cell, respectively). These DN individuals, contrarily to healthy controls and some types of tumor patients whose cells are hypersensitive to mutagenic agents, did not show increased SCE rates as a consequence of cigarette smoking, alcohol consumption and diagnostic radiation treatments. These observations are in contrast with clinical evidence that similar lesions are both markers or risk and precursors of malignancy in individuals with multiple nevi, affected by the dysplastic nevus syndrome (DNS) or belonging to FMM (familial malignant melanoma) families. Three HLA class I alleles out of 72 tested were found more frequently in sporadic DN individuals compared with controls: B37 (p < 0.05), B52 (p < 0.01) and B70 (p < 0.01). Whether the greater chromosomal stability (as shown by the SCE analysis), and/or the altered frequency of some HLA alleles could influence the chance of developing cutaneous malignancy in DN individuals is yet to be evaluated.

  14. Cumulative frequency distribution of past species extinctions

    NASA Technical Reports Server (NTRS)

    Raup, D. M.

    1991-01-01

    Analysis of Sepkoski's compendium of the time ranges of 30,000+ taxa yields a mean duration of 28.4 ma for genera of fossil invertebrates. This converts to an average extinction rate of 3.5 percent per million years or about one percent every 286,000 years. Using survivorship techniques, these estimates can be converted to the species level, yielding a Phanerozoic average of one percent species extinction every 40,000 years. Variation in extinction rates through time is far greater than the null expectation of a homogeneous birth-death model and this reflects the well-known episodicity of extinction ranging from a few large mass extinctions to so-called background extinction. The observed variation in rates can be used to construct a cumulative frequency distribution of extinction intensity, and this distribution, in the form of a kill curve for species, shows the expected waiting times between extinction events of a given intensity. The kill curve is an average description of the extinction events of a given intensity. The kill curve is an average description of the extinction record and does not imply any cause or causes of extinction. The kill curve shows, among other things, that only about five percent of total species extinctions in the Phanerozoic were involved in the five largest mass extinctions. The other 95 percent were distributed among large and small events not normally called mass extinctions. As an exploration of the possibly absurd proposition that most past extinctions were produced by the effects of large-body impact, the kill curve for species was mapped on the comparable distribution for comet and asteroid impacts. The result is a curve predicting the species kill for a given size of impacting object (expressed as crater size). The results are reasonable in that impacts producing craters less than 30 km (diameter) cause negligible extinction but those producing craters 100-150 km (diameter) cause extinction of species in the range of 45

  15. Apolipoprotein E Allelic Frequency Altered in Women with Early-onset Breast Cancer.

    PubMed

    Porrata-Doria, Tirtsa; Matta, Jaime L; Acevedo, Summer F

    2010-05-24

    Among women, the most prevalent type of cancer is breast cancer, affecting 1 out of every 8 women in the United States; in Puerto Rico, 70 out of every 100,000 will develop some type of breast cancer. Therefore, a better understand of the potential risk factors for breast cancer could lead to the development of early detection tools. A gene that has been proposed as a risk factor in several populations around the world is Apolipoprotein E (apoE). ApoE functions as a mechanism of transport for lipoproteins and cholesterol throughout the body, with 3 main isoforms present in humans (apoE2, apoE3, and apoE4). Whether or not apoE4 is a risk factor for breast cancer remains controversial. Previous studies have either included test subjects of all ages (20-80) or have focused on late-onset (after age 50) breast cancer; none has concentrated specifically on early-onset (aged 50 and younger) breast cancer. The objectives of this study was to examine (in a Puerto Rican population) the differences in the relative frequency of occurrence of apoE4 in non-breast cancer versus breast cancer patients and to examine, as well, the potential differences of same in early- versus late-onset patients. We found an increased frequency of apoE4 (odds ratio 2.15) only in early-onset breast cancer survivors, which is similar to the findings of those studies that combined or adjusted for age as well as for an association between apoE4 and decreased tumor size. ApoE is also a potential risk factor for long-term cognitive effects after chemotherapy and affects response to hormone replacement. Our data supports the theory that knowing the apoE genotype of women who are at risk of developing breast cancer may be beneficial, as such knowledge would aid in the prediction of tumor size and the development of treatment regimens.

  16. Allele and genotype frequencies of CYP2C9, CYP2C19 and CYP2D6 in an Italian population.

    PubMed

    Scordo, Maria Gabriella; Caputi, Achille P; D'Arrigo, Concetta; Fava, Giuseppina; Spina, Edoardo

    2004-08-01

    The polymorphic cytochrome P450 isoenzymes (CYPs) 2C9, 2C19 and 2D6 metabolise many important drugs, as well as other xenobiotics. Their polymorphism gives rise to important interindividual and interethnic variability in the metabolism and disposition of several therapeutic agents and may cause differences in the clinical response to these drugs. In this study, we determined the genotype profile of a random Italian population in order to compare the CYP2C9, CYP2C19 and CYP2D6 allele frequencies among Italians with previous findings in other Caucasian populations. Frequencies for the major CYP2C9, CYP2C19 and CYP2D6 mutated alleles and genotypes have been evaluated in 360 unrelated healthy Italian volunteers (210 males and 150 females, aged 19-52 years). Genotyping has been carried out on peripheral leukocytes DNA by molecular biology techniques (PCR, RFLP, long-PCR). CYP2C9, CYP2C19 and CYP2D6 allele and genotype frequencies resulted in equilibrium with the Hardy-Weinberg equation. One hundred and fourteen subjects (31.7%) carried one and 23 subjects (6.4%) carried two CYP2C9 mutated alleles. Sixty-eight (18.9%) volunteers were found to be heterozygous and six (1.7%) homozygous for the CYP2C19*2, while no CYP2C19*3 was detected in the evaluated population. Volunteers could be divided into four CYP2D6 genotypes groups: 192 subjects (53.3%) with no mutated alleles (homozygous extensive metabolisers, EM), 126 (35.0%) with one mutated allele (heterozygous EM), 12 (3.4%) with two mutated alleles (poor metabolisers, PM) and 30 (8.3%) with extracopies of a functional gene (ultrarapid metabolisers, UM). Frequencies of both CYP2C9 and CYP2C19 allelic variants, as well as CYP2D6 detrimental alleles, in Italian subjects were similar to those of other Caucasian populations. Conversely, the prevalence of CYP2D6 gene duplication among Italians resulted very high, confirming the higher frequency of CYP2D6 UM in the Mediterranean area compared to Northern Europe. PMID:15177309

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

    PubMed

    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

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

    PubMed

    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.

  19. Zipfian Frequency Distributions Facilitate Word Segmentation in Context

    ERIC Educational Resources Information Center

    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…

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

    PubMed

    Lucotte, Gérard

    2002-05-01

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

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

    PubMed Central

    Kiesler, Kevin M.; Vallone, Peter M.

    2013-01-01

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

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

    PubMed

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

    2015-11-01

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

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

    PubMed

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

    2014-06-01

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

  4. Variant allele frequency enrichment analysis in vitro reveals sonic hedgehog pathway to impede sustained temozolomide response in GBM

    PubMed Central

    Biswas, Nidhan K.; Chandra, Vikas; Sarkar-Roy, Neeta; Das, Tapojyoti; Bhattacharya, Rabindra N.; Tripathy, Laxmi N.; Basu, Sunandan K.; Kumar, Shantanu; Das, Subrata; Chatterjee, Ankita; Mukherjee, Ankur; Basu, Pryiadarshi; Maitra, Arindam; Chattopadhyay, Ansuman; Basu, Analabha; Dhara, Surajit

    2015-01-01

    Neoplastic cells of Glioblastoma multiforme (GBM) may or may not show sustained response to temozolomide (TMZ) chemotherapy. We hypothesize that TMZ chemotherapy response in GBM is predetermined in its neoplastic clones via a specific set of mutations that alter relevant pathways. We describe exome-wide enrichment of variant allele frequencies (VAFs) in neurospheres displaying contrasting phenotypes of sustained versus reversible TMZ-responses in vitro. Enrichment of VAFs was found on genes ST5, RP6KA1 and PRKDC in cells showing sustained TMZ-effect whereas on genes FREM2, AASDH and STK36, in cells showing reversible TMZ-effect. Ingenuity pathway analysis (IPA) revealed that these genes alter cell-cycle, G2/M-checkpoint-regulation and NHEJ pathways in sustained TMZ-effect cells whereas the lysine-II&V/phenylalanine degradation and sonic hedgehog (Hh) pathways in reversible TMZ-effect cells. Next, we validated the likely involvement of the Hh-pathway in TMZ-response on additional GBM neurospheres as well as on GBM patients, by extracting RNA-sequencing-based gene expression data from the TCGA-GBM database. Finally, we demonstrated TMZ-sensitization of a TMZ non-responder neurosphere in vitro by treating them with the FDA-approved pharmacological Hh-pathway inhibitor vismodegib. Altogether, our results indicate that the Hh-pathway impedes sustained TMZ-response in GBM and could be a potential therapeutic target to enhance TMZ-response in this malignancy. PMID:25604826

  5. Beyond orchids and dandelions: Testing the 5HTT “risky” allele for evidence of phenotypic capacitance and frequency dependent selection

    PubMed Central

    Conley, Dalton; Rauscher, Emily; Siegal, Mark L.

    2013-01-01

    The persistence of behaviorally deleterious genes in the human population poses an interesting question for population genetics: If certain alleles at these loci are deleterious, why have they survived in the population? We consider evidence for phenotypic capacitance and/or frequency dependent selection for an allele that has been putatively shown to have negative associations with human behaviors (the “short” 5-HTT promoter region allele) yet which has persisted in human and non-human primate populations. Using National Longitudinal Study of Adolescent Health data, we compare sibling and twin variation in depression by 5-HTT genotype (specified in several ways) and investigate sibship-level cross-person gene-gene interactions. In support of the “orchid / dandelion” hypothesis, we find evidence that the short allele increases variation in phenotypes in response to environmental (or genetic) differences (i.e. acts as a perturbation of a phenotypic capacitor). Further, we also find some evidence that the effects of allelic variation at this locus are moderated by the genetic environment of the sibship unit (i.e. may be susceptible to frequency dependent selection). We discuss implications of these findings for genetic models in general, specifically with respect to stable unit treatment value assumption violations (i.e. non-independence of units of analysis). PMID:23701535

  6. Note on a Strongly Unimodal Bibliometric Size Frequency Distribution.

    ERIC Educational Resources Information Center

    Sichel, H. S.

    1992-01-01

    This study demonstrates that the number of references at the end of scientific research papers forms a strongly unimodal frequency distribution and that the generalized Gaussian-Poisson distribution fits such unimodal data extremely well. (three references) (Author/MES)

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

    KOHYAMA, Moeko; TADA, Naomi; MITSUI, Hiroko; TOMIOKA, Hitomi; TSUTSUI, Toshihiko; YABUKI, Akira; RAHMAN, Mohammad Mahbubur; KUSHIDA, Kazuya; MIZUKAMI, Keijiro; YAMATO, Osamu

    2015-01-01

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

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

    PubMed

    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.

  10. Frequencies of 23 Functionally Significant Variant Alleles Related with Metabolism of Antineoplastic Drugs in the Chilean Population: Comparison with Caucasian and Asian Populations

    PubMed Central

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

    2012-01-01

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

  11. Allele Distributions at Hybrid Incompatibility Loci Facilitate the Potential for Gene Flow between Cultivated and Weedy Rice in the US

    PubMed Central

    Craig, Stephanie M.; Reagon, Michael; Resnick, Lauren E.; Caicedo, Ana L.

    2014-01-01

    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. PMID:24489758

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

    PubMed

    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.

  13. Radio frequency distribution assembly, operations and maintenance manual

    NASA Astrophysics Data System (ADS)

    1983-09-01

    The Naval Research Laboratory (NRL) Radio Frequency Distribution Assembly (RFDA) is an interface between the Sperry four-channel, fast-switching synthesizer and the EF-111 jamming system antenna ports. The RFDA will distribute the RF energy while providing controlled RF amplitude to simulate the antenna patterns of the EF-111 Electronic Warfare (EW) systems. The RFDA is capable of operating over the frequency range of 0.5 to 18 GHz, and can rapidly switch between varying frequencies and attenuation levels.

  14. Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program

    PubMed Central

    Gragert, Loren; Maiers, Martin; Chatterjee, Ansu; Albrecht, Mark

    2015-01-01

    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 estimates). This

  15. [Distribution of allelic variants of promotor sites of cytokine genes and endothelial growth factor gene among healthy subjects and patients with rheumatoid arthritis in a Russian Europeoid population].

    PubMed

    Konenkov, V I; Golovanova, O V; Prokof'ev, V F; Shevchenko, A V; Zonova, E V; Korolev, M A; Leonova, Iu B; Khalaĭdzhi, N A; Lapsina, S A

    2010-01-01

    The article reports results of the first study of cytokine gene polymorphic sites and analysis of distribution of their complexes among healthy subjects and patients with rheumatoid arthritis (RA) representative of the Russian Europeoid population; their possible prognostic significance is evaluated. Comprehensive analysis of the frequency of allelic variants of cytokine genes IL1B C-31T, IL6 G-174C, TNFA A-238G, TNFA A-308G, TNFA A-863C, IL4 C-590T, IL10 A-592C and VEGF C-2578A was performed for 513 residents of the Novosibirsk region showing no obvious signs of any diseases and 125 RA patients. The results suggest association of RA with certain alleles of pro- and anti-inflammatory cytokine genes. Complex indices reflecting combinations of genotypes of two, three, four, five, six and seven loci of the explored cytokine genes found in individual patient demonstrate their high specificity for RA. It is supposed that these findings can be used in further clinical studies for the development of algorithm designed to detect risk groups among clinically healthy subjects.

  16. Magnitude-frequency distribution of volcanic explosion earthquakes

    NASA Astrophysics Data System (ADS)

    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.

  17. A microsatellite polymorphism in the von Willebrand factor gene: comparison of allele frequencies in different population samples and evaluation for forensic medicine.

    PubMed

    Sajantila, A; Pacek, P; Lukka, M; Syvänen, A C; Nokelainen, P; Sistonen, P; Peltonen, L; Budowle, B

    1994-09-16

    The allele frequencies at the tetranucleotide repeat (TCTA) vWA locus in the vWF gene were determined in the general Finnish population, in a population representing an internal isolate of Finland, in the Vologda-Russian population, and in US Black population samples. The allele and genotype frequencies from these population samples were compared with each other and with those reported from Spanish and British population samples. Statistically significant differences were demonstrated between most of the different groups (Finns vs. Vologda-Russians, Finns vs. US Blacks, Finns vs. Spanish, Vologda-Russians vs. US Blacks, Vologda-Russians vs. Spanish, US Blacks vs. Spanish and US Blacks vs. British Caucasians), but not between the two Caucasoid population samples from Finland and Great Britain, nor between or within the subpopulation samples from Finland and those from Vologda-Russia. In addition, the vWA marker was evaluated and demonstrated to be reliable for forensic purposes and paternity testing.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    Arango, Eliana; Carmona-Fonseca, Jaime

    2013-01-01

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

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

    PubMed

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

    2016-09-01

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

  1. Allele frequencies of the major milk proteins in the Finnish Ayrshire and detection of a new kappa-casein variant.

    PubMed

    Ikonen, T; Ruottinen, O; Erhardt, G; Ojala, M

    1996-06-01

    A total of 20990 Finnish Ayrshire cows were phenotyped for the major milk proteins by isoelectric focusing in polyacrylamide gels. The predominant alleles in the Finnish Ayrshire were alpha S1-casein B (0.999), alpha S2-casein A (0.991), beta-casein A1 (0.509) and alpha 2 (0.490), kappa-casein A (0.612) and beta-lactoglobulin B (0.716). The kappa-casein E allele (0.307) was also rather common in the Finnish Ayrshire. A new kappa-casein variant (kappa-casein F) was demonstrated in two Finnish Ayrshire cows, a dam and a daughter.

  2. ABO and Rh (D) group distribution and gene frequency; the first multicentric study in India

    PubMed Central

    Agrawal, Amit; Tiwari, Aseem Kumar; Mehta, Nidhi; Bhattacharya, Prasun; Wankhede, Ravi; Tulsiani, Sunita; Kamath, Susheela

    2014-01-01

    Background and Objectives: The study was undertaken with the objective to provide data on the ABO and Rh(D) blood group distribution and gene frequency across India. Materials and Methods: A total of 10,000 healthy blood donors donating in blood banks situated in five different geographical regions of the country (North, South, East and Center) were included in the study. ABO and Rh (D) grouping was performed on all these samples. Data on the frequency of ABO and Rh(D) blood groups was reported in simple numbers and percentages. Results: The study showed that O was the most common blood group (37.12%) in the country closely followed by B at 32.26%, followed by A at 22.88% while AB was the least prevalent group at 7.74%. 94.61% of the donor population was Rh positive and the rest were Rh negative. Regional variations were observed in the distribution. Using the maximum likelihood method, the frequencies of the IA, IB and IO alleles were calculated and tested according to the Hardy Weinberg law of Equilibrium. The calculated gene frequencies are 0.1653 for IA (p), 0.2254 for IB (q) and 0.6093 for IO (r). In Indian Population, O (r) records the highest value followed by B (q) and A (p); O > B > A. Conclusion: The study provides information about the relative distribution of various alleles in the Indian population both on a pan-India basis as well as region-wise. This vital information may be helpful in planning for future health challenges, particularly planning with regards to blood transfusion services. PMID:25161353

  3. The frequency of the mitochondrial aldehyde dehydrogenase I2 (atypical) allele in Caucasian, Oriental and African black populations determined by the restriction profile of PCR-amplified DNA.

    PubMed

    Dandré, F; Cassaigne, A; Iron, A

    1995-06-01

    The aldehyde dehydrogenase I (ALDH I) gene codes for a mitochondrial enzyme which plays a major role in hepatic alcohol detoxication. It has been related to alcohol flushing in Orientals bearing the atypical ALDH I2 gene. The variant protein results from a lysine for glutamate substitution at position 487 (G-->A change in exon 12). A procedure for ALDH I2 detection consisting in a differentiation between the 'atypical' allele and the 'wild' allele has been improved through PCR and subsequent MboII digestion. Blood samples collected on anticoagulant or directly absorbed on blotting paper were used for DNA amplification in the presence of two specific oligonucleotidic primers, each one able to incorporate a restriction site in the amplimer. After MboII digestion, PCR products were separated by polyacrylamide gel electrophoresis and then visualized with ethidium bromide. This technique permits a rapid and non-radioactive detection of atypical ALDH I2 on a PCR product without the use of allele specific oligonucleotides. It was applied to the study of ALDH I2 allele frequency in random population samples of three ethnic groups: Caucasians, Orientals and African blacks.

  4. Distributed Bragg reflector laser for frequency modulated communication systems

    SciTech Connect

    Chraplyvy, A.R.; Koch, T.L.; Tkach, R.W.

    1990-02-27

    This patent describes a lightwave transmitter. It includes a distributed Bragg reflector laser and means for frequency modulating said laser. The laser comprises first and second semiconductor heterostructure regions.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  8. Low frequency noise distributed-feedback ytterbium fibre laser

    SciTech Connect

    Nikulin, M A; Babin, S A; Kablukov, S I; Dmitriev, Aleksandr K; Dychkov, Aleksandr S; Lugovoy, Aleksei A; Pecherskii, Yu Ya

    2009-10-31

    We report a single-frequency 1-W fibre laser source emitting at 1093 nm, composed of a distributed-feedback ytterbium fibre laser and fibre-optic amplifier. The laser frequency was stabilised by side-locking to a transmission peak of a Fabry - Perot interferometer, and the residual frequency noise spectrum of the laser was measured. Our results indicate that the laser linewidth can be narrowed down below 1 kHz. (lasers)

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

    PubMed

    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

  10. Distribution of VP4 gene alleles in human rotaviruses by using probes to the hyperdivergent region of the VP4 gene.

    PubMed Central

    Steele, A D; Garcia, D; Sears, J; Gerna, G; Nakagomi, O; Flores, J

    1993-01-01

    The rotavirus VP4 protein elicits the production of neutralizing antibodies and is known to play a role in inducing resistance to disease. At least five human rotavirus VP4 gene alleles have been described on the basis of antigenic polymorphism and/or nucleotide sequence differences. In the present study, we developed cDNA probes directed at the hyperdivergent region of the VP4 gene of the five described human rotavirus VP4 alleles (Wa, DS1, M37, AU228, and 69M) and used them in hybridization assays with human rotavirus strains from Latin America and Europe to determine the distribution of the VP4 gene alleles in nature. The Wa-like allele was detected most frequently, occurring in 57% of the 402 rotavirus strains tested, and the DS1-like allele was the next most common, occurring in 14% of the strains tested. The M37- and AU228-like alleles were detected in only 4 and 3% of the rotavirus strains tested, respectively, whereas the 69M-like VP4 gene allele was not detected. Several rotavirus strains from Europe did not react with any of the VP4 gene probes, although they did hybridize to a probe generated from a representative strain from the group. These data indicate the global distribution of various VP4 gene alleles and raise the possibility that other, unrecognized human VP4 alleles exist in nature because almost one-fourth of the strains could not be classified into any of the established VP4 groups. Images PMID:8394374

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

    PubMed

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

    2015-06-01

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

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

    PubMed

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

    1997-04-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2011-01-01

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

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

    PubMed

    Sulcebe, Genc; Shyti, Erkena

    2016-08-01

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

  16. Distributional Effects of Word Frequency on Eye Fixation Durations

    ERIC Educational Resources Information Center

    Staub, Adrian; White, Sarah J.; Drieghe, Denis; Hollway, Elizabeth C.; Rayner, Keith

    2010-01-01

    Recent research using word recognition paradigms, such as lexical decision and speeded pronunciation, has investigated how a range of variables affect the location and shape of response time distributions, using both parametric and non-parametric techniques. In this article, we explore the distributional effects of a word frequency manipulation on…

  17. Distributed Frequency Control of Prosumer-Based Electric Energy Systems

    SciTech Connect

    Nazari, MH; Costello, Z; Feizollahi, MJ; Grijalva, S; Egerstedt, M

    2014-11-01

    In this paper, we propose a distributed frequency regulation framework for prosumer-based electric energy systems, where a prosumer (producer-consumer) is defined as an intelligent agentwhich can produce, consume, and/or store electricity. Despite the frequency regulators being distributed, stability can be ensured while avoiding inter-area oscillations using a limited control effort. To achieve this, a fully distributed one-step model-predictive control protocol is proposed and analyzed, whereby each prosumer communicates solely with its neighbors in the network. The efficacy of the proposed frequency regulation framework is shown through simulations on two real-world electric energy systems of different scale and complexity. We show that prosumers can indeed bring frequency and power deviations to their desired values after small perturbations.

  18. Visualization of EEG using time-frequency distributions.

    PubMed

    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.

  19. Allele and Haplotype Frequencies of Human Leukocyte Antigen-A, -B, -C, -DRB1, and -DQB1 From Sequence-Based DNA Typing Data in Koreans

    PubMed Central

    In, Ji Won; Roh, Eun Youn; Oh, Sohee; Shin, Sue; Park, Kyoung Un

    2015-01-01

    Background Data on allele frequencies (AFs) and haplotype frequencies (HFs) of HLA-C and -DQB1 are limited in Koreans. We investigated AFs and HFs of HLA-A, -B, -C, -DRB1, and -DQB1 in Koreans by high-resolution sequence-based typing (SBT). Methods Hematopoietic stem cells were obtained from 613 healthy, unrelated donors to analyze HLA-A, -B, -C, -DRB1, and -DQB1 genotypes by using AlleleSEQR HLA-A, -B, -C, -DRB1, and -DQB1 SBT kits (Abbott Molecular, USA), respectively. Alleles belonging to HLA-C*07:01/07:06 group were further discriminated by using PCR-sequence specific primer analysis. AFs and HFs were calculated by direct counting and maximum likelihood method, respectively. Results In all, 24 HLA-A, 46 HLA-B, 24 HLA-C, 29 HLA-DRB1, and 15 HLA-DQB1 alleles were identified. AFs and HFs of HLA-A, -B, and -DRB1 were similar to those reported previously. For the HLA-C locus, C*01:02 was the most common allele, followed by C*03:03, C*03:04, C*14:02, C*03:02, and C*07:02 (AF ≥7%). AFs of C*07:01 and C*07:06 were 0.16% and 3.18%, respectively. For the HLA-DQB1 locus, DQB1*03:01 was the most common allele, followed by DQB1*03:03, *03:02, *06:01, *05:01, *04:01, and *06:02 (AF ≥7%). AFs of DQB1*02:01 and DQB1*02:02 were 2.12% and 6.69%, respectively. HFs of A*33:03-C*07:06 and C*07:06-B*44:03 were 3.09% and 3.10%, respectively, while those of DRB1*07:01-DQB1*02:02 and DRB1*03:01-DQB1*02:01 were 6.61% and 2.04%, respectively. Conclusions This study reported AFs and HFs of HLA, including HLA-C and -DQB1, in Koreans by using high-resolution SBT. These data can be used to resolve ambiguous results of HLA typing for organ and hematopoietic stem cell transplantations. PMID:26131415

  20. Highly flexible distributions to fit multiple frequency financial returns

    NASA Astrophysics Data System (ADS)

    BenSaïda, Ahmed; Slim, Skander

    2016-01-01

    Financial data are usually studied via low flexible distributions, independently of the frequency of the data, due to their simplicity and analytical tractability. In this paper we analyze two highly flexible five-parameter distributions into fitting financial returns, these are the skewed generalized t (SGT) and the generalized hyperbolic (GH). Applications carried on two exchange rates (Euro-Dollar and Dollar-Yen), and two indexes (S&P 500 and Nikkei 225) over four frequencies: weekly, daily, 30-min and 5-min, confirm the superiority of the SGT and GH in approximating the distribution of a given data at a remarkable precision. Moreover, as we move from higher to lower frequency, the distribution's overall shape does indeed change radically, and the estimated parameters refute the tendency to normality, which calls into question the aggregational Gaussianity's stylized fact.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. Frequency distribution histograms for the rapid analysis of data

    NASA Technical Reports Server (NTRS)

    Burke, P. V.; Bullen, B. L.; Poff, K. L.

    1988-01-01

    The mean and standard error are good representations for the response of a population to an experimental parameter and are frequently used for this purpose. Frequency distribution histograms show, in addition, responses of individuals in the population. Both the statistics and a visual display of the distribution of the responses can be obtained easily using a microcomputer and available programs. The type of distribution shown by the histogram may suggest different mechanisms to be tested.

  4. Universal distribution of component frequencies in biological and technological systems.

    PubMed

    Pang, Tin Yau; Maslov, Sergei

    2013-04-01

    Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual systems, and their use frequencies vary over many orders of magnitude. We study this frequency distribution in genomes of ∼500 bacterial species and in over 2 million Linux computers and find that in both cases it is described by the same scale-free power-law distribution with an additional peak near the tail of the distribution corresponding to nearly universal components. We argue that the existence of a power law distribution of frequencies of components is a general property of any modular system with a multilayered dependency network. We demonstrate that the frequency of a component is positively correlated with its dependency degree given by the total number of upstream components whose operation directly or indirectly depends on the selected component. The observed frequency/dependency degree distributions are reproduced in a simple mathematically tractable model introduced and analyzed in this study. PMID:23530195

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

    PubMed

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

    PubMed Central

    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

    2013-01-01

    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. PMID:24273426

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2015-04-01

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

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

    PubMed

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

    2015-04-01

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

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

    PubMed Central

    Dabiri, Sasan; Ghadimi, Fatemeh; Firouzifar, Mohammadreza; Yazdani, Nasrin; Mohammad-Amoli, Mahsa; Vakili, Varasteh; Mahvi, Zahra

    2016-01-01

    Introduction Several lines of evidence support the contribution of autoimmune mechanisms in the pathogenesis of Meniere’s disease. The aim of this study was determining the association between HLA-Cw Alleles in patients with definite Meniere’s disease and patients with probable Meniere’s disease and a control group. Materials and Methods: HLA-Cw genotyping was performed in 23 patients with definite Meniere’s disease, 24 with probable Meniere’s disease, and 91 healthy normal subjects, using sequence specific primers polymerase chain reaction technique. The statistical analysis was performed using stata 8 software. Results: There was a significant association between HLA-Cw*04 and HLA-Cw*16 in both definite and probable Meniere’s disease compared to normal healthy controls. We observed a significant difference in HLA-Cw*12 frequencies between patients with definite Meniere’s disease compared to patients with probable Meniere’s disease (P=0.04). The frequency of HLA-Cw*18 is significantly higher in healthy controls (P=0.002). Conclusion: Our findings support the rule of HLA-Cw Alleles in both definite and probable Meniere’s disease. In addition, differences in HLA-Cw*12 frequency in definite and probable Meniere’s disease in our study’s population might indicate distinct immune and inflammatory mechanisms involved in each condition. PMID:27602337

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

    Dabiri, Sasan; Ghadimi, Fatemeh; Firouzifar, Mohammadreza; Yazdani, Nasrin; Mohammad-Amoli, Mahsa; Vakili, Varasteh; Mahvi, Zahra

    2016-01-01

    Introduction Several lines of evidence support the contribution of autoimmune mechanisms in the pathogenesis of Meniere’s disease. The aim of this study was determining the association between HLA-Cw Alleles in patients with definite Meniere’s disease and patients with probable Meniere’s disease and a control group. Materials and Methods: HLA-Cw genotyping was performed in 23 patients with definite Meniere’s disease, 24 with probable Meniere’s disease, and 91 healthy normal subjects, using sequence specific primers polymerase chain reaction technique. The statistical analysis was performed using stata 8 software. Results: There was a significant association between HLA-Cw*04 and HLA-Cw*16 in both definite and probable Meniere’s disease compared to normal healthy controls. We observed a significant difference in HLA-Cw*12 frequencies between patients with definite Meniere’s disease compared to patients with probable Meniere’s disease (P=0.04). The frequency of HLA-Cw*18 is significantly higher in healthy controls (P=0.002). Conclusion: Our findings support the rule of HLA-Cw Alleles in both definite and probable Meniere’s disease. In addition, differences in HLA-Cw*12 frequency in definite and probable Meniere’s disease in our study’s population might indicate distinct immune and inflammatory mechanisms involved in each condition.

  13. Correcting length-frequency distributions for imperfect detection

    USGS Publications Warehouse

    Breton, André R.; Hawkins, John A.; Winkelman, Dana L.

    2013-01-01

    Sampling gear selects for specific sizes of fish, which may bias length-frequency distributions that are commonly used to assess population size structure, recruitment patterns, growth, and survival. To properly correct for sampling biases caused by gear and other sources, length-frequency distributions need to be corrected for imperfect detection. We describe a method for adjusting length-frequency distributions when capture and recapture probabilities are a function of fish length, temporal variation, and capture history. The method is applied to a study involving the removal of Smallmouth Bass Micropterus dolomieu by boat electrofishing from a 38.6-km reach on the Yampa River, Colorado. Smallmouth Bass longer than 100 mm were marked and released alive from 2005 to 2010 on one or more electrofishing passes and removed on all other passes from the population. Using the Huggins mark–recapture model, we detected a significant effect of fish total length, previous capture history (behavior), year, pass, year×behavior, and year×pass on capture and recapture probabilities. We demonstrate how to partition the Huggins estimate of abundance into length frequencies to correct for these effects. Uncorrected length frequencies of fish removed from Little Yampa Canyon were negatively biased in every year by as much as 88% relative to mark–recapture estimates for the smallest length-class in our analysis (100–110 mm). Bias declined but remained high even for adult length-classes (≥200 mm). The pattern of bias across length-classes was variable across years. The percentage of unadjusted counts that were below the lower 95% confidence interval from our adjusted length-frequency estimates were 95, 89, 84, 78, 81, and 92% from 2005 to 2010, respectively. Length-frequency distributions are widely used in fisheries science and management. Our simple method for correcting length-frequency estimates for imperfect detection could be widely applied when mark–recapture data

  14. Os zygomaticum bipartitum: frequency distribution in major human populations

    PubMed Central

    HANIHARA, TSUNEHIKO; ISHIDA, HAJIME; DODO, YUKIO

    1998-01-01

    The frequency of the Os zygomaticum bipartitum was examined in major human populations around the world. Eastern Asians have a higher frequency of the bipartite zygomatic bone than any other geographical groups. The arctic peoples, Amerindians and the Oceanians, who all may have derived from eastern Asian population stocks, have a considerably low frequency of this trait. The frequency distribution from East/Southeast Asia to Africa and Europe through South/Central/West Asia suggests some clinality for the bipartite zygomatic bone. The second peak in the frequency is seen in Subsaharan Africa. The clinal variation with no identifiable regulation by subsistence patterns and environmental factors suggested a genetic background for the occurrence of the Os zygomaticum bipartitum. PMID:9723981

  15. Distribution of the CCR5delta32 allele (gene variant CCR5) in Rondônia, Western Amazonian region, Brazil

    PubMed Central

    de Farias, Josileide Duarte; Santos, Marlene Guimarães; de França, Andonai Krauze; Delani, Daniel; Tada, Mauro Shugiro; Casseb, Almeida Andrade; Simões, Aguinaldo Luiz; Engracia, Vera

    2012-01-01

    Since around 1723, on the occasion of its initial colonization by Europeans, Rondonia has received successive waves of immigrants. This has been further swelled by individuals from northeastern Brazil, who began entering at the beginning of the twentieth century. The ethnic composition varies across the state according to the various sites of settlement of each wave of immigrants. We analyzed the frequency of the CCR5Δ32 allele of the CCR5 chemokine receptor, which is considered a Caucasian marker, in five sample sets from the population. Four were collected in Porto Velho, the state capital and the site of several waves of migration. Of these, two, from the Hospital de Base were comprised of HB Mothers and HB Newborns presenting allele frequencies of 3.5% and 3.1%, respectively, a third from the peri-urban neighborhoods of Candelária/Bate-Estaca (1.8%), whereas a fourth, from the Research Center on Tropical Medicine/CEPEM (0.6%), was composed of malaria patients under treament. The fifth sample (3.4%) came from the inland Quilombola village of Pedras Negras. Two homozygous individuals (CCR5Δ32/CCR5Δ32) were detected among the HB Mother samples. The frequency of this allele was heterogeneous and higher where the European inflow was more pronounced. The presence of the allele in Pedras Negras revealed European miscegenation in a community largely comprising Quilombolas. PMID:22481870

  16. Fiber optic reference frequency distribution to remote beam waveguide antennas

    NASA Technical Reports Server (NTRS)

    Calhoun, Malcolm; Kuhnle, Paul; Law, Julius

    1995-01-01

    In the NASA/JPL Deep Space Network (DSN), radio science experiments (probing outer planet atmospheres, rings, gravitational waves, etc.) and very long-base interferometry (VLBI) require ultra-stable, low phase noise reference frequency signals at the user locations. Typical locations for radio science/VLBI exciters and down-converters are the cone areas of the 34 m high efficiency antennas or the 70 m antennas, located several hundred meters from the reference frequency standards. Over the past three years, fiber optic distribution links have replaced coaxial cable distribution for reference frequencies to these antenna sites. Optical fibers are the preferred medium for distribution because of their low attenuation, immunity to EMI/IWI, and temperature stability. A new network of Beam Waveguide (BWG) antennas presently under construction in the DSN requires hydrogen maser stability at tens of kilometers distance from the frequency standards central location. The topic of this paper is the design and implementation of an optical fiber distribution link which provides ultra-stable reference frequencies to users at a remote BWG antenna. The temperature profile from the earth's surface to a depth of six feet over a time period of six months was used to optimize the placement of the fiber optic cables. In-situ evaluation of the fiber optic link performance indicates Allan deviation on the order of parts in 10(exp -15) at 1000 and 10,000 seconds averaging time; thus, the link stability degradation due to environmental conditions still preserves hydrogen maser stability at the user locations. This paper reports on the implementation of optical fibers and electro-optic devices for distributing very stable, low phase noise reference signals to remote BWG antenna locations. Allan deviation and phase noise test results for a 16 km fiber optic distribution link are presented in the paper.

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

    PubMed

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

    2015-07-03

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

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

    PubMed

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

    2016-03-01

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

  19. Frequency distribution signatures and classification of within-object pixels

    PubMed Central

    Stow, Douglas A.; Toure, Sory I.; Lippitt, Christopher D.; Lippitt, Caitlin L.; Lee, Chung-rui

    2011-01-01

    The premise of geographic object-based image analysis (GEOBIA) is that image objects are composed of aggregates of pixels that correspond to earth surface features of interest. Most commonly, image-derived objects (segments) or objects associated with predefined land units (e.g., agricultural fields) are classified using parametric statistical characteristics (e.g., mean and standard deviation) of the within-object pixels. The objective of this exploratory study was to examine the between- and within-class variability of frequency distributions of multispectral pixel values, and to evaluate a quantitative measure and classification rule that exploits the full pixel frequency distribution of within object pixels (i.e., histogram signatures) compared to simple parametric statistical characteristics. High spatial resolution Quickbird satellite multispectral data of Accra, Ghana were evaluated in the context of mapping land cover and land use and socioeconomic status. Results show that image objects associated with land cover and land use types can have characteristic, non-normal frequency distributions (histograms). Signatures of most image objects tended to match closely the training signature of a single class or sub-class. Curve matching approaches to classifying multi-pixel frequency distributions were found to be slightly more effective than standard statistical classifiers based on a nearest neighbor classifier. PMID:22408575

  20. Randomness versus specifics for word-frequency distributions

    NASA Astrophysics Data System (ADS)

    Yan, Xiaoyong; Minnhagen, Petter

    2016-02-01

    The text-length-dependence of real word-frequency distributions can be connected to the general properties of a random book. It is pointed out that this finding has strong implications, when deciding between two conceptually different views on word-frequency distributions, i.e. the specific 'Zipf's-view' and the non-specific 'Randomness-view', as is discussed. It is also noticed that the text-length transformation of a random book does have an exact scaling property precisely for the power-law index γ = 1, as opposed to the Zipf's exponent γ = 2 and the implication of this exact scaling property is discussed. However a real text has γ > 1 and as a consequence γ increases when shortening a real text. The connections to the predictions from the RGF (Random Group Formation) and to the infinite length-limit of a meta-book are also discussed. The difference between 'curve-fitting' and 'predicting' word-frequency distributions is stressed. It is pointed out that the question of randomness versus specifics for the distribution of outcomes in case of sufficiently complex systems has a much wider relevance than just the word-frequency example analyzed in the present work.

  1. Similarity of Symbol Frequency Distributions with Heavy Tails

    NASA Astrophysics Data System (ADS)

    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.

  2. Distribution of MICB diversity in the Zhejiang Han population: PCR sequence-based typing for exons 2-6 and identification of five novel MICB alleles.

    PubMed

    Ying, Yanling; He, Yanmin; Tao, Sudan; Han, Zhedong; Wang, Wei; Chen, Nanying; He, Junjun; Zhang, Wei; He, Ji; Zhu, Faming; Lv, Hangjun

    2013-07-01

    The polymorphism of major histocompatibility complex class I chain-related gene B (MICB) and variations in MICB alleles in a variety of populations have been characterized using several genotyping approaches. In the present study, a novel polymerase chain reaction sequence-based typing (PCR-SBT) method was established for the genotyping of MICB exons 2-6, and the allelic frequency of MICB in the Zhejiang Han population was investigated. Among 400 unrelated healthy Han individuals from Zhejiang Province, China, a total of 20 MICB alleles were identified, of which MICB*005:02:01, MICB*002:01:01, and MICB*004:01:01 were the most predominant alleles, with frequencies of 0.57375, 0.1225, and 0.08375, respectively. Nine MICB alleles were detected on only one occasion, giving a frequency of 0.00125. Of the 118 distinct MICB ∼ HLA-B haplotypes identified, 42 showed significant linkage disequilibrium (P < 0.05). Haplotypes MICB*005:02:01 ∼ B*46:01, MICB*005:02:01 ∼ B*40:01, and MICB*008 ∼ B*58:01 were the most common haplotypes, with frequencies of 0.0978, 0.0761, and 0.0616, respectively. Five novel alleles, MICB*005:07, MICB*005:08, MICB*027, MICB*028, and MICB*029 were identified. Compared with the MICB*005:02:01 sequence, a G > A substitution was observed at nucleotide position 210 in MICB*005:07, and a 1,134 T > C substitution in MICB*005:08 and an 862 G > A substitution in MICB*027 were detected. In addition, it appears that MICB*028 probably arose from MICB*004:01:01 with an A to G substitution at position 1,147 in exon 6. MICB*029 had a G > T transversion at nucleotide position 730 in exon 4, compared with that of MICB*002:01:01. On the basis of the new PCR-SBT assay, these observed results demonstrated MICB allelic variations in the Zhejiang Han population.

  3. Distributed coupling and multi-frequency microwave accelerators

    DOEpatents

    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.

  4. Stabilized Fiber-Optic Distribution of Reference Frequency

    NASA Technical Reports Server (NTRS)

    Calhoun, Malcolm; Tjoelker, Robert; Diener, William; Dick, G. John; Wang, Rabi; Kirk, Albert

    2003-01-01

    An optoelectronic system distributes a reference signal of low noise and highly stabilized phase and frequency (100 MHz) from an atomic frequency standard to a remote facility at a distance up to tens of kilometers. The reference signal is transmitted to the remote station as amplitude modulation of an optical carrier signal propagating in an optical fiber. The stabilization scheme implemented in this system is intended particularly to suppress phase and frequency fluctuations caused by vibrations and by expansion and contraction of the optical fiber and other components in diurnal and seasonal heating and cooling cycles. The system (see figure) comprises several subsystems, the main one being (1) a hydrogen-maser or linear-ion-trap frequency standard in an environmentally controlled room in a signal-processing center (SPC), (2) a stabilized fiber-optic distribution assembly (SFODA), (3) a compensated sapphire oscillator (CSO) in an environmentally controlled room in the remote facility, (4) thermally stabilized distribution amplifiers and cabling from the environmentally controlled room to end users, and (5) performance- measuring equipment.

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

    PubMed

    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.

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

    PubMed Central

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

    2002-01-01

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

  7. The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference.

    PubMed

    Trolle, Thomas; McMurtrey, Curtis P; Sidney, John; Bardet, Wilfried; Osborn, Sean C; Kaever, Thomas; Sette, Alessandro; Hildebrand, William H; Nielsen, Morten; Peters, Bjoern

    2016-02-15

    HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8(+) T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8(+) T cell epitopes. PMID:26783342

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

    PubMed Central

    Amos, Christopher I.

    2015-01-01

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

  9. Distribution and genotype frequency of the C1431T and pro12ala polymorphisms of the peroxisome proliferator activator receptor gamma gene in an Iranian population

    PubMed Central

    Rooki, Hassan; Haerian, Monir-Sadat; Azimzadeh, Pedram; Ebrahimi, Mahmoud; Mirhafez, Reza; Ferns, Gordon; Ghayour-Mobarhan, Majid; Zali, Mohammad-Reza

    2013-01-01

    BACKGROUND: Peroxisome proliferator activator receptor gamma (PPARγ) is a nuclear transcription factor regulating multiple genes involved in cell growth, differentiation, carbohydrate and lipid metabolism and energy production. Several genetic variations in the PPARγ gene have been identified to be associated with diabetes, obesity, dyslipidemia, insulin resistance, metabolic syndrome and coronary artery disease. The present study was designed to explore the distribution of two common single nucleotide polymorphisms of the PPARγ gene (C1431T and Pro12Ala) in an Iranian population. MATERIALS AND METHODS: Genotype frequencies for these two polymorphisms were compared for 160 healthy Iranian individuals with reports from other populations. The Genotyping was performed using real-time polymerase chain reaction. RESULTS: The genotype distribution of the C1431T PPARγ polymorphism was 0.869 for the CC genotype, 0.119 for the CT genotype and 0.013 for uncommon TT genotype. Allelic frequencies were 0.93 for C and 0.07 for T allele respectively. For the Pro12Ala polymorphism of PPARγ gene, genotypic distributions and allelic frequencies were, 0.813 for CC, 0.181 for CG and 0.06 for GG and 0.903 for C and 0.097 for G respectively. Allelic and genotypic frequencies for both polymorphisms of PPARγ gene were in Hardy-Weinberg equilibrium. CONCLUSIONS: Iran is a country with an ethnically diverse population and a comparison of allelic and genotypic frequencies of PPARγ C1431T and Pro12Ala polymorphisms between our population and others showed significant differences. PMID:24497707

  10. Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class II BoLA-DRB3 allele.

    PubMed

    Takeshima, S-N; Miyasaka, T; Matsumoto, Y; Xue, G; Diaz, V de la Barra; Rogberg-Muñoz, A; Giovambattista, G; Ortiz, M; Oltra, J; Kanemaki, M; Onuma, M; Aida, Y

    2015-01-01

    Bovine leukocyte antigens (BoLAs) are used extensively as markers for bovine disease and immunological traits. In this study, we estimated BoLA-DRB3 allele frequencies using 888 cattle from 10 groups, including seven cattle breeds and three crossbreeds: 99 Red Angus, 100 Black Angus, 81 Chilean Wagyu, 49 Hereford, 95 Hereford × Angus, 71 Hereford × Jersey, 20 Hereford × Overo Colorado, 113 Holstein, 136 Overo Colorado, and 124 Overo Negro cattle. Forty-six BoLA-DRB3 alleles were identified, and each group had between 12 and 29 different BoLA-DRB3 alleles. Overo Negro had the highest number of alleles (29); this breed is considered in Chile to be an 'Old type' European Holstein Friesian descendant. By contrast, we detected 21 alleles in Holstein cattle, which are considered to be a 'Present type' Holstein Friesian cattle. Chilean cattle groups and four Japanese breeds were compared by neighbor-joining trees and a principal component analysis (PCA). The phylogenetic tree showed that Red Angus and Black Angus cattle were in the same clade, crossbreeds were closely related to their parent breeds, and Holstein cattle from Chile were closely related to Holstein cattle in Japan. Overall, the tree provided a thorough description of breed history. It also showed that the Overo Negro breed was closely related to the Holstein breed, consistent with historical data indicating that Overo Negro is an 'Old type' Holstein Friesian cattle. This allelic information will be important for investigating the relationship between major histocompatibility complex (MHC) and disease.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Towards the distribution network of time and frequency

    NASA Astrophysics Data System (ADS)

    Lipiński, M.; Krehlik, P.; Śliwczyński, Ł.; Buczek, Ł.; Kołodziej, J.; Nawrocki, J.; Nogaś, P.; Dunst, P.; Lemański, D.; Czubla, A.; Pieczerak, J.; Adamowicz, W.; Pawszak, T.; Igalson, J.; Binczewski, A.; Bogacki, W.; Ostapowicz, P.; Stroiński, M.; Turza, K.

    2014-05-01

    In the paper the genesis, current stage and perspectives of the OPTIME project are described. The main goal of the project is to demonstrate that the newdeveloped at AGH technology of fiber optic transfer of the atomic clocks reference signals is ready to be used in building the domestic Time and Frequency distribution network. In the first part we summarize the two-year continuous operation of 420 kmlong link connecting the Laboratory of Time and Frequency at Central Office of Measures GUM in Warsaw and Time Service Laboratory at Astrogeodynamic Obserwatory AOS in Borowiec near Poznan. For the first time, we are reporting the two year comparison of UTC(PL) and UTC(AOS) atomic timescales with this link, and we refer it to the results of comparisons performed by GPS-based methods. We also address some practical aspects of maintaining time and frequency dissemination over fiber optical network. In the second part of the paper the concept of the general architecture of the distribution network with two Reference Time and Frequency Laboratories and local repositories is proposed. Moreover the brief project of the second branch connecting repositories in Poznan Polish Supercomputing and Networking Center and Torun Nicolaus Copernicus University with the first end-users in Torun such as National Laboratory of Atomic, Molecular and Optical Physics and Nicolaus Copernicus Astronomical Center is described. In the final part the perspective of developing the network both in the domestic range as far as extention with the international connections possibilities are presented.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    2012-01-01

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

  15. Apparent LFE Magnitude-Frequency Distributions and the Tremor Source

    NASA Astrophysics Data System (ADS)

    Rubin, A. M.; Bostock, M. G.

    2015-12-01

    Over a decade since its discovery, it is disconcerting that we know so little about the kinematics of the tremor source. One could say we are hampered by low signal-to-noise ratio, but often the LFE signal is large and the "noise" is just other LFEs, often nearly co-located. Here we exploit this feature to better characterize the tremor source. A quick examination of LFE catalogs shows, unsurprisingly, that detected magnitudes are large when the background tremor amplitude is large. A simple interpretation is that small LFEs are missed when tremor is loud. An unanswered question is whether, in addition, there is a paucity of small LFEs when tremor is loud. Because we have both the LFE Green's function (from stacks) and some minimum bound on the overall LFE rate (from our catalogs), tremor waveforms provide a consistency check on any assumed magnitude-frequency (M-f) distribution. Beneath southern Vancouver Island, the magnitudes of >10^5 LFEs range from about 1.2-2.4 (Bostock et al. 2015). Interpreted in terms of a power-law distribution, the b-value is >5. But missed small events make even this large value only a lower bound. Binning by background tremor amplitude, and assuming a time-invariant M-f distribution, the b-value increases to >7, implying (e.g.) more than 10 million M>1.2 events for every M=2.2 event. Such numbers are inconsistent with the observed modest increase in tremor amplitude with LFE magnitude, as well as with geodetically-allowable slips. Similar considerations apply to exponential and log-normal moment-frequency distributions. Our preliminary interpretation is that when LFE magnitudes are large, the same portion of the fault is producing larger LFEs, rather than a greater rate of LFEs pulled from the same distribution. If correct, this distinguishes LFEs from repeating earthquakes, where larger background fault slip rates lead not to larger earthquakes but to more frequent earthquakes of similar magnitude. One possible explanation, that LFEs

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

    PubMed

    Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  17. Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe

    PubMed Central

    Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

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

    PubMed

    Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  19. Distribution selection for hydrologic frequency analysis using subsampling method

    NASA Astrophysics Data System (ADS)

    Das, S.

    2016-08-01

    This paper investigates the potential utility of subsampling, a resampling technique with the aid of a goodness of fit test to select the best distribution for frequency analysis. Subsampling draws samples (of smaller size) from the original sample without replacement. The performance of the methodology is assessed by applying the methodology to an observed annual maximum (AM) hydrologic data series. Several AM discharge series of different record lengths are used as case studies to determine the performance. Overall, it is found that the methodology is suitable for a longer data series and a good performance can be obtained when the subsample size is around half of the underlying data sample. The methodology has also outperformed the standard AD test in terms of effectively discriminating between distributions. All results indicate that the subsampling technique can be a promising tool in discriminating between distributions.

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

    PubMed

    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

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

    PubMed Central

    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

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

    PubMed

    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.

  3. Frequency distributions: from the sun to the earth

    NASA Astrophysics Data System (ADS)

    Crosby, N. B.

    2011-11-01

    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.

  4. Frequency dependence of microparticle charge in a radio frequency discharge with Margenau electron velocity distribution

    SciTech Connect

    Du, Cheng-Ran; Khrapak, Sergey A.; Antonova, Tetyana; Steffes, Bernd; Thomas, Hubertus M.; Morfill, Gregor E.

    2011-01-15

    rf discharges are widely used in complex plasma experiments. In this paper, we theoretically investigate the dependence of the particle floating potential on the discharge frequency, assuming the model Margenau expression for the electron velocity distribution function. In doing so we use the orbital motion limited cross section to calculate the electron flux to the particle and collision enhanced collection approximation for the ion flux to the particle. The floating potential is then obtained from the flux balance condition. It is shown that for typical plasma conditions in laboratory rf discharges, normalized floating potential grows with increase of the discharge frequency in collisionless regime and decreases in weakly collisional regime. However, variations in the floating potential are usually small when plasma parameters do not depend on the rf frequency.

  5. Ion energy distributions in dual frequency RF plasmas

    NASA Astrophysics Data System (ADS)

    Hatton, Peter; Rees, John; Bort, Sam; Seymour, Dave

    2015-09-01

    For many surface-processing applications involving plasmas operated at RF frequencies it has been found helpful to combine two sources of power operating at different frequencies. By choosing suitable input powers at the two frequencies and varying the phase relationship set between the two inputs, the energy distributions (IEDs) for the ions arriving at the target surface can be optimised. There have been, however, only a limited number of published reports of measured or modelled distributions. In the present work IEDs for both positive and negative ions formed in plasmas in argon and nitrous oxide have been measured for mass-identified ions in two different reactors, one of which is a parallel-plate, capacitatively-coupled, system and the other is an inductively-coupled system. Typical data for 13.56 and 27.1 MHz inputs are presented for a range of phase relationships. The IEDs show clearly significant differences between the data for different species of ions which result in part from the ion-molecule collisions occurring, particularly in the plasma/surface sheath regions.

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2016-09-01

    In this data article we present data on the distribution of alleles and genotypes of the interleukin (IL)-6 c.-174 G>C polymorphism (rs 1800795) in patients with coronary heart disease (CHD) in dependence of the incidence of new cardiovascular events (combined endpoint: myocardial infarction, stroke/TIA, cardiac death, death according to stroke) within three years follow-up. Moreover, we investigated putative associations between individual expression of IL-6 genotypes and IL-6 serum level. This investigation is a subanalysis of the article entitled "The Interleukin 6 c.-174 CC genotype is a predictor for new cardiovascular events in patients with coronary heart disease within three years follow-up" (ClinicalTrials.gov identifier: NCT01045070) (Reichert et al., 2016) [1]. PMID:27570807

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

    PubMed

    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

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

    PubMed

    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.

  11. Frequency doubling of Raman fiber lasers with random distributed feedback.

    PubMed

    Dontsova, E I; Kablukov, S I; Vatnik, I D; Babin, S A

    2016-04-01

    This Letter presents what we believe is the first experimental study of frequency doubling of a Raman fiber laser (RFL) with random distributed feedback (RDFB) in an MgO:PPLN crystal. We compared two laser configurations, each with a half-open cavity. The cavity contained either a broadband Sagnac mirror or a narrowband fiber Bragg grating (FBG). We found that spectral broadening in the studied configurations of the RDFB RFLs differed from that found in a conventional RFL with a linear cavity, as well as from each other. We also compared the second harmonic generation (SHG) efficiency for these three types of lasers. The highest SHG efficiency was obtained for the RDFB RFL with the FBG delivering >100  mW power at 654 nm. PMID:27192256

  12. Orthogonal Frequency-Division Multiplexed Quantum Key Distribution

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2014-02-01

    Umbilical cord blood (UCB) is a widely accepted source of progenitor cells, and now, many cord blood banks were established. Here, we analysed the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies, HLA matching possibilities for searching potential donors and outcome of UCB transplantations in Zhejiang cord blood bank of China. A total of 6384 UCB units were characterized for 17 HLA-A, 30 HLA-B and 13 HLA-DRB1 alleles at the first field resolution level. Additionally, B*14, B*15 and B*40 were typed to the second field level. A total of 1372 distinct A-B-DRB1 haplotypes were identified. The frequencies of 7 haplotypes were more than 1%, and 439 haplotypes were <0.01%. A*02-B*46-DRB1*09, A*33-B*58-DRB1*03 and A*30-B*13-DRB1*07 were the most common haplotypes, with frequencies of 4.4%, 3.3%, and 2.9%, respectively. Linkage disequilibrium(LD) analysis showed that there were 83 A-B, 106 B-DRB1, 54 A-DRB1 haplotypes with positive LD, in which 51 A-B, 60 B-DRB1, 32 A-DRB1 haplotypes exhibited a significant LD (P < 0.05). In 682 search requests, 12.9%, 40.0% and 42.7% of patients were found to have 6 of 6, 5 of 6 and 4 of 6 HLA-A, HLA-B and HLA-DRB1 matching donors, respectively. A total of 30 UCB units were transplanted to 24 patients (3 patients not evaluated due to early death); 14 of 21 patients (66.7%) engrafted. This study reveals the HLA distribution and its transplantation application in the cord blood bank of Zhejiang province. These data can help to select potential UCB donors for transplantation and used to assess the scale of new cord blood banking endeavours.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Frequencies and ethnic distribution of ABO and Rh(D) blood groups in Mauritania: results of first nationwide study.

    PubMed

    Hamed, C T; Bollahi, M A; Abdelhamid, I; Med Mahmoud, M A; Ba, B; Ghaber, S; Habti, N; Houmeida, A

    2012-04-01

    There is no data available on the ABO/Rh(D) frequencies in the Mauritanian population. We retrospectively analysed records of a 5-year database that contained ABO/Rh phenotype and ethnic origin of 10 116 volunteers giving blood at the national blood transfusion centre to derive the frequencies of ABO/Rh(D) groups in the Mauritanian population. The two race categories in the country and their sub-ethnic groups: the Moors (whites and black) and the black Africans (Pulhars, Soninkes and Wolof) were included in this study. Globally, group O had the highest frequency (49.10%) followed by A (28.28%), B (18.56%) and AB (4.05%). This order more common in North African populations was found in four of the five ethnic groups composing our population. Allele frequencies were, respectively, 70.20%, 17.74% and 12.04% giving the same order of O > A > B. We observed no significant variation in these frequencies between the different ethnic groups. Rhesus study showed that with a percentage of 94.23% Rh(D) positive is by far the most prevalent, while Rh(D) negative is present only in 5.77% of the total population. This frequency distribution supports the mixed-race composition of the Mauritanian population.

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

    ERIC Educational Resources Information Center

    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)

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

    PubMed

    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

  18. Film thickness frequency distribution of different vehicles determines sunscreen efficacy

    NASA Astrophysics Data System (ADS)

    Sohn, Myriam; Hêche, Adeline; Herzog, Bernd; Imanidis, Georgios

    2014-11-01

    Sun protection factor (SPF) frequently differs between sunscreens containing the same composition of ultraviolet (UV) filters that primarily define sunscreen efficacy. We tested the hypothesis that the thickness frequency distribution of the sunscreen film is also responsible for and can explain the divergence in the measured SPF. For this, we developed a method to measure film thickness from the difference of topography before and after application of 2 mg/cm2 of sunscreen on pig ear epidermal membrane. The influence of five vehicle formulations and of application pressure and spreading time on mean thickness (S), S to median ratio, and SPF in vitro was investigated. The vehicle had a significant impact, low vehicle viscosity resulting in a smaller S, larger S to median ratio, and lower SPF in vitro than high viscosity; continuous oil phase produced the largest S and SPF values. A long spreading time reduced S and SPF and increased application pressure reduced SPF. There was a positive correlation between S and SPF in vitro, underlining the relevance of film thickness for interpreting UV protection differences of formulations with the same filter composition. This work demonstrated a strong influence of vehicle and application conditions on sunscreen efficacy arising from differences in film thickness distribution.

  19. Film thickness frequency distribution of different vehicles determines sunscreen efficacy.

    PubMed

    Sohn, Myriam; Hêche, Adeline; Herzog, Bernd; Imanidis, Georgios

    2014-11-01

    Sun protection factor (SPF) frequently differs between sunscreens containing the same composition of ultraviolet (UV) filters that primarily define sunscreen efficacy. We tested the hypothesis that the thickness frequency distribution of the sunscreen film is also responsible for and can explain the divergence in the measured SPF. For this, we developed a method to measure film thickness from the difference of topography before and after application of of sunscreen on pig ear epidermal membrane. The influence of five vehicle formulations and of application pressure and spreading time on mean thickness ( ), to median ratio, and SPF in vitro was investigated. The vehicle had a significant impact, low vehicle viscosity resulting in a smaller , larger to median ratio, and lower SPF in vitro than high viscosity; continuous oil phase produced the largest and SPF values. A long spreading time reduced and SPF and increased application pressure reduced SPF. There was a positive correlation between and SPF in vitro, underlining the relevance of film thickness for interpreting UV protection differences of formulations with the same filter composition. This work demonstrated a strong influence of vehicle and application conditions on sunscreen efficacy arising from differences in film thickness distribution.

  20. Distribution of the HLA class I allele in chronic hepatitis C and its association with serum ALT level in chronic hepatitis C.

    PubMed

    Kondo, Yasuteru; Kobayashi, Koju; Kobayashi, Tomoo; Shiina, Masaaki; Ueno, Yoshiyuki; Satoh, Takaomi; Shimosegawa, Tooru

    2003-10-01

    An essential process for resolution of viral infections is the efficient recognition and elimination of intracellular virus. Recognition of viral antigens in the form of short peptides associated with HLA class I molecule is a major task of CD8+ cytotoxic T lymphocytes. In this study, we have evaluated the frequency of the HLA class I alleles in patients with chronic hepatitis C. HLA-B51, -B52, -B55, -B56, -B61, B70, -Cw1, -Cw3, and -Cw4 are less frequent in patients with chronic hepatitis C than in Japanese individuals. The frequency of HLA-A2 is slightly lower in the patients but tends to be higher in patients with normal alanine aminotransferase (ALT) level than in those with elevated ALT level (p = 0.07). Other HLA alleles are not significantly different between two groups. Comparison of HLA homozygosity at HLA-A and -B or -C or at two or three loci did not show a significant association with levels of serum ALT or with the clinical outcome of interferon therapy in patients with hepatitis C. These results suggest a possibility that the alterations of host response, which depends on genetic background, influence disease activities of HCV infection.

  1. Sensitivity of rat inferior colliculus neurons to frequency distributions.

    PubMed

    Herrmann, Björn; Parthasarathy, Aravindakshan; Han, Emily X; Obleser, Jonas; Bartlett, Edward L

    2015-11-01

    Stimulus-specific adaptation refers to a neural response reduction to a repeated stimulus that does not generalize to other stimuli. However, stimulus-specific adaptation appears to be influenced by additional factors. For example, the statistical distribution of tone frequencies has recently been shown to dynamically alter stimulus-specific adaptation in human auditory cortex. The present study investigated whether statistical stimulus distributions also affect stimulus-specific adaptation at an earlier stage of the auditory hierarchy. Neural spiking activity and local field potentials were recorded from inferior colliculus neurons of rats while tones were presented in oddball sequences that formed two different statistical contexts. Each sequence consisted of a repeatedly presented tone (standard) and three rare deviants of different magnitudes (small, moderate, large spectral change). The critical manipulation was the relative probability with which large spectral changes occurred. In one context the probability was high (relative to all deviants), while it was low in the other context. We observed larger responses for deviants compared with standards, confirming previous reports of increased response adaptation for frequently presented tones. Importantly, the statistical context in which tones were presented strongly modulated stimulus-specific adaptation. Physically and probabilistically identical stimuli (moderate deviants) in the two statistical contexts elicited different response magnitudes consistent with neural gain changes and thus neural sensitivity adjustments induced by the spectral range of a stimulus distribution. The data show that already at the level of the inferior colliculus stimulus-specific adaptation is dynamically altered by the statistical context in which stimuli occur. PMID:26354316

  2. High CYP2A6 Enzyme Activity as Measured by a Caffeine Test and Unique Distribution of CYP2A6 Variant Alleles in Ethiopian Population

    PubMed Central

    Djordjevic, Natasa; Carrillo, Juan Antonio; Makonnen, Eyasu; Bertilsson, Leif; Ingelman-Sundberg, Magnus

    2014-01-01

    Abstract CYP2A6 metabolizes clinically relevant drugs, including antiretroviral and antimalarial drugs of major public health importance for the African populations. CYP2A6 genotype–phenotype relationship in African populations, and implications of geographic differences on enzyme activity, remain to be investigated. We evaluated the influence of CYP2A6 genotype, geographical differences, gender, and cigarette smoking on enzyme activity, using caffeine as a probe in 100 healthy unrelated Ethiopians living in Ethiopia, and 72 living in Sweden. CYP2A6 phenotype was estimated by urinary 1,7-dimethyluric acid (17U)/1,7-dimethylxanthine or paraxanthine (17X) ratio. The frequencies of CYP2A6*1B, *1D, *2, *4, *9, and *1x2 in Ethiopians were 31.3, 29.4, 0.6, 0.6, 2.8, and 0.3%, respectively. The overall mean±SD for log 17U/17X was 0.12±0.24 and coefficient of variation 199%. No significant difference in the mean log 17U/17X ratio between Ethiopians living in Sweden versus Ethiopia was observed. Analysis of variance revealed CYP2A6 genotype (p=0.04, F=2.01) but not geographical differences, sex, or cigarette smoking as predictors of CYP2A6 activity. Importantly, the median (interquartile range) of 17U/17X ratio in Ethiopians 1.35 (0.99 to 1.84) was 3- and 11-fold higher than the previously reported value in Swedes 0.52 (0.27 to 1.00) and Koreans 0.13 (0.0 to 0.35), respectively (Djordjevic et al., 2013). Taken together, we report here the relevance of CYP2A6 genotype for enzyme activity in this Ethiopian sample, as well as high CYP2A6 activity and unique distribution of the CYP2A6 variant alleles in Ethiopians as compared other populations described hitherto. Because Omics biomarker research is rapidly accelerating in Africa, CYP2A6 pharmacogenetics and clinical pharmacology observations reported herein for the Ethiopian populations have clinical and biological importance to plan for future rational therapeutics efforts in the African continent as well as therapeutics

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

    PubMed

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

    2015-02-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-08-01

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

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

    PubMed

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

    2014-08-01

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

  7. The frequency distribution of daily global irradiation at Kumasi

    SciTech Connect

    Akuffo, F.O.; Brew-Hammond, A. )

    1993-02-01

    Cumulative frequency distribution curves (CDC) for daily global irradiation on the horizontal produced by Liu and Jordan in 1963 have until recently been considered to have universal validity. Results obtained by Saunier et al. in 1987 and Ideriah and Suleman in 1989 for two tropical locations, Ibadan in Nigeria and Bangkok in Thailand, respectively, have thrown into question the universal validity of the Liu and Jordan generalized CDC. Saunier et al., in particular, showed that their results disagreed with the generalized CDC mainly because of differences in the values of the maximum clearness index (Kmax), as well as the underlying probability density functions. Consequently, they proposed two expressions for determining Kmax and probability densities in tropical locations. This paper presents the results of statistical analysis of daily global irradiation for Kumasi, Ghana, also a tropical location. The results show that the expressions of Saunier et al. provide a better description of the observations than the generalized CDC and, in particular, the empirical equation for Kmax may be valid for Kumasi. Furthermore, the results show that the values of the minimum clearness index (Kmin) for Kumasi are much higher than the generally accepted value of 0.05 for overcast sky conditions. A comparison of the results for Kumasi and Ibadan shows that there is satisfactory agreement when the values of Kmax and Kmin are comparable; in cases where there are discrepancies in the Kmax and Kmin values, the CDC also disagree. 13 refs., 3 figs., 5 tabs.

  8. On the frequency-magnitude distribution of converging boundaries

    NASA Astrophysics Data System (ADS)

    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.

  9. Frequency and Spatial Distribution of Environmental Campylobacter spp.

    PubMed Central

    Brown, P. E.; Christensen, O. F.; Clough, H. E.; Diggle, P. J.; Hart, C. A.; Hazel, S.; Kemp, R.; Leatherbarrow, A. J. H.; Moore, A.; Sutherst, J.; Turner, J.; Williams, N. J.; Wright, E. J.; French, N. P.

    2004-01-01

    Humans are exposed to Campylobacter spp. in a range of sources via both food and environmental pathways. For this study, we explored the frequency and distribution of thermophilic Campylobacter spp. in a 10- by 10-km square rural area of Cheshire, United Kingdom. The area contains approximately 70, mainly dairy, farms and is used extensively for outdoor recreational activities. Campylobacter spp. were isolated from a range of environmental samples by use of a systematic sampling grid. Livestock (mainly cattle) and wildlife feces and environmental water and soil samples were cultured, and isolates were presumptively identified by standard techniques. These isolates were further characterized by PCR. Campylobacter jejuni was the most prevalent species in all animal samples, ranging from 11% in samples from nonavian wildlife to 36% in cattle feces, and was isolated from 15% of water samples. Campylobacter coli was commonly found in water (17%) and sheep (21%) samples, but rarely in other samples. Campylobacter lari was recovered from all sample types, with the exception of sheep feces, and was found in moderate numbers in birds (7%) and water (5%). Campylobacter hyointestinalis was only recovered from cattle (7%) and birds (1%). The spatial distribution and determinants of C. jejuni in cattle feces were examined by the use of model-based spatial statistics. The distribution was consistent with very localized within-farm or within-field transmission and showed little evidence of any larger-scale spatial dependence. We concluded that there is a potentially high risk of human exposure to Campylobacter spp., particularly C. jejuni, in the environment of our study area. The prevalence and likely risk posed by C. jejuni-positive cattle feces in the environment diminished as the fecal material aged. After we took into account the age of the fecal material, the absence or presence of rain, and the presence of bird feces, there was evidence of significant variation in the

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

    PubMed Central

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

    2011-01-01

    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. PMID:23136478

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

    PubMed

    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.

  12. Effect of photogrammetric reading error on slope-frequency distributions. [obtained from Apollo 17 mission

    NASA Technical Reports Server (NTRS)

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

    1973-01-01

    The effect of reading error on two hypothetical slope frequency distributions and two slope frequency distributions from actual lunar data in order to ensure that these errors do not cause excessive overestimates of algebraic standard deviations for the slope frequency distributions. The errors introduced are insignificant when the reading error is small and the slope length is large. A method for correcting the errors in slope frequency distributions is presented and applied to 11 distributions obtained from Apollo 15, 16, and 17 panoramic camera photographs and Apollo 16 metric camera photographs.

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

    PubMed Central

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

    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 in Chilean 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 vacA 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 m2 recedes H Pylori strain distribution in Spain and Portugal. PMID:16419167

  14. Dual matrilineal geographic distribution of Korean type 2 diabetes mellitus-associated -11,377 G adiponectin allele.

    PubMed

    Choi, Jee-Hye; Min, Na Young; Park, Sang Kil; Gavaachimed, Lkhagvasuren; Ko, Young Jong; Han, Sung Hoon; Kim, Kyung Yong; Kim, Kijung; Lee, Kwang Ho; Park, Ae Ja

    2014-12-01

    The present study was performed to identify the susceptible single nucleotide polymorphisms (SNPs) for the prediction of Korean type 2 diabetes mellitus (T2DM) and to clarify the matrilineal origin of Korean T2DM‑specific SNPs. Fourteen SNPs from the adiponectin (ADIPOQ), hepatocyte nuclear factor 4α, phosphoenolpyruvate carboxykinase 1 and glucokinase genes in the Korean population were analyzed. Only one SNP, ‑11,377 C/G on the ADIPOQ gene, was finally determined to be responsible for the incidence of Korean T2DM (P=0.028). The G‑T‑T‑A haplotype at positions ‑11,377, +45, +276 and +349 on the ADIPOQ gene was also associated with a high incidence of Korean T2DM (P=0.023). In addition, the susceptibility of Korean individuals to T2DM appears to be affected by their matrilineal origin. Of note, the group of Southern origin, consisting of mitochondrial DNA macrohaplogroups F and R, was predisposed to T2DM, whereas the group of Northern origin, consisting of haplogroups A and Y, was resistant to T2DM. This implied that the differential genetics between the two groups, which were formed from the initial peopling of the proto‑Korean population via Southern and Northern routes to the present time, may explain their differing susceptibility to T2DM. In conclusion, from Southern Asia Northward, a matrilineal origin of Korean individuals appears to be responsible for the prevalence of Korean T2DM caused by the ‑11,377 G allele.

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

    PubMed

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

    2012-09-01

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

  16. Features of electromagnetic radiation time-and-frequency fluctuation intensity distributions from human brain structures.

    PubMed

    Kublanov, V S; Gasilov, V L; Kazakov, Y E

    2000-01-01

    Time-and-frequency fluctuation intensity distributions' analysis is made of the electromagnetic radiation obtained from deep human brain structures. The role of monitoring the distribution changes due to various cerebral circulation disorders is explained.

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

    SciTech Connect

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

    1993-01-01

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

  18. The Effects of Frequency, Distribution, Mode of Presentation, and First Language on Learning an Artificial Language

    ERIC Educational Resources Information Center

    Miyata, Munehiko

    2011-01-01

    This dissertation presents results from a series of experiments investigating adult learning of an artificial language and the effects that input frequency (high vs. low token frequency), frequency distribution (skewed vs. balanced), presentation mode (structured vs. scrambled), and first language (English vs. Japanese) have on such learning.…

  19. Investigation of effect of excitation frequency on electron energy distribution functions in low pressure radio frequency bounded plasmas

    SciTech Connect

    Bhattacharjee, Sudeep; Lafleur, Trevor; Charles, Christine; Boswell, Rod

    2011-07-15

    Particle in cell (PIC) simulations are employed to investigate the effect of excitation frequency {omega} on electron energy distribution functions (EEDFs) in a low pressure radio frequency (rf) discharge. The discharge is maintained over a length of 0.10 m, bounded by two infinite parallel plates, with the coherent heating field localized at the center of the discharge over a distance of 0.05 m and applied perpendicularly along the y and z directions. On varying the excitation frequency f (={omega}/2{pi}) in the range 0.01-50 MHz, it is observed that for f {<=} 5 MHz the EEDF shows a trend toward a convex (Druyvesteyn-like) distribution. For f > 5 MHz, the distribution resembles more like a Maxwellian with the familiar break energy visible in most of the distributions. A prominent ''hot tail'' is observed at f{>=} 20 MHz and the temperature of the tail is seen to decrease with further increase in frequency (e.g., at 30 MHz and 50 MHz). The mechanism for the generation of the ''hot tail'' is considered to be due to preferential transit time heating of energetic electrons as a function of {omega}, in the antenna heating field. There exists an optimum frequency for which high energy electrons are maximally heated. The occurrence of the Druyvesteyn-like distributions at lower {omega} may be explained by a balance between the heating of the electrons in the effective electric field and elastic cooling due to electron neutral collision frequency {nu}{sub en}; the transition being dictated by {omega} {approx} 2{pi}{nu}{sub en}.

  20. Investigation of effect of excitation frequency on electron energy distribution functions in low pressure radio frequency bounded plasmas

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, Sudeep; Lafleur, Trevor; Charles, Christine; Boswell, Rod

    2011-07-01

    Particle in cell (PIC) simulations are employed to investigate the effect of excitation frequency ω on electron energy distribution functions (EEDFs) in a low pressure radio frequency (rf) discharge. The discharge is maintained over a length of 0.10 m, bounded by two infinite parallel plates, with the coherent heating field localized at the center of the discharge over a distance of 0.05 m and applied perpendicularly along the y and z directions. On varying the excitation frequency f (=ω/2π) in the range 0.01-50 MHz, it is observed that for f ≤ 5 MHz the EEDF shows a trend toward a convex (Druyvesteyn-like) distribution. For f > 5 MHz, the distribution resembles more like a Maxwellian with the familiar break energy visible in most of the distributions. A prominent "hot tail" is observed at f ≥ 20 MHz and the temperature of the tail is seen to decrease with further increase in frequency (e.g., at 30 MHz and 50 MHz). The mechanism for the generation of the "hot tail" is considered to be due to preferential transit time heating of energetic electrons as a function of ω, in the antenna heating field. There exists an optimum frequency for which high energy electrons are maximally heated. The occurrence of the Druyvesteyn-like distributions at lower ω may be explained by a balance between the heating of the electrons in the effective electric field and elastic cooling due to electron neutral collision frequency νen; the transition being dictated by ω ˜ 2πνen.

  1. The Size Frequency Distribution of Small Main-Belt Asteroids

    NASA Technical Reports Server (NTRS)

    Burt, Brian J.; Trilling, David E.; Hines, Dean C.; Stapelfeldt, Karl R.; Rebull, Luisa M.; Fuentes, Cesar I.; Hulsebus, Alan

    2012-01-01

    The asteroid size distribution informs us about the formation and composition of the Solar System. We build on our previous work in which we harvest serendipitously observed data of the Taurus region and measure the brightness and size distributions of Main-belt asteroids. This is accomplished with the highly sensitive MIPS 24 micron channel. We expect to catalog 104 asteroids, giving us a statistically significant data set. Results from this investigation will allow us to characterize the total population of small, Main-belt asteroids. Here we will present new results on the completeness of our study; on the presence of size distribution variations with inclination and radial distance in the belt; and early result on other archival fields.

  2. Distribution of mating-type alleles and M13 PCR markers in the black leaf spot fungus Mycosphaerella fijiensis of bananas in Brazil.

    PubMed

    Queiroz, C B; Miranda, E C; Hanada, R E; Sousa, N R; Gasparotto, L; Soares, M A; Silva, G F

    2013-02-08

    The fungus Mycosphaerella fijiensis is the causative agent of black sigatoka, which is one of the most destructive diseases of banana plants. Infection with this pathogen results in underdeveloped fruit, with no commercial value. We analyzed the distribution of the M. fijiensis mating-type system and its genetic variability using M13 phage DNA markers. We found a 1:1 distribution of mating-type alleles, indicating MAT1-1 and MAT1-2 idiomorphs. A polymorphism analysis using three different primers for M13 markers showed that only the M13 minisatellite primers generated polymorphic products. We then utilized this polymorphism to characterize 40 isolates from various Brazilian states. The largest genetic distances were found between isolates from the same location and between isolates from different parts of the country. Therefore, there was no correlation between the genetic similarity and the geographic origin of the isolates. The M13 marker was used to generate genetic fingerprints for five isolates; these fingerprints were compared with the band profiles obtained from inter-simple sequence repeat (UBC861) and inter-retrotransposon amplified polymorphism analyses. We found that the M13 marker was more effective than the other two markers for differentiating these isolates.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  4. Frequency-wavenumber processing for infrasound distributed arrays.

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2015-09-01

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

  7. Frequencies of immune hypersensitivity reaction-associated HLA class I alleles in healthy South African Indian and mixed ancestry populations determined by a novel real-time PCR assay.

    PubMed

    Loubser, S; Paximadis, M; Gentle, N; Puren, A; Gray, C M; Tiemessen, C T

    2014-10-01

    We have determined the frequencies of human leucocyte antigen (HLA)-B*57:01, HLA-B*35:05, HLA-C*04 and HLA-C*08 in healthy individuals of South African Indian (SAI) ethnicity (n = 50) and South African mixed (SAM) ancestry (n = 50) using real-time allele-specific polymerase chain reaction (AS-PCR) assay. HLA-B*57:01 associates with immune hypersensitivity reaction (IHR) in individuals exposed to abacavir (ABC), while nevirapine (NVP) IHR associates with HLA-B*35:05, HLA-C*04 and HLA-C*08. Real-time AS-PCR assays typically use less DNA, are more cost-effective and rapid compared with conventional genotyping methods, such as sequence-based typing (SBT). The assay was developed using samples of known HLA class I genotype and subsequently applied to the SAI and SAM samples. HLA-B*57:01 was detected in SAM and SAI populations at frequencies of 8.0% and 12.0%, respectively, while HLA-B*35:05 was not found in SAI individuals, but was present in 6.0% of SAM individuals. HLA-C*04 was detected in 22.0% and 24.0% of SAM and SAI individuals, respectively, while 10.0% and 8.0% of SAM and SAI individuals, respectively, were HLA-C*08 positive. This study reports the development of a novel real-time AS-PCR assay to identify HLA class I alleles associated with ABC and NVP IHR and has established the frequencies of these alleles present in healthy SAI and SAM populations. Using South African demographic data, our hypothetical analysis suggests that a substantial number of individuals would benefit from the assay.

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

    PubMed

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

    2015-09-01

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

  9. Construction Learning as a Function of Frequency, Frequency Distribution, and Function

    ERIC Educational Resources Information Center

    Ellis, Nick C.; Ferreira-Junior, Fernando

    2009-01-01

    This article considers effects of construction frequency, form, function, and prototypicality on second language acquisition (SLA). It investigates these relationships by focusing on naturalistic SLA in the European Science Foundation corpus (Perdue, 1993) of the English verb-argument constructions (VACs): verb locative (VL), verb object locative…

  10. Reviving oscillation with optimal spatial period of frequency distribution in coupled oscillators

    NASA Astrophysics Data System (ADS)

    Deng, Tongfa; Liu, Weiqing; Zhu, Yun; Xiao, Jinghua; Kurths, Jürgen

    2016-09-01

    The spatial distributions of system's frequencies have significant influences on the critical coupling strengths for amplitude death (AD) in coupled oscillators. We find that the left and right critical coupling strengths for AD have quite different relations to the increasing spatial period m of the frequency distribution in coupled oscillators. The left one has a negative linear relationship with m in log-log axis for small initial frequency mismatches while remains constant for large initial frequency mismatches. The right one is in quadratic function relation with spatial period m of the frequency distribution in log-log axis. There is an optimal spatial period m0 of frequency distribution with which the coupled system has a minimal critical strength to transit from an AD regime to reviving oscillation. Moreover, the optimal spatial period m0 of the frequency distribution is found to be related to the system size √{ N } . Numerical examples are explored to reveal the inner regimes of effects of the spatial frequency distribution on AD.

  11. High-Frequency ac Power-Distribution System

    NASA Technical Reports Server (NTRS)

    Hansen, Irving G.; Mildice, James

    1987-01-01

    Loads managed automatically under cycle-by-cycle control. 440-V rms, 20-kHz ac power system developed. System flexible, versatile, and "transparent" to user equipment, while maintaining high efficiency and low weight. Electrical source, from dc to 2,200-Hz ac converted to 440-V rms, 20-kHz, single-phase ac. Power distributed through low-inductance cables. Output power either dc or variable ac. Energy transferred per cycle reduced by factor of 50. Number of parts reduced by factor of about 5 and power loss reduced by two-thirds. Factors result in increased reliability and reduced costs. Used in any power-distribution system requiring high efficiency, high reliability, low weight, and flexibility to handle variety of sources and loads.

  12. Linkage disequilibrium in the insulin gene region: size variation at the 5' flanking polymorphism and bimodality among "class I" alleles.

    PubMed Central

    McGinnis, R. E.; Spielman, R. S.

    1994-01-01

    The 5' flanking polymorphism (5'FP), a hypervariable region at the 5' end of the insulin gene, has "class 1" alleles (650-900 bp long) that are in positive linkage disequilibrium with insulin-dependent diabetes mellitus (IDDM). We report that precise sizing of the 5'FP yields a bimodal frequency distribution of class 1 allele lengths. Class 1 alleles belonging to the lower component (650-750 bp) of the bimodal distribution were somewhat more highly associated with IDDM than were alleles from the upper component (760-900 bp), but the difference was not statistically significant. We also examined 5'FP length variation in relation to allelic variation at nearby polymorphisms. At biallelic RFLPs on both sides of the 5'FP, we found that one allele exhibits near-total association with the upper component of the 5'FP class 1 distribution. Such associations represent a little-known but potentially widespread form of linkage disequilibrium. In this type of disequilibrium, a flanking allele has near-complete association with a single mode of VNTR alleles whose lengths represent consecutive numbers of tandem repeats (CNTR). Such extreme disequilibrium between a CNTR mode and flanking alleles may originate and persist because length mutations at some VNTR loci usually add or delete only one or two repeat units. PMID:7915880

  13. Trinucleotide repeats at the FRAXF locus: Frequency and distribution in the general population

    SciTech Connect

    Holden, J.J.A.; Walker, M.

    1996-08-09

    FRAXF the third X-chromosomal fragile site to be cloned, has been shown to harbor a polymorphic compound triplet array: (GC-CGTC){sub n} (GCC){sub n}. Expansion and methylation of the GCC-repeat and the neighboring CpG-rich region result in chromosomal fragility. DNAs from 500 anonymous consecutive newborn males were examined to determine the incidence of various repeat numbers. The range of repeats was from 10-38, with the most common alleles having 14 (52.7%), 12 (16.6%), 21 (9.0%), and 22 (5.2%) triplets. Based on the distribution of repeat numbers, we suggest that the 21-repeat allele resulted from hairpin formation involving 7 GCC-repeats in a 14-repeat allele, accompanied by polymerase slippage. Examination of dinucleotide repeats near the FRAXF repeat will be important in testing this hypothesis. Since the clinical phenotype, if any, of FRAXF is unknown, this database will also be valuable for comparisons with repeat numbers in individuals from special populations. 20 refs., 1 fig., 1 tab.

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

    PubMed

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

    2010-10-01

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

  15. Text mixing shapes the anatomy of rank-frequency distributions

    NASA Astrophysics Data System (ADS)

    Williams, Jake Ryland; Bagrow, James P.; Danforth, Christopher M.; Dodds, Peter Sheridan

    2015-05-01

    Natural languages are full of rules and exceptions. One of the most famous quantitative rules is Zipf's law, which states that the frequency of occurrence of a word is approximately inversely proportional to its rank. Though this "law" of ranks has been found to hold across disparate texts and forms of data, analyses of increasingly large corpora since the late 1990s have revealed the existence of two scaling regimes. These regimes have thus far been explained by a hypothesis suggesting a separability of languages into core and noncore lexica. Here we present and defend an alternative hypothesis that the two scaling regimes result from the act of aggregating texts. We observe that text mixing leads to an effective decay of word introduction, which we show provides accurate predictions of the location and severity of breaks in scaling. Upon examining large corpora from 10 languages in the Project Gutenberg eBooks collection, we find emphatic empirical support for the universality of our claim.

  16. Text mixing shapes the anatomy of rank-frequency distributions.

    PubMed

    Williams, Jake Ryland; Bagrow, James P; Danforth, Christopher M; Dodds, Peter Sheridan

    2015-05-01

    Natural languages are full of rules and exceptions. One of the most famous quantitative rules is Zipf's law, which states that the frequency of occurrence of a word is approximately inversely proportional to its rank. Though this "law" of ranks has been found to hold across disparate texts and forms of data, analyses of increasingly large corpora since the late 1990s have revealed the existence of two scaling regimes. These regimes have thus far been explained by a hypothesis suggesting a separability of languages into core and noncore lexica. Here we present and defend an alternative hypothesis that the two scaling regimes result from the act of aggregating texts. We observe that text mixing leads to an effective decay of word introduction, which we show provides accurate predictions of the location and severity of breaks in scaling. Upon examining large corpora from 10 languages in the Project Gutenberg eBooks collection, we find emphatic empirical support for the universality of our claim.

  17. Text mixing shapes the anatomy of rank-frequency distributions.

    PubMed

    Williams, Jake Ryland; Bagrow, James P; Danforth, Christopher M; Dodds, Peter Sheridan

    2015-05-01

    Natural languages are full of rules and exceptions. One of the most famous quantitative rules is Zipf's law, which states that the frequency of occurrence of a word is approximately inversely proportional to its rank. Though this "law" of ranks has been found to hold across disparate texts and forms of data, analyses of increasingly large corpora since the late 1990s have revealed the existence of two scaling regimes. These regimes have thus far been explained by a hypothesis suggesting a separability of languages into core and noncore lexica. Here we present and defend an alternative hypothesis that the two scaling regimes result from the act of aggregating texts. We observe that text mixing leads to an effective decay of word introduction, which we show provides accurate predictions of the location and severity of breaks in scaling. Upon examining large corpora from 10 languages in the Project Gutenberg eBooks collection, we find emphatic empirical support for the universality of our claim. PMID:26066216

  18. Distributed Hierarchical Control of Multi-Area Power Systems with Improved Primary Frequency Regulation

    SciTech Connect

    Lian, Jianming; Marinovici, Laurentiu D.; Kalsi, Karanjit; Du, Pengwei; Elizondo, Marcelo A.

    2012-12-12

    The conventional distributed hierarchical control architecture for multi-area power systems is revisited. In this paper, a new distributed hierarchical control architecture is proposed. In the proposed architecture, pilot generators are selected in each area to be equipped with decentralized robust control as a supplementary to the conventional droop speed control. With the improved primary frequency control, the system frequency can be restored to the nominal value without the help of secondary frequency control, which reduces the burden of the automatic generation control for frequency restoration. Moreover, the low frequency inter-area electromechanical oscillations can also be effectively damped. The effectiveness of the proposed distributed hierarchical control architecture is validated through detailed simulations.

  19. Cross-language distributions of high frequency and phonetically similar cognates.

    PubMed

    Schepens, Job; Dijkstra, Ton; Grootjen, Franc; van Heuven, Walter J B

    2013-01-01

    The coinciding form and meaning similarity of cognates, e.g. 'flamme' (French), 'Flamme' (German), 'vlam' (Dutch), meaning 'flame' in English, facilitates learning of additional languages. The cross-language frequency and similarity distributions of cognates vary according to evolutionary change and language contact. We compare frequency and orthographic (O), phonetic (P), and semantic similarity of cognates, automatically identified in semi-complete lexicons of six widely spoken languages. Comparisons of P and O similarity reveal inconsistent mappings in language pairs with deep orthographies. The frequency distributions show that cognate frequency is reduced in less closely related language pairs as compared to more closely related languages (e.g., French-English vs. German-English). These frequency and similarity patterns may support a better understanding of cognate processing in natural and experimental settings. The automatically identified cognates are available in the supplementary materials, including the frequency and similarity measurements.

  20. Frequency distributions and correlations of solar X-ray flare parameters

    NASA Technical Reports Server (NTRS)

    Crosby, Norma B.; Aschwanden, Markus J.; Dennis, Brian R.

    1993-01-01

    Frequency distributions of flare parameters are determined from over 12,000 solar flares. The flare duration, the peak counting rate, the peak hard X-ray flux, the total energy in electrons, and the peak energy flux in electrons are among the parameters studied. Linear regression fits, as well as the slopes of the frequency distributions, are used to determine the correlations between these parameters. The relationship between the variations of the frequency distributions and the solar activity cycle is also investigated. Theoretical models for the frequency distribution of flare parameters are dependent on the probability of flaring and the temporal evolution of the flare energy build-up. The results of this study are consistent with stochastic flaring and exponential energy build-up. The average build-up time constant is found to be 0.5 times the mean time between flares.

  1. Algae-P Relationships, Thresholds, and Frequency Distributions Guide Nutrient Criterion Development

    EPA Science Inventory

    The complementary use of frequency distribution methods and stressor-response relationships that we used to develop candidates for TP criteria in this study should provide the fundamental analytical basis for criteria development to protect multiple attributes in ecosystems where...

  2. Effects of Massed vs. Distributed Practice and Word Frequency on Young Children's Free Recall.

    ERIC Educational Resources Information Center

    Hohn, Robert L.

    Research on massed practice (MP) and distributed practice effects to preschool children in free recall tasks is reported. A total of 40 kindergarten children were randomly assigned to High Frequency and Low Frequency word groups. No significant differences were found between the two groups on the dimensions of IQ and age. Lists of 32 high…

  3. The Influence of Orthographic Neighborhood Density and Word Frequency on Visual Word Recognition: Insights from RT Distributional Analyses

    PubMed Central

    Lim, Stephen Wee Hun

    2016-01-01

    The effects of orthographic neighborhood density and word frequency in visual word recognition were investigated using distributional analyses of response latencies in visual lexical decision. Main effects of density and frequency were observed in mean latencies. Distributional analyses additionally revealed a density × frequency interaction: for low-frequency words, density effects were mediated predominantly by distributional shifting whereas for high-frequency words, density effects were absent except at the slower RTs, implicating distributional skewing. The present findings suggest that density effects in low-frequency words reflect processes involved in early lexical access, while the effects observed in high-frequency words reflect late postlexical checking processes. PMID:27065902

  4. [Prevalence of VRN1 Locus Alleles among Spring Common Wheat Cultivars Cultivated in Western Siberia].

    PubMed

    Efremova, T T; Chumanova, E V; Trubacheeva, N V; Arbuzova, V S; Belan, I A; Pershina, L A

    2016-02-01

    With the use of allele-specific primers developed for the VRN1 loci, the allelic diversity of the VRN-A1, VRN-B1, and VRN-D1 genes was studied in 148 spring common wheat cultivars cultivated under the conditions of Western Siberia. It was demonstrated that modern Western Siberian cultivars have the VRN-A1a allele, which is widely distributed in the world (alone or in combination with the VRN-B1a and VRN-B1c alleles). It was established that the main contribution in acceleration of the.seedling-heading time is determined by a dominant VRN-A1a allele, while the VRN-A1b allele, on the contrary, determines later plant heading. Cultivars that have the VRN-A1b allele in the genotype are found with a frequency of 8%. It was shown that cultivars with different allele combinations of two dominant genes (VRN-A1a + VRN-B1c and VRN-A1a + VRN-B1a) are characterized by earlier heading and maturing.

  5. Time-frequency representation of a highly nonstationary signal via the modified Wigner distribution

    NASA Technical Reports Server (NTRS)

    Zoladz, T. F.; Jones, J. H.; Jong, J.

    1992-01-01

    A new signal analysis technique called the modified Wigner distribution (MWD) is presented. The new signal processing tool has been very successful in determining time frequency representations of highly non-stationary multicomponent signals in both simulations and trials involving actual Space Shuttle Main Engine (SSME) high frequency data. The MWD departs from the classic Wigner distribution (WD) in that it effectively eliminates the cross coupling among positive frequency components in a multiple component signal. This attribute of the MWD, which prevents the generation of 'phantom' spectral peaks, will undoubtedly increase the utility of the WD for real world signal analysis applications which more often than not involve multicomponent signals.

  6. Beat frequency is bimodally distributed in spermatozoa from T/t12 mice.

    PubMed

    Katz, D F; Erickson, R P; Nathanson, M

    1979-12-01

    Flagellar beat frequencies of spermatozoa from mice of varying genotype were studied using highspeed cinemicrography. Beat frequency was variable but unimodal in two inbred lines, their F1, and an outbred line. In contrast, beat frequency in spermatozoa from T-complex, balanced lethal stocks (T/t6 and T/t12) tended not to vary between individual males of each genotype up to four hours after collection. The two-hour distribution of beat frequency for T/t12 was, moreover, bimodal, suggesting the possible existence of two subpopulations of spermatozoa.

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

    PubMed

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

    PubMed

    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. PMID:26502227

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Frequency distributions of the concentrations of essential and nonessential elements in largemouth bass, Micropterus salmoides

    SciTech Connect

    Pinder, J.E. III; Giesy, J.P.

    1981-04-01

    From data on elemental concentrations in human tissues, Liebscher and Smith (1968) hypothesized that the frequency distributions of concentrations for essential elements were normal distributions, whereas the frequency distributions for nonessential elements were lognormal distributions. Although Liebscher and Smith's justifications for this hypothesis are flawed, other researchers have reported similar observations. The concentrations of Cd, Ca, Cr, Co, Cu, Fe, Pb, Mn, Hg, K, Se, Na, and Zn were measured in the muscle, liver, and egg tissues of female largemouth bass to determine (1) to what extent the frequency distributions of elemental concentrations are affected by errors in measuring concentrations and (2) whether the previously observed differences between essential and nonessential elements could be demonstrated if we restricted our comparisons to only those elements whose concentrations can be accurately measured. Variance component analyses of elemental concentrations in muscle tissue indicated that variations among replicate tissue samples due to measuring errors were large relative to the variations among individual fish for Cd, Ca, Mn, K, and Na. For elements where variation among individuals was not obscured by errors in measuring concentrations, there were no apparent differences between the frequency distributions for the essential elements, Cr, Cu, Fe, Se, and Zn, and the distributions for the nonessential elements, Pb and Hg. The hypothesis of Liebscher and Smith was not supported by our data.

  11. The time-frequency characteristics of violin vibrato: modal distribution analysis and synthesis

    PubMed

    Mellody; Wakefield

    2000-01-01

    A high-resolution time-frequency distribution, the modal distribution, is applied to the study of violin vibrato. The analysis indicates that the frequency modulation induced by the motion of the stopped finger on the string is accompanied by a significant amplitude variation in each partial of that note. Amplitude and frequency estimates for each partial are extracted from the modal distribution of ten pitches that span the range of the violin instrument. The frequency modulation is well-represented by a single sinusoid with a mean rate of 5.9 Hz and a mean excursion of +/- 15.2 cents. A spectral decomposition of the amplitude envelopes of the partials shows that the peaks lie primarily at integer multiples of the vibrato rate. These amplitude and frequency estimates are used in an additive synthesis model to generate synthetic replicates of violin vibrato. Simple approximations to these estimates are created, and synthesized sounds using these are evaluated perceptually by seven subjects using discrimination, nonmetric multidimensional scaling (MDS), and sound quality scoring tasks. It is found that the absence of frequency modulation has little effect on the perceptual response to violin vibrato, while the absence of amplitude modulation causes marked changes in both sound quality and MDS results. Low-order spectral decompositions of the amplitude and frequency estimates also occupy the same perceptual space as the original recording for a subset of the pitches studied.

  12. The time-frequency characteristics of violin vibrato: modal distribution analysis and synthesis

    PubMed

    Mellody; Wakefield

    2000-01-01

    A high-resolution time-frequency distribution, the modal distribution, is applied to the study of violin vibrato. The analysis indicates that the frequency modulation induced by the motion of the stopped finger on the string is accompanied by a significant amplitude variation in each partial of that note. Amplitude and frequency estimates for each partial are extracted from the modal distribution of ten pitches that span the range of the violin instrument. The frequency modulation is well-represented by a single sinusoid with a mean rate of 5.9 Hz and a mean excursion of +/- 15.2 cents. A spectral decomposition of the amplitude envelopes of the partials shows that the peaks lie primarily at integer multiples of the vibrato rate. These amplitude and frequency estimates are used in an additive synthesis model to generate synthetic replicates of violin vibrato. Simple approximations to these estimates are created, and synthesized sounds using these are evaluated perceptually by seven subjects using discrimination, nonmetric multidimensional scaling (MDS), and sound quality scoring tasks. It is found that the absence of frequency modulation has little effect on the perceptual response to violin vibrato, while the absence of amplitude modulation causes marked changes in both sound quality and MDS results. Low-order spectral decompositions of the amplitude and frequency estimates also occupy the same perceptual space as the original recording for a subset of the pitches studied. PMID:10641668

  13. 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.

    PubMed

    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.

  14. Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape.

    PubMed

    Delourme, R; Bousset, L; Ermel, M; Duffé, P; Besnard, A L; Marquer, B; Fudal, I; Linglin, J; Chadœuf, J; Brun, H

    2014-10-01

    Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for durability of major resistance genes. This was demonstrated in the Leptosphaeria maculans/Brassica napus pathosystem in a 5year recurrent selection field experiment on lines harboring the qualitative resistance gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of the virulent isolate population. In this study we continued this recurrent selection experiment in the same way to examine whether the pathogen population could adapt and render the major gene ineffective in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an effective approach for controlling the pathogen epidemics over time. This combination did not prevent isolates virulent against the major gene from amplifying in the long term but the quantitative resistance significantly delayed for 5years the loss of effectiveness of the qualitative resistance and disease severity was maintained at a low level on the genotype with both types of resistance after the fungus population had adapted to the major gene. We also showed that diversity of AvrLm6 virulence alleles was comparable in isolates recovered after the recurrent selection on lines carrying either the major gene alone or in combination with quantitative resistance: a single repeat-induced point mutation and deletion events were observed in both situations. Breeding varieties which combine qualitative and quantitative resistance can effectively contribute to disease control by increasing the potential for durability of major resistance genes.

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Longitudinal clines in the frequency distribution of 'super-clones' in an aphid crop pest.

    PubMed

    Gilabert, A; Dedryver, C-A; Stoeckel, S; Plantegenest, M; Simon, J-C

    2015-12-01

    Parthenogenesis is the main mode of reproduction of aphids. Their populations are therefore composed of clones whose frequency distribution varies in space and time. Previous population genetic studies on aphids have highlighted the existence of highly abundant clones ('super-clones'), distributed over large geographic areas and persisting over time. Whether the abundance of 'super-clones' results from their ecological success or from stochastic forces, such as drift and migration, is an open question. Here, we looked for the existence of clines in clonal frequency along a climatic gradient in the cereal aphid Rhopalosiphum padi (Linnaeus, 1758) and examined the possible influence of geographical distance and environmental variables in the buildup and maintenance of such clonal clines. We investigated the spatial distribution of the commonest genotypes of R. padi by sampling populations along an east-west transect in maize fields in the northern half of France in both spring and late summer. Individual aphids were genotyped at several polymorphic loci, allowing the assessment of frequency distributions of multilocus genotypes (MLGs) across the cropping season. We found several MLGs showing longitudinal clines in their frequency distribution in both spring and summer. In particular, two dominant asexual genotypes of R. padi showed inverted geographical clines, which could suggest divergent adaptations to environmental conditions. We concluded that while the distribution of some 'super-clones' of R. padi seems most likely driven by the action of migration and genetic drift, selection could be also involved in the establishment of longitudinal clines of others. PMID:26278064

  17. Enhanced Recovery Utilizing Variable Frequency Drives and a Distributed Power System

    SciTech Connect

    Randy Peden; Sanjiv Shah

    2005-07-26

    This report describes complete results of the project entitled ''Enhanced Recovery Utilizing Variable Frequency Drives and a Distributed Power System''. This demonstration project was initiated in July 2003 and completed in March 2005. The objective of the project was to develop an integrated power production/variable frequency drive system that could easily be deployed in the oil field that would increase production and decrease operating costs. This report describes all the activities occurred and documents results of the demonstration.

  18. Genetic parameters and allele frequencies of five new European Standard Set STR loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in the population of Romania

    PubMed Central

    Stanciu, Florin; Vladu, Simona; Cuţăr, Veronica; Cocioabă, Daniela; Iancu, Florentina; Cotolea, Adnana; Stoian, Ionel Marius

    2013-01-01

    Aim To establish allele frequencies and genetic parameters for 5 new European Standard Set short tandem repeat (STR) loci in the population of Romania and to compare them with those in other populations. Methods DNA was isolated using QIAamp 96 DNA Swab BioRobot Kit and Chelex 100 methods. Polymerase chain reaction amplification was done using Investigator ESSplexPlus Kit (D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, and vWA). For DNA typing, Applied Biosystems 3500/3500xL Genetic Analyzer was used. Statistical analysis was done using Powerstats, GDA, and Arlequin software. Results Power of discrimination and polymorphism information content was highest for two new ESS loci, D1S1656 and D12S391. Comparison of allele frequencies for 5 new ESS loci in Romanian population with previously published population data showed significant differences for all compared populations, with the exception of Hungary. Geographically more distant populations, such as Spain, Sweden, United Kingdom, Germany, and Portugal differed more than closer populations. Conclusion New ESS STR loci are very useful for the analysis of forensic samples (persons or traces) due to their characteristics (shortness and high polymorphism). In comparisons with other common STR markers, they have a higher power of discrimination and also higher polymorphism information content, and could be used in any national DNA database. PMID:23771753

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

    PubMed

    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.

  20. Investigating low frequency dielectric properties of a composite using the distribution of relaxation times technique

    SciTech Connect

    Tuncer, Enis

    2006-01-01

    The distribution of relaxation times approach, a less frequently employed dielectric data analysis technique, is utilized to better understand the relaxation characteristics of composites consisting of metal-coated, hollow glass spheres dispersed in a paraffin wax matrix. The dielectric properties of the composite samples are measured by means of impedance spectroscopy in the frequency range 0.1mHz to 10 MHz. The application of a mixture law is not appropriate for the analysis of the frequency-dependent properties of the considered system on this broad frequency range. However, utilization of the distribution of relaxation times procedure to study the dielectric behaviour shows clear trends in the mixtures' relaxation spectra. Relaxation processes of the paraffin wax and those specific to the composites are found from the extracted distribution of relaxation times spectra. The influence of the filler concentration, q, on the dielectric properties is examined; a relaxation with a narrow distribution at intermediate frequencies becomes broad with the addition of the filler. This relaxation, in the form of the low-frequency-dispersions (also known as constant phase angle) phenomenon, dominates the dielectric properties of the composites with high bead concentration, q > 0:15. The variation in dielectric properties of individual samples whose bead concentrations q are nominally the same is discussed in terms of possible microstructural variations.

  1. Investigating low-frequency dielectric properties of a composite using the distribution of relaxation times technique

    SciTech Connect

    Tuncer, Enis; Bowler, Nicola; Youngs, I. J.; Lymer, K. P.

    2006-01-01

    The distribution of relaxation times approach, a less frequently employed dielectric data analysis technique, is utilized to better understand the relaxation characteristics of composites consisting of metal-coated, hollow glass spheres dispersed in a paraffin wax matrix. The dielectric properties of the composite samples are measured by means of impedance spectroscopy in the frequency range 0.1 mHz to 10 MHz. The application of a mixture law is not appropriate for the analysis of the frequency-dependent properties of the considered system on this broad frequency range. However, utilization of the distribution of relaxation times procedure to study the dielectric behaviour shows clear trends in the mixtures' relaxation spectra. Relaxation processes of the paraffin wax and those specific to the composites are found from the extracted distribution of relaxation times spectra. The influence of the filler concentration, q, on the dielectric properties is examined; a relaxation with a narrow distribution at intermediate frequencies becomes broad with the addition of the filler. This relaxation, in the form of the low-frequency-dispersions (also known as constant phase angle) phenomenon, dominates the dielectric properties of the composites with high bead concentration, q>0.15. The variation in dielectric properties of individual samples whose bead concentrations q are nominally the same is discussed in terms of possible microstructural variations.

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

    SciTech Connect

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

    2015-01-05

    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 terahertz (THz) emission at angles tuned by design between 0° and 50° was realized, leading to an original phase-matching approach for highly collimated THz quantum cascade lasers.

  3. Single-frequency distributed Bragg reflector Nd doped silica fiber laser at 930 nm.

    PubMed

    Fang, Qiang; Xu, Yang; Fu, Shijie; Shi, Wei

    2016-04-15

    We report a single-frequency distributed Bragg reflector (DBR) fiber laser at 930 nm for the first time, to the best of our knowledge. A ∼2.5 cm long commercial highly neodymium-doped silica fiber was utilized as the gain medium to achieve ∼1.9 mW laser output. The single longitudinal mode operation of this laser was verified by a scanning Fabry-Perot interferometer. This fiber laser is suited for seeding high-power 930 nm narrow-linewidth laser amplifiers, which can be used to generate coherent single-frequency pure blue light through frequency doubling. PMID:27082356

  4. [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].

    PubMed

    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

  5. The impact of frequency mixing on sheath properties: Ion energy distribution and Vdc/Vrf interaction

    NASA Astrophysics Data System (ADS)

    Shannon, Steven; Hoffman, Daniel; Yang, Jang-Gyoo; Paterson, Alex; Holland, John

    2005-05-01

    A dual frequency rf sheath is analyzed using a simple rf sheath model to study the interaction between the two driving rf currents and their effect on sheath parameters. A symmetric rf discharge with defined electron density and dc sheath potential is modeled using a sharp boundary sheath approximation. Three results of this study are reported: (1) reproduction of trends in ion energy distribution functions predicted and measured in previous studies, (2) a frequency-mixing-dependent relationship between the dc sheath potential and applied rf potential, and (3) an additional asymmetry in the ion energy distribution function generated by the intermodulation components resulting from the nonlinear sheath.

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

    SciTech Connect

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

    2013-11-15

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

  7. Model for radial dependence of frequency distributions for energy imparted in nanometer volumes from HZE particles

    NASA Technical Reports Server (NTRS)

    Cucinotta, F. A.; Nikjoo, H.; Goodhead, D. T.; Decillo, J. F. (Principal Investigator)

    2000-01-01

    This paper develops a deterministic model of frequency distributions for energy imparted (total energy deposition) in small volumes similar to DNA molecules from high-energy ions of interest for space radiation protection and cancer therapy. Frequency distributions for energy imparted are useful for considering radiation quality and for modeling biological damage produced by ionizing radiation. For high-energy ions, secondary electron (delta-ray) tracks originating from a primary ion track make dominant contributions to energy deposition events in small volumes. Our method uses the distribution of electrons produced about an ion's path and incorporates results from Monte Carlo simulation of electron tracks to predict frequency distributions for ions, including their dependence on radial distance. The contribution from primary ion events is treated using an impact parameter formalism of spatially restricted linear energy transfer (LET) and energy-transfer straggling. We validate our model by comparing it directly to results from Monte Carlo simulations for proton and alpha-particle tracks. We show for the first time frequency distributions of energy imparted in DNA structures by several high-energy ions such as cosmic-ray iron ions. Our comparison with results from Monte Carlo simulations at low energies indicates the accuracy of the method.

  8. Model for radial dependence of frequency distributions for energy imparted in nanometer volumes from HZE particles.

    PubMed

    Cucinotta, F A; Nikjoo, H; Goodhead, D T

    2000-04-01

    This paper develops a deterministic model of frequency distributions for energy imparted (total energy deposition) in small volumes similar to DNA molecules from high-energy ions of interest for space radiation protection and cancer therapy. Frequency distributions for energy imparted are useful for considering radiation quality and for modeling biological damage produced by ionizing radiation. For high-energy ions, secondary electron (delta-ray) tracks originating from a primary ion track make dominant contributions to energy deposition events in small volumes. Our method uses the distribution of electrons produced about an ion's path and incorporates results from Monte Carlo simulation of electron tracks to predict frequency distributions for ions, including their dependence on radial distance. The contribution from primary ion events is treated using an impact parameter formalism of spatially restricted linear energy transfer (LET) and energy-transfer straggling. We validate our model by comparing it directly to results from Monte Carlo simulations for proton and alpha-particle tracks. We show for the first time frequency distributions of energy imparted in DNA structures by several high-energy ions such as cosmic-ray iron ions. Our comparison with results from Monte Carlo simulations at low energies indicates the accuracy of the method. PMID:10761008

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

    NASA Astrophysics Data System (ADS)

    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

  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

    PubMed Central

    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

  11. Linkage disequilibrium in the insulin gene region: Size variation at the 5{prime} flanking polymorphism and bimodality among {open_quotes}Class I{close_quotes} alleles

    SciTech Connect

    McGinnis, R.E.; Spielman, R.S.

    1994-09-01

    The 5{prime} flanking polymorphism (5{prime}FP), a hypervariable region at the 5{prime} end of the insulin gene, has {open_quotes}class 1{close_quotes} alleles (650-900 bp long) that are in positive linkage disequilibrium with insulin-dependent diabetes mellitus (IDDM). The authors report that precise sizing of the 5{prime}FP yields a bimodal frequency distribution of class 1 allele lengths. Class 1 alleles belonging to the lower component (650-750 bp) of the bimodal distribution were somewhat more highly associated with IDDM than were alleles from the upper component (760-900 bp), but the difference was not statistically significant. They also examined 5{prime}FP length variation in relation to allelic variation at nearby polymorphisms. At biallelic RFLPs on both sides of the 5{prime}FP, they found that one allele exhibits near-total association with the upper component of the 5FP class 1 distribution. Such associations represent a little-known but potentially wide-spread form of linkage disequilibrium. In this type of disequilibrium, a flanking allele has near-complete association with a single mode of VNTR alleles whose lengths represent consecutive numbers of tandem repeats (CNTR). Such extreme disequilibrium between a CNTR mode and flanking alleles may originate and persist because length mutations at some VNTR loci usually add or delete only one or two repeat units. 22 refs., 5 figs., 6 tabs.

  12. Measurement of High Frequency Perturbations to the Ion Velocity Distribution in the HELIX Helicon Plasma Source

    NASA Astrophysics Data System (ADS)

    Kline, J. L.; Boivin, R. F.; Franck, C.; Klinger, T.; Scime, E. E.

    2001-10-01

    Using lasers to measure plasma parameters has become more common in recent years. Lasers can provide information about plasma parameters without perturbing the plasma. The most common technique for ion parameter measurements is Laser Induced Fluorescence (LIF). LIF typically measures the ion velocity distribution and provides information about the ion temperatures and ion flows in the plasma. More recently, Skiff and Anderegg [1987] and Safarty et al. [1996] have shown that measurements of the perturbed ion velocity distribution can provide wave number information for waves propagating in a plasma due the non-local nature of the dielectric tensor. In the past two years, attempts have been made to measure the perturbed ion velocity distribution function at frequencies relevant to Helicon plasma sources. The objective of the measurements is to identify electrostatic oscillation associated to the slow wave or "Trivelpeice Gould modes" in helicon plasma sources. Past efforts to measure the perturbed ion velocity distribution function have been unsuccessful due to technical difficulties associated with measuring the cross correlation of the photon and reference signals. Using a high frequency SR544 Stanford Research lock-in amplifier, high frequency perturbations to the ion velocity distribution in a helicon source have been measured. Perturbed ion velocity distribution measurements, along with the related theory will be presented.

  13. Simulation of multi-frequency EPR spectra for a distribution of the zero-field splitting

    NASA Astrophysics Data System (ADS)

    Azarkh, Mykhailo; Groenen, Edgar J. J.

    2015-06-01

    We present a numerical procedure called 'grid-of-errors' to extract the distribution of magnetic interactions from continuous-wave electron-paramagnetic-resonance (EPR) spectra at multiple microwave frequencies. The approach is based on the analysis of the lineshape of the spectra and explicitly worked out for high-spin systems for which the lineshape is determined by a distribution of the zero-field splitting. Initial principal values of the zero-field splitting tensor are obtained from the EPR spectrum at a microwave frequency in the high-field limit, and the initial distribution is taken Gaussian. Subsequently, the grid-of-errors procedure optimizes this distribution, without any restriction to its shape, taking into account spectra at various microwave frequencies. The numerical procedure is illustrated for the Fe(III)-EDTA complex. An optimized distribution of the zero-field splitting is obtained, which provides a proper description of the EPR spectra at 9.5, 34, 94, and 275 GHz. The proposed approach can be used as well for distributions of magnetic interactions other than the zero-field splitting.

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

    PubMed

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

    2014-08-22

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

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

    PubMed

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

    2014-08-22

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

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

    SciTech Connect

    Alonso, S.; Castro, A.; Fernandez-Fernandez, I.; Pancorbo, M.M. de

    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.

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

    PubMed Central

    Alonso, S; Castro, A; Fernández-Fernández, I; de Pancorbo, M M

    1997-01-01

    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. Images Figure 2 Figure 3 PMID:9012415

  18. Exploring empirical rank-frequency distributions longitudinally through a simple stochastic process.

    PubMed

    Finley, Benjamin J; Kilkki, Kalevi

    2014-01-01

    The frequent appearance of empirical rank-frequency laws, such as Zipf's law, in a wide range of domains reinforces the importance of understanding and modeling these laws and rank-frequency distributions in general. In this spirit, we utilize a simple stochastic cascade process to simulate several empirical rank-frequency distributions longitudinally. We focus especially on limiting the process's complexity to increase accessibility for non-experts in mathematics. The process provides a good fit for many empirical distributions because the stochastic multiplicative nature of the process leads to an often observed concave rank-frequency distribution (on a log-log scale) and the finiteness of the cascade replicates real-world finite size effects. Furthermore, we show that repeated trials of the process can roughly simulate the longitudinal variation of empirical ranks. However, we find that the empirical variation is often less that the average simulated process variation, likely due to longitudinal dependencies in the empirical datasets. Finally, we discuss the process limitations and practical applications.

  19. Exploring Empirical Rank-Frequency Distributions Longitudinally through a Simple Stochastic Process

    PubMed Central

    Finley, Benjamin J.; Kilkki, Kalevi

    2014-01-01

    The frequent appearance of empirical rank-frequency laws, such as Zipf’s law, in a wide range of domains reinforces the importance of understanding and modeling these laws and rank-frequency distributions in general. In this spirit, we utilize a simple stochastic cascade process to simulate several empirical rank-frequency distributions longitudinally. We focus especially on limiting the process’s complexity to increase accessibility for non-experts in mathematics. The process provides a good fit for many empirical distributions because the stochastic multiplicative nature of the process leads to an often observed concave rank-frequency distribution (on a log-log scale) and the finiteness of the cascade replicates real-world finite size effects. Furthermore, we show that repeated trials of the process can roughly simulate the longitudinal variation of empirical ranks. However, we find that the empirical variation is often less that the average simulated process variation, likely due to longitudinal dependencies in the empirical datasets. Finally, we discuss the process limitations and practical applications. PMID:24755621

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

    SciTech Connect

    Slatkin, M.; Rannala, B.

    1997-02-01

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

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

    PubMed

    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

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

    PubMed Central

    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

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

    NASA Astrophysics Data System (ADS)

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

    2005-06-01

    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 and 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. Though, 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 distribution. We show that this adjustment is not always possible, and that it depends on the shape of the original and desired distributions, as well as on the relative number of data points that can be added. Applying this theorem to radiative equilibrium Monte Carlo calculations, we provide a firm theoretical basis for the frequency distribution adjustment method of Bjorkman and Wood, and we demonstrate that this method provides the correct frequency distribution through the additional requirement of radiative equilibrium. We discuss the advantages and limitations of this approach, and show that it can easily be combined with the presence of additional heating sources and the concept of photon weighting. However, the method may fail if small dust grains are included, or if the absorption rate is estimated from the mean intensity of the radiation field.

  4. Characterization of the treefrog null allele, 1991

    SciTech Connect

    Guttman, S.I.

    1992-04-01

    Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

  5. Characterization of the treefrog null allele

    SciTech Connect

    Guttman, S.I. . Dept. of Zoology)

    1990-12-01

    As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

  6. Visualizing disease associations: graphic analysis of frequency distributions as a function of age using moving average plots (MAP) with application to Alzheimer's and Parkinson's disease.

    PubMed

    Payami, Haydeh; Kay, Denise M; Zabetian, Cyrus P; Schellenberg, Gerard D; Factor, Stewart A; McCulloch, Colin C

    2010-01-01

    Age-related variation in marker frequency can be a confounder in association studies, leading to both false-positive and false-negative findings and subsequently to inconsistent reproducibility. We have developed a simple method, based on a novel extension of moving average plots (MAP), which allows investigators to inspect the frequency data for hidden age-related variations. MAP uses the standard case-control association data and generates a birds-eye view of the frequency distributions across the age spectrum; a picture in which one can see if, how, and when the marker frequencies in cases differ from that in controls. The marker can be specified as an allele, genotype, haplotype, or environmental factor; and age can be age-at-onset, age when subject was last known to be unaffected, or duration of exposure. Signature patterns that emerge can help distinguish true disease associations from spurious associations due to age effects, age-varying associations from associations that are uniform across all ages, and associations with risk from associations with age-at-onset. Utility of MAP is illustrated by application to genetic and epidemiological association data for Alzheimer's and Parkinson's disease. MAP is intended as a descriptive method, to complement standard statistical techniques. Although originally developed for age patterns, MAP is equally useful for visualizing any quantitative trait.

  7. Effect of rotational disruption on the size-frequency distribution of the Main Belt asteroid population

    NASA Astrophysics Data System (ADS)

    Jacobson, Seth A.; Marzari, Francesco; Rossi, Alessandro; Scheeres, Daniel J.; Davis, Donald R.

    2014-03-01

    The size distribution of small asteroids in the Main Belt is assumed to be determined by an equilibrium between the creation of new bodies out of the impact debris of larger asteroids and the destruction of small asteroids by collisions with smaller projectiles. However, for a diameter less than 6 km, we find that YORP-induced rotational disruption significantly contributes to the erosion even exceeding the effects of collisional fragmentation. Including this additional grinding mechanism in a collision evolution model for the asteroid belt, we generate size-frequency distributions from either an accretional or an `Asteroids were born big' initial size-frequency distribution that are consistent with observations reported in Gladman et al. Rotational disruption is a new mechanism that must be included in all future collisional evolution models of asteroids.

  8. The Gaussian atmospheric transport model and its sensitivity to the joint frequency distribution and parametric variability.

    PubMed

    Hamby, D M

    2002-01-01

    Reconstructed meteorological data are often used in some form of long-term wind trajectory models for estimating the historical impacts of atmospheric emissions. Meteorological data for the straight-line Gaussian plume model are put into a joint frequency distribution, a three-dimensional array describing atmospheric wind direction, speed, and stability. Methods using the Gaussian model and joint frequency distribution inputs provide reasonable estimates of downwind concentration and have been shown to be accurate to within a factor of four. We have used multiple joint frequency distributions and probabilistic techniques to assess the Gaussian plume model and determine concentration-estimate uncertainty and model sensitivity. We examine the straight-line Gaussian model while calculating both sector-averaged and annual-averaged relative concentrations at various downwind distances. The sector-average concentration model was found to be most sensitive to wind speed, followed by horizontal dispersion (sigmaZ), the importance of which increases as stability increases. The Gaussian model is not sensitive to stack height uncertainty. Precision of the frequency data appears to be most important to meteorological inputs when calculations are made for near-field receptors, increasing as stack height increases.

  9. Frequency-Range Distribution of Boulders Around Cone Crater: Relevance to Landing Site Hazard Avoidance

    NASA Technical Reports Server (NTRS)

    Clegg-Watkins, R. N.; Jolliff, B. L.; Lawrence, S. J.

    2016-01-01

    Boulders represent a landing hazard that must be addressed in the planning of future landings on the Moon. A boulder under a landing leg can contribute to deck tilt and boulders can damage spacecraft during landing. Using orbital data to characterize boulder populations at locations where landers have safely touched down (Apollo, Luna, Surveyor, and Chang'e-3 sites) is important for determining landing hazard criteria for future missions. Additionally, assessing the distribution of boulders can address broader science issues, e.g., how far craters distribute boulders and how this distribution varies as a function of crater size and age. The availability of new Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images [1] enables the use of boulder size- and range frequency distributions for a variety of purposes [2-6]. Boulders degrade over time and primarily occur around young or fresh craters that are large enough to excavate bedrock. Here we use NAC images to analyze boulder distributions around Cone crater (340 m diameter) at the Apollo 14 site. Cone crater (CC) was selected because it is the largest crater where astronaut surface photography is available for a radial traverse to the rim. Cone crater is young (approximately 29 Ma [7]) relative to the time required to break down boulders [3,8], giving us a data point for boulder range-frequency distributions (BRFDs) as a function of crater age.

  10. Unique frequency distribution of ice and dust cloud observations over Gale Crater on Mars

    NASA Astrophysics Data System (ADS)

    de la Torre Juarez, M.; Cantor, B. A.

    2012-12-01

    A normalized cloud index was tested to detect clouds using the MARs Camera Imager (MARCI) on the Mars Reconaissance orbiter. The algorithm and its validation are described. After validation it was used to extract the frequency of ice and dust clouds over the region around Gale. The analysis suggests a higher frequency of hazes and ice clouds over this region than over the other three final candidate sites for landing the Mars Science Laboratory at Mawrth, Eberswalde and Holding and a different type of non-guassian distribution raising the question about what properties around Gale could be causing a different cloud cycle.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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).

  13. A maximum likelihood approach to jointly estimating seasonal and annual flood frequency distributions

    NASA Astrophysics Data System (ADS)

    Baratti, E.; Montanari, A.; Castellarin, A.; Salinas, J. L.; Viglione, A.; Blöschl, G.

    2012-04-01

    Flood frequency analysis is often used by practitioners to support the design of river engineering works, flood miti- gation procedures and civil protection strategies. It is often carried out at annual time scale, by fitting observations of annual maximum peak flows. However, in many cases one is also interested in inferring the flood frequency distribution for given intra-annual periods, for instance when one needs to estimate the risk of flood in different seasons. Such information is needed, for instance, when planning the schedule of river engineering works whose building area is in close proximity to the river bed for several months. A key issue in seasonal flood frequency analysis is to ensure the compatibility between intra-annual and annual flood probability distributions. We propose an approach to jointly estimate the parameters of seasonal and annual probability distribution of floods. The approach is based on the preliminary identification of an optimal number of seasons within the year,which is carried out by analysing the timing of flood flows. Then, parameters of intra-annual and annual flood distributions are jointly estimated by using (a) an approximate optimisation technique and (b) a formal maximum likelihood approach. The proposed methodology is applied to some case studies for which extended hydrological information is available at annual and seasonal scale.

  14. Maximum-likelihood methods for array processing based on time-frequency distributions

    NASA Astrophysics Data System (ADS)

    Zhang, Yimin; Mu, Weifeng; Amin, Moeness G.

    1999-11-01

    This paper proposes a novel time-frequency maximum likelihood (t-f ML) method for direction-of-arrival (DOA) estimation for non- stationary signals, and compares this method with conventional maximum likelihood DOA estimation techniques. Time-frequency distributions localize the signal power in the time-frequency domain, and as such enhance the effective SNR, leading to improved DOA estimation. The localization of signals with different t-f signatures permits the division of the time-frequency domain into smaller regions, each contains fewer signals than those incident on the array. The reduction of the number of signals within different time-frequency regions not only reduces the required number of sensors, but also decreases the computational load in multi- dimensional optimizations. Compared to the recently proposed time- frequency MUSIC (t-f MUSIC), the proposed t-f ML method can be applied in coherent environments, without the need to perform any type of preprocessing that is subject to both array geometry and array aperture.

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

    PubMed

    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

  16. Study of HLA-DQA1 alleles in celiac children.

    PubMed

    Nieto, A; Blanco Quirós, A; Arranz, E; Alonso Franch, M; Garrote, J A; Calvo, C

    1995-01-01

    The familial incidence of celiac disease (CD) confirms its genetic basis, although acquired factors are also involved. Many authors have reported a linkage between celiac disease and HLA antigens, but there are differences which depend on geographical areas, and nowadays the study must be done at the genetic level. Thirty-eight celiac children and 52 normal controls were included in this study. All individuals were chosen from the Castilla and Leon area. We used the reverse ¿dot block¿ technique, using sequence-specific oligonucleotide DNA probes (Cetus, USA) to determine the HLA-DQA1 alleles in DNA samples previously amplified by PCR (polymerase chain reaction). The different frequency of alleles in patients and controls was assessed by 3 statistical tests: chi square (chi(2)), relative risk (RR) and etiologic fraction (EF). A very high frequency of DQA1*0201 (chi(2):p <0.0001) and DQA1*0501 (chi(2): p <0.0001) alleles was observed in patients; all but one (97%) had the DQA1*0501 allele vs. 40% of controls (RR: 37.00; EF: 0.955). The DQA1*0201 allele also had a high prevalence in celiacs (58%)(RR: 1.375: EF:0.438). The DQA1*01 allele was only found in 10.5% of patients compared to 79% of controls (chi(2): p <0.0001) and the DQA1*03 allele was also decreased in celiacs. There was only one celiac girl without the DQA1*0501 allele. She had no other clinical or serological differences, as compared to the other patients. In the study of allele subtypes, among the DQA1*01 allele, 50% of patients were positive for DQA1*101 and the remaining 50% had DQA1*0102, but none of the individuals were positive for DQA1*0103. Among normal controls, 32 individuals (61.5%) expressed the DQA1*0102 subtype, 15 (28.9%) the DQA1*0101 subtype and 5 (9.6%) the DQA1*0103 subtype. All positive cases for DQA1-*05 belong to the DQA1* 0501 subtype, in both celiac and control groups. There were 10 possible combinations of HLA-DQA1 genes, but we found a very unequal distribution in both celiacs

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

    SciTech Connect

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

    2012-07-20

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

  18. Bivariate Frequency Analysis with Nonstationary Gumbel/GEV Marginal Distributions for Rainfall Event

    NASA Astrophysics Data System (ADS)

    Joo, Kyungwon; Kim, Sunghun; Kim, Hanbeen; Ahn, Hyunjun; Heo, Jun-Haeng

    2016-04-01

    Multivariate frequency analysis has been developing for hydrological data recently. Particularly, the copula model has been used as an effective method which has no limitation on deciding marginal distributions. The time-series rainfall data can be characterized to rainfall event by inter-event time definition and each rainfall event has rainfall depth and duration. In addition, changes in rainfall depth have been studied recently due to climate change. The nonstationary (time-varying) Gumbel and Generalized Extreme Value (GEV) have been developed and their performances have been investigated from many studies. In the current study, bivariate frequency analysis has performed for rainfall depth and duration using Archimedean copula on stationary and nonstationary hourly rainfall data to consider the effect of climate change. The parameter of copula model is estimated by inference function for margin (IFM) method and stationary/nonstationary Gumbel and GEV distributions are used for marginal distributions. As a result, level curve of copula model is obtained and goodness-of-fit test is performed to choose appropriate marginal distribution among the applied stationary and nonstationary Gumbel and GEV distributions.

  19. A FEMTOSECOND-LEVEL FIBER-OPTICS TIMING DISTRIBUTION SYSTEM USING FREQUENCY-OFFSET INTERFEROMETRY

    SciTech Connect

    Staples, J.W.; Byrd, J.; Doolittle, L.; Huang, G.; Wilcox, R.

    2009-10-17

    An optical fiber-based frequency and timing distribution system based on the principle of heterodyne interferometry has been in development at LBNL for several years. The fiber drift corrector has evolved from an RF-based to an optical-based system, from mechanical correctors (piezo and optical trombone) to fully electronic, and the electronics from analog to fully digital, all using inexpensive off-the-shelf commodity fiber components. Short-term optical phase jitter and long-term phase drift are both in the femtosecond range over distribution paths of 2 km or more.

  20. Distributed fiber sensing system with wide frequency response and accurate location

    NASA Astrophysics Data System (ADS)

    Shi, Yi; Feng, Hao; Zeng, Zhoumo

    2016-02-01

    A distributed fiber sensing system merging Mach-Zehnder interferometer and phase-sensitive optical time domain reflectometer (Φ-OTDR) is demonstrated for vibration measurement, which requires wide frequency response and accurate location. Two narrow line-width lasers with delicately different wavelengths are used to constitute the interferometer and reflectometer respectively. A narrow band Fiber Bragg Grating is responsible for separating the two wavelengths. In addition, heterodyne detection is applied to maintain the signal to noise rate of the locating signal. Experiment results show that the novel system has a wide frequency from 1 Hz to 50 MHz, limited by the sample frequency of data acquisition card, and a spatial resolution of 20 m, according to 200 ns pulse width, along 2.5 km fiber link.

  1. 976 nm single-frequency distributed Bragg reflector fiber laser.

    PubMed

    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

  2. Single-frequency Yb-doped fiber laser with distributed feedback based on a random FBG

    NASA Astrophysics Data System (ADS)

    Abdullina, S. R.; Vlasov, A. A.; Lobach, I. A.; Belai, O. V.; Shapiro, D. A.; Babin, S. A.

    2016-07-01

    Single-frequency operation of a 1.03 μm fiber laser with random distributed feedback (RDFB) is demonstrated. The laser cavity is based on a 4 cm long fiber Bragg grating (FBG) consisting of 10 homogeneous subgratings with random phase and amplitude of refractive index modulation inscribed in a polarization maintaining (PM) Yb-doped fiber. Such RDFB laser generates single longitudinal mode with output power up to 25 mW, which is 3.5 times higher than that for a DFB laser based on regular π-shifted FBG of the same length in the same fiber. The single-frequency linewidth is measured to be  <100 kHz in both cases. The observed difference of the DFB and RDFB lasers is confirmed by numerical simulation showing different longitudinal distribution of intra-cavity radiation in these cases, analogous to those in the experiment.

  3. Simulation and analysis of an intermediate frequency (IF) distribution system with applications for Space Station

    NASA Technical Reports Server (NTRS)

    Costello, Thomas A.; Brandt, C. Maite

    1989-01-01

    Simulation and analysis results are described for a wideband fiber optic intermediate frequency distribution channel for a frequency division multiple access (FDMA) system where antenna equipment is remotely located from the signal processing equipment. The fiber optic distribution channel accommodates multiple signals received from a single antenna with differing power levels. Performance parameters addressed are intermodulation degradations, laser noise, and adjacent channel interference, as they impact the overall system design. Simulation results showed that the laser diode modulation level can be allowed to reach 100 percent without considerable degradation. The laser noise must be controlled as to provide a noise floor of less than -90 dBW/Hz. The fiber optic link increases the degradation due to power imbalance yet diminishes the effects of the transmit amplifier nonlinearity. Overall, optimal operation conditions can be found to yield a degradation level of about .1 dB caused by the fiber optic link.

  4. Relationships among solar activity SEP occurrence frequency, and solar energetic particle event distribution function

    NASA Astrophysics Data System (ADS)

    Nymmik, Rikho

    The solar cycle 20-22 direct spacecraft measurement results are used to analyze the occurrence frequency and distribution function of solar energetic particle (SEP) events as dependent on solar activity. The analysis has shown that • the mean occurrence frequency of the SEP events with ≥30 MeV proton fluence sizes exceeding 106 is proportional to sunspot number, • the SEP event proton distribution functions for periods of different solar activity levels can be described to be power-law functions whose spectral form (spectral indices and cutoff values) are the same. The above results permit the following conclusions: a) to within statistical deviations, the total number of SEP events observed during any given time interval is proportional to the sum of mean-yearly sunspot numbers; b) large SEP events can occur to within quite a definite probability even during solar minima.

  5. Size frequency distribution of Martian craters and relative age of light and dark terrains.

    NASA Technical Reports Server (NTRS)

    Woronow, A.; King, E. A., Jr.

    1972-01-01

    Light and dark terrains in and around Meridiani Sinus, mapped on the imagery from Mariner 6 and Mariner 7, were found to have significantly different cumulative size frequency distributions of craters. The light terrain on a mosaic of frames 6N11, 6N13, and 6N19 has a greater proportion of large craters and a lesser proportion of smaller craters than the dark terrain on the same frames. The light terrain is interpreted to be generally older than the dark terrain. The filling or partial filling of the smaller craters on the light terrain by surface detritus is suggested. Several wide-angle frames have remarkably similar cumulative crater size frequency distributions that may be representative of a large portion of the Martian surface.

  6. Identification of the third/extra allele for forensic application in cases with TPOX tri-allelic pattern.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; da Motta, Carlos Henrique Ares Silveira; Rodenbusch, Rodrigo; Gusmão, Leonor; Alho, Clarice Sampaio

    2015-05-01

    Genotyping of polymorphic short tandem repeats (STRs) loci is widely used in forensic DNA analysis. STR loci eventually present tri-allelic pattern as a genotyping irregularity and, in that situation, the doubt about the tri-allele locus frequency calculation can reduce the analysis strength. In the TPOX human STR locus, tri-allelic genotypes have been reported with a widely varied frequency among human populations. We investigate whether there is a single extra allele (the third allele) in the TPOX tri-allelic pattern, what it is, and where it is, aiming to understand its genomic anatomy and to propose the knowledge of this TPOX extra allele from genetic profile, thus preserving the two standard TPOX alleles in forensic analyses. We looked for TPOX tri-allelic subjects in 75,113 Brazilian families. Considering only the parental generation (mother+father) we had 150,226 unrelated subjects evaluated. From this total, we found 88 unrelated subjects with tri-allelic pattern in the TPOX locus (0.06%; 88/150,226). Seventy three of these 88 subjects (73/88; 83%) had the Clayton's original Type 2 tri-allelic pattern (three peaks of even intensity). The remaining 17% (15/88) show a new Type 2 derived category with heterozygote peak imbalance (one double dose peak plus one regular sized peak). In this paper we present detailed data from 66 trios (mother+father+child) with true biological relationships. In 39 of these families (39/66; 59%) the extra TPOX allele was transmitted either from the mother or from the father to the child. Evidences indicated the allele 10 as the extra TPOX allele, and it is on the X chromosome. The present data, which support the previous Lane hypothesis, improve the knowledge about tri-allelic pattern of TPOX CODIS' locus allowing the use of TPOX profile in forensic analyses even when with tri-allelic pattern. This evaluation is now available for different forensic applications.

  7. Power conversion distribution system using a resonant high-frequency AC link

    NASA Technical Reports Server (NTRS)

    Sood, P. K.; Lipo, T. A.

    1986-01-01

    Static power conversion systems based on a resonant high frequency (HF) link offers a significant reduction in the size and weight of the equipment over that achieved with conventional approaches, especially when multiple sources and loads are to be integrated. A faster system response and absence of audible noise are the other principal characteristics of such systems. A conversion configuration based on a HF link which is suitable for applications requiring distributed power is proposed.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Oxide vapor distribution from a high-frequency sweep e-beam system

    SciTech Connect

    Chow, R.; Tassano, P.L.; Tsujimoto, N.

    1995-03-01

    Oxide vapor distributions have been determined as a function of operating parameters of a high frequency sweep e-beam source combined with a programmable sweep controller. We will show which parameters are significant, the parameters that yield the broadest oxide deposition distribution, and the procedure used to arrive at these conclusions. A design-of-experimental strategy was used with five operating parameters: evaporation rate, sweep speed, sweep pattern (pre-programmed), phase speed (azimuthal rotation of the pattern), profile (dwell time as a function of radial position). A design was chosen that would show which of the parameters and parameter pairs have a statistically significant effect on the vapor distribution. Witness flats were placed symmetrically across a 25 inches diameter platen. The stationary platen was centered 24 inches above the e-gun crucible. An oxide material was evaporated under 27 different conditions. Thickness measurements were made with a stylus profilometer. The information will enable users of the high frequency e-gun systems to optimally locate the source in a vacuum system and understand which parameters have a major effect on the vapor distribution.

  13. Bayesian analysis of size-dependent overwinter mortality from size-frequency distributions.

    PubMed

    Carlson, Stephanie M; Kottas, Athanasios; Mangel, Marc

    2010-04-01

    Understanding the relationship between body size and mortality is an important problem in ecology. We introduce a novel Bayesian method that can be used to quantify this relationship when the only data available are size-frequency distributions of unmarked individuals measured at two successive time periods. The inverse Gaussian distribution provides a parametric form for the statistical model development, and we use Markov chain Monte Carlo methods to evaluate posterior distributions. We illustrate the method using data on threespine stickleback (Gasterosteus aculeatus) collected before and after the winter season in an Alaskan lake. Our method allows us to compare the intensity of size-biased mortality in different years. We discuss generalizations that include more complicated relationships between size and survival as well as time-series modeling.

  14. Scaling of frequency-magnitude distributions of fluid-induced seismicity

    NASA Astrophysics Data System (ADS)

    Dinske, Carsten; Shapiro, Serge A.

    2015-04-01

    We compare b value and seismogenic index Σ estimates using two different approaches: a standard Gutenberg-Richter power-law fitting and a frequency-magnitude lower bound probability fitting. The latter takes into account the finite size of the perturbed rock volume. Our results reveal that the smaller is the perturbed rock volume the larger are the deviations between the two sets of derived parameters. It means that the magnitude statistics of the induced events is most affected for low injection volumes and/or short injection times. In sufficiently large stimulated volumes both fitting approaches provide comparable b value and seismogenic index estimates. In particular, the b value is then in the range universally obtained for tectonic earthquakes (b 0.8 - 1.2). We introduce the specific magnitude MΣ as a seismotectonic characteristic of a reservoir location. Defined as the ratio between seismogenic index Σ and b value, this magnitude scaling parameter is unaffected by the size of perturbed rock volumes. Using both seismogenic index model and specific magnitude model we predict frequency-magnitude distributions for two different scenarios and compare these to observed data. We conclude that the seismogenic index model provides reliable predictions which confirm its applicability as a forecast tool. On the other hand, the specific magnitude model can be applied to predict the asymptotical limit of probable frequency-magnitude distributions.

  15. Constructing the frequency and wave normal distribution of whistler-mode wave power

    NASA Astrophysics Data System (ADS)

    Watt, C. E. J.; Degeling, A. W.; Rankin, R.

    2013-05-01

    We introduce a new methodology that allows the construction of wave frequency distributions due to growing incoherent whistler-mode waves in the magnetosphere. The technique combines the equations of geometric optics (i.e., raytracing) with the equation of transfer of radiation in an anisotropic lossy medium to obtain spectral energy density as a function of frequency and wavenormal angle. We describe the method in detail and then demonstrate how it could be used in an idealized magnetosphere during quiet geomagnetic conditions. For a specific set of plasma conditions, we predict that the wave power peaks off the equator at ˜15° magnetic latitude. The new calculations predict that wave power as a function of frequency can be adequately described using a Gaussian function, but as a function of wavenormal angle, it more closely resembles a skew normal distribution. The technique described in this paper is the first known estimate of the parallel and oblique incoherent wave spectrum as a result of growing whistler-mode waves and provides a means to incorporate self-consistent wave-particle interactions in a kinetic model of the magnetosphere over a large volume.

  16. Frequency distribution of gastro esophageal reflux disease in inhalation injury: A historical cohort study

    PubMed Central

    Karbasi, Ashraf; Aliannejad, Rasoul; Ghanei, Mostafa; Sanamy, Mehran Noory; Alaeddini, Farshid; Harandi, Ali Amini

    2015-01-01

    Background: There is no data on the prevalence and the association of gastro esophageal reflux disease (GERD) with toxic fume inhalation. Therefore, we aimed to evaluate the frequency distribution of GERD symptoms among the individuals with mild respiratory disorder due to the past history of toxic fume exposure to sulfur mustard (SM). Materials and Methods: In a historical cohort study, subjects were randomly selected from 7000 patients in a database of all those who had a history of previous exposure to a single high dose of SM gas during war. The control group was randomly selected from adjacent neighbors of the patients, and two healthy male subjects were chosen per patient. In this study, we used the validated Persian translation of Mayo Gastroesophageal Reflux Questionnaire to assess the frequency distribution of reflux disease. Results: Relative frequency of GERD symptoms, was found to be significantly higher in the inhalation injury patients with an odds ratio of 8.30 (95% confidence interval [CI]: 4.73-14.55), and after adjustment for cigarette smoking, tea consumption, age, and body mass index, aspirin and chronic cough the odds ratio was found to be 4.41 (95% CI: 1.61-12.07). Conclusion: The most important finding of our study was the major GERD symptoms (heartburn and/or acid regurgitation once or more per week) among the individuals with the past history of exposure to SM toxic gas is substantially higher (4.4-fold) than normal populations. PMID:26622251

  17. The frequency and distribution of recent landslides in three montane tropical regions of Puerto Rico

    USGS Publications Warehouse

    Larsen, M.C.; Torres-Sanchez, A. J.

    1998-01-01

    Landslides are common in sttep mountainous areas of Puerto Rico where mean annual rainfall and the frequency of intense storms are high. Each year, landslides cause extensive damage to property and coccasionally result in loss of life. Average population density is high, 422 people/km2, and is increasing. This increase in population density is accompanied by growing stress on the natural environment and physical infrastructure. As a result, human populations are more vulnerable to landslide hazards. The Blanco, Cibuco, and Coamo study areas range in surface area from 276 to 350 km2 and represent the climatologic, geographic, and geologic conditions that typify Puerto Rico. Maps of recent landslides developed from 1:20 000-scale aerial photographs, in combination with a computerized geographic information system, were used to evaluate the frequency and distribution of shallow landslides in these areas. Several types of landslides were documented-rainfall-triggered debris flows, shallow soil slips, and slumps were most abundant. Hillslopes in the study area that have been anthropogenically modified, exceed 12?? in gradient, and greater than 300 m in elevation, and face the east-northeast, are most prone to landsliding. A set of simplified matrices representing geographic conditions in the three study areas was developed and provides a basis for the estimation of the spatial controls on the frequency of landslides in Puerto Rico. this approach is an example of an analysis of the frequency of landslides that is computationally simple,. and therefore, may be easily transferable to other settings.

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

    NASA Astrophysics Data System (ADS)

    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.

  19. The Interannual Stability of Cumulative Frequency Distributions for Convective System Size and Intensity

    NASA Technical Reports Server (NTRS)

    Mohr, Karen I.; Molinari, John; Thorncroft, Chris D,

    2010-01-01

    The characteristics of convective system populations in West Africa and the western Pacific tropical cyclone basin were analyzed to investigate whether interannual variability in convective activity in tropical continental and oceanic environments is driven by variations in the number of events during the wet season or by favoring large and/or intense convective systems. Convective systems were defined from TRMM data as a cluster of pixels with an 85 GHz polarization-corrected brightness temperature below 255 K and with an area at least 64 km 2. The study database consisted of convective systems in West Africa from May Sep for 1998-2007 and in the western Pacific from May Nov 1998-2007. Annual cumulative frequency distributions for system minimum brightness temperature and system area were constructed for both regions. For both regions, there were no statistically significant differences among the annual curves for system minimum brightness temperature. There were two groups of system area curves, split by the TRMM altitude boost in 2001. Within each set, there was no statistically significant interannual variability. Sub-setting the database revealed some sensitivity in distribution shape to the size of the sampling area, length of sample period, and climate zone. From a regional perspective, the stability of the cumulative frequency distributions implied that the probability that a convective system would attain a particular size or intensity does not change interannually. Variability in the number of convective events appeared to be more important in determining whether a year is wetter or drier than normal.

  20. Beyond Word Frequency: Bursts, Lulls, and Scaling in the Temporal Distributions of Words

    PubMed Central

    Altmann, Eduardo G.; Pierrehumbert, Janet B.; Motter, Adilson E.

    2009-01-01

    Background Zipf's discovery that word frequency distributions obey a power law established parallels between biological and physical processes, and language, laying the groundwork for a complex systems perspective on human communication. More recent research has also identified scaling regularities in the dynamics underlying the successive occurrences of events, suggesting the possibility of similar findings for language as well. Methodology/Principal Findings By considering frequent words in USENET discussion groups and in disparate databases where the language has different levels of formality, here we show that the distributions of distances between successive occurrences of the same word display bursty deviations from a Poisson process and are well characterized by a stretched exponential (Weibull) scaling. The extent of this deviation depends strongly on semantic type – a measure of the logicality of each word – and less strongly on frequency. We develop a generative model of this behavior that fully determines the dynamics of word usage. Conclusions/Significance Recurrence patterns of words are well described by a stretched exponential distribution of recurrence times, an empirical scaling that cannot be anticipated from Zipf's law. Because the use of words provides a uniquely precise and powerful lens on human thought and activity, our findings also have implications for other overt manifestations of collective human dynamics. PMID:19907645

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

    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.

  3. Distribution and deposition of organic fouling on the microfiltration membrane evaluated by high-frequency ultrasound

    PubMed Central

    Lin, Yi-Hsun; Tung, Kuo-Lun; Wang, Shyh-Hau; Zhou, Qifa; Shung, K. Kirk

    2014-01-01

    A 50 MHz high-frequency ultrasound and analysis method were developed to further improve the in situ assessment of deposition and distribution of organic fouling on the polyvinylidene fluoride (PVDF) membranes. Measurements of fouling depositions were performed from PVDF membranes filtrated with aqueous humic acid solutions (HAS) of 2 and 4 ppm concentrations in a flat-sheet module. Ultrasound signals reflected from the PVDF membranes, following filtrations at various durations including 0, 5, 15, 30, 60, and 100 min, were acquired. The thickness and distribution of fouling estimated and assessed by peak-to-peak echo voltage (Vpp) and C-mode images were found to be non-homogeneously deposited on the membranes. Following the filtrations with 2 and 4 ppm HAS for 100 min, the corresponding thickness of fouling deposition increased from 1.81±9 to 2.4571.57 mm, respectively; those average Vpp decreased from 2.05±07 to 1.13±16 V and from 2.11±08 to 0.94±15 V. These results demonstrated that the deposition and distribution of organic fouling could be sensitively and rapidly evaluated by high-frequency ultrasound image incorporated with the analysis method. PMID:25309028

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

    PubMed

    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.

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

    PubMed

    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. PMID:27575129

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Sampling frequency of ciliated protozoan microfauna for seasonal distribution research in marine ecosystems.

    PubMed

    Xu, Henglong; Yong, Jiang; Xu, Guangjian

    2015-12-30

    Sampling frequency is important to obtain sufficient information for temporal research of microfauna. To determine an optimal strategy for exploring the seasonal variation in ciliated protozoa, a dataset from the Yellow Sea, northern China was studied. Samples were collected with 24 (biweekly), 12 (monthly), 8 (bimonthly per season) and 4 (seasonally) sampling events. Compared to the 24 samplings (100%), the 12-, 8- and 4-samplings recovered 94%, 94%, and 78% of the total species, respectively. To reveal the seasonal distribution, the 8-sampling regime may result in >75% information of the seasonal variance, while the traditional 4-sampling may only explain <65% of the total variance. With the increase of the sampling frequency, the biotic data showed stronger correlations with seasonal variables (e.g., temperature, salinity) in combination with nutrients. It is suggested that the 8-sampling events per year may be an optimal sampling strategy for ciliated protozoan seasonal research in marine ecosystems.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. Polymorphisms in the cytochrome P450 CYP1A2 gene (CYP1A2) in colorectal cancer patients and controls: allele frequencies, linkage disequilibrium and influence on caffeine metabolism

    PubMed Central

    Sachse, Christoph; Bhambra, Upinder; Smith, Gillian; Lightfoot, Tracy J; Barrett, Jennifer H; Scollay, Jenna; Garner, R Colin; Boobis, Alan R; Wolf, C Roland; Gooderham, Nigel J

    2003-01-01

    Aim Several single nucleotide polymorphisms (SNPs) of the cytochrome P450 enzyme 1A2 gene (CYP1A2) have been reported. Here, frequencies, linkage disequilibrium and phenotypic consequences of six SNPs are described. Methods From genomic DNA, 114 British Caucasians (49 colorectal cancer cases and 65 controls) were genotyped for the CYP1A2 polymorphisms −3858G→A (allele CYP1A2*1C), −2464T→delT (CYP1A2*1D), −740T→G (CYP1A2*1E and *1G), −164A→C (CYP1A2*1F), 63C→G (CYP1A2*2), and 1545T→C (alleles CYP1A2*1B, *1G, *1H and *3), using polymerase chain reaction–restriction fragment length polymorphism assays. All patients and controls were phenotyped for CYP1A2 by h.p.l.c. analysis of urinary caffeine metabolites. Results In 114 samples, the most frequent CYP1A2 SNPs were 1545T→C (38.2% of tested chromosomes), −164A→C (CYP1A2*1F, 33.3%) and −2464T→delT (CYP1A2*1D, 4.82%). The SNPs were in linkage disequilibrium: the most frequent constellations were found to be −3858G/−2464T/−740T/−164A/63C/1545T (61.8%), −3858G/−2464T/−740T/−164C/63C/1545C (33.3%), and −3858G/−2464delT/−740T/−164A/63C/1545C (3.51%), with no significant frequency differences between cases and controls. In the phenotype analysis, lower caffeine metabolic ratios were detected in cases than in controls. This was significant in smokers (n = 14, P = 0.020), and in a subgroup of 15 matched case-control pairs (P = 0.007), but it was not significant in nonsmokers (n = 100, P = 0.39). There was no detectable association between CYP1A2 genotype and caffeine phenotype. Conclusions (i) CYP1A2 polymorphisms are in linkage disequilibrium. Therefore, only −164A→C (CYP1A2*1F) and −2464T→delT (CYP1A2*1D) need to be analysed in the routine assessment of CYP1A2 genotype; (ii) in vivo CYP1A2 activity is lower in colorectal cancer patients than in controls, and (iii) CYP1A2 genotype had no effect on phenotype (based on the caffeine metabolite ratio). However, this

  11. Frequency Distributions of Geochemical Data, Scaling Laws, and Properties of Compositions

    NASA Astrophysics Data System (ADS)

    Buccianti, Antonella

    2015-07-01

    Many random processes occur in geochemistry. Accurate predictions of the manner in which elements or chemical species interact with each other are needed to construct models able to treat the presence of random components. Although modelling of frequency distributions with some probabilistic models (for example Gaussian, log-normal, Pareto) has been well discussed in several fields of application, little attention has been devoted to the features of compositional data and, in particular, to their multivariate nature. In this contribution an approach coherent with the properties of compositional information is proposed and used to investigate the shape of the frequency distribution of geochemical indices obtained by robust multivariate analysis. The purpose is to understand data-generation processes from the perspective of compositional theory. The approach is based on use of transformations of the log-ratio family, each with peculiar theoretical and practical advantages, depending on the statistical methods adopted. Accordingly, because, in compositional data, all the relevant information about one term ( x i ) of a D-part composition is contained in the ratios to each of the remaining parts x 2,…, x D , analysis of single variables is abandoned. The proposed methodology directs attention to modelling of the frequency distribution of more complex indices, linking all the terms of the composition to better represent the dynamics of geochemical processes. An example of its application is presented and discussed on the basis of consideration of the chemistry of 616 ocean floor basaltic (OFB) glasses from the abyssal volcanic glass data file (AVGDF) of the Smithsonian Institution.

  12. Uncertainty in the frequency distribution of water quality parameters: comparing three Bayesian approaches

    NASA Astrophysics Data System (ADS)

    Krueger, T.

    2012-04-01

    Observational uncertainties are a notably under-researched area in environmental science, despite their impact on process understanding, model prediction (via the input, calibration and validation stages) and decision making. In this paper I focus on water quality parameters, such as sediment, phosphorus, nitrogen, chloride and oxygen concentrations, which are routinely monitored by environmental regulators to assess the status of surface waters and inform water resources management. This assessment is typically done based on a low temporal monitoring resolution, which in the UK, for example, is fortnightly or monthly so that no more than 12-26 samples per year are typically available. This sampling pattern introduces an unknown bias to the empirical frequency distribution of the parameters, particularly those that are highly variable in time, such as sediment and phosphorus. This bias translates into uncertainty about the statistical moments and percentiles which are ultimately compared to environmental standards or used to drive, calibrate and validate models. In this paper I estimate this uncertainty probabilistically comparing three Bayesian inference models: (1) estimating the parameters of a theoretical frequency distribution, (2) averaging over multiple hypotheses of the frequency distribution, (3) the Bayesian Bootstrap. Uncertainty estimates are propagated through to percentiles of key water quality parameters for practical cases of rural pollution management in the UK and compared to existing standards to illustrate the impact of observational uncertainty on the assessment of surface waters. I also demonstrate a case of model calibration against these uncertain data. The three inference models compared all have limitations and rely on more or less subjective assumptions about the data not collected which are illustrated and discussed. As the science here offers multiple solutions, I will argue that the methodological choice is best made together with

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

    PubMed Central

    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.

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

    PubMed

    Lozano-Cortés, Diego F; Berumen, Michael L

    2016-04-30

    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.

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

    PubMed

    Lozano-Cortés, Diego F; Berumen, Michael L

    2016-04-30

    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. PMID:26520210

  16. An Array of Frequency Selective Bolometers (FSB) for the Spectral Energy Distribution (SPEED) Camera

    NASA Technical Reports Server (NTRS)

    Silverberg, R. F.; Ali, S.; O'Dell, C.; Timbie, P. T.; Bier, A.; Campano, B.; Chen, T. C.; Cottingham, D. A.; Sharp, E.; Cheng, E. S.

    2003-01-01

    The SPEED camera is being developed to study the spectral energy distributions of high redshift galaxies using the Heinrich Hertz Telescope (HHT) in Arizona. SPEED requires a small cryogenic detector array of 2x2 pixels with each pixel having four frequency bands in the 150-350 GHz range. Here we describe the development of the detector array of these high efficiency FSBs. The FSB design provides the multi-pixel multi-spectral band capability required for SPEED in a compact stackable array. The SPEED bolometers will use proximity effect superconducting transition edge sensors as their temperature-sensing element allowing for higher levels of multiplexing in future applications.

  17. [An EMD based time-frequency distribution and its application in EEG analysis].

    PubMed

    Li, Xiaobing; Chu, Meng; Qiu, Tianshuang; Bao, Haiping

    2007-10-01

    Hilbert-Huang transform (HHT) is a new time-frequency analytic method to analyze the nonlinear and the non-stationary signals. The key step of this method is the empirical mode decomposition (EMD), with which any complicated signal can be decomposed into a finite and small number of intrinsic mode functions (IMF). In this paper, a new EMD based method for suppressing the cross-term of Wigner-Ville distribution (WVD) is developed and is applied to analyze the epileptic EEG signals. The simulation data and analysis results show that the new method suppresses the cross-term of the WVD effectively with an excellent resolution.

  18. Size-Frequency Distribution of Boulders ≥ 10 m on Comet 103P/Hartley 2

    NASA Astrophysics Data System (ADS)

    Pajola, M.; Lucchetti, A.; A'Hearn, M. F.; Bertini, I.; Marzari, F.; La Forgia, F.; Lazzarin, M.; Naletto, G.; Barbieri, C.

    2015-12-01

    We present the first size-frequency distribution of boulders ≥ 10 m identified on comet 103P/Hartley 2, computed from the images taken by the Deep Impact/High Resolution Imager - Visible CCD camera on 4 November 2010. We derived the size-frequency distribution of the illuminated side of the comet (˜ 50%), as well as identified the power-law indexes characterizing the two lobes of 103P. 332 boulders larger than 10 m were identified 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 close indexes, i.e. -2.7 ± 0.2 for the bigger lobe (L1) and -2.6 +0.2/-0.5 for the smaller one (L2). Both the similar power-law indexes and the similar maximum boulder sizes derived for the two lobes point towards a similar fracturing/disintegration phenomena of the boulders as well as similar lifting processes that may occur in L1 and L2. Nonetheless, the significative difference in the number of boulders per km2 between the two lobes suggests that the more diffuse H2O sublimation on the bigger lobe produce twice the boulders per km2 with respect to those produced on the small lobe (primary activity CO2 driven). If we compare the boulder distribution of the hyperactive 103P comet with similar studies performed on 67P (67P/Churyumov-Gerasimenko, i.e. the comet studied by Rosetta spacecraft), we derive that 103P shows a lower global power-law index (-2.7 vs -3.6). The size-frequency boulder trend of 103P is somehow closer to the -2.2 value measured on the neck region of 67P, i.e. the most active region of the northern hemisphere of 67P; nevertheless the hyperactivity of 103P works in a very different way than the normal activity of 67P in the neck/Hapi area. In addition to the global differences between the two comets' activities, the absence of cliffs and walls on 103P show a completely different surface geomorphology between

  19. Low noise buffer amplifiers and buffered phase comparators for precise time and frequency measurement and distribution

    NASA Technical Reports Server (NTRS)

    Eichinger, R. A.; Dachel, P.; Miller, W. H.; Ingold, J. S.

    1982-01-01

    Extremely low noise, high performance, wideband buffer amplifiers and buffered phase comparators were developed. These buffer amplifiers are designed to distribute reference frequencies from 30 KHz to 45 MHz from a hydrogen maser without degrading the hydrogen maser's performance. The buffered phase comparators are designed to intercompare the phase of state of the art hydrogen masers without adding any significant measurement system noise. These devices have a 27 femtosecond phase stability floor and are stable to better than one picosecond for long periods of time. Their temperature coefficient is less than one picosecond per degree C, and they have shown virtually no voltage coefficients.

  20. Crater size-frequency distributions and a revised Martian relative chronology

    NASA Technical Reports Server (NTRS)

    Barlow, Nadine G.

    1988-01-01

    A relative plotting technique is applied to Viking 1:2M photomosaics of 25,826 Martian craters of diameter greater than 8 km and age younger than that of the Martian surface. The size-frequency distribution curves are calculated and analyzed in detail, and the results are presented in extensive tables and maps. It is found that about 60 percent of the crater-containing lithologic units, including many small volcanoes and the ridged planes, were formed during the heavy-bombardment period (HBP), while 40 percent arose after the HBP. Wide region-to-region variation in the crater density is noted, and localized age estimates are provided.

  1. Does the geographical gradient of ApoE4 allele exist in China? A systemic comparison among multiple Chinese populations.

    PubMed

    Hu, Peng; Qin, Yuan Han; Jing, Cheng Xue; Lu, Ling; Hu, Bo; Du, Peng Fei

    2011-01-01

    The allelic frequencies of apolipoprotein E (apoE) vary substantially around the world. There is a conspicuous south-to-north gradient of e4 frequencies in Europe, with the proportion of e4 carriers from only 10-15% in the south to 40-50% in the north. The mechanism may be related to the possibility that e4 carriers are less likely to develop vitamin D deficiency. In addition, Asian populations traditionally have lower e4 frequency than Europeans, which may be attributed in part to the scarce or irregular food supplies in Western world in the recent past. However, whether these geographical distribution gradients exist in China is yet unknown. ApoE genotypes of 200 children from Nanning City were determined by PCR-restriction fragment length polymorphism (RFLP) analysis. Allele frequency data of 18 other populations were collected from published sources and correlated with latitude and longitude information from different geographic resources. In our subjects, the frequencies of apoE genotypes were E3/E3: 73.0%, E3/E2: 15.0%, E4/E3: 5.0%, E4/E4: 5.0%, and E4/E2: 2.0%; the frequencies of apoE alleles were e2: 8.5%, e3: 83.0%, and e4: 8.5%, respectively. The total sample consisted of 3,679 individuals from 19 Chinese populations; the allelic frequencies were e2: 7.6%, e3: 85.5%, and e4: 6.9%, respectively; the proportion of e4 carriers was from 4.9% in Kunming to 17.5% in Harbin. Systemic comparison among multiple Chinese populations revealed that positive correlation existed between the e4 allele frequency distribution and latitude north (r=0.586, P=0.008), but no correlation of the e4 allele frequency distribution with longitude east was found (r=-0.018, P=0.942). We conclude that there is a south-to-north, but not an east-to-west gradient for the apoE4 allele in China.

  2. SAR imagery of moving targets: application of time-frequency distributions for estimating motion parameters

    NASA Astrophysics Data System (ADS)

    Haimovich, Alexander M.; Peckham, C. D.; Teti, Joseph G., Jr.

    1994-06-01

    It is well known that targets moving along track within a Synthetic Aperture Radar (SAR) field of view are imaged as defocused objects. The SAR stripmap mode is tuned to stationary ground targets and the mismatch between the SAR processing parameters and the target motion parameters causes the energy to spill over to adjacent image pixels, thus not only hindering target feature extraction, but also reducing the probability of detection. The problem can be remedied by generating the image using a filter matched to the actual target motion parameters, effectively focusing the SAR image on the target. For a fixed rate of motion the target velocity can be estimated from the slope of the Doppler frequency characteristic. The processing is carried out on the range compressed data but before azimuth compression. The problem is similar to the classical problem of estimating the instantaneous frequency of a linear FM signal (chirp). This paper investigates the application of three different time-frequency analysis techniques to estimate the instantaneous Doppler frequency of range compressed SAR data. In particular, we compare the Wigner-Ville distribution, the Gabor expansion and the Short-Time Fourier transform with respect to their performance in noisy SAR data. Criteria are suggested to quantify the performance of each method in the joint time- frequency domain. It is shown that these methods exhibit sharp signal-to-noise threshold effects, i.e., a certain SNR below which the accuracy of the velocity estimation deteriorates rapidly. It is also shown that the methods differ with respect to their representation of the SAR data.

  3. Frequency-dependent spatiotemporal distribution of cerebral oscillatory changes during silent reading: a magnetoencephalograhic group analysis.

    PubMed

    Goto, Tetsu; Hirata, Masayuki; Umekawa, Yuka; Yanagisawa, Takufumi; Shayne, Morris; Saitoh, Youichi; Kishima, Haruhiko; Yorifuji, Shirou; Yoshimine, Toshiki

    2011-01-01

    The frequency profiles and time courses of oscillatory changes when reading words are not fully understood, although there have been many reports that oscillatory dynamics reflect local brain function. In order to clarify oscillatory dynamics, we investigated the frequency and spatiotemporal distributions of neuromagnetic activities during silent reading of words in 23 healthy subjects. Individual data were divided into the following frequency bands: theta (5-8 Hz), alpha (8-13 Hz), beta (13-25 Hz), low gamma (25-50 Hz), and high gamma (50-100 Hz), and were analyzed by synthetic aperture magnetometry (SAM). The time window was consecutively moved in steps of 50 ms. Group analysis was performed to delineate common areas of brain activation. A transient power increase in the theta band occurred first in the bilateral occipital cortices, and then rapidly propagated to the left temporo-occipital areas, left inferior and middle frontal gyri, bilateral medial prefrontal cortices, and finally to the left anterior temporal cortices, which possibly reflects a serial cognitive process. This serial propagation of the transient power increase in the theta band was followed by sustained power decreases in the alpha, beta and low gamma bands. These results suggest that the transient power increase in the theta bands may be associated with priming and propagation of local activities, while sustained power decreases in the alpha, beta and low gamma bands reflect parallel neural processes related to silent reading words. Our results showed a relationship between frequency bands of oscillatory changes and locations. This may have implications in the relationship between frequency bands and functions.

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

    NASA Technical Reports Server (NTRS)

    Shoemaker, Eugene M.; Shoemaker, Carolyn S.

    1987-01-01

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

  5. The spatial distribution of precipitation frequency for atmospheric river storms in Northern California

    NASA Astrophysics Data System (ADS)

    Yuter, S. E.; Kingsmill, D.; White, C.; Wilbanks, M.; Hardin, N.; Cunningham, J.

    2011-12-01

    A key missing piece on the role of atmospheric rivers (ARs ) in flooding events in California is knowledge of the detailed spatial distribution of precipitation over the slopes of the Coastal Range and Sierra Nevada. Existing rain gauges provide incomplete information on precipitation in this region, particularly over rugged mountainous terrain. We utilize operational radar data from National Weather Service WSR-88D radars at six locations in California and Nevada to determine the spatial distribution of precipitation frequency for selected AR events. Preliminary results suggest that the southerly moisture transport by the Sierra Barrier Jet becomes more southeasterly toward the north end of the Sacramento Valley and enhances precipitation in the lee of the Coastal Range.

  6. Phase retrieval in digital speckle pattern interferometry by use of a smoothed space-frequency distribution.

    PubMed

    Federico, Alejandro; Kaufmann, Guillermo H

    2003-12-10

    We evaluate the use of a smoothed space-frequency distribution (SSFD) to retrieve optical phase maps in digital speckle pattern interferometry (DSPI). The performance of this method is tested by use of computer-simulated DSPI fringes. Phase gradients are found along a pixel path from a single DSPI image, and the phase map is finally determined by integration. This technique does not need the application of a phase unwrapping algorithm or the introduction of carrier fringes in the interferometer. It is shown that a Wigner-Ville distribution with a smoothing Gaussian kernel gives more-accurate results than methods based on the continuous wavelet transform. We also discuss the influence of filtering on smoothing of the DSPI fringes and some additional limitations that emerge when this technique is applied. The performance of the SSFD method for processing experimental data is then illustrated.

  7. Statistical Tests of the Coalescent Model Based on the Haplotype Frequency Distribution and the Number of Segregating Sites

    PubMed Central

    Innan, Hideki; Zhang, Kangyu; Marjoram, Paul; Tavaré, Simon; Rosenberg, Noah A.

    2005-01-01

    Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain rejection probabilities. Here we develop a “haplotype configuration test” of neutrality (HCT) based on the full haplotype frequency distribution. To enable exact computation of rejection probabilities for small samples, we derive a recursion under the standard coalescent model for the joint distribution of the haplotype frequencies and the number of segregating sites. For larger samples, we consider simulation-based approaches. The utility of the HCT is demonstrated in simulations of alternative models and in application to data from Drosophila melanogaster. PMID:15654103

  8. Loss of Mhc and Neutral Variation in Peary Caribou: Genetic Drift Is Not Mitigated by Balancing Selection or Exacerbated by Mhc Allele Distributions

    PubMed Central

    Taylor, Sabrina S.; Jenkins, Deborah A.; Arcese, Peter

    2012-01-01

    Theory and empirical results suggest that the rate of loss of variation at Mhc and neutral microsatellite loci may differ because selection influences Mhc genes, and because a high proportion of rare alleles at Mhc loci may result in high rates of loss via drift. Most published studies compare Mhc and microsatellite variation in various contemporary populations to infer the effects of population size on genetic variation, even though different populations are likely to have different demographic histories that may also affect contemporary genetic variation. We directly compared loss of variation at Mhc and microsatellite loci in Peary caribou by comparing historical and contemporary samples. We observed that similar proportions of genetic variation were lost over time at each type of marker despite strong evidence for selection at Mhc genes. These results suggest that microsatellites can be used to estimate genome-wide levels of variation, but also that adaptive potential is likely to be lost following population bottlenecks. However, gene conversion and recombination at Mhc loci may act to increase variation following bottlenecks. PMID:22655029

  9. Loss of MHC and neutral variation in Peary caribou: genetic drift is not mitigated by balancing selection or exacerbated by MHC allele distributions.

    PubMed

    Taylor, Sabrina S; Jenkins, Deborah A; Arcese, Peter

    2012-01-01

    Theory and empirical results suggest that the rate of loss of variation at Mhc and neutral microsatellite loci may differ because selection influences Mhc genes, and because a high proportion of rare alleles at Mhc loci may result in high rates of loss via drift. Most published studies compare Mhc and microsatellite variation in various contemporary populations to infer the effects of population size on genetic variation, even though different populations are likely to have different demographic histories that may also affect contemporary genetic variation. We directly compared loss of variation at Mhc and microsatellite loci in Peary caribou by comparing historical and contemporary samples. We observed that similar proportions of genetic variation were lost over time at each type of marker despite strong evidence for selection at Mhc genes. These results suggest that microsatellites can be used to estimate genome-wide levels of variation, but also that adaptive potential is likely to be lost following population bottlenecks. However, gene conversion and recombination at Mhc loci may act to increase variation following bottlenecks.

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

    NASA Astrophysics Data System (ADS)

    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

  11. Improved accuracy of the NPL-CsF2 primary frequency standard: evaluation of distributed cavity phase and microwave lensing frequency shifts

    NASA Astrophysics Data System (ADS)

    Li, Ruoxin; Gibble, Kurt; Szymaniec, Krzysztof

    2011-10-01

    We evaluate the distributed cavity phase (DCP) and microwave lensing frequency shifts, which were the two largest sources of uncertainty for the NPL-CsF2 caesium fountain clock. We report measurements that confirm a detailed theoretical model of the microwave cavity fields and the frequency shifts of the clock that they produce. The model and measurements significantly reduce the DCP uncertainty to 1.1 × 10-16. We derive the microwave lensing frequency shift for a cylindrical cavity with circular apertures. An analytic result with reasonable approximations is given, in addition to a full calculation that indicates a shift of 6.2 × 10-17. The measurements and theoretical models we report, along with improved evaluations of collisional and microwave leakage induced frequency shifts, reduce the frequency uncertainty of the NPL-CsF2 standard to 2.3 × 10-16, nearly a factor of two lower than its most recent complete evaluation.

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

    NASA Astrophysics Data System (ADS)

    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

  13. Scaling, stability and distribution of the high-frequency returns of the IBEX35 index

    NASA Astrophysics Data System (ADS)

    Suárez-García, Pablo; Gómez-Ullate, David

    2013-03-01

    In this paper we perform a statistical analysis of the high-frequency returns of the IBEX35 Madrid stock exchange index. We find that its probability distribution seems to be stable over different time scales, a stylized fact observed in many different financial time series. However, an in-depth analysis of the data using maximum likelihood estimation and different goodness-of-fit tests rejects the Lévy-stable law as a plausible underlying probabilistic model. The analysis shows that the Normal Inverse Gaussian distribution provides an overall fit for the data better than any of the other subclasses of the family of Generalized Hyperbolic distributions and certainly much better than the Lévy-stable laws. Furthermore, the right (resp. left) tail of the distribution seems to follow a power-law with exponent α≈4.60 (resp. α≈4.28). Finally, we present evidence that the observed stability is due to temporal correlations or non-stationarities of the data.

  14. Estimating the frequency distributions of particulate matter and their metal elements in a temple.

    PubMed

    Lu, Hsin-Chung; Fang, Gour-Cheng; Wu, Yuh-Shen

    2006-07-01

    Air quality inside Asian temples is typically poor because of the burning of incense. This study measured and analyzed concentrations of fine (PM2.5) and coarse (PM2.5-10) particulate matter and their metal elements inside a temple in central Taiwan. Experimental results showed that the concentrations of metals Cd, Ni, Pb, and Cr inside the temple were higher than those at rural, suburban, urban, and industrial areas in other studies. Three theoretical parent distributions (lognormal, Weibull, and gamma) were used to fit the measured data. The lognormal distribution was the most appropriate distribution for representing frequency distributions of PM10, PM2.5, and their metal elements. Furthermore, the central limit theorem, H-statistic-based scheme, and parametric and nonparametric bootstrap methods were used to estimate confidence intervals for mean pollutant concentrations. The estimated upper confidence limits (UCLs) of means between different methods were very consistent, because the sample coefficient of variation (CV) was < 1. When the sample CV was > 1, the UCL based on H-statistical method tended to overestimate the UCLs when compared with other methods. Confidence intervals for pollutant concentrations at different percentiles were evaluated using parametric and nonparametric bootstrap methods. The probabilities of pollutants exceeding a critical concentration were also calculated.

  15. 0. 04 Hz relative optical-frequency stability in a 1. 5. mu. m distributed-Bragg-reflector (DBR) laser

    SciTech Connect

    Ishida, O.; Toba, H. ); Tohmori, Y. )

    1989-12-01

    The optical frequency of a 1.5 {mu}m distributed-Bragg-reflector (DBR) laser is stabilized against that of a master laser by heterodyne-type frequency locking with a phase-locked loop (PLL). Despite its wide linewidth of 16 MHz, stable PLL operation with an optical hold-in range of 26 GHz is realized, and residual frequency fluctuations are reduced to 0.04 Hz at an averaging time of 500 s. The combination of DBR laser and PLL is, therefore, suitable for future frequency-controlled light sources. The offset error from the settled frequency caused by the band-limited beat spectrum is also discussed.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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

  18. An earthquake-like magnitude-frequency distribution of slow slip in northern Cascadia

    NASA Astrophysics Data System (ADS)

    Wech, Aaron G.; Creager, Kenneth C.; Houston, Heidi; Vidale, John E.

    2010-11-01

    Major episodic tremor and slip (ETS) events with Mw 6.4 to 6.7 repeat every 15 ± 2 months within the Cascadia subduction zone under the Olympic Peninsula. Although these major ETS events are observed to release strain, smaller “tremor swarms” without detectable geodetic deformation are more frequent. An automatic search from 2006-2009 reveals 20,000 five-minute windows containing tremor which cluster in space and time into 96 tremor swarms. The 93 inter-ETS tremor swarms account for 45% of the total duration of tremor detection during the last three ETS cycles. The number of tremor swarms, N, exceeding duration τ follow a power-law distribution N $\\propto$ τ-0.66. If duration is proportional to moment release, the slip inferred from these swarms follows a standard Gutenberg-Richter logarithmic frequency-magnitude relation, with the major ETS events and smaller inter-ETS swarms lying on the same trend. This relationship implies that 1) inter-ETS slip is fundamentally similar to the major events, just smaller and more frequent; and 2) despite fundamental differences in moment-duration scaling, the slow slip magnitude-frequency distribution is the same as normal earthquakes with a b-value of 1.

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

    NASA Astrophysics Data System (ADS)

    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

  20. Prevalence of the CYP2D6*10 (C100T), *4 (G1846A), and *14 (G1758A) alleles among Iranians of different ethnicities.

    PubMed

    Bagheri, Ali; Kamalidehghan, Behnam; Haghshenas, Maryam; Azadfar, Parisa; Akbari, Leila; Sangtarash, Mohammad Hossein; Vejdandoust, Faramarz; Ahmadipour, Fatemeh; Meng, Goh Yong; Houshmand, Massoud

    2015-01-01

    The presence of polymorphisms in the CYP2D6 gene may modulate enzyme level and activity, thereby affecting individual responses to pharmacological treatment. Here, we compared the prevalence of the CYP2D6*10, *4, and 14* alleles in an Iranian population of different ethnicities with those of other populations. Allele and genotype frequency distributions of CYP2D6*10 variants and predicted phenotypes including extensive metabolizers, intermediate metabolizers, and poor metabolizers were analysed in blood samples of 300 unrelated healthy individuals in an Iranian population using polymerase chain reaction (PCR)-restriction fragment length polymorphism, PCR-single-strand conformation polymorphism, and direct genomic DNA sequencing. The CYP2D6*4 (G1846A) and *14 (G1758A) allelic frequencies were not detected in different ethnicities, demonstrating the absence of a significant contribution of these alleles in Iranian populations. However, the T/T, C/T, and C/C genotype frequencies of the CYP2D6*10 allele were significantly different (P<0.01) in all Iranian ethnic groups. Additionally, the frequency of the homozygous T/T variant of the CYP2D6*10 allele was significantly high in the Lure (P<0.017) and low in the Kurd (P<0.002) ethnicities. The frequency of the T/T variant of the CYP2D6*10 allele in central Iran was the highest (P<0.001), while the south of Iran had the lowest frequency (P<0.001). The frequency of the C/T variant of the CYP2D6*10 allele was significantly a bit high (P<0.001) in females compare to males, while the frequencies of the T/T variant in females is similar to males, which are 24.4% and 24.3%, respectively. In contrast to absence of the CYP2D6*4 (G1846A) and *14 (G1758A) alleles in Iranian populations of different ethnicities, the prediction of the CYP2D6*10 allele is required in drug research and routine treatment, where the information would be helpful for clinicians to optimize therapy or identify persons at risk of adverse drug reactions before

  1. A simple, semi-deterministic approximation to the distribution of selective sweeps in large populations.

    PubMed

    Martin, Guillaume; Lambert, Amaury

    2015-05-01

    In large populations, the distribution of the trajectory of allele frequencies under selection and genetic drift approaches a semi-deterministic behavior: a deterministic trajectory started and ended at stochastic boundary values. This provides simple yet accurate approximations for the distribution of allelic frequencies over time (conditional on fixation), and of extinction and fixation times, for both hard and soft sweeps, and under arbitrary inbreeding and dominance.

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

    NASA Astrophysics Data System (ADS)

    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.

  3. High-Frequency Pulsed-Electro-Acoustic (PEA) Measurements for Mapping Charge Distribution

    NASA Astrophysics Data System (ADS)

    Sorensen, Kristina; Pearson, Lee; Dennison, J. R.; Doyle, Timothy; Hartley, Kent

    2012-10-01

    High-frequency pulsed-electro-acoustic (PEA) measurements are a non-destructive method used to investigate internal charge distributions in dielectric materials. This presentation discusses the theory and signal processing of simple PEA experiments and shows results of PEA measurements. PEA experiments involve a thin dielectric positioned between two conducting electrodes. A voltage signal on the two electrodes generates an electric field across the dielectric, which stimulates embedded charge and creates a pressure wave that propagates within the capacitor. A coupled acoustic sensor then measures the ensuing pressure pulse response. Spatial distributions of the charge profile are obtained from the resultant pressure waveform. Gaussian filters and other signal processing methods are used to increase the signal-to-noise ratio in this waveform. Estimates of the charge distribution inside the dielectric are extracted from this analysis. Our ultimate objective is to develop high resolution PEA methods to investigate in vacuo charge deposition in thin film polymeric, ceramic, or glass dielectric materials using medium to high energy (approximately 103 to 107 eV) electron beams.

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

    NASA Astrophysics Data System (ADS)

    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

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

    NASA Astrophysics Data System (ADS)

    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

  6. New classification scheme for ozone monitoring stations based on frequency distribution of hourly data.

    PubMed

    Tapia, O; Escudero, M; Lozano, Á; Anzano, J; Mantilla, E

    2016-02-15

    According to European Union (EU) legislation, ozone (O3) monitoring sites can be classified regarding their location (rural background, rural, suburban, urban) or based on the presence of emission sources (background, traffic, industrial). There have been attempts to improve these classifications aiming to reduce their ambiguity and subjectivity, but although scientifically sound, they lack the simplicity needed for operational purposes. We present a simple methodology for classifying O3 stations based on the characteristics of frequency distribution curves which are indicative of the actual impact of combustion sources emitting NO that consumes O3 via titration. Four classes are identified using 1998-2012 hourly data from 72 stations widely distributed in mainland Spain and the Balearic Islands. Types 1 and 2 present unimodal bell-shaped distribution with very low amount of data near zero reflecting a limited influence of combustion sources while Type 4 has a primary mode close to zero, showing the impact of combustion sources, and a minor mode for higher concentrations. Type 3 stations present bimodal distributions with the main mode in the higher levels. We propose a quantitative metric based on the Gini index with the objective of reproducing this classification and finding empirical ranges potentially useful for future classifications. The analysis of the correspondence with the EUROAIRNET classes for the 72 stations reveals that the proposed scheme is only dependent on the impact of combustion sources and not on climatic or orographic aspects. It is demonstrated that this classification is robust since in 87% of the occasions the classification obtained for individual years coincide with the global classification obtained for the 1998-2012 period. Finally, case studies showing the applicability of the new classification sche